title: Jinhua Hecha-a fermented green tea improves sleep via regulating glutamatergic synapses and gut microbiota

city: Hangzhou

first: Yingying

address: No. 260, Baichuan Street, Fuyang District, Hangzhou City

institute: Zhejiang Chinese Medical University

summary: In animal experiments, the potential beneficial effects of JHHC on sleep quality were evaluated.

overall_design: Randomly, 3 mice from each of the NC group, FFZR group, and JHHCG group were used to extract total RNA from colon tissues.

first: Xunjie

last: Zheng

first: Ke

first: Jianli

last: Gao

first: Jianbo

last: huang

first: Zhaohuan

last: Lou


title: Raw sequence reads of the transcriptomics for rapamycin-treated HeLa cells

status: Public on May 01 2025

city: Beijing

first: Xinyuan

last: Fan

address: No.292 Chengfu Road, Haidian District

country: China

institute: Peking University

type: Expression profiling by high throughput sequencing

summary: Rapamycin, known for its ability to inhibit the mammalian target of rapamycin (mTOR) pathway, which is a key player in metabolism, autophagy, tumorigensis and other crucial processes. However, due to the highly complexed, transient and context-dependent nature, the molecular details on how mTOR impacts cellular processes as well as specific diseases remained largely elusive. Given that mTOR is significantly associated with lysosome both physically and functionally, we have performed a proteomic study via the CAT-Lyso method to profile lysosomal dynamics upon mTOR perturbation in HeLa cells. Here, we further present the transcriptomic profiling of HeLa cells treated with rapamycin, in order to generate a multi-omic picture for mining biological information.

overall_design: To investigate the transcriptional regulations of genes, we prepared HeLa cells treated with or without rapamycin (100 nM, 24 h) and performed the bulk RNA-sequcing of the samples, followed by comparative gene expression analysis.

first: Ziqi

last: Liu

first: Peng

middle: R

last: Chen


title: 5G-exposed human skin cells do not respond with altered gene expression and methylation profiles [RNA-Seq]

city: Bremen

first: Jyoti

last: Jyoti

state: Bremen

address: Campus Ring 6

department: School of Science

country: Germany

institute: Constructor University

summary: Due to the ever-increasing wirelessly transmitted data, the development of new transmission standards and higher frequencies in the 5G band is required. Despite basic biophysical considerations that argue against health effects, there is public concern about this technology. Because the skin penetration depth at these frequencies is only 1 millimeter or less, we exposed fibroblasts and keratinocytes to electromagnetic fields up to ten times the permissible limits, for 2 and 48 hours in a fully blinded experimental design. Sham-exposed cells served as negative, and UV-exposed cells as positive controls. Differences in gene expression and methylation due to exposure were small and not higher than expected by chance. These data strongly support the assessment that there is no evidence for exposure-induced damage to human skin cells.

overall_design: Strictly blinded, temperature-controlled transcriptomics and methylation study in human keratinocytes (HaCaT) and human dermal fibroblasts (HDF) exposed to 5G electromagnetic fields at different frequencies (27 GHz and 40.5 GHz), power flux densities (1 mW/cm2 and 10 mW/cm2) and exposure times (2h and 48h). There are total 96 samples, with 3 technical replicates per experiment for exposed as well as sham-exposed cells. Additionally, 24 samples (12 HaCat, 12 HDF) were considered for UV, and 5G exposure without temperature compensation treatment, respectively. Differential RNA expression analysis and differential DNA methylation analysis were performed on exposure category variable (exposed/sham) for each treatment combination.

first: Isabel

last: Gronau

first: Eda

last: Cakir

first: Marc-Thorsten

last: Hütt

first: Alexander

last: Lerchl

first: Vivian

last: Meyer


title: ALKBH1-mediated DNA N6-methyladenine Modification Regulates H3K9me3-dependent Heterochromatin in Neural Tube Development [scRNA-Seq]

city: beijing

first: Xuejia

last: He

address: 2 yabao road

institute: Capital Institute of Pediatrics

summary: Neural Tube Defects (NTDs) are a class of severe congenital developmental defects caused by abnormal closure of the neural tube during early embryonic development, including conditions such as anencephaly, spina bifida, and encephalocele. Currently, NTDs are considered to result from the combined effects of genetic and environmental factors, particularly maternal folate intake during pregnancy, leading to widespread epigenetic dysregulation. However, the role of N6-methyladenine (N6-mA) in embryonic neural development remains largely unknown. Here, we found significant upregulation of Alkbh1 and concomitant significant downregulation of overall 6mA in brain tissue of a mouse model of NTDs. Further investigation through RNA-seq，MeDIP, CUT&TAG, and single-cell sequencing revealed crosstalk between N6-mA and H3K9me3-marked heterochromatin, primarily impacting the involvement of embryonic glial cells in the formation of the hindbrain during embryonic neural tube development. These findings collectively suggest a potential epigenetic role of N6-mA in mammalian brain development, potentially exhibiting cell type specificity.

overall_design: Establishment of NTD Mouse Model: MTX is a folate antagonist. Under conditions of low folate diet in pregnant mice, we intraperitoneally injected MTX (1.5 mg/kg) at gestational day 7.5. We began observing the closure status of the neural tube in fetal mice during the neural tube closure window at E9.5-10.5. Normal mice appeared plump and round, with fully closed neural tubes, and were categorized into the normal group. Embryos from mice on low folate diet and injected with MTX exhibited varying degrees of developmental delay, smaller embryos, and primarily showed phenotypes of hindbrain malformations and spina bifida, and were categorized into the NTD group. RNA-seq is used to identify differentially expressed genes between two groups, with three replicates in each group.To delve deeper into the specific mechanisms of N6-mA and H3K9me3 epigenetic inheritance in the occurrence and development of NTDs, we obtained single-cell RNA expression profiles of Con and NTDs fetal mouse brain tissues using the 10x Genomics Chromium platform.

first: Jinying

last: Shen

first: Shan

last: Wang


title: Study of kidney state in 70% liver resection in experiment in mice

city: Moscow

first: Evgeny

last: Karpulevich

address: Alexandra Solzhenitsina

department: Information Systems

country: Russia

institute: ISP RAS

summary: A model of liver regeneration after 70% resection was reproduced in sexually mature male C57 black mice. The animals were removed from the experiment after 1,3 and 7 days. Kidneys were taken from the animals. Kidneys of intact animals were used as a control.

overall_design: Twelve sexually mature males of the C57 black line were used in the experiment. The model of liver regeneration after 70% resection was reproduced in 9 mice, 3 mice were used as an intact control. The operated mice were removed from the experiment using a CO2 chamber after 1 (n=3), 3 (n=3) and 7 (n=3) days. Kidneys were used for NGS study.

first: Andrey

last: Elchaninov


title: ALKBH1-mediated DNA N6-methyladenine Modification Regulates H3K9me3-dependent Heterochromatin in Neural Tube Development [RNA-Seq]

overall_design: 1.Establishment of NTD Mouse Model: MTX is a folate antagonist. Under conditions of low folate diet in pregnant mice, we intraperitoneally injected MTX (1.5 mg/kg) at gestational day 7.5. We began observing the closure status of the neural tube in fetal mice during the neural tube closure window at E9.5-10.5. Normal mice appeared plump and round, with fully closed neural tubes, and were categorized into the normal group. Embryos from mice on low folate diet and injected with MTX exhibited varying degrees of developmental delay, smaller embryos, and primarily showed phenotypes of hindbrain malformations and spina bifida, and were categorized into the NTD group. RNA-seq is used to identify differentially expressed genes between two groups, with three replicates in each group. 2.Constructing a low-folate cell line：After resuscitating normal mESCs, Sv129 cells were randomly split into FA4 and FA0. The FA0 group uses folate-free mESCs culture medium.Folate (Sigma) was added to the medium of FA0 as medium of the FA4 group(final concentration: 4 mg/L).  Next, two groups were added correspond medium and were cultured at 37°C with 5% CO2 in a humidified incubator and passaged every 2–3 days. The culture medium was changed daily. Identifying differentially expressed genes between two groups using RNA-seq technology.


title: 5G-exposed human skin cells do not respond with altered gene expression and methylation profiles [methylation]


title: EZH2-targeted PROTACs target the EZH2/FOXM1 axis and reduce breast cancer cell growth [CUT&Tag]

city: Durham

first: Joshua

last: Corbin

state: NC

address: 3 Genome Ct

country: USA

institute: Duke University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Breast cancer (BCa) remains the second leading cause of cancer-related mortalities in women, and acquired resistance to hormone therapies, such as tamoxifen, an estrogen receptor inhibitor, is a major hurdle in the treatment of luminal BCa. Another subtype, triple negative BCa (TNBC), is associated with aggressive disease and poor prognosis. The enhancer of zeste homolog 2 (EZH2), the methyltransferase component of the polycomb repressive complex 2 (PRC2), is overexpressed in BCa and has been implicated in tamoxifen resistance. In addition to its PRC2-dependent canonical transcription repressive role through catalyzing histone 3 lysine 27 trimethylation (H3K27me3), evidence suggests that EZH2 can function noncanonically, in a methyltransferase-independent manner, as a transcription activator through interacting with hormone receptors and oncogenic transcription factors. Unlike methyltransferase inhibitors, proteolysis targeting chimeras (PROTAC), which target EZH2 and interacting proteins for degradation, can suppress both activating and repressive functions of EZH2. Previous studies have suggested that PROTACs can be leveraged to inhibit TNBC cell growth. In this study, we expand our scope to test whether EZH2 targeted PROTACs can effectively inhibit luminal BCa cell growth. We find that EZH2-targeted PROTACs, MS177 and MS8815, effectively inhibited the growth luminal BCa cells, including those with acquired tamoxifen resistance, to a much greater degree when compared to methyltransferase inhibitors. Similarly, PROTACs uniquely reduced the expression of genes involved in cell cycle progression, including forkhead box M1 (FOXM1) target genes, in BCa cell lines. Likewise, promoter regions with EZH2 binding in the absence of H3K27me3 were enriched with FOXM1 target genes in both luminal BCa and TNBC cell lines, suggesting a regulatory mechanism independent of hormone receptor status. EZH2 PROTAC treatment reduced FOXM1 protein expression and increased its degradation. In clinical samples, EZH2 mRNA expression tightly correlated with FOXM1 and FOXM1 target genes. Together, this study suggests that EZH2 targeted PROTACs represent a promising avenue of research for the future treatment of BCa, including in the setting of tamoxifen resistance.

overall_design: We used CUT&Tag to assess the genome-wide binding of YY1, H3K27ac, H3K9ac, and H3K27me3 in 22Rv1 and VCaP cells, either parental lines or those with the knock-out/down (KO/KD) of endogenous YY1, with rescued re-expression of YY1 WT or YY1_del30aa mutant in cells

first: Gang

middle: G

first: Ling

last: Cai


title: Angelicin regulated NIH3T3 activity by stimultate by TGF-β and H2O2

city: Ji'nan

first: Kai

last: Cheng

address: Qingdao Road,6699

institute: Shandong First Medical University

summary: Murine NIH3T3 cells were commonly used as an in vitro cell model to study the malignant transformation of fibroblasts. We  examined the effect of Angelicin(IPRN) on NIH3T3 activity stimulated by TGF-β and H2O2.

overall_design: To investigate the regulatory effects of IPRN on cancer-associated fibroblasts, we induced NIH3T3 cells by adding hydrogen peroxide and TGF-β. After adding IPRN, we explored the signaling pathways affected by IPRN through sequencing.


title: DNA methylation profiles in 3 mutant NPCs and wt NPCs (control, empty vector) at 10 days

city: Palo Alto

first: Lingjun

last: Meng

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

type: Methylation profiling by genome tiling array

summary: To investigate temporal DNA methylation changes occurring during human neural progenitor cells (NPCs) maintenance in later times via genomic DNA methylation measurement by Infinium MethylationEPIC BeadChip assay, we introduced IDH1-R132H, KRAS-G12C, and TP53-R273C mutations separately into NPCs at day 0, with dox induction for 10 days to overexpress the oncogenes. After 10 days of induction, we investigated the DNA methylation profiles in NPCs, in order to investigate the epigenetic change during oncogene induction.

overall_design: We introduced each oncogene into individual wt NPCs, using dox to overexpress the GoF mutation gene for 10 days, then performed an Infinium MethylationEPIC BeadChip assays. Stanford Functional Genomics Facility (SFGF) using the Infinium MethylationEPIC array which interrogates over 850,000 methylation sites at single-nucleotide resolution.

first: Alice

last: Yu

first: Huanwei

last: Huang

first: Jodie


title: ALKBH1-mediated DNA N6-methyladenine Modification Regulates H3K9me3-dependent Heterochromatin in Neural Tube Development

first: shan

last: wang

address: 2yabao road

type: Methylation profiling by high throughput sequencing

summary: Neural Tube Defects (NTDs) are a class of severe congenital developmental defects caused by abnormal closure of the neural tube during early embryonic development, including conditions such as anencephaly, spina bifida, and encephalocele. Currently, NTDs are considered to result from the combined effects of genetic and environmental factors, particularly maternal folate intake during pregnancy, leading to widespread epigenetic dysregulation. However, the role of N6-methyladenine (N6-mA) in embryonic neural development remains largely unknown. Here, we found significant upregulation of Alkbh1 and concomitant significant downregulation of overall 6mA in brain tissue of a mouse model of NTDs. Further investigation through MeDIP, CUT&TAG, and single-cell sequencing revealed crosstalk between N6-mA and H3K9me3-marked heterochromatin, primarily impacting the involvement of embryonic glial cells in the formation of the hindbrain during embryonic neural tube development. These findings collectively suggest a potential epigenetic role of N6-mA in mammalian brain development, potentially exhibiting cell type specificity.

overall_design: 1.Establishment of NTD Mouse Model: MTX is a folate antagonist. Under conditions of low folate diet in pregnant mice, we intraperitoneally injected MTX (1.5 mg/kg) at gestational day 7.5. We began observing the closure status of the neural tube in fetal mice during the neural tube closure window at E9.5-10.5. Normal mice appeared plump and round, with fully closed neural tubes, and were categorized into the normal group. Embryos from mice on low folate diet and injected with MTX exhibited varying degrees of developmental delay, smaller embryos, and primarily showed phenotypes of hindbrain malformations and spina bifida, and were categorized into the NTD group. 6mA MeDIP was performed on normal and NTD fetal brains to investigate the genomic localization of DNA 6mA and identify genomic regions enriched with DNA 6mA（IP Repeat in groups of three）. 2.Constructing a low-folate cell line：After resuscitating normal mESCs, Sv129 cells were randomly split into FA4 and FA0. The FA0 group uses folate-free mESCs culture medium.Folate (Sigma) was added to the medium of FA0 as medium of the FA4 group(final concentration: 4 mg/L).  Next, two groups were added correspond medium and were cultured at 37°C with 5% CO2 in a humidified incubator and passaged every 2–3 days. The culture medium was changed daily. 6mA MeDIP was performed on FA4 and FA0 groups to investigate the genomic localization of DNA 6mA and identify genomic regions enriched with DNA 6mA.


title: DNA methylation profiles in seven mutant NPCs and wt NPCs (control, empty vector) at 2 days [LM17-Lm24]

summary: To investigate temporal DNA methylation changes occurring during human neural progenitor cells (NPCs) maintenance in early times via genomic DNA methylation measurement by Infinium MethylationEPIC BeadChip assay, we introduced IDH1-R132H, KRAS-G12C, TP53-R273C, BRAF-V600E, NRAS-Q61R, HRAS-Q61R, and SOX17-S403I mutations separately into NPCs at day 0, with dox induction for 2 days to overexpress the oncogenes. After 2 days of induction, we investigated the DNA methylation profiles in NPCs, in order to investigate the epigenetic change during oncogene induction.

overall_design: We introduced each oncogene into individual wt NPCs, using dox to overexpress the GoF mutation gene for 2 days, then performed an Infinium MethylationEPIC BeadChip assays. Stanford Functional Genomics Facility (SFGF) using the Infinium MethylationEPIC array which interrogates over 850,000 methylation sites at single-nucleotide resolution.


title: DNA methylation profiles in seven mutant hESCs and wt hESCs(control, empty vector) at 9 days

summary: To investigate the effect of oncogenic mutations on genome-wide DNA methylation in stem cells, we performed an Infinium MethylationEPIC BeadChip assays. To clarify that the epigenetic change is caused only by one oncogenic mutation, we introduced each oncogene into individual wt hESCs, using dox to overexpress the GoF mutation gene for nine days. The DNA methylation profiles demonstrated that the seven mutant hESCs and wt hESCs as control (empty vector) were distinguished by DNA methylated gene loci.

overall_design: We introduced each oncogene into individual wt hESCs, using dox to overexpress the GoF mutation gene for nine days, then performed an Infinium MethylationEPIC BeadChip assays. Stanford Functional Genomics Facility (SFGF) using the Infinium MethylationEPIC array which interrogates over 850,000 methylation sites at single-nucleotide resolution.

first: Yongjin

last: Yoo


title: DNA methylation profiles in 3 mutant iN cells and wt iN cells (control, empty vector) at 2 days

summary: To investigate temporal DNA methylation changes occurring during NPC maintenance in later times via genomic DNA methylation measurement by Infinium MethylationEPIC BeadChip assay, we introduced IDH1-R132H, KRAS-G12C, and TP53-R273C, mutations separately into NPCs at day 0, with dox induction for 10 days to overexpress the oncogenes. After 10 days of induction, we differentiated the NPCs into iN cells for two more days, in order to investigate the epigenetic change during differentiation at increase temporal resolution.

overall_design: We introduced each oncogene into individual wt NPCs, using dox to overexpress the GoF mutation gene for 10 days, then differentiated the NPCs into iN cells for two more days,  performed an Infinium MethylationEPIC BeadChip assays. Stanford Functional Genomics Facility (SFGF) using the Infinium MethylationEPIC array which interrogates over 850,000 methylation sites at single-nucleotide resolution.


title: DNA methylation profiles in seven mutant NPCs and wt NPCs (control, empty vector) at 2 days


title: rRNA processing is surveilled by the mRNA guard protein Npl3

city: Göttingen

first: Heike

last: Krebber

address: Grisebachstraße 8

department: Molecular Genetics

institute: Georg-August Universität Göttingen

summary: Ribosomes mature stepwise on a long precursor-rRNA, the 35S rRNA in Saccharomyces cerevisiae. Successive cleavage and protein association generates the small and large subunits that join each other for translation. If the maturation encounters difficulties, pre-rRNA cleavage occurs irrevocably at site A3, generating the aberrant 23S rRNA that is degraded. We show that the mRNA guard protein Npl3 functions in rRNA maturation and its surveillance. In its absence, the early SSU processome assembly is disturbed as the ETS1 accumulates and some proteins are not loaded properly onto the rRNA. Additionally, the amount of the 23S rRNA increases, which indicates a novel role of Npl3 its removal. For this quality control function, Npl3 binds to the nascent pre-rRNA in a complex with the TRAMP-complex component Air1, but independently of Trf5. Although Trf5 is still able to mark such RNAs with an oligo d(T) sequence in npl3∆, this signal is not sufficient for full TRAMP complex assembly. Rather, the Npl3-mediated loading of Air1 supports the exosome recruitment and the elimination of the 23S rRNA. Thus, Npl3 represents a general RNA surveillance factor that clears the cell from faulty mRNA and rRNA products by recognition of processing defects and guiding degrading enzymes.

overall_design: To investigate the role of Npl3 in the rRNA quality control, we sequenced rRNA in wild type cells and in the deletion strain npl3∆.

first: Anne-Sophie

last: Lindemann

first: Ivo

last: Coban


title: JAK-STAT SIGNALING DRIVES AUTOIMMUNE DIABETES IN LEW.1WR1 RATS

city: Worcester

first: Alan

last: Derr

state: Massachusetts

address: 55 Lake Ave North

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

summary: Pancreatic islet cell populations in poly I:C + KRV-infected Ifnar1-/- LEW.1WR1 rats were compared to those of WT LEW.1WR1 rats to identify compensatory mechanism in endocrine cells that appear to lead to autoimmume diabetes in the infected Ifnar1-/- rats.

overall_design:
Pancreatic islet cells were extracted from LEW.1WR1 rats on Day 11 post-treatment under three conditions - PBS (no-treatment control), injections of polyinosine-polycytidylic acid (poly I:C) on days -3, -2, and -1 (no-KRV control), and poly I:C treatment followed by injection of KRV (Kilham rat virus) on day 0. For the poly IC+KRV treatment pancreatic islet cells were also extracted on days 7 and 9 post-treatment to observe the onset of insulitis over time.
10X single-cell RNA-Seq was performed on each sample and bioinformatic and imaging analysis was applied to identify the cell type subsets and identify the genes and spatial distribution of cells involved in the onset of autoimmune diabetes.

first: Adediwura

last: Arowosegbe

first: Zhiru

last: Guo

first: Emma

last: Vanderleeden

first: Jennifer

middle: P


title: Tracing immunological interaction in trimethylamine N-oxide hydrogel-derived zwitterionic microenvironment during promoted diabetic wound regeneration

city: ｂｅｉｊｉｎｇ

first: Zheng

last: Li

address: 22 Zhongguancun South Avenue

institute: Peking University School and Hospital of Stomatology

summary: The diabetic wound healing is challenging due to the sabotaged delicate balance of immune regulation via an undetermined pathophysiological mechanism, so it is crucial to decipher multicellular signatures underlying diabetic wound healing and seek therapeutic strategies. Here, we develop a strategy using novel trimethylamine N-oxide (TMAO)-derived zwitterionic hydrogel to promote diabetic wound healing, and explore the multi-cellular ecosystem around zwitterionic hydrogel, mapping out an overview of different cells in the zwitterionic microenvironment using single-cell RNA sequencing. The diverse cellular heterogeneity has been revealed, highlighting the critical role of macrophage and neutrophils in managing diabetic wound healing. It is found that zwitterionic hydrogel can upregulate chemokine-secreted macrophages and downregulate extracellular traps (NETs)-neutrophils and facilitate their interactions compared with polyanionic and polycationic hydrogels, validating the underlying effect of zwitterionic microenvironment on the activation of adaptive immune system. These findings expand our horizons of the sophisticated orchestration of immune systems in zwitterion-directed diabetic wound repair and uncover new strategies of novel immunoregulatory biomaterials.

overall_design: We examined the role of zwitterionic hydrogel, polyanionic hydrogel (A1-A4) and a polycationic hydrogel (C1-C4) on diabetic wound regeneration. Then we explored how the zwitterionic hydrogel regulate immune microenvironment by scRNA-seq.

first: Longwei

first: Muxin

last: Yue

first: Qingyu

last: Peng

first: Xiong

last: Pu

first: Yongsheng

last: Zhou


title: EZH2-targeted PROTACs target the EZH2/FOXM1 axis and reduce breast cancer cell growth

first: Joshua

last: Corbin

overall_design: RNA-seq was utilized to assess transcriptomic profiles of T47D, T47D-TR and BT-549 cell lines treated with 2.5 uM MS177 (EZH2-targeted PROTAC) in addition to negative controls (MS177-N1 and MS177-N2), C24 (EZH2 methyltransferase inhibitor) or 0.125% DMSO vehicle control. Cells were treated for 48 hours prior to RNA extraction. RNA-seq was also utilized to assess transcriptomic profiles of the T47D-TR cell line treated with 2.5 uM MS8815 (EZH2-targeted PROTAC), MS8815-N (negative control), EPZ-6438 (EZH2 methyltransferase inhibitor) or 0.05% DMSO vehicle control. Cells were treated for 30 hours prior to RNA extraction.

first: Gang

last: Wang

first: Ling

last: Cai


title: STAG3 promotes exit from pluripotency through post-transcriptional mRNA regulation in the cytoplasm.

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building

department: Cancer Institute

country: United Kingdom

institute: University College London

summary: STAG proteins are key regulators of the cohesin complex and are often linked to alterations in cell identity and disease. Among the mammalian STAG paralogs, STAG3 has been less extensively studied beyond its known roles in meiosis. In this study, we demonstrate that STAG3 is expressed in mouse embryonic stem cells (mESCs) and primordial germ cell-like cells (PGCLCs), where it is required for cell fate decisions. Distinct from the other STAG proteins, STAG3 mediates its effects in the cytoplasm, facilitating the post-transcriptional regulation of gene expression. Furthermore, STAG3 localizes to the centrosome independently of cohesin and interacts with proteins involved in mRNA localization and stability. The knockdown of STAG3 in mESCs using siRNAs results in the destabilization of the centrosome and the key P-body RNA-induced silencing complex (RISC) component TNRC6C, leading to the derepression of P-body localised mRNAs, such as DPPA3. Our results propose a model in which STAG3 collaborates with RNA-binding proteins (RBPs) and specific target mRNAs to control post-transcriptional gene expression and facilitate the transition from pluripotency in mESCs. Given that STAG3 is upregulated in various cancers, our results provide a novel perspective on how STAG proteins might contribute to cell identity and disease.

overall_design: Wildtype (WT) E14 mouse embryonic stem cells (mESC) were cultured in naïve (2i/LIF) conditions. Three biological replicates of either untreated (UT) mESCs or mESCs treated for 48hrs with control (Luciferase, siLuc) or Stag3 siRNAs were collected.  Total RNA was isolated using NEB Monarch RNA prep kit for transcriptome analysis by bulk Illumina RNA sequencing .

first: Sam

middle: L

last: Weeks

first: Dubravka

last: Pezic

first: Martin

last: Dodel

first: Kunal

last: Shah

first: Amandeep

last: Bharma

first: Benjamin

last: Taylor

first: Tyson

middle: V

last: Sharp

first: Faraz

last: Mardakheh

first: Suzana

last: Hadjur


title: Chemical Screening Identified Compounds That Trigger Differentiation and Augment ATRA-Induced Myeloid Cell Differentiation

city: Shanghai

first: Xiaona

last: Wei

address: Shanghai Jiaotong University, Shanghai, China

institute: Shanghai Jiaotong University

summary: Acute myeloid leukemia (AML) is a blood cancer characterized by abnormal proliferation and differentiation arrest of myeloid progenitor cells. Clinical treatment of AMLs remains challenging. Promoting AML cell differentiation is a valid therapeutic strategy. But most AMLs lack effective differentiation drugs. In this study, we generated Tg(drl:hoxa9) zebrafish, which drives hoxa9 overexpression in hematopoietic cells and exhibits myeloid differentiation arrest. Using Tg(drl:hoxa9) embryos, we performed a chemical screen and identified four FDA-approved drugs, ethacrynic acid, khellin, oxcarbazepine and alendronate, that efficiently restored myeloid differentiation in embryos. The four drugs also induced the differentiation of AML cells, with ethacrynic acid being the most effective. By RNA-seq analysis, we found that during induction of differentiation, ethacrynic acid activates the IL-17 and MAPK signaling pathways, which are known to promote granulopoiesis. Furthermore, we found that ethacrynic acid enhances all-trans retinoic acid (ATRA)-induced myeloid differentiation, and the two signaling are convergent on the IL-17/MAPK pathways. Inhibition of IL-17 /MAPK pathways impairs ethacrynic acid and ATRA-induced differentiation. In addition, we showed that ethacrynic acid is less toxic to embryonic development and less disruptive to normal hematopoietic processes than ATRA. Thus, the combination of ethacrynic acid and ATRA may have a broader clinical application. In conclusion, through zebrafish-aided screening, our study identified four drugs repurposed to induce AML differentiation and provided new agents for AML therapy.

overall_design: To investigate the effects of Ethacrynic acid on myeloid differentiation, we performed RNA-sequencing analysis for transcriptomic changes of AML cells after Ethacrynic acid treatment.

first: Wei


title: Uchl1 maintains energy and metabolic homeostatic balance during spermatogenesis

city: xian yang

first: donghui

last: Yang

state: shaanxi

address: No. 3rd, Taicheng Road, Yangling, Shaanxi

institute: Northwest A&F University

summary: In mammals, spermatogenesis plays a critical role in upholding the genetic stability of the male germline; however, disruptions such as viral and bacterial infections, toxic damage, genetic mutations, or deletions can disturb the delicate equilibrium of the testicular microenvironment, ultimately resulting in impaired spermatogenesis and male infertility. One key protein involved in this process is UCHL1, which possesses deubiquitinating enzyme, multiple ligases, and hydrolase activities. In addition to its roles in maintaining neuronal activity and memory function in the brain, UCHL1 is also implicated in spermatogenesis. Nevertheless, the precise mechanism by which it sustains metabolic homeostasis during spermatogenesis remains unclear. To investigate this, we generated Uchl1_KO mice and subjected their testes to snRNA-seq and metabolomics sequencing. Our analysis revealed that Uchl1_KO mice exhibited abnormal spermatogenesis, decreased testicular OXHPOS levels, and disrupted ADIPONECTIN signaling, concomitant with heightened inflammatory signaling and disturbances in lipid metabolism and energy homeostasis in the testes. These findings suggest that Uchl1 plays a crucial role in spermatogenesis by modulating energy and metabolic pathways within the testes to maintain orderly spermatogenesis. This study contributes to the understanding of the energy and metabolic balance required for successful male spermatogenesis.

overall_design: The precise mechanism by which it sustains metabolic homeostasis during spermatogenesis remains unclear. To investigate this, we generated Uchl1_KO mice and subjected their testes to snRNA-seq and metabolomics sequencing.

first: Donghui

first: Wenbo

last: Chen

first: Ning

last: Zhang

first: Mengfei


title: Engineered methionine adenosyltransferase cascades for metabolic labeling of individual DNA methylomes in live cells

city: Vilnius

first: Kotryna

last: Kvederaviciute

address: Sauletekio av. 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

summary: Methylation, a widely occurring natural modification serving diverse regulatory and structural functions, is carried out by a myriad of S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases (MTases). The AdoMet cofactor is produced from L-methionine  and ATP by a family of multimeric methionine adenosyltransferases (MAT). To advance mechanistic and functional studies, strategies for repurposing the MAT and MTase reactions to accept extended versions of the transferable group have been exploited. We installed two of the engineered variants as Mat2a-Dnmt1 cascades in mouse embryonic stem cells using CRISPR-Cas genome editing. The resulting cell lines showed Dnmt1-dependent DNA modification with extended azide tags upon exposure to methionine analogs in the presence of physiological levels of Met.

overall_design: Genetically stable system for biosynthetic production of an extended AdoMet analog which enables metabolic labeling of a DNMT-specific methylome under methionine abundance in mouse embryonic stem cells. Mouse Dnmt1-directed DNA modifications were analyzed in E14TG2a cells bearing engineered Dnmt1 and Mat2a following the incubation with S-(6-azidohex-2-ynyl)-l-homocysteine. Wild-type Dnmt1 and Mat2a cells were used as a control. All experiments were carried out in triplicates.

first: Liepa

last: Gasiule

first: Vaidotas

last: Stankevius

first: Saulius

last: Klimasauskas


title: Deep Mutational Scan of a DNA Polymerase via Compartmentalized Self-Replication

city: Seattle

first: Nicholas

middle: Anthony

last: Popp

email: poppn@uw.edu, poppn13@gmail.com

state: Washington

address: 3720 15th Avenue NE, S-320

department: Genome Sciences

institute: University of Washington School of Medicine

summary: We present a novel platform for high-resolution mapping of DNA polymerase activity and stability under the effects of harsh chemistries that are incompatible with most other mutational scanning methods. This approach pairs compartmentalized self-replication (CSR), a high-throughput method for polymerase directed evolution, with deep mutational scanning (DMS), a method of quantifying variant effect via next-generation sequencing of libraries that are subjected to a functional selection. We demonstrate the validity of this “CSR-DMS” platform by showing that it identifies loss-of-function variants at sites with known DNA binding or catalytic activity in the wild-type protein. We further explore the efficacy of this method by imposing denaturing selective pressures (heat or guanidinium thiocyanate) during screening and showing that variants with high positive enrichment under these selective pressures possess higher resistance to denaturation in activity assays. These variants may be useful for “direct” diagnostic workflows that detect biomarkers from crude sample matrices with little to no sample purification. Furthermore, the mechanisms of stabilizing mutations can be inferred from trends in the scores of similar mutations in sequence-to-function heatmaps and corroborated by the behavior of residues of interest in molecular dynamics simulations of the wild-type protein. These mechanisms, uncovered by CSR-DMS, inform future approaches to rational design of extremely stable DNA polymerases. Overall, we propose that CSR-DMS could be used both for the study of the biophysical mechanisms of selective pressures and for the engineering of polymerases with novel capabilities.

overall_design: A barcoded single amino acid variant library of DNA polymerase spanning its entire sequence was expressed in E. coli. Cells were encapsulated in oil-aqueous emulsion droplets and subjected to PCR cycling either alone, in conjunction with excessive heat treatment, or in conjunction with added guanidinium. The PCR cycling forced variant polymerases to amplify barcode sequences from their own coding plasmids under a "compartmentalized self-replication" selection scheme. The emulsion was broken after 20 cycles of PCR and barcoded DNA fragments were isolated and sequenced with Illumina sequencing. Barcodes were associated back to corresponding DNA polymerase variants by comparison with a barcode-variant map created by sequencing the variant library plasmid using PacBio HiFi long-read sequencing.

first: Ian

middle: T

last: Hull

middle: A

first: Enos

middle: C

last: Kline

first: Rachel

last: Powell

first: Melinda

middle: K

last: Wheelock

first: Matthew

last: Childers

first: Qin

last: Wang

first: Valerie

last: Daggett

first: Douglas

middle: M

last: Fowler

first: Barry

last: Lutz


title: Transcriptome reveals Fusarium graminearum gene expression patterns under pH stress

city: Shenzhen

first: Yuping

last: Shang

address: Dapeng district

institute: Chinese Agricultral Academay

summary: 【Objective】 The objective of this study is to study the transcriptome regulation mechanism of F. graminearum under different pH stress conditions, analyze the gene expression level and its differences, and explore the metabolic pathways related to the anti-stress response of F. graminearum cells under acidic or alkaline conditions, and reveal how F. graminearum actively regulates intracellular metabolism and synthesis processes to adapt to the changes of extracellular pH environment. 【Method】 F. graminearum was cultured in PDB (potato dextrose broth) medium with initial pH of 4.5, 6.5 and 8.0 for 48 h, and the total RNA of the strain was extracted to construct a cDNA library. Transcriptome sequencing and bioinformatics techniques were used to identify the related differentially expressed genes (DEGs), and the metabolic pathways involved were further analyzed. 【Result】 A total of 4283 DEGs were detected under acidic conditions, of which 2232 were up-regulated and 2252 were down-regulated. Under alkaline conditions, there were a total of 498 DEGs, of which 269 were up-regulated and 229 were down-regulated. The results of Gene Ontology (GO) functional enrichment analysis showed that 211 GO terms were significantly enriched and 72 were down-regulated under acidic conditions. There were 33 GO terms that were revised upwards and 40 downwards under alkaline conditions. The results of KEGG encyclopedia of genes and Genomes (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis showed that 22 pathways were significantly enriched and 32 pathways were down-regulated under acidic conditions. There were 8 up-regulated pathways and 13 down-regulated pathways under alkaline conditions. The expression of membrane transporters and hydrolysis of carbohydrate compounds and other related genes were up-regulated, and the expression of genes related to protein metabolism was down-regulated, which assisted F. graminearum cells to adapt to changes in the external environment. At the same time, F. graminearum maintained the internal environment balance of its own cells by reducing secondary metabolism and amino acid metabolism under acidic and alkaline conditions, respectively, so as to resist extracellular pH stress. 【Conclusion】 In the acidic environment, Fusarium graminearum adapts to the changes in the extracellular environment by promoting the production of riboprotein complexes and secondary metabolism. In an alkaline environment, Fusarium graminearum cells respond to and sense external stresses through amino acid metabolism. The analysis of the metabolic pathways of F. graminearum cells provides important gene expression data for the response of F. graminearum to different pH environments, and the results of this study are helpful to understand the pathogenesis of F. graminearum.

overall_design: In order to further understand the gene expression pattern of Fusarium graminearum under acid-base stress, we cultured Fusarium graminearum in PDB (potato dextrose broth) medium with initial pH of 4.5, 6.5 and 8.0 for 48 h, extracted the total RNA of the strains, and constructed a cDNA library. The mRNA-seq libraries were constructed according to the manufacturer's protocol (NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)) and duplexed on the Illumina NovaSeq 6000 platform.

first: Cuijun


title: Xap5 protects against necrotic apoptosis induced by overdevelopment in adipocytes.

city: Wuhan

first: Haochen

last: Jiang

address: No.9. BoXue Road, economic development District

institute: Jianghan university

summary: The development and death of adipocytes play a crucial role in the metabolic stability of the body. We report that Xap5 plays a significant role in the development and death of adipocytes. The specific knockout of Xap5 in mature adipocytes leads to severe lipodystrophy in mice, subsequently causing metabolic disorders. By analyzing the development process of wild-type and Xap5 knockout adipocytes in vivo and in vitro, we found that the adipose deficiency caused by Xap5 knockout is mainly due to necroptosis caused by excessive development of adipocytes. Our results reveal a previously unrecognized role of Xap5 in adipocyte development and homeostasis.

overall_design: To understand the physiological significance and function of Xap5 in regulating adipocyte development and cell death, we generated mature adipocyte-specific Xap5 knockout (KO) mice (Adiponectin-cKO mice). We then conducted gene expression profiling analysis using data from RNA-seq from white adipose tissue (WAT) of Xap5 wild-type (WT) and Adiponectin-cKO mice at postnatal day 42 (P42), and in-vitro cultured adipocytes of Xap5 WT and cKO mice after 8 days of adipogenic induction.

first: Mengting

last: Hua

first: Mei

last: Ding

first: Zhangfeng

last: Hu


title: A humanized neuronal model system reveals key roles for the trace element manganese in neuronal endocytosis, calcium flux and mitochondrial bioenergetics

first: Dimitri

last: Budinger

address: 30 guilford street

institute: university college london

summary: Manganese (Mn) is an essential trace metal that is necessary for life. Its duality as both a crucial micronutrient and potential neurotoxicant necessitates tight control of intracellular and extracellular Mn levels. Dysregulation of Mn is implicated in a broad range of human diseases, from neurodevelopmental sequelae related to Mn levels in drinking water, to acquired forms of manganism, rare inherited Mn transportopathies and more common disorders such as Parkinson’s and Alzheimer’s disease. Despite the clear association between Mn dysregulation and neurodevelopmental or neurodegenerative diseases, the underlying cellular mechanisms that govern neuropathology remain poorly understood. We established a humanised midbrain neuronal system to better understand the neuronal sequelae of Mn dysregulation. By integrating transcriptomic and functional approaches, we show that Mn dyshomeostasis leads to dysregulation of key cellular pathways that are crucial to normal neuronal function, including defects in mitochondrial bioenergetics, calcium signalling, endocytosis, and glycosylation, as well as cellular stress and early neurodegeneration. Our humanized model has enhanced understanding of the role of Mn in the human brain, and the consequences of both acquired and genetic disorders associated with Mn dysregulation. Better understanding of these underlying pathophysiological processes will identify potential targets for future therapeutic intervention.

overall_design: Aged-matched healthy Controls (2) and 6 patient lines with SLC39A14, SLC30A10 and SLC39A8 deficient patients iPSCs-derived midbrain dopaminergic neurons (3 biological replicates each). These lines were analysed in both basal condition and manganese toxic overexposure (100uM for 48h). Neurons were 65 days when collected.

first: Manju

last: Kurian


title: Gata2 promotes drug resistance in Acute Myeloid Leukemia (AML)

city: Philadelphia

first: Kathrin

last: Bernt

state: PA

address: 3501 Civic Center Boulevard,

institute: Children's Hospital of philadelphia

summary: In this study, we generated mouse models of MLL-AF9-driven AML (MA9) harboring conditional alleles for Gata2 gene to precisely investigate the role of Gata2 in drug resistance and progression of MLL-rearranged (MLL-r) AML. Our findings revealed a novel mechanism for Gata2 in blunting p53 mediated apoptosis via transcriptional repression of Rassf4, a regulator of Mdm2 protein stability.

overall_design: ChIP-seq of  H3K27ac in murine Gata2 f/f and Gata2 -/- (Gata2 KO) MA9 cells.

first: Fatemeh

last: Alikarami

first: Michael

last: Xie


title: Expression data of brain arteries from Wistar rats

city: Puerto Real

first: Maria del Carmen

last: González Montelongo

state: Cádiz

address: Calle Esparraguera 111

country: Spain

institute: University of Cádiz

summary:
Aneurismal subarachnoid hemorrhage (aSAH) is a neurovascular disease characterized by blood released into the subarachnoid space due to cerebral arteries rupture. After the onset of bleeding, secondary associated vasospasm (VSP) remains a dramatic side effect that causes severe comorbidities.
In brain arteries from SAH (and control) animals we performed a total RNA extraction and a microarray analysis of cerebral arteries from animals 7 days after surgery to study the long-term transcriptional effects induced by SAH

overall_design: Male wistar rats (400 g approximately and six months old) were divided into three groups: control, sham7d, and SAH7d. 100 µL of cerebrospinal fluid was removed from the cisterna magna through the posterior atlanto-occipital membrane. Then, in the SAH group, 100 µL of blood was obtained from the caudal vein and immediately injected intracisternally. In the sham group the same procedures were performed, using the same volume of saline. The control group did not receive any surgery. For RNA analysis, whole brains were obtained and arteries were cleaned under a magnifying glass in ice-cold RNAses-free Hank’s solution, immediately frozen in liquid nitrogen and stored at -80 ºC.The homogenization of the arteries was performed the RNeasy® Micro Kit.The amplified cDNA was quantified, fragmented and labeled for hybridization with GeneChip® Clariom S Rat Array.

first: Gonzalo

last: Revilla-González

first: Francisco

last: Morón-Civantos


title: Wars1 loss-of-function in the liver identifies a unique cytosol-to-mitochondria stress response.

city: Lausanne

first: Francesca

last: Pontanari

address: Route Cantonale

department: SV

country: Switzerland

institute: EPFL

summary: Several laboratories, including ours, have used the Slc25a47tm1c(EUCOMM)Hmgu mouse model to characterize the role of SLC25A47, an hepatocyte-specific mitochondrial carrier, in hepatic metabolism and systemic physiology. In this study, we report that the hepatic and systemic phenotypes observed in Slc25a47tm1c(EUCOMM)Hmgu mouse model upon recombination of the Slc25a47-Wars1 locus, are driven by the unanticipated downregulation of Wars1, the cytosolic tryptophan aminoacyl-tRNA synthetase whose gene is located in close vicinity to Slc25a47. We show that downregulation of Wars1 in hepatocytes not only impacts on cytosolic translation, as expected, but also impairs the ability of hepatic mitochondria to translate proteins eventually leading to a profound activation of the mitochondrial unfolded protein response (UPRmt), an integral part of the mitochondrial stress response (MSR). Our results clarify the respective roles of Slc25a47 and Wars1 in both systemic and hepatic metabolism and suggest that a bidirectional stress communication system operates in the mammalian liver between the cytosol and mitochondria highlighting the complexity and promiscuity of cellular stress mechanisms. This newly identified anterograde pathway complements the previously recognized Mitochondrial-to-Cytosolic Stress Response (MCSR), which we propose to call the Cytosolic-to-Mitochondrial Stress Response (CMSR).

overall_design: Slc25a47-Wars1lox/lox mice were injected with AAV8_hAAT_Cre to induce the recombination of the locus. These mice were co-injected with Slc25a47 or Wars1 to validate which gene was the main driver of the observed phenotypes upon locus recombination. Control mice for Cre were co-injected with Gfp while mice not undergoing recombination were injected with Gfp alone. The viruses were under the hAAT promoter, therefore the recombination is specifically targeted to hepatocytes. Each condition was replicated in 6 mice.

first: Hadrien

last: Demagny

first: Adrien

last: Faure

first: Xiaoxu

last: Li

first: Giorgia

last: Benegiamo

first: Antoine

last: Jalil

first: Alessia

last: Perino

first: Kristina

last: Schoonjans

first: Johan

last: Auwerx


title: Adaptive immunity to retroelements promotes barrier integrity [bulk_CD8]

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

summary: The skin is the body’s largest and outermost barrier tissue. Whether environmental exposures reinforce barrier resilience remains poorly understood. Here, we show that xenobiotic-induced retroelement-specific immunity enhances tissue repair; more specifically, mild detergent exposure promotes the reactivation of defined retroelements, and retroelement-specific CD8+ responses, in a Langerhans cell-dependent manner. This discrete population of retroelement-specific CD8 T cells are recruited to the skin, where they develop as tissue-resident cells and are enriched for genes associated with wound repair. Upon injury, retroelement-specific CD8+ T cells significantly accelerate wound repair via IL-17A. Collectively, this work demonstrates that tonic environmental exposures promote the accumulation of tissue-resident retroelement-specific T cells that preemptively set the tissue for maximal resilience to barrier breaches.

overall_design: RNA-seq from CD8+ T cells (CCR6+ and CCR6-) from ear skin of mice treated with HSV1 (CCR6- cells) and BHI-tween (CCR6+ cells)

first: Alexandria

last: Wells


title: Adaptive immunity to retroelements promotes barrier integrity [single_cell_CD8]

overall_design: single cell RNA-seq from CD8 T cells from mouse skin in mice treated with BHI-tween or HSV-1


title: Adaptive immunity to retroelements promotes barrier integrity [bulk_DC_KC_LC]

overall_design: bulk RNA-seq from dendritic cells, keratinocytes and langerhans cells from mouse ear skin under control conditions or treated with BHI-tween.


title: Experimental treatment of gonarthrosis using infrared laser

city: Moscow

first: Evgeny

last: Karpulevich

address: Alexandra Solzhenitsina

institute: ISP RAS

summary: Study of single cell transcriptomics of synovial fluid of patients with gonarthrosis before and after exposure to infrared laser.

overall_design: In a patient with secondary post-traumatic arthrosis of the 2nd degree and a patient with local injuries of the knee joint, synovial fluid was collected, cells were isolated and frozen. Then the first patient underwent irradiation with an infrared laser (10 sessions), his pain syndrome was assessed and the synovial fluid was re-sampled, cells were isolated and frozen from it. The samples were then analyzed using single cell transcriptomic analysis

first: Polina

last: Vishnyakova

first: Pavel

last: Petrov

first: Tatiana

last: Gerashchenko

first: Miroslava

last: Chirkova


title: Adaptive immunity to retroelements promotes barrier integrity [bulk_whole_tissue]

overall_design: RNA-seq from whole ear tissue from untreated mice, mice treated with BHI-tween or Stapholococcus epidermidis


title: Transcriptomic analysis after proton and neutron therapy

summary: Study of molecular signatures in three types of objects after proton (human) and neutron (cell model, xenograft) irradiation

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: The aim of the study was to establish common and distinct molecular signatures activated by particle therapy in three types of objects - patient material (tumor tissue and peritumoral tissue) from patients with head and neck cancer, in a cell line of a human larynx strain in the form of a tumoroid obtained at ultra-low adhesion plastic and in a cell strain of the larynx, implanted subcutaneously in an immunodeficient mouse. Irradiation was carried out at an installation at the Medical Radiological Research Center named after. A.F. Tsyba with a final total dose of 10 Gy.

first: Konstantin

last: Gordon


title: Long‐term combination therapy with metformin and oxymetholone in a Fanconi anemia mouse model

city: Portland

first: Craig

last: Dorrell

state: OR

address: 3181 SW Sam Jackson Park Rd.

department: Pediatrics

institute: OHSU

summary: Fanconi anemia (FA) is a disease caused by defective deoxyribonucleic acid (DNA) repair that manifests as bone marrow failure, cancer predisposition, and developmental defects. We previously reported that monotherapy with either metformin (MET) or oxymetholone (OXM) improved peripheral blood (PB) counts and the number and functionality of bone marrow hematopoietic stem progenitor cells (HSPCs) number inFancd2−/−mice. To evaluate whether the combination treatment of these drugs has a synergistic effect to prevent bone marrow failure in FA, we treated cohorts ofFancd2−/−mice and wildtype controls with either MET alone, OXM alone, MET+OXM, or placebo diet from age 3weeks to 18months. The OXM treated animals showed modest improvements in blood parameters including platelet count (p=.01) and hemoglobin levels (p<.05). In addition, the percentage of quiescent hematopoietic stem cell (HSC) (LSK [Lin−Sca+c‐Kit+]) was significantly increased (p=.001) by long‐term treatment with MET alone. The combination of metformin and oxymetholone did not result in a significant synergistic effect in any hematopoietic parameter. Gene expression analysis of liver tissue from these animals showed that some of the expression changes caused byFancd2deletion were partially normalized by metformin treatment. Importantly, no adverse effects of the individual or combination therapies were observed, despite the long‐term administration. We conclude that androgen therapy is not a contraindication to concurrent metformin administration in clinical trials.

overall_design: Liver samples were collected from sex-matched (male) mice after 18 months of treatment. RNA was isolated and cDNA libraries constructed from five groups: wildtype untreated, Fancd2 mutant untreated, Fancd2 mutant metformin-treated, fancd2 mutant oxymetholone-treated, and fancd2 mutant metformin+oxymetholone treated

first: Suzanne

last: Fei


title: Computational design of potent and selective BAK and BAX binders

first: David

last: Baker

state: WA

address: Molecular Engineering and Sciences, Box 351655

institute: University of Washington

summary: There are numerous binders of the pro-survival BCL2 family proteins such as BCL2, MCL1, and BCL-XL, but development of potent and selective binders of their pro-apoptotic counterparts BAK and BAX has remained a major unsolved challenge. We use computational protein design to generate 13 kDa binders of BAK and BAX with 400 pM and 3 nM affinity, orders of magnitude higher than any existing native or designed binder, and with greater than 100-fold specificity against pro-survival BCL2 family members. The crystal structure of the BAKᐧɑBAK2 complex is very close to the computational design model, with the binder making specific interactions extending out from the canonical BH3-binding groove. Liposome- and cell-based analyses reveal that ɑBAK2 inhibits membrane permeabilization when in excess of BAK, but activates BAK when BAK is in excess. Structural analyses indicate that binding of ɑBAK2 results in partial unfolding and exposure of BAK’s BH3 domain. Similar to ɑBAK2, ɑBAX2 activates BAX at low concentrations and does not activate BAX at high concentrations. This work provides valuable insight into design of small molecule or protein inhibitors of BAK and BAX; inhibition requires high affinity binding as well as a saturating concentration of binder at the site of action. Our designs are the first binders with the high specificity required for efficient modulation of apoptosis via direct interaction with BAK and BAX and they provide highly selective molecular probes for addressing outstanding cell biological questions about cell death.

overall_design: In the related work, proteins were computationally designed to bind BAK or BAX. Site-directed saturation mutagenesis libraries were generated based on the sequences of sub-optimal minibinders, transformed into yeast for surface display, and selected for high-affinity binding to each target, optionally in the presence of unlabeled competitors (other BCL2 homologs). Next generation sequencing analysis of the naive and selected pools was used to determine the fitness of each mutation for affinity and specificity.

first: Stephanie

last: Berger


title: Transcriptomic Analysis of C918 Cells Treated with 400μM Tetracaine Hydrochloride (TTC) for 24 Hours

city: luzhou

first: yi

last: peng

address: xianglinlu

institute: 西南医科大学

summary: This study aimed to investigate the transcriptomic changes in C918 cells upon treatment with 400μM tetracaine hydrochloride (TTC) for 24 hours. RNA-seq data were generated from TTC-treated and untreated control C918 cells to identify differentially expressed genes and pathways involved in the cellular response to TTC exposure. The findings may provide insights into the molecular mechanisms underlying the effects of TTC on C918 cells.

overall_design: The experiment involved two conditions: 1) C918 cells treated with 400μM TTC for 24 hours, and 2) C918 cells treated with an equivalent dose of PBS as a control. Three biological replicates were prepared for each condition. Total RNA was extracted, and RNA-seq libraries were constructed and sequenced using Illumina technology.

first: Jianguo

last: Feng

first: Peng

last: Yi

first: Ran

last: Zhang

first: Li

last: Liu


title: Transcriptome profiling of RBM3 overexpression in A431 cells

summary: This study aims to investigate the transcriptional changes induced by overexpression of RNA-binding protein RBM3 in A431 human epidermoid carcinoma cells. Lentiviral transduction was used to stably overexpress RBM3 in A431 cells. Total RNA was extracted from RBM3 overexpressing cells and control cells, followed by RNA-seq library preparation and sequencing on Illumina platform. Differential gene expression analysis will be performed to identify RBM3 targets and regulatory networks.

overall_design: A431 cells were transduced with lentivirus expressing RBM3 or EGFP control lentivirus. After puromycin selection, stable overexpressing cell lines were established and validated by western blot. Three biological replicates were prepared for each condition. Total RNA was extracted from validated stable cell lines and RNA integrity was verified. Poly(A) RNA was purified and used for strand-specific RNA-seq library construction with unique barcode indices. Libraries were multiplexed and sequenced on Illumina NovaSeq 6000 using paired-end 150bp reads.


title: scRNA-seq of Abdominal aortic  aneurysm tissues in Gsdme-KO mice

city: 上海

first: Zhen

state: 上海

address: 延长中路

department: Pharmacy

institute: Shanghai Tenth People's Hospital Tongji University School of Medicine

summary: The aim of this study was to explore the transciptome of the diverse vascular smooth muscle cells subsets from abdominal aortic aneurysm tissues in Gsdme deletion mice.The model was established by exposing the infrarenal aorta to PPE (porcine pancreatic elastase) under pressure to induce aneurysmal degeneration for 4 weeks.we compared the characteristics of SMC subpopulation beteew the WT and KO groupsto reveal the effect of GSDME in the progression of Abdomanl Aortic Aneurysm.

overall_design: AAA model was established by PPE infusion. The control group mice is C57BL/6J,the model group mice is Gsdme global deletion.the analysed sample was abdominal aorta.

first: Zhang

last: Zhen


title: A humanized therapeutic monoclonal anti-ASC antibody alleviates oxygen-induced retinopathy in mice

city: Miami

first: Augusto

middle: F

last: Schmidt

state: FL

address: 1611 NW 12th ave

institute: University of Miami Miller School of Medicine

summary: This study was to test the efficacy of a humanized monoclonal antibody, IC100 for ASC, an apoptosis-associated speck-like protein containing a caspase recruitment domain that is pivotal in inflammasome assembly, in the prevention and treatment of an oxygen-induced retinopathy (OIR) mouse model.

overall_design: To assess the effects of IC100, newborn mice (C57BL/6) were randomized to the following groups: room air (RA) with placebo (PBS) (RA-PBS), 75% O2 with PBS (O2-PBS), O2 + IC100 intravitreal injection (O2-IC100-IVT), and O2 + IC100 intraperitoneal injection (O2-IC100-IP). The mice were grown in RA from P1 to P6, then in 75% O2 from P7 to P11, and then to RA from P12 to P18. IC100 was given via IVT at P12 and IP at P12, P14, and P16.

first: Huijin

last: Yun

first: Shaoyi

last: Chen

first: Mattthew

last: Duncan

first: Juan

last: Rivero de Vaccari

first: Robert

last: Keane

first: Tsung-Han

last: Chou

first: Merline

last: Benny

first: Karen

last: Young

first: Vittorio

last: Porciatti

first: Mary

last: Harnett

first: Shu

last: Wu


title: Single cell transcriptomics of blood mononuclear cells in patients with preeclampsia

first: Evgeny

last: Karpulevich

summary: Study of single cell transcriptomics of PBMC from patients with preeclampsia and normal pregnancy

overall_design: The study compared changes occurring at the transcriptome level in umbilical cord blood PBMС during normal pregnancy and preeclampsia. During a cesarean section, after the placenta was removed, the umbilical vessel was punctured and blood was collected into EDTA tubes. Isolation of PBMC was carried out in a Ficoll density gradient for 20 min at 800 g with break 0. The PBMС ring was rinsed in PBS and frozen. The samples were then analyzed using single cell transcriptomic analysis

first: Polina

last: Vishnyakova

first: Tatiana

last: Gerashchenko

first: Miroslava

last: Chirkova


title: Characterization of the human testicular primary cells

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

summary: In this study, we carried out experiments using commercially available human testicular primary cells - hTPc (Celprogen, CA, USA), obtained from a 25-years old Caucasian man with normal karyotype 46,XY. To characterize the hTP cells, we used the commercial total RNA obtained from normal testicular tissues with preserved spermatogenesis (n=3) (Clontech Laboratories; Agilent Life Technologies, Carlsbad, CA, USA; Ambion Life Technologies, Carlsbad, CA, USA)

overall_design: We performed a comparative analysis of gene expression profiles by RNA-seq between: human testicular primary cells (hTPc) (n=3), the human testicular primary cells from another vial (hTPcIM) (n=3) and human testis with normal spermatogenesis (n=3)

first: Malcher

last: Agnieszka


title: Disulfide Tethering to Map Small Molecule Binding Sites Transcriptome-Wide

city: New Haven

first: Matthew

last: Simon

state: CT

address: 266 Whitney Ave

department: Molecular Biophysics and Biochemistry

institute: Yale University

summary: Tether-seq uses s4U metabolic labeling to provide sites for reversible and covalent attachment of small molecule disulfides to the transcriptome. By screening under reducing conditions, we are able to highlight interactions that are stabilized by binding over those driven by the reactivity of the RNA sites. When applied to cellular RNA, Tether-seq with a disulfide analogue of risdiplam (compound 2) revealed a number of potential binding sites. Structure probing by SHAPE-MaP revealed a structured motif and confirmed binding to the lead molecule.

overall_design: Tether-seq was performed using RNA from s4U-fed HEK293T cells, extracted under non-denaturing conditions. PNA samples were prepared using trizol-extracted s4U RNA. This involved xyz. Enrichment. TL chemistry. RNA sequencing libraries were prepared for all enrichment samples.

first: Michelle

middle: H

last: Moon

first: Isaac

middle: W

last: Vock

first: Andrew

middle: D

last: Streit

first: Leah

middle: J

last: Connor

first: Julia

last: Senkina

first: Jonathan

last: Ellman


title: Nucleoptosis: Nucleolar ISG20L2 mediates cell death through genomic DNA degradation

city: hangzhou

first: Hongyu

last: Lin

address: Zijingang Campus of Zhejiang University, 866 Yuhangtang Road, Xihu District

institute: Zhejiang University School of Medicine

summary: In this study, we employed  ChIP-seq to identify ISG20L2 directly interacts with genomic DNA during nucleoptosis in A549 cells

overall_design: A549 cells were infected with HSV-1 (MOI: 1) for 8 hours, and then collected, fixed and undergone chromatin cross-linking according to the manufacturer’s instructions using the SimpleChIP® Enzymatic Chromatin IP Kit (9003S, CST). The chromatin fragments specifically binding to ISG20L2 were enriched by anti-ISG20L2 antibody (24639-1-AP, Proteintech), and then the DNA was purified by QIAquick PCR Purification Kit (28104, QIANGEN). The purified DNA was then constructed for ChIP-seq library by Novogene (Beijing, China). The clean reads were aligned to human genome (GRCh38.p14) using BWA mem (v 0.7.12), and the IP enriched peaks were then analyzed by MACS2 (version 2.1.0).

first: Fengjiao

last: Lu

first: Jiang

last: Yang

first: Renjie

last: Song

first: Yang

last: Liu

first: Xuetao

last: Cao


title: Age-dependent transcriptome characterization of the rat neurohypophysis

city: Grand Forks

first: John

middle: Andrew

last: Watt

state: North Dakota

address: 504 Nth Hameline St

department: Biomedical Sciences

institute: University of North Dakota

summary: Our prior studies indicat age-dependent contralateral axonal sprouting within the neurohypophysis following unilateral lesion of magnocellular neurons.

overall_design: To understand the changes in the transcriptome that underlies this phenomenon, we performed RNA-seq and functional analysis of the rat neurohypophysis to determine changes in gene expression with age.

first: Derick

last: Thompson

first: Malak

last: Alzidaneen


title: Age-dependent DNA methylation characterization of the rat neurohypophysis

summary: Our prior studies indicat age-dependent contralateral axonal sprouting in the neurohypophysis following unilateral lesion of magnocellular neurons.

overall_design: We performed Oxford Nanopore sequencing of the rat neurohypophysis to determine changes in DNA methylation with age.


title: Tetrahydroberberrubine produces anti-obesity effect by activating PGC1α-mediated thermogenesis in white and brown adipose tissue

city: Harbin

first: yang

last: shi

address: No.157 Baojian Rd, Harbin, HEILONGJIANG

institute: Harbin medical university

summary: The increasing incidence of obesity poses great challenges and demands for developing effective therapeutic approaches. We aimed to reveal the anti-obesity effects of tetrahydroberberrubine (THBru), a derivative of berberine (BBR) and elucidate its underlying mechanism. The anti-obesity effects of THBru and BBR were assessed and compared using an obese mouse model induced by high fat diet (HFD). THBru was found to markedly ameliorated obesity, indicated by reduced body weight, decreased Lee’s index, lowered epididymal white adipose tissue (WAT) and brown adipose tissue (BAT) fat mass as well as improved dyslipidemia. At the same dose, THBru produced greater anti-obesity effects than BBR. RNA-sequencing and gene set enrichment analysis indicated THBru activated thermogenesis, which was further confirmed in WAT, BAT, and 3T3-L1 cells. Bioinformatics analysis of RNA-sequencing data revealed the candidate gene Pgc1α, a key regulator involved in thermogenesis. Moreover, THBru was demonstrated to elevate the expression of PGC1α by stabilizing its mRNA in WAT, BAT and 3T3-L1 cells. Furthermore, PGC1α knockdown blocked the pro-thermogenic and anti-obesity action of THBru both in vivo and in vitro. This study indicated THBru exerted anti-obesity effects by activating PGC1α-mediated thermogenesis and outlined its potential preventive and therapeutic implications for obesity and related diseases.

overall_design: To dissect the biological processes THBru regulated, WAT from HFD-induced mice with or without THBru (50 mg·kg-1·d-1) treatment was conducted RNA-sequencing

first: Yong

last: Zhang

first: Xin

first: Xueqing

last: Tang

last: Shi


title: Effects of Nogo-B receptor overexpression on transcriptomic profiling in the NIH3T3 fibroblast cell line

city: Mineola

first: Qing

middle: Robert

last: Miao

state: NY

address: 101 Mineola Blvd

department: Foundations of Medicine

institute: NYU Long Island School of Medicine

summary: Unrestrained receptor tyrosine kinase (RTK) signaling and epigenetic dysregulation are responsible in part for tumorigenesis. Aberrant RTK signaling results in the remodeling of histone modification. As a Ras modulator, NgBR promotes Ras-mediated RTK signaling pathways. Meanwhile, we observed that NgBR overexpression in NIH3T3 cells significantly increased the acetylation of histone H3 and histone H4. To further elucidate the underlying mechanism that NgBR upregulates histone acetylation in tumorigenesis, we carried out RNA-seq analysis to examine the transcriptome alternation in NIH3T3 cells and NgBR-overexpressed NIH3T3 cells (3T3NgBR cells) and revealed that overexpression of NgBR up-regulates ACSS2 expression, but not ACSS1 and ACSS3. Moreover. ACSS2 overexpression abrogated NgBR deficiency-caused decrease of histone acetylation in NIH3T3 cells. Taken together, all the data suggested that NgBR regulates tumorigenesis in NIH3T3 cells via ACSS2-mediated histone acetylation.

overall_design: Comparative gene expression analysis of RNASeq data for NIH3T3 cells (wild type) and NgBR overexpressed NIH3T3 cell (3T3NgBR).

first: Wenquan

last: Hu

first: Xiang

last: Wang

first: Munichandra

middle: B

last: Tirumalasetty

middle: R


title: Single-cell mass cytometry and transcriptomic profiling of circulating immune cells identifies an expansion of CD25hi switched memory B cells in Osteoarthritis

city: Palo Alto

first: Nidhi

last: Bhutani

state: California

address: 240 Pasteur Drive

department: Orthopaedic Surgery

institute: Stanford

summary: Osteoarthritis (OA) is a chronic, debilitating disease with no available disease-modifying drugs with end-stage surgery being the only treatment option. Biomarker identification in blood specimens of OA patients has hitherto been limited to serum proteins and bulk transcriptomics and epigenomic feature identification. We sought to capitalize on high resolution, single-cell techniques of mass cytometry by time-of-flight (cyTOF) and sc-RNA-seq to identify OA-associated features in the immune cells of the patients’ peripheral blood. Comparison of healthy donors and OA patients’ peripheral blood mononuclear cells (PBMC) revealed that frequencies of specific subpopulations of B cells, monocytes, CD4+ and CD8+T cells were distinctly perturbed in OA. While many immune subtypes were depleted, a CD25hiCD27+IgD- switched memory B cell population was identified to be significantly expanded in OA blood. Sc-RNA seq revealed a dysfunction of IL2/Stat3 and Notch signaling in the switched memory B cells expanded in OA. Upon profiling peripheral blood of patients with degenerative meniscal tears (DMT), a population known to be at enhanced risk for OA, we observed a similar expansion of CD25hiCD27+IgD- switched memory B cells suggesting that it can be a biomarker of early and late OA. Unsupervised clustering utilizing immune cell correlates stratified the profiled OA patients into three distinct subsets. Development of such single cell platforms can be a powerful clinical tool for OA prognosis as well as precision therapeutics.

overall_design: PBMC samples from OA patients and healthy donors (3 samples pooled as 1 replicate, n = 2/group) were enriched for B-cells and profiled using scRNAseq. 3 samples each were pooled to obtain 2 single cell cDNA libraries per group.

first: Yudhishtar

middle: S

last: Bedi

first: Neety

last: Sahu


title: LFA-1 regulated by IL-2/STAT5 pathway boosts antitumor function of intratumoral CD8+ T cells for improving anti-PD-1 antibody therapy

city: Zhengzhou

first: Jiqi

last: Shan

state: Henan

address: 1 Jianshe East Road, Erqi District, Zhengzhou City, Henan Province

institute: The First Affiliated Hospital of Zhengzhou University, Zhengzhou,

summary: These findings indicate that LFA-1-midiated immune synapse acts as a regulator of the antitumor function of intratumoral CD8+ T cells, which can be applied to improve anti-PD-1 antibody therapy.

overall_design: Female C57BL/6J mice (aged 6–8 weeks) were purchased from SPF Biotechnology Co., Ltd. (Beijing, China).mice were subcutaneously implanted with 1×106 B16 cells into the right flank on day 0. CD8+ T cells in TILs from B16 tumor-bearing mice were sorted on day 7 and day 14 using mouse CD8a microbeads (Miltenyi Biotec, 130-117-044) according to the manufacturer’s protocol. In brief, single-cell suspensions from tumor tissues were incubated with mouse CD8a microbeads for 10 min at 4 ℃. After magnetic labeling, the CD8+ T cells were isolated using a column. RNA was isolated using a TRIzol reagent (Invitrogen, cat, #15596026CN). RNA-seq and data analyses were conducted by SeqHealth Technology Co., Ltd. (Wuhan, China).

first: Wei

last: Jing

first: Yu

last: Ping


title: Effects of ACSS2 deficiency on transcriptomic profiling in BE(2)-C neuroblastoma cells

summary: Tumorigenesis also relies on the reprogramming of cellular metabolism, which greatly influences epigenetic and transcriptomic regulation. Specifically, the metabolite acetate serves as an important bioenergetic fuel and a precursor of acetyl-CoA, the substrate for histone acetylation. The enzyme ACSS2, responsible for converting acetate to acetyl-CoA in the cytosol and nucleus, has been associated with substantial reductions in tumor burden in various types of cancer. Our reports have shown that ACSS2 is highly expressed in neuroblastoma, and its expression level is usually associated with unfavorable clinical outcomes and poor survival. In this study, to further elucidate the underlying mechanism that ACSS2 overexpression regulates neuroblastoma tumorigenesis, we performed RNA-seq to examine the transcriptome alternation in neuroblastoma. We discovered that increased MYCN expression in human NB tumors correlates with elevated ACSS2 expression. Furthermore, we found that ACSS2-mediated biosynthesis of acetyl-CoA in regulating MYCN expression in MYCN-amplified neuroblastoma. Together, These results suggested that ACSS2-mediated biosynthesis of acetyl-CoA may be crucial for MYCN expression and progressive malignancy of neuroblastoma by capturing acetate as a carbon source in the cytosol and nucleus.

overall_design: Comparative gene expression analysis of RNASeq data for BE(2)-C cells (NB_NS) and ACSS2 deficient BE(2)-C cells (NB_siACSS2).


title: RNA-sequencing from fetal thymocytes and thymus, lung and bronchus epithelial cells.

first: Abdulvasey

last: Mohammed

state: CA

address: 240 Pasteur Dr

summary: To investigate the contributions of immune and stromal cells to the production of interferon in the thymus, we performed bulk RNA-sequencing on thymocytes, thymic epithelial cels, bronchial epithelial cells and lung epithelial cells.

overall_design: Bulk RNA-seq profiling of magnetic bead enriched populations from select human fetal (pcw 16-18) anterior foregut-derived organs.

first: Andrew

last: Gentles

first: Katja

last: Weinacht


title: Immune-epithelial networks characterise the cellular ecosystem of the small intestine in celiac disease

city: University of Oxford

first: Agne

last: Antanaviciute

address: MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: The immune-epithelial interactions driving intestinal damage in coeliac disease (CD) are incompletely understood.We applied single-cell (scRNA-seq) and spatial transcriptomics to define this. scRNA-seq of 76,824 immune and epithelial cells in 23 subjects with and without CD showed epithelial populations shifted towards a progenitor state, with interferon-driven transcriptional responses, and perturbation of secretory and enteroendocrine populations. Mucosal T-cells showed numeric and functional changes in regulatory, T follicular helper-like CD4+T-cell, natural intraepithelial lymphocytes, and CD8+T-cell subsets with a skewed TCR repertoire.Mucosal changes persisted despite treatment, representing a persistent immune-epithelial 'scar'. Spatial transcriptomics defined transcriptionally-distinct niches beyond that described in conventional histological scores,including CD-specific lymphoid structures containing localised T-B cell interactions. Spatial transcriptomics-driven receptor-ligand analyses and examination of disease susceptibility gene expression defined networks of altered chemokine and morphogen signalling, which may drive crypt axis distortion andallowed spatial/cellular resolution of where genetic drivers of CD act in tissue.

overall_design: 10x visium spatial transcriptomics of duodenal biopsies from study subjects with and without celiac disease

first: Michael

middle: E

last: FitzPatrick

first: Nicholas

last: Provine

first: Melanie

last: Dunstan

first: Dominik

last: Trzupek

first: Jia-Yuan

first: Sophie

middle: L

last: Irwin

first: Lucy

last: Garner

first: Jane

last: Pernes

first: Riccardo

last: Ferreira

first: Sarah

last: Sasson

last: Aschenbrenner

first: Astor

last: Rodrigues

last: Howarth

first: Oliver

last: Brain

first: Elizabeth

last: Soilleux

last: Teichmann

first: Calliope

last: Dendrou

first: Alison

last: Simmons

first: Holm

last: Uhlig

first: John

last: Todd

first: Paul

last: Klenerman


title: Maturational alterations in the transcriptome and methylome of the rat neurohypophysis

last: Watt

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Interferon Gamma signaling triggers dysplastic alveolar remodeling during respiratory viral infection

city: Shanghai

first: Guilin

last: Yang

address: Yueyang road 320

institute: Center for Excellence in Molecular Cell Science

summary: A single-cell transcriptional analysis was performed on lung immune cellsisolated from influenza PR8 infected mice at 14 days post injury. The goal is to investigate the potential signaling pathway that regulates dysplastic KRT5 cells expansion. The left lung lobe from influenza infected mice were dissociated to single cells and subjected to fluorescence activated cell sorting (FACS) to select all CD45+ cells. We found that the regulation of actin cytoskeleton, focal adhesion, Hippo signaling pathway are highly activated in dysplastic KRT5+ cells, suggesting that these signaling pathway may play a role in the expansion of dysplastic KRT5 cells in influenza infected lungs.

overall_design: Influenza PR8 infected 14 days post injury wild type mice left lung lobe were dissociated to single cells and  cells were subjected to fluorescence activated cell sorting (FACS) to select all CD45+cells. The sorted cells were using for scRNA-seq with a 10x Genomics platform.

first: Xiuyu

last: Lin

first: Pengfei

last: Sui


title: FACT-mediated depletion of macroH2A-nucleosome regulates the cell response of macrophage

city: beijing

first: ji

last: dengyu

address: 10 Xitoutiao, Youanmen, Fengtai District

institute: Capital Medical Universit

summary: The histone variant macroH2A has been shown to generally associate with transcriptionally silent chromatin states. However, how macroH2A regulates the chromatin structure and functions in transcriptional process still remains elusive at the molecular level. In this study, we demonstrate that the incorporation of macroH2A does not affect the stability and the folding dynamics of nucleosome, but greatly impairs the FACT’s maintenance function at the nucleosome level. FACT can greatly impair the stability of macroH2A nucleosome, and quickly deplete the macroH2A nucleosome after the first unfolding process. Furthermore, we identify the key residue S139 of macroH2A, whose mutation can rescue the FACT’s function to maintain nucleosome integrity. Genome-wide analyses show that S139 mutation in macroH2A reshapes the position of macroH2A and regulates the stimulation-induced transcription in macrophage. Our findings provide mechanistic insights of how histone variant macroH2A coregulates with FACT at the nucleosome level and functions in cell response of macrophage in immunity.

overall_design: ChIP-seq for vector,overexpress macroH2A and macroH2AS139A in RAW264.7 cells

first: Ping

last: Chen


title: TKTL1: a new candidate gene in nonobstructive azoospermia

first: Tomasz

last: Stokowy

summary: The genetic background of the non-obstructive azoospermia (NOA) remains poorly known. However, recent studies employing next generation sequencing techniques were able to uncover some NOA causative genes, among which was the TKTL1 gene. In this article we aim to understand the function of the TKTL1 gene in human spermatogenesis by inducing its overexpression in human testicular primary cells (hTPc), which we verified in male gonad tissue samples collected from NOA patients by uncovering the genes cluster regulated by TKTL1. Successful overexpression of the TKTL1 gene was achieved in hTP cells, the TKTL1 gene expression level was significantly higher in modified cells compared to both control groups (p<0.01). Using RNA-seq, we selected 20 genes which expression levels significantly differed in the modified hTP cells overexpressing TKTL1 gene in comparison to both controls. Male gonad tissue samples collected from NOA patients harbouring a mutation in the TKTL1 gene showed a significant downregulation (p<0.05) in HERC5, CSF3, HES1 and HSPA1B genes, compared to both controls, which was in accordance with the results obtained for hTPc cells, as the overexpression of the TKTL1 gene correlated with an increased expression level of the named genes compared to control groups.

overall_design: The comparative analysis of gene expression profiles by RNA-Seq between modified human testicular primary cells (hTPc) with overexpressed TKTL1 (n=3) compared to WT cells (n=3) and negative control with expression of GFP (n=3)

first: Malcher

last: Agnieszka


title: Single cell level characterization of Cdh11 deficiency-induced changes in pancreatic cancer

city: Livermore

first: Stephen

middle: Patrick

last: Wilson

address: 7000 East Ave

department: BBTD

institute: LLNL

summary: Cadherin 11 (Cdh11), a cell-to-cell adhesion molecule, has been suggested to promote tumor growth and immunosuppression in PDAC, and Cdh11 inhibition significantly extended survival in mice with PDAC. However, the mechanisms by which Cdh11 deficiency influences PDAC progression and anti-tumor immune responses has yet to be fully elucidated. To investigate Cdh11-deficiency induced changes in PDAC tumor microenvironment (TME), we crossed p48-Cre; LSL-KrasG12D/+; LSL-Trp53R172H/+ (KPC) mice with Cdh11+/- mice and performed single-cell RNA sequencing (scRNA-seq) of the non-immune (CD45-) and immune (CD45+) compartment of KPC tumor bearing Cdh11 proficient (KPC-Cdh11+/+) and Cdh11 deficient (KPC-Cdh11+/-) mice.

overall_design: KPC-Cdh11+/+, KPC-Cdh11+/- and Cdh11+/+ cohorts (n>=4) were euthanized at 4-5 months of age. Pancreases were excised, CD45-/7-AAD-  (non-immune) and CD45+/7-AAD- (immune) cells populations were sorted via fluorescently activated cell sorting (FACS) and profiled using scRNA-seq.

first: Aimy

last: Sebastian

first: Kelly

last: Martin

first: Gabriela

last: Loots


title: The effect of IL-1β on the expression of small RNA in mouse chondrocyte

first: Chuandong

last: Wang

address: 320 Yueyang Road

institute: SJTU

type: Non-coding RNA profiling by high throughput sequencing

summary: IL-1β is a key inflammatory factor that leads to cartilage degeneration. Small RNA plays an important regulatory role in cell function. Small RNA sequencing and qPCR were used to detect the effect of inflammatory factor IL-1β on small RNA expression in chondrocytes

overall_design: Chondrocyte stimulated with 10 ng/ml IL-1β for 24 hours and the expression of small RNA in chondrocyte were detected by small RNA sequencing.

first: Yuxin

last: Zhang


title: Single-cell transcriptome atlas reveals developmental trajectories in the leaves of two kiwifruit (Actinidia chinensis) genotypes

first: Miaomiao

address: Hanghai east road

institute: Zhengzhou Fruit Research Institute, CAAS

summary: we constructed the first single-cell transcriptional atlas in vine leaves of kiwifruit.

overall_design: Two genotypes


title: RNA Sequencing of induced pluripotent stem cell derived motor neurons from C9orf72 hexanucleotide repeat expansion carriers and controls

city: Oxford

first: Jakub

last: Scaber

state: Oxfordshire

address: West Wing, John Radcliffe Hospital, Headley Way

department: Nuffield Department of Clinical Neurosciences

summary: Transcriptomic signature of the C9orf72 hexonucleotide repeat expansion in induce pluripotent stem cell derived neurons.

overall_design: iPSC-MNs for RNA sequencing were harvested on DIV 39 from 3 control lines and 4 patient lines (from 3 individuals, with one providing two clones) from ALS patients carrying the C9orf72 hexonucleotide repeat expansion.

first: Kevin

last: Talbot

first: Yinyan

last: Xu


title: A SCAN-box containing KRAB-ZFP maintains DNA methylation and inhibits gene expression

city: Guangzhou

first: Bo

state: Guangdong

address: Guangzhou, 510150, Guangdong Province, China.

institute: The Third Affiliated Hospital of Guangzhou Medical University


title: A transcriptome analysis of serum-starved nucleus pulposus cells

city: Chongqing

first: Fanli

last: Chong

address: 183 Xinqiao Street, Shapingba District

institute: Xinqiao Hospital, Army Medical University

summary: This study sought to elucidate the transcriptomic changes of nucleus pulposus cells in serum starvation. The findings will lead to a better understanding of quiescent nucleus pulposus cells and provide insights into disc degeneration at the molecular level.

overall_design: There are two groups in the data set: serum starvation group and control group cultured in a 10% serum medium

first: Bin

last: Li


title: A SCAN-box containing KRAB-ZFP maintains DNA methylation and inhibits gene expression [RRBS]

last: Yang

summary: DNA methylation is one of the most characteristic epigenetic modifications. In mammals, it is involved in a variety of biological processes, including transposable element silencing, gene expression regulation, genomic imprinting, and X chromosome inactivation. Here, through a medium-scale analysis of CpG islands loci coupled with ChIP-seq of Krüppel associated box zinc finger proteins (KRAB-ZFPs), we identified a murine ZFP, ZFP202, that bind to methylated CpG loci. We found that ZFP202 not only maintain CpG loci methylation, but also inhibit downstream gene expression in specific tissues. Disruption of ZFP202 in mouse led to genes upregulation in testis and placenta. Thus, our research identified a novel transcription factor that binding to methylated DNA and maintaining DNA methylation and promoting gene inhibition.

overall_design: As ZFP202 is highly expressed in brain, testis and placenta, we harvested genomic DNA from adult testis, 12.5 embryo days (E12.5) placenta and whole brain of Zfp202 KO and WT mice, respectively. We then performed reduced representation bisulfite sequencing (RRBS) after MspI digestion of genomic DNA.


title: A SCAN-box containing KRAB-ZFP maintains DNA methylation and inhibits gene expression [MeDIP-seq]

overall_design: As ZFP202 is highly expressed in brain, testis and placenta, we harvested genomic DNA from adult testis, 12.5 embryo days (E12.5) placenta and whole brain of Zfp202 KO and WT mice, respectively,  which were then subjected to Methylated DNA Immunoprecipitation-Sequencing (MeDIP-seq) with 5mC antibodies.


title: Hypoxia-induced LncRNA SLC1A5-AS Enhances Glutamine Uptake by Increasing the Protein Level of ASCT2 in Hepatocellular Carcinoma Cells [mito]

first: Jiawen

last: Jiang

address: 130 Dongan Road, Xuhui District

institute: Fudan University

summary: To identify differentially expressed oncogenic lncRNAs in the mitochondria of HCC cells under hypoxia, hypoxia cell models of PHH and two HCC cell lines (Huh-7 and Hep-3B) were constructed, then we isolated mitochondrial RNA from the different groups after treatment with CoCl2 for 0, 6, and 12 hours for RNA-seq.

overall_design: Screening of the oncogenic mitochondria-associated lncRNAs under the cutoffs with Log 2 (Fold Change) > 5 (Wilcoxon Test < 0.01) in Huh-7 and Hep-3B cells compared with PHH cells.

first: Wei

last: Dong

first: Jiao

first: Wen

first: Qian

first: Ruyi

first: Jiaxu

first: Hao

last: Wu

first: Hui

first: Zhe

first: Robert

last: Zhao


title: Protective effect of Qing Hua Chang Yin (QHCY) on ulcerative colitis

city: Fuzhou

first: Aling

last: Shen

state: Fujian

address: 1 Qiuyang road, Minhou Shangjie

institute: Fujian university of Traditional Chinese Medicine

summary: The goal of this study is to compare the differently expressed genes in colon tissue of Control and DSS induced chronic colitis mouse model with or without Qing Hua Chang Yin (QHCY) treatment. The DSS induced chronic colitis mouse model were randomly divided into 3 groups: Model, Model + QHCY and Model + Mesalazine groups (n=6 for each group). Control mice (n=6) were set as control. Mice in Control and Model groups were intragastrically with double distilled water, while mice in Model + QHCY group was intragastrically with 1.6 g/kg/day of QHCY and mice in Model + Mesalazine group was intragastrically with 0.2 g/kg/d of Mesalazine. Then the colon tissues were used to identify differentially expressed genes among different groups.

overall_design: RNA sequencing was performed with colonic mice in 4 groups: Control, Model, Model + QHCY and Model + Mesalazine treated (n=6 for each group) to identify the differently expressed genes and related pathway.

first: Jun

last: Peng

first: Liya

last: Liu


title: Chromatin accessibility of PD1 knockout tissue resident memory T cells

city: New York

first: Ashley

middle: Stephen

last: Doane

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: OT1 cells were sorted on : Size, singlets live dead CD8 Va2 + and donor OT1 using congenic markers to distinguish donor cells (eg CD45.2, Thy1.1, Thy1.2, CD45.1) from recipient (host cells), and between PD1+/+ OT1 and PD1-/- OT1 donors.

overall_design: ATAC-Seq

first: Niroshana

last: Anandasabapathy


title: A SCAN-box containing KRAB-ZFP maintains DNA methylation and inhibits gene expression [ChIP-seq]

first: Bo

overall_design: We performed ChIP-seq on GFP-fused ZFP202 overexpressed mouse NIH3T3 cells with GFP antibodies.


title: Role of the transcription factor Nur77 (Nr4a1) in the effects of antipsychotic drugs

city: Montreal

first: Daniel

last: Levesque

state: Qc

address: CP 6128, Succ. Centre-ville

country: Canada

institute: University of Montreal

summary: To better understand the role of Nur77 in antipsychotic drug effects we performed a transcriptional analysis (RNAseq) to compare gene expression patterns between wild type and Nur77-deficient rats exposed to haloperidol.

overall_design: Comparison of gene expression between wild type and Nur77 deficient rats treated with saline or haloperidol (4 groups, N=3/group)

first: Simon

last: Majeur

first: Giovanni

last: Hernandez

first: Catherine

last: Lévesque

first: Pierre

last: Blanchet

first: Claude

last: Rouillard


title: A SCAN-box containing KRAB-ZFP maintains DNA methylation and inhibits gene expression [RNA-seq]

overall_design: To investigate the functional consequences in the absence of ZFP202 in mouse, we performed RNA-seq on Zfp202 KO mouse E12.5 placenta.


title: A pro B cell population forms the apex of the leukemic hierarchy in Hoxa9/Meis1-dependent AML

city: Hannover

first: Tobias

last: Maetzig

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

summary: In the murine HoxA9/Meis1 (H9M) AML model leukemic stem cell (LSC) potential lies in three different heterogeneous immunophenotypes including Lin-cKit+ progenitor cells (Lin-), Gr1+CD11b+cKit+ myeloid cells and lymphoid cells (Lym+). We performed scRNA-seq to reveal the cell type contribution of HoxA9/Meis1 bone marrow and the hierarchical organization of different immunophenotypes. Therefore, primary and secondary bone marrow of HoxA9/Meis1 tranplanted animals were isolated, sorted and sequenced. We could identify that in the HoxA9/Meis1 AML model a pro-B cell population resides at the apex.

overall_design: In total, 3 bone marrow samples from 3 HoxA9/Meis1 mice were analyzed. 1 sample contained bone marrow from a primary recipient and two samples contained bone marrow from its secondary recipiemts transplanted with Lin- and Lym+ LSCs. For parallel sequencing, the samples were labeled with hashtag probes: primary HoxA9/Meis1 bone marrow (Hash #4), secondary bone marrow tranplanted with Lin- LSCs (Hash #5), and secondary bone marrow transplanted with Lym+ LSCs (Hash #6).

first: Anna

last: Lieske

first: Eric

last: Ageyeman-Duah


title: Hypoxia-induced LncRNA SLC1A5-AS Enhances Glutamine Uptake by Increasing the Protein Level of ASCT2 in Hepatocellular Carcinoma Cells [ctb]

first: Jiawen

last: Jiang

summary: To analyze the whole-genome profile regulated by SLC1A5-AS in HCC, we treated Huh-7 cells using two independent siRNAs and a negative control (NC), followed by RNA-seq.

overall_design: Clustering analysis of dysregulated gene expression patterns was performed and visualized using a heatmap. To further process the sequencing data, we used KEGG and GO analyses to find the top six enriched signaling pathways and biological processes.

first: Wei

last: Dong

first: Jiao

last: Wang

first: Wen

last: Zhang

first: Qian

first: Ruyi

first: Jiaxu

first: Hao

first: Hui

first: Zhe

last: Li

middle: C


title: RNA-seq from murine Rag2-/- and Rag2-/-NE1-/- primary pro-B cells

city: Chicago

first: Amy

last: Kenter

state: IL

address: 835 S Wolcott

institute: UIC

summary: We report the gene expression profile from the RNA-seq data generated from BM derived Rag2-/- and Rag2-/-NE1-/- pro-B cells.

overall_design: RNA-seq was performed on Rag deficient murine pro-B cells following 5 days of ex vivo IL7 expansion.

first: Sarah

last: Naiyer

first: Saurabh

last: Priyadarshi

first: Ann

last: Feeney


title: Small RNA sequencing of extracellular vesicles extracted from adipose tissue of nondiabetic or diabetic human subjects

city: Nanjing

first: jin

last: wang

address: No. 321 Zhongshan Road

department: Department of Endocrinology

institute: Drum Tower hospital affiliated to Nanjing university medical school

summary: We demonstrated that adipose tissue derived extracellular vesicles from diabetic subjects could induce cognitive impairment. miRNAs in adipose tissue-derived EVs could be transferred to the hippocampus, which promotes synaptic damage and cognitive impairment. To identify the specific subtypes of miRNAs that responsible for cognitive impairment, we examined the sRNA profiles of EVs extracted from adipose tissue of nondiabetic and diabetic subjects by RNA deep sequencing.

overall_design: EVs were extracted from adipose tissues of nondiabetic and diabetic subjects and processed for RNA extraction by Trizol. All sRNA library construction and deep sequencing were performed by Novogene (Tianjin, China).

first: Jin


title: Effect of DDX24 knockdown on gene expression in Vascular Smooth Muscle Cells

city: Zhuhai

first: Yujiao

last: Gong

address: No. 52 Mei Hua Dong Road

institute: The Fifth Affiliated Hospital of Sun Yat-sen University

summary: To investigate the role of DDX24 in vascular smooth muscle cells, RNA-seq of HUASMC/HUVSMC with DDX24 knockdown was performed. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HUASMC/HUVSMC cells and HUASMC/HUVSMC cells with DDX24 knockdown.

first: Jiaxing

last: Wei


title: Small RNA sequencing of adipose tissue derived extracellular vesicles and hippocampus from chow- or HFD-fed male mice

summary: We demonstrated that adipose tissue derived extracellular vesicles from HFD-fed mice could induce cognitive impairment. miRNAs in adipose tissue-derived EVs could be transferred to the hippocampus, which promotes synaptic damage and cognitive impairment. To identify the specific subtypes of miRNAs that responsible for cognitive impairment, we examined the sRNA profiles of hippocampus and EVs extracted from adipose tissue of Chow and HFD mice by RNA deep sequencing.

overall_design: Adipose tissue derived EVs and hippocampus were extracted from male mice of the 12-week Chow- or HFD-fed C57BL/6J backgrounds and processed for RNA extraction by Trizol. All sRNA library construction and deep sequencing were performed by Novogene (Tianjin, China).

first: Wang

last: Jin


title: Gene expression of bone marrow cells from PHF6-deficiency of RUNX1-ETO9a induced acute myeloid leukemia mouse model

city: Tianjin

first: shuaibing

last: hou

address: Nanjing road 288

institute: State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases

summary: To explore the underlying molecular mechanisms of Phf6 loss in delaying AML progression, we analyzed the transcriptional profiles of VC Phf6,RE9a and WT Phf6,RE9a AML cells via RNA-sequencing

overall_design: Comparative gene expression profiling analysis of RNA-seq data for GFP+ leukemia cells from bone marrow of VC Phf6,RE9a and WT Phf6,RE9a mouse models

first: Shuaibing

last: Hou

first: Tengxiao

last: Guo

first: Xiaomin

first: Weiping

last: Yuan


title: Effect of depletion of LINC00938 on gene expression of SH-SY5Y cells

first: xiaohua

last: dong

address: 1111 XianXia Road

institute: Tongren Hospital, Shanghai Jiao Tong University School of Medicine,

summary: To investigate the function of LINC00938 in the regulation of cell apoptosis, we established  cell lines SH-SY5Y in which LINC00938 gene has been knocked down by shRNA.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SH-SY5Y cells and its KD derivatives (shLINC00938). We then detected the enriched KEGG pathway analysis using data obtained from RNA-seq of SH-SY5Y.

first: Xiaohua