title: Differential gene expression in paired H841-Tre vs. H841

city: Tianjin

first: Yujie

last: Hao

address: 22 Qixiangtai Road

institute: Tianjin Medical University

summary: Small cell lung cancer (SCLC) is characterized by significant heterogeneity and plasticity, which contribute to its aggressive progression and resistance to therapy. Understanding the underlying mechanisms of these features is essential for improving treatment outcomes. Autophagy, a conserved cellular process, plays a role in many cancers; however, its specific function in SCLC remains unclear. Utilizing a genetically engineered mouse model (Rb1fl/fl; Trp53fl/fl; GFP-LC3-RFP-LC3△G), we tracked autophagic flux in vivo to assess its effects on SCLC biology. Tumor subpopulations with high autophagic flux exhibited increased proliferation, enhanced metastatic potential, and neuroendocrine (NE) characteristics, whereas those with low autophagic flux displayed more immune-related signals and non-NE traits. In vitro modulation of autophagic flux further corroborated these findings: the autophagy activator trehalose induced NE features in non-NE cell lines (H841), while the autophagy inhibitor Bafilomycin A1 promoted non-NE characteristics in NE cell lines (H1092). This study provides a model for investigating autophagy in vivo and underscores its role in the heterogeneity and plasticity of SCLC.

overall_design: Sequencing was performed on both the control H841 cell line and the H841 cell line treated with 200 mM trehalose for 12 hours.

first: Zhe

last: Liu


title: PLAC8 attenuates pulmonary fibrosis and inhibits apoptosis of alveolar epithelial cells via facilitating autophagy

status: Public on Dec 17 2024

city: Shenyang

first: Yingying

last: Chen

address: 39 Huaxiang Road

country: China

institute: Shengjing Hospital of China Medical University

type: Expression profiling by high throughput sequencing

summary: Idiopathic pulmonary fibrosis (IPF) is an irreversible lung condition that progresses over time, which ultimately results in respiratory failure and mortality. In this study, we found that PLAC8 was downregulated in the lungs of IPF patients based on GEO data, in bleomycin (BLM)-induced lungs of mice, and in primary murine alveolar epithelial type II (pmATII) cells and human lung epithelial cell A549 cells. Overexpression of PLAC8 facilitated autophagy and inhibited apoptosis of pmATII cells and A549 cells in vitro. Moreover, inhibition of autophagy or overexpression of p53 partially abolished the effects of PLAC8 on cell apoptosis. ATII cell-specific overexpression of PLAC8 alleviated BLM-induced pulmonary fibrosis in mice. Mechanistically, PLAC8 interacts with VCP-UFD1-NPLOC4 complex to promote p53 degradation and facilitate autophagy, resulting in inhibiting apoptosis of alveolar epithelial cells and attenuating pulmonary fibrosis. In summary, these findings indicate that PLAC8 may be a key target for therapeutic interventions in pulmonary fibrosis.

overall_design: C57BL/6 mice at the age of 8 week were received bleomycin (BLM, 3 U/kg) or saline solution (Control) in 50 μL by intratracheal instillation (I.T.) at day 0. Mouse lungs were isolated for RNA extract at day 3.

first: Wei

last: Sun

first: Bo

last: Zhao

first: Zhong

last: He

first: Lihua

last: Chang

last: Song


title: Male specific conserved LncRNA TSCL1 regulated target mRNA translation by interaction with PIWIL1 [Ribo-seq]

city: Nanjing

first: Zhongyu

last: Zou

state: Jiangsu

address: 101 Longmian Road, Jiangning Campus, Nanjing Medical University, Nanjing, Jiangsu Province, China

institute: Nanjing Medical University

summary: Long non-coding RNAs are known to play crucial roles in various physiological processes in mammals, yet their functions in spermatogenesis remain largely underexplored. Here, we have identified a distinct category of conserved haploid spermatids-associated long non-coding RNAs (cHS-LncRNAs) characterized by their sequence-based conservation, specific expression in the testis, and elevated expression levels in haploid spermatids. Among these, we found that the testis specific conserved LncRNA 1 (Tscl1) exhibits the highest expression in round spermatids. Deletion of Tscl1 in mice exhibits reduced sperm motility, disordered mitochondrial sheath structure, abnormal fatty acid metabolism, and results in male infertility. Mechanistically, Tscl1 directly interacts with PIWIL1 and HuR via its 5′ end stem-loop  structure and multiple AU-rich elements, respectively. This binding pattern promotes the formation of the PIWIL1/eIF3f/HuR/eIF4G3 supercomplex, regulating the translation efficiency of fatty acid metabolism-associated mRNAs within the chromatoid body. Furthermore, the region where TSCL1 interacts with PIWIL1 is significantly enriched with TSCL1 variants identified in patients with non-obstructive azoospermia (NOA) compared to those in the fertile controls (OR=5.992, P=0.020,  NCase=1,338, NControl=2,664). Taken together, our findings elucidate the critical role of Tscl1 in regulating the translation efficiency of target mRNAs through its collaboration with PIWIL1 and HuR during spermiogenesis.

overall_design: Ribo-seq in TSCL1_Lnc_KO and TSCL1_WT

first: Shuai

last: Lu

first: Yang

last: Li

first: Chenmeijie


title: Male specific conserved LncRNA TSCL1 regulated target mRNA translation by interaction with PIWIL1 [lncRNA-seq]

type: Non-coding RNA profiling by high throughput sequencing

overall_design: lncRNA-seq profiling of PAC, RS, and ES cells isolated from mouse testes, with three biological replicates for each group


title: Transcriptome reshaping of the evolved thermotolerant Saccharomyces cerevisiae strain compared with the parental strain by RNA-Seq

status: Public on Dec 18 2024

first: Qinhong

last: Wang

address: 32 West 7th Avenue, Tianjin Airport Economic Area

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

summary: Elevated thermotolerance is an important desired property of Saccharomyces cerevisiae for its industrial applications. Here, adaptive laboratory evolution experiments were employed to further improve the thermotolerance of an industrial strain ScY. The resulting evolved strain showing enhanced thermotolerance was named ScY01. We sequenced mRNA from the cultures of the evolved strain ScY01 and the parental strain ScY grown on YP medium containing 200 g/l glucose at 40ºC at 200 rpm for 14 h ~ 16 h to the early-log phase. Differences in gene expression in ScY01 versus ScY revealed by RNA deep sequencing revealled that genes involved into glycolysis, amino acid biosynthesis and translation showed increased gene expressions, whereas mitochondrial translation and respiration associated genes showed decreased gene expressions. This suggested that the evolved strain might suppress its mitochondrial respiratory activity but boost its fermentation capacity, thereby providing enough ATP required for its more active energy-consuming pathways including amino acid and protein biosynthetic pathways.

overall_design: mRNA levels in Saccharomyces cerevisiae strain ScY and ScY01 was examined by RNA-Seq without replication

first: Xianni

last: Qi

first: Zhen

first: Yufeng

last: Guo

first: Yanqing

last: Cai

first: Qi

first: Yuping

last: Lin


title: JUNB O-GlcNAcylation-mediated Promoter Accessibility of Metabolic Genes Modulates Distinct Epithelial Lineage in Pulmonary Fibrosis [ipf_saec_bulk]

city: Biberach

first: Meshal

last: Ansari

address: Birkendorfer Straße 65

country: Germany

institute: Boehringer Ingelheim

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Harnessing a 3D patient derived organoid model and multi-omics approach, we provide the first inventory of the connection between metabolic alteration, chromatin accessibility, and transcriptional regulation in IPF aberrant epithelial remodeling. This remodeling is characterized by an increase in chromatin accessibility, particularly at JUNB motif-enriched promoter regions proximal to transcription start sites of metabolic and pro-fibrotic genes. Mechanistically, JUNB undergoes O-linked β-N-acetylglucosamine modification (O-GlcNAcylation), a critical step in modulating pro-fibrotic responses to chronic injury. This modification is pivotal in fostering the emergence of aberrant epithelial basal cells in the alveolar niche, a proposed driver of IPF pathology. Our findings reveal a novel link between metabolic dysregulation and cell fate regulation at the chromatin level in fibrosis, mediated by the O-GlcNAc-JUNB axis.

overall_design: To investigate the role of metabolic dysregulation in IPF basal cells, we utilized a 3D organoid system, derived from lung tissue samples obtained from IPF patients and healthy, control resections from tumor explants. We isolated EPCAM+ distal airway epithelial cells through tissue dissection and multiple sorting steps to obtain a pure epithelial cell fraction. The harvested cells were cultured in Cultrex basement membrane extract to promote the formation and growth of distal airway organoids. 6 of the 12 AOs were additionally treated with a pro-fibrotic stimuli in form of a disease-relevant cocktail (IPFrc). Finally, we performed bulk RNA sequencing and ATAC sequencing on the IPF and control AOs (n = 12 across 4 conditions).

first: Marie-Therese

last: Bammert

first: Leoni

last: Haag

first: Fidel

last: Ramirez

first: Huy Q

last: Le


title: JUNB O-GlcNAcylation-mediated Promoter Accessibility of Metabolic Genes Modulates Distinct Epithelial Lineage in Pulmonary Fibrosis

overall_design: To investigate the role of metabolic dysregulation in IPF basal cells, we utilized a 3D organoid system, derived from lung tissue samples obtained from IPF patients and healthy, control resections from tumor explants. We isolated EPCAM+ distal airway epithelial cells through tissue dissection and multiple sorting steps to obtain a pure epithelial cell fraction.  The harvested cells were cultured in Cultrex basement membrane extract to promote the formation and growth of distal airway organoids. Finally, the 10x Chromium Single Cell Multiome ATAC + Gene Expression platform was used to measure transcriptome and chromatin accessibility in IPF (n = 2) and control (n = 2) airway organoids on a single-cell level.

first: Huy

middle: Q


title: Palmitic acid regulates the biological function of Ovarian Cancer

city: Dalian

first: Jianxin

state: Liaoning

address: West Lushun South Road

institute: Dalian Medical University

summary: Palmitic acid was positively correlated with the invasion ability of ovarian cancer cells, its up-regulation inhibited the migrative, invasive and cloning capacity of cancer cells in vitro and suppressed the tumor proliferation and intraperitoneal diffusion in vivo, while its up-regulation did the opposite.

overall_design: Ovarian Cancer TOV-112D cells treatment with Palmitic acid of 200 μM for 24h and BSA as a negative control.

first: Wang

last: Jianxin

first: Meng

last: Songshu


title: Exploring the epigenetic landscape of spermatozoa: impact of oxidative stress and antioxidant supplementation on DNA methylation and hydroxymethylation

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

country: France

institute: igred

type: Methylation profiling by high throughput sequencing

summary: Oxidative stress in the epididymal compartment of snGpx4-/-;Gpx5-/- male mice has been shown to increase the percentage of spermatozoa with 8OHdG positive staining (DNA oxidation). In these mice, the total amount of sperm nuclear 5-hydroxymethylCytosine (5hmC) is significantly higher than in wild type mice. As the transormation of the epigenetic mark 5-methyCytosine (5mC) into 5hmC is an oxidative process, normally driven by enzymes, this work was aimed to test whether the increase in 5hmC was driven by the oxidative stress. Mice were given an oral antioxidant supplementation  (Fertilix®) for 14 days in their drinking water, a treatment previously shown by our group to decrease epididymal oxidative stress, shown by a significant decrease in the percentage of 8OHdG positive sperm cells.  Genomic DNA was then extracted from cauda epididymsi spermatozao and sequenced, using EM-seq and EhM-seq to respectively determine 5mC and 5hmC bases in a reduced representation protocol.

overall_design: Wild-type and snGpx4-/-;Gpx5-/- male mice were used in the study. They were given (Fx-samples) or not an oral antioxidant supplementation (Fertilix®) for 14 days in their drinking water. Cauda epididymal spermatozoa were then retrieved and their genomic DNA extracted. EM-seq and EhM-seq were performed for each individual in order to determine the occurence of 5mC and 5hmC, respectively.

first: Fabrice

last: Saez

first: Yoan

last: Renaud


title: Effect of metal ion on itaconic acid fermentability for Aspergillus terreus

city: Changzhou

first: Xia

last: Yi

address: Gehu Middle Road #21

institute: Changzhou University

summary: Zn (Ⅱ) and Fe (Ⅱ) are the essential metal elements for the growth of microorganisms. It illustrated that more itaconic acid was achieved for 0.25 g/L ZnSO4·2H2O and 0.40 g/L FeSO4·2H2O than the control with 0.15 g/L ZnSO4·2H2O and 0.16 g/L FeSO4·2H2O after single factor assays for Aspergillus terreus.We furhter carried out transcriptome assays to uncover molecular mechanism of the enhanced itaconic acid fermentability for A. terreus with metal ion.Therefore, our study would provide a reference metal ion concentration ratio for itaconic and other biochemicals production.

overall_design: Comparative of gene expression profiling using RNA-seq data between the control groups and the optimized metal ion groups for the wild Aspergillus terreus.


title: SPTLC2 mediates AKT pathway and regulates the biological function of Ovarian Cancer

summary: Ovarian cancer is a leading cause of death among gynecologic malignancies. This disappointing prognosis is closely related to intrinsic or acquired resistance to conventional platinum-based chemotherapy, which can affect a third of patients. As such, investigating relevant molecular targets is crucial in the fight against this disease. So far, many mutations involved in ovarian cancer pathogenesis have been identified. Among them, a few pathways were implicated. One such pathway is the P13K/AKT/mTOR with abnormalities found in many cases. This pathway is considered to have an instrumental role in proliferation, migration, invasion and, more recently, in chemotherapy resistance. Serine Palmitoyltransferase (SPTLC2) have been found to influence P13K/AKT/mTOR pathway with different potential role in tumor genesis behavior. In particular, their biological function was recently investigated as regards chemoresistance, therefore, leading to the identification of potential specific indirect biomarker of platinum sensitivity in ovarian cancer

overall_design: Ovarian Cancer Hey-A8 cells with stable knockdown of SPTLC2 and shCON as a negative control.  shCON and shSPTLC2 cells were extracted for RNA sequencing

first: Xingyue

last: Zhai

first: Songshu

last: Meng


title: The Core Circadian Clock Factor, Bmal1, Transduces Sex-specific Differences in Both Rhythmic and Nonrhythmic Gene Expression in the Mouse Heart

city: Gainesville

first: Spencer

last: Procopio

state: FL

address: 1345 Center Drive

country: USA

institute: University of Florida

summary: Sexual dimorphism in mammals, including humans and laboratory rodents, has primarily been attributed to hormonal and sex chromosomal differences. Accumulating evidence now suggests that circadian rhythms also contribute to sexual dimorphism in cardiac physiology and cardiovascular diseases. Here, we show that the circadian transcriptome of the mouse heart exhibits sexual dimorphism. We determined that female hearts express significantly more rhythmically expressed genes (REGs) and that the temporal distribution of the REGs was different between males and females. In addition, the overlap in genes and functional pathways were modest between males and females. All aspects of the sexual dimorphism in the circadian transcriptome was significantly diminished with cardiomyocyte specific loss of the core clock gene, Bmal1. Analysis of all differentially expressed genes (DEGs) between males and females showed that differential expression between sexes was largely diminished with loss of cardiomyocyte Bmal1. We conclude that cardiomyocyte specific Bmal1, and likely the core clock mechanism, plays a vital role in conferring a sexually dimorphic program of gene expression in the adult mouse heart.

overall_design: To investigate the role of BMAL1 in the sex differences of the heart circadian transcriptome in mice, we generated an inducible cardiomyocyte specific BMAL1 knockout (icsBmal1 KO) mouse.

first: Xiping

last: Zhang

middle: B

first: Zhiguang

last: Huo

first: Karyn

middle: A

last: Esser


title: ERF114/115/109 are essential for Jasmonate-repressed non-canonical JAZ8 activity in JA signaling.

city: Qingdao

first: XUAN

middle: JIA]

last: SUI

state: 山东省

address: Binhai Road

institute: ShanDong university

summary: As an important part of the plant root system, the root hair has a high degree of plasticity, which can help the plant to improve the absorption of water and nutrients and efficiency when the plant encounters stress. It is well known that jasmonic acid can promote the elongation of JA and this promotion is achieved by degrading JAZs to release RHD6. However, not all JAZs are degraded by SCFCOI1. We found that ERF114 in the ERF family interacts with most JAZs, and the erf114 mutant has a short root hair phenotype. This may provide a new idea for how to inhibit the function of JAZs that cannot be degraded. That is, the binding of the target protein is inhibited by the competition between proteins. Through biochemical experiments, genetic analysis and RNA-seq results analysis, it was proved that ERF114 participated in JA signal transmission and affected the transcriptional activity of MYC2 for downstream JA-responding genes. At the same time, MYC2 can directly affect the transcription of ERF114, form a positive feedback signal, and participate in the growth and development process of root hair mediated by JA. RHD6 also plays a role in this process.

overall_design: In order to further investigate the role of ERF114 in JA signaling pathway, we processed Col-0 and erf114 by applying exogenous MeJA (50μM). By analyzing the results of RNA-seq before and after treatment, ERF114 was further determined to participate in JA signaling pathway

first: Jiaxuan

last: Sui

first: Qianlan

last: Yin

first: Yiying

last: Chen

first: Min

last: Sun


title: SPTLC2 mediates EGFR/STAT3 pathway regulates the biological function of Ovarian Cancer

first: Jianxin

last: Wang

summary: Serine Palmitoyltransferase (SPTLC2) was positively correlated with the invasion ability of ovarian cancer cells, its down-regulation inhibited the migrative, invasive and cloning capacity of cancer cells in vitro and suppressed the tumor proliferation and intraperitoneal diffusion in vivo, while its up-regulation did the opposite. Moreover, SPTLC2 could bind to EGFR to induce PD-L1 regulation in ovarian cancer, which was caused by the activation of EGFR/STAT3 signaling. Afatinib combined with trametinib had an obvious effect of inhibiting the intraperitoneal diffusion of ovarian cancer cells, especially in the group with low expression of SPTLC2, while overexpression of PD-L1 could reverse this phenomenon.

overall_design: Ovarian Cancer OVCAR-3 cells with stable knockdown of SPTLC2 and shCON as a negative control.  shCON and shSPTLC2 cells were extracted for RNA sequencing


title: Small bowel RNA-seq data from patients with Crohn's disease and patients with colon cancer (non-CD controls)

city: Seoul

first: Yoonho

last: Lee

address: 88, Olympic-ro 43-gil, Songpa-gu, Seoul, Republic of Korea

department: Department of Biochemistry and Molecular Biology

country: South Korea

institute: University of Ulsan College of Medicine

summary: To identify the dysregulated molecular pathways and core genes associated with the chronic and progressive course of CD, we evaluated the gene expression profiles of uninflamed small bowel tissues from CD patients who underwent small bowel resection and compared the results with those of patients with right colon cancer, who served as uninflamed non-CD controls.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for patients with CD and non-CD controls.
***submitter declares that the raw data can not  provided due to patient privacy concerns/hospital policy***

first: Ho-Su


title: The role of XBP1 in regulating the progression of non-alcoholic steatohepatitis [XCON/XCKO hepatocytes]

city: nanjing

first: Qi

address: The First Affiliated Hospital of Nanjing Medical University, 300 Guang Zhou Road

institute: The first affliated hospital of nanjing medical university

summary: Our study demonstrated that XBP1 is upregulated in liver tissues of patients with NASH. Conditional knockout of Xbp1 in the hepatocytes resulted in decreased lipid accumulation in mice. Genetic specific deletion of Xbp1 in macrophages ameliorated nutritional steatohepatitis and fibrosis in mice by reducing the secretion of pro-inflammatory cytokine, increasing M2 macrophage polarization, and decreasing TGF-β1 expression. Pharmacological inhibition of XBP1 protects against steatohepatitis and fibrosis, highlighting a promising strategy for NASH therapy.

overall_design: Xbp1FL/FL（XCON） and Xbp1ΔHep （XCKO）hepatocytes were isolated from mice fed with HFD for 26 weeks（n=3/group）.

first: Haoming

last: Zhou

first: Qingfa

last: Bu

first: Ling

last: Lu


title: The role of XBP1 in regulating the progression of non-alcoholic steatohepatitis [XWT/XKO BMDMs]

overall_design: LPS-primed Xbp1FL/FL（XWT）or Xbp1ΔMf（XKO）bone marrow-derived macrophages (BMDMs) were incubated with WT primary hepatocytes conditioned media (CM) for 48 h, and then Xbp1FL/FL or Xbp1ΔMf BMDMs were subjected to RNA sequencing analysis (n = 3/group).


title: Heat production from adipose-tissue macrophages regulates lipolysis and diet-induced obesity

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

institute: Ewha Womans University

summary: Recently white adipose tissues (WAT) have been shown to be able to generate heat upon cold exposure through the expression of uncoupling protein-1 (UCP1), a molecule regulating mitochondrial proton gradient.  Although the role of UCP1 has been extensively investigated in adipocytes, it is currently unknown whether UCP1 in the microenvironment of WAT such as adipose-tissue macrophages (ATM) could play a role in thermogenesis.  Given the critical role of hypoxia in regulating obesity and insulin resistance, we challenged our myeloid-specific hypoxia-inducible factor-1α (Hif-1α) knockout (KO) mice to high fat diet and observed that these mice were not only protected from diet-induced obesity but also resistant to the body temperature changes upon cold exposure, the latter effect being completely lost upon surgical removal of WAT.  Mechanistically, ATM deficient for HIF-1α generated heat production through increased expression of UCP1 and increased mitochondrial functions, all of which lead to an enhanced lipolysis in neighboring adipocytes.  Lastly, we observed a number of co-localized areas between UCP-1 and CD68 in WAT of lean mice as well as individuals whereas such areas were not observed in an obese mice or human subjects.  In conclusion, we demonstrate a novel mechanism by which ATM regulate obesity through UCP1-mediated heat generation.

overall_design: The investigation of gene expression change in FACS-sorted adipose tissue macrophages (ATM) from hMRP8cre+;Hif-1αfl/fl;ApoE-/- mice or hMRP8cre-;Hif-1αfl/fl;ApoE-/- mice.

first: Hyeongrin

last: Jeon


title: Topical ABT-263 treatment reduces aged skin senescence and improves subsequent wound healing

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Senescent cells accumulate in aging tissues, impairing their ability to undergo repair and regeneration following injury. Previous research has demonstrated that targeting tissue senescence with senolytics can enhance tissue regeneration and repair by selectively eliminating senescent cells in specific aged tissues. In this study, we focused on eliminating senescent skin cells in aged mice to assess the effects on subsequent wound healing. We applied ABT-263 (Navitoclax) and a DMSO control directly to the skin of 24-month-old mice over a 5-day period. Following ABT-263 treatment, aged skin showed decreased gene expression of senescent markers p16 and p21, accompanied by reductions in SA-β-gal and p21-positive cells compared to the DMSO-treated skin. However, ABT-263 treatment also triggered a temporary inflammatory response and macrophage infiltration in the skin. Bulk RNA sequencing of ABT-263-treated skin revealed prompt upregulation of genes associated with wound healing pathways, including hemostasis, inflammation, cell proliferation, angiogenesis, collagen synthesis, and extracellular matrix organization. Aged mice treated with ABT-263 exhibited accelerated wound closure compared to the DMSO control group. In conclusion, topical ABT-263 effectively reduced several senescence markers in aged skin, thereby priming the skin for improved subsequent wound healing. This enhancement may be attributed to ABT-263-induced senolysis and the resulting inflammation, which in turn stimulated the expression of genes involved in extracellular matrix remodeling and wound repair pathways.

overall_design: In this study, we focused on eliminating senescent skin cells in aged mice to assess the effects on subsequent wound healing. We applied ABT-263 (Navitoclax) and a DMSO control directly to the skin of 24-month-old mice over a 5-day period, excised and homogenized the skin, and profiled gene expression in the skin homogenate using RNA sequencing.

first: Maria

last: Shvedova

first: Daniel


title: Single-cell transcriptomics of human organoid-derived enteroendocrine cell populations from the small intestine.

status: Public on Dec 16 2024

city: Cambridge

first: Fiona

last: Gribble

state: Cambridgeshire

address: Box 289 Addenbrooke's Hospital, Hills Road

department: Medical Research Laboratories

country: United Kingdom

institute: University of Cambridge

summary: Enteroendocrine cells (EECs) are the source of a variety of gut hormones that control local intestinal functions such as gallbladder contraction, pancreatic enzyme secretion and intestinal motility, as well as peripheral nutrient metabolism and appetite. This study aimed to map human EECs isolated from organoids derived from duodenum and ileum using single-cell RNA sequencing.

overall_design: Organoids derived from human duodenum and ileum were genetically modified using CRISPR-Cas9 to express the fluorescent protein Venus driven by the chromogranin-A promoter. Fluorescent cells from CHGA-Venus organoids were purified by flow cytometry and analysed by 10X single-cell RNA sequencing.

first: Christopher

last: Smith

middle: M


title: AXL-TBK1 driven AKT3 activation promotes metastasis

city: Dallas

first: Rolf

last: Brekken

state: TX

address: 6000 Harry Hines Blvd

institute: The University of Texas Southwestern Medical Center

summary: The receptor tyrosine kinase AXL promotes tumor progression, metastasis and therapy resistance through the induction of epithelial-mesenchymal transition (EMT). Here, we report that activation of AXL results in TANK-binding kinase 1 (TBK1) phosphorylation, subsequent TBK1-dependent phosphorylation of AKT3 (pAKT3) and nuclear accumulation of pAKT3 and the EMT transcription factor (EMT-TF) Snail. Mechanistically, we show that (i) TBK1 directly binds and phosphorylates AKT3, in an mTORC1 dependent manner. Once activated, AKT3 interacts with Snail and promotes the accumulation of nuclear Snail to drive EMT. Congruently, in human pancreatic ductaladenocarcinoma tissue, nuclear AKT3 co-localizes with Snail and correlates with worse clinical outcome. AKT3 knockout in tumor cells significantly reduced metastatic spread in mice suggesting that selective AKT3 inhibition represents a novel therapeutic avenue for targeting EMT in aggressive cancers.

overall_design: The investigate the role of AKT3 expression in MCF10A cells. We established MCF10A cells overexpressing AKT3 and compare the effects to control vector.

first: James

last: Lorens

first: Stefan

last: Hinz


title: The role of XBP1 in regulating the progression of non-alcoholic steatohepatitis

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

overall_design: Refer to individual Series


title: Self-balanced regulation by the long non-coding RNA Lockd on the cell cycle progression of cortical neural progenitor cells through counteracting cis and trans roles

city: Suzhou

first: shaojun

last: Qi

address: B8, Lane 21, Dong Yan Li Rd, Suzhou Industry Park,Suzhou ,Jiang Su, China

department: Department of mRNA Sciences

institute: Suzhou Abogen Biosciences Co., Ltd.

summary: Neural stem/progenitor cells (NSPCs) undergo active proliferation and exit the cell cycle upon precise regulation to produce differentiated progenies in order. Long non-coding RNAs (lncRNAs) have emerged as critical players in the developmental processes of NSPCs; however, relatively few have been shown to regulate the cell cycle in vivo directly. Here, we identified an NSPC-expressed lncRNA Lockd (lncRNA downstream of Cdkn1b) in the developing forebrain. Using in vivo loss of function models by premature termination of Lockd transcription via knockin polyadenylation signals or shRNA-mediated knockdown of Lockd (Lockd-KD), we show that Lockd is required for proper cell cycle progression of cortical NSPCs and the production of TBR2+ intermediate neural progenitor cells during cortical development. Interestingly, a comparison of genetic profiling in the two models reveals that Lockd promotes the expression of two counteracting cell cycle-related genes, Cdkn1b in cis and Ccnd1 in trans. Overexpression of Ccnd1 or Cdkn1b-KD can rescue the cellular phenotypes of reduced cycling progenitors in Lockd-KD. Our results imply that lncRNA could act through distinct cis and trans mechanisms to achieve a self-balanced function.

overall_design: Set 1: The control and Lockd-shRNA expressing plasmids were electroporated into NSPCs at E14.5, and GFP positive cells were sorted by flow cytometry at E16.5 (two biological replicates for control or Lockd-shRNA). Set 2: E13.5 cortices of wild type (WT) and PlyA-KI mice were also dissected and pooled for transcriptome profiling (two biological replicates for WT or PlyA-KI).

first: Shaojun

first: Jiangli

last: Zheng

first: Qin

last: Shen


title: Epigenetic programming by trithorax supports the translation capacity of Drosophila memory neurons [RNA-seq trx]

city: Nijmegen

first: Nicholas

last: Raun

address: Geert Grooteplein 10

country: Netherlands

institute: Radboudumc

summary: We have analyzed changes in histone H3 lysine 4 methylation (H3K4me) and gene expression resulting from trx knockdown (KD) in adult mushroom body neurons of Drosophila melanogaster.

overall_design: Examination of H3k4me1 and H3K4me3 levels, and gene expression in mushroom body neurons of adult naïve or trained trx-KD flies and their genetic background controls. Genetic material was collected from pools of 50-60 fly heads in least 3 replicates per condition.

first: Jamie

last: Kramer


title: Epigenetic programming by trithorax supports the translation capacity of Drosophila memory neurons [ChIP-seq]


title: Increased PTCHD4 expression via m6A modification of PTCHD4 mRNA promotes senescent-cell survival

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH


title: CFTR acts as a potential therapeutic target for attention deficit-hyperactivity disorder

city: Chengdu

first: Huaqin

last: Sun

address: Renmin Nanlu

institute: Sichuan University

summary: The occurrence of attention deficit-hyperactivity disorder (ADHD) symptoms in patients with cystic fibrosis (CF) is substantially higher than in the general population, and the cystic fibrosis transmembrane conductance regulator (CFTR) is the pathogenic gene of cystic fibrosis, suggesting the potentially critical role of CFTR in ADHD. Here, we identified three heterozygous missense mutations (p.E217G, p.F316L and p.T1220I) in CFTR, segregating with ADHD in two consanguineous families with 6 affected individuals. Using the zebrafish model, we found that the cftr knockout line displays hyperactive, impulsive-like, and attention deficit-like behaviors, reminiscent of human ADHD patients. Single-cell RNA-seq of 7 dpf larvae identified clusters of neuron cells that were sensitive to cftr, especially, the number of dopaminergic neuron cells decreased in the cftr mutant fish. Bulk RNA-seq and proteomic analysis at the early gastrulation period showed that the expression of nerve system genes was abnormal. Notably, we tried to use CFTR activitors Lumacaftor (VX-809) and Ivacaftor (VX-770) to treat the ADHD zebrafish model (established by per1b mutant), and found enhanced CFTR activity could rescue the ADHD-like behaviors. In brief, we uncover the role of CFTR in ADHD pathogenesis and explore novel diagnoses and therapy for ADHD by targeting CFTR.

overall_design: To further investigate the molecular mechanism of ADHD like behavior induced by cftr deficiency. We collected the 7 hpf larval samples of WT and cftr+/- line, and carried out single-cell RNA-sequencing analysis to explore the molecular regulation of the nervous system.

first: Qianqian

last: Li


title: Cerebral Venous Blood Flow Regulates Brain Fluid Clearance via Dural Lymphatics

city: Paris

first: Ruchith

last: Singhabahu

address: 47 bd de l'Hôpital

institute: Institut du Cerveau

summary: Previous studies have shown that the vascular system regulates brain clearance via arterial blood flow and the lymphatic drainage of CSF. Here, we examined the hypothesis that cerebral venous blood flow may participate in brain clearance as an intermediate compartment between the arterial and lymphatic poles of the vascular system. Transcriptomic analyses provided insights into the molecular mechanisms driving dural lymphatic remodeling within the dura mater.

overall_design: Mice after sham surgery (controls) as well as mice 14 days after jugular venous ligature were used. Skullcaps were dissected and dural meninges were carefully peeled off the skullcaps. Viable singlets were isolated by flow cytometry and scRNA-seq analysis was performed.

first: Marie-Renée

last: El Kamouh

first: Jean-Leon

last: Thomas


title: Elane mediates neutrophil infiltration into the brain and neuroinflammation

city: Hangzhou

first: Xinjiang

last: Lu

address: Yuhangtang road No.866

institute: Zhejiang University

summary: In CUMS mice, neutrophils can infiltrate brain parenchyma and induce neuroinflammatory responses. To identify potential mediators, we analyzed the gene expression profiles of bone marrow neutrophils from mice subjected to CUMS and compared them with those of control mice. Interestingly, among the genes notably associated with neutrophil functions were Elane and Mpo, the crucial granule proteins of neutrophils that mediate chronic inflammation. Our study demonstrated that neutrophil-specific Elane knockout reduced neutrophil infiltration into the brain parenchyma and alleviated neuroinflammation. Elane plays a critical role in modulating the influence of peripheral neutrophils on brain.

overall_design: We performed transcriptional profiling using RNA-seq in flow cytometry sorted neutrophils from the bone marrow of control and CUMS mice

first: Rong

last: Mou

first: Yixin

last: Wu


title: Regulatory T cells converted from T helper 1 cells in tumors suppress cancer immunity via CD39

city: Zhejiang

first: Sang Nee

last: Tan

address: Hangzhou

department: School of Medicine

institute: Westlake University

summary: Although regulatory T (Treg) cells are widely believed to impede anti-tumor immunity, their regulation and functional mechanisms are not well understood. Here, through characterization of multiple cancer models, we identified substantial periphery-induced Treg cells in the tumor microenvironment (TME), depletion of which provoked anti-tumor responses and conferred potent therapeutic effects by increasing functional CD8+ T cells. Through fate-mapping and transfer experiments, we found IFN-γ-expressing T helper (Th) 1 cells developed into Treg cells in tumors, in response to TGF-β signaling. Pseudotime trajectory further revealed the terminal differentiation of Th1-like Treg cells from Th1 cells in the TME. Hence, tumor-resident Treg cells highly expressed T-bet, which was essential for their function in the TME. CD39, highly expressed by T-bet+ Treg cells in both mouse and human tumors, is required for Treg suppression of CD8+ T cell response. In summary, our study has elucidated a developmental pathway of intra-tumoral Treg cells and implicated new ways of targeting them in cancer patients.

overall_design: We sorted tTreg cells from spleen and lymph nodes (LNs) of CD45.1 Foxp3YFP-cre mice, and sorted conventional Foxp3- CD4+ T cells and CD8+ T cells from CD45.2 Foxp3YFP-cre mice. We then co-transferred tTreg cells, conventional CD4+ T cells and CD8+ T cells at ratios of 1: 10: 8 into TCRbd-/- mice, followed by the inoculation of Hepa1-6 tumor cells 3 days later. We generated bulk RNA sequencing of intra-tumoral pTreg and tTreg cells isolated from the Hepa1-6 tumor model. Treg cells purified from tumor-free LNs were included as a control.

first: Sang-Nee

first: Jing

last: Hao

last: Ge

first: Meng

last: Lin

first: Genyu

last: Wang

first: Ni

last: Ling

first: Chen

last: Dong


title: Spatial Transcriptomics of Colorectal Carcinoma Sample with Different Level of Differentiation

city: Philadelphia

first: Jiazhen

last: Rong

state: PA

address: Academic Research Building

department: Genomics and Computational Biology

institute: University of Pennsylvannia

summary: Cancer cells gain survival advantages through forming heterogeneous clones. Colorectal Carcinoma (CRC) is a known hetergenuus cancer type. In order to understand the heterogeneity of gene expression of different tumor clones, the spatial transcirptomics of a human CRC sample is measured. Copy number variations (CNV) were inferred at cell level and utilized for clustering the tumor cells into clones.

overall_design: Spatial Transcriptomics profiling of a human CRC FFPE sample was measured by 10X Genomics Visium Spatial Gene Expression.

first: Nancy

last: Zhang


title: scRNAseq gene expression profile of zebrafish jaw joint cells after complete resection of the synovial jaw joint

city: New York

first: Joanna

last: Smeeton

state: NY

address: 650 W 168TH ST, ROOM 1103A, William Black Building

department: Rehabilitation and Regenerative Medicine

institute: Columbia University Irving Medical Center

summary: Adult mammalian synovial joints have limited regenerative capacity, where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole-joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single-cell RNA sequencing, we profile RNA expression from live-sorted jaw joint cells throughout the time course of joint regeneration (1 to 70 days-post-joint-resection (dpjr)). Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage.

overall_design: scRNAseq was performed on live-sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post-joint-resection (1, 3, 7, 14, 28, and 70 dpjr) to capture the major stages of healing post-resection.

first: Maria

last: Blumenkrantz

first: Ernesto

last: Gagarin

first: Everett

last: Weinstein

first: Troy

last: Anderson

first: Julia

last: Mo

first: Desmarie

last: Sherwood


title: Cancer cells restrict immunogenicity of retrotransposon expression via distinct mechanisms [PDAClines_RNAseq]

city: New york city

first: Siyu

last: Sun

address: 321 61E street

institute: Memorial Sloan Kettering Cancer Center

summary: To thrive, cancers must navigate acute inflammatory signaling accompanying oncogenic transformation, such as via overexpression of retrotransposable elements. We examined the relationship between immunostimulatory repeat expression, tumor evolution and the tumor-immune microenvironment. Integration of multimodal data from a cohort of pancreatic ductal adenocarcinoma (PDAC) patients revealed expression of specific Alu repeats predicted to form double-stranded RNA (dsRNAs) and trigger RIG-I-like receptor-associated (RLR) type-I interferon (IFN) signaling. Alu-derived dsRNA anti-correlated with pro-tumorigenic macrophage infiltration. We defined two complementary pathways whereby PDAC may adapt to such anti-tumorigenic signaling. In mutant p53 tumors, ORF1p from LINE-1 preferentially binds  Alus and decreases their expression, whereas ADAR1 editing primarily reduces dsRNA formation in wild-type p53 tumors. Depletion of either ORF1p or ADAR1 reduced tumor growth in vitro. That tumors utilize multiple pathways to mitigate immunostimulatory repeats implies that the stress from their expression is a fundamental phenomenon to which PDAC, and other tumors, adapt.

overall_design: To investigate the repeat expression in PDAC cell lines with different level of L1 ORF1p expression, totall RNA was sequenced from 11 different patient derived cell lines.


title: Transcriptional dysregulation in a Mecp2 methyl-binding domain point mutant model (Mecp2 G118E)

city: Houston

first: Sameer

middle: Subhash

last: Bajikar

address: 1250 Moursund St

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: We recently identified a mutation in the methyl-binding domain of MECP2 (MECP2 G118E) in a male patient with Rett syndrome. To ask whether this mutation conferred similar molecular dysregulation as observed in previous mouse models of Rett syndrome, we generated a knockin mouse model of this mutation and collected the cortex for RNA-sequencing.

overall_design: Cortical tissue from Mecp2 G118E or litter-mate control wild-types were collected to isolate RNA. PolyA RNA-seq was performed from collected RNA and expression was analyzed for differential expression.


title: Carrier Subclass Year 4

first: exRNA

last: BRL

address: One Baylor Plaza

department: Molecular & Human Genetics - Milosavljevic

summary: To evaluate performance of immunomagnetic separation and size exclusion chromatography in the isolation of different extracellular RNA carriers from biofluids.

overall_design: Plasma, placental explant supernatant and cell culture supernatants were collected. Extracellular RNA carriers were isolated using immunomagnetic separation and size exclusion chromatography and analysed using small RNA seq

first: Louise

middle: C

last: Laurent

first: Srimeenakshi

last: Srinivasan

first: Peter

middle: D

last: Hoff

first: Abbas

last: Hakim

first: Tyler

last: Ostrander

first: Willi

last: Cheung

first: Priyadarshini

last: Pantham

first: Jeff

last: Franklin

first: Saumya

last: Das


title: Epigenetic programming by trithorax supports the translation capacity of Drosophila memory neurons [RNA-seq Set1 & trr]

first: Nicholas

last: Raun

overall_design: Examination of gene expression in mushroom body neurons of adult Set1 or trr-KD flies and their genetic background controls. Genetic material was collected from pools of 50-60 fly heads in least 4 replicates per condition.

first: Raun

last: Nicholas

first: Kramer

last: Jamie


title: A pan-family screen of Nuclear Receptors in immunocytes reveals ligand-dependent inflammasome control [RNA-seq 2]

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: We performed RNAseq profiling of  sorted LYVE1+CD206+ MFs  from WT, RARγ mutant and RXRα mutant  converting macrophages (Conv.MF).

overall_design: RNA-seq was performed on purified Conv.MFs sorted from “Rainbow-CRISPR” mice 25 days after reconstitution, mutant cells and WT cells were matched from the same BMC mouse. Biological replicates were obtained for each NR ablation.

first: Yutao

last: Wang

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Transcriptional profiling of DNA sensing signal activation of THP-1 cells using bulk RNA-seq and single cell RNA-seq

city: Daejeon

first: In-Hwan

last: Jang

address: 125, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea

department: Immunotherapy Research Center

institute: Korea Research Institute of Bioscience and Biotechnology

summary: This study observed that reporter protein from plasmid DNA transfection expression levels were dose-nonlinear after transfection in THP-1 cells caused by activation of DNA sensing. The expression levels of target genes were significantly upregulated after blocking the STING pathway. Through analysis of changes in the bulk and single cell RNA-seq of heterozygous cellular response to DNA transfection, we clarified the DNA sensing-induced innate immune response and apoptosis.

overall_design: DNA sensing signal activated THP-1 cells compared to control cells, under the condition with or without STING inhibitor (H151) were used to perform transcriptome analysis. Bulk RNA-seq based on time course analysis (12-24-36 hours) of four conditions experiment: negative control (NC), H151-treatment, plasmid DNA-transfected (pDNA), H151-treatment and pDNA-transfected (pDNA_H151). To characterize reporter proteins (GFP, Green fluorescent protein)-translated cells , bulk RNA-seq of sorted cells with biological replicates of 2. Samples were derived from total RNA extracted from EGFP protein negative (GFP_neg) and positive(GFP_pos) THP-1 cells sorted by fluorescence-activated cell sorter (FACS) after of pDNA transfection. To investigate heterogeity of cellular response of pDNA transfection ,single cell RNA-seq of THP-1 cells was performed after transfection.

first: Ling-Zu

last: Kong

first: Tae-Don

last: Kim


title: OPG promotes lung metastasis by blocking the RANKL-RANK-CXCL10 axis to drive NK cell paucity (CRISPR)

city: Beijing

first: Hu

last: Haitian

address: Haidian Beijing

institute: Tsinghua University

summary: Metastasis is the major cause of cancer-related mortality. In the lung metastasis, monocyte-derived macrophages (Mo-macs) exhibit a complex function. However, tumor cells how to derive lung metastasis through Mo-macs remains unclear. Here we show that a tumor-secreted protein osteoprotegerin (OPG) contributes to the lung metastasis of cancer depends on the Mo-macs by an in vivo screening. OPG binds with RANKL to block the signaling between RANKL-RANK on Mo-macs. RANKL-RANK signals induce Mo-macs to secrete CXCL10, recruiting NK cells to control the lung metastasis. Increased expression of OPG in the metastases is regulated by TGF-β. Consistent with our findings, enrichment of OPG amplifications was observed in metastatic cancer patients, and increased expression of OPG was also shown in the lung metastatic sites compared with the paired primary breast cancer samples. Overall, our findings reveal a mechanism of how tumor cells promote lung metastasis via inhibiting the function of Mo-macs.

overall_design: To identify the lung metastatic derivers dependent on the Mo-macs. Anti-Csf1R antibody was used to deplete Mo-macs and then B16F10 cells transfected with a druggable sgRNA library were injected into mice via tail vein. IgG was used as control. Last, metastases were harvested to extract genomic DNA for PCR of sgRNAs. Data was analyzed by MAGeCK.

first: Haitian

last: Hu

first: Xuan

last: Li

first: Zhanao

last: Xu

first: Hanqiu

last: Zheng


title: Integrated multi-omic high-throughput strategies across-species identified potential key diagnostic, prognostic, and therapeutic targets for atherosclerosis under high glucose conditions

first: Zhida

last: Shen

state: Zhejiang

address: Qingchun East Road 3

department: Department of Cardiology

institute: Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University,

summary: Diabetes is a well-known risk factor for atherosclerosis (AS), but the underlying molecular mechanism remains unknown.Hyperglycemia is a hallmark of diabetes and high glucose is proven to induce foam cell formation mainly derived from macrophages. In this study, we aimed to explore systematic regulatory gene programs under this complicated situation. Following by induction of macrophage-derived foam cells in vitro, the high-throughput sequencing was performed. Coexpression gene modules were constructed using weighted gene co-expression network analysis (WGCNA) and relevant modules were identified. Genes with high intramodular connectivity were further screened to select hub genes related to foam cell formation in foam cells annotated by integrated scRNA datasets. The potential roles of selected genes were further validated in bulk-RNA and scRNA datasets of human plaques.   Two modules were found to be both positively related to high glucose and ox-LDL. Further enrichment analyses confirmed the association between the brown module and AS. The high correlation between the brown module and macrophages was identified and 4 genes (Aldoa, Creg1, Lgmn, and Pkm) were screened. Further validation in external bulk-RNA and scRNA datasets of human plaques was performed. In addition, the survival analysis confirmed the prognostic value of Aldoa. Knocking down Aldoa expression alleviated the foam cell formation in vitro.

overall_design:
Mice aged 8 weeks were intraperitoneally injected with 6% soluble starch and the peritoneal macrophages (PM) were isolated. For foam cell induction, the isolated peritoneal macrophages were incubated with 50 mg/ml ox-LDL (Yiyuan Biotech, China) for 48 h. As for high glucose induction, the cells were treated with high glucose (33mmol/L) medium, while mannitol (27.5mM) was added in DMEM as an osmotic control. 4 groups were set, low glucose without ox-LDL (L_C), high glucose without ox-LDL (H_C), low glucose with ox-LDL (L_O), high glucose with ox-LDL (H_O)
The mouse strain (background) used in these experiments is C57BL/6.

first: He

last: Huang


title: Single cell RNA sequencing of embryonic limb skeletal muscles

city: Haifa

first: Peleg

last: Hasson

address: Efron 1

department: Medicine

country: Israel

institute: Technion

summary: Fibroblasts are the most common cell type found in connective tissues, known to play major roles in development, homeostasis, regeneration and disease. Although specific fibroblast subpopulations were associated with different biological processes, the mechanisms and unique activities underlying their diversity has not been thoroughly examined. Turning to skeletal muscle development, we set to dissect the variation of muscle-resident fibroblasts (mrFibroblasts). Our results demonstrate mrFibroblasts diversify following the transition from embryonic to fetal myogenesis prior to birth. We find mrFibroblast segregate into two major subpopulations occupying distinct niches, with interstitial fibroblasts residing between the muscle fibers, and delineating fibroblasts sheathing the muscle mass. We further show these subpopulations entail distinct cellular dynamics and transcriptomes. Notably, we find mrFibroblast subpopulations exert distinct regulatory roles on myoblast proliferation and differentiation. Finally, we demonstrate this diversification depends on muscle contraction. Altogether, these findings establish mrFibroblast diversify in a spatio-temporal embryonic process into distinct cell types, entailing different characteristics and roles.

overall_design: We report the single cell RNA sequencing from skeletal muscles of  E12.5&E15.5 embryos taken from both forelimbs and hindlimbs

first: Lavi

last: Coren

first: Shelly

last: Zaffryar-Eilot

first: Anas

last: Odeh

first: Anna

last: Kaganovsky


title: Holt-Oram syndrome at single cell resolution

first: Yi

last: Zhao

state: Texas

address: 6770 Bertner Avenue

institute: The Texas Heart Institute at Baylor College of Medicine

summary: Holt-Oram syndrome (HOS), characterized by heart and forelimb defects, is caused by mutations in the T-box transcription factor, TBX5. While much has been done to elucidate TBX5’s transcriptional mechanisms in animal and human induced pluripotent stem cell (iPSC) models, transcriptomics from HOS patient tissue is lacking.

overall_design: Here, we report single nuclear transcriptional profiling (snRNA-seq) of left ventricular (LV) tissue from a 10-year-old female HOS patient undergoing cardiac transplant surgery.

first: Zhao

last: Yi

first: Li

last: Xiao

first: Jeffrey

last: Steimle

first: Martin

last: James


title: OPG promotes lung metastasis by blocking the RANKL-RANK-CXCL10 axis to drive NK cell paucity

first: Hu

last: Haitian

overall_design: Murine lung CD11b+F4/80+ Mo-macs were isolated by FACS. Then, these cells were stimulated by PBS and RANKL for 24 hors. DEGs of these cells were analyzed by RNA-seq.


title: A pan-family screen of Nuclear Receptors in immunocytes reveals ligand-dependent inflammasome control

city: Boston

first: CBDM

last: Lab

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

overall_design: Refer to individual Series


title: A pan-family screen of Nuclear Receptors in immunocytes reveals ligand-dependent inflammasome control [scRNA-seq]

summary: To examine more closely the varied effects of RA receptor deletions on peritoneal MFs, and determine whether inactivation of RXRα and RARγ elicited superimposable effects on different LPM clusters (as predicted if they operate as a heterodimer, a known propensity of RXR proteins), we performed single-cell RNA sequencing (scRNAseq) analyses on total CD11b+CD115+ peritoneal cells from BMC mice edited for several RA receptors, 17 days after reconstitution.

overall_design: Total CD11b+CD115+ peritoneal macrophages were sorted from BMC mice carrying  RA receptor mutants (i.e., RORα, RXRβ ,RARγ and RXRα) and internal controls, 17 days after reconstitution. Each in biological duplicate, and all multiplexed by hashtagging into the same run for optimal comparability.

first: Yutao

last: Wang

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: A pan-family screen of Nuclear Receptors in immunocytes reveals ligand-dependent inflammasome control [ChIPmentation]

summary: We profiled RXRα binding to genomic loci in peritoneal macrophages using ChIPmentation.

overall_design: Chip with RXRα antibody in total peritoneal macrophages with sequencing library preparation by Tn5 transposase(tagmentation).


title: A pan-family screen of Nuclear Receptors in immunocytes reveals ligand-dependent inflammasome control [RNA-seq 1]

summary: We profiled the transcriptional effects of NR deficiencies on peritoneal macrophages.

overall_design: RNA-seq of peritoneal macrophages from bone marrow chimera mice carrying different NR mutants.


title: RNA sequencing to determine gene expression changes in SQLE knockdown osteosarcoma cells

city: Shanghai

first: YongJie

address: Zhabei District

department: Department of Orthopaedic Surgery

institute: Shanghai Tenth People’s Hospital Affiliated to Tongji University

summary: In our study, we found that SQLE was critical to osteosarcoma progression. To identify the mechanism of SQLE in osteosarcoma, we conducted the RNA-seq analysis of SQLE knockdown in osteosarcoma cell line U2OS cells.

overall_design: Compare the transcritome profile of U2OS stably expressing SQLE-shRNA or scrambled-shRNA using RNA-seq.

first: Yongjie

first: Yang

last: Dong

first: Kunpeng

last: Zhu

first: Chunlin

last: Zhang


title: Temporal single-cell profiling of distinct mesenchymal, epithelial, endothelial, and immune cell lineages in the lung after injury

city: Iowa City

first: Dakota

middle: L

last: Jones

state: IA

address: 51 Newton Road

department: Department of Anatomy and Cell Biology

institute: University of Iowa

summary: Upon severe injury to the lungs, a poorly understood multistep process results in either euplastic regeneration or dysplastic repair which leads to a loss of functional gas-exchanging alveolar tissue. We show that the dysplastic repair process consists of an injury-induced tissue niche (iTCH) containing Keratin 5+ epithelial cells and Pdgfra-derived Pdgfrb+ mesenchymal cells, which proliferate and transit across multiple cells states before localizing to dysplastic regions. Temporal and spatial single cell analysis reveals that Pdgfra-derived Pdgfrb+ cells communicate via Notch signaling to dysplastic keratinized epithelium. Inactivation of proliferation and Notch signaling in these Pdgfra+ progenitor mesenchymal cells prevents the establishment of iTCHs. Mesenchymal Notch signaling in iTCHs suppresses Wnt and Fgf signaling, whereas loss of Notch rewires alveolar signaling patterns to promote euplastic regeneration and restore functional gas exchange in the lung. iTCH presence and signaling patterns can be used to differentially phenotype fibrotic from degenerative chronic lung disease, with associated apposing flows of FGF and WNT signaling discriminating these disease states. These data reveal the emergence of an injury and disease associated niche in the lung, its regulation by mesenchymal Notch signaling, and the impact these cellular decisions have on discriminating the choice between dysplastic repair or euplastic regeneration.

overall_design: Mesenchymal, epithelial, endothelial, and immune cells were isolated by fluoresence-activated cell sorting (FACS) and analyzed using scRNA-seq.

first: Michael

middle: P

last: Morley

first: Edward

middle: E

last: Morrisey


title: High-Resolution Genome-Wide Maps Reveal Widespread Presence of Torsional Insulation

city: Ithaca

first: Michelle

middle: D.

address: 142 Sciences Dr B08

department: LASSP

institute: Cornell University, HHMI

summary: Torsional stress in chromatin plays a fundamental role in cellular functions, influencing key processes such as transcription, replication, and chromatin organization. Transcription and other processes may generate and be regulated by torsional stress. In the genome, the interplay of these processes creates complicated patterns of both positive (+) and negative (-) torsion. However, a challenge in generating an accurate torsion map is determining the zero-torsion baseline signal, which is conflated with chromatin accessibility. Here, we introduce a high-resolution method based on the intercalator trimethylpsoralen (TMP) to address this challenge. We describe a method to establish the zero-torsion baseline while preserving the chromatin state of the genome of S. cerevisiae. This approach enables both high-resolution mapping of accessibility and torsional stress in chromatin in the cell. Our analysis shows transcription-generated torsional domains consistent with the twin-supercoiled-domain model of transcription and suggests a role for torsional stress in recruiting topoisomerases and in regulating 3D genome architecture via cohesin. Significantly, we reveal that insulator sequence-specific transcription factors decouple torsion between divergent promoters, whereas torsion spreads between divergent promoters lacking these factors, suggesting that torsion serves as a regulatory mechanism in these regions. Although insulators are known to decouple gene expression, our finding provides a physical explanation of how such decoupling may occur. This new method provides a potential path forward for using TMP to measure torsional stress in the genome without the confounding contribution of accessibility in chromatin.

overall_design: TMP-seq of s. cerevisiae cells with and without torsion was performed as a means of measuring the genome wide distribution of torsional stress.  This method allows the subtraction of both DNA sequence and protein mediated accesibility biases from the resulting psoralen crosslinking distribution.

first: Porter

last: Hall

first: Lauren

last: Mayse

first: Lu

last: Bai

first: Marcus

last: Smolka

first: B

middle: F

last: Pugh


title: Longitudinal gene expression profiling in Nodal-induced and control zebrafish embryonic explants

first: Amrit

last: Koirala

address: 1 Baylor Plaza

summary: We report RNA-sequencing from zebrafish explants generated from embryos injected with mRNA encoding the Nodal ligand ndr2 (N), constitutively active Nodal receptor CA-acvr1b* (T), and uninjected (U) controls. Explants of all 3 conditions were compared at each of 7 developmental stages: sphere (SR), 30% epiboly (30), 50% epiboly (50), shield (SH), 75% epiboly (75), 90% epiboly (90), and 2-somite (2S) (corresponding to 4, 4.7, 5.3, 6, 8, 9, and 11 hours post fertilization, respectively).

overall_design: Sequencing of polyadenylated mRNAs from ndr2 (N), CA-acvr1b*(T), and uninjected (U) explants with 3 biological replicates (A-C) per condition per stage (SR - 2S).

first: Margot

last: Kossmann Williams

first: Cristian

last: Coarfa


title: METTL3 mediates m6A modification of hsa_circ_0072380 to regulate the progression of gestational diabetes mellitus

city: Guangzhou

first: chen

middle: wei

last: fen

address: 4F, Building 1, Standard Property Unit 3, International Biotech Island

institute: Forevergen

summary: M6A modification plays a vital role in gestational diabetes mellitus (GDM) progression. However, the role of METTL3 and differential m6A-modified circRNAs in GDM stay to be investigated. Placental tissue samples from GDM patients and normal controls (NC) were collected to measure changes in m6A modification levels. MeRIP-seq on placental tissue was performed to detect differential m6A-modified circRNAs.High glucose (HG)-treated JEG3 cells were used to establish the GDM cell model. Differentially expressed circRNAs levels in GDM and NC groups was measured by qRT-PCR. We knocked down METTL3 to study its function. Additionally, we conducted functional recovery experiments. Dot blot assay was utilized to assess changes in m6A levels. MeRIP-qPCR was performed to evaluate the effect of knocking down METTL3 on m6A modification of hsa_circ_0072380 in JEG3 cells. Compared with NC group, GDM group exhibited increased levels of m6A modification and METTL3 expression. Differences in m6A modification of circRNAs exist between the GDM and NC groups. Hsa_circ_0000994, hsa_circ_0058733, and hsa_circ_0072380 were significantly down-regulated in GDM group while hsa_circ_0036376, hsa_circ_0000471, and hsa_circ_0001173 showed no significant differences between two groups. HG treatment promoted METTL3 expression and m6A level of JEG3 cells, and inhibited cell proliferation, migration, and invasion abilities. Knocking down METTL3 reversed these effects. After HG treatment, hsa_circ_0072380 was significantly down-regulated. Knocking down METTL3 led to up-regulation of hsa_circ_0072380, while knocking down hsa_circ_0072380 restored the function of SiMETTL3. Additionally, knocking down METTL3 significantly reduced m6A modification of hsa_circ_0072380. METTL3 mediated m6A modification of hsa_circ_0072380 to regulate GDM progression.

first: Shaofeng

first: Shiqin

last: Cai

first: Lisha

last: Ye

first: Zilian

last: Wang

first: Haitian

last: Chen


title: Expression data from Myotonic dystrophy type 1 (DM1) patient-derived induced pluripotent cell

city: Kodaira

first: Masayoshi

last: Kamon

state: Tokyo

address: 4-1-1 Ogawa-Higashi

department: Department of PNS Research

country: Japan

institute: National Center of Neurology and Psychiatry

summary:
DM1-iPSCs were generated from the peripheral blood of male adult patients. All clones were generated using episomal vectors. For skeletal muscle differentiation of the DM1-iPSCs, tet-on MYOD1 expression vector was transfected into DM1-iPSCs.
To examine whether DM1-iPSC clones with different repeat sizes have acquired different characteristics, we isolated DM1-iPSC clones with different repeat sizes. We isolated 2 clones (S45 and S118) showing repeat size of 400~900, 2 clones (S14 and S24) showing repeat size of 1200~1600, and 2 clones (S1 and S16) showing repeat size of 1800~2800.

overall_design: Cells were harvested at undifferentiated stages for RNA extraction and hybridization on Affymetrix microarrays. We performed gene expression profiles of 6 DM1-iPSC subclones and 1 healthy control iPS cell (normal).

first: M

first: T

last: Araki


title: Conserved functions of angiosperm ε-clade 14-3-3 proteins in growth, flowering, and abiotic stress resilience

city: Northfield

first: Heather

middle: Elizabeth

last: Driscoll

state: VT

address: 158 Harmon Drive

department: Biology

institute: Norwich University

summary: 14-3-3 proteins are involved in a number of developmental processes in plants, largely acting through the control of transcription factor localization within the cytoplasm or nucleus. The temperate Pooideae grass 14-3-3 gene GF14h in particular was previously found to be co-expressed with flowering activators in the vernalization pathway, leading to the hypotheses that its protein product is involved in vernalization responsive flowering and/or cold acclimation. To test predictions of these non-exclusive hypotheses, and to assess functional conservation broadly across angiosperms, we generated CRISPR lines of GF14h in Brachypodium distachyon (Pooideae) and compared their mutant phenotypes with those of the co-orthologous Arabidopsis thaliana (Brassicaceae) grf9 T-DNA mutant. Contrary to our first prediction, we found that rather than promoting flowering as part of the vernalization pathway, both BdGF14h and AtGRF9 repress flowering under different conditions. Our data also support a conserved role for GF14h/GRF9 genes in the promotion of growth at the expense of abiotic stress resilience. We discuss these results in the light of crop improvement and climate change.

overall_design: Total RNA was extracted from whole aboveground tissues of plants at the five leaf stage at the end of a 15 day drought treatment. Drought was conducted by withholding water. All material was collected three hours post dawn to control for circadian rhythms in gene expression. RNAseq was conducted for cDNA libraries on three biological replicates of wild type Brachypodium distachyon 21-3 and mutant (CR:GF14h-1 and CR:HDAC19-2b) plants of the same genotypic background as the wild type. Mutations were specific to the 14-3-3 protein encoding gene GF14h or HISTONE DEACETYLASE 19 (HDAC19) based on CRISPR/Cas9 editing and subsequent genotyping. Mutants for both genes are homozygous for a mutation in exon 1 and the mutations cause a premature stop codon.

first: Jill

last: Preston


title: Primary human hepatocyte transcriptomic statin response

city: Oakland

first: Marisa

last: Medina

state: CA

address: 5700 Martin Luther King Jr. Way

department: Pediatrics

institute: UCSF

summary: We have previously identified a number of statin-responsive genes in human cell lines, but in some cases, these findings may not be relevant in vivo. Here, we statin exposed primary human hepatocytes from four different donors to identify statin-responsive genes in this biologically relevant cell type. We also compared the effects of statin on gene expression between these primary cells and our previous datasets in other cell lines to identify overlapping effects of interest.

overall_design: Primary human hepatocytes from 4 different donors treated with 0 nM, 500 nM or 2000 nM activated simvastatin

middle: W

first: Elizabeth

last: Theusch

first: Kristen

last: Stevens


title: The gene expression profile of primary BMMs differentiating into osteoclasts after knockout of solute carrier family 11 member 2 (SLC11A2)

status: Public on Dec 15 2024

city: Hangzhou

first: Siyue

last: Tao

state: Please Select

address: 3rd, Qingchun Road, Shangcheng district

department: Orthopedics department

institute: Sir run run shaw hospital affiliated to zhejiang university

summary: To investigate the effect of solute carrier family 11 member 2 (SLC11A2) knockout on osteoclast differentiation, BMMs were extracted from the femurs of SLC11A2 knockout mice and the same litter of control mice, treated with RANKL, and then rna sequencing was performed.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BMMs extracted from the femurs of LysmCre-Slc11a2flox/flox mice and litters of control Slc11a2flox/flox mice, and were treated with 50ng/mL RANKL for 48 hours

first: Xiaoan

last: Wei

first: Xiangxi

last: Kong

first: Fengdong

last: Zhao

first: Jian


title: Transcriptome variation between wild type and five-foliate leaf mutant in Glycine max

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois


title: Transcriptome variation between wild type and five-foliate leaf mutant in Glycine max (RNA)

summary: Molecular characterization of leaf development has not been well studied in soybean. Studies have shown that genomic regions controlling multifoliate leaf morphology in Glycine max also regulates important agronomic characters including yield, seed weight, seed number, shattering, plant growth, and flowering. Two soybean isolines that differed in leaf phenotype were profiled by high throughput RNA and small RNA (sRNA) sequencing. A Clark isoline, homozygous for a dominant mutant allele, Lf1, that specifies a five-foliate compound leaf was compared to wild type Clark that is homozygous for the standard allele that produces trifoliate leaves. Although Lf1 is dominant, it presents variable expressivity as the young plantlets with the Lf1Lf1 genotype initially have trifoliate leaves in the first few weeks, after which they transition to five-foliate leaves. At later developmental stages, they begin to produce four-foliate or trifoliate leaves.  In RNA-Seq experiments, a total of 91 and 95 million reads were generated in each lane of Illumina sequencing for the shoot tip of wild type Clark standard (CS) and mutant Clark five-foliate (CF) libraries, respectively. Of these, ~70% million reads aligned to the 78,743 target Glyma models from the reference soybean genome (cv. Williams 82) with maximum of 3 mismatches and up to 25 alignments.  Where as in vegetative bud, 56 (CS) to 59 (CF) million reads were produced and of these ~80% aligned to the soybean reference genome.  The comparative studies of the transcript profiles of the wild-type versus mutant line revealed a number of differentially expressed genes. A total of 1,296 and 2,083 genes were up-regulated in the shoot tip of CS and CF, respectively that showed ≥2-fold expression difference.  On the contrary in the vegetative bud, much smaller number of genes 14 (CS) and 94 (CF) showed increased transcript abundance. In sRNA analysis, a collection of 200,447 and 268,508 unique sRNA sequences isolated from shoot tip tissue of CS and CF were aligned to the soybean reference genome and their target glyma models were predicted using bioinformatics. This sRNA analysis at genome level reveals differences in size distribution of classes in the CS and CF. This study provides insight into the initial understanding of leaf development in soybean by revealing a number of genes and sRNAs differentially expressed between the CS and CF.

overall_design: Examination of two soybean isolines: Clark standard (CS, wild type) & Clark five-foliate (CF, mutant) from two different tissues.

first: Navneet

last: Kaur


title: Effects of SARS-CoV-2 S protein on endothelial cell thrombosis

city: Changchun

first: xizi

last: luo

state: jilin

address: 126 Xinmin Street, Changchun, Jilin, China

institute: Jilin University

summary: The outbreak of Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection, has led to an unparalleled global health crisis. While the majority of COVID-19 patients present with mild respiratory issues, a subset of patients still develop severe symptoms and life-threatening complications. Notably, abnormal coagulation and thrombosis are significant contributors to mortality in severe COVID-19 patients. Therefore, this study stimulated aortic endothelial cells with SARS-Cov-2 S protein and performed transcriptome sequencing analysis.

overall_design: RNA sequencing was conducted on endothelial cells with and without exposure to the SARS-CoV-2 S protein. Following 24 h of treatment with SARS-CoV-2 S protein at 10 nM, the cells were collected for RNA sequencing at Kidio Bio.


title: Small RNA variation between trifoliate and five-foliate shoot tips of Glycine max isolines

summary: Two soybean isolines that differed in leaf phenotype were profiled by high throughput RNA and small RNA (sRNA) sequencing. A Clark isoline abbreviated as CF and homozygous for a dominant mutant allele, Lf1, that specifies a five-foliate compound leaf was compared to wild type Clark, designated CS, which is homozygous for the standard allele that produces trifoliate leaves. Although Lf1 is dominant, it presents variable expressivity as the young plantlets with the Lf1Lf1 genotype initially have trifoliate leaves in the first few weeks, after which they transition to five-foliate leaves. This study provides insight into the initial understanding of leaf development in soybean by revealing a number of small RNAs differentially expressed between the CS and CF. Out of over 200,000 unique sequences, 913 showed similarities to 122 known miRNAs in soybean.

overall_design: Small RNAs from shoot tips from two soybean isolines of Glycine max were compared: Clark standard trifoliate line (PI 547402, L58-231, abbreviated as CS) and Clark five-foliate (PI 547425, L64-1344, abbreviated as CF).  These lines were obtained from the USDA Soybean Germplasm Collection GRIN (USDA/ARS, University of Illinois, Urbana IL).


title: Tau accumulation induces microglial state alterations in Alzheimer’s disease model mice

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University


title: Gene expression in amiRNA-VQ1,VQ10 compared to wild type Col-0 plants under normoxia.

city: Valencia

first: Jose

last: Leon

address: CPI Edificio 8E, Ingeniero Fausto Elio s/n

country: Spain

institute: IBMCP (CSIC-UPV)

summary: Comparative expression analysis of amiRNA-VQ1,VQ10 versus wild type Col-0 in normoxic plants.

overall_design: 3´RNA-Seq data from three independent biological replicates for every genotype were used to perform the comparative analysis.

first: José

last: León


title: AXL and MERTK receptor tyrosine kinases inhibition protects against pancreatic necrosis via limiting CXCL2-mediated neutrophil infiltration

first: Jingpiao

last: Bao

address: South Chongqing Road no. 227  Copyright © 2013 Shanghai jiaotong university school of medicine

institute: Shanghai Jiao Tong University School of Medicine

summary: We aimed to investigate the strategies to protect against pancreatitis severity and we focused on AXL and MERTK tyrosine kinases receptors, which are the negative regulator of the innate immune response. In order to investigate the underlying mechanism of AXL and MERTK in mediating pancreatic necrosis, we performed high-throughput mRNA sequencing on the pancreatic tissues of 6 C57BL/6J wild type mice and 6 Axl-/-Mertk-/-  mice under hyperstimulation of caerulein.

overall_design: Pancreas were collected from caerulein-treated C57BL/6J wild type mice and Axl-/-Mertk-/- mice. Total RNA from pancreatic tissue was processed for RNAsequencing.

first: L

last: Wen

first: J

first: X

last: Zhang


title: Chronic Stress Exacerbates Cerebral Amyloid Angiopathy through Promoting NET formation

first: Huipeng

last: Huang

address: 600 Tianhe Road

institute: the Third Affiliated Hospital of Sun Yat-sen University

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

overall_design: Refer to individual Series


title: Chronic Stress Exacerbates Cerebral Amyloid Angiopathy through Promoting NET formation [I]

summary: Cerebral amyloid angiopathy (CAA) is the leading cause of vascular dementia among the elderly. Neuropsychiatric symptoms are commonly manifested in CAA patients but are usually considered as consequences of CAA pathology. Here, we report that chronic stress promotes CAA progression, which enhances deposition of amyloid protein beta (Aβ) in brain blood vessels and exacerbates subsequent brain injury. Mechanistically, neutrophil is implicated in CAA development. Aβ that accumulated in brain vasculature induces neutrophil extracellular traps (NETs) by activating STAT6 signaling, which inhibits neutrophil apoptosis and switches the programmed cell death toward NETosis. During chronic stress, circulatory Norepinephrine (NE) strengthens STAT6 activation in neutrophil and promotes NET formation, thus exacerbates the NET-dependent angiopathy. We demonstrate that inhibiting neutrophil chemotaxis towards brain or suppressing NET formation both ameliorate CAA severity in the context of chronic stress. Therefore, we propose that stress-associated psychological disorders and NETs are promising therapeutic targets in CAA.

overall_design: To investigate the underlying mechanism of Aß40-induced NETs, bone marrow derived neutrophils of mice were separated and treated with 20ug/ml Aß40 for 4h.


title: Chronic Stress Exacerbates Cerebral Amyloid Angiopathy through Promoting NET formation [II]

overall_design: To study how chronic stress exacerbated NET formation and the consequent brain injury in CAA, WT or CAA mice subjected to chronic restraint stress were perfused with PBS. Brains were isolated and half of the brains were subjected to RNA extraction.


title: Transcriptome profiling reveals different expression pattern between beard and scalp hair follicle  in androgenetic alopecia.

first: Lian

middle: Shu

last: Wu

state: Guangdong

address: No.1838, North Guangzhou Avenue, Baiyun District

department: Department of Plastic and Aesthetic Surgery

institute: Nanfang Hospital of Southern Medical University

summary: Androgenetic alopecia (AGA) is a progressive dermatological disorder of scalp hair loss, while beard growth in AGA is normally unaffected. In an attempt to identify genes that contribute to the androgen-responsive phenotype, we performed a thorough transcriptome profiling of hair follicles (HFs) from frontal and occipital scalp, chin and armpit. Through this analysis, three specifiic different expressed genes(LGALS7B, FABP4, FOS) were identified using qPCR, immunofluorescence. The differences in the expression of these genes in cultured beard and frontal HF reflected less inflammation and immune response, more active keratinization and PPARs signaling in beard HFs compared to frontal HFs. This profiling results be used to understand the different molecular mechanism of hair growth between AGA beard and HF, and those provided a possibility for the enlarged beard phenotype and AGA treatment.

overall_design: hair follicle mRNA profiles of hair follicles from frontal and occipital scalp, chin and armpit in androgenetic alopecia.

first: Shulian

first: Qian

last: Qu


title: Screening of reference genes by qRT-PCR in Chelonus formosanus

status: Public on Dec 14 2024

city: haikou

first: qiujiu

last: cai

address: No. 14 Xingdan Road

institute: Institute of Plant Protection, Hainan Academy of Agricultural Sciences, China

summary: Chelonus formosanus is an important parasitic natural enemy of Lepidopteran insects and has great value in the biological control of insect pests. To screen the reference genes in the real-time fluorescence quantitative PCR (qRT-PCR) assay of Chelonus formosanus, six candidate reference genes were selected based on transcriptome data, including GAPDH, ACT, TU, TF, HSP, and RP. The expression stability of these six internal reference genes was determined by qRT-PCR in different tissues (head, chest, abdomen) and at different temperatures (11℃and 41℃), as well as with two insecticides (dinotefuran and chlorantraniliprole).

overall_design: To screen the reference genes in the real-time fluorescence quantitative PCR (qRT-PCR) assay of Chelonus formosanus, six candidate reference genes were selected based on transcriptome data, including GAPDH, ACT, TU, TF, HSP, and RP. The expression stability of these six internal reference genes was determined by qRT-PCR in different tissues (head, chest, abdomen) and at different temperatures (11℃and 41℃), as well as with two insecticides (dinotefuran and chlorantraniliprole). The BestKeeper, GeNorm, NormFinder, Delta, and RefFinder were used to evaluate the expression stability of each gene after treatments.

first: Qiujiu

last: Cai

first: Jingjing

last: Jia

first: Weikang

first: Zhufeng

last: Lin

first: Qing

last: Feng

first: Qi

last: Yao

first: Xuncong

last: Ji


title: Transcriptome characterization of human highly osteoblastic/cementoblastic periodontal ligament cell clones (OM medium)

city: Campinas

first: Luciana

middle: Souto

last: Mofatto

state: Sao Paulo

address: R. Carl Von Linaeus

department: Genetics, Evolution and Bioagents

country: Brazil

institute: Institute of Biology - University of Campinas

summary: we isolated single-cell-derived clones and evaluated their potential to differentiation into osteo/cementoblastic (O/C) phenotype (C-O clones) or fibroblastic phenotype (C-F clones) in vitro, and evaluated the transcriptomic profile of the groups of clones in  osteogenic induction medium, using next-generation sequencing technology (RNA-seq).

overall_design: 2 clones of each phenotype [ osteo/cementoblastic (O/C) phenotype (C-O clones) or fibroblastic phenotype (C-F clones)] were compared

first: Miki

middle: T

last: Saito

middle: S

first: Francisco

middle: H

last: Nociti-Jr

first: Karina

middle: G

last: Silvério


title: Host and rabies virus gene expression is shaped by human brain cell type and reveals a preexisting pro-viral transcriptional state in astrocytes

city: Portland

first: Arpiar

middle: B

last: Saunders

state: OR

address: 3232 SW Research Dr

institute: Vollum Institute (Oregon Health and Sciences University)

summary: Rabies virus (RABV) proteins play dual roles during the infection of complex neural tissue, the generation and spread of new virions and the active inhibition of cellular innate immune pathways, both contributing to rabies’ lethality. While spatially-distinct RABV protein residues specializing in virus-centric and immune-inhibitory functions have been identified, how these dual functions interact to shape infection outcomes across diverse types of host brain cells is unknown. To “unmask” and study how innate immune inhibition affects the transcriptional regulation of the human and viral genome with cellular resolution, we performed single-cell RNA sequencing of co-cultured human brain cell types, comparing infection dynamics of a wild-type RABV isolate virus to a mutant virus in which six critical point mutations in the P and M RABV proteins selectively neuter antagonism of interferon- and NF-κB- dependent cellular responses. Our analysis reveals that RABV gene expression is shaped by host cell type and that wild-type RABV infection induces small-scale, cell-type conserved transcriptional programs that may support infection by hijacking transcriptional feedback systems that control pro-viral host cell factors while minimizing anti-viral responses. In contrast to accepted models, disinhibited innate immune signaling increases RABV transcriptional output across infected cell types. Most strikingly, we discovered a sub-population of “pro-viral” astrocytes that supports an average of 6-fold higher viral mRNA expression through a massive host cell transcriptional change involving ~38% of the astrocyte-expressed human genome. Our analysis suggests that “pro-viral”-like astrocytes are a rare subtype found in the human brain and are poised to play a protective role during viral infection by advertising pathogens to microglia.

overall_design: Single-cell RNA-seq data was generated from co-cultured human brain cell types following various infection conditions of Tha isolate rabies virus (RABV). One experimental axis was viral titer (either 0.5 or 5.0 MOI). The second experimental axis was the rabies virus infection condition, which included 1) "No Infection" (in which no rabies virus was introduced into the culture well) as well 2) wild-type "Tha" RABV or 3) Tha2P4M RABV ("2P4M" denotes six amino acid mutations in RABV P and M proteins that block antagonism of host cell innate immune pathways by P and M protein).

first: Lena

last: Feige

first: Karl

last: Young

first: Juan Pablo

last: Cerapio

first: Tatsuya

last: Kozaki

first: Lauriane

last: Kergoat

first: Valentina

last: Libri

first: Florent

last: Ginhoux

first: Milena

last: Hasan

first: Lamya

last: Ben Ameur

first: Gregory

last: Chin

first: Zach

last: Goode

first: Hervé

last: Bourhy


title: DNA methylation analysis of parental and p53-null human fibroblasts

city: Solna

first: Gema

last: Sanz Santos

state: Stockholm

address: Nobels väg 16

country: Sweden

institute: Karolinska Institutet

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of parental and p53-null human fibroblasts. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Samples included 3 parental human fibroblast replicates and 3 p53-null human fibroblasts replicates.

overall_design: Bisulphite converted DNA from the 6 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip. Samples included 3 parental human fibroblast replicates and 3 p53-null human fibroblasts replicates.

first: G

last: Sanz

first: M

last: Singh


title: High-throughout sequencing of ovarian cancer cells treated with Annonacin and Carboplation

city: Wenzhou

first: Kejie

last: Chen

address: Chashan

institute: Wenzhou Medical University

summary: The high-throughput sequencing technology was performed after the treatment of human ovarian cancer cells A2780 and ES2 with Annonacin and Carboplation purchased from MCE, to explore the expression of genes related to cell proliferationand DNA damage of ovarian cancer cells A2780 and ES2 after the treatment of Annonacin and Carboplation, and to find an interesting target pathway,p53 signaling pathway.

overall_design: A2780 and ES2 cells (3 × 105 cells/well in 6-well plates) were treated with Annonacin or carboplatin or the combination of Annonacin and carboplatin for 48 h. After treatment, the cells were collected, and total RNA from each group was extracted using TRIzol (TaKaRa, Japan). Paired-end sequencing was ultimately carried out on an Illumina HiSeq 4000 platform at LC-BIO Technologies (Hangzhou, China).

first: Yeying

last: He

first: Jiaying

last: TONG

first: Xiaohui

last: Zheng


title: bulk RNA-seq of lichen planus

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

summary: An early and sustained clinical response was seen, with 83.3% of patients responsive at week 16. Our molecular data identified a unique, oligoclonal IFN-γ, CD8+, CXCL13+ cytotoxic T-cell population in LP skin and demonstrated a rapid decrease in IFN signature within 2 weeks of treatment, most prominently in the basal layer of the epidermis.

overall_design: Whole transcriptomic analysis using bulk RNA-seq was performed on lesional and non-lesional skin prior to therapy (n=11, 12, respectively).

first: Johann

last: Gudjonsson

first: Lam

middle: C

last: Tsoi

first: Mangold

last: Aaron


title: Genomic Analysis of genetically perturbed Xenopus laevis embryos

city: Williamsburg

first: Margaret

last: Saha

state: Virginia

address: 540 Landrum Drive

institute: College of Wiliam & Mary

summary: To investigate the genes involved in the compensatory behavior observed in Xenopus laevis following a genetic perturbation on the Notch signaling pathway, we analyzed the gene expression of the embryos using RNA-Seq for three developmental stages and three treatments

overall_design: Differential gene expression analysis of RNA-seq data for Xenopus laevis embryos injected with either DBM or ICD constructs (as well as control GFP) at three time points

first: Sahan

last: Raghavan

first: Matthew

last: Luchs


title: Differential effects of p95HER2 and FL-HER2 on gene expression in PB2 mouse breast tumor xenografts at early and late stages.

city: Pittsburgh

first: Dong

last: Hu

address: 530 45th Street

institute: University of Pittsburgh

summary: To explore how p95HER2 regulates gene expression to promote tumor growth in immunocompetent mice, we engineered PB2 mouse breast cancer cells to express either p95HER2 or control FL-HER2 under the control of doxycycline. Both FL-HER2 and p95HER2 cells were implanted to the mammary fat pads of immunocompetent C57BL/6 mice that were placed under a DOX625 doxycycline diet. Tumor xenografts were harvested 10 and 22 days after inoculation. We then performed transcriptomic analysis using RNA-seq data from PB2-FL-HER2 and PB2-p95HER2 tumors.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from PB2-FL-HER2 and PB2-p95HER2 tumors collected 10 and 22 days after implantation.

first: Linda

middle: M

last: McAllister-Lucas

first: Peter

last: Lucas


title: Thymic mimetic cells in zebrafish

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: We profiled the zebrafish thymus by single-cell RNA sequencing to investigate the heterogeneity of zebrafish thymic epithelial cells and determine whether similar mimetic cell populations to those found in mice and humans might also exist in the zebrafish.

overall_design:
To assess the heterogeneity of zebrafish thymic epithelial cells, a total of 11 zebrafish samples derived from 14 adult and 21 juvenile zebrafish were studied. Specifically, we re-processed single-cell RNA sequencing (scRNA-seq) data from 8 zebrafish thymus samples derived from 4 adult zebrafish and 21 juvenile zebrafish previously described in GSE190794 (GSM5732067, GSM5732070, GSM5732077,  GSM5732078, GSM5732079, GSM5732080, GSM5732081, GSM5732082) so that reads mapping to intronic regions were included in the analysis to increase sensitivity and be consistent with mouse and human scRNA-seq studies for cross-species comparison. In addition, we generated 3 new scRNA-seq datasets derived from a total of 10 adult lck:mCherry;cd79a:eGFP transgenic zebrafish. The thymi from 5 of these adult zebrafish were subjected to mechanical dissociation, filtering, and cell sorting on a BD FACSAriaII, whereas thymi from the other 5 adult zebrafish underwent enzymatic dissociation with Liberase TM prior to quenching, filtering, and cell sorting. The live, non-autofluorescent, GFP-negative, mCherry-negative cells (a population depleted of T and B cells, thus providing a relative enrichment of thymic epithelial cells) were sorted and collected for 10x scRNA-seq. One 10x lane was used for the mechanically dissociated sample (untreated) and two lanes were used for the liberase-treated sample to obtain 2 technical replicates.

Re-analysed Samples in GSE190794/PRJNA788489 and their processed data file:

SampleName Experiment BioSample processed data file
GSM5732067 Adult, Thymus, 3 SRX13397695 SAMN24007722 Fish_22_Thymus_.filtered_feature_bc_matrix.h5
GSM5732070 Adult, Thymus, 4 SRX13397698 SAMN24007725 Fish_24_Thymus_.filtered_feature_bc_matrix.h5
GSM5732077 Adult, Thymus, 1 SRX13397705 SAMN24007732 lck-eGFP_Thymus_1_.filtered_feature_bc_matrix.h5
GSM5732078 Adult, Thymus, 2 SRX13397706 SAMN24007733 lck-eGFP_Thymus_2_.filtered_feature_bc_matrix.h5
GSM5732079 Juvenile, Thymus, 1 SRX13397707 SAMN24007734 4wpfThymus_1.filtered_feature_bc_matrix.h5
GSM5732080 Juvenile, Thymus, 2 SRX13397708 SAMN24007735 4wpfThymus_3.filtered_feature_bc_matrix.h5
GSM5732081 Juvenile, Thymus, 3 SRX13397709 SAMN24007736 4wpfThymus_5.filtered_feature_bc_matrix.h5
GSM5732082 Juvenile, Thymus, 4 SRX13397710 SAMN24007737 4wpfThymus_6.filtered_feature_bc_matrix.h5

first: Sara

middle: A

last: Rubin

first: Alexandra

last: Corbin

first: Song

middle: P

last: Yang

middle: I


title: IRF2BP2-mediated MHC-I expression controls cytotoxic T cell responses in acute myeloid leukemia

city: New York

first: Zhengxi

last: Sun

state: NY

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Medical Center


title: IRF2BP2-mediated MHC-I expression controls cytotoxic T cell responses in acute myeloid leukemia [RNA-Seq]

summary: Immunotherapy, including immune checkpoint blockade (ICB), has become an effective option for treating patients with cancer, especially those with solid tumors. Recently, T cell-based cellular therapies have extended the scope of immunotherapy to B-cell malignancies. Immunotherapy options for patients with acute myeloid leukemia (AML), however, are limited. To identify new immunotherapy approaches for AML, we performed CRISPR/Cas9 AML T cell co-culture screens. We determined that depletion of the transcription factor IRF2BP2 leads to enhanced T cell killing both in vitro and in vivo. Gene expression profiling and flow cytometry studies confirmed enhanced MHC-I expression upon IRF2BP2 loss. Chromatin binding analysis further revealed a regulatory axis whereby MHC-I expression is repressed by IRF2BP2 through its repression of the interferon alpha pathway. Our studies have identified the inhibition of IRF2BP2 as a potential strategy for enhancing T-cell-based therapies in patients with AML

overall_design: To investigate the transcriptional regulation function of IRF2BP2 in acute myeloid leukemia, we established THP-1 and MOLM-13 human AML cell lines with control and IRF2BP2 knockout using sgRNAs. We then acquired gene expression profiles of these cell lines by performing RNA-seq.

first: Xufeng

last: Chen

first: Iannis

last: Aifantis


title: Cardiac reprogramming and Gata4 overexpression reduce fibrosis and improve diastolic dysfunction in heart failure with preserved ejection fraction [scRNA-seq]

city: Tsukuba

first: Yu

last: Yamada

state: Ibaraki

address: 1-1-1 Tennoudai

department: Cardiovascular

institute: University of Tsukuba

summary: Fibrosis is important pathogenesis in heart failure with preserved ejection fraction (HFpEF). We previously reported that the overexpression of cardiac transcription factors, Mef2c/Gata4/Tbx5/Hand2 (MGTH) could directly reprogram cardiac fibroblasts (CFs) into induced CMs (iCMs) and reduce fibrosis. Here we show that in vivo cardiac reprogramming generated iCMs from resident CFs, improved cardiac function, and reversed fibrosis in HFpEF model using a novel transgenic mouse system. scRNA-seq of non-cardiomyocytes revealed that cardiac reprogramming suppressed fibroblastic gene expression via conversion of profibrotic profile to a quiescent state. Thus, in vivo cardiac reprogramming may be a promising approach for HFpEF.

overall_design: Hearts were harvested 15 weeks after the start of the experiment from three groups (Ctrl, Ctrl_HF, and TTg_HF) for scRNA-seq.

first: Masaki

last: Ieda


title: Cardiac reprogramming and Gata4 overexpression reduce fibrosis and improve diastolic dysfunction in heart failure with preserved ejection fraction [Visium]

summary: Fibrosis is important pathogenesis in heart failure with preserved ejection fraction (HFpEF). We previously reported that the overexpression of cardiac transcription factors, Mef2c/Gata4/Tbx5/Hand2 (MGTH) could directly reprogram cardiac fibroblasts (CFs) into induced CMs (iCMs) and reduce fibrosis. Here we show that in vivo cardiac reprogramming generated iCMs from resident CFs, improved cardiac function, and reversed fibrosis in HFpEF model using a novel transgenic mouse system. Visium revealed spatial information on changes in gene expression in HFpEF.

overall_design: Hearts were harvested 15 weeks after the start of the experiment from three groups (Ctrl, Ctrl_HF, and TTg_HF) for Visium.


title: Effect of p95HER2 overexpression on gene expression in PB2 mouse breast tumor xenografts.

summary: To explore how p95HER2 regulates gene expression to promote tumor growth in immunocompetent mice, we engineered PB2 mouse breast cancer cells to express p95HER2 under the control of doxycycline. Both empty vector (EV) and p95HER2 cells were implanted to the mammary fat pads of immunocompetent C57BL/6 mice, which were placed under a DOX625 doxycycline diet. Tumor xenografts were harvested 3 weeks after inoculation. We then performed transcriptomic analysis using the RNA-seq data from PB2-EV and PB2-p95HER2 tumors.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from PB2-EV and PB2-p95HER2 tumors.


title: Genomic Analysis of genetically perturbed Xenopus Borealis embryos

summary: To investigate the genes involved in the compensatory behavior observed in Xenopus Borealis following a genetic perturbation on the Notch signaling pathway, we analyzed the gene expression of the embryos using RNA-Seq for three developmental stages and three treatments

overall_design: Differential gene expression analysis of RNA-seq data for Xenopus Borealis embryos injected with either DBM or ICD constructs (as well as control GFP) at three time points


title: IRF2BP2-mediated MHC-I expression controls cytotoxic T cell responses in acute myeloid leukemia [ChIP-Seq]

overall_design: Chromatin immunoprecipitation DNA-seq (ChIP-seq) for histone modication H3K27ac in THP-1 cells with control or IRF2BP2 knockdown


title: Cardiac reprogramming and Gata4 overexpression reduce fibrosis and improve diastolic dysfunction in heart failure with preserved ejection fraction

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

overall_design: Refer to individual Series