title: Genome-wide methylation profiles of post-mortem tissue samples (human) 1

summary: In this study, 60 post-mortem tissue samples comprising three tissue types (blood, brain, and heart) were collected from autopsies of 20 Koreans aged 18 to 78. 250 ng of genomic DNA (gDNA) was employed to generate DNA methylation profiles utilizing the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA, USA) at Macrogen Inc. (Macrogen, Seoul, Korea).


title: Genome-wide methylation profiles of post-mortem tissue samples (human)

status: Public on Oct 22 2023

city: Seoul

first: Hwan Young

last: Lee

address: 103 Daehak-ro, Jongno-gu

department: Forensic Medicine

country: South Korea

institute: Seoul National University College of Medicine

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Phosphorylation of AHR by PLK1 promotes metastasis of LUAD via DIO2-TH signaling

city: Houston

first: Chaohao

last: Li

state: TX

address: 1881 East Rd

country: USA

institute: MD Anderson Cancer Center

type: Expression profiling by high throughput sequencing

summary: Metastasis of Lung adenocarcinoma (LUAD) is a major cause of death in patients. Aryl hydrocarbon receptor (AHR) is an important transcription factor involved in the initiation and progression of lung cancer. Polo-like kinase 1 (PLK1), a serine/threonine kinase, is an oncogene that promotes the malignancy of multiple cancer types. Nonetheless, the interaction between these two factors and significance in lung cancer remains to be determined. Here, we demonstrate that PLK1 phosphorylates AHR at S489 in LUAD, which leads to epithelial-mesenchymal transition (EMT) and metastatic events. RNA-seq analyses show that type 2 deiodinase (DIO2) is responsible for EMT and enhanced metastatic potential. DIO2 converts tetraiodothyronine (T4) to triiodothyronine (T3), which then activates thyroid hormone signaling. In vitro and in vivo experiments demonstrate that treatment with T3 or T4 promotes the metastasis of LUAD, whereas depletion of DIO2 or deiodinase inhibitor disrupts this property. Taken together, our results identify the phosphorylation of AHR by PLK1 as a mechanism leading to the progression of LUAD and provide possible therapeutic interventions for this event.

overall_design: To investigate the mechanisms behind enhanced metastasis after AHR is phosphorylated by PLK1 at S489, we established four cell lines (V, WT, SA, SD) derived from A549 lung adenocarcinoma cancer cell line, by overexpressing AHR with different mutations. We performed RNA-seq analysis of four cell lines and identified genes that were most differentially expressed in SD cells

first: Xiaoqi

last: Liu

first: Daheng

last: He

first: Chi

last: Wang


title: Efficacy of tafasitamab in combination with rituximab in subtypes of aggressive lymphoma

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

country: Germany

institute: University of Münster

summary: Purpose: Despite recent advances in the treatment of patients with aggressive lymphomas, still a significant fraction of patients will succumb to their disease. Thus, novel therapeutic strategies are urgently needed. As the anti-CD20 antibody rituximab and the CD19-targeting antibody tafasitamab share distinct modes of actions, we investigated if dual-targeting of aggressive lymphoma B-cells by combining rituximab and tafasitamab might increase cytotoxic effects.  Experimental Design: Antibody single and combination efficacy was determined investigating different modes of action including direct cytotoxicity, antibody-dependent cell-mediated cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP) in vitro and in vivo models of aggressive B-cell lymphoma comprising diffuse large B-cell lymphoma (DLBCL) and Burkitt lymphoma (BL).  Results: Overall, three different sensitivity profiles to antibody monotherapy or combination treatment were observed in in vitro models: while 2/11 cell lines were primarily sensitive to tafasitamab and 2/11 were predominantly sensitive to rituximab treatment, the combination of tafasitamab and rituximab resulted in enhanced cell death in 7/11 cell lines in at least one mode of action. Treatment with either antibody or the combination   resulted in decreased expression of the oncogenic transcription factor MYC and inhibition of AKT signaling which mirrored the cell line-specific sensitivities to direct cytotoxicity. At last, the combinatorial approach of the two antibodies resulted in a synergistic survival benefit in a PBMC-humanized Ramos NOD/SCID mouse model.   Conclusions: This study demonstrates that the combination of tafasitamab and rituximab improves efficacy compared to antibody mono treatment in models of aggressive B-cell lymphoma in vitro and in vivo.  Translational Relevance: The immunochemotherapy of rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) remains the standard of care for newly diagnosed DLBCL patients. However, 30-40% of patients are refractory or relapse after initial response to the immunochemotherapy, indicating a high-unmet medical need for these patients. Tafasitamab and rituximab target the B-cell surface proteins CD19 and CD20, respectively, and both antibodies feature overlapping modes of action , namely direct cytotoxicity, ADCC and ADCP. In this study, we show that the combination of tafasitamab and rituximab had additive and synergistic efficacy both in vitro and in vivo. Our findings shed new light on the underlying mechanism of the combination of both antibodies and lay the ground to translate the results into improved outcome for patients with aggressive lymphoma in future clinical trials.

overall_design: For gene expression profiling, we performed RNA-sequencing of SU-DHL-6 cells after 6, 12, 18 and 24h of treatment with either 5nM tafasitamab, or 5nM rituximab, or the combination of 5nM tafasitamab and 5nM rituximab, compared to control (just solvent). Each time point and treatment was measured by two replicates. The same solvent measurements serve as control for each of the three treatments, resulting in 32 samples in total.

first: Georg

last: Lenz

first: Maria

last: Patra-Kneuer


title: RNA-seq analysis of the developmental mechanisms of Mongolian sheep embryos in different periods

city: Inner Mongolia

first: Hong

last: Su

state: Inner Mongolia

address: No. 306, Zhaowuda Road, Saihan District, Hohhot, Inner Mongolia Autonomous Region

country: China

institute: Inner MongoliaAgricultural University

summary: Analyze the developmental mechanism of Mongolian sheep embryos in different periods．

overall_design: Hulunbeier sheep was the experimental group, and Wuzhumuqin sheep was the control group. In each group (n = 3), 16-day and 25-day embryos of each sheep were taken, digested into single cells with enzymes, and performed RNA-seq.

first: Guifang

last: Cao


title: Microassay analysis of the lncRNAs expression profile in human aortic vascular smooth muscle cells(hAoSMCs) treated with PDGF-BB at 24 h.

city: shanghai

first: Xian

last: Guo

address: changhai road 168

institute: Changhai hospital

summary: Atherosclerosis is the most important mechanism of cardiovascular and cerebrovascular diseases and has become one of the most serious diseases that threaten human health. Vascular smooth muscle cells (VSMCs) are the main cellular components that constitute the structure of the blood vessel wall. The excessive proliferation and migration are pivotal pathological basis of atherosclerosis, in-stent restenosis, pulmonary hypertension and other vascular proliferative diseases. PDGF-BB is a potent proliferative agent for VSMCs, but the specific mechanism of PDGF-BB signaling pathway involved in biological processes such as proliferation and migration of VSMCs is not elusive.

overall_design: Used the lncRNAs microarray technology to screen the target lncRNA in hAoSMCs proliferation model treated with PDGF-BB (20ng/mL).Total RNAs of 3 replicates of hAoSMCs treated with vehicle or PDGF-BB at 24 h were sequenced and analyzed for identification of novel lncRNAs.

first: P

first: X


title: Post-mortem gene expression from mouse brain

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

summary:
Every biological system interacts with the surrounding environment, both during life and after death. We investigated three concealment simulations (air exposed, water submerged, and buried) to understand how the environment can influence the post-mortem transcription to add knowledge about the biology of death and also to identify possible molecules for forensic applications.
We used microarrays to detect upregulated and downregulated genes in the brains of concealed mouse (48h after death) and to identify molecular markes specifically associated to each environmental condition or the gene expression programme shared by all conditions analysed.

overall_design: 12 mice were used for the experiments in triplicate. All animals were euthanized by CO2 exposure at the same time and then distributed on the groups (control, exposed, submerged and buried). Full brains were macerated with liquid nitrogen and an aliquote was used for the analyses (control immediately after death and treated groups 48h after death)

first: Raphael

middle: S

last: Bonadio

first: Larissa

middle: B

last: Nunes

first: Mariana

middle: M

last: Pedreira

first: Patricia

last: Moretti

first: Juliana

middle: F

last: Mazzeu

first: Aline

last: Pic-Taylor

first: Stefano

last: Cagnin

first: Silviene

last: Oliveira


title: Inactivation of Gas6/Axl signaling aggravated Microglia-Astrocyte cross regulation after spinal cord injury

status: Public on Oct 21 2023

city: Guangzhou

first: Xiao

middle: Lin

last: Zeng

state: Guangdong

address: 58 Zhongshan 2nd Road

institute: Sun Yat-sen University

summary: Aggressive inflammation and excessive scar formation are the main cause to the difficulty of neural tissue repair after spinal cord injury (SCI). Microglia and astrocytes act as important role in this micro-environment of SCI and there is cross regulation between microglia and astrocytes. After SCI, MG0 polarized into MG1 and MG3 which were belong to pro-inflammatory phenotype microglia; Naive astrocytes polarized into Reactive and Scar-forming astrocytes. Growth arrest-specific 6 (Gas6) and its receptor Axl was declined in all these cells after SCI. In vitro study, Gas6 had the negative effect on cytotoxic astrocytes and pro-inflammatory microglia polarization and even the cross regulation between cytotoxic astrocytes and pro-inflammatory microglia. Further mechanism study indicated that Gas6 suppressed cytotoxic phenotype polarization of astrocytes through inhibited the activation of YES-associated protein (YAP) signal pathway and suppressed pro-inflammatory phenotype polarization of microglia through inhibited the activation of NF-κB/p65 and JAK/Stat3 signal pathways. In vivo study, Gas6 treatment suppressed cytotoxic astrocytes and pro-inflammatory microglia polarization at the injured site of spinal cord to facilitate tissue repair and loco-motor recovery.

overall_design: Spinal cord damage can lead to sensory, motor, and autonomic dysfunction distal to the site of injury. The lack of effective treatment measures and the poor prognosis after injury are heavy burdens to patients and their families and greatly endanger human health. After spinal cord injury, the microenvironment localized to the injury is dramatically altered. The purpose of this RNA-seq analysis was to examine the differences in the transcriptomes of normal wild-type mice and mice with spinal cord injury. Total RNA was purified from the spinal cord injury center, and differential expression analysis was performed to compare the transcriptomes of spinal cord injured mice with those of wild-type mice (Sham group, n=3 and SCI group, n=3).

first: Jiewen

last: Chen

first: Xiaolin

first: Yong

last: Wan

first: Xiang

last: Li


title: VU-0365114-treated AsPC-1 and PANC-1

city: New Taipei City

first: Pei-Ming

last: Yang

address: No. 301, Yuantong Rd., Zhonghe Dist.

department: Graduate Institute of Cancer Biology and Drug Discovery

country: Taiwan

institute: Taipei Medical University

summary: To analyze the VU-0365114-induced gene expression changes in pancreatic cancer cells.

overall_design: AsPC-1 and PANC-1 cells treated with 10 uM VU-0365114 for 24 h.


title: Identification of the target gene expression of peptide SK56 in human macrophage cells during pyroptosis

city: kunming

first: Gan

last: Wang

address: jiaochang dobg lu 32#

institute: Kunming Institute of Zoology

summary: To gain insight into the  peptide SK56 target gene profile in macrophage cells, we performed RNA-seq analysis in PMA-differentiated THP-1 cells upon LPS+nigericin with or without SK56, to analyze the signaling pathway of cell pyroptosis blocked by SK56..

overall_design: Transcriptomics analysis of pyroptosis or SK56 treatment expression in human macrophage cells

first: Wang

last: Gan

first: Ping

last: Meng


title: H3mm18 interferes with transcription on H3.3 incorporated chromatin.

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We focused on H3mm18 (one of the histone H3.3 subvariants that is expressed in skeletal muscle stem cells) to understand the function of a group that is not incorporated into chromatin.

overall_design: We performed CEL-Seq2 in C2C12 cells, BRB-seq, ChIL-seq and ATAC-seq in NIH3T3 cells, and BRB-Seq in mouse tissues.

first: Kosuke

last: Tomimatsu

first: Atsuko

last: Miyawaki-Kuwakado

first: Tetsuro

last: Komatsu

first: Yukari

last: Kondo

first: Kazumitsu

last: Maehara

first: Daijiro

last: Konno

first: Seiji

last: Okada

first: Akihito

last: Harada

first: Kaori

last: Tanaka

first: Yasuo

last: Kitajima

first: Hitoshi

last: Kurumizaka

first: Hiroshi

last: Kimura

first: Taro

last: Tachibana

first: Yusuke

last: Ono

first: Tatsuya

last: Takemoto


title: Comparison of gene change after pneumonectomy

city: New York

first: Bi-Sen

last: Ding

state: NY

address: York Avenue

institute: Weill Cornell

summary: Pneumonectomy, resection of left lung lobe, induces regenerative responses that consist of numerous genetic changes. To identify genetic changes, we compare the isolated vascular cells from young and old mice that underwent pneumonectomy.

overall_design: The experiment compared gene change in the lung vascular cells isolated from young and old mice after pneumonectomy.

first: B


title: Repurposing FDA-approved drugs for the treatment of malignant peripheral nerve sheath tumors

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

summary: Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive soft tissue sarcomas developed from Schwann cell lineage. They account for up to 10% of all soft tissue sarcomas. Although there is an unmet need for new therapeutic agents for MPNSTs, to date there have been few transcriptomic analyses of this tumor type. We studied FDA approved drugs for MPNST treatment and compared their transcriptomic changes in cell lines before and after treatment. We demonstrated that Fludarabine treated NF1 MPNST cells exhibited altered signaling pathways such as the upregulation of the Wnt/Ca+ pathway and downregulation of the hedgehog and hypoxia signaling pathways in the Ingenuity Pathway Analysis (IPA) and Gene Set Enrichment Analysis (GSEA) analysis. The combined Colchicine and Fludarabine treatment enhanced the cytotoxicity of sporadic MPNST cells through altered signaling pathways, including increased Wnt/β-catenin pathway and others. The transcriptomic analysis comparing NF1/sporadic MPNST cells and normal Schwann cells indicated that NF1 MPNST cells had more splicing events, fewer single nucleotide variants, and induced RNA expression than sporadic MPNST cells. In summary, we identified a transcriptomic differences between MPNSTs and Schwann cells, between sporadic MPNST cells and NF1 MPNST cells, and between drug treated MPNST cells and vehicle treated cells.

overall_design:
The overnight cultured cells (~2 x 10^6 per 100 mm dish) were exposed with various concentrations of a drug(s) or vehicle for 24 h.
Total 20 samples were analyzed; 2 replicates each group, respectively.

first: Ming

last: Leung

first: Vonn

last: Walter

first: Sang

last: Lee


title: The RNA methylation level of A549 was altered by nanomaterial incubation.

city: xiamen

first: jie

last: zeng

state: fujian

address: No. 4221-120, Xiang An Nan Road

institute: School of Life Sciences, Xiamen University

summary: We reported changes in RNA methylation levels in A549 cells caused by black phosphorus quantum dots and titanium dioxide nanoparticles.

overall_design: Detection of RNA methylation in lung cancer cells by 2 nanomaterials respectively.

first: Fengkai

last: Ruan

first: Jie

last: Zeng

first: Shengwei

last: Jiang

first: Hanying

last: Yin

first: Chengyong

last: He


title: Effect of PF-429242 on gene expression in liver cancer cells

first: Pei-Ming

last: Yang

summary: To analyze the PF-429242-induced gene expression changes in PLC/PRF/5 and HepG2 liver cancer cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PF-429242-treated PLC/PRF/5 and HepG2 cells.


title: The non-canonical poly(A) polymerase FAM46C promotes erythropoiesis

status: Public on Oct 20 2023

city: hangzhou

first: ke

last: yang

state: zhejiang

address: 1369 West Wenyi Road, Hangzhou

institute: Liangzhu Laboratory, Zhejiang University


title: The non-canonical poly(A) polymerase FAM46C promotes erythropoiesis [RIP]

summary: Posttranscriptional regulation of mRNA is a crucial component of gene expression. The disruption of this process can have detrimental effects on normal development and give rise to various diseases.  The search for novel posttranscriptional regulators and the exploration of their roles are essential for understanding development and disease. Through a multimodal analysis of red blood cell trait GWASs and transcriptomes of erythropoiesis, we identified FAM46C, a non-canonical RNA poly(A) polymerase, as a necessary factor for proper red blood cell development. FAM46C is highly expressed in late stages of the erythroid lineage, and its developmental upregulation is controlled by an erythroid-specific enhancer. We demonstrate that FAM46C stabilizes mRNA in an enzyme activity dependent manner by maintaining the poly(A) tails of its targets. Furthermore, we identified transcripts of lysosome and mitochondria components as highly confident in vivo targets of FAM46C, which aligns with the need of maturing red blood cells for substantial clearance of organelles and maintenance of cellular redox homeostasis. In conclusion, our study unveils a novel role of FAM46C in positively regulating the level of lysosome and mitochondria components, thereby promoting erythropoiesis.

overall_design: RNA Immunoprecipitation Sequencing (RIP-seq) for FAM46C-strep in HUDEP-2 cells

first: Ke

last: Liu


title: The non-canonical poly(A) polymerase FAM46C promotes erythropoiesis [CUT&RUN]

overall_design: CUT&RUN for TBP, GATA1, TAL1, as well as histone variants H3K4me1 and H3K27ac in HUDEP-2 cells


title: The non-canonical poly(A) polymerase FAM46C promotes erythropoiesis [RNA-seq]

overall_design: RNA-seq for FAM46C knockdown, knockout clonal and overxpression in HUDEP-2 cells.

first: Xiang

last: Lv


title: The non-canonical poly(A) polymerase FAM46C promotes erythropoiesis [Capture-C]

overall_design: Next generation (NG) Capture-C of FAM46C promoter in HUDEP-2 cells


title: Stepwise differentiation of follicular helper T cells reveals distinct developmental and functional states [RNA-Seq 2]

city: Boston

first: Peter

last: Sage

address: 221 Longwood Ave

department: Medicine/Renal

institute: Brigham and Women's Hospital

summary: Assessment of transcriptional changes in TfhFull or TfhProg with FoxP1 deletion

overall_design: Control versus FoxP1 deleted Tfh-Prog and Tfh-Full RNASeq


title: Non-canonical function of histone methyltransferase G9a in the translational regulation of chronic inflammation

city: Chapel Hill

first: Adil

last: Muneer

state: North Carolina

address: 120 Mason Farm Rd, Genetic Medicine Building

department: Biochemistry and Biophysics

institute: University of North Carolina Chapel Hill

summary: We report a novel translation-regulatory function of G9a, a histone methyltransferase and well-understood transcriptional repressor, in promoting hyperinflammation and lymphopenia; two hallmarks of endotoxin tolerance (ET)-associated chronic inflammatory complications. Using multiple approaches, we demonstrate that G9a interacts with multiple translation regulators during ET, particularly the N6-methyladenosine (m6A) RNA methyltransferase METTL3, to co-upregulate expression of certain m6A-modified mRNAs that encode immune-checkpoint and anti-inflammatory proteins. Mechanistically, G9a promotes m6A methyltransferase activity of METTL3 at translational/post-translational level by regulating its expression, its methylation, and its cytosolic localization during ET. Additionally, from a broader view extended from the G9a-METTL3-m6A translation regulatory axis, our translatome proteomics approach identified numerous “G9a-translated” proteins that unite the networks associated with inflammation dysregulation, T cell dysfunction, and systemic cytokine response. In sum, we identified a previously unrecognized function of G9a in protein-specific translation that can be leveraged to treat ET-related chronic inflammatory diseases.

overall_design: MeRIP-Seq/m6A-seq was performed using THP-1 cells (wildtype, G9a knockout, METTL3 knockout) under different inflammatory conditions (N, NL, TL) to identify G9a/METTL3-corregulated transcripts showing differential m6A modification.

first: Li

last: Wang

first: Feng

last: Zhang

first: Xian

last: Chen


title: The non-canonical poly(A) polymerase FAM46C promotes erythropoiesis [ADAR_APOBEC]

overall_design: FAM46C-ADARcd/APOBEC1 dox induction expression 24h in HUDEP-2 cells, and then RNA-seq.


title: Transcriptome Analysis Reveals Differentially Expressed Genes and Pathways for Oviduct Development and Defense in Prelaying and Laying Hens

city: Chengdu

first: Lingqian

address: 211 Huimin Road, Wenjiang, Chengdu, Sichuan Province

institute: Sichuan Agricultural University

summary: The oviduct plays an indispensable role in the formation of eggs, especially the magnum and uterus. The identification of oviduct development in different stages will help to target candidate genes and pathways in regulation of albumen and eggshell formation, as well as defense mechanism in oviduct and egg. To identify the function differences and the molecular defense mechanism of the oviduct and egg, we performed transcriptome sequencing analysis of the magnum and uterus in 120d and 300d old Lohmann layers, three birds in each group. With fold changes (log2 Ratio)>=2 and false discovery rate (FDR)<0.01, RNA-Seq revealed 1040 genes expressed differentially in the magnum and 595 genes in the uterus. By combining GO enrichment and KEGG pathway analysis, it served to show that genes activities of the magnum and uterus in prelaying chickens were more likely to concentrate on growth and development, and after egg-laying, they were mainly inclined to enhance the substances transmembrane transport and secretion activities. We further characterized 1579 new genes, while only 803 of them were functionally annotated. A complex mixture of proteins related to defense was measured in this study. A subset of avian β-defensins (AvBDs) and ovodefensins (OvoDs), that is, AvBD12, AvBD11, AvBD10, OvoDA1, OvoDB1, OvoDA2, OvoDA3 and OvoDBβ were detected to express in the magnum of laying hens at high levels. Collectively, the identification and functional analysis of these differentially expressed genes (DEGs), as well as specific expression of avian defensins may contribute to understand the development and defense mechanisms of oviduct and eggs.

overall_design: To identify the function differences and the molecular defense mechanism of the oviduct and egg, we performed transcriptome sequencing analysis of the magnum and uterus in 120d and 300d old Lohmann layers.

first: Lintian

last: Yu

first: Long

first: Jinshan

last: Ran


title: Mutations from IPEX patients elicit a range of phenotypes in mice [scATAC-Seq]

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: scATAC analysis of mouse Treg from Foxp3 missense mutant mice heterozygous females : R51Q, K199del, R51Q, WT

overall_design: Mouse CD4+ regulatory Tregs in 6-10 weeks old Foxp3 missense mutant heterozygous female mice were isolated from spleen by FACS for scATAC-seq using 10x Genomics.

first: Juliette

last: Leon

first: Kaitavjeet

last: Chowdhary

first: Christophe

last: Benoist


title: Mutations from IPEX patients elicit a range of phenotypes in mice

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

overall_design: Refer to individual Series


title: Mutations from IPEX patients elicit a range of phenotypes in mice [RNAseq]

summary: RNAseq analysis of mouse Treg from Foxp3 missense mutant mice hemizygous male and heterozygous female : R51Q, C168Y, K199del, R309Q, F324L, R337Q

overall_design: Mouse CD4+ regulatory Tregs in 6-10 weeks old Foxp3 missense mutant mice hemizygous male and heterozygous female were isolated from spleen by flow cytometry, as DAPI–CD19-TCRβ+CD4+CD25+. 1,000 cells were double-sorted directly into lysis buffer for RNA-seq (Smart-seq2)  library preparation following the standard ImmGen low-input protocol (www.immgen.org).


title: A subset of temporary resident cardiac macrophages induced by myocardial infarction limits adverse ventricular remodeling

city: Shanghai

first: Yaozu

last: Xiang

address: 1239 Siping Road, Yangpu District

institute: Tongji University


title: A subset of temporary resident cardiac macrophages induced by myocardial infarction limits adverse ventricular remodeling [spatial RNA-seq]

summary: We provided an analysis of mouse macrophage heterogeneity in the heart after MI using spatial transcriptome sequencing.

overall_design: Spatial gene profiles of mouse heart cell populations derived from MI and MI-E.

first: Yue

last: Xu

first: Kai

last: Jiang

first: Dandan


title: PTEN facilitates lysosome biogenesis and decreases exosome secretion by directly dephosphorylating TFEB

first: Yuanyuan

last: Shi

address: changhailu 168

institute: the First Affiliated Hospital of Naval Medical University

summary: To investigate the differentially expressed genes in the PTEN_x005f_x0002_intact CCA cells, compared with the PTEN-deficient CCA cells. group.cooperative function KDM4D/NFIB/MLL1 complex in the regulation of adipogenic differentiation, we established

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different cells.

first: Tianyi

first: Xiaowen

last: Cui

first: Liwei

last: Dong

first: Hongyang


title: A subset of temporary resident cardiac macrophages induced by Myocardial infarction limits adverse ventricular remodeling

summary: We provided an mRNA-seq analysis of mouse macrophage heterogeneity in the heart after MI.

overall_design: Macrophage RNA profiles derived from WT and Bhlhe41dTomato-Cre+/- mice post MI.


title: Gene expression in dormant, germinating and thermoinhibited Arabidopsis seeds

city: Kawasaki

first: Naoto

last: Kawakami

state: Kanagawa

address: 1-1-1 Higashimita, Tama-ku

department: Department of Life Sciences

institute: Meiji University

summary: To establish the basis for understanding molecular mechanism of seed germination response to temperature, we analyzed transcriptomes in freshly harvested dormant and dry stored after-ripened seeds.  The after-ripened seeds started to show visible germination from 36h after the start of imbibition, and almost all the seeds germinated after 3 days. The freshly harvested seeds stayed dormant by imbibition at 26°C, and germination of the after-ripened seeds was almost completely inhibited at 34°C. Total RNA was prepared from 0 (dry), 6 and 24h imbibed seeds to find regulatory genes of seed dormancy and germination.

overall_design: Transcriptomes in Arabidopsis thaliana Col-0 dormant seeds (imbibed at 26°C ) and after-ripened seeds (imbibed at 26°C and 34°C) were analyzed at 0, 6 and 24 hours after imbibition.  Three independent experiments were performed at each time point using different seed batches for each experiment.

first: Natsuki

last: Tachibana

first: Tomohiro

last: Sano

first: Yuki

last: Nakazawa

first: Shizuka

last: Koshimizu


title: A subset of temporary resident cardiac macrophages induced by myocardial infarction limits adverse ventricular remodeling [scRNA-seq]

summary: We provided a single cell mRNA-seq analyses of mouse macrophage heterogeneity in the heart after MI.

overall_design: Gene profiles of mouse heart cell populations derived from Sham, MI and MI-E.

first: Feng

last: Chen

last: Wang


title: Stepwise differentiation of follicular helper T cells reveals distinct developmental and functional states [ATAC-Seq]

first: Peter

last: Sage

summary: Follicular helper T (Tfh) cells are essential for the formation of high affinity antibodies. However, the signals that promote Tfh development after initial differentiation are unknown. Here we use fate mapping and reporter strategies to show that, after initial differentiation, Tfh cells transition from a progenitor-like Tfh (Tfh-Prog) stage to an IL-21-expressing fully developed Tfh (Tfh-Full) stage which is regulated by follicular regulatory T (Tfr) cells. Using single cell RNA sequencing and epigenomic analysis, we uncover additional developmental stages including an early Tfh transitory (Tfh-Trans) stage prior to full development, as well as an Tfh-Ex stage that occurs after full development marked by loss of IL-21 expression. The transcriptional and epigenetic landscape is formed in the Tfh-Transitory stage and is maintained throughout the Tfh-Ex state, suggesting terminal development. We also find the transcription factor Foxp1 regulates the transitions between these stages in Tfh cells to balance the ratio of stem-like progenitor and effector Tfh cells. Through selective in vivo deletion of Tfh-Full and Tfh-Ex cells, we show that these cells control antigen-specific germinal center formation, maintenance and somatic hypermutation at distinct stages of responses to a SARS-CoV-2 vaccine. Together, these studies demonstrate the transitionary phases of Tfh development and how control of the progression through these stages regulates humoral immunity.

overall_design: Lymph node T follicular helper cells/duplicates or triplicates/Lymph node conventional CD4 T cells as controls

middle: T

first: Manuel

middle: A

last: Podesta

first: Cecilia

last: Cavazzoni

first: Debattama

last: Sen

first: Alos

last: Diallo


title: High sodium reduced the expression of PTH1R and Klotho by inhibiting 1,25 (OH)2D3 synthesis in cultured proximal tubule epithelial cells

city: Shang hai

first: Jie

last: Gu

address: No. 12, middle Urumqi Road, Shanghai

institute: Division of Nephrology, Huashan Hospital, Fudan University, Shanghai, China.

summary: The proximal tubule is the sensing site of sodium and phosphorus and the main place for the synthesis and metabolism of 1,25 (OH)2D3. Sodium may share the sensing mechanism with phosphate in proximal tubule epithelial cells; whether sodium cooperates with phosphate or plays an independent role in the regulation of phosphorus homeostasis remains unknown. In this in vitro study, we investigated the effects of high sodium on the synthesis and function of active vitamin D and local phosphorus regulation in proximal tubular epithelial cells. Human proximal tubule epithelial (HK-2) cells were treated with different concentrations of sodium/phosphorus. The expression of 1α-OHase (Cyp27b1) and 24-OHase (Cyp24a1) was determined by RT-PCR and Western Blot. Liquid chromatography/mass spectrometry (LC/MS) and enzyme-linked immunosorbent assay (ELISA) were used to detect the levels of 1,25 (OH)2D3. Intracellular Ca2+ ([Ca2+]i) was detected with the Ca2+ indicator dye Fura-4. Chromatin samples were immunoprecipitated with antibodies against parathyroid receptor 1 (PTH1R) and Klotho. High sodium decreased the expression of 1,25 (OH)2D3 by reducing 1α-OHase and 24-OHase in HK-2 cells, reduced the expression of PTH1R and Klotho, and increased the intracellular calcium concentration. These effects were reversed by sodium phosphorus transporter inhibitor (PFA), sodium hydrogen transporter inhibitor (Caliporide), and a chelator of the extracellular calcium, whereas enhanced by ouabain. Vitamin D receptor agonists significantly increased the recruitment of VDR to the Vitamin D response element (VDRE) of PTH1R and Klotho promoter, thus increasing the expression of PTH1R and Klotho. High extracellular sodium can decrease the synthesis of active vitamin D in the proximal tubules, affect the gene regulation of 1,25 (OH)2D3/VDR, and significantly reduce the expression of PTH1R and Klotho. The data reveal the influence of a high-sodium diet on mineral metabolism and the core role of vitamin D in kidney mineral metabolism.

overall_design: High phosphate/sodium induced gene expression in the HK-2 cells was measured at 24 hours after exposure to high phosphate/sodium.

first: Jialin

first: Xujiao

first: Jianping

last: Mao

first: Huaizhou

last: You

first: Jing


title: Stepwise differentiation of follicular helper T cells reveals distinct developmental and functional states [scRNA-seq]


title: Pien Tze Huang induces reactive oxygen species to inhibit colorectal cancer growth

status: Public on Oct 19 2023

city: fuzhou

first: yangfan

last: zhang

address: Fujian Normal University Qishan Campus, College Town, Fuzhou, Fujian Province

institute: FJNU

summary: In this study, we investigated the impact of PZH on inducing reactive oxygen species (ROS) to inhibit colorectal cancer (CRC) growth. CRC cell line HCT116 was exposed to PZH for 24 hours, then RNA-Sequencing was conducted and showed that PZH modulated ROS-related signaling pathways, including DNA repair and the unfolded protein response, concomitant with the suppression of proliferation-related genes such as PCNA and Ki-67.

overall_design: CRC cell line HCT116 was treated by PZH for 24 h and then performed RNA-Sequencing (RNA-Seq) by sequencing company.

first: Qin

last: Lu

first: Zhiyun

last: Cao

first: Jian

last: Du


title: An aptamer-based bionic spinal cord scaffold elicits robust neurogenesis in situ after spinal cord injury in rats

first: Rongjie

last: Wu

address: Yuexiu District, 106, Zhongshan Road

institute: Guangdong Pronvincial People's Hospital

summary: Transected spinal cord injury (SCI) results in significant structural disruption of the spinal cord. The reconstruction of neural pathways following SCI faces several key challenges, including inadequate endogenous neural stem cells (NSCs) and poor neurogenesis in natural repair process, and concerns related to the long-term survival of neurons following exogenous transplantation. In the current study, we report an oligonucleotide aptamer drug (Apt19S) which is first proven to recruit endogenous NSCs to the site of injury following SCI, and therefore develop a bionic spinal cord scaffold that can sustainedly release Apt19S and neurotrophin-3 (NT-3) to provide the neurogenic niche with the necessary mechanical properties and support for in situ spinal cord repair. The bionic scaffold successfully recruited a significant number of endogenous NSCs in vivo and established a neurogenic niche that was abundant in NT-3, thereby promoting neuronal differentiation and the formation of neuronal networks Regenerated nerve fibers including 5-hydroxytryptamine-positive nerve fibers and corticospinal tract grew robustly into the injury site and generated synaptic connections with the newborn neurons. Collectively, our findings indicate that our aptamer-based bionic spinal cord scaffold elicits a robust neurogenesis process in situ, breaking the limitations imposed by poor self-repair ability in the adult spinal cord.

overall_design: Six adult female SD rats (220–250 g, supplied by the Experimental Animal Center of Sun Yat-sen University) were randomly divided into two groups: 1) Apt19S-decellularized optic nerve (A-DON) scaffold implant. 2) decellularized optic nerve scaffold implant. (n=3 for each group).Two weeks after SCI, three rats were selected from each of the DON and A-DON groups for mRNA sequencing in the spinal cord.

first: Biqin

last: Lai

last: Liu


title: NQO1 regulates expression and alternative splicing of apoptotic genes associated with Alzheimer's disease in PC-12 cells

city: LanZhou

first: yingshi

last: du

address: NO.1 Donggang West Road

department: First Department of Geriatrics

institute: The First Hospital of Lanzhou University

summary: Quinone oxidoreductase I (NQO1), an important antioxidant enzyme which plays an important role in monitoring cellular redox state, was altered in the brain tissues of Alzheimer’s disease (AD) patients. In addition to its traditional antioxidant effect, NQO1 is also a multifunctional RNA-binding protein (RBP) in post-transcriptional regulation. However, NQO1 in AD pathology by acting as an RBP is not studied. In the present study, the RBP functions of NQO1 in rat PC12 cells, a cell line widely used in neurological disease studies, were investigated using siRNA knock-down (KD) and following whole transcriptome (RNA-seq) analysis. Reduced levels of NQO1 led to a significant increase in cellular apoptosis, compared with control cells. Notably, RNA-seq analysis of the transcriptome of PC12 cells by NQO1-KD revealed that genes in certain apoptosis pathways, were under global transcriptional and alternative splicing regulation. Quantitative RT-PCR confirmed the NQO1-regulated transcription of apoptotic genes Cryab, Lgmn , Ngf, Apoe, Brd7, Stat3, and alternative splicing of Bin1, Picalm, Fyn. These NQO1-regulated genes have been found to be closely related to AD pathogenesis. Our findings suggest that NQO1 acts as an RBP and participates in the pathology of AD by regulating expression and alternative splicing of genes involved in apoptosis. The results of present study extend our understanding of the cellular and molecular mechanisms in AD pathogenesis, which might contribute to the development of novel therapeutic targets.

overall_design: Transcrptional analysis of nqo1 knockdown and control in PC12 cells

first: Yingshi

first: Gejing

first: Yongming


title: DNA methylation alternations in the offspring hypothalamic tissue from inulin treatment dams

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

summary: Maternal inulin treatment may moderate the metabolism in offspring. Hypothalamic tissue from maternal inulin treatment has CpG sites that exhibit differential DNA methylationregulated compared to maternal obesity.

overall_design: We performed DNA methylation array analyses of offspring hypothalamic tissue from inulin treatment dams and obesity dams (n=3 per group).

first: Xinhua

last: Xiao

first: Jia

last: Zheng

first: Ming

last: Li

first: Miao

last: Yu

first: Fan

last: Ping

first: Tong

last: Wang

first: Xiaojing


title: Target gene regulatory network of miR-497 in angiosarcoma

city: West Lafayette

first: Jason

last: Hanna

state: IN

address: 201 S. University St. Hans219

department: Biological Sciences

institute: Purdue University

summary: Angiosarcoma (AS) is a vascular sarcoma that is highly aggressive and metastatic. Due to its rarity, treatment options for patients are limited, therefore more research is needed to identify possible therapeutic vulnerabilities. We previously found that endothelial deletion of Dicer1 drives AS development in mice. Given the role of DICER1 in canonical microRNA (miRNA) biogenesis, this suggests that miRNA loss may be important in AS development. After testing miRNAs previously suggested to have a tumor-suppressive role in AS, microRNA-497-5p (miR-497) suppressed cell viability most significantly. We also found that miR-497 expression led to significantly reduced cell migration and tumor formation. To understand the mechanism of miR-497 tumor suppression, we identified clinically relevant target genes using a combination of RNA-sequencing data in an AS cell line, expression data from AS patients, and target prediction algorithms. This work provides insight into the mechanisms of miR-497 and its target genes in AS pathogenesis.

overall_design: To characterize the target gene network of miR-497, mouse angiosarcoma cell line, ADC106, was transfected with NC and miR-497 mimics, and RNA was extracted 3 days post-transfection. RNA-seq was performed to identify differential gene expression in response to miR-497 overexpression.

first: Annaleigh

last: Benton


title: Distinct Mucosal and Systemic Immunological Characteristics in Transgender Women Potentially Relating to HIV Acquisition

first: Michael

last: Corley

address: 413 East 69th Street

department: Medicine, Division of Infectious Diseases

institute: Weill Cornell Medicine

summary: Genome-wide DNA methylation profiling of human sigmoid biopsy

overall_design: Bisulfite converted DNA from FACS sorted cells were hybridized to the Illumina MethylationEPIC Beadchip

middle: J


title: FLOT2 promotes nasopharyngeal carcinoma progression through suppression of TGF-β pathway via facilitating CD109 expression

city: Changsha

first: caiping

last: ren

address: No 87 Xiangya Road

institute: Xiangya Hospital, Central South University

summary: In nasopharyngeal carcinoma (NPC), the TGF-β/SMAD pathway genes are altered with inactive TGF-β signal, but the mechanisms remain unclear. Flotillin 2 (FLOT2) is a highly expressed protein in NPC, and is crucial for NPC progression. We show that FLOT2 negatively regulated TGF-β signaling pathway via up-regulating CD109 expression. FLOT2 increased CD109 transcription by stabilizing STAT3, which is identified as the activating transcription factor of CD109. FLOT2 interacted with STAT3 directly and increased the stability of STAT3 by inhibiting K48-linked polyubiquitination. CD109 could rescue the functional changes of NPC cells resulted from FLOT2 alteration. Expression of FLOT2 and CD109 was positively correlated, and was significantly higher in NPC tissues than in the normal nasopharyngeal epithelial tissues. Patients with high expression of both FLOT2 and CD109 presented poorer overall survival and disease-free survival compared those with high expression of one protein alone. In conclusion, FLOT2 promotes the development of NPC by inhibiting TGF-β signaling pathway via stimulating the expression of CD109 by stabilizing STAT3, which provides novel potential therapeutic strategy for NPC treatment.

overall_design: Expression data and the differentially expressed mRNAs in 5-8F-control and 5-8F-shFLOT2 cells were analysed using RNA-seq

first: Hongjuan

last: Xu

first: Weidong

first: Xingjun

last: Jiang

first: Caiping

last: Ren


title: Transcriptome changes after Nobiletin treatment in mammospheres

city: Yogyakarta

first: Adam

last: Hermawan

state: DI Yogyakarta

address: Sekip Utara II

department: Pharmacy

country: Indonesia

institute: Universitas Gadjah Mada

summary: Mammospheres from MCF-7 cells  were treated with Nobiletin and analyzed mRNA expression through mRNA sequencing

overall_design: We performed mRNA sequencing to find differentially expressed genes in Nobiletin treated mammospheres from MCF-7 cells

first: Muthi

last: Ikawati

first: Nurul

last: Fatimah

first: Heri

last: Himawan Prasetio


title: Effect of the autoimmune suppressor Gadd45a on radiation biodosimetry

first: Constantinos

last: Broustas

address: 630 168th Street

department: Center for Radiological Research

institute: Columbia University

summary: Radiation biodosimetry based on transcriptomic analysis of peripheral blood is a valuable tool to detect radiation exposure after a radiological/nuclear event and obtain useful biological information that could predict tissue and organismal injury. However, confounding factors, including inflammation, can potentially obscure the predictive power of the method. The Gadd45 (growth arrest and DNA damage-inducible genes) family is composed of three members, Gadd45a, Gadd45b, and Gadd45g, that play important roles in cell growth control, differentiation, DNA repair, and apoptosis.  Gadd45b and Gadd45g are important for inflammatory responses as well as mediating signals of the innate immune system, whereas Gadd45a is a negative regulator of activation-induced T cell proliferation. T cells from Gadd45a null mice are hyper-responsive to activating stimuli due to spontaneously increased p38MAPK activity. Importantly, Gadd45a-deficient mice develop an autoimmune disease, similar to human systemic lupus erythematosus, characterized by severe hematological disorders, kidney disease, and premature death. The goal of this study was to elucidate how pre-existing inflammatory condition in mice can affect radiation biodosimetry. We exposed wild-type and Gadd45a knockout C57BL/6J mice to 7 Gy x-rays and 24 h later we isolated whole blood and performed genome microarray and gene ontology analysis.

overall_design: Radiation induced gene expression in  blood from Gadd45aWT and Gadd45aKO mice was measured 24 h after 7 Gy of x-rays. Five or 9 (gadd45aKO_IR) independent experiments were performed at each Gadd45 genotype and treatment.

middle: G


title: Integrating network pharmacology, transcriptomics to reveal neuroprotective of curcumin activate PI3K / AKT pathway in Parkinson’s disease

city: haikou

first: benchi

last: cai

address: xiuyin road

institute: hainan general hospital

summary:
Background: Parkinson’s disease (PD), a severe threat in aging society, is a significant cause of disable. Curcumin, a polyphenol with hydrophobic properties, has been proved to against Parkinson. Our previous study provides an initial understanding of the neuroprotective mechanisms of curcumin in treating Parkinson’s disease. However, further exploration in this area is needed. The present study was designed to investigate the potential mechanism of curcumin for treating PD.
Methods: The therapeutic efficacy of curcumin was evaluated using behavioral tests, immunofluorescence of tyrosine hydroxylase (TH). Network pharmacology and transcriptomics predicted the active pathway and bioprocess of curcumin in PD. Activation of the PI3K / AKT signaling pathway was confirmed by quantitative real-time PCR and immunofluorescence.
Result:  Curcumin restored the dyskinesia and dopaminergic neurons damage of MPTP-induced mice. The results of network pharmacology and transcriptomics showed that curcumin against Parkinson's disease by regulating inflammation, oxidative stress, and aging. The mechanisms of these were associated with activation of PI3K / AKT pathway.
Conclusion: In conclusion, the mechanism of curcumin against PD was revealed by our study which lays a foundation for the application of curcumin in treating.

overall_design:
Animals and Treatments,30 male C57BL/6J mice (8 weeks old) were obtained from Hunan Slaughter Jingda Laboratory Animal Co., Ltd. Prior to the commencement of the experiments, the mice were housed in a standard environment with unlimited access to food and water. They were kept in a pathogen-free facility for one week. The animal procedures were approved by the Ethics Committee of Hainan Hospital, Hainan Medical College. Carbon dioxide asphyxiation was used as a humane method to euthanize all the mice. The mice were then randomly divided into three groups: control, MPTP, and MPTP + Curcumin. To induce Parkinson's disease in the mouse model, MPTP (Sigma-Aldrich, United States) was administered through intraperitoneal injections at a dose of 20 mg/kg in saline, along with probenecid (250 mg/kg in tris-HCl buffer) every 3.5 days for a total of 10 doses over a period of 5 weeks. Starting from day 1 of the experiment, curcumin (Macklin, Shanghai, China) was administered daily via gavage at a dose of 60 mg/kg for 7 weeks in the MPTP + Curcumin group.
Transcriptome,RNA extraction was performed using the TRIzol reagent (Invitrogen, CA, USA) as per the manufacturer's instructions. The quality and quantity of the extracted RNA were assessed using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). The integrity of the RNA was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Subsequently, libraries were prepared using the VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer's protocol. The libraries were sequenced on an Illumina Novaseq 6000 platform, generating 150 bp paired-end reads. The raw reads in fastq format were processed using fastp24 to remove low quality reads, resulting in clean reads. Approximately 50 clean reads were retained for each sample for further analysis. The clean reads were then aligned to the reference genome using HISAT225. The FPKM26 of each gene was calculated and the read counts of each gene were obtained using HTSeq-count27. Principal component analysis (PCA) was performed using R (v 3.2.0) to assess the biological duplication of samples. Differential expression analysis was conducted using DESeq228, with a threshold of Q value < 0.05 and foldchange > 2 to determine significantly differentially expressed genes (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to visualize the expression patterns of genes in different groups and samples. We would like to acknowledge the assistance of OE Biotech, Inc., (Shanghai, China) in sequencing and bioinformatics analysis.


title: Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

type: Methylation profiling by high throughput sequencing

summary: In dinoflagellates, the most unique and divergent nuclear organization among the known diversity of eukaryotes has evolved. The list of highly unusual features of dinoflagellate nuclei and genomes is long -- permanently condensed liquid crystalline chromosomes, in which histones are not the main packaging component, genes organized as very long unidirectional gene arrays, general absence of transcriptional regulation, high abundance of the otherwise very rare DNA modification 5-hydroxymethyluracil (5-hmU), and many others. Most of these fascinating properties were originally identified in the 1970s and 1980s but have received very little attention in recent decades using modern genomic tools. In this work, we address some of the outstanding questions regarding dinoflagellate genome organization by mapping the genome-wide distribution of 5-hmU (using both immunoprecipitation-based and basepair-resolution chemical mapping approaches) and of chromatin accessibility in the genome of the dinoflagellate Breviolum minutum. We find that the 5-hmU modification is preferentially enriched over certain classes of repetitive elements, and also often coincides with the boundaries between gene arrays. It is generally anti-correlated with chromatin accessibility, the levels of which are lower in those regions. We discuss the potential roles of 5-hmU in the functional organization of dinoflagellate genomes and its relationship to the transcriptional landscape of gene arrays.

sample_organism:
Saccharomyces cerevisiae
Candida albicans
Homo sapiens
Bigelowiella natans
Breviolum minutum

overall_design: ATAC-seq in B. minutum; mapping of 5-hmU in B. minutum using MeDIP-seq and chemical mapping; SMF and ATAC-seq on yeast cells exogenously expressing various dinoflagellate DVNP proteins

middle: K

first: Xinyi

last: Chen

first: Matthew

middle: P

last: Swaffer

first: Chuan

last: He

first: Tingting

last: Xiang

first: Anshul

last: Kundaje

first: Arthur

middle: R

last: Grossman

first: William

last: Greenleaf


title: Human cerebrospinal fluid impacts chemo-radiotherapy sensitivities in tumour cells from glioblastoma patients

city: Adelaide

first: Cedric

last: Bardy

state: SA

address: North Terrace

country: Australia

institute: South Australian Health and Medical Research Institute (SAHMRI)

summary: Cancers in the central nervous system resist therapies effective in other cancers, possibly due to the unique biochemistry of the human brain microenvironment comprised of cerebrospinal fluid (CSF). However, the impact of CSF on cancer cells and therapeutic efficacy is unknown. Here we examined the effect of human CSF on glioblastoma (GBM) tumours from 25 patients. We found that CSF induces tumour cell plasticity and resistance to standard GBM treatments (temozolomide and irradiation). We identified nuclear-protein-1 (NUPR1), a transcription factor hampering ferroptosis, as a mediator of therapeutic resistance in CSF. NUPR1 inhibition with a repurposed antipsychotic, trifluoperazine, enhanced the killing of GBM cells resistant to chemoradiation in CSF. The same chemo-effective doses of trifluoperazine were safe for human neurons and astrocytes derived from pluripotent stem cells. These findings reveal that chemoradiation efficacy decreases in human CSF and suggest that combining trifluoperazine with standard care may improve GBM patient survival.

overall_design: Whole transcriptome, single-cell mRNA seq profiles of 10 GBM patient-derived cell lines  cultured in glioma medium (termed GM or TME) or CSF generated using 10X genomics.

first: Brett

middle: W

last: Stringer

first: Manam

middle: I

last: De Silva

first: Zarina

last: Greenberg

first: Alejandra

middle: N

last: Puerta

first: Robert

last: Adams

first: Bridget

last: Milky

first: Michael

last: Zabolocki

first: Mark

last: van den Hurk

first: Lisa

last: Ebert

first: Christine

last: Bishop

first: Simon

last: Conn

first: Ganessan

last: Kichenadasse

last: Michael

first: Rebecca

last: Ormsby

first: Santosh

last: Poonoose


title: Integrative analysis in WGBS and transcriptome profiles of an temperature sensitive etiolation tea plant cultivar ‘Zhonghuang 2’

city: Hangzhou

first: Kexin

last: Zhang

address: No.9, Meiling South Road

institute: Tea Research Institute,Chinese Academy of Agricultural Science

summary: The green tea made from the etiolation shoots and leaves have fresh taste and strong aroma. ‘Zhonghuang 2 (ZH2) is a natural etiolation mutant and its shoots are etiolation in spring and turn green in summer. Two conditions including the relative high temperature (LT, 26 / 22oC) and the relative low temperature (LT, 18 / 14oC) were to find out the etiolated reason of ZH2. We confirmed ZH2 was a low-temperature sensitive tea plant cultivar, and the reason of shoots etiolation at LT was the reduction of stacked grana, which could cause the lack of photoreaction. We identified 1279 differentially expressed genes (DEGs), most of them were related to cytochrome synthesis and chloroplast development and function by RNA-seq. Through the whole-genome bisulfite sequencing (WGBS) assay, we found that the dynamic of DNA methylation level in three contexts (CG, CHG and CHH) was all decreased at LT, and the change was most obvious in the CHH context. According the result of cross analysis, 56 genes were identified with significant changes in both expression and DNA methylation levels. A large number of them were related to chloroplast development and chlorophyll synthesis. This study demonstrated that the DNA methylation was involved in the low-temperature regulated etiolation process of young shoots in ZH2. Change of the DNA methylation level was associated with the gene expression level, thus affecting the structure and function of chlorophyll and chloroplast, even reduced photosynthesis, which might have a phenotypic impact on the color of shoots and leaves. And it laid the foundation for studying the etiolation process from an epigenetic perspective.

overall_design: we set up two treatments of high temperature (HT) and low temperature (LT) to investigate the etiolation mechanism of young shoots of 'Zhonghuang 2' cultivar under the low temperature. And the HT is the control group and the LT is the treatment group.

first: Ying

last: Liu

first: Yajun

last: Yang

first: Lu

last: Wang

first: Xincao


title: Altered chromatin occupancy of patient-associated H4 mutants misregulate neuronal differentiation

city: New York

first: Douglas

last: Barrows

address: 1230 York Ave

institute: Rockefeller University

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

overall_design: Refer to individual Series


title: Altered chromatin occupancy of patient-associated H4 mutants misregulate neuronal differentiation [RNA-seq]

summary: Chromatin integrates extracellular signals to regulate gene expression and, therefore, tightly controls development. Mutations in histone genes, including H3.3 and H4, were recently identified in children with developmental disorders characterized by intellectual disability and dysmorphic facial features1–7. However, the mechanistic and functional roles of these de novo, heterozygous germline mutations remain largely unknown. Here, we focus on the histone H4 lysine 91 to arginine (H4K91R) or glutamine (H4K91Q) mutations located within the highly conserved core histone fold domain. Our findings demonstrate that H4K91 mutants form aberrant nuclear puncta in mouse embryonic stem cells (mESCs), as well as in differentiated neural cells in vitro and in vivo. Genome-wide analyses revealed that H4K91 mutants accumulate ectopically at H3.3 and H3K9me3-enriched heterochromatin regions. Mechanistically, H4K91 mutants demonstrated enhanced binding to histone H3 variant H3.3, and ablation of H3.3 or the H3.3-specific chaperone DAXX diminished the formation of H4 mutant puncta and enrichment at heterochromatin regions. Additionally, H4 mutant expression increased chromatin accessibility in mammalian cells. Phenotypically, H4 mutant mice exhibit reduced brain size and altered cortical neuron layers, reminiscent of microcephaly phenotypes observed in patients. Consistent with the altered brain development in vivo, the expression of H4 mutants alter developmental gene expression and accelerate pro-neural differentiation in cell culture models. Together, these studies reveal multiple concurrent pathogenic mechanisms of H4 mutants found in developmental disorders and further our understanding of how histone mutants regulate cell fate during development.

overall_design: We determined genes that change in expression with the expression of H4K91 mutants in differentiated neural cells from mESCs, using RNA-Seq followed by gene expression analyses.

first: Lijuan

last: Feng

first: Thomas

last: Carroll

first: C

middle: D

last: Allis


title: Bioprinting of Injectable Centimeter-scale Architectures with a Visible-light Crosslinking Bioink

city: 北京

first: yixue

last: Luo

state: 北京市

address: Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Department of Mechanical Engineering, Tsinghua University, Beijing 100084, China

institute: 清华大学

summary: This study propose a novel visible-light crosslinking hydrogel bioink (termed GP) to fabricate injectable centimeter-scale architectures. Composed of GelMA with large molecular weight PEGDA, GP can form a reinforced dual-crosslinking network, presenting excellent superelasticity and stability, supporting injection pass nozzles with 1.5mm inner diameter after bioprinted as 15mm×15mm scale architectures. Moreover, when printing with living cells, even for sensitive cell lines like genome-edited cells, the transcriptome of cells after printing shows no difference, suggesting the high cell printing suitability of GP and the visible-light extrusion printing technique. The printed architectures can support long-term culture for at least 14 days, and GP provides cells with a biocompatible microenvironment, supporting cell survival, proliferation, and function maintenance.

overall_design: For plate cultured samples, HepaRG and gene-edited HepaRG cells (M14A) were cultured in culture flasks. To extract RNA, cells were digested from culture flasks, centrifuged to separate liquid supernatant, and then collected in TRIzol. For after printing samples, M14A cells were digested from culture flasks and gently mixed with GP bioink. 4 hours after printing, the GP printed arhitectures were quick-frozen with liquid nitrogen and ground with mortar and pestle to fracture materials and cell structures. RNA was then extracted using TRIzol.

first: Rui

last: Yao

first: Ruoyu

last: Chen


title: Exonuclease Xrn1 regulates TORC1 signaling in response to SAM availability

city: Dallas

first: Benjamin

last: Tu

state: TEXAS

address: 5323 Harry Hines Blvd.

department: Biochemistry

institute: UT Southwestern Medical Center

summary:
Autophagy is a conserved process of cellular self-digestion that promotes survival during nutrient stress. In yeast, methionine starvation is sufficient to induce autophagy. One pathway of autophagy induction is governed by the SEACIT complex, which regulates TORC1 activity in response to amino acids through the Rag GTPases Gtr1 and Gtr2
This work identifies an unexpected yet critical role for Xrn1 in nutrient sensing and growth control that extends beyond its canonical housekeeping function in RNA degradation and indicates an avenue for RNA  metabolism to function in amino acid signaling into TORC1.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in cells lacking Xrn1 under methionine-replete or -depleted conditions.

first: Madeline

last: McGinnis

last: Sutte

first: Samira

last: Jahangiri


title: Stepwise differentiation of follicular helper T cells reveals distinct developmental and functional states

city: Boston

first: Peter

last: Sage

address: 221 Longwood Ave

institute: Brigham and Women's Hospital


title: Role of AEBP1 in LX-2 cells

first: Wei

state: Beijing

address: No. 95 Yong’an road, Xicheng District

department: Beijing Friendship Hospital

institute: Capital Medical University

summary: To investigate the role of AEBP1 involved in hepatic stellate cells (HSCs), we inhibited AEBP1 expression by specific siRNA in human HSC line LX-2 cells. Total RNA was loaded for bulk RNA sequencing.

overall_design: Human HSC line LX-2 cells were cultured in minimum essential medium (MEM) supplemented with 10% fetal bovine serum (Thermo Scientific) and 100 U/mL penicillin and streptomycin (Thermo Scientific). Human AEBP1 gene specific siRNA (50 nM, Ribobio, China) or scrambled siRNA (50 nM, Ribobio, China) were transfected into LX-2 cells using Lipofectamine 3000 regent (Invitrogen, USA) for 48 hours.

first: Wen

first: Hong

last: You


title: RNA-Sequencing  of semimembranosus muscles from iliac vein stenosis mice and diosmin-treated mice with iliac vein stenosis

city: Nanjing

first: Zhiguang

last: Shi

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

institute: Nanjing Medical University

summary: Diosmin is a classic venoactive drug, which has been shown to have a vascular protective effect in the inflammatory response. However, due to the limitations of experimental methods, the mechanism underlying the venous dysfunction has not been explored yet. It is necessary for us to identify the mechanism underlying whether micronized diosmin protects against venous dysfunction in iliac vein stenosis model. In this study, diosmin was administrated to mice 40 mg/kg per day by intraperitoneal injection after surgery. The characteristics of tight junctions between muscle cells around IVS-induced ligation sites have been detected. GO analysis after RNA sequencing indicated that diosmin can significantly improve the muscle system, involving actin filament organization and muscle contraction.

overall_design: Examination of 2 different semimembranosus muscles from IVS-induced mice and diosmin (40 mg/kd/day)-treated mice with IVS.

first: Zhiye

last: Guo

first: Xiaolong

last: Du

first: Yihua

last: Zhang

first: Chunwan

last: Su

first: Feng

last: Ran

first: Qiulun

last: Lu


title: RNF185 control of COL3A1 expression limits prostate cancer migration and metastatic potential

status: Public on Oct 18 2023

city: Vancouver

first: Yen-Yi

last: Lin

state: British Columbia

address: 2660 Oak St

country: Canada

institute: University of British Columbia

summary: RNF185 is a RING finger domain-containing ubiquitin ligase implicated in ER-associated degradation. Prostate tumor patient data analysis revealed a negative correlation between RNF185 expression and prostate cancer progression and metastasis. Likewise, several prostate cancer cell lines exhibited greater migration and invasion capabilities in culture upon RNF185 depletion. Subcutaneous inoculation of mouse prostate cancer MPC3 cells stably expressing shRNA against RNF185 into mice resulted in larger tumors and more frequent lung metastases. RNA-sequencing and Ingenuity Pathway Analysis identified wound healing and cellular movement among the most significant pathways upregulated in RNF185-depleted, compared to control prostate cancer cells. Gene Set Enrichment Analyses performed in samples from patients harboring low RNF185 expression and in RNF185- depleted lines confirmed the deregulation of genes implicated in EMT. Among those, COL3A1 was identified as the primary mediator of RNF185's ability to impact migration phenotypes. Correspondingly, enhanced migration and metastasis of RNF185 KD prostate cancer cells were attenuated upon coinhibition of COL3A1. Our results identify RNF185 as a gatekeeper of prostate cancer metastasis, partly via its control of COL3A1 availability.

overall_design: RNF185-depleted prostate cancer cells exhibited enhanced COL3A1 mRNA expression, and in specimens from prostate cancer patients, high COL3A1 expression was correlated with poor prognosis.

last: Van Espen

first: Htoo

last: Zarni Oo

first: Colin

last: Collins

first: Ladan

last: Fazli

first: Alfredo

last: Molinolo

first: Rabi

last: Murad

first: Martin

last: Gleave

first: Ze’ev

last: Ronai


title: Functional Pdgfra fibroblast heterogeneity in normal and fibrotic mouse lung

city: Research Triangle Park

first: Stavros

last: Garantziotis

state: NC

address: 111 TW Alexander Drive, Room 109

department: DIR

institute: NIH/NIEHS

summary: Using, scRNA Seq transcriptomic analysis, we report that Pdgra+ fibroblasts in mouse lung have significant heterogenity in normal and fibrotic lung, and key pathways involved in lipogenic and fibrogenic pathways govern the transition of normal lipofibroblasts from a normal to a myofibroblast phenotype following lung injury

overall_design:
Pdgfra-GFP reporter mice were dosed with either 2 U/Kg bleomycin or PBS. On day 14 post-exposure, lungs (3 mice/treatment) were harvested, cells enzymatically digested, and GFP+ cells sorted using FACS to prepare live cells for scRNA Seq. Sequencing was done using the 10X Genomics Chromium Platform, and following processing with Cell Ranger v3.0.1 was done to generate an initial cell by gene count matrix. Samples were combined in Seurat v3 and clustered into 11 unique clusters based on top gene marker expression. Data was analyzed using Ingenuity Pathway Analysis, Pseudotime trajectories prepared with SlingShot, and IF staining conducted for verification.
For repetive bleomyin exposure, Pdgfra-GFP mice  were dosed with bleomycin or PBS once weekly for 3 weeks (bleomycin at 1, 1, and 0.5 U/Kg). Two weeks after the last exposure, lungs (3 mice/treatment) were harvested, cells enzymatically digested, and GFP+ cells sorted using FACS.   Sequencing was done using the 10X Genomics Chromium Platform, and following processing with Cell Ranger v3.0.1 was done to generate an initial cell by gene count matrix. Samples were combined in Seurat v3 and clustered into 11 unique clusters based on top gene marker expression. Data was analyzed using Ingenuity Pathway Analysis, Pseudotime trajectories prepared with SlingShot, and IF staining conducted for verification.

first: Carol

middle: S

last: Trempus


title: Low input lipidomics analysis reveals remodeling of lipid metabolism and saturation during mouse and human preimplantation embryo development

first: Hua

last: Yu

address: No.18 Shilongshan Road

institute: Westlake University

summary: Scd1 is responsible for forming a carbon-carbon double bound at the 9-10th position from the C-terminus of saturated fatty acids such as palmitic acid and stearic acid (C16:0 and C18:0), to generate the products of palmitoleic acid (C16:1) and oleic acid (C18:1).Here, we found SCD1 is required for in vitro blastocyst embryo development, and one of the mechanisms is through regulating unsaturated fatty acid-mediated membrane fluidity and formation of apical domain. Overall, our study provides invaluable resources for lipid reprogramming in mammalian preimplantation embryo development and mechanistic insights on regulation of embryogenesis by lipid unsaturation.

overall_design: Examination of gene expression in wide-type and scd1 knocking down embryo

first: Ling

first: Jing

last: Zhao

first: Jin


title: ChIP-seq of Phytophthora infestans (3 days post incubation)

city: nanjing

first: Han

last: Chen

state: jiangsu

address: weigang no.1,xuanwu district

institute: Nanjing Agricultural University

summary: Phytophthora infestans, the causal agent of potato late blight, is a devastating plant disease that was responsible for the Irish potato famine and continues to threaten global food security. While the P. infestans genome is an excellent resource for studying the aggressiveness of this pandemic pathogen, its epigenome remains poorly understood. In this study, utilizing liquid chromatography-tandem mass spectrometry (LC-MS/MS), we identified post-translational modifications (PTMs) at the P. infestans core histone H3. The PTMs include prevalent modifications in eukaryotes, as well as some novel marks, such as H3K53me2 and H3K122me3. We focused on trimethylations of H3K4, H3K9, H3K27, and H3K36, and profiled the P. infestans epigenome using native chromatin immunoprecipitation followed by sequencing (N-ChIP-seq). In parallel, we mapped P. infestans chromatin accessibility using the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). We found that adaptive genomic compartments display significantly higher levels of H3K9me3 and H3K27me3 and are generally found in condensed chromatin. Interestingly, highly accessible regions with ATAC-seq peaks are also found in this compartment. We observed that genes encoding virulence factors, such as effectors, are enriched in open chromatin regions with few histone modifications. Based on N-ChIP-seq at 3 days post-incubation, we revealed the PTM dynamics in secretome genes from the mycelium to the infection stage. Using a combination of genomic, epigenomic, and transcriptomic strategies, our study illustrates the epigenetic states and changes in P. infestans, helping to elucidate genomic functions and regulation in this pathogen.

overall_design: Two replicates of P. infestans 3 dpi stage samples were performed.


title: Transcriptomes of maize seedlings in wild-type and Gβ knockout lines.

city: Yangzhou

first: Yijun

last: Wang

address: Wenhui

institute: Yangzhou University

summary:
Purpose: We aim to reveal maize transcriptomic changes in wild-type and Gβ knockout lines.
Methods: RNA-seq was used to reveal transcriptome of maize biological replicates of wild-type and Gβ knockout lines.
Results: Differnentically expressed transcritps were identified by the comparison of biological replicates of wild-type and Gβ knockout lines.
Conclusions: We identified differentially expressed genes in Gβ knockout lines.

overall_design: RNA-seq of biological replicates of seedlings (roots removed) from wild-type and Gβ knockout lines using HiSeq 2500 System with a 150 bp paired-end module.


title: Gene Expression and Chromatin Accessibility of Nephron Progenitor Cells in Mice

city: Chongqing

first: Lei

last: Li

address: yixueyuan road

institute: CQMU

summary: We report the use of high-throughput sequencing, including RNA-seq and ATAC-seq, to compare the gene expression patterns and chromatin accessibility in uninduced (mK3) and epithelial-differentiated (mK4) metanephric mesenchymal cells.

overall_design: Examination of 2 different metanephric mesenchymal cells mK3 and mK4

first: Li

last: Lei

first: Qin

last: Zhou

first: Yajun

last: Xie


title: Effect of hemoglobin or hemin on human pulmonary microvascular endothelial cells

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

summary: HLMVEC treated with Ctrl, Hb2+, Hb3+, or hemin for 30 min or 1.5 hours

overall_design: Each treatment repeated in three different primary cell donors

first: Jamie

last: Meegan

first: Julie

last: Bastarache

first: Lorraine

last: Ware


title: Meiotic prophase length modulates Tel1-dependent DNA double-strand break interference

city: Brighton

first: Matthew

last: Neale

address: Science Park Road

department: Genome Damage and Stability Centre

country: United Kingdom

institute: University of Sussex

summary: During meiosis, genetic recombination is initiated by the formation of many DNA double-strand breaks (DSBs) catalysed by the evolutionarily conserved topoisomerase-like enzyme, Spo11, in preferred genomic sites known as hotspots. DSB formation activates the Tel1/ATM DNA damage responsive (DDR) kinase, locally inhibiting Spo11 activity in adjacent hotspots via a process known as DSB interference. Intriguingly, in S. cerevisiae, over short genomic distances (<15 kb), Spo11 activity displays characteristics of concerted activity or clustering, wherein the frequency of DSB formation in adjacent hotspots is greater than expected by chance. We have proposed that clustering is caused by a limited number of sub-chromosomal domains becoming primed for DSB formation. Here, we provide evidence that DSB clustering is abolished when meiotic prophase timing is extended via deletion of the NDT80 transcription factor. We propose that extension of meiotic prophase enables most cells, and therefore most chromosomal domains within them, to reach an equilibrium state of similar Spo11-DSB potential, reducing the impact that priming has on estimates of coincident DSB formation. Consistent with this view, when Tel1 is absent but Ndt80 is present and thus cells are able to rapidly exit meiotic prophase, genome-wide maps of Spo11-DSB formation are skewed towards pericentromeric regions and regions that load pro-DSB factors early—revealing regions of preferential priming—but this effect is abolished when NDT80 is deleted. Our work highlights how the stochastic nature of Spo11-DSB formation in individual cells within the limited temporal window of meiotic prophase can cause localised DSB clustering—a phenomenon that is exacerbated in tel1∆ cells due to the dual roles that Tel1 has in DSB interference and meiotic prophase checkpoint control.

overall_design: CC-seq libraries from sae2D meiotic SK1 S. cerevisiae cells isolated at 6 hours after sporulation induction

first: Luz

last: Lopez Ruiz

first: Dominic

last: Johnson

first: George

last: Brown


title: Cla4 phosphorylates histone methyltransferase Set1 to prevent its degradation by the APC/CCdh1 complex

city: wuhan

first: Yu

last: Qi

state: Hubei

address: xujiapeng

department: College of life sciences

institute: Hubei university

summary: The expression of chromatin modifying enzymes needs to be tightly controlled to ensure proper distribution of chromatin modifications. H3 lysine 4 trimethylation (H3K4me3) is a conserved histone modification catalyzed by histone methyltransferase Set1 and its dysregulation is associated with pathologies. Here, we show that Set1 is intrinsically unstable and its protein levels are strictly controlled by ubiquitin-dependent proteasomal degradation within the cell cycle and during gene transcription. Specifically, Set1 contains a destruction box (D-box) that can be recognized by the E3 ligase APC/CCdh1 complex and degraded by the ubiquitin-proteasome pathway. Cla4 phosphorylates serine 228 (S228) within Set1 D-box, which inhibits APC/CCdh1-mediated Set1 proteolysis. During gene transcription, the RNA polymerase II-associated PAF complex facilitates Cla4 to phosphorylate Set1-S228 and protect the chromatin-bound Set1 from degradation. By modulating the stability of Set1, Cla4 and the APC/CCdh1 complex control H3K4me3 levels, which then regulates gene transcription, cell cycle progression and chronological aging. In addition to Set1, there are 141 proteins containing the D-box that can be potentially phosphorylated by Cla4 to prevent their degradation by the APC/CCdh1 complex. Thus, we not only addressed the long-standing question about how Set1 stability is controlled, but also uncovered a new mechanism to regulate protein stability

overall_design: ChIP-Seq examination

first: X

last: Gong

first: Q


title: Altered chromatin occupancy of patient-associated H4 mutants misregulate neuronal differentiation [ChIP-seq]

first: Douglas

last: Barrows

state: NY

overall_design: Characterization of the genome-wide incorporation of H4WT and H4K91 mutants in mouse embryonic stem cells (mESCs) as well as in differentiated neural cells.

first: Lijuan

last: Feng

first: Thomas

last: Carroll

first: C

last: Allis


title: Characterization of DNA methylation changes induced by albuterol in airway epithelial cultures

city: La Laguna

first: Javier

last: Perez-Garcia

address: Avenida Astrofisico Francisco Sanchez s/n

department: Biochemistry, Microbiology, Cell Biology, and Genetics

country: Spain

institute: Universidad de La Laguna

summary: Albuterol is the first-line asthma medication used in diverse populations. Although DNA methylation (DNAm) is an epigenetic mechanism involved in asthma and bronchodilator drug response (BDR), no study has assessed whether albuterol could induce changes in the airway epithelial methylome. We aimed to characterize albuterol-induced changes in DNAm in airway epithelial cells and assess the potential functional consequences and biological pathways implicated. We followed a discovery and validation study design to characterize albuterol-induced DNAm changes in paired airway epithelial cultures stimulated in vitro with albuterol. In the discovery phase, an epigenome-wide association study (EWAS) using paired nasal epithelial cultures from Puerto Rican children (n=97) identified 22 CpGs genome-wide associated with repeated-use albuterol treatment (p<9x10-8). Albuterol predominantly induced a hypomethylation effect on CpGs captured by the EPIC array across the genome (probability of hypomethylation: 76%, p-value=3.3x10-5). DNAm changes on the CpGs cg23032799 (CREB3L1), cg00483640 (MYLK4-LINC01600), and cg05673431 (KSR1) were validated in nasal epithelia from 10 independent donors (false discovery rate [FDR]<0.05). The effect on the CpG cg23032799 (CREB3L1) was cross-tissue validated in bronchial epithelial cells at nominal level (p=0.030). DNAm changes in these three CpGs showed to be influenced by three independent genetic variants (FDR<0.05). In silico analyses showed these polymorphisms regulated gene expression of nearby genes in lungs and/or fibroblasts including KSR1 and LINC01600 (6.30x10 14≤p≤6.60x10-5). Additionally, the hypomethylation at the CpGs cg10290200 (FLNC) and  cg05673431 (KSR1) was associated with reduced gene expression of the genes where they are located (FDR<0.05). Furthermore, while the epigenetic effect of albuterol was independent of the asthma status, severity, and use of medication, BDR was nominally associated with the effect on the CpG cg23032799 (CREB3L1) (p=0.004). Gene-set enrichment analyses revealed that epigenomic modifications of albuterol could participate in asthma-relevant processes (e.g., IL-2, TNF-α, and NF-κB signaling pathways) and that albuterol-affected genes are likely regulated by Trichostatin A (FDR<0.05). Finally, nine differentially methylated regions were associated with albuterol treatment, including CREB3L1, MYLK4, and KSR1 (adjusted p-value<0.05). In conclusion, this study reveals, for the first time, evidence of epigenetic modifications induced by albuterol in the mucociliary airway epithelium. The epigenomic response induced by albuterol might have potential clinical implications by affecting biological pathways relevant to asthma

overall_design: Bisulphite converted DNA from 100 pairs of epithelial cell samples treated with albuterol or mock solution were hybridized to the Illumina Infinium MethylationEPIC Beadchip v1

first: Esteban

last: Burchard


title: NAA enhances cell yields by inhibiting apoptosis pathway

city: Tianjin

first: Dongpeng

last: Zheng

state: Tianjin

address: No. 92, Weijin Road, Xuefu Street, Nankai District

department: School of Pharmaceutical Science and Technology

institute: Tianjin university

summary: The in vitro cell culturing witnessed its applications in both scientific research and industrial activities, its optimization leads to practical benefits, either through shortening the doubling time, or simplification of engineering requests, or both. Literature searching highlighted a role of a synthetic auxin derivative 1-Naphthaleneacetic acid (NAA) in optimizing plant cell culturing. Here, by measuring  cell counts and their activities via CCK8 tests, we observed an up to 2-fold increase in the yield of in vitro cultured human cells. We tested different types of human cell lines and primary natural killer cells, found that NAA was effective in all the cells tested. The PI staining and FACS analysis suggested that NAA did not affect the cell cycling. Apoptosis-specific dye staining analysis implicated that NAA rescued cell death. We further did bulk RNA sequencing and identified the lipid metabolism-engaging and anti-apoptosis gene, ANGPTL4, was enhanced in expression upon NAA treatment. Studies on ANGPTL4 knockout cells indicated that ANGPTL4 is required for NAA-mediated response. Thus, our data identified a beneficial role of NAA in human cell culturing and highlighted its potency in the in vitro cell culturing

overall_design: In order to explore the effect of plant auxin NAA on the function of mammalian cells, we tested NAA in different cancer cells. It was found that 300um NAA could improve the proliferation of many cell lines, and this proliferation effect was caused by inhibiting apoptosis. RNA-seq analysis showed that NAA interacted with intracellular ANGPTL4 to exert anti-apoptosis effect, and explored the functional effect of NAA in animal cells.

first: Zhongyi

last: Wang

first: Fengqi

last: Li

first: Zhaojun

last: Pang

first: Chunjing

first: Yue

last: Ma

first: Ying

last: Xu

first: Ce

last: Yang

first: Xueren

first: Shouchun

last: Peng

first: Zichuan

last: Liu

first: Xin

last: Mu


title: CSF3R T618I collaborates with RUNX1-RUNX1T1 to expand hematopoietic progenitors and sensitizes to GLI-inhibition [single-cell RNA-seq]

city: Munich

first: Vanessa

last: Arfelli

state: Bavaria

address: Max-Lebsche-Platz 30

department: Medical Clinic and Polyclinic III

institute: Munich University Hospital, Ludwig-Maximilians University (LMU)

summary: Activating CSF3R mutations are recurrent in AML with t(8;21) translocation. However, the nature of oncogenic collaboration between alterations of CSF3R and the t(8;21) associated RUNX1-RUNX1T1 fusion remains unclear. In CD34+ hematopoietic stem and progenitor cells from healthy donors, double oncogene expression led to a clonal advantage, increased self-renewal potential, as well as blast-like morphology and distinct immunophenotype. Gene expression profiling revealed hedgehog-signaling as a potential mechanism, with upregulation of GLI2 constituting a putative pharmacological target. Both primary hematopoietic cells and the t(8;21) positive AML cell line SKNO-1 showed increased sensitivity to the GLI-inhibitor GANT61 when expressing CSF3R T618I. Our findings suggest that during leukemogenesis the RUNX1-RUNXT1 fusion and CSF3R mutation act in a synergistic manner to alter hedgehog signaling which can be exploited therapeutically.

overall_design:
Comparative gene expression profiling analysis of single cell RNA-seq data for human CD34+ cells (hematopoietic progenitors) co-transduced with RUNX1-RUNX1T1tr and CSF3RWT or CSF3RT618I. The data comprise 1 biological replicate, with cells collected in 2 timepoints (day 30 and day 60), each containing 10.000 cells per library for each experimental arm.
>>>NOTE FROM SUBMITTER: According to the German law, the submission of raw sequencing data from human samples is prohibited.<<<

first: Anja

last: Swoboda

first: Michael

last: Sterr

first: Stefan

last: Krebs

first: Anna

last: Danese


title: CSF3R T618I collaborates with RUNX1-RUNX1T1 to expand hematopoietic progenitors and sensitizes to GLI-inhibition

overall_design:
Comparative gene expression profiling analysis of bulk RNA-seq data for human CD34+ cells (hematopoietic progenitors) transduced with RUNX1-RUNX1T1tr and CSF3RWT, CSF3RT618I or empty vector (EV MIG). The data comprise 2 biological replicates, each containing 6 technical replicates for each experimental arm.
NOTE FROM SUBMITTER: According to the German law, the submission of raw sequencing data from human samples is prohibited.

first: Swoboda

last: Anja

first: Arfelli

last: Vanessa

first: Bagnoli

last: Johannes

first: Kerbs

last: Paul


title: ChIP Seq Analysis of H3K4me3 in Wild Type and Set1 S228A S228E mutants

first: Yu

last: Qi

summary: Cells need to coordinate gene expression with their metabolic states to maintain cell homeostasis and growth. However, how cells transduce nutrient availability to appropriate gene expression response via histone modifications remains poorly understood. Here,we reported cla4 catalyzed Set1 phosphorylaton regulates cell cycle and histone gene transcription.

overall_design: ChIP-Seq analysis. Yeast strain were grown in 200 ml YPD  media at 30°C until OD600 of ~0.7-1.0. The crosslinking was performed in 1% formaldehyde and quenched by adding 10 ml of 2.5 M glycine. Cells were harvested, washed once   with cold TBS + PMSF, lysed in FA-SDS buffer (40 mM HEPES-KOH pH7.5, 1 mM EDTA pH8.0, 0.1% SDS, 1% Triton X-100, 0.1% Na deoxycholate, 1 mM PMSF, 2 μg/ml leupeptin, 1 μg/ml pepstatin A, protease inhibitor cocktail, phosphatase inhibitor cocktail). Chromatin was sonicated to an average size of ~500 bp and then subjected to immunoprecipitation with antibodies pre-bound to Protein G Dynabeads (Invitrogen) at 4°C overnight. The beads were washed successively with FA buffer, FA buffer + 1 M NaCl, FA buffer + 0.5 M NaCl, TEL buffer (10 mM Tris pH8.0, 1 mM EDTA, 0.25 M LiCl, 1% NP-40, 1% Na deoxycholate) and TE buffer (10 mM Tris pH7.4, 1 mM EDTA). The eluted DNA/protein complex was treated with 20 µg Proteinase K at 55°C for 1 h followed by treatment at 65°C overnight. After removing RNA by RNase (Roche), the DNA was purified with ethanol precipitation and sequenced . Yeast strains WT (BY4741 in Open Biosystem) and Rif1-FLAG were the in same group, yeast strains Sen1-FLAG and Glc7-FLAG cultured both in YPD medium and SD-C medium were the other group.

first: Xuanyunjing

last: Gong


title: Truncated DAZL mutation reduces NANOS3 expression in primordial germ cells and leads to premature ovarian insufficiency

city: BEIJING

first: QINGYUAN

last: LIU

state: BEIJING

address: QINGHUAYUAN street，HAIDIAN distribute

institute: Tsinghua University

summary: Primary ovarian insufficiency (POI) is a complex disorder that affects many genes and the underlying molecular mechanisms remain to be fully elucidated. In this study, a homozygous point mutation, c.808C>T, in the DAZL gene of a POI patient was identified. This homozygous variant causes a C-terminal truncation of DAZL and down-regulation of germ-line gene NANOS3 expression, among other dysregulated genes, in human primordial germ cells (hPGCs) in vitro. Mechanistically, we discovered that the truncated DAZL had defects in regulating mRNA translation for NANOS3, VASA, and SYCP3 - all essential for gametogenesis. Additionally, the truncated DAZL showed impaired interaction with Poly(A)-binding proteins (PABPs), a crucial component of the translation initiation complex. At the cellular level, the truncated mutation resulted in increased apoptosis of in vitro hPGCs. Our findings reveal that the c.808C>T mutation in DAZL causes dysregulated expressions of many genes, increases germ cell apoptosis and ultimately leads to POI.

overall_design: To examine the potential effect of the mutant DAZL on PGC gene expressions, WT DAZL or the truncated DAZL was overexpressed in hPGCLCs during in vitro differentiation. We then performed gene expression profiling analysis using data obtained from RNA-seq at two time points. Comparative gene expression profiling analysis of RNA-seq data for WT DAZL hPGCLCs and c.808C>T DAZL hPGCLCs.

first: Qingyuan


title: Comprehensive analysis of differentially expressed microRNAs involved in diabetic trigeminal ganglion

city: Fuzhou

first: jianzhang

last: Hu

address: Fuzhou

institute: Fujian Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Diabetic keratopathy(DK) is a common ocular complication of diabetes that seriously threatens diabetic patients' vision. Here, by sequencing of microRNAs (miRNAs) from diabetic and normal TG tissues, we aimed to uncover potential miRNAs involved in the pathogenesis of diabetic corneal neuropathy.

overall_design: miRNA profiles in the trigeminal ganglion of C57BL/6J diabetic and normal mice

first: Jianzhang

first: Danling

last: Liao

first: Shijia

last: Wei


title: Hepatic steatosis promotes atherosclerosis progression via extracellular vesicles  mediated inhibition of cholesterol efflux in foam cells

city: Guangzhou

first: Shen

last: Chen

state: Guangdong Sheng

address: No.74 Zhongshan Road 2, Guangzhou

institute: Sun Yat-sen University

summary: To determine the functional miRNA mediated the inhibition role of exosomes (EVs) on the, cholesterol efflux, miRNA sequencing was conducted to compare the expression profile of miRNA content in EVs isolated from primary hepatocytes of chow diet-fed ApoE-/- mice (Chow-EVs) or HFHC-fed ApoE-/- mice (HFHC-EVs).

overall_design: Comparative gene expression profiling analysis of miRNA sequencing data for EVs derived from primary hepatocytes of chow diet-fed ApoE-/- mice (Chow-EVs) or HFHC-fed ApoE-/- mice (HFHC-EVs).

first: Xu

first: Juan

last: Pang

first: Rong

last: Huang

first: Yiran

last: You

first: Haoyang

last: Zhang

first: Jinghe

last: Xiao

first: Hongliang

last: Xue

first: Wenhua

last: Ling


title: The research on transcriptional profiling in plasma exosomes of SD rats: SAH vs Sham

first: Zhaosi

state: Chongqing

address: No.1 Youyi Road, Yuzhong District

institute: The First Affiliated Hospital of Chongqing medical university

summary: Transcriptional profiling of plasma exosomes came from SD rats that underwent subarachnoid hemorrhage (SAH) and sham operation (Sham) rats. The goal was to identify the changes of RNA in plasma exosomes after subarachnoid hemorrhage in SD rats.

overall_design: Two-condition experiment, SAH, Sham. Biological replicates: 3 SAH replicates, 3 Sham replicates. Six samples were analyzed.

first: Xiaoshuang

last: Liu


title: CITE-seq of peripheral immune cells after SARS-COV-2 vaccination in patients with MM

city: Frankfurt

first: Julius

middle: C

last: Enssle

address: Theodor-Stern-Kai 7

department: Hematology/Oncology

institute: University Hospital Frankfurt

summary:
Patients with multiple myeloma (MM) routinely receive mRNA-based vaccines to reduce COVID-19-related mortality, but whether disease- and therapy-related alterations in immune cells and cytokine-responsiveness contribute to the observed heterogeneous vaccination responses is unclear. Thus, we analyzed PBMCs from patients with MM during/after SARS-CoV-2 vaccination and breakthrough infection (BTI) using combined whole-transcriptome and surface proteome single-cell profiling with functional serological and T-cell validation in additional 58 patients with MM.
Our results demonstrate that vaccination responders showed a significant overrepresentation of cytotoxic CD4+ T-cells and mature CD38+ NK-cells expressing FAS+/TIM3+ with a strong enrichment for cytokine-responsiveness such as type-I-interferon-, IL-12- and TNF-alpha-mediated signaling. Patients with MM experiencing BTI developed higher serological and cellular responses and displayed similar cytokine-responsive immune cell patterns as observed in vaccination responders.
Finally, these results expand our understanding of molecular and cellular patterns associated with immunization responses and may benefit the design of improved vaccination strategies in immunocompromised patients.

overall_design:
For single-cell CITE sequencing of T-, B-, NK- and NKT-cells of patients with Multiple Myeloma (MM) and age-matched healthy controls, we selected 11 representative individuals from our previously published cohort (Enssle JC, Cancer Cell, 2022) resulting in 24 samples. Samples were obtained from serological and T-cell responders and non-responders after the 2nd (TP3) and 3rd (TP5) vaccination. To limit potential disease- or treatment-related bias, we selected patients which are representative of the group that was in the 1st line of treatment for MM, in at least very-good-partial-remission (VGPR) and without corticosteroid treatment 14 days before and after vaccination. We also included samples from 2 healthy controls (HC) after their respective 2nd and 3rd vaccination. As some patients with MM from our main cohort exhibited a breakthrough infection (BTI) after the 3rd vaccination at timepoint of data cut-off, we additionally included 2 full responders and 2 full non-responders MM patients together with 2 HC which all developed a BTI after the 3rd vaccination. Here, we subjected samples after the 3rd vaccination and after BTI (TP6) for CITEseq analysis. One patient with MM donated samples after TP3, TP5 and BTI.
>>>Raw data for human samples not available due to patient privacy concerns<<<

first: Julia

last: Campe

first: Alina

last: Moter

first: Isabel

last: Voit

first: Alec

last: Gessner

first: Ika

last: Yu

first: Sebastian

last: Wolf

first: Björn

last: Steffen

first: Hubert

last: Serve

first: Melanie

last: Bremm

first: Sabine

last: Huenecke

first: Michael

last: Lohoff

first: Maria

last: Vehreschild

first: Holger

last: Rabenau

first: Marek

last: Widera

first: Sandra

last: Ciesek

first: Thomas

last: Oellerich

first: Katharina

last: Imkeller

last: Rieger

first: Ivana

last: von Metzler

first: Evelyn

last: Ullrich


title: T cell-Macrophage Interactions Mediate Innate and Adaptive Immune Responses in Histidyl-tRNA Synthetase-Induced Myositis

city: Pittsburgh

first: Tracy

last: Tabib

state: PA

address: 200 Lothrop Street

department: Department of Medicine

institute: University of Pittsburgh

summary: The relative contribution of innate and adaptive immunity to idiopathic inflammatory myopathy is poorly defined. We therefore sought to clarify these components of disease pathogenesis using our novel murine model of histidyl-tRNA synthetase (HRS)-induced myositis. Myositis was induced in WT and various congenic strains of C57BL/6 mice through intramuscular immunization with recombinant HRS. Histopathological, immunohistochemical, flow cytometric, and transcriptomic assessments were used to characterize muscle-infiltrating cell populations in these congenic strains. RAG1 KO mice developed markedly reduced muscle inflammation relative to WT mice, demonstrating a key requirement for T cells in driving HRS-induced myositis. Diminished cellular infiltration in CD4-Cre.MyD88fl/fl conditional knockout and OT-II TCR transgenic mice highlighted roles for innate and TCR-mediated/adaptive immune signaling in T cells. Transcriptionally-based pathway analyses showed that disruption of T cell signaling alters the function of macrophages, fibroblasts, and other non-lymphoid cell populations. Overall, these findings demonstrate that HRS-induced myositis reflects complex cellular interactions requiring the activation of both innate and adaptive T cell-mediated signaling pathways.

overall_design: Groups of n=3-5 mice from indicated congenic strains of C57BL/6 mice were immunized intramuscularly with PBS versus recombinant HRS.  17-21 days post immunization, muscle tissue was harvested from mice and pooled by experimental group.  Physical and enzymatic digestion of pooled muscle samples yielded single cell preparations that were then subjected to flow cytometry as well as scRNAseq using the 10X Genomics platform and 5'V2 chemistry.

first: Daniel

last: Reay

first: Ying

last: Wang

first: Timothy

middle: B

last: Oriss

first: Nicholas

last: Young

first: Robert

last: Lafyatis

first: Wael

last: Jarjou

first: Paula

last: Clemens

first: Dana

last: Ascherman