title: Analysis of gene expressions of mast cells in murine atopic dermatitis-like skin

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

institute: Singapore Immunology Network (SIgN)

summary: Purpose: To compare gene expressions of resident and integrinβ7-positive mast cells (MCs) in atopic-dermatitis (AD) like skin.   Methods: Each MC population from skin was sorted by flow cytometry, and sequencing was performed on Illumina HiSeq 4000 platform. Sequencing data in the form of FASTQ files were mapped onto the Mus musculus genome build GRCm38 using the STAR aligner (version 2.5.2b) with gene annotations obtained from GENCODE (version M22). Differential expression analysis was performed using the edgeR package (version 3.28.1) in R (version 3.6.2) and differentially expressed genes were defined as those with false discovery rate (FDR) < 0.05.   Results: Principal component analysis demonstrated three distinct MC populations, and 1157 differentially expressed genes were detected. Integrinβ7-positive MC showed both mucosal type mast cell signatures and skin type mast cell signatures, and they specifically expressed migration related genes.

overall_design: mRNA profiles of skin resident and integrinβ7-positive MCs in non-treated and AD-like skin.

first: Yuki

middle: H

last: Keith

first: Bernett

last: Lee

first: Sho

last: Hanakawa

first: Satoshi

last: Nakamizo

first: Yoshihiro

last: Ishida

first: Kenji

last: Kabashima


title: Enteric glial cells favor accumulation of anti-inflammatory macrophages during the resolution of muscularis inflammation

status: Public on Sep 12 2022

city: Leuven

first: Gianluca

last: Matteoli

address: Herestraat 49

country: Belgium

institute: KU Leuven

type: Expression profiling by high throughput sequencing

summary: Monocyte-derived macrophages (Mφs) are crucial regulators during muscularis inflammation. However, it is unclear which micro-environmental factors are responsible for monocyte recruitment and anti-inflammatory Mφ differentiation in this paradigm. Here, we investigate Mφ heterogeneity at different stages of muscularis inflammation and determine how environmental cues can attract and activate tissue-protective Mφs. Results showed that muscularis inflammation induced marked alterations in mononuclear phagocyte populations associated with a rapid infiltration of Ly6c+ monocytes that locally acquired unique transcriptional states. Trajectory inference analysis revealed two main pro-resolving Mφ subpopulations during the resolution of muscularis inflammation, i.e. Cd206+ MhcIIhi and Timp2+ MhcIIlo Mφs. Interestingly, we found that damage to the micro-environment upon muscularis inflammation resulted in EGC activation, which in turn stimulated monocyte infiltration and the consequent differentiation in anti-inflammatory CD206+ Mφs via CCL2 and CSF1, respectively. In addition, CSF1-CSF1R signaling was shown to be essential for the differentiation of monocytes into CD206+ Mφs and EGC proliferation during muscularis inflammation. Our study provides a comprehensive insight into pro-resolving Mφ differentiation and their regulators during muscularis inflammation. We deepened our understanding in the interaction between EGCs and Mφs, thereby highlighting pro-resolving Mφ differentiation as a potential novel therapeutic strategy for the treatment of intestinal inflammation.

overall_design: Cells isolated from the muscularis of the small intestine of the mice (WT or CCR2 KO) 24 hours or 72 hours after intestinal manipulation were sorted for cd45+ cells. Cells were loaded onto 10x chip targeting the recovery of 1000 cells. Single cell RNA sequencing libraries were prepared using 10x genomics platform according to manufacturer’s instructions (Single cell 3’ solution). Sequencing libraries were loaded at 1.4 pM on an Illumina NextSeq500 with NextSeq 500/550 Mid Output v2 kit (150 cycles) (Illumina). Cell Ranger software (v3.0.2) (10x Genomics) was used to demultiplex Illumina BCL files to FASTQ files (cellranger mkfastq) to perform alignment (to mouse GRCm38/mm10 genome), filtering, UMI counting and to produce gene-barcode matrices. Library preparation, sequencing and sample demultiplexing was done at the Genomics Platform of the GIGA Institute (Liège University, Belgium). Counts from the data of naive mice, 24 hour post intestinal manipulation and 72 hour post intestinal manipulation were concatenated and analysed using Seurat R package. Cells with less than 200 gene and 10% percent of mitochondrial genes were removed from the analysis.

first: Michelle

last: Stakenborg

first: Saeed

last: Abdurahiman

first: Veronica

last: De Simone

first: Gera

last: Goverse

first: Nathalie

first: Lies

last: Van Baarle

first: Qin

last: Wu

first: Dimitri

last: Pirottin

first: Jung-Seok

last: Kim

first: Louise

last: Maor

first: Isabel

last: Pintelon

first: Sofie

last: Thys

first: Emilie

last: Pollenus

first: Louis

last: Boon

first: Philippe

last: Van den Steen

first: Marlene

last: Hao

first: Jo

last: Van Ginderachter

first: Guy

middle: E

last: Boeckxstaens

first: Jean-Pierre

last: Timmermans

first: Steffen

last: Jung

first: Thomas

last: Marichal

first: Sales

last: Ibiza


title: Microarray-based gene expression profiling in mouse bleomycin-induced systemic sclerosis model treated with MT-7117

status: Public on Sep 09 2022

city: Yokohama-shi Aoba-ku

first: Shinji

last: Kojima

address: Kamoshida-cho 1000

country: Japan

institute: Mitsubishi Tanabe Pharma Corporation

summary: In this study, we analyzed the gene expression profiles of the lung in mouse bleomycin (BLM)-induced systemic sclerosis (SSc) model treated with MT-7117. Gene array analysis using the BLM-induced SSc model demonstrated changes in numerous categories related to macrophages, monocytes, and neutrophils, followed by endothelial cell-related categories after treatment with MT-7117 (Dersimelagon). In the analysis that focused on biological functions, categories of inflammatory response, activation of antigen-presenting cells, angiogenesis, atherosclerosis, vasculogenesis, and vaso-occlusion were suppressed by MT-7117. In the analysis that focused on molecular signaling pathways, triggering receptor expressed on myeloid cells-1, IL-6, and oncostatin M involved in inflammation, and peroxisome proliferator-activated receptor that is related to fibrosis were all affected by MT-7117.

overall_design: Total RNA of mouse lung tissue samples of PBS_vehicle (control group without disease), BLM_vehicle (control group with disease), and BLM_MT-7117 (0.3 mg/kg) obtained from the BLM-induced SSc model (prophylactic evaluation) was used for analysis

first: Masahiro

last: Kondo

first: Tsuyoshi

last: Suzuki

first: Yuko

last: Kawano

first: Atsuhiro

last: Matsumoto


title: miRNA-Mediated Suppression of a Cardioprotective Cardiokine as a Novel Mechanism Exacerbating Post-MI Remodeling by Sleep Breathing Disorders

city: beijing

first: hui

middle: yun

last: du

state: beijing

address: 2 Anzhen Rd, Chaoyang District, Beijing

department: the Beijing Institute of Heart, Lung, and Blood Vessel Diseases

country: China

institute: Beijing Anzhen Hospital, Capital Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: This study provides the first evidence that MI+CIH upregulates miR-214-3p, suppresses cardiac CTRP9 expression, and exacerbates cardiac remodeling, suggesting that CTRP9 may be a novel therapeutic target against pathologic remodeling in MI patients with OSA

overall_design: Cardiac miRNA profiles of C57BL/6J mice in four different groups (Sham,MI, CIH, MI+CIH) were generated by deep sequencing.

first: Yunhui

last: Du

first: Xinliang

last: Ma


title: ARRB1 inhibits the progression of non-alcoholic steatohepatitis by promoting the intracellular processing of GDF15

city: Nanjing

first: Zechuan

last: Zhang

address: Zhongshan Road

institute: Nanjing Medical University

summary: ARRB1 is a vital regulator in the development of NASH via facilitating GDF15 translocate to Golgi apparatus and maturation. ARRB1 is a potential therapeutic target for the treatment of NASH.

overall_design: Hepatocytes mRNA profiles of ARRB1-/- and WT mice fed with HFD for 26 weeks were generated by deep sequencing, in triplicate.

first: Beicheng

last: Sun


title: Blood transcriptome of human sepsis in an Indian cohort [Illumina array]

city: Kalyani

first: SAMANWOY

last: MUKHOPADHYAY

state: West Bengal, INDIA

country: India

institute: NATIONAL INSTITUTE OF BIOMEDICAL GENOMICS

summary: Sepsis remains a lethal ailment with imprecise treatment and ill-understood biology. A clinical transcriptomic analysis of sepsis patients was performed for the first time in India and revealed large-scale change in blood gene expression in patients of severe sepsis and septic shock admitted to ICU. Three biological processes were quantified using scores derived from the corresponding transcriptional modules. Comparison of the module scores revealed that genes associated with immune response were more suppressed compared to the inflammation-associated genes. These findings will have great implication in the treatment and prognosis of severe sepsis/septic shock if translated into a bedside tool.

overall_design: Transcriptomic profiling was performed on sepsis cases and on matched (by age and gender) healthy controls, who were not suffering from any inflammatory diseases, and were not related to the patients. Samples were collected at two different time points in the cases. Two blood samples from the sepsis cases were collected, the first at the time of diagnosis (D1), and a second sample after 24 hours (D2) . Representative single blood sample was collected from each of the healthy control individuals. A total of 27 patients (23 with paired transcriptome data for two time points) and 12 healthy control subjects (for the single time point) were recruited in this study.

first: Samanwoy

last: Mukhopadhay

first: Saroj

middle: K

last: Mohapatra


title: Next Generation Sequencing Facilitates Quantitative Analysis of lncRNA PART1 Regulated Transcriptomes

city: Peiking

first: haibo

last: Han

address: 52 Fucheng Road, Haidian District

department: Department of Cell Biology

institute: Peking University School of Oncology

summary: The goals of this study are to analyze the transcriptome profiling (RNA-seq) after lncRNA PART1 overexpression in MGC-803 cells.

overall_design: MGC-803 cells were transfected by lncRNA PART1 expression and blank vectors as control.Total RNA was extraced by Qiagen kit and the RNA profiles were generated by RNA sequencing, using Illumina Hiseq 2000.

first: Jiafu

last: Ji

first: Haibo


title: Genetic engineered primary human natural killer cells targeting TIGIT via CRISPR/Cas9 enhanced anti-tumor activity against GBM spheroids and 2D culture.

status: Public on Sep 11 2022

city: Kashihara

first: Takayuki

last: Morimoto

state: Nara prefecture

address: 840 Shijo-Cho

department: Department of Neurosurgery

institute: Nara Medical University

summary: Background. Although several immunotherapies against glioblastoma (GBM) have been investigated for long time, only limited effective results are acquired. Therefore, we developed immunotherapy based on genome edited NK cells knocking out the checkpoint receptor, which would overcome the immunosuppressive tumor microenvironment in GBM.  Methods.  We generated T cell immunoglobulin and ITIM domain (TIGIT), an inhibitory receptor expressed on lymphocytes, knockout (KO) human primary NK cells using the clustered regularly interspaced short palindromic repeats (CRISPR)/ CRISPR-associated protein9 (Cas9), each single guide RNA targeting different genome sites on TIGIT coding exons. To detect anti-tumor activity of genome edited NK cells against GBM, we utilized 2D adherent model and spheroids derived from GBM cell lines, U87, T98G, LN18, and U251. Subsequently, we performed real time cell growth assays, flow cytometry based apoptosis assays, and ELISA for investigating anti-tumor activity.  Result. We established TIGIT KO human primary NK cells using CRISPR/Cas9. Flow cytometry indicated effective knockout of TIGIT and unchanged expression of immune checkpoint receptors other than TIGIT. T7 endonuclease I mutation detection assays showed that RNPs disrupted the intended genome sites. Using real time cell growth assays, we revealed enhanced anti-tumor activity of genome edited NK cells against 2D adherent GBM cells. The genome edited NK cells also exhibits enhanced anti-tumor effect against GBM spheroids derived from GBM cell lines.Conclusion. Our founding suggests that immunotherapy based on TIGIT KO NK cells using CRISPR/Cas9 is a promising therapy against GBM.

overall_design: Despite multimodality treatment, patients with glioblastoma (GBM) exhibits poor outcome. A novel strategy is needed and the immunotherapy is one of them. Although immunotherapies like chimeric antigen receptors (CAR) T therapy, immune checkpoint inhibitors, vaccine therapy and oncolytic virus therapy are investigated, it is difficult to change the severe immunosuppressive tumor microenvironment, so called “cold tumor”. To activate cancer immunity cycle, NK cells, which recognize tumor cells via several receptors and promote each step of cancer immunity cycle, are the suitable agents for immunotherapy against GBM. Furthermore, Genome edited NK cells targeting TIGIT, an immune checkpoint receptor, have an advantage in that be able to maintain brockage of TIGIT signal in result avoiding exhausted status, whereas the effect of anti TIGIT antibody depends on its dose and administration timing. Here, we established TIGIT KO human primary NK cells and demonstrated enhanced anti-tumor activity. This designer NK cells will thus provide more insight into the GBM treatment.

first: Tsutomu

last: Nakazawa

first: Ryosuke

last: Matsuda

first: Fumihiko

last: Nishimura

first: Mitsutoshi

last: Nakamura

first: Shuichi

last: Yamada

first: Ichiro

last: Nakagawa

first: Young-Soo

last: Park

first: Takahiro

last: Tsujimura

first: Hiroyuki

last: Nakase


title: Blood transcriptome of human sepsis in an Indian cohort [Affymetrix array]

summary: Sepsis remains a lethal ailment with imprecise treatment and ill-understood biology. A clinical transcriptomic analysis of sepsis patients was performed for the first time in India and revealed large-scale change in blood gene expression in patients of severe sepsis and septic shock admitted to ICU. Three biological processes were quantified using scores derived from the corresponding transcriptional modules. Comparison of the module scores  revealed that genes associated with immune response were more suppressed compared to the inflammation-associated genes. These findings will have great implication in the treatment and prognosis of severe sepsis/septic shock if it can be translated into a bedside tool.

last: Mukhopadhyay


title: Epigambogic acid A inhibits the tumorigenesis of non-small cell lung cancer through inhibiting the expression of DIRC1

city: Shenzhen

first: huibin

last: song

address: No.1017, Dongmen North Road, Luohu District

institute: Shenzhen People's Hospital

summary: Non-small cell lung cancer (NSCLC) is the leading life-threatening cancer in the world. Gamboge, a type of desiccating resin excreted from gamboge stalk, has been reported to have antitumor effects in various malignancies. However, little is known about the underlying mechanism in lung cancer. In this study, we discovered a novel compound in gamboge, epigambogic acid A, which significantly inhibited lung cancer cell growth with 99.94% inhibition. In addition, epigambogic acid A suppressed cell invasion and metastasis, and promoted apoptosis in NSCLC cells. The combinatorial analysis of transcriptome sequencing and The Cancer Genome Atlas (TCGA) database indicated that epigambogic acid A could remarkably decrease the expression of oncogenes such as disrupted in renal cancer 1 (DIRC1) and collagen type III alpha 1 chain (COL3A1). Moreover, DIRC1 promoted cell proliferation and clone formation in NSCLC cells. Overall, these results identify a key role of epigambogic acid A in tumor suppression and uncover the mechanism of action of epigambogic acid A and DIRC1, which provides potential implications in NSCLC therapy.

overall_design: mRNA profiles of PC9 cells treated by different concentrations of epigambogic acid A

first: Chen

last: Chen

first: Huibin

last: Song

first: Zheng

last: Peng

first: Ke-Ming

last: Li

first: Guangsuo

last: Wang

first: Li

last: Zhao

first: Hui

last: He

first: Jian

first: Qiaoyun

last: Long

first: Pan

first: Chang

last: Zou

first: Yong-Xian

last: Cheng

first: Zhiwei


title: Next Generation Sequencing  Quantitative Analysis of TEAD Palmitoylation Inhibitor MGH-CP1 in MDA-MB-231 cells

city: Charlestown

first: Yang

last: Sun

state: MA

address: 149 13th Street, CBRC 3050E

department: CBRC

country: USA

institute: Massachusetts General Hospital

summary: Purpose: The goal of this study is to understand the signaling pathway alteration inMDA-MB-231cells treated with TEAD autopalmitoylation inhibitor MGH-CP1,  and to further validate TEAD inhibitor for specifity in TEAD-YAP interuption. Methods:Breast cancer cell line MDA-MB-231 was chosen to be treated with TEAD palmitoylation inhibitor MGH-CP1 at 10μM for 24 hours. Total RNA was isolated for the analysis. RNA samples were sent to Novogen for library construction, RNA sequencing and raw data process.  Conclusions: Our study privides gene expression profiling evidence to validate our TEAD palmitoylation inhibitor MGH-CP1 as specific small molecule to block TEAD transcriptional activity.

overall_design: Examination of vehicle control and MGH-CP1 in one breast cancer cell line.

first: Xu

last: Wu


status: Public on Sep 10 2022

first: Songcheng

last: Yin

address: 628 Zhenyuan Road

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

summary: In order to explore the effect of RNA-binding protein PUM1 on proliferation, metastasis and metabolism of gastric cancer, we established PUM1 stable knockdown SGC-7901 cell lines. We then performed gene expression profiling analysis using data obtained from RNA-seq of PUM1-knockdown and negative control SGC-7901 cells.

overall_design: RNA-sequencing of SGC-7901 cells with and without PUM1 knockdown by shRNA, 3 replications.

first: Huifang

last: Liu


title: Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury

status: Public on Sep 08 2022

city: Hannover

first: Christian

last: Hinze

address: Carl-Neuberg-Str. 1

department: Department of Nephrology and Hypertension

country: Germany

institute: Hannover Medical School

summary: Background: Acute kidney injury (AKI) occurs frequently in critically ill patients and is associated with adverse outcomes. Cellular mechanisms underlying AKI and kidney cell responses to injury remain incompletely understood.   Methods: We performed single-nuclei transcriptomics, bulk transcriptomics, molecular imaging studies, and conventional histology on kidney tissues from 8 individuals with severe AKI (stage 2 or 3 according to Kidney Disease: Improving Global Outcomes (KDIGO) criteria). Specimens were obtained within 1-2 hours after individuals had succumbed to critical illness associated with respiratory infections, with 4 of 8 individuals diagnosed with COVID-19. Control kidney tissues were obtained post-mortem or after nephrectomy from individuals without AKI.   Results: High-depth single cell-resolved gene expression data of human kidneys affected by AKI revealed enrichment of novel injury-associated cell states within the major cell types of the tubular epithelium, in particular in proximal tubules, thick ascending limbs and distal convoluted tubules. Four distinct, hierarchically interconnected injured cell states were distinguishable and characterized by transcriptome patterns associated with oxidative stress, hypoxia, interferon response, and epithelial-to-mesenchymal transition, respectively. Transcriptome differences between individuals with AKI were driven primarily by the cell type-specific abundance of these four injury subtypes rather than by private molecular responses. AKI-associated changes in gene expression between individuals with and without COVID-19 were similar.   Conclusions: The study provides an extensive resource of the cell type-specific transcriptomic responses associated with critical illness-associated AKI in humans, highlighting recurrent disease-associated signatures and inter-individual heterogeneity. Personalized molecular disease assessment in human AKI may foster the development of tailored therapies.

overall_design:
The provided data comprise single nuclei sequencing data from AKI and control patients as presented in detail in https://www.biorxiv.org/content/10.1101/2021.12.15.472619v1.

>>>Submitter states that raw data are not available due to patient privacy concerns<<<

first: Christine

last: Kocks

first: Janna

last: Leiz

first: Nikos

last: Karaiskos

first: Anastasiya

last: Boltengagen

first: Shuang

last: Cao

first: Christopher

middle: M

last: Skopnik

first: Jan

last: Klocke

first: Jan-Hendrik

last: Hardenberg

first: Helena

last: Stockmann

first: Inka

last: Gotthardt

first: Benedikt

last: Obermayer

first: Laleh

last: Haghverdi

first: Emanuel

last: Wyler

first: Markus

last: Landthaler

first: Sebastian

last: Bachmann

first: Andreas

middle: C

last: Hocke

first: Victor

last: Corman

first: Jonas

last: Busch

first: Wolfgang

last: Schneider

first: Nina

last: Himmerkus

last: Bleich

first: Kai

middle: U

last: Eckardt

first: Philipp

last: Enghard

first: Nikolaus

last: Rajewsky

last: Schmidt-Ott


title: Effect of depletion of Rcrin on gene expression in mouse liver tissues

city: Beijing

first: Yanying

last: Wang

address: 15 Datun Road, Chaoyang District,Beijing 100101, China

institute: Institute of Biophysics, Chinese Academy of Sciences

summary:
To investigate the function of Rcrin in liver, we established Rcrin flox mice and crossed with Alb-cre mice, then we generated Rcrin conditional knockout mice. Then we got liver tissues from Rcrin conditional knockout mice and Rcrin flox mice.
We then performed gene expression profiling analysis using data obtained from RNA-seq of Rcrin conditional knockout mice (Rcrin knockout) and Rcrin flox mice (WT) at age of 8 weeks old.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for liver tissues from Rcrin conditional knockout mice (Rcrin  knockout) and Rcrin flox mice (WT).


title: To explore read-through circRNA profiles in human normal and NASH livers

summary:
To investigate the function of read-through circRNAs in liver, we obtained human NASH liver tissues and normal liver tissues patients without NAFLD undergoing surgery for hepatic hemangioma.Patients with positive hepatitis B surface antigen or anti-hepatitis C virus (HCV) antibody with detectable HCV RNA, excessive alcohol consumption (20 g/day in men or 10 g/day in women), secondary fatty liver (e.g., use of systemic steroids or tamoxifen), or malignancies before baseline were excluded.
We then performed exome capture mRNA sequencing using livers from three NASH patients and three patients with hepatic hemangioma.

overall_design: Comparative gene expression profiling analysis of exome capture mRNA-seq data for liver tissues from human normal and NASH livers.


title: RPRD1B is required for proper heat shock response [TTchem-seq]

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

country: United Kingdom

institute: The Francis Crick Institute

summary: The Heat Shock response (HSR) is a highly conserved transcriptional program induced by the exposure to a variety of environmental stressors. Following an insult, a small subset of genes, known as the Heat Shock genes, are rapidly induced by the Heat Shock Factors (HSFs) to maintain protein homeostasis and ensure cell survival. In this study, we demonstrate that the RNAPII interactor RPRD1B is required for proper transcription of heat shock induced genes and for survival to heat shock.

overall_design: Generating a snapshot of transcriptional activity at different times of HS exposure by pulse-labelling nascent RNA with 4SU in cells depleted for RPRD1B.

first: Simona

last: Cugusi

first: Prashanth

last: Bajpe

first: Harshil

last: Patel

first: Jesper

middle: Q

last: Svejstrup


title: Chromatin accessibility landscapes of intestinal WT Nkp46-CC6- ILC3 (Double Negative, DN ILC3) and BATF-deficient cKO DN ILC3s sorted from intestine

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Group 3 innate lymphoid cells (ILC3s) are crucial for the maintenance of host-microbiota homeostasis in gastrointestinal mucosal tissues. The mechanisms that maintain lineage identity of intestinal ILC3s, and ILC3s-mediated orchestration of microbiota and mucosal T cell immunity are elusive. Here, we identified BATF as a gatekeeper of ILC3s homeostasis in the gut. Depletion of BATF in ILC3s resulted in excessive interferon-γ production, dysbiosis, aberrant T cell immune responses and spontaneous inflammatory bowel disease (IBD), which was considerably ameliorated by removal of adaptive immunity or antibiotic treatment. Mechanistically, BATF directly regulates ILC3s identity by globally shapes chromatin landscape of ILC3s. BATF directly binds to the cis-regulatory elements of type 1 effector genes, restrains their chromatin accessibility and inhibits their expression. Conversely, BATF promotes chromatin accessibility of genes involved in MHCII antigen processing and presentation pathways. Collectively, our findings reveal BATF is a promising candidate to maintain ILC3s stability and coordinate ILC3s–mediated control of intestinal homeostasis.

overall_design: ATACseq, 2 samples (WT and cKO DN ILC3s), 2 biological replicates per sample, from intestine.

first: Xiaopeng

last: Wu


title: Effect of depletion of OGT on gene expression during M2 polarization  of macrophages

city: shang hai

first: Qian

last: Zhang

address: xiangyin road 800

institute: Second military medical university

summary:
To investigate the function OGT in the regulation of M2 polarization of macrophages, we established IL-4-activated bone marrow-derived macrophages (BMDMs) from mice of wild-type control or Lyz2-Cre/Loxp-mediated knockout of OGT.
We then performed gene expression profiling analysis using data obtained from RNA-seq of wild-type (WT) and OGT-knockout (OGT-KO) macrophages at two time points during IL-4 (20ng/μl) sitmulation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and OGT-KO BMDMs.

first: Xuetao

last: Cao

first: Qingzhu

last: Shi


title: Transgenerational inheritance of acquired memory and epigenetic imprints through maternal gametes

city: Shanghai

first: Xiwei

last: Liu

address: 1239 Siping Road

institute: Tongji University

summary: Transgenerational inheritance of acquired traits/characteristics from ancestors is believed to play important roles in evolution, as well as health problems/symptoms not due to “classical genetic inheritance”. However, the central enigma, such as how the acquired transgenerational characteristics are developed, and how the acquired traits are transmitted from generations to generations of offspring, largely remained veiled. In this study, we used C elegans as a model system and provide evidence that the dynamic of H3K27me3 as a hallmark and regulator for the gut-mediated transgenerational inheritance of acquired traits. Further, we demonstrate that yolk proteins guide the establishment of the acquired epigenetic imprints in soma, as well as determines the transgenerational inheritance of epigenetic imprints and subsequent acquired behavior in offspring by maternal provision. Taken together, our findings support that yolk proteins both function as a systemic “non-nuclear factor” for establishing the somatic epigenetic imprints and as a “cargo” to transmit acquired epigenetic information to the subsequent generations through oocytes.

overall_design: For bulk RNA-Seq, 6 samples were analyzed. For both naïve and trained condition samples there are 3 replicates. The naïve samples were considered reference sample.  For barcoded single organ RNA-Seq, 4 samples were analyzed. For germline and intestine, one naïve sample and one PA14 trained sample were used. The naïve samples were considered reference sample.  For barcoded single cell RNA-Seq of worm PVD and OLL neuron, 2 samples were analyzed, one naïve sample and one PA14 trained sample. The naïve sample was considered reference sample.

first: Wei

last: Li

first: Qiang

last: Fang

first: Qiuyu

first: Haowei

first: Yonghao

first: Fanglin

last: Sun


title: Loss of p53 suppresses replication stress-induced DNA damage in ATRX-deficient neuroblastoma

city: Kitaadachi-gun

first: Hisanori

last: Takenobu

state: Saitama

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

institute: Saitama Cancer Center

summary: To elucidate ATRX-dependent transcriptional alterations and their functional consequences, we performed a microarray analysis of Ctrl and ATRX KO NGP cells.

overall_design: Total RNA was extracted from Ctrl and two ATRX KO NGP clones, and a microarray analysis was performed using the Agilent-072363 SurePrint G3 Human GEv3 8 × 60 K Microarray  G4851C (Agilent Technologies, Santa Clara, CA, USA).

first: Takehiko

last: Kamijo

first: Jesmin

last: Akter

first: Miki

last: Ohira

first: Ryuichi

middle: P

last: Sugino


title: Differentially expressed genes in the transition from callus proliferation to differentiation in Ceratopteris richardii

city: Jishou

first: Gui-Sheng

address: 120 Renmin South Street

institute: Jishou University

summary: Regeneration is common in plants and transcription factors greatly contribute to this versatility of flowering plants; however, the evolution of this capability has hardly been explored. The callus can be induced from an intact plant rather than an explant in the water fern Ceratopteris richardii and the employed media are very different. The callus was verified having resulted in indirect de novo shoot organogenesis (IDNSO). Hundreds of genes were differentially expressed between the proliferating and the differentiating callus, hinting at significant changes in photosynthesis and hormone response. Many transcription factors were also differentially expressed, providing cues on how the callus proliferated and differentiated. STM-, ANT-, and ESE3-like transcription factor were simultaneously expressed in the vascular-initial-like cells in the callus, thus identifying a key tissue in callus differentiation; furthermore, they might have undergone subfunctionalization or neofunctionalization during evolution. Therefore, IDNSO was considered both conserved and diversified throughout vascular plants.

overall_design: The callus is employed, and there are three reference samples of the differentiating callus and three control samples of the proliferating callus


title: Lymphatic endothelial cells, together with Rspo3+Grem1+ fibroblasts, support intestinal stem cells through the production of R-spondin3 in homeostasis and injury [200211YilA]

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

summary: Intestinal stem cells (ISCs) depend on niche factors for proper function. Here, we focus on RSPO3, an essential ISC niche factor, that engages the Lgr5 receptor on ISCs to potentiate WNT signaling, an interaction that is critical for maintaining intestinal stemness. Leveraging novel Rspo3-GFP and Grem1-tdTomato-CreERT2 genetically engineered mice together with single-cell mRNA profiling, we find that RSPO3 is expressed by lymphatic endothelial cells (LECs) and Rspo3+Grem1+ (RG) fibroblasts in the intestinal stroma where RG fibroblasts surround lymphatics and are in close proximity to Lgr5+ ISCs near the crypt base. Functionally, RG fibroblasts through the production of RSPO3 and GREM1 and LECs through the production of RSPO3 foster intestinal organoid propagation in vitro. Rspo3 loss in either or both of these niche cells in vivo compromises ISC numbers, villi length, and repair after irradiation-induced injury. Mechanistically, irradiation-induced damage expands LEC and RG fibroblast numbers and enhances the latters’ generation of RSPO3 through IL-1 receptor activation. We propose that LECs represent a novel component of the ISC niche, which together with RG fibroblasts, provide essential RSPO3 to sustain ISCs in homeostasis and regeneration.

overall_design: Three replicates each of small intestinal or colonic Epcam negative, CD45 negative stromal cells positive or negative for CD31 or Rspo3.

first: Norihiro

last: Goto

first: Omer

last: Yilmaz


title: Lymphatic endothelial cells, together with Rspo3+Grem1+ fibroblasts, support intestinal stem cells through the production of R-spondin3 in homeostasis and injury [200909Yil]


title: Lymphatic endothelial cells, together with Rspo3+Grem1+ fibroblasts, support intestinal stem cells through the production of R-spondin3 in homeostasis and injury [scRNAseq]

overall_design: Rspondin3 postive,  Epcam negative, CD45 negative stromal cells from two replicates of untreated, 2 replicates of irradiated, 2 replicates of unirradiated controls and one normal colon.


title: RNA sequencing of human breast cancer cells with CUL4B knockdown

city: Jinan

first: Yuxing

last: Wang

state: Shandong

address: 44 Wenhuaxi Rd

institute: Institute of Molecular Medicine and Genetics Shandong University School of Medicine

summary: Approximately 30% of cases are resistant to TAM, which has become a major obstacle for breast cancer therapy.In this study, we demonstrated that CUL4B promotes TAM resistance in breast cancer cells through miR-32-5p/ER-α36 axis. CUL4B is overexpressed in TAM-resistant breast cancer cells and positively correlates with the levels of ER-α36 protein in human breast cancer specimens. Mechanistically, CUL4B positively regulates ER-α36 expression by epigenetically repressing the transcription of miR-32-5p. These findings provide not only a mechanistic insight into the role of CUL4B in regulating TAM sensitivity but also a potential target for the therapy of breast cancer.

overall_design: We generated transciptome data from human breast cancer cells that Knockdown CUL4B and its control

first: Molin

first: Yaoqin

last: Gong


title: Comparison of transcript profiles of Arabidopsis WT and VPZ plants to fluctuating light and high light

city: Cerdanyola del Vallès

first: ANTONI

last: GARCIA-MOLINA

state: Barcelona

address: Campus UAB - CRAG Building

department: Plant Development and Signal Transduction

country: Spain

institute: Centre for Research in Agrigenomics

summary:
Purpose: Overexpression of VDE, ZEP and PsbS (VPZ) in plants confers enhanced dynamics of non-photochemical quenching of NPQ under FL light. VPZ overexpression in tobacco has been reported to increase plant biomass under fluctuating light. However, our work demonstrates that such strategy had no advantageous effect when asssayed in Arabidopsis thaliana. To investigate whether this observation is due to  impairements in signaling pathways due to the expression of VPZ in Arabidopsis thaliana, transcriptome profiles of VPZ plants exposed to fluctuating light or high light were conducted.
Methods: mRNA-Seq libraries were prepared from 21-d-old Col0 plants and VPZ lines #2 and #4  cultivated under standard control conditions and then exposed to fluctuating light or high light for 6h and 30 h.  Standard Illumina protocols were used for mRNA-Seq sequencing. Triplicates for 3 independent plants were used. Adaptor sequences were removed with Trimmomatic and resulting reads mapped to the Arabidopsis genome (Araport11) with Tophat 2.1.1. Normalised counts reads were quantified with featureCounts to provide processed data files and differential expression analysis were conducted with the DEseq2 pipeline.
Results: mRNA-Seq libraries contained app. 9 milion reads each. Transcript analysis for differential gene expression was conducted according to the Tophat/featureCounts/DESeq2 pipeline. To declare significant differences, a cut-off for absolute log2(FC) ≥ 1 compared to the initial timepoint (0h) and FDR ≤ 0.05 was applied. Significant transcripts exclusively found for Col0 and both VPZ lines in each time-point were considered for subsequent analysis. Accordingly,  528 and 415 transcripts (6h and 30h) were found for Col0, and 326 and 896  (6h and 30h) for the VPZ under control conditions. For FL, 490 and 591 transcripts qualified as specific  (6h and 30h) for Col0 and 938 and 401 (6h and 30h) for VPZ. Strikingly, the amount of transcripts raised to 2847 and 2902 DEGs (6h and 30h) for Col0, whereas only 546 and 304  (6h and 30h) were detected for VPZ under HL. transcripts).
Conclusions: the overexpression of VPZ in Arabidopsis leads to particular transcriptome response under fluctuating light related to changes in photosynthesis and response to abscisic acid, among all. However, Col0 displayed wider transcriptome responses than VPZ after exposure to high light .

overall_design: Transcriptome profiling of leafs of 21-d-old Arabidopsis Col0 and VPZ lines #2 and #4 plants treated with fluctuating light or high light for 6h and 30h. Illumina Sequencing protocols were applied to biologically independent triplicates.

first: Antoni

last: Garcia-Molina

first: Dario

last: Leister


title: Transcriptome-wide profiling of acute stress induced changes in ribosome occupancy level using external standards

city: Houston

first: Annie

middle: W.

last: Shieh

state: Texas

address: 1825 Pressler St

department: Brown Foundation Institute Of Molecular Medicine

institute: University of Texas Health Science Center

summary: Acute cellular stress is known to induce a global reduction in protein translation through suppression of cap dependent translation. However, selective translation in response to acute stress has been shown to play important roles in regulating the stress response. An accurate transcriptome-wide profile of acute cellular stress-induced translational changes has been challenging to obtain. Commonly used data normalization methods, such as quantile normalization, operate based on the assumption that any systematic shifts are artifacts introduced from experimental procedures. Consequently, if applied to profiling acute cellular stress-induced protein translation changes, these methods are expected to produce biased estimates. To address this issue, here we designed, generated, and evaluated a panel of 16 oligomers to serve as external standards for ribosome profiling studies. Using Sodium Arsenite treatment-induced oxidative stress in lymphoblastoid cell lines as a model system, we applied spike-in oligomers as external standards based on quantifications of monosomal RNA extracted from each sample. We found our spike-in oligomers to display a linear correlation between the observed and the expected, with small but significant ratio compression at the lower concentration range, and span the expected quantitative range in the observed data, which covers 97 % of the quantitated endogenous genes. We found popular global scaling normalization approaches to introduce both high levels of false positives and false negatives in differential expression analysis. Using the expected fold changes constructed from spike-in external controls, we found in our dataset that TMM normalization produced 87.5% false positives when a P value cutoff of 0.1 is used (i.e. 10% expected false positive rate) and on average produced a systematic shift of fold change by 3.25 fold. These results highlight the consequences of applying global scaling approaches to conditions that clearly violate their key assumptions. As an alternative, we found using spike-in quantifications as control genes in RUVg normalization recapitulated the expected stress induced global reduction of translation, and resulted in little, if any, systematic shifts in spike-in constructed true positives. Finally, using spike-in constructed true positives and true negatives, we explored alternative normalization approaches for acute cellular stress response ribo-seq studies. We found that a simple approach that quantile normalized data from control and treated samples separately, which we termed respective quantile normalization, produced expected results in spike-in quantification, and resulted in little, if any, systematic bias on fold change in endogenous genes. Additionally, we found that under certain parameters, using endogenous control genes for RUVg normalization best recapitulate the expected. Our results clearly demonstrated the utility of our spike-in oligomers, both for constructing expected results as controls and for data normalization. Our exploration of different normalization approaches highlights the issues in applying global scaling normalization when key assumptions are clearly not met. We show that a respective quantile normalization approach or normalization with endogenous control genes are viable options worth considering as a more generalizable approach for stress response ribo-seq studies. This conclusion is likely applicable to other types of studies that involve global shifts in expression profiles between comparison groups of interests.

overall_design: Ribosome profiling of LCL in response to sodium arsenite induced stress

middle: W

first: Sandeep

last: Bansal

first: Zhen

last: Zuo

first: Sidney


title: Aoatg11 and Aoatg33 are indispensable for mitophagy, and contribute to conidiation, the stress response, and pathogenicity in the nematode-trapping fungus Arthrobotrys oligospora

city: Kunming

first: Xuemei

last: Li

state: Yunnan

address: wuhuaqu

institute: majorbio

summary: Mitophagy is one of the most important cellular processes to ensure mitochondrial quality control, which aims to transport damaged, dysfunctional, or excess mitochondria for degradation and reuse. Here, we determined the function of AoAtg11 and AoAtg33, two orthologous autophagy-related proteins involved in yeast mitophagy, in the typical nematode-trapping fungus Arthrobotrys oligospora . Deletion of Aoatg11  and Aoatg33 impairs mitophagy, mitochondrial morphology and activity, autophagy,cell apoptosis, reactive oxygen species levels, lipid droplet accumulation, and endocytosis. These combined effects resulted in slow vegetative growth; reduced conidiation, trap formation, cell nucleus, and extracellular protease activity; increased susceptibility to the stress response; and arthrobotrisin production in the Δ Aoatg11 and Δ Aoatg33 mutants, compared with the wild-type strain. In addition, the absence of Aoatg11 caused an endoplasmic reticulum stress response. Transcriptome analysis revealed that many differentially expressed genes in the Δ Aoatg11 mutants were involved in various important cellular processes, such as lipid metabolism, the TCA cycle, mitophagy, nitrogen metabolism, endocytosis, and the MAPK signaling pathway. In conclusion, our study revealed that Aoatg11 and Aoatg33 mediate autophagy and mitophagy in A. oligospora , and provides a basis for elucidating the links between mitophagy and fungal vegetative growth, conidiation, and pathogenicity.

overall_design: RNA-seq analysis between six wild-type samples and six ΔAoatg11 mutant samples, with three biological replicates per sample, and prediction of multiple cytological processes that may affect trap formation in Arthrobotrys oligospora.

first: Meichen

last: Zhu

first: Yankun

last: Liu

first: Le

last: Yang

first: Keqing

last: Zhang

first: Jinkui


title: transcriptome analysis for luteolin or siVRK1 treated ovarian cancer cells

status: Public on Sep 07 2022

city: 名古屋市昭和区

first: xuboya

last: chang

state: 愛知県

address: 日本愛知県名古屋市昭和区鶴舞町６５

institute: Nagoya University

summary: To investigate the function of Luteolin and siVRK1 on ovarian cancer, we use A2780 and ES2 cell lines treated with siCtrl, siVRK1, DMSO and luteolin to do the experiment. We then performed gene expression profiling analysis using data obtained from RNA-seq .

overall_design: Comparative gene expression profiling analysis of RNA-seq data for A2780 and ES2 cells(siCtrl, siVRK1, DMSO and luteolin)

first: Xuboya

last: Chang

first: Tamauchi

last: Satoshi

first: Kosuke

last: Yoshida

first: Akira

last: Yokoi


title: Mechanisms of Restoring T Cell Immunity after Cure of Chronic Viral Infection

city: Boston

first: Sonu

last: Subudhi

address: 100 Blossom St, Cox 7

department: Radiation Oncology

summary: Understanding the molecular mechanisms of T cell exhaustion and reinvigoration is crucial to improving T cell based immunotherapy. In this study we confirmed key differences between memory and exhausted antigen-specific CD8+ T cells in hepatitis C virus infection before and after antiviral treatment. After viral cure, we observed the although phenotypically they seem to recover, functionally they showed little improvement and critical transcriptional regulators remained in exhausted state.

overall_design:
We analyzed hepatitis C virus (HCV)-specific T cells and non-specific memory T cell populations from 6 patients with chronic HCV infection receiving 12 weeks of direct-acting antiviral therapy with aritaprevir/ritonavir/ombitasvir + dasabuvir + ribavirin. All patients were treated successfully. Peripheral blood mononuclear cells were obtained from blood draws right before treatment initiation and 12 months after the end of treatment. In each patient, HCV-specific cells were sorted using two different HCV multimers: One representing an epitope present in the circulating HCV genome and one epitope where the virus had escaped the T cell response and thus the corresponding T cells did not receive a TCR signal in vivo. Sorted specific T-cell populations and memory T cell subpopulations were analyzed by extracting RNA and performing RNA sequencing using the Smart-Seq2 protocol. A group of 8 patients with acute self-limited HCV infection were included as control representing natural control of infection. These patients were studied 24 weeks after their last detectable HCV viremia. Finally, we confirmed the data from chronically treated patients in a confirmatory cohort, consisting of 9 patients after successful antiviral treatment.

>>>Submitter states: Raw data have been submitted to dbGaP: phs002510.v1.p1<<<

first: Pierre

last: Tonnerre

first: David

last: Wolski

first: Georg

last: Lauer


title: Gene expression profile at single cell level of liver immune cells from the liver Rcrin conditional knockout mice (Rcrin knockout) and  Rcrin flox mice (WT)

first: Yanying

last: Wang

summary: Immune cells in liver are considered to contribute to NASH. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of immune cells in the liver.

overall_design: immune cells in the livers of the Rcrin knockout mice and WT mice were isolated by collagenase digestion and analyzed using scRNAseq.


title: Gene expression profile at single cell level of CD45+ from the spinal cords of WT and STAP-1 mice 15 days after EAE induction

city: Sapporo

first: Junichi

last: Kashiwakura

state: Hokkaido

address: 15-4-1, Maeda 7-jo, Teine-ku

institute: Hokkaido University of Science

summary: T cells are considered to be an important cell type for pathogenesis of multiple screlosis. We used single cell RNA sequencing (scRNA-seq) to analyze popluation of inflitrating CD45+ cells in spinal cords of WT and STAP-1 KO mice to figure out whehter STAP-1 is required for infiltration of T cells in the spinal cords after EAE induction.

overall_design: The cells in spinal cords were collected, CD45+ clell were stained with antbodies conjugated with hashtag and analyzed using scRNAseq.

first: Jun-ichi

first: Kota

last: Kagohashi

first: Tadashi

last: Matsuda


title: Hepatic CPT1A facilitates liver-adipose cross-talk via induction of FGF21

city: Guangzhou

first: Wei

last: Sun

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

summary: Hepatosteatosis, defined as excessive intrahepatic lipid accumulation, represents the first step in the development of NAFLD. However, the molecular events directly caused by hepatic lipid build-up, in terms of its impact on liver biology and other peripheral organs, remain unclear. Carnitine palmitoyltransferase 1A (CPT1A) is the rate limiting enzyme for long chain fatty acid beta-oxidation in the liver. Here we utilise hepatocyte-specific Cpt1a knockout (LKO) mice to investigate the physiological consequences of abolishing hepatic long chain fatty acid metabolism to NAFLD and systemic metabolic homeostasis. We show that LKO mice displayed more severe hepatosteatosis but were otherwise protected against diet-induced weight gain, insulin resistance, hepatic ER stress and damage in response to high fat diets. Furthermore, increased energy expenditure accompanied by enhanced adipose tissue browning was observed in LKO mice. Mechanistically, hepatic CPT1A deficiency actives the peroxisome proliferator activator alpha (PPARα)- fibroblast growth factor 21 (FGF21) axis and the elevation of FGF21 contributes to the improved liver pathology and adipose browning in HFD-treated LKO mice. Thus, our study demonstrates that liver with deficient CPT1A expression adopts a healthy steatotic status that protects against HFD-evoked liver damage and potentiates adipose browning in an FGF21-dependent manner. Inhibition of hepatic CPT1A may serve as a viable strategy for the treatment of obesity and NAFLD.

overall_design: Liver mRNA profiles of  wild type (WT) and Cpt1a L-/- mice on HFD

first: Tao

last: Nie

first: Kuai

last: Li

first: Xiaoyan

last: Hui

first: Donghai

last: Wu

first: Shaoqiang

last: Lin


title: Gene expression profile at single cell level of intratumor myeloid cells

first: Qian

last: Zhang

summary: Tumor-infiltrating myeloid cells play important roles in tumor development. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of myeloid cells in tumor.

overall_design: CD45+CD19-CD3-NK1.1- cells from B16-F10 allografts were sorted were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Xuetao

last: Cao

first: Qingzhu

last: Shi


title: Identification of miRNAs and their target genes associated with improved corn seed vigor induced by gibberellin (GA3) through small RNAs and degradome sequencing

city: Zhengzhou

first: yanyong

last: cao

state: henan

address: No. 116, Huayuan Road

institute: Henan Academy of Agricultural Sciences

summary:
Background: High seed vigor is crucial for agricultural production owing to its potential in high quality and yield of crops. A better understanding of the underlying mechanisms is highly necessary.
Results: To better understand the involvement and regulatory mechanism of miRNAs correlated with maize seed vigor, small RNAs and degradome sequencing of two inbred lines Yu537A and Yu82 were performed. A total of 791 mature miRNAs were obtained with different expressions, among of which 505 miRNAs were newly identified and the rest miRNAs were more or less reported before by comparing the miRNAs with the sequences in miRbase database. Analysis of miRNA families showed maize seeds contain fewer miRNA families and larger miRNA families compared with animals, indicating that functions of miRNAs in maize seeds were more synergistic than animals. Degradome sequencing was used to identify the targets of miRNAs and the results showed a total of 6196 targets were obtained. Function analysis of diﬀerentially expressed miRNAs and targets showed Glycan degradation and galactose metabolism were closely correlated with improved corn seed vigor.
Conclusions: These findings provide valuable information to understand the involvement of miRNAs with corn seed vigor and these putative genes will be valuable resources for improving the seed vigor in future corn breeding.

overall_design:
A total of 18 samples were sequenced with 3 biological replicates per group.
Please note that
"S" represents the late germination variety YU537A,
"E" represents the early germination cultivar YU82,
6h, 53h, and 78h represent the time of germination,
and "SGA_53h" represents the late germination variety YU537A treated with GA to germinate at 53h after imbibition.

first: Zanping

last: Han

first: Bin

first: Yunqian

last: Jin


title: LNCAP xenograft prostate cancer progression model in NOD-SCID mice

city: Brisbane

first: Colleen

last: Nelson

state: Queensland

address: 199 Ipswich Road

department: Institute of Health and Biomedical Innovation; Vancouver Prostate Centre

country: Australia

institute: Queensland University of Technology; University of British Columbia

summary: Xenografts are useful in vivo tumour models for investigating cancer progression, therapeutic responses and predicting anti-cancer drug response in patients with cancer of a similar phenotype. We have generated bulk RNA-seq data from LNCaP xenografts of a large and well-annotated prostate cancer progression study, investigating responsiveness and subsequent resistance to therapies targeting the androgen receptor (AR). LNCaP xenograft tumour establishment and initial growth are dependent on androgens in male mice (PRE-CX / pre-castration group). Upon castration, AR activity and tumour growth are suppressed (POST-CX / post-castration group), however, this initial responsiveness to castration reproducibly gives way to castration-resistance (CRPC / castration-resistant prostate cancer).  Further treatment of CRPC with the AR targeting drug enzalutamide (ENZ) initially provides a therapeutic response (ENZ Sensitive; ENZS), however, resistance emerges in time (ENZ Resistant; ENZR).

overall_design: 54 samples, multiple biological repeats of each condition/treatment group: PRE-CX (pre-castration / intact, 9), POST-CX (post-castration, 8), CRPC (castrate-resistant, 10), ENZ (enzalutamide treated, 27 = 12 ENZS and 15 ENZR).

first: Ellca

last: Ratther

first: Brett

last: Hollier

first: Rachel

last: Hu

first: Elizabeth

last: Williams

first: Lisa

last: Philp

first: Nataly

last: Stylianou

first: Marianna

last: Volpert

first: Katrina

last: Sweeney

first: Nenad

last: Bartonicek

first: Melanie

last: Lehman

first: Anja

last: Rockstroh


title: RPRD1B is required for proper heat shock response

city: London

first: Richard

last: Mitter

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

overall_design: Refer to individual Series


title: RPRD1B is required for proper heat shock response [RNA-seq]

summary: The Heat Shock response (HSR) is a highly conserved transcriptional program induced by the exposure to a variety of environmental stressors. Following an insult, a small subset of genes, known as the Heat Shock genes, are rapidly induced by the Heat Shock Factors (HSFs) to maintain protein homeostasis and ensure cell survival. In this study, we demonstrate that the RNAPII interactor RPRD1B is required for proper transcription of heat shock induced genes and for survival to heat shock.

overall_design: RNA was extracted and mRNA was obtained by selecting the polyA(+) fraction of the labelled RNA.

first: Simona

last: Cugusi

first: Prashanth

last: Bajpe

first: Harshil

last: Patel

first: Jesper

last: Svejstrup


title: Resident Macrophage Subpopulations Occupy Distinct Microenvironments in the Kidney

city: Birmingham

first: Matthew

middle: David

last: Cheung

state: AL

address: 1825 University Blvd

institute: University of Alabama at Birmingham School of Medicine

summary: The kidney contains a population of resident macrophages from birth that expands as it grows and forms a contiguous network throughout the tissue. Kidney resident macrophages (KRMs) are important in homeostasis and the response to acute kidney injury (AKI). While the kidney contains many microenvironments, it is unknown whether KRMs are a heterogeneous population differentiated by function and location. We combined single-cell RNA sequencing (scRNAseq), spatial transcriptomics, flow cytometry, and immunofluorescence imaging to localize, characterize, and validate KRM populations during quiescence and following 19 minutes of bilateral ischemic kidney injury. scRNAseq and spatial transcriptomics revealed seven distinct KRM subpopulations, which are organized into zones corresponding to regions of the nephron. Each subpopulation was identifiable by a unique transcriptomic signature suggesting distinct functions. Specific protein markers were identified for two clusters allowing analysis by flow cytometry or immunofluorescence imaging. Following injury, the original localization of each subpopulation is lost, either from changing locations or transcriptomic signatures. The original spatial distribution of KRMs is not fully restored for at least 28 days post-injury. The change in KRM localization confirms a long hypothesized dysregulation of the local immune system following acute injury and may explain the increased risk for chronic kidney disease.

overall_design: Single-cell RNA sequencing of kidneys leukocytes and spatial transcriptomics of whole kidneys obtained mice before and after bilateral ischemia reperfusion injury. There are five timepoints (quiescent/day 0, day 1, day 6, and day 28 with n=3 per timepoint for both single-cell and spatial transcriptomics

middle: D

first: Elise

middle: N

last: Erman

first: Kyle

last: Moore

first: Jeremie

last: Lever

first: Zhang

last: Li

first: Jennifer

middle: R

last: LaFontaine

first: Gelare

last: Ghajar-Rahimi

first: Shanrun

last: Liu

first: Zhengqin

last: Yang

first: Rafay

last: Karim

first: Bradley

last: Yoder

first: Anupam

last: Agarwal

first: James

middle: F

last: George


title: Single cell RNA-seq analysis for early erythroblasts in spleen and bone marrow (BM) with or without mitochondria transfer

city: Singapore

first: Rui

last: Yokomori

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore, National University of Singapore

summary: Single cell RNA-seq analysis for early erythroblasts in spleen and BM with or without mito-Dendra2 fluorescence signal after macrophage infusion upon PHZ treatment

overall_design: Mito-dendra2 labelled macrophages were intravenously injected into PHZ treated mice, early erythroblasts were isolated based on the presence of mito-dendra2 signal to be identified as mito- and mito+

first: Yang

last: Chong

first: R

first: T

last: Sanda

first: Toshio

last: Suda


title: Human centromere repositioning activates transcription and opens chromatin fibre structure [RNAseq]

city: Edinburgh

first: Catherine

last: Naughton

address: Crewe Road

department: MRC Human Genetics Unit

institute: University of Edinburgh

summary: Human centromeres appear as constrictions on mitotic chromosomes and form a platform for kinetochore assembly in mitosis. Biophysical experiments led to a suggestion that repetitive DNA at centromeric regions form a compact scaffold necessary for function, but this was revised when neocentromeres were discovered on non-repetitive DNA. To test whether centromeres have a special chromatin structure we have analysed the architecture of a neocentromere. Centromere formation is accompanied by RNA pol II recruitment and active transcription to form a decompacted, negatively supercoiled domain enriched in ‘open’ chromatin fibres. In contrast, centromerisation causes a spreading of repressive epigenetic marks to surrounding regions, delimited by H3K27me3 polycomb boundaries and divergent genes. This flanking domain is transcriptionally silent and partially remodelled to form ‘compact’ chromatin, similar to satellite-containing DNA sequences, and exhibits genomic instability. We suggest transcription disrupts chromatin to provide a foundation for kinetochore formation whilst compact pericentromeric heterochromatin generates mechanical rigidity.

sample_organism:
Homo sapiens
Cricetulus griseus

platform_organism:
Homo sapiens
Cricetulus griseus

overall_design: RNA-Seq was used to examine transcription across the neocentromere region in HybNeo3 and GM10253A cells. Two replicates for each cell line (GM10253A and HybNeo3) were processed.

first: Nick

last: Gilbert


title: Human centromere repositioning activates transcription and opens chromatin fibre structure [Agilent ChIP-chip]

type: Genome binding/occupancy profiling by genome tiling array

summary:
This study was designed to investigate the chromatin structure of human centromeres.
Human centromeres appear as constrictions on mitotic chromosomes and form a platform for kinetochore assembly in mitosis. Biophysical experiments led to a suggestion that repetitive DNA at centromeric regions form a compact scaffold necessary for function, but this was revised when neocentromeres were discovered on non-repetitive DNA. To test whether centromeres have a special chromatin structure we have analysed the architecture of a neocentromere. Centromere formation is accompanied by RNA pol II recruitment and active transcription to form a decompacted, negatively supercoiled domain enriched in ‘open’ chromatin fibres. In contrast, centromerisation causes a spreading of repressive epigenetic marks to surrounding regions, delimited by H3K27me3 polycomb boundaries and divergent genes. This flanking domain is transcriptionally silent and partially remodelled to form ‘compact’ chromatin, similar to satellite-containing DNA sequences, and exhibits genomic instability. We suggest transcription disrupts chromatin to provide a foundation for kinetochore formation whilst compact pericentromeric heterochromatin generates mechanical rigidity.

overall_design: Agilent ChIP-chip


title: Lymphatic endothelial cells, together with Rspo3+Grem1+ fibroblasts, support intestinal stem cells through the production of R-spondin3 in homeostasis and injury

first: Charles

last: Whittaker


title: Prostate Cancer Cell Line Transcriptomes

first: Colleen

last: Nelson

summary: Gene expression of 5 prostate cancer cell lines (LNCaP, VCaP, DU-145, PC-3, DuCaP) in standard culture conditions, harvested during exponential growth phase.

overall_design: 10 samples, biological duplicates of LNCaP, VCaP, DU-145, PC-3 and DuCaP cell line, respectively.

first: Stephen

last: McPherson

first: Mei-Chun

last: Yeh

first: Lisa

last: Philp

last: Gunter

first: Nenad

last: Bartonicek

first: Melanie

last: Lehman

first: Anja

last: Rockstroh


title: RNA-seq of Eca109 cells.

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

summary: Investigate the underlying mechanisms by which Evo suppressed ESCC growth in vitro.

overall_design: Eca109 cells were treated with 1‰ DMSO or Evodiamine (1μM) for 24 h, and total RNAs were subjected to RNA isolation and RNA-seq analyses were generated by deep sequencing using Illumina Hiseq.

first: Li

last: Zhang

first: Shuying

last: Yuan


title: Human centromere repositioning activates transcription and opens chromatin fibre structure [TTseq]

overall_design: TT-Seq was used to examine nascent transcription accross the neocentromere region in HybNeo3 and GM10253A cells. TTseq is an adaptation of 4sU-Seq whereby the labeled RNA is fragmented prior to 4sU-purification and results in an enrichment of transient transcripts. TTseq was performed on 8 samples, 2 control untreated samples for each cell line GM10253A and HybNeo3 and also 2 exosome RNAi knockdown treated samples for each cell line.


title: Genes that were altered after chemogenetic activation of endogenous oxytocin in the dorsal horn

city: Kitakyushu-shi

first: Mitsuhiro

last: Yoshimura

state: Fukuoka

address: 1-12-8 Koshiki-hibikino, Wakamatsu-ku

institute: University of Occupational and Environmental Health, Japan

summary: Purpose: RNAseq analysis was carried out to investigate the alterd genes by chemogenetic activation of endogenous oxytocin in the superficial layer (laminae I-II) and deep layer (laminae III-VI) of the dorsal horn. Methods: At 120 min after the s.c. administration of Saline or CNO (1 mg/kg) (n=3, each), adult male oxytocin-hM3Dq-mCherry transgenic rats were decapitated immediately without being anesthetized. Spinal cords specimens including laminae I-II and III-VI were collected separately. Results: 254 genes in the laminae I-II, and 191 genes in the laminae III-VI of the dorsal horn were significantly altered after chemogenetic activation of endogenous oxytocin.

overall_design: Dorsal horn mRNA profiles after chemogenetic activation of endogenous oxytocin

first: Nishimura

last: Haruki

first: Yoshimura

last: Mitsuhiro

first: Masafumi

last: Muratani

first: Ueta

last: Yoichi


title: Human centromere repositioning activates transcription and opens chromatin fibre structure [Agilent bTMP-chip]

first: Catherine

last: Naughton

overall_design: Agilent bTMP-chip

first: Nick

last: Gilbert


title: Stem Cell transcriptional response to Microglia-Conditioned Media

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

summary: This paper demonstrates that whereas SOX2+ cells in HDB are highly susceptible to ZKV, SOX2+ primary GBM samples exhibit moderate to high resistance to infection. Expression profiling revealed an innate immune signature due to microglia infiltration in highly resistant GBM samples that was lacking in HDB. This data was generated to proflile the transcriptional response to microglia-secreted factors in stem cells from glioma cell lines and human developing brain. We find that Interferon-stimulated genes are the main targets upregulated in response to microglia conditioned media exposure.

overall_design: GCGR glioma stem cell lines (G322, G334) and primary human developing brain cultures (BRC2251) were exposed to microglia-conditioned media (067,069,070) or  to GSC-conditioned control media (G322, G334, BRC2251) media

first: Harry

last: Bulstrode

first: Ilias

last: Moutsopoulos

first: David

last: Rowitch


title: Human centromere repositioning activates transcription and opens chromatin fibre structure [Agilent 'open' chromatin-chip]

overall_design: Agilent 'open' chromatin-chip


title: Gene expression differences between low IL2/7- and high IL-2-expanded CD8+ T effectors at day 8 of LCMV Armtrong infection

city: Chongqing

first: Haiyang

last: He

address: Gaotanyan street

institute: Arm medical university

summary: Here, we reported a novel subset of CD8+ T effectors with transcriptional similarity to central memory CD8+ T cells (Tcm). Such CD8+ T effectors were characterized with abundant surface expression of both Cxcr3 and CD62L and possessed strong stemness. These CD8+ T effectors mainly developed into Tcm in adoptive transfer and exclusively possessed the capacity to generate Tcm in antigen re-stimulation, indicating they functioned to be Tcm precursors. These Cxcr3+CD62L+ Tcm precursors were determined by high expression of T cell transcription factor 1 (TCF-1), which guaranteed CD62L expression by binding to distal enhancers of Sell (gene symbol for CD62L). Cxcr3+CD62L+ Tcm precursors could be massively obtained by expansion of anti-CD3/28 activated CD8+ T cells with low IL-2 plus IL-7, and these in vitro-expanded Cxcr3+CD62L+ Tcm precursors exhibited strong effective in tumor elimination and were better than conventional high IL-2 expanded-CD8+ T effectors for clearance of tumors.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for low IL2/7 or high IL-2 expanded CD8+ T effecotors.

first: Xinyuan

last: Zhou


title: Haplotype-specific chromatin looping reveals genetic interactions of regulatory regions modulating gene expression in 8p23.1

city: Cincinnati

first: Iouri

last: Chepelev

state: OH

address: 3200 Vine St

institute: US Department of Veterans Affairs Medical Center

summary:
A major goal of genetics research is to elucidate mechanisms explaining how genetic variation contributes to phenotypic variation. The genetic variants identified in genome-wide association studies (GWASs) generally explain only a small proportion of heritability of phenotypic traits, the so-called missing heritability problem. Recent evidence suggests that additional common variants beyond lead GWAS variants contribute to phenotypic variation; however, their mechanistic underpinnings generally remain unexplored.

Herein, we undertake a study of haplotype-specific mechanisms of gene regulation at 8p23.1 in the human genome, a region associated with a number of complex diseases. The FAM167A-BLK locus in this region has been consistently found in the genome-wide association studies (GWASs) of systemic lupus erythematosus (SLE) in all major ancestries. Our haplotype-specific chromatin interaction (Hi-C) experiments, allele-specific enhancer activity measurements, genetic analyses, and epigenome editing experiments revealed that: (1) haplotype-specific long-range chromatin interactions are prevalent in 8p23.1; (2) BLK promoter and cis-regulatory elements cooperatively interact with haplotype-specificity; (3) genetic variants at distal regulatory elements are allele-specific modifiers of the promoter variants at FAM167A-BLK; (4) the BLK promoter interacts with and, as an enhancer-like promoter, regulates FAM167A expression and (5) local allele-specific enhancer activities are influenced by global haplotype structure due to chromatin looping.

Although SLE causal variants at the FAM167A-BLK locus are thought to reside in the BLK promoter region, our results reveal that genetic variants at distal regulatory elements modulate promoter activity, changing BLK and FAM167A gene expression and disease risk. Our results suggest that global haplotype-specific 3-dimensional chromatin looping architecture has a strong influence on local allelic BLK and FAM167A gene expression, providing mechanistic details for how regional variants controlling the BLK promoter may influence disease risk.

overall_design: Comparative analysis of chromatin looping strengths on SLE non-risk (G1) and risk (G2) haplotypes at the FAM167A-BLK locus in two lymphoblastoid cell lines heterozygous for the SLE associated SNP rs922483. We prepared 10 capture Hi-C libraries from 5 independent batches of NA07000 cells and 4 capture Hi-C libraries from 2 independent batches of NA07056 cells (2 biological replicates per cell batch).

first: Mariana Saint-Just

last: Ribeiro

first: Pulak

last: Tripathi

first: Bahram

last: Namjou

first: John

middle: B

last: Harley


title: Gene expression change after inactivation of MEF2D or PU.1 by CRISPR-Cas9

city: PHILADELPHIA

first: Zhendong

last: Cao

state: PA

address: BRB Rm620, 421 Curie Blvd

department: Cancer biology

institute: university of pennsylvania

summary: Transcriptional dysregulation is a prominent feature in leukemia. Here, we systematically surveyed the transcription factor (TF) vulnerabilities in leukemia, and uncovered TF clusters that exhibit context-specific addictions within and between different subtypes of leukemia. We focused on and  validated MEF2D as a requirement exclusively in AML with high IRF8 expression. Transcriptomic and chromatin-binding profiling revealed a key TF circuit composed of MEF2D-IRF8 vital for AML maintenance. AML can acquire dependence on this circuit through various mechanisms, including enhancer activation of the circuit via MLL-rearrangement. IRF8 cooperates with PU.1 to control PU.1/MEIS1 co-regulated transcriptional outputs, meanwhile coordinating with MEF2D to directly regulate genes in a non-redundant manner. Collectively, our study nominates a TF circuit in support of the pathogenesis of AML.

overall_design: mRNA profiles of Cas9 sgRNA-expressing human cell lines

first: Bianca

last: Pingul

first: Hua

last: Huang

first: Junwei

last: Shi


title: Dissection of the MEF2D-IRF8 transcriptional circuit dependency in acute myeloid leukemia


title: The Skeletal Muscle Molecular Clock Regulates Sarcomere Length Through Titin Splicing [2]

city: Nashville

first: Lance

last: Riley

state: TN

address: 9445 MRB4, 2213 Garland Ave

department: Biomedical Engineering

institute: Vanderbilt University

summary: Circadian rhythms have been implicated in regulating skeletal muscle structure and function, but no mechanisms have connected the molecular clock to sarcomeric proteins. We identified an isoform shift in the sarcomeric ruler, titin, and showed that the skeletal muscle molecular clock regulates titin isoform and subsequently sarcomere length through RBM20, an RNA binding protein that controls titin splicing. Restoring RBM20 expression in iMSBmal1-/- TA muscle partially restored titin isoform.

overall_design: Tibialis anterior muscles were collected from inducible, skeletal muscle specific Bmal1 fl/fl mice 8 weeks after treatment with either tamoxifen solution and 4 weeks after AAV treatment. Muscles were pulverized under liquid nitrogen to prevent fiber type bias prior to total RNA colleciton.

middle: A

first: Karyn

last: Esser


title: Human centromere repositioning activates transcription and opens chromatin fibre structure

first: Catherine

last: Naughton

overall_design: Refer to individual Series


title: The Skeletal Muscle Molecular Clock Regulates Sarcomere Length Through Titin Splicing [1]

summary: Circadian rhythms have been implicated in regulating skeletal muscle structure and function, but no mechanisms have connected the molecular clock to sarcomeric proteins. We identified an isoform shift in the sarcomeric ruler, titin, and showed that the skeletal muscle molecular clock regulates titin isoform and subsequently sarcomere length through RBM20, an RNA binding protein that controls titin splicing.

overall_design: Tibialis anterior muscles were collected from inducible, skeletal muscle specific Bmal1 fl/fl mice 5 weeks after reatment with either vehicle or tamoxifen solution. Muscles were pulverized under liquid nitrogen to prevent fiber type bias prior to total RNA colleciton.


title: Microglia regulate Zika virus infection in human developing brain and glioma; Stem Cell transcriptional response to Microglia-Conditioned Media

first: Irina

last: Mohorianu


title: mRNA profiling in primary AML cells

summary: Transcriptional dysregulation is a prominent feature in leukemia. Here, we systematically surveyed the transcription factor (TF) vulnerabilities in leukemia, and uncovered TF clusters that exhibit context-specific addictions within and between different subtypes of leukemia. We focused on and validated MEF2D as a requirement exclusively in AML with high IRF8 expression. Transcriptomic and chromatin-binding profiling revealed a key TF circuit composed of MEF2D-IRF8 vital for AML maintenance. AML can acquire dependence on this circuit through various mechanisms, including enhancer activation of the circuit via MLL-rearrangement. IRF8 cooperates with PU.1 to control PU.1/MEIS1 co-regulated transcriptional outputs, meanwhile coordinating with MEF2D to directly regulate genes in a non-redundant manner. Collectively, our study nominates a TF circuit in support of the pathogenesis of AML.

overall_design: mRNA profiling in primary AML cells


title: Gut biopsies from patients with Crohn's Disease and Ulcerative Colitis and healthy controls

city: Copenhagen

first: Lasse

last: Folkersen

address: Artellerivej

department: Bioinformatics

country: Denmark

institute: National Genome Center

summary: For IBD, >163 susceptibility loci have been revealed by Genome-wide association studies (GWAS). Still only 13.6% of the heritability in CD and 7.5% in UC can be explained by the loci that have been revealed (23128233). In an endeavor to pinpoint additional IBD genes and pathways involved in the disease, we have made a large scale transcriptome analysis of human pince 380 biopsies from 109 donors. We identified novel genes and protein-protein interaction networks that are strongly associated with disease and gives new insight to the pathology of both CD and UC and the resulting inflammation

overall_design: Cross-sectional sample collection from patient

first: Klaus

middle: S

last: Frederiksen

first: Kirstine

last: Belling

first: Jan

last: Gorodkin

first: Flemming

last: Pociot

first: Mogens

last: Vilien

first: Claus

last: Bang-Berthelsen


title: Dissection of the MEF2D-IRF8 transcriptional circuit dependency in acute myeloid leukemia [CUT&RUN]

overall_design: Protein binding profiles on chromatin in human AML cells


title: RNA sequencing/Gene expression studies of N-glycosylation inhibitors in diffuse lymphoma

status: Public on Sep 06 2022

city: Bethesda

first: David

state: Maryland

address: 9000 Rockville Pike

institute: National Cancer Institute

summary: We determined that N-linked glycosylation p[lays a role in oncogenic signaling in diffuse lymphoma.  We sought to obtain gene expression data and gene signatures in diffuse lymphoma cells by examining changes in gene expression by RNA seq following treatment with the N-linked glycosylation inhibitor NGI-1 and as a comparator the BTK inhibitor acalabrutinib and the PI3K inhibitor copanlisib

overall_design: RNA sequencing to determine gene expression in HBL1 and TMD8 diffuse cells treated in duplicates with vehicle (DMSO), 5 µM NGI-1, 50 nM acalabrutinib or 20 nM copanlisib for 3, 6 and 24 hours.

first: Sebastian

last: Scheich

first: Louis

middle: M

last: Staudt


title: Analysis of Aqp4+ Edem1+/- astrocytes by scPACS

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

summary: Samples were analyzed by scPACS from WT or EAE mice

overall_design: Samples were sorted on Aqp4 expression, then analyzed for Edem1 in WT or EAE

first: Michael

last: Wheeler

first: Iain

last: Clark

first: Francisco

last: Quintana


title: Temporal transcriptional profiles of colonic tissue during DSS-induce colitis

city: JiNan

first: Shiyang

address: Wenhua West Road

institute: Shandong University

summary: Inflammation dramatically alters the gut microenvironment. To investigate the transcriptome changes the temporal profile of multiple signaling pathways throughout the progression of colitis, we collected the colonic tissue at a series of time points during DSS colitis for bulk RNA sequencing.

overall_design: 7-week-old SPF mice received clean water or 3% DSS for 6 days, and the mid-colon tissues were harvested for bulk RNA sequencing at day 0, day 2, day 4 and day 6.

first: Mengqi

last: Zheng

first: Yunjiao

last: Zhai

first: Yanbo

last: Yu


title: Arabidopsis mRNA decay landscape shaped by XRN 5′-3′ exoribonucleases

city: Nankang

first: Ho-Ming

last: Chen

state: Taipei

address: No. 128, Sec. 2, Academia Road

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

summary: XRN 5′-3′ exoribonucleases play crucial roles in the control of RNA processing, quality, and quantity in eukaryotes. Although genome-wide profiling of RNA decay fragments is now feasible, how XRNs shape the plant mRNA degradome remains elusive. Here, we profiled and analyzed the RNA degradomes of the Arabidopsis wild type and mutants with defects in XRN activity. Deficiency of nuclear XRN3 or cytoplasmic XRN4 but not nuclear XRN2 activity largely altered Arabidopsis mRNA decay profiles. In addition to the primary XRN4 substrates derived from decapping and microRNA-directed slicing, terminating ribosome- and exon junction complex-protected fragments produced from XRN4-mediated cytoplasmic decay also represent the most abundant decay intermediates of Arabidopsis mRNAs. Short excised linear introns and cleaved pre-mRNA fragments downstream of polyadenylation sites were polyadenylated and stabilized in the xrn3 mutant, demonstrating the function of XRN3 in the removal of cleavage remnants from pre-mRNA processing. Further analysis of stabilized XRN3 substrates confirmed that polyadenylation cleavage frequently occurs after an adenosine. An increase in decay intermediates with 5′ ends upstream of a consensus motif in the xrn4 mutant suggests an endonucleolytic cleavage mechanism targeting the 3′ untranslated region of many Arabidopsis mRNAs. However, analysis of decay fragments stabilized in the xrn4 mutant indicated that, except for microRNA-directed slicing, endonucleolytic cleavage events in the coding sequence might rarely result in major decay intermediates. Together, the results of this study reveal major substrates and products of nuclear and cytoplasmic XRNs along Arabidopsis transcripts and provide a basis for precise interpretation of RNA degradome data.

overall_design: Profiling 5' ends of RNA degradation intermediate in Arabidopsis thaliana rosette leaves by parallel analysis of RNA ends (PARE)

first: Wan-Yin

last: Han

first: Bo-Han

last: Hou

first: Wen-Chi

last: Lee

first: Tze-Ching

last: Chan

first: Tzu-Hsiang

last: Lin


title: Dissection of the MEF2D-IRF8 transcriptional circuit dependency in acute myeloid leukemia [ChIP-seq]

first: Zhendong

last: Cao

overall_design: PU.1 binding profiles upon IRF8 targeted degradation in human AML cells

first: Bianca

last: Pingul

first: Hua

last: Huang

first: Junwei

last: Shi


title: Cell atlas of mouse colon tissue from the initial stage of colitis

last: Li

summary: Inflammation dramatically alters the gut microenvironment. To investigate the composition and transcriptome changes of various intestinal cell populations during the initial phase of inflammation, and the underlying cellular interactions, we delineated a single-cell atlas of the mouse colon treated with DSS on the day 2 of colitis.

overall_design: 7-week-old SPF mice received clean water or 3% DSS for two days, and the mid-colon tissues were harvested for single-cell RNA sequencing.


title: Targeting KDM4 for treating PAX3-FOXO1-driven alveolar rhabdomyosarcoma [RNAseq_LHCN_hg19]

city: Memphis

first: Hongjian

last: Jin

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

summary: Chimeric transcription factors drive lineage-specific oncogenesis but are notoriously difficult to target. Alveolar rhabdomyosarcoma (RMS) is an aggressive childhood soft tissue sarcoma transformed by the pathognomonic PAX3–FOXO1 fusion protein, which governs a core regulatory circuitry transcription factor (CRC TF) network. Here we show that the histone lysine demethylase KDM4B is a therapeutic vulnerability for PAX3–FOXO1+ RMS. Genetic and pharmacologic inhibition of KDM4B significantly delays tumor growth by disrupting the expression of CRC TFs caused by epigenetic alterations of PAX3–FOXO1-governed super enhancers.  Combining KDM4B inhibition with cytotoxic chemotherapy leads to significant tumor regression in preclinical PAX3–FOXO1+ RMS models.  In summary, we have identified a targetable mechanism required for maintenance of PAX3-FOXO1-related CRC TF network, which may translate to a novel therapeutic approach for fusion-positive RMS.

overall_design: Examination of gene profile changes by comparing LHCN-M2 cells with and without PAX3-FOXO1 overexpression  by using RNA-seq method

first: Ahmed

last: Abuzaid

first: Jie

last: Fang

first: Yiping

last: Fan

first: Jun

last: Yang


title: Nintedanib induces senolytic effect via STAT3 inhibition

city: Daegu

first: Young-Sam

address: 333 Technojungang-Daero, Hyeonpung-Eup, Dalsung-Gun

department: Department of New Biology

country: South Korea

institute: DGIST

summary: Selective removal of senescent cells, or the concept of senolytic therapy, has been proposed to be a potent strategy for overcoming age-related diseases and even reversing aging. We found that nintedanib, a tyrosine kinase inhibitor, selectively induced cell death in primary human diploid fibroblasts undergoing replicative senescence. Similar to ABT263, a well-known senolytic agent, nintedanib triggered intrinsic apoptosis in senescent cells. Additionally, at the concentration producing the senolytic effect, nintedanib arrested the cell cycle of nonsenescent cells in the G1 phase without cytotoxicity. Interestingly, compared with ABT263, nintedanib showed a different mode of activating caspase-9 in the intrinsic apoptotic pathway, in that nintedanib did not suppress the levels of Bcl-2 family proteins in senescent cells. In more detail, nintedanib suppressed the activation of the JAK2/STAT3 pathway, which caused drug-induced cell death in senescent cells. STAT3 knockdown in senescent cells also induced caspase activation. Moreover, nintedanib reduced the number of senescent cells stained based on senescence-associated β-galactosidase activity and airway resistance in a mouse model of bleomycin-induced lung fibrosis. Overall, we identified that nintedanib could be used as a new senolytic agent and that inhibiting STAT3 could be a potential approach for inducing selective cell death in senescent cells. Our findings will pave the way for expanding senolytic toolkits in response to various aging statuses and age-related diseases.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human diploid fibroblasts treated by nintedanib as a senolytic compound.

first: Hyun-Ji

last: Cho


title: Genome-wide profiling of H3K4me3 and H3K27me3 in rice male meiocytes using low cell number ChIP-seq

city: Xuzhou

first: Cen

middle: Ai

last: Zhang

state: Jiangsu

address: No.2 Kunpeng

institute: Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District

summary: Meiotic cell-specific chromatin profiling at the gene level is still not fully elucidated, which is largely due to techniques challenges for collection of enough synchronized cells of interest for conventional chromatin immunoprecipitation. This leaves the open question in a state of incomprehension, which is about how chromatin reprogramming links to transcriptional dynamics at individual well-defined meiotic cell-type or stage. To address this, we developed a low cell number ChIP-seq (LCN ChIP-seq) approach by using 8-10K cells, which was for the first time applied for profiling of an active mark H3K4me3 and a repressive mark H3K27me3 genome-wide for male meiocytes at prophase I stage.

overall_design: ChIP-seq

first: Aicen

first: Yining

first: Yi

last: Shen

first: Wenli

first: Zhukuan

last: Cheng


title: Transcriptome analysis implicates MYC as a driver of early onset colorectal cancer

city: Hershey

first: Gregory

last: Yochum

address: 700 HMC Crescent Road

institute: Penn State College of Medicine

summary: Despite a global decrease in colorectal cancer (CRC) incidence, the prevalence of early onset colorectal cancer (EOCRC), or those occurring in individuals before the age of 50, has been steadily increasing over the past several decades. When compared to later onset colorectal cancers (LOCRCs) in individuals over 50, our understanding of the genetic and molecular underpinnings of EOCRCs is limited. Here, we conducted transcriptomic analysis of patient-matched normal colonic segments and tumors to identify gene expression programs involved in carcinogenesis. Amongst differentially expressed genes, we found increased expression of the c-MYC (MYC) proto-oncogene and its downstream targets in tumor samples. We identify tumors with high and low differential MYC expression, and patients with high-MYC tumors were older and overweight or obese. We also detect elevated expression of the PVT1 long-non-coding RNA (lncRNA) in most tumors and find gains in copy number for both MYC and PVT1 gene loci in 35% of tumors evaluated. Our transcriptome analysis indicates that EOCRC can be sub-classified into groups based on differential MYC expression and suggests that MYC is a critical driver of most CRCs that develop in younger patients.

overall_design: Gene expression profiles of 21 surgically resected tumors and patient-matched adjacent colonic segments from early onset colorectal cancer patients were generated by deep sequencing.

first: Olivia

last: Marx

first: Walter

last: Koltun


title: Targeting KDM4 for treating PAX3-FOXO1-driven alveolar rhabdomyosarcoma [RNA-Seq]

overall_design: Examination of gene expression profile change with KDM4B mutation by RNA-seq

first: Abuzaid

last: Ahmed


title: Targeting KDM4 for treating PAX3-FOXO1-driven alveolar rhabdomyosarcoma [CUT&Tag]

first: Hongjian

overall_design: Examination of chromatin changes with various treatments by CUT&TAG


title: Targeting KDM4 for treating PAX3-FOXO1-driven alveolar rhabdomyosarcoma [CUT&RUN, 2]

overall_design: Examination of chromatin changes with QC6352 treatment by CUT&RUN

first: Maxham

last: Lily

first: Shao

last: Ying


title: Transcripts identified by microarray analysis that were deregulated in E14.5 Tbx18(cre/+);FGFR1(fl/fl);FGFR2(fl/fl) (Fgfr1/2cDKO) ureters

city: Hannover

first: Mark-Oliver

last: Trowe

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

institute: Medizinische Hochschule Hannover

summary: Evaluation of the transcriptional changes in E14.5 ureters upon loss of Fgfr1 and Fgfr2 in the ureteric mesenchyme.

overall_design: Total RNA from dissected ureters of E14.5 Fgfr1/2cDKO and control embryos was analyzed by microarray analysis.

first: Andreas

last: Kispert


first: Douglas

last: Green

state: United States

address: 262 Danny Thomas Pl

department: Immunology

summary: We performed scRNAseq of PC9 parental (PT) and persister cells (PS) at d1, d3 and d7 after being generated by treatment with BH3-mimetics. Trajectory analysis and differential expression along the pseudotime revealed the upregulation of the integrated stress response (ISR) and EMT signatures at early pseudotime, while gene expression profiles for cell cycle progression were upregulated at late pseudotime, characteristic for late PS and PT.

overall_design: scRNAseq of PC9 parental and persister cells at d1, d3 and d7 generated by treatment with BH3-mimetics

first: Halime

last: Kalkavan

first: Mark

middle: J

last: Chen

first: Jeremy

middle: C

last: Crawford


title: Targeting KDM4 for treating PAX3-FOXO1-driven alveolar rhabdomyosarcoma [ChIP-Seq, 2]

last: Jin

overall_design: Examination of chromatin changes with various treatments by Chip-seq

first: Jie

last: Fang

first: Jun

last: Yang


title: The iron starvation response of the Staphylococcus aureus hemB small colony variant (SCV)

city: London

first: David

last: Heinrichs

state: ON

address: Microbiology and Immunology, 3014 Dental Sciences Building, 1151 Richmond Street

country: Canada

institute: University of Western Ontario

summary: Respiration deficient S. aureus small colony variants (SCVs) frequently cause persistent infections, which necessitates they acquire iron, yet how SCVs obtain iron remains unknown. To address this, we created a stable hemB mutant in S. aureus USA300 strain LAC. The hemB SCV utilized exogenously supplied heme but was attenuated for growth under conditions of iron starvation. RNA-seq showed that both WT S. aureus and the hemB mutant sense and respond to iron starvation.

sample_organism: Staphylococcus aureus subsp. aureus USA300

overall_design: A total of 15 samples were analyzed. Samples were acquired from 2 independent experiments, each consisting of 1-3 biological replicates per strain. All samples were grown in iron restricted medium. 4 samples were WT S. aureus treated with ferric ammonium sulfate, 3 samples were WT S. aureus untreated, 3 samples were hemB S. aureus treated with ferric ammonium sulfate, 5 samples were hemB S. aureus untreated.

first: Izabela

middle: Z

last: Batko

first: Veronica

last: Guariglia-Oropeza

middle: E


title: Gene Therapy with the N-terminus of Junctophilin-2 Improves Hypertrophy and Heart Failure in Mice

city: Iowa City

first: Long-Sheng

last: Song

state: IA

address: 285 Newton Rd

department: Internal Medicine

institute: University of Iowa

summary: Our previous work found a variety of cardiac stresses initiate site-specific cleavage of junctophilin-2 (JP2), an essential component of the E-C coupling apparatus, producing a 75-kDa N-terminal fragment (JP2NT) which unexpectedly translocates into cardiomyocyte nuclei and functions as a transcriptional repressor. We also determined that transgenic overexpression of JP2NT in cardiomyocytes attenuates pressure-overload induced hypertrophy and heart failure by blunting the induction of maladaptive transcripts. To test whether JP2NT could be utilized by gene therapy approaches for treating heart failure, we developed cardiotropic adeno-associated GFP and JP2NT expressing viruses for testing in a preclinical model of heart failure. Our results show that the transcriptional and pathological changes from pressure overload can be reduced through viral expression of JP2NT once hypertrophy and heart failure has already begun.

overall_design: Sham or trans-aortic constriction (TAC) surgery was performed on 9–10-week-old mice. After two weeks, echocardiography was performed to identify TAC operated mice with moderate cardiac dysfunction (ejection fractions 40-60%, n=30) and sham operated mice with normal function (n=10). Mice were further divided into two groups each for receiving AAV2/9 virus expressing either GFP or JP2NT (tail vein injection, 1x10E12 viral genomes, 100 ul). Heart tissue was collected 8 weeks after surgery for RNA analysis.

first: Hall

last: Duane

first: Song

last: Long-Sheng


title: Transcripts identified by microarray analysis that were deregulated in E15.5+6d Tbx18(cre/+);FGFR1(fl/fl);FGFR2(fl/fl) (Fgfr1/2cDKO) ureter cultures

summary: Evaluation of the transcriptional changes in E15.5+6d ureter cultures upon loss of Fgfr1 and Fgfr2 in the ureteric mesenchyme.

overall_design: E15.5 ureters of Fgfr1/2cDKO and control embryos were dissected and cultured for 6 days.Total RNA from these ureters was analyzed by microarray analysis.


title: Targeting KDM4B to disrupt the core regulatory transcription network governed by PAX3-FOXO1 in high-risk rhabdomyosarcoma [ATAC-seq]

first: Hongjian

summary: Chimeric transcription factors drive lineage-specific oncogenesis but are notoriously difficult to target. Alveolar rhabdomyosarcoma is an aggressive childhood soft tissue sarcoma, mainly driven by the pathognomonic PAX3–FOXO1, which governs a core regulatory circuitry transcription factor (CRC TF) network. Here we show that the histone lysine demethylase KDM4B is a therapeutic vulnerability to the PAX3–FOXO1+ RMS. Genetic and pharmacologic inhibition of KDM4B significantly delays tumor growth, disrupting the expression of CRC TFs in accordance with the alterations of PAX3–FOXO1-determining super enhancers.  Combination of KDM4B inhibitor with cytotoxic chemotherapy leads to significant tumor regression in preclinical PAX3–FOXO1+ RMS models.  In summary, we have identified a targetable epigenetic modifier required for the functions of PAX3–FOXO1, which may translate to a novel therapeutic approach for the high-risk RMS.

overall_design: Examination of chromatin accessibility, histone modification  post QC6352 treatments, KDM4B shRNA knockdown and overexpression Pax3-FOXO1 in RH30 or LHCN.

first: Fang

last: Jie

first: Singh

last: Shivendra

first: Jin

last: Hongjian

first: Yang

last: Jun


title: Lung eosinophil RNA-Seq for P2ry14-deficient and wild-type mice

city: Research Triangle Park

first: Donald

middle: Nelson

last: Cook

state: NC

address: 111 T.W. Alexander Drive

department: IIDL

institute: NIEHS

summary: Transcriptome analysis of P2ry14-sufficient and P2ry14-deficient mouse lung eosinophils in protease model of asthma.

overall_design: Lung eosinophils were purified after OVA challenge in Aspergillus protease-mediated model of asthma

first: Tadeusz

middle: P

last: Karcz

first: Keiko

last: Nakano

first: Sara

last: Grimm


title: DMSO effect on HepaRG differentiation

city: Vandœuvre-lès-Nancy

first: Hélène

last: Dubois-Pot-Schneider

address: Site CRAN/Faculté de Médecine - Bâtiment D, 1er étage 9 avenue de la Forêt de Haye, BP 184

department: CRAN

country: France

institute: Université de Lorraine - UMR7039 CRAN

summary: Gene expression profile analysis allowed to identify a panel of genes characteristic of HepaRG differentiation and DMSO effect on the differentiation process.

overall_design: We performed transcriptomic analysis at various time-points during this process; day 4, day 15, day 30 - DMSO, day 30 + DMSO and D34 +/- DMSO.  Four independent experiments were performed

first: Anne

last: Corlu


title: Targeting KDM4B to disrupt the core regulatory transcription network governed by PAX3-FOXO1 in high-risk rhabdomyosarcoma [CUT&RUN]

last: Jin

overall_design: Examination of chromatin accessibility, histone modification post QC6352 treatment in RH30.


title: Whole-genome bisulfite sequencing anlaysis of in vitro fertilized mouse hybrid blastocysts

city: Fukuoka

first: Wan Kin

last: Au Yeung

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Molecular and Structural Biology

institute: Kyushu University

type: Methylation profiling by high throughput sequencing

summary: We report a deeply-sequenced profile of mouse blastocysts which is able for allele-specific analysis.

overall_design: Whole-genome bisulfite sequencing anlaysis was performed on in vitro fertilized mouse blastocysts (Female strain: C57BL/6; male strain: JF1) by post bisilfite adaptor tagging method.

first: Hiroyuki

last: Sasaki


title: The Skeletal Muscle Molecular Clock Regulates Sarcomere Length Through Titin Splicing

first: Lance

last: Riley

address: 9445 MRB4, 2213 Garland Ave

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

overall_design: Refer to individual Series


title: Ribosome profiling of ZPR1-depleted S.cerevisiae cells

status: Public on Sep 05 2022

city: Cambridge

first: Vladimir

last: Denic

state: MA

address: 52 Oxford St

institute: Harvard University

summary: The aim of this study was to gain insight into the ribosome occupancy on different genes and codons in Zpr1-depleted cells vs. WT Zpr1 cells

overall_design: S. cerevisiae ribosome profiling in prGAL1-mAID-ZPR1 cells depleted of Zpr1 for 8 hours vs. ZPR1 wild type cells

first: Ibrahim

last: Sabbarini

first: Dvir

last: Reif

first: Alexander

last: McQuown

first: Anjali

last: Nelliat

first: Jeffrey

last: Prince

first: Britnie

last: Membreno

first: Colin

last: Wu

first: Andrew

middle: W

last: Murray