title: The effects of WTAP on m6A mRNA modification in the heart [meRIP-seq]

city: Harbin

first: Zheng

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

summary: Through  m6A mRNA-profiling, we aim to characterize the  m6A mRNA changes in the hearts of Wtapflox/flox and Wtap-CKO mice.

overall_design:
To map the mRNA m6A modification caused by WTAP in the hearts, MeRIP-seq was performed in the hearts of Wtapflox/flox and Wtap-CKO mice.
Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from the hearts of Wtapflox/flox and Wtap-CKO mice at 4 days old. A total of 300 μg RNAs were pooled from seven Wtapflox/flox mice and eight Wtap-CKO mice, respectively. Fragmented RNA (~100 nt) was incubated for 2 hr at 4℃ with anti-m6A polyclonal antibody (Merk Millipore) in the immunoprecipitation experiment. Then, immunoprecipitated RNAs or Input was used for library construction with Ovation SoLo RNA-Seq System Core Kit (NuGEN). The library preparations were sequenced on an Illumina Novaseq platform with a paired-end read length of 150 bp according to the standard protocols. After mapping reads to the reference genome, exomePeak R package (version 2.16.0) was used for the m6A peak identification in each anti-m6A immunoprecipitation group with the corresponding input samples serving as a control, and q-value threshold of enrichment of 0.05 was used for all data sets. The m6A-enriched motifs of each group were identified by HOMER (version 4.9.1).
The heart mRNA m6A profiles in Wtapflox/flox and Wtap-CKO mice were characterized.

first: Xinzhi

last: Li

first: Lei

last: Shi


title: The effects of WTAP on heart development [WTAPCKO]

status: Public on Jan 14 2024

last: Chen

country: China

type: Expression profiling by high throughput sequencing

summary: The goal of this study is to investigate how WTAP regulates heart development.

overall_design:
mRNA profiles in the hearts of Wtapflox/flox and Wtap-CKO mice were generated by deep sequencing using Illumina Novaseq 6000 platform (n=3 for each group).
Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from the hearts of Wtapflox/flox and Wtap-CKO mice at 4 days old. Three independent biological replicates for each group were used for RNA-seq. RNA-seq was performed by deep sequencing using an Illumina Novaseq 6000 platform. Paired-end clean reads were aligned to the mouse reference genome(GRCm39) with Hisat2 v2.0.5, and the aligned reads were used to quantify mRNA expression by using featureCounts v1.5.0-p3.
Our study represents the first detailed analysis of heart transcriptomes from Wtapflox/flox and Wtap-CKO mice, generated by RNA-seq technology. The RNA-seq analysis showed that 2348 genes were downregulated and 2764 genes were upregulated in the hearts of Wtap-CKO mice.

first: Zhiguo

last: Zhang


title: Myocardial GR epigenomic changes with single ZT0 prednisone pulse

city: Cincinnati

first: Mattia

last: Quattrocelli

state: OH

address: 240 Sabin Way

country: USA

institute: Cincinnati Children's Hospital Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: this dataset encompasses the cardiac GR epigenomic changes elicited in 4-month-old mice with a single ZT0 prednisone (1mg/kg i.p.) injection

overall_design: 4 months-old mice (WT, C57BL/6J background) were injected with either vehicle, or one i.p. injection of 1mg/kg prednisone (#P6254; Sigma-Aldrich; St. Louis, MO) at ZT0. The injectable solution was diluted from a 5mg/ml stock in DMSO (#D2650; Sigma-Aldrich; St. Louis, MO) in 50ml volume. Injections were conducted at the beginning of the light-phase (ZT0; lights-on). Hearts were collected 4 hours after last injection.

first: Hima

middle: B

last: Durumutla

first: Fadoua

last: El Abdellaoui Soussi


title: Comparative Multi-omic Mapping of Human Pancreatic Islet Endoplasmic Reticulum and Cytokine Stress Responses Provide Insights into Type 2 Diabetes Genetics [scRNA-seq]

status: Public on Jan 15 2024

city: Farmington

first: Eishani

middle: Kumar

last: Sokolowski

state: CT

address: 263 Farmington Avenue

institute: University of Connecticut Health Center

summary: Endoplasmic reticulum (ER) and inflammatory stress responses are two pathophysiologic factors contributing to islet dysfunction and failure in Type 2 Diabetes (T2D). However, how human islet cells respond to these stressors and whether T2D-associated genetic variants modulate these responses is unknown. To fill this knowledge gap, we profiled transcriptional (RNA-seq) and epigenetic (ATAC-seq) remodeling in human islets exposed to ex vivo ER (thapsigargin) or inflammatory (IL-1β+IFN-γ) stress. 5,427 genes (~32%) were associated with stress responses; most were stressor-specific, including upregulation of genes mediating unfolded protein response (e.g. DDIT3, ATF4) and NFKB signaling (e.g. NFKB1, NFKBIA) in ER stress and cytokine-induced inflammation respectively. Islet single-cell RNA-seq profiling revealed strong but heterogeneous beta cell ER stress responses, including a distinct beta cell subset that highly expressed apoptotic genes. Epigenetic profiling uncovered 14,968 stress-responsive cis-regulatory elements (CREs; ~14%), the majority of which were stressor-specific, and revealed increased accessibility at binding sites of transcription factors that were induced upon stress (e.g. ATF4 for ER stress, IRF8 for cytokine-induced inflammation). Eighty-six stress-responsive CREs overlapped known T2D-associated variants, including 20 residing within CREs that were more accessible upon ER stress. Among these, we linked the rs6917676 T2D risk allele (T) to increased in vivo accessibility of an islet ER stress-responsive CRE and allele-specific beta cell nuclear factor binding in vitro. We showed that MAP3K5, the only ER stress-responsive gene in this locus, promotes beta cell apoptosis. Consistent with its pro-apoptotic and putative diabetogenic roles, MAP3K5 expression inversely correlated with beta cell abundance in human islets and was induced in beta cells from T2D donors. Together, this study provides new genome-wide insights into human islet stress responses and putative mechanisms of T2D genetic variants.

overall_design: To uncover the transcriptional responses of islets to stress, we procured primary human pancreatic islets from non-diabetic donors and exposed them to a 24-hour treatment with either thapsigargin vs. DMSO (solvent control) or pro-inflammatory cytokines (IL-1β+IFN-γ) vs. untreated (control), respectively.

middle: K

first: Romy

last: Kursawe

first: Vijay

last: Selvam

first: Redwan

middle: M

last: Bhuiyan

first: Asa

last: Thibodeau

first: Chi

last: Zhao

first: Cassandra

middle: N

last: Spracklen

first: Duygu

last: Ucar

first: Michael

middle: L

last: Stitzel


title: Liver-restricted Type I Interferon Signature Precedes Liver Damage in Chronic Hepatitis B Patients Stopping Antiviral Therapy

city: Toronto

first: Adam

last: Gehring

state: ON

address: 101 College St

country: Canada

institute: UHN

summary: Immune-mediated liver damage is the driver of disease progression in patients with chronic Hepatitis B virus (HBV) infection. Liver damage is an antigen-independent process caused by bystander activation of CD8 T cells and NK cells. How bystander lymphocyte activation is initiated in chronic hepatitis B (CHB) patients remains unclear. Periods of liver damage, called hepatic flares, occur unpredictably, making early events difficult to capture. To address this obstacle, we longitudinally sampled the liver of CHB patients stopping antiviral therapy and analyzed immune composition and activation using flow cytometry and single-cell RNA sequencing (scRNA-seq). At 4 weeks after stopping therapy, HBV replication rebounded but no liver damage was detectable. There were no changes in cell frequencies at viral rebound. ScRNA-seq revealed upregulation of IFN stimulated genes (ISGs) and pro-inflammatory cytokine MIF at viral rebound in patients that go on to develop hepatic flares 6 – 18 w after stopping therapy. The type I IFN signature was only detectable within the liver and neither IFN-α/β or ISG induction could be detected in the peripheral blood. In vitro experiments confirmed the type I IFN-dependent ISG profile whereas MIF was induced primarily by IL-12. MIF exposure further amplified inflammatory cytokine production by myeloid cells. Our data show that innate immune activation is detectable in the liver before clinically significant liver damage is evident. The combination of type I IFN and enhanced cytokine production upon MIF exposure represent the earliest immunological triggers of lymphocyte bystander activation observed in hepatic flares associated with chronic HBV infection.

overall_design:
To investigate for early immune signatures preceding liver damage among CHB patients undergoing nucleotide analogue cessation. Liver FNAs were collected for scRNA-seq and flow cytmetry analysis at two timepoints; upon stopping  therapy and 4 weeks after stopping therapy. Upon identifying ISG and MIF being upregulated as key drivers of liver inflammation, in vitro experiments were executed to identify the soluble factors and immune pathways that trigger the inflammatory gene upregulations.
**Raw data for human samples not available due to patient privacy concerns***

first: Conan

last: Chua

first: Deeqa

last: Mahamed

first: Shirin

last: Nkongolo

first: Juan

middle: D

last: Vasquez

first: Aman

last: Mehrotra

first: David

last: Wong

first: Raymond

middle: T

last: Chung

first: Jordan

middle: J

last: Feld

first: Harry

last: Janssen


title: Assay for transposase-accessible chromatin-sequencing (ATAC-seq) of heart samples from  Wtapflox/flox and Wtap-CKO mice, respectively.

first: Zheng

last: Chen

summary: The goal of this study is to determine whether cardiac deletion of Wtap affects chromatin accessibility.

overall_design:
To assess chromatin accessibility in the heart casued by cardiac deletion of Wtap, ATAC-seq analysis of heart samples in Wtapflox/flox and cardiomyocyte-specific Wtap knockout (Wtap-CKO) mice was performed.
Each heart sample was pooled from six Wtap-CKO and seven Wtapflox/flox mice, respectively. Nuclei was extracted from heart samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min. Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufactuer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina NovaSeq 6000 platform and 150 bp paired-end reads were generated. ATAC-seq analysis was performed using a standard protocol.
The chromatin accessibility in the hearts of Wtapflox/flox and Wtap-CKO mice were characterized.

first: Xinzhi

last: Li

first: Lei

last: Shi

first: Zhiguo

last: Zhang


title: Effect of roots subjected to 300 mg/l PS-COOH treatments and to control conditions for RNA-Seq in cotton

city: Anyang

first: Junjie

last: Zhao

address: No.38 of Huanghe Street

institute: Institute of Cotton Research

summary: Roots from 10 independent plants subjected to 300 mg/l PS-COOH treatments and to control conditions were pooled separately to form single biological replicates for RNA-seq analysis. Transcriptomics analyses showed that antioxidant activity-related genes were significantly upregulated after PS-COOH treatments, indicating that oxidative stress was induced in cotton.

overall_design: Roots cultured on 0 and 300 mg/l PS-COOHs concentrations for 9 days are used to extract RNA.The total RNA was extracted using TRIzol reagent (Invitrogen, California, USA). Then, the RNAs’ purity and quantity were checked using an RNA Nano 6000 Assay Kit for the Bioanalyzer 2100 system (Agilent Technologies, California, USA). Afterwards, approximately 10 µg of total RNA was used for RNA-seq library  construction.

first: Xiongfeng

last: Ma

first: Daigang

last: Yang

first: Wei


title: Dynamics of chromatin and transcriptome in the HSPCs at different hematopoietic developmental stages

city: shanghai

first: deng

middle: li

last: Hong

address: 280 chongqing south road

institute: shanghai jiao tong univerisity

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

overall_design: Refer to individual Series


title: Heart transcriptional changes with prednisone with inducible cardiomyocyte-specific KLF15 ablation

status: Public on Jan 13 2024

first: Mattia

last: Quattrocelli

summary: this dataset encompasses the cardiac transcriptomic changes elicited in myocardial tissues of 4months-old mice at 4 hours after a single ZT0 prednisone (1mg/kg i.p.) injection, or vehicle, in cardiomyocyte-KLF15-WT versus cardiomyocyte-KLF15-KO conditions (inducible, tamoxifen-driven ablation right prior to drug pulse).

overall_design: Mice were obtained and interbred from the Jackson Laboratories (Bar Harbor, ME; JAX strain number listed) or from collaborators: Myh6-MerCreMer mice #005657, Klf15-flox mice #029787 (provided by Dr. Jain, Brown U). Gene ablation was induced with tamoxifen at ~8 weeks of age using a combination of i.p. (20 mg/kg/day for 5 days; Sigma #T5648) and chow-mediated (40mg/kg for 3 weeks; Harlan #TD.130,860) administration. Analyses were performed after 4 weeks of tamoxifen washout, i.e. at ~16 weeks of age. Drug treatment consisted of single intraperitoneal injection of prednisone (1 mg/kg; #P6254, Sigma-Aldrich, St. Louis, MO). The injectable solution was diluted from a stock (5 mg/ml) in dimethyl sulfoxide (DMSO; #D2650, Sigma-Aldrich, St. Louis, MO) in a 50-µl volume. Injections were conducted at the beginning of the light phase (ZT0; lights on) in mice kept on 12h/12h light/dark cycles. Tissues were harvested at 4 hours post-injection.

first: Hima

last: Durumutla

first: Fadoua

last: El Abdellaouoi Soussi

first: Mukesh

last: Jain


title: Heart transcriptional changes with prednisone with inducible cardiomyocyte-specific GR ablation

summary: this dataset encompasses the cardiac transcriptomic changes elicited in myocardial tissues of 4months-old male mice at 4 hours after a single ZT0 prednisone (1mg/kg i.p.) injection, or vehicle, in cardiomyocyte-GR-WT versus cardiomyocyte-GR-KO conditions (inducible, tamoxifen-driven ablation right prior to drug pulse).

overall_design: Mice were obtained and interbred from the Jackson Laboratories (Bar Harbor, ME; JAX strain number listed) or from collaborators: Myh6-MerCreMer mice #005657, GR-flox mice #021021. Gene ablation was induced with tamoxifen at ~8 weeks of age using a combination of i.p. (20 mg/kg/day for 5 days; Sigma #T5648) and chow-mediated (40mg/kg for 3 weeks; Harlan #TD.130,860) administration. Analyses were performed after 4 weeks of tamoxifen washout, i.e. at ~16 weeks of age. Drug treatment consisted of single intraperitoneal injection of prednisone (1 mg/kg; #P6254, Sigma-Aldrich, St. Louis, MO). The injectable solution was diluted from a stock (5 mg/ml) in dimethyl sulfoxide (DMSO; #D2650, Sigma-Aldrich, St. Louis, MO) in a 50-µl volume. Injections were conducted at the beginning of the light phase (ZT0; lights on) in mice kept on 12h/12h light/dark cycles. Tissues were harvested at 4 hours post-injection.


title: CDK5RAP3 regulates hepatocyte differentiation in human

city: Kunming，Yunnan

first: Yang

last: Shao

address: Room 1405, Administration Building, No.727 Jingming South Road, Chenggong District, Kunming

institute: Kunming University of Science and Technology

summary: CDK5RAP3, an UFL1 adaptor for UFMylation, is crucial for liver development in mouse. However, the function of CDK5RAP3 in human hepatocyte differentiation remains unclear. The stepwise generation of hepatocyte-like cells derived from human embryonic cells simulates human hepatocyte differentiation in vitro. Here, the human embryonic cells were conducted to differentiate into hepatocytes and ScRNA-Seq analysis was performed to elucidate the molecular mechanism of CDK5RAP3 in human liver development. We found CDK5RAP3 was important for human hepatocytes differentiation. The CDK5RAP3 deficiency upregulated ER stress in hepatic-endoderm stage, and impaired ribosome homeostasis in mature hepatocytes.

overall_design: Firstly, CDK5RAP3 gene is knockout in human embryonic cell (hESCs) line H9. Secondly, CDK5RAP3-null hESCs were conducted to differentiate into hepatocytes. The cells were collected on differentiated stage (10 and 25 days). Finally, ScRNA-Seq analysis was performed to elucidate the molecular mechanism of CDK5RAP3 in human liver development.

first: Li

last: Wang

first: Ran

last: Gao

first: Shuchun


title: Transcriptome analysis of pulsed activation of MAPK signaling in HEK-RAF-ER cells [RNA_seq_pulse_time_series]

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

country: Germany

institute: Charite Universitätsmedizin Berlin

summary: In this study we performed pulsed activation of MAPK signalling by inducing RAF activity of the RAF-ER constract by tamoxifen, and subsequently blocking MAPK activity using MEK inhibitor at different times. Transcriptomes were sampled 0.5 h to 8h after induction

overall_design: Tamoxifen (4OHT, 0.5uM) was induced at t=0h, and the MEK inhibitor (U01126, 20uM) was added after 0.5h, 1h, 2h, and 4h. Transcriptomes were sampled at 0.5h, 1h, 2h, and 4h.

first: Florian

last: Uhlitz

first: Anja

last: Sieber


title: MAPK


title: Transcriptome analysis of human endothelial subtypes by RNA-seq analysis

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: RNA was isolated from HLEC, HAEC, HMVEC and HUVEC cells. Sequencing was performed on the NextSeq500 instrument (Illumina). Processing of raw reads was performed as previously described (Zhang T et al., 2015)

overall_design: mRNA expression profiles of 4 types of human endothelial cells grown in cell culture were analyzed by RNA-seq in triplicate.

first: Zimmermann

last: Barbara

first: Guenther

last: Stefan


title: Targeted Perturb-seq of regulators of the transcriptional network downstream of RAF-MAPK signaling [perturb_seq]

summary: In this study we use a (targeted) perturb seq experiment in which we knock out 22 transcription factors downstream of MAPK signalling in order to reconstruct the transcriptional network downstream of RAF/MAPK signaling.

overall_design: HEK-RAF-ER were transduced with a pooled CRISPR/Cas9 library targeting 22 transcription factors and the RAF-ER transgene with 4 guides each. Additionally, 10 non-targeting controls and 10 safe-cutters were included as negative controls. After a period of editing, the RAF/MAPK pathway was induced by 4OHT (tamoxifen), and single cell transcriptome gene expression and CRISPR libraries were generated using the 10x Chromium Single Cell 3' V3 with Feature Barcoding technology. Additionally, we performed targeted PCR amplification of 140 genes that yielded better coverage of these genes. These dial-out libraries were sequenced seperately.

first: Ghanem

last: El

first: Bertram

last: Klinger

first: Michael

last: Böttcher


title: A novel 2-iminobenzimidazole compound, XYA1353, displays in vitro and in vivo anti-myeloma activity via targeting NF-κB signaling

city: xuzhou

first: Ruosi

last: Yao

state: China

institute: Xuzhou Medical University

summary:
To determine the pharmacological mechanism of XYA1353 to MM, RNA-seq was performed to compare gene expression in RPMI-8226 cells treated by compound XYA1353 or not.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for RPMI-8226 cells(CON, P17 (XYA1353)).


title: Gene expression profile of CD11b+ Gr1+ Myeloid derived suppressor cells isolated from tumor microenviroment and bone marrow oat different stages of tumor bearing animals and control animals.

city: Purulia

first: Sankar

last: Bhattacharyya

state: West Bengal

address: Ranchi Road Sainik School

department: Zoology

country: India

institute: Sidho Kanho Birsha University

summary: To understand changes in  gene expression profile of myeloid derived suppressor cells in tumor microenvironment and bone marrow with the shift of immune paradigm in response to progressive tumor developments.

overall_design: CD11b+ Gr1+ Myeloid derived suppressor cells were isolated using FACS from ascites and bone marrow from S-180 tumor bearing animals of 4 stages of tumor as 3day post tumor innoculation, 7day post tumor innoculation, 14day post tumor innoclation, 21day pos tumor innoculation which is early to late phase tumor transition and the normal counter part  also isolated to compare the gene expression profile difference between control and tumor microenvironment derived MDSC. Whole cell mRNA were isolated using ambion RNA isolateion mini kit. Each group of sample represents two biological replicates (Control1, Control2), each replicate contains pulled RNA from 12 animals. 5 groups of samples as control, 3day, 7day, 14day, 21day containg one replicate in both ascites and bone marrow in total 20 samples were analysed.

first: Krishna

last: Mahanti

first: Jayasree

last: Saha

first: Debanjan

last: Sarkar

first: Anik

last: Pramanik


title: YTHDF3 modulates the stability of Cbln1 mRNA by recruiting BTG2 and is implicated in the impaired cognition of prenatal hypoxia offspring

status: Public on Jan 17 2024

city: soochow

first: Miao

last: Sun

institute: Institute for Fetology, The First Affiliated Hospital of Soochow University

summary: The “Fetal Origins of Adult Disease (FOAD)” hypothesis holds that adverse factors during pregnancy can increase the risk of chronic diseases in offspring. Here, we investigated the effects of prenatal hypoxia (PH) on brain structure and function in adult offspring and explored the role of the N6-methyladenosine (m6A) pathway. The results suggest that abnormal cognition in PH offspring may be related to dysregulation of the m6A pathway, specifically increased levels of YTHDF3 in the hippocampus. YTHDF3 interacts with BTG2 and is involved in the decay of Cbln1 mRNA, leading to the down-regulation of Cbln1 expression. Deficiency of Cbln1 may contribute to abnormal synaptic function, which in turn causes cognitive impairment in PH offspring. This study provides new scientific clues for understanding the mechanisms of impaired cognition in PH offspring and provides a theoretical basis for the treatment of cognitive impairment in offspring exposed to PH.

overall_design: To investigated the effects of prenatal hypoxia (PH) on brain structure and function in adult offspring , we established a PH modle of C57BL/6J mice. Then performed and comparative gene expression profiling analysis using data obtained from RNA-seq of control and PH offspring.

first: Likui

last: Lu


title: Effects of kockouts of EGR1, FOS and their combination on the MAPK induced transcriptome [RNA_KO_clones]

first: Nils

last: Blüthgen

summary: In this study we used CRISPR/Cas9 to generate KO clones of the HEK-RAF-ER cell line that lack expression of EGR1, FOS  and profiled the transcriptome after inducing RAF/MAPK signaling.

overall_design: We generated multiple KO clones of EGR1 and FOS using guides that target the promoter and the first exon. From these clones, we also generated combinatorial KOs. We then profiled the transcriptome before and 6h-18h after induction of RAF/MAPK in those KO clones and in selected WT clones.

first: David

last: Steinbrecht


title: Inherited blood cancer predisposition through altered transcription elongation [ChIP-seq]

city: Boston

first: Jiawei

last: Zhao

state: Massachusetts

address: 1 Blackfan Circle

institute: Boston Children's Hospital

summary: We identified CTR9 mutants as rare heritible contributing factors to several blood cancers. We later identified partial loss of CTR9 is capable of driving key hematopoietic maintenance and self-renewal gene expression through altered transcription elongation.

overall_design: ChIP-seq for H3K4me3, H3K36me3, H3K79me2,MLLT3, PAF1, LEO1, CDC73, RNA polII on AAVS1 or partial CTR9 edited sorted CD34+CD45RA-CD90+ cells

first: Vijay

last: Sankaran


title: Inherited blood cancer predisposition through altered transcription elongation


title: Inherited blood cancer predisposition through altered transcription elongation [single-cell RNA-seq]

overall_design: CD34+ HSPCs edited by AAVS1, CTR9 guide RNAs were subject to single cell RNA-seq analysis

middle: G


title: Comparison of Blood Transcriptomic Profiles of Healthy, T2D and  Diabetic Nephropathy (DN) Reveals FTO as a potential target for DN

city: Yiwu

first: Qiang

state: Zhejiang

address: No. N1, Shangcheng Avenue

institute: Zhejiang University

summary: To identify the potential regulators in the progression of diabetic nephropathy (DN), we performed RNA sequencing of blood samples from healthy volunteers, patients with T2D,  and patients with  DN. Further analyses revealed that FTO was significantly downregulated in blood samples of T2D and DN patients, while the expression of other erasers, writers or readers remained unchanged between disease and healthy groups . Our study thus provides potential molecular mechanisms for DN progression and association of differential gene expression with the functional and structural changes observed in patients with DN.

overall_design: A total of 28 patients with biopsy-proven DN hospitalized from January 2015 to December 2016 in Shanghai Jiao Tong University Affiliated Sixth People’s Hospital were enrolled in the study. Nine control human kidney samples were obtained from the unaffected portion of tumor nephrectomies. RNA-seq was performed on 28 DN and 9 control samples.

first: Mengzhe

last: Guo

first: Qian

last: Sha

first: Xi

last: Chen


title: TEAD1 in cardiac fibroblast activation

status: Public on Jan 12 2024

city: Shanghai

first: shuai

last: song

address: No. 1609 Xietu Road, Xuhui District, Shanghai

department: Department of Cardiology

institute: Zhongshan  Hospital, Fudan University


title: Inherited blood cancer predisposition through altered transcription elongation [Pro-seq]

overall_design: Examination of transcription elongation by Pro-seq on CD34+ HSPCs edited by AAVS1 and CTR9 sgRNAs

first: Seth

last: Goldman


title: Gene expression data from endometrial cancer patient-derived cells (EDC-PDCs) treated with Efp siRNA

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

country: Japan

institute: Saitama Medical University

summary: To examine the role of Efp in endometrial cancer, patient-derived cells were treated with siRNA targeting Efp (siEfp) or control siRNA (siControl). siRNA-mediated Efp silencing resulted in suppressed spheroid proliferation and altered gene expression profile, featuring downregulation of genes related to cell cycle and inflammation/immune responses. This study provides an insight into alternative endometrial cancer therapeutic strategies targeting Efp.

overall_design: Total RNA was extracted from endometrial cancer patient-derived cells (EC-PDCs) treated with siRNAs targeting Efp (siEfp #A) or control siRNA (siControl) and then used for Affymetrix microarrays analysis.

first: Kuniko

last: Horie-Inoue

first: Satoshi

last: Inoue


title: Single-cell transcriptomics of precursor lung adenocarcinoma reveals intratumoral heterogeneity and shifting immune network

city: Guangzhou

first: Chao

last: Zhang

address: Zhongshan Er Road

department: Thoracic Oncology

institute: Guangdong Lung Cancer Institute

summary: We conducted a multi-omics analysis including single-cell RNA transcriptome, single-cell T cell receptor (scTCR), whole exome sequencing and multiplex immunohistochemistry (mIHC) to decipher single cell atlas of precursor lung adenocarcinoma and mechanisms of diverse immune cells during precursor lesions development in hopes of digging out potential therapeutic targets.

overall_design: 78 (62 scRNA and 16 scTCR)

first: Wen-Zhao

last: Zhong


title: Notch inhibition in microRNA-mediated neuronal reprogramming promotes neurite extension

city: St Louis

first: Kyle

last: Burbach

state: MO

address: 660 S Euclid Ave

department: Developmental Biology

institute: Washington University in St Louis School of Medicine

summary: Although the importance of Notch signaling in brain development is well-known, its specific contribution to cellular reprogramming remains less defined. Here, we use microRNA-induced neurons (miNs) that are directly reprogrammed from human fibroblasts to determine how Notch signaling contributes to neuronal identity. We found that inhibiting Notch signaling led to an increase in neurite extension, while activating Notch signaling had the opposite effect. Surprisingly, Notch inhibition during the first week of reprogramming was both necessary and sufficient to enhance neurite outgrowth at a later timepoint. This timeframe is when the reprogramming miRNAs, miR-9/9* and miR-124, primarily induce a post-mitotic state and erase fibroblast identity. Accordingly, transcriptomic analysis showed that the effect of Notch inhibition was likely due to improvements in fibroblast fate erasure and silencing of anti-neuronal genes. To this effect, we identify MYLIP, whose downregulation in response to Notch inhibition significantly promoted neurite outgrowth. Moreover, Notch inhibition resulted in cells with neuronal transcriptome signature defined by long gene expression at a faster rate than the control, demonstrating the effect of accelerated fate erasure on neuronal fate acquisition. Our results demonstrate the critical role of Notch signaling in mediating morphological changes in miRNA-based neuronal reprogramming of human adult fibroblasts.

overall_design: We inhibited Notch signaling using SAHM1 and activated it using NICD overexpression and sequenced at PID7 to investigate the time specific differences in neuronal reprogramming with Notch inhibition

middle: F

first: Andrew

middle: S

last: Yoo


title: Notch inhibition in microRNA-mediated neuronal reprogramming promotes neurite extension (PID21)

overall_design: We used two Notch Inhibitors, DAPT and SAHM1, to investigate the effect of inhibiting notch on microRNA induced reprogramming of neurons at PID21.


title: Transcriptome profiling of mRNAs in cortex of normal rats with electroacupuncture

first: Ming-Shu

last: Xu

address: No. 650 South Wanping Road, Xuhui District

department: Shanghai Research Institute of Acupuncture and Meridian

institute: Shanghai University of Traditional Chinese Medicine

summary: We analyzed transcriptomic characteristic of motor cortex from Sprague-Dawley rat brain treated with electroacupuncture.

overall_design: We selected 3 normal Sprague-Dawley rats with electroacupuncture at GB20 (Fengchi acupoints). The motor cortex was stripped from brain tissue, and total RNAs were extracted according to the manufacturer’s instructions. Qualified total RNA was further purified. We complete the construction of sequencing sample library. The number of fragments of each gene was counted, and then normalized. Finally, the FPKM value of each gene was calculated by Perl script.


title: Toll-Like Receptor-induced Nucleosome Remodeling Achieved by Broadly Acting NF-kB in Collaboration with Transcription Factors Conferring Selectivity [BMDM_ATAC]

city: Los Angeles

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

institute: University of California Los Angeles

summary: Macrophages play a critical role in bridging the innate and adaptive immune systems, which requires timely and precise transcription control when responding to danger signals. Gene expression networks in macrophages have been profiled extensively in recent decades with the advancement of high-throughput sequencing technologies. However, unveiling critical mechanistic insights into control of diverse transcriptional networks has proven to be challenging. Recent evidence has suggested that the accessibility of chromatin structure can provide an integral means of transcription regulation. We have used the relatively recent Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-seq) method to assess chromatin accessibility with optimal resolution in mouse bone marrow derived macrophages during the course of lipid- A stimulation. This advanced method enabled us to characterize the chromatin state of genome-wide regulatory regions. By applying a quantitative systematic approach, we obtained mechanistic insights into the highly selective role of the major transcription factors, NF-κB and IRF3, in nucleosome remodeling and transcription regulation.

overall_design: Bone-marrow derived macrophages were derived from C57/B16 and Irf3-/- mice. C57/B16 macrophages were stimulated with lipid-A for 0, 30, 60 or 120 minutes and in the presence of cycloheximide for 120 minutes. Irf3-/- macrophages were treated with lipid A with or without the presence of cycloheximide for 0 and 120 minutes. Chromatin was collected and treated with Tn5 transposase to profile DNA accessibility.

first: An-Chieh

last: Feng

first: Brandon

last: Thomas


title: Transcriptome profiling of mRNAs in cortex of rats with cerebral ischemia and reperfusion treated by acupuncture

summary: We analyzed transcriptomic characteristic of motor cortex from Sprague-Dawley rats brain with cerebral ischemia and reperfusion (CIR) treated by acupuncture.

overall_design: We selected 3 Sprague-Dawley rats with CIR treated by electroacupuncture at GB20 (Fengchi acupoints). The motor cortex was stripped from brain tissue, and total RNAs were extracted according to the manufacturer’s instructions. Qualified total RNA was further purified. We complete the construction of sequencing sample library. The number of fragments of each gene was counted, and then normalized. Finally, the FPKM value of each gene was calculated by Perl script.


title: Structural analysis of the lncRNA SChLAP1 reveals protein binding interfaces and a conformationally heterogenous retroviral insertion

city: Durham

first: Amanda

last: Hargrove

state: NC

address: 124 Science Dr

department: Chemistry

institute: Duke University

summary: The lncRNA Second Chromosome Locus Associated with Prostate 1 (SChLAP1) was previously identified as a predictive biomarker and potential driver of aggressive prostate cancer. Recent work suggests that SChLAP1 may bind the SWI/SNF chromatin remodeling complex to promote prostate cancer metastasis, though the exact role of SWI/SNF recognition is debated. To date, there are no detailed biochemical studies of apo SChLAP1 or SChLAP1:protein complexes. Herein, we report the first secondary structure model of SChLAP1 using SHAPE-MaP in vitro, in cellulo, and ex cellulo (protein-free). Comparison of the ex cellulo and in cellulo data via ΔSHAPE identified putative protein binding sites within SChLAP1. In addition, we identified primate conserved exons of SChLAP1 as well as regions that appear to have been incorporated through retroviral insertion. In particular, we characterized a complex structural landscape in a protein binding region at the 3′-end of SChLAP1 derived from a THE1B-type retroviral insertion, suggesting a role for an exapted RNA structure in SChLAP1:protein recognition and prostate cancer progression. This work lays the foundation for future efforts to selectively target and disrupt the SChLAP1:protein interface and to develop new therapeutic avenues in prostate cancer treatment.

overall_design:
DNA-seq of libraries derived from mock (DMSO) or SHAPE-probed SChLAP1 RNA. Biological duplicate obtained for in cellulo and ex cellulo samples, and unicate obtained of in vitro samples. DMS probing performed with ethanol control of in vitro SChLAP1 in biological unicate.
Please note that the processed data generated from both DMSO and SHAPE samples is linked to the corresponding DMSO sample records.

first: James

middle: P

last: Falese

first: Emily

last: McFadden

first: Christopher

middle: A

last: D'Inzeo

middle: E


title: CD38-RyR2 axis mediated signaling impedes CD8+  T cell response to anti-PD1 therapy in  cancer

city: KOLKATA

first: Puspendu

last: Ghosh

state: WEST BENGAL

address: CNO6,SECTOR V, BIDHANNAGAR

department: CBID

institute: CSIR-IICB

summary: PD-1 blockade therapy, harnessing the cytotoxic potential of CD8+  T cells, has yielded clinical success in treating malignancies. However, its efficacy is often limited due to the progressive differentiation of intratumoral CD8+ T cells into a hypofunctional state known as terminal exhaustion. Despite identifying CD8+ T cell subsets associated with immunotherapy resistance, the molecular pathway triggering the resistance remains elusive. Given the clear association of CD38 with CD8+ T cell subsets resistant to anti-PD1 therapy, we investigated its role in inducing resistance. Phenotypic and functional characterization, along with single-cell RNA sequencing analysis of both in vitro chronically stimulated and intratumoral CD8+ T cells, revealed that CD38-expressing CD8+ T cells are terminally exhausted. Exploring the molecular mechanism, we discovered that CD38 expression was crucial in promoting terminal differentiation of CD8+ T cells by suppressing TCF1 expression, thereby rendering them unresponsive to anti-PD1 therapy. Genetic ablation of CD38 in tumor reactive CD8+ T cells restored TCF1 levels and improved the responsiveness to anti-PD1 therapy in mice. Mechanistically, CD38 expression on exhausted CD8+ T cells elevated intracellular Ca2+ levels through RyR2 calcium channel activation. This, in turn, promoted chronic AKT activation, leading to TCF1 loss. Knockdown of RyR2 or inhibition of AKT in CD8+ T cells maintained TCF1 levels, induced a sustained anti-tumor response, and enhanced responsiveness to anti-PD1 therapy. Thus, targeting CD38 represents a potential strategy to improve the efficacy of anti-PD1 treatment in cancer.

overall_design:
Peripheral blood mononuclear cells (PBMCs) were isolated via Ficoll-hypaque gradient centrifugation from de-identified buffy coats obtained from two healthy human subjects (Donor 1 and Donor2). Naïve CD3 T cells were purified using the Dynabeads Untouched Human CD3+ T-cell isolation kit (Invitrogen). Purified CD3+ T cells were activated with plate-bound anti-CD3 (5 μg/ml) and anti-CD28 (2 μg/ml), along with recombinant human IL-2 (100 units/ml), in complete RPMI-1640 supplemented with 10% FBS (Invitrogen) for 72 hours. Following 72 h of activation, T cells were passaged at every 48h at 1×10^6 cells/ml in RPMI-1640 medium containing 10% FBS, with (chronic) or without (referred to as control in the text) plate-bound anti-CD3 (2 μg/ml) until 11 days. The chronic group was maintained in recombinant human IL-2 (25 units/ml), while the control group was maintained in recombinant human IL-2 (100 units/ml). On day 11, live cells were sorted using FACS. Cell viability was determined using Trypan Blue on the ThermoFisher Scientific, Countess® II FL Automated Cell Counter. Approximately, 0.1X10^6 T cells were labelled using BDTM Single-Cell Multiplexing Kit-Human with unique tags. The control samples i.e. Control1 (obtained from Donor1) and Control2 (obtained from Donor2) were labelled with SampleTag 1 and Sample Tag3 respectively while the chronically stimulated samples i.e. Chr. St. 1 (obtained from Donor1) and Chr. St. 2 (obtained from Donor2) were labelled with SampleTag 2 and Sample Tag 4 respectively. Thereafter, these samples were taken for further steps of single cell sequencing. Finally, all sequencing libraries were prepared using BD RhapsodyTM WTA Amplification kit as per the manufacturer’s guideline. The unique nucleotide sequences of individual sampleTag are provided as text file.
The raw data fastq file is a pooled sample file, while the processed files are matrix tables containing raw gene counts for individual genes and single cells. Each processed file represents one sample and is generated from processing the aforementioned FASTQ file.

first: Anupam

last: Gautam


title: Bulk RNA-seq analysis of Mycobacterium tuberculosis infected Sp140-sufficient and -deficient mouse lungs with and without pDC depletion

city: Berkeley

first: Dmitri

middle: I

last: Kotov

state: CA

address: 415 Weill Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary: Mycobacterium tuberculosis (Mtb) causes 1.5 million deaths annually. Active tuberculosis correlates with a neutrophil-driven type I interferon (IFN) signature, but the underlying cellular mechanisms remain poorly understood. We found that interstitial macrophages (IMs) and plasmacytoid dendritic cells (pDCs) are dominant producers of type I IFN during Mtb infection in mice and non-human primates, and pDCs localize near human Mtb granulomas. Depletion of pDCs reduces Mtb burdens, implicating pDCs in tuberculosis pathogenesis. During IFN-driven disease, we observe abundant DNA-containing neutrophil extracellular traps (NETs) known to activate pDCs. Single cell RNA-seq indicates that type I IFNs act on IMs to impair their responses to IFNg, a cytokine critical for Mtb control. Cell type-specific disruption of the type I IFN receptor suggests IFNs act on IMs to inhibit Mtb control. We propose pDC-derived type I IFNs, driven by NETs, act on IMs to drive bacterial replication, further neutrophil recruitment, and active tuberculosis disease.

overall_design: RNA-Seq

first: Ophelia

middle: V

last: Lee

first: Stefan

last: Fattinger

first: Charlotte

last: Langner

first: Jaresley

last: Guillen

first: Joshua

last: Peters

first: Andres

last: Moon

first: Eileen

last: Burd

first: Kristen

middle: C

last: Witt

first: Daniel

last: Stetson

first: David

last: Jaye

first: Bryan

last: Bryson

first: Russell

last: Vance


title: The clock gene Per1 may exert diurnal control over hippocampal memory consolidation

city: State College

first: Aswathy

last: Sebastian

address: University Park

institute: PennState

summary: The circadian system influences many different biological processes, including memory performance. While the suprachiasmatic nucleus (SCN) functions as the brain’s central pacemaker, downstream “satellite clocks” may also regulate local functions based on the time of day. Within the dorsal hippocampus (DH), for example, local molecular oscillations may contribute to time-of-day effects on memory. Here, we used the hippocampus-dependent Object Location Memory task to determine how memory is regulated across the day/night cycle in mice. First, we systematically determined which phase of memory (acquisition, consolidation, or retrieval) is modulated across the 24h day. We found that mice show better long-term memory performance during the day than at night, an effect that was specifically attributed to diurnal changes in memory consolidation, as neither memory acquisition nor memory retrieval fluctuated across the day/night cycle. Using RNA-sequencing we identified the circadian clock gene Period1 (Per1) as a key mechanism capable of supporting this diurnal fluctuation in memory consolidation, as Per1 oscillates in tandem with memory performance. We then show that local knockdown of Per1 within the DH has no effect on either the circadian rhythm or sleep behavior, although previous work has shown this manipulation impairs memory. Thus, Per1 may independently function within the DH to regulate memory in addition to its known role in regulating the circadian system within the SCN. Per1 may therefore exert local diurnal control over memory consolidation within the DH.

overall_design: Differential gene expression analyses of RNA-seq data from dorsal hippocampus punches for naive homecage (HC) mice compare to mice trained with object location memory (OLM) at 6 diurnal timepoints (ZT1, ZT5, ZT9, ZT13, ZT17, and ZT21) and sacrificed 60m after training.

first: Lauren

last: Bellfy

first: Chad

middle: W

last: Smies

first: Alicia

middle: R

last: Bernhardt

first: Kasuni

middle: K

last: Bodinayake

first: Chen-Yu

last: Lo

first: Shoko

last: Murakami

first: Hannah

last: Boyd

first: Megan

last: von Abo

first: Istvan

last: Albert

first: Janine

last: Kwapis


title: Transcriptome profiling of mRNAs in cortex of rats with cerebral ischemia and reperfusion

first: Ming-Shu

last: Xu

summary: We analyzed transcriptomic characteristic of motor cortex from Sprague-Dawley rats brain with cerebral ischemia and reperfusion (CIR).

overall_design: We selected 3 Sprague-Dawley rats with CIR. The motor cortex was stripped from brain tissue, and total RNAs were extracted according to the manufacturer’s instructions. Qualified total RNA was further purified. We complete the construction of sequencing sample library. The number of fragments of each gene was counted, and then normalized. Finally, the FPKM value of each gene was calculated by Perl script.


title: CITE-seq analysis of Mycobacterium tuberculosis infected B6 and Sp140-deficient mouse lungs

first: Dmitri

last: Kotov

overall_design: Lungs were harvested from C57BL/6 and Sp140-deficient naïve mice (2 animals per genotype) or mice infected with Mycobacterium tuberculosis for 25 days  (3 animals per genotype).  Myeloid cells were magnetically enriched based on Ly6G and CD64. After enrichment, infected cells were isolated by Fluorescence-activated cell sorting (FACS)  to separate Mtb infected and bystander myeloid cells based on Wasabi expression. Naive samples where isolated by FACS into macrophages and a monocyte/neutrophil mixture, which were pooled at a 1 to 2 ratio for greater macrophage representation.

first: Ophelia

last: Lee

first: Stefan

last: Fattinger

first: Charlotte

last: Langner

first: Jaresley

last: Guillen

first: Joshua

middle: M

last: Peters

first: Andres

last: Moon

first: Eileen

last: Burd

first: Kristen

last: Witt

middle: B

middle: L


title: S1 basic leucine zipper transcription factors shape plant architecture by controlling C/N partitioning to apical and lateral organs

city: Wuerzburg

first: Christoph

last: Weiste

address: Julius-von-Sachs Platz 2

department: Julius-von-Sachs Institute

institute: Julius-Maximilians-Universitaet

summary: To decipher gene expression controlled by the five highly homologous group S1 bZIP transcription factors during the reproductive growth phase of Arabidopsis thaliana, we generated triple (bzip2/-11/-44) and quintuple (bzip1/-2/-11/-44/-53) mutants of these factors using CRISPR/Cas9 and analysed gene expression in distinct C source (source leaves) or C sink (sink leaves, rosette buds, flowers) tissues.

overall_design: We performed RNAseq from 3 biological replicates per genotype (wild type (WT, Arabidopsis ecotype Col-0), triple and quintuple bZIP mutants) and tissue (source leaves, sink leaves, rosette buds, flowers)

first: Philipp

last: Kreisz


title: Bulk RNA-seq analysis of bone marrow-derived macrophages stimulated with various cytokines

first: Daniel

last: Stetson

first: David

last: Jaye

first: Bryan

middle: D

last: Bryson

first: Russell

last: Vance


title: Cortical miR-709 links glutamatergic signaling to NREM sleep EEG slow waves in an activity-dependent manner [RNA-seq]

city: Lausanne

first: Leonore

last: Wigger

address: Amphipôle Building

country: Switzerland

institute: Swiss Institute of Bioinformatics

summary: Micro-RNAs (miRNAs) are key, post-transcriptional regulators of gene expression that have been implicated in a plethora of biological processes. Their role in sleep, however, has received little attention. In the current experiment, we investigated the effects of in vitro miR-709 inhibition on the transcriptome of primary cortical neurons.

overall_design: Eighteen primary cortical neuronal cultures from C57BL6/J mice were distributed in 3 groups, each one following a different treatment, namely miR-709 inhibition (i-miR-709, n=6), scrambled control (scr, n=6) or ddH2O control (ctrl, n=6), and their transcriptome was subsequently assessed by RNA-sequencing.

first: Konstantinos

last: Kompotis

first: Geraldine

last: Mang

first: Paul

last: Franken


title: Cortical miR-709 links glutamatergic signaling to NREM sleep EEG slow waves in an activity-dependent manner

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

overall_design: Refer to individual Series


title: Cortical miR-709 links glutamatergic signaling to NREM sleep EEG slow waves in an activity-dependent manner [agilent_cortex_hippocampus]

summary: Micro-RNAs (miRNAs) are key, post-transcriptional regulators of gene expression that have been implicated in a plethora of biological processes. Their role in sleep, however, has received little attention. In this experiment we investigated the effects of sleep deprivation on the cortex and hippocampus miRNA transcriptome. In this experiment we observed  different miRNAs being affected by sleep deprivation in the cortex and hippocampus.

overall_design: Eight C57BL/6J male mice (12 weeks old) were used in total, divided in the sleep-drepived group (n=2) and the non-treated control group (n=2) for cortex or hippocampus.


title: ChIP-Seq  of Wild Type pDC Transcriptomes  (CpG 0h, 2h)

city: Duesseldorf

first: Stefanie

last: Scheu

state: Nordrhein-Westfalen

address: Universitaetsstr. 1

department: Institute of Medical Microbiology and Hospital Hygiene

institute: University of Duesseldorf

summary:
Purpose: The goals of this study are to identify BATF binding sites in purified BM-d Flt3-L cultured pDCs (ChIP-seq) at steady state and at 2h after CpG activation.
Methods: Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine, and sent to Active Motif Services (Carlsbad, CA) to be processed for ChIP-Seq. In brief, chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (20 µg, spiked-in with 200 ng of Drosophila chromatin) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 ug of antibody against BATF (CST, 8638BF). Antibody against H2Av (0.4 ug) was also present in the reaction to ensure efficient pull-down of the spike-in chromatin (Egan et al., 2016). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 °C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Quantitative PCR (QPCR) reactions were carried out in triplicate on specific genomic regions using SYBR Green Supermix (Bio-Rad).  The resulting signals were normalized for primer efficiency by carrying out QPCR for each primer pair using Input DNA.
Results: For ChIP Sequencing Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end). Reads were aligned consecutively to the mouse genome (mm10) and to the Drosophila genome (dm3) using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis. The number of mouse alignments used in the analysis was adjusted according to the number of Drosophila alignments that were counted in the samples that were compared. Mouse alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of p-value = 1e-7. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed. Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations. The results were further visualized using Integrative Genomics Viewer (IGV) (Robinson et al., 2011) and modified with Inkscape.
Conclusions: Our study represents a detailed analysis of global BATF binding sites in naive and activated pDCs. Our results show that BATF binds not only to promoter regions of genes but extensively to enhancer elements as well. We identify key role players important for pDC biology that are regulated by BATF binding onto their DNA.

overall_design: BATF binding profiles of bone marrow-derived Flt3-L FACS purified pDCs from wild type mice that were left naïve or stimulated with TLR9 agonist CpG for 2h.

first: Shafaqat

last: Ali

first: Ritu

last: Mann-Nüttel


title: Common chromosomal aberrations detected by array comparative genomic hybridization in bladder cancer

city: Beijing

first: HUANG

last: CHEN

address: Yinghuadongjie 2#, Chaoyang District, Beijing

department: Department of Etiology and Carcinogenesis

institute: China-Japan Friendship Hospital

type: Genome variation profiling by genome tiling array

summary: Analysis of Copy Number for bladder cancer using Agilent Human Genome CGH Microarray Kit 4x44K

overall_design: 65 Samples

first: Chen

last: Huang

first: Cai

last: Zhao


title: Cortical miR-709 links glutamatergic signaling to NREM sleep EEG slow waves in an activity-dependent manner [agilent_forebrain]

summary: Micro-RNAs (miRNAs) are key, post-transcriptional regulators of gene expression that have been implicated in a plethora of biological processes. Their role in sleep, however, has received little attention. We first investigated the effects of sleep deprivation on the brain miRNA transcriptome. Sleep deprivation affected 52 miRNAs in the whole brain, and particularly miR-709, an activity-dependent microRNA, enriched in the cerebral cortex.

overall_design: Sixteen C57BL/6J male mice (12 weeks old) were used, divided in the sleep-drepived group (n=8) and the non-treated control group (n=8). After removal of an outlier miRNA sample, data from 7 sleep-deprived and 8 control mice were retained in the data set for statistical analysis.


title: Crosstalk between chromatin and the transcription factor Svb

city: Toulouse

first: Cedric

last: Polesello

address: 118 Route de Narbonne

country: France

institute: Centre de Biologie Intégrative de Toulouse

summary: The transcription factor Shavenbaby (Svb), the only member of the OvoL family in Drosophila, controls intestinal stem cell differentiation. Post-translational modification of Svb produces two protein isoforms, Svb-ACT and Svb-REP, which promote intestinal stem cell renewal or differentiation, respectively. Using engineered cell lines, we express either isoform to define their mode of action, and develop an unbiased method to identify Svb target genes in intestinal cells.  Within a given cell type, Svb-ACT and Svb-REP antagonistically regulate the expression of a set of target genes, binding specific enhancers whose accessibility is constrained by. During intestinal differentiation, the set of target genes progressively changes, together with chromatin accessibility. Moreover, Svb-REP binding stabilizes three-dimensional enhancer-promoter loops, while influencing the local chromatin landscape to repress target genes. We propose that SvbACT-to-REP switch promotes enterocyte differentiation of intestinal stem cells through direct gene regulation and chromatin remodeling.

overall_design: We used the technology of Hi-C to quantifiy long-range interactions resulting from the 3D organization of the genome, in drosophila S2 cells expressing the Svb repressor or activator isoforms (Svb-REP and Svb ACT, respectively)

first: Mancheno-Ferris

last: Alexandra

first: Fosseprez

last: Olivier

first: Depierre

last: David

first: Cuvier

first: Polesello

last: Cedric


title: Organism-level analysis of sepsis reveals mechanisms of systemic inflammation

status: Public on Jan 11 2024

city: Chicago

first: Michihiro

last: Takahama

state: Illinois

department: Pritzker School of Molecular Engineering

institute: University of Chicago

summary: Sepsis is an uncontrolled, systemic response to infection with life-threatening consequences. Our understanding of the pathogenesis of sepsis across organs of the body is rudimentary. Here, using mouse models of sepsis, we generate a dynamic, organism-wide map of the pathogenesis of the disease, revealing the spatiotemporal patterns of well-known and previously unrecognized effects of sepsis on the body. By combining functional perturbations with organism-wide profiling, we discover two interorgan mechanisms that are key to the pathophysiology of sepsis. First, we find that a hierarchical cytokine circuit arising from the pairwise effects of TNF plus IL-18, IFN-γ, or IL-1β suffices to explain a large fraction of the molecular effects of sepsis on the body. Moreover, the effects of these three cytokine pairs on the abundance of nearly two hundred cell types across nine organ types recapitulate half of all the cellular effects of sepsis. Second, we uncover an interorgan pathway whereby a gut-derived, secreted phospholipase, Pla2g5, mediates hemolysis in the blood circulation and contributes to multi-organ failure during sepsis. Thus, a simplifying principle in the systemic behavior of the cytokine network and a lipase misdirected from gut to blood provide fundamental insights to help build a unifying mechanistic framework for the pathophysiological effects of sepsis on the organ systems of the body.

overall_design: We performed the experiments and 2 datasets were generated from the following experiments and samples: (1) Lysophosphatidic acid injection, (2) Dexamethasone.

first: Nicolas

last: Chevrier


title: Secreted Phospholipase PLA2G5 Acts as a Self-Venom in Sepsis by Mediating Hemolysis

summary: Sepsis is a systemic response to infection with life-threatening consequences such as hemolysis, a predictor of mortality risks for the disease. Here, by measuring organism-wide changes in gene expression, we discovered that the secreted phospholipase PLA2G5 is induced in colon cell types during sepsis. The genetic deletion and antibody blockade of PLA2G5 abrogated the lethal effects of sepsis. PLA2G5 blockade during sepsis led to an increase in splenic red pulp macrophages and iron homeostasis, linking PLA2G5 to red blood cell homeostasis during sepsis. Mechanistically, bloodborne PLA2G5 led to intravascular hemolysis through its lipolytic activity on red blood cell membranes. In humans with sepsis, the plasma level of PLA2G5 was elevated and predictive of disease severity and mortality. We conclude that sepsis corrupts PLA2G5 from the gut into becoming a systemic self-venom which is toxic for host red blood cells.

overall_design: We performed the experiment and 1 dataset was generated from the following experiments and samples: (1) Pla2g5 neutralizing antibody.


title: Cortical miR-709 links glutamatergic signaling to NREM sleep EEG slow waves in an activity-dependent manner [NanoString]

first: Leonore

last: Wigger

summary: Micro-RNAs (miRNAs) are key, post-transcriptional regulators of gene expression that have been implicated in a plethora of biological processes. Their role in sleep, however, has received little attention. In this experiment, we investigated the effects of in vivo miR-709 inhibition on the cortical transcriptome of adult mice.

overall_design: Cortical tissues from five i-miR-709- and five scrambled-injected mice were dissected and assessed for the expression of specific genes of interest, defined by a previous in vitro screening. After removal of an outlier sample, four i-miR-709- and five scrambled-injected cortex samples were retained in the data set for statistical analysis.

first: Konstantinos


title: N6-methyladenosine reader YTHDF1 promotes stemness and therapeutic resistance in hepatocellular carcinoma by enhancing NOTCH1 expression

first: Xinyue

last: Zhang

state: guangdong

address: zhongshan road 2

institute: Sun Yat-sen University First Affiliated Hospital

summary: N6-methyladenosine (m6A) RNA modification is the most common and conserved epigenetic modification in mRNA and has been shown to play important roles in cancer biology. As the m6A reader YTHDF1 has been reported to promote progression of hepatocellular carcinoma (HCC), it represents a potential therapeutic target. In this study, we evaluated the clinical significance of YTHDF1 using human HCC samples and found that YTHDF1 was significantly upregulated in HCCs with high stemness scores and was positively associated with recurrence and poor prognosis. Analysis of hepatoma spheroids revealed that YTHDF1 was highly expressed in liver cancer stem cells (CSCs). Stem cell-specific conditional Ythdf1 knock-in (CKI) mice treated with diethylnitrosamine showed elevated tumor burden compared with wild type mice. YTHDF1 promoted CSC renewal and resistance to the multiple tyrosine kinase inhibitors lenvatinib and sorafenib in patient-derived organoids and HCC cell lines, which could be abolished by catalytically inactive mutant YTHDF1. RNA immunoprecipitation sequencing, m6A methylated RNA immunoprecipitation sequencing, ribosome profiling, and RNA sequencing identified NOTCH1 as a direct downstream of YTHDF1. YTHDF1 bound to m6A modified NOTCH1 mRNA to enhance its stability and translation, which led to increased NOTCH1 target genes expression. NOTCH1 overexpression rescued HCC stemness in YTHDF1 deficient cells in vitro and in vivo. Lipid nanoparticles targeting YTHDF1 significantly enhanced the efficacy of lenvatinib and sorafenib in HCC in vivo. Taken together, YTHDF1 drives HCC stemness and drug resistance through a YTHDF1-m6A-NOTCH1 epitranscriptomic axis, and YTHDF1 is a potential therapeutic target for treating HCC.

overall_design:
To decipher whether YTHDF1 modulates HCC stemness in m6A-dependent manner, we applied RNA immunoprecipitation sequencing, m6A methylated RNA immunoprecipitation sequencing, ribosome profiling, and RNA sequencing to pinpoint downstream targets regulated by YTHDF1-m6A epigenetic axis in HCC.
To investigate the molecular mechanism that silencing of YTHFD1 increased sensitivities against lenvatinib/sorafenib, we performed RNA-seq on tumor tissues from orthotopic xenograft implants treated with LNP-siYTHDF1 in combination with either lenvatinib or sorafenib.

first: Lixia

last: Xu

first: Jun

last: Yu

first: Tianhong

last: Su

first: Yifan

last: Wu


title: Analysis of MTX-3937-treated human peripheral NK cells

city: Jinan

first: Rong

last: Xiao

address: Lixia strict Wenhuaxi street No. 44

institute: Shandong University

summary: Siglec-9 has been of particular interest for their potential as immune checkpoints. Here, we employed docking-based virtual screening combined with bio-layer interferometry assays to identify a potential Siglec-9 inhibitor, MTX-3937. Analysis showed that MTX-3937-treatment significantly enhanced the production of IFN-γ, TNF-α, perforin and CD107a in human NK cells. Consistently, MTX-3937 largely promoted NK cells tumor killing activities both in vitro and in vivo. In mechanism, MTX-3937 inhibited the phosphorylation level of SHP-1/2 in NK92 cells.

overall_design: To globally characterize MTX-3937-mediated improvement of NK cell functions, we assessed the transcriptional profiles of MTX-3937- and DMSO-treated human peripheral NK cells from healthy donors.

first: Chunhong

last: Ma


title: The Transcription factor NF-YA is Crucial for Neural Progenitor Maintenance during Brain Development

city: Niigata

first: Tomoyuki

last: Yamanaka

address: 1-757 Asahimachidori, Chuo-ku

department: Brain Research Institute

institute: Niigata University

summary: In contrast to stage-specific transcription factors, the role of ubiquitous transcription factors in neuronal development remains a matter of scrutiny. Here, we demonstrated that a ubiquitous factor NF-Y is essential for neural progenitor maintenance during brain morphogenesis. Deletion of the NF-YA subunit in neural progenitors by using nestin-cre transgene in mice resulted in significant abnormalities in brain morphology, including a thinner cerebral cortex and loss of striatum during embryogenesis. Detailed analyses revealed a progressive decline in multiple neural progenitors in the cerebral cortex and ganglionic eminences, accompanied by induced apoptotic cell death and reduced cell proliferation. In neural progenitors, the NF-YA short isoform lacking exon 3 is dominant and co-expressed with cell cycle genes. ChIP-seq analysis from the cortex during early corticogenesis revealed preferential binding of NF-Y to the cell cycle genes, some of which were confirmed to be downregulated following NF-YA deletion. Notably, the NF-YA short isoform disappears and is replaced by its long isoform during neuronal differentiation. Forced expression of the NF-YA long isoform in neural progenitors resulted in a significant decline in neuronal count, possibly due to the suppression of cell proliferation. Collectively, we elucidated a critical role of the NF-YA short isoform in maintaining neural progenitors, possibly by regulating cell proliferation and apoptosis. Moreover, we identified an isoform switch in NF-YA within the neuronal lineage in vivo, which may explain the stage-specific role of NF-Y during neuronal development.

overall_design: E13.5 mouse brain cortices were fixed, lyzed and sonicated. The lysates (input) were subjected to chromatin immunoprecipitation (ChIP) using anti-NF-YC and anti-H3K4me3 antibodies. The DNA libraries of the input and two ChIP samples were generated by Takara ThruPLEX DNA-seq Kit, and sequenced by Illumina NextSeq 2000 using P1 regent (100 cycles).

first: Nobuyuki

last: Nukina


title: Bulk RNA-seq of healthy and senescent mouse fibro-adipogenic progenitors (FAPs)

city: Rochester

first: Xu

state: MN

address: 200 First St SW

department: Physical Medicine and Rehabilitation

institute: Mayo Clinic

summary: We report the bulk RNA-seq of healthy and senescent mouse fibro-adipogenic progenitors (FAPs)

overall_design: We isolated FAPs from skeletal muscle of young C57BL/6 mice and induced senescence with Etoposide treatment (20uM for 48 hours and then cultured in normal medium for 5 more days). We then collected the RNA and performed the RNA-seq.

first: Nathan

last: LeBrasseur


title: Airway Microfold (M) Cells Emerge in the Post-IAV Lung

city: La Jolla

first: Xin

last: Sun

address: Cellular and Molecular Medicine East 1087, 9500 Gilman Drive

institute: University of California San Diego

summary: Airway cell fates are altered during repair and regeneration following lung injury. Here we survey mouse airway epithelium using single nucleus RNA-sequencing after influenza (PR8) infection and uncovered the emergence of Microfold (M) cells in the post-IAV intrapulmonary lung. These pulmonary M cells share expression signatures with the better-characterized intestinal M cells. Furthermore, similar to intestinal M cells  that function by overlying lymphoid follicles in Peyer’s Patches, the post-IAV pulmonary M cells are enriched over bronchus associated lymphoid tissue (BALT), suggestive an interactive relationship.

overall_design: single nucleus RNA-seq from lineage labelled airway cells (Sox2-creER;SUN1-GFP) from control and 25 days post PR8 (IAV) infection

first: Justinn

last: Barr

first: Le

first: Jamie

last: Verheyden


title: Tuft cells and fibroblasts promote thymus regeneration through activation of a type-2 immune response [CITE-Seq]

city: Rehovot

first: Jakub

last: Abramson

address: 234 Herzl st.

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

summary: The goal of this study was to examine the effect of dexamethasone-induced involution on the thymus cellular composition, and highlight cell populations which participate in the regeneration process. For this purpose we treated WT mice with dexamethasone, sorted non-T hematopoietic cells from their thymi 4 days after treatment when the thymus begins its recovery, or at an earlier time point (18 hours) for comparison, and performed CITE-Seq.

overall_design: Young WT male mice were treated with dexamethasone 4 days/18 hours before sacrifice, then perfused and stained with CITE-Seq antibodies. Thymic hematopoietic cells excluding mature T cells were then isolated by FACS sorting for 10x single cell RNA sequencing. 2 replicates were used for each condition. The control was untreated age-matched WT mice.

first: Shir

last: Nevo

first: Dena

last: Leshkowitz


title: Tuft cells and fibroblasts promote thymus regeneration through activation of a type-2 immune response [ex_vivo_tuft]

summary: The goal of this study was to determine whether thymic tuft cells activation during acute thymic involution is mediated by IL-13, which is produced by ILC2 upon involution and the receptor for which is expressed by tuft cells. For this purpose we sorted thymic tuft cells from WT mice, treated them ex vivo with recombinant IL-13 for 24 hours, and performed bulk RNA-Seq.

overall_design: Tuft cells from thymi of young male WT mice were sorted and grown ex vivo, then treated with rIL-13 or vehicle only (PBS) for 24 hours and then mRNA profiles were generated by deep sequencing using the MARSseq method. 3 replicates were used.


title: Tuft cells and fibroblasts promote thymus regeneration through activation of a type-2 immune response [IL25KO_ILC2_untreated]

summary: The goal of this study was to determine whether the alarmin IL-25 has an effect on thymic innate lymphoid cells type-2 (ILC2) at steady state. For this purpose we sorted thymic ILC2 from WT or Il25 KO mice and performed bulk RNA-Seq.

overall_design: Thymic ILC2 from young Il25 KO male mice were isolated and mRNA profiles were generated by deep sequencing using the MARSseq method. 4 replicates were used. The control was WT age-matched mice.


title: Tuft cells and fibroblasts promote thymus regeneration through activation of a type-2 immune response [ex_vivo_ILC2]

summary: The goal of this study was to determine whether thymic innate lymphoid cells type-2 (ILC2) activation during acute thymic involution is mediated by the alarmins IL-25 and IL-33. For this purpose we sorted thymic ILC2 from WT mice, treated them ex vivo with recombinant IL-25/IL-33 or both for 24 hours, and performed bulk RNA Seq.

overall_design: ILC2 from thymi of young male WT mice were sorted and grown ex vivo, then treated with rIL-25, rIL-33, both, or vehicle only (PBS) for 24 hours and then mRNA profiles were generated by deep sequencing using the MARSseq method. 3-4 replicates were used.


title: Tuft cells and fibroblasts promote thymus regeneration through activation of a type-2 immune response [Tuft_after_Dex]

summary: The goal of this study was to understand the role of thymic tuft cells in thymic regeneration following dexamethasone-induced acute involution, and determine whether this is affected by IL-13, which is produced by ILC2 upon involution and the receptor for which is expressed by tuft cells. For this purpose we treated WT and Il13ra1 KO mice with dexamethasone, sorted tuft cells from their thymi 3 days after treatment when the thymus begins its recovery, at an earlier time point (18 hours) for comparison, or at a later time point (6d) when IL-13 has been released, and performed bulk RNA Seq.

overall_design: Young male WT and Il13ra1 KO mice were treated with dexamethasone 6 days/3 days/18 hours before sacrifice, and then thymic tuft cells were isolated and mRNA profiles were generated by deep sequencing using the MARSseq method. 3-5 replicates were used. The control for treated WT mice was untreated WT mice, and the control for treated Il13ra1 KO mice was treated age-matched WT mice.


title: A mutation in the low complexity domain of splicing factor hnRNPA1 linked to amyotrophic lateral sclerosis disrupts distinct neuronal RNA splicing networks

first: Yeon

last: Lee

address: 1 Barker Hall

institute: UC Berkeley

summary: Amyotrophic lateral sclerosis (ALS) is a debilitating neurodegenerative disease characterized by loss of motor neurons. Human genetic studies have linked mutations in RNA binding proteins as causative for this disease. The hnRNPA1 protein, a known pre-mRNA splicing factor, is mutated in some ALS patients. Here, two human cell models were generated to investigate how a mutation in the C-terminal low complexity domain (LCD) of hnRNPA1 can cause splicing changes of thousands of transcripts that collectively are linked to the DNA damage response, cilia organization and translation. We show that the hnRNPA1 D262V mutant protein binds to new binding sites on differentially spliced transcripts from genes that are linked to ALS. We demonstrate that this ALS-linked hnRNPA1 mutation alters normal RNA-dependent protein-protein interactions. Furthermore, cells expressing this hnRNPA1 mutant exhibit a cell aggregation phenotype, markedly reduced growth rates, changes in stress granule kinetics and aberrant growth of neuronal processes. This study provides insight into how a single amino acid mutation in a splicing factor can alter RNA splicing networks of genes linked to ALS.

overall_design: We investigated a mutation in the C-terminal low complexity domain (LCD) of hnRNPA1 can alter RNA splicing networks of genes linked to ALS.

first: Donald

last: Rio


title: Tuft cells and fibroblasts promote thymus regeneration through activation of a type-2 immune response [NKT_after_Dex]

summary: The goal of this study was to understand the role of thymic natural killer T cells (NKT) in thymic regeneration following dexamethasone-induced acute involution. For this purpose we treated WT mice with dexamethasone, sorted NKT from their thymi 3 days after treatment when the thymus begins its recovery, or at an earlier time point (18 hours) for comparison, and performed bulk RNA Seq.

overall_design: Young male WT mice were treated with dexamethasone 3 days/18 hours before sacrifice, and then thymic NKT were isolated and mRNA profiles were generated by deep sequencing using the MARSseq method. 4-5 replicates were used. The control was 3 days vehicle-treated age-matched WT mice.


title: Tuft cells and fibroblasts promote thymus regeneration through activation of a type-2 immune response [Tuft_after_irr]

summary: The goal of this study was to understand the role of thymic tuft cells in thymic regeneration following irradiation-induced acute involution. For this purpose we treated WT mice with sublethal irradiation, sorted tuft cells from their thymi 3 days after treatment when the thymus begins its recovery, and performed bulk RNA Seq.

overall_design: Young female WT mice were treated with sublethal irradiation 3 days before sacrifice, and then thymic tuft cells were isolated and mRNA profiles were generated by deep sequencing using the MARSseq method. 4-5 replicates were used. The control was untreated age-matched WT mice.


title: Tuft cells and fibroblasts promote thymus regeneration through activation of a type-2 immune response [TEC_after_rAREG_inj]

summary: The goal of this study was to determine how thymic epithelial cells (TEC) differentiation and gene expression is affected by amphiregulin (AREG), which is produced by ILC2 upon thymic involution and the receptor for which is expressed by early TEC subsets. For this purpose we treated WT mice with recombinant AREG, sorted TEC from their thymi 10 days after treatment when the thymus is recovering and AREG has been released, and performed bulk RNA-Seq.

overall_design: Young male WT mice were injected intrathymically with rAREG 10 days before sacrifice, and then TEC were isolated and mRNA profiles were generated by deep sequencing using the MARSseq method. 4-5 replicates were used. The control was vehicle (PBS) treated age-matched WT mice.


title: Tuft cells and fibroblasts promote thymus regeneration through activation of a type-2 immune response [Fibroblasts_after_irr]

summary: The goal of this study was to understand the role of fibroblasts in thymic regeneration following irradiation-induced acute involution. For this purpose we treated WT mice with sublethal irradiation, sorted fibroblasts from their thymi 3 days after treatment when the thymus begins its recovery, or at an earlier time point (1 day) for comparison, and performed bulk RNA Seq.

overall_design: Young male WT mice were treated with sublethal irradiation 3 days/1 day before sacrifice, and then fibroblasts were isolated and mRNA profiles were generated by deep sequencing using the MARSseq method. 5 replicates were used. The control was untreated age-matched WT mice.


title: Tuft cells and fibroblasts promote thymus regeneration through activation of a type-2 immune response [ILC2_after_Dex]

summary: The goal of this study was to understand the role of thymic innate lymphoid cells (ILC2) in thymic regeneration following dexamethasone-induced acute involution, and determine whether this is activated by the alarmins IL-25 and IL-33. For this purpose we treated WT, Il25 KO or Il33 mice with dexamethasone, sorted ILC2 cells from their thymi 3 days after treatment when the thymus begins its recovery, or at an earlier time point (18 hours) for comparison, and performed bulk RNA-Seq.

overall_design: Young male WT, Il25 KO or Il33 KO mice were treated with dexamethasone, 3 days/18 hours before sacrifice, and then ILC2 were isolated and mRNA profiles were generated by deep sequencing using the MARSseq method. 3-5 replicates were used. For treated WT mice, the control was untreated age-matched WT mice, and for Il25 and Il33 KO treated mice, the control was treated WT age-matched mice.


title: Tuft cells and fibroblasts promote thymus regeneration through activation of a type-2 immune response [Fibroblasts_after_Dex]

summary: The goal of this study was to understand the role of fibroblasts in thymic regeneration following dexamethasone-induced acute involution. For this purpose we treated WT mice with dexamethasone, sorted fibroblasts from their thymi 4 days after treatment when the thymus begins its recovery, or at an earlier time point (18 hours) for comparison, and performed bulk RNA Seq.

overall_design: Young male WT mice were treated with dexamethasone 4 days/18 hours before sacrifice, and then fibroblasts were isolated and mRNA profiles were generated by deep sequencing using the MARSseq method. 3-4 replicates were used. The control was untreated age-matched WT mice.


title: Analysis of differential gene expression related to steroid metabolism in the granulosa cell transcriptome of PCOS patients based on single-cell level

city: Hainan

first: Dandan

address: No.3 Xueyuan Road, Longhua District

institute: Hainan Medical College

summary: The development of granulosa cells has an impact on the development of pcos. We performed single-cell RNA-seq sequencing (scRNA-seq) of granulosa cells to analyse the heterogeneity of PCOS.

overall_design: We performed single-cell RNA-seq sequencing (scRNA-seq) of granulosa cells from three polycystic ovary syndrome (PCOS) infertile groups and three control groups and identified differential genes in PCOS GCs.

first: Jinjing

last: Li

first: Baoguo

last: Xie


title: Tuft cells and fibroblasts promote thymus regeneration through activation of a type-2 immune response [ILC2_after_irr]

summary: The goal of this study was to understand the role of thymic innate lymphoid cells (ILC2) in thymic regeneration following irradiation-induced acute involution, and determine whether this is activated by the alarmin IL-25. For this purpose we treated WT or Il25 KO mice with sublethal irradiation and/or recombinant IL-25, sorted ILC2 cells from their thymi 3 days after treatment when the thymus begins its recovery, and performed bulk RNA Seq.

overall_design: Young WT and Il25 KO mice were treated with sublethal irradiation, rIL-25, or both, 3 days before sacrifice, and then ILC2 were isolated and mRNA profiles were generated by deep sequencing using the MARSseq method. 3-4 replicates were used. For treated WT mice, the control was untreated age-matched WT mice, and for Il25 KO irradiated mice, the control was treated WT age-matched mice.


title: Acquisition of suppressive function by CD4+ conventional T cells limits anti-tumor immunity driven by Treg depletion [RNA-seq II]

city: Cambridge

first: Rahul

last: Roychoudhuri

address: Tennis Court Road

department: Department of Pathology

country: United Kingdom

institute: University of Cambridge

summary: Regulatory T (Treg) cells are essential for immune homeostasis but inhibit immune rejection of cancer. Strategies to disrupt Treg-mediated cancer immunosuppression have been met with limited clinical success, but the underlying mechanisms for this failure are poorly understood. By modeling Treg-targeted immunotherapy in mice, we find that a subset of CD4+ Foxp3- conventional T (Tconv) cells with potent suppressive function undergoes activation and expansion upon depletion of Foxp3+ Treg cells and limits therapeutic efficacy. We noted that Foxp3- Tconv cells within tumors adopt a Treg-like transcriptional profile upon Treg depletion and acquire suppressive function. This is attributable to a Th2-like subset of CD4+ Tconv cells marked by expression of (C-C motif) receptor 8 (CCR8) and enriched in Treg-associated transcripts. CCR8+ Tconv cells are found in mouse and human tumors. Upon Treg depletion, CCR8+ Tconv cells undergo systemic and intratumoral activation and expansion, resulting in IL-10 dependent suppression of anti-tumor immunity. Consequently, conditional deletion of Il10 within T cells augments anti-tumor efficacy upon Treg-depletion in mice, and antibody blockade of IL-10 signaling synergizes with Treg depletion to overcome treatment resistance. These findings reveal a secondary layer of immunosuppression by Tconv cells released upon therapeutic Treg depletion and suggest that broader consideration of suppressive function within the T cell lineage is required for development of effective Treg-targeted therapies.

overall_design: Syngeneic B16-F10 melanoma cells were subcutaneously implanted into Foxp3EGFP-DTR mice and ablated  Treg cells through administration of DTx. T cells were isolated by FACS and subjected to RNA-Seq analysis

first: Sarah

last: Whiteside

first: Francis

last: Grant

first: James

last: Clarke

first: Alex

last: Evans


title: Identification of early gene expression profiles governing long-lasting antibody responses to the Ebola vaccine Ad26.ZEBOV/MVA-BN-Filo

city: CRETEIL

first: Cecile

last: LEFEBVRE

address: 51 Avenue du Maréchal de Lattre de Tassigny, Bât R+1 Eq16 U955

institute: INSERM

summary: Ebolavirus disease (EVD) is a severe hemorrhagic fever with a high fatality rate. In this study, we comprehensively investigated transcriptome profiles at 0, 3 hours, 1 and 7 days after vaccination with Ad26.ZEBOV and MVA-BN-Filo. Three hours after Ad26.ZEBOV injection, we observed an increase in gene abundance related to antigen presentation, sensing, and T- and B-cell receptors. The highest response occurred one day after Ad26.ZEBOV injection, with an increase in the expression of genes for interferon-induced antiviral molecules, monocyte activation, and sensing receptors. This response was mainly shaped by the HESX1, ATF3, ANKRD22, and ETV7 transcription factors. A plasma-cell signature was observed on day 7 post-Ad26.ZEBOV vaccination, with an increase of the abundance of CD138, MZB1, CD38, and CD79A, as well as that of immunoglobulin genes. Importantly, we identified early-expressed genes correlated with the magnitude of the antibody response 21 days after the MVA-BN-Filo and 364 days after Ad26.ZEBOV vaccinations. Our results provide early gene signatures that characterize an effective vaccine antibody response against Ebola.

overall_design: Gene expression profiles of blood samples from subjects vaccinated volunters with Ad26.ZEBOV/MVA-BN-Filo (EBOVAC trial)

first: Cécile

last: Lefebvre

first: Mélany

last: Durand

first: Hakim

last: Hocini

first: Fabiola

last: Blengio

first: Laura

last: Richert

first: Rodolphe

last: Thiébaut

first: Yves

last: Lévy


title: Tuft cells and fibroblasts promote thymus regeneration through activation of a type-2 immune response

first: Jakub

last: Abramson

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

overall_design: Refer to individual Series


title: Acquisition of suppressive function by CD4+ conventional T cells limits anti-tumor immunity driven by Treg depletion.


title: Acquisition of suppressive function by CD4+ conventional T cells limits anti-tumor immunity driven by Treg depletion [scRNA-seq]

overall_design: Syngeneic B16-F10 melanoma cells were subcutaneously implanted into Foxp3EGFP-DTR mice and ablated  Treg cells through administration of DTx. T cells were isolated by FACS and subjected to scRNA-Seq analysis


title: Single Cell sequencing analysis of intrapulmonary airway cells from wildtype mouse and Sox2 conditional knockout mouse

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: The goal of this study was to compare intrapulmonary airway cells obtained from wildtype mice to Sox2cKO mice.

overall_design: One sample of adult mouse airway epithelial cells and one sample of adult Sox2-CreERT2; Sox2-flox; R26R-EYFP lineage traced mice were prepared for library preparation.

first: Kazushige

last: Shiraishi

first: Edward

last: Morrisey


title: Effect of pre-miR-1307 overexpression on isomiR levels in MDA-MB-231 breast cancer cells

city: Heidelberg

first: Birgitta

middle: E.

last: Michels

address: Im Neuenheimer Feld 580

department: Molecular Genome Analysis

institute: DKFZ

type: Non-coding RNA profiling by high throughput sequencing

summary: In the recent past, the impact of isomiR expression changes in cancer has gained increasing interest. Here, we stably overexpress pre-miR-1307, a pre-miRNA which is frequently upregulated in cancer, and assess the effect on isomiR expression. While we see robust and significant upregulation of the canonical form miR-1307-3p|0 and its abundant 5'isomiR miR-1307-3p|1, as well as of the canonical miR from the 5p arm (miR-1307-5p|0), the overexpression of pre-miR-1307 did not lead to global alterations in isomiR expression patterns. These data validate the suitability of our model cell line for the analysis of the effects of joint upregulation of miR-1307-3p|0, -3p|1 and -5p|0.

overall_design: MDA-MB-231 breast cancer cells were stably lentivirally transduced with constructs overexpressing pre-miR-1307 or two independent C.elegans pre-miRNA constructs and isomiR expression levels were quantified by small RNA sequencing of three biological replicates per condition.

first: Cindy

last: Körner

first: Angelika

last: Wörner


title: An evolutionary epigenetic clock in plants [Accessions]

city: Freising

first: Zhilin

last: Zhang

state: Bavaria

address: Emil-Ramann-Str. 4

department: School of Life Sciences

institute: Technical University of Munich

type: Methylation profiling by high throughput sequencing

summary: Molecular clocks are the basis for dating the divergence between lineages over macro-evolutionary timescales (~104-108 years). However, classical DNA-based clocks tick too slowly to inform us about the recent past. Here, we demonstrate that stochastic DNA methylation changes at a subset of cytosines in plant genomes possess a clock-like behavior. This ‘epimutation-clock’ is orders of magnitude faster than DNA-based clocks and enables phylogenetic explorations on a scale of years to centuries. We show experimentally that epimutation-clocks recapitulate known topologies and branching times of intra-species phylogenetic trees in the selfing plant A. thaliana and the clonal seagrass Z. marina, which represent the two primary modes of plant reproduction. This discovery will open new possibilities for high-resolution temporal studies of plant biodiversity.

overall_design: We used the selfing plant Arabidopsis thaliana as a model to generate mutation accumulation lines (MA-lines) from seven diverse natural accessions (i.e., genotypes) as founders.

first: Robert

middle: J

last: Schmitz

first: Frank

last: Johannes


title: Acquisition of suppressive function by CD4+ conventional T cells limits anti-tumor immunity driven by Treg depletion [RNA-seq]

first: Rahul

last: Roychoudhuri

first: Sarah

last: Whiteside

first: Francis

last: Grant

first: James

last: Clarke

first: Alex

last: Evans


title: Maternal KLF17 regulates zygotic genome activation in the mouse

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

summary: To investigate the change of embryo transcriptome upon the inhibition of transition, we treated  the late zygote with CHX and performed RNA-seq; To test KLF17 necessity for ZGA transcripts expression and embryo development, we next generated conditional knockout mouse models for Klf17 and collected embryo to perform RNA-seq and Stacc-seq.

overall_design: We selected seven stages of oocyte and embryo when we treated embyo with CHX; For the transcriptome of maternal Klf17 knockout embryo, We selected two stages of embryo; For the Stacc-seq of maternal Klf17 knockout embryo, only early 2 cell stage of embryo was used.

first: Yue

last: Hu

first: Ran

last: Huo

first: Jiongshong

first: Yuxiang

last: Wang

first: Chao

last: Ren


title: Type 2 inflammation reduces SARS-CoV-2 replication in the airway epithelium in allergic asthma through functional alteration of ciliated epithelial cells II

status: Public on Jan 10 2024

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Despite well-known susceptibilities to other respiratory viral infections, individuals with allergic asthma have shown reduced susceptibility to severe coronavirus disease 2019 (COVID-19).

overall_design: Bronchial AECs from healthy nonsensitized children (n= 17) and children with allergic asthma (n= 15) aged 6 to 18 years (Tables I and II) were obtained from subjects while under general anesthesia; the cells were obtained by using 4-mm Harrell unsheathed bronchoscope cytology brushes (ConMed, Utica, NY). As we and others have described33,34 an unprotected brush was inserted through an endotracheal tube, advanced until resistance was felt, and rubbed against the airway surface for 2 seconds. Cells were then seeded onto T-25 cell culture flasks precoated with type I collagen and proliferated under submerged culture conditions

first: Naresh

last: Jayavelu

first: Matthew

last: Altman

first: Basilin

last: Benson

last: Dufort

first: Elizabeth

last: Vanderwall

first: Lucille

last: Rich

first: Maria

last: White

first: Patrice

last: Becker

first: Alkis

last: Togias

first: Daniel

last: Jackson

first: Jason

middle: S

last: Debley


title: FLUAV RAM-IGIP: A modified live influenza virus vaccine that enhances humoral and mucosal responses against influenza.  Vaccine Encoding the IgA-Inducing Protein

city: Athens

middle: Roberto

last: Perez

state: GA

address: 953 College Station Road

institute: University of Georgia

summary: Influenza A virus (FLUAV) poses a significant threat to both humans and animals. While vaccination serves as the primary defense against influenza, the effectiveness of currently approved vaccines is suboptimal. To address this issue, we have developed modified live virus (MLV) vaccines against influenza using genome rearrangement techniques targeting the internal gene segments of FLUAV. The rearranged M2 (RAM) strategy involves cloning the M2 ORF downstream of the PB1 ORF in segment 2 and incorporating multiple early stop codons within the M2 ORF in segment 7. Additionally, the IgA-inducing protein (IGIP) coding region was inserted into the HA segment to further attenuate the virus and enhance protective mucosal responses. RAM-IGIP viruses exhibit similar growth rates to wild type (WT) viruses in vitro and remain stable during multiple passages in cells and embryonated eggs. The safety, immunogenicity, and protective efficacy of the RAM-IGIP MLV vaccine against the prototypical 2009 pandemic H1N1 strain A/California/04/2009 (H1N1) (Ca/04) were evaluated in Balb/c mice and compared to a prototypic cold-adapted live attenuated virus vaccine. The results demonstrate that the RAM-IGIP virus exhibits attenuated virulence in vivo. Mice vaccinated with RAM-IGIP and subsequently challenged with an aggressive lethal dose of the Ca/04 strain exhibited complete protection. Analysis of the humoral immune response revealed that the inclusion of IGIP enhanced the production of neutralizing antibodies and augmented the antibody-dependent cellular cytotoxicity response. Similarly, the RAM-IGIP potentiated the mucosal immune response against various FLUAV subtypes. Moreover, increased antibodies against NP and NA responses were observed. These findings support the development of MLVs utilizing genome rearrangement strategies in conjunction with the incorporation of immunomodulators.

first: C

last: Caceres

first: L

last: Gay

first: Aarti

last: Jain

first: Teresa

last: Mejias

first: Matias

last: Cardenas

first: Brittany

last: Seibert

first: Flavio

last: Cargnin

first: Brianna

last: Cowan

first: Ginger

last: Geiger

first: Amy

last: Vincent

first: Silvia

last: Carnaccini

first: D

middle: H

last: Davies

first: Daniela

last: Rajao


title: Type 2 inflammation reduces SARS-CoV-2 replication in the airway epithelium in allergic asthma through functional alteration of ciliated epithelial cells I

first: Stephanie

last: Osmond

first: Naresh

last: Jayavelu

first: Matthew

last: Altman

first: Basilin

last: Benson

last: Dufort

first: Elizabeth

last: Vanderwall

first: Lucille

last: Rich

first: Maria

middle: P

last: White

first: Patrice

last: Becker

last: Togias


title: HuR promotes triglyceride synthesis and intestinal fat absorption

first: liu

last: cihang

address: Xueyuan Road

institute: Peking University Health Science Center

summary: Triacylglyceride (TAG) synthesis in the small intestine determines the absorption of dietary fat, but the mechanisms underlying are largely unknown. Here, we report that the RNA-binding protein HuR (ELAVL1) promotes TAG synthesis in the small intestine. HuR associates with the 3’UTR of Dgat2 mRNA and the introns 1 of Mgat2 pre-mRNA. Association of HuR with Dgat2 3’UTR stabilizes Dgat2 mRNA, while association of HuR with intron 1 of Mgat2 pre-mRNA promotes the processing of Mgat2 pre-mRNA. Intestinal epithelium-specific HuR knockout reduces the expression of DGAT2 and MGAT2, thereby reducing the dietary fat absorption through TAG synthesis and mitigating high-fat diet (HFD)-induced non-alcoholic fatty liver disease (NAFLD) and obesity. Our findings highlight a critical role of HuR in promoting dietary fat absorption.

overall_design: To investigate the function of HuR in intestinal fat absorption, we generated a conditional intestinal epithelium-specific HuR knockout (cKO) mouse. RNA was extracted from the proximal jejunum in HuR cKO and their wild-type (WT) littermates. We then performed gene expression profiling analysis using data obtained from RNA-seq of 5 WT and cKO mice. Comparative gene expression profiling analysis of RNA-seq data  for cKO mice and its WT littermates.

first: Cihang

last: Liu

first: Yunping

last: Lin

first: Ying

last: Wang

first: Shuyong


title: Paraspeckle protein NONO attenuates vascular calcification by inhibiting BMP2 transcription

first: Yue

last: Lu

state: Shandong

address: 44# Wenhua Xi Road

institute: Shandong university

summary: Vascular calcification is a common and life-threatening complication in patients with chronic kidney disease, in which osteogenic differentiation of vascular smooth muscle cells (VSMCs) plays an essential role. Paraspeckle protein NONO is a multifunctional protein involved in many nuclear biological processes but its role in vascular calcification and osteogenic differentiation of VSMCs remains unclear.By RNA sequencing analysis in primary mouse VSMCs with or without NONO knockout, we observed significant changes of genes important in regulating vascular function and osteogenic differentiation of VSMCs.

overall_design: The gene expression of 3 samples from NONO-knockout (ko) VSMC was compared to 3 wide-type (wt) samples by RNA sequencing

first: Meng

last: Zhang

first: Yun

first: Cheng


title: Role of IGF2R in beta cells

city: Maebashi

first: Jun

last: Shirakawa

address: 3-39-15 Showa-machi

department: Institute for Molecular and Cellular Regulation

institute: Gunma University

summary: RNA-seq data of isolated pancreatic islets of one-year-old  wild type and IGF2 receptor knock out mice.

overall_design: We then performed differntially expressed genes analysis using data obtained from RNA-seq of above-mentioned isolated islets

first: Rohit

middle: N

last: Kulkarni