title: Lineage tracking reveals origins and relative affinities of antibodies produced by two subsets of memory B cells

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

summary: Memory B cells comprise a heterogenous group of cells that differ in origin, and phenotype. During the early phases of the immune response, activated B cells can differentiate into IgM expressing memory cells, short-lived plasma cells or seed germinal centers (GCs). The memory compartment is subsequently enriched by B cells that have been through several rounds of division and selection in the GC. Here we report on the use of an unbiased lineage tracking approach to explore the origins and properties of memory B cell subsets in mice with an intact immune system. We find that activated B cells continue to differentiate into memory B cells throughout the immune response. When defined on the basis of their origins, the memory B cells originating from activated B cells or GCs differ in isotype and overall gene expression, somatic hypermutation, and in their affinity for antigen.

overall_design:
Memory B cell subsets in mice with an intact immune system were examined.
Cells were sorted directly into a solution of 1% 2-β-mercaptoethanol (Sigma) in TCL Buffer (Qiagen, 1031576) and RNA was isolated using RNAClean XP Beads (Beckman Coulter, A63987). Near full-length mRNA was reverse transcribed as previously described (Islam et al., 2014) (Trombetta et al., 2014). Multiplexed libraries were prepared for sequencing using a Nextera XT DNA Library Preparation Kit (Illumina). Libraries were sequenced on an Illumina NovaSeq 6000 at the Rockefeller University Genomics Core.

first: Charlotte

last: Viant

first: Tobias

last: Wirthmiller

first: Mohamed

middle: A

last: ElTanbouly

first: Spencer

middle: T

last: Chen

first: Melissa

last: Cipollac

first: Victor

last: Ramos

first: Leonidas

last: Stamatatos

first: Michel

last: Nussenzweig


title: Targeting P300/CBP reveals discrete regulation of transcription and chromatin accessibility by histone acetylation [ATACseq]

status: Public on May 11 2021

city: South San Francisco

first: Simon

middle: J

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

country: USA

institute: AbbVie

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To test the long-standing paradigm directly linking histone acetylation with chromatin decompaction and transcriptional output, we used integrated epigenomic and transcriptomic analyses following acute inhibition of major cellular lysine acetyltransferases P300 and CBP. We discovered that P300/CBP inhibition dynamically perturbs acetylation kinetics and dramatically suppresses core-transcriptional networks in the absence of changes to chromatin accessibility. CRISPR/Cas9 screening identified NCOR1 and HDAC3 transcriptional co-repressors as the principle antagonists of P300/CBP by counteracting acetylation turnover kinetics. Finally, deacetylation of H3K27 provides nucleation sites for reciprocal methylation switching, a feature that can be exploited therapeutically by concomitant KDM6A and P300 inhibition. Overall, this study indicates that the steady-state histone acetylation-methylation equilibrium functions as a molecular rheostat governing cellular transcription that is amenable to therapeutic exploitation as an anti-cancer regimen.

overall_design: Examination of changes in chromatin accessibility by ATAC-seq following catalytic inhibition of P300/CBP


title: Apolipoprotein E promotes immune suppression in pancreatic cancer through NF-kB-mediated production of CXCL1

status: Public on May 12 2021

city: Ann Arbor

first: Marina

last: Pasca di Magliano

state: Michigan

address: 1500 E Medical Center Drive

department: Surgery

institute: University of Michigan

type: Expression profiling by high throughput sequencing

summary: This study sought to determine the role of Apolipoprotein E (ApoE) in mediating immune suppresion in pancreatic cancer. Our data show ApoE regulates T cell infiltration through NF-kB mediated Cxcl1 production.

overall_design: This dataset includes 7940b tumor cells derived from the KrasLSL-G12D/+; Trp53LSL-R172H/+; Pdx1-Cre (KPC) mouse model of pancreatic cancer treated with either vehicle or 0.3ug/mL of murine recombinant ApoE (rApoE). Vehicle (n=3) and rApoE (n=3).

first: Howard

middle: C

last: Crawford

first: Samantha

middle: B

last: Kemp


title: Identification of LARP1 targets in naive CD4 T cells [eCLIP]

status: Public on May 13 2021

city: Glasgow

first: Alison

last: Galloway

address: Garscube Estate, Switchback Road

country: United Kingdom

institute: Beatson CRUK

summary: We investigated the role of RNMT in T cells using an Rnmt conditional knockout mouse model. We report that the mRNA cap methyltransferase, RNMT, supports naïve T cell survival and activation-induced proliferation. We demonstrate that RNMT has gene-specific impacts in T cells, selectively regulating expression of terminal polypyrimidine tract (TOP) mRNAs which are targets of the m7G-cap binding protein LARP1. These LARP1 eCLIP experiments determine the RNA binding sites of LARP1 in naive CD4 T cells from Rnmt cKO and control mice.

overall_design: LARP1 seCLIP (single end cross linking immunoprecipitation- an enhanced iCLIP method) libraries were prepared from naïve CD4 T cells magnet sorted from mouse lymph nodes. Proteins were crosslinked to RNA using UV light prior to cell lysis, RNA was partially digested, then LARP1-crosslinked RNA immunoprecipitated and used to prepare libraries. Here we first compared three different antibodies for LARP1 seCLIP in CD4 T cells, then selected one antibody to prepare libraries from Rnmt fl/fl (control) and Rnmt fl/fl CD4cre+ (Rnmt cKO) CD4 T cells. Each experiment has libraries prepared with a LARP1 antibody, an isotype control antibody, and a size matched input control.

first: Victoria

middle: H

last: Cowling


title: RNMT regulates the naïve CD4 T cell transcriptome

summary: We investigated the role of RNMT in T cells using an Rnmt conditional knockout mouse model. We report that the mRNA cap methyltransferase, RNMT, supports naïve T cell survival and activation-induced proliferation. We demonstrate that RNMT has gene-specific impacts in T cells, selectively regulating expression of terminal polypyrimidine tract (TOP) mRNAs which are targets of the m7G-cap binding protein LARP1. These RNAseq experiments investigate the effect of Rnmt cKO on the naïve CD4 T cell transcriptome.

overall_design: Sequencing of rRNA-depleted RNA from naïve CD4 T cells sorted from the lymph nodes of Rnmt fl/fl CD4cre (Rnmt cKO) and Rnmt fl/fl (control) mice.

first: Aneesa

last: Kaskar

first: Olga

last: Suska


title: A customizable purification assay designed for small-RNA biomarker identification and functional evaluation of circulating exosomes: Exosome Capture by AnTibody of CHoice and Enzymatic Release (exo-CATCHER)

city: Jerusalem

first: Iddo

middle: Z.

last: Ben-Dov

address: Ein Kerem

department: Nephrology and Hypertension

country: Israel

institute: Hadassah Medical Center

summary: Circulating nucleic acids, encapsulated within exosomes, can provide a remote cellular snapshot of biomarkers associated with disease, however selective exosome isolation is critical. Current laboratory-based purification techniques rely on the physical properties of exosomes for selection, rather than their inherited cellular characteristics. Therefore, we established a highly selective purification assay, termed exosome Capture by AnTibody of CHoice and Enzymatic Release (exo-CATCHER), designed for high-throughput analysis of low-abundance small-RNA cargos by next-generation sequencing. We demonstrated its sensitivity by specifically isolating and sequencing small-RNA from mouse exosomes spiked into human plasma. Furthermore, we used Western blotting, nanoparticle tracking, and transmission electron microscopy to validate, quantify, and demonstrate capture and release of intact exosomes. As proof of principle, we utilized exo-CATCHER to purify serum exosomes from mildly and severely ill Covid-19 patients, identified, and validated hsa-miR-146a and hsa-miR-126-3p to be significantly downregulated in a small sample set of severely ill patients. We used exo-CATCHER to purify intact exosomes from high IgG titer convalescent sera and confirmed unexpected neutralizing properties, against SARS-CoV-2 in vitro, identified using ultracentrifuged exosomes, not observable with exosomes from sera with IgG titers below quantification level. Exo-CATCHER represents a versatile molecular assay for highly specific purification of circulating exosomes.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: miRNA profiling of serum, plasma and antibody-captured circulating exosomes

first: Megan

last: Mitchell

middle: Z

first: Masood

last: Kamali‐Moghaddam

first: Olivier

last: Loudig


title: Targeting P300/CBP reveals discrete regulation of transcription and chromatin accessibility by histone acetylation [RNAseq]

overall_design: Profile changes in transcription following catalytic inhibition of P300/CBP in multiple myeloma by RNA-sequencing


title: Targeting P300/CBP reveals discrete regulation of transcription and chromatin accessibility by histone acetylation [NOMEseq]

type: Methylation profiling by high throughput sequencing

overall_design: Examination of changes in nucleosome position and DNA methylation by NOMe-seq following catalytic inhibition of P300/CBP


title: TF ChIP-seq from HepG2 (ENCSR660ENW)

status: Public on May 23 2021

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
ChIP-Seq on HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and pervasive recursive splicing [nascent RNA profiling]

city: Bethesda

first: Daniel

middle: R

last: Larson

address: 41 Medlar Dr.

institute: NIH

summary: The coupled activities of RNA polymerase and the spliceosome are responsible for the abundance and isoform composition of mRNA in human cells. However, the dynamics of these megadalton enzymatic complexes working in concert on endogenous genes have not been described. Here, we establish a quasi-genome-scale platform for observing synthesis and processing kinetics of single nascent RNA molecules in real time. We find that all observed genes show transcriptional bursting. We also observe large kinetic variation in intron removal for single introns in single cells which is inconsistent with deterministic splice site selection. Transcriptome-wide footprinting of the U2AF complex further reveals widespread splice site selection within introns. We propose and validate a unified theoretical model for transcription and splicing based on pervasive stochastic recursive splicing.

overall_design: Nascent RNA profiling in HBEC cells

first: Yihan

last: Wan


title: Targeting P300/CBP reveals discrete regulation of transcription and chromatin accessibility by histone acetylation [Hi-C]

overall_design: Examination of changes in chromosome conformation by Hi-C following catalytic inhibition of P300/CBP


title: Targeting P300/CBP reveals discrete regulation of transcription and chromatin accessibility by histone acetylation [CRISPR]

overall_design: Determining mechanisms of acquired resistance to catalytic P300/CBP inhibition by genome-scale CRISPR/Cas9 screening


title: Targeting P300/CBP reveals discrete regulation of transcription and chromatin accessibility by histone acetylation [singlecellseq]

overall_design: Examination of changes in gene expression and chromatin accessability by single cell seuqencing in CLL following catalytic inhibition of P300/CBP


title: Targeting P300/CBP reveals discrete regulation of transcription and chromatin accessibility by histone acetylation [PRO-seq]

overall_design: Examination of changes in transcriptionally engaged RNA polymerase II by PRO-seq following catalytic inhibition of P300/CBP


title: Targeting P300/CBP reveals discrete regulation of transcription and chromatin accessibility by histone acetylation [ChIPseq]

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: Examination of changes in histone marks and chromatin occupancy by ChIP-seq following catalytic inhibition of P300/CBP


title: ACAA2 genome-binding patterns before and after transverse aortic constriction in C57Bl/6J mice on different diets [ACAA2]

city: Newark

first: Maha

last: Abdellatif

state: NJ

address: 185 S. Orange Ave.

department: Cell Biology and Molecular Medicine

institute: Rutgers-University

summary: Acetyl-CoA acyltransferace 2 (ACAA2) associates with chromatin at promoter sites in the heart of C57Bl/6J mice. A high-fat vs. low-fat diet reduces it promoter abundance, whereas, transverse aortic constriction (TAC) increases it slight.

overall_design: C57Bl/6J mice were fed either a low-fat (10 Kcal%, Fat 10 or control),  or high-fat (60 Kcal%, Fat 60 or HiFat) diet for 4 days before subjecting them to a sham or transverse aortic constriction (TAC) surgeries. The mice were maintained on the same diet for another week, before they were assessed by echocardiography, the hearts isolated, chromatin extracted , and subjected to anti-ACAA2 ChIP-Seq

last: Adellatif


title: The effect of diet on H3K9-butyryl and H3K9-acetyl in the heart before and after transverse aortic constriction in C57Bl/6J mice

summary: Mice (C57Bl/6J) that are fed increasing levels of dietary fat (0, 10, and 60 Kcal%) show a parallel increasing decline in global promoter-H3K9-butyryl (H3K9Bu), but none in promoter-H3K9-acetyl (H3K9ac), in the heart. Additionally, transverse aortic constriction (TAC) induces a further decline in H3K9Bu, compared to an increase in H3K9ac.

overall_design: C57Bl/6J mice were fed either a fat-free (0 Kcal%, Fat 0), low-fat (10 Kcal%, Fat 10 or control),  or high-fat (60 Kcal%, Fat 60 or HiFat) diet for 4 days before subjecting them to a sham or transverse aortic constriction (TAC) surgeries. The mice were maintained on the same diet for another week, before they were assessed by echocardiography, the hearts isolated, chromatin extracted , and subjected to anti-H3K9Bu and anti-H3K9ac ChIP-Seq


title: New insights into the maize disease lesion mimics-conferred defense response revealed by integrated transcriptomics and metabolomics analysis

city: zheng zhou

first: xiaohuan

last: mu

address: zhengzhou long zi hu

country: China

institute: Henan Agricultural University

summary: We performed integrated transcriptomics and metabolomics analysis on three dominant Les mutants Les4, Les10 and Les17.

overall_design: Transcriptomics analysis on three dominant Les mutants Les4, Les10 and Les17.

first: Jiankun

last: Li

first: Liping

last: Xu

first: Zhuangzhuang

last: Dai

first: Tianyuan

last: Fan

first: Teng

last: Jing

first: Mengyao

last: Chen

first: Mingyue

last: Gou


title: H3K9-butyryl (H3K9Bu) and H3K9-acetyi (H3K9ac) genome patterns before and after transverse aortic constriction in Balb/cJ and Balc/cByJ mice

summary: Balb/cJ mice on a low-fat diet show a decline in promoter H3K9-butyryl (H3K9Bu) in the heart, after subjecting them to transverse aortic constriction (TAC). In contrast, Balb/cByJ, which has a deletion in the ACADS gene, exhibit an increase in promoter H3K9Bu. Conversely, H3K9ac increases in the former and declines in the latter.

overall_design: Balb/cJ and Balb/cByJ mice were fed either a low-fat (10 Kcal%) diet for 4 days before subjecting them to a sham or transverse aortic constriction (TAC) surgeries. The mice were maintained on the same diet for another week, before they were assessed by echocardiography, the hearts isolated, chromatin extracted , and subjected to anti-H3K9Bu and anti-H3K9ac ChIP-Seq


title: Targeting P300/CBP reveals discrete regulation of transcription and chromatin accessibility by histone acetylation [TTseq]

first: Simon

last: Hogg

overall_design: Examination of changes in nascent RNA production by TT-seq following catalytic inhibition of P300/CBP


title: Diet- and stress-induced changes of RNA in mouse heart

summary: RNA-Seq data show that stress combined with a high-fat versus a fat-free diet, evokes greater changes in gene expression

overall_design: Mice were fed either a fat-free (0 Kcal%) or a high-fat (60 Kcal%) diet for 4 days before subjecting them to a sham or transverse aortic constriction (TAC) surgeries. The mice were maintained on the same diet for another week, before they were assessed by echocardiography, the hearts isolated, RNA extracted, sequenced using Illumina NextSeq 500, and analyzed by DESeq2 at 10%FDR (adjusted p-value).


title: Liver transcriptome dynamics during hibernation are shaped by a shifting balance between transcription and RNA stability

status: Public on May 10 2021

city: Aurora

first: Sandy

last: Martin

state: CO

department: Cell and Developmental Biology

institute: University of Colorado School of Medicine

summary: Hibernators dramatically lower metabolism to save energy while fasting for months. Prolonged fasting challenges metabolic homeostasis, yet small-bodied hibernators emerge each spring ready to resume all aspects of active life, including immediate reproduction. The liver is the body’s metabolic hub, processing and detoxifying macromolecules to provide essential fuels to brain, muscle and other organs throughout the body. Here we quantify changes in liver gene expression across several distinct physiological states of hibernation in 13-lined ground squirrels, using RNA-seq to measure the steady-state transcriptome and GRO-seq to measure transcription for the first time in a hibernator. Our data capture key timepoints in both the seasonal and torpor-arousal cycles of hibernation. Strong positive correlation between transcription and the transcriptome indicates that transcriptional control dominates the known seasonal reprogramming of metabolic gene expression in liver for hibernation. During the torpor-arousal cycle, however, discordance develops between transcription and the steady-state transcriptome by at least two mechanisms: 1) although not transcribed during torpor, some transcripts are unusually stable across the torpor bout; and 2) unexpectedly, on some genes, we document continuing, slow elongation with a failure to terminate transcription across the torpor bout. While the steady-state RNAs corresponding to these readthrough transcripts did not increase during torpor, they did increase shortly after rewarming despite their simultaneously low transcription. Both of these mechanisms would assure the immediate availability of functional transcripts upon rewarming. Integration of transcriptional, post-transcriptional and RNA stability control mechanisms, all demonstrated in these data, likely initiate a serial gene expression program across the short euthermic period that restores the tissue and prepares the animal for the next bout of torpor.

overall_design: RNA-seq libraries were prepared from replicate samples (n=5) from five physiolocial groups to capture key changes in circannual hibernation plus one extra liver sequenced more deeply for  annotation purposes only (L200); 26 samples total

first: Sandra

middle: L


title: The effect of transverse aortic constriction on gene expression in Balb/cJ versus Balb/cByJ(∆ACADS) mice hearts

summary: RNA-Seq data show that ACADS knockout curbs gene expression after transverse aortic constriction in mice

overall_design: Balb/cJ and Balb/cByJ mice were fed either a low-fat (10 Kcal%) diet for 4 days before subjecting them to a sham or transverse aortic constriction (TAC) surgeries. The mice were maintained on the same diet for another week, before they were assessed by echocardiography, the hearts isolated, RNA extracted, sequenced using Illumina NextSeq 500, and analyzed by DESeq2 at 10%FDR (adjusted p-value).


title: Immune checkpoint blockade reprograms systemic immune landscape and tumor microenvironment in obesity-associated breast cancer

status: Public on May 08 2021

city: Memphis

first: Liza

last: Makowski

state: Tennessee

address: 19 South Manassas St

department: Medicine- Heme Onc

institute: UTHSC

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

overall_design: Refer to individual Series


title: Immune checkpoint blockade reprograms systemic immune landscape and tumor microenvironment in obesity-associated breast cancer [tumor]

summary: Immune checkpoint blockade (ICB) has improved outcomes in some cancers. A major limitation of ICB is that a majority of patients fail to respond, which is partly attributable to immunosuppression. Obesity appears to improve immune checkpoint therapies in some cancers but impacts on breast cancer (BC) remain unknown. In obese mice fed an obesogenic or lean controls on a low fat  diet, mice are injected with BC cells andtreated with anti-PD-1 or control. Obesity leads to immunosuppression systemically in tumor-free mice that is exacerbated in tumor-bearing mice. Obesity augments tumor incidence and progression. Anti-PD-1 induces regression in lean mice and potently abrogates progression in obese mice. Anti PD-1 significantly reduces immunosuppressive cells and elevates anti-tumor immune cells. Lamb2, downregulated by anti-PD1, significantly predict patient survival. Last, we identify a microbial signature associated with anti-PD-1 efficacy. In sum, anti-PD-1 is highly efficacious in obese mice by reinvigorating durable antitumor immunity.

overall_design: RNA-seq data from bulk tumors in obese mice treated with anti-PD-1 or IgG2a isotype control

first: Joe

last: Pierre

first: David

middle: N

last: Hayes


title: Spatial Transcriptomics of human fetal liver

city: Shenzhen

first: Hou

last: Xianliang

address: 1017 Dongmen North Road, Luohu District, Shenzhen

institute: The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital)

summary: We use single-cell RNA-seq technology for unbiased analysis of fetal livers over developmental time from 8 postconception weeks (PCW) and 17 PCW in humans.

overall_design: The sample contained one  8-postconception weeks and one 17-postconception weeks fetal livers.

first: Xianliang

last: Hou

first: Yong


title: Methylome patterns of cattle adaptation to heat stress

status: Public on May 07 2021

city: Piacenza

first: Marcello

last: Del Corvo

address: Via Emilia Parmense, 84

department: Institute of Zootechnics, Faculty of Agricultural, Food and Environmental Sciences

country: Italy

institute: Università Cattolica del S. Cuore

summary: Heat stress has a detrimental impact on cattle health, welfare and productivity by affecting gene expression, metabolism and immune response, but little is known on the epigenetic mechanisms mediating the effect of temperatureat the cellular and organism level. In this study, we investigated genome-wide DNA methylation in blood samples collected from 5 bulls of the heat stress resilient Nellore breed and 5 bulls of the Angus that are more heat stress susceptible, exposed to the sun and high temperature-high humidity during the summer season of the Brazilian South-East region. The methylomes were analyzed during and after the exposure by Reduced Representation Bisulfite Sequencing, which provided genome-wide single-base resolution methylation profiles. Significant methylation changes between stressful and recovery periods were observed in 822 genes. Among these, 352 were only seen in Angus, 367 were specific to Nellore, and 103 showed significant changes in methylation patterns in both breeds. KEGG and Gene Ontology (GO) enrichment analyses showed that responses were breed-specific. Interestingly, in Nellore significant genes and pathways were mainly involved in stress responses and cellular defense and were undermethylated during heat stress. Whereas in Angus the response was less focused. These preliminary results suggest that heat challenge induces changes in methylation patterns in specific loci, which should be further scrutinized to assess their role in heat tolerance.

overall_design: Methylation profile of Nellore and Angus bulls exposed to the sun and high temperature-high humidity during the summer season of the Brazilian South-East region.

first: Barbara

last: Lazzari

first: Emanuele

last: Capra

first: Ludmilla

last: Zavarez

first: Marco

last: Milanesi

first: Yuri

last: Utsunomiya

first: Adam

last: Taiti

first: Alessandra

last: Stella

first: Guillerme

last: De Paula Nogueira

first: Josè

middle: F

last: Garcia

first: Paolo

last: Marsan


title: A regulatory role for CHD4 in maintenance of the spermatogonial stem cell pool

status: Public on May 06 2021

city: Callaghan

first: Tessa

last: Lord

state: NSW

address: University Dr

country: Australia

institute: University of Newcastle

summary: To understand the role of the nucleosome remodelling protein CHD4 in regulating spermatogonial stem cell function, we performed single cell RNA-sequencing on undifferentiated spermatogonia from primary culture that had been transfected with either control (non-targeting) siRNA or Chd4 siRNA. Transcriptome profiling revealed reduced expression of ‘self-renewal’ genes following Chd4 knockdown, along with increased expression of signature progenitor genes. Overall, CHD4 was demonstrated to primarily act as an activator of gene expression in SSCs. In pairing these data with additional analyses, including use of an Id4-eGfp transgenic mouse line, spermatogonial transplantation, and co-immunoprecipitation experiments: the findings of our study demonstrated a previously unappreciated and fundamental role for CHD4 in controlling fate decisions in the spermatogonial pool.

overall_design: Examination of undifferentiated spermatogonia from primary culture at 24h post-transfection with control or Chd4 siRNA

first: Jon

middle: M

last: Oatley


title: Reduced representation bisulfite sequencing (RRBS) of chronic lymphocytic leukemia (CLL) samples

city: Beijing

first: Heng

last: Pan

address: 49 North Garden Rd., Haidian District

institute: Peking University Third Hospital

summary: The field of cancer genomics has been empowered by increasingly sophisticated inference tools to distinguish driver mutations from the vastly greater number of passenger mutations. Similarly, promoter DNA hypermethylation has been shown to drive cancer through inactivation of tumor suppressor genes (TSGs), but growing malignant populations also accrue pervasive stochastic epigenetic changes in DNA methylation (DNAme), which likely carry little functional impact. However, the development of DNAme inference methods has lagged behind, providing limited ability to robustly differentiate driver DNAme changes (epidrivers) from stochastic, passenger DNAme changes. To address this challenge, we developed MethSig, a statistical inference framework that accounts for the varying stochastic hypermethylation rates across the genome and between samples. MethSig estimates the background expected DNAme changes, thereby allowing the identification of epigenetically disrupted loci, where observed hypermethylation significantly exceeds expectation, potentially reflecting positive selection. We applied MethSig to reduced representation bisulfite sequencing (RRBS) data of 407 chronic lymphocytic leukemia (CLL) samples, including 304 CLLs collected in a prospective clinical trial. MethSig resulted in well-calibrated quantile-quantile (Q-Q) plots in contrast to ubiquitously used statistical methods, and reproducible inference of epidrivers across independent cohorts. MethSig provided robust inference in additional cancer types, including multiple myeloma (MM, n = 44) and ductal carcinoma in situ (DCIS, n = 24).  To further validate MethSig’s inferences, selected CLL candidate epidrivers (DUSP22, RPRM, or SASH1) underwent CRISPR/Cas9 knockout in CLL cells, showing superior fitness in ibrutinib and fludarabine treatment compared with controls. Candidate epidrivers are enriched in known TSGs, and in genes hypermethylated or inactivated across cancer types. Notably, greater number of epidrivers was closely associated with adverse outcome in CLL in a multivariable model accounting for additional adverse prognostic marks. Application of MethSig to CLL relapsed after chemoimmunotherapy further identified relapse-specific epidrivers, enriched in TP53 targets as well as DNA damage pathway. Collectively, MethSig represents a novel framework for robust identification of epidrivers to chart the role of aberrant DNAme in cancer.

overall_design: Using RRBS, we profiled DNA methylation patterns of CLL tumor samples.

first: Pan

last: Heng


title: Human blastocyst model by self-organization of naïve pluripotent stem cells

status: Public on May 05 2021

city: Exeter

first: Daniel

last: Spindlow

state: Devon

address: Stocker Road

department: Living Systems Institute

institute: University of Exeter

summary: Human naïve pluripotent cells can differentiate to extraembryonic trophoblast and hypoblast cells. Here we report formation of human blastocyst models by self-organization solely of naïve pluripotent stem cells. The embryo models comprise the three founding lineages, epiblast, trophoblast and hypoblast, arranged to mimic the natural blastocyst. Single-cell RNA sequencing validated the identity of each cell type.

overall_design: Single cells of human E5, E6 and E7 blastocysts and human blastocyst models by self-organization solely of naïve pluripotent stem cells mRNA profiles were generated using Smart-seq2.

first: Ayaka

last: Yanagida


title: Impaired inhibitory GABAergic synaptic transmission and transcription studied in single neurons by Patch-seq in Huntington’s disease

city: Edinburgh

first: Poorya

last: Parvizi

address: 9 Little France Rd

institute: The University of Edinburgh

summary: Transcriptional dysregulation in Huntington’s disease (HD) causes functional deficits in striatal neurons. Here, we performed Patch-seq in an in vitro HD model to investigate the effects of mutant huntingtin (Htt) on synaptic transmission and gene transcription in single striatal neurons. We found that expression of mutant Htt decreased the synaptic output of striatal neurons in a cell autonomous fashion and identified a number of genes, whose dysregulation was correlated with physiological deficiencies in mutant Htt neurons. In support of a pivotal role for epigenetic mechanisms in HD pathophysiology, we found that inhibiting histone deacetylase 1/3 activities rectified several functional and morphological deficits and alleviated the aberrant transcriptional profiles in mutant Htt neurons. With this study, we demonstrate that Patch-seq technology can be applied both to better understand molecular mechanisms underlying a complex neurological disease at single-cell level and to provide a platform for screening for therapeutics for the disease.

overall_design: Isolated striatal neurons from newborn C57BL6 mice were infected with lentiviruses expressing human HTT exon 1 fused to GFP with normal (25Q-Htt) or expanded (97Q-Htt) number of glutamine (Q) repeats. Also, we treated cultured striatal neurons with RGFP109, a specific HDAC1/3 inhibitor (100 nM treatments at DIV 6, 9, 12). To assess phenotypic differences between the groups, we used 25Q-Htt, and 97Q-Htt neurons treated with vehicle or RGFP109. As an overall control construct, an empty vector alone (without the inserted gene cassette) was used to infect cultured striatal neurons. In total, we sequenced RNA-seq libraries from 117 single striatal GABAergic neurons and 14 astrocytes.

first: Foteini

last: Paraskevopoulou

first: Gökçe

last: Senger

first: Nurcan

last: Tuncbag

first: Christian

last: Rosenmund

first: Ferah

last: Yildirim


title: Characterization of myeloid cells in acute and chronic LCMV infection by scRNA-seq

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

summary: The immune response to a chronic viral infection is uniquely tailored to balance viral control and immunopathology. The role of myeloid cells in shaping the response to chronic viral infection, however, is poorly understood. Single-cell RNA sequencing of myeloid cells during acute and chronic LCMV infection was performed to address this question. We discovered a cluster of suppressive neutrophils that is enriched in chronic versus acute infection. Furthermore, suppressive neutrophils highly expressed the gene encoding PIM1, a kinase known to promote mitochondrial fitness and cell survival. Pharmacological inhibition of PIM1 selectively diminished suppressive neutrophil-mediated immunosuppression without affecting the function of monocytic myeloid derived suppressor cells (M-MDSCs). Decreased accumulation of suppressive neutrophils led to increased CD8 T cell function and viral control. Mechanistically, PIM kinase activity was required for maintaining fused mitochondrial networks in suppressive neutrophils, but not in M-MDSCs, and loss of PIM kinase function caused increased apoptosis of suppressive neutrophils.

overall_design: Mice were infected with 200 or 2,000,000 PFU LCMV Clone 13 to establish acute and chronic infection, respectively. Spleens were harvested 7 days post-infection. Myeloid cells (B220- CD3- NK1.1- CD11b+) were purified by FACS sorting and subjected to the 10x Genomics scRNA-seq protocol.

first: Peter

last: Volberding

first: Moujtaba

last: Kasmani


title: An integrated transcriptomic approach to identify molecular markers of calcineurin inhibitor nephrotoxicity in pediatric kidney transplant recipients

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

summary:
Calcineurin inhibitor nephrotoxicity (CNIT) has been associated with the development of chronic renal allograft dysfunction and decreased graft survival. This study evaluated 37 formalin-fixed paraffin-embedded biopsies from pediatric kidney transplant recipients using gene expression profiling.
Oxidative phosphorylation and mitochondrial dysfunction were the top molecular pathways as-sociated with overexpressed genes in CNIT samples. Decreased ATP synthesis was identified as a significant biological function in CNIT, while key toxicology pathways included NRF2-mediated oxidative stress response and increased permeability transition of mitochondria.

overall_design: To identify a unique molecular signature for accurate pediatric CNIT diagnosis.

first: Valeria

last: Mas

middle: I

last: Maluf


title: Macropinocytosis requires Gal-3 in a subset of patient-derived glioblastoma stem cells

status: Public on May 04 2021

city: Genève

first: Eliana

last: Marinari

address: Rue Michel-Servet 1

country: Switzerland

institute: UNIGE

summary: GBM cells were treated with GAL3 shRNA vs sh ctrl. Gal3 forms a complex with Rab10 to potentiate macropinocytosis in the mesenchymal subpopulation of GBM tumors

overall_design: GAL3 shRNA vs Ctrl

first: Erika

last: Cosset


title: Single cell RNA-seq analysis of endothelial cells during diabetic atherosclerosis

city: Ann Arbor

first: Guizhen

last: Zhao

state: MI

address: 2800 Plymouth Rd

department: Cardiovascular Center

institute: University of Michigan

summary: Single-cell RNA sequencing (scRNA-seq) was performed on the  CD31-mircrobeads enriched endothelial cells isolated from aorta and heart from eight-week-old, male Ldlr-/- mice fed standard chow (Chow) or diabetogenic high-fat diet with 0.15% cholesterol (DDC) diet for 12 weeks. This study report the changes of EC subpopulations, fractions, transcriptomic and metabolic profiles during diabetic atherosclerosis.

overall_design: Examination of the transcriptomic profiles of endothelial cells isolated from aorta and heart pooled  from three Ldlr-/- mice fedstandard chow (Chow) or diabetogenic high-fat diet with 0.15% cholesterol (DDC) diet for 12 weeks

first: Jifeng

last: Zhang

first: Y

middle: E

last: Chen


title: Analysis of genes regulated by DUX4 via oxidative stress reveals potential therapeutic targets for treatment of facioscapulohumeral dystrophy

city: Villejuif

first: Anna

last: Schwager

state: Please Select

address: 114 Rue Edouard Vaillant

country: France

institute: Institut Gustave Roussy

summary: Muscles of patients with facioscapulohumeral dystrophy (FSHD) are characterized by sporadic DUX4 expression and oxidative stress which is at least partially induced by DUX4 protein. Nevertheless, targeting oxidative stress with antioxidants has a limited impact on FSHD patients, and the exact role of oxidative stress in the pathology of FSHD, as well as its interplay with the DUX4 expression, remain unclear. Here we set up a screen for genes that are upregulated by DUX4 via oxidative stress with the aim to target these genes rather than the oxidative stress itself. Immortalized human myoblasts expressing DUX4 (MB135-DUX4) have an increased level of reactive oxygen species (ROS) and exhibit differentiation defects which can be reduced by treating the cells with classic (Tempol) or mitochondria-targeted antioxidants (SkQ1). The transcriptome analysis of antioxidant-treated MB135 and MB135-DUX4 myoblasts allowed us to identify 200 genes with expression deregulated by DUX4 but normalized upon antioxidant treatment. Several of these genes, including PITX1, have been already associated with FSHD and/or muscle differentiation. We confirmed that PITX1 was indeed deregulated in MB135-DUX4 cells and primary FSHD myoblasts and revealed a redox component in PITX1 regulation. PITX1 silencing partially reversed the differentiation defects of MB135-DUX4 myoblasts. Our approach can be used to identify and target redox-dependent genes involved in human diseases.

overall_design: mRNA profiles of immortalized human myoblasts MB135 (control) and myoblasts MB135-DUX4 expressing DUX4, non-treated or treated with antioxidants (Tempol 100 uM or SkQ1 40nM) for 4 days. The experiments were caried out in biological duplicates.

last: Karpukhina

first: Yegor

last: Vassetzky


title: Immune checkpoint blockade reprograms systemic immune landscape and tumor microenvironment in obesity-associated breast cancer [Mammary fat pad, MFP]

first: Liza

last: Makowski

overall_design: RNA-seq data from breast cancer tumor adjacent adipose mammary fat pad (MFP) in lean and obese mice treated with anti-PD-1 or IgG2a isotype control

first: Joseph

last: Pierre

first: David

last: Hayes


title: Targeting P300/CBP reveals discrete regulation of transcription and chromatin accessibility by histone acetylation

city: South San Francisco

first: Simon

last: Hogg

address: 1000 Gateway Boulevard

institute: AbbVie


title: The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle

city: Mexico City

first: Mayra

last: Furlan-Magaril

state: Mexico City

address: Circuito exterior s/n

department: Molecular Genetics

country: Mexico

institute: IFC-UNAM


title: The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle [RNA-Seq]

summary: Circadian gene expression is essential for organisms to adjust cellular responses and anticipate daily changes in the environment. In addition to its physiological importance, the clock circuit represents an ideal, temporally resolved, system to study transcription regulation. Here, we analysed changes in spatial mouse liver chromatin conformation using genome-wide and promoter-capture Hi-C alongside daily oscillations in gene transcription in mouse liver. We found circadian topologically associated domains switched assignments to the transcriptionally active, open chromatin compartment and the inactive compartment at different hours of the day while their boundaries stably maintain their structure over time. Individual circadian gene promoters displayed maximal chromatin contacts at times of peak transcriptional output and the expression of circadian genes and contacted transcribed regulatory elements, or other circadian genes, was phase-coherent. Anchor sites of promoter chromatin loops were enriched in binding sites for liver nuclear receptors and transcription factors, some exclusively present in either rhythmic or stable contacts. The circadian 3D chromatin maps provided here identify the scales of chromatin conformation that parallel oscillatory gene expression and protein factors specifically associated with circadian or stable chromatin configurations.

overall_design: Total stranded RNAseq on mouse liver samples at four timepoints (ZT0, 6, 12, 18) during a circadian cycle. ZT0=lights on, ZT12=lights off

first: Masami

last: Ando-Kuri

first: Rodrigo

last: Arzate-Mejia

first: Jorg

last: Morg

first: Jonathan

last: Cairns

first: Cesar

last: Poot-Hernandez

last: Andrews

first: Csilla

last: Varnai

first: Boo

last: Virk

first: Steven

middle: W

last: Wingett

last: Fraser


title: Gene expression regulated by let-607 RNAi in C. elegans

city: Chongqing

first: Yuxi

last: Dai

address: Daxuecheng west street, Huxi town, Shapingba

institute: Chongqing university

summary: Coordinated regulation of stress response pathways is crucial for cellular homeostasis. However, crosstalk between the different stress pathways and the physiological significance of this crosstalk remain poorly understood. In this study, using the model organism C. elegans, we discovered that suppression of the transcription factor LET-607/CREBH, a regulator of cellular defense and proteostatic responses, triggers adaptive induction of DAF-16-dependent stress responses. Suppression of LET-607 improves stress resistance and extends C. elegans lifespan in a DAF-16-dependent manner. We identified the sphingomyelin synthase SMS-5 to be a central mediator in the communication between LET-607 and DAF-16. SMS-5 reduces the contents of unsaturated phosphatidylcholine (PC), which activates DAF-16 through ITR-1-dependent calcium signaling and calcium-sensitive kinase PKC-2. Our data reveal the significance of crosstalk between different stress pathways in animal fitness and identify LET-607/CREBH and specific PC as regulators of DAF-16 and longevity.

overall_design: Total mRNA profiles of  let-607 RNAi wild type C. elegans developed to the L4 stage were generated by deep sequencing, in triplicate, using Novaseq6000.

first: Bin

last: He

first: Jie

last: Xu

first: Shanshan

last: Pang

first: Haiqing

last: Tang


title: The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle [ChIP-seq]

overall_design: CTCF ChIPseq on mouse liver samples at two timepoints (ZT0 and 12) during a circadian cycle. ZT0=lights on, ZT12=lights off

first: Peter


title: Massively parallel quantification of SpCas9 gRNA efficiencies by surrogate lentiviral libraries

status: Public on May 03 2021

city: Aarhus

first: Lin

last: Lin

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

country: Denmark

institute: Aarhus University

summary: In this study, we used a surrogate lentivirus library to capture CRISPR editing outcome in HEK cells. The dataset include quantification of indel frequencies for SpCas9 gRNAs in 12,000 surrogate sites. After filtering low quality sites, the high quality SpCas9 gRNA activities from a total of 10592 sites have been used to develop an improved deep learning-based prediction model CRISPRon (https://rth.dk/resources/crispr/.).

overall_design: The surrogate lentivirus library contains 12,000 (12K) synthetic DNAs, each expressing a gRNA and contain a surrogate target site. The surrogate site is designed to capture CRISPR editing efficiency and outcomes, representing the corresponding endogenous site (37 nt). The 12K surrogate lentivirus library was generated by array-based oligo synthesis, followed by inserting the oligo pool into a lentiviral vector by Golden-Gate Assembly. The 12K library was then transduced to wildtype and SpCas9 expressing HEK293T cells using a MOI of 0.3. The transduced cells were changed to selection medium (puromycin) to enrich transduced days. For the SpCas9 HEK293T cells, overexpression of SpCas9 was also induced by addition of doxycycline. Indel frequencies introduced in the surrogate sites was quantified in cells 2, 8 and 10 days after transduction by deep sequencing. As an important QC step for filtering indels introduced by oligo synthesis and PCR, the synthetic oligo pool and the 12K surrogate plasmids were also deep sequenced. Deep sequencing was performed by MGISEQ-500, pair-end 150 cycles.

first: Xi

last: Xiang

first: Kunli

last: Qu

first: Xiaoguang

last: Pan

first: Xue

last: Liang

first: Yonglun

last: Luo


title: GRO-seq analysis of liver gene transcription in hibernating 13-lined ground squirrels

city: Aurora

first: Sandy

last: Martin

institute: University of Colorado School of Medicine

summary: Hibernators dramatically lower metabolism to save energy while fasting for months. Prolonged fasting challenges metabolic homeostasis, yet small-bodied hibernators emerge each spring ready to resume all aspects of active life, including immediate reproduction. The liver is the body’s metabolic hub, processing and detoxifying macromolecules to provide essential fuels to brain, muscle and other organs throughout the body. Here we quantify changes in liver gene expression using RNA-seq to measure the steady-state transcriptome and GRO-seq to measure transcription across several distinct physiological states of hibernation in 13-lined ground squirrels. Our data capture key timepoints in both the seasonal and torpor-arousal cycles of hibernation. Strong positive correlation between transcription and the transcriptome indicates that transcriptional control dominates the known seasonal reprogramming of metabolic gene expression in liver for hibernation. During the torpor-arousal cycle, however, discordance develops between transcription and the steady-state transcriptome by at least two mechanisms: 1) although not transcribed during torpor, some liver transcripts are unusually stable, consistent with data from other tissues; and 2) unexpectedly, on some genes, we document continuing, slow elongation with a failure to terminate transcription across the torpor bout. While the steady-state RNAs corresponding to these readthrough transcripts did not increase during torpor, they did increase shortly after rewarming despite then low transcription. Both of these mechanisms assure the availability of functional transcripts immediately upon rewarming. Integration of transcriptional, post-transcriptional and RNA stability control mechanisms, all demonstrated in these data, likely initiate a serial gene expression program across the short euthermic period that restores the tissue and prepares the animal for the next bout of torpor.

overall_design: triplicate samples from four stages of hibernation plus the control active season were studied by GRO-seq on nuclei isolated from liver tissue, 15 samples total

first: Sandra


title: Cervical mucosa exposed to free and complement opsonized HIV

city: Linköping

first: Rada

last: Ellegård

state: Ostergotlands Lan

address: Vallmogatan 16

country: Sweden

institute: Linköping University

summary: Whole transcriptome amplification of RNA purified from cervical explants (endocervix/ectocervix) cultured with different forms of HIV (free, complement opsonized and complement and antibody opsonized HIV) or mock treated for 6h or 24h.

overall_design:
9 donors - mock, free HIV (F-HIV), complement opsonized HIV (C-HIV ), complement and antibody opsonized HIV (CI-HIV)

**RAW DATA NOT PROVIDED due to Swedish GDPR law**

first: Cecilia

last: Svanberg

first: Elisa

last: Crisci

first: Mohammad

last: Khalid

first: Ninnie

last: Wodlin

first: Maria

last: Svenvik

first: Julian

last: Bess

first: Jeffrey

last: Lifson

first: Sofia

last: Nyström

first: Kenzie

last: Birse

first: Adam

last: Burgener

first: Esaki

last: Shankar

first: Marie

last: Larsson


title: Analysis of the transcriptomic changes of activated satellite cells lacking Hira

city: Creteil

first: Joana

last: Esteves de Lima

address: 8 rue du general sarrail

department: IMRB INSERM U955

institute: INSERM

summary: The epigenetic mechanisms coordinating the maintenance of adult cellular lineages and the inhibition of alternative cell fates are poorly understood. Here we show that targeted ablation of the histone chaperone HIRA in myogenic cells leads to extensive transcriptional modifications consistent with a major role in maintaining skeletal muscle cellular identity. Conditional ablation of HIRA in muscle stem cells of adult mice compromised their capacity to regenerate and self-renew, leading to tissue repair failure. Epigenetic analysis of Hira-deficient cells showed a drastic reduction of histone variant H3.3 deposition and H3K27ac modification at regulatory regions of muscle genes. By contrast, genes from alternative lineages were ectopically expressed in Hira-mutant cells via MLL1/MLL2-mediated increase of H3K4me3 mark at silent promoter regions. Therefore, HIRA sustains the epigenetic landscape governing muscle cell lineage identity via incorporation of H3.3 at muscle gene regulatory regions, while preventing the expression of alternative lineage genes.

overall_design: Examining the transcriptomic changes in activated satellite cells lacking Hira

first: Reem

last: Bou Akar

first: Leo

last: Machado

first: Yuefeng

last: Li

first: Bernadette

last: Drayton-Libotte

first: F Jeffrey

last: Dilworth

first: Frederic

last: Relaix


title: The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle [PChi-C]

first: Mayra

last: Furlan-Magaril

overall_design: Promoter Capture Hi-C (PChi-C) on mouse liver samples at four timepoints (ZT0, 6, 12, 18) during a circadian cycle. ZT0=lights on, ZT12=lights off

first: Masami

last: Ando-Kuri

first: Rodrigo

last: Arzate-Mejia

first: Jorg

last: Morg

first: Jonathan

last: Cairns

first: Cesar

last: Poot-Hernandez

first: Simon

last: Andrews

first: Csilla

last: Varnai

first: Boo

last: Virk

first: Steven

last: Wingett

first: Peter

last: Fraser


title: Acetylation of PAX7 Controls Muscle Stem Cell Self-Renewal and Differentiation Potential

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

summary: It has been suggested that muscle stem cell function is regulated by Acetyl-CoA and NAD+ availability, but the mechanisms remain unclear. We identified two acetylation sites on PAX7 that positively regulate its transcriptional activity. Lack of PAX7 acetylation reduces DNA binding, specifically to the homeobox motif. The acetyltransferase MYST1 stimulated by Acetyl-CoA, and the deacetylase SIRT2 stimulated by NAD+, were identified as direct regulators of PAX7 acetylation and asymmetric division in muscle stem cells. Abolishing PAX7 acetylation in mice using CRISPR/Cas9 mutagenesis led to an expansion of the satellite stem cell pool, reduced numbers of asymmetric stem cell divisions, and increased numbers of oxidative IIA myofibers. Gene expression analysis confirmed that lack of PAX7 acetylation preferentially affects the expression of target genes regulated by homeodomain binding motifs. Thus, PAX7 acetylation status regulates muscle stem cell function and differentiation potential to facilitate metabolic adaptation of muscle tissue.

overall_design: Gene expression in freshly isolated satellite cells from Pax7WT and Pax7KR mice (3 biological replicates of each)

first: Marie-Claude

last: Sincennes

first: Caroline

last: Brun

first: Alexander

middle: Y

last: Lin

first: Tabitha

last: Rosembert

first: David

last: Datzkiw

first: John

last: Saber

first: Hong

last: Ming

first: Yoh-ichi

last: Kawabe

first: Michael

last: Rudnicki


title: Stylophora pistillata cell atlas illuminates stony coral symbiosis, calcification and immunity

city: Barcelona

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

summary: We performed single-cell transcriptome analysis (using MARS-seq) in the stony coral Stylophora pistillata.

overall_design: Several specimens from each stage (adult colony polyps, settling polyps and free swimming larva) were dissociated and pooled before sorting single-cells for scRNAseq.


title: RNA Sequencing of Fetal and Adult Mature Thymic Vγ1+ γδ T-Cells

status: Public on May 01 2021

city: Toronto

first: Juan Carlos

last: Zuniga-Pflucker

state: Ontario

address: 2075 Bayview Avenue

department: Immunology

institute: University of Toronto

summary: γδ T-cells form an integral arm of the immune system through their rapid and potent effector functions, and are critical players during both protective and destructive immunity. However, the factors that dictate γδ T-cell functional programming in vivo remain to be fully elucidated. Here, we employed RBPJ-inducible and KN6-transgenic mice to assess the roles of ontogenic timing, T-cell receptor (TCR) signal strength, and Notch signaling in the generation of γδ T-cell functional subsets in vivo. We found skewed generation of Vγ1+ cells toward the PLZF+ γδ T-cell lineage at the fetal stage. Similarly, generation of interleukin (IL)-17 producing γδ T-cells was favored during, although not exclusive to, the fetal stage. Strong TCR signals, in conjunction with Notch, were necessary for the generation of IL-4 producing γδ T-cells. Conversely, weak TCR signals were amenable for the generation of IL-17 producing γδ T-cells, which was Notch-independent. Additionally and surprisingly, Notch signaling was also dispensable for peripheral γδ T-cell IL-17 production. Thus, our results precisely defined the roles of ontogenic timing, TCR signal strength, and Notch signaling in γδ T-cell functional programming in vivo.

overall_design: Mature CD24- Vγ1+ γδ T-cells were sorted from thymi using BD FACSAria Fusion. RNA was extracted using TRIzol. Library construction was done using Takara SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian. RNA sequencing was performed using Illumina NovaSeq 6000. Raw data were aligned to GRCm38 using HISAT2 version 2.1 and raw read counts were obtained using HTSeq version 0.1.

first: Edward

last: Chen

first: Christina

last: Lee

first: Patrycja

middle: K

last: Thompson

last: Wiest

first: Michele

last: Anderson

first: Juan

last: Zúñiga-Pflücker


title: Global methylation in Arabidopsis plants after multigenerational exposure to high temperatures

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

summary: We conducted whole-genome bisulfite sequencing (WGBS) of Arabidopsis thaliana mutation accumulation (MA) lines under different temperature treatments over sucessive generations, and then we identified the global methylation in each MA line. Our result showed taht DNA methylation was observed more frequently at DNA mutation sites, indicating its contribution to the mutation process at elevated temperatures.

overall_design: Whole-genome bisulfite sequencing (WGBS) of Arabidopsis MA lines at different temperature treatments over sucessive generations.

first: Zhaogeng

last: Lu


title: Poly(I:C) transfection time course in Xenopus laevis A6 cells

city: Salt Lake City

first: Ian

last: Boys

state: Utah

department: Human Genetics

institute: University of Utah

summary: This study was designed to identify Xenopus laevis genes that respond to stimulation with an immune agonist, poly(I:C).

overall_design: 12 samples in 4 groups with 3 biological replicates each. Treatment time course of 6 12 and 24 hours of poly(I:C) transfection, with a mock-transfected reference.

last: Schoggins


title: The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle [Hi-C]

first: Mayra

last: Furlan-Magaril

overall_design: Hi-C on mouse liver samples at four timepoints (ZT0, 6, 12, 18) during a circadian cycle. ZT0=lights on, ZT12=lights off

first: Masami

last: Ando-Kuri

first: Rodrigo

last: Arzate-Mejia

first: Jorg

last: Morg

first: Jonathan

last: Cairns

first: Cesar

middle: A

last: Poot-Hernandez

first: Simon

last: Andrews

first: Csilla

last: Varnai

first: Boo

last: Virk

first: Steven

last: Wingett

first: Peter

last: Fraser


title: Genetic effects on liver chromatin accessibility identify disease regulatory variants [genotypes]

city: Chapel Hill

first: Karen

last: Mohlke

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: Identifying the molecular mechanisms by which genome-wide association study (GWAS) loci influence traits remains challenging. Chromatin accessibility quantitative trait loci (caQTL) help identify GWAS loci that may alter GWAS traits by modulating chromatin structure, but caQTL have been identified in a limited set of human tissues. Here we mapped caQTL in human liver tissue in 20 liver samples and identified 3,123 caQTL. The caQTL variants are enriched in liver tissue promoter and enhancer states and frequently disrupt binding motifs of transcription factors expressed in liver. We predicted target genes for 861 caQTL peaks using proximity, chromatin interactions, correlation with promoter accessibility or gene expression, and colocalization with expression QTL. Using GWAS signals for 19 liver function and/or cardiometabolic traits, we identified 110 colocalized caQTL and GWAS signals, 56 of which contained a predicted caPeak target gene. At the LITAF LDL-cholesterol GWAS locus, we validated that a caQTL variant showed allelic differences in protein binding and transcriptional activity. These caQTL contribute to the epigenomic characterization of human liver and help identify molecular mechanisms and genes at GWAS loci.

overall_design: liver tissue samples from 20 individuals

first: Kevin

last: Currin

first: Michael

last: Erdos

first: Narisu

last: Narisu

first: Vivek

last: Rai

first: Swarooparani

last: Vadlamudi

first: Hannah

middle: J

last: Perrin

first: Jacqueline

last: Idol

first: Tingfen

last: Yan

first: Ricardo

middle: D

last: Albanus

first: K

last: Broadaway

first: Amy

middle: S

last: Etheridge

first: Lori

last: Bonnycastle

last: Orchard

first: John

middle: P

last: Didion

first: Amarjit

last: Chaudhry

first: Federico

last: Innocenti

first: Erin

middle: G

last: Schuetz

first: Laura

last: Scott

first: Stephen

last: Parker

first: Francis

last: Collins


title: Genetic effects on liver chromatin accessibility identify disease regulatory variants

first: Karen

last: Mohlke

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

overall_design: Refer to individual Series


title: Investigation of gene expression profiles in the kidneys of Cnnm2fl/fl;Six2-Cre mice.

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary: To elucidate the molecular mechanism of blood pressure regulation, we performed DNA microarray analyses to investigate gene expression in the kidneys of Cnnm2fl/fl;Six2-Cre mice.

overall_design: A dye-swap experiment was performed onto a Mouse GE 4×44K V2 (G4846A; Agilent Technologies).

first: Yosuke

last: Funato

first: Hiroaki

last: Miki


title: Gene expression profiles of HiDEP after treatment with Fluoro-SAHA or M344

city: Kumamoto

first: Kenichi

last: Miharada

address: 2-2-1 Honjo, Chuo-ku

institute: Kumamoto University

summary:
Total RNA was extrected from HiDEP-1 (Immortalized erythroid cell line derived from human induced pluripotent stem cells; PMID: 23533656) cultured with HDAC inhibitors, Fluoro-SAHA (FS) or M344 or Valproic acid (VPA), for 24 hours using Rneasy Mini Kit (QIAGEN) by following the manufacture's protocol.
After the quality/quantity determination, RNA was subjected to expression analyses using Affymetrix GeneChip® Array / Human Gene 2.0 ST Array

overall_design: HiDEP-1 were treated with DMSO or FS or VPA or M344 for 24 hours. The experiment was repeated 3 times.

first: Svetlana

last: Soboleva

first: Ryo

last: Kurita

first: Fredrik

last: Ek

first: Hugo

last: Åkerstrand

first: Rita

last: Alves

first: Roger

last: Olsson

first: Yukio

last: Nakamura


title: Comparative transcriptome analysis reveals conserved defense responses in maize and sorghum to Setosphaeria turcica

city: Urbana

first: Tiffany

last: Jamann

address: 1102 S Goodwin Ave, Turner Hall

department: Crop Sciences

institute: University of Illinois at Urbana-Champaign

summary: The goal of this study was to examine the transcriptional response of maize and sorghum during compatible and incompatible interactions with Setosphaeria turcica.

sample_organism:
Sorghum bicolor
Zea mays

platform_organism:
Sorghum bicolor
Zea mays

overall_design: Greenhouse-grown maize and sorghum were inoculated with maize-specific S. turcica (Et28A), sorghum-specific S. turcica (15St008) or a mock treatment. Interactions are classified as compatible when the plant was inoculated with an isolate from that host (ie. maize and Et28A) and incompatible when a plant was inoculated with a strain that was isolated from a different host. Two timepoints were sampled- 24 and 48 hours after inoculation.

first: Pragya

last: Adhikari

first: Santiago

middle: X

last: Mideros


title: Genetic effects on liver chromatin accessibility identify disease regulatory variants [RNA-seq]

overall_design: RNA-seq on liver tissue from 20 individuals

first: Kevin

last: Currin

first: Michael

middle: R

last: Erdos

first: Narisu

last: Narisu

first: Vivek

last: Rai

first: Swarooparani

last: Vadlamudi

first: Hannah

last: Perrin

first: Jacqueline

last: Idol

first: Tingfen

last: Yan

first: Ricardo

last: Albanus

first: K

last: Broadaway

first: Amy

last: Etheridge

first: Lori

last: Bonnycastle

first: Peter

last: Orchard

first: John

last: Didion

first: Amarjit

last: Chaudhry

first: Federico

last: Innocenti

first: Erin

last: Schuetz

first: Laura

last: Scott

first: Stephen

middle: C

last: Parker


title: Integrated analysis of long noncoding RNAs and mRNA expression profiles reveals the potential role of lncRNAs in early stage of post-peripheral nerve injury in Sprague-Dawley rats

status: Public on Apr 30 2021

city: Guangzhou

first: Yu-Jing

last: Zhang

address: No.2 Zhongshan Road #58

institute: Sun Yat-sen University

type: Non-coding RNA profiling by high throughput sequencing

summary: The regulatory role of lncRNAs in the early stage post peripheral nerve injury (PNI) is not yet clear. In this study, next-generation sequencing was used to perform deep sequencing on normal sciatic nerves (control) and lesional tissues derived on the 4th (D4) and 7th days (D7) after sciatic nerve injury in rats. Time-point unique differentially expressed lncRNAs (DElncRNAs) were analyzed for functional enrichment. The results showed that 776 DElncRNAs were unique to D4, and their functions were mainly enriched in wound healing, phosphatase binding and MAPK signaling pathways; 317 DElncRNAs were unique to D7, and their functions were mainly enriched in ion transmembrane transporter channel activity; 579 DElncRNAs were shared by these two days, and their functions were mainly enriched in axongenesis, the PI3K-Akt signaling pathway and cell cycle. Furthermore, lncRNA-mRNA interaction networks were constructed in functions or pathways with a high enrichment rate. Finally, 3 mRNAs and 4 lncRNAs in the axongenesis interaction network were selected, and their expression levels were verified by RT-qPCR. This study preliminarily revealed the regulatory role of lncRNAs at different time points in the early stage post PNI, which provides potential targets for basic research and clinical treatment of PNI.

overall_design: Examination of lncRNA and mRNA expression profiles of the rat sciatic nerve under 3 conditions (uninjuerd, 4 days post nerve crush and 7 days post nerve crush), with 2 replicates in each group

first: Yujing

first: Zhaowei

last: Zhu

first: Yangbin

last: Xu

first: Bo

last: He


title: Genetic effects on liver chromatin accessibility identify disease regulatory variants [ATAC-seq]

first: Karen

middle: L

last: Mohlke

overall_design: ATAC-seq on liver tissue from 20 individuals

first: Kevin

last: Currin

first: Michael

last: Erdos

first: Narisu

last: Narisu

first: Vivek

last: Rai

first: Swarooparani

last: Vadlamudi

first: Hannah

last: Perrin

first: Jacqueline

last: Idol

first: Tingfen

first: Francis

last: Collins


title: A TORC1/histone axis regulates chromatin organization and non-canonical induction of autophagy to ameliorate ageing

city: Cologne

first: Yu-Xuan

last: Lu

address: Joseph-Stelzmann-Str. 9b

department: Biological Mechanisms of Ageing

country: Germany

institute: Max-Planck-Institute for Biology of Ageing

summary: Modulation of histone levels is commonly seen during ageing in many species. However, any role for histone levels in longevity of multicellular organisms remains undiscovered. Here we show that inhibition of mTORC1 by rapamycin post-transcriptionally increases expression of histone proteins H3 and H4 in Drosophila intestine. Expression of H3/H4 in enterocytes alters chromatin organization, induces intestinal autophagy through transcriptional regulation, and prevents age-related structural and functional decline in the intestine. Increased H3/H4 expression in enterocytes is essential for rapamycin-dependent longevity and intestinal health. Histones H3/H4 regulate expression of a selective autophagy cargo adaptor Bchs (ALFY in mammals), increased expression of which in enterocytes is necessary and sufficient for increased H3/H4-dependent healthy longevity. In mice, rapamycin treatment increases expression of histone proteins and ALFY transcript, and alters chromatin organisation in small intestine, suggesting the mTORC1-histone axis is at least partially conserved in mammals and may offer new targets for anti-ageing interventions.

overall_design: RNA-seq in rapamycin-treated and control guts in wild type D. melanogaster at the age of 10 days, 30 days and 50 days. Three biological replicates and 25 guts per replicate.

first: Jennifer

last: Regan

last: Eßer

first: Lisa

middle: F

last: Drews

first: Thomas

last: Weinseis

first: Julia

last: Stinn

first: Oliver

last: Hahn

first: Richard

last: Miller

first: Sebastian

last: Grönke

first: Linda

last: Partridge


title: Phospholipid composition of APOE lipoproteins affects microglia activation in an isoform-specific manner

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto Street

department: Enviromantal and Occupational health

institute: University of Pittsburgh

summary: Apolipoprotein E4 (APOE) is the strongest genetic risk factor for Alzheimer's disease (AD). Our lipidomic analysis identified a common phospholipid signature with a high level of correlation between APOEε3/3 and APOEε4/4 AD postmortem brain samples and native lipoproteins isolated from astrocyte conditioned media of mice expressing human APOE3 or APOE4. Behavioral testing demonstrated that native E3 lipoproteins were more effective than E4 at ameliorating the harmful effects of Aβ on cognition. We posit that APOE isoform-specific differences in the phospholipid composition of native lipoproteins prompt a differential microglial response. Using time-lapse in vivo two-photon imaging, we compared the effect of E3 or E4 infused with Aβ and determined that E3 lipoproteins induced a faster microglial migration towards Aβ. To determine how E3 and E4 lipoproteins affect microglial transcriptome in response to Aβ, we performed bulk and single cell RNA-seq of WT and Trem2ko mice. We show that compared to E4, cortical infusion of E3 lipoproteins upregulated a higher proportion of genes associated with an activated immune response accompanied by a downregulation of homeostatic genes. scRNA-seq identified microglia-specific clusters affected by Trem2 deficiency, suggesting that lack of Trem2 impairs the transition of microglia from homeostatic to an activated state. Compared to E3, E4-expressing microglia showed a reduced Aβ uptake that was additionally aggravated by Trem2 deficiency. Together, our findings have elucidated unique phenotypic and transcriptional differences in the microglial response to Aβ in the presence of E3 or E4 lipoproteins which could impact AD pathogenesis.

overall_design: Isolated microglia and neuron from wild-type C57BL/6J, 129P2(Cg)-Cx3cr1tm1Litt/J (Cx3cr1GFP) and Trem2em2ADiuj/J mice (Trem2ko) were used to reveal transcriptomic changes in response to Aβ injection using bulk and single cell RNA-seq.

first: Nicholas

last: Fitz

first: KyongNyon

last: Nam

first: Cody

middle: M

last: Wolfe

first: Florent

last: Letronne

first: Brittany

last: Playso

first: Bistra

last: Iordanova

first: Takashi

last: Kozai

last: Biedrzycki

first: Valerian

last: Kagan

first: Yulia

last: Tyurina

first: Xianlin

last: Han

first: Radosveta

last: Koldamova


title: Identification of differential DNA methylation associated with multiple sclerosis: a family-based study

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

institute: OSR - San Raffaele Scientific Institute

summary: Multiple Sclerosis (MS) is known to be caused by a genetic predisposition triggered by environmental factors. Despite the knowledge of genetic factors and environmental agents involved, it is largely unclear how they interact. Epigenetics, particularly DNA methylation, represents a model for environmental factors to influence the genome. In this paper, we studied 26 affected and 26 unaffected relatives from 8 MS multiplex families (≥ 3 affected relatives) as part of a multicentric Italian cohort study using Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) run on an Illumina® HiSeq 2500 (2x100 bp). Technical validation in 6/8 of the original families and biological replication in 2 additional families (FDR < 0.1 and a concordant fold change, FC) were performed in suggestive differentially methylated regions (DMRs) between affected and unaffected relatives using SeqCap Epi Choice Enrichment (Roche®).  Evidence of association from MeDIP-Seq across 8 families was combined with aggregation statistics, separately for hypo- and hyper-methylated regions with concordant FC in ≥ 6/8 families, yielding 162 DMRs at FDR ≤ 0.1. Technical validation and biological replication led to 2 hypomethylated regions, which point to NTM and BAI3 genes, and 2 hypermethylated regions in PIK3R1 and CAPN13 (mean size: 3.1 kb).  Multiplex families represent a privileged setting for the study of regions of differential methylation as they reduce the impact of potential confounders like shared genetics and environmental factors. We identified 4 novel regions which contain genes of potential interest that need to be tested in larger cohorts of patients.

overall_design: Whole Blood samples from both MS affected individuals and healthy realatives were collected from 8 families and were subjected to MeDIP Sequencing. After quality filtering reads and identifying peaks of methylated regions, differentially methylated regions were called (DMRs). An aggregation strategy was used to select for thos regions with hyper or hypomethylation in MS compared to Healthy individuals based on metaanalyzed p.values across the 8 families. After increasing those DMRs by 1kb down and upstream, a bisulfite panel of methylation sequencing (by Roche) was used to validate DMRs using 6 families of the discovery phase and replicate them on two unrelated MS families

first: J

first: F

last: Clarelli

first: E

last: Mascia

first: S

last: Bonfiglio

last: Martinelli-Boneschi


title: Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens

status: Public on Apr 29 2021

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

institute: Universitaet Hamburg

summary: We present evidence of mechanistically diverse allosteric relays converging on a few peptidyltransferase center (PTC) nucleotides, and propose a general model of antibiotic resistance mediated by these ARE-ABCFs

overall_design: E. faecalis cell lysate and RqcH 50s-bound (i.e. immunopreciptated, RqcH 50s-IP) tRNAs used for tRNA microarrays to measure tRNA abundance – 2 biological replicates in total; 2 – RqcH 50s-IP and 1 - total tRNA (lysate)

first: Hiraku

last: Takada

first: Caillan

last: Crowe-McAuliffe

first: Christine

last: Polte

first: Vasily

last: Hairyliuk

first: Daniel

last: Wilson


title: Human lymphoid stromal cell heterogeneity and functional alteration in follicular lymphoma

city: RENNES

first: vonick

last: sibut

address: avenue du Prof Leon BERNARD

summary: Despite recent advances in the characterization of stromal cell origin, heterogeneity, and function in mice, little is known in human. Follicular lymphoma (FL) is the most frequent indolent lymphoma. It corresponds to the accumulation of germinal center B-cell clones within lymph nodes. FL B cells interact with a reprogrammed immune and stromal cells that provide crucial contributions to the licensing of tumor growth and immune evasion. Most of transcriptomics approaches in human was performed on cultured, and amplified stromal cells modifying their phenotype and function. We purified native stromal cells from LN FL patients, healthy tonsil, and healthy bone marrow. Gene expression profiling based on three lymphoid stromal cell types provides new insights on the characterization of those cells in human and highlight new signalling pathways involved in the crosstalk between stromal cells and tumoral FL B cells.

overall_design:
Tonsil tissues from 8 healthy donors and LN from 4 FL patients were collected and enzymatically dissociated. After depletion of hematopoietic cells three stromal cell subsets where sorted by FACS based on their phenotype. DN: CD45[neg] /CD11b[neg] /CD235a[neg] /CD31[neg] /Podoplanin[neg] /CD21[neg] /CD49a[pos] ; FDC: CD45[neg] /CD11b[neg] /CD235a[neg] /CD31[neg] /Podoplanin[pos] /CD21[pos] ; FRC: CD45[neg] /CD11b[neg– /CD235a[neg] /CD31[neg] /Podoplanin[pos] /CD21[neg] /CD49a[pos]). RNA extraction was performed on 10 000 cells for each stromal cell subsets.

Bone marrow aspirates from 4 healthy donors were collected and enzymatically dissociated. After depletion of hematopoietic cells, stromal cell subsets where sorted by FACS based on the phenotype: CD45[neg] /CD11b[neg] /CD235a[neg] /CD31[neg] /CD271[pos] /CD49a[pos]. RNA extraction was performed on 10 000 cells.

first: Léa

last: Verdière

first: Delphine

last: Rossille

first: David

last: Roulois

first: Frédéric

last: Mourcin

first: Karin

last: Tarte


title: Post-translational Modification of RNA m6A Demethylase ALKBH5 Regulates ROS-induced DNA Damage Response

city: Chicago

first: Xiaolong

last: Cui

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

summary: Faithful genome integrity maintenance plays an essential role in cell survival. Here, we identify the RNA demethylase ALKBH5 as a key regulator that protects cells from DNA damage and apoptosis during reactive oxygen species (ROS)-induced stress. We find that ROS significantly induces global mRNA N6-methyladenosine (m6A) levels by modulating ALKBH5 post-translational modifications (PTMs), leading to the rapid and efficient induction of thousands of genes involved in a variety of biological processes including DNA damage repair. Mechanistically, ROS promotes ALKBH5 SUMOylation through activating ERK/JNK signaling, leading to inhibition of ALKBH5 m6A demethylase activity by blocking substrate accessibility. Moreover, ERK/JNK/ALKBH5-PTMs/m6A axis is activated by ROS in hematopoietic stem/progenitor cells (HSPCs) in vivo in mice, suggesting a physiological role of this molecular pathway in the maintenance of genome stability in HSPCs. Together, our study uncovers a molecular mechanism involving ALKBH5 PTMs and increased mRNA m6A levels that protect genomic integrity of cells in response to ROS.

overall_design: m6A-Seq was performed in wild type and AlKBH5 over-expressed HEK cells.

first: Jiangbo

last: Wei

first: Zhijian

last: Qian

first: Chuan

last: He


title: Gene Expression Profiling of Cancer Cells after STBD1 overexpression

status: Public on Apr 28 2021

city: Chengdu

first: Han

last: Zhu

state: China, Sichuan

address: No.17 People's South Road

institute: Sichuan University

summary: We compare the gene expression profiles of shSTBD1/plvx neo, shSTBD1/WT, and shSTBD1/W203C cells

overall_design: Three biological replicates of shSTBD1/plvx neo, shSTBD1/WT, and shSTBD1/W203C HCT116 cells

first: Zhu

last: Han


title: Resolving cellular and molecular diversity along the hippocampal anterior-to-posterior axis in humans

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

summary: The hippocampus supports many facets of cognition, including learning, memory, and emotional processing. Anatomically, the hippocampus runs along a longitudinal axis, posterior-to-anterior in primates (corresponding to dorsal-to-ventral in rodents). The structure, function, and connectivity of the hippocampus vary along this axis.  In rodents, experiments have established the cellular, molecular, and functional heterogeneity along the hippocampal axis, resulting in comprehensive models of specialization that integrate these different types of information.  In humans however, functional heterogeneity remains an active area of investigation, and structural heterogeneity has not been described.  To better understand the cellular composition and molecular diversity along the hippocampal long axis in the human brain and define distinct molecular signatures corresponding to functional domains we performed single-nuclei RNA-sequencing on surgically resected human anterior and posterior hippocampus. Analysis of 131,325 nuclei revealed differentially expressed genes between the anterior and posterior human hippocampus at cellular resolution. We determine the program of these axis- and cell-type specific genes that are conserved in the mouse hippocampus, and we also identify patterns that are differential between the human and mouse. We further identify axis- and cell-type specific gene expression signatures that differentially intersect with human cognitive and neuropsychiatric genetic signals, identifying cell type-specific genes in the posterior hippocampus for cognitive function and in the anterior hippocampus for mood and affect. Our data illuminate a region- and cell-type-specific transcriptional landscape within the hippocampus. This data is accessible as a public resource through an interactive website (https://human-hippo-axis.cells.ucsc.edu/) and will act as a reference atlas for the human hippocampus.

overall_design: We carried out single-nuclei RNA-sequencing of human resected hippocampus. Anterior and posterior hippocampus from 5 donors were processed and sequenced as separate libraries.

first: Fatma

last: Ahyan

first: Stefano

last: Berto

first: Ashwinikumar

last: Kulkarni


title: Adaptation of white adipose tissue to cool environmental temperatures

city: Ann Arbor

first: Ormond

middle: A.

last: MacDougald

address: 2800 Plymouth Rd

department: Molecular & Integrative Physiology

institute: University of Michigan

summary: To map changes in RNAs that occur to the gluteal portion of the posterior subcutaneous adipose tissue of mice housed under cool temperature, we performed RNA-Seq on gluteal WAT of mice housed at 22°C compared with thermoneutral housing (29°C; control).

overall_design: Mice were housed from birth to 13 weeks of age at 22°C or 29°C. After weaning, posterior hair was removed. RNAs were isolated from Gluteal WAT of mice housed both at 22°C and 29°C

first: Akira

last: Nishii

first: Hiroyuki

last: Mori


title: Gene Expression Profiling of Cancer Cells after STBD1 depletion

summary: To understand how STBD1 inhibits tumor growth, we compare the gene expression profiles of shControl and shSTBD1 HCT116 cells using RNA-seq

overall_design: Three biological replicates of shControl and shSTBD1 HCT116 cells


title: Mammary epithelial cells have lineage-rooted metabolic identities

city: Toronto

first: Curtis

middle: William

last: McCloskey

address: 101 College Street, PMCRT, Room 13-303

department: Medical Biophysics

institute: University Health Network

summary: Cancer metabolism adapts the metabolic network of its tissue-of-origin. However, breast cancer is not a disease of a singular origin. Multiple epithelial populations serve as the culprit cell-of-origin for specific breast cancer subtypes, yet our knowledge of the metabolic network of normal mammary epithelial cells is limited. Using a multi-OMIC approach, here we identify the diverse metabolic programs operating in normal mammary populations. The proteomes of basal, luminal progenitor, and mature luminal cell populations revealed enrichment of glycolysis in basal cells and of oxidative phosphorylation in luminal progenitors. Single-cell transcriptomes corroborated lineage-specific metabolic identities and additional intra-lineage heterogeneity. Mitochondrial form-and-function differed across lineages, with clonogenicity correlating to mitochondrial activity. Targeting oxidative phosphorylation and glycolysis with inhibitors exposed lineage-rooted metabolic vulnerabilities of mammary progenitors. Bioinformatics indicated breast cancer subtypes retain metabolic features of their putative cell-of-origin. Thus, lineage-rooted metabolic identities of normal mammary cells may underlie breast cancer metabolic heterogeneity and targeting these vulnerabilities could advance breast cancer therapy.

overall_design:
Single-cell RNA sequencing of  primary human reduction mammoplasty samples Multiplexed using lipid-tagged indices (MULTI-seq)

*** Submitter comment: Raw fastq files not supplied as this data is derived from multiplexed samples over mutliple runs as indicated in the RM_count_matrix_metadata.csv file. Additionally, all data presented in the publication can be repeated using the two processed data files uploaded here ***

middle: W

first: Rama

last: Khokha


title: Single-Cell RNA Sequencing of Thymic KN6 γδ T-Cells Modulated by TCR Signal Strength and Notch Signaling

first: Juan Carlos

last: Zuniga-Pflucker

address: 2075 Bayview Avenue

institute: University of Toronto

summary: γδ T-cells form an integral arm of the immune system through their rapid and potent effector functions, and are critical players during both protective and destructive immunity. However, the factors that dictate γδ T-cell functional programming in vivo remain to be fully elucidated. Here, we employed RBPJ-inducible and KN6-transgenic mice to assess the roles of ontogenic timing, T-cell receptor (TCR) signal strength, and Notch signaling in the generation of γδ T-cell functional subsets in vivo. We found skewed generation of Vγ1+ cells toward the PLZF+ γδ T-cell lineage at the fetal stage. Similarly, generation of interleukin (IL)-17 producing γδ T-cells was favored during, although not exclusive to, the fetal stage. Strong TCR signals, in conjunction with Notch, were necessary for the generation of IL-4 producing γδ T-cells. Conversely, weak TCR signals were amenable for the generation of IL-17 producing γδ T-cells, which was Notch-independent. Additionally and surprisingly, Notch signaling was also dispensable for peripheral γδ T-cell IL-17 production. Thus, our results precisely defined the roles of ontogenic timing, TCR signal strength, and Notch signaling in γδ T-cell functional programming in vivo.

overall_design: CD3+Vγ4+ KN6 cells were sorted from thymi using BD FACSAria Fusion. Library construction was done using 10x Genomics Chromium Controller v3. Single-cell RNA sequencing was performed using Illumina NovaSeq 6000. Raw data were aligned to GRCm38, and raw read counts were obtained using Cell Ranger version 5.0.

first: Edward

last: Chen

first: Christina

last: Lee

first: Patrycja

middle: K

last: Thompson

first: David

last: Wiest

first: Michele

last: Anderson

first: Juan

last: Zúñiga-Pflücker


title: Transcriptome-wide N6-methyladenosine modification profiling of long non-coding RNAs and circular RNA during growth of Marek’s disease virus in vitro

city: Zhengzhou

first: ZHU Xiaojing

middle: Xiaojing

last: ZHU

state: Henan

address: 15 Longzihu University Park, Zhengdong New District

institute: Henan Agricultural University

summary: we profiled the transcriptome-wide m6A modification in lncRNAs and circRNA in MDV-infected chicken embryo fibroblast (CEF) cells. Methylated RNA immunoprecipitation sequencing results revealed that the lncRNA m6A modification is highly conserved with MDV infection increasing the expression of lncRNA m6A modified sites compared to uninfected cell controls. m6A modification was highly conserved in circRNAs. Comparing to the uninfected group, the number of peaks, conserved motifs, and abundance of circRNA m6A modification, was not significantly different in cells that were infected with MDV. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) analysis revealed that lncRNA m6A modifications were highly associated with signaling pathways associated with MDV infection. The alterations seen in transcriptome-wide m6A occurring in lncRNAs following MDV-infection suggest this process plays important regulatory roles during MDV replication.  And the insulin signaling pathway was associated with the regulation of m6A modified circRNAs in MDV infection. In summary, we report for the first time profiling of the alterations in transcriptome-wide m6A modification in lncRNAs and circRNA of MDV-infected CEF cells.

overall_design: Examing 2 conditions, each with 3 replicates

first: Guoqing

last: Zhuang

first: Aijun

last: Sun


title: RNA sequencing of poly(A+) transcriptome of quadriceps muscles from wildtype and CaMK2gVV/CaMK2gVV mice under sedentary and post-acute exercise conditions

city: Baltimore

first: Mark

middle: E

state: MD

address: Rangos 471, 855 N. Wolfe Street

department: Department of Medicine

institute: Johns Hopkins School of Medicine

summary:
Reactive oxygen species (ROS) contribute to health and disease.  CaMKII is a widely expressed enzyme whose activation by oxidation of regulatory domain methionines (ox-CaMKII) contributes to cardiovascular disease, asthma, and cancer.  Here we integrate comparative genomic and experimental data to show that CaMKII activation by ROS arose more than half-a-billion years ago on the vertebrate stem lineage where it constituted a bridge between ROS and increased intracellular Ca2+ release, exercise responsive gene transcription, and improved performance in skeletal muscle.  These enhancements to fight-or-flight physiology were likely key in facilitating a well-evidenced shift in the behavioural ecology of our immediate chordate ancestors, and, in turn, the evolutionary success of vertebrates.  Still, the ox-CaMKII innovation must be considered a critical evolutionary trade-off, as it rendered us more susceptible to common and often fatal diseases by providing ROS an expanded role in those processes.
This poly(A+) transcriptome profiling study examined the actue transcriptional response of mouse skeletal muscles three hours after a single bout of submaximal exericse in wildtype and mutant mice whose CaMKIIg cannot be activated by reactive oxygen species.

overall_design: Wildtype and CaMK2gVV/CaMK2gVV mice were either kept sedentary or forced to performed a submaximal running exercise. Four mice per genotype were used for each condition. Three hours after the group of exercised mice finished running, all mice were sacrifed for mRNA sequencing by Illumina NovaSeq 6000.

first: Qinchuan

last: Wang

first: Erick

middle: O

last: Hernández-Ochoa

first: Jonathan

last: Granger

first: Corina

last: Antonescu

first: Liliana

last: Florea

first: C

last: Talbot Jr

last: Mohr


title: mRNA-seq of peripheral blood monocyte- and human pluripotent stem cell-derived macrophages

status: Public on Apr 27 2021

city: Melbourne

first: Jarny

last: Choi

state: Victoria

address: The University of Melbourne

department: Anatomy and Neuroscience

institute: Centre for Stem Cell Systems

summary: We investigate the impact of an initial stimulation and a re-stimulation in altering transcriptional responses in both peripheral blood-monocyte derived macrophages and human pluripotent stem cell derived macrophages.

overall_design: mRNA-seq in 2-3 replicates of LPS stimulated macrophages derived from peripheral blood or human pluripotent stem cell-derived macrophages

first: Nadia

last: Rajab

first: Andrew

last: Laslett

first: Christine

middle: A

last: Wells


title: Effect of N1-acetylspermidine treatment on hair follicle stem cell organoid cultures

city: Koln

first: Jorge

last: Boucas

department: Bioinformatics

institute: Max Planck Institute for Biology of Ageing

summary: Stem cell differentiation has been shown to involve an increase in mRNA translation. Amongst others, the rate of translation is influenced by availability of the natural polyamines putrescine, spermidine, and spermine that are essential for cell growth and modulate stem cell maintenance. However, the link between polyamines and translation in cell fate decisions remains obscure. Here, we used hair follicle stem cell (HFSC) organoids to study the role of polyamines as key regulators of mRNA translation in stem cell fate decisions. HFSCs showed lower translation than progenitor cells, and a forced suppression of translation by direct targeting of the ribosome or through specific depletion of natural polyamines elevated stemness. In addition, we identified N1-acetylspermidine as a novel parallel regulator of cell fate decisions. To identify the molecular mechanism by which N1-AcSpd supplementation promotes stemness, we performed RNA-sequencing. We unravel an increase in proliferation. Overall, this study delineates the diverse routes of polyamine metabolism-mediated regulation of stem cell fate decisions.

overall_design: UMI-RNA-Seq of sorted HFSC organoids (alpha6+CD34- and alpha6+CD34+ cells), 16 samples, 4 biological replicates, WT and treated with N1-acetylspermidine for 72h

first: Kira

last: Allmeroth

first: Andromachi

last: Pouikli

first: Peter

last: Tessarz

first: Martin

last: Denzel

first: Franziska

last: Metge


title: Adaptation of cultured adipocytes to cool temperatures

first: Hiroyuki

last: Mori

address: 1000 Wall Street

summary: The experiment mapped changes in RNA that occur as adipocytes adapt to cool temperatures (31°C ) in vitro. We performed RNA-Seq on mature adipocytes exposed to 31°C for 0, 1 or 12 days. 0 day refers to the control, where cells were cultured at 37°C only.

overall_design: Mesenchymal stem cells (MSCs) were isolated from C57BL/6J mice. Mature adipocytes were exposed to 31°C for 0, 1 or 12 days. For the cells cold exposed for 12 days, the MSCs were cultured at 37°C prior to and for the first four days of adipogenesis, after which cells were moved to 31°C for 12 days. The cells cold exposed for 1 day were moved to 31°C 15 days after adipocyte differentiation. The cells cold exposed for 0 days were cultured at 37°C consistently.  All cells were harvested 16 days after adipocyte differentiation.

first: Ormond

last: MacDougald

first: Akira

last: Nishii


title: HEC regulation at high ambient temperature gene expression in Arabidopsis thaliana

status: Public on Apr 26 2021

city: Austin

first: Enamul

last: Huq

address: Department of MBS, NHB 2.606, Stop A5000, 100 East 24th St.

institute: The University of Texas at Austin

summary: The mRNA expression profiles of the WT, hec1hec2, and pifQ were analyzed in 24 hour 22degC and 28degC treated conditions. The gene expression changes was analyzed and compared within 22degC and 28degC.

overall_design: Total eighteen 24h 22degC and 28degC treated Arabidopsis samples were used. These include three replicates of the following genotypes: Col-0, hec1hec2, and pifQ. Therefore, three replicates of following genotypes and conditions: Col-0 (22degC), hec1hec2 (22degC), pifQ (22degC), Col-0 (28degC), hec1hec2 (28degC), and pifQ (28degC).

first: Sanghwa

last: Lee


title: A healthy human liver cell atlas reveals hepatic stellate cell heterogeneity

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

summary: We generated a high-resolution cellular atlas of the healthy human liver by profiling the transcriptome of more than 25,000 individual liver cells using droplet-based RNA-sequencing. Recently published datasets and in situ hybridization were integrated to confirm, validate and locate newly identified cell populations. We identified, annotated and characterized a total of 23 cell subpopulations that represent the degree of heterogeneity of parenchymal (i.e. hepatocytes and cholangiocytes) and non-parenchymal liver cells (i.e. endothelial cells, stellate cells, macrophages and lymphoid cells). We successfully classified human hepatocytes and liver sinusoidal endothelial cells along the porto-central axis and for the first time reveal the existence of functionally specialized pericentral GPC3+ and periportal HHIP+ DBH+ hepatic stellate cells in the healthy human liver. Our study provides a description of the different cell compartments that enter into the composition of a healthy human liver and currently constitutes the biggest single-cell RNA sequencing dataset available on human healthy hepatocytes and hepatic stellate cells. We identified subsets of hepatic stellate cells characterized by distinct localization and physiological functions.

overall_design: Single-cell RNA sequencing for two livers. First liver is represented by 2 samples for the parenchymal fraction and 2 samples for the non-parenchymal fraction. Second liver is represented by 1 sample for the parenchymal fraction, 2 samples for the non-parenchymal fraction and 1 sample for the whole fraction.

first: Valéry

last: Payen

first: Niki

last: Alevra Sarika

first: Megan

last: Colonval

first: Latifa

last: Karim

first: Manon

last: Deckers

first: Mustapha

last: Najimi

first: Wouter

last: Coppierters

first: Benoît

last: Charloteaux

first: Etienne

last: Sokal

first: Adil

last: El Taghdouini


title: Dynamics of alternative splicing during somatic cell reprogramming reveals functions for RNA-binding proteins CPSF3, hnRNP UL1 and TIA1

city: Barcelona

first: Claudia

last: Vivori

address: Carrer Dr Aiguader 88

institute: Centre for Genomic Regulation

summary:
Background.
Somatic cell reprogramming is the process that allows differentiated cells to revert to a pluripotent state. In contrast to the extensively studied rewiring of epigenetic and transcriptional programs required for reprogramming, the dynamics of post-transcriptional changes and their associated regulatory mechanisms remain poorly understood. Here we study the dynamics of alternative splicing changes occurring during efficient reprogramming of mouse B cells into induced pluripotent stem (iPS) cells and compare them to those occurring during reprogramming of mouse embryonic fibroblasts.

Results.
We observe a significant overlap between alternative splicing changes detected in the two reprogramming systems, which are generally uncoupled from changes in transcriptional levels. Correlation between gene expression of potential regulators and specific clusters of alternative splicing changes enable the identification and subsequent validation of CPSF3 and hnRNP UL1 as facilitators, and TIA1 as repressor of mouse embryonic fibroblasts reprogramming. We further find that these RNAbinding proteins control partially overlapping programs of splicing regulation, involving genes relevant for developmental and morphogenetic processes.

Conclusions.
Our results reveal common programs of splicing regulation during reprogramming of different cell types and identify three novel regulators of this process and their targets.

overall_design: RNA-seq of MEFs reprogramming upon shRNA-mediated knockdown of Cpsf3 or Hnrnpul1 (vs. scrambled shRNA control) or overexpression of Tia1 (vs. empty vector control). Sequencing was performed  in duplicates at day 0 and day 12 post-OSKM induction.

first: Panagiotis

last: Papasaikas

first: Ralph

last: Stadhouders

first: Bruno

last: Di Stefano

first: Anna

last: Ribó Rubio

first: Clara

last: Berenguer Balaguer

first: Serena

last: Generoso

last: Mallol

first: José

last: Sardina

first: Bernhard

last: Payer

first: Thomas

last: Graf

first: Juan

last: Valcárcel