title: Transcriptome analysis of human 293T cells transfected with Ehhadh WT and different mutants (K329R, K335R, K344R, K572R)

city: SHANGHAI

first: XIANGYU

last: ZHOU

state: SHANGHAI

address: Shanghai First Maternity and Infant Hospital

institute: Tongji University

summary: We previously identified four lysine crotonylation (Kcr) sites at EHHADH (K329, K335, K344, K572).  Ehhadh mutants in which lysine Kcr sites were simultaneously mutated to arginine by site-specific mutagenesis to mimic a decrotonylated status.To investigate the possible site-specific regulatory role of Ehhadh Kcr on biological processes, we performed transcriptome analysis on 293T cells that transfected with  Ehhadh WT or mutants (K to R) recombinant Myc-tagged plasmids.

overall_design: Examination the differentiation expressed genes (DEGs) in cells transfected with Ehhadh mutations (K329R, K335R, K344R, K572R) and WT

first: Xiangyu

last: Zhou


title: ChIP-Seq in LNCaP prostate cancer cells

status: Public on Jan 28 2022

city: Philadelphia

first: Peter

last: Choi

state: PA

address: 3501 Civic Center Blvd, CTRB 4400

department: Pathology and Laboratory Medicine

country: USA

institute: The Children's Hospital of Philadelphia

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We used ChIP-Seq to profile AR binding and H3K27 acetylation genome-wide in LNCaP cells with and without PRMT inhibition and knockdown.

overall_design: ChIP-Seq of AR and H3K27ac in LNCaP cells treated with DMSO or Furamidine, or infected with shLacZ or shPRMT1. Two replicates and matched input controls for each condition.

first: Stephen

last: Tang

first: Srinivas

last: Viswanathan

middle: S


title: Whole ileal tissue from day 6 Dextran Sodium Sulfate (DSS) administered Il17rafl/fl;Atoh1-cre+/- mice

status: Public on Jan 25 2022

city: Stony Brook

first: Pawan

last: Kumar

address: 100 Nicolls Road

institute: Stony Brook University

type: Expression profiling by high throughput sequencing

summary: Total RNA sequencing (RNA-seq) of the terminal ileum of day 6 Dextran Sodium Sulfate (DSS) administered Il17rafl/fl;Atoh1-cre+ mice and littermate cre- mice was performed.

overall_design: N = 3 Il17rafl/fl;Atoh1-cre+ mice.  N = 3 Il17rafl/fl;Atoh1-cre- mice


title: Glutathione-dependent redox balance characterizes the distinct metabolic properties of follicular and marginal zone B cells

city: Esch-sur-Alzette

first: Dirk

last: Brenner

address: 29, rue Henri Koch

department: Department of Infection and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

summary: The metabolic principles underlying the differences between follicular and marginal zone B cells (FoB and MZB, respectively) are not well understood. Here we show, by studying mice with B cell-specific ablation of the catalytic subunit of glutamate cysteine ligase (Gclc), that glutathione synthesis affects homeostasis and differentiation of MZB to a larger extent than FoB, while glutathione-dependent redox control contributes to the metabolic dependencies of FoB. Specifically, Gclc ablation in FoB induces metabolic features of wild-type MZB such as increased ATP levels, glucose metabolism, mTOR activation and protein synthesis. Furthermore, Gclc-deficient FoB have a block in the mitochondrial electron transport chain (ETC) due to diminished complex I and II activity and thereby accumulate the tricarboxylic acid cycle metabolite succinate. Finally, Gclc deficiency hampers FoB activation and antibody responses in vitro and in vivo, and induces susceptibility to viral infections. In summary, Gclc is required to ensure the development of MZB, the integrity of the mitochondrial ETC in FoB and it is crucial for antibody-mediated immunity.

overall_design: Total B cells from spleen were FACS-sorted from 4 mutant and control mice and pooled with cell hashing.

first: Davide

middle: G

last: Franchina

first: Niels

last: Vandamme


title: A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis [Cut&Run IFNgvsCtr]

city: Stockholm

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

summary: Multiple sclerosis (MS) is a disease characterized by a targeted immune attack on myelin in the central nervous system (CNS). We have previously shown that oligodendrocytes (OLs), myelin producing cells in the CNS, and their precursors (OPCs), acquire disease-specific transcriptional states in MS. To understand how these alternative transcriptional programs are activated in disease, we performed single-cell assay for transposase accessible chromatin using sequencing (scATAC-seq) on the OL lineage in the experimental autoimmune encephalomyelitis (EAE) mouse model of MS. We identified regulatory regions with increased accessibility in oligodendroglia (OLG) in EAE, some of which in the proximity of immune genes. A similar remodeling of chromatin accessibility was observed upon treatment of postnatal OPCs with interferon-gamma (IFNg), but not with dexamethasone. These changes in accessibility were not exclusive to distal enhancers, but also occurred at promoter regions, suggesting a role for promoters in mediating cell-state transitions. Notably, we found that a subset of immune genes already exhibited chromatin accessibility in OPCs ex vivo and in vivo, suggesting a primed chromatin state in OLG compatible with rapid transitions to an immune-competent state. Several primed genes presented bivalency of H3K4me3 and H3K27me3 at promoters in OPCs, with loss of H3K27me3 upon IFNg treatment. Inhibition of JMJD3/KDM6B, mediating removal of H3K27me3, led to the inability to activate these genes upon IFNg treatment. Importantly, OLGs from the adult human brain showed chromatin accessibility at immune gene loci, particularly at MHC-I pathway genes. A subset of single-nucleotide polymorphisms (SNPs) associated with MS susceptibility overlapped with these primed regulatory regions in OLG from both mouse and human CNS. Our data suggest that susceptibility for MS may involve activation of immune gene programs in OLG. These programs are under tight control at the chromatin level in OLG and may therefore constitute novel targets for immunological-based therapies for MS.

overall_design: We have performed bulk CUT&RUN for H3K27ac, H3K27me3, H3K4me3 and Ctcf from FACS sorted Sox10GFP+ oligodendrocyte precursor cells  treated with IFN-gamma fro 48 hours.

first: Mandy

last: Meijer

first: Gonçalo

last: Castelo-Branco


title: Rixosomal RNA degradation contributes to silencing of Polycomb target genes

status: Public on Jan 26 2022

city: boston

first: Danesh

last: Moazed

state: MA

address: 240 longwood avenue

department: cell biology

institute: Harvard medical school

summary: Polycomb Repressive Complex (PRC) 1 and 2 are histone-modifying and chromatin-binding complexes that are required for silencing of developmental regulatory and other genes. Their silencing functions are thought to involve chromatin compaction and condensate formation but whether other mechanisms contribute to silencing is unknown. Here we show that the rixosome, a conserved RNA degradation complex with roles in ribosomal RNA processing and heterochromatic RNA degradation in fission yeast, associates with human PRC complexes, is recruited to promoters of Polycomb target genes in differentiated cell lines and embryonic stem cells, and is required for efficient silencing of Polycomb target genes. These findings reveal an unanticipated role for RNA degradation in Polycomb-mediated gene silencing.

overall_design:
ChIP-seq analysis of histone modifications and chromatin associated proteins
PRO-seq analysis of histone modifications and chromatin associated proteins

first: Haining


title: SARS-CoV-2 Infection Induces Ferroptosis of Human Pluripotent Stem Cell-Derived Sinoatrial Nodal like Pacemaker Cells [bulk RNA-seq]

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: We established an efficient strategy to derive functional human SAN like pacemaker cells for disease modeling and drug screening. And we found SARS-CoV-2 infection causes dysfunction of human SAN like pacemaker cells and induces ferroptosis.  And we also found that Deferoxamine and imatinib can block SARS-CoV-2 infection and infection-associated ferroptosis. Our study using functional human SAN like pacemaker cells demonstrates a potential mechanism for some COVID-19 cardiac abnormalities and identifies candidate drugs to protect the SAN like pacemaker from SARS-CoV-2 infection.

sample_organism:
Homo sapiens
Mesocricetus auratus

platform_organism:
Homo sapiens
Mesocricetus auratus

overall_design: 21 total samples. At least three sample replicates were done for each group.

first: Yuling

last: Han

first: Jiajun

last: Zhu


title: Differential DNA methylation in the hippocampus of arsenic-exposed offspring mice

city: Shanghai

first: Ni

last: Yan

address: 197, Ruijin Er Street

country: China

institute: Shanghaijiaotong University

type: Methylation profiling by high throughput sequencing

summary: Determining the DNA methylation profiles in the hippocampus of developmental arsenic-exposed offspring mice by target-capture MethylC-Seq.

overall_design: Compare the differences in DNA methylation profiles (MethylC-Seq) between the hippocampal DNA samples from developmental exposure of 5000 ppb ATO and control groups.

first: Min

last: Lu


title: In vivo CRISPR screening reveals druggable regulators of mammalian tissue regeneration [liver-RNA-seq]

city: Dallas

first: Hao

state: TX

address: 6000 Harry Hines Blvd

institute: UT Southwestern Medical Cetern

summary: Identifying new pathways that regulate mammalian regeneration is challenging due to the paucity of in vivo screening approaches. We employed pooled CRISPR knockout and activation screening in the regenerating liver to evaluate 164 chromatin regulatory proteins. Both screens identified imitation-SWI chromatin remodeling components Baz2a and Baz2b, not previously implicated in regeneration. In vivo sgRNA, siRNA, and knockout strategies against either paralog confirmed increased regeneration. Distinct BAZ2-specific bromodomain inhibitors GSK2801 and BAZ2-ICR resulted in accelerated liver healing after diverse injuries. Inhibitor treated mice also exhibited improved regeneration in an inflammatory bowel disease model, suggesting multi-tissue applicability. Transcriptomics on regenerating livers showed increases in ribosomal and cell cycle mRNAs. Surprisingly, CRISPRa screening to define mechanisms showed that overproducing ribosomal proteins was sufficient to drive regeneration, while Rpl24 haploinsufficiency was rate limiting for BAZ2 inhibition mediated regeneration. The discovery of regenerative roles for imitation-SWI components provides immediate strategies to enhance tissue repair.

overall_design: Examination of  transcriptional changes after BAZ2 inhibition in regenerating mouse liver


title: Differential mRNA Expression in the hippocampus of arsenic-exposed offspring mice

summary: Determining the mRNA expression profiles in the hippocampus of developmental arsenic-exposed offspring mice by RNA-seq.

overall_design: Compare the differences in transcriptome profiles between the hippocampal samples from 5000 ppb ATO and control groups.


title: In vivo CRISPR screening reveals druggable regulators of mammalian tissue regeneration [liver-ChIP-seq]

overall_design: Examination of changes in H3K27ac binding after BAZ2 inhibition in regenerating mouse liver

first: Yuemeng

last: Jia


title: Cell Type-Specific Genomic Profiling of the Hepatic Fasting Response

status: Public on Jan 27 2022

city: Odense M

first: Anne

last: Loft

address: Campusvej 55

department: Biochemistry & Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: We generated time-resolved profiles of fasting-induced changes in the genomic landscapes of hepatocytes and liver macrophages using the INTACT methodology

overall_design: We subjected female HEP-INTACT and MAC-INTACT mice to a fast starting at the onset of the mouse active phase, ZT12, and after 3, 8, 16, and 24h livers were collected for INTACT followed by ATAC-seq analyses. Ad libitum fed controls were sacrificed at each time point to account for diurnal variations in gene expression.

first: Søren

last: Fisker Schmidt

first: Thomas

last: Schwarzmayr

first: Stephan

last: Herzig


title: Tet1 regulates embryonic stem cell differentiation programs and development independent of its catalytic activity.

first: Meelad

middle: M

last: Dawlaty

state: New York

address: 1301 Morris Park Ave, Price 419, Bronx

department: Genetics

institute: Albert Einstein College of Medicine

summary: In this study: (1) we characterized the Tet1 non-catalytic functions in the regulation of ESC gene expression programs by performing transcriptomic analysis of Tet1 wild type (WT), Tet1 catalytic mutant (Mut) and Tet1 knockout (KO) mouse ESCs by RNA-seq to identify differentially expressed genes. (2) We mapped the genome-wide occupancy of endogenously FLAG-tagged Tet1-WT and  Tet1-Mut in ESCs by CUT&Tag using a specific antibody against FLAG. (3) We determined how the genome-wide occupancy of the epigenetic modifiers: Ezh2, Sin3a, Chd4 and the enrichment of histone marks: H3K27me3, H3K4me3 and H3K27ac, are affected in Tet1-KO ESCs versus Tet1-WT and Tet1-Mut by CUT&Tag or CUT&RUN. (4) We analyzed methylation levels and distribution in Tet1-WT, Tet1-Mut and Tet1-KO ESCs by WGBS, to confirm Tet1 non-catalytic targets with no differential methylation. (5) We explored whether Tet1 non-catalytic functions play a role in chromatin accessibility by performing ATAC-seq in Tet1-WT, Tet1-Mut and Tet1-KO ESCs.

overall_design: We examined the role of Tet1 non-catalytic functions in regulation of ESC gene expression programs by performing transcriptomic analysis of Tet1-WT,  Tet1-Mut, Tet1-KO ESCs by RNA-seq to identify differentially expressed genes. RNA-Seq: Three independent ESC of each genotype (Tet1-WT (Tet1+/+), Tet1-Mut (Tet1m/m), Tet1-KO (Tet1–/–)) were cultured on feeders, pre-plated to remove feeders and seeded on gelatin overnight. Total RNA was extracted (Omega E.Z.N.A Total RNA kit), barcoded and used to prepare libraries. ERCC spike in controls were included. The libraries were subjected to 100 bp paired-end sequencing using Illumina NextSeq 500 platform at the Einstein Epigenomics core following their protocols. We generated ~37 million reads per sample. Details of RNA-seq and data analysis are described in the methods sections of the manuscript. CUT&Tag/CUT&RUN-seq: Genome-wide occupancy experiments were performed on one ESC line of each genotype, which was cultured on feeders, pre-plated to remove feeders and seeded on gelatin overnight. CUT&Tag sequencing analysis of embryonic stem cells expressing FLAG-tagged WT-Tet1 and FLAG-tagged Tet1-catalytic mutant from the endogenous Tet1 locus. FLAG-Tet1-WT and FLAG-Tet1-Mut binding sites were defined by enrichment over non-specific enriched regions identified in IgG and parental untagged Tet1-WT cells. Ezh2/H3K27me3/H3K4me3/Sin3a/HEK27ac CUT&Tag and Chd4 CUT&RUN sequencing analysis of Tet1-WT,  Tet1-Mut, Tet1-KO ESCs: Specific binding sites were defined by enrichment over IgG control. CUT&Tag and CUT&RUN libraries were subjected to 75 bp and 35 bp paired-end sequencing, respectively, using Illumina NextSeq 500 platform at the Einstein Epigenomics core following their protocols. Details of CUT&Tag/CUT&RUN and data analysis are described in the methods sections of the manuscript. WGBS-seq: WGBS was performed on two independent ESC lines of each genotype (Tet1-WT,  Tet1-Mut, Tet1-KO) which were pre-plated and seeded on gelatin overnight.  High quality DNA (extracted by Quick-DNA Miniprep Kit) was bisulfite converted and sequenced by BGI company (https://en.genomics.cn/). Lamda DNA spike-in was added to confirm the bisulfite conversion efficiency. Details of WGBS and data analysis are described in the methods sections of the manuscript. ATAC-seq: Three independent ESC lines of each genotype (Tet1-WT,  Tet1-Mut, Tet1-KO) were used to identify differences in chromatin accessibility by ATAC-seq. Transposed DNA fragments were used to prepare 200-1000 bp libraries. Libraries were sequenced at the Einstein Epigenomics core with a 75 bp paired-end protocol on an Illumina NextSeq 500 platform. Details of WGBS and data analysis are described in the methods sections of the manuscript.

first: Qin

last: Tang

first: Stephanie

last: Chrysanthou

first: Deyou

last: Zheng


title: In vivo CRISPR screening reveals druggable regulators of mammalian tissue regeneration [H2-ATAC-seq]

overall_design: Examination of changes in chromatin accessbility after BAZ2 inhibition


title: Amino acids and IGF1 regulation of fish muscle growth revealed by transcriptome and microRNAome integrative analyses of pacu (Piaractus mesopotamicus) myotubes [RNA-seq]

city: Jatai

first: Bruna

middle: Tereza Thomazini

last: Zanella

state: Goias

country: Brazil

institute: Federal University of Jatai (UFJ)

summary: Amino acids (AA) and IGF1 have demonstrated to play essential roles in protein synthesis and fish muscle growth. The myoblast cell culture is useful to study the muscle regulation, and omics data have contributed enormously to understand its molecular biology. However, to our knowledge, no study has performed large-scale sequencing of fish cultured muscle cells stimulated with pro-growth signals. In this work, we obtained the transcriptome and microRNAome of pacu (Piaractus mesopotamicus) cultured myotubes treated with AA or IGF1. We identified 1228 and 534 genes differentially expressed by AA and IGF1. Enrichment analysis showed that AA treatment induced chromosomal changes, mitosis, and muscle differentiation, while IGF1 modulated IGF/PI3K signalling, metabolic alteration, and matrix structure. In addition, potential molecular markers were similarly modulated by both treatments. Muscle-miRNAs (miR-1, -133, -206 and -499) were up-regulated especially in AA samples, and we identified molecular networks with omics integration. Two pairs of genes and miRNAs showed high level of relationship, and involvement in myogenesis and muscle growth: marcksb and miR-29b in AA, and mmp14b and miR-338-5p in IGF1. Our work helps to elucidate fish muscle physiology and metabolism, highlights potential molecular markers, and creates perspective for improvements in aquaculture and in vitro meat production.

overall_design: To obtain the transcriptional profile of pacu (Piaractus mesopotamicus) muscle cells treated with amino acids (AA), IGF1 or cultived in nutrient restriction medium

first: Bruno

middle: O

last: Duran

middle: T

first: Erika

last: Perez

first: Edson

middle: A

last: Mareco

first: Maeli

last: Dal-Pai-Silva

first: Daniel

last: de la serrana


title: Siwi cooperates with Par-1 kinase to regulate mitochondrial Papi scaffolding Siwi-piRISC biogenesis

city: Tokyo

first: Yuka

middle: W.

last: Iwasaki

address: 35 Shinanomachi, Shinjuku-ku,

department: Department of Molecular Biology

country: Japan

institute: Keio University School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Bombyx Papi contains two K-homology (KH) domains and one Tudor domain, and acts as a scaffold for Siwi-piRISC biogenesis on the mitochondrial surface. To initiate this process, Papi binds first to Siwi via the Tudor domain and subsequently to piRNA precursors loaded onto Siwi via the KH domains. This second action depends on phosphorylation of Papi. However, its underlying mechanism remains unknown. Here, we show that Siwi targets Par-1 kinase to mitochondrial Papi to promote its phosphorylation at Ser547 in the auxiliary domain and that this modification enhances the ability of Papi to bind Siwi-bound piRNA precursors via the KH domains. Papi S547A mutant still bound to Siwi, like wild-type (WT) Papi, although it evaded phosphorylation by Par-1: Consequently, Papi lost the ability to bind RNAs, abrogating the generation of Siwi-piRISC. Papi mutant lacking the Tudor and auxiliary domains escaped coordinated regulation by Siwi and Par-1 and lost their bias to bind piRNA precursors. Pseudo-phosphorylation mutants of Papi restored Siwi-piRISC formation in Papi-lacking cells, but their ability to bind RNAs required Siwi, similar to WT Papi. Par-1-dependent, multilayered mechanism by which Siwi regulates the role of Papi in Siwi-piRISC biogenesis was revealed.

first: Hiromi

last: Yamada

first: Mikiko

middle: C

last: Siomi


title: WGBS on prospermatogonia at E18.5

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

country: France

institute: institut curie

summary: To evaluate the impact of the Dnmt3C, Dnmt3L and Dnmt3A mutations in the methylome of male germ cells, mutant and control whole genome bisulfite sequencing experiments were conducted starting from genomic DNA obtained from FACS-sorted germ cells.

overall_design: Comparison of whole genome methylome maps of male germ cells of mutant and wildtype isolated from fetal testis at E18.5

first: Mathilde

last: Dura

first: Déborah

last: Bourc'his


title: scRNA-seq on germ cells or whole testis at 10dpp

summary: To allow identification of differentially expressed genes in Dnmt3A and Dnmt3L mutants and wildtype germ cells at a single cell level at 10dpp

overall_design: Comparison of scRNA-seq results from germ cells of mutants Dnmt3A, Dnmt3L and wildtype at 10dpp

first: Deborah


title: Cut&Run on Id4-GFP bright + med germ cells (~SSC) at 10dpp for H3K27me3, H3K27ac and H3K9me3

summary: To evaluate the impacts of Dnmt3A mutation in the methylome of male germ cells, mutant and control whole genome bisulfite sequencing experiments were conducted starting from genomic DNA obtained from FACS-sorted germ cells.

overall_design: Examination of 3 different histone modifications in Dnmt3A mutant and wildtype context.


title: ADARs act as potent regulators of circular transcriptome in cancer

city: Singapore

first: Polly Leilei

last: Chen

address: #12-01, MD6, 14 Medical Drive

department: Department of Anatomy

country: Singapore

institute: Cancer Science Institute of Singapore NUS

summary: Circular RNAs (circRNAs) are produced by head-to-tail back-splicing which is mainly facilitated by base-pairing of reverse complementary matches (RCMs) in circRNA flanking introns. Adenosine deaminases acting on RNA (ADARs) are known to bind double-stranded RNAs for adenosine to inosine (A-to-I) RNA editing. Here we characterize ADARs as potent regulators of circular transcriptome by identifying over a thousand of circRNAs regulated by ADARs in a bidirectional manner through and beyond their editing function. We found that editing can stabilize or destabilize secondary structures formed between RCMs via correcting A:C mismatches to I(G)-C pairs or creating I(G).U wobble pairs, respectively. We provided experimental evidence that editing also favors the binding of RNA-binding proteins such as PTBP1 to regulate back-splicing. These ADARs-regulated circRNAs which are ubiquitously expressed in multiple types of cancers, demonstrate high functional relevance to cancer. Our findings support a hitherto unappreciated bidirectional regulation of circular transcriptome by ADARs and highlights the complexity of cross-talk in RNA processing and its contributions to tumorigenesis.

overall_design: We constructed cDNA libraries of 6 circular RNA samples and sequenced the libraries using Illumina Hiseq 4000 platform achieving over 100 millions pairs of mappable reads per sample. Then we examined circular RNA events in EC109 cells after depletion or overexpression of ADAR1 or ADAR2.

first: Leilei

first: Haoqing

last: Shen

first: Omer

last: An


title: germ cells

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

overall_design: Refer to individual Series


title: RNAseq on whole testis at 19dpp and 25dpp

summary: To allow identification of differentially expressed genes and transposons in Dnmt3A mutants at 19dpp and 25dpp; mutant and wildtype RNA-Seq experiments were conducted starting from whole testis RNA.

overall_design: Comparison of RNA-seq results from whole testis RNA of mutant Dnmt3A and wildtype at 19dpp and 25dpp.


first: Danesh

last: Moazed

overall_design: ChIP-seq analysis of histone modifications and chromatin associated proteins in hES cells

first: Haining

last: zhou


title: RNAseq on Id4-GFP bright + med germ cells (~SSC) at 10dpp

summary: To allow identification of differentially expressed genes in Dnmt3A mutant and wildtype Id4-GFPbright+med cells (~SSC) at 10dpp

overall_design: Comparison of RNA-seq results from Id4-GFPbright+med cells RNA of mutant Dnmt3A and wildtype at 10dpp


title: Single nuclei transcriptomic profiling of human astrocytes and oligodendrocytes in Alzheimer’s disease

status: Public on Apr 01 2022

first: Shane

middle: A.

last: Liddelow

address: 435 E. 30th Street

department: Neuroscience Institute

institute: NYU Langone Medical Center


title: Inhibition of the renal production of glucose associates with a worse prognosis in chronic kidney disease

city: Lugano

first: Anna

last: Rinaldi

state: Ticino

address: Tesserete

department: Nephrology

country: Switzerland

institute: Ente Ospedaliero Cantonale

summary: Single-cell transcriptomics revealed that gluconeogenesis is impaired in proximal tubule cells during CKD in mice.

overall_design: Normal mouse kidney was analysed by single-nucleus RNA-sequencing using 10X Genomics Chromium Drop-Seq. Normal kidney was harvested from 10- to 12-week-old, 25–28-g, male C57BL6/J Pten pc-/-. Illumina Next-Seq sequencing of barcoded single nuclei libraries was performed and aligned to a pre-mrna genome with STAR/CellRanger. Seurat v3.2.0 in R v4 was used for downstream analyses, including normalization, scaling, and clustering of nuclei.

first: Thomas

last: Verissimo

last: Faivre

first: Carolyn

last: Heckenmeyer

first: Marylise

last: Fernandez

last: Cagarelli

first: Maja

last: Lindenmeyer

first: Clemens

last: Cohen

first: Maarten

last: Naesens

first: Joseph

last: Rutkowski

first: Solange

last: Moll

first: Pietro

last: Cippà

first: David

last: Legouis

first: Sophie

last: de Seigneux


title: SUMOylation of Jra regulates the immune response in the gut of Drosophila

status: Public on Jan 24 2022

city: PUNE

first: Girish

last: Ratnaparkhi

state: MH

address: Dr. Homi Bhabha Road Pashan Pune 411008

department: Biology

country: India

institute: Indian Institute of Science Education & Research

summary:
Purpose: To understand how SUMOylation of Jra regulates the gut immune response in Drosophila in a Pseudomonas infection model. To answer this, we performed 2 RNA-seq experiments one with knockdown of Jra in the gut and the other with a SUMO-conjugation resistant mutant (SCR) line generated by CRISPR/Cas9 technology.
Methods: 50-60 midguts from adult female flies were dissected and total RNA was extracted in trizol. The total RNA was used to generate a cDNA library using Quantseq 3' mRNA kit Fwd. Expereiments done in triplicates
Results: Phenotypically, JraRNAi is protective to the host and JraSCR is detrimental to the host during infection. Transcriptional profiling revealed that genes involved in immune response are differentially regulated in JraRNAi and JraSCR.
Conclusions: Our study demonstrates the first detailed analysis of gut transcriptomes with varied activity of Jra using an RNAi and an allele that is resistant to SUMO conjugation. Our results show that genes important for a robust immune response are elevated in JraRNAi where as the same genes are dampened in JraSCR. This suggests that SUMO conjugation of Jra is a crucial step for robust immune activation in the gut of Drosophila.

overall_design: 42 samples

first: Soory

last: Amarendranath

first: Ratnaparkhi

last: Girsh


title: A sandbox for prediction and integration of DNA, RNA, and proteins in single cells

city: Somerville

first: Daniel

middle: B

last: Burkhardt

address: 101 South Street, 6th Floor

institute: Cellarity

summary: Single-cell multiomics data collected from bone marrow mononuclear cells of 12 healthy human donors. Half the samples were measured using the 10X Multiome Gene Expression and Chromatin Accessability kit and half were measured using the 10X 3' Single-Cell Gene Expression kit with Feature Barcoding in combination with the BioLegend TotalSeq B Universal Human Panel v1.0.  The dataset was generated to support Multimodal Single-Cell Data Integration Challenge at NeurIPS 2021. Samples were prepared using a standard protocol at four sites. The resulting data was then annotated to identify cell types and remove doublets. The dataset was designed with a nested batch layout such that some donor samples were measured at multiple sites with some donors measured at a single site. In the competition, participants were tasked with challenges including modality prediction, matching profiles from different modalities, and learning a joint embedding from multiple modalities.

first: Malte

middle: D

last: Lücken

first: Christopher

last: Lance

first: Robrecht

last: Cannoodt

first: Angela

last: Pisco

first: Smita

last: Krishnaswamy

first: Fabian

middle: J

last: Theis

first: Jonathan

last: Bloom


title: Integrative genome-wide analysis in mouse mammary tumors in response to maternal long-term genistein (LT-GE) treatment

city: Columbia

first: Yuanyuan

middle: R

last: Li

state: MO

address: University of Missouri School of Medicine, One Hospital Dr., Medical Sciences Building, NW508, Medical Sciences Building, NW508, Medical Sciences Building, M659

department: Ob&Gyn

institute: University of Missouri

summary: We tested global gene transcriptome changes by RNA-sequencing analysis and genome-wide methylation profiles by reduced representation bisulfite sequencing (RRBS) analysis in the offspring mammary tumors of C3(1)-SV40 Tag (SV40) transgenic mice to further identify key epigenetic-controlled genes in regulation of maternal GE diet-mediated early breast cancer prevention.

overall_design: Total RNA and genomic DNA samples obtained from the offspring mammary tumors of SV40 transgenic mice with mothers fed either control or LT-GE diets (maternal GE dietary administration began in early life from 4 weeks of age in mothers until weaning) were subjected RNA-seq analysis and RRBS analysis.

first: Vinodh

last: Srinivasasainagendra


title: SARS-CoV-2 Infection Induces Ferroptosis of Human Pluripotent Stem Cell-Derived Sinoatrial Nodal like Pacemaker Cells

first: Shuibing

last: Chen


title: Human iPSC-Derived Fallopian Tube Organoids with BRCA1 Mutation Recapitulate Early Stage Carcinogenesis

city: Los Angeles

first: Michael

last: Workman

state: CA

address: 8700 Beverly Blvd., AHSP Suite 8405

institute: Cedars-Sinai Medical Center

summary: We generate induced pluripotent stem cells (iPSCs) from healthy individuals and young ovarian cancer patients with germline pathogenic BRCA1 mutations. We then differentiate them into a human iPSC-derived fallopian tube organoid model. We recapitulated BRCA1 mutant ovarian carcinogenesis in vitro and showed tumors in vivo. Using the IPSC derived fallopian tube organoid model, we identify a unique transcriptional profile associated with BRCA1 mutation similar to the ovarian cancer profile.

overall_design: Bulk RNA-seq profiles of BRCA1 mutant and conrtol iPSC derived fallopian tube organoids

first: Nur

last: Yucer

first: Clive

middle: N

last: Svendsen


title: Activation of the Mitochondrial ClpP protease is Synthetically Lethal with HDAC1/2 Inhibition in Glioblastoma Model Systems

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
By integration of transcriptome and metabolite analyses, we showed that pharmacological activation of the mitochondrial ClpP protease through utilization of enhanced imipridone compounds (ONC206 and ONC212) in combination with global (Panobinostat) and selective (romidepsin) HDAC – inhibitors caused synergistic reduction of viability in established and patient-derived xenograft (PDX) cultures of human GBM. This effect occurred independent of TP53 status and was partially mediated by activation of a cell death with apoptotic features accompanied by activation of initiator and effector caspases as well as cleavage of PARP. Consistently, the combination treatment altered the expression of anti-apoptotic and pro-apoptotic Bcl-2 family members, resulting in down-regulation of Bcl-xL and Mcl-1. Knockdown experiments targeting Noxa, BIM, Bcl-xL and Mcl-1 confirmed a functional implication of these proteins in the reduction of cellular viability mediated by the combination treatment. Importantly, knockdown of the ClpP protease significantly rescued the reduction of cellular viability by ClpP activators and the combination treatment, respectively, suggesting critical involvement of this protein.
We used microarrays to detail the global programme of gene expression underlying cellularization and identified distinct classes of up-regulated and down-regulated genes in cells treated with ONC206 and Romidepsin.

overall_design: GBM14 cells were treated with 10µM ONC206 and/or 2.5nM Romidepsin (or DMSO vehicle control) for 24h and samples were extracted for total RNA by miRNAeasy Mini Kit.

first: Thi

last: Nguyen

first: Markus

last: Siegelin


title: ATAC-seq data of control and Activin-treated amphioxus ectodermal explants at 11 hpf and 19 hpf.

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

summary: The goal of this projet was to identify genomic region showing differential accessibility  between control and Activin-treated amphioxus explants at two time points (gastrula and neurula stage)

overall_design: Two replicates were obtained for each condition (time/treatment).

first: Anthony

last: Leon

first: Lucie

last: Subirana

first: Ildefonso

last: Cases

first: Manuel

last: Irimia

first: Jose

middle: L

last: Gomez-Skarmeta

first: Hector

last: Escriva

first: Stephanie

last: Bertrand


title: In vivo CRISPR screening reveals druggable regulators of mammalian tissue regeneration [H2-ChIP-seq]

first: Hao

last: Zhu

summary: Identifying new pathways that regulate mammalian regeneration is challenging due to the paucity of in vivo screening approaches. We employed pooled CRISPR knockout and activation screening in the regenerating liver to evaluate 164 chromatin regulatory proteins. Both screens identified imitation-SWI chromatin remodeling components Baz2a and Baz2b, not previously implicated in regeneration. In vivo sgRNA, siRNA, and knockout strategies against either paralog confirmed increased regeneration. Distinct BAZ2-specific bromodomain inhibitors GSK2801 and BAZ2-ICR resulted in accelerated liver healing after diverse injuries. Inhibitor treated mice also exhibited improved regeneration in an inflammatory bowel disease model, suggesting multi-tissue applicability. Transcriptomics on regenerating livers showed increases in ribosomal and cell cycle mRNAs. Surprisingly, CRISPRa screening to define mechanisms showed that overproducing ribosomal proteins was sufficient to drive regeneration, while Rpl24 haploinsufficiency was rate limiting for BAZ2 inhibition mediated regeneration. The discovery of regenerative roles for imitation-SWI components provides immediate strategies to enhance tissue repair.

overall_design: Examination of genome-wide BAZ2A and BAZ2B binding  and epigenetic changes after BAZ2 inhibition.

first: Yuemeng

last: Jia


title: Amino acids and IGF1 regulation of fish muscle growth revealed by transcriptome and microRNAome integrative analyses of pacu (Piaractus mesopotamicus) myotubes

first: Bruna

last: Zanella


title: Expression Patterns of SOX10 deficient BRAFi/MEKi tolerant and SOX10 KO A375 cell lines

city: Philadelphia

first: Andrew

middle: E

last: Aplin

address: 233 South 10th St.

institute: Thomas Jefferson University

summary: Given the heterogeneous expression of SOX10 in naïve melanoma, we sought to characterize SOX10 deficient population. To this end, we generated SOX10 CRISPR/Cas9 knockouts using two different guide RNAs (gRNA, #2 and #4) in the A375 (BRAF mutant) metastatic cell line.  Using this approach, we identified multiple clones with loss of SOX10 expression. RNA-seq was performed to characterize the SOX10-regulated transcriptome. We used GSEA analysis to evaluate significant pathway changes in SOX10 knockout cells when compared to parental cells. We observed an enrichment in pathways associated with the tumor microenvironment (epithelial-mesenchymal transition; TGF beta signaling; extracellular structure organization; apical junction; hypoxia; angiogenesis), alterations in metabolic pathways (increase in the glycolysis pathway), a reduction in MYC and E2F targets and upregulation in p53 pathway and TNFA signaling via NFkB in the SOX10 knockout cells compared to parental cells.  SOX10 negative clones have been identified in the minimal residual disease in BRAF mutant PDX models following BRAF and MEK inhibition and in patient samples  while on treatment and SOX10 loss has been described as a resistant mechanism in BRAF mutant melanoma patients following vemurafenib treatment. Thus, we also analyzed the transcriptome profile of SOX10 low/deficient cells that arose following BRAFi+MEKi treatment in vivo. We performed GSEA analysis on RNA-seq data of CRT34 and CRT35 cells compared to parental A375 cells. CRT34 and CRT35 showed a very similar transcriptome profile to SOX10 KO cells when compared to A375 parental cells

overall_design: RNAs were obtained from parental and CRISPR SOX10 KO A375 cells and from in vitro cultures of BRAFi/MEKi tolerant/resistant A375 cells generated in vivo, SOX10 deficient (CRT34 and CRT35) treated with or without a combination of BRAF and MEK inhibitor

first: Mai

middle: Q

first: Claudia

last: Capparrelli

first: Timothy

last: Purwin


title: Genetic and epigenetic determinants of reactivation of Mecp2 and the inactive X chromosome in neural stem cells

city: Rotterdam

first: Beatrice

last: Tan

address: Dr. Molewaterplein 40

department: Developmental Biology

country: Netherlands

institute: Erasmus MC


title: Limited extent and consequences of pancreatic SARS-CoV-2 infection

status: Public on Jan 23 2022

city: New York

first: Brad

last: Rosenberg

address: 1 Gustave L Levy Place, Box 1124

department: Department of Microbiology

institute: Icahn School of Medicine at Mount Sinai

summary: Several studies have suggested a relationship between SARS-CoV-2 infection and diabetes. This study examined the consequences of infection of human pancreatic islets with SARS-CoV-2 virus. This GEO submission contains the raw and processed data from single-cell RNA sequencing (scRNAseq) experiments evaluating the tropism of SARS-CoV-2 in pancreatic islets and transcriptional changes induced by infection of these cells. Overall we observed limited infection of pancreatic islets (0.2 - 3.4% of all cells infected per donor) and identified multiple pancreatic cell types as targets of infection; due to the preponderance of major endocrine cell populations in our islet cell preparations, downstream analyses were primarily focused on alpha and beta cells. Within beta cells we identified an upregulation of interferon stimulated genes in both infected and bystander cells as well as an NFκB mediated genes in infected cells only. Within alpha cells we detected a non-specific downregulation of a large number of host genes in infected cells.

overall_design: Pancreatic islets from three donors were infected or mock infected with SARS-CoV-2 for 48 hours then analyzed by scRNAseq.

first: Dirk

last: Homann


title: Control and Activin-treated amphioxus ectodermal explants at 11 hpf and 19 hpf.

first: Juan

last: Tena


title: RNA-seq data of control and Activin-treated amphioxus ectodermal explants at 11 hpf and 19 hpf.

summary: The goal of this projet was to identify genes differentially expressed between control and Activin-treated explants at two time points (gastrula and neurula stage)

overall_design: Two repliactes were obtained for each condition (time/treatment) by mixing explants obtained from different fecondations.

first: Anthony

last: Leon

first: Lucie


title: The protective effect of spermine on diabetic cardiomyopathy.

city: Harbin

first: Can

last: Wei

address: Baojian Road

department: Department of Pathophysiology

institute: Harbin Medical University

summary: Diabetic cardiomyopathy (DCM) is a specific form of cardiomyopathy that is independent of coronary artery disease and hypertension. Exploring the transcriptomics and proteomics of DCM is of great significance for understanding the biology of the disease and for guiding new therapeutic targets for the potential therapeutic effect of spermine (SPM).

overall_design: The mRNA profiles of myocardial tissue of C57BL / 6 mice that divived into normal control group (CK), diabetic cardiomyopathy model group (DCM) and spermine treated group (SPM)


title: RNASeq analysis of human ALDH- and ALDH+ DU145 xenografts in nu/nu mice upon radiotherapy treatment

status: Public on Jan 22 2022

city: Dresden

last: Peitzsch

country: Germany

institute: Center for Regenerative Therapies Dresden (CRTD)

summary:
Purpose: we aimed at identify and compare the transcriptional changes of ALDH- and ALDH+ DU145 xenografts upon radiotherapy treatment.
Method: Xenografts were generated by injection of ALDH- and ALDH+ DU145 cells in male NMRI-Foxn1 nu/nu immune-deficient mice and subjected to fractionated irradiation to a final dose of 50 Gy. Tumors were excised and processed for total RNA extraction and RNAseq analysis.

overall_design: Expression profiling by high throughput sequencing of snap-frozen ALDH- and ALDH+ DU145 xenograft tumors upon fractionated irradiation.

first: Franziska

middle: M

last: Schwarz

first: Maria

last: Besso

first: Ina

last: Kurth


title: Genome-wide transcriptional profiling of C. elegans in a heavy metal contaminated soil after nZVI treatment

city: Madrid

first: Pedro

last: Botias

address: Jose Antonio Nováis 12

institute: Universidad Complutense de Madrid

summary: Classical ecotoxicological test and high-throughput molecular tools (microarray) were conducted on C. elegans to assess the effectiveness and ecosafety of a nanoremediation strategy applied to a highly polluted soil environment with heavy metals (HMs). We stablished a profiled gene expression in C. elegans exposed to the polluted soil, treated and untreated with nZVI. The results obtained showed that the percentage of differentially expressed genes decreased with the exposure time to nZVI. The expression profile of genes associated with stress response, metal toxicity, proteolysis, immune response, and cuticle development resulted affected. At short term, when a more effective HMs immobilization has occurred genes related to specific heavy metal detoxification mechanisms or to response to metal stress, were down regulated. After longer exposure time, we found decreased effectiveness of nZVI and increased HMs toxicity, whereas the transcriptional oxidative and metal-induced responses were attenuated.

overall_design: For each experimental condition (control and nZVI-treated soil, at three different sampling times), three microarray experiments corresponding to three independent RNA from the collected nematodes were processed and analyzed. The samples were processed with GeneChip® WT PLUS Reagent Kit (Applied Biosystems), hybridized with GeneChip™ C. elegans Gene 1.0 ST Arrays (Applied Biosystems) and scanned with a GeneChip® Scanner 3000 7G (Applied Biosystems).

first: Carmen

last: Fajardo

first: Margarita

last: Martín

first: Mar

last: Nande

last: Botías

first: Jesús

last: García-Cantalejo

first: Gerardo

last: Mengs

first: Gonzalo

last: Costa


title: Expression data from Skeletal Stem Cells cultured in 3-dimensional (3D) Collagen

status: Public on Jan 21 2022

city: Ann Arbor

first: Stephen

last: Weiss

state: MI

address: 210 Washtenaw Ave

department: Life Sciences Institute

institute: University of Michigan

summary:
Skeletal stem cells (SSCs) reside in a 3-dimensional extracellular matrix (ECM) compartment and differentiate into multiple cell lineages, thereby controlling tissue maintenance and regeneration. Within this environment, SSCs can proteolytically remodel the surrounding ECM in response to growth factors that direct lineage commitment. In the bone tissue, type I collagen is the most abundant ECM.  The dominant type I collagenolytic proteinase found in mammals is the type I transmembrane MMP, MMP14. Therefore, SSCs from  Mmp14+/+ or Mmp14-/- mice were cultured  in collagen hydrogels to explore the gene expression regulated by ECM remodeling.
Microarrays were used to detail the gene expression underlying ECM remodeling process in SSCs.

overall_design: mRNA was harvested from collagen-embedded wild-type and Mmp14 knockout SSCs after a 48 h culture period and hybridization on Affymetrix microarrays to screen for transcriptional changes.

first: Yi

last: Tang

first: Lingxin

last: Zhu

first: Jung-Sun

last: Cho

first: Xiao-Yan

last: Li


title: Transcriptomic cell types of ventromedial hypothalamus in female mouse: 10x cells

city: Pasadena

first: Mengyu

last: Liu

state: California

address: 1200 E California Blvd

department: BBE

institute: Caltech

summary: The ventrolateral subdivision of the ventromedial hypothalamus (VMHvl) is essential for innate social behaviors including aggression and mating in female mice at different reproductive states. However, the female VMHvl transcriptomes in different reproducive states and their relationship behavioral functions are unknown. We performed single-cell RNA 10x sequencing and investigated correspondence between transcriptomic identity in different reproductive states and behavioral activation. Immediate early gene analysis from our Act-seq dataset identified that distinct T-types function in female aggression and mating behaviors.

overall_design: Single cell characterization of VMHvl in virgin, lactaing and post-lactation female mice

first: David

last: Anderson


title: Transcriptional co-activators YAP1-TAZ of Hippo signalling in doxorubicin-induced cardiomyopathy

city: London

first: Angela

last: Yiu

address: Hammersmith Campus, Du Cane Road

department: Department of Surgery and Cancer

country: United Kingdom

institute: Imperial College London

summary: Aims: Hippo signalling is an evolutionarily conserved pathway that controls organ size by regulating apoptosis, cell proliferation and stem cell self-renewal. Recently, the pathway has been shown to exert powerful growth regulatory activity in cardiomyocytes. However, the functional role of this stress- and cell death-related pathway in the human heart and cardiomyocytes is not known. In this study, we investigated the role of the transcriptional co-activators of Hippo signalling, YAP and TAZ, in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) in response to cardiotoxic agents and investigated the effects of modulating the pathway on cardiomyocyte function and survival. Methods and Results: RNA sequencing analysis of human heart samples with doxorubicin-induced end-stage heart failure and healthy controls showed YAP and ERBB2 (HER2) as upstream regulators of differentially expressed genes correlated with doxorubicin treatment. Thus, we tested the effects of doxorubicin and/or small molecule inhibitor lapatinib on hiPSC-CM in vitro . Using an automated high contentscreen of 96 clinically relevant chemotherapeutic drugs, we showed that doxorubicin induced the highest activation of YAP/TAZ nuclear translocation in both hiPSC-CM and  control MCF7 breast cancer cells. The overexpression of YAP rescued doxorubicin- induced cell loss in hiPSC-CM by inhibiting apoptosis and inducing proliferation. In  contrast, silencing of YAP and TAZ by siRNAs resulted in elevated mitochondrial membrane potential loss in response to doxorubicin. Human iPSC-CM calcium transients did not change in response to YAP/TAZ silencing. Conclusions: Our results suggest that Hippo signalling is involved in clinical anthracycline-induced cardiomyopathy. Modelling with hiPSC-CM in vitro showed similar responses to doxorubicin as adult cardiomyocytes and revealed a potential cardioprotective effect of YAP in doxorubicin-induced cardiotoxicity.

overall_design: 5 left ventricular

first: Tunde

last: Berecz

first: Gabor

last: Foldes


title: Two subsets of human marginal zone B cells resolved by global analysis of lymphoid tissues and blood [human appendix, spleen, mLN]

city: Oxford

first: Jacqueline

middle: HY

last: Siu

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

institute: University of Oxford

summary: B cells generate antibodies that are essential for immune protection, but their subgroups are poorly defined. Here we perform undirected deep profiling of B cells in matched human lymphoid tissues from deceased transplant organ donors and blood. In addition to identifying unanticipated features of tissue-based B cell differentiation, we resolve two subsets of marginal zone B (MZB) cells differing in cell surface and transcriptomic profiles, clonal relationships to other subsets, enrichment of genes in the NOTCH pathway, distribution bias within splenic marginal zone microenvironment, and immunoglobulin repertoire diversity and hypermutation frequency. Each subset is present in spleen, gut-associated lymphoid tissue, mesenteric lymph nodes, and blood. MZB cells and the lineage from which they are derived are depleted in lupus nephritis. Here we show that this depletion is of only one MZB subset.  The other remains unchanged as a proportion of total B cells compared to health. Thus, it is important to factor MZB cell heterogeneity into studies of human B cell responses and pathology.

overall_design: Single cell transcriptomic analysis of B cells from human appendix, spleen, mLN

first: Jo

last: Spencer

middle: H


title: In vivo CRISPR screening reveals druggable regulators of mammalian tissue regeneration

city: Dallas

first: Hao

address: 6000 Harry Hines Blvd

institute: UT Southwestern Medical Cetern

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

overall_design: Refer to individual Series


city: Ribeirão Preto

first: Carla

middle: Barbosa

last: Nonino

address: Av. Bandeirantes, 3900

institute: Universidade de São Paulo

type: Methylation profiling by genome tiling array

summary:
Introduction: Nutriepigenetic markers are predictive responses associated with changes in human "surrounding" environmental conditions, which may influence metabolic diseases. Although rich in calories, Western diets could be linked with the deficiency of micronutrients, resulting in the downstream of epigenetic and metabolic effects and consequently in obesity. Zinc (Zn) is an essential nutrient associated with distinct biological roles in human health. Despite its importance in metabolic processes, little is known about the Zn-epigenetic. Thus, the present study aimed to identify the epigenetic variables associated with Zn daily ingestion (ZnDI) and serum Zinc (ZnS) levels in women with and without obesity.
Materials and methods: this is a case-control, non-randomized, single-center study conducted with 21 women allocated into two groups: Control Group (CG), composed of 11 women without obesity, and Study Group (SG), composed of 10 women with obesity. Anthropometric measurements, ZnDI, and ZnS levels were evaluated. Also, the leukocyte DNA was extracted for DNA methylation analysis using the 450k Illumina BeadChips. The Epigenetic Clock was calculated by the Horvath method. The ChAMP package selected the Differentially Methylated Regions (DMRs).
Results: The SG had lower ZnS levels than the CG. Moreover, in SG, the ZnS levels were negatively associated with the epigenetic age acceleration. The DMR analysis revealed 37 DMRs associated with ZnDI and ZnS levels. The DMR of the PM20D1 gene was commonly associated with ZnDI and ZnS levels and was hypomethylated in the SG.
Conclusion: Our findings provide new information on Zn's modulation of DNA methylation patterns and bring new perspectives for understanding the nutriepigenetic mechanisms in obesity.

overall_design:
MethylationBrazil
Novel Zinc-related Differentially Methylated Regions in leukocytes of women with and without obesity using the Champ pipeline


title: Two subsets of human marginal zone B cells resolved by global analysis of lymphoid tissues and blood [healthy and lupus human blood]

overall_design: Single cell transcriptomic analysis of B cells from healthy and lupus human blood

first: Thomas

last: Tull

first: Michael

last: Pitcher


title: CDK7 inhibition by LDC4297 in Mia-Paca2 and Panc89 cells

city: Muenster

last: Meisterernst

address: Robert-Koch-Straße 43

department: Faculty of Medicine

institute: University of Muenster

summary: Inhibition of the dual function cell cycle and transcription kinase CDK7 is known to affect the viability of cancer cells, but the mechanisms underlying cell line-specific growth control remain poorly understood. Here, we employed a previously developed, highly specific small molecule inhibitor that non-covalently blocks ATP binding to CDK7 (LDC4297) to study the mechanisms underlying cell line-specific growth using a panel of genetically heterogeneous human pancre-atic tumor lines as model system. Although LDC4297 diminished both transcription rates and CDK T-loop phosphorylation in a comparable manner, some PDAC lines displayed significantly higher sensitivity than others. We focused our analyses on two well-responsive lines (Mia-Paca2 and Panc89) that, however, showed significant differences in their viability response to extended exposure to limiting LDC4297 concentrations. Biochemical and RNAseq analysis revealed strik-ing differences in gene expression and cell cycle control. Especially the downregulation of a group of cell cycle control genes, among them CDK1/2 and CDC25A/C, correlated well to the observed viability differences in Panc89 versus Mia-Paca2 cells. A parallel downregulation of regulatory pathways supported the hypothesis of a feedforward programmatic effect of CDK7 inhibitors, eventually causing hypersensitivity of PDAC lines.

overall_design: In total 12 samples were analyzed reflecting two conditions (untreated and LDC4297 treated) in two different cell lines.

first: Lina

last: Kolloch

first: Andrea

last: Oeckinghaus


title: Xist spatially amplifies SHARP recruitment to balance chromosome-wide silencing and specificity to the X chromosome

first: Mario

last: Blanco


title: Xist spatially amplifies SHARP recruitment to balance chromosome-wide silencing and specificity to the X chromosome [CLAP]

summary: Although thousands of lncRNAs are encoded in mammalian genomes, their mechanisms of action are largely uncharacterized because they are often expressed at significantly lower levels than their proposed targets. One such lncRNA is Xist, which mediates chromosome-wide gene silencing on one of the two X chromosomes to achieve gene expression balance between males and females. How a limited number of Xist molecules can mediate robust silencing of a significantly larger number of target genes (~1 Xist RNA: 10 gene targets) while maintaining specificity to genes on the X within each cell is unknown. Here, we show that Xist drives non-stoichiometric recruitment of the essential silencing protein SHARP to amplify its abundance across the inactive X, including at regions not directly occupied by Xist. This amplification is achieved through concentration-dependent homotypic assemblies of SHARP on the X and is required for chromosome-wide silencing. We find that expressing Xist at higher levels leads to increased localization at autosomal regions, demonstrating that low levels of Xist are critical for ensuring its specificity to the X chromosome. We show that Xist (through SHARP) acts to suppress production of its own RNA which may act to constrain overall RNA levels and restrict its ability to spread beyond the X. Together, our results demonstrate a spatial amplification mechanism that allows Xist to achieve two essential but countervailing regulatory objectives: specificity to the X and chromosome-wide gene silencing, and suggest a more general mechanism by which other low abundance lncRNAs can balance specificity to, and robust control of, their regulatory targets.

overall_design: Using UV crosslinking we created covalent bonds between all proteins and RNAs that were directly interacting. We utilized Halo-tagged variants of SHARP protein to purify the interacting RNAs and subsequently sequenced to identify binding sites.

first: Mitchell

last: Guttman

first: Joanna

middle: W

last: Jachowicz

first: Mackenzie

last: Strehle


title: Xist spatially amplifies SHARP recruitment to balance chromosome-wide silencing and specificity to the X chromosome [RAP-DNA]

overall_design: Mouse embryonic stem cells expressing Xist under a Dox inducible promoter were treated with increasing amounts of Dox to titrate expression of Xist. After Dox induction, cells were harvested and crosslinked using 3% Formaldehyde + DSG. Lysates prepared from cells were subsequently hybridized with biotinylated antisense probes to Xist and resulting complexes purified using streptavidin beads. DNA crosslinked to Xist was purified and subjected to next-generation sequencing technologies.


title: Two novel proteins with opposing m6A writing functions interact with HAKAI [RNA-seq]

city: Loughborough

first: Nathan

last: Archer

state: East Midlands

address: Sutton Bonington

department: School of Veterinary Medicine and Sciences

institute: University of Nottingham

summary: Using in vivo interaction proteomics, two HAKAI-interacting zinc finger proteins, HIZ1 and HIZ2, were discovered as novel components of the Arabidopsis m6A writer complex. HAKAI is required for the interaction between HIZ1 and MTA. Whilst HIZ1 knockout plants have normal levels of m6A, plants in which it is overexpressed show reduced methylation. In addition, HIZ1 was found to be involved in root hair development upon auxin transport inhibition in a HAKAI-dependent manner. Mutant plants lacking HIZ2 are viable but have an 85% reduction in m6A abundance and show severe developmental defects. Our findings suggest that HIZ1 appears to be a HAKAI-dependent negative regulator of m6A deposition and HIZ2 is a novel and essential member of the Arabidopsis m6A writer complex.

overall_design: Differential expression analysis of Arabidopsis m6A writer complex member mutants including HAKAI, Virilizer and FIP37. We used 6 replicates for wt, 5 reps were used for fip37, 4 reps for vir and 3 for hakai. These data are related to the input data used for MeRIPSeq, which are available on GEO, accession number GSE174573.

first: Mi

last: Zhang

first: Zsuzsanna

last: Bodi

first: Kasia

last: Rataj

first: Silin

last: Zhong

first: Nigel

middle: P

last: Mongan

first: Gordon

middle: G

last: Simpson

first: Rupert

last: Fray


title: Dual role of Ovol2 on the germ cell lineage segregation during gastrulation in mouse embryogenesis.

city: Fukuoka city

first: Yuki

last: Naitou

state: Japan

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

institute: Kyushu university


title: CECR2 Drives Breast Cancer Metastasis by Suppressing Macrophage Inflammatory Responses

city: New Haven

first: Qin

last: Yan

email: qin.yan@yale.edu, craig.wilen@yale.edu

address: 310 Cedar St.

department: Pathology

institute: Yale University

summary:
Purpose: Metastasis are responsible for the most majority of cancer-related deaths due to the lack of effective targeted therapies. Therefore, specific targets which tackle that complex process are needed to improve the therapeutic outcomes of metastatic breast cancer.
Methods: ATAC-Seq analysis of CECR2 knockout and control LM2 cells.
Results: CECR2 knockout  regulate chromatin accessibility of  NF-kB target genes .
Conclusions: Our work confirmed that CECR2 knockout attenuates chromatin accessibility at promoters or enhancers of the downstream NF-kB target genes.

overall_design: ATAC-seq analysis in LM2 cell lines

first: Meiling

first: Wesley

last: Cai


title: Gene expression in sorted myeloid population from mice

city: Adelaide

first: Andrew

last: Zannettino

state: SA

address: SAHMRI, North Terrace

department: Faculty of Health and Medical Sciences

country: Australia

institute: University of Adelaide

summary: Cells expressing macrophage markers (Cd11b+F4/80+CD169+CX3CR1neg) were sorted from the bone marrow of C57BL/6 mice and their gene expression profile analysed using RNA sequencing. Analysis of the most highly expressed genes revealed a gene expression signature consistent with a granulocyte population (i..e high expression of Ly6g and Cxcr2), rather than macrophages (i.e. low/negligible expression of Adgre1, Cd163 and Mertk). Collectively these data demonstrate that cells which stain positive for conventional macrophage markers exhibit a gene expression signature consistent with cells of the granulocyte lineage.

overall_design: RNAseq analysis of sorted Cd11b+F4/80+CD169+CX3CR1neg "macrophages" from the bone marrow of C57BL/6 mice (n=3)

middle: C

first: Jacqueline

last: Noll

first: Khatora

middle: S

last: Opperman


title: Treatment and Resistance to Paradox-Breaker PLX8394 in cutaneous melanoma

city: Philadelphia

last: Aplin

institute: Thomas Jefferson University

summary: FDA-approved BRAF inhibitors produce high response rates and improve overall survival in patients with BRAF V600E/K mutant melanoma, but are linked to pathologies associated with paradoxical ERK1/2 activation in wild-type BRAF cells. To overcome this limitation, a next-generation paradox breaking RAF inhibitor (PLX8394) has been designed. Here we show that by using a quantitative reporter assay, PLX8394 rapidly suppressed ERK1/2 reporter activity and growth of mutant BRAF melanoma xenografts. Ex vivo treatment of xenografts and use of a patient-derived explant system (PDeX) revealed that PLX8394 suppressed ERK1/2 signaling and elicited apoptosis more effectively than the FDA-approved BRAF inhibitor, vemurafenib. Furthermore, PLX8394 was efficacious against vemurafenib-resistant BRAF splice-variant expressing tumors and reduced splice-variant homodimerization. Importantly, PLX8394 did not induce paradoxical activation of ERK1/2 in wild-type BRAF cell lines or PDeX. Continued in vivo dosing of xenografts with PLX8394 led to the development of acquired resistance via ERK1/2 reactivation through heterogeneous mechanisms; however, resistant cells were found to have differential sensitivity to ERK1/2 inhibitor. These findings highlight the efficacy of a paradox-breaking selective BRAF inhibitor and the use of PDeX system to test efficacy of therapeutic agents.

overall_design: RNAs were obtained from parental and PBRT resistant cell lines established from in vivo tumors PBRT15 and PBRT16 were treated with 500 nM PLX8394

first: Timothy

last: Purwin

first: Edward

last: Hartsough


title: RNA sequencing of control and PTPN2 knocked down transcriptomes in EndoC-𝛽H1 cells with or without the treatment of pro-inflammatory cytokines

city: Anderlecht

first: Valerie

last: Vandenbempt

state: Vlaams-Brabant

address: Lenniksebaan 808

country: Belgium

institute: Université Libre de Bruxelles

summary: Type 1 diabetes (T1D) results from autoimmune destruction of β-cells in the pancreas. Protein tyrosine phosphatases (PTPs) are candidate genes for T1D and play a key role in autoimmune disease development and β-cell function. Here, we assessed the global protein and individual PTP profile in the pancreas from diabetic NOD mice treated with anti-CD3 monoclonal antibody and IL-1 receptor antagonist (IL-1RA). The treatment reversed hyperglycemia compared to the anti-CD3 alone control group. We observed enhanced expression of PTPN2, a T1D candidate gene, and endoplasmic reticulum (ER) chaperones in islets from mice with reversed diabetes. To address the functional role of PTPN2 in β-cells, we generated PTPN2 deficient stem cell-derived β-like and human EndoC-βH1 cells. Mechanistically, we demonstrated that PTPN2 inactivation in β-cells exacerbates the type I and type II IFN signalling networks, and the potential progression towards autoimmunity. Moreover, we established the capacity of PTPN2 to modulate the Ca2+-dependent unfolded protein response in β-cells. Adenovirus-induced overexpression of PTPN2 decreased BiP expression and partially protected from ER-stress induced β-cell death. Our results postulate PTPN2 as a key protective factor in β-cells during inflammation and ER stress in autoimmune diabetes.

overall_design: mRNA profiles of control and PTPN2 knocked down 𝛽-cells with or without treatment of human interferon-𝛾 or interferon-α

first: Bernat

last: Elvira

first: Julia

middle: B

last: Martinez

first: Javier

last: Negueruela

first: Beata

last: Vekeriotaite

first: Singh

last: Pal

first: Fernando

last: Rossello

first: Pascale

last: Lybaert

first: Timo

last: Otonkoski

first: Wei

last: Wu

first: Conny

last: Gysemans

first: Esteban

last: Gurzov


title: Integrated analysis of single-cell and spatial transcriptomics in keloids

city: Seoul

first: Jong Hee

last: Lee

address: 81, Irwon-ro, Gangnam-gu

department: Department of Dermatology

country: South Korea

institute: Samsung Medical Center

summary: To uncover the underlying pathophysiology of keloids, we used two technologies, single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST). we focused on the molecular signature of keloids. In this study, we provide the comprehensive transcriptomic atlas of keloids and its matched spatial information, essential to understanding intercellular crosstalk in the skin microenvironments.

overall_design: We employed scRNA-seq on two keloid samples using the platform of 10X Genomics. To further assess the spatial heterogeneity and organization of keloid FBs, we performed ST analysis on tissue from keloid specimens (2 sections from 2 samples including one scRNA-seq paired sample). To confirm the study results, we further applied ST on two independent normal skin sections . Normal skin samples from skin cancer excision were used for ST analysis.

first: Jong

first: Joonho

last: Shim


title: Licochalcone A activate glycolysis by via PI3K / AKT pathway to play an anti-aging effect on adipose stem cells and aging mice [hADSCs]

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

summary: We implemented transcriptomic analyses of hADSCs treated with Licochalcone A  6 days


title: The Arabidopsis NuA4 histone acetyltransferase complex is required for chlorophyll biosynthesis and photosynthesis. [RNA-Seq]

status: Public on Jan 20 2022

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

summary: Although two Enhancer of Polycomb-like proteins, EPL1A and EPL1B (EPL1A/B), are known to be conserved and characteristic subunits of the NuA4-type histone acetyltransferase complex in Arabidopsis thaliana, the biological function of EPL1A/B and the mechanism by which EPL1A/B function in the complex remain unknown. Here, we report that EPL1A/B are required for the histone acetyltransferase activity of the NuA4 complex on the nucleosomal histone H4 in vitro and for the enrichment of histone H4K5 acetylation at thousands of protein-coding genes in vivo. We demonstrate that EPL1A/B are required for linking the NuA4 catalytic subunit HAM1 with accessory subunits in the NuA4 complex. EPL1A/B function redundantly in regulating plant development especially in chlorophyll biosynthesis and de-etiolation. The EPL1A/B-dependent transcription and H4K5Ac are enriched at genes involved in chlorophyll biosynthesis and photosynthesis. We also find that EAF6, another characteristic subunit of the NuA4 complex, contribute to de-etiolation. These results suggest that the Arabidopsis NuA4 complex components function as a whole to mediate histone acetylation and transcriptional activation specifically at light-responsive genes and are critical for photomorphogenesis.

overall_design: Examination of the mRNA expression of wild type and epl1a/b mutant.


title: The Arabidopsis NuA4 histone acetyltransferase complex is required for chlorophyll biosynthesis and photosynthesis.


title: Post-transcriptional Fibroblast Fate Switching By MBNL1 Regulates Fibrotic and Myocardial Remodeling During Cardiac Wound Healing

city: Seattle

first: Jennifer

last: Davis

state: WA

address: 850 Republican St, Brotman #343

department: Lab Medicine and Pathology

country: USA

institute: University of Washington

summary: Dynamic fibroblast state transitions underlie the heart’s fibrotic response, raising the possibility that tactical control of these transitions could alter maladaptive fibrotic outcomes. Transcriptome maturation by Muscleblind-like 1 (MBNL1) has emerged as a driver of differentiated cell states. Indeed, MBNL1 expression is elevated in conjunction with profibrotic transcripts in lineage traced myofibroblasts and modeling this gain in function by fibroblast-specific overexpression of an MBNL1 transgene induced a myofibroblast transcriptional identity in healthy hearts and promoted maladaptive myocyte remodeling and scar maturation following injury. Both fibroblast-specific and myofibroblast-specific loss of MBNL1 limited scar production and maturation, which was ascribed to negligible myofibroblast activity. MBNL1 deletion drove expansion of all quiescent cardiac fibroblast states and promoted mesenchymal stem cell characteristics while forced MBNL1 expression restricted state diversity by transitioning most fibroblasts to the most mature myofibroblast identity. These data suggest MBNL1 is a post-transcriptional switch controlling quiescent to myofibroblast transitions during cardiac wound healing.

overall_design: Examination of single cell gene expression in isolated cardiac fibroblasts in SHAM and myocardial infarction (MI) conditions in Wild Type/Non-transgenic (NTG), MBNL1 knockout (Fl-Tcf21iCre), and MBNL1 overexpression (Tg-Tcf21iCre) mice.


title: Two subsets of human marginal zone B cells resolved by global analysis of lymphoid tissues and blood

first: Jacqueline

last: Siu


title: The Arabidopsis NuA4 histone acetyltransferase complex is required for chlorophyll biosynthesis and photosynthesis. [ChIP-Seq]

overall_design: Examination of H4K5Ac levels in wild type and epl1a/b mutant.


title: Two novel proteins with opposing m6A writing functions interact with HAKAI [meRIP-seq]

city: Nottingham

first: Nigel

last: Mongan

address: University Park

department: Biodiscovery Institute

overall_design: MeRIPSeq analysis of Arabidopsis m6A writer complex member mutants including HAKAI, Virilizer and FIP37. We used 3 replicates of each mutants and wt. Each experiment had an input and an IP sample

first: Mi

last: Zhang

first: Zsuzsanna

last: Bodi

first: Kasia

last: Rataj

first: Silin

last: Zhong

first: Gordon

last: Simpson

first: Rupert

last: Fray


title: Analysis of gene expression in zebrafish cornea during wound healing

city: Montpellier

first: Frederic

last: Michon

address: 80, rue Augustin Fliche

department: Institute for Neurosciences of Montpellier

institute: Inserm

summary: The cornea, transparent and outermost structure of camera-type eyes, is prone to environmental challenges, but has remarkable wound healing capabilities which enables to preserve vision. The manner in which cell plasticity impacts wound healing remains to be determined. In this study, we report rapid wound closure after zebrafish corneal epithelium abrasion. Furthermore, by investigating the cellular and molecular events taking place during corneal epithelial closure, we show the induction of a bilateral response to a unilateral wound. Our transcriptomic results, together with our TGF-beta receptor inhibition experiments, demonstrate conclusively the crucial role of TGF-beta signaling in corneal wound healing. Finally, our results on Pax6 expression and bilateral wound healing, demonstrate the decisive impact of epithelial cell plasticity on the pace of healing. Altogether, our study describes terminally differentiated cell competencies in the healing of an injured cornea. These findings will enhance the translation of research on cell plasticity to organ regeneration.

overall_design: For RNA-sequencing, same-age fish were grouped one day prior to the experiment into four tanks (14 fish per 3 litres). Aged-matched (145, 148, 180 or 183 day-old) control and wound specimens were collected from the same tank. With respect to wounding, abrasion in both corneas of the animals was performed as described above. Control animals were anesthetized and placed onto a sponge for an equal duration as for the wounded animals. After 1.5hrs’ recovery, the fish were anesthetized again in 0.02% Tricaine and decapitated. Eyes were enucleated and cornea dissected in PBS. For one sample, 6 corneas from 3 individuals were pooled in 100µl of Tri reagent (T9424, Sigma). RNA was isolated from TRI reagent (T9424, Sigma) using Precellys beads and standard protocols (P000912-LYSK0-A.0, Bertin Technologies, Montigny-Le-Bretonneux, France). RNA was further purified using the Qiagen Rneasy MiniElute Cleanup kit (#74204, Qiagen, Hilden, Germany). Polyadenylated mRNA was purified from 50ng of Total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Ipswich, Massachusetts, USA).  The following steps were performed by the Biomedicum Functional Genomics Unit (FuGu) at the Helsinki Institute of Life Science and Biocenter Finland at the University of Helsinki. Library preparation was completed on purified mRNA using the NEBNext Ultra Directional RNA Library prep kit ( #E7420L, New England Biolabs) using 14 cycles of PCR amplification and indexed using single (i7) indexing. Indexed library preps from each sample were then pooled and sequenced at a pool concentration of 1.3pM on the NextSeq 500 using a NextSeq High Output 75 cycle flow cell (Illumina, San Diego, California, USA) with 75SE reads. Basecalling and demultiplexing was performed using Illumina bcl2fastq (v2.20.0.422) software. Reads were mapped to zebrafish GRCz11 genome using STAR aligner (2.6.0c). Gene counts were calculated using the featureCounts tool from the Subread package (v1.22.2) using Ensembl release 97 zebrafish gtf-files. Differential expression analysis was performed using R package DESeq2 (v1.22.2 [63]). One sample was excluded based on visual PCA inspection (Fig S2A). For downstream analyses, only genes with an entrezgene id were consider, therefore excluding predicted genes (Table S1). Gene Ontology (GO) term analysis was performed using g:Profiler (version e98_eg45_p14_ce5b097, [64]) online tool with default parameters. Volcano plots and heatmaps were generated using GraphPad Prism 8 (version 8.3.0, Graphpad Software, San Diego, California, USA).

first: Kaisa

last: Ikkala

first: Vassilis

last: Stratoulias


title: Gene expression profiles of HSCs from P0 livers.

city: New York

first: Yeojin

address: 650 WEST 168TH STREET, BB 1108

institute: Columbia University Medical Center

summary:
Purpose: The study was designed to identify transcriptional differences of P0 liver HSCs with different genotypes or different cell size.
Method: For RNA-seq, libraries were prepared according to the Smart-seq2 protocol from 100-200 sorted HSCs. Samples were sequenced by NextSeq500 (Illumina) with single-end 75-bp read length using the NextSeq 500/550 High Output v2 Kit (75 cycles, Illumina). The RNA-seq pipeline from Basepair (www.basepairtech.com) was used for the analysis. Expression count was analyzed by STAR and differential expression by DESeq2 (P < 0.05 and fold-change > 2).

overall_design: HSC mRNA profiles from P0 livers.

first: Lei

last: Ding


title: Single nucleus RNA-seq of genetically labeled Esr1+ neurons from the bed nucleus of the stria terminalis (BNST), preoptic area (POA), ventromedial hypothalamus (VMH), and medial amygdala (MeA)

city: Palo Alto

first: Joseph

middle: Riley

last: Knoedler

address: 1201 Welch Road

department: Psychiatry and Behavioral Sciences

institute: Stanford Univesity

summary: We used genetic methods to label Esr1+ neurons with nuclear membran GFP to all purificiation of nuclei from these cells followed by single-nucleus sequencing.

overall_design: We generated libraries from male, FR females (ovariectomized, hormonally primed, sexually receptive) and FNR (ovariectomized, not hormonaly primed, sexually unreceptive) mice in order to compare cell type composition and gene expression between these conditions. We generated one library from each condition in each brain region surveyed. Full count matrices for each region and associated metadata represent filtered data reported in paper; the unfiltered count matrices have not undergone QC filtering.

first: Nirao

last: Shah


title: Translating ribosome affinity purification of Esr1+ neuronal populations to identify sex and estrus-stage differentially expressed genes

summary: We used translating ribosome affinity purification (TRAPseq) to profile genetically labeled neurons in the bed nucleus of the stria terminalis (BNST), preoptic area (POA), medial amygdala (MeA) and ventromedial hypothalamus (VMH) from adult male mice, and from adult female mice modeled to be in two distinct stages of the estrus cycle (estrus, sexually receptive, FR; and diestrues, sexually unreceptive, FNR).

overall_design: We analyzed 36 bulk RNA-seq samples (each pooled from 3-5 mice) with three biological replicates per region and condition. Full DESeq2 output is available for each pairwise comparison.

middle: R


title: WGD paralog evolution

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

summary: Studying the evolution of binding preferences for 30 paralog TF pairs in S.cerevisiae

overall_design: Genome-wide binding of wt TFs and orthologs in different backgrounds was profiled using ChEC-seq

first: Tamar

last: Gera

first: Felix

last: Jonas


title: Cannabidiol Inhibits SARS-CoV-2 Replication through Induction of the Host ER Stress and Innate Immune Responses

city: Chicago

first: Dongbo

last: Yang

state: IL

address: 929 E 57th St

institute: University of Chicago

summary: The spread of SARS-CoV-2 and ongoing COVID-19 pandemic underscores the need for new treatments.  Here we report that cannabidiol (CBD) inhibits infection of SARS-CoV-2 in cells and mice. CBD and its metabolite 7-OH-CBD, but not THC or other congeneric cannabinoids tested, potently block SARS-CoV-2 replication in lung epithelial cells. CBD acts after viral entry, inhibiting viral gene expression and reversing many effects of SARS-CoV-2 on host gene transcription. CBD inhibits SARS-CoV-2 replication in part by up-regulating the host IRE1a RNase endoplasmic reticulum (ER) stress response and interferon signaling pathways. In matched groups of human patients from the National COVID Cohort Collaborative, CBD (100 mg/ml oral solution per medical records) had a significant negative association with positive SARS-CoV-2 tests. This study highlights CBD as a potential preventative agent for early-stage SARS-CoV-2 infection and merits future clinical trials.  We caution against use of non-medical formulations including edibles, inhalants or topicals as a preventative or treatment therapy at the present time.

overall_design: Lung aveolar A549 cells were stably overexpressed with human angiotensin converting enzyme 2 (ACE2) protein and seeded at 10,000 cells per well in a 96-well plate. Cannabidiol or vehicle were added together to the cells. Cannabidiol (Cayman Chemical, 90080) was dissolved in a 10mM stock solution with DMSO (Sigma-Aldrich, D2650-100mL). Final concentration of CBD was 10 µM. The virus stock was then removed and replaced with fresh 2% FBS DMEM media with drug. The cells were incubated for another 24 hours before total RNA extraction using the NucleoSpin 96 RNA kit (Takarabio, 740709).  Three independent biological replicates were performed per experimental condition, with 12 total RNA samples. RNA sample quality check, library construction, and sequencing were performed by the University of Chicago Genomics Facility following standard protocols. The average RNA Integrity Score was 8.9. All 12 samples were sequenced in two runs by a NovaSeq 6000 sequencer to generate paired-end 100bp reads. For each sample, the raw FASTQ files from two flow cells were combined before downstream processing.  Cannabidivarin (CBDV) was isolated from the hemp oil using centrifugal partition chromatography (CPC), a countercurrent separation technique, and a biphasic liquid-liquid solvent system. Identical experimentation to the above CBD experiment was then performed. The average RNA Integrity Score was also 8.9. RNA-seq data for both experiments were analyzed separately using a local Galaxy 20.05 instance for the following steps. Quality and adapter trimming were performed on the raw sequencing reads using Trim Galore! 0.6.3. The reads were mapped to both the human genome (UCSC hg19 with GENCODE annotation) and the SARS-COV-2 genome (NCBI Assembly ASM985889v3 with Ensembl annotation) using RNA STAR 2.7.5b. The resulting mapped reads from each sample were counted by featureCounts 1.6.4 for per gene read counts. The raw counts were analyzed for differential expression between experimental conditions using DESeq2 1.22.1.

first: Vlad

last: Nicolaescu

first: Marsha

last: Rosner


title: Transcriptional Inactivation of TP53 and BMP Pathway Components Mediates Therapy-induced Dedifferentiation and Metastasis in Prostate Cancer (ATAC-seq)

city: Houston

first: Filippo

last: Giancotti

state: Texas

address: 1881 East Road

department: Cancer Biology

institute: UT MD Anderson Cancer Center

summary: AR blockade instigates two separate and complementary processes: 1) transcriptional silencing of TP53 and hence acquisition of hybrid E/M and stem-like traits; and 2) inhibition of the BMP signaling, which promotes resistance to the pro-apoptotic and anti-proliferative effects of AR inhibition. The drug tolerant prostate cancer cells generated through reprogramming are rescued by neuregulin and generate metastases in mice.

overall_design: Bulk ATAC sequencing of the samples from various time points over the course of enzalutamide treatment of human prostate adenocarcinoma cells LNCaP.

first: Yan

last: Wang


title: Transcriptional Inactivation of TP53 and BMP Pathway Components Mediates Therapy-induced Dedifferentiation and Metastasis in Prostate Cancer (ChIP-seq)

overall_design: Bulk ChIP sequencing of the samples from various time points over the course of enzalutamide treatment of human prostate adenocarcinoma cells LNCaP.


title: Transcriptional Inactivation of TP53 and BMP Pathway Components Mediates Therapy-induced Dedifferentiation and Metastasis in Prostate Cancer

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

overall_design: Refer to individual Series


title: RNA sequencing of porcine smooth muscle cells, after treatments with platelet derived growth factor and S100A4 protein

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

institute: University of Geneva Medical School

summary: Smooth muscle cells were treated with platelet derived growth factor (PDGF-BB) and S100A4 protein to decipher the mechanisms by which they contribute to smooth muscle cell phenotypic transition. We report that PDGF-BB treatment upregulates genes related to growth response or to extracellular matrix component proteases, while S100A4 upregulates pro-inflammatory genes. When used in combination, PDGF-BB and S100A4 show synergistic action by enhancing the upregulation of genes already affected by S100A4 and by inducing the upregulation of genes exclusive for this condition.

overall_design: Cells were exposed to different treatments (i.e. PDGF-BB, oS100A4 and PDGF-BB+oS100A4) for 4 hours. Experiments were performed with cells isolated from 3 different animals.

last: Lemeille


title: Transcriptional Inactivation of TP53 and BMP Pathway Components Mediates Therapy-induced Dedifferentiation and Metastasis in Prostate Cancer (RNA-seq)

overall_design: Bulk RNA sequencing of the samples from various time points over the course of enzalutamide treatment of human prostate adenocarcinoma cells LNCaP; the samples from neuregulin rescued cells and LDN193189 treated cells, respectively.  Also, we performed RNA-seq in the LNCaP cells with shRNA knock-down of TP53 or BRCA1.

first: Hyunho

last: Han

first: Alekya

last: Rumandla

first: Xiaobo


title: A comprehensive immune cell atlas of cystic kidney disease reveals the involvement of adaptive immune cells in injury mediated cyst progression

status: Public on Jan 19 2022

city: Oklahoma City

first: Kurt

last: Zimmerman

state: Oklahoma

address: 940 Stanton L Young Blvd

department: Internal Medicine

institute: University of Oklahoma Health Sciences Center

summary: It is widely accepted that injuries to cilia mutant mice accelerate the rate of cystic kidney disease; however, cellular factors that drive the accelerated rate of cystic disease are unknown. By performing single cell RNA sequencing of all CD45+ immune cells, we find that the subtype and gene expression of adaptive immune cells is significantly altered between non-injured, aged cystic mice, injury-accelerated cystic mice, and non-cystic controls. Deletion of all adaptive immune cells reduced cystic disease in the injury-accelerated model but had no effect on cystic disease in the non-injured model. This differential rescue may be due to unique adaptive immune cell subtypes and ligands that are only present in the injury accelerated model of cystic disease.

overall_design: To unbiasedly identify modifier cells that may be influencing the differential rate of cyst growth observed in injured versus non-injured cilia mutant kidneys at a time of similar cyst severity, we generated a single cell atlas of cystic kidney disease by sequencing 79,355 cells from control mice and adult induced conditional Ift88 mice (hereafter referred to as cilia mutant mice) that were harvested ~7 months post induction or 8 weeks post 30-minute unilateral ischemia reperfusion injury.

first: Cheng

middle: J

last: Song

first: Zhang

last: Li

first: Ummey

last: Ahmed

first: Sarah

last: Bland

first: Alex

last: Yashchenko

first: Shanrun

last: Liu

first: Ernald

last: Aloria

first: Jeremie

last: Lever

first: Nancy

last: Gonzalez

first: Marissa

middle: A

last: Bickel

first: Cory

last: Giles

first: Constantin

last: Georgescu

first: Jonathan

middle: D

last: Wren

first: Mark

last: Lang

first: Etty

middle: N

last: Benveniste

first: Laruie

last: Harrington

first: Leo

last: Tsiokas

first: James

middle: F

last: George

first: Kenneth

last: Jones

first: David

middle: K

last: Crossman

first: Anupam

last: Agarwal

first: Michal

last: Mrug

first: Bradley

last: Yoder

first: Katharina

last: Hopp


title: Electrical Modulation of Transplanted Stem Cells Improves Functional Stroke Recovery

city: San Francisco

first: Alex

last: Lee

address: 1550 Fourth St.

institute: UCSF

summary: This study evaluated the effect of electrical stimulation on human neural progenitor cells using RNAsequencing

overall_design: Cells were loaded onto conductive polymer scaffolds. One group of cells received electrical stimulation (800mV, 100Hz for 1 hour) from the conductive polymer scaffold and compared to a group of unstimulated cells on the conductive polymer.

first: George

last: Paul

first: Oh

last: Byeongtaek

first: Lee

last: Alex


title: Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Mitochondrial DNA base editing in vivo via viral DdCBE delivery to somatic cells

city: Cambridge

first: Lindsey

last: Van Haute

address: Hills Road

department: MRC Mitochondrial Biology Unit

institute: University of Cambridge

summary: We show that delivering the mitochondrial base editor DdCBEs via AAV transduction of somatic cells efficiently produces precise base editing of the intended region.

overall_design: Base editing of cytosine to thymine of total DNA of mouse heart and cells.

first: Pedro

last: Silva-Pinheiro


title: Yin Yang 1 regulates ITGAV and ITGB1, contributing to better prognosis of colorectal cancer

city: Chiba city

first: Nami

last: Sato

state: Chiba purefecture

address: Chuo-ku, Inohana 1-8-1

department: General Surgery

institute: Chiba university


title: Combined VEGFR and MAPK pathway inhibition in angiosarcoma

first: Michael

last: Wagner

state: Washington

address: 825 Eastlake Ave E

summary: Combined inhibition of the VEGF and MAPK pathways with cediranib and trametinib had an additive effect in in vitro models, and a combinatorial effect in an in vivo model. Combined treatment led to smaller tumors than treatment with either agent alone. RNA-seq demonstrated distinct expression signatures between the trametinib treated tumors and those treated with both trametinib and cediranib.

overall_design: Mice with murine SVR xenografts were treated with vehicle, trametinib, cediranib, or the combination and RNA was isolated from whole tumor lysate


title: CCL22 mutations in chronic lymphoproliferative disorder of NK cells (CLPD-NK)

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Institute

summary: We engrafted empty vector, wild type CCL22, and Pro79Arg-CCL22 mutant-expressing NK-92 cells into NOD.Cg-Prkdcscid Il2rgtm1Wjl Tg(IL15)1Sz/SzJ mice to assess in vivo function of detected CCL22 mutations. Engrafted Pro79Arg NK-92 cells recapitulated the phenotype of CLPD-NK patients with CCL22 mutations.

overall_design: 3 replicates of wild type, empty vector and CCL22-P79R mutant infected NK-92 cell line

first: S

last: Kimura

first: Charles

last: Mullighan


title: Transcriptional profile of B cell susbets

city: Newark

first: Jason

last: Weinstein

state: NJ

address: New Jersey Medical School Cancer Center 205 South Orange Ave

department: Center for Immunity and Inflmmation

institute: Rutgers New Jersey Medical School

summary: Inflammatory (B220+ CD19+ CD44+ CD11c+ Tbet-AmCyanhi), GC (B220+ IgDlo CD95+ GL-7+), and naive follicular B cells (B220+ CD19+ IgDhi CD23+) were sorted from male Tbet-AmCyan reporter mice at day 12 post infection with LCMV-Armstrong. RNA-seq was employed to compare the transcriptomes of these three B cell populations.

overall_design: Mice were infected i.p. with 2 × 10^5 pfu LCMV Armstrong and  B cell subsets were sorted from Tbet-AmCyan reporter mice at 12 days post LCMV infection

last: Lemenze

first: Wenzhi

last: Song


title: single cell analysis of hematopoietic stem/progenitor cells(HSPC) and microenvironmental cells from fetal mouse bone marrow

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

summary: We use scRNA-seq to analyze HSPC and microenvironmental cells in embryonic mouse bone marrow. The embryonic cells are compared with corresponding cells from Bmx-CreER Wls mice. conditional knockout mice, in which artery derived Wnt secretion is blocked.

overall_design: We use single cell RNA-sequencing to analyze the HSPC and microenvironmental cells together in fetal mouse bone marrow.We also analyze Bmx-CreER Wls conditional KO mouse embryos.

first: Ralf

last: Adams

first: Yang

last: Liu

first: Qi

last: Chen


title: Expression of mutated genes in tumor samples in patients with hepatocellular carcinoma

status: Public on Jan 18 2022

city: Pamplona

first: Pablo

last: Sarobe

address: Avda. Pio XII, 55

institute: CIMA

summary: Expression of mutated genes (mRNA) in tumor cells may originate new protein sequences potentially recognized by lymphocytes, denominated neoantigens. The purpose of this study is the chracterization of the expression of mutated genes in tumor samples in patients with hepatocellular carcinoma. Expression of the mutated genes are compared with that of the wild-type (WT) version in the tumor cells, Moreover, expression of these mutated and WT genes is also analyzed in non-tumoral lver tissue. Thse comparative experiments have allowed to demostrated specific expression of mutated genes in tumor cells obtained from patients.

overall_design: RNAseq experiments have been carried out using tumor and non-tumor samples obtained from 10 patients with hepatocellular carcinoma.


title: New insights into the role of lncRNA after spaceflight

city: Yerevan

first: Arsen

last: Arakelyan

state: Yerevan

address: 7 Hasratyan St.

department: Bioinformatics

country: Armenia

institute: Institute of Molecular Biology NAS RA

summary: We analyzed the transcriptional profile by RNA-sequencing of exosomal content isolated from blood plasma of three astronauts who flew on various ISS missions between 1998-2001. Computational analysis of the transcriptome of these exosomes identified 27 differentially expressed lncRNAs with possible functions and clinical implications.

overall_design: Comparison of lncRNA expression from blood sEVs at 2 time points.

first: David

last: Goukassian

first: Sankar

last: Addya

first: Mattew

last: Coleman

first: Venkata

last: Garikipati

first: Paul

last: Mills


title: Activation of innate immune pathways after brain injury promotes scar formation and impairs tissue recovery

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary: Scar formation is a major hindrance to central nervous system regeneration upon traumatic injury. Glial cells are key players during the wound healing process, and their reaction to injury determines the extent of tissue restoration. Here, we used the regenerative potential of the zebrafish telencephalon to identify specific molecular and cellular mechanisms regulating glial scar formation. We demonstrated that contact of the cerebrospinal fluid with the brain parenchyma after injury activates toll-like receptor 2 (Tlr2) and the chemokine receptor 3 (Cxcr3) innate immunity pathways leading to initiation of a glial scar. These pathways were critical for scarring even after ablation of microglia and infiltrating monocytes. Our data support a specific role for the injury-induced Tlr1/2 and Cxcr3 signaling pathways in controlling proliferation of the oligodendrocyte progenitors and therefore exacerbated glial reactivity, contributing to scar formation. Interference with the Tlr1/2 and Cxcr3 pathways after injury alleviated glial scar formation and improved tissue restoration.

overall_design: We performed gene expression microarray analysis in the whole telencephalon at different time points during the course of regeneration after nostril or skull brain injury

first: Rosario

last: Sanchez-Gonzalez

first: Christina

last: Koupourtidou

first: Tjasa

last: Lepko

first: Alessandro

last: Zambusi

first: Klara

middle: T

last: Novoselc

first: Tamara

last: Durovic

first: Sven

last: Aschenbroich

first: Veronika

last: Schwarz

first: Christopher

last: Breunig

first: Hans

last: Straka

first: Hagen

last: Huttner

first: Martin

last: Irmler

first: Wolfgang

last: Wurst

first: Andreas

last: Zwergal

first: Tamas

last: Schauer

first: Tobias

last: Straub

first: Tim

last: Tschopka

first: Dietrich

last: Trumbach

first: Magdalena

last: Götz

first: Stefan

last: Stricker

first: Jovica

last: Ninkovic


title: Pharmacologically enhanced regulatory hematopoietic stem cells (HSC.Regs) reverts experimental autoimmune diabetes

city: San Diego

first: Dave

last: Robbins

state: CA

address: 3535 General Atomics Court Ste. 200

institute: Fate Therapeutics

summary:
Ex-vivo pharmacological modulation enhances the immunoregulatory and trafficking properties of HSCs which mitigated autoimmune diabetes and other autoimmune disorders.
We used GeneChip microarrays to compare the whole transcriptomes of vehicle (DMSO) and dmPGE2 (10uM) + Dexamenthasone (uM) modulated human CD34+ HSPCs.

overall_design: Total RNA was extracted from in vitro modulated (4hr) human mobilized peripheral blood CD34+ (HSPCs). Each sample was processed with triplicate donors (or samples) when possible and gene expression was compared.

first: D

middle: L


title: Hyperaccumulation of gadolinium by Methylorubrum extorquens AM1 reveals impacts of lanthanides on cellular processes beyond methylotrophy

status: Public on Jan 17 2022

city: Berkeley

first: Nathan

last: Good

address: 111 Koshland Hall

department: Plant and Microbial Biology

institute: UC-Berkeley

summary: We report a genetic variant of Methylorubrum extorquens AM1 that hyperaccumulates the heavy lanthanide gadolinium. Using RNA-seq transcriptomics we identified wide-spread metabolic and physiological changes in this strain and experimentally validate several of them, including increased gadolinium transport and storage in an intracellular compartment we name the lanthasome.

overall_design: RNA-seq transcriptomics of evo-HLn variant compared to the ancestral genetic background, in the presence of lanthanum, gadolinium

middle: M

first: Harvey

last: Lee

first: Emily

last: Hawker

first: Morgan

middle: Z

last: Su

first: Assaf

last: Gilad

first: N

last: Martinez-Gomez