title: Microbiota-dependent indole production is required for the development of collagen-induced arthritis

city: Aurora

first: Kristine

last: Kuhn

state: Colorado

address: 1775 Aurora Ct. Mail Stop B115

department: Medicine

institute: University of Colorado School of Medicine

summary: Altered tryptophan catabolism has been identified in inflammatory diseases like rheumatoid arthritis (RA) and spondyloarthritis (SpA), but the causal mechanisms linking tryptophan metabolites to disease are unknown. Using the collagen-induced arthritis (CIA) model we identify alterations in tryptophan metabolism, and specifically indole, that correlate with disease. We demonstrate that both bacteria and dietary tryptophan are required for disease, and indole supplementation is sufficient to induce disease in their absence. When mice with CIA on a low-tryptophan diet were supplemented with indole, we observed significant increases in serum IL-6, TNF, and IL-1β; splenic RORγt+CD4+ T cells and ex vivo collagen-stimulated IL-17 production; and a pattern of anti-collagen antibody isotype switching and glycosylation that corresponded with increased complement fixation. IL-23 neutralization reduced disease severity in indole-induced CIA. Finally, exposure of human colon lymphocytes to indole increased expression of genes involved in IL-17 signaling and plasma cell activation. Altogether, we propose a mechanism by which intestinal dysbiosis during inflammatory arthritis results in altered tryptophan catabolism, leading to indole stimulation of arthritis development. Blockade of indole generation may present a novel therapeutic pathway for RA and SpA.

overall_design:
To investigate the effect of indole on human colon lymphocytes, we stimulated colon lamina propria mononuclear cells with 1mM indole or vehicle control for 4 hours.
Stimulated LPMCs were then flow sorted into CD3+ T cells and CD19+ B cells, and bulk RNAsequencing was performed on the sorted samples.
Differentially expressed genes were analyzed in Ingenuity Pathway Analysis (Qiagen) to identify differentially expressed pathways.

first: Kuhn

last: Kristi

first: Berlinberg

last: Adam

first: Stahly

last: Andrew

first: Seymour

last: Brenda


title: Translation-coupled sensing and degradation of RNA-protein crosslinks

status: Public on Nov 13 2023

city: Baltimore

first: Allen

middle: R

last: Buskirk

state: MD

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

country: USA

institute: Johns Hopkins University School of Medicine

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

overall_design: Refer to individual Series


title: Nt-acetylation independent turnover of SQUALENE EPOXIDASE 1 by Arabidopsis DOA10-like E3 ligases

city: Birmingham

first: Daniel

middle: James

last: Gibbs

state: West Midlands

address: Edgbaston

department: School of Biosicences

country: United Kingdom

institute: The University of Birmingham

type: Expression profiling by high throughput sequencing

summary: The Acetylation-dependent (Ac/) N-degron pathway degrades proteins through recognition of their acetylated N-termini (Nt) by E3-ligases called Ac/N-recognins.  To date, specific Ac/N-recognins have not been defined in plants.  Here we used molecular, genetic, and multi-omics approaches to characterise potential roles for Arabidopsis (Arabidopsis thaliana) DEGRADATION OF ALPHA2 10 (DOA10)-like E3-ligases in the Nt-acetylation-(NTA-) dependent turnover of proteins at global and protein-specific scales. Arabidopsis has two ER-localised DOA10-like proteins. AtDOA10A, but not the Brassicaceae-specific AtDOA10B, can compensate for loss of yeast (Saccharmoyces cerevisiae) ScDOA10 function. Transcriptome and Nt-acetylome profiling of an Atdoa10a/b RNAi mutant revealed no obvious differences in the global NTA profile compared to wildtype, suggesting that AtDOA10s do not regulate the bulk turnover of NTA substrates.  Using protein steady-state and cycloheximide-chase degradation assays in yeast and Arabidopsis, we showed that turnover of ER-localised squalene epoxidase 1 (AtSQE1), a critical sterol biosynthesis enzyme, is mediated by AtDOA10s.  Degradation of AtSQE1 in planta did not depend on NTA, but Nt-acetyltransferases indirectly impacted its turnover in yeast, indicating kingdom-specific differences in NTA and cellular proteostasis. Our work suggests that, in contrast to yeast and mammals, targeting of Nt-acetylated proteins is not a major function of DOA10-like E3 ligases in Arabidopsis and provides further insight into plant ERAD and the conservation of regulatory mechanisms controlling sterol biosynthesis in eukaryotes.

overall_design: RNA was extracted from pooled 10-day old seedlings grown vertically on ½ MS plates. Three biological replicates for each treatment were used for subsequent RNA sequencing.

first: D

middle: J


title: The transcription factor Zfp281 serves redundantly with Zfp148 to support CD4+ T cell development and functions [Th2 ChIP]

city: Bethesda

first: Remy

last: Bosselut

address: 9000 Rockville Pike, Building 37

department: Laboratory of Immune Cell Biology

institute: National Cancer Institute, National Institute of Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The transcription factor Gata3 is essential both for CD4+ T cell development in the thymus and for the differentiation of Th2 cells, which mediate responses against extracellular parasites and contribute to asthma and allergies. Here we report that the transcription factor Zfp281, in part redundantly with its paralog Zfp148, cooperates with Gata3 to promote CD4+ T cell development and Th2 cell differentiation. Disruption of both factors in T cells resulted in reduced numbers of spleen CD4+ T cells. Additionally, we show that Zfp281 interacts with Gata3, and that Zfp281 binds to Th2 cytokine loci in Th2 cells. Finally, we found that Zfp148 and Zfp281 promote Th2 cytokine expression. During airway inflammation, Zfp148/281-deficient CD4+ T cells failed to express Th2 cytokines, despite normal expression of Gata3. Altogether our data identify Zfp148 and Zfp281 as essential for enabling Gata3 functions in both CD4+ T cell development and Th2 function.

overall_design: CD4+ T cells were activated with IL-4, anti-IFNg, and anti-IL12 (Th2 conditions) for 5 days, then processed for ChIP-Seq

first: Laura

middle: B

last: Chopp


title: Multi-omics profiling of PcG proteins and related factors in Drosophila cell lines (ChIP-Seq)

status: Public on Nov 14 2023

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

summary: To understand the combinatorial binding of different PcG proteins and their binding dynamics across cell types, we performed multi-omics profiling in three Drosophila cell lines, including S2, Kc167 and/or D17-c3 cells. The profiled data included: 1) RNA-seq; 2) ATAC-seq; 3) ChIP-seq of multiple PcG proteins and other related proteins, including E(z), GAGA, Pc, Pcl, Ph, Psc, Scm, Sfmbt, Pho, Spps; 4) Multiple active and repressive histone modifications, including H3K27ac, H3K27me3, H3Krme2, H3K4me3, H3K36me2, H3K36me3.

overall_design: We generated RNA-seq, ATAC-seq and ChIP-seq data in S2, K167 and/or D17-c3 cells.

first: Lesley

last: Brown

first: Pedro

last: Rocha

first: Ming-an

first: Judith

last: Kassis


title: An integrative single-cell multiomics profiling of human pancreatic islets identifies T1D associated genes, regulatory regions, and single nucleotide polymorphism [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: To investigate the mechanism of DLK1 and RASGRP1 knockout in inducing beta cell apoptosis, we performed gene expression profiling analysis using data obtained from RNA-seq of DLK1 WT vs DLK1-/- and RASGRP1 WT VS RASGRP1-/- hPSCs differentiated beta cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for DLK1 WT vs DLK1-/- and RASGRP1 WT VS RASGRP1-/- hPSCs differentiated beta cells.

first: Zeping

last: Zhao

first: Tuo

last: Zhang


title: An integrative single-cell multiomics profiling of human pancreatic islets identifies T1D associated genes, regulatory regions, and single nucleotide polymorphism


title: Effect of estrogen and testesterone on muscle primary cultures

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

summary: Male and female muscle primary cultures were obtained from healthy young individuals. Cultures were treated with either estrogen, testesterone or DMSO. Gene expression was measured as response to the treatment

overall_design: Skeletal muscle biopsies were taken from a total of five male and five female subjects and primary cultures were derived. Each subject's cultures were separated into three aliquots and each were treated with either estrogen, testesterone or control media.

first: Mark

last: Pataky

first: Sree

last: Nair


title: Expression analysis suggests that DNMT3L is required for oocyte de novo DNA methylation only in Muridae and Cricetidae rodents

city: Ceske Budejovice

first: Lenka

last: Gahurova

address: Branisovska 1760

department: Department of molecular biology and genetics

country: Czech Republic

institute: University of South Bohemia

summary: During early mammalian development, DNA methylation undergoes two waves of reprogramming, enabling transitions between somatic cells, oocyte and embryo. The first wave of de novo DNA methylation establishment occurs in the oocytes. Its molecular mechanisms has been studied in mouse, a classical mammalian model. Current dogma describes DNA methyltransferase 3A (DNMT3A) and its cofactor DNMT3L as two essential factors for oocyte DNA methylation – the ablation of either leads to nearly complete abrogation of DNA methylation. However, DNMT3L is not expressed in human oocytes, suggesting that the mechanism uncovered in mouse is not universal across mammals. We analyzed available RNA-seq datasets from oocytes of multiple mammals including our novel naked mole-rat oocytes dataset, and revealed that Dnmt3l is expressed only in the oocytes of mouse, rat and golden hamster. We identified a specific promoter sequence recognised by an oocyte transcription factor complex associated with Dnmt3l activity and demonstrated that it emerged in the rodent clade Eumuroida, comprising the families Muridae (mice, rats, gerbils) and Cricetidae (hamsters). Therefore, Dnmt3l is expressed and consequently plays a role in de novo DNA methylation only in the oocytes of these species, instead of being an essential pan-mammalian factor.

sample_organism:
Cavia porcellus
Heterocephalus glaber
Spalacopus cyanus

overall_design: RNA-sequencing of naked mole-rat (5 replicates, natural conditions), guinea pig (1 replicate) and coruro (1 replicate) oocytes


title: Characterization of the zinc finger µ-protein HVO_0758 from Haloferax volcanii: biological roles, zinc binding, and NMR solution structure

city: Freiburg

first: Rick

last: Gelhausen

state: Baden Württemberg

address: Georges-Köhler-Allee 106

department: Department of Computer Science

country: Germany

institute: Albert-Ludwigs-University Freiburg

summary: Transcriptome analysis based on total RNA-seq was performed on different Haloferax volcanii strains including mutants strains iincluding deletion strains for two small proteins. Differential expression analysis showed that a subset of genes were found to be regulated in the absence of the small proteins.

overall_design: 2 replicates of Total RNA-seq from different Haloferax volcanii strains

first: Lydia

last: Hadjeras

first: Jörg

last: Soppa

first: Deniz

last: Üresin

first: Cynthia

middle: M

last: Sharma

first: Rolf

last: Backofen


title: Next generation sequencing of chicken otocyst with genetically induced loss-of-Wnt signalling

city: London

first: Magdalena

last: Zak

address: 332 Grays Inn Road

institute: UCL Ear Institute

summary: Bulk RNA-sequencing of individual E3 chicken otocyst, in which Wnt signaling activity was reduced by genetic manipulation. The E2 otic placodes were in ovo transfected with a construct overexpressing truncated form of B-catenin reducing Wnt activity or a control plasmid expressing mCherry and collected 24h later. Transcripts abundance was mapped to a chicken reference genome using Kallisto package and differentially expressed genes were identify using Sleuth package (genes with p-value < 0.05 were considered as significant).

overall_design: Identification of genes deregulated in E3 otocyst in response to reduction of Wnt signalling activity

last: Żak

first: Nicolas

last: Daudet


title: Effectors enabling adaptation to mitochondrial complex I loss in Hürthle cell carcinoma

city: Boston

first: Russell

last: Jenkins

state: MA

address: 55 Fruit Street

institute: Masschussetts General Hospital

summary: We report the results of bulk RNA-seq from human Hürthle cell carcinoma (HCC) samples and matched normal thyroids. The bulk RNA-seq data reveals the molecular programs that are activated in HCC. These activated programs include mTOR and Myc signaling, the mitochondrial unfolded protein response, lipid peroxide scavenging, and amino acid biosynthesis.

overall_design: Bulk RNA-seq in human Hürthle cell carcinoma (n=24) and matched normal thyroid (n=18) samples.

first: Vamsi

middle: K

last: Mootha

first: Sareh

last: Parangi

first: Raj

last: Gopal


title: The transcription factor Zfp281 serves redundantly with Zfp148 to support CD4+ T cell development and functions [Thymus Visium]

first: Remy

last: Bosselut

overall_design: Tissue sections from FFPE fixed thymi from C5YBL/6 and tdKO mice were first destained and decrosslinked according to the 10X Demonstrated Protocol CG000520.  Probe hybridization and all subsequent steps were performed as per 10X User guide for Visium CytAssist Spatial Gene Expression (CG000495). In brief, probe hybridization was performed overnight on the destained and decrosslinked tissue sections followed by probe ligation, and CytAssist enabled RNA digestion and tissue removal. Subsequently, probe extension was carried out and the ligation product was eluted, and a pre-amplification step performed. A subset of the pre-amplification product was used for library construction. Quality and concentration of the resulting sequencing library was checked using Bioanalyzer instrument (Agilent 2100).

first: Laura

last: Chopp


title: TP53 loss and TET2 deficiency cooperate to drive lineage-plastic leukemogenesis by transforming progenitors and establishing immune suppressive environment

city: Columbus

first: Bradley

middle: Wayne

last: Blaser

state: OH

address: 400 W 12th Ave

department: Comprehensive Cancer Center

institute: Ohio State University

summary: Loss-of-function mutations of TET2 and TP53 genes are frequently co-observed in AML patients receiving intensive chemotherapy and represent independent predictors for inferior survival in patients after stem cell transplantation. Here we show that TET2 biallelic loss or haploinsufficiency is observed in >10% AML patients with TP53 mutations and associated with poor outcome. In mice, double deletions of TET2 and P53 leads to development of T-ALL, B-ALL or AML and stimulation of pre-leukemic mice via TLR2-TRAF6-A20 axis skews leukemia development toward AML. scRNA-seq of murine blasts reveals that B cell leukemia differentiation is accompanied by transcriptional changes of ll7r and Myb while AML commitment is associated with dynamic elevation of Klf4 and Flt3. Notably, mice with AML exhibit T cell exhaustion, NK dysfunction, and MDSC-like properties which are similarly observed in AML patients with TP53/TET2 co-mutations.  Lastly, we demonstrated that silencing of MEK/ERK, JAK/STAT or TLR-A20 signaling pathways, that are overexpressed in TP53/TET2-mutant AML, restores normal differentiation in vitro and in vivo. Collectively, these findings provide evidence that TP53 deficiency and TET2 loss cooperate to transform hematopoietic progenitors and play a role in AML development and identify novel targets to deliver therapy for this high-risk AML group.

overall_design: 16 samples are provided.  Genotypes are WT, TP53-/- and TET2-/-TP53-/-.  Animals with primary disease and recipients of transplanted tissues are included.  Tissues analyzed include spleen and marrow.  All samples were processed using 10X Genomics 3' capture scRNA-seq technology.

first: Pu

last: Zhang

first: Mehdi

last: Gharghabi

first: Moray

last: Campbell

first: Steven

last: Sher

first: Eric

middle: D

last: Eisenmann

first: Lai

last: Tzung-Huei

first: Bonnie

last: Harrington

first: Wing

last: Chan

first: Youssef

last: Youssef

first: Brandi

last: Walker

first: Tierney

last: Kauffman

first: Alice

last: Mims

first: Daniel

last: Canfield

first: Hannah

last: Phillips

first: Katie

last: William

first: Arleta

last: Lozanski

first: Tzyy-Jye

last: Doong

first: Charlene

last: Mao

first: Jessica

last: Kohlschmidt

first: Ann-Kathrin

last: Eisfeld

first: James

middle: S

last: Blachly

first: Lapo

last: Alinari

first: Robert

last: Baiocchi

first: Yiping

last: Yang

first: Nicole

last: Grieselhuber

first: Ross

middle: L

last: Levine

first: Sharyn

last: Baker

first: John

middle: C

last: Byrd

middle: W

first: Rosa

last: Lapalombella


title: An in vitro model of human hematopoiesis identifies a regulatory role for the aryl hydrocarbon receptor

city: East Lansing

first: D M Isha Olive

last: Khan

state: Michigan

address: 1129 Farm Lane

department: Pharmacology and Toxicology

institute: Michigan State University

summary: An in vitro model of human hematopoietic stem cell differentiation is found to allow development of multiple immune lineages through use of single-cell methods. Using this model, we demonstrate that activation of aryl hydrocarbon receptor (AHR) signaling drives human hematopoietic stem and progenitor cells (HSPCs) to differentiate towards myeloid lineages at the expense of lymphoid lineages. Gene perturbations in progenitor cells and lineage-specified immune cells by AHR ligand, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) are identified.

overall_design: Human cord-blood derived CD34+ HSPCs were cultured over a 28-day period in vitro in media enriched with cytokines/growth factors and treated with either the control vehicle (0.02% DMSO) or 1 nM TCDD. Cells were harvested on day 0 and every 7 days from both the vehicle and TCDD-treated experimental groups and sequenced at a single cell level for a total of 5 kinetic endpoints.

first: D

first: Peer

last: Karmaus

first: Norbert

middle: E

last: Kaminski


title: Single-cell transcriptomic analysis of peripheral blood mononuclear cells (PBMCs) from autism patients before and after metabolic stimulation with long-term L-serine treatment

city: Daegu

first: Jong Pil

last: Kim

address: Cheomdan-ro 61

country: South Korea

institute: Korea Brain Research Institute

summary: ASD patients who were assessed using the ADI-R (Autism Diagnostic Interview-Revised) showed improvements in the Clinical Global Impression (CGI) after oral medication of L-serine. We analyzed single-cell transcriptome changes in PBMCs obtained from two ASD patients (both male, 3 and 4 years old) and compared the transcriptomic features with those of the same patients after treatment with L-serine (400 mg) for 12 weeks. The transcriptional profiles of PBMCs from autism patients showed a large portion of immature CD4 T cells were partially caused by an atypical developmental trajectory. Treatment with L-serine for 12 weeks at a 400 mg dose significantly reduced atypical naive CD4 T cells and drastically restored the transcriptome features of biosynthetic processes involved in normal development of CD4 T cells. This study illustrates that the transcriptomic signatures of  CD4 T cells have prognostic values of ASD and metabolic reprogramming of adaptive immune cells may restore immune development and delay ASD progression.

overall_design: Single-cell mRNA sequencing of peripheral blood mononuclear cells (PBMCs) using the inDrop (v2) platform  Supplementary file 1 : single cell mRNA sequencing libraries of PBMCs from 2 donor before oral-medication of L-serine  Supplementary file 2 : single cell mRNA sequencing libraries  of PBMCs from 2 donor after oral-medication of L-serine (400mg/day, 2 weeks)

first: Youngshik

last: Choe

first: Jaemyung

last: Jang

first: Jong

middle: P

first: Soonbong

last: Baek

first: Hyun

last: Jung

first: Seungeun

last: Yeo

first: Su-Kyeong

last: Hwang


title: The transcription factor Zfp281 serves redundantly with Zfp148 to support CD4+ T cell development and functions [Papain multiome]

first: Remy

last: Bosselut

overall_design: Anesthetized mice were injected intranasally with 40 ug of papain suspended in 20 l of PBS once per day over two 3-day periods separated by a 10-day rest, and analyzed on day 16 after the initial injection. CD44hiCD4+ cells were sorted from dLN of papain treated mice and prepared for Chromium NextGem Multiome ATAC + Gene Expression by following the 10X protocol for nuclei isolation with a lysis time of 3 minutes.

first: Laura

last: Chopp


title: Short-term transcriptomic points-of-departure are consistent with chronic points-of departure for three organophosphate pesticides across mouse and fathead minnow.

city: Durham

first: Leah

last: Wehmas

state: NC

address: 109 T.W. Alexander Drive

institute: US EPA

summary: New approach methods (NAMs) can reduce the need for chronic, animal-based toxicity and carcinogenicity bioassays. Here, we apply benchmark dose (BMD) response modeling (BMDExpress 2.3) to transcriptomic data after short-term exposures to three organophosphate pesticides (OPPs) to estimate chronic adverse effect levels in mouse. Specifically, mouse-liver were collected for RNA sequencing after 7-days of exposure, respectively, to several dose-levels of well-known OPPs: fenthion, methidathion and parathion. Transcriptional points-of-departure (TPODs) were compared to chronic, apical points-of-departures (APOD) for each OPP to inform more efficient means of estimating chemical potency and risk. The mouse-liver TPODs for fenthion, methidathion, and parathion were 0.009, 0.093, and 0.046 mg/Kg-day, respectively. These short-term TPODs reflected the relative potencies of the most sensitive, apical effects from the chronic studies with fenthion identified as the most potent OPP. Moreover, the TPODs were 2.3 to 17-fold more sensitive than the chronic APODs for mouse, suggesting utility in using short-term gene response for estimating long-term chemical risk. Further investigation into OPPs’ modes of action identified significant impacts on acetylcholinesterase mRNA abundance (FDR p-value <0.05, |FC|>2) as well as enrichment of canonical pathways (IPA, z-score>|2|) associated with organism death and neurological and immune dysfunctions, which have been known to be affected by OPPs. Despite bioassay-related differences, our results indicate the conservation of key events potentially important to OPPs biological activity and potency across species. While additional research is needed, these results build confidence in using short-term, molecular-based assays for the characterization of toxicity and risk, thereby reducing reliance on chronic, rodent-based studies.

overall_design: B6C3F1 male mouse livers (mix of left lateral, caudate, and right medial lobes) were collected for RNA sequencing after 7-days of exposure to several dose-levels of well-known organophosphate pesticides: fenthion at 2.5, 5, 10, 20 ppm; methidathion at 10, 25, 50, 100 ppm; and parathion at at 20, 40, 80 ppm (n=7/dose/OPP). OPPs were incorporated into AIN-93G rodent diet (or not for controls) and provided ad libitum with consumption monitored.

first: Rubia

last: Martin


title: An integrative single-cell multiomics profiling of human pancreatic islets identifies T1D associated genes, regulatory regions, and single nucleotide polymorphism [ATAC-seq]

first: Shuibing

last: Chen

summary: To investigate the mechanism of DLK1 and RASGRP1 knockout in inducing beta cell apoptosis, we performed chromatin access profiling analysis using data obtained from ATAC-seq of DLK1 WT vs DLK1-/- and RASGRP1 WT VS RASGRP1-/- hPSCs differentiated beta cells.

overall_design: Comparative chromatin accessibility profiling analysis of ATAC-seq data for DLK1 WT vs DLK1-/- and RASGRP1 WT VS RASGRP1-/- hPSCs differentiated beta cells.

first: Zeping

last: Zhao

first: Tuo

last: Zhang


title: Zfp281 and Zfp148 control CD4+ T cell thymic development and Th2 functions. (ChIP-seq)

summary: How CD4+-lineage gene expression is initiated in differentiating thymocytes remains poorly understood. Here, we show that the paralog transcription factors Zfp281 and Zfp148 control both this process and cytokine expression by Th2 effector cells. Genetic, single-cell, and spatial transcriptomic analyses show that these factors promote the intrathymic CD4+ T cell differentiation of MHC II-restricted thymocytes, including expression of the CD4+ lineage-committing factor Thpok. In peripheral T cells, Zfp281 and Zfp148 promote chromatin opening at and expression of Th2 cytokine genes, but not of the Th2 lineage determining transcription factor Gata3. Zfp281 interacts with Gata3, and binds Gata3 genomic binding sites at loci encoding Thpok and Th2 cytokines. Thus, Zfp148 and Zfp281 collaborate with Gata3 to promote CD4+ T cell development and Th2 cell responses.

overall_design: CD4+ T cells were activated with IL-4, anti-IFNg, and anti-IL12 (Th2 conditions) for 5 days, then processed for ChIP-Seq.


title: Antibody Dependent Cell-Mediated Cytotoxicity Selection Pressure Induces Diverse Mechanisms of Resistance

first: Rossin

last: Erbe

address: 401 N Broadway

institute: Johns Hopkins School of Medicine

overall_design: Refer to individual Series


title: Antibody Dependent Cell-Mediated Cytotoxicity Selection Pressure Induces Diverse Mechanisms of Resistance (scATAC-Seq)

summary:
Targeted monoclonal antibody therapy has emerged as a powerful therapeutic strategy for cancer. Unfortunately, only a minority of patients haves durable responses and the development of resistance remains a major clinical obstacle. Antibody-dependent cell-mediated cytotoxicity (ADCC) represents a crucial therapeutic mechanism of action; however few studies have explored ADCC resistance. Using multiple in vitro models of ADCC selection pressure, we have uncovered both shared and distinct resistance mechanisms.
We employed CITE sequencing and single-cell ATAC-seqeuncing to interrogate molecular mechanisms of resistance.

overall_design: Comparative DNA accessibility analysis of scATACseq data for A431, FaDu, and SKOV3 cell lines, both sensitive to and with acquired resistance to ADCC

first: David

last: Zahavi

first: Elana

last: Fertig

first: Louis

last: Weiner


title: Antibody Dependent Cell-Mediated Cytotoxicity Selection Pressure Induces Diverse Mechanisms of Resistance (CITE-Seq)

overall_design: Comparative gene and protein expression profiling analysis of CITE-seq data for A431, FaDu, and SKOV3 cell lines, both sensitive to and with acquired resistance to ADCC


title: Genome-wide analysis of long noncoding RNA expression profile in gastric cancer

city: Wuhan

first: Rongzhang

last: Dou

state: Hubei

address: No.169 Donghu Road

department: Department of Gastrointestinal Surgery

country: China

institute: Zhongnan Hospital, Wuhan University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Gastric cancer (GC) remains one of the most prevalent tumor worldwide, and ranks third in cancer-related deaths globally. Long non-coding RNAs (lncRNAs) have been reported to play significant role in the progression and metastasis in gastric cancer (GC), however, the molecular mechanism are largely elusive. We aim to identify up-regulated lncRNA in GC and study their function in promoting tumor progression and metastasis.

overall_design: Microarray expression profiling of mRNAs and lncRNAs were conducted using RNA extracted from six gastric cancer samples and matched adjacent normal tissues.

first: Chaogang

last: Yang

first: Yan

last: Fang

first: Jinseng

last: Zhen

first: Chenxi

last: Liang

first: Jialin

last: Song

first: Lei

last: Han

first: Sihao

last: Huang

first: Panyi

last: Zhong

first: Keshu

last: Liu

first: Zaihuan

last: Lin

first: Guoquan

first: Qian

last: Peng

first: Chunwei

first: Bin

last: Xiong

first: Shuyi

last: Wang


title: The transcription factor Zfp281 serves redundantly with Zfp148 to support CD4+ T cell development and functions [Population RNA-seq]

first: Remy

last: Bosselut

overall_design: Thymocytes were sorted for population RNAseq.

first: Laura

last: Chopp


title: Transcriptomes and metabolism define heterogeneous mouse and human MAIT cells [mouse]

city: San Diego

first: Viankail

middle: Osiris

last: Cedillo-Castelan

email: vcastelan@lji.org, viancastelan@gmail.com, gascui@lji.org, gabrielascuigac@gmail.com

state: CA

address: 4334 Rous st

department: Bioinformatics

institute: La jolla institute for immunology

summary: Mucosal-associated invariant T (MAIT) cells are a subpopulation of T lymphocytes that respond to microbial metabolites.  We performed single-cell RNA sequencing and metabolic analyses in MAIT cell subsets in thymus and peripheral tissues from mice and humans to define the heterogeneity and developmental path of these innate-like lymphocytes.  We show that the predominant mouse subset, which produces IL-17 (MAIT17), and the subset that produces IFN (MAIT1), have greatly different transcriptomes and metabolic states in the thymus and periphery.  A subset has a transcriptome similar to circulating lymphocytes, and in mice these are found in recent thymic emigrants, suggesting partially mature cells emigrate from the thymus.  Human MAIT cells are predominantly MAIT1 cells, but have a different metabolism from naïve CD8 T cells with increased fatty acid uptake and storage.  Although mouse and human subsets are similar in thymus, in the periphery they are divergent, likely reflecting environmental and genetic differences.

overall_design: Single cell RNA sequencing of mouse MAIT cells from thymus, liver, lung and spleen.

first: Shilpi

last: Chandra

first: Gabriel

last: Ascui

first: Thomas

last: Riffelmacher

first: Ashu

last: Sethi

first: Ciro

last: Ramirez

last: Castelan

first: Gregory

last: Seumois

first: Hayley

last: Simon

first: Mallory

last: Murray

first: Goo-Young

last: Seo

first: Ashmitaa

last: Premlal

first: Greet

last: Verstichel

first: Yingcong

last: Li

first: Chia-Hao

first: Jason

last: Greenbaum

first: John

last: Lamberti

first: Raghav

last: Murthy

last: Nigro

first: Hilde

last: Cheroutre

first: Christian

last: Ottensmeier

first: Li-Fan

last: Lu

first: Pandurangan

last: Vijayanand

first: Mitchell

last: Kronenberg


title: The transcription factor Zfp281 serves redundantly with Zfp148 to support CD4+ T cell development and functions [scRNA-seq]

first: Remy

last: Bosselut

summary: The transcription factor Gata3 is essential both for CD4+ T cell development in the thymus and for the differentiation of Th2 cells, which mediate responses against extracellular parasites and contribute to asthma and allergies. Here we report that the transcription factor Zfp281, in part redundantly with its paralog Zfp148, cooperates with Gata3 to promote CD4+ T cell development and Th2 cell differentiation. Disruption of both factors in T cells resulted in reduced numbers of spleen CD4+ T cells. Additionally, we show that Zfp281 interacts with Gata3, and that Zfp281 binds to Th2 cytokine loci in Th2 cells. Finally, we found that Zfp148 and Zfp281 promote Th2 cytokine expression. During airway inflammation, Zfp148/281-deficient CD4+ T cells failed to express Th2 cytokines, despite normal expression of Gata3. Altogether our data identify Zfp148 and Zfp281 as essential for enabling Gata3 functions in both CD4+ T cell development and Th2 function.

overall_design: Thymocytes were sorted as CD69+, CD69- DP, and CD69- DN, mixed in an 8:1:1 ratio, then processed for 10X Genomics 5' V1.1 scRNAseq

first: Laura

last: Chopp


title: USF1 transcriptionally regulated UGT1A3 and promoted lung adenocarcinoma progression by regulating neurotrophin signaling pathway

city: Jinan

first: Wei

last: Dong

state: Shandong

address: Jing Wu Road 324#

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

summary: Lung cancer remains the leading cause of oncological death. There is an urgent need to discover new molecular targets and to develop new treatments. Our previous study showed that one of the UDP-glucuronosyltransferases (UGTs) family, UGT1A3, is an important prognostic factor for lung adenocarcinoma (LUAD), inhibiting UGT1A3 could significantly improve the efficacy of anti-tumor drugs. In this study, we aimed to explore the upstream transcriptional factor (USF1) of UGT1A3 and its way of playing a role in LUAD.

overall_design: H1299 cells were transfected with shRNAs specific against UGT1A3 or USF1, and DEGs in cell was analyzed by DNA micro-assay.


title: CLIP-Seq Analysis Enables the Design of Ribosomal RNA Bait Oligonucleotides That Protect Against C9ORF72 ALS/FTD-Associated Poly-GR Pathophysiology

city: Chicago

first: Evangelos

last: Kiskinis

state: IL

address: 233 E Erie St #500

department: Neurology

institute: Northwestern University

summary: We report CLIP-Seq results for GFP tagged poly-GR in order to define poly-GR interacting RNAs in vivo.

overall_design: Two independent CLIP-Seq experiments were performed for GFP-(GR)50 in HEK-293 cells using GFP, GFP-(GP)10 and untransfected cells as controls.

first: Marco

last: Boccitto

first: Juan

middle: A

last: Ortega

first: Sandra

last: Wolin


title: RNASeq VDR knockout TAMOX or control vehicle treated VDRActinCre+ mice gastrocnemius

first: Raji

last: Kumar

state: MINNESOTA

address: 200 1st street SW

department: Nephrology and Hypertension

summary: Deletion of the Vitamin D Receptor in Skeletal Muscle is Associated with Improved Glucose Tolerance and Reduced Muscle Function

overall_design: We deleted the skeletal muscle Vdr in adult mice, and assessed glucose disposal, insulin sensitivity and concentrations, skeletal muscle gene expression and muscle strength.

first: Louis

last: Losbanos

first: Theodore

last: Craig

first: Numrah

last: Fadra

first: Asha

last: Nair

first: Aleksey

last: Matveyenko

first: Rajiv


title: The effects of the prolonged Cd exposure on gene expression changes in in Uterine Leiomyoma Cells [cancer pathways]

city: RTP

first: Rick

middle: David

last: Fannin

address: 111 Tw Alexander Dr, MD D204

department: NIEHS/NIH

institute: Mr.

summary: The heavy metal Cadmium (Cd), a widespread environmental contaminant, poses serious hazards to human health, and is considered a metallohormone and carcinogen. In women with uterine fibroids, there is a significant association between blood Cd levels and fibroid tumor size. The aim of this study was to determine if benign uterine fibroid cells could be malignantly transformed in vitro by continuous Cd exposure, and if so, explore a molecular mechanism by which this could occur. We found when fibroid cells were exposed to 10 µM CdCl2 for 8 weeks, a robust and fast-growing Cd- Resistant Leiomyoma (CR-LM) culture was established. The CR-LM cells showed the ability to form viable colonies in soft agar, increased glycogen aggregates, enhanced cell motility, a higher percentage of cells in G2/M phase, and increased expression of the proliferation marker Ki-67. NanoString analysis showed downregulation of genes encoding for ECM components, such as collagens, fibronectins, laminins, and SLRP family proteins; whereas, genes involved in ECM degradation (MMP1, MMP3 and MMP10) were significantly upregulated. A volcano plot  showed that the direction of expression changes of the top differentially genes favored cancer progression. Functional analysis by IPA predicted a significant inhibition of TGFβ signaling, leading to enhanced  proliferation and attenuated fibrosis. Prolonged Cd exposure altered phenotypic characteristics and dysregulated genes in fibroid cells predicative of progression towards a cancer phenotype. Therefore, continuous  Cd exposures changes the phenotype of benign fibroid cells in vitro and could possibly pose a health risk for women with uterine fibroids.

overall_design: A human uterine leiomyoma cell line immortalized via retroviral transfection of telomerase (ht-UtLM) was generated by our laboratory. For 8-week Cd-exposure experiment, the ht-UtLM cultures were maintained continuously in ht-UtLM culture medium supplemented with 10 μM CdCl2 for 8 weeks. The culture medium was replaced with fresh medium with 10 μM CdCl2 every 3 days. Passage-matched control ht-UtLM cultures were run concurrently with Cd exposed cells. All cultures were kept in a standard tissue culture incubator at 37°C with 5% CO2.

first: Yitang

last: Yan

first: Jingli

last: Liu

first: Michael

last: Dykstra

first: Arianna

last: Lawrence

first: Kevin

last: Gerrish

first: Charles

last: Tucker

first: Erica

last: Scappini

first: Darlene

last: Dixon


title: The effects of the prolonged Cd exposure on gene expression changes in in Uterine Leiomyoma Cells [cancer progression]


title: Transcriptomes and metabolism define heterogeneous mouse and human MAIT cells [human]

first: Viankail

last: Cedillo-Castelan

overall_design: Single cell RNA sequencing of human MAIT cells from thymus,lung and PBMCs.

first: Shilpi

last: Chandra

first: Gabriel

last: Ascui

first: Thomas

last: Riffelmacher

first: Ashu

last: Sethi

first: Ciro

last: Ramirez

last: Castelan

first: Gregory

last: Seumois

first: Hayley

last: Simon

first: Mallory

last: Murray

first: Goo-Young

last: Seo

first: Ashmitaa

last: Premlal

first: Greet

last: Verstichel

first: Yingcong

last: Li

first: Chia-Hao

last: Lin

first: Jason

last: Greenbaum

first: John

last: Lamberti

first: Raghav

last: Murthy

last: Nigro

first: Hilde

last: Cheroutre

first: Christian

last: Ottensmeier

first: Li-Fan

last: Lu

first: Pandurangan

last: Vijayanand

first: Mitchell

last: Kronenberg


title: From computer simulation to therapeutic potential: ETA53 for myocardial infarction

status: Public on Nov 12 2023

city: Suwon-si

first: Uisuk

last: Jeong

state: Gyeonggi-do

address: 206, World cup-ro

department: Molecular Science and Engineering

institute: Ajou university

summary: In the severity of myocardial infarction, Toll-like receptor (TLR) 9 plays a pivotal role in the inflammatory responses induced through damage-associated molecular patterns involving mitochondrial DNA and HMGB1. However, the therapeutic agents currently available for myocardial infarction substantially lack any association with the effects on immune responses. In this study, we applied a comprehensive drug discovery approach, which integrates in silico, in vitro, and in vivo processes, as well as determined therapeutic effects and mechanisms free from side effects. In an animal model of myocardial infarction, conditioned based on pharmacological properties, improved effects compared to the FDA-approved Rosuvastatin were detected. In summary, a small molecular inhibitor, ETA53 (endosomal Toll-like receptor antagonist 53), which selectively acts on TLR9 in nano-molar units, was developed. ETA53 was found to be effective for treating myocardial infarction caused by permanent ligation of the left anterior descending coronary artery, based on indicators such as cardiac function, inflammation, infarct size, and fibrosis. The results offered insights that varied from those of conventional drug development perspectives; consequently, the novel inhibitor may provide an alternative treatment with a mechanism different from that of the commercially available drugs for myocardial infarction.

overall_design: Gene expression profiling analysis of RNA-seq data to verify the effect of ETA53 in a myocardial infarction model.

first: Muhammad

last: Haseeb

first: Kang-Gon

last: Lee

first: Yongdoo

last: Park

first: Sangdun

last: Cho


title: SERPINA11 related novel Serpinopathy- a perinatal lethal disorder

city: Hyderabad

first: Rashna

last: Bhandari

state: Telangana

address: Bldg 7, Gruhakalpa, 5-4-399/B Nampally

country: India

institute: Centre for DNA Fingerprinting and Diagnostics

summary: SERPINA11 is a hitherto poorly characterised gene belonging to Clade A of the SERPIN superfamily. The exact functional significance and expression pattern of this gene remains unknown. Here we report a perinatal lethal phenotype associated with biallelic loss of function variants in SERPINA11, and characterised by gross and histopathological features of extracellular matrix disruption. We found SERPINA11 protein expression in multiple mouse tissues and human fetal lungs. Immunofluorescence of the affected fetal lung revealed markedly reduced expression of SERPINA11 protein compared with healthy, gestation matched human fetal lung. Protein expression data from HEK293T cell lines following site directed mutagenesis is also presented to support the loss of function nature of the variant. This novel serpinopathy appears to be a consequence of loss of inhibition of serine proteases involved in extracellular matrix remodelling, revealing SERPINA11 as a protease inhibitor critical for embryonic development.

overall_design: We conducted RNA-seq from liver tissue of a 19 week old human fetus carrying a homozygous nonsense variant in SERPINA11 gene, to study any alterations in the SERPINA11 transcript levels.

first: Shagun

last: Aggarwal

first: Shrutika

last: Padwal

first: Pragna

last: Thotakura

first: Karthik

last: Tallapaka

first: Ashwin

last: Dalal


title: Hepatic tissue expression profiles of Acsm3 konckout and control mice.

city: Beijing

first: Yibo

last: Wang

state: Beijin

address: 167 Beilishi Road, Xicheng District, Beijing

institute: Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Acyl-CoA synthetase medium-chain family member 3 (ACSM3) is one member of ACSM family and localized on the outer membrane of mitochondria, which catalyzes the activation of medium-chain (C4-C14) length FAs and xenobiotic carboxylic acids. We found that ACSM3 was lower expressed in the metabolic syndrome (MetS) patients and mice. ACSM3 mainly expressed in the liver. We speculated that ACSM3 deficiency may participated in the MetS progression and then constructed Acsm3 global knockout mice (C57BL/6J background) by CRISPR/Cas9 system. The knockout mice exhibited profound depletion of Acsm3 expression in liver extracts. Male mice are more sensitive to diet-induced MetS than female mice, and thus male mice were used in this study. The phenotype of Acsm3 knockout mice was analyzed with wild type littermates as controls. 12 weeks, livers from three male Acsm3 knockout mice and three male control mice were removed for RNA sequencing.

overall_design: To elucidate the molecular differences in hepatic expression profiles between Acsm3 knockout mice and control mice, at 12 weeks of age, we performed RNA sequencing analysis with three male Acsm3 knockout mice and three male control mice. Before that, all mice were housed under a 12 h light/dark cycle at a temperature of 24 °C and relative humidity of (56 ± 10) %, with free access to water and normal diet.

first: Xiao

last: Xiao

first: Ruofei

last: Li

first: Bing

last: Cui


title: Microglia sense astrocyte dysfunction and prevent disease progression in an Alexander disease model

city: Chuo

first: Kozo

last: Saito

address: 1110 Shimokato

department: Department of Neuropharmacology

country: Japan

institute: University of Yamanashi

summary: Alexander disease is a neurodegenerative diseases caused by mutations of GFAP, an astrocyte-specific gene. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of astrocytes.

overall_design: Cells of hippocampi of GFAP-hGFAP mice (60TM line, n = 3 mice) or WT mice (C57BL6/J, n = 3 mice) were isolated by a papain-based protocol, and analyzed using scRNA-seq.

first: Eiji

last: Shigetomi

first: Youichi

last: Shinozaki

first: Kenji

last: Kobayashi

first: Bijay

last: Parajuli

first: Yuto

last: Kubota

first: Kent

last: Sakai

first: Hiroshi

last: Horiuchi

first: Junichi

last: Nabekura

first: Schuichi

last: Koizumi


title: Effects of O2 concentration on endeometrial organoids within collagen-based gel (70% type I collagen and 30% matrigel)

city: Sendai

first: Shun

last: Shibata

address: 2-1 Seiryo-chou

department: Graduate School of Medicine

institute: Tohoku University

summary: We investgated effect of O2 concentration on gene expression of EMO within collagen-based gel (70% type I collagen and 30% matrigel).

overall_design: We cultured human endometrial organoids in collagen-based gels (70% type-I collagen and 30% matrigel) for 7 days with ECSY medium under normoxic (20% O2) and hypoxic (5% O2) conditions. The composition of the ECSY medium was as follows: DMEM/F-12  supplemented with 1% ITS-X supplement, 0.15% BSA, 1% Knockout Serum Replacement, 200 mM L-ascorbic acid, 50 ng/ml EGF, 2 μM CHIR99021, 2 μM SB202190, and 10 μM Y27632.

first: Takahiro

last: Arima


title: Peripheral RNA biomarkers for neurocognitive impairment shared by prenatal alcohol exposure (PAE) and offspring from mother with diabetes (OMD) in mice.

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

summary: Our study reports peripheral RNA biomarkers for neurocognitive impairment shared by PAE and OMD in mice. We extracted RNA from three subtypes (T cell, B cell and monocytes) of white blood cells sorted by flow cytometer. We performed both differential expression and splicing analyses. Common differential alternative splicing (AS) events between OMD and FASD were found. This study posits that AS of lymphocyte RNA is a rich resource, and deep-learning is an effective tool, for discovery of peripheral biomarkers of neurobehavioral deficits in children of diverse adverse pregnancies.

overall_design: RNA profiling extracted from peripheral blood mononuclear cells (PBMCs) of offspring from PAE, OMD and controls

first: Junko

last: Sasaki

first: Dipankar

last: Dutta

first: Banerjee

last: Payal

first: Ankush

last: Bansal

first: Toru

first: Satoshi

last: Yamashita

first: Kazue

last: Hashimoto-Torii


title: snRNA-seq analysis of apical-out endometrial organoids including endometrial stromal cells and human umbilical vein endothelial cells

status: Public on Nov 11 2023

summary: In this study, we developed an apical-out-endometrial organoids (AO-EMO + eSC/HUVEC), which exposes the apical surface of the epithelium and contains eSC and an endothelial network. To evaluate this model, we conducted a single-nucleus RNA-sequencing (snRNA-seq).

overall_design: The endometrial organoids (EMO) fragments were centrifuged at 500 × g for 3 min, after which the supernatant was meticulously aspirated. Subsequently, a blend of 70% type I collagen and 30% Matrigel was incorporated into a pellet of EMO fragments, and 20 µl of the resulting mixture was dispensed into a non-treated 48-well plate. The plates were then incubated at 37°C for 30 min. ECSY medium supplemented with 50 ng/ml FGF2 and 20 ng/ml VEGF were added and replaced every two or three days. The composition of the ECSY medium was as follows: DMEM/F-12 supplemented with 1% ITS-X supplement, 0.15% BSA, 1% Knockout Serum Replacement, 200 mM L-ascorbic acid, 50 ng/ml EGF, 2 μM CHIR99021, 2 μM SB202190, and 10 μM Y27632. We conducted snRNA-seq following nuclear extraction and DAPI+ sorting.

first: Luis

last: Nagai

first: Ryuichiro

last: Nakato


title: Cellular quiescence is dependent upon the HIRA histone chaperone

city: Newcastle upon Tyne

first: Simon

last: Whitehall

address: Framlington Place

department: Biosciences Institute

institute: Newcastle University

summary: Quiescence (G0) is a reversible non-dividing state that facilitates cellular survival in adverse conditions. Here we demonstrate that the function of the HIRA histone chaperone complex is required for viability during nitrogen-starvation induced quiescence in Schizosaccharomyces pombe. G0 cells lacking the HIRA protein, Hip1 exhibit elevated levels of antisense ncRNAs and an increase in unrepaired DNA double strand breaks. Nitrogen-starved hip1∆ cells retain metabolic activity but, in contrast to wild type, rapidly lose the ability to resume proliferation. After a short period in G0 (1 day), hip1∆ mutants are able to resume cell growth in response to the restoration of a nitrogen source, but do not efficiently induce Start-specific gene expression and re-enter the cell cycle. However, hip1∆ cells rapidly progress to an unresponsive state and by 4 days in G0, the majority no longer initiate growth following nitrogen source restoration. Analysis using a conditional hip1 allele is consistent with these findings and indicates that HIRA is required for efficient exit from quiescence and prevents a permanent cell cycle arrest.

overall_design: Examination of nitrogen starved (quiescent) and re-fed fission yeast cells (wildtype and hip1 mutant)

first: S

first: C

last: Gal


title: The effects of the prolonged Cd exposure on gene expression changes in in Uterine Leiomyoma Cells

first: Rick

last: Fannin

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

overall_design: Refer to individual Series


title: RNA-seq of dorsal root ganglia (DRG) neurons of dry skin (AEW) mice

city: Incheon

first: WOOK-JOO

last: LEE

address: 191, Hambangmoe-ro, Yeonsu-gu

department: College of Pharmacy

institute: Gachon University

summary: Dry skin evokes itch (pruritus), but underlying mechanisms are still elusive. To examine alterations of itch-related genes, dry skin condition was induced by AEW (Acetone/Ether/Water) treatment. In this study, RNA-seq was performed with dorsal root ganglia neurons obtained from AEW-treated ICR male mice (12-week-old) or control mice.

overall_design: AEW treatment was applied for 5 consecutive days, and DRG neurons were obtained in day 6. Total RNAs were from both AEW-treated (n = 6) and control (n = 6) mice were pooled

first: Wook-Joo

last: Lee

first: Won-Sik

last: Shim


title: Aberrant Expression Profile of Circular RNAs in Human Lung Adenocarcinoma   by Microarray Analysis

city: Xi'an

first: shi

last: hongyang

address: 157 Xiwu Road, Xi'an City

department: Department of respiratory and critical care medicine

institute: The Second Affiliated Hospital of Xi'an Jiaotong University

summary: To determine the circRNA expression profile in  lung adenocarcinoma compared with adjacent normal tissues, we used circRNA microArray analysis form Arraystar to examine the expression of circRNAs in  lung adenocarcinoma compared with adjacent normal tissues

overall_design: Tissue specimens from lung adenocarcinomas and paired adjacent normal tissues were collected, then perform circRNAs chips by Arraystar Human circRNAs chip (Arraystar)

first: Hongyang

last: Shi

first: Yuqiang

last: Ji


title: Transcriptomes and metabolism define heterogeneous mouse and human MAIT cells

first: Viankail

last: Cedillo-Castelan

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Effects of substrates on gene expression of human endometrial organoids

first: Shun

last: Shibata

summary: To investigate the effects of different substrates on  human endometrial organoids , we compared the transcriptomes of EMO cultured within Matrigel and collagen-based gels.

overall_design: We cultured human endometrial organoids in Matrigel or collagen-based gels (70% type-I collagen and 30% matrigel) for 7 days. Human endometrial organoids were established and maintained in the ECSY medium. The composition of the ECSY medium was as follows: DMEM/F-12 (Life Technologies) supplemented with 1% ITS-X supplement, 0.15% BSA (FUJIFILM Wako), 1% Knockout Serum Replacement (KSR, Thermo Fisher Scientific), 200 mM L-ascorbic acid (FUJIFILM Wako), 50 ng/ml EGF, 2 μM CHIR99021, 2 μM SB202190, and 10 μM Y27632. We used 2 independent organoids from 2 donors.

last: Endo

first: Takahiro

last: Arima


title: The intrinsically disordered region of the E3 ubiquitin ligaseTRIP12 induces the formation of chromatin condensates and interferes withDNA damage response.

city: Toulouse

first: Claire

last: Vargas

address: 2 Avenue Hubert Curien

country: France

institute: Centre de Recherches en Cancérologie de Toulouse

summary: Chromatin compaction is crucial for the expression and the integrity of the genome. We previously showed that the nuclear HECT-type E3 ubiquitin ligase TRIP12 (Thyroid hormone Receptor Interacting Protein 12) is tightly associated to chromatin. Overexpressed in several types of cancers, we explored herein the consequences of TRIP12 overexpression on chromatin homeostasis. First, we established the proxisome of TRIP12 by BioID and unveiled its pleiotropic role in chromatin regulation. Second, we demonstrated that an overexpression of TRIP12, via its intrinsically disordered region, leads to the formation of chromatin condensates enriched in heterochromatin epigenetic marks. We further discovered that the formation of TRIP12 mediated-chromatin condensates is highly dynamic and driven by a mechanism of polymer-polymer phase separation (PPPS). Chromatin condensates formation is dependent not only on the concentration, the length of TRIP12-IDR but also electrostatic interactions. Chromatin compaction is a determinant parameter in several biological processes. Indeed, we measured that the formation of TRIP12 mediated-chromatin condensates alters cell cycle progression, genome accessibility, transcription as well as DNA damage response (DDR) by inhibiting the accumulation of Mediator DNA Damage Checkpoint (MDC1). Altogether, this study reveals a novel dynamic role for TRIP12 in chromatin compaction independently of its ubiquitin ligase activity with important consequences on cellular processes.

overall_design: Comparative gene accessibility analysis of ATAC-seq data from two experiments of HeLaS3 cells transfected with TRIP12-IDR-GFP versus non transfected HeLaS3 cells.

first: Jérôme

last: Torrisani

first: Marlène

last: Dufresne


title: SHORT-ROOT 1 is critical to cell division and tracheary element development in rice roots

city: Chongqing

first: yadi

last: xing

address: Beibei District

institute: Southwest University

summary: The exocyst is a key factor in vesicle transport and is involved in cell secretion, cell growth, cell division, and other cytological processes in eukaryotes. EXO70 is the key exocyst subunit. We obtained a mutant SHORT-ROOT gene, SR1, through map-based cloning and genetic complementation. SR1 encodes a plant-conserved protein with an EXO70 domain. SR1 mutation affected the whole root-development process, producing shorter radicles, adventitious roots, and lateral roots, abnormal xylem development, causing dwarfing, and decreasing the water potential and moisture content. SR1 was largely expressed in the roots, but only in developing root meristems and tracheary elements. The shortness of the sr1 mutant roots was caused by the presence of fewer meristem cells. The in situ histone H4 expression patterns confirmed that cell proliferation during root development was impaired. Tracheary element dysplasia was caused by marked decreases in the inner diameters of and distances between the perforations of adjacent tracheary elements. The membrane transport of the sr1 mutants was blocked, affecting cell division in the root apical region and root tracheary element development. The study of SR1 will improve our understanding of the function of the EXO70 gene in rice and guide future studies on the molecular mechanisms involved in plant root development.

overall_design: Development of two rice transcriptome sequencing and analysis software RNAseq

first: Guanghua

last: He

first: Yadi

last: Xing

last: Wang

first: Tianquan

last: Zhang


title: Characterization of the genes that were regulated by infection with enterotoxigenic E. coli (ETEC)

city: Kyoto

first: Eriko

last: Kage-Nakadai

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Koyto Univ.

summary: In the present study, we investigated the pathogenicity of infection with enterotoxigenic E. coli (ETEC)  using Caenorhabditis elegans as a model animal. The lifespan of the adult C. elegans infeted with ETEC was significantly longer than that of uninfected animals (control). Transcriptional profiling comparing infected- and uninfected animals suggested that genes related to the insulin-like peptide were upregulated by infection with ETEC.

overall_design: Transcriptional profiling of three-day-old worms that were infected or uninfected with ETEC for five days, by deep sequencing, using Illumina HiSeq.


title: Hormone responsiveness and spatial heterogeneityof apical-out endometrial organoids

summary: We have developed apical-out (AO)- endometrial organoids (EMO) that emulate the in vivo archtecture of endometrial epithelium. The AO-EMO exposes the apical surface of the epithelium. To explore the hormone responsiveness and spatial heterogeneity of AO-EMO, we conducted transcriptomic analysis.

overall_design: We cultured human endometrial organoids in collagen-based gels (70% type-I collagen and 30% matrigel) for 7-10 days with ECSY medium. The composition of the ECSY medium was as follows: DMEM/F-12  supplemented with 1% ITS-X supplement, 0.15% BSA, 1% Knockout Serum Replacement, 200 mM L-ascorbic acid, 50 ng/ml EGF, 2 μM CHIR99021, 2 μM SB202190, and 10 μM Y27632. Following the ECSY culture, we sequentially introduced 17β-estradiol(E2), medroxyprogesterone acetate (MPA), 8-bromoadenosine 3′,5′-cyclic monophosphate (8-Br-cAMP), and prolactin. The treatment durations were as follows: 2 days for E2 and 4 days for the combined treatment of E2, MPA, 8-Br-cAMP, and prolactin (EPCP).  As a control, we prepared AO-EMO without any hormone treatment as well as AO-EMO treated exclusively with E2. To isolate the outer and inner cells of AO-EMO, the culture medium was aspirated, and PBS was added to wash. Subsequently, TrypLE Express was added to the culture dish, and plates were incubated at 37℃ for 30 min. Following the incubation, TrypLE was removed and AO-EMO were washed with PBS. The outer cells were detached by pipetting PBS onto the surface of the AO-EMO several times using a manual pipette. We used 4 independent organoids from 4 donors.


title: Maternal DBP exposure promotes synaptic formation in offspring by activiting astrocytes via AKT/NF-κB/IL-6/JAK2/STAT3 signaling pathway

city: Nanjing

first: Yun

middle: hui

last: Xia

address: 22 Hankou Road

institute: Nanjing university

summary: In summary, we revealed that maternal DBP exposure activated astrocytes through the AKT/NF-κB/IL-6/JAK2/STAT3 signaling pathway and up-regulated the expression of TSP1, which then affected the density and morphology of dendritic spines and synaptic formation of hippocampal neurons, ultimately leading to decreased autonomy and exploration behavior of offspring.

overall_design: C8-D1A cells were treated with 1 mM MBP for 24 h

first: Yunhui


title: Identification and characterization analysis of the different  genes in CUS mouse treated with RVG-circDYM-EVs using RNA-seq.

city: 南京

first: Xiaoyu

last: Yu

state: 选择所在的省份

address: 南京鼓楼丁家桥87号

institute: 东南大学

summary: Whole RNA-sequencing analysis was performed and analyzed by Lc. Biotech Co. Ltd. (Hangzhou, China). hippocampus tissue from the Ctrl + Ctrl group, Ctrl + circDYM group, CUS + Ctrl group, and CUS + circDYM group were collected in TRIzol. Total RNAs were extracted from Trizol. UMI technology was used to label each sequence fragment with sequence tags, which minimized the interference of duplication caused by PCR amplification on the quantitative accuracy of the transcriptome. RNA sequencing reads were aligned to the mouse genome (GRCh37/hg19) using the software Hisat2 (2.0.4). Transcript abundance was evaluated by calculating fragments per kilo base of exon per million fragments mapped (FPKM).

overall_design: Examination of different genes by RVG-circDYM-EV in CUS mice by RNA-seq.


title: Multi-omics Analysis Reveals the Effects of LPS-induced Acute Lung Injury in Mice

city: Guangzhou

first: Zhuohui

last: Luo

address: Jichang Road 12th

institute: Guangzhou University of Chinese Medicine

summary:
To investigate the molecular alterations in the pathogenesis of ALI induced by LPS.
We then performed gene expression profiling analysis using data obtained from RNA-seq of lung tissues from the two comparison groups.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for lung tissues.

first: Jia

last: Huang

first: Xiu

last: Xi

first: Zai

last: Xu

first: Xiao

last: Shen

first: Zhui

middle: H


title: High-throughput Sequencing Facilitates Quantitative Analysis of  Bone Marrow Macrophages and Spleenic Macrophages MicroRNA Expression in mouse MLL-AF9 acute myelogenous leukemia

city: Tianjin

first: Lina

address: 288 nanjing Road

institute: institute of blood disease

type: Non-coding RNA profiling by high throughput sequencing

summary: The goals of this study aim to reveal microRNA expression profiles of leukemia-associated macrophages and regulatory mechanism in response to the microenvironmental cues in mouse MLL-AF9 acute myelogenous leukemia

overall_design: Compare microRNA expression of macrophages in MLL-AF9 acute myelogenous leukemia which are suggested as leukemia-associated macrophages (LAMs) with homeostasis

first: GuoGuang

last: Zheng

first: Xiaoli

last: Liu


title: Analysis of the mechanism of curcumin against osteoarthritis using transcriptomics

status: Public on Nov 10 2023

city: Changsha

first: Wenxiang

last: Deng

address: 300 Bachelor's Road, Hanpu Science and Education Park, Yuelu District

institute: Hunan University of Medicine

summary: Curcumin is a polyphenolic compound extracted from the turmeric plant (Curcuma longa) and has been extensively studied for its anti-inflammatory and anti-proliferative properties. The safety and effectiveness of curcumin have been thoroughly proven. However, the mechanisms underlying the treatment of osteoarthritis remain unclear. This study aimed to reveal the potential mechanism of curcumin in the treatment of osteoarthritis through metabolomics and transcriptomics. First, we verified the effect of curcumin on inflammatory factors in human articular chondrocytes. Secondly, we used cellular metabolomics to explore the cellular metabolic mechanism of curcumin against osteoarthritis. Third, we evaluated differences in gene expression in human articular chondrocytes by transcriptomics. Finally, to evaluate essential targets and elucidate the underlying mechanisms of curcumin in the treatment of osteoarthritis, we performed a screen for proteins in pathways shared by metabolomics and transcriptomics. Our results showed that curcumin significantly reduced the levels of inflammatory markers, such as IL-β, IL-6, and TNF-α, in human articular chondrocytes. Cellular metabolomics identified 106 differential metabolites, including beta-aminopropionitrile, 3-amino-2-piperidone, pyrrole-2-carboxaldehyde, and various other components. Transcriptome analysis yielded 1050 differential mRNAs. Enrichment analysis showed that differential metabolites and mRNA were significantly enriched in 7 pathways including glycine, serine, and threonine metabolism; interconversion of pentose and glucuronic acid; glycerolipid metabolism; histidine metabolism; mucin type O-glycan biosynthesis; phosphoinositide metabolism; and cysteine and methionine metabolism. A total of 23 key targets were identified to be involved in these pathways. We speculate that curcumin may alleviate osteoarthritis by targeting key proteins involved in glycine, serine, and threonine metabolism, inhibiting pyruvate production, and regulating glycolysis.

overall_design: Using transcriptomics to analyze the expression differences of curcumin in normal chondrocytes and osteoarthritis cells

first: WenXiang


title: Integrative transcriptome- and DNA methylation analysis of brain tissue from the temporal pole in suicide decedents and their controls (Methylation)

city: Grand Rapids

first: Lena

last: Brundin

address: 333 Bostwick Ave NE

institute: Van Andel Institute

summary: To investige gene expression and methylation changes in the suicide decedents group from postmortem brain tissues

overall_design: We compared genome wide gene expression and methylation differences between the suicide decedents group (n=29) and mental healthy group who died by natural causes (n =31).

first: Qiong

last: Sha

first: John

last: Mann


title: Mouse trophoblast cells have attenuated responses to TNFα and IFNγ that allow them to avoid synergic cytotoxicity of the two cytokines

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

summary: TNFα and IFNg are two inflammatory cytokines that play critical roles in immune responses, but they can also negatively affect cell proliferation and viability. In particular, the combination of the two cytokines (TNFα/IFNγ) synergistically causes death in many cell types. We recently demonstrated that, mouse embryonic stem cells (ESCs) isolated from the inner cell mass of the blastocyst stage embryo, do not respond to TNFα and IFNg, thereby avoiding TNFα/IFNγ cytotoxicity. This study expanded our investigation to mouse trophoblast stem cells (TSCs) and differentiated trophoblasts (TSC-TBs), the major cellular constituents in trophectoderm of the blastocyst. We report here that TNFα or IFNγ alone has limited negative effect on the viability of mouse fibroblasts, but TNFα/IFNγ effectively kill these cells. However, TSCs and TSC-TBs are markedly resistant to the cytotoxicity of TNFα/IFNγ. With molecular and cellular approaches and transcriptomic analysis, we demonstrated that TSCs and TSC-TBs have attenuated responses to TNFα and IFNγ and the underlying molecular mechanisms that allow these cells to avoid the synergistic cytotoxicity of TNFα/IFNγ.  Together with our previous findings in ESCs, we propose that the attenuated responses of TSCs, TSC-TBs, and ESCs to TNFα and IFNγ may serve as a protective mechanism that limits cytokine cytotoxicity in the blastocyst.

overall_design: Mouse TSCs, differentiated TSCs, and MEFs  confluence (60–70% confluence) were treated with mouse TNFα and IFNγ (20 ng/ml, PeproTech, Rocky Hill, NJ) individual or in combination (TNFα/IFNγ), then total RNA was extracted, followed by RNA-sequencing analysis.

first: Zongliagn

first: Yan-Lin

last: Guo


title: Next Generation Sequencing Quantitative Analysis of altered expression of genes in DHCR24 overexpressing bladder cancer cells

city: 广东省广州市越秀区

first: jian

middle: cheng

address: 孙逸仙纪念医院沿江西路107号

institute: Sun Yat-sen Memorial Hospital

summary: Bladder cancer (BCa) is one of the most commonly diagnosed urinary malignancies with an estimated yearly 550,000 new cases worldwide. Previous study revealed that DHCR24 was a crucial oncogene that widely involved in tumor initiation and progression. Yet the biological role and underlying regulatory mechanism of DHCR24 in lymph node (LN) metastasis of bladder cancer (BCa) remain unclear. Our study aims to explore the target genes of DHCR24 and the underlying mechanism in the LN metastasis of BCa.

overall_design: To detect the precise mechanism of DHCR24 in LN metastasis of BCa, the total RNA of UM-UC-3 cells transfected with Vector plasmids or DHCR24-overexpressing plasmids was extracted and the next generation sequencing was conducted to explore the expressing profile difference between Vector and overexpression group. The result was obtained from three independent experiments.

first: Yue

last: Zhao

first: Changhao

last: Chen

first: Jiancheng

first: hanhao

last: zheng


title: Spatial transcriptomic profiling reveals local and domain-establishing regulatory signaling networks within the bone marrow

city: Dallas

first: Robert

middle: J

last: Tower

address: 5323 Harry Hines Blvd

institute: UTSW

summary: The application of single-cell RNA sequencing (scRNAseq) to the bone field has led to significant advancements in our understanding of skeletal stem cell (SSC) heterogeneity, yet disparity remains in the characterization of these cells in the context of their native environment. To resolve these limitations, we combined scRNAseq and spatial transcriptomics in adult femurs to provide endogenous, in vivo context. First, predictive modeling was used to determine the spatial location of SSCs within the bone marrow. These results localized CXCL12-abundant reticular cells to the bone marrow, while PDGFRα+SCA1+ were found to enrich within the outer periosteum. Correlative analyses were next used to define the cellular niche composition, identifying smooth muscle cells, as well as endothelial cell and macrophage subtypes overrepresented within the SSC niche. Using cell-cell communication prediction and spatial transcriptomics, we defined ligand-receptor pairs specifically expressed within the niche and mapped their expression back to niche-resident cells. Finally, these SSC niches were placed in the context of bone microdomains. Signaling gradients derived from the vasculature and bone surfaces were unbiasedly assessed using SpatialTime. This data indicated a striking, spatially-restricted activation of metabolic and major morphogenetic pathways. This project demonstrates the ability of this technique to spatially localize SSC subpopulations, define the cellular components of the stem cell niche, unravel cell-cell communication and place this niche in the context of its bone microdomain to gain a comprehensive understanding of local and global SSC regulatory networks within the bone.

overall_design: Femurs from 10 week old C57BL/6 mice


title: Integrative transcriptome- and DNA methylation analysis of brain tissue from the temporal pole in suicide decedents and their controls

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

overall_design: Refer to individual Series


title: Cancer immunotherapy via synergistic co-activation of myeloid cells

city: Philadelphia

first: Max

middle: M

last: Wattenberg

state: PENNSYLVANIA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania


title: Epigenetic regulator landscape of HOX/MEIS expression in AML

city: La Jolla

first: Karina

middle: Ofelia

last: Barbosa Guerra

address: 10901 North Torrey Pines Rd, Deshpande Lab RM6210B

department: Tumor Initiation & Maintenance Program

institute: Sanford Burnham Prebys Medical Discovery Institute


title: Polyamine metabolite spermidine rejuvenates the oocyte quality by enhancing mitophagy during female reproductive aging

first: Zhang

last: Yu

address: No. 1 Weigang

institute: Nanjing Agricultural University

summary: Advanced age is a primary risk factor for female infertility due to reduced ovarian reserve and declining oocyte quality. However, as an important contributing factor, the role of metabolic regulation during reproductive aging is poorly understood. Here, we applied untargeted metabolomics to identify spermidine as a critical metabolite in ovaries to protect oocytes against aging. In particular, we found that spermidine level was reduced in aged ovaries and supplementation of spermidine promoted follicle development, oocyte maturation, early embryonic development and female fertility of aged mice. By micro-transcriptomic analysis, we further discovered that recovery of oocyte quality by spermidine was mediated by enhancement of mitophagy activity and mitochondrial function in aged mice, and this action mechanism was conserved in porcine oocytes under oxidative stress. Altogether, our findings demonstrate that spermidine supplementation is a potentially effective strategy to ameliorate oocyte quality and reproductive outcome of women at an advanced age.

overall_design: To gain insight into the potential mechanisms regarding how spermidine improves the quality of aged oocytes, micro-transcriptome was carried out to compare the change of young, aged and spermidine-rescue group transcript levels.

first: Yu

last: Zhang

first: Jie

last: Bai

first: Zhaokang

last: Cui

last: Li

first: Qian

last: Gao

first: Yilong

last: Miao

first: Bo

last: Xiong


title: AS1842856 treatment in BT549 cells

status: Public on Nov 15 2023

city: Edinburg

first: Megan

middle: Erin

last: Keniry

state: TX

address: 1201 W. University Dr.

department: Biology

institute: UTRGV

summary: Basal-like breast cancer (BBC) is a poor prognosis cancer that lacks effective targeted therapy. Recently our group and others found that forkhead box transcription factor FOXO1 promotes stem gene expression in BBC and GBM cell lines. Given the critical role of cancer stem cells in promoting cancer progression, we examined the impact of FOXO1 inhibition with AS1842856 on BBC cells. We treated BT549 cells with 200nM AS1842856 for 48 hours and found that FOXO1 inhibition induced a set of WNT Pathway genes.

overall_design: AS1842856 treatment in BT549 cells


title: Mapping of genome-wide histone modifications in SGF29 knockout vs NTC U937 AML cells. Mapping of binding of SGF29 and Tudor-domain mutant SGF29_D196R by FLAG ChIP [ChIP-seq SGF29]

summary:
ChIP-seq was performed to investigate the genomic binding of SGF29 in U937 cells using FLAG-tagged SGF29-wild-type or SGF29_D196R mutant overexpression constructs. To assess the effects SGF29 in histone mark deposition, ChIP-seq was performed for different histone modifications in U937 cells with CRISPR-knockout of SGF29 or the expression of a control sgRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K9ac, H3K9me3, H2K120Ub1, H3K4me3 in U937 cells with SGF29 knockout or control sgRNA. ChIP-seq for FLAG-tagged wild-type or Tudor domain mutant SGF29 in U937 cells.

first: Anagha

last: Deshpande

last: Barbosa

first: Xue

last: Lei

first: Rabi

last: Murad

first: Aniruddha


title: Effect of CRISPR knockout of MLL, CSNK2A1 and SGF29 on gene expression profiles in acute myeloid leukemia U937 cells [RNA-seq]

summary:
To investigate the transcriptomic effects upon loss of CSNK2A1 (Casein kinase 2, CK2), MLL and SGF29 in the AML cell line U937 we performed CRISPR knockouts, as well as transduction with non-targeting controls, and harvested samples for bulk RNA-Seq.
We then performed gene expression profiling analysis using data obtained from RNA-seq of the different CRISPRko perturbations compared to non-targeting controls.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for U937 cells and their knockout or control derivatives (MLL knockout, CSNK2A1 knockout, SGF29 knockout and non-targeting control).

last: Murad.


title: Anylasis of the diatom Phaeodactylum tricornutum under 64-75-5,Tetracycline hydrochloride stress

city: shantou

first: jichen

last: chen

address: university road

institute: shantou university

overall_design: 24h examined cell density, Fv/Fm, sugar and protein content

first: Yuqiu

last: wu

first: Wanna

last: wang

first: Jichen

first: Hua

last: du

first: Xiaojuan

last: liu

first: Hong


title: OGFOD1 Regulates Translation to Alter Hypertrophy Susceptibility

city: Bethesda

first: Philip

last: Murphy

state: MD

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

summary: Cardiac hypertrophy, a precursor for heart failure, requires increased translation. However, little is known of the mechanisms that regulate translation in hypertrophy. Members of the 2-oxoglutarate-dependent dioxygenase family regulate several aspects of gene expression, including translation. An important member of this family is OGFOD1. Here, we show OGFOD1 accumulates in failing human hearts. Upon OGFOD1 deletion, murine hearts showed transcriptomic and proteomic changes, with only 21 factors (0.6%) changing in the same direction at both the mRNA and protein levels. Additionally, OGFOD1-KO mice were protected from induced hypertrophy, supporting a role for OGFOD1 in the cardiac response to chronic stress.

overall_design: WT and OGFOD1-KO mice aged 3-5 months were treated with either vehicle (1X PBS and Sodium Ascorbate) or isoproterenol (1X PBS, Sodium Ascorbate, and Isoproterenol) for 2 weeks by osmotic minipump. Hearts were isolated from these mice and RNA was extracted and subjected to RNAsequencing.

first: Leslie

last: Kennedy

first: Elizabeth

first: Poching

last: Liu

first: Yan

last: Luo

first: Ilker

last: Tunc

first: Mehdi

last: Pirooznia


title: Transcriptomic analysis of J0951/Col, J0951/UAS_YUC4, J0571/UAS_YUC4, Q2500/UAS_YUC4, J0121/UAS_YUC4 andQ0990/UAS_YUC4.

city: qingdao

first: Ting

middle: Ting

last: Ding

address: binhai street  NO.72

institute: shandong university

summary: The goal of this study is to investigate the effect of enhanced auxin biosynthesis on gene expression in specific root tissues. We isolated total RNA from the roots of 5_day_old J0951/Col, J0951/UAS_YUC4, J0571/UAS_YUC4, Q2500/UAS_YUC4, J0121/UAS_YUC4 andQ0990/UAS_YUC4 seedlings. We found that there was a statistically significant enrichment in genes annotated as being linked to cell wall related genes.

first: Tingting

first: ZhaoJun


title: The Epigenetic Regulator Landscape of HOX/MEIS Expression in AML [scRNA-seq]

first: Karina

last: Barbosa Guerra

summary: Aberrant and constitutive activation of the clustered homeobox (HOX) genes and the three-amino-acid loop extension (TALE) domain-containing HOX co-factor MEIS1 (henceforth termed HOX/MEIS) is a recurrent feature in several types of myeloid and lymphoid leukemias. HOX/MEIS misexpression is linked to aberrant self-renewal and therapy resistance in leukemia, but the therapeutic targeting of this important pathway has remained elusive. Using AF10-rearranged leukemia as a prototypical example of HOX/MEIS dysregulation, we sought to comprehensively characterize  chromatin regulators that sustain aberrant expression of these genes. We deployed a GFP-MEIS1 knock-in reporter cell line to conduct small-molecule inhibitor screens and a high-density domain-focused CRISPR-Cas9 screen targeting epigenetic regulators. We identified members of at least six distinct chromatin-modifying complexes as HOX/MEIS regulators, including previously characterized HOX/MEIS regulators such as DOT1L, AF10, ENL, and HBO1 as well as less well-characterized and completely novel HOX/MEIS regulators including AFF2, JADE3, casein kinase 2 and the chromatin reader SGF29. These HOX/MEIS regulators were important for the growth of AML cell lines representing diverse leukemia subtypes characterized by HOX/MEIS dysregulation including leukemias with AF10 rearrangements, MLL rearrangements, and NPM1 mutation. Determination of gene expression changes after perturbing each of these MEIS1 regulators in parallel using CROP-seq demonstrated that the deletion of DOT1L, ENL, AFF2, or SGF29 led to the downregulation of several genes associated with stem cell self-renewal and upregulation of differentiation-associated genes.

overall_design: We selected sgRNAs targeting MLLT10, MLLT6, MLLT1, SGF29, MLLT3, CSNK2A1, KAT7, BRD4, DOT1L, CSNK2B, AFF4, KMT2A, AFF2 and a non-targeting control and cloned them into the CROPseq-guide-puro vector (Addgene #86708). Plasmid preparations were mixed in equimolar ratios and the pool was used to prepare lentivirus. U937 cells were transduced in duplicate and sequenced. A total of 18,000 cells per sample were loaded on a Chromium Single Cell Instrument with a targeted capture of 10,000 cells/sample. RNAseq libraries were prepared using the 10X Genomics Chromium Single Cell 3′ v3 Library, Gel Beads & Mutiplex Kit. Sequencing was performed on the Illumina NovaSeq using the S4 200 kit and PE100 run configuration. A custom script was used to deduplicate reads by UMI.

first: Anagha

last: Deshpande

first: Anna

last: Minkina

first: Jay

last: Shendure

first: Aniruddha


title: Serca2b inhibition aids T cell activation and selectively promotes tumor cell death

city: Amsterdam

first: Oscar

last: Krijgsman

state: Outside the US or Canada

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

summary: We found that T cells and tumor cells are differentially dependent on Atp2a2 for their survival. In fact, Atp2a2 KO T cells have increased function, whereas Atp2a2 KO tumor cells die. Thapsigargin is a drug that targets the protein product of Atp2a2: Serca2b. We found that in tumor cells, the SAGA complex transmits TG signals to induce tumor cell death, principally via Ccdc101.

overall_design: Here, we treated tumor cells (either WT or Ccdc101 KO) or T cells (WT or Atp2a2 KO) with TG (50ng/mL) or Veh (DMSO) for 8 hours. The T cells were additionally activated with anti-CD3 antibodies (2.5ug/mL in PBS) for 24 hours (Act) or not (Rest).

first: David

last: Vredevoogd

first: Daniel

last: Peeper


title: CTCF Loss Potentiates P53 Mediated Gene Transcription in Breast Tissue

city: Montreal

first: Meredyth

middle: Laurel Georgia

last: Elisseou

state: Quebec

address: 3999 ch de la Cote-Sainte-Catherine

department: Experimental Medicine

country: Canada

institute: McGill

summary: A single copy loss of CTCF is found in about 50% of breast cancer patients. Based on clinical TCGA data we hypothesized that the loss of CTCF may potentiate TP53 target gene expression in patients. Using MCF10A cells as a model, we deleted a single copy of CTCF using CRISPR/Cas9. We found, using qPCR and RNA-seq, that cells carrying low CTCF displayed an enhanced TP53 response after exposure to chemotherapeutics. Using ATAC-seq, we aimed to explore whether the elevated induction of TP53 target gene transcription was associated with changes in open or closed chromatin structure. Specifically, we were interested in comparing chromatin accessibility at TP53 target genes within MCF10A CTCF +/- cells compared to control cells following the induction of DNA damage (6uM cisplatin for 8h). We discovered that accessibility of the transcription start site is associated with heightened gene expression in CTCF+/- compared to the control. Interestingly, for a subset of TP53 response genes, there is increased accessibility on both transcriptional start sites and termination sites following the induction of DNA damage. The importance of chromatin accessibility at these two regions is still under investigation. Additionally, accessible gene regions at both sites also appear to have greater enrichment within TADS in the CTCF+/- cell compared to the control. We propose that the increased accessibility of TP53 target genes following damage represents a mechanism enhancing the efficacy of the TP53-regulated DNA damage response.

overall_design: Using MCF10A cells as a model, we deleted a single copy of CTCF using CRISPR/Cas9, creating two knockdowns: #17 and # 22. Triplicates were utilized for treatments of the control, #17, and #22 where we utilized 6uM Cisplatin to investigate DNA damage at 0h and 8h after treatment.

first: Benjamin

last: Lebeau


title: Identification of transcriptional changes after QYHJ treatment in mouse model with pancreatic cancer

city: Shanghai

first: Libin

last: Song

address: 270 Dongan Road

institute: Fudan University Shanghai Cancer Center

summary:
Purpose: The goals of this study are to characterize the transcriptional changes after QYHJ treatment. More importantly, the transcriptome differences betweeen QYHJ treatment and control mice are compared to identify RNAs that may be targets of QYHJ.
Methods: High-throughput RNA sequencing (RNA-seq) was employed to capture the transcriptional changes in QYHJ treatment samples. StringTie was used to quantify gene expression and DESeq2 was utilized to compared expression changes between different sample groups.

overall_design: Tanscriptome-wide characterization of QYHJ treatment pancreatic cancer mouse model


title: Zfp281 and Zfp148 control CD4+ T cell thymic development and Th2 functions

first: Remy

last: Bosselut

address: 9000 Rockville Pike, Building 37

department: Laboratory of Immune Cell Biology

institute: National Cancer Institute, National Institute of Health

summary:
How CD4+ lineage gene expression is initiated in differentiating thymocytes remains poorly understood. Here, we show that the paralog transcription factors Zfp281 and Zfp148 control both this process and cytokine expression by T helper cell type 2 (TH2) effector cells. Genetic, single-cell, and spatial transcriptomic analyses showed that these factors promote the intrathymic CD4+ T cell differentiation of class II major histocompatibility complex (MHC II)–restricted thymocytes, including expression of the CD4+ lineage–committing factor Thpok. In peripheral T cells, Zfp281 and Zfp148 promoted chromatin opening at and expression of TH2 cytokine genes but not of the TH2 lineage–determining transcription factor Gata3. We found that Zfp281 interacts with Gata3 and is recruited to Gata3 genomic binding sites at loci encoding Thpok and TH2 cytokines. Thus, Zfp148 and Zfp281 collaborate with Gata3 to promote CD4+ T cell development and TH2 cell responses.

This SuperSeries is composed of the SubSeries listed below.


title: Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1 [EMSA-seq]

status: Public on Nov 09 2023

city: University Park

first: Lu

last: Bai

address: 406 South Frear Building

institute: Penn State University

summary: Pioneer factors (PFs) are a subset of transcription factors (TFs) that can bind to nucleosomal DNA and invade closed chromatin. Despite that nucleosomes do not present a strong barrier to PF binding, PF can only bind to a small fraction of motifs in the genome. The underlying mechanism of such binding selectivity is not well understood. Here, we design a high-throughput assay named Chromatin Immunoprecipitation over Integrated Synthetic Oligonucleotides (ChIP-ISO) to systematically dissect the sequence features affecting the binding specificity of a classic PF, FOXA1, in A549 human lung carcinoma cells. This method involves integrating thousands of synthetic sequences containing FOXA1 motifs into a fixed genomic locus, followed by FOXA1 chromatin immunoprecipitation (ChIP) and amplicon sequencing. We find that 1) FOXA1 binding is affected by motif strength and co-binding TFs AP-1 and CEBPB, with AP-1 playing a major role in promoting FOXA1 binding, 2) FOXA1 binding in vivo and in vitro are poorly correlated, and FOXA1 and AP-1 show binding cooperativity in vitro, 3) FoxA1’s binding specificity is mostly determined by the local sequences, whereas chromatin context, including heterochromatin marks, only plays a minor role, and 4) AP-1 is at least partially responsible for differential binding of FOXA1 in different cell types. Finally, neural network analysis shows that AP-1 and CEBPB motifs are predictive of FOXA1 ChIP-seq peaks in A549, but not in some other cell types. In summary, combining ChIP-ISO with in vitro and in silico analyses, our study provides insights into the genetic rules underlying PF binding specificity and reveals a mechanism for its regulation during cell differentiation.

overall_design: Electrophoretic mobility shift assay with high-throughput sequencing (EMSA-seq) on a synthetic oligonucleotide library incubated with 1-60 nM purified FOXA1 and separated on a native polyacrylamide gel to separate FOXA1 bound and unbound oligonucleotides for purification followed by high-throughput sequencing

first: Cheng

last: Xu

first: Holly

last: Kleinschmidt

first: Jianyu

last: Yang

first: Erik

last: Leith

first: Jenna

last: Johnson

first: Song

last: Tan

first: Shaun

last: Mahony


title: Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct


title: Effect of  CLK2 expression in the regulation of intron retention during heat shock

city: Wuhan

first: Wei

last: Wang

state: Hubei

address: 13 Hangkong Road

institute: Huazhong University of Science and Technology Tongji Medical College

summary: We established the HeLa cells expressing the GFP (control) or CLK2 (WT) and subjected them to heat shock. These cells were subjected to RNA-seq for the alternative splicing analysis.

overall_design: Four HeLa cell groups (GFP, HS-GFP, WT, HS-WT) were subjected to RNA-seq

first: Bing


title: Discrete hippocampal projections are differentially regulated by parvalbumin and somatostatin interneurons

city: Austin

first: Jennifer

last: Donegan

address: 1701 Trinity

department: Psychiatry

institute: UT Austin

summary: People with schizophrenia show hyperactivity in the ventral hippocampus (vHipp) and we have previously demonstrated distinct behavioral roles for vHipp cell populations. Here, we test the hypothesis that parvalbumin (PV) and somatostatin (SST) interneurons differentially innervate and regulate hippocampal pyramidal neurons based on their projection target. First, we use eGRASP to show that PV-positive interneurons form a similar number of synaptic connections with pyramidal cells regardless of their projection target while SST-positive interneurons preferentially target nucleus accumbens (NAc) projections. To determine if these anatomical differences result in functional changes, we used in vivo opto-electrophysiology to show that SST cells also preferentially regulate the activity of NAc-projecting cells. These results suggest vHipp interneurons differentially regulate that vHipp neurons that project to the medial prefrontal cortex (mPFC) and NAc. Characterization of these cell populations may provide potential molecular targets for the treatment schizophrenia and other psychiatric disorders associated with vHipp dysfunction.

overall_design:
Retrograde virus was used to fluorescently label vHipp neurons that project to the mPFC or NAc in C57BL/6 mice.
Six weeks after viral injection, flow cytometry was used to sort out fluorescently labeled cells.
RNASeq was used to determine the transcriptional profile of mPFC- or NAc-projecting pyramidal cells from 5-6 animals per group.

last: Lodge

first: Hannah

middle: B

last: Elam

first: Angela

last: Boley


title: Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1 [ChIP-ISO]

overall_design: Chromatin Immunoprecipitation with Integrated Synthetic Oligonucleotides (ChIP-ISO) for TF FOXA1 and histone modifications H3K9me3 and H3K27me3 in a mixed population of WT A549 human lung carcinoma cells with 3,203 synthetic oligonucleotides integrated individually into the AAVS1 locus.


title: Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1 [ChIP-seq]

overall_design: Chromatin immunoprecipitation with sequencing (ChIP-seq) for TF FOXA1 and histone modifications H3K9me3 and H3K27me3 in WT A549 human lung carcinoma cells, as well as for TFs FOXA1 and FOSL2 in A549 cells induced with doxycycline to overexpress dominant-negative A-Fos.


title: Next Generation Sequencing Facilitates Quantitative Analysis of WT and BES1-RNAi in dark and Green light Transcriptomes

first: Yuhan

last: Hao

address: #300 Fenglin Road

institute: CAS Center for Excellence in Molecular Plant Science

summary: Analysis of differential differential gene expression regulated by green light.

overall_design: mRNA profiles of 3 days of WT and BES1-RNAi seedlings  grown in the dark and then exposed to continuous Green light (10 μmol·m-2·s-1) for 1 hours were generated by deep sequencing, in triplicate, using Illumina Hiseq 4000

first: Hongtao

last: Liu


title: SUL1 deficiency reduces PKA activity to increase replicative lifespan in yeast Saccharomyces cerevisiae

city: Cheng Du

first: Yan

last: Pan

address: Northern Jianshe Road

institute: University of Electronic Science and Technology of China

summary: The process of sulfate uptake plays a crucial role in cellular metabolism and growth. SUL1, a plasma membrane transporter responsible for regulating the entry of extracellular sulfate in S. cerevisiae. Our previous work verified SUL1 as a fundamental gene involved in the regulation of lifespan. This study aimed to undertake a more comprehensive analysis of the role of SUL1 in regulating longevity. Our data showed that that sulfate transport is not required for the effect of SUL1 deletion on increased longevity. The SUL1 mutant demonstrates decreased functionality within the PKA signaling pathway, resulting in a variety of effects, such as increased stress-protective trehalose and glycogen, enhanced autophagy, elevated expression of stress response genes, and reduced expression of ribosomal genes. Concurrently, the observed increase in lifespan resulting from the deletion of SUL1 may be partially attributed to the stimulation of autophagy and MSN2-mediated transcriptional activity. The findings of this study provide additional evidence for the association between sulfate transporter and longevity, thereby identifying a novel potential intervention target for extending lifespan.

overall_design: To investigate the mechanism by which SUL1 mutations extend lifespan, exponential phase cells from the SUL1 mutant and wild-type (WT) groups were harvested and subjected to total RNA extraction for the construction of mRNA libraries intended for sequencing analysis. The WT strain was utilized as a control group, with three biological replicates per group.

first: Juan

last: Long

first: Hao

last: Li

first: Jing


title: A Cell Atlas of the Dahl SS Thoracic Aortic Perivascular Adipose Tissue

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

summary: Perivascular adipose tissue (PVAT) is increasingly recognized for its function in mechanotransduction. To examine the cell-specificity of recognized mechanotransducers we use single nuclei RNA sequencing (snRNAseq) of the thoracic aorta PVAT (taPVAT) from male Dahl SS rats compared to subscapular brown adipose tissue (BAT). Approximately 30,000 nuclei from taPVAT and BAT each were characterized by snRNAseq, identifying 8 major cell types expected and one unexpected (nuclei with oligodendrocyte marker genes). Cell-specific differential gene expression analysis between taPVAT and BAT identified up to 511 genes (adipocytes) with many (≥20%) being unique to individual cell types. Piezo1 was the most highly, widely expressed mechanotransducer. Presence of PIEZO1 in the PVAT was confirmed by RNAscope® and IHC; antagonism of PIEZO1 impaired the tissue’s ability to hold tension. Collectively, the cell compositions of taPVAT and BAT are highly similar, and PIEZO1 is likely a mechanotransducer in taPVAT.

overall_design: Nuclei isolated from 2 naïve male Dahl SS rats each from subscapular brown adipose tissue and thoracic aorta perivascular adipose tissue.

first: Janice

last: Thompson

first: Stephanie

last: Watts

first: Leah

last: Terrian

first: G

last: Contreras

first: Cheryl

last: Rockwell

first: Christian

last: Mora

first: Emma

last: Wabel

first: Lizbeth

last: Lockwood

first: Sudin

last: Bhattacharya


title: Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1 [RNA-seq]

first: Lu

last: Bai

overall_design: Extraction of polyA-enriched RNA followed by high-throughput sequencing in A549 human lung carcinoma cells with the dox-inducible A-FOS protein integrated randomly into the genome with piggyBac transposase.

first: Cheng

last: Xu

first: Holly

last: Kleinschmidt

first: Jianyu

last: Yang

first: Erik

last: Leith

first: Jenna

last: Johnson

first: Song

last: Tan

first: Shaun

last: Mahony


title: Effect of the antifungal protein PeAfpA in the expression profile of Saccharomyces cerevisiae BY4741 strain.

city: Paterna

first: Moisés

last: Giner Llorca

state: Valencia

address: Catedrático Agustín Escardino, 7

department: Department of Food Biotechnology

country: Spain

institute: Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC)

summary: Transcriptomic study to characterize the interaction of the Penicillium expansum antifungal protein PeAfpA with the the model yeast Saccharomyces cerevisiae. For this, the transcriptome of S. cerevisiae BY4741 strain was compared among samples treated with increasing concentrations of PeAfpA.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BY4741 strain under different PeAfpA treatments (three replicates per sample)

last: Giner-Llorca

first: Antonella

last: Locascio

first: Javier

last: Alonso-del-Real

first: Jose

middle: F

last: Marcos

first: Paloma

last: Manzanares


title: A flexible Transcriptomic Analysis Pipeline (TAP) for quality control and functional assessment of transcriptomes

city: Burlington

first: Seth

last: Frietze

state: Vermont

address: 111 Colchester Ave

institute: University of Vermont

summary: We developed a Transcriptomic Analysis Pipeline (TAP) as a flexible workflow for comprehensive transcriptome analysis from any species with a reference genome. We tested TAP in a case study to compare polyA+ and rRNA-depletion RNA-seq library protocols using Drosophila melanogaster following different thermal stress temperatures. TAP provides a flexible and complete pipeline to enable researchers to extract more biologically relevant interpretations by integrated and interactive transcriptome analysis.

overall_design: Adult flies were subjected to 5 different temps with 3 biological replicates, total RNA extracted and used to construct polyA-selected and rRNA-depleted RNA-Seq libraries.

first: Emily

last: Nadeau

first: Joseph

last: Boyd