title: Microarray data of TPLL samples and normal T cell fractions

city: Rotterdam

first: Stefan

middle: J.

last: Erkeland

state: Zuid-Holland

address: Dr. Molewaterplein 40

department: Department of Immunology

country: Netherlands

institute: Erasmus University Medical Center

summary:
T cell prolymphocytic leukemia (T-PLL) is mostly characterized by aberrant expansion of small to medium sized pro-lymphocytes with a mature post-thymic phenotype, high aggressiveness of the disease and poor prognosis. However, T-PLL is more heterogeneous with a wide-range of clinical, morphological, and molecular features, which occasionally impedes the diagnosis. We hypothesized that T-PLL consists of phenotypic and genotypic subgroups that may explain the heterogeneity of the disease. We found that T-PLL does not show a clear skewing in T cell receptor alpha (TRA), TRB gene usage and CDR3 stereotypy. In addition, multi-dimensional immuno-phenotyping and gene expression profiling did not reveal clear T-PLL subgroups. However, based on miRNA expression profiles, T-PLL samples did clearly cluster in subgroups. We identified 35 miRNAs that were aberrantly expressed in T-PLL with miR-200c/141 as the most differentially expressed cluster. High miR-200c/141 expression was significantly correlated with increased white blood cell counts and poor survival. Furthermore, we found that overexpression of miR-200c/141 in T-PLL correlated with downregulation of their targets ZEB2 and TGFβR3, indicating that the TGFβ pathway is affected. Our results thus highlight the emerging role for aberrantly expressed oncogenic miRNAs in T-PLL, thereby paving the way for new therapeutic targets in this disease.
We used gene expression profiling by microarray to determine gene expression differences between T-PLL samples and normal T-cell subets.

overall_design: Gene expression analysis was performed on peripheral blood/bone marrow mononuclear cells of 23 TPLL cases and 6 normal T-cell subsets (naïve, memory and effector of CD4+ and CD8+ cells) of 2  healthy donors. When the tumor load of a patient was below 85%, cells were purified using cell sorting on a FACSAria III, based on the CD4 and CD8 expression on T-PLL cells.

first: Christiaan

last: Stavast

first: Anton

last: Langerak


title: Characterization of CD8 T cells during acute LCMV infection using scRNA-seq

status: Public on Apr 02 2021

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

country: USA

institute: Northwestern University

type: Expression profiling by high throughput sequencing

summary: During a viral infection, CD8 T cells encounter a myriad of antigenic and inflammatory signals of variable strength, which sets off each individual T cell on a unique differentiation trajectory. However, the developmental path for each of these cells will ultimately lead to one of only two potential outcomes after clearance of the infection—death or survival and development into memory CD8 T cells. How this cell fate decision is made remains incompletely understood. In this study, we explore the dynamic transcriptional changes during effector and memory CD8 T cell differentiation at the single cell level.

overall_design: Three samples (Day 0, 9, and 129) prepared using 10x Genomics Chromium platform

first: David

middle: M

last: Schauder


title: P14 CD8 T cells during acute LCMV infection

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: MIG, MIG-E47, or MIG-ID2 transduced CD8 T cells in vitro


title: TPLL samples and normal T cell fractions


title: Identification of the lncRNA DINOR as a global stress regulator in the super fungus Candida auris

status: Public on Apr 01 2021

city: Beijing

first: Yabing

last: Song

state: Beijing

address: Chaoyang District

department: Institute of Microbiology

country: China

institute: Chinese Academy of Sciences

summary: The goal of this RNA-Seq study is to elucidate DINOR’s function in regulating C. auris morphogenesis.

overall_design: mRNA profiles of WT, dinorΔ, and dinorΔ:DINOR cells.

first: Jiaxin

last: Gao

first: Eve

middle: W

last: Chow

first: Haitao

last: Wang

first: Jianbin


title: Next generation sequencing of small non-coding RNAs of T-PLL patients and normal T-cell fractions

type: Non-coding RNA profiling by high throughput sequencing

summary: T cell prolymphocytic leukemia (T-PLL) is mostly characterized by aberrant expansion of small to medium sized pro-lymphocytes with a mature post-thymic phenotype, high aggressiveness of the disease and poor prognosis. However, T-PLL is more heterogeneous with a wide-range of clinical, morphological, and molecular features, which occasionally impedes the diagnosis. We hypothesized that T-PLL consists of phenotypic and genotypic subgroups that may explain the heterogeneity of the disease. We found that T-PLL does not show a clear skewing in T cell receptor alpha (TRA), TRB gene usage and CDR3 stereotypy. In addition, multi-dimensional immuno-phenotyping and gene expression profiling did not reveal clear T-PLL subgroups. However, based on miRNA expression profiles, T-PLL samples did clearly cluster in subgroups. We identified 35 miRNAs that were aberrantly expressed in T-PLL with miR-200c/141 as the most differentially expressed cluster. High miR-200c/141 expression was significantly correlated with increased white blood cell counts and poor survival. Furthermore, we found that overexpression of miR-200c/141 in T-PLL correlated with downregulation of their targets ZEB2 and TGFβR3, indicating that the TGFβ pathway is affected. Our results thus highlight the emerging role for aberrantly expressed oncogenic miRNAs in T-PLL, thereby paving the way for new therapeutic targets in this disease.

overall_design: small non-coding RNA seq of T-PLL patients compared to normal T cell fractions

middle: J


title: Metabolic Reprogramming of Terminally Exhausted CD8+ T-cells by Interleukin-10 Enhances Anti-Tumour Immunity

city: Lausanne

first: Li

last: Tang

state: Vaud

address: MED 1 2826, Station 9, CH-1015 Lausanne

department: Institute of Bioengineering (IBI) / Institute of Materials (IMX)

country: Switzerland

institute: École polytechnique fédérale de Lausanne (EPFL)

summary: Terminally exhausted CD8+ T-cells, which hold certain level of anti-tumour cytotoxicity but largely reduced proliferation capacity, contribute directly to tumour growth control. However, this subpopulation do not respond to immune checkpoint blockades or most existing immunotherapies and are difficult to be reactivated. Here, we show that a half-life extended interleukin (IL)-10/Fc fusion protein directly expands the terminally exhausted CD8+ TILs and sustains their effector functions through in vivo metabolic reprogramming, leading to eradication of established solid tumours and durable cures in a majority of treated mice when combined with adoptive T-cell transfer immunotherapy. Our results provide preclinical evidence that IL-10/Fc is a safe and highly effective therapy that acts on a specific subset of CD8+ TILs distinct from those responding to immune checkpoint blockades. Thus, IL-10/Fc could complement and synergize with existing cancer immunotherapies for enhanced efficacy and response rates. We find that IL-10/Fc reprograms T-cell metabolism by promoting oxidative phosphorylation through the mitochondrial pyruvate carrier, suggesting that metabolic reprogramming is sufficient to revitalize terminally exhausted CD8+ TILs.

overall_design: The goals of this study are to use NGS to perform transcriptome profiling (RNA-seq) to find the changes of the global gene expression programs of tumor-infiltrating terminally exhausted CD8+ T-cells from IL-10/Fc treated mice. PBS treated mice were used as controls. Total RNA was extracted and submitted to RNA-seq

first: Yugang

last: Guo

first: Yu-Qing

last: Xie


title: Prenatal Stress-induced Depressive-like Behavior is Associated with Brain Metabotranscriptome Remodeling and is Reversed by Acetyl-carnitine

city: Irvine, CA

first: Amal

last: Alachkar

address: 355 Med Surge II

institute: University of California Irvine

summary: Intergenerational stress increases lifetime susceptibility to depression and other psychiatric disorders. Whether intergenerational stress transmission is a consequence of in-utero neurodevelopmental disruptions or early-life mother-infant interaction is largely unknown, due to the complexity, superposition, and inseparability between the prenatal and postnatal mechanisms. Here we show that prenatal stress, through exposing pregnant mice to predator scent, induces depressive-like behavior and social deficits. Cross-fostering experiments indicate divergent and convergent mechanisms of both in utero and early-life parenting environments and support a two-hit model of stress transmission. According to this model, prenatal stress (first-hit) primes brain metabolome and transcriptome (metabotranscriptome), and increases vulnerability to the second-hit in early life, triggered by poor caregiving by the traumatized mothers. Metabolomics, transcriptomic and bioinformatics analyses reveal mechanisms that involve stress- and hypoxia- response metabolic pathways in the brains of the newborn mice, likely through the production of the epigenetic modifiers 2-Hydroxyglutaric acid and succinic acid. These responses produce long-lasting alterations in mitochondrial-energy metabolism, and epigenetic processes pertaining to DNA and chromatin modifications. We demonstrate that an early pharmacological intervention – correction of the mitochondria metabolism, and epigenetic modifications with acetyl-L-carnitine (ALCAR) supplementation - produces long-lasting protection against the behavioral deficits associated with intergenerational transmission of traumatic stress.

overall_design: Stress vs. control

first: Sammy

last: Alhassen

first: Siwei

last: Chen

first: Lamees

first: Alvin

last: Phan

first: Mohammad

last: Khoudari

first: Angele

last: De Silva

first: Huda

last: Barhoosh

first: Zitong

first: Chelsea

last: Parrocha

first: Emily

last: Shapiro

first: Charity

last: Henrich

first: Zicheng

first: Leon

last: Mutesa

first: Pierre

last: Baldi

first: Geoffrey

last: Abbott


title: Defining the transcriptional regulon of ChvI in Caulobacter crescentus

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

summary: We sought to define the transcriptional regulon of the ChvI response regulator in Caulobacter crescentus. This study compares gene expression between ∆chvI cells and cells overexpressing the constitutively-active chvI(D52E) mutant. Our work provides a global view of the genes directly and indirectly regulated by the ChvGI two-component system in C. crescentus.

overall_design: 6 replicates of Caulobacter cresentus ∆chvI EV and ∆chvI chvI(D52E)++ cultures were grown in PYE + 0.15% xylose before total RNA extraction using TRIzol. RNA-seq reads were mapped to the NA1000 reference genome (CP001340).

first: Benjamin

last: Stein

first: Aretha

last: Fiebig


title: Generation of caudal-type serotonin neurons and hindbrain fate organoids from hPSCs

city: Bongmyeongdong

first: Vincencius

last: Vidyawan

state: Cheonan

address: 25, Bongjeong-ro, Dongnam-gu, Cheonan-si, 31151, Korea

department: Department of Integrated Biomedical Science

country: South Korea

institute: Soonchunhyang Institute of Medi-bio Science (SIMS)

summary:
Serotonin (5-HT) neurons, the major components of the raphe nuclei, arise from ventral hindbrain progenitors. Based on the anatomical location and axonal projection, 5-HT neurons are coarsely divided into rostral and caudal groups. Here, we propose a novel strategy to generate hindbrain 5-HT neurons from human pluripotent stem cells (hPSCs), which involves the formation of ventral-type neural progenitor cells (NPCs) and stimulation of the hindbrain 5-HT neural development. A caudalizing agent, retinoid acid (RA), was used to direct the cells into the hindbrain cell fate.
Approximately 30-40% of hPSCs successfully developed into 5-HT-expressing neurons using our protocol, with the majority acquiring a caudal rhombomere identity (r5-8). We further modified our monolayer differentiation system to generate 5-HT neuron-enriched hindbrain-like organoids. We have also suggested downstream applications of our 5-HT monolayer and organoid cultures to study neuronal response to gut microbiota. Our methodology could become a powerful tool for future studies related to 5-HT neurotransmission.

overall_design: To investigate the regional identity of the 5-HT neurons, we performed a transcriptome analysis by comparing the microarray profiles from undifferentiated hESCs (group E), non-patterned neurons (group N; differentiation day 25), and 5-HT neurons (group S; differentiation day 30). For each sample group (S, N, and E), samples were collected from three independent cultures that each consisted of 3 wells of 24-well plate. Total RNA was isolated using TRIZOL (Life Technology), and RNA quality was checked by OD 260/280 ratio and analyzed by Agilent 2100 Bioanalyzer, Transcriptome analysis was executed using The Affymetrix Whole Transcript (WT) Expression Array, cDNA was synthesized using the GeneChip WT Amplification kit.

first: Parvin

last: Valiulahi

first: Jae-won

last: Shim


title: Transcriptomic profiling of caruncular and cotyledonary tissues of 83 days fetuses in response to early maternal nutrient supplementation

city: Auburn

first: Wellison

middle: J. S.

last: Diniz

state: Alabama

address: CASIC Building 559 Devall Drive Auburn University, 205

department: Animal Sciences

institute: Auburn University

summary: We measured the gene expression profiles of maternal (caruncular; CAR) and fetal (cotyledonary; COT) portions of the placenta to identify differentially expressed genes (DEG), biological processes (BP), and pathways underlying placental development and function in response to early maternal nutrition. To this end, we used the RNA-Seq-based differential expression analysis of bovine placental tissues. The factors examined included vitamin and mineral supplementation (VTM or NoVTM) and rate of gain (low gain – LG or moderate gain – MG). The treatments were arranged as follows: (1) no vitamin and mineral supplementation and low gain (NoVTM_LG, n = 9); (2) vitamin and mineral supplementation and low gain (VTM_LG, n = 9); (3) no vitamin and mineral supplementation and moderate gain (NoVTM_MG, n = 9), and (4) vitamin and mineral supplementation and moderate gain (VTM_MG, n = 8). On day 83 ± 0.27 of gestation the uteroplacental tissues were collected through ovariohysterectomy and the largest placentome closest to the fetus was collected. Then, maternal (CAR) and fetal (COT) portions were manually dissected, snap-frozen, and stored at −80 °C. After RNA quality control, read mapping was performed with STAR aligner to the bovine ARS-UCD1.2 reference genome.  Genes with expression values lower than 1 count per million in 50% of the samples were filtered out. After filtering, the genes of CAR and COT tissues were analyzed using the DESeq2 v.1.22.1 software to identify DEGs. The DESEq2 model was used to measure the treatment effect while controlling for batch effect differences that included the surrogated variables (sva) and the heifer’s birthplace (farm of origin). Genes were identified as differentially expressed for each one of the contrasts when the adjusted p-value (padj) cutoff < 0.1 and classified as up- or down-regulated based on the sign of the log2 fold change.   We identified 267 unique DEGs throughout all tissues and group contrasts. The over-represented functions are essential to fetal growth and development, and included fatty acid metabolism, hormone synthesis, nutrient transport, energy metabolism, and biosynthesis of amino acids.

overall_design: Angus-cross heifers (n = 35) were randomly assigned by initial body weight (X ̅  = 359.5 ± 7.1 kg) to a 2×2 factorial arrangement of treatments. The factors examined included vitamin and mineral supplementation (VTM or NoVTM) and rate of gain (low gain – LG or moderate gain – MG). The treatments were arranged as follows: (1) no vitamin and mineral supplementation and low gain (NoVTM_LG, n = 9); (2) vitamin and mineral supplementation and low gain (VTM_LG, n = 9); (3) no vitamin and mineral supplementation and moderate gain (NoVTM_MG, n = 9), and (4) vitamin and mineral supplementation and moderate gain (VTM_MG, n = 8).  Diets were delivered once daily via total mixed ration and consisted of triticale hay, corn silage, modified distillers grains plus solubles, ground corn, and if indicated by treatment, mineral premix. To achieve MG (0.79 kg/d), heifers were fed the total mixed ration with the addition of the starch-based protein/energy supplement (a blend of ground corn, dried distillers grains plus solubles, wheat midds, fish oil, urea, and ethoxyquin). The LG heifers were maintained on the basal total mixed ration and targeted to gain 0.28 kg/d. The VTM treatment started 71 to 148 days before artificial insemination by providing 0.45 kg/heifer daily of a ground corn and vitamin and mineral premix (Purina Wind & Rain  Storm All-Season 7.5 Complete, Land O’Lakes, Inc., Arden Hills, MN). Based on the VTM starting date, heifers were assigned to one of seven breeding groups so that the supplementation period was at least 60 days for all. At breeding, heifers were randomly assigned to either LG or MG treatments within their respective VTM treatment. Heifers were bred by artificial insemination using female-sexed semen from a single sire. The VTM and rate of gain treatments were carried out until day 83 ± 0.27 of gestation, when uteroplacental tissues were collected through ovariohysterectomy. After QC, 29 and 31 samples (seven or eight samples per group) remained for further analyses from CAR and COT, respectively.   To make all pair-wise comparisons between the four treatment groups, six contrasts were created as follows: (1) VTM_MG vs. NoVTM_LG, (2) VTM_MG vs. VTM_LG, (3) VTM_MG vs. NoVTM_MG, (4) VTM_LG vs. NoVTM_LG, (5) VTM_LG vs. NoVTM_MG, (6) NoVTM_MG vs. NoVTM_LG. Multiple testing adjustment of the p-values (padj) was adopted using the Benjamini–Hochberg procedure for false discovery rate (FDR).

first: Lawrence

middle: P

last: Reynolds

first: Alison

middle: K

last: Ward

first: Joel

middle: S

last: Caton

first: Carl

middle: R

last: Dahlen


title: Epigenome-wide study of brain DNA methylation following acute opioid intoxication

city: Baltimore

first: Brion

last: Maher

state: MD

address: 624 N. Broadway

department: Mental Health

institute: Johns Hopkins Bloomberg School of Public Health

type: Methylation profiling by high throughput sequencing

summary: Opioid abuse poses significant risk to individuals in the United States and epigenetic changes are a leading potential biomarker of opioid abuse. Current evidence, however, is mostly limited to candidate gene analysis in whole blood. Here, we provide Illumina HumanMethylationEPIC array data generated in dorsolateral prefrontal cortex tissue from 153 deceased invidiuals: 72 who died of acute opioid intoxication, 53 psychiatric controls, and 28 normal controls. Using these data, we conducted an epigenome-wide association study and identified one CpG site within a gene (NTN1) that may be related to opioid use. We also detected accelerated PhenoAge in opioid samples compared to control samples.

overall_design: Genome-wide DNA methylation data were measured in postmortem tissue from the dorsolateral prefrontal cortex with the HumanMethylationEPIC array. The dataset includes 153 tissue samples (72 opioid samples; 53 psychiatric controls; 28 normal controls).


title: Defining the lineage of thermogenic perivascular adipose tissue [PVAT v IWAT]

city: Philadelphia

first: Patrick

last: Seale

state: PA

address: Smilow Center for Translational Research, 12th Floor 3400 Civic Center Blvd.

institute: University of Pennsylvania

summary: Brown adipose tissue can expend large amounts of energy and thus increasing its amount or activity is a promising therapeutic approach to combat metabolic disease. In humans, major deposits of brown fat cells are found intimately associated with large blood vessels, corresponding to perivascular adipose tissue (PVAT). However, the cellular origins of PVAT are poorly understood. We applied single cell transcriptomic analyses, ex vivo adipogenesis assays, and genetic fate mapping to determine the identity of perivascular adipocyte progenitors. In mice, we found that thoracic PVAT develops from a fibroblastic lineage, consisting of progenitor cells (Pdgfra+; Ly6a+; Pparg-) and preadipocytes (Pdgfra+; Ly6a+; Pparg+). Progenitor and preadipocyte cells in PVAT shared transcriptional similarity with analogous cell types in inguinal white adipose tissue (IWAT), pointing towards a conserved hierarchical structure of adipose lineage cells. Interestingly, the aortic adventitia of adult animals contained a novel population of adipogenic smooth muscle cells (SMCs) (Myh11+; Pdgfra-; Pparg+) that contributed to perivascular adipocyte formation. Similarly, human PVAT contained presumptive fibroblastic and SMC-like adipocyte progenitors, as revealed by single nucleus RNAseq. Taken together, these studies define distinct populations of progenitor cells for thermogenic PVAT, providing a foundation for developing strategies to augment brown fat activity

overall_design: Transcriptome (mRNA) profiles of FACS isolated cell populations from the thoracic aorta perivascular fat (PVAT Progenitor cells and PVAT Preadipocytes) and inguinal white adipose tissue (IWAT) (DPP4+ Progenitors and ICAM1+ PreAdipocytes) from wild type 3 day old (P3) mixed male and female mouse pups were generated by deep sequencing, in triplicate, followed by DESeq2 analysis for differential expression of genes between the various groups.

first: Anthony

last: Angueira

first: Alexander

last: Sakers


title: Defining the lineage of thermogenic perivascular adipose tissue [Pup Aorta]

summary: Brown adipose tissue can expend large amounts of energy and thus increasing its amount or activity is a promising therapeutic approach to combat metabolic disease. In humans, major deposits of brown fat cells are found intimately associated with large blood vessels, corresponding to perivascular adipose tissue (PVAT). However, the cellular origins of PVAT are poorly understood. We applied single cell transcriptomic analyses, ex vivo adipogenesis assays, and genetic fate mapping to determine the identity of perivascular adipocyte progenitors. In mice, we found that thoracic PVAT develops from a fibroblastic lineage, consisting of progenitor cells (Pdgfra+; Ly6a+; Pparg-) and preadipocytes (Pdgfra+; Ly6a+; Pparg+). Progenitor and preadipocyte cells in PVAT shared transcriptional similarity with analogous cell types in white adipose tissue, pointing towards a conserved hierarchical structure of adipose lineage cells. Interestingly, the aortic adventitia of adult animals contained a novel population of adipogenic smooth muscle cells (SMCs) (Myh11+; Pdgfra-; Pparg+) that contributed to perivascular adipocyte formation. Similarly, human PVAT contained presumptive fibroblastic and SMC-like adipocyte progenitors, as revealed by single nucleus RNAseq. Taken together, these studies define distinct populations of progenitor cells for thermogenic PVAT, providing a foundation for developing strategies to augment brown fat activity

overall_design: Transcriptome (mRNA) profiles of FACS isolated cell populations from the aorta and perivascular fat (intermediate cells, progenitor cells, preadipocytes, and smooth muscle cells (SMC)) from wild type (WT) 3 day old (P3) mixed male and female mouse pups were generated by deep sequencing, in triplicate, followed by DESeq2 analysis for differential expression of genes between the various groups.


title: Comparison of splicing tools

city: Amsterdam

first: Ittai

middle: Bernardo

last: Muller

address: De Boelelaan 1118

institute: Amsterdam UMC

summary: Study that compares three commonly used event-based differential splicing tools: rMATS, MISO, and SUPPA2

overall_design: Three tools were investigated for their analysis speed, usage of RAM as well as CPU load average. Different datasets of varying read depth (30MM, 100MM, and 300MM, 2v2) and amount of replicates (2, 3, 10 replicates) were analysed with three differential splicing tools rMATS, MISO and SUPPA2.

first: I

middle: B


title: Defining the lineage of thermogenic perivascular adipose tissue

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Whole transcriptome analysis of mouse aortas and kidneys with or without deletion of the EGFR in endothelial cells after 18 weeks of high fat diet

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

country: Germany

institute: Martin Luther University - Halle-Wittenberg

summary: Vascular EGF receptors (EGFR) are supposed to be relevant for function and structure of arterial vessels. Recently, we showed in genetic mouse models that vascular smooth muscle (VSMC) EGFR is required for proper physiological function and structure as well as for pathophysiological alterations induced by angiotensin II or obesity. The importance of endothelial (EC) EGFR in vivo is unknown. Therefore we analyzed the impact of EC-EGFR knockout on vascular and renal function under control condition as well as in obesity in comparison to VSMC-KO.

overall_design:
RNASequencing of aorta and kidney samples from wild-type mice and mice with knock-out of their endothelial cells-EGFR. Mice were fed with standard or high fat diets (60% fat share of energy versus 10%).
Raw RNASequencing data were treated successively with HISAT2 (mapping) and featureCounts (counting).

first: Barbara

last: Schreier

first: Christian

last: Stern

last: Nolze

first: Sindy

last: Rabe

first: Sigrid

last: Mildenberger

first: Michael

last: Gekle


title: Chromosomal Silencing Induced by Xist Expression from Autosomal Transgenes

city: Irvine

first: Sha

last: Sun

state: CA

address: 4232 McGaugh Hall

department: Development and cell biology

institute: University of california Irvine

summary: Xist transgenes (Tg) integrated into an autosome can induce transcriptional silencing of flanking genes. We investigate an autosomal integration of Xist Tg that is compatible with mouse viability but causes male sterility in homozygous transgenic mice. We show ectopic Xist expression in the transgenic male cells along with a transcriptional reduction of genes clustered in two regions of Chromosome 1. RNA-seq and DNA Fluorescent in situ Hybridization (FISH) confirms that Xist Tg is associated with Chromosome 1.

overall_design: TgBAC8 mouse lines were generated and described previously as transgenic mice carrying 200 kb of sequence from the Xic including Xist (Sun et al. 2015). C57BL/6J-TgBAC8-2087 line was used in this study, for which Tg2087/+ mice were crossed to wildtype C57B1/6J mice to obtain offspring that contain littermates of transgenic (Tg2087/+) and wildtype (+/+) animals. Tail tip fibroblasts (TTF) were isolated from tail tip tissues of transgenic and wildtype mice from the same litter and grown in DMEM medium containing 10% FBS supplemented with MEM non-essential amino acids, 25mM HEPES pH 7.2-7.5, 0.1mM 2-mercaptoethanl, penicillin, and streptomycin. TTFs were then immortalized with Simian virus 40 large T cDNA following the protocol as previously described (Brown et al. 1986). Transgenic samples and wildtype (control) samples were processed in parallel following the same procedure for RNA-seq.

first: Ikrame

last: NACIRI

first: Shan

last: JIANG

first: Benjamin

last: LIN

first: Ali

last: MORTAZAVI

last: SUN

first: Chui-Ho

last: WEBB


title: Downregulation of anti-inflammatory A20 promotes immune escape of lung adenocarcinomas

city: Vienna

first: Herwig

last: Moll

address: Waehringer Strasse 13a

country: Austria

institute: Medical University of Vienna

summary: We found that the potent anti-inflammatory enzyme A20 is a potent tumor suppressor and hence often downregulated in human and mouse lung adenocarcinoma. Comparison of gene expression profiles of A20 expressing versus A20 deficient lung tumor tissue samples revealed that loss of A20 enhanced the cellular response to interferons. This hypersensitivity to interferons was responsible to drive immune evasion of A20 deficient lung adenocarcinomas. ,

overall_design: KRASG12D mutated, p53 and A20 deficient tumors were induced in mice via inhalation with a Cre recombinase expressing adenovirus. After 10 weeks, tumors were macroscopically dissected and RNA was processed for RNAseq analysis.

first: Kristina

last: Breitenecker


title: Defining the lineage of thermogenic perivascular adipose tissue [Adult Aorta]

first: Patrick

last: Seale

overall_design: Transcriptome (mRNA) profiles of FACS isolated cell populations from the aorta and perivascular fat ( intermediate cells, progenitor cells, and smooth muscle cell (SMC) populations SMC1 and SMC2) from wild type (WT) adult (13 week old) male mice were generated by deep sequencing, in triplicate, followed by DESeq2 analysis for differential expression of genes between the various groups.

first: Anthony

last: Angueira

first: Alexander

last: Sakers


title: PELP1/SRC-3-dependent regulation of metabolic kinases drives therapy resistant ER+ breast cancer [3D]

city: Minneapolis

first: Nuri

middle: Alpay

last: Temiz

state: MN

address: 2231 6th St SE

department: Masonic Cancer Center

institute: University of Minnesota

summary: Trascriptome analysis of mcf7 cell lines were performed

overall_design: MCF-7 PELP1 cells expressing LXSN, WT PELP1, or cytoplasmic (cyto) PELP1 were used to create tumorsphere 3D culture: Single cells were plated serum-free mammary epithelial basal medium containing 1% methylcellulose, 1% B27 supplement, 1% penicillin–streptomycin, 5 mg/mL insulin,  20 ng/mL EGF, 1 ng/mL hydrocortisone, and 100 mmol/L beta-mercaptoethanol in ultra-low attachment plates and cultured for 6 days prior to RNA isolation. RNA was extracted with RNAeasy Mini Kit and sequenced with Illumina HiSeq 2000

first: Carol

middle: E

last: Lange

first: Julie

middle: H

last: Ostrander


title: Nitazoxanide impairs mitophagy flux through ROS-mediated mitophagy initiation and lysosomal dysfunction in bladder cancer

status: Public on Mar 31 2021

city: Shen Zhen

first: Haiyan

state: Guang Dong

address: 47 Youyi Road, Luohu District

institute: The Third Affiliated Hospital of Shenzhen University (LuoHu Hospital Group)

summary: Bladder cancer is one of the most common malignancy in the urinary tract with high recurrence and drug resistance in clinics. Alternative treatments from existing drugs might be a promising strategy. Nitazoxanide (NTZ), an FDA-approved antiprotozoal drug, has got increasingly noticed because of its favorable safety profile and antitumor potential, yet the effects in bladder cancer and underlying mechanisms remain poorly understood. Herein, we find that NTZ induces mitochondrial damage and mitophagy initiation through PINK1-generated phospho-ubiquitin(pS65-Ub) and autophagy receptor-mediated pathway even in the absence of Atg5/Beclin1. Meanwhile, NTZ inhibits lysosomal degradation activity, leading to mitophagy flux impairment at late stage. Mitochondrial reactive oxygen species (ROS) production is critical in this process, as eliminating ROS with N-acetylcysteine (NAC) efficiently inhibits PINK1 signaling-mediated mitophagy initiation and alleviates lysosomal dysfunction. Co-treatment with NTZ and autophagy inhibitor Chloroquine (CQ) to aggravate mitophagy flux impairment promotes NTZ-induced apoptosis, while alleviation of mitophagy flux impairment with ROS scavenger reduced cell death. Moreover, we also discover a similar signaling response in the 3D bladder tumor spheroid after NTZ exposure. In vivo study reveals a significant inhibition of orthotopic bladder tumors with no obvious systemic toxicity. Together, our results uncover the anti-tumor activities of NTZ with the involvement of ROS-mediated mitophagy modulation at different stages and demonstrate it as a potential drug candidate for fighting against bladder tumors.

overall_design: Examination of mRNA profiles of MGHU3 cells with or without Nitazoxanide treatment


title: Prostate H3K4me3 ChIP-seq

city: Rennes

first: Fatima

last: SMAGULOVA

address: 9 av. Prof. Léon Bernard

country: France

institute: Irset - U1085

summary: Exposure to pesticide chlordecone is associated with high risk of prostate cancer.We hypothesised that changes in histone H3K4me3 could be involved in pathological processes in prostate induced by chlordecone. We exposed mice to chlordecone during embryonic development (E6.5-E15.5) and we analysed F1 progeny male epigenetic H3K4me3 marks in prostate tissue, as well as H3K4me3 in the prostate of F3 progeny to reveal the transgenerational effects resulting from the ancestral exposure to CD. We performed ChIP using H3K4me3 commercial antibody (Merck Millipore, 07-473) and pooled prostate tissues from 4 mice. DNA-protein complex was immunoprecipitated, eluted and DNA purified.

overall_design:
The DNA from ChIP, samples of F1 animals: 1. PS1 control 2. PS2 control 3. PS3 chlordecone 4. PS4 chlordecone 5. PS5 input
Four libraries (H3K4me3 ChIP) were prepared from prostate of F3 mice.  Two replicates from control-derived mice (C5, C7) and two replicates from CD-derived mice (K4, K11).

last: Smagulova

first: Louis

last: Legoff


title: Haploinsufficiency of the Sin3/HDAC corepressor complex member SIN3B causes a syndromic intellectual disability/autism disorder

city: Nantes

first: Alice

last: Mollé

address: 30 bd Jean Monnet

institute: University of Nantes

summary: Proteins involved in transcriptional regulation harbor a demonstrated enrichment of mutations in neurodevelopmental disorders. The Sin3 (Swi-independent 3)/histone deacetylase (HDAC) complex plays a central role in histone deacetylation and transcriptional repression. Among the two vertebrate paralogs encoding the Sin3 complex, SIN3A variants cause syndromic intellectual disability, but the clinical consequences of SIN3B haploinsufficiency in humans are uncharacterized. Here, we describe a syndrome hallmarked by intellectual disability, developmental delay, and dysmorphic facial features with variably penetrant autism spectrum disorder, congenital malformations, corpus callosum defects, and impaired growth caused by disruptive SIN3B variants. Using chromosomal microarray or exome sequencing, and through international data sharing efforts, we identified nine individuals with heterozygous SIN3B deletion or single-nucleotide variants. Five individuals harbor heterozygous deletions encompassing SIN3B that reside within a ~230 kb minimal region of overlap on 19p13.11, two individuals have a rare nonsynonymous substitution, and two individuals have a single-nucleotide deletion that results in a frameshift and predicted premature termination codon. To test the relevance of SIN3B impairment to measurable aspects of the human phenotype, we disrupted the orthologous zebrafish locus by genome editing and transient suppression. The mutant and morphant larvae display altered craniofacial patterning, commissural axon defects, and reduced body length supportive of an essential role for Sin3 function in growth and patterning of anterior structures. To investigate further the molecular consequences of SIN3B variants, we quantified genome-wide enhancer and promoter activity states by using H3K27ac ChIP-seq. We show that, similar to SIN3A mutations, SIN3B disruption causes hyperacetylation of a subset of enhancers and promoters in peripheral blood mononuclear cells. Together, these data demonstrate that SIN3B haploinsufficiency leads to a hitherto unknown intellectual disability/autism syndrome, uncover a crucial role of SIN3B in the central nervous system, and define the epigenetic landscape associated with Sin3 complex impairment.

overall_design: H3K27ac modifications in PBMCs from individuals carrying a SIN3B or SIN3A deletion and healthy family members

first: Xenia

last: Latypova

first: Marie

last: Vincent

first: Oluwadamilare

middle: A

last: Adebambo

first: Cynthia

last: Fourgeux

first: Tahir

middle: N

last: Khan

first: Alfonso

last: Caro

first: Monica

last: Rosello

first: Dmitriy

last: Niyazov

first: Damien

last: Lederer

last: Deprez

first: Yline

last: Capri

first: Peter

last: Kannu

first: Anne

middle: C

last: Tabet

first: Jonathan

last: Levy

first: Emmelien

last: Aten

first: Nicolette

last: den Hollander

first: Miranda

last: Splitt

first: Jagdeep

last: Walia

first: Ladonna

middle: L

last: Immken

first: Pawel

last: Stankiewicz

first: Kirsty

last: McWalter

first: Sharon

last: Suchy

first: Raymond

last: Louie

first: Shannon

last: Bell

first: Roger

last: Stevenson

first: Justine

last: Rousseau

first: Catherine

last: Willem

first: Christelle

last: Retiere

first: Xiang-Jiao

last: Yang

first: Philippe

last: Campeau

first: Francisco

last: Martinez

first: Jill

last: Rosenfeld

first: Cédric

last: Le Caignec

first: Sébastien

last: Küry

first: Sandra

last: Mercier

first: Kamran

last: Moradkhani

first: Solène

last: Conrad

first: Thomas

last: Besnard

last: Cogné

first: Nicholas

last: Katsanis

first: Stéphane

last: Bézieau

first: Jeremie


title: Dynamic post-transcriptional regulation by Mrn1 links cell wall homeostasis to mitochondrial structure and function

city: Berkeley

middle: T

last: Ingolia

email: ingolia@berkeley.edu, nick@ingolia.org

address: 1 Barker Hall # 3202

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary: The RNA-binding protein Mrn1 in Saccharomyces cerevisiae targets over 300 messenger RNAs, including many involved in cell wall biogenesis. The impact of Mrn1 on these target transcripts is not known, however, nor is the cellular role for this regulation. We have shown that Mrn1 represses target mRNAs through the action of its disordered, asparagine-rich amino-terminus. Its endogenous targets include the paralogous SUN domain proteins Nca3 and Uth1, which affect mitochondrial structure and function as well as the cell wall, as well as other nuclear-encoded mitochondrial proteins. While loss of MRN1 has no effect on fermentative growth, we found that mrn1Δ yeast adapt more quickly to respiratory conditions. These cells also have enlarged mitochondria in fermentative conditions, an observation that may explain their faster switch to respiration. Our analyses indicated that Mrn1 acts as a hub for integrating cell wall integrity and mitochondrial biosynthesis in a carbon-source responsive manner.

overall_design: mRNA profiling in wild-type and mrn1Δ budding yeast, during fermentative (glucose) and respiratory (ethanol + glycerol) growth

first: Kendra

last: Reynaud

first: Molly

last: Brothers

first: Michael

last: Ly


title: HIV-1-driven aberrant host gene expression may contribute to HIV-1 persistence

city: New Haven

first: Ya-Chi

last: Ho

state: CT

address: BCMM 349, 295 Congress Ave, BCMM 349

department: Microbial Pathogenesis

institute: Yale University School of Medicine

summary: Using HIV-1 RNASortSeq, we identified HIV-1-infected cells containing inducible HIV-1 for RNAseq from resting CD4+ T cells treated with PMA/ionomycin for 16 hours from eight antiretroviral therapy treated, virally suppressed, HIV-1-infected individuals. Using custom bioinformatic pipeline, we identified HIV-1 genomic RNA, host RNA and HIV-1-host chimeric RNA junctions.

overall_design: We used custom bioinformatic pipelines to identify HIV-1 RNA sequences and HIV-1-host chimeric RNA sequences to examine HIV-1-host RNA interactions.

first: C

last: Talbot Jr.

first: Ales

last: Varabyou


title: Chromatin accessibility in human K562 erythroleukemia cells profiled upon heat shock, recovery, and heat-induced transcriptional memory

city: Stockholm

first: Anniina

last: Vihervaara

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: KTH Royal Institute of Technology

summary: ATAC-seq in human K562 erythroleukemia cells that were either unconditioned (s_uC and HSS_uC), preconditioned with a single heat shock exposure (s_pC), or preconditioned with multiple heat exposures (HSS_pC). After two day recovery from the preconditioning, during which the cells underwent two mitotic divisions, the cells were additionally subjected to a single heat shock to analyze heat-induced changes in chromatin accessibility in unconditioned versus preconditioned cells.

overall_design: ATAC-seq measures of chromatin accessibility in human K562 cells. The cells were either untreated, heat shocked to monitor the changes that occur at chromatin accessibility during the heat-induced transcriptional reprogramming, or allowed to recover 48-hours from a single (s_) or multiple (HSS_) heat shock exposured. Additionally, the kinetics of heat-induced changes to chromatin state were compared between uncoditioned and preconditioned cells.

first: John

last: Lis


title: Macrophages of embryonic origin function during early life to determine host iNKT cell levels at barrier surfaces I

city: Boston

last: Gensollen

address: 77 Avenue Louis Pasteur

department: Gastroenterology

institute: Brigham and Women's Hospital/Harvard Medical School

summary: It is increasingly recognized that immune development within mucosal tissues is under the control of environmental factors during early life. However, the cellular mechanisms that underlie such temporally and regionally restrictive governance of these processes is unclear. Here, we uncover an extrathymic pathway of immune development within the colon that is controlled by embryonic, but not bone-marrow derived, macrophages which determines the ability of these organs to receive invariant natural killer T (iNKT) cells and allow them to establish local residency. Consequently, early life perturbations of fetal-derived macrophages result in persistent decreases of mucosal iNKT cells and is associated with later life susceptibility or resistance to iNKT cell associated mucosal disorders. These studies uncover a host developmental program orchestrated by ontogenically distinct macrophages that is regulated by microbiota and reveal an important post-natal function of macrophages that emerge in fetal life.

overall_design: Macrophages from colon tissue at two time points.

first: Xi

last: Lin

first: Ting

last: Zhang

first: Michal

last: Pyzik

first: Peter

last: See

first: Jonathan

last: Glickman

first: Florent

last: Ginhoux

first: Matthew

last: Waldor

first: Marko

last: Salmi

first: Pia

last: Rantakari

first: Richard

last: Blumberg


title: Bacterial defenses against natural antibiotics promote collateral resilience to clinical antibiotics

city: Pasadena

first: Dianne

last: Newman

address: 1200 E California Blvd, MC 147-75

institute: Caltech

summary: To characterize the defense mechanisms P. aeruginosa has evolved in response to its most toxic phenazine, pyocyanin, we performed a genome-wide transposon sequencing (TnSeq) screen in which the mutant library was exposed to PYO under carbon starvation in order to maximize PYO toxicity, and genes for which transposon mutants were significantly enriched or depleted were identified.

overall_design: Assessment of transposon mutant frequency per gene in a pooled library of approximately 145,000 random Tn5 transposon insertion mutants, following exposure to 100 µM pyocyanin for 26 hours in the absence of a carbon source, or to the same conditions without pyocyanin. The experiment was performed with two biological replicates.

first: Lucas

last: Meirelles

first: Elena

last: Perry

first: Megan

last: Bergkessel


title: Constrained chromatin accessibility in PU.1-mutated agammaglobulinemia patients

first: James

last: Garifallou

state: Pennsylvania

address: 3615 Civic Center Boulevard, ARC1014

department: Neonatology

institute: Children's Hospital of Philadelphia

summary: Using CITE-seq we measured expression of 132 proteins on the cell surfaces of single human bone marrow aspirate cells. Expression of each protein was normalized with a isotype-specific control on a single cell basis. Principal compenent analysis of normalized proteins was used to produce UMAP plots that clustered like cell types. After identifying pro-B cells on UMAP plots and further refining these populations by filtering on CD19 expression and absent CD20/IgM expression, we identified differentially expressed genes between patient and control pro-B cells.

overall_design: 2 CITE-seq data sets were analyzed

first: Michael

last: Gonzalez

first: Carole

last: Le Coz

first: Neil

last: Romberg


title: RUNX1/ETO and mutant KIT both contribute to programming the transcriptional and chromatin landscape in t(8;21) AML

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

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

overall_design: Refer to individual Series


title: Cattle lymph nodes: Control  vs. Larva tick-infested;  Control vs. Adult tick-infested; Larva tick-infested vs. Adult tick-infested

city: Pretoria

first: Dave

middle: Kenneth

last: Berger

state: Gauteng

address: Lynnwood Road

department: Plant and Soil Science

country: South Africa

institute: University of Pretoria

summary: Transcriptional profiling of lymph nodes of three cattle breeds (Bonsmara, Brahman, Holstein-Friesian) in response to the cattle tick (Rhipicephalus microplus) larvae and adult infestation. Emphasis is placed on firstly, comparing transcriptional responses within a cattle breed, before and after infestation, and secondly, comparing differentially expressed genes common between the breeds.

overall_design: Three-condition experiment. Control (baseline)  vs. Larva tick-infested;  Control (baseline) vs. Adult tick-infested; Larva tick-infested vs. Adult tick-infested. Biological replicates: 3 Bonsmara baseline replicates; 3 Bonsmara larvae infested replicates; 3 Bonsmara adult infested replicates; 3 Brahman baseline replicates; 3 Brahman larva-infested replicates; 3 Brahman adult-infested replicates; 3 Holstein-Friesian baseline replicates; 3 Holstein-Friesian larva-infested replicates; 3 Holstein-Friesain adult-infested replicates.

first: Christine

last: Maritz-Olivier

first: Luïse

last: Robbertse

first: Christian

last: Stutzer

first: Sabine

last: Richards

first: Andrew

last: Leisewitz

first: Jan

last: Crafford


title: Gene expression analysis of bladder cancer cell line, its BCG resistant and AR knockdown subline.

city: Rochester

first: Taichi

last: Mizushima

state: NY

address: 601 Elmwood

institute: University of Rochester

summary: BCG resistant and AR konckdown subline from UMUC3 were compared with the original cell line.

overall_design: These sublines were awnalyzed by the Affymetrix GeneChip™ Human Gene 2.0 ST Array platform. Array data was processed by Affymetrix Exon Array Computational Tool. Two replicates were performed.

first: Satoshi

last: Inoue

first: Hiroshi

last: Miyamoto


title: Transcriptional response to low temperature in Thioalkalivibrio versutus AL2 and Tv. nitratis ALJ2

first: Anne-Catherine

last: Ahn

address: Science Park 904

department: IBED

institute: University of Amsterdam

summary: Transcriptional response to growth at low temperature in the haloalkaliphilic sulfur-oxidizer Thioalkalivibrio versutus AL2 and Tv. nitratis ALJ2 by performing RNA-seq analysis

sample_organism:
Thioalkalivibrio nitratis
Thioalkalivibrio versutus AL 2

overall_design: Transcriptomic analysis was performed using Ion Proton platform with an Ion PI Chip v3 on continious culture samples of Thioalkalivibrio versutus AL2 and Tv. nitratis ALJ2 both grown  in quadruplicates at 10 and 30°C.

first: Gerard

last: Muyzer


title: Genomic instability is an early event driving chromatin organization and “escape” from oncogene-induced senescence

city: Göttingen

first: Argyris

last: Papantonis

address: Robert-Koch-Straße 40

department: Institute of Pathology

institute: University Medical Centre Göttingen

summary: Oncogene-induced senescence (OIS) is an inherent and important tumor suppressor mechanism. However, if not timely removed via immune surveillance, senescent cells will also present a detrimental side. Although this has mostly been attributed to the senescence-associated-secretory-phenotype (SASP) of these cells, we recently suggested that “escape” from the senescent state represents another unfavorable outcome. Here, we exploit genomic and functional data from a prototypical human epithelial cell model carrying an inducible CDC6 oncogene to identify an early-acquired recurrent chromosomal inversion, which harbors a locus encoding the circadian transcription factor BHLHE40. This inversion alone suffices for activation of BHLHE40 upon CDC6 induction and for driving cell cycle re-entry and malignant transformation. In summary, we provide strong evidence in support of genomic instability underlying “escape” from oncogene-induced senescence.

overall_design: In situ Hi-C performed in two states (“OFF” and “Bypass”) of a single cell-derived HBEC clone carrying a CRISPR-generated >3-Mbp inversion on chr3 that encompasses the BHLHE40 gene locus

first: Vassilis

middle: G

last: Gorgoulis

first: Yajie

last: Zhu


title: Microbially competent 3D skin - a novel test system for studying host-microbe interaction

city: Berlin

first: Lisa

middle: Lotte

last: Lemoine

address: Max-Dohrnstraße 8-10

institute: German Federal Institute for Risk Assessment

summary: The skin`s microbiome is predominantly commensalic, harbouring a metabolic potential far exceeding that of its host. While toxicologically relevant there is still a lack of suitable models.  We now report on a new biologically characterised co-culture that allows studying microbe-host interactions for extended periods of time  in situ  . The system is based on a commercially available 3D skin model. In a proof of concept this model was colonised with single and mixed cultures of two selected skin commensals. Two different methods were used to quantify the bacteria on the surface of the skin models. While  M. luteus  established a stable co-culture,  P. oleovorans  maintained slow continuous growth over the 8 day cultivation period. A detailed skin transcriptome analysis showed bacterial colonisation leading to up to 3318 significant changes. Additionally FACS, ELISA and Western blot analyses were carried out to analyse secretion of cytokines and growth factors. Changes found in colonised skin were varied dependent on the bacterial species used and comprised immunomodulatory functions, such as secretion of IL-1α/β, Il-6, antimicrobial peptides and increased gene transcription of IL-10 and TLR2. The colonisation also influenced the secretion of many grows factors as VFGFA and FGF2. Notably, many of these changes have already previously been associated with the presence of skin commensals. Concomitantly the model gained first insights on the microbiome’s influence on skin xenobiotic metabolism (i.e., CYP1A1, CYP1B1 and CYP2D6) and olfactory receptor expression. The system provides urgently needed experimental access for assessing the toxicological impact of the microbiome’s xenobiotic metabolism  in situ.

overall_design: Development of a microbial competent skin model and its characterization. For this purpose we analyzed transcription of co-cultures of EpiDermFT™ (MatTek) skin tissue and two different skin isolates (M. luteus and P. oleovorans) using the Affymetrix Human Clariom S. Array data was processed by the company ATLAS Biolabs GmbH (Friedrichstraße 147, 10117 Berlin, Germany). Three biological replicates were performed for each condition.

first: Tewes

last: Tralau

first: Ralf

last: Dieckmann

first: Sascha

last: Al Dahouk

first: Andreas

last: Luch


title: Gene expression profiles in colon cancer spheroids treated with a ROCK inhibitor

city: Chuo-ku

first: Hirokazu

last: Ohata

state: Tokyo

address: Tsukiji 5-1-1

country: Japan

institute: National Cancer Center Research Institute

summary: Spheroid cells derived from colon cancer patients was treated with Y-27632, a ROCK inhibitor, and we have performed whole genome microarray expression assay.

overall_design: Human colon cancer spheroids derived from two colon cancer patients were treated with 20 microM Y-27632 for 7 days.


title: CD22 blockage restores age-related impairments of microglia surveillance capacity

status: Public on Mar 30 2021

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

institute: F. Hoffmann - La Roche AG

summary: We report that antibody-mediated CD22 blockage leads to an altered transcriptomic signature profile which, by further evaluating the affected genes, resembles a homeostatic phenotype.

overall_design: Assessment of RNA expression levels following antibody-mediated blockage of CD22 in human iPSC-derived macrophages.

first: Erich

last: Kueng

first: Martin

last: Ebeling

first: Simon

last: Gutbier

first: Eva

last: Harde


title: Next generation sequencing of mRNA of T-PLL patients and normal T-cell fractions

city: Rotterdam

first: Stefan

middle: J.

last: Erkeland

state: Zuid-Holland

address: Dr. Molewaterplein 40

department: Department of Immunology

institute: Erasmus University Medical Center

summary: T cell prolymphocytic leukemia (T-PLL) is mostly characterized by aberrant expansion of small to medium sized pro-lymphocytes with a mature post-thymic phenotype, high aggressiveness of the disease and poor prognosis. However, T-PLL is more heterogeneous with a wide-range of clinical, morphological, and molecular features, which occasionally impedes the diagnosis. We hypothesized that T-PLL consists of phenotypic and genotypic subgroups that may explain the heterogeneity of the disease. We found that T-PLL does not show a clear skewing in T cell receptor alpha (TRA), TRB gene usage and CDR3 stereotypy. In addition, multi-dimensional immuno-phenotyping and gene expression profiling did not reveal clear T-PLL subgroups. However, based on miRNA expression profiles, T-PLL samples did clearly cluster in subgroups. We identified 35 miRNAs that were aberrantly expressed in T-PLL with miR-200c/141 as the most differentially expressed cluster. High miR-200c/141 expression was significantly correlated with increased white blood cell counts and poor survival. Furthermore, we found that overexpression of miR-200c/141 in T-PLL correlated with downregulation of their targets ZEB2 and TGFβR3, indicating that the TGFβ pathway is affected. Our results thus highlight the emerging role for aberrantly expressed oncogenic miRNAs in T-PLL, thereby paving the way for new therapeutic targets in this disease.

overall_design: mRNA seq of T-PLL patients compared to normal T cell fractions

middle: J

first: Christiaan

last: Stavast

first: Anton

middle: W

last: Langerak


title: Macrophages of embryonic origin function during early life to determine host iNKT cell levels at barrier surfaces

first: Thomas

last: Gensollen


title: Macrophages of embryonic origin function during early life to determine host iNKT cell levels at barrier surfaces II

overall_design: Specific pathogen free and germ free macrophages

first: Xi

last: Lin

first: Ting

last: Zhang

first: Michal

last: Pyzik

first: Peter

last: See

first: Jonathan

last: Glickman

first: Florent

last: Ginhoux

first: Matthew

last: Waldor

first: Marko

last: Salmi

first: Pia

last: Rantakari

first: Richard

middle: S

last: Blumberg


title: Impact of negative energy balance on transcriptomic profiles of three endometrial cell types isolated by laser capture microdissection in postpartum dairy cows

status: Public on Mar 26 2021

city: JOUY-en-JOSAS

first: gilles

last: charpigny

state: ILe de France

address: domaine de Vilvert

department: Physiologie Animale Systeme Elevage

institute: INRAE

summary: The three different main cells types of the endometrium, have very different patterns of gene expression. The severity of NEB after calving is associated with changes in gene expression at time of breeding. Specific alterations in GEs are associated with activation of pro-inflammatory mechanisms. Concomitantly, changes in the expression of genes related to cell to cell interactions and maternal recognition of pregnancy takes place in ST. The combination of these effects possibly altering the uterine environment and embryo maternal interactions may negatively influence the establishment of pregnancy.

overall_design: Twelve Swedish Red cows receiving a control diet or a mild restricted diet to induce differences of energy balance were categorized into mild (MNEB, n = 5) and severe negative energy balance (SNEB, n = 4). The three endometrial cell types: luminal (LE), glandular (GE) epithelium and stroma (ST) were collected by laser microdissection from endometrial biopsies performed at 80 days postpartum.

first: Wiruntita

last: Chankeaw

first: Sandra

last: Lignier

first: Christophe

last: Richard

first: Theodoros

last: Ntallaris

first: Mariam

last: Raliou

first: Yongzhi

last: Guo

first: Damien

last: Plassard

first: Claudia

last: Bevilacqua

first: Olivier

last: Sandra

first: Göran

last: Andersson

first: Patrice

last: Humblot

first: Gilles

last: Charpigny


title: Frozen bone marrow (BM) samples belonging to pediatric acute myeloid leukemia (AML) cohort analyzed by Human Transcriptome Array 2.0 (HTA 2.0)

city: Catania

first: Daniele

middle: F

last: Condorelli

state: Italy

address: Via S. Sofia 64

department: Biomedical and Biotechnological Sciences

country: Italy

institute: University of Catania

summary: We analyzed 12 pediatric AML bone marrow RNA in order to determine the whole transcriptome expression levels  by HTA 2.0 microarrays.  Results provided insights into the regulation, at transcript level, of driver genes involved in primary chemiotherapy failure (after two cycles of Induction phase; blasts>5%).

overall_design: Frozen bone marrow (BM) samples belonging to pediatric cohort have been collected. Four of these patients, named Primary Induction Failure (PIF),  failed to achieve complete remission (CR) after two cycles of induction therapy (ICE), reporting all but one a blast rate between 10-20%. On the contrary, other 8 cases were named Primary Induction Responses (PIR).


title: Defining the lineage of thermogenic perivascular adipose tissue [Thoracic PVAT]

city: Philadelphia

first: Patrick

last: Seale

address: Smilow Center for Translational Research, 12th Floor 3400 Civic Center Blvd.

institute: University of Pennsylvania

summary: Brown adipose tissue can expend large amounts of energy and thus increasing its amount or activity is a promising therapeutic approach to combat metabolic disease. In humans, major deposits of brown fat cells are found intimately associated with large blood vessels, corresponding to perivascular adipose tissue (PVAT). However, the cellular origins of PVAT are poorly understood. We applied single cell transcriptomic analyses, ex vivo adipogenesis assays, and genetic fate mapping to determine the identity of perivascular adipocyte progenitors. In mice, we found that thoracic PVAT develops from a fibroblastic lineage, consisting of progenitor cells (Pdgfra+; Ly6a+; Pparg-) and preadipocytes (Pdgfra+; Ly6a+; Pparg+). Progenitor and preadipocyte cells in PVAT shared transcriptional similarity with analogous cell types in white adipose tissue, pointing towards a conserved hierarchical structure of adipose lineage cells. Interestingly, the aortic adventitia of adult animals contained a novel population of adipogenic smooth muscle cells (SMCs) (Myh11+; Pdgfra-; Pparg+) that contributed to perivascular adipocyte formation. Similarly, human PVAT contained presumptive fibroblastic and SMC-like adipocyte progenitors, as revealed by single nucleus RNAseq. Taken together, these studies define distinct populations of progenitor cells for thermogenic PVAT, providing a foundation for developing strategies to augment brown fat activity.

overall_design: Single Cell RNA Sequencing of cells from digested mosue aortas and associated perivascular adipose tissue at ages E18,P3, Adulthood (13 weeks) and single nucleus sequencing of human perivascular adipose tissue. For mice, individual analysis of each sample as well as integration of E18 and P3 datasets was performed. For humans samples, datasets were integrated and analyzed.

first: Alexander

last: Sakers

first: Anthony

last: Angueira


title: Functional mapping of androgen receptor enhancer activity [I]

status: Public on Mar 28 2021

city: Vancouver

first: Nathan

last: Lack

state: BC

address: 2260 Oak St

department: Vancouver Prostate Centre

country: Canada

institute: University of British Columbia

summary: In this study we functionally quantified the enhancer activity of all clinical ARBS. We demonstrated that only 7% of  ARBS demonstrate androgen-dependent enhancer activation, while 11% have enhancer activity independent of AR binding. Almost all of these AR enhancers have not been previously studied. Surprisingly the vast majority of ARBS (81%) do not have significant enhancer activity. This in vitro annotation strongly correlated to clinical PCa samples. Integrating long-range chromatin interactome and transcriptomic data, we found androgen inducible enhancers were significantly more enriched to serve as anchors for gene looping and acted as a ‘hub’ to activate AR-regulated genes. To characterize the mechanism of AR enhancers we developed a deep neural network that can successfully predict active enhancers and identify key features for active enhancers. Finally, combining these results with whole genome sequencing of primary and metastatic PCa, we identified and characterized non-coding somatic SNVs that significantly impacted AR enhancer activity of a critical tumour suppressor.

overall_design: We conducted STARRseq experiment to quantify high confidence AR binding regions with DHT and EtOH with three replicates.

first: Chia-Chi

last: Huang

first: Shreyas

last: Lingadahalli

first: Tunc

last: Morova

first: Dogancan

last: Ozturan


title: Chromatin interactions at risk loci links ATP5MD to schizophrenia

city: Guangzhou

first: Zhongju

last: Wang

state: Guangdong

address: No. 1023-1063, South Sha-tai Road, Baiyun District

institute: Southern Medical University

summary: Genome-wide association studies (GWAS) have accelerated the discovery of numerous genetic variants associated with schizophrenia. However, most risk variants show a small effect size (odds ratio (OR)<1.2), suggesting that more functional risk variants remain to be identified. Here, we employed region-based multi-marker analysis of genomic annotation (MAGMA) to identify additional risk loci containing variants with large OR value from Psychiatry Genomics Consortium (PGC2) schizophrenia GWAS data and then employed summary-data-based mendelian randomization (SMR) to prioritize schizophrenia susceptibility genes. The top-ranked susceptibility gene ATP5MD, encoding an ATP synthase membrane subunit, is observed to be downregulated in schizophrenia by the risk allele of CNNM2-rs1926032 in the schizophrenia-associated 10q24.32 locus.

overall_design: Examination of chromatin interaction between rs1926032 and ATP5MD.

first: Yongchang

last: Zhu

first: Linyan

last: Ye

first: Qiyang

last: Li

first: Bo

first: Hao

last: Zhao

first: Xiuqin

last: Bao

first: Qiqi

last: Zhuo

first: Tengfei

last: Yang

first: Zhaoqiang

first: Shufen

first: Bingtao

last: Hao

first: Cunyou


title: Splicing Variation Contributes to Functional Dysregulation of Genes in Acute Myeloid Leukemia

first: Kristen

last: Lynch

address: 906 Stellar Chance Labs 422 Curie Blvd

department: Biochemistry and Molecular Biophysics

summary: Acute Myeloid Leukemia (AML) has been associated with somatic mutations in numerous genes; however, the penetrance of these mutations is low. Here we investigate the contribution of alternative splicing as an additional layer of gene dysregulation in AML. By analyzing splicing variations across two patient datasets, we find a consistent set of splicing events that disrupt the coding potential of a subset of AML-associated genes. Importantly, most of these splicing variations are independent of any currently-identified somatic mutations.  We have further validated that for EZH2 and ZRSR2 these splicing events reduce the expression of full-length protein. Together these results highlight the contribution of splicing to gene dysregulation and demonstrate that mutation analysis underestimates the burden of functional gene disruption in patient populations.

overall_design: 29 AML samples, 2 normal donors, 2 cel lines

first: Osvaldo

middle: D

last: Rivera

first: Martin

last: Carroll

first: Sara

last: Cherry

first: David

last: Schultz

first: Yoseph

last: Barash


title: Expression data MCF-7 Breast cancer cells with Graphene Oxide and Graphene nitrite Treatments

city: Chennai

first: Sailaja

middle: V

last: Elchuri

state: Tamil Nadu

address: No18, College Road, Nungambakkam

department: Nanobiotechnology

country: India

institute: Vision Research Foundation

summary:
Breast cancer is one of the fatal diseases, Graphene has a property that can be used for Imaging and Therapy. Global gene expression changes leading to these changes were investigated presently in Breast cancer subtypes. The pathological staging of the cancers is compared to global gene expression profiles.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: Graphene Oxide and Graphene Nitrite was treated with IC25 vvalue in MCF-7 Breast cancer cell lines respectively. RNA extraction extraction and hybridization on Affymetrix microarrays were performed to under stand tumour progression with an intent to identify candidate markers for Imaging and therapy.

first: Prasanna

middle: K

last: Athyala

first: Srujana

last: Chittipothi

first: D

last: Narayanan


title: Identification of SRSF6 downstream regulatory genes and  its impact on pleural fibrosis progression

city: Wuhan

first: Li-Mei

last: Liang

state: Hubei

address: 1277 JieFang Avenue

department: Department of Respiratory and Critical Care Medicine, Union Hospital

institute: Huazhong University of Science and Technology

summary: Pleural fibrosis is defined as an excessive deposition of extracellular matrix that results in destruction of the normal pleural tissue architecture and compromised function. There is no effective medication for this disorder. Pleural mesothelial cells (PMCs/ Met-5A) play a key role in the process of pleural fibrosis. However, the detailed mechanisms are poorly understood. In our study, firstly SRSF6 protein has a major role in pleural fibrosis progression. To explore downstream of SRSF6, RNA sequencing was performed in Met-5A treated by bleomycin(0.2ug/ml) with SRSF6 siRNA or negtive control siRNA (siRNA NC).  In conclusion, SRSF6 induced pleural fibrosis through a cluster pathway including SRSF6/WNT5A and SRSF6/SMAD1/5/9 signaling. SRSF6 is involved in pleural fibrosis, inhibition of SRSF6 is a novel strategy for treatment.

overall_design: Two independent preparations of Met-5A cells exposed to control siRNAs+Bleomycin or SRSF6 siRNAs+ Bleomycin

first: Liang

last: Xiong

first: Hong

last: Ye

first: Wan-Li

last: Ma


title: Functional mapping of androgen receptor enhancer activity [II]

first: Nathan

middle: A

last: Lack

summary: In this study we functionally quantified the enhancer activity of all clinical ARBS. We demonstrated that only 7% of  ARBS demonstrate androgen-dependent enhancer activation, while 11% have enhancer activity independent of AR binding. Almost all of these AR enhancers have not been previously studied. Surprisingly the vast majority of ARBS (81%) do not have significant enhancer activity. This in vitro annotation strongly correlated to clinical PCa samples. Integrating long-range chromatin interactome and transcriptomic data, we found androgen inducible enhancers were significantly more enriched to serve as anchors for gene looping and acted as a ?hub? to activate AR-regulated genes. To characterize the mechanism of AR enhancers we developed a deep neural network that can successfully predict active enhancers and identify key features for active enhancers. Finally, combining these results with whole genome sequencing of primary and metastatic PCa, we identified and characterized non-coding somatic SNVs that significantly impacted AR enhancer activity of a critical tumour suppressor.

first: Chia-Chi

last: Huang

first: Shreyas

last: Lingadahalli

first: Tunc

last: Morova

first: Dogancan

last: Ozturan


title: Light-induced Changes in the Suprachiasmatic Nucleus Transcriptome Regulated by the ERK/MAPK Pathway

status: Public on Mar 24 2021

city: Columbus

first: Diego

middle: Fernando

last: Alzate Correa

state: OH

address: 333 W 10th Avenue

department: Neuroscience

institute: The Ohio State University

summary:
The mammalian master circadian pacemaker within the suprachiasmatic nucleus (SCN) maintains tight entrainment to the 24 hr light/dark cycle via a sophisticated clock-gated rhythm in the responsiveness of the oscillator to light. Intriguingly, entrainment is not merely a passive response, instead the internal oscillator responds and adjust its own timing to entrainment signals discriminating the time of day. For example, exposure to brief light pulses in the first and final hours of the subjective generate circadian phase delays and advances respectively; whereas similar photic pulses during the subjective day does not modify the phase. A central event in this light entrainment process appears to be the rapid induction of gene expression via the ERK/MAPK pathway.
We used microarray-based expression profiling of the suprachiasmatic nucleus to examine the role of MAPK signaling in the light-evoked transcriptional response. We focused on three circadian timepoints that define the unique, clock-time delimited response properties of the SCN to light: the subjective day, early subjective night, and late subjective night.

overall_design: To profile the light-evoked, clock-gated, transcriptional profile in the suprachiasmatic nucleus, mice were infused with U0126 (or DMSO as vehicle) and exposed to light (or sham light-treated) at the three noted time points: the subjective day (CT4), early subjective night (CT15, and late subjective night (CT22) After light exposure, animals were returned to darkness for 50 minutes (corresponding to 1 hour after the onset of light),  then sacrificed and total SCN RNA was extracted and prepared for microarray analysis. For each individual sample, the SCN from two different mice under the same treatment were pool togetther. Each grouop was run by tryplicate.

last: Correa

first: Moray

last: Campbell

first: Kari

middle: R

last: Hoyt

first: Karl

last: Obrietan


title: Single-cell RNA sequencing of chicken skin

city: Vienna

first: Julia

last: Lachner

address: Waehringer Guertel 18-20

institute: Medical University of Vienna

summary: Cells were isolated from the back skin of 1-day old chicks after plucking down feathers. Cells were dissociated and enriched for epidermal cells according to a published protocol (PMID: 33157095). Single‐cell separation (10X Genomics Chromium), library preparation (10X Genomics Cell Ranger, version 3.0.2), sequencing (Illumina HiSeq 3000/4000) and data analysis (Seurat Version 3, Satija Lab, NY) were performed according to a published protocol (PMID: 31930613).

overall_design: Comparison of gene expression in chicken suprabasal keratinocytes versus basal keratinocytes

first: Sophia

last: Derdak

first: Leopold

last: Eckhart


title: RNA-seq of WT and ID2KO CD8+ T cells in iLN of tumor-bearing mice after oxaliplatin treatment

city: Beijing

first: Liuhui

last: Fu

address: Zhongguancun North Street

department: Institute for Immunology

institute: Tsinghua university

summary: Recent studies in both mice and human have suggested that the gut microbiota could modulate tumor response to chemotherapeutic agents or immunotherapies. However, the underlying mechanism has not been well characterized. Here, we found that disruption of the intestinal microbiota with antibiotics impaired the anti-cancer efficacy of oxaliplatin, which was correlated with the reduction of lots of the intestinal microbial metabolites including butyrate, one of the short chain fatty acids. Re-supplementation of either the whole intestinal microbial metabolites or butyrate could rescue the therapeutic responses of oxaliplatin in the microbiota-destroyed tumor-bearing mice by modulating CD8+ T cell function in the tumor microenvironment. Further experiments showed butyrate boosted the anti-tumor cytotoxic CD8+ T cell responses through ID2, a key transcription regulator highly expressed by tumor-infiltrating CD8+ T cells. Butyrate induced ID2 expression in CD8+ T cells, while ID2 further promoted the proliferation and function of CD8+ T cells through IL-12 signaling. Together, our findings suggest that gut microbial metabolite butyrate could promote the anti-tumor therapeutic efficacy through the ID2-dependent regulation of CD8+ T cell immunity.

overall_design: 6 samples: 3 WT CD8+ T cells, 3 ID2KO CD8+ T cells

first: Yao

last: He

first: Xiaohuan

last: Guo


title: RNA-seq of Ctrl and NaBu-treated CD8+ T cells in vitro

overall_design: 4 samples: 2 Ctrl CD8+ T cells, 2  NaBu-treated  CD8+ T cells


title: Genome-wide mapping to profile histone H3-associated epigenetic marks and chromatin conformation in senescent human stromal cells

status: Public on Mar 23 2021

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary:
Cellular senescence, one of the major driving forces of organismal aging and age-related pathologies, is modulated by interconnected molecular changes. Combinational analysis of high-throughput 'multi-omics' datasets can provide a multi-dimensional and integrated profile of cellular senescence to unravel the heterogeneous aging process with unprecedented throughput and details.
Linear chromatin is compacted into eukaryotic nucleus through a complex and multi-layered architecture. Consequently, chromatin conformation in a local or long-distance manner is strongly correlated with gene expression. Epigenetic study approaches such as chromosome conformation capture (3C) technology, together with its variants like 4C/5C/Hi-C, have been well developed to characterize chromatin looping and whole genome structure. DNA-binding proteins, including transcription factors, epigenetic and chromatin modifiers, govern gene expression in a highly intricate manner. To pinpoint the binding sites of DNA-binding proteins is crucial for decoding gene regulatory networks. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is a widely used technique to identify DNA regions bound by a specific protein. Information derived from ChIP-seq has tremendously advanced the research of mechanisms of transcription factors, cofactors and histone modifications in regulating gene expression during cellular senescence.

overall_design: Using the ChIP-seq strategy to establish epigenome signatures and generate a wide-spectrum chromatin landscape of senescent human stromal cells, the major components of tissue microenvironment in diverse solid organs. To profile the genomic DNA sequences associated with histone H3-specific alterations including H3K9me3 and H3K36me3, and to identify epigenomes that are highly occupied by these H3 sites but potentially subject to significant changes in the course of cellular senescence. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of human stromal cells. We find that lysine 9 and lysine 36 trimethylation of histone H3 effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect a distinct cellular state between proliferation and senescence or cell cycle arrest, and image overall expression status. Finally, we show that chromatin state can be read in a spatiotemporal and cell lineage-specific manner when systematically taking advantage of ChIP-seq, ATAC-seq and RNA-seq data. This study provides a basic framework for future application of comprehensive chromatin profiling towards characterization of human senescent cells in the course of organismal aging.

first: Boyi

last: Zhang


title: Genome-wide tracking of Escherichia coli DNA polymerase V to the lagging strand during the SOS response

status: Public on Mar 22 2021

city: Göteborg

first: Anders R.

last: Clausen

address: Box 440

institute: University of Gothenburg

summary: Ribonucleotides are frequently incorporated into DNA and can be used as a marker of DNA replication enzymology. To investigate on a genome-wide scale, how E. coli pol V accesses undamaged chromosomal DNA during the SOS response, we mapped the location of ribonucleotides incorporated by steric gate variants of pol V across the entire E. coli genome. To do so, we used strains that are deficient in ribonucleotide excision repair (DrnhB), constitutively express all SOS-regulated genes [lexA(Def)] and constitutively “activated” RecA* (recA730).  The strains also harbor two steric gate variants of E. coli pol V (Y11A or F10L), or a homolog of pol V, (pol VR391-Y13A). Ribonucleotides are frequently incorporated by the pol V-Y11A and pol VR391-Y13A variants, with a preference to the lagging strand.  In contrast, the pol V-F10L variant incorporates less ribonucleotides and no strand preference was observed. Sharp transitions in strand specificity are observed at replication origin (oriC), while a gradient is observed at the termination region. To activate RecA* in a recA+ strain, we treated the strains with ciprofloxacin and genome-wide mapped the location of the incorporated ribonucleotides. Again, the polV-Y11A steric gate variant, exhibited a lagging strand preference. Our data is consistent with a specific role for pol V in lagging strand DNA synthesis across the entire E. coli genome during the SOS response.

overall_design: Mapping ribonucleotides in DNA from E. coli  that induced SOS-response in combination with various steric gate variants of polV that allow more ribonucleotides to be incororated with HydEn-seq (5´end sequencing of genomic fragments generated by alkaline hydrolysis).

first: Mahmood

last: Faraz

first: Roger

last: Woodgate

first: Anders


title: Transcriptome analysis of the role of SMAD6 in mediating endothelial cell response to laminar shear stress by high throughput RNA sequencing

status: Public on Mar 29 2021

city: WAUWATOSA

first: ZIQING

last: LIU

state: WI

address: 8701 W Watertown Plank Rd, BSB 5320

department: Biology

institute: Medical College of Wisconsin

summary: Laminar shear stress regulates blood vessel morphogenesis and subsequent quiescence, but how endothelial cells (EC) enact and maintain the vascular homeostasis required in most vessels for proper vessel function is poorly understood. SMAD6, a scaffold for several signaling pathways, is expressed in developing arteries and its expression is flow-regulated. We found that SMAD6 is essential for endothelial cell flow-mediated responses, and that it functions downstream of the mechanosensor Notch1. Endothelial cells with reduced SMAD6 levels failed to align under stable laminar shear flow that promotes vascular homeostasis, while forced SMAD6 expression rescued misalignment induced by reduced Notch1 signaling. SMAD6-dependent homeostatic laminar flow required the Notch ligand Dll4 and Notch transcriptional activity. Mechanistically, neither the N-terminal nor the C-terminal domain of SMAD6 alone rescued flow alignment upon loss of Notch signaling. Endothelial cells with reduced Smad6 levels has compromised barrier function, and RNA profiling revealed upregulation of proliferation-associated genes and down regulation of junction-associated genes. Among junction-related genes affected by SMAD6 levels, the proto-cadherin PCDH12 was upregulated by homeostatic flow and required for proper flow-mediated endothelial cell alignment. Thus, SMAD6 is a critical integrator of flow-mediated signaling inputs downstream of Notch1, as vessels transition from an angiogenic to a homeostatic phenotype.

overall_design: To understand how SMAD6 mediate EC flow response, we performed bulk RNAseq of human umbilical vein endothelial cells (HUVEC) transfected with siNT non-targeting control siRNA or siSMAD6 (30 hrs of transfection) and then cultured under static condition or flowed under 15 dynes/cm2 laminar shear for 72 hrs.

first: Ziqing

last: Liu

first: Dana

middle: L

last: Ruter

first: Victoria

last: Bautch


title: Transcriptome analysis of mouse NSN and SN oocytes classified by Fibrillarin-GFP.

status: Public on Mar 27 2021

first: Ting

last: WANG

address: Qinghuayuan Street

institute: Tsinghua University

summary: We selected NSN and SN GV oocytes based on FBL-GFP localization, and performed transcriptome profiling of single NSN and SN GV oocytes, and MII oocytes in vitro matured from NSN and SN GV oocytes.

overall_design: Microinjection of mRNA encoding FBL-GFP into mouse GV oocytes, then classify according to FBL-GFP marked nucleolus pattern, then perform high-throughput RNA-sequencing of NSN and SN oocytes.

first: Jie

last: Wang


title: ChIP-seq and RNA-seq analyses in human multiple myeloma cell line MM.1S

city: Kumamoto

first: Hiroto

last: Ohguchi

state: Kumamoto

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

department: IRDA

institute: Kumamoto University

summary:
Recent studies have highlighted the oncogenic roles of KDM5A; however, its molecular mechanism has not been fully delineated. Here we identifies KDM5A as a transcriptional activator of MYC target genes in multiple myeloma (MM). Genetic ablation of KDM5A or pharmacologic inhibition of KDM5 by novel inhibitor JQKD82 impairs MM cell growth. Gene expression profile reveals that JQKD82 decreases expression of MYC targets. Expression of MYC targets is similarly downregulated by KDM5A depletion, but little affected by KDM5B knockdown. Mechanistically, KDM5A co-localizes with MYC across the genome, and KDM5A and MYC coordinately promote MYC target gene transcription. The treatment with JQKD82 reduces phosphorylation level of RNA polymerase II (RNAPII), resulting in RNAPII pausing, accompanied by hyper-H3K4me3 status at the MYC loci. Finally, we shows that JQKD82 exerts anti-MM activity and prolongs overall survival in vivo mouse xenograft models. Our results delineate KDM5A function that reinforces MYC transcriptional program, and identify KDM5A as a potential therapeutic target in MM.
This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series

first: Berkley

middle: E

last: Gryder


title: Skin expression data from psoriasis patients treated with secukinumab

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

country: Denmark

institute: University of Copenhagen

summary:
Psoriasis is a common chronic inflammatory skin disease where IκBζ is known to play an important role by mediating IL-17A-driven effects. However, the molecular mechanism by which IL-17A regulates IκBζ expression is not known.
We assessed global gene expression by microarray analysis to explore the molecular transformation in skin samples from psoriatic patients during anti-IL-17A (secukinumab) treatment.

overall_design: Skin punch biopsies were taken from nonlesional (NL) and lesional (LS) psoriatic skin of psoriatic patients before secukinumab treatment and from lesional psoriatic skin at day 4, 14, 42 and 84 during secukinumab treatment. RNA was extracted from the skin biopsies and used for microarray analysis.

first: Claus

last: Johansen

first: Trine

last: Bertelsen

first: Lars

last: Iversen


title: Gene expression profile of metabolic dysfunction in the aorta of male Sprague-Dawley rats following a short-term high fat diet

status: Public on Mar 21 2021

city: Socorro

first: Rebecca

last: Reiss

state: NM

address: 801 Leroy Place

institute: New Mexico Institute of Mining and Technology

summary: Diet-induced metabolic dysfunction precedes multiple disease states, including diabetes, heart disease, and atherosclerosis. The critical role of the vasculature in disease progression is established, yet the details of how gene expression changes in early cardiovascular disease remain an enigma. The objective of the current project was to evaluate whether a quantitative assessment of gene expression within the aorta of six-week old healthy male Sprague-Dawley rats compared to those exhibiting metabolic dysfunction symptoms could reveal potential mediators of vascular dysfunction.

overall_design: RNA was extracted from the aorta of four rats; two animals fed high-fat diet (HFD) shown to stimulate symptoms of metabolic dysfunction (including hypertension, weight gain, glucose intolerance, and insulin insensitivity) and two healthy animals that were fed a standard chow diet (CHOW) served as age-matched controls. Sequencing libraries were constructed from polyA-selected transcripts and 36-basepair reads were obtained from an Illumina Genome Analyzer IIx run. Data quality was examined with FASTQC.  Reads were mapped to ENSEMBL release 79 of the rat genome (Rnor_5.0; GCA_000001895.3) using two methods, the Genomic Mapping and Alignment Program (GMAP) and Tophat, which uses splice site junction mapping (SJM).The results for each mapping program was quantitated per gene using HTSeq count. A low count cutoff was determined by a Zipf graph, in which the log abundance per gene is graphed against the log rank.  Statistical analysis with Empirical Analysis of Digital Gene Expression data in R (EdgeR). Transcripts with a p(adj) ≤ 0.05 in at least one of the mapping techniques were subjected to Gene Ontology (GO) biological process term enrichment and network analysis using Cytoscape (v3.7.1) and the App ClueGO/CluePedia (v2.5.5).  The resulting network was reframed by taking into consideration the tissue type and the experimental protocol.

first: Alex

last: Mohr

first: Monique

last: Beaudet

first: Johnny

last: Sena

first: Jay

last: Naik

first: Benjimen

last: Walker

first: Karen

last: Sweazea


title: Effect of Actn3 genotype on dexamethasone response in skeletal muscle

status: Public on Mar 25 2021

city: Parkville

first: Jane

middle: T

last: Seto

state: VIC

address: 50 Flemington Road

country: Australia

institute: Murdoch Children's Research Institute, Royal Children's Hospital

summary: To examine the effect of alpha-actinin-3 deficiency on muscle atrophy response following dexamethasone treatment.

overall_design: Adult male C57BL6 WT and Actn3 null mice were given a single bolus of  20 mg/kg dexamethasone sodium phosphate by intraperitoneal injection. Controls were injected with saline. Quadriceps muscles were harvested and RNA extracted for RNA-seq analysis at 3 hr or 24 hr post injection.

first: Harrison

last: Wood

first: Kathryn

middle: N

last: North


title: Anti-PDGFcc antibody treatment increases adipogenesis pathways in inguinal white adipose tissue

status: Public on Mar 20 2021

city: New York

first: Jessica

last: White

address: 1305 York Ave

institute: Weill Cornell

summary:
Purpose: The goals of this experiment were to examine the transcriptional profiles (RNA-seq) of inguinal white adipose tissue (iWAT) in mice subjected to the indicated diets and treatments for eight weeks.
Methods: 6-week-old C57BL6/J mice fed a control or a high-fat diet were treated with anti-PDGFcc neutralizing antibodies or Goat IgG for 2 weeks of treatment. Antibodies were administered by i.p. every two days. Four animals were treated in each condition. The resulting iWAT from these mice were sequenced in duplicates, aligned with STAR, quantified with featureCounts, and then differential gene expression analyses were performed using limma.
Results: An unbiased analysis of hallmark pathways in iWAT of anti-PDGFcc antibody-treated mice and control animals using a pre-ranked Gene Set Enrichment Analysis (GSEA) identified adipogenesis as the pathway most differentially regulated by PDGFcc blockade when accounting for diet effects. By contrast, the hallmark fatty acid metabolism pathway which includes genes involved in lipid uptake, lipid oxidation, and lipid mobilization was not significantly enriched after anti-PDGFcc treatment. Similarly, hallmark pathways glycolysis, MTORC1 signaling, or TGFb signaling were not differentially regulated by anti-PDGFcc treatment after accounting for diet effects. An additional GSEA analysis of genes involved in lipid synthesis and storage identified a subset of genes up-regulated by PDGFcc blockade regardless of diet, which included several negative regulators of lipid synthesis and storage such as Insig1, Ppara, and Idh2.
Conclusions: A GSEA identified adipogenesis as the pathway most differentially regulated by PDGFcc blockade when accounting for diet effects. Key genes involved included several negative regulators of lipid synthesis and storage such as Insig1, Ppara, and Idh2.

overall_design: iWAT mRNA profiles in mice fed with either control or high-fat diets and then either treated or untreated with anti-PDGFcc antibody.

first: Nehemiah

last: Cox

middle: B

first: Olivier

last: Elemento

first: Frederic

last: Geissmann


title: A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker (NG_Capture-C)

city: Oxford

first: Yavor

last: Bozhilov

state: Oxfordshire

address: John Radcliffe Hospital, Headington, Weatherall Institiute of Molecular Medicine

institute: WIMM, Oxford University

summary: Many SNVs associated with human traits and genetic diseases are thought to alter the activity of existing regulatory elements. Some SNVs may also create entirely new regulatory elements which change gene expression, but the mechanism by which they do so is largely unknown. Here we show that a single base change in an otherwise unremarkable region of the human alpha-globin cluster creates an entirely new promoter and an associated unidirectional transcript. This SNV downregulates alpha-globin expression causing alpha-thalassaemia. Rather than competing for the activity of the enhancers, the new promoter lying between the α-globin genes and their associated super-enhancer acts as an orientation-dependent boundary element. Together these observations show how both the order and orientation of the fundamental elements of the genome determine patterns of gene expression and support the concept that promoters may act as boundary elements in mammals as in drosophila. Finally, these findings should prompt others to fully evaluate SNVs lying outside of known regulatory elements as causing changes in gene expression by creating new regulatory elements.

overall_design:
To identify regulatory interactions in the α-globin locus we performed high resolution chromatin conformation capture (3C) using NG CaptureC (Downes, D.J. et al 2020). NG CaptureC was performed in triplicate for Day 21 of hiPSC erythroid differentiation. Capture was performed with biotinylated oligonucleotides targeting sequences adjacent to NlaIII sites in two separate designs. Probes were divided into pools targeting the R2 enhancer, HBA1/2 promoters or the C-SNV promoter region. Lines: LA01, LA06, LA13 (homozygous C-SNV allele); Vas_Clone1, Vas_Clone2, Vas_Clone3 (promoter insertion in anti-sense orientation, parental line SBAD02); INV_Clone1, INV_Clone2, INV_Clone3 (C-SNV promoter inversion, parental line LA01); AH017 wild type line; SBAD02 wild type line; SBAD03 wild type line;
The SNV for both the C-SNV (C/C) lines, and CtoT (T/T) and TtoC (C/C) edited clones is the same and is at position 209,709 of chr16 in genome build hg19.


title: A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker

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


title: A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker (RNA-seq)

overall_design:
To characterise the expression profile of iPSC-derived erythroid cells from day 21 of differentiation PolyA+ and PolyA- RNA-seq was carried out. Lines: LA01, LA06, LA13 (homozygous C-SNV allele); Vas_Clone1, Vas_Clone2, Vas_Clone3 (promoter insertion in anti-sense orientation, parental line SBAD02); Vs_Clone1, Vs_Clone2, Vs_Clone3 (promoter insertion in sense orientation, parental line SBAD02); INV_Clone1, INV_Clone2, (C-SNV promoter inversion, parental line LA01); AH017 wild type line; SBAD02 wild type line;
The SNV for both the C-SNV (C/C) lines, and CtoT (T/T) and TtoC (C/C) edited clones is the same and is at position 209,709 of chr16 in genome build hg19.


title: A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker (ChIP-seq)

overall_design:
To characterise the epigenetic landscape and identify chromatin modifications, ChIP-seq was carried out at day 21 of hiPSC erythroid differentiation. ChIP was performed for enhancer (H3K4me1), promoter (H3K4me3) and active transcription (H3K27ac) marks, as well as for the boundary protein CTCF. All ChIPs were performed on the same material simultaneously and a 5% input was stored prior to immunoprecipitation as a control. Lines: LA01, LA06, LA13 (homozygous C-SNV allele); Vas_Clone1, Vas_Clone2, Vas_Clone3 (promoter insertion in anti-sense orientation, parental line SBAD02); Vs_Clone1, Vs_Clone2, Vs_Clone3 (promoter insertion in sense orientation, parental line SBAD02); INV_Clone1, INV_Clone2, (C-SNV promoter inversion, parental line LA01); AH017 wild type line; SBAD02 wild type line;
The SNV for both the C-SNV (C/C) lines, and CtoT (T/T) and TtoC (C/C) edited clones is the same and is at position 209,709 of chr16 in genome build hg19.


title: Genes differentially expressed during early osteoblast (OB)  differentiation

city: guangzhou

first: zhipeng

last: zou

state: guangdong

address: tonghe road

department: Cell Biology

institute: southern medical university

summary: RNA-seq analysis was performed to identify early OB-regulating genes in C3H10T1/2 MSCs.

overall_design: C3H10T1/2 MSCs were left untreated (control) or induced for osteoblast differentiation (OB)  for 3 days. There are 3 biological replicates for the control group and 4 for the OB group.

first: Zhipeng

last: Zou

first: Chen

last: Tao


title: A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker (ATAC-seq)

overall_design:
To characterise the epigenetic landscape and identify nucleosome depleted regions during erythropoiesis, ATAC-seq was carried out at day 21 of hiPSC erythroid differentiation. Lines: LA01, LA06, LA13 (homozygous C-SNV allele); CtoT_Clone1, CtoT_Clone2, CtoT_Clone3, CtoT_Clone4 (edited C-SNV line LA01 to homozygous T allele); TtoC_Clone1, TtoC_Clone2, TtoC_Clone3, TtoC_Clone4 (edited wild type line SBAD02 to homozygous C-SNV allele); Vas_Clone1, Vas_Clone2, Vas_Clone3 (promoter insertion in anti-sense orientation, parental line SBAD02); Vs_Clone1, Vs_Clone2, Vs_Clone3 (promoter insertion in sense orientation, parental line SBAD02); nonINV_Clone1, nonINV_Clone2, nonINV_Clone3 (Lox site inserted non-inverted, parental line LA01); INV_Clone1, INV_Clone2, INV_Clone3 (C-SNV promoter inversion, parental line LA01); AH017 wild type line; SBAD02 wild type line; SBAD03 wild type line;
The SNV for both the C-SNV (C/C) lines, and CtoT (T/T) and TtoC (C/C) edited clones is the same and is at position 209,709 of chr16 in genome build hg19.