title: Whole transcriptome sequencing of chemotherapy-resistant muscle-invasive urothelial bladder cancer

summary: To identify the therapeutic targets in a treatment-refractroy cancer patient, we performed single-cell RNA sequencing for 3,115 cells from primary bladder cancer (BC159-T#3) and patient-derived xenografts (BC159-T#3-PDX-vehicle and BC159-T#3-PDX-tipifarnib). Matched time-series bulk tumor tissues were also sequenced using whole exome target probe (WES) and whole transcriptome target probe (WTS).

overall_design:
All mRNA sequencing data were acquired from single patients (BC159T) at a different time (BC159-T#1, BC159-T#2, and BC159-T#3). The first transurethral resection of bladder tumor (TUR-BT) (BC159-T#1) was diagnosed with non-MIUBC (muscle-invasive urothelial bladder cancer). Despite of intravesical bacillus Calmette-Guerin (BCG), the patient progressed into MIUBC at the second TUR-BT (BC159-T#2). After undergoing multiple neoadjuvant chemotherapy regimens (gemcitabine/paclitaxel and sequential paclitaxel), the patient developed local recurrence and multiple lung metastases and removed following palliative partial cystectomy (BC159-T#3).
The raw data at EGA archive due to patient privacy concerns [EGAD00001005978].

first: W

first: H

middle: W

last: Lee

first: S

last: Park

first: K

last: Joo


title: Single-cell RNA sequencing of chemotherapy-resistant muscle-invasive urothelial bladder cancer

status: Public on Mar 26 2020

city: Seoul

first: Woosung

last: Chung

state: State...

address: Samsung Medical Center

country: South Korea

institute: Samsung Genome Institute

type: Expression profiling by high throughput sequencing

summary: To identify the therapeutic targets in a treatment-refractory cancer patient, we performed single-cell RNA sequencing for 3,115 cells from primary bladder cancer (BC159-T#3) and patient-derived xenografts (BC159-T#3-PDX-vehicle and BC159-T#3-PDX-tipifarnib). Matched time-series bulk tumor tissues were also sequenced using whole exome target probe (WES) and whole transcriptome target probe (WTS).

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
All single-cell mRNA sequencing data were acquired from a single patient (BC159-T#3) and patient-derived xenografts (BC159-T#3-PDX-vehicle and BC159-T#3-PDX-tipifarnib). The PDX samples were mapped to the human and mouse genome, respectively. To remove the cells with low sequencing quality, we applied filtering criteria using nUMI, nGene, proportion of mitochondiral genes, and averaged expression of housekeeping genes. Additional filtering criteria was applied to the PDX samples to eliminate human-mouse mixed cells. Total 3,934 cells met the criteria. After identification of cell type, the strict criteria were applied to tumor cells using nGene and inferred copy number variations. Thereafter, we removed outliers in nGene to eliminate potential multiplets in nontumor cell population.
The raw data at EGA archive due to patient privacy concerns [EGAD00001005978].

first: SH


title: DNMT1 drives 4D genome rewiring during oncogene induced senescence

status: Public on Mar 27 2020

city: Philadelphia

first: Satish

last: Sati

state: Pennsylvania

address: 421 Curie Blvd, BRB 1039

department: Dermatology

country: USA

institute: University of Pennsylvania

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: While, transcriptional and epigenetic changes associated senescence processes are well studied, the 3D chromatin changes associated with it remains elusive. In this study, we have generated genome wide chromatin interaction maps (Hi-C), epigenetic (ChIP-Seq), replication-timing and gene expression (RNA-Seq) profiles from replication induced (RS) and oncogene induced (OIS) senescent cells. As senescence associated heterochromatin foci (SAHFs) differentiates both RS and OIS nuclei, we identified the regions that constitute SAHFs and called them Senescence Associated Heterochromatin Domains (SAHDs).  Further, screening of candidate factors for SAHF induction allowed us to identify DNMT1 as a novel component that induces SAHFs by stimulation of HMGA2 expression. DNMT1 depletion does not reverse the senescence process, however, instead, depleted cells transition to a 3D genome conformation akin to that of cells in replicative senescence, suggesting that acute senescence induction (OIS) involves SAHF formation in addition to the RS-dependent 3D genome rewiring.

overall_design: Hi-C, RNAseq, ChIPseq, WGBS in huamn proliferative and senescent fibroblats

first: Boyan

last: Bonev

first: Quentin

last: Szabo

first: Paul

last: Bensadoun

first: Vincent

last: Loubiere

first: Giorgio

middle: L

last: Papadopoulos

first: Frederic

last: Bantignies

first: Lauriane

last: Fritsch

first: Jean-Marc

last: Lemaitre

first: Giacomo

last: Cavalli


title: In vivo atlas of RNA secondary structures recognized by ADARs [RNA-Seq]

city: Guangzhou

first: Rui

last: Zhang

address: No. 135, Xingang Xi Road

country: China

institute: Sun Yat-sen University

summary: We performed irCLASH and HiCLIP for ADAR1-3 in HEK293 cells. In addition, we performed mRNA-seq in ADAR1-3 overexpressed HEK293 cells and control HEK293 cells

overall_design: Three ADAR genes are present in the human genome. ADAR1 and ADAR2 bind to dsRNA and catalyze adenosine-to-inosine RNA editing, whereas ADAR3 is thought to be catalytically inactive and predominantly acts as an inhibitor of editing. Despite the importance of ADARs in a variety of regulatory processes, little is known about the in vivo structures of their RNA substrates. Therefore we developed irCLASH to generate the in vivo atlas of RNA secondary structures recognized by ADARs in this study.

first: Wenbing

last: Yang


title: In vivo atlas of RNA secondary structures recognized by ADARs [irCLASH-seq&hiCLIP-seq]

first: Yulong

last: Song


title: RNA-seq on AML patient samples and umbilical cord blood derived CD34+

city: Palo Alto

first: Ritika

last: Dutta

state: CA

address: 265 Campus Drive

institute: Stanford School of Medicine

summary: We aim to identify differentially expressed genes between AML patient samples and normal hematopoeitic progenitor cells.

overall_design: In collaboration with Girihlet, we performed RNA-seq on sorted blasts from 7 AML patient samples and sorted CD34+ cells from UCB after 72 hours of culture in StemSpan media with TPO, Flt3L, SCF

first: Tian

middle: Y


title: Loss of CHD1 promotes chromatin dysregulation leading to heterogeneous mechanisms of resistance to hormone therapy in prostate cancer [RNA-seq]

city: Dallas

first: Ping

last: Mu

state: TX

address: 6000 Harry Hines Blvd., NA6.308A

department: Human Oncology and Pathogenesis

institute: UT Southwestern Medical Center

summary: Next generation androgen receptor (AR) signaling inhibitors have significantly improved the survival of men with metastatic castration-resistant prostate cancer (mCPRC) but resistance remains a problem.  Genomic alterations at the AR locus are present in ~50% of mCRPC patients, typically in association with large numbers of copy number gains and losses across the genome.  To explore the functional consequences of these copy number alterations, we screened an shRNA library targeting all genes deleted in prostate cancer (the prostate cancer deletome: 4380 shRNAs targeting 730 genes) for next generation antiandrogen resistance using a clinically-validated model of enzalutamide-sensitive, AR-driven mCRPC LNCaP/AR.  The Chromatin helicase DNA-binding factor (CHD1) scored as a top candidate and was validated in vitro and in vivo using multiple independent shRNAs and CRISPR guides.  Mechanistically, CHD1 loss led to global changes in open and closed chromatin (ATAC-seq) as well as downregulation of canonical AR target genes upon the challenge of antiandrogen, despite robust AR expression.  Integrative analysis of ATAC- and RNA-seq changes following CHD1 deletion identified 23 candidate transcription factor drivers of enzalutamide resistance. CRISPR-based unbiased functional screening identified 4 of these drivers may drive the AR-independent resistance, including glucocorticoid receptor (GR), BRN2, NR2F1 and TBX2. Genetic studies further establish that CHD1 loss confers antiandrogen resistance by converting mCRPC cells from AR-dependence to GR-dependence in one of the resistant LNCaP/AR clone. Thus, CHD1 functions as a molecular tuner to regulate chromatin plasticity and maintain oncogenic AR signaling, as well as AR dependency.

overall_design: Compare the transcriptome changes after the deletion of CHD1 genes. There are 5 different conditions with 3 biological replicates and 2 technical replicates each. shNT samples are controls. XE means xenografts treated with enzalutamide.


title: Loss of CHD1 promotes chromatin dysregulation leading to heterogeneous mechanisms of resistance to hormone therapy in prostate cancer [ATAC-seq]

overall_design: Compare the chromatin accessibility changes after the deletion of CHD1 genes. There are 5 conditions with 3 biological replicates each. shNT is the control. XE means xenografts treated with enzalutamide.


title: Loss of CHD1 promotes chromatin dysregulation leading to heterogeneous mechanisms of resistance to hormone therapy in prostate cancer [shRNA screen]

summary: Next generation androgen receptor (AR) signaling inhibitors have significantly improved the survival of men with metastatic castration-resistant prostate cancer (mCPRC) but resistance remains a problem. Genomic alterations at the AR locus are present in ~50% of mCRPC patients, typically in association with large numbers of copy number gains and losses across the genome. To explore the functional consequences of these copy number alterations, we screened an shRNA library targeting all genes deleted in prostate cancer (the prostate cancer deletome: 4380 shRNAs targeting 730 genes) for next generation antiandrogen resistance using a clinically-validated model of enzalutamide-sensitive, AR-driven mCRPC LNCaP/AR. The Chromatin helicase DNA-binding factor (CHD1) scored as a top candidate and was validated in vitro and in vivo using multiple independent shRNAs and CRISPR guides. Mechanistically, CHD1 loss led to global changes in open and closed chromatin (ATAC-seq) as well as downregulation of canonical AR target genes upon the challenge of antiandrogen, despite robust AR expression. Integrative analysis of ATAC- and RNA-seq changes following CHD1 deletion identified 23 candidate transcription factor drivers of enzalutamide resistance. CRISPR-based unbiased functional screening identified 4 of these drivers may drive the AR-independent resistance, including glucocorticoid receptor (GR), BRN2, NR2F1 and TBX2. Genetic studies further establish that CHD1 loss confers antiandrogen resistance by converting mCRPC cells from AR-dependence to GR-dependence in one of the resistant LNCaP/AR clone. Thus, CHD1 functions as a molecular tuner to regulate chromatin plasticity and maintain oncogenic AR signaling, as well as AR dependency.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design:
Identification of shRNA enrichment in enzalutamide resistant tumors compared to plasmid and pregraft samples.
The plasmid library was sequenced and provides the 'plasmid' samples. The library was transduced into human CRPC tumor cell line LNCaP/AR, these transduced LNCaP/AR cells serve as "pregrafts". Transduced LNCaP/AR cells were selected for 4 days using 2 ug/ml puromycin (Invitrogen) and 2 million cells were subcutaneously injected bilaterally into 5 castrated SCID mice. Genomic DNA from plasmids, pregrafts, and resistant tumors was isolated, and normalized reads of all shRNAs present in resistant tumors or starting materials (plasmids and pregrafts) were quantified using HiSeq 2500 sequencing of shRNA guide strands PCR amplified from the isolated genomic DNA.


title: Loss of CHD1 promotes chromatin dysregulation leading to heterogeneous mechanisms of resistance to hormone therapy in prostate cancer

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

overall_design: Refer to individual Series


title: Skeletal muscle enhancer interactions identify genes controlling whole body metabolism in humans [cHiC-seq]

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: Obesity and type 2 diabetes (T2D) are metabolic disorders influenced by lifestyle and genetic factors, and characterized by insulin resistance in skeletal muscle, a prominent site of glucose disposal. Numerous genetic variants have been associated with obesity and T2D, of which the majority is located in non-coding DNA regions. This suggest that most variants mediate their effect by altering the activity of gene-regulatory elements, including enhancers. Here, we map skeletal muscle genomic enhancer elements that are dynamically regulated after exposure to the free fatty acid palmitate or the inflammatory cytokine TNFα. By overlapping enhancer positions with the location of disease-associated genetic variants, and resolving long-range chromatin interactions between enhancers and gene promoters, we identify target genes involved in metabolic dysfunction in skeletal muscle. The majority of these genes also associate with altered whole-body metabolic phenotypes in the murine BXD genetic reference population. Thus, our combined genomic investigations identified genes that are involved in skeletal muscle metabolism and linked to SNPs associated with the development of obesity and T2D.

overall_design: Promoter capture HiC (cHiC) of human primary muscle cells treated with palmitate or TNFa.

first: Kristine

last: Williams

middle: R

first: Jette

last: Bork-Jensen

first: Martin

last: Wohlwend

first: Ann

middle: N

last: Hansen

first: Lewin

last: Small

first: Rasmus

last: Ribel-Madsen

first: Arne

last: Astrup

first: Oluf

last: Pedersen

first: Johan

last: Auwerx

first: Christopher

middle: T

last: Workman

first: Niels

last: Grarup

first: Torben

first: Romain

last: Barrès


title: Enhancing Cardiac Cell Proliferation and Survival Suppresses Dilated Cardiomyopathy caused by Ttn-insufficiency

city: Singapore

first: Roger

last: Foo

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

summary: Dilated cardiomyopathy (DCM), defined by left ventricular (LV) enlargement associated with impaired cardiac performance, is a major cause of heart failure (HF). This results in a dilated, thin-walled left ventricle that fails to supply sufficient blood to the body. Truncating variants in TTN (TTNtv), coding for the largest structural protein in the sarcomere, contribute to the largest portion of familial and ambulatory DCM. The mechanisms for how TTNtv lead to cardiac dilation are unclear. Here, we show that reduction of Ttn expression by shRNA (Ttn shRNA) generated DCM in both mouse and rat. Ttn shRNA transduced mice developed typical DCM manifestations including impaired cardiac performance, enlarged LV and reduced LV wall thickness. Gene profiling indicates cardiac metabolism, cell proliferation and survival related genes are significantly dysregulated in Ttn shRNA-induced DCM. TUNEL assay showed Ttn shRNA induced a significant increase of cardiac cell apoptosis. A screen of 15 dysregulated downstream genes identified candidates, including Esrra, Esrrb and Yy1 significantly suppressed Ttn shRNA-induced cardiac dilation and/or DCM. Ttn shRNA induced cardiac cell apoptosis was ameliorated by Yy1. Importantly, by inducing D-type cyclin, Yy1 initiated cardiomyocyte cell cycle reentry facilitating the restoration of cardiac performance. Our findings demonstrate that DCM caused by Ttn insufficiency can be treated by therapeutically enhancing cardiac cell proliferation and survival.

overall_design: In total, 7 RNA-seq samples were sequenced. 3 Controls and 4 Ttn-KO mice.

first: Jiang

last: Jianming

first: Liao

last: Dan


title: Skeletal muscle enhancer interactions identify genes controlling whole body metabolism in humans [RNA-seq]

first: Lars

overall_design: RNA-Seq of human primary muscle cells treated with palmitate or TNFa.


title: Skeletal muscle enhancer interactions identify genes controlling whole body metabolism in humans [ChIP-seq]

overall_design: H3K27ac & H3K4me1 ChIP of human primary muscle cells treated with palmitate or TNFa.

first: Kristine


title: Microarray expression profile of circular RNAs in cervical cancer

status: Public on Mar 25 2020

city: Shenyang

first: XH

last: Li

state: Liaoning

address: No. 36, Sanhao Street

institute: China Medical University

summary: Human immortal cervical cell line H8, human cervical cancer cell line SiHa and SiHa transfected with Wnt11-overexpression vector were included in the study. We identified circRNAs differentially expressed between H8 and SiHa or between SiHa and SiHa transfected with OV-Wnt11.

overall_design: In the study presented here, we designed to analyze the circRNA expression in H8 cells, SiHa cells and SiHa cells transfected with OV-Wnt11.

first: X

middle: H

first: Heng

last: Wei

first: N

last: Ma


title: Skeletal muscle enhancer interactions identify genes controlling whole body metabolism in humans

last: Ingerslev


title: Transcriptome analysis of the facial processes in Rspo2, WNT9b and Rspo2;Wnt9b double mutant mice

city: Cheonan

first: Jeong Kyo

last: Yoon

address: 25 Bonjeong-ro, Dongnam-gu

institute: Soonchunhyang University

summary:
Purpose: To determine transcriptome profile of the facial processes of Wnt9b, Rspo2 and double gene knockout embryos by NG RNA sequencing
Method: Embryonic facial process RNA samples isolated from wild type, Rspo2, Wnt9b and Rspo2;Wnt9b double mutants in triplicate (except wild type (n=2)) at embryonic day 10.5
Results: single-end 50bp reads, 19.8 million reads - 30.7 million reads.

overall_design: NG RNA seq on the samples isolated from the facial processes of wild type, Rspo2, Wnt9b and Rspo2;Wnt9b double mutant embryos in triplicate (except wild type (n=2))

first: Jeong

middle: K

first: Yongri

last: Jin


title: Impact of protein on muscle transcriptome to endurance training

city: Leeds

first: Pim

last: Knuiman

address: Clarendon Way

department: Biological Sciences

country: United Kingdom

institute: University of Leeds

summary: The present analysis was executed to determine the impact of protein supplementation on changes in the muscle transcriptome following prolonged endurance training

overall_design: Expression profiling of human male vastus lateralus muscle at baseline and midterm during protein supplmentation.  Average age of controls: 22.5. Average age of Protein-treated subjects: 21.5. All biometrics available for subjects are included in the file GSE147494_sample_biometrics.txt.

first: Roland

last: Hangelbroek

first: Mark

last: Boekschoten

first: Maria

last: Hopman

first: Marco

last: Mensink


title: Gene expression of cell populations sorted from exocrine cells infected with PNM (M3) or NGN3 and LacZ or REST

city: Rehovot

first: Ofer

last: Elhanani

address: Herzl St 234

department: Dept. of Biomolecular Sciences

country: Israel

institute: Weizmann Institute of Science

summary: Bulk MARS-seq analysis of gene expression identified genes induced by PNM or NGN3 that are inhibited by REST expression.

overall_design: Primary exocrine cells were isolated from C57BL/6 mice and infected with Ad-M3-mCherry (PNM expressing) or Ad-NGN3-GFP and Ad-LacZ or Ad-REST viruses. Cell populations were FACS sorted according to mCherry and GFP expression. RNA from 4 biological replicates of these samples was used for library construction using Bulk MARS-seq protocol and sequenced.

first: Dena

last: Leshkowitz

first: Michael

last: Walker


title: H3K79me2/3 controls enhancer promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells (RNA-seq)

city: Oxford

first: Thomas

middle: A

last: Milne

address: John Radcliffe Hospital, Headington

department: MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: MLL gene rearrangements (MLLr) are a common cause of aggressive, incurable acute lymphoblastic leukemias (ALL) in infants and children, most of which originate in utero. The most common MLLr produces an MLL-AF4 fusion protein. MLL-AF4 promotes leukemogenesis by activating key target genes, mainly through recruitment of DOT1L and increased histone H3 lysine 79 methylation (H3K79me2/3). One key MLL-AF4 target gene is PROM1 which encodes CD133 (Prominin-1). CD133 is a pentaspan transmembrane glycoprotein that represents a potential pan-cancer target as it is found on multiple cancer stem cells. Here we demonstrate that aberrant PROM1/CD133 expression is essential for leukemic cell growth, mediated by direct binding of MLL-AF4. Activation is controlled by an intragenic H3K79me2/3 enhancer element (KEE) leading to increased enhancer-promoter interactions between PROM1 and the nearby gene TAPT1. This dual locus regulation is reflected in a strong correlation of expression in leukemia. We find that in PROM1/CD133 non-expressing cells, the PROM1 locus is repressed by polycomb repressive complex 2 (PRC2) binding, associated with reduced expression of TAPT1, partially due to loss of interactions with the PROM1 locus. Together, these results provide the first detailed analysis of PROM1/CD133 regulation that explains CD133 expression in MLLr ALL.

overall_design: RNA-seq

first: Laura

last: Godfrey

first: Nicholas

last: Crump

first: I-Jun

last: Lau


title: H3K79me2/3 controls enhancer promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells (ChIP-seq)

overall_design: ChIP-seq


title: H3K79me2/3 controls enhancer promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells (ATAC-seq)

overall_design: ATAC-seq


title: H3K79me2/3 controls enhancer promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells


title: Hair-bearing human skin generated entirely from pluripotent stem cells

city: Boston

first: Karl

middle: Russell

last: Koehler

state: MA

address: 3 Blackfan Circle

department: Otolaryngology-Head and Neck Surgery

institute: Boston Children's Hospital-Harvard Medical School

summary: In this study, we defined a differentiation approach for guiding human pluripotent stem cells in to complex hair-bearing skin tissue, known as skin organoids. The primary goal of this single-cell RNA-sequencing analysis was to define the cellular composition of skin organoids, which we have shown using histology contain multiple embryonic cell lineages. The secondary goal was to determine whether skin organoids generated using different cell lines (WA25 hESCs and DSP-GFP hiPSCs) contain similar cell types.

overall_design: Single-cell RNA-sequencing data from three different timepoints using two different stem cell lines.

first: Jiyoon

last: Lee

first: Hongyu

last: Gao

first: Yunlong

last: Liu


title: Gene expression of Cell populations sorted from exocrine cells reprogrammed to beta-like cells

summary: Bulk MARS-seq analysis of gene expression in reprogrammed exocrine cells exhibit many similarities to native beta cells. Reprogrammed cells are enriched for expression of genes that are direct targets of the transcriptional repressor REST.

overall_design: Primary exocrine cells were isolated from MIP-GFP mice and infected with Ad-M3-mCherry virus or Ad-mCherry control virus. Cell populations were FACS sorted according to mChery and GFP expression. Additionaly, GFP positive beta cells were sorted from islets of MIP-GFP mice. RNA from 4 biological replicates of these samples was used for library construction using Bulk MARS-seq protocol and sequenced.


title: Gene expression of the combined effect of PDX1 and dominant-negative REST (DN-REST) on primary pancreatic exocrine cells

summary: Bulk MARS-seq analysis of gene expression in exocrine cells infected with Ad-PDX1, Ad-DN-REST or both. DN-REST activated endocrine genes, many of which exhibited a synergistic effect in coexpression with PDX1. PDX1 alone activated exocrine genes.

overall_design: Primary exocrine cells were isolated from C57BL/6 mice and infected with Ad-mCherry control virus Ad-PDX1, Ad-DN-REST or Ad-PDX1+ Ad-DN-REST. Total RNA was obtained from 4 biological replicates 5 days post infection. This RNA was used for library construction using Bulk MARS-seq protocol and sequencing.


title: Gene expression of Cell populations


title: Noise-driven Cellular Heterogeneity in Circadian Periodicity

status: Public on Mar 24 2020

city: San Francisco

first: Ravi

last: Desai

address: 1650 Owens Street

department: Biochemistry and Biophysics

institute: University of California, San Francisco

summary: Idoxuridine increases cell-to-cell variabillity of expression from the HIV LTR promoter. To test what effect Idoxuridine has on the global structure of mRNA variability, single-cell RNA-sequencing was performed on mouse embryonic stem cells (E14) treated with either 10uM Idoxuridine or DMSO as a control for 24hrs.

overall_design: 2 samples


title: 16s rDNA sequencing of feces from C9orf72 loss of function mice

city: Cambridge

first: Aaron

last: Burberry

state: Massachusetts

address: 7 Divinity Avenue SF 258

department: HSCRB

institute: Harvard University

summary: We report the sequencing of bacterial species across four environments in which C9orf72 loss of function mice were studied as well as mice that received fecal transplantation. Our study elucidates bacterial communities that associate with pro-inflammatory or pro-survival outcomes in this model of ALS/FTD with features of autoimmunity and systemic and neural inflammation.

overall_design: In one round of sequencing, 5 fecal pellets from 2 pro-inflammatory environments (Harvard BRI/Johns Hopkins) and 2 pro-survival environments (Broad Institute/Jackson Labs) were sequenced at the 16s rDNA locus. In a second round of sequencing, 9 fecal pellets from Harvard BRI, 9 fecal pellets from Broad Institute, 6 fecal pellets from Harvard BRI mice transplanted with Harvard BRI feces, and 6 pellets from Harvard BRI mice transplanted with Broad feces were sequenced at the 16S rDNA locus.

first: Kevin

last: Eggan


title: Transcription and export complex (THO/TREX) coordinates transcription termination in Arabidopsis

city: Illkirch-Graffenstaden

first: Jules

last: Deforges

address: Boulevard Gonthier d'Andernach

country: France

institute: Transgene SA

summary: Transcription termination of mRNAs transcribed from a given locus has a decisive role in regulating the gene function as it determines the coding potential and inclusion of regulatory sequence elements. Failure in appropriate transcription termination leads to read-through transcription, resulting in the synthesis of antisense RNAs which can have profound impact on overall gene expression. However, molecular mechanisms which regulate transcription termination and chimeric RNA formation are poorly understood.   We explored the regulatory function of transcription and export complex (THO/TREX) in transcription termination. We show that two members of THO/TREX complex, TREX COMPONENT 1 (TEX1) and HYPER RECOMBINATION1(HPR1) are critical for the correct transcription termination in Arabidopsis. We first demonstrate this by showing defective termination of the bacterial nopaline synthase (NOS) terminator on a transgene in tex1 and hpr1 mutants. Additionally, we show that RNA termination defects in tex1 and hpr1 mutants are widespread at the whole genome levels leading to 3’UTR extensions, truncations and in some cases in the formation of intergenic chimeric transcripts. Chromatin immunoprecipitation coupled with quantitative PCR experiments confirmed the presence of RNA polymerase II beyond the canonical termination sites on genes with defective RNA termination in tex1 and hpr1 mutants. These results demonstrate that THO/TREX complex is a novel regulator of transcription termination in Arabidopsis.

overall_design: RNAs from Arabidopsis thaliana roots with different genotypes (WT, tex1-4, pho1-7, pho1-7tex1-4 and pho1-7hpr1-5 were extracted and sequenced, with 2 or 3 biological replicate per genotype.

first: Ghazanfar

last: Khan

first: Yves

last: Poirier


title: Interdependence of a mammary-specific super-enhancer and its native promoter facilitates gene activation during pregnancy

city: Bethesda

first: Hye Kyung

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

summary: Lineage-specific genetic programs rely on cell-restricted super-enhancers, platforms for high-density occupation by transcription factors. It is not known whether super-enhancers synergize specifically with their native promoters or provide autonomous regulatory platforms. Here we investigate the ability of the mammary Wap super-enhancer to activate the promoter of the juxtaposed and ubiquitously expressed Tbrg4 gene in the mouse mammary gland. The Wap super-enhancer was fused, by itself or in combination with its promoter, with the Tbrg4 gene. While the Wap super-enhancer activated the Tbrg4 promoter five-fold, the combination of Wap super-enhancer and promoter resulted in an 80-fold gene activation, demonstrating lineage-specific promoter-enhancer synergy. Employing ChIP-seq profiling, we uncover a chromatin platform permissive for high level expression that develops in the native promoter-enhancer context but not with a heterologous promoter. Post-transcriptional mechanisms through the Wap 3’UTR have been proposed to account for the exceptional high mRNA levels during lactation, but our mouse genetic experiments failed to support this. Lastly, we discovered that the CREB transcription factor is an integral part of the Tbrg4 promoter but not essential for its function. Taken together, our data reveal that lineage-specific enhancer-promoter synergy is critical for mammary gene regulation during pregnancy and lactation.

overall_design: ChIP-seq for STAT5A, CREB, RNA Pol II, H3K27ac and H3K4me3 in the mammary tissues of wild type, SE-Tbrg4, Wap-Tbrg4 and △CREB mutant mice at day one and ten of lactation.

first: Xianke

last: Zeng


title: RNA-sequencing of dephostatin-treated Salmonella

city: Hamilton

first: Brian

last: Coombes

state: ON

address: MDCL 2108, 1200 Main St W, McMaster University

department: Biochemistry

country: Canada

institute: McMaster University

summary: We report the effect of dephostatin treatment on the Salmonella transcriptome. High-throughput sequencing was used to quantify transcript levels under different growth conditions.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Salmonella was grown in the presence of dephostatin and DMSO in SPI-2 inducing (LPM) and non-inducing (LB) media types. RNA was isolated and sequenced to quantify differential gene expression induced by dephostatin treatment.

first: Caressa

last: Tsai

first: Craig

last: MacNair

first: My

middle: P

last: Cao

first: Jordyn

last: Perry

first: Jakob

last: Magolan

first: Eric

middle: D

last: Brown


title: Protein Acetylation Mediated by YfiQ and CobB Is Involved in the Virulence and Stress  II

city: Beijing

first: Zongmin

last: Du

address: No. 20, Fengtai Dongdajie Street

institute: Beijing Institute of Microbiology and Epidemiology

summary: Our comparative transcriptomic studies found that the cobB and yfiQ deletions resulted in differential expression of a large number of genes,we found 399 DEGs in the cobB mutant, among which 142 were down-regulated and 257 were up-regulated and there were 594 DEGs in the yfiQ mutant, among which 219 were down-regulated and 375 were up-regulated in comparison with the Yersinia pestis wild-type strain.Interestingly, expression of the virulence-related genes hmsHFRS, psaABEF were significantly lower in both ΔcobB and ΔyfiQ. Moreover, the stress response-related genes involved in the heat- and cold-shock response, acid resistance, and the universal stress response were significantly differentially expressed.most of these genes were expressed at significantly lower levels than in the wild-type strain.The mouse infection experiments and the phenotype analysis confirmedthe virulence attenuation of ΔcobB and ΔyfiQ. Our results demonstrate that protein acetylation mediated by YfiQ and CobB is involved in the virulence and stress.

overall_design: We compared the transcriptional profiles of the cobB and yfiQ mutants with that of the wild-type strain using RNA-sequencing (RNA-seq)

first: Wanbing


title: Gene expression of primary tumor and lung metastases in 4T1 mouse mammry tumor model

status: Public on Mar 23 2020

first: Jae Young

last: So

address: 37 Convent Drive, Rm 3134

department: LCBG

institute: NCI/NIH

summary: We sorted GFP-labeled 4T1 cells from primary tumor and lung metastases and performed mRNA sequencing.

overall_design: Identify differentially expressed genes between primary tumor and lung metastases

first: Jae

first: Li

last: Yang


title: DNMT3B enrichment in lung metastases of 4T1 mouse mammry tumor model

summary: We sorted GFP-labeled 4T1 cells from lung metastases and performed DNMT3B ChIP-seq.

overall_design: Identify genomic region with DNMT3B enrichment in lung metastases.


title: Single Cell RNA sequencing of MAFB +/+ and -/- cells at the pancreatic progenitor and beta-like stages

first: Simone

last: Giacometti

address: 513 Parnassus Avenue

institute: UCSF

summary: Pancreatic Beta-cells are essential for regulating blood glucose levels. Much of our knowledge relating to human Beta-cell development and function has depended on rodent models, which have provided a blueprint to confirm important cellular features in humans. The advent of next generation sequencing studies, however, has highlighted discrepancies in Beta-cells which exist between mice and men. The precise contribution of such differences has not yet been fully appreciated. Numerous studies have identified MAFB to be present in human Beta-cells postnatally, while its expression is restricted to embryonic and neo-natal Beta-cells in mice. Conversely, the related transcription factor MAFA is only active in mature murine Beta-cells and notably, knockout of MAFB has minimal effect on murine Beta-cell development and function, in contrast to MAFA. Using CRISPR/Cas9-mediated gene editing, coupled with endocrine cell differentiation strategies, we dissect the contribution of MAFB to Beta-cell development and function specifically in humans. MAFB knockout hPSCs have normal pancreatic differentiation capacity up to the progenitor stage, but favor somatostatin- and pancreatic polypeptide–positive cells at the expense of insulin- and glucagon-producing cells during endocrine cell specification. Our results uncover a requirement for MAFB late in the human pancreatic developmental program and identify it as a distinguishing transcription factor within islet cell subtype specification. Taken together, the current study demonstrates that MAFB has synonymous functions in mice and human Alfa and Beta-cell specification and uncovers previously unappreciated roles in other pancreatic endocrine cell types, in particular Gamma-cells. We propose that under-appreciated differences in rodent versus human pancreatic islet biology may be alleviated by expanding genetic observations in animal models by utilizing hPSCs to better model human Beta-cell development and associated disease pathophysiology such as diabetes.

overall_design: MAFB+/+ and MAFB-/- hESCs differentiated towards pancreatic progenitor cells and beta-like cells were digested and prepared using v2 10X single cell kits according to standard protocol, then sequenced using HiSeq4000.

first: Ronan

last: Russell

first: Phichitpol

last: Carnese

first: Thomas

middle: G

last: Hennings

first: Emily

middle: M

last: Walker

first: Holger

last: Russ

first: Jennifer

middle: S

last: Liu

first: Roland

last: Stein

first: Matthias

last: Hebrok


title: Targeted single-cell transcriptome readouts for high-throughput genetics and functional genomics

city: Barcelona

first: Lars

last: Velten

address: C. Dr. Aiguader 88, P05

department: Bioinformatics and Genomics

country: Spain

institute: CRG

summary: We show that targeted single-cell RNA-sequencing (TAP-seq) permits reliable mapping of cell (sub)types with as little as 100 reads per cell and reduces the sequencing costs for differential expression testing by a factor of 10-30, thereby enabling a cost-effective profiling of a large number of genotypes at the single cell level. We demonstrate the use of TAP-seq by generating comprehensive perturbation-based enhancer-target gene maps for 1.5% of the human genome.

overall_design:
The performance of targeted single-cell RNA-seq (TAP) was compared to whole transcriptome seq (WTX) in various scenarios (for detail, refer to sample description):
- TAP_DEEP: Comparison of targeting panels, targeted seq (deeply sequenced)
- WTX_REF: Unperturbed K562 reference, whole Tx
- TAP_CT: Cell type mapping (mouse bone marrow panel), targeted seq.
- WTX_CT: Cell type mapping, whole Tx - see series GSE122465
- TAP_DIFFEX: Dataset for evaluation of differential expression, targeted seq.
- WTX_DIFFEX: Dataset for evaluation of differential expression, whole tx.
- TAP_SCREEN: Enhancer screen on chromosome 8 and 11, targeted seq.

Additional datasets (supplement only):
- TAP_TAR: Initial test experiments
- TAP_REDESIGN: Redesign of Targeting panel 2

first: Daniel

last: Schraivogel

first: Andreas

last: Gschwind

last: Steinmetz


title: Evolutionary and Molecular Characterization of liver enriched gene 1

city: Hangzhou

first: Yanna

last: Dang

email: yannadang@126.com, yannadang@zju.edu.cn

state: Zhejiang

address: 866 Yuhangtang Rd

department: College of Animal Sciences

institute: Zhejiang University

summary: Liver enriched gene 1 (Leg1) is a newly identified gene with few functional information. To know the function of Leg1 in mammals, a phylogenetic study was first conducted and indicated that Leg1 is an ancient gene, existing from bacteria to mammals. Analysis of pig genome shows the presence of three copies of pig Leg1s (pLeg1), which could be grouped to Leg1a, Leg1b, and Leg1c clades, respectively. Purifying force acts upon the evolution of Leg1 genes, making them highly likely be functional constraint.Additionally, expression analysis of pLeg1 in combination with the available expression data of human and mouse Leg1s suggests that the eutherian Leg1s might preserve similar function in contrary to those of zebrafish and platypus. Therefore, pLeg1a might provide essential information regarding eutherian Leg1a. In our work, pLeg1a and its coding protein pLEG1a display high similarities to its human and mouse counterparts in terms of gene organization, expression pattern, glycosylation, structures. Moreover, preliminary functional study using RNA-seq suggested that pLeg1a involves in the lipid homeostasis. In conclusion, our study has provided some basic information regarding the evolution, and function of Leg1 genes, which could be applied to further validation of Leg1.

overall_design: HEK293T cells were cultured in DMEM (Hyclone) with 10% fetal bovine serum (Hyclone) in a 6-well plate until reaching 80% confluency.Then,the cells were transfected with 3 μg pCAG-pleg1a-3×FLAG vector (pleg1a) or 3 μg empty pCAG-3×FLAG vector (NC) using Lipofectamine 3000 (Thermofisher). After 48 hours, cells are harvested (n=4), and total RNA was isolated. Then mRNA was seperated with oligo(dT)25 and was used to  prepare sequencing libraries.

first: Jin

last: He


title: The effect of rifampicin on human mononuclear cell gene expression

city: Kuopio

first: Jaana

last: Rysae

address: Yliopistonranta 1C

department: School of Pharmacy

country: Finland

institute: University of Eastern Finland

summary: The aim of the study was to elucidate the effects of pregnane receptor X (PXR) activation by rifampicin on the mononuclear cell gene expression in vivo.

overall_design: Twelve individuals (healthy volunteers, aged 19-38 years) were administered 600 mg rifampicin (Rimapen; Orion Corporation, Espoo, Finland) or placebo daily for a week with at least a 4-week washout period before the next treatment arm. At the end of each arm, blood samples were collected on the morning of the eighth day. The study had randomized, open, and placebo-controlled crossover design. This trial was registered at ClinicalTrials.gov as NCT00985270.

first: Janne

last: Hukkanen

last: Rysä


title: Gene expression analysis of anti-tuberculous drug responses in a whole blood transcriptome model

first: Philip

middle: Kam Weng

last: Kwan

address: 21 Lower Kent Ridge Rd

institute: National University of Singapore

summary:
There is a need for better tools to evaluate new or repurposed TB drugs. The whole blood bactericidal activity (WBA) assay has been advocated for this purpose. We investigated whether transcriptional responses in the WBA assay resemble TB responses in vivo, and whether the approach might additionally reveal mechanisms of response.
Microarray analysis was performed on Mycobacterium tuberculosis (Mtb) RNA extracted from whole blood cultures, sputum from TB patients on combination treatment, and drug-free broth cultures

overall_design: Microarray analysis was performed on Mtb RNA taken from whole blood cultures from 4 volunteers, 9 sputum of TB patients on standard combination treatment, and 5 drug-free broth cultures. Mtb (H37Rv strain) was incubated in whole blood cultures for one hour with rifampicin, isoniazid, pyrazinamide, ethambutol individually and in 4-drug combination; with moxifloxacin, faropenem (with amoxicillin and clavulanic acid), and a drug-free control (drugs at Cmax concentrations; each replicate assay prepared from the blood of one of the 4 healthy volunteers).

first: Wenwei

last: Lin

first: Ahmad

last: M Naim

first: Balamurugan

last: Periaswamy

first: Paola

middle: F

last: De Sessions

first: Martin

last: Hibberd

first: Nicholas

middle: I

last: Paton


title: RNA-seq analysis of the transfer of R388 plasmid with or without ardC, from E. coli to P. putida

status: Public on Mar 22 2020

city: Santander

first: Gabriel

last: Moncalian

address: Albert Einstein 22

department: Molecular Biology

institute: University of Cantabria

summary: P. putida KT2440 was mixed in a conjugation filter with either E. coli BW27783-NxR bearing no plasmid (NP), E. coli BW27783-NxR bearing pSU2007 (ardC+) or E. coli BW27783-NxR bearing pLGM25 (ardC-). RNA-seq results showed that: (a) R388 genes involved in conjugation are highly upregulated in the ardC+ condition with respect to the ardC- condition. (b) a number of  donor E. coli genes and pathways involved in flagellar motility, SOS and stress responses and different metabolic pathways are downregulated in the ardC- condition with respect to NP or ardC+ conditions. (c) SOS genes are upregulated in recipient P. putida cells when receiving ardC+ containing plasmid with respect to NP or ardC- conditions.

sample_organism:
Escherichia coli
Pseudomonas putida KT2440

overall_design: R388, E. coli or P putida gene expression during the transfer of R388 plasmis with or without ardC

first: Lorena

last: Gonzalez-Montes


title: RNA-Seq of whole Drosophila brains (mid-pupal stage) with panneuronal pdm3 knockdown and controls

city: Philadelphia

first: Matthew

last: Kayser

state: PA

address: 415 Curie Boulevard, CRB 320

department: Psychiatry

institute: University of Pennsylvania

summary: Through an RNAi-based screen, we identified a gene, pdm3, required for sleep maturation in Drosophila. Pdm3, a transcription factor, coordinates an early developmental program that prepares the brain to later execute high levels of juvenile adult sleep. Through temporal mapping, we found that pdm3 acts during the mid-pupal stage of Drosophila development to control sleep ontogeny. As such, we profiled RNA expression in whole brains at this stage of development to identify possible downstream transcriptional changes in the setting of panneuronal pdm3 knockdown (Elav-GAL4> UAS pdm3 RNAi) and controls (Elav-GAL4 / +).

overall_design: Experimental: Elav-GAL4 > UAS pdm3 RNAi (4 replicates) versus controls: Elav-GAL4 / + (4 replicates). All samples were from the mid-pupal stage, defined visually as brown pupae (~6 days post-egg lay at 25c)

first: Leela

last: Chakravarti Dilley

first: Milan

last: Szuperak

first: Naihua

last: Gong

first: Charlette

last: Williams

first: Ricardo

last: Linares Saldana

first: David

last: Garbe

first: Mubarak

last: Syed

first: Rajan

last: Jain


title: Single-cell RNA sequencing of wildtype and miR-146a deficient T cells from mice treated with anti-PD-1 therapy

city: Freiburg

first: Severin

last: Dicks

address: Breisacherstr. 153

department: Institute of Medical Bioinformatics and Systems Medicine

country: Germany

institute: University Freiburg Medical Center

summary: We observed increased severity of immune related adverse events (irAEs) to anti-PD-1 therapy as well as enhanced T cell effector function in miR-146a deficient mice compared to wildtype (WT) mice. The aim of this experiment was to analyze differences in gene expression between WT and miR-146a deficient T cells at the single cell level.

overall_design: Single-cell RNA sequencing was performed from splenic MACS purified T cells from 2 WT and 2 miR-146a deficient mice that had been treated with anti-PD-1 antibody twice a week for three weeks.To induce irAEs, mice were additionally treated with low-dose LPS once a week.

first: Natalie

last: Köhler

first: Robert

last: Zeiser

first: Melanie

last: Boerries


title: Transcriptome changes accompany mitochondrial membrane potential heterogeneity in mouse embryonic and induced pluripotent stem cells

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Stem cells are uniquely dependent on both oxidative phosphorylation and glycolysis to maintain pluripotency and drive differentiation. Here, we identified that stem cells sorted by their inherent differences in mitochondrial activity exhibited significantly altered germline differentiation potential. Stem cells with lower average mitochondrial membrane potential were less proliferative and generated less ROS and ATP despite having a similar mitochondrial DNA copy number as cells with higher membrane potential. We demonstrate that pluripotent stem cells exhibit a large range of mitochondrial activity from an otherwise homogenous population, and that they are dependent on this activity to drive differentiation.

overall_design: Mouse embryonic and induced pluripotent stem cells from a C57BL/6 background were stained with mitochondrial membrane potential dye tetramethylrhodamine methyl ester (TMRM) and sorted by fluorescence activated cell sorting into populations of low or high mitochondrial membrane potential. RNA was extracted from each population and analyzed by Affymetrix arrays.

first: Alisha

last: Bothun

first: Dori

middle: C

last: Woods


title: RNA sequencing analysis of HCT116 cells following 24 hours of metabolic recovery from methionine restriction +/- small molecule treatment.

city: Madison

first: Spencer

last: Haws

state: WI

address: 330 N. Orchard St.

institute: University of Wisconsin-Madison

summary: We determined small molecule inhibition of H3K9 HMTs G9a/GLP during methionine restriction results in lasting changes in transcriptional profiles following metabolic recovery.

overall_design: Examination of transcript profiles before and after metabolic recovery from methionine restriction +/- small molecule treatment.

first: John

last: Denu


title: The cyanobacterial phytochrome 2 regulates the expression of motility-related genes through the second messenger cyclic di-GMP

first: Thomas

last: Wallner

address: Schaenzlestrasse 1

department: Institute of Biology III

institute: University of Freiburg

summary: The cyanobacterial phytochrome Cph2 is a light-dependent diguanylate cyclase producing the second messenger c-di-GMP. Under blue light, the Cph2-dependent increase in the cellular c-di-GMP concentration leads to inhibition of motility in the cyanobacterium Synechocystis 6803. However, the targets of c-di-GMP in this cyanobacterium and its mechanism of action remained unclear. Here, we determined the cellular concentrations of three cyclic nucleotides in wild-type and Δcph2 cells after blue- and green light illumination. Inactivation of the photoreceptor gene completely abolished the blue-light dependent increase in the c-di-GMP content. Microarray analysis revealed that in the wild type in comparison to the Δcph2 mutant, blue light mainly led to a change in accumulation of mRNAs encoding minor pilins, putative chaperone usher pili as well as several chemotaxis regulators. The mRNA encoding the minor pilins pilA5-pilA6 is negatively affected by high c-di GMP content under blue light, whereas the minor pilin encoding operon pilA9-slr2018 accumulates under the same conditions, suggesting opposing functions of the respective gene sets. Based on mutational and gene expression analysis, we further suggest that the second Synechocystis 6803 homolog of a CRP-like transcription factor, SyCRP2, is the regulator of minor pilin gene expression and of putative chaperone usher pili genes slr1667/slr1668. Thus, our work indicates that the Cph2-mediated increase in cellular c-di-GMP concentration upon blue-light illumination specifically changes the transcriptome of Synechocystis 6803.

overall_design: We analyzed gene expression of an Synechocystis sp. PCC 6083 mutant strain Δcph2 lacking the unique bacteriophytochrome Cph2 (Wilde et al., 2002; Mol Microbiol 44: 04) and a control strain (WT) 48 hours after transfer to blue light (5 µmols photons m-2 s-1). Blue light induce production of c-di-GMP in the WT but not in the Δcph2 mutant strain. Green light treatment served as control where no changes of the c-di-GMP content between WT and Δcph2 mutant strain could be detected. For the timepoint (48h) we sampled biological triplicates with two technical replicates. The microarray was finally hybridized with RNA derived from two biological replicates.

first: Laura

last: Pedroza

first: Karsten

last: Voigt

first: Volkhard

last: Kaever

first: Annegret

last: Wilde


title: MITF Expression Predicts Therapeutic Vulnerability to p300 Inhibition in Human Melanoma

summary: Histone modifications, largely regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs) have been recognized as major regulatory mechanisms governing human diseases including cancer.  Despite significant effort and recent advances, the mechanism by which the p300 transcriptional coactivator mediates tumorigenesis remains unclear.  Here, we use a genetic and chemical approach to identify the Microphthalmia-associated transcription factor (MITF) as a critical downstream target of p300 driving human melanoma growth.  We find that direct transcriptional control of MITF by p300-dependent histone acetylation within proximal gene regulatory regions is coupled to cellular proliferation, suggesting a significant growth regulatory axis. Further analysis revealed Forkhead Box M1 (FOXM1) as a key effector of the p300-MITF axis driving cell growth, which is selectively activated in human melanomas. Targeted chemical inhibition of p300 histone acetyltransferase activity using a potent and selective catalytic p300/CBP inhibitor confirmed the critical role of the p300-MITF-FOXM1 axis in melanoma and demonstrated significant growth inhibitory effects in melanoma cells expressing high levels of MITF.  These data support p300 as a promising novel epigenetic therapeutic target in human melanoma.

overall_design: In order to obtain a comprehensive assessment of p300 downstream effector genes in human melanoma, we performed genome-wide expression profiling analysis of WM983B and SK-Mel5 melanoma cells following p300 depletion. RNA from melanoma cells transduced with either shp300 or scrambled lentiviruses was purified, and the RNA samples were submitted to Boston University Microarray and Sequencing Resource Core Facility for analysis on the Affymetrix GeneChip Human Gene 2.0 ST.

first: Edward

last: Kim

first: Rhoda

last: Alani


title: iPSCs from people with MS can differentiate into oligodendrocytes in a homeostatic but not an inflammatory milieu

status: Public on Mar 21 2020

city: Baltimore

first: Matthew

last: Smith

address: 600 N Wolfe Street

department: Neurology

institute: Johns Hopkins University

summary: Multiple sclerosis (MS) is an inflammatory and demyelinating disease of the central nervous system (CNS) that results in variable severities of neurodegeneration. The understanding of MS has been limited by the inaccessibility of the affected cells and the lengthy timeframe of disease development. However, recent advances in stem cell technology have facilitated the bypassing of some of these challenges. Towards gaining a greater understanding of the innate potential of stem cells from people with varying degrees of disability, we generated induced pluripotent stem cells (iPSCs) from peripheral blood mononuclear cells derived from stable and progressive MS patients, and then further differentiated them into oligodendrocyte (OL) lineage cells.  We analyzed differentiation under both homeostatic and inflammatory conditions, via sustained exposure to low-dose interferon gamma (IFNγ), a prominent cytokine in MS. We found that all iPSCs differentiated into mature myelinating OLs, but chronic exposure to IFNγ dramatically inhibited differentiation in both MS groups, particularly if exposure was initiated during the pre-progenitor stage. Low dose IFNγ was not toxic but led to an early upregulation of interferon response genes in OPCs followed by an apparent redirection in lineage commitment from OL to a neuron-like phenotype in a significant portion of the treated cells. Our results reveal that a chronic low-grade inflammatory environment may have profound effects on the efficacy of regenerative therapies

overall_design: 3 Multiple Sclerosis and 2 Healthy Control iPSC lines were differentiated into oligodendrocyte precursor cells and stimulated with IFNg vs vehicle overnight

first: Itzy

last: Morales-Pantoja

first: Labchan

last: Rajbhandari

first: Linzhao

last: Cheng

first: Yongxing

last: Gao

first: Vasiliki

last: Machairaki

first: Arun

last: Venkatesan

first: Peter

last: Calabresi

first: Kathryn

last: Fitzgerald

first: Katharine

last: Whartenby


title: Epigenome-Wide Methylation Profile in sustemic lupus erythematosus: Impact of ethnicity and SLEDAI score

city: Jefferson

first: Stancy

last: Joseph

state: Ar

address: 3900 NCTR Road

department: Biochemical Toxicology

institute: FDA/NCTR

summary: Epienome-wide DNA methylation profiling of systemic lupus erythematosus (SLE). The Illumina HumanMethylation450K Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in normal human blood samples from females.  Samples included 33 non-SLE female patients (control) and 57 SLE  female patients. SLE patients:- Ethnicity included 39 African americans and 18 European Americans. SLEDAI score ranged from 2-30. Non-SLE pateients:-Ethnicity indclued 17 African Americans and 16 European Americans, all with a SLEDAI score of zero.

overall_design: Bisulphite converted DNA from the 90 samples were hybridized to the Illumina Infinium HumanMethylation450K Beadchip

first: Biridgett

last: Green-Knox

first: Nysia

last: George

first: Beverly

last: Lyn-Cook


title: Stem cells utilize m6A-mediated decay via YTHDF2 to regulate neural differentiation and promote pluripotency

city: Fort Collins

first: Carol

middle: J

last: Wilusz

state: Colorado

address: 1682 Campus Delivery

department: Microbiology, Immunology and Patholgy

institute: Colorado State University

summary: The m6A methylation pathway has previously been shown to influence pluripotency.  YTHDF2 is an RNA binding protein that interacts with m6A-modified RNAs to facilitate their degradation.  We sought to identify the cohort of RNAs targeted by YTHDF2 in human induced pluripotent stem cells (iPSC).

overall_design: To investigate the impact of YTHDF2 on relative transcript abundances in human iPSCs, we analyzed RNA samples of cells subjected to control or YTHDF2 siRNA-mediated depletion and compared their transcriptional profiles.  Three replicates of control and four of YTHDF2 knockdown were evaluated for a total of seven samples.

first: Adam

last: Heck

first: Joseph

last: Russo

first: Jeffrey

first: Erin

last: Osborne Nishimura


title: Resolving molecular mechanisms of autoimmune disease in primary CD4 T cells

city: London

first: James

last: Lee

address: The Francis Crick Institute, 1 Midland Rd

institute: The Francis Crick Institute

summary: Numerous genomic loci have been implicated in autoimmune disorders, but attempts to identify causal variants, and thereby disease mechanisms, have been hampered by strong linkage disequilibrium – leaving most loci unresolved and the potential of GWAS unfulfilled. To overcome this, we developed a massively-parallel reporter assay for use in primary CD4 T-cells, a key effector of many autoimmune diseases, and sought to resolve potential causal variants via their functional effects. This provided testable hypotheses into disease mechanisms, which can provide previously unappreciated insights into molecular mechanisms of disease

overall_design: The study consists of a massively parallel reporter assay, in which the minimal promoter in the vector was replaced by the RSV promoter. This was necessary in order for the assay to work in primary CD4 T cells. A 99,990 oligo library was designed to test 264 candidate SNPs at 14 autoimmune disease-associated gene deserts, and to tile each haplotype at 50bp intervals. Allelic constructs were tiled across each SNP in triplicate, and each was tagged by 30 unique 11nt barcodes. Each tiling construct was tagged by 6 unique barcodes. Transfections were performed into resting and activated CD4 T cells from 12 healthy individuals, and resting and activated Jurkats in 4 independent replicates. Raw data are provided as Illumina reads of the 11nt barcode from RNA extracted 24 hours after transfection, or from 4 replicates of the MPRA vector library. We also provide a tab-delimited file containing the unnormalized barcode counts for each sample and metadata relating to the sequence tagged by the barcode.


title: ChIP-chip by SNP array of a case of a patient with TCF3-HLF-positive BCP-ALL

status: Public on Mar 20 2020

city: Lublin

first: Monika

last: Szelest

address: ul. Antoniego Gębali 6

department: Laboratory of Genetic Diagnostics

country: Poland

institute: Medical University of Lublin

summary: The TCF3-HLF translocation is a very rare rearrangement in ALL that is associated with an extremely poor prognosis. The TCF3-HLF fusion gene in the described case resulted in the fusion of the homeobox-related gene of TCF3 to the leucine zipper domain of HLF. The TCF3-HLF fusion gene product acts as a transcriptional factor leading to the dedifferentiation of mature B lymphocytes into an immature state (lymphoid stem cells). This process initiates the formation of pre-leukaemic cells. Due to the rarity of this chromosomal aberration, only a few cases have been described in the literature. The advantage of this work is the presentation of an interesting case of clonal evolution of cancer cells and the cumulative implications (diagnostic and prognostic) of the patient’s genetic alterations.

overall_design: The microarray analyses were performed with the use of a CytoScan HD array. All laboratory procedures were carried out according to the manufacturers' protocols. The study was based on an analysis of scanned data files that was generated with the Chromosome Analysis Suite v 3.3 (ChAS, Thermo Fisher Scientific, Waltham, MA). Furthermore, the copy numbers of altered regions (CNAs) were calculated, and the data were normalized to a reference model (Thermo Fisher Scientific) of baseline reference intensities, NA 33 (hg19/CRCh37). The copy number states (CNS) and their breakpoints were determined with the use of the hidden Markov model (HMM) software package. The threshold levels of log2 ratio ≥0.5 and ≤0.5 were used for the categorization of the altered chromosomal regions as CNV gains and losses, respectively. The obtained data were analyzed based on two different criteria: genome-wide CNVs and leukaemia-associated region/gene-specific CNAs (leukaemia genes_all_20150505; Fullerton Overlap Map_hg19).

first: M

last: Lejman

last: Włodarczyk


title: Whole transcriptomic analysis of mechanisms of tolerance and resistance to chlorhexidine in carbapenemase-producing Klebsiella pneumoniae clinical strains

city: A Coruña

first: Maria

last: Tomas-Carmona

address: As Xubias, 84

department: Microbiology Department

institute: Instituto de Investigación Biomédica de A Coruña (INIBIC) / Complexo Hospitalario Universitario de A Coruña (CHUAC)

summary: The increasing resistence and/or bacterial tolerance to bactericides, such as chlorhexidine, causes worrisome public health problems. Using transcriptomical and microbiological studies, we analysed the molecular mechanisms associated with the adaptation to chlorhexidine in two carbapenemase-producing strains of Klebsiella pneumoniae belonging ST258-KPC3 and ST846-OXA48.

overall_design: In this study, we analized four clinical strains of Klebsiella pneumoniae producing carpabenemase, two of them adapted to chlorhexidine (ST258-KPC3CA and ST846-OXA48CA) and their respective controls (ST258-KPC3 and ST846-OXA48). For each strain there are four replicate. Statical analysis by DESeq2 and EdgeR.

first: Ines

last: Bleriot

first: Lucia

last: Blasco

first: Mercedes

last: Delgado

first: Ana

last: Gual de Torella

first: Anton

last: Ambroa

first: Laura

last: Fernandez-García

last: Lopez

first: Olga

last: Pacios

first: Jesus

last: Oteo

first: Alvaro

last: Pascual

first: German

last: Bou

first: Felipe

last: Fernandez-Cuenca

last: Tomas


title: H3K27ac ChIP in stimulated primary CD4 T cells - effect of disease-associated haplotype on 6q23

last: Lee

summary: Numerous genomic loci have been implicated in autoimmune disorders, but attempts to identify causal variants, and thereby disease mechanisms, have been hampered by strong linkage disequilibrium – leaving most loci unresolved and the potential of GWAS unfulfilled. To overcome this, we developed a massively-parallel reporter assay for use in primary CD4 T-cells, a key effector of many autoimmune diseases, and sought to resolve potential causal variants via their functional effects. We identified a specific functional variant at a pleiotropic locus that has been associated with multiple immune mediated diseases, and confirmed that this modulated expression by disrupting an NFKB binding site. To determine the resulting effect on enhancer activity we performed H3K27ac ChIP in stimulated CD4 T cells from 3 major allele homozygotes and 3 minor allele homozygotes at rs6927172.

overall_design: We performed H3K27ac ChIP in stimulated CD4 T cells that were freshly purified from 3 minor allele homozygotes and 3 major allele homozygotes at rs6927172. Stimulations were performed for 4 days using anti-biotin beads coated with anti-CD3, anti-CD2 and anti-CD28 (1:2 bead-to-cell ratio) and IL-2 (10ng/ml). Raw data are provided as 50bp single-end Illumina reads from both the immunoprecipitated DNA and the input chromatin. We also provide bigWig files for individual samples and the output from ROSE (rank ordering of super-enhancers) for merged samples - according to genotype at rs6927172.


title: Genome-wide maps of H3K9 PTMs in HCT116 cells before and after 24 hours of methionine restriction.

first: Spencer

last: Haws

summary: We determined H3K9me3 enrichment is lost at constitutively reppressed chromatin regions in response to 24 hours of methonine restriction and is subsequently replaced by H3K9me1.

overall_design: Examination of 2 histone modifications before and after 24 hours of  methionine/SAM depletion.

first: John

last: Denu


title: Identification of miRNA signatures associated with radiation-induced late lung injury in mice (plasma)

city: Monrovia

first: Claude

last: Rogers

address: 1225 S. Shamrock Ave.

institute: ChromoLogic

type: Non-coding RNA profiling by high throughput sequencing

summary: Acute radiation exposure of the thorax can lead to late serious, and even life-threatening, pulmonary and cardiac damage. Sporadic in nature, late complications tend to be difficult to predict, which prompted this investigation into identifying non-invasive, tissue-specific biomarkers for the early detection of late radiation injury. Levels of circulating microRNA (miRNA) were measured in C3H and C57Bl/6 mice after whole thorax irradiation at doses yielding approximately 50% mortality in 150 or 180 days, respectively (LD50/150 or 180). Within the first two weeks after exposure, weight gain slowed compared to sham treated mice along with a temporary drop in white blood cell counts. 52% of C3H (33 of 64) and 72% of C57Bl/6 (46 of 64) irradiated mice died due to late radiation injury. Lung and heart damage, as assessed by computed tomography (CT) and histology at 150 (C3H mice) and 180 (C57Bl/6 mice) days, correlated well with the appearance of a local, miRNA signature in the lung and heart tissue of irradiated animals, consistent with inherent differences in the C3H and C57Bl/6 strains in their propensity for developing radiation-induced pneumonitis or fibrosis, respectively. Radiation-induced changes in the circulating miRNA profile were most prominent within the first 30 days after exposure and included miRNA known to regulate inflammation and fibrosis. Importantly, early changes in plasma miRNA expression predicted survival with reasonable accuracy (88-92%). The miRNA signature that predicted survival in C3H mice, including miR-34a-5p, -100-5p, and -150-5p, were associated with pro-inflammatory NF-κB-mediated signaling pathways, whereas the signature identified in C57Bl/6 mice (miR-34b-3p, -96-5p, and -802-5p) was associated with TGF-β/SMAD signaling. This study supports the hypothesis that plasma miRNA profiles could be used to identify individuals at high risk of organ-specific late radiation damage, with applications for radiation oncology clinical practice or in the context of a radiological incident.

overall_design: Two stains of mice, C3Hf/Sed/Kam and C57Bl/6, were exposed to a single dose of whole thorax lung irradiation (N = 64 for both strain) or sham irradiation (control; N = 32). Plasma samples were taken prior to radiation (PT), at day 2 or 5 post-irradiation (D2 or D5), and at monthly intervals thereafter (M1, M2, M3, etc.) until the study endpoint (M4 for C3H and M6 for C57).

first: Agnes

last: Lukaszewicz

first: Jason

last: Yamada-Hanff

first: Ewa

last: Micewicz

first: Josephine

last: Ratikan

first: Mark

last: Starbird

first: Thomas

last: Miller

first: Christine

last: Nguyen

first: Tove

last: Olafsen

first: Keisuke

last: Iwamoto

first: William

last: McBride

first: Dörthe

last: Schaue

first: Naresh

last: Menon


title: Comparative Transcriptomic Analysis of Vascular Endothelial Cells after Hypoxia/Reoxygenation Induction

first: Yuan-Qiang

last: Lu

address: 79 Qingchun Road

department: Emergency Medicine

institute: the First Affiliated Hospital, School of Medicine, Zhejiang University

summary: Hypoxia and re-oxygenation are common features in many physiological and pathological processes such as, inflammation and tumorigenesis. Vascular endothelial (VEC) participates in the regulation of a variety of important balances in the body and the regulation of cellular functions, plays an important role in the reaction of organs such as ischemia, hypoxia, and inflammatory immunity.

overall_design: HUVEC (Procell Life Science ＆ Technology Co,. Ltid.) were replaced with fresh medium at 37℃ in a humidified atmosphere of 5% CO2 and 95% air which the O2 concentration was about 20% for 12 hours before exposure to hypoxia. Hypoxia cultures (5% O2) were incubated under 5% O2, 5% CO2 and 90% N2 by 3131 Single Tri-gas 184L incubator (Thermo Fisher scientific, Shanghai, China). Hypoxia/re-oxygenation group HUVEC were incubated under hypoxia for 3 hours followed by 1 hour 95% air/5% CO2. HUVEC cultured only in 95% air/5% CO2 were used as the normoxia control group.


title: Grad-seq in a Gram-positive bacterium reveals exonucleolytic sRNA activation in competence control

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: RNA-protein interactions crucially underlie many steps of bacterial gene expression including post-transcriptional control by small regulatory RNAs (sRNAs). In stark contrast with recent progress in Gram-negative bacteria, knowledge about RNA and protein complexes in Gram-positive species remains scarce. Here, we used Grad-seq to draft a landscape of such complexes in Streptococcus pneumoniae, determining the sedimentation profiles of ~88% of the transcripts and ~62% of the proteins of this important human pathogen. Analysis of in-gradient distributions and subsequent tag-based protein capture identified interactions of the exoribonuclease Cbf1 (a.k.a. YhaM) with sRNAs that control bacterial competence. Contrary to expectation, the nucleolytic activity of Cbf1 stabilized these sRNAs, thereby promoting their function as repressors of competence. These results illustrate how this first RNA/protein complexome resource for a Gram-positive species can be utilized to identify new molecular factors in RNA-based regulation of pathways with relevance to bacterial virulence.

overall_design: 6 CLIP-seq samples from S. pneumoniae TIGR4 cbf1-3xFLAG including 3 crosslinked samples and 3 non-crosslinked control samples.

first: Jens

last: Hör

first: Geneviève

last: Garriss

first: Silvia

last: Di Giorgio

first: Lisa-Marie

last: Hack

last: Vanselow

middle: U

first: Andreas

last: Schlosser

first: Birgitta

last: Henriques-Normark

first: Jörg

last: Vogel


title: Exonuclease-mediated sRNA activation in competence regulation in a Gram-positive bacterium

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

overall_design: Refer to individual Series


title: Regulation of DNA methylome in metastatic progression

city: Bethesda

first: Jae Young

last: So

address: 37 Convent Drive, Rm 3134

institute: NCI/NIH

summary: We sorted GFP-labeled 4T1 cells from primary tumors and lung metastases and performed methylation-seq.

overall_design: Compare DNA methylation levels between primary tumors and lung metastases in 4T1 mouse mammary turmo model

first: Jae

middle: Y

first: Li

last: Yang


title: Identification of miRNA signatures associated with radiation-induced late lung injury in mice (heart)

first: Claude

last: Rogers

overall_design: Two stains of mice, C3Hf/Sed/Kam and C57Bl/6, were exposed to a single dose of whole thorax lung irradiation (N = 64 for both strain) or sham irradiation (control; N = 32).  Heart, lung, and brain tissue, as well as red and white blood cells (RBC and WBC) were colected from animals that survived until the study endpoint (M4 for C3H, N = 15; and M6 for C57, N = 20). The tissues were homogenized and miRNA was extracted and sequenced to identify radiation-induced changes in miRNA abundance.

first: Agnes

last: Lukaszewicz

first: Jason

last: Yamada-Hanff

first: Ewa

last: Micewicz

first: Josephine

last: Ratikan

first: Mark

last: Starbird

first: Thomas

last: Miller

first: Christine

last: Nguyen

middle: T

last: Lee

first: Tove

last: Olafsen

middle: H


title: Lipopolysaccharide induced inflammatory response in mouse intestinal epithelial cells

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: Lipopolysaccharides (LPS) can lead to a lethal endotoxemia, which is a systemic inflammatory response syndrome (SIRS) characterized by a systemic release of cytokines, such as TNF. Endotoxemia is studied intensely, as a model system of gram-negative infections. LPS- as well as TNF-induced SIRS involve a strong induction of pro-inflammatory genes. In this study we investigate the response of  the intestinal epithelium cells (IECs) ot LPS and may produce pro-inflammatory cytokines or suffer cell death.

overall_design: 6 samples total, 3 LPS stimulated sampels, 3 PBS controls. All samples from the same condition are biological replicates

first: Kelly

last: Van Looveren

first: Jolien

last: Vandewalle

last: Libert


title: Complete LKB1 loss results in lethal metastatic prostate cancer

city: Madrid

first: Cristian

last: Suarez Cabrera

state: Madrid

address: Av. Complutense 40

institute: CIEMAT

summary: In order to identify the contribution of Lkb1 loss to Pten driven prostate cancer progression, we engineered a prostate conditional mutant mice in which was induced the loss of Lkb1 in combination with heterozygous loss of the prostate tumor suppressor Pten (Ptenpc+/- Lkb1pc-/-). This mouse model developed metastatic prostate squamous cell carcinoma. We compared this tumor type with the adenocarcinomas developed in Ptenpc-/- Lkb1pc+/+ mice. We carried out microdissection and RNA extraction of tumor tissues embedded in paraffin of Ptenpc+/- Lkb1pc-/- and Ptenpc-/- Lkb1pc+/+. To distinguish between early and late phenotype of prostate squamous cell carcinoma, we compared Ptenpc+/- Lkb1pc-/- tumor tissues collected at the age of six and ten months of age among them and with Ptenpc-/- Lkb1pc+/+ mouse prostate tissue.

overall_design: Gene expression was compared among prostate tumors generated in Ptenpc+/- Lkb1pc-/-  and Ptenpc-/- Lkb1pc+/+ mouse models. Specifically, early (six months) and late (ten months) stages of carcinomas developed in Ptenpc+/- Lkb1pc-/- mice were compared with prostate adenocarcinoma originated in Ptenpc-/- Lkb1pc+/+ mice. In this transcriptomic study, we included 4 samples of early stage prostate carcinomas (Ptenpc+/- Lkb1pc-/-), 4 samples of late stage prostate carcinomas (Ptenpc+/- Lkb1pc-/-) and 5 samples of prostate adenocarcinomas (Ptenpc-/- Lkb1pc+/+).

first: Ivana

last: Hermanova

first: Patricia

last: Zúñiga-García

first: Sonia

last: Fernandez-Ruiz

first: Arkaitz

last: Carracedo

last: Suárez-Cabrera

first: Iris

last: Lodewijk

first: Jesús

last: Paramio


title: mTORC2/Rac1 pathway predisposes cancer aggressiveness in IDH1-mutated glioma

first: Chunzhang

last: Yang

state: Maryland

address: 37 Convent Dr.

department: NOB

institute: NCI

summary: The present study aims to investigation alterations in the transcriptional profile when cells acquire pathogenic IDH mutants

overall_design: U251 MG cells were infected with lentivirus with IDH1 R132C or IDH1 R132H coding sequences. Cells were harvested and proceeded for mRNA sequencing analysis


title: Whole transcriptomes analyses of HEK293FT cell line treated with ISLR secreted supernatant or empty vector control supernatant

city: shanghai

first: yang

last: tang

address: Yueyang Road 320

institute: Shanghai Institute of Biochemistry and Cell Biology

summary:
Purpose: To explore the molecular mechanisms of ISLR protein, RNA sequencing was performed to analyze the geome-wide change of ISLR secreted supernatant treated HEK293FT cells compared to those of control supernatant treated cells.
Methods: Total mRNA was extracted from HEK293FT cells in triplicate respectively. Then RNA quality was assessed using an Agilent Bioanalyzer 2100 and the sample reads were sequenced using Illumina Hiseq 4000 platform. As a reasult, we got the transcript data using Hisat2 followed by Stringtie. qRT–PCR validation was performed using TaqMan and SYBR Green assays.
Results: We mapped about 60 million sequence reads per sample to the human genome and identified about 58,000 transcripts in HEK293FT cells. Many transcripts showed different expression between ISLR secreted supernatant and control treated HEK293FT cells, with a fold change ≥2 and p value <0.05. Gene set enrichment analysis (GSEA) showed a significantly positive enrichment of Hippo target genes.
Conclusion: Our study present the datiled transcripts analysis of  HEK293FT cells, with biologic replicates. Based on RNA-seq transcriptome characterization , we conclude a molecular mechanism of ISLR regulating multiple pathways related to tissue repair.

overall_design: Total mRNA was extracted from HEK293FT cells treated with ISLR secreted supernatant or empty vector control supernatant in triplicate. The quality was assessed using Agilent 2100, and the profiles were sequenced on the Illumina NovaSeq 6000.

first: Yang

last: Tang

first: Jiuzhi

last: Xu

first: Zhengquan

last: Yu


title: A transcriptional roadmap for 2C-like to pluripotent state transition  [bulk RNA]

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

summary: In mouse embryonic stem cell (ESC) culture, a small proportion of cells display totipotent features by expressing a set of genes that are only active in 2-cell-stage embryos. These 2-cell-like (2C-like) cells spontaneously transit back into pluripotent state. We previously dissected the transcriptional dynamics of pluripotent to 2C-like transition and identified factors that modulate the transition. However, how 2C-like cells transits back to the pluripotent state and what factors drive this process remains largely unknown. To address these questions, we examined the transcriptional dynamics during the reverse transition from the 2C-like state to ESCs and identified an intermediate state involved in the transition. Interestingly, we found that mESCs exit from the 2C-like state through a molecular path characterized by a two-wave upregulation of pluripotent genes different from the one observed during the 2C-like entry transition. We also showed that nonsense-mediated mRNA decay (NMD) targets Dux mRNA and affects 2C-like state maintenance, suggesting that Dux degradation contributes to the reversal of 2C-like state.

overall_design: Here we performed bulk RNA-seq on 24h Dux-induced 2C-Like cells (D1 2C+) and the cells obtained after 24h from D1 2C+ cells, D2 2C-negative, and D2 2C-positive cells. We also perfomred single cell RNA-seq on cells obtained from Dux-induced 2C-like at 0h and 24h.

first: Xudong

last: Fu

first: Yi

last: Zhang


title: RNA-seq analysis of dolastatin 15 treatment in HCT116 cells

city: Gainesville

first: Tongjun

last: Gu

state: FL

address: 2033 Mowry Road

department: ICBR

institute: The University of Florida

summary: Dolastatin 15 is a known tubulin binding agent and shows remarkable differential cytotoxicity against a panel of colorectal HCT116 isogenic cells. The compound causes anti-vascularization effect in human endothelial cells (HUVEC) in a dose dependent manner. Antiangiogenic effect was further validated in a zebrafish genetic model with activated HIF

overall_design: Examination of Dolastatin 15 effect on HCT116 cells relative to solvent controls using two different concentrations of 20 nM and 100 nM at 16 and 24 hour time points

first: Hendrik

last: Luesch

first: Ranjala

last: Ratnayake


title: Transcriptome profiling of 786-O RCC cells transduced with control vector or PRDM16 lentivirus.

city: Birmingham

first: Sunil

last: Sudarshan

state: Alabama

address: 1824 6th Avenue South

department: Urology

institute: UAB

summary: Recent large-scale data sets indicate the emerging importance of alterations of the epigenome in renal cell carcinoma (RCC).  Analysis of transcriptomic data of patient samples including normal kidney, primary tumor, and metastatic tumor deposits demonstrates epigenetic silencing of the gene encoding the transcription factor PR domain-containing 16 (PRDM16).  PRDM16 has a prominent role in adipocyte metabolism but is also highly expressed in the kidney.  The role of PRDM16 in renal cancer has not been investigated. RNAseq analysis reveals that PRDM16 imparts a predominantly repressive effect on the RCC transcriptome including suppression of SEMA5B (semaphorin 5B), a target gene of hypoxia inducible factor (HIF).  Collectively, our data uncover a novel epigenetic basis by which HIF target gene expression is amplified in kidney cancer.  Moreover, they demonstrate a new mechanism by which PRDM16 exerts its tumor suppressive effects.

overall_design: Total RNA were isolated from 786-O RCC cells transduced with control vector or PRDM16 lentivirus. Two replicates were considered for both control and PRDM16 overexpressed cells. RNA-seq was performed to find out impact of PRDM16 overexpression on global transcriptome of RCC cells.

first: Darshan

last: Chandrashekar


title: DDX3X suppresses neural lineage susceptibility to medulloblastoma [DNA-Seq]

status: Public on Mar 19 2020

city: Cambridge

first: Richard

last: Gilbertson

address: Robinson way

department: Cancer Research UK Cambridge Institute

institute: University of Cambridge

type: Genome variation profiling by high throughput sequencing

summary: DDX3X is frequently mutated in the WNT and SHH subtypes of medulloblastoma Ð the commonest malignant childhood brain tumor. But whether DDX3X functions as a medulloblastoma oncogene or tumor suppressor gene is not known. Here  we show that Ddx3x regulates hindbrain patterning and development by controlling Hox gene expression and cell stress signaling. In mice predisposed to Wnt or Shh-medulloblastoma  Ddx3x sensed oncogenic stress and suppressed tumor formation. WNT and SHH-medulloblastomas normally arise only in the lower and upper rhombic lips  respectively. Deletion of Ddx3x relived this lineage restriction  enabling both medulloblastoma subtypes to arise in either germinal zone. Thus  DDX3X is a medulloblastoma tumor suppressor that regulates hindbrain development and restricts the competence of cell lineages to form medulloblastoma subtypes.

overall_design: DNA-sequencing profiles of tumors formed from aberrant Wnt or Shh signalling. At least 3 replicates per genotype.  The 2 Normal samples represent tumors caused by aberrant wnt or shh signalling but DO NOT have loss of ddx3x in any form.

first: Deanna

last: Patmore

first: Amir

last: Jassim


title: DDX3X suppresses neural lineage susceptibility to medulloblastoma


title: Construction of brest cancer cell line BT20-specific interactome

status: Public on Mar 28 2020

city: Pittsburgh

first: Xiaosong

last: Wang

state: Pennsylvania

address: 5150 Centre Ave

department: Pathology

institute: University of Pittsburgh

summary:
Experiment type: Expression profiling by microarray and RNA-seq data, Third-party re-analysis

The purpose of our study is to construct breast cancer cell line BT20-specific interactome by aggregating publically available microarray or RNA-seq samples, and identify novel transcriptional regulators that control breast cancer progression.

We collected 101 samples of BT20 cell line microarray or RNA-seq from 12 prior studies and our own study data, GSE120919. We performed normalization for Affymetrix microarray platform and Illumina HiSeq and NovaSeq platform datasets. For the normalization, we used SCAN.UPC R package (ver.2.24.0, PMID: 22959562, https://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html) on Affymetrix microarray platform datasets. We use Rsubread R package (ver.1.30.5, PMID: 23558742, http://bioconductor.org/packages/Rsubread/), TPM log2 values on Illumina HiSeq and NovaSeq platform datasets. And then, we performed batch effect adjusting to combine the datasets which came from different laboratories. The matrix data we deposited in GEO has normalized log2 signal intensity for 12,360 genes, and the genes were mapped to human Entrez Gene IDs that overlapped across 13 datasets (a total number of 101 samples).

BT20-specific interactome was assembled by Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe, PMID: 16723010). Then, we used Master Regulator Analysis-Fisher?s Extact Test (MRA-FET, PMID: 20531406) to infer transcription factors which control a gene signature dysregulated by a fusion gene in BT20 cell line (please refer to GSE120919). We discovered SNAI2 as a master regulator candidate to modulate the gene signature in the fusion gene expressing BT20. Our findings will provide biological insights into the role of the fusion gene in breast cancer.

overall_design:
A total number of 13 data sets containing 50 microarray samples, 39 RNA-seq samples, and 12 beadchip samples were downloaded from NCBI GEO (http://ncbi.nlm.nih.gov/geo). For Affymetrix platform datasets, we used SCAN.UPC R package, and for Illumina RNA-seq platforms datasets, we used Rsubread R packages to normalize the data. For other platform datasets, we downloaded series_matrix.txt.gz files and used their normalized data. SCAN.UPC is excellent to adjust intra- and inter-study batch effects across individual samples. In RNA-seq data normalization, we used Rsubread (version 1.30.5) to align sequence reads to reference genome sequence, and used edgeR (version 3.22.3) and limma (version 3.36.2) R packages to normalize gene expression level to log2 transcripts per million (TPM) (PMID: 22872506). We aligned sequence reads to GRCh38 human genome reference sequence (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/GRCh38.primary_assembly.genome.fa.gz) and mapped the aligned sequences to NCBI gene IDs by using NCBI gene annotation data (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.38_GRCh38.p12/GCF_000001405.38_GRCh38.p12_genomic.gff.gz). After normalization, we included only protein-coding genes, non-coding RNAs, and pseudogenes which have poly A tails. We removed genes of which expression level is zero across all samples.

Significant gene signature: Limma analysis (PMID: 25605792) was used to identify differentially expressed genes out of the between the control samples and the fusion gene expressing samples in GSE120919 data. We found out the gene signature specifically enriched in the fusion gene expressing samples and applied this gene signature to MRA-FET analysis to infer transcription factors that control the gene signature.

Gene Set Enrichment Analysis (GSEA): we performed Gene Set Enrichment Analysis (GSEA) using the Hallmark Pathway dataset,  to identify the pathways enriched in the BCL2L14-ETV6 variants expressing BT20 cells. Several pathways involved in cancer progression are upregulated in fusion expressing cells, such as epithelial mesenchymal transition (EMT), angiogenesis, and kras signaling (Please refer to GSE120919).

BT20-specific interactome and Master Regulator Analysis (MRA): From the 101 microarray samples that have done with normalization, and batch adjusting, ARACNe built up regulatory interactions between the 12,360 genes and 1,032 human transcription factors (TFs) through mutual information (MI) calculation. From the built BT20-specific interactome, MRA-FET inferred master regulator (MR) candidates which control the gene signature, which are specific in the fusion gene expressing BT20 cells and identified by GSEA.

The information of the 101 samples of 13 dataset are summarized in the meta-data spreadsheet. The meta-data have sample names with GSE accession number, and information of array or RNA-seq platform, how to obtain expression data, original experiment type. The matrix data txt file has normalized log2 expression values of 101 samples.

first: Sanghoon

last: Lee

first: Yiheng

last: Hu


title: HNF4α nuclear localization correlates with the clinical progression of terminal hepatic failure in humans

first: Sarah

last: Hainer

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

summary: HNF4α is a transcription factor that plays a critical role in terminal hepatocyte failure. HNF4α-based reprogramming therapy can correct terminal liver failure in rats and humans. As liver disease progresses, HNF4α expression decreases in the nuclei of hepatocytes, leading to impaired regulation and hepatic function. Post-translational modifications (PTMs) are a fundamental regulatory mechanism of protein function and localization. In this study, we analyzed HNF4α localization and pathways involved in HNF4α PTMs in human hepatocytes at different stages of decompensated liver function upon Child-Pugh classification. RNA-seq analysis revealed that HNF4α and the PTMs-pathway related to AKT are down-regulation in cirrhotic hepatocytes with terminal failure. These findings were confirmed by protein expression, where the HNF4α nuclear levels are significantly reduced in Child‐Pugh B and C hepatocytes, whereas cytoplasmic expression of HNF4α was increased. Moreover, cMET and phospho-AKT were significantly reduced in Child‐Pugh B and C hepatocytes. The association and statistical contribution of cMET and phospho-AKT to the nuclear localization of HNF4α were confirmed by Spearman’s rank correlation test and pathway analysis. Principal component analysis was used to characterize the protein profiles related to the degree of liver dysfunction. Additionally, HNF4α acetylation was significantly reduced in failing human hepatocytes when compared to normal controls, demonstrating a significant correlation to the degree of hepatic function. Conclusion: These results suggest that the alterations in the cMET-AKT pathway directly correlate to HNF4α localization and the level of hepatic dysfunction. In conclusion, this study has therapeutic implications and suggests that manipulation of these pathways may restore hepatocyte function in terminal liver failure.

overall_design: RNA-seq analysis of hepatocytes from normal patients, NASH patients, and alcohol-mediated Laennec's cirrhotic patients.

first: Nicolas

middle: A

last: Fraunhoffer

first: Kazuki

last: Takeishi

first: Alina

last: Ostrowska

first: Nandini

last: Agarwal

first: Alexandra

last: Collin de l'Hortet

first: Jorge

last: Guzman-Lepe

first: Kazutoyo

last: Morita

first: Edgar

middle: N

last: Tafaleng

first: Kris

last: Troy

first: Swati

last: Banerjee

first: Shirish

last: Paranjpe

first: George

middle: K

last: Michalopoulos

first: Aaron

last: Bell

first: Ira

last: Fox

first: Alejandro

last: Soto-Gutierrez


title: DDX3X suppresses neural lineage susceptibility to medulloblastoma [RNA-seq]

first: Richard

last: Gilbertson

overall_design: RNA-sequencing profiles of developmental time points in the cerebullum of WT and DDX3X perturbed Blbp positive cells and in tumors formed from aberrant Wnt or Shh signalling. BCP and BPtcH DO NOT have DDX3X perturbations. 3 to 5 replicates per time point per condition.

first: Deanna

last: Patmore

first: Amir

last: Jassim


title: Gene expression data from epididymal fat of systemic Iah1-knockout in A/J-12SM mouse

city: Nagoya

first: Misato

last: Kobayashi

state: Aichi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

summary:
The QTL for fatty liver was mapped on mouse chromosome 12, designated as Fl1sa. Iah1 gene is a candidate gene for Fl1sa . In mammal, Iah1 function has been largely unknown.
We constructed Iah1-knockout mouse in A/J-12SM background. Iah1 gene is abundantly expressed in epididymal fat of mouse. We compared the epididymal fat's gene expressions between Iah1-WT mouse and Iah1-KO mouse.

overall_design: Total RNA of male Iah1-WT mice and Iah1-KO mice fed a high-fat diet for 12 weeks were extracted from epididymal fat of three mice. The RNAs form three mice were pooled and hybridized on one Affymetrix microarry.

first: Tomomi

last: Masuya

first: Miyako

last: Suzuki

first: Junko

last: Tsujimura

first: Shinsaku

last: Kanamori

first: Tamio

last: Ohno

first: Yuki

last: Miyasaka

first: Atsuhi

last: Murai

first: Fumihiko

last: Horio


title: transcriptional analysis of bulk monocytes isolated from patients post-bariatric surgery undergoing a standardized liquid mixed-meal test intended to provoque postprandial hypoglycemia, upon treatment with either placebo, anakinra or empagliflozin

city: Basel

first: Marc

middle: Yves

last: Donath

state: Basel-Stadt

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University Hospital of Basel

summary: Postprandial hypoglycemia is a disabling complication of bariatric surgery. So far, no therapy exists, and the underlying mechanisms remain unclear. Here, we hypothesized that glucose-induced IL-1β leads to an exaggerated insulin response in this condition. Therefore, we conducted a placebo controlled, randomized, double-blind, cross-over study with the SGLT2-inhibitor empagliflozin (Jardiance [10mg]) and the IL-1 receptor antagonist anakinra (Kineret [100mg]). Both drugs reduced postprandial insulin release and prevented hypoglycemia. Moreover, analysis of monocytes taken from this patient population ex-vivo revealed a hyper-reactive inflammatory state in these cells. Our study proposes a role for glucose-induced IL-1β in postprandial hypoglycemia after bariatric surgery and suggests that SGLT2-inhibitors and IL-1 antagonism may improve this condition.

overall_design: We conducted a placebo controlled, double-blind, randomized, cross-over proof-of concept study in patients with postprandial hypoglycemia after bariatric surgery. Patients were randomly assigned to receive either anakinra, empagliflozin or placebos on three study days followed by a standardized liquid mixed-meal test. Episodes of hypoglycemia were defined as (1) the appearance of typical symptoms, (2) low plasma glucose and (3) relief of symptoms following glucose administration (Whipple's triad). Following our hypothesis of an overactivation of the innate immune-system in patients experiencing post-bariatric hypoglycemia, we assessed transcriptional changes in our patient population’s innate immune cells, using an unbiased RNA sequencing approach. Therefore, we isolated monocytes from peripheral blood samples taken immediately before and 60 min (i.e. before rescue glucose application when needed) after ingestion of the mixed meal test on all three treatment days. Due to scheduling conflicts, only a subset of patients enrolled in the trial could be processed (11 patients in total). Furthermore, two samples failed library preparation, leaving us with 64 samples for sequencing. Out of these 64 samples, 16 were obtained on study visits where hypoglycemia occured, while 48 were not. For more details regarding the protocol, see publication.

first: Matthias

last: Hepprich

first: Sophia

last: Wiedemann

first: Benjamin

middle: L

last: Schelker

first: Beckey

last: Trinh

first: Alessandra

last: Stärkle

first: Marco

last: Geigges

first: Jordan

last: Löliger

first: Marianne

last: Böni-Schnetzler

first: Gottfried

last: Rudofsky


title: Systemic approaches reveal anti-adipogenic signals at the onset of obesity–related inflammation in white adipose tissue [ChIP-seq]

city: Lausanne

first: Federica

last: Gilardi

state: Vaud

address: Lausanne 1015

department: CIG - Center of Integrative Genomics

institute: University of Lausanne

summary: HFD feeding induces a rapid adipocyte progenitors (APs) proliferation in visceral adipose tissue (vWAT), followed by a block of differentiation. In contrast, subcutaneous adipose tissue (scWAT), in obesity, undergoes trans-differentiation of beige adipocytes to white and, consequently, a hyperplastic growth at later stages. We performed ChIP-seq to profile RNA pol II recruitment and the global epigenetic changes of H3K4me1 and H3K27Ac induced by HFD feeding.

overall_design: We had 6 experimental conditions in C67Bl/6 mice: 1) mice fed with CTR diet for 1 week, 2) mice fed with HFD diet for 1 week, 3) mice fed with CTR diet for 8 weeks, 4) mice fed with HFD diet for 8 weeks, 5) mice fed with CTR diet for 20 weeks, 6) mice fed with HFD diet for 20 weeks. For all the experimental group we analyzed both vWAT and scWAT with 2 biological replicate per condition.

first: Tiziana

last: Caputo

first: Gabriela

last: Aguileta

first: Khanh

middle: B

last: Trang

first: Nicolas

last: Guex

first: Béatrice

last: Desvergne


title: Polymerase occupancy (ChIP-Seq) in WT and mutants of Caulobacter crescentus NA1000

city: Geneva

first: Patrick

last: Viollier

address: Rue michel Servet,1

institute: University of Geneva

summary: Coordination of cell cycle progression with central metabolism is fundamental to all cell types and likely underlies differentiation into dispersal cells in bacteria. How central metabolism is monitored to regulate cell cycle functions is poorly understood. A forward genetic selection for cell cycle regulators in the polarized alpha-proteobacterium Caulobacter crescentus unearthed the uncharacterized CitA citrate synthase, a TCA (tricarboxylic acid) cycle enzyme, as unprecedented checkpoint regulator of the G1→S transition. We show that loss of the CitA protein provokes a (p)ppGpp alarmone-dependent G1-phase arrest without apparent metabolic or energy insufficiency. While S-phase entry is still conferred when CitA is rendered catalytically inactive, the paralogous CitB citrate synthase has no overt role other than sustaining TCA cycle activity when CitA is absent. With eukaryotic citrate synthase paralogs known to fulfill regulatory functions, our work extends the moonlighting paradigm to citrate synthase coordinating central (TCA) metabolism with development and perhaps antibiotic tolerance in bacteria.

overall_design: Examination of polymerase whole genome binding/occupancy (ChIP-Seq) in WT Caulobacter crescentus and comparison with ∆citA mutant or a strain producing the (p)ppGpp alarmone. 3 samples were analyzed in monoplicate

first: Matthieu

last: Bergé

first: Laurence

last: Degeorges