title: Cobalt resistance via detoxification and mineralization in the iron-reducing bacterium Geobacter sulfurreducens

status: Public on Dec 21 2020

city: EAST LANSING

first: MARCELA

last: TABARES

state: MI

address: 567 WILSON RD

department: MMG

institute: MICHIGAN STATE UNIVERSITY

summary: We gained insights into the environmental controls of Geobacter activities in cobamide-driven microbiomes by investigating the adaptive responses of the model representative G. sulfurreducens to growth and reproduction in the presence of CoII. Consistent with environmental exposure, we demonstrate high CoII resistance in this species and describe from genomic rand transcriptomic data multiple pathways for protein and DNA repair, cell envelope modifications, and biofilm formation that allow the cells to effectively cope with CoII stress. Importantly, we show that metal acclimation also involves respiratory chains for the reductive precipitation of the metal on the cell’s surface. These adaptive responses allow Geobacter species to grow in CoII-rich environments, sustaining the productivity of the native microbiomes and contributing to hitherto abiotic reactions of the Co cycle.

overall_design: We extracted total RNA from exponential phase of growth in Geobacter sulfurreducens PCA when growth with or without cobalt chloride.

first: Marcela

last: Tabares

first: Hunter

last: Dulay

first: Kazem

last: Kashefi

first: Gemma

last: Reguera


title: Exosome-mediated interaction in the tumor microenvironment modulates MIR211 response via the DUSP6-ERK5 axis and contributes to BRAFV600E inhibitor resistance in melanoma

status: Public on Jan 29 2021

city: St. Petersburg

first: Bongyong

last: Lee

state: Florida

address: 501 6th Ave S

country: USA

institute: The Johns Hopkins University

type: Expression profiling by high throughput sequencing

summary: It is uncertain whether the microRNA MIR211 is a tumor suppressor or an oncogene. To resolve this, we ectopically expressed MIR211 in BRAFV600E-mutant A375 melanoma cells and examined its effect in mouse xenografts. Ectopic MIR211 expression promoted aggressive tumor growth accompanied by increased cellular proliferation and angiogenesis. We provide evidence that MIR211 transfers to adjacent mouse endothelial cells via exosomes and alter the cellular properties.  Cross-species transcriptomic analysis showed that human tumor-derived MIR211 interacts with the mouse transcriptome and activates ERK5 signaling in tumor cells via modulation of a feedback loop. MIR211 directly inhibited the DUSP6 protein phosphatase, a novel MIR211 target, as confirmed by RNA immunopurification with RNA-seq and target cleavage assays. Finally, MIR211 expression conferred resistance to the BRAF inhibitor vemurafenib and the MEK inhibitor cobimetinib, with associated increases in ERK5 phosphorylation. These findings are consistent with a model in which MIR211 regulates melanoma tumor proliferation and BRAF inhibitor resistance by inducing ERK5 signaling within the complex tumor microenvironment. We propose that the MIR211-ERK5 axis represents an important and sensitive regulatory arm in melanoma with potential theranostic applications.

overall_design: A375, A375/211, and A375/211/PDK cells were injected into SCID mice and tumors were excised after 14 days. RNAs were isolated from tumors and sequenced. For Ago2 RIP-seq, A375 and A375/211 cells were subjected to immunopurification using an anti-Ago2 antibody and co-purified RNAs were sequenced.

first: Ranjan

last: Perera


title: Epigenome-Wide Association Study (EWAS) Identifies Transgenerational Disease Biomarkers in Sperm Following Ancestral Exposure to the Pesticide Methoxychlor

status: Public on Dec 16 2020

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

type: Methylation profiling by high throughput sequencing

summary: Environmental exposures such as chemical toxicants can alter gene expression and disease susceptibility through epigenetic processes. Epigenetic changes can be passed to future generations through germ cells through epigenetic transgenerational inheritance of increased disease susceptibility. The current study used an epigenome-wide association study (EWAS) to investigate whether specific transgenerational epigenetic signatures of differential DNA methylation regions (DMRs) exist that are associated with particular disease states in the F3 generation great-grand offspring of F0 generation rats exposed during gestation to the agricultural pesticide methoxychlor. The transgenerational epigenetic profile of sperm from F3 generation methoxychlor lineage rats that have only one disease state was compared to those that have no disease. Observations identify disease specific patterns of DMRs for these transgenerational rats that can potentially serve as epigenetic biomarkers for prostate disease, kidney disease, obesity, and the presence of multiple diseases. The chromosomal locations, genomic features, and gene associations of the DMRs are characterized. Disease specific DMR sets contained DMR associated genes that have previously been shown to be associated with that specific disease. Future epigenetic biomarkers could potentially be developed and validated for humans as a disease susceptibility diagnostic tool to facilitate preventative medicine and management of disease.

overall_design:
Analysis of the transgenerational actions of methoxychlor used outbred Sprague Dawley female rats (F0 generation) transiently exposed (200mg/kg body weight) methoxychlor during days 8 to 14 of gestation. The F1 generation animals (direct fetal exposure) were bred to generate the F2 generation (direct germline exposure), which were bred to generate the F3 generation (transgenerational so no direct exposure).  The methoxychlor lineage animals were aged to 1 year and euthanized for pathology and sperm epigenetic analysis. No sibling or cousin breedings (crosses) were used to avoid any inbreeding artifacts. Generally 6–8 founder gestating females from different litters were bred and 25–50 individuals of each sex obtained for each generation.
---------------------------
Authors state"Samples MX12, MX13, MX22, and MX24 were not included in any analysis and thus have no processed data files", "MX12 and MX13 were removed due to low sequence quality", and "MX22 and MX24 did not have any relevant disease association".

first: Eric

middle: E

last: Nilsson

first: Jennifer

middle: M

last: Thorson

first: Millissia

last: Ben Maamar

first: Daniel

last: Beck


title: Androgen Receptor splice variant V7 (AR-V7) mediates AR signalling in castration resistant prostate cancer (CRPC) [RNA-seq]

status: Public on Jan 21 2021

city: Houston

first: Basil

last: Paul

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

summary: CRPC remains AR dependent. There are multiple mechanisms for reactivation of AR including expression of constitutively active AR splices variant AR-V7 (AR3). Earlier studies suggest that though the variants regulate many of the same genes as AR, they also have unique targets. Another argument is that the variant is a “weak” AR. We have used an LNCaP cell line that expresses AR-V7 in response to doxycycline (LNCaP AR-V7) to compare the activities of the two isoforms and to identify differential regulation of target genes. We also used VCaP cell line that expresses AR-V7 in response to doxycycline (VCaP AR-V7) to validate the activities of the two isoforms in an alternative prostate cancer cell line. The transcriptomes for AR and AR-V7 in these cell lines were identified using RNA-Seq.

overall_design: Biological replicates of LNCaP AR-V7 and VCaP AR-V7 cells treated with ethanol, 10uM R1881 or 20ng/mL Doxycycline for 24 hours were harvested into PureXtract RNAzol solution. Total RNA was extracted, and column purified using RNAeasy kit (Qiagen, USA). Equal amounts of clean total RNA samples from biological replicates were pooled together for library preparation.

first: Paul

last: Basil

first: Nancy

last: Weigel


title: NGLY1-deficient cerebral organiods display abnormal neuronal differentiation

city: Fort Worth

first: Yu-Chieh

last: Wang

state: Texas

address: 3500 Camp Bowie Boulevard

department: Department of Pharmaceutical Sciences

institute: University of North Texas Health Science Center

summary: We report using a single-cell transcriptomic study of cerebral organiods (COs) developed from WA09 hESCs with gene editing-induced NGLY1 mutations and from NGLY1-deficient patient's hiPSCs at 40 or 80 days of development.  WA09 hESC-derived COs with and without mutant NGLY1 and patient's hiPSC-derived COs with and without the ectopic expression NGLY1 were analyzed.

overall_design: The COs of two hESC clones with (NGLY1-deficient or NGLY1-functional) were cultured for 80 days of developments. Replicate deficient and functional CO samples were taken at 80 days and an additional sample was taken at day 40. The COs of two hiPSC clones (one NGLY1-deficient, one NGLY1-functional due to ectopic expression) were also cultured and sampled at 40 days of development.


title: Cooperative genetic networks drive embryonic stem cell transition from naïve to formative pluripotency

status: Public on Dec 22 2020

city: Cologne

first: Andreas

last: Beyer

address: Joseph-Stelzmann-Str. 26

department: CECAD

country: Germany

institute: University of Cologne

summary: In the mammalian embryo, epiblast cells must exit the naïve state and acquire formative pluripotency. This cell state transition is recapitulated by mouse embryonic stem cells (ESCs), which undergo pluripotency progression in defined conditions in vitro. However, our understanding of the molecular cascades and gene networks involved in the exit from naïve pluripotency remains fragmentary. Here, we employed a combination of genetic screens in haploid ESCs, CRISPR/Cas9 gene disruption, large-scale transcriptomics and computational systems biology to delineate the regulatory circuits governing naïve state exit. Transcriptome profiles for 73 ESC lines deficient for regulators of the exit from naïve pluripotency predominantly manifest delays on the trajectory from naïve to formative epiblast. We find that gene networks operative in ESCs are also active during transition from pre- to post-implantation epiblast in utero. We identified 496 naïve state-associated genes tightly connected to the in vivo epiblast state transition and largely conserved in primate embryos. Integrated analysis of mutant transcriptomes revealed funnelling of multiple gene activities into discrete regulatory modules. Finally, we delineate how intersections with signalling pathways direct this pivotal mammalian cell state transition.

overall_design: A total number of 340 samples were analyzed as part of this  project. 319 samples of 73 different KO cell lines and WT cell lines at two different conditions were used for the analysis. KOs were done in replicates (pairs) for each condition. The number of WT replicates is higher as WT samples were included in all batches. 21 additional samples were used in a WT differentiation time course. Time points from 0 to 32 hours are included (in steps of 2 hours). 0 hour and 32 hour samples were done in pairs and two different conditions at 0 hours were included.

last: Lackner

first: Robert

last: Sehlke

first: Marius

last: Garmhausen

first: Giuliano

last: Stirparo

first: Michelle

last: Huth

first: Fabian

last: Titz-Teixeira

first: Julia

last: Ramesmayer

first: Petra

last: van der Lelij

first: Henry

middle: F

last: Thomas

first: Meryem

last: Ralser

first: Laura

last: Santini

first: Elena

last: Galimberti

first: Mihail

last: Sarov

first: A. Francis

last: Stewart

first: Austin

last: Smith

first: Martin

last: Leeb


title: Comparative efficacy of serum lactate dehydrogenase levels versus circulating cell-free microRNAs in monitoring response to checkpoint inhibitor immunotherapy treatment in metastatic melanoma patients

status: Public on Dec 07 2020

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

type: Non-coding RNA profiling by high throughput sequencing

summary: This study compares the efficiency of cfmiR signatures versus sLDH levels in assessing and monitoring melanoma patients' responses during the course of their CII treatment.

overall_design: The cfmiRs were evaluated using a next generation HTG EdgeSeq microRNA (miR) Whole Transcriptome Assay (WTA) in 161 serial bleed samples obtained during the course of the CII treatment from 48 stage III and IV melanoma patients. Initially, cfmiRs were profiled in pre- and post-treatment plasma samples of stage IV non-responsive melanoma patients and compared to normal donors’ plasma samples. A 9 cfmiR signature was identified in pre- and post-treatment samples that was associated with having no response to CII. These cfmiRs were then compared in pre- and post-treatment plasma samples from stage IV responsive melanoma patients. MiR-4745-3p, miR-615-3p, and miR-6511-3p showed potential predictive abilities in assessing CII response. In stage III melanoma patients, miRs found in pre-treatment plasma samples were associated with response to CII therapy. Our results showed that compared to elevated baseline LDH levels, cfmiRs were consistently more efficient in detecting melanoma patients undergoing CII therapy who will develop progressive disease. By using this minimally invasive assay, we identified a cfmiR signature that could assess responses and allow for potential real-time monitoring of patients receiving CII treatment.

first: Matias

middle: A

last: Bustos

middle: S

first: Negin

last: Rahimzadeh


title: WWOX gene and estrogen receptor interplay in breast cancer

city: Lodz

first: Andrzej

middle: K.

last: Bednarek

address: Zeligowskiego St. 7/9

department: Department of Molecular Carcinogenesis

country: Poland

institute: Medical University in Lodz

summary: The aim of presented study was to assess the relationship between the presence of estrogen receptor and WWOX gene in breast cancer cell lines.

overall_design: The study was based on estrogen-responsive (MCF7) and estrogen-unresponsive (MDA-MB-231, BT20) cell lines, for which depending on native expression, WWOX gene was either induced by retroviral transfection (MDA-MB-231) or silenced with shRNA (MCF7, BT20), and changes in the phenotype were estrogen stimulated. We have employed nAnT-iCAGE methodology for high-throughput gene expression profiling.

first: Karolina

last: Pospiech


title: Validation of Baboon Pluripotent Cells as a Model for Translational Stem Cell Research [ChIP-Seq]

city: Yiwu

first: keren

last: cheng

state: Zhejiang

address: 1575 chouzhou bei road

department: School of Medicine

country: China

institute: Zhejiang University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To investigate the extent of similarity in epigenetic programming among human, baboon and mouse PSCs, we examined genome-wide patterns of four chromatin modifications (H3K4me3, H3K9me3, H3K27me3, H3K27ac) and DNA methylation in baboon iPSC and ESCs. We show that baboon pluripotent cells (PSCs) recapitulate key molecular features of human PSCs with much greater accuracy than that found in PSCs from non-primate species. Specifically, baboon and human PSCs exhibit significantly greater conservation of gene expression patterns, higher sequence and structural homology among pluripotency factors, more equivalent genome-wide patterns of histone and DNA methylation modifications, and similar maintenance of bivalent programming of developmental genes than that found between human and non-primate PSCs.

overall_design: Examination of transcriptome, H3K4me3, H3K27ac, H3K9me3, H3K27me3 and DNA methylation in baboon iPSC and ESC.

first: Keren

last: Cheng

first: Megan

last: Mahlke

first: John

middle: R

last: McCarrey


title: Emergence of Dynamic Neuro-Immune Profile During Mid-life Aging in the Female Brain: Implications for Alzheimer’s Disease Risk [P3]

status: Public on Dec 08 2020

city: TUCSON

first: Roberta

last: Brinton

state: Arizona

address: 1230 N Cherry Ave, PO Box 210242

department: The Center for Innovation in Brain Science

institute: University of Arizona

summary: Aging and endocrine transition states can significantly impact inflammation across organ systems. Neuroinflammation is a well-documented feature in Alzheimer’s disease (AD). Herein, we investigated neuro-inflammation that emerges during mid-life aging, chronological and endocrinological, in the female brain as an early initiating mechanism driving AD risk later in life.  Analyses were conducted in a translational rodent model of mid-life chronological and endocrinological aging followed by validation in transcriptomic profiles from women versus age-matched men. In the translational model, the neuroinflammatory profile of mid-life aging in females was endocrine and chronological  state specific, dynamic, anatomically distributed and persistent. Microarray dataset analyses of aging human hippocampus indicated a sex difference in neuroinflammatory profile in which women exhibited a profile comparable to the pattern discovered in our translational rodent model, whereas age-matched men exhibited a profile consistent with low neuro-immune activation. Translationally, these findings have implications for therapeutic interventions during mid-life to decrease late-onset AD risk.

overall_design: 6 animals/group. Female  animals were aged from 6 months to 16 months with different menapausing status.

first: Shang

last: Yuan

first: Yin

last: Fei

first: Mishra

last: Aarti


title: Identification and Analysis of Dysregulated lncRNA, microRNA and mRNA expression profiles and construction of ceRNA network in THP-1 macrophage infected with Talaromyces marneffei [RNA-seq]

status: Public on Dec 01 2020

city: Nanning

first: Yueqi

last: Li

state: Guangxi

address: NO.22 Shuangyong Road

institute: Guangxi Medical University

summary:
BACKGROUND: Competitive endogenous RNA (ceRNA) reveals new mechanisms for interactions between RNAs. However, knowledge of ceRNA regulatory networks in macrophages infected with Talaromyces marneffei (T. marneffei, TM) is still limited. This study aims to explore the expression profiles of lncRNA, miRNA and mRNA, and the changes of ceRNA network related to immunity, inflammation, metabolism in TM-infected macrophage.
METHODS: Next-generation sequencing technology (NGS) was used to obtain mRNA, miRNA and lncRNA expression profiles in TM-infected macrophages and normal macrophages. Cuffdiff and DESeq2 software packages are used to identify differentially expressed lncRNA, miRNA and mRNA. The function enrichment analysis was performed by GOseq package in R platform, and the lncRNA–miRNA–mRNA interaction ceRNA network was established in Cytoscape. Functional enrichment analysis was performed on genes contained in the ceRNA network, and genes significantly enriched in functional pathways were selected for qRT-PCR verification.
RESULTS: A total of 119 lncRNAs, 28 miRNAs and 208 mRNAs were identified as differentially expressed RNAs in TM-infected macrophages. Among them, 38 lncRNAs, 10 miRNAs and 109 mRNAs are contained in the ceRNA regulatory network. GO analysis and KEGG pathway of mRNA in the ceRNA network showed that macrophages infected with TM activated pathways and functions related to immune response, metabolic response and inflammatory response. Select genes that are significantly abundant in GO analysis and KEGG pathway. The core genes were selected for quantitative real-time PCR (qRT-PCR) to verify consistency with the sequencing results. Eight groups of ceRNAs consisting of 3 mRNAs, 5 lncRNAs, and 2 miRNAs were verified. They are mRNA CSF3, IL24, LIF. lncRNA IL6R-AS1, LINC02009, AC068831.1, AC006252.1, LINC02466. These genes may be involved in immune response and inflammatory response-related pathways and functions in TM-infected macrophages.
CONCLUSIONS: The CeRNA network plays an important role in understanding the mechanism of TM infection in macrophages. This study may provide effective and novel insights for further understanding the underlying mechanism of Talaromyces marneffei.

overall_design: LncRNA, miRNA, and mRNA profiles of macrophage infected with Talaromyces marneffei

first: Wudi

last: Wei


title: Identification and Analysis of Dysregulated lncRNA, microRNA and mRNA expression profiles and construction of ceRNA network in THP-1 macrophage infected with Talaromyces marneffei [miRNA-seq]


title: Comparative evaluation for the globin gene depletion methods  for mRNA sequencing using the whole blood-derived total RNAs

status: Public on Nov 30 2020

city: Rochester

first: Jin Sung

last: Jang

state: MN

address: 200 First St SW

institute: Mayo Clinic

summary: Background:  There are challenges in generating mRNA-Seq data from whole-blood derived RNA as globin gene and rRNA are frequent contaminants.  Given the abundance of erythrocytes in whole blood, globin genes comprise some 80% or more of the total RNA. Therefore, depletion of globin gene RNA and rRNA are critical steps required to have adequate coverage of reads mapping to the reference transcripts and thus reduce the total cost of sequencing. In this study, we directly compared the performance of probe hybridization (GLOBINClear Kit and Globin-Zero Gold rRNA Removal Kit) and RNAse-H enzymatic depletion (NEBNext® Globin & rRNA Depletion Kit and Ribo-Zero Plus rRNA Depletion Kit) methods from 1 ug of whole blood-derived RNA on mRNA-Seq profiling. All RNA samples were treated DNaseI for additional cleanup before the depletion step and were processed for poly-A selection for library generation. Results: Probe hybridization revealed a better overall performance than the RNAse-H enzymatic depletion method, detecting a higher number of genes and transcripts without 3’ region bias. After depletion, samples treated with probe hybridization showed globin genes at 0.5% (±0.6%) of the total mapped reads;  the RNAse-H enzymatic depletion had 3.2% (±3.8%). Probe hybridization showed more junction reads and transcripts compared with RNAse-H enzymatic depletion and also had a higher correlation (R>0.9) than RNAse-H enzymatic depletion (R>0.85). Conclusion: In this study, our results showed that 1 µg of high-quality RNA from whole blood could be routinely used for transcriptional profiling analysis studies with globin gene and rRNA depletion pre-processing.  We also demonstrated that the probe hybridization depletion method is better suited to mRNA sequencing analysis with minimal effect on RNA quality during depletion procedures.

first: Jin


title: RNA-seq data exhibit distinct colonic function in colonic tissues

status: Public on Nov 24 2020

city: Beijing

first: shimeng

last: Huang

address: No. 2 Yuanmingyuan West Road, Haidian District

department: College of Animal Science and Technology

institute: China Agricultural University

summary: Investigation of whole genome gene expression level changes in colonic tissue response to DSS and CMFG administration

overall_design: C57BL/6 mice (female, 8 week of age) were obtained from the SPF Biotechnology Co., Ltd, Beijing, China. Throughout the acclimatization and study periods, all animals were maintained on a 12 hr light-dark cycle (21 ± 2°C) under specific pathogen-free conditions and had access to food and water ad libitum. CMFG administration suspended in PBS was administered by oral gavage in CMFG + DSS group mice from day 0 to day 21. Mice in the DSS group underwent oral gavage of PBS. DSS colitis (DSS group and CMFG+DSS group) was induced by administration of 2.5% DSS (w/v; molecular weight, 36-50 kDa; MP Biomedicals, UK) in drinking water ad libitum for 7 days. Colonic tissues were immediately snap-frozen in liquid nitrogen and homogenized. Total RNA recovered from four separate group include DSS and CMFG with DSS.

first: Junjun

last: Wang

first: Cong

last: Liu

first: Shimeng


title: Identification and Analysis of Dysregulated lncRNA, microRNA and mRNA expression profiles and construction of ceRNA network in THP-1 macrophage infected with Talaromyces marneffei

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

overall_design: Refer to individual Series


title: Genome-wide analysis of PTBP1-regulated retained introns in mESCs

status: Public on Nov 18 2020

city: LOS ANGELES

first: Chia-ho

last: Lin

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

summary: Intron retention (IR) is an alternative splicing event where mRNAs containing unspliced introns are exported to the cytoplasm and then either translated, giving rise to new protein isoforms, or degraded via the nonsense-mediated decay pathway. However, unspliced introns are also seen in nuclear RNA. Some of these are spliced at a low rate but do eventually become fully spliced and their respective mRNAs exported, while others stay retained and are recognized by nuclear decay machineries. IR has been shown to be regulated during granulocyte and neuronal differentiation and in some cancers, and a subset of the nuclear retained introns, called detained introns, have been implicated in growth control pathways. Despite many findings on IR and its biological significance, it is still not clear whether an incompletely spliced intron observed is a true retained intron that is exported as an mRNA or is a product of slow splicing that remains in the nucleus. A better understanding is needed of the molecular events that reduce intron excision rate and determine the release of an RNA for export. We have found that some genes in mouse embryonic stem cells (mESCs) produce RNAs that are highly associated with the high molecular-weight nuclear pellet (chromatin), rather than the soluble nucleoplasm or cytoplasm. This chromatin-associated RNA is polyadenylated, usually contains one or more incompletely spliced introns, and is often extensively bound by polypyrimidine tract-binding protein 1 (PTBP1). We hypothesize that PTBP1 inhibits splicing of these introns, and this causes sequestration of the transcript on chromatin. We are studying the role of PTBP1 in inhibiting intron excision and anchoring RNAs in the nuclear and chromatin compartments of mESCs.

overall_design: E14 mESCs were treated with eGFP (negative control), PTBP1 and PTBP1+PTBP2 siRNAs for 48 hours. The cells were fractionated, and total RNA from each subcellular compartment was extracted. PolyA+ RNA was isolated for RNA sequencing and intron retention analyses. Three biological replicates from each condition were used.

first: Han

middle: Y

last: Lim

first: Douglas

middle: L

last: Black


title: Transcription factor enrichment analysis (TFEA): Quantifying the activity of hundreds of TFs from a single experiment

status: Public on Dec 18 2020

city: Boulder

first: Dylan

middle: J

last: Taatjes

state: CO

address: Campus Box 596

department: Biochemistry

institute: University of Colorado Boulder

summary: Detecting differential activation of transcription factors (TFs) in response to perturbation provides insight into global cellular processes. We present here Transcription Factor Enrichment Analysis (TFEA), a robust and reliable computational method that can detect differential activity of hundreds of TFs given any set of perturbation data. TFEA draws inspiration from GSEA and detects positional motif enrichment within an ordered list of regions of interest (ROI). As ROI are typically directly inferred from the data, we also introduce muMerge, a statistically principled method that generates a consensus list of ROIs from multiple replicates and conditions. TFEA is broadly applicable to data types that inform on transcriptional regulation, including CAGE data, ChIP-Seq, and accessibility data (e.g. ATAC-Seq). We demonstrate that TFEA can not only identify key TFs that respond to a perturbation, but also temporally unravel complex regulatory networks with time series data. Consequently, TFEA serves as a “hypothesis-generating engine” that provides an easy, rigorous, and cost-effective means to broadly assess TF activity to yield new biological insights about basic cellular processes.

overall_design: CRISPR/Cas9 edited MCF10A cells (full length wild type p53 cDNA was inserted at transcriptional start site in exon 2) were treated with 10uM nutlin3a and 0.01% DMSO (control) for 3 hours with a total of 2 biological replicates. Nuclei were isolated and PRO-seq libraries were constructed and sequenced.

first: Cecilia

middle: B

last: Levandowski

first: Zachary

last: Maas

first: Jonathan

middle: D

last: Rubin


title: Profiling of aPL response in mouse monocytes

status: Public on Nov 17 2020

city: Mainz

first: Johannes

last: Braun

address: Langenbeckstr. 1

department: Center for Thrombosis and Hemostasis (CTH)

institute: University Medical Center, Johannes Gutenberg-University Mainz

summary: We profiled CD115-selected mouse spleen monocytes after stimulation with aPL HL7G and after stimulation with Tlr7 agonist R848, Tlr9 agonist CpGB and Tlr3 agonist Poly I/C

overall_design: Monocytes were stimulated for 3 hours followed by total RNA extraction

first: Wolfram

last: Ruf

first: Anna

last: Etzold

first: Ulrich

last: Zechner


title: Apc and ApcKras

status: Public on Nov 11 2020

city: Glasgow

first: Andrew

last: Campbell

address: Switchback Road

country: United Kingdom

institute: CRUK Beatson Institute


title: miRNA expression analysis of DICER1 knock-out cell lines

status: Public on Nov 14 2020

city: Shinjuku-ku

first: Shin-ichiro

last: Ohno

state: Tokyo

address: 6-1-1 Shinjuku

department: Molecular Pathology

country: Japan

institute: Tokyo Medical University

summary:
To confirm the lack of expression of most miRNAs in DICER1 knock-out cell lines, we performed miRNA microarray analysis.
The purpose of this study is to classify DICER1-dependent Small RNA and independent Small RNA using DICER1 cells using deficient cell lines, and to identify novel small RNA and small RNA processing mechanisms.

overall_design: DICER1 knock-out cell clones (DICER1 KO #1, #2) were made by CRSPR/Cas9 system. The deletion of DICER1 gene were cofirmed by sequence and immunoblotting.


title: Gene expression analysis of WT, Apc and ApcKras mouse intestine

summary: Oncogenic KRAS mutations and inactivation of the APC tumour suppressor co-occur in colorectal cancer (CRC). Despite efforts to target mutant KRAS directly, most therapeutic approaches focus upon downstream pathways, albeit with limited efficacy. Moreover, mutant KRAS alters the basal metabolism of cancer cells, rendering them ‘addicted’ to glutamine supporting proliferation. We show that concomitant mutation of Apc and Kras in the mouse intestinal epithelium profoundly rewires metabolism, increasing glutamine consumption. Furthermore, SLC7A5, a glutamine antiporter, is critical for colorectal tumorigenesis in models of both early and late-stage metastatic disease. Mechanistically, SLC7A5 maintains intracellular amino-acid levels following KRAS activation through transcriptional and metabolic reprogramming. This supports the increased demand for bulk protein synthesis that underpins enhanced proliferation of KRAS-mutant cells. Moreover, targeting protein synthesis, via mTORC1 inhibition, cooperates with Slc7a5 deletion to abrogate growth of established KRAS-mutant tumours. Together, these data suggest SLC7A5 as an attractive target for therapy-resistant KRAS-mutant CRC.

overall_design: Whole mouse intestinal tissue was removed from WT, Apc fl/fl, Kras G12D/+ or Apc fl/fl Kras G12D/+ mice, RNA was extracted and gene expression analysis was performed using the Affymetrix GeneChip Mouse Genome 420 2.0 microarray.

first: Arafath

last: Najumudeen

first: Kathryn

last: Gilroy

first: Owen

last: Sansom


title: Acute CD8+ T cell responses to viral infection harbor Tcf1-dependent stem-like cells that quantitatively yield central memory

status: Public on Oct 30 2020

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics


title: Time course transcriptome of Plasmodium falciparum parasite of 3D7 strain

status: Public on Oct 20 2020

city: Singapore

first: Zbynek

last: Bozdech

state: Select if applicable

department: Molecular Genetics&Cell Biology

country: Singapore

institute: Nanyang Technological University

summary: The time course transcriptome were generated in Plasmodium falciparum parasite of 3D7 strain by collecting RNA samples every 2 hours during 48 hours of the full intraerythrocytic developmental cycle.

overall_design: A total of 25 transcriptome collected every 2 hours over the 48-hour parasite's intraerythrocytic life cycle

first: Grennady

last: Wirjanata

first: Jaishree

last: Tripathi

first: Michal

last: Kucharski

first: Sourav

last: Nayak

first: Lei

last: Zhu


title: Transgenerational Disease Specific Epigenetic Sperm Biomarkers after Ancestral Exposure to Dioxin

status: Public on Dec 02 2020

city: Pullman

first: Michael

last: Skinner

address: Abelson 507

institute: WSU

summary: Dioxin is one of the most common historic industrial contaminants with several major industry and government accidents having exposed large numbers of the worldwide population over the past century. Previous rat studies have demonstrated the ability of dioxin (2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)) exposure to promote the epigenetic transgenerational inheritance of disease susceptibility in subsequent generations. The types of disease observed include testis, ovary, kidney, prostate and obesity pathologies. The current study was designed to use an epigenome-wide association study (EWAS) to identify potential sperm DNA methylation biomarkers for specific transgenerational diseases. The transgenerational F3 generation dioxin lineage male rats with and without a specific disease were compared to identify differential DNA methylation regions (DMRs). The genomic features of the DMRs are characterized. Observations demonstrate that disease specific epimutation DMRs exist for the transgenerational dioxin lineage rats that can potentially be used as epigenetic biomarkers for testis, ovary, kidney, prostate and obesity diseases. These disease specific DMRs were associated with genes that have previously been shown to be linked with these diseases. This EWAS for transgenerational disease identified epigenetic biomarkers and provides the proof of concept of the potential to develop similar biomarkers for humans to diagnose disease susceptibilities and facilitate preventative medicine.

overall_design: Analysis of the transgenerational actions of dioxin used outbred Sprague Dawley female rats (F0 generation) transiently exposed (TCDD 100 ng/kg BW/day) during days 8 to 14 of gestation. The F1 generation animals (direct fetal exposure) were bred to generate the F2 generation (direct germline exposure), which were bred to generate the F3 generation (transgenerational so no direct exposure). The dioxin lineage was aged to 1 year and euthanized for pathology and sperm epigenetic analysis. No sibling or cousin breedings (crosses) were used to avoid any inbreeding artifacts. Generally 6–8 founder gestating females from different litters were bred and 25–50 individuals of each sex obtained for each generation.

first: Millissia

last: Ben Maamar

first: Eric

last: Nilsson

first: Jennifer

last: Thorson

first: Daniel

last: Beck


title: RNA binding of Saccharomyces cerevisiae Ssd1

status: Public on Oct 23 2020

city: Edinburgh

first: Edward

middle: William Joseph

last: Wallace

address: Waddington Building, Max Born Crescent

department: Institute for Cell Biology, School of Biological Sciences

institute: University of Edinburgh

summary: We quantified the exact RNA binding sites of the Ssd1 protein in Saccharomyces cerevisiae, in exponential growth and heat shock conditions, using the CRAC protocol. We used a His-TEV-protein A tag (HTP) on the C-terminal of the genomic copy of Ssd1, with the 3'UTR replaced by the 3'UTR/terminator from the K. lactis Ssd1 homolog, followed by a KlURA3 selection marker.

overall_design: Five samples: two biological replicates of CRAC binding to Ssd1-HTP tagged protein at both of 30C and 42C 16min, and a negative control sample of background strain BY4741 with no tagged protein.

first: Rosey

last: Bayne


title: Elimination of Saccharomyces paradoxus viral dsRNA leads to transcriptional and phenotypic alterations

city: Vilnius

first: Elena

last: Serviene

address: Akademijos 2

country: Lithuania

institute: Nature Research Centre

summary: Here we determine the impact upon the loss of M66 dsRNA alone and both L-A-66 along with M66 on the host S. paradoxus transcriptional changes. In Pet [L+M-] and [L-M-] cells we have found 941 and 651 differently expressed genes (DEGs), respectively. In total, there were 1234 and 535 DEGs in Spo [L+M-] and [L-M-] cells, respectively.

overall_design: Examination of transcriptional and phenotypic alterations in response to S. paradoxus viral dsRNA elimination

first: Juliana

last: Luksa

first: Bazilė

last: Ravoityte


title: Epigenome analysis of cord blood DNA from infants born into the UPBEAT study

status: Public on Nov 05 2020

city: Oxford

first: Elie

last: Antoun

state: United Kingdom

address: Nuffield Department of Medicine

department: CAMS China Oxford Institute (CAMS-COI

institute: University of Oxford

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling of umbilical cord blood buffy coat DNA samples. The Illumina Infinium MethylationEPIC array was used to obtain DNA methylation profiles across approximately 850,000 CpGs. Samples included 557 cord blood samples born to obese women in the UPBEAT trial, with and without gestational diabetes mellitus (GDM), to determine the association between maternal GDM and hyperglycaemia during pregnancy on the methylation in the infant.

overall_design: Bisulphite converted DNA from the 557 samples were hybridised to the Illumina Human Infinium MethylationEPIC array.


title: Acute CD8+ T cell responses to viral infection harbor Tcf1-dependent stem-like cells that quantitatively yield central memory [ATAC-seq]

first: Tania

last: Wyss

summary: Central memory CD8+ T cells (TCM) can protect from secondary pathogen infection, from chronic infection and cancer as a result of their stem cell-like properties. However, the developmental origin of central memory cells and consequently the basis of their stemness have not been resolved. By monitoring the expression of the transcription factor Tcf1 (Tcf7), which is essential for central memory formation, we identified a small subset of CD8+ T cells present during the acute response to primary infection. These cells lacked cytotoxic effector function, resembled TCM both transcriptionally and epigenetically, had stem cell-like properties, and quantitatively yielded TCM. Stemness effector phase Tcf7+ CD8+ T cells depended on Tcf1 protein expression and on a set of Tcf1-dependent genes associated with adult stem cells. Stemness was thus not acquired subsequent to antigen clearance but was maintained in rare CD8+ T cells responding to acute infection and these cells quantitatively yielded TCM.

overall_design: Naive Tcf7GFP P14 cells (CD45.2+) were transferred into B6 recipient mice (CD45.1) prior to infection with LCMV Armstrong (Arm). Tcf7GFPhi and Tcf7GFP- P14 cells were flow sorted on day 8 or day 28 post infection based CD45.2+ CD45.1-. In addition P14 cells were flow sorted from the spleen of naive mice based CD8+ CD62L+ (Naive). Regions of open chromatin were assessed by ATACseq, using Illumina HiSeq 4000 technology.

first: Daniela

last: Pais Ferreira

first: Werner

last: Held


title: Gene expression profiling of rice developing leaves in response to elevated CO2

status: Public on Oct 10 2020

city: Sendai

first: Yonghyun

last: Kim

state: Miyagi

address: Aramaki, Aoba-ku

department: Graduate School of Agricultural Science

institute: Tohoku University

summary: Elevated CO2 (eCO2) condition has influence on developing leaf growth of rice (Oryza sativa cv. Nipponbare), specifically lower than P4 (plastochron number) stage, resulting in decrease in leaf size compared with that grown at ambient CO2 (aCO2). In this case, decrease in leaf size seems to be one of acclimation process at CO2 replete environment despite of the fact that number of tiller increase during CO2 replete periods; however, it is not yet elucidated which endogenous signal play a precise role in depression of developing leaf growth in those process. In this context, to elucidate precise signal interaction between mature and developing leaf of rice at eCO2 environment, we profiled gene expressions of developing rice leaf (P4) using oligo DNA microarray 4X44K RAP-DB (Agilent Technologies, Santa clara, CA).

overall_design: eCO2 induced gene expression in rice developing leaf  at eCO2 was measured at 7 h and 13.5 h after elevated CO2 treatment on daytime. Four independent experiments were performed at each time (7 and 13.5 h) using different samples

first: Mitsue

last: Miyao


title: Epigenome-Wide Association Study for Transgenerational Disease Epimutation Sperm Biomarkers following Ancestral Exposure to Jet Fuel Hydrocarbons

status: Public on Oct 01 2020

summary: Jet fuel hydrocarbons is the generic name for aviation fuels used in gas-turbine engine powered aircrafts. Due to the widespread use of jet fuel hydrocarbons, this compound has been recognized as the single largest chemical exposure for military personnel. Previous animal studies have demonstrated the ability of jet fuel (JP-8) exposure to promote the epigenetic transgenerational inheritance of disease susceptibility in subsequent generations. The diseases observed include late puberty, kidney, obesity and multiple disease pathologies. The current study was designed to identify potential sperm DNA methylation biomarkers for specific transgenerational diseases. Observations identify few disease specific differential DNA methylation regions (DMRs) called epimutations in the transgenerational F3 generation great-grand-offspring rats ancestrally exposed to jet fuel. The potential epigenetic DMRs were identified for late puberty, kidney, obesity, and multiple diseases, and found to be predominantly disease specific. These disease specific DMRs have associated genes previously shown to be linked with each of these specific diseases. Therefore, the germline (i.e. sperm) has environmentally induced ancestrally derived epimutations that have the potential to transgenerationally transmit disease susceptibilities to subsequent generations. Epigenetic biomarkers for specific diseases could be developed as medical diagnostics to facilitate clinical management of disease and allow preventative medicine therapeutics.

overall_design: From embryonic day E8 to E14 the F0 generation gestating females were administered daily intraperitoneal injections of JP-8 hydrocarbon (jet fuel obtained from Lt Dean Wagner, Dayton, OH), 500 mg/kg BW/day, or dimethyl sulfoxide (DMSO) (vehicle) with an equal volume of sesame oil (Sigma) to prevent irritation at the injection site. The no observable adverse effect level (NOAEL) for JP-8 is 500-1000 mg/kg BW/day. The offspring F1, F2 and F3 generations were all aged to 90 days of age and bred within the generation and within the jet fuel lineage. The F3 generation is the first without a direct exposure to jet fuel and is thus called the transgenerational generation. All the animals were aged to 1 year and euthanized for pathology and sperm collected for epigenetic analyses. No sibling or cousin breeding was used to prevent any inbreeding artifacts in the control or jet fuel lineages. An MeDIP-seq approach was used to identify DMRs associated with specific transgenerational diseases.


title: Lung type II alveolar epithelial cells collaborate with CCR2+ inflammatory monocytes in host defense against acute viral infection

status: Public on Sep 22 2020

city: New York

first: Joseph

last: Luna

state: NY

address: 1230 York Ave #64

institute: The Rockefeller University

summary: The pulmonary immune system consists of a network of tissue-resident cells as well as immune cells that are recruited to the lungs during infection and/or inflammation. How these immune components communicate during an acute DNA viral infection is not well understood. Intranasal infection of mice with vaccinia virus causes lethal pneumonia and systemic dissemination. Here we report that vaccinia host range protein C7 is a critical virulence factor. We provide evidence that lung type II alveolar epithelial cells (AECIIs) provide first-line of defense against viral  infection by inducing IFN-b and IFN-stimulated genes via the activation of the MDA5 and STING-mediated nucleic acid-sensing pathways and the type I IFN positive feedback loop. This leads to the recruitment and activation of CCR2+ inflammatory monocytes in the lungs, which are indispensable to fight against viral dissemination. Our data provide novel insights into how the lung AECIIs orchestrate innate immune responses to defend pulmonary viral infection.

overall_design: RNAseq of delta C7 vaccinia virus infection in lung AECII cells from WT or MDA5/STING KO mice; RNAseq of lung AECII cells  treated with interferon beta; RNAseq of lung monocytes with WT or delta C7 vaccinia virus

first: Ning

last: Yang

first: Peihong

last: Dai

first: Yi

last: Wang

first: Charles

last: Rice

first: Liang

last: Deng


title: Characterization of epigenomic and transcriptomic changes upon TGF-beta treatment in NMuMG cells [DnaseI-seq]

city: Sevilla

first: Jose

middle: C.

last: Reyes

address: Av. Américo Vespucio

department: Genome biology

country: Spain

institute: CABIMER

summary: TGFβ cytokines have crucial roles in development, proliferation, tissue homeostasis, differentiation, and immune regulation. Consequently, alterations in TGFβ signaling underlie numerous diseases, including cancer.  Moreover TGFβ is one of the most potent inductors of EMT (epithelial to mesenchymal transition) in normal and oncogenic epithelial cells from different origins. During EMT, cells undergo an extensive reorganization of cell adhesion complexes, cytoskeletal architecture, and extracellular matrix interactions and acquire increased motility and invasion properties. However, little is known about the genomic repertoire of enhancers activated by TGFβ, the chromatin dynamics during this process, or the SMAD (main effectors of TGFβ pathway) partners in epithelial cells. To address these outstanding questions about the genomic regulation mediated by TGFβ in epithelial cells we determine and characterize the enhancer atlas of the TGFβ response in normal murine mammary gland (NMuMG) epithelial cells, a well-established model for TGFβ-dependent EMT. To achieve this we performed ATAC-seq, ChIP-seq against typical histone modifications for enhancers and promoters (H3K27ac, H3K4me1 and H3K4me3) and ChromRNA-seq (to identify enhancer RNAs) analyses at two different time points after TGFβ treatment (2h and 12h) to study the enhancers dynamics during this process. We also performed a transcriptomic analyses (RNA-seq) at same time points to correlate genomic regulation to transcriptional changes upon TGFβ treatment. We show that TGFβ promotes a fast and widespread increase of chromatin accessibility in most enhancers of the cell line, irrespectively of whether the enhancer will become activated or repressed. We also observed that activated enhancers are strongly enriched for SMAD2/3/4 and AP-1 footprints. In contrast, decommissioned enhancers present footprints for TEAD, HNF1A, or HNF1B TF (and not for SMAD2/3/4). Strikingly, analyses of the regulated genes around TGFβ-regulated enhancers revealed TGFβ regulatory domains that can encompass several genes and that are constrained by 3D chromatin conformation. In these domains enhancer targeting is more promiscuous than previously anticipated.

overall_design: DNaseI-seq analysis of NMuMG mouse glandular epithelial cells  treated with TGFβ1 at  2 hours with vehicle as control (after 6 hours of serum and insulin starvation) were generated by deep sequencing, in duplicates, using Illumina HiSeq2000.

middle: C

last: Guerrero-Martínez


title: Characterization of epigenomic and transcriptomic changes upon TGF-beta treatment in NMuMG cells [ATAC-seq_2]

overall_design: ATAC-seq analysis of NMuMG mouse glandular epithelial cells  treated with TGFβ1 at 10 minutes or 2 hours with vehicle as control (in starvation or complete medium conditions respectively) were generated by deep sequencing, in duplicates, using Illumina HiSeq2000.


title: Characterization of epigenomic and transcriptomic changes upon TGF-beta treatment in NMuMG cells [ChromRNA-seq]

overall_design: Chromatin-enriched RNA sequencing of NMuMG mouse glandular epithelial cells  treated with TGFβ1 at 2h and 12h or with vehicle as control were generated by deep sequencing, in duplicates, using Illumina HiSeq2000.


title: Search for a novel diagnostic marker for liver cancer.

status: Public on Oct 09 2020

city: Hefei

first: yongwei

last: zhang

state: China

address: anhui medical university

institute: First Affiliated Hospital of Anhui Medical University

summary: Analysis of the circular RNA expression proﬁles of tumor and normal tissue samples from Hepatocellular carcinoma (HCC).Find potential circular RNA to serve as diagnostic marker for liver cancer.

overall_design: Tumor and non-tumor parts are extracted from obtained HCC tissues.

first: Yongwei

last: Zhang

first: Yeben

last: Qian


title: Epigenome-Wide Association Study for Pesticide (Permethrin and DEET) Induced DNA Methylation Epimutation Biomarkers for Specific Transgenerational Disease

status: Public on Nov 12 2020

first: Michael

last: Skinner

summary: Permethrin and N,N-diethyl-meta-toluamide (DEET) are the pesticides and insect repellent most commonly used by humans. These pesticides have been shown to promote the epigenetic transgenerational inheritance of disease in rats. The current study was designed as an epigenome-wide association study (EWAS) to identify potential sperm differential DNA methylation regions (DMRs) for specific transgenerational disease. Outbred Sprague Dawley gestating female rats (F0) were exposed to the pesticide combination including Permethrin and DEET. Their great-grand offspring (F3) were only transgenerationally exposed to pesticides. The transgenerational adult male rat sperm were collected from individuals with single and multiple diseases and compared to non-diseased animals to identify DMRs associated with transgenerational disease transmission. The exposure of gestating female rats to a permethrin and DEET pesticide combination promoted testis disease, prostate disease, kidney disease, and the presence of multiple disease in the subsequent great-grand offspring F3 generation. Interestingly, the majority of the disease specific sperm DMR associated genes were previously found to be linked to relevant disease specific genes.

overall_design: Analysis of the transgenerational actions of multiple pesticide chemicals used outbred Sprague Dawley female rats (F0 generation) transiently exposed to pharmacological doses of permethrin (150 mg/kg bodyweight/day) and DEET (40 mg/kg bodyweight/day) during days 8 to 14 of gestation. The F1 generation animals (direct fetal exposure) were bred to generate the F2 generation (direct germline exposure), which were bred to generate the F3 generation (transgenerational so no direct exposure).  The pesticides lineage animals were aged to 1 year and euthanized for pathology and sperm epigenetic analysis. No sibling or cousin breedings (crosses) were used to avoid any inbreeding artifacts. Generally 6–8 founder gestating females from different litters were bred and 25–50 individuals of each sex obtained for each generation.

first: Jennifer

last: Thorson

first: Daniel

last: Beck

first: Millissia

last: Ben Maamar

first: Eric

last: Nilsson


title: Characterization of epigenomic and transcriptomic changes upon TGF-beta treatment in NMuMG cells

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

overall_design: Refer to individual Series


title: Characterization of epigenomic and transcriptomic changes upon TGF-beta treatment in NMuMG cells [ChIP-seq]

overall_design: Binding profiles of H3K27ac, H3K4me1 and H3K4me3 from NMuMG mouse glandular epithelial cells  treated with TGFβ1 at 2h and 12h or with vehicle as control were generated by deep sequencing, in duplicates, using Illumina HiSeq2000.


title: The amino acid transporter SLC7A5 is required for efficient growth of KRAS-mutant colorectal cancer

first: Andrew

last: Campbell

overall_design: RNA samples were prepared from 1) small intestinal tissue samples of 3 independent animals per genotype or 2) from small intestinal tissue samples of 4 indepdent animals treated with vehicle or rapamycin per group or from 3 Apc iKras organoid tumour lines isolated from intestinal tissue of 3 independent animals per group treated with or without doxycycline for 24 or 48h. Each experimental setting includes a control group of 3 animals/lines - these are samples (tissue) or (organoid).

first: Arafath

last: Najumudeen

first: Kathryn

last: Gilroy

first: Owen

last: Sansom


title: Chemicals orchestrate reprogramming with hierarchical activation of master transcription factors primed by endogenous Sox17 activation

first: Fan

last: Guo

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Mouse somatic cells can be chemically reprogrammed into pluripotent stem cells (CiPSCs) through an intermediate extraembryonic endoderm (XEN)-like state. However, it is elusive how the chemicals orchestrate the cell fate alteration. In this study, we analyze molecular dynamics in chemical reprogramming from fibroblasts to a XEN-like state. We find that Sox17 is initially activated by the chemical cocktails, and XEN cell fate specialization is subsequently mediated by Sox17 activated expression of other XEN master genes, such as Sall4 and Gata4. Furthermore, this stepwise process is differentially regulated. The core reprogramming chemicals CHIR99021, 616452 and Forskolin are all necessary for Sox17 activation, while differently required for Gata4 and Sall4 expression. The addition of chemical boosters in different phases further improves the generation efficiency of XEN-like cells. Taken together, our work demonstrates that chemical reprogramming is regulated in 3 distinct “prime–specify–transit” phases initiated with endogenous Sox17 activation, providing a new framework to understand cell fate determination.

overall_design: The transcriptomes of 808 single cells were detected during the reprogramming process (from d0 to d20)

first: Chan

last: Gu

first: Zhenghao

last: Yang

first: Xiaochan

last: Xu

first: Chao

last: Tang

first: Yang

last: Zhao


title: Characterization of epigenomic and transcriptomic changes upon TGF-beta treatment in NMuMG cells [ATAC-seq]

first: Jose

last: Reyes

overall_design:
ATAC-seq analysis of NMuMG mouse glandular epithelial cells  treated with TGFβ1 at 2h and 12h or with vehicle as control were generated by deep sequencing, in duplicates, using Illumina HiSeq2000.

Please note that each processed data file was generated from both replicate samples and is linked to the corresponding rep1 sample records.

last: Guerrero-Martínez


title: Single-cell RNA sequencing elucidates cell populations in the murine and human tympanic membrane

status: Public on Nov 03 2020

city: San Francisco

first: Aaron

last: Tward

address: 505 Parnassus AVE

institute: UCSF

summary: Previous descriptions of the cellular makeup of the tympanic membrane (TM) describe three basic cell types: keratinocytes, fibrofblasts, and muscosal cells. To better understand the diversity of cells in this tissue, we performed single-cell RNA sequencing on dissociated murine and human TMs. We identified the basic cell types previously known, as well as subtypes of cells in each group. Notably, keratinocyte cell clusters spanning the known differentiation kierarchy were identified, including two groups of undifferentiated keratinocytes which we propose make distinct contributions to maintaining the TM epidermis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-cell RNA sequencing of two samples from murine TMs (epidermal and fibrous/mucosal) and two samples from a healthy human TM (lateral and medial)

first: Stacey

last: Frumm

first: Shengyang

last: Yu


title: Gene expression profiling of hypertrophic and failing cardiomyocytes identifies new players in heart failure

status: Public on Sep 15 2020

city: Utrecht

first: Cornelis

middle: J.

last: Boogerd

address: Uppsalalaan 8

department: Developmental Biology and Stem Cell Research

country: Netherlands

institute: Hubrecht Institute

summary:
Aim - Pathological cardiac remodeling is characterized by cardiomyocyte hypertrophy and fibroblast activation, which can ultimately lead to heart failure (HF). Genome-wide expression analysis on heart tissue has been instrumental for the identification of molecular mechanisms at play. However, these data were based on signals derived from all cardiac cell types. Here we aimed for a more detailed view on molecular changes driving cardiomyocyte hypertrophy and failure to aid in the development of therapies to reverse maladaptive remodeling.
Methods and results - Utilizing cardiomyocyte-specific reporter mice exposed to pressure overload by transverse aortic banding (TAB), we obtained gene expression profiles of hypertrophic (one-week TAB) and failing (eight-weeks TAB) cardiomyocytes. We identified subsets of genes differentially regulated and specific for either stage. Among these, we found upregulation of known marker genes for HF, such as Nppb and Myh7. Additionally, we identified a set of genes specifically upregulated in failing cardiomyocytes and that so far have not been studied in HF, including the platelet isoform of phosphofructokinase (PFKP). Human cardiomyocytes subjected to 7-day NE/AngII treatment recapitulated the upregulation of the failure-induced genes indicating conservation. RNA-seq on failing and healthy human hearts confirmed increased expression for several failure-induced genes and allowed for expressional correlation to NPPB/MYH7. Finally, suppression of Pfkp in PE-treated primary cardiomyocytes reduced stress-induced gene expression and hypertrophy, suggesting a role in cardiomyocyte failure.
Conclusion - Using cardiomyocyte-specific transcriptomic analysis we identified novel failure-induced genes relevant for human HF, and show that PFKP is a conserved failure-induced gene that can modulate cardiomyocyte stress response.

overall_design: RNA-sequencing on cardiomyocytes from 12 ventricule samples from mice of sham, hypertrophic or failing hearts.

first: Marta

last: Vigil-Garcia

first: Charlotte

last: Demkes

first: Joep

last: Eding

first: Danielle

last: Versteeg

first: Hesther

last: de Ruiter

first: Ilaria

last: Perini

first: Monika

last: Gladka

first: Folkert

middle: W

last: Asselbergs

first: Aryan

last: Vink

first: Magdalena

last: Harakalova

first: Alexander

last: Bossu

first: Eva

last: van Rooij


title: Early termination of the Shiga toxin transcript generates a regulatory small RNA

status: Public on Sep 16 2020

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

summary: Enterohaemorrhagic E. coli is significant human pathogen that causes disease ranging from haemorrhagic colitis to haemolytic uremic syndrome. The later can lead to potentially fatal renal failure and is caused by the release of Shiga toxins that are encoded within lambdoid bacteriophages. The toxins are encoded within the late transcript of the phage and are regulated by anti-termination of the PR’ late promoter during lytic induction of the phage. During lysogeny, the late transcript is prematurely terminated at tR’ immediately downstream of PR’, generating a short RNA that is a by-product of anti-termination regulation. We demonstrate that this short transcript binds the small RNA chaperone Hfq, and is processed into a stable 74 nt regulatory small RNA that we have termed, StxS. StxS activates expression of the general stress response sigma factor, RpoS, through direct interactions with an activating seed sequence within the 5’ UTR. StxS represses expression of Shiga toxin 1 and activation of RpoS promotes high cell density growth under nutrient limiting conditions. Many phages utilise anti-termination to regulate the lytic/lysogenic switch and our results demonstrate that short RNAs generated as a by-product of this regulation can acquire regulatory small RNA features and modulate host fitness.

overall_design: The study includes three sequencing datasets that mapped 1. Total RNA-seq reads (biological triplicate data), 2. RNA 5' ends using dRNA-seq (single TEX+ and TEX- datasets), and 3. RNA 3' ends using Term-seq (triplicated datasets).

first: Brandon

last: Sy


title: Glyphosate Induced Transgenerational DNA Methylation and Histone Retention Sperm Epigenetic Biomarkers for Disease

status: Public on Sep 12 2020

first: Michael

middle: K

last: Skinner

department: SBS

summary: The herbicide glyphosate has been shown to promote the epigenetic transgenerational inheritance of pathology and disease in subsequent great-grand offspring (F3 generation). This generational toxicology suggests the impacts of environmental exposures need to assess subsequent generations. The current study was designed to identify epigenetic biomarkers for glyphosate induced transgenerational disease. Following a transient glyphosate exposure of a gestating female rat (F0 generation), the subsequent transgenerational F3 generation, with no direct exposure, were aged to 1 year and animals with specific pathologies identified. The pathologies investigated included prostate disease, kidney disease, obesity, and presence of multiple disease. The sperm were collected from the males and used to identify specific differential DNA methylation regions (DMRs) associated with the pathologies. In addition, the differential histone retention sites (DHRs) were examined for the various pathologies as well. Unique signatures of DMRs and DHRs for each pathology were identified for the specific diseases. Interestingly, at a lower statistical threshold overlapping sets of DMRs and DHRs were identified that were common for all the pathologies. The DMR and DHR gene associations were identified and correlated with known pathology associated genes. While the disease biomarker DMR and DHR did not meet typical statistical significance levels, these results may help design future studies with reduced variability. Observations indicate transgenerational epigenetic biomarkers of disease pathology can potentially be identified in the sperm that can assess disease susceptibility. These biomarkers may also suggest epigenetic diagnostics could be used to facilitate preventative medicine.

overall_design: Analysis of the transgenerational actions of glyphosate used outbred Sprague Dawley female rats (F0 generation) transiently exposed (25 mg/kg body weight glyphosate daily) during days 8 to 14 of gestation. The F1 generation animals (direct fetal exposure) were bred to generate the F2 generation (direct germline exposure), which were bred to generate the F3 generation (transgenerational so no direct exposure). A control lineage used F0 generation gestating females administered vehicle control dimethyl sulfoxide (DMSO) or phosphate buffered saline (PBS). The control and glyphosate lineages were aged to 1 year and euthanized for pathology and sperm epigenetic analysis. No sibling or cousin breedings (crosses) were used to avoid any inbreeding artifacts in either the control or glyphosate lineages. Generally 6–8 founder gestating females from different litters were bred and 25–50 individuals of each sex obtained for each generation.

first: Millissia

last: Maamar

first: Daniel

last: Beck

first: Jennifer

last: Thorson

first: Eric

last: Nilsson

first: Deepika

last: Kubsad


title: Identification of genes regulated by Fer2 in PAM neurons using an overexpression approach

status: Public on Sep 08 2020

city: Geneva

first: Federico

last: Miozzo

address: 30 Quai Ernest-Ansermet, CH-1211

institute: University of Geneva

summary: The transcription factor Fer2 plays a neuroprotective role in the dopaminergic neurons of the fly brain, but the underlying molecular mechanisms are not understood. By performing RNA-seq on isolated dopaminergic PAM neurons after Fer2 constitutive overexpression, we identified over one hundred genes differentially regulated in response to PAM-specific Fer2 overexpression.

overall_design: RNA-seq on isolated dopaminergic PAM neurons from 14 day-old flies overexpressing a UAS-Fer2::FLAG transgene driven by a PAM specific GAL4 (R58-GAL4). Flies not carrying the UAS-Fer2::FLAG transgene were used as controls. N=3 per group.

first: Nicolas

last: Loncle

first: Emi

last: Nagoshi


title: ANTICANCER AGENT P-bi-TAT LINKS THE THYROID HORMONE RECEPTOR ON INTEGRIN αvβ3 TO CANCER CELL METABOLISM/ATP GENERATION II

status: Public on Aug 28 2020

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary: Microarray analysis was carried out on human GBM cells exposed to P-bi-TAT (10-6 M tetrac equivalent) for 24 h. P-bi-TAT significantly downregulated electron transport chain genes ATP5A1 (ATP synthase A1), ATP51, ATP5G2, COX6B1 (cytochrome c oxidase subunit 6B1), NDUFA8 (NADH dehydrogenase [ubiquinone] FA8), NDUFV2 and other NDUF genes, SLC25A6 (solute carrier group 2), UCP2 ([mitochondrial] uncoupling protein 2) and COX5A. The NDUF and ATP genes are also relevant to control of oxidative phosphorylation and transcription. Six additional NDUF genes linked to oxidative phosphorylation were affected. Conclusions. P-bi-TAT caused downregulation of expression of a panel of genes involved in electron transport, oxidative phosphorylation, and cytoplasmic ribosomal protein generation in GBM cells. A key component of the anticancer activity of P-bi-TAT relates to disordering of ATP generation mechanisms in tumor cells.

overall_design: Studied the anticancer functions of P-bi-TAT in GBM cells in terms of modulation of transcription by the drug of genes essential to cancer cell mitochondrial function. Compared with triplicate GBM U87MG cells with GBM U87MG cells treated with P-bi-TAT (30 µM) for 24 h.

first: Gennadi

last: Glinsky

first: Kavitha

last: Godugu

first: Thangirala

last: Sudha

first: Mehdi

last: Rajabi

first: Shaker

last: Mousa

first: Paul

last: Davis


title: Mis-regulation of Nucleoporins 98 and 96 leads to translational stress that promotes hallmarks of tumorigenesis.

status: Public on Sep 01 2020

city: Ann Arbor

first: Laura

last: Buttitta

state: MI

address: 5218 Biological Sciences Bldg., 1105 North University Ave.

department: Molecular, Cellular, Developmental Biology

institute: University of Michigan

summary: Compromising Nups 98 and 96 triggers cell death and compensatory proliferation via JNK and TNF signaling that becomes tumorigenic when apoptosis is blocked.

overall_design: Transcriptome changes were determined by comparing levels of transcripts in L3 wings expressing the apoptosis inhibitor (P35) in combination with either Nup98-96 RNAi or white RNAi.

first: Kiriaki

last: Kanakousaki

first: Ajai

last: Pulianmackal

first: Kerry

middle: A

last: Flegel

first: Olga

last: Grushko


title: ANTICANCER AGENT P-bi-TAT LINKS THE THYROID HORMONE RECEPTOR ON INTEGRIN αvβ3 TO CANCER CELL METABOLISM/ATP GENERATION

overall_design: Studied the anticancer functions of P-bi-TAT in GBM cells in terms of modulation of transcription by the drug of genes essential to cancer cell mitochondrial function. Compared with triplicate GBM primary cells samples with GBM primary cells treated with P-bi-TAT (30 µM) for 24 h.

first: G

first: K

first: T

first: M

first: S

first: P


title: Fer2 in the fly brain

status: Public on Aug 27 2020

first: Federico


title: Identification of genes regulated by Fer2 in the fly brain using an overexpression approach

summary: The transcription factor Fer2 plays a neuroprotective role in the dopaminergic neurons of the fly brain, but the underlying molecular mechanisms are not understood. By performing RNA-seq on fly heads after Fer2 inducible overexpression, we identified hundreds of genes differentially regulated in response to Fer2 overexpression. Combining this dataset with Fer2 ChIP-seq on the fly head, we obtained a list of 26 direct target genes, bound and regulated by Fer2.

overall_design: RNA-seq on fly heads from 14 day-old flies overexpressing a UAS-Fer2::FLAG transgene driven by a heat-inducible GAL4 (hs-GAL4). Heat-shock treatment was used to induce Fer2 overexpression. Flies not carrying the UAS-Fer2::FLAG transgene were used as controls. N=3 per group.

first: Emi


title: Genome-wide map of the binding sites of the transcription factor Fer2 in the fly brain

summary: The transcription factor Fer2 plays a neuroprotective role in the dopaminergic neurons of the fly brain, but the underlying molecular mechanisms are not understood. By using chromatin immunoprecipitation coupled to sequecing (ChIP-seq), we identified over 250 genomic binding sites bound by Fer2 in the fly brain. Combining this dataset with RNA-seq of fly heads upon inducible Fer2 overexpression, we obtained a list of 26 direct target genes, bound and regulated by Fer2.

overall_design: ChIP-seq on fly heads from 14 day-old flies expressing a GFP::V5-tagged Fer2 genomic transgene (Fer2::GFP::V5) in a Fer2 mutant background. Anti-V5 antivbody was used to immunoprecipitate Fer2. As a negative control, ChIP-seq was performed on w1118 flies. N=2 per genotype.


title: Single cell transcriptomics of human islet ontogeny defines the molecular basis of beta cell dedifferentiation in T2D

city: Philadelphia

first: Jonathan

last: Schug

state: Pennsylvania

address: 12-156 Smilow Ctr Trans Research

department: School of Medicine

institute: University of Pennsylvania

summary: Dedifferentiation of pancreatic beta cells may reduce islet function in type 2 diabetes (T2D). However, the prevalence, plasticity and functional consequences of this cellular state remain unknown.  We employed single-cell RNAseq to detail the maturation program of alpha and beta cells during human ontogeny. We show that although both alpha and beta cells mature in part by repressing non-endocrine genes, alpha-cells retain hallmarks of an immature state, while beta-cells attain a full beta-cell specific gene expression program. In islets from T2D donors, both alpha- and beta-cells return to a less mature expression profile, de-repressing the juvenile genetic program and exocrine genes while increasing expression of exocytosis, inflammation and stress response signaling pathways. These changes support the increased proportion of beta-cells displaying suboptimal function observed in T2D islets. These findings provide new insights into the molecular program underlying islet cell maturation during human ontogeny and the loss of transcriptomic maturity  that occurs in islets of type 2 diabetics.

overall_design: More that 619 cells from islets of one newborn (84), five toddlers (27, 17, 15, 12, 23), two adolescents (14, 22), four adult (22, 22, 37, 54) controls, and ten T2D donors (24, 13, 11, 30, 15, 23, 11, 19, 34, 24) were sequenced using Fluidigm C1 single-cell RNA-Seq. Numbers in parathesis indicates number of cells sequenced that were assigned a cell type following rigorous evalution.

first: Dana

last: Avrahami

first: Yue

last: Wang

first: Eseye

last: Feleke

first: Chengyang

last: Liu

first: Ali

last: Naji

first: Benjamin

last: Glaser

first: Klaus

middle: H

last: Kaestner


title: Identification of ALPPL2 as a novel specific and functional surface marker for naïve pluripotency

status: Public on Aug 11 2020

city: Shanghai

first: Bi

last: Yan

address: Siping Road 1239

institute: Tongji university

summary: We report ALPPL2 as a prominently specific and functional surface marker for naïve pluripotency. By performing RNA-seq analysis of TJ-1# and iCRISPR nESCs and pESCs, APG+ cells at different time points during naïve reprogramming, we validate ALPPL2’s specificity for naïve pluripotent state at transcriptional level. Deep analysis of the transcriptome differences between Wild Type (WT), ALPPL2 knockdown (AKD) cells via RNA-seq, Wild Type (WT), ALPPL2 knockout (AKO) and IGFBP1 knockout (IKO) individual colonies in detail via Smart-seq, and performing RNA immunoprecipitation (RIP) using IGF2BP1 antibody in nESCs followed by RNA-seq or qPCR analysis, we identify that ALPPL2 is essential for both establishment and maintenance of naïve pluripotency via interacting with IGF2BP1 to stabilize TFCP2L1 and STAT3 mRNA level.

overall_design: Examination of mRNA profiles of WT, ALPPL2 KO, ALPPL2 KD, IGF2BP1 KO and IGF2BP1 enrichment by deep sequencing.

first: Yan

last: Bi

first: Yanping

last: Zhang

first: Yixuan


title: Characterization of epigenomic and transcriptomic changes upon TGF-beta treatment in NMuMG cells [RNA-seq]

first: Jose

last: Reyes

overall_design: Transcriptome profiles of NMuMG mouse glandular epithelial cells  treated with TGFβ1 at 2h and 12h or with vehicle as control were generated by deep sequencing, in duplicates, using Illumina HiSeq2000.

last: Guerrero-Martínez


title: RNA sequencing of mouse bone marrow dendritic cells

city: La Jolla

first: Paul

last: Insel

address: 9500 Gilman Drive

department: Pharmacology

institute: UC San Diego

summary: Bulk mRNA from mouse bone marrow-derived dendritic cells (BMDCs) was sequenced. Samples were obtained from Wild Type (C57BL/6J) mice, or mice with GNAS knocked out specifically in CD11c +ve cells.

overall_design: 4 mice with GNAS knockout and 5 WT mice

first: Amy

middle: M

last: Chinn

first: Krishna

last: Sriram


title: Common Marmoset Gut Microbiome Profiles in Health and Intestinal Disease

status: Public on Aug 26 2020

city: Cambridge

first: Alexander

last: Sheh

state: ma

address: 77 Massachusetts ave 16-828

department: Biological Engineering

institute: MIT

summary: We report the RNAseq data from captive common marmosets with gastrointestinal diseases housed at MIT. Samples were collected at necropsy from the duodenum and jejunum from 3 animals presenting with intestinal bowel disease (IBD) and 3 animals with duodenal strictures/ulcers. To determine the transcriptomic profile of animals with strictures, we evaluated the duodenal tissue immediately adjacent to the stricture lesion and compared it to the duodenum of non-stricture (IBD) animals as a non-stricture control. To determine the transcriptomic profile of animals with IBD, we evaluated the jejunum of animals with IBD with the jejunum of non-IBD (stricture) animals as a non-IBD control.  Minimal pathology was observed in the non-IBD control but enteritis was noted in non-stricture controls. We report that stricture may affect the intestinal absorption and lipid metabolism in marmosets, while IBD increases immune responses.

overall_design: Examination of ulcers/stricture in the duodenum and IBD in the jejunum of marmosets.


title: MiR-520b inhibits endothelial activation by targeting NF-κB p65

status: Public on Aug 08 2020

city: Beijing

first: Yang

last: Bin

address: 167 Beilishi Road

institute: Chinese Academy of  Medical Sciences and Peking Union Medical College

summary: We aimed to elucidate the impact of miR-520b on endothelial cell (EC) activation. To determine the potential targets of miR-520b, we performed RNA-seq analysis by transfecting miR-520b mimics in primary human umbilical vein endothelial cells (HUVECs).

overall_design: To determine the potential targets of hsa-miR-520b, we synthesized the oligonucleotide sequence of mature miR-520b and then transfected it into HUVECs. MiR-520b mimics or control were transfected into cells at a final concentration of 100 nM using Lipofectamine RNAiMAX (Invitrogen) following manufacturer’s protocol. 48 hours later, the cells were harvested for further use.

first: Bin

last: Yang

first: Huijun


title: Transcriptomic analysis of human spermatogenesis

status: Public on Aug 01 2020

city: Fontenay aux roses

first: Pierre

last: Fouchet

address: 10, route du panorama

country: France

institute: CEA

summary: Microarray analysis was performed in order to detail the global changes of gene expression in human spermatogenesis and decipher molecular pathways underlying spermatogonial stem cell fate

overall_design: Human germinal cells from adult testicular biopsies were sorted by flow cytometry, RNA exracted and used for Affymetrix microarray analysis. Three individual samples of 10,000 cells were processed for each germinal population

first: M

last: Givelet

first: V

last: Firlej

first: B

last: Lassalle

last: Barraud-Lange

first: P


title: Sequencing of Induced pluripotent stem cell derived retinal progenitor cells

city: Bangalore

first: Rajarshi

last: Pal

address: CCAMP, NCBS

country: India

institute: Eyestem research

summary: Age-related macular degeneration (AMD) is a result of degeneration/damage of the retinal pigment epithelium (RPE) while retinitis pigmentosa (RP), an inherited early-onset disease, results from premature loss of photoreceptors. A promising therapeutic approach for both is the replacement of lost/damaged cells with human induced pluripotent stem cell (hiPSC)-derived retinal cells. We studied the chemistry of retinal progenitor cells derived from iPSC through our patented unified differentiation protocol with the aim to take the cells for clincal benefits to needly patients. RPE expressed tight junction proteins, showed pigmentation and ciliation, and secreted polarization-related factors vascular endothelial growth factor (VEGF) and pigment epithelium-derived factor (PEDF). PRP expressed neural retina proteins and cone and rod markers, and responded to KCl-induced polarization. Transcriptomic analysis demonstrated an increase in the expression of mature retinal tissue-specific genes coupled with concomitant downregulation of genes from undesired lineages. RPE transplantation rescued visual function in RCS rats shown via optokinetic tracking and photoreceptor rescue. PRP transplantation improved light perception in NOD.SCID-rd1 mice, and positive electroretinography signals indicated functional photoreceptor activity in the host's outer nuclear layer. Graft survival and integration were confirmed using immunohistochemistry, and no animals showed teratoma formation or any kind of ectopic growth in the eye.

overall_design: We analysed Induced pluripotent stem cell and their derivatives -RPE and photoreceptor progenitor (PRP) cells at different timepoints. Following are the samples included in the study (1) Induced pluripotent stem cell (2) Retinal progenitors- obtained by dual SMAD and WNT inhibition from iPSC (3)  RPE progenitors - obtained by removing the rosettes and culturing the epithelial pockets (4) Retinal Pigment Epithelium - pigmented RPE progenitors (5) Photoreceptor precursors - Rosette structures obtained in retinal progenitors enzymatically selected and expanded in culture.  De novo-generated RPE and PRP were analyzed by Next generation sequencing.


title: Transcriptomic analysis of mouse spermatogonia and human spermatogenesis

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

overall_design: Refer to individual Series


title: Transcriptomic analysis of mouse spermatogonia

summary: Microarray analysis was performed in order to detail the gene expression profiles in murine  b-2M-SPa-6+c-kit-undifferentiated  and b-2M-SPa-6+c-kit+ differentiating  spermatogonia. These data were used to compare human and mouse transcriptomes of undifferentiated spermatogonia.

overall_design: Mouse germinal cells from adult testicular biopsies were sorted by flow cytometry, RNA extracted and used for Affymetrix microarray analysis. Three samples of 10,000 cells (one mice per sample) were processed for each germinal population


title: Pancreatic and intestinal endocrine cells share common transcriptomic signatures and gene regulatory networks

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

summary:
Background: Endocrine cells of the digestive system, including the pancreatic endocrine cells (PECs) clustered in the islets of Langerhans and the enteroendocrine cells (EECs) scattered in the intestinal epithelium, play an important role in metabolism. Although EECs and PECs are located in distinct organs, they share many features and several common genes control their differentiation.  In this study, we investigated comprehensively the similarity of EECs and PECs by defining their transcriptomic landscape and comparing the regulatory networks controlled by pax6b, a key player in both EECs and PECs.
Results: RNA-sequencing was performed on EECs and PECs isolated from wild-type and pax6b mutant zebrafish. Data mining of wild-type zebrafish EEC data confirmed the expression of orthologs for most known mammalian EEC hormones but also revealed the expression of three additional neuropeptide hormones (Proenkephalin-a, Calcitonin-a and Adcyap1a) not yet reported to be expressed by EECs in any species. Comparison of transcriptomes from EECs, PECs and other zebrafish tissues highlights a very close similarity between EECs and PECs, with more than 70 % of genes being expressed in both endocrine cell types. Comparison of Pax6b-regulated genes in EECs and PECs revealed a significant overlap.  pax6b loss-of-function does not affect the total number of EECs and PECs but instead disrupts the balance between cell subtypes, leading to an increase of ghrelin- and motilin-like expressing cells in both the intestine and pancreas at the expense of other endocrine cells such as beta- and delta-cells in the pancreas and pyyb-expressing cells in the intestine. Finally, we show that the homeodomain of Pax6b is dispensable for its action in both EECs and PECs.
Conclusion:  This study highlights the close relatedness of EECs and PECs at the transcriptomic and regulatory levels, supporting the hypothesis of a common phylogenetic origin and underscoring the potential implication of EECs in metabolic diseases such as Type 2 diabetes.

overall_design: RNA-sequencing of 13 samples. Pancreatic endocrine cell (pax6b:GFP +) transcriptomic profiles of 27 hpf (hours post fertilization) wild type (WT) and pax6b-/- (MUT) zebrafish embryos were generated in triplicates. Enteroendocrine cell (pax6b:GFP +) transcriptomic profiles of 4d wild type (WT) and pax6b-/- (MUT) zebrafish emryos were generated in 4 replicates and 3 replicates, respectively.

first: Estefania

last: Tarifeño-Saldivia

first: Justine

last: Pirson

first: Anne-Sophie

last: Reuter

first: Isabelle

last: Manfroid

first: Marianne

last: Voz

first: Bernard

last: Peers


title: p53-inducible long non-coding RNAs encode functional peptides in hepatocellular carcinoma cells

status: Public on Jul 18 2020

city: Guangzhou

first: Jian-Hua

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: Sun Yat-sen University


title: p53-inducible long non-coding RNAs encode functional peptides in hepatocellular carcinoma cells [RNA-seq]

summary: To identify p53-regulated lncRNAs responsive to DNA damage in human hepatocellular carcinoma (HCC) cells, we conducted paired-end and strand-specific RNA-seq using HepG2 wild-type and p53-knockout (HepG2-KO-p53) cells, which were devoid of p53 protein, using the CRISPR-Cas9 system treated with or without the DNA-damaging agent adriamycin (ADR)

overall_design: RNA-seq profiles of HepG2 p53 wild-type (WT) and HepG2 p53 knockout (p53−/−) treated with ADR or not were generated by deep sequencing, in two independent experiments, using Illumina Xten. Raw RNA-seq data reads were aligned to the UCSC hg19 reference genome using Hisat2 (version 2.0.5) with default parameters.

first: Wen-Li

last: Xu

first: Bing

last: Deng

first: Peng-Hui

last: Lin

first: Chang

last: Liu

last: Li

first: Ke-Ren

last: Zhou

first: Hui

first: Liang-Hu

last: Qu


title: Consequences of postnatal Tshz3 deletion: implications for autism spectrum disorder

status: Public on Sep 09 2020

first: Bianca

last: Habermann

address: 163, Avenue de Luminy

institute: Aix-Marseille University, CNRS, IBDM UMR 7288

summary: We recently identified heterozygous deletions of the gene TSHZ3, which encodes a Zn-finger transcription factor, in patients with a syndrome including autistic features and provided evidence in mice for a link between Tshz3 haploinsufficiency, defects in cortical projection neurons (CPNs) and autism spectrum disorder (ASD)-like abnormalities. To get more insight into when and where TSHZ3 is required for the proper development of the brain, we generated and characterized a novel mouse model of conditional Tshz3 deletion in projection neurons from postnatal day 2-3 onward. These mice exhibit altered striatal expression of genes encoding for synaptic components, electrophysiological and synaptic changes in striatal cholinergic interneurons, , as well as  ASD-relevant behavioral deficits. These data, by revealing a crucial postnatal role of TSHZ3 in the development and function of the corticostriatal circuitry that might be determinant for ASD pathogenesis, offer a novel ASD model and further open the possibility for an early postnatal therapeutic window for the syndrome linked to TSHZ3 haploinsufficiency.

overall_design: mRNA sequencing of TSHZ3 deletion in striatum versus wild-type, 3 replicates each at P34, 3-4 mice per replicate

first: Xavier

last: Caubit

first: Emeric

last: Dubois

first: Laurent

last: Fasano

first: Ahmed

last: Fatmi

first: Dany

last: Severac


title: mDrop-seq: Massively parallel single-cell RNA-seq of Saccharomyces Cerevisiae and Candida Albicans

status: Public on Jul 22 2020

city: Chicago

first: Ryan

middle: Patrick

last: Dohn

state: IL

address: 5841 S. Maryland Ave.

department: Department of Medicine

institute: University of Chicago

summary: We present microbial Drop-seq or mDrop-seq, a high-throughput scRNA-seq technique that is used on two yeast species, Saccharomyces cerevisiae, a popular model organism and Candida albicans, a common opportunistic pathogen. We benchmarked mDrop-seq for sensitivity and specificity and used it to profile 35,109 S. cerevisiae cells to detect variation in mRNA levels between them. As a proof of concept, we quantified expression differences in heat-shocked S. cerevisiae using mDrop-seq. We detected differential activation of stress response genes within a seemingly homogenous population of S. cerevisiae under heat-shock. We also applied mDrop-seq to C. albicans cells, a polymorphic and clinically relevant yeast species with thicker cell wall compared to S. cerevisiae. Single cell transcriptomes in 39,705 C. albicans cells was characterized using mDrop-seq under different conditions, including exposure to fluconazole, a common anti-fungal drug.

sample_organism:
Saccharomyces cerevisiae
Candida albicans

overall_design: scRNA-seq data of S. cerevisiae with and without heat shock treatment and C. albicans with and without fluconazole treatment.

first: Rebecca

last: Back

first: Alan

last: Selewa

first: Heather

last: Eckart

first: Anindita

last: Basu


title: Whole transcriptome analysis for kidney aging in mice [miRNA-seq]

status: Public on Jul 11 2020

city: Xi’an

first: Fan

middle: Fan

last: Gao

state: Shaanxi

address: West Yanta Road 277

department: Dialysis Department of Nephrology Hospital

institute: the First Affiliated Hospital of Xi’an Jiaotong University

summary: The goals of this study are to explore the differential expression of non-coding RNAs in mice kidne during aging

overall_design: The non-coding RNA expression of  3-month-old, 12-month-old and 24-month-old C57BL/6 mice kidney  was performed using RNA-sequencing.

first: Hongli

last: Jiang

first: Lei

last: Chen

first: Fanfan


title: Whole transcriptome analysis for kidney aging in mice [non-coding RNA]

summary: The goals of this study are to explore the differential expression of non-coding RNAs in mice kideny during aging


title: Whole transcriptome analysis for kidney aging in mice


title: Role of FTO in ovarian cancer

status: Public on Jul 01 2020

city: CHICAGO

first: Manoj

last: Kandpal

state: Illinois

address: 1256 W NORTHSHORE AVE, 3R

institute: Northwestern University


title: Role of FTO in ovarian cancer (MeRIP-Seq)

summary: RNA methylation plays an important role fine tuning translation and subsequently regulating cellular responses and cell fate. The fat mass- and obesity-associated protein (FTO) was recognized as an m6A demethylase and described as an oncogenic factor in leukemia and brain tumors. FTO expression levels are suppressed in ovarian tumors and ovarian cancer stem cells (CSCs). FTO induce cyclic AMP activity through targeting PDE4B and PDE1C by down-regulation of m6A levels in the mRNA transcript. In all or findings point to a tumor suppressor function of FTO in high grade serous OC

overall_design:
GFP (control) or FTO-GFP (treatment) over-expression in OVCAR-5 cells
3 biological replicates for IgG input for GFP, 3 biological replicates for m6A pull-down for GFP, 3 biological replicates for IgG input for FTO-GFP, and 3 biological replicates for m6A pull-down for FTO-GFP

first: Kandpal

last: Manoj

first: Hao

last: Huang

first: Daniela

last: Matei


title: Transcriptional profiling of pax2a-Low and pax2a-High thyroid follicular cells in zebrafish

status: Public on Jun 25 2020

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

institute: Shiv Nadar Institution of Eminence

summary: Thyroid follicular cells (TFCs) are responsible for generation, storage and release of thyroid hormone. Single-cell analysis of zebrafish thyroid gland demonstrated transcriptional heterogeneity within the TFC population (Gillotay et al., bioRxiv, 2020. doi: 10.1101/2020.01.13.891630. GEO dataset for single-cell RNA-Seq.: GSE133466). Particularly, TFC displayed transcriptional heterogeneity in the expression of pax2a, a transcription factor involved in differentiation and maturation of TFCs. To validate the genetic heterogeneity, we generated a pax2a knock-in line, in which mKO2 expression is driven by endogenous pax2a locus. Using Tg(tg:nls-EGFP); pax2a:mKO2-Knock-in, we sorted for TFCs (GFP+) and separated the pax2a-Low (mKO2-Low) and pax2a-High (mKO2-High) populations for NGS.

overall_design: We used fluorescence-activated cell sorting (FACS) coupled with next generation RNA-Sequencing to profile pax2a-high and pax2a-low TFCs from 5 mpf animals. Cells were sorted directly into lysis buffer provided in ReliaPrep™ RNA Miniprep Systems (Promega Z6011) and mRNA isolated according to the manufactor’s protocol. cDNA was generated using Ribozome depletion protocol followed by adapter ligation. Sequencing was performed on llumina NextSeq500. Reads were splice-aligned to the zebrafish genome, GRCz11, using HISAT2. Featurecounts was used to assign reads to exons thus eventually getting counts per gene.

middle: P


title: Small RNA sequencing  of HCV infected hepatoma cells

status: Public on Aug 18 2020

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

summary: HCV infection requires both virus and host factors, including endogenous genes, a large proportion of which are noncoding RNAs (ncRNAs). The identification and mechanistic elucidation of these stably and conservatively expressed RNAs will shed light on HCV gene diagnosis and therapy. Nevertheless, most studied ncRNAs in HCV are microRNAs, with numerous other types of ncRNAs being neglected, such as long noncoding RNAs (lncRNAs) or small nucleolar RNAs (snoRNAs). Here, using two different hepatoma cell lines, we performed small RNA sequencing and analyzed the differential expression of microRNAs and snoRNAs, which provide data for further functional validation of snoRNAs and microRNAs during HCV infection.

overall_design: Huh7 and Huh7.5.1 cells were infected with JFH-1 HCVcc, and total RNA was extracted at specific time points (0, 6, 24, and 48 h) postinfection using TRIzol reagent (Invitrogen, Carlsbad, USA) according to the manufacturer’s instructions for transcriptome sequencing. For small RNA sequencing, 10 μg of total RNA for each sample was used for small RNA cDNA library preparation, and microRNA and snoRNA were mapped and analyzed.

first: Xijing

last: Qian

first: Zhongtian

last: Qi


title: ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer

status: Public on Jun 24 2020

first: Lu

last: Wang

address: 303 E. Superior Street Simpson Querrey 7-414

department: Biochemistry and Molecular Genetics

summary: The bromodomain and extra-terminal (BET) protein BRD4 functions as a transcriptional activator and is a therapeutic target for different human cancers. Here, we report a critical link between Polycomb repressive deubiquitinase-BAP1 (PR-DUB) complex and BRD4, which is bridged by the physical interaction between additional sex combs-like protein 3 (ASXL3) in small cell lung cancer (SCLC). We further showed that ASXL3 functions as an adaptor protein, which directly interacts with BRD4-extra-terminal (ET) domain via a novel BRD4 binding motif (BBM), and maintains chromatin occupancy of BRD4 at active enhancers. Genetic depletion of ASXL3 leads to a genome-wide reduction of histone H3K27Ac levels as well as BRD4 occupancy, resulting in a similar change of gene expression profile induced by BET inhibitors. Pharmacologically-induced inhibition with BET specific chemical degrader (dBET6) selectively inhibits cell proliferation of a subtype of SCLC, characterized with high expression of ASXL3. Collectively, this study provides mechanistic insight into the oncogenic function of ASXL3-BRD4 axis in SCLC.

overall_design: To determine gene expression and histone modification change in ASXL3 depleted cells

first: Zibo

last: Zhao

first: Elizabeth

last: Bartom


title: Downregulation of the Ubiquitin-E3 Ligase KPC1 promotes glioblastoma progression through upregulation of SerpinE1 [array]

status: Public on Jun 17 2020

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

summary: Two glioblastoma cell lines (LN18 and HS863) were stable transfected with control empty vector (EV) or RNF123-vector (KPC1). The objective of this experiment was to determine NFKB1-targets regulated by RNF123 overexpression in glioblastoma cell lines. To do that LN18 and HS863 cell lines with RNF123 overexpression were compared to control empty vector. In the present study, we utilized the combination of RPPA and RNA-Sequencing. By comparing both datasets, we identified commonly proteins and genes differentially expressed in control versus RNF123-overexpressing cells.

overall_design: Total protein and RNA were extracted from glioblastoma cell lines

first: Xiaowen

first: Matias

last: Bustos

first: Matthew

last: Salomon

first: Gordon

middle: B

last: Mills

first: Ying

last: Mao

middle: S


title: Transcriptomic profiles of the nasal epithelium from the Genes-environments & Admixture in Latino Americans (GALA) II study

status: Public on Jul 13 2020

city: Denver

first: Satria

last: Sajuthi

state: Colorado

address: 1400 Jackson St.

institute: National Jewish Health

summary:
Childhood asthma is a complex disease historically defined by partially overlapping clinical features, including recurrent respiratory symptoms and reversible airway obstruction. However, the heterogeneity observed in clinical disease and airway pathology suggests that the “traditionally” defined asthma population is composed of multiple subgroups (i.e., endotypes), each with a distinct pathogenesis. Gene expression profiling of bronchial airway brushings identified the type 2-high asthma endotype, defined by excessive airway inflammation driven by type 2 cytokines, which was found in ~50% of subjects. Importantly, response to inhaled corticosteroid treatment was limited to this type 2-high endotype. The clinical utility of type 2-high asthma endotyping and the discovery of other endotypes have been limited by the need to perform an invasive bronchoscopy to obtain the bronchial brushings for analysis. Moreover, research bronchoscopies cannot be performed in children. Less invasive methods for the identification of asthma endotypes are needed.

To this end, we found that the type 2-high asthma endotype can be identified by gene expression profiling of minimally invasive nasal airway epithelium brushings. Moreover, we found high nasal expression of the type 2 cytokine, IL-13,4 was associated with higher risk of asthma exacerbations among Puerto Ricans, who have the highest asthma morbidity and mortality in the U.S. Herein, we propose to use whole transcriptome sequencing of nasal airway epithelial brushings from Puerto Rican children with asthma to identify the type 2-high and other asthma endotypes, which relate to severity and drug response.

overall_design: We sought to identify clinically relevant endotypes using nasal brushing samples from 695 asthmatic and healthy Puerto Rican children.

first: Cydney

middle: L

last: Rios

first: Jamie

last: Everman

first: Michael

middle: T

last: Montgomery

first: Benjamin

last: Saef

first: Nathan

middle: D

last: Jackson

first: Angel

last: Mak

first: Sam

last: Oh

first: Celeste

last: Eng

first: Vivian

last: Medina

first: Jennifer

last: Elhawary

first: Scott

last: Huntsman

first: Jose

last: Rodriguez-Santana

first: Esteban

middle: G

last: Burchard

first: Max

last: Seibold