title: Transcriptional checkpoints control Neutrophil-driven inflammation

status: Public on May 09 2021

first: Erinke

last: van Grinsven

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

summary: This dataset combines transcriptional and chromatin analysis of neutrophils from the air pouch mouse model, an in vivo model of acute inflammation, with transcriptional analysis of Hoxb8 neutrophils, an in vitro model of neutrophil development.

overall_design: At 6 days after the creation of the air pouch, mice were challenged with 100 µg zymosan injected directly into the pouch. Four hours after zymosan injection the bone marrow, blood, membrane, and exudate were harvested for ATAC-sequencing and RNA-sequencing analysis. Additionally, we used an ex vivo system of murine ER-Hoxb8 neutrophils that phenotypically and morphologically recapitulate neutrophil maturation stages during five days of in vitro culture in the presence of G-CSF. The Hoxb8 cells of day 0, 1, 3, or 5 of development with or without 2 hours of incubation with zymosan were prepared for RNA-sequencing analysis.

first: Tariq

last: Khoyratty

first: Zhichao

last: Ai

first: Sara

last: Mathie

first: Hayley

last: Eames

last: Udalova


title: Nrf1 promotes heart regeneration and repair by regulating proteostasis and redox balance [scRNA-Seq]

status: Public on May 01 2021

city: Dallas

first: Miao

last: Cui

state: Texas

address: UT Southwestern Medical Center Department of Molecular Biology 6000 Harry Hines Blvd.

country: USA

institute: UTSW

type: Expression profiling by high throughput sequencing

summary: Heart disease can be caused by ischemic coronary artery injury, hypertension, and chemotherapy, all of which lead to loss or dysfunction of cardiac muscle. The adult mammalian heart lacks the ability to regenerate. In contrast, the heart of neonatal mice, within the first week after birth, possesses a unique ability to regenerate lost myocardium following injury, mediated by proliferation of cardiomyocytes. The mechanisms whereby neonatal cardiomyocytes adapt to injury-induced stress conditions and activate regenerative cellular programs remain to be defined. Here, we show that Nrf1, an endoplasmic reticulum (ER) bound transcription factor, is expressed in regenerating cardiomyocytes. Genetic deletion of Nrf1 prevented cardiomyocytes from activating a transcriptional program required for heart regeneration, revealed by single-nucleus RNA sequencing (snRNA-seq).  Conversely, adeno-associated virial (AAV) overexpression of Nrf1 protected the adult mouse heart from ischemia/reperfusion (I/R) injury.  Nrf1 also protected human induced pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) from doxorubicin-induced cardiotoxicity. The protective function of Nrf1 is mediated by a dual stress response mechanism involving activation of the proteasome and redox balance. Our findings reveal a mechanistic interplay between adaptive stress responses and heart regeneration, and highlight the central role of Nrf1 in these processes.

overall_design: Exmination of transcriptome changes in neonatal rat ventricular cardiomyocytes overexpresing Nrf1 or Nrf2 .

first: Ning

last: Liu

first: Rhonda

last: Bassel-Duby

first: Eric

middle: N

last: Olson


title: TAK-981

status: Public on Apr 23 2021

city: Cambridge

middle: Scott

last: Lightcap

state: MA

address: 40 Landsdowne Street

institute: Takeda Pharmaceuticals

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Single cell RNA-Seq analysis of A20 tumors derived from tumor-bearing Balb/c mice treated with vehicle or 7.5 mg/kg TAK-981 for 8 h demonstrates induction of IFN1 gene expression in monocytes and T-cells

summary: Single cell RNA-Seq analysis of A20 tumors indicated that the IFN1 signature was derived primarily from monocytes and T cells, not the B cell population which includes A20 tumor cells.  Single cell RNA-Seq analysis characterized the effect of TAK-981 on B cells (n=4513, includes both A20 B lymphoma tumor cells and WT B cells), erythrocytes (n=238), monocytes (n=85) and T cells (n=107) from A20 tumors responding to treatment with TAK-981. Tumors were harvested 8 h after treatment of A20 tumor-bearing Balb/c mice with either vehicle or 7.5 mg/kg TAK-981 and subjected to scRNA-Seq.

overall_design: In vivo treatment of Balb/c mice bearing the A20 tumor with either 7.5 mg/kg TAK-981 or vehicle for 8 h, with tumor harvested and prepared for scRNA-Seq.

middle: S

first: Stephen

last: Grossman

first: Keli

last: Song

first: Pooja

last: Shah

first: Yu

last: Fu

first: Min

middle: Y

last: Lee

first: Dennis

last: Huszar


title: Sex-specific phenotypic effects and evolutionary history of an ancient polymorphic deletion of the human growth hormone receptor

status: Public on Apr 30 2021

city: Buffalo

first: Omer

last: Gokcumen

state: NY

address: 639 Cooke Hall

department: Biological Sciences

institute: University at Buffalo

summary: The deletion of the third exon of the growth hormone receptor (GHR) is one of the most common genomic structural variants in the human genome. This deletion (GHRd3) has been linked to response to growth hormone, placenta size, birth weight, growth after birth, time of puberty, adult height, and longevity. However, its evolutionary history and the molecular mechanisms through which it affects phenotypes remain unresolved. Here, we analyzed thousands of genomes and provide evidence that this deletion was nearly fixed in the ancestral population of anatomically modern humans and Neanderthals. However, it underwent a paradoxical adaptive reduction in frequency approximately 30 thousand years ago in East Asia that roughly corresponds with the emergence of archaeological evidence for multiple modern human behaviors, dramatic changes in climate, and a concurrent population expansion. Further, we provide evidence that GHRd3 is associated with protection from edematous severe acute malnutrition primarily in males. Using a mouse line engineered to contain the deletion, we found Ghrd3's effect on the liver transcriptome of male mice grown without any calorie restriction mimics response to calorie restriction through regulation of circadian pathways. In contrast, under calorie restriction, Ghrd3 leads to the female-like gene expression in male livers. As a likely consequence, the dramatic weight difference between male and female mice disappears among GHRd3 mice under calorie restriction. Our data provide evidence for sex- and environment-dependent effects of GHRd3 and are consistent with a model in which the allele frequency of GHRd3 varies throughout human evolution as a response to fluctuations in resource availability.

overall_design: Liver RNAseq of 8 cohorts mice (each n=5) based on all possible combinations of sex (female or male), diet (constantly available, i.e., ad libitum (AL) or 40% calorie restricted (CR)), and genotype (wt/wt or d3/d3) under controlled settings. We raised all of the cohorts under identical conditions until weaning at 30 days old and provided the differential diets for the next 30 days.


title: Nrf1 promotes heart regeneration and repair by regulating proteostasis and redox balance


title: Nrf1 promotes heart regeneration and repair by regulating proteostasis and redox balance [bulkRNA-Seq]


title: Columbia University/NYP COVID-19 Lung Atlas

status: Public on Apr 29 2021

city: New York

first: Jana

last: Biermann

address: 622 West 168th St

institute: Columbia University

summary: We profiled 116,314 cells using snRNA-seq  of 20 frozen lungs obtained from 19 COVID-19 decedents and seven control patients with short postmortem interval (PMI) autopsies. The COVID-19 cohort comprises seven female and 12 male decedents, including 13 patients of Hispanic ethnicity, with an age range from 58 to >89 years who had acquired SARS-CoV-2 infection and succumbed to the disease. The average time from symptom onset to death was 27.5 days (range, 4–63 days). After rapid autopsy with a median PMI of 4 hours (range 2–9 hours) collected tissues were either flash-frozen or frozen following OCT (optimal cutting temperature) embedment and subjected to snRNA-seq using a droplet-based platform (10x Genomics). All included patients had underlying hypertensive disorder and frequently one or more additional co-morbidities associated with increased risk for severe COVID-19.

overall_design:
Single-nuclei RNA sequencing of 116,314 cells from 20 frozen lungs obtained from 19 COVID-19 decedents and seven control patients.

Raw read files to be uploaded to DUOS (https://duos.broadinstitute.org/) due to patient privacy concerns.

first: Benjamin

last: Izar

first: Johannes

middle: C

last: Melms


title: Comparison of gene expression profiles of neonate rat cardiomyocytes (NRCMs) transfected with LacZ, 23k prolactin (PRL), or 16k PRL.

city: Bunkyo-ku

first: Takashi

last: Shimizu

country: Japan

institute: University of Tokyo

summary: Recently, it is reported that multiple signaling pathways are involved with the pathogenesis of PPCM. Here, we show that 23k PRL activates PERK signaling.

overall_design: Total 9 samples were derived from NRCMs with plasmids of LacZ, 23k PRL, or 16k PRL.

first: Ryo

last: Nakaki


title: Chacterization of Day 1 and Day 5 Atlantic salmon adherent head kidney leukocytes (HKLs)

city: St. John's

first: Nicole

last: Smith

state: NL

address: 0 Marine Lab Rd

department: Ocean Sciences

country: Canada

institute: Memorial University

summary: Transcriptional profiling of Atlantic salmon adherent HKLs that were cultured for 1 day (24 h) and cultured for 5 days (120 h). Our previous data (RNA-seq, morphology and phagocytosis) indicate that Day 1 cells are predominatly monocytes while Day 5 cells are predominatly macrophages.

overall_design: Two condition experiment (Day 1 cells and Day 5 cells). 4 biological replicates: 4 Day 1 cells, 4 Day 5 cells.

first: Navaneethaiyer

last: Umasuthan

first: Surendra

last: Kumar

first: Nardos

middle: T

last: Woldemariam

first: Rune

last: Andreassean

first: Sherri

middle: L

last: Christian

first: Matther

last: Rise


title: Genome-wide analysis of gene expression of cutaneous lupus skin samples and lupus nephritis kidney samples

status: Public on Apr 22 2021

city: Worcester

first: John

middle: E

last: Harris

address: 364 Plantation St

department: Dermatology

institute: University of Massachusetts Medical School

summary: Microarray gene expression analyses were performed on human skin samples from cutaneous lupus subtypes (SCLE and CCLE) and normal patients along with human kidney samples from lupus nephritis and normal patients

overall_design: 47 deidentified human samples from formalin fixed, paraffin-embedded skin (6 chronic cutaneous lupus, 10 subacute cutaneous lupus, 10 control skin) and formalin fixed paraffin-embedded kidney (14 lupus nephritis, 7 control kidney)

first: Wei-Che

last: Ko


title: Transcriptional profiling of primary human keratinocytes treated with interferon gamma and/or infected with HSV-2 using Illumina beadarray

status: Public on Apr 21 2021

city: Seattle

first: Tao

last: Peng

state: WA

address: 1100 Fairview Ave N/FHCRC/E5-110

department: Medicine

institute: University of Washington

summary: We aim to analyze the transcriptional profiles of primary human keratinocytes in response to interferon gamma (IFNG) treatment and/or HSV-2 (strain HG-52) infection. The goal is to define IFNG regulated intrinsic immunity of primary human keratinocytes and how HSV-2 infection regulates the intrinsic immunity of primary human keratinocyte.

overall_design: Primary human keratinocytes were untreated or treated with IFNG (100 u/ml) for 48 hours and then mock infected or infected with HG-52 (a HSV-2 strain) for 4 hours. The total RNA were extracted and converted into cDNA. The cRNA transcribed from the cDNA were labled and hybridized to Illumina beadarray (HT-12 v4).


status: Public on May 05 2021

city: Biberach

first: Bernd

last: Weigle

address: Birkendorfer Str. 65

department: Cancer Immunology & Immune Modulation

country: Germany

institute: Boehringer Ingelheim Pharma GmbH&Co KG

summary: Macrophages are pivotal effectors of host immunity and regulators of tissue homeostasis. Understanding of human macrophage biology has been hampered by the lack of reliable and scalable models for cellular and genetic studies. Human iPSC-derived monocytes and macrophages, as an unlimited source of subject genotype-specific cells, will undoubtedly play an important role in advancing our understanding of the role of macrophage biology and implication in human diseases. Here, we present RNA-Seq data of hiPSC-derived monocytes and GM-CSF or M-CSF macrophages generated by a fully optimized differentiation protocol as well as primary myeloid cells.

overall_design: Analysis of bulk RNA-Seq samples from hiPSC-derived monocytes and GM-CSF or M-CSF macrophages (n=5) as well as primary myeloid cells (monocytes, GM-CSF or M-CSF macrophages, n=6). One hiPSC-derived M-CSF macrophages sequencing library did not pass quality check.

first: Di

last: Cui

first: Alexandra

last: Franz

first: Sophie

middle: A

last: Fillon

first: Linda

last: Jannetti

first: Timo

last: Isambert

first: Katrin

last: Fundel-Clemens

first: Heinrich

middle: J

last: Huber

first: Coralie

last: Viollet

first: Alexander

last: Ghanem

first: Akira

last: Niwa

first: Stefan

last: Pflanz


title: Nrf1 promotes heart regeneration and repair by regulating proteostasis and redox balance [Spatial transcriptome]

first: Miao

first: Ning

last: Liu

first: Rhonda

last: Bassel-Duby

first: Eric

last: Olson


title: Identification and functional characterization of long non-coding RNAs associated with epithelial-to-mesenchymal transition

city: Paris

first: Marina

last: Pinskaya

address: rue d'Ulm

country: France

institute: Institut Curie

summary: In the last decade, new high-throughput sequencing techniques have revealed the complexity of the human transcriptome, allowing the characterization of long non-coding (lnc)RNAs. Since their expression has been reported as very specific to tissue, developmental stage and pathological variations, some lncRNAs have been proposed as biomarkers for diagnosis as well as prognosis of tumors. In this project, we aime in identification  of  lncRNAs associated with  the epithelial-to-mesenchymal transition (EMT), a biological process that promotes metastasis. This was performed on an in vitro model (Castro Vega et al, 2015) in which primary HEK cells naturally undergo EMT. Cells were immortalized prior and after EMT, therefore giving rise to the Epi (HA5-Early) and Mes (HA5-Late) cell-lines, which respectively display epithelial and mesenchymal phenotypes. HOTAIR is one the lcnRNAs functionning as a scaffold to tether PRC2 and Lsd1/REST/coREST complexes to gene promoter to epigenetically repress transcription. Its high expression is associated with poor-prognosis cancer and promotes EMT. To decipher a role of PRC2 and Lsd1 interacting domains in HOTAIR function we generated Epi cell lines expressing full length and truncated versions of HOTAIR missing first 5'-300 bp and last 3'-500 bp interacting with HOTAIR partners. Total RNA form these cell lines was extracted and sequenced to reveal HOTAIR targets dependent of its intercation with PRC2 and/or Lsd1.

overall_design: The experiment was performed in biological duplicates of each cell-line (Epi-CTR, Epi-HOT, Epi-HOTΔP and Epi-HOTΔL).

first: Julien

last: Jarroux

first: Claire

last: Bertrand

first: Marc

last: Descrimes

first: Camille

last: Gautier

first: Antonin

last: Morillon


title: HOTAIR lncRNA role in epithelial-mesenchymal transition

type: Genome binding/occupancy profiling by high throughput sequencing


title: Most cancer cell lines give very modest transcriptional regulation following treatment with the SUMO activating enzyme inhibitors TAK-981 or ML-792

last: Lightcap

summary: Modest transcriptional changes has been previously observed in solid tumor cell lines in response to inhibition of SUMOylation by ML-792 and here confirmed with TAK-981, lacking a robust induction of IFN1 genes. Comparable modulation of gene expression in HCT116, MDA-MB-231 and Colo-205 cells by TAK-981 and ML-792. Biological triplicates of HCT116, MDA-MB-231 and Colo-205 cells treated with DMSO, 1 μM ML-792 or 1 μM TAK-981 in vitro for 16 h were analyzed by RNA-Seq. The number of differentially expressed genes (DEGs) with false discovery rate corrected p- values of <0.05 and fold-change values greater than 2 are captured. The degree of gene regulation by TAK-981 is plotted against the degree of gene regulation by ML-792 for the union of their DEGs for each cell line. Data are fitted by linear regression after outliers were removed (7 DEGs from Colo- 205, r^2 = 0.951; 2 DEGs from HCT116, r^2 = 0.836; and 2 DEGs from MDA-MB-231, r^2 = 0.971). Limited and comparable upregulation of human IFN1 mRNA signature in Colo-205, and MDA-MB-231 cells, but not in HCT116 cells, following 16h of treatment with 1uM ML-792 or 1uM TAK-981, as determined by human IFN1 ssGSEA gene signature scores. In vitro treatment of the A20, B16F10, CT26 and MC38 mouse tumor cell lines with TAK-981 did not result in induction of the IFN1 pathway. The overall degree of transcriptional modulation by TAK-981 was relatively modest in the mouse tumor cell lines, with only limited overlap observed in the transcriptional responses to TAK-981, as also observed for the human solid tumor cell lines.

overall_design: In vitro treatment of human cell lines with DMSO, 1 uM TAK-981 or 1 uM ML-792 for 16 h. In vitro treatment of mouse cell lines with DMSO or 1 uM TAK-981 for 16 h.

first: Dennis

last: Huszar


title: Bisulfte sequnencing of Wild Type (Col-0), and miP1aOX in Arabidopsis thaliana

status: Public on Apr 24 2021

city: Frederiksberg C

first: Bin

last: Sun

address: Thorvaldsensvej 40

department: Department of Plant and Environmental Sciences

country: Denmark

institute: Copenhagen Plant Science Centre – University of Copenhagen

type: Methylation profiling by high throughput sequencing

summary: Plants were grown on 1/2 MS for 12 days under LD conditions and DNA was extracted and sequenced

overall_design: Examination of two genotypes (wild type/miP1aOX) and one condition with one replicates each

first: Daniel

last: Straub

first: Stephan

last: Wenkel


title: Profiling of Lsd1 and chromatin marks in epithelial cells overexpressing HOTAIR variants

summary: Epithelial-to-mesenchymal transitions (EMT) underlie a loss of epithelial traits by normal cells during development and neoplastic cells during cancer metastasis. The long noncoding RNA HOTAIR triggers EMT, in part by serving as a scaffold for Polycomb Repressive Complex 2 (PRC2) and thus promoting repressive histone H3 Lys27 methylation. In addition to PRC2, HOTAIR interacts with the Lsd1 lysine demethylase, an epigenetic regulator of cell fate during development and differentiation. Here, we showed that HOTAIR requires the Lsd1-interacting domain, but not the PRC2-interacting domain, to promote migration of epithelial cells. Our results suggest that the HOTAIR-Lsd1 asociation redistributes Lsd1 on chromatin and hence reprograms the epithelial transcriptome.

overall_design: The experiment was performed in biological duplicates for each cell line  following the protocol of CUT&RUN (Skene et al 2018). Immunoprecipitated DNA was sequenced.

first: Dominika

last: Foretek

last: Gabriel

first: Ugo

last: Szachnowski


title: Next Generation Sequencing  of miP1aOX and sum20.1 in Arabidopsis thaliana

overall_design: Examination of two genotypes and one condition with three replicates each


title: Melanoma dedifferentiation induced by interferon-gamma epigenetic remodeling in response to anti-PD-1 therapy

status: Public on May 10 2021

city: Los Angeles

first: Yeon Joo

last: Kim

state: CA

address: Center for Health Sciences 54-200

institute: UCLA

summary: Melanoma dedifferentiation has been reported as a state of cellular resistance to targeted therapies and immunotherapies as cancer cells revert to a more primitive cellular phenotype. Here we show that, counterintuitively, the biopsies of patient tumors that respond to anti-programmed cell death receptor 1 (PD-1) therapy decreased expression of melanocytic markers and increased neural crest markers, suggesting treatment-induced dedifferentiation. When modeling the effects in vitro, we documented that melanoma cell lines that were originally melanocytic differentiated underwent a process of neural crest dedifferentiation when continuously exposed to interferon gamma (IFNγ), through a global chromatin landscape changes leading to enrichment in specific hyperaccessible chromatin regions. The IFNγ-induced dedifferentiation signature corresponded with improved outcomes in patients with melanoma, challenging the notion that neural crest dedifferentiation is entirely an adverse phenotype.

overall_design: RNA sequencing of eight different human melanoma cell lines at baseline, following three days of TNF exposure, or following 2-5 weeks of IFNg exposure.

first: Katherine

middle: M

last: Sheu

first: Jennifer

last: Tsoi

first: Antoni

last: Ribas


title: circRNAs microarray analysis in colorectal caner tissues

status: Public on Apr 17 2021

city: Nanjing

first: yueming

last: sun

state: jiangsu

address: Nanjing medical university

country: China

institute: The First Affiliated Hospital of Nanjing Medical University

summary: Circular RNA (circRNA) is a kind of transcripts characterized by originating from the back-splicing of pre-mRNA. CircRNAs have higher stability than liner transcripts and are more resistant to RNase R due to their loop structure, which makes circRNAs potential diagnostic markers and therapeutic targets for cancer . The biological functions of circRNAs are widely involved in the proliferation, metastasis, apoptosis, and autophagy of various cancers via multiple ways.  To further investage the role of circRNA in CRC, a circRNA micoarray was performed.

overall_design: CapitalBio Technology Human CircRNA Array v2 was designed with four identical arrays per slide (4 x 180K format), with each array containing probes interrogating about 170,340 human circRNAs. Those circRNA target sequences were all from Circbase，Deepbase and Rybak-Wolf20151. Each circRNA was simultaneous detected by a long probe and a short probe. The circRNA array also contain 4974 Agilent control probes.The circRNA array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V13.0 (Agilent). To select the differentially expressed genes, we used threshold values of ≥2 and ≤−2-fold change and a Benjamini-Hochberg corrected p vlaue of 0.05. The data was Log2 transformed and median centered by genes using the Adjust Data function of CLUSTER 3.0 software then further analyzed with hierarchical clustering with average linkage (Eisen et al., 1998). Finally, we performed tree visualization by using Java Treeview (Stanford University School of Medicine, Stanford, CA, USA).

first: Junwei

last: Tang


title: Inhibition of nuclear receptor RORα attenuates cartilage damage in osteoarthritis by modulating IL-6/STAT3 pathwa

status: Public on Apr 20 2021

city: Hong Kong

first: Tongzhou

last: Liang

state: Hong Kong

address: 30 Ngan Ching Street

department: Department of Orthopaedics and Traumatology

institute: The Chinese University of Hong Kong

summary: Osteoarthritis is characterized by cartilage destruction, chronic inflammation, and subchondral sclerosis. Evidence showed that nuclear receptor family is closely associated with cartilage damage in an unclear molecular mechanism. Here, we investigated the role and molecular mechanism of the retinoic acid receptor-related orphan receptor-α (RORα), an important member of nuclear receptor, in regulating cartilage degradation and osteoarthritis pathogenesis. Investigation to osteoarthritis clinical specimen showed that the degree of RORα elevation is positively correlated with the severity of osteoarthritis and cartilage damage. In an in vivo osteoarthritis models induced by anterior crucial ligament transaction, intraarticularly injection of siRora adenovirus reversed the cartilage damage. RORα knock-down increased the protein expression level of anabolic factor such as type II collagen, Aggrecan, and decreased the expression of catabolic factor. RNA-seq data suggested IL-6/STAT3 pathway is significantly down-regulated. Mechanistically, RORα knock-down decreased the expression level of both IL-6 and phosphorylated STAT3. RORα exerted its effect on IL-6/STAT3 signaling in two different ways, which includes interaction with STAT3 and IL6 promoter. Taken together, our findings indicated the pivotal role of RORα/IL-6/STAT3 axis in osteoarthritis progression and confirmed RORα knock-down exerted therapeutic effect in human chondrocyte thus providing a potential drug target in osteoarthritis therapy.

overall_design: mRNA profiles of Vehicle treated and SR3335 treated chondrocyte

first: Bo

last: Gao

first: Dongsheng

last: Huang


title: BAP1 constrains pervasive H2AK119ub1 to control the transcriptional potential of the genome [ChIP-seq]

status: Public on May 03 2021

city: Oxford

first: Nadezda

last: Fursova

address: South Parks Rd

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

summary: Histone-modifying systems play fundamental roles in gene regulation and the development of multicellular organisms. Histone modifications that are enriched at gene regulatory elements have been heavily studied, but the function of modifications found more broadly throughout the genome remains poorly understood. This is exemplified by histone H2A monoubiquitylation (H2AK119ub1), which is enriched at Polycomb-repressed gene promoters but also covers the genome at lower levels. Here, using inducible genetic perturbations and quantitative genomics, we found that the BAP1 deubiquitylase plays an essential role in constraining H2AK119ub1 throughout the genome. Removal of BAP1 leads to pervasive genome-wide accumulation of H2AK119ub1, which causes widespread reductions in gene expression. We show that elevated H2AK119ub1 preferentially counteracts Ser5 phosphorylation on the C-terminal domain of RNA polymerase II at gene regulatory elements and causes reductions in transcription and transcription-associated histone modifications. Furthermore, failure to constrain pervasive H2AK119ub1 compromises Polycomb complex occupancy at a subset of Polycomb target genes, which leads to their derepression, providing a potential molecular rationale for why the BAP1 ortholog in Drosophila has been characterized as a Polycomb group gene. Together, these observations reveal that the transcriptional potential of the genome can be modulated by regulating the levels of a pervasive histone modification.

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design:
Mouse embryonic stem cells in which BAP1 can be conditionally removed were profiled for genomic distribution of histone modifications associated with active transcription (H3K27ac, H3K4me3, and H3K4me1) or Polycomb-mediated gene repression (H2AK119ub1 and H3K27me3), Polycomb factors (RING1B and SUZ12) and RNA Polymerase II (total occupancy (Pol II NTD) and phosphorylated forms associated with transcription initiation or elongation (Pol II Ser5P or Ser2P respectively)), using spike-in calibrated ChIP-seq (cross-linked - for Polycomb factors and Pol II, and native - for histone modifications).
Please note that, as each processed data is associated with multiple samples, they are linked as Series supplementary file and described in the corresponding sample description field.

first: Anne

middle: H

last: Turberfield

first: Emma

last: Findlater

first: Robert

last: Klose


title: HCMV infected Human Fibroblasts UL84 IE2 ChIPSeq

status: Public on Apr 19 2021

city: Reno

first: Cyprian

last: Rossettto

state: NV

address: 1664 North Virginia Street

department: Microbiology & Immunology

institute: University of Nevada, Reno

summary: We report ChIP-seq analsyis of human fibroblasts infected with HCMV strains AD169 and TB40E. ChIP was performed at 20 hpi for IE2 and 3 dpi for IE2 and UL84.

overall_design: ChIP-seq analysis UL84 and IE2 in human fibroblasts infected with HCMV strains AD169 and TB40E

first: Salome

last: Manska

last: Rossetto


title: Bioengineered embryoids mimic post-implantation development in vitro [Embryoids10XG]

status: Public on Apr 12 2021

city: Lausanne

first: Nicolas

last: Broguiere

address: AI 1208 Station 15

department: Sciences de la vie

country: Switzerland

institute: EPFL

summary: Here, we report a bioengineering-inspired approach to simultaneously coax mouse embryonic stem cells (ESCs) into hundreds of uniform epiblast-like (EPI) aggregates in a solid matrix-free manner. When co-cultured with mouse trophoblast stem cell (TSC) aggregates, the resulting hybrid structures initiate gastrulation-like events and undergo axial morphogenesis to yield structures, termed EpiTS embryoids, with a pronounced anterior development, including brain-like regions.

overall_design: Testing the effect of epiblast epithelialization on the development of hybrid embryoids

first: Mehmet

middle: U

last: Girgin

first: Sylke

last: Hoehnel

first: Nathalie

last: Brandenberg

first: Bastien

last: Mercier

first: Alfonso

last: Arias

first: Matthias

middle: P

last: Lutolf


title: Macrophage miR-210 induction and metabolic reprogramming in response to pathogen interaction boost life-threatening inflammation.

status: Public on Apr 01 2021

city: Indianapolis

first: Mircea

last: Ivan

state: IN

address: 980 W. Walnut St.

department: HEMATOLOGY/ONCOLOGY

institute: Indiana University School of Medicine

summary: RNAseq was performed on murine bone marrow-derived macrophages (BMDMs) untreated and following 42 hours LPS/IFN-g treatment.

overall_design: MicroRNAs (miRs) are important regulators of gene expression.The goal of the present study is to compare at transcriptional levels the effect of miR-210 deletion in murine bone marrow-derived macrophages (BMDMs) untreated and following a 42 hours LPS/IFN-g treatment.

first: Massimiliano

last: Mazzone

first: Federico

last: Virga

first: Federica

last: Cappellesso

first: Daniela

last: Taverna

first: Cristina


title: Multipotent progenitors and hematopoietic stem cells arise independently from hemogenic endothelium in the mouse embryo

status: Public on Apr 06 2021

first: Brandon

last: Hadland

address: 1100 Fairview Avenue N., D2-115, P.O. Box 19024

institute: Fred Hutchinson Cancer Research Center

summary: During embryogenesis, waves of hematopoietic progenitors develop from hemogenic endothelium (HE) prior to the emergence of self-renewing hematopoietic stem cells (HSC). Although previous studies have shown that yolk sac-derived erythromyeloid progenitors and HSC emerge from distinct populations of HE, it remains unknown whether the earliest lymphoid-competent progenitors, multipotent progenitors, and HSC originate from common HE. Here we demonstrate by clonal assays and single cell transcriptomics that rare HE with functional HSC potential in the early murine embryo are distinct from more abundant HE with multilineage hematopoietic potential that fail to generate HSC. Specifically, HSC-competent HE are characterized by expression of CXCR4 surface marker and by higher expression of genes tied to arterial programs regulating HSC dormancy and self-renewal. Together, these findings suggest a revised model of developmental hematopoiesis in which the initial populations of multipotent progenitors and HSC arise independently from HE with distinct phenotypic and transcriptional properties.

overall_design: single cell RNA-sequencing (10X Genomics platform) of murine E9-9.5 P-Sp/AGM-derived FACS-isolated VE-Cadherin+CD61+EPCR+ cells.


title: PHF10 subunit of PBAF complex mediates transcriptional activation by MYC

status: Public on Apr 08 2021

city: Moscow

first: Natalia

last: Klimenko

address: 34/5 Vavilova Street

country: Russia

institute: Institute of Gene Biology (IGB) of the Russian Academy of Sciences

summary: The PBAF complex, a member of SWI/SNF family of chromatin remodelers, plays an essential role in transcriptional regulation. We revealed a disease progression associated elevation of PHF10 subunit of PBAF in clinical samples of melanoma. We demonstrated that in melanoma cell lines, PHF10 interacts with MYC and facilitates the recruitment of PBAF complex to target gene promoters, therefore augmenting MYC transcriptional activation of genes involved in the cell cycle progression. Depletion of either PHF10 or MYC induced G1 accumulation and a senescence-like phenotype. Our data identify PHF10 as a pro-oncogenic mechanism and an essential novel link between chromatin remodeling and MYC-dependent gene transcription.

overall_design: RNASeq assay was performed in A375 melanoma cells transfected with control siRNA (two replica), siRNA to PHF10 (four replica), or MYC (two replica). Knockdown of PHF10 and knockdown of MYC were performed as two independent experiments with appropriate controls.

first: N

last: Soshnikova


title: RNA-Seq study on root samples from Olea europaea cultivars

status: Public on Apr 07 2021

city: JAEN

first: Jorge

middle: Antolín

last: Ramirez

state: --- Select a state ---

address: Campus Las Lagunillas s/n 23071

department: Experimental Biology

country: Spain

institute: University of Jaen

summary: Cultivated olive tree (Olea europaea L. subsp. europaea var. europaea) is one of most relevant  worldwide-extended crops. Since this plant has a huge effect on the economy of several regions,  especially in those located in the Mediterranean basin, all efforts focused on its protection have a  great relevance in agriculture sustainability. As all extended crops, olive tree cultivars are under the  threat of a wide range of pathogens. Among them, Verticillium dahliae has been in the spotlight in  the last decades because the disease caused by this soil-borne fungus (Verticillium wilt) is easily  spread and can eventually kill the tree. In this line, many different factors have been studied in order  to shed some light on the molecular/genetic mechanisms underlying the Olea europaea-Verticillium  dahliae interaction, some of them focused on the gene expression pattern of the host. In this study,  the expression pattern of roots from thirty-six O. europaea cultivars with different  resistance/susceptibility degree to Verticillium wilt has been analyzed by RNA-Seq. As a result,  processes involved in plant defense, transcription and root development have emerged as potential  players in the differential response to Verticillium wilt of these cultivars. Additionally, a quite  interesting set of 421 genes with an opposite expression pattern in those cultivars showing extreme  resistance/susceptibility to Verticillium wilt has been discovered, establishing a solid group of  candidates to take into account in future genetic improvement programs.

overall_design: This RNA-Seq study was conducted on 2 biological replicates from 36 Olea europaea root samples (72 individuals).

last: Ramírez-Tejero

first: Francisco

last: Luque


title: IFNγ modulates the immunopeptidome of triple negative breast cancer cells by enhancing and diversifying antigen processing and presentation

city: Clayton

first: Gabriel

last: Goncalves

state: VICTORIA

address: 15 Innovation walk

country: Australia

institute: Monash University

summary: To identify potential T-cell targets for Triple-Negative Breast Cancer (TNBC) vaccination, we examined the effect of the pro-inflammatory cytokine interferon-γ (IFNγ) on the transcriptome, proteome and immunopeptidome of the TNBC cell line MDA-MB-231. Using high resolution mass spectrometry, we identified a total of 84,131 peptides from 9,647 source proteins presented by human leukocyte antigen (HLA)-I and HLA-II alleles. Treatment with IFNγ resulted in a remarkable remoulding of the immunopeptidome, with only a 34% overlap between untreated and treated cells across the HLA-I immunopeptidome, and expression of HLA-II only on treated cells. IFNγ increased the overall number, diversity and abundance of the immunopeptidome, as well as the proportion of coverage of source antigens. The suite of peptides displayed under conditions of IFNγ treatment included many known tumour associated antigens, with the HLA-II repertoire sampling 265 breast cancer associated antigens absent from those sampled by HLA-I. Quantitative analysis of the transcriptome (10,248 transcripts) and proteome (6783 proteins) of these cells revealed 229 proteins and transcripts were commonly differentially  expressed, most of which involved in downstream targets of IFNγ signalling including components of the antigen processing machinery such as tapasin and HLA. However, these changes in protein expression did not explain the dramatic modulation of the immunopeptidome following IFNγ treatment.  These results demonstrate the high degree of plasticity in the immunopeptidome TNBC cells following cytokine stimulation and provide evidence that under pro-inflammatory conditions a greater variety of HLA-I and HLA-II vaccine targets are unveiled to the immune system. This has important implications for the development of personalised cancer vaccination strategies.

overall_design: To study the effects of IFNγ on the transcriptome of TNBC cells in three replicates

first: Kerry

last: Mullan

first: Divya

last: Duscharla

first: Rochelle

last: Ayala

first: Nathan

last: Croft

first: Pouya

last: Faridi

first: Anthony

last: Purcell


title: Transcriptome of human monocyte-derived macrophages infected with live-Mycobacterium leprae

status: Public on Apr 16 2021

city: Berkeley

first: Thyago

middle: Leal

last: Calvo

state: California

address: 2151 Berkeley Way

department: IGI

institute: UC Berkeley

summary: To this date, host transcriptome studies in leprosy have focused on Schwann cells, as well as mouse-footpad and skin biopsies.  Despite macrophages being  the most infected cell types in leprosy lesions, there is no genome-wide experiments with this model. Here, we aimed at identifying host macrophages transcriptional changes induced by live-Mycobacterium leprae infection for 48 hours.

overall_design: Peripheral blood from female and male healthy individuals were collected. PBMCs were isolated by the density gradient method (histopaque 1077) with further monocyte purification using anti-CD14 magnetic beads. Monocytes (95% purity checked by flow cytometry) were seeded  (5x10^5 cells/well) in 24-well plates and grown in Iscove’s modified Dubelcco’s medium supplemented with antibiotics and pooled human sera for 6 days at 37 °C in 5% CO2. After macrophage differentiation, cultures were fed by replacing half of medium volume every 3 days.  Macrophages were infected with live-M. leprae (Thai-53 strain) with MOI of 10:1 (bacteria:host) for 48 hours.

last: Leal-Calvo

first: Bruna

last: Martins

first: Daniele

middle: F

last: Bertoluci

first: Patricia

last: Rosa

first: Rodrigo

last: de Camargo

first: Giovanna

middle: V

last: Germano

first: Vania

last: de Souza

first: Ana

last: Latini

first: Milton

middle: O

last: Moraes


title: Transcriptional profiling of human genital skin biopsies at lesion, 2- and 8-weeks post healing  and contra-lateral control genital skin biopsies during recurrent HSV-2 infection

first: Tao

last: Peng

summary: Analysis of host response at the gene expression level during lesion and post healing periods (2- & 8-weeks after HSV-2 reactivation induced lesion is resolved). We would like to get a comprehensive overview on host gene expression of genital skin during lesion and post healing periods of recurrent HSV-2 infection as compared to those in control skin.

overall_design: Total RNA were extracted from tissue slices of genital skin biopsies isolated from patients with recurrent HSV-2 infection using PicoPure kits (Thermo Scientific). cDNA were amlified and biotin labled using NuGEN kit, and hybridized to Illumina beadarrays (HT-12 v4).


title: Endometrial Microbiota is More Diverse in Women with Endometriosis than Symptomatic Controls

city: Hamilton

first: Jocelyn

last: Wessels

state: Ontario

address: 1280 Main Street West

department: Obstetrics and Gynecology

institute: McMaster University

summary: Endometriosis is a chronic, estrogen-dependent gynecological condition that affects approximately 10% of women of reproductive age. The most widely accepted theory of the etiology of endometriosis includes the process of retrograde menstruation, where menstrual effluent travels up the Fallopian tubes, accesses the peritoneal cavity, and in some people is able to establish endometriotic lesions. Recent reports suggest the uterus is not devoid of bacteria, as was once believed. Thus, the refluxed menstrual effluent may also carry bacteria along with it, and this bacteria has been suggested to contribute to inflammation, and establishment and growth of endometriotic lesions. Here, we sought to compare and contrast the uterine bacteria (endometrial microbiota) in women with surgically confirmed presence or absence of endometriosis using next-generation 16S rRNA gene sequencing. We obtained an average of more than 9000 sequence reads per endometrial biopsy, and found that the endometrial microbiota of women with endometriosis was more diverse (greater Shannon Diversity Index and greater proportion of ‘Other’ taxa) than that of symptomatic controls (women with pelvic pain, but with surgically confirmed absence of endometriosis; diagnosed with other benign gynecological conditions at surgery). The difference in endometrial microbiotas was supported in unsupervised cluster analyses where some clustering of endometrial microbiota by disease status (endometriosis vs. controls) was observed. The bacterial taxa enriched in the endometrial microbiota of women with endometriosis belonged to the Actinobacteria phylum, Oxalobacteraceae and Streptococcaceae families, and Tepidimonas genus, while those enriched in the symptomatic controls (without endometriosis) belonged to the Burkholderiaceae family, and Ralstonia genus. Taken together, our findings suggest the endometrial microbiota is perturbed in people with endometriosis.

overall_design: Endometrial bacterial profiles of people with and without endometriosis were generated by 16S rRNA gene sequencing using the Illumina MiSeq platform.

first: Warren

middle: G

last: Foster


title: Activation of IFN1 signaling by TAK-981 in blood, spleen, or tumor of A20-tumor bearing or B16F10-tumor bearing mice

status: Public on Apr 23 2021

city: Cambridge

first: Eric

middle: Scott

last: Lightcap

address: 40 Landsdowne Street

institute: Takeda Pharmaceuticals

summary: Intravenous administration of TAK-981 to Balb/c or C57BL/6 mice bearing A20 or B16F10 syngeneic tumors, respectively, resulted in a strong induction of IFN1 pathway genes in peripheral blood leukocytes, spleen and A20 tumor tissues. TAK- 981 dependent upregulation of IFN1 mRNA signature was determined from RNA-Seq data in peripheral blood, spleen and tumor of BALB/c mice bearing A20 tumors. Upregulation of IFN1 ssGSEA scores were calculated in peripheral blood at 4h (P = 0.0011) and 8h (P = 0.0001), in spleen at 4h (P = 0.0002) and 8h (P = 0.0020), and in tumor at 4h (P = 0.0095) and 8h (P = 0.0033) after treatment with the indicated doses of TAK-981. Dose dependent upregulation of IFN1 mRNA signature by TAK-981 was determined from RNA-Seq data in peripheral blood and spleen of C57BL/6 mice bearing B16F10 tumors. Upregulation of IFN1 ssGSEA scores in the blood at 4h (P = 0.001) and 8h (P = 0.0125) and in the spleen at 4h (P = 0.0019) and 8h (P = 0.0796) after treatment with the indicated concentrations of TAK-981. No upregulation of ssGSEA scores was detected in tumors at 4h (P=0.4295) or 8h (P=0.9706) after treatment with TAK-981. P values were calculated by Welch’s ANOVA test.

overall_design: Blood, spleen and tumor profiles from tissues isolated from Balb/c mice bearing A20 tumors or C57BL/6 mice bearing B16F10 tumors, treated with different doses of TAK-981, 4 or 8 hours after dosing

middle: S

first: Stephen

last: Grossman

first: Keli

last: Song

first: Pooja

last: Shah

first: Yu

last: Fu

first: Min

middle: Y

last: Lee

first: Dennis

last: Huszar


title: Programmed suppression of oxidative phosphorylation and mitochondrial function by gestational alcohol exposure correlate with global increases in H3K9me2 that do not suppress transcription

status: Public on Mar 31 2021

city: College Station

first: Michael

last: Golding

state: TX

address: 4466 TAMU

department: VTPP

institute: Texas A&M University

summary:
Purpose: A critical question emerging in the field of developmental toxicology is whether alterations in chromatin structure induced by toxicant exposure control patterns of gene expression or instead are structural changes that arise due to a nuclear stress response. Previously, we used a mouse model to conduct a three-way comparison between control offspring, alcohol-exposed but phenotypically normal animals, and alcohol-exposed offspring exhibiting craniofacial and central nervous system structural defects.In the cerebral cortex of animals exhibiting alcohol-induced dysgenesis, we identified a dramatic increase in the enrichment of dimethylated histone H3, lysine 9 (H3K9me2) within the regulatory regions of key developmental factors driving histogenesis in the brain. Whether this change in chromatin structure is causally involved in the development of structural defects remains unknown.
Methods: We isolated total RNA from the GD17 cortex using the RNeasy Plus Mini Kit (catalog # 74134, Qiagen) according to the manufacturer's instructions. Before RNASeq library preparation, we randomized samples and generated sequencing libraries using the TruSeq RNA Sample Preparation kit (catalog # RS-122-2001, Illumina). We sequenced pooled samples using an Illumina HiSeq 2500 at Whitehead Genomic Services (Cambridge, MA). The sequencing data were demultiplexed, aligned using STAR with default parameters (Dobin et al., 2013), and referenced against the Mus musculus genome (UCSC version mm10).
Results: To identify transcriptional differences distinguishing affected fetuses from unaffected offspring, we returned to our previously published, early gestational binge model of maternal alcohol exposure (Veazey et al., 2015). Here, dams were intraperitoneally administered injections of either vehicle or alcohol on gestational-day seven. On gestational-day 17 (GD17), stage-matched control and alcohol- exposed fetuses were dissected and scored for both ocular and craniofacial congenital defects. After determining the sex of each fetus using PCR analysis targeting the Y-chromosome, we found that the majority of affected samples (13/17; 76%) were female. We then isolated RNA from the GD17 fetal cortex of three (n=3) control, EtOH-exposed unaffected, and EtOH-exposed affected offspring and conducted deep-sequencing analysis of the cortex transcriptome. Our sequencing analyses identified a small number (88) of differentially expressed transcripts between the control and unaffected samples. In contrast, comparisons between control and affected, as well as unaffected and affected, identified 876 (412 downregulated, 522 upregulated) and 2281 (1432 downregulated, 1041 upregulated) differentially expressed genes, respectively
Conclusions: Alterations in the genetic pathways regulating oxidative phosphorylation and mitochondrial dysfunction distinguish alcohol-exposed affected vs. unaffected offspring.

overall_design: Cortical mRNA profiles of gestation day 17 alcohol exposed offspring

first: Richard

middle: C

last: Chang


title: Stem cell niche organisation in the Drosophila ovary requires the ECM component Perlecan

city: Hobart

first: Owen

last: Marshall

state: Tas

address: 17 Liverpool St

institute: Menzies Institute for Medical Research

summary: Stem cells reside in specialised microenvironments or niches that balance stem cell proliferation and differentiation. The extracellular matrix (ECM) is an essential component of most niches, as it controls niche homeostasis, provides physical support and conveys extracellular signals. Basement membranes (BMs) are thin ECM sheets constituted mainly by Laminins, Perlecan, Collagen IV and Entactin/Nidogen and that surround epithelia and other tissues. Perlecans are secreted proteoglycans that interact with ECM proteins, ligands, receptors and growth factors such as FGF, PDGF, VEGF, Hedgehog and Wingless. Thus, Perlecans have structural and signalling functions through the binding, storage or sequestering of specific ligands. We have used the Drosophila ovary to assess the importance of Perlecan in the functioning of a stem cell niche. Ovarioles in the adult ovary are enveloped by an ECM sheath and possess a tapered structure at their anterior apex termed the germarium. The anterior tip of the germarium hosts the germline niche, where two to four germline stem cells (GSCs) reside together with few somatic cells: terminal filament (TF) cells, cap cells (CpCs) and escort cells (ECs). We report that niche architecture in the developing gonad requires trol, that niche cells secrete an isoform-specific, Perlecan-rich interstitial matrix and that DE-cadherin-dependent stem cell-niche adhesion necessitates trol. Hence, we provide evidence to support a structural role for Perlecan in germline niche establishment during larval stages and in the maintenance of a normal pool of stem cells in the adult niche.

overall_design: Targeted DamID.  Two biological replicates for tj-GAL4, one replicate each of en-GAL4 and Bab1-GAL4 driving TaDa-RpII215 in Drosophila ovaries.

first: Alfonsa

last: Díaz-Torres

first: Alicia

middle: E

last: Rosales-Nieves

first: John

middle: R

last: Pearson

first: Carmen

last: Santa-Cruz Mateos

first: Miriam

last: Marín-Menguiano

first: Andrea

last: Brand

first: Acaimo

last: González-Reyes


title: SARS-CoV-2 Invades the Central Nervous System via the Olfactory Route in Rhesus Monkeys

status: Public on Apr 14 2021

city: Kunming

first: Yun

last: Yang

address: Jiao Ling Lu road

institute: Institute of Medical Biology,Chinese Academy of Medical Sciences

summary:
Purpose: Neurological manifestations are frequently reported in the Coronavirus Disease 2019 (COVID-19) patients. However, the neuroinvasion mechanism of SARS-CoV-2 remains to be determined. In this study, we explored the neuroinvasion of SARS-CoV-2 via our established non-human primate (NHP) model of COVID-19. Single-cell sequencing was conducted to comprehensively determine effects of SARS-CoV-2 infection on the CNS in consideration of the its cellular heterogeneity.
Methods: Rhesus monkeys (3-5 kg, 3-5years old) were used for this study. One monkey were intranasally infected with 1x 10^7 PFU of SARS-CoV-2 in 1mL of PBS, and another monkey was intracranially injected with 1x10^6 of SARS-CoV-2 in 200 µl of PBS. One monkey was intranasally and intracranially treated with PBS as a control. We analyzed the tissues collected on the 4 dpi and 7dpi following intranasal inoculation and on the 9 dpi following intracranial inoculation. Two thousand cells were used to create 5 different clusters, including microglia, mature neurons, oligodendrocytes, endothelial vascular cells, and astrocytes. Single-cell sequencing of were sequenced by an Illumina Novaseq6000 sequencer, the sequencing depth of each cell was at least 100,000 reads, and the paired-end 150 bp (PE150) reading strategy was adopted.
Results and Conclusions: Single-cell sequencing data showed that mitochondrial-related genes ND3, ATP6 and COX3 were down-regulated in mature neurons, oligodendrocytes, endothelial vascular cells and microglia in the hippocampus, primary olfactory cortex, and cerebral cortex infected with SARS-CoV-2.

overall_design: We analyzed the hippocampus, primary olfactory cortex and cerebral cortex collected on the 4 dpi and 7dpi following intranasal inoculation and on the 9 dpi following intracranial inoculation.

first: Li

last: Jiao

first: Wenhai

last: Yu

first: Yuan

last: Zhao


title: RNA sequencing reveals that withaferin A reduces overexpression of Bruton's tyrosine kinase in glucocorticoid resistant multiple myeloma cells

city: Wilrijk

first: Emilie

last: Logie

state: Antwerp

address: Universiteitsplein 1

department: Biomedical Sciences

country: Belgium

institute: University of Antwerp

summary: Multiple myeloma (MM) is an incurable hematological malignancy characterized by the uncontrolled growth of plasma cells in the bone marrow. The major barrier in treating MM is the occurrence of primary and acquired therapy resistance to multiple existing anti-cancer drugs. Often, this therapy resistance is associated with constitutive activation of Bruton tyrosine kinase (BTK) dependent B-cell receptor (BCR) signaling. Novel kinase inhibitors covalently targeting BCR signaling, including the clinically approved BTK inhibitor ibrutinib (IBR) and the preclinical phytochemical Withaferin A (WA), have therefore gained pharmaceutical interest. Remarkably, glucocorticoid (GC)-resistant MM cells overexpressing BTK are more sensitive to WA then to IBR. To further characterize the kinase inhibitor profiles of WA and IBR in GC-resistant MM cells, we applied phosphopeptidome- and transcriptome-specific tyrosine kinome profiling. Our results demonstrate that WA treatment triggers dual inhibition of BCR signaling by transcriptional downregulation and covalent cysteine-dependent kinase inhibition of BTK. Covalent interaction between WA and BTK could further be confirmed by biotin-based affinity purification and confocal imaging microscopy. Altogether, we show that covalent BCR-BTK kinase inhibition by WA represents an attractive strategy to treat GC-resistant MM.

overall_design: mRNA profiles of glucocorticoid sensitive MM1.S and glucocorticoid resistant MM1.R cell lines after treatment with withaferin A

first: Bart

last: Cuypers

first: Nicolas

last: De Neuter


title: Bioengineered embryoids mimic post-implantation development in vitro [EmbryoidsTruseq3]

last: Broguiere

first: Mehmet

last: Girgin

first: Sylke

last: Hoehnel

first: Nathalie

last: Brandenberg

first: Bastien

last: Mercier

first: Alfonso

last: Arias

first: Matthias

last: Lutolf


title: Bortezomib induces anti-multiple myeloma immune response mediated by cGAS/STING pathway activation

city: Boston

middle: Kemal

last: Samur

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: Proteasome inhibitor bortezomib (BTZ) induces apoptosis in myeloma (MM) cells, and has transformed patient outcome. Using in vitro as well as in vivo immunodeficient and immunocompetent murine MM models, we here show that BTZ also triggers immunogenic cell death (ICD) characterized by exposure of calreticulin (CALR) on dying MM cells, phagocytosis of tumor cells by dendritic cells, and induction of MM specific immunity. We identify a BTZ-triggered specific ICD-gene signature which confers improved outcome in two independent MM patient cohorts. Importantly, BTZ stimulates MM cells immunogenicity via activation of cGAS/STING pathway and production of type-I interferons; and STING agonists significantly potentiate BTZ-induced ICD. Our studies therefore delineate mechanisms whereby BTZ exerts immunotherapeutic activity, and provide the framework for clinical trials of STING agonists with BTZ to induce potent tumor-specific immunity and improve patient outcome in MM.

overall_design: For in vitro study we have triplicates for AMO1 cell line wild type (WT), STING patwhway knockout (KO), WT treated with bortezomib (WT+BTZ) and STING KO treated with BTZ. For in vivo study we have triplicates for 5TGM1 tumors that grew in in C57BL/KaLwRijHsd mice and specifically: 5TGM1 WT, 5TGM1 WT treated with BTZ, 5TGM1 CALR KO, 5TGM1 CALR KO treated with BTZ.

first: Annamaria

last: Gulla

first: Kenneth

last: Anderson


title: RNA seq data examining response to chemical treatment to build the first gene co-expression network of zebrafish

status: Public on Apr 13 2021

city: Richland

first: Ryan

last: McClure

state: Washington

address: 11829272 Battelle for the US DOE, 790 6th Street

department: Microbiology

institute: Pacific Northwest National Laboratory

summary: This study combines RNA seq data from a number of different expeirments examining response to chemical treatment to build the first gene co-expression network of zebrafish.  We interrogate this network to determine how the transcriptomic map responds to different types of chemicals and what pathways and processes are critical to chemical response

overall_design: Integration and network analysis of 170 RNA seq datasets across 37 different chemical (or control) treatments.

first: McClure

last: Ryan

first: Shankar

last: Prarthana

first: Waters

last: Katrina

first: Tanguay

last: Robyn


title: Next Generation Sequencing - An Analysis of the Role of Human-Specific Isoform transcription factor Oct-1 in Nerve Cell Differentiation

status: Public on Mar 30 2021

first: Tatiana

last: Portseva

address: Vavilova street 32

institute: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

summary: The aim of this study is to compare the NGS-derived profiling of human transcriptome (RNA-seq) in wild-type neuroblastoma cells with neuroblastoma transcript with a high level of expression of Oct-1 transcription factor and evaluate the effect of Oct-1 transcription factor on the regulation of nerve cell differentiation. Methods: Human mRNA profiles of 16-day differentiating wild-type neuroblastoma IMR32  and neuroblastoma IMR32 with overexpression primate-specific isoform of transcription factor Oct-1 were generated by deep sequencing, in triplicate, using Illumina NovaSeq. Mapping reads to the human genome (hg38) using hisat program. On average, about 89-90% of all received data was uniquely aligned in each library. The htseq-count utility calculated the number of reads that were mapped to known genes (ncbi - entrezID). The obtained values (cpm - countpermillion) for each gene for each library were combined into one matrix for further analysis. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the human genome (hg38). Filtration, normalization by the method (TMM), variance estimation and evaluation of differentially expressed genes were performed in the edgeR module. Genes in which cpm did not exceed 1 in any three libraries were considered low-expressing. After filtering the low-expressing genes, 15,108 entries remained. RNA-Seq data confirmed that approximately 8% of the transcripts showed differential expression between the WT and Oct-1 overexpressed differentiating neuroblastoma cells, with FDR<0.01 (p-value adjusted for multiple testing).

overall_design: Human neuroblastoma mRNA profiles of 16-days differentiating wild-type neuroblastoma IMR32  and neuroblastoma IMR32 with overexpression primate-specific isoform of transcription factor Oct-1Z. Differentiation in MEM, 10% FCS, 2.5 mkM BrdU.

first: E

last: Pankratova

first: A

last: Stepchenko

first: T

middle: N


title: RNA-Seq Quantitative Analysis of the regulation of SARS-CoV-2 infection on autophagy and apoptosis related gene transcriptome in infected cells

status: Public on Mar 23 2021

city: Guangzhou

first: Fei

last: Li

address: Xingang West Road

department: School of Life Science

institute: Sun Yat-sen university

summary: In our study, we found that SARS-CoV-2-S pseudovirions infection induced high levels of autophagy and apoptosis in infected cells. To further investigate the underlying regualtion of SARS-CoV-2-S pseudovirions infection in infected cells, ACE2-expressing HEK293T-hACE2 and Vero E6 cells were treated with Mock or SARS-CoV-2-S pseudovirions for RNA-Seq analysis to exame the expression of autophagy- and apoptosis-related genes. Our results indicate that the majority of autophagy- and apoptosis-promoting genes were significantly increased in SARS-CoV-2-S pseudovirions treated HEK293T-hACE2 and Vero E6 cells. In contrast, the subset of autophagy- and apoptosis-suppressing genes was significantly decreased in SARS-CoV-2-S pseudovirions-treated HEK293T-hACE2 and Vero E6 cells than Mock-treated HEK293T-hACE2 and Vero E6 cells. Meanwhile, SARS-CoV-2-S pseudovirions infection enhanced the expression of pro-inflammatory cytokines in infected cells.

sample_organism:
Homo sapiens
Chlorocebus sabaeus

platform_organism:
Homo sapiens
Chlorocebus sabaeus

overall_design: Examination of SARS-CoV-2-S pseudovirions infected HEK293T-hACE2 and Vero E6 cells and Mock treated HEK293T-hACE2 and Vero E6 control group

first: Qing

last: Zhang

first: Jingyao

first: Peihui

last: Wang


title: Integrative analysis of miRNA-mRNA expression profiles in esophageal fibrosis after ESD

city: 常州市

first: Yin

state: 江苏省

address: No.185 Juqianjie Road, Changzhou, Jiangsu, China

institute: Changzhou First People's Hospital

summary: The present results provided an improved understanding of the changes in the microenvironment during the process of esophageal fibrosis, as well as novel potential targets for the treatment of esophageal fibrosis and BES.

overall_design: During the esophageal ESD procedure, the esophageal tissue in the remaining submucosal layer, referred to as normal esophageal (NE) tissue, was collected, and 1 week thereafter, post-operative esophageal (PE) tissue was obtained. High-throughput sequencing was used to identify dysregulated microRNAs (miRNAs/miRs) between NE and PE tissues.

first: Chunfang

last: Xu


title: DL4-ubeads Induce T Cell Differentiation from Stem Cells in a Stromal Cell-Free System

status: Public on Mar 22 2021

city: Toronto

first: Juan-Carlos

last: Zúñiga-Pflücker

address: 2075 Bayview Avenue

institute: Sunnybrook Research Institute

summary: T cells serve as pivotal effectors of the immune system and can be harnessed as therapeutic agents for regenerative medicine and cancer immunotherapy. An unmet challenge in the field is the development of a clinically relevant system that is readily scalable to generate large numbers of T-lineage cells from hematopoietic stem/progenitor cells (HSPCs). Here, we report a stromal cell-free, microbead-based approach that supports the efficient in vitro development of both human progenitor T (proT) cells and mature T cells from CD34+ cells sourced from cord blood, GCSF-mobilized peripheral blood, and pluripotent stem cells (PSCs). DL4-μbeads, along with lymphopoietic cytokines, induced an ordered sequence of differentiation from CD34+ cells to CD34+CD7+CD5+ proT cells to CD3+ T cells. Single-cell RNA sequencing of human PSC-derived proT cells revealed a transcriptional profile similar to the earliest thymocytes found in the embryonic and fetal thymus. Furthermore, the adoptive transfer of CD34+CD7+ proT cells into immunodeficient mice demonstrated efficient thymic engraftment and functional maturation of peripheral T cells. DL4-μbeads provide a simple and robust platform to both study human T cell development and facilitate the development of engineered T cell therapies from renewable sources.

overall_design: Single-cell RNA sequencing of 2,761 human iPSC-derived progenitor T cells using 10x Genomics platform and using the Illumina NovaSeq 6000.

first: Ashton

last: Trotman-Grant

first: Juan


title: A transcriptomics approach identifies DR5-AS as a cisplatin-inducible long non-coding RNA that modulates cell cycle and proliferation

city: Izmir

first: Bünyamin

last: Akgül

state: Urla

address: Gulbahce Campus

department: Molecular Biology and Genetics

country: Turkey

institute: Izmir Institute of Technology

summary: We have performed a transcriptomics study in which we first applied 80 uM of cisplatin for 16h. Total RNA was isolated from control as well as drug treated cells and apoptosis induction was confirmed by Annexin V and 7AAD staining. Total RNAs were subjected to deep-sequencing to identify differentially expressed RNAs. We then took advantage of bioinformatic tools to identify which lncRNAs are differentially expressed upon cisplatin treatment

overall_design: Total RNA was isolated from negative control (0.1 % DMSO) and cisplatin (80 uM, 16h) treated HeLa cells in triplicate to perform deep-sequencing. 0.1% DMSO was used as control and denoted as 150605_SND405_A_L007_GDU-14, 150605_SND405_A_L007_GDU-15, 150605_SND405_A_L007_GDU-16.

first: Dilek

last: Gurer

first: Ipek

last: Erdogan

first: Ulvi

last: Ahmadov

first: Osama

last: Sweef

first: Bunyamin

last: Akgul


title: LsAP2 regulates leaf morphology by inhibiting CIN-like TCP transcription factors and repressing LsKAN2 in lettuce

status: Public on Mar 29 2021

city: Beijing

first: Chen

last: Luo

address: No.2 Yuanmingyuan West Road, Haidian District

institute: China Agricultural University

summary: Leaf size and flatness directly affect photosynthesis and are closely related to agricultural yield. The final leaf size and shape are coordinately determined by cell proliferation, differentiation, and expansion during leaf development. Lettuce (Lactuca sativa L.) is one of the most important leafy vegetables worldwide, and lettuce leaves vary in shape and size. However, the molecular mechanisms of leaf development in lettuce are largely unknown. In this study, we showed that the lettuce APETALA2 (LsAP2) gene regulates leaf morphology. LsAP2 encodes a transcriptional repressor that contains the conserved EAR motif, which mediates interactions with the TOPLESS/TOPLESS-RELATED (TPL/TPR) corepressors. Overexpression of LsAP2 led to small and crinkly leaves, and many bulges were seen on the surface of the leaf blade. LsAP2 physically interacted with the CINCINNATA (CIN)-like TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factors and inhibited their transcriptional activation activity. RNA sequencing analysis showed that LsAP2 affected the expression of auxin- and polarity-related genes. In addition, LsAP2 directly repressed the abaxial identity gene KANADI2 (LsKAN2). Together, these results indicate that LsAP2 regulates leaf morphology by inhibiting CIN-like TCP transcription factors and repressing LsKAN2, and our work provides insights into the regulatory mechanisms of leaf development in lettuce.

overall_design: Young leaves of one-month-old WT and LsAP2-OE plants were used for RNA-seq experiments, and three biological replicates were performed for each sample.

first: Shenglin

first: Kang

last: Ning

first: Zijing

last: Chen

first: Yixin

first: Jingjing

last: Yang

first: Qian


title: Relating the transcriptome and microbiome by paired terminal ileal Crohn's disease

city: Shanghai

first: Sibo

last: Zhu

state: China

address: songhulu 2005

institute: Fudan University

summary: Management of terminal ileal Crohn's disease (CD) is difficult due to fibrotic prognosis and failure to achieve mucosal healing. A limited number of synchronous analyses have been conducted on the transcriptome and microbiome in unpaired terminal ileum tissues. Therefore, our study focused on the transcriptome and mucosal microbiome in terminal ileal tissues of CD patients with the aim of determining the role of cross-talk between the microbiome and transcriptome in the pathogenesis of terminal ileal CD. Mucosa-attached microbial communities were significantly associated with segmental inflammation status. Interaction-related transcription factors (TFs) are the panel nodes for crosstalk between the gene patterns and microbiome for terminal ileal CD. The transcriptome and microbiome in terminal ileal CD can be different related to local inflammatory status, and specific differentially expressed genes (DEGs) may be targeted for mucosal healing. TFs connect gene patterns with the microbiome by reflecting environmental stimuli and signals from microbiota.

overall_design: Approximately 5 mg (four mucosal biopsies) of tissue samples were extracted from the inflamed and proximal non-inflamed ileum of CD patients (n=10). IMCD and NMCD were extracted from the biopsy samples, and they were confirmed by light microcopy. Three months prior to recruitment, all patients were instructed to avoid antibiotics, steroids, immunosuppressants, and biologics.

first: Chenwen

last: Cai

first: Jinlu

last: Tong

first: Tianrong

first: Qi

last: Feng

first: Yuqi

last: Qiao

first: Jun

last: Shen


title: The expression profiles of circRNA, lncRNA, mRNA, and miRNA in the testis of STZ-induced diabetic rats

status: Public on Mar 17 2021

city: Shenzhen

last: Wu

state: Guangdong

address: Xueyuan Road 1098

institute: Shenzhen University

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Sex-specific control of human heart maturation by the progesterone receptor [bulk_RNAseq_human]

city: Melbourne

first: Enzo

last: Porrello

state: Victoria

address: c/o Royal Children’s Hospital

department: Cell Biology

institute: Murdoch Children's Research Institute

summary: The physiological adaptation of the heart to the postnatal environment is one of the most critical developmental transitions in the life of mammals. Despite in depth knowledge of the molecular mechanisms controlling embryonic heart development, little is known about the signals that govern postnatal maturation of the heart in humans. Here, we analyse the transcriptome of more than 50,000 single cells in the developing human heart from early gestation to adulthood, which enabled mapping of developmental trajectories across 7 main classes of cardiac cells over time. Striking sex-specific differences in cardiomyocyte maturation were identified and subsequently confirmed via deep RNA sequencing of purified cardiomyocytes. To identify transcriptional drivers of these changes, ATAC-seq was used to assay the open chromatin landscape, which unveiled the progesterone receptor as a key mediator of sex-dependent transcriptional changes during cardiomyocyte maturation. Functional studies in mice, as well as human pluripotent stem cell-derived cardiomyocytes and organoids, validated the progesterone receptor as a mediator of sex-specific metabolic programs and as a cardiac inotrope, consistent with a role in developmental maturation. These datasets provide a blueprint for understanding sex-specific mechanisms governing human heart development and unveil an important role for the progesterone receptor in cardiomyocyte maturation.

overall_design: Transcriptional analysis of cardiomyocytes from 3 different human developmental stages.

first: Choon

middle: B

last: Sim


title: The expression profile of circRNA, lncRNA and mRNA in the testis of STZ-induced diabetic rats

summary: The number of patients with diabetes is increasing worldwide. Diabetic testicular damage can cause spermiogenesis disorders and sexual dysfunction. We thus explored the role of circRNA, lncRNA and mRNA in diabetic testicular damage, and revealed that they could serve as effective prevention and treatment therapeutic targets. Streptozotocin (STZ) was used to generate a rat model of type 2 diabetes. Rat testicular tissues were used for circRNA, lncRNA and mRNA sequencing.

overall_design: Testicular tissues circRNA, lncRNA and mRNA profiles of rat after 8 weeks of STZ-induced diabetes were generated by high-throughput sequencing using Illumina Hiseq 3000.

first: Li

last: Hu

first: Pei

last: zhu

first: Danian

last: Qin


title: Next Generation Sequencing  of Wild Type pDC Transcriptomes in a longitudinal activation study (CpG 0h, 2h, 6h, 12)

city: Duesseldorf

first: Stefanie

last: Scheu

state: Nordrhein-Westfalen

address: Universitaetsstr. 1

department: Institute of Medical Microbiology and Hospital Hygiene

institute: University of Duesseldorf

summary:
Purpose: The goals of this study are to compare NGS-derived pDC transcriptome profiling (RNA-seq) normalized counts and differential expression of genes between different pDC states (steady state, or TLR9 activated for 2h, 6h, or 12h with CpG) in Batf presence and absence.
Methods: mRNA profiles of Bone marrow-derived Flt3-L cultured FACS purified pDCs from wild-type and Batf-knockout mice that were left naive or stimulated with TLR9 agonist CpG for 2h, 6h r 12h were generated by deep sequencing, in triplicate, using the Illumina HiSeq3000 platform. DNase digested total RNA samples used for transcriptome analyses were quantified (Qubit RNA HS Assay, Thermo Fisher Scientific) and quality measured by capillary electrophoresis using the Fragment Analyzer and the ‘Total RNA Standard Sensitivity Assay’ (Agilent Technologies, Inc. Santa Clara, USA). All samples in this study showed high quality RNA Quality Numbers (RQN; mean = 9.9). The library preparation was performed according to the manufacturer’s protocol using the Illumina® ‘TruSeq Stranded mRNA Library Prep Kit’. Briefly, 200 ng total RNA were used for mRNA capturing, fragmentation, the synthesis of cDNA, adapter ligation and library amplification. Bead purified libraries were normalized and finally sequenced on the HiSeq 3000/4000 system (Illumina Inc. San Diego, USA) with a read setup of SR 1x150 bp. The bcl2fastq tool was used to convert the bcl files to fastq files as well for adapter trimming and demultiplexing.
Results: Data analyses on fastq files were conducted with CLC Genomics Workbench (version 11.0.1, QIAGEN, Venlo. NL). The reads of all probes were adapter trimmed (Illumina TruSeq) and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides maximal 2). Mapping was done against the Mus musculus (mm10; GRCm38.86) (March 24, 2017) genome sequence. After grouping of samples (three biological replicates each) according to their respective experimental condition, multi-group comparisons were made and statistically determined using edgeR on usegalaxy.org The Resulting 𝑃 values were corrected for multiple testing by FDR. A 𝑃 value of ≤0.05 was considered significant.
Conclusions: Our study represents the first detailed analysis of Batf-dependent gene expression in naive and activated pDC transcriptomes in a longitduinal study. Our results show that Batf absence significantly altered the global gene expression patterns in pDCs, modulating many biological pathways important for cell development and effector function.

overall_design: mRNA profiles of Bone marrow-derived Flt3-L FACS purified pDCs from wild type and Batf-deficient mice that were left naïve or stimulated with TLR9 agonist CpG for 2h, 6h or 12h.

first: Shafaqat

last: Ali

first: Ritu

last: Mann-Nüttel


title: Study of the pathology and the underlying molecular mechanism of tissue injury around hematoma following intracerebral hemorrhage

city: Nantong

first: Jinglei

last: Wang

state: Jiangsu

address: 20 Xisi Road

institute: Affiliated Hospital of Nantong University

summary: We compare the perihematoma tissues before and after intracerebral hemorrhage in rats. Gene Ontology functional annotation, Protein interaction network analysis, reverse transcription quantitative PCR technology, Western blot technology, immunofluorescence technology and Causal network analysis are used to detect the changes of RET before and after intracerebral hemorrhage and the pathways in which RET might be involved.

overall_design: Two-condition experiment, Sham vs. ICH. Biological replicates: 3 control replicates, 3 transfected replicates.

first: Jiabing


title: Expression data of OVCAR8 cells with and without mesothelial cells

city: Sydney

first: Chenkai

last: Ma

state: NSW

address: 11 Julius Avenue

institute: CSIRO

summary: To characterize the mesothelial cell-mediated changes of gene expression in ovarian cancer cells, we performed RNA sequencing in OVCAR8 cells with and without mesothelial cell co-culture.

overall_design: OVCAR8 cells were indirectly co-cultured with mesothelial cells. Total RNA from the co-cultured OVCAR8 cells and OVCAR8 monoculture was extracted using Trizol and sujected to RNA-seq analysis

first: Jin

last: Qian

first: Erinn

last: Rankin

first: Bauer

middle: L

last: LeSavage

first: Suchitra

last: Natarajan

first: Kelsea

middle: M

last: Hubka

first: Joshua

middle: T

last: Eggold

first: Yiren

last: Xiao

first: Katherine

last: Fuh

first: Venkatesh

last: Krishnan

first: Annika

last: Enejder

first: Sarah

last: Heilshorn

first: Oliver

last: Dorigo


title: Epigenetic inactivation of the autophagy-lysosomal system in the Parkinson’s disease appendix (8: ChIP)

status: Public on Mar 01 2021

city: Grand Rapids

first: Peipei

last: Li

state: MI

address: 333 Bostwick Ave N.E.

department: Center for Neurodegenerative Science

institute: Van Andel Research Institute

summary: The gastrointestinal tract may be a site of origin for α-synuclein (α-syn) pathology in idiopathic Parkinson’s disease (PD), and an abundance of aggregated α-syn has recently been demonstrated in both the healthy and PD appendix. However, the molecular changes that enable gut α-syn aggregates to contribute to the development and progression of PD remain unclear. Here, our deep-sequencing of DNA methylation changes at 521 autophagy-lysosomal pathway (ALP) genes in the human appendix and brain in PD and healthy controls indicates a pattern of widespread hypermethylation in the PD appendix that is recapitulated in the PD brain. There is significant overlap in the individual ALP genes affected across the PD appendix and brain, with lysosomal genes specifically downregulated in both regions. Healthy epigenetic aging, which involves a hypermethylation of macroautophagy and selective autophagy genes in the appendix and brain, is disrupted in both areas in PD. In mice, DNA methylation changes at ALP genes induced by chronic gut inflammation are greatly exacerbated by the presence of α-syn pathology. DNA methylation changes at ALP genes induced by α-synucleinopathy are significantly associated with the ALP abnormalities observed in the PD appendix, specifically involving lysosomal genes. Our work, which constitutes an in-depth, unbiased investigation of epigenetic changes in the ALP of the PD gut and brain, identifies the epigenetic misregulation of the ALP, especially a downregulation of lysosomal genes, as a potential culprit for the initiation and spread of α-syn pathology in idiopathic PD.

overall_design: Chromatin immunoprecipitation (ChIP) was used to identify active enhancers and promoters in the healthy human appendix (n = 3 individuals)

first: Juozas

last: Gordevicius

first: Lee

last: Marshall

first: Bryan

last: Killinger

first: Sean

last: Lang

first: Elizabeth

last: Ensink

first: Nathan

last: Kuhn

first: Wei

last: Cui

first: Nazia

last: Maroof

first: Irving

last: Vega

first: Fredric

last: Manfredsson

first: Markus

last: Britschgi

first: Viviane

last: Labrie


title: KDM5A suppresses PML-RARα target gene expression and APL differentiation through repressing H3K4me2

city: Philadelphia

first: Siqing

last: Wang

state: PENNSYLVANIA

address: 3401 Civic Center Blvd

department: Department of Pediatrics, Division of Hematology

institute: Children’s Hospital of Philadelphia

summary: Epigenetic abnormalities are frequently involved in the initiation and progression of cancers including acute myeloid leukemia (AML). A subtype of AML, Acute promyelocytic leukemia (APL), is mainly driven by a specific oncogenic fusion event of PML-RARα. PML-RARα was reported as a transcription repressor through the interaction with NCoR/HDAC complexes leading to the mis-suppression of its target genes and differentiation blockage. While previous studies were mainly focused on the connection of histone acetylation, it is still largely unknown whether alternative epigenetics mechanisms are involved in APL progression. KDM5A is a demethylase of histone H3 lysine 4 di- and tri- methylations (H3K4me2/3) and a transcription corepressor. Here, we found that the loss of KDM5A led to APL NB4 cell differentiation and retarded growth. Mechanistically, through epigenomics and transcriptomics analyses, we detected KDM5A binding in 1,889 genes, with the majority of the binding events at promoter regions. KDM5A suppressed the expression of 621 genes, including 42 PML-RARα target genes primarily by controlling the H3K4me2 in the promoters and 5’ end intragenic regions. In addition, a recently reported pan-KDM5 inhibitor, CPI-455 on its own could phenocopy the differentiation effects as KDM5A loss in NB4 cells. CPI-455 treatment or KDM5A knockout could greatly sensitize NB4 cells to ATRA induced differentiation. Our findings indicated that KDM5A contributed to the differentiation blockage in the APL cell line NB4, and inhibition of KDM5A could greatly potentiate NB4 differentiation.

overall_design: We deleted KDM5A by CRISPR-Cas9 in NB4 cell line, which is an APL cell line carrying the gene fusion of PML-RARa.To further investigate the underlining mechanism, we profiled genome-wide distribution pattern of KDM5A in NB4 cells, and H3K4me2 and H3K4me3 in both control and KDM5A. We also did RNA-seq for control (SCR1 and SCR2) and KDM5A-KO (KO1 and KO2) NB4 cells.

first: Siyuan

last: Xu


title: Single cell RNA sequencing of liver macrophages from Noonan mice

status: Public on Mar 10 2021

city: Toulouse

first: Armelle

last: YART

address: 4bis avenue H. Curien

department: RESTORE

institute: INSERM U1301

summary: We report the use of single cell RNA sequencing to identify differentially-expressed genes in liver macrophages from a mouse model of Noonan syndrome (NS) and highlight specific subpopulation clusters that may contribute to the associated insulin resistance phenotype.

overall_design: Single cell RNA sequencing of F4/80+ cells purified by flow cytometry from liver of wild type and Noonan mice

last: Yart

first: Romain

last: Paccoud

first: Jean-Philippe

last: Pradere

first: Delphine

last: Labourdette


title: Sex-specific control of human heart maturation by the progesterone receptor [bulk_RNAseq_PrKO]

first: Enzo

last: Porrello

overall_design: Transcriptional analysis of cardiomyocytes from 2 mouse strains (Pgr_WT and Pgr_KO).

first: Choon

last: Sim


title: Single-cell multiomics sequencing (RNA, ADT and VDJ) of CD4+ T cells from peripheral blood of CMV+ and CMV- healthy humans.

city: Atlanta

first: Haydn

last: Kissick

address: 1462 Clifton Rd.

institute: Emory University

summary: The goal of this study is to understand the transcriptional features of CD4+ memory T cells induced by CMV seropositivity and explore their TCR repertoire clonality.

overall_design: We selected CMV-associated CD4+ T cells based on ADT expression matrix. Differential expression analysis based on gene expression matrix was performed to extract transcriptiomes upregulated within these cells. Clonotypes of CD4+ T cells were assigned based on their unique combination of paired V(D)J gene usage and paired productive CDR3 sequences of alpha and beta chain. Simpson's Reciprocal Index was calculated to compare the clonal diversity of CMV-associated CD4+ T cells with other T cell subsets.

first: Christian

last: Larsen

first: Weiwen

last: Zhang

first: Anna

last: Morris

first: Erica

last: Peek

first: Geeta

last: Karadkhele

first: Jennifer

last: Robertson


title: Gene expression profiling of sarcoma cells treated with mithramycin A (MTA), nano-encapsulated MTA or MTA-analogs

city: Oviedo

first: Rene

last: Rodríguez

state: Asturias

address: Av. Roma s/n

department: Sarcomas and Experimental Therapeutics

institute: Health Research Institute of Asturias (ISPA)

summary: This study was designed to gain insight about the mechanisms involved in the anti-tumor effects of mithramycin A (MTA) and the MTA analog EC-8042 in sarcoma cells. In addition, we also studied whether this molecular features could be influenced by the nano-encapsulation of MTA.

overall_design: we have performed RNA seq analyses in myxoid liposarcoma T-5H-FC#1 cells treated in triplicate with either DMSO (control), or the IC50 values of free MTA (M_F) (25 nM), MTA loaded in polymeric PLG-nanoparticles (M_NP) (25 nM) or EC-8042 (300 nM) for 24 hours. In addition, this study includes RNA seq analyses of 143B osteosarcoma cells treated with DMSO (control) or the IC50 values of EC-8042 (100 nM) for 24 hours.

last: Rodriguez

first: Oscar

last: Estupiñan


title: Sex-specific control of human heart maturation by the progesterone receptor [snRNAseq_human]

overall_design: Single nuclei transcriptional analysis of cardiomyocytes from 3 different human developmental stages.


title: Sex-specific control of human heart maturation by the progesterone receptor [bulk_RNAseq_AAV_PGR]

overall_design: Transcriptional analysis of cardiomyocytes from mouse strain treated with 2 different adeno-associated viral vectors.


title: Genomic Fabric Remodeling in Prostate Cancer

status: Public on Mar 12 2021

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: Prostate cancer is a leading cause of death among men but its genomic characterization and best therapeutic strategy are still under debate. The Genomic Fabric Paradigm (GFP) considers the transcriptome as a multi-dimensional mathematical object subjected to a dynamic set of expres-sion correlations among the genes. Here, GFP is applied to gene expression profiles of three (one primary, and two secondary) cancer nodules and the surrounding normal tissue from a surgically removed prostate tumor. GFP was used to determine the regulation and rewiring of the P53 signaling, apoptosis, prostate cancer and several other pathways involved in survival and pro-liferation of the cancer cells. Genes responsible for the block of differentiation, evading apoptosis, immortality, insensitivity to anti-growth signals, proliferation, resistance to chemotherapy and sustained angiogenesis were found as differently regulated in the three cancer nodules with re-spect to the normal tissue. The analysis indicates that even histo-pathologically equally graded cancer nodules from the same tumor have substantially different transcriptomic organizations, raising legitimate questions about the validity of meta-analyses comparing large populations of healthy and cancer humans. The study suggests that GFP may provide a personalized alternative to the biomarkers’ approach of cancer genomics.

overall_design:
Gene expressions were profiled in two equally graded (Gleason score 4+4=8/10) cancer nodules from a surgically removed prostate cancer

Please note that [1] multiple yellow strategy was used to hybridize differently labelleld biological replicas with the microarray and then iteratively normalizing the expression data to the intra-array and inter-array median expression until the maximum error of estimate becomes less than 5% [2] Each raw data file contains raw data for two samples as indicated in the corresponding sample description field.

first: Sanda

middle: A


title: Sex-specific control of human heart maturation by the progesterone receptor


title: RNA-Seq and ChIP-Seq from Tbr2+ and Tbr2- nuclei

status: Public on Mar 05 2021

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: We performed RNA-Seq and H3K9ac ChIP-Seq from Tbr2+ and Tbr2- nuclei sorted by FACS from E16.5 embryonic cortex treated with either vehicle or HDAC inhibitor (TSA).

first: Cemil

last: Kerimoglu


title: Comparison of gene expression profiles of hearts in nulloparous (NP) or postpartum (PP) PERK wild type (flx) or PERK cardiac-specific knockout (cko) mice.

city: Bunkyo-ku

first: Takashi

last: Shimizu

institute: University of Tokyo

summary: Recently, it is reported that multiple signaling pathways are involved with the pathogenesis of PPCM. Here, we show that PERK kockout affect these pathways in postpartum period.

overall_design: Total 12 samples were derived from hearts in nulloparous (NP) or postpartum (PP) PERK wild type (flx) or PERK cardiac-specific knockout (cko) mice.

first: Ryo

last: Nakaki


title: Epigenetic inactivation of the autophagy-lysosomal system in the Parkinson’s disease appendix (7: PFC_neuron primary cohort)

first: Peipei

last: Li

overall_design: DNA methylation at 521 known ALP genes and surrounding genomic area (± 300 kb) was profiled in isolated prefrontal cortex neurons of PD patients and controls (primary cohort)

first: Juozas

last: Gordevicius

first: Lee

last: Marshall

first: Bryan

last: Killinger

first: Sean

last: Lang

first: Elizabeth

last: Ensink

first: Nathan

last: Kuhn

first: Wei

last: Cui

first: Nazia

last: Maroof

first: Irving

last: Vega

first: Fredric

last: Manfredsson

first: Markus

last: Britschgi

first: Viviane

last: Labrie


title: Epigenetic inactivation of the autophagy-lysosomal system in the Parkinson’s disease appendix (4: Mice_rAAV a-syn)

overall_design: DNA methylation changes at ALP genes (n=571 ALP genes ± 50 kb) in response to α-synuclein aggregation were examined in the mouse equivalent of the appendix, the cecal patch


title: Epigenetic inactivation of the autophagy-lysosomal system in the Parkinson’s disease appendix (1: PD_Appendix)

overall_design: To determine whether epigenetic disruption of the ALP in the appendix could contribute to PD, we profiled DNA methylation at 521 known ALP genes and surrounding genomic area (± 300 kb) in the PD and control appendix


title: Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution

city: Stanford

first: Alex

last: Trevino

state: California

address: 279 Campus Drive West

department: Genetics

institute: Enable Medicine

summary: In this study, we map chromatin accessibility and gene expression at single-cell resolution in the developing human cerebral cortex.

overall_design:
We generated single-cell ATAC-seq and single-cell RNA-seq libraries from 4 samples of mid-gestation human cerebral cortex, spanning 8 weeks of development

**RAW DATA not provided due to patient privacy**

first: Alexandro

first: Fabian

last: Müller

first: Jimena

last: Andersen

first: Laksshman

last: Sundaram

first: Arwa

last: Kathiria

first: Anna

last: Shcherbina

first: Kyle

last: Farh

first: Howard

last: Chang

first: Anca

last: Pașca

first: Anshul

last: Kundaje

first: Sergiu

middle: P

first: William

middle: J

last: Greenleaf


title: Epigenetic inactivation of the autophagy-lysosomal system in the Parkinson’s disease appendix (6: PFC_neuron replication cohort)

first: Peipei

last: Li

overall_design: DNA methylation at 521 known ALP genes and surrounding genomic area (± 300 kb) was profiled in isolated prefrontal cortex neurons of PD patients and controls (replication cohort)

first: Juozas

last: Gordevicius

first: Lee

last: Marshall

first: Bryan

last: Killinger

first: Sean

last: Lang

first: Elizabeth

last: Ensink

first: Nathan

last: Kuhn

first: Wei

last: Cui

first: Nazia

first: Irving


title: The expression profile of miRNA in the testis of STZ-induced diabetic rats

first: Yuqi

last: Wu

summary: The number of patients with diabetes is increasing worldwide. Diabetic testicular damage can cause spermiogenesis disorders and sexual dysfunction. We thus explored the role of miRNAs in diabetic testicular damage, and revealed that they could serve as effective prevention and treatment therapeutic targets.Streptozotocin (STZ) was used to generate a rat model of type 2 diabetes. Rat testicular tissues were used for miRNA sequencing. we identified 19 differentially expressed miRNAs in the testes of diabetic rats.

overall_design: Testicular tissues miRNA profiles of rat after 8 weeks of STZ-induced diabetes were generated by high throughput sequencing using Illumina Hiseq 3000.

first: Li

last: Hu

first: Pei

last: Zhu

first: Danian

last: Qin


title: Epigenetic inactivation of the autophagy-lysosomal system in the Parkinson’s disease appendix (5: OFB)

overall_design: DNA methylation at 521 known ALP genes and surrounding genomic area (± 300 kb) was profiled in the PD and control olfactory bulb

last: Maroof

last: Vega

first: Fredric

last: Manfredsson

first: Markus

last: Britschgi

first: Viviane

last: Labrie


title: Disrupting Mechanotransduction Promotes Regenerative Phenotypes in Human Cells

status: Public on Feb 24 2021

city: Tucson

first: Kellen

last: Chen

state: AZ

address: 1501 N Campbell Ave

department: Surgery

institute: University of Arizona

summary: We quantify the effects of FAK inhibition on three-dimensional (3D) cultured human fibroblasts at the cellular and transcriptomic level using single cell RNA-sequencing. We demonstrate that mechanical stress induces pro-fibrotic fibroblast differentiation fates in large organisms, which can effectively be averted by FAK inhibition, which induces discrete fibroblast clusters that promote wound regeneration.

overall_design: scRNA-seq was performed on human fibroblasts from 3 different human patients in a physiologically relevant, 3-dimensional, in vitro, collagen scar system

first: Dominic

last: Henn

first: Michael

last: Januszyk

first: Geoffrey

last: Gurtner


title: Transcriptional profiling of fission yeast RNA polymerase II CTD mutants

status: Public on Feb 25 2021

city: New York

first: Angad

last: Garg

state: New York

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: This RNA-Seq analysis compares gene expression of the RNA polymerase II CTD-mutants contrasting to the WT RNA polymerase II CTD (with isogenic 3' selection marker) in the fission yeast S. pombe

overall_design:
8 test samples were analyzed, of which rpb1-CTD-T4A29 was previously submitted under GEO accession number GSE155609; 2 parental control samples (rpb1-CTD-WT29) were processed (each control set indicates which test samples were compared). Each sample has at least 3 replicate experiments.

rpb1-CTD-WT18 [truncated CTD with 18 consensus repeats] has 4 replicates where two replicates processed were deposited under GEO accession no. GSE52370)

first: Beate

last: Schwer

first: Stewart

last: Shuman


title: Epigenetic inactivation of the autophagy-lysosomal system in the Parkinson’s disease appendix (3: Mice_DSS)

first: Peipei

last: Li

overall_design: DNA methylation changes at ALP genes (n=571 ALP genes ± 50 kb) in response to gut inflammation were examined in the mouse equivalent of the appendix, the cecal patch

first: Juozas

last: Gordevicius

first: Lee

last: Marshall

first: Bryan

last: Killinger

first: Sean

last: Lang

first: Elizabeth

last: Ensink

first: Nathan

last: Kuhn

first: Wei

last: Cui


title: Sex-specific control of human heart maturation by the progesterone receptor [bulk_ATACseq_human]

first: Enzo

last: Porrello

summary: The physiological adaptation of the heart to the postnatal environment is one of the most critical developmental transitions in the life of mammals. Despite in depth knowledge of the molecular mechanisms controlling embryonic heart development, little is known about the signals that govern postnatal maturation of the heart in humans. Here, we analyse the transcriptome of more than 50,000 single cells in the developing human heart from early gestation to adulthood, which enabled mapping of developmental trajectories across 7 main classes of cardiac cells over time. Striking sex-specific differences in cardiomyocyte maturation were identified and subsequently confirmed via deep RNA sequencing of purified cardiomyocytes. To identify transcriptional drivers of these changes, ATAC-seq was used to assay the open chromatin landscape, which unveiled the progesterone receptor as a key mediator of sex-dependent transcriptional changes during cardiomyocyte maturation. Functional studies in mice, as well as human pluripotent stem cell-derived cardiomyocytes and organoids, validated the progesterone receptor as a mediator of sex-specific metabolic programs and as a cardiac inotrope, consistent with a role in developmental maturation. These datasets provide a blueprint for understanding sex-specific mechanisms governing human heart development and unveil an important role for the progesterone receptor in cardiomyocyte maturation.

overall_design: Chromatin landscape analysis of cardiomyocytes from 3 different human developmental stages and 2 induced human pluripotent stem cell differentiated cardiomyocyte lines.

first: Choon

last: Sim


title: Functional dissection of the PTS provides insight into the prevalence of Faecalibacterium prausnitzii in the host intestinal environment

status: Public on Mar 06 2021

city: Seoul

first: Chang Kyu

last: Yoon

state: Seoul

address: 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea

country: South Korea

institute: Seoul National University

summary: Faecalibacterium prausnitzii is a dominant member of healthy human colon microbiota, regarded as a beneficial gut bacterium due to its ability to produce anti-inflammatory substances. However, little is known about how F. prausnitzii utilizes the nutrients present in the human gut, influencing its prevalence in the host intestinal environment. The phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS) is a widely distributed and highly efficient carbohydrate transport system found in most bacterial species that catalyses the simultaneous phosphorylation and import of cognate carbohydrates; its components play physiological roles through interaction with other regulatory proteins. Here, we performed a systematic analysis of the 16 genes encoding putative PTS components (2 enzyme I, 2 HPr, and 12 enzyme II components) in F. prausnitzii A2-165. We identified the general PTS components responsible for the PEP-dependent phosphotransfer reaction and the sugar-specific PTS components involved in the transport of two carbohydrates, N-acetylglucosamine and fructose, among five enzyme II complexes. We suggest that the dissection of the functional PTS in F. prausnitzii may help to understand how this species outcompetes other bacterial species in the human intestine.

overall_design: Transcriptome profiles of F. prausnitzii cells grown on a single carbohydrate as a sole carbon source (galactose, fructose, glucose, N-acetylglucosamine)

first: Deborah

last: Kang

first: Hyeong-In

last: Ham

first: Seung-Hwan

last: Lee

first: Yong-Joon

last: Cho

first: Yeon-Ran

last: Kim

first: Chang-Kyu

first: Yeong-Jae

last: Seok