title: Characterization of the potential role of NTPCR in epithelial ovarian cancer by integrating transcriptomic and metabolomic analysis

status: Public on Dec 31 2021

city: Hangzhou City

first: HongKai

last: Shang

address: 388 Yuhangtang Road, Xihu District

institute: Zhejiang University

summary:
Background: Epithelial ovarian carcinoma (EOC) is a malignant tumor with high motility in women. Our previous study found that dysregulated NTPCR was associated with the prognosis of ovarian cancer patients, and thus this present study attempted to explore the potential roles of nucleoside-triphosphatase cancer-related (NTPCR) in disease progression.
Methods: Expressed level of NTPCR was investigated in ovarian cancer cell lines by RT-qPCR analysis. shRNA targeting NTPCR was generated and transfected into SKOV3 cells to detect the effect of knocking out NTPCR on cell proliferation, cell cycle, cell migration, and invasion. Transcriptomic sequencing and metabolite profiling analysis were performed in shNTPCR groups to identify transcriptome or metabolites alteration that might contribute to ovarian cancer. And finally, we searched the overlapped signaling pathways correlated with differential metabolites and DEGs by integrating analysis.
Results: NTPCR was upregulated in EOC cell lines compared with human ovarian epithelium cell IOSE80, especially in SKOV3 and OVCAR-3 (SKOV3 vs IOSE80, P<0.001; OVCAR-3 vs IOSE80, P<0.001). Knocking out NTPCR can induce cell proliferation and S phase arrest, promote migration and invasion in SKOV3 cells. RNA sequencing analysis demonstrated cohorts of differential expressed genes (DEGs) were identified in shNTPCR samples. PPI networks were constructed for DEGs. STAT1 (degree = 43) and OAS2 (degree = 36) were identified as hub genes in network. Several miRNAs together with target genes were predicted to be crucial genes related to disease progression, including hsa-miR-124-3p, hsa-miR-30a-5p, hsa-miR-146a-5, EP300, GATA2, and STAT3. We also screened the differential metabolites from shNTPCR samples, including 22 upregulated and 22 downregulated metabolites. By integrating analysis, eight overlapped pathways were correlated with these DEGs and differential metabolites, such as primary bile acid biosynthesis, protein digestion, and absorption, pentose and glucuronate interconversions.
Conclusion: NTPCR might serve as a tumor suppressor in EOC progression. Our results demonstrated that DEGs and differential metabolites were mainly related to several signaling pathways, which might be a crucial role in the progression of ovarian cancer.

overall_design: Observe the effect of down-regulation of NTPCR on gene expression in ovarian cancer cells by transcriptomic sequencing

first: Hongkai

first: Huizhi

last: Zhang

first: Hongjang

last: Zhao

first: Jinyi

last: Tong


title: Whole Transcriptomic analysis of placenta and its released extracellular vesicles in normal and preeclampsia pregnancies: insigths into novel biomarkers and mechanisms of disease

status: Public on Dec 17 2021

city: Oxford

first: Toluwalase

last: Awoyemi

state: Oxfordshire

address: John Radcliffe Hospital, Level 3

department: Nuffield Department's of Women's and reproductive health

country: United Kingdom

institute: University of Oxford

type: Expression profiling by high throughput sequencing

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: Homeostatic calcium fluxes, ER calcium release, SOCE, and calcium oscillations in cultured astrocytes are interlinked by a small calcium toolkit

status: Public on Dec 14 2021

city: Würzburg

first: Robert

last: Blum

address: Josef-Schneider-Str. 11

department: Department of Neurology

country: Germany

institute: University Hospital Würzburg

summary: We report the application of RNA-seq for molecular profiling of cultured, cortical astrocytes. Our data set is based on about 40 million unique reads per sample in four independent mRNA preparations. Cortical astrocytes are a prototypical cell model for investigating calcium signaling. For analysis of calcium fluxes, we performed direct calcium imaging in the endoplasmic reticulum and in the cytosol. We describe in our study the physiological profile of homeostatic and agonist-induced calcium fluxes. Furthermore, we show how ER calcium release shapes the cytosolic calcium signal. This transcriptome dataset was used to profile the calcium toolkit of astrocytes. The data suggest that a small number of calcium signaling-related proteins mediate calcium homeostasis in astrocytes.

overall_design: Profiling of  calcium signalling components that are expressed in cultured cortical astrocytes of the mouse based on 4 biological replicates.

first: Thorsten

last: Bischler


title: Transcriptomic analysis of placenta and its released extracellular vesicles in normal and preeclampsia pregnancies: insigths into novel biomarkers and mechanisms of disease

summary:
Purpose:  The goals of this study is to compare and profile the transcriptome of the placenta in preeclamptic and normal patients using RNA sequencing.
Methods: Placental and Placental vesicles (STB-EVs)  mRNA profiles of normal and preeclamptic patients were generated by deep sequencing using Illumina HISEQ. The sequence reads that passed quality filters were analyzed at the gene level HISAT2 followed by featureCounts. Quantitative PCR validation was performed using TaqMan gene expression assays
Results: This contains a set of three parallel mRNA sequencing experiments involving placenta tissue, medium/large STB-EVs and small STB-EVs. Comparison between PE and normal pregnancy placental tissue revealed 18,070 genes from which 580 were upregulated and 563 were downregulated (p-value of <0.05 ) while in medium/large STB-EVs, revealed 14,216 genes from which 1,128 were upregulated and 833 were downregulated. In small STB-EVs, out of 23,322 genes, 232 were upregulated and 106 were downregulated) (adjusted P-value of <0.05)  We identified a number of mechanistic and biomarker targets,  which were validated with qRT–PCR and confirmed to be signifficantly DE. The differentially expressed analysis identified potential yet undescribed genes that may contribute to the pathogenesis of preeclampsia or/and may act as biomarkers of the disease.
Conclusions: Our study represents the first detailed analysis of combined Placenta and placental extracellular vesicles (STB-EVs)   transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results have identified potential STB-EV based small RNA biomarkers in preeclampsia.

overall_design: Placental small RNA profiles of 8 preeclamptic (PE) and 6 normal pregnant (NP) women and medium/large STB-Evs small RNA profiles of 8 preeclamptic (PE) and 7 normal pregnant (NP) women

first: Wei

first: Maryam

last: Rahbar

first: Adam

last: Cribbs

first: Prassana

last: Logenthiran

first: Shuhan

last: Jiang

first: Sofia

last: Cerdeira

first: Chris

last: Redman

first: Manu

last: Vatish


title: Transcriptomic insights into the roles of the transcription factors Clr1, Clr2 and Clr4 in lignocellulose degradation of the thermophilic fungal platform Thermothelomyces thermophilus

status: Public on Dec 15 2021

city: Berlin

first: Benedikt

last: Siebecker

address: Gustav-Meyer-Allee 25

institute: Technische Universität Berlin

summary: Thermothelomyces thermophilus, formerly known as Myceliophthora thermophila, is used in industry to produce lignocellulolytic enzymes and heterologous proteins. However, the transcriptional network driving the expression of these proteins remains elusive. As a first step to systematically uncover this network, we investigated growth, protein secretion, and transcriptomic fingerprints of strains deficient in the cellulolytic transcriptional regulators Clr1, Clr2, and Clr4, respectively.  The genes encoding Clr1, Clr2, and Clr4 were individually deleted using split marker or the CRISPR/Cas12a technology and the resulting strains as well as the parental strain were cultivated in bioreactors under chemostat conditions using glucose as carbon source. During steady state conditions, cellulose was added instead of glucose to study the genetic and cellular responses in all four strains to the shift in carbon source availability. Notably, the clr1 and clr2 deletion strains were unable to continue to grow on cellulose, demonstrating a key role of both regulators in cellulose catabolism. Their transcriptomic fingerprints uncovered not only a lack of cellulase gene expression but also reduced expression of genes predicted to encode hemicellulases, pectinases, and esterases. In contrast, the growth of the clr4 deletion strain was very similar compared to the parental strain. However, a much stronger expression of cellulases, hemicellulases, pectinases, and esterases was observed.   The data gained in this study suggest that both transcriptional regulators Clr1 and Clr2 activate the expression of genes predicted to encode cellulases as well as hemicellulases, pectinases, and esterases. They further suggest that Clr1 controls the basal expression of cellulases and initiates the main lignocellulolytic response to cellulose via induction of clr2 expression. In contrast, Clr4 seems to act as a repressor of the lignocellulolytic response presumably via controlling clr2 expression. Comparative transcriptomics in all four strains revealed potentially new regulators in carbohydrate catabolism and lignocellulolytic enzyme expression that define a candidate gene list for future analyses.

overall_design: Investigation of gene expression in response to cellulose in comparison to glucose in 3 different T. thermophilus transcription factor knockout mutants and their parental strain; ex= exponential state, SS= steady state, t1= 0.5 h, t2= 1 h, t3= 2 h, and t4= 4 h after spiking cellulose (duplicates for each condition/strain: R1, R2).

first: Tabea

last: Schütze

first: Sebastian

last: Spohner

first: Stefan

last: Haefner

first: Vera

last: Meyer


title: Dnase1l3 enhances antitumor immunity and suppresses tumor progression [bulk RNAseq]

status: Public on Feb 07 2022

city: Durham

first: Leping

last: Li

state: NC

address: 111 TW Alexander Dr.

department: Biostatistics and Computational Biology

country: USA

institute: NIEHS

summary: For the chronic inflammation-related colon cancer model (AOM/DSS-colon cancer model), 3-month-old Dnase1l3 WT and KO mice were injected with AOM (8 mg/kg, body weight). One week later, mice were challenged with 2.5% DSS water for 7 days followed by a 14-day recovery with regular drinking water for three cycles. Body weight, rectal bleeding and diarrhea were monitored during the entire experiment. Mice with more than 25% weight loss were removed during the experiment. For the AOM model, 2-month-old Dnase1l3 WT and KO mice were injected intraperitoneally with AOM (8 mg/kg, body weight). Colon tissues were isolated 9 hours, or five days after injection. All animal experiments were conducted in accordance with guidelines of NIEHS/NIH Animal Care and Use Committee.

overall_design: RNA was extracted from the whole colon tissue of Dnase1l3 WT and KO mice at basal condition, after one cycle of AOM/DSS, after three cycles of AOM/DSS and from final tumors from Dnase1l3 WT and KO mice after the three cycles of AOM/DSS. For each group, three to five samples were used. Comparisons were carried out between the two genotypes for each group. RNA was extracted using RNeasy mini kit (QIAGEN) and were of sufficient quality.


title: SmallRNA analysis of placenta and its released extracellular vesicles in normal and preeclampsia pregnancies: insigths into novel biomarkers and mechanisms of disease

first: Toluwalase

summary:
Purpose:  The goals of this study is to compare and profile the smallRNA transcriptome of the placenta in preeclamptic and normal patients using RNA sequencing.
Methods: Placental and Placental vesicles (STB-EVs)  smallRNA profiles of normal and preeclamptic patients were generated by deep sequencing using Illumina HISEQ. FASTq.gz files were compressed with OASIS compressor and alignment was done with OASIS 2.0 ( by trimmimng with trimmomatic, aligning using default OASIS 2.0 aligning papameters). Quantitative PCR validation was performed using TaqMan gene expression assays
Results: This  contains a set of three parallel smallRNA sequencing experiments involving placenta tissue, medium/large STB-EVs and small STB-EVs. Comparison between PE and normal pregnancy placental tissue revealed 134 (p-value of <0.05 ) while in medium/large STB-EVs, 101 and in small STB-EVs, 16  (adjusted P-value of <0.05) differentially expressed small RNA  We identified a number of mechanistic and biomarker targets,  which were validated with qRT–PCR and confirmed to be signifficantly DE. The differentially expressed analysis identified potential yet undescribed small RNAs that may contribute to the pathogenesis of preeclampsia or/and may act as biomarkers of the disease.
Conclusions: Our study represents the first combined analysis of placenta, medium/large and small STB-EV transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results identified potential Placenta EV small RNA biomarkers that can help diagnose the preeclampsia

last: Zhang

first: William

last: Cooke

first: Neva

last: Kandzija


title: Potent stimulation of the androgen receptor instigates a viral mimicry response in prostate cancer [RNA-seq]

status: Public on Feb 01 2022

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

summary: Inhibiting the androgen receptor (AR), a ligand-activated transcription factor, with androgen deprivation therapy is a standard-of-care treatment for metastatic prostate cancer (PCa). Paradoxically, activation of AR can also inhibit the growth of PCa in some patients and experimental systems, but the mechanisms underlying this phenomenon are poorly understood. This study exploited a potent synthetic androgen, methyltestosterone (MeT), to investigate AR agonist-induced growth inhibition. MeT strongly inhibited growth of PCa cells expressing AR, but not AR-negative models. Genes and pathways regulated by MeT were highly analogous to those regulated by DHT, although MeT induced a quantitatively greater androgenic response in PCa cells. MeT potently down-regulated DNA methyltransferases, leading to global DNA hypomethylation. These epigenomic changes were associated with dysregulation of transposable element expression, with long-term MeT treatment resulting in upregulation of endogenous retrovirus (ERV) transcripts. Increased ERV expression led to accumulation of double-stranded RNA and a “viral mimicry” response characterised by activation of interferon signalling, upregulation of MHC Class I molecules and enhanced recognition of murine PCa cells by CD8+ T cells. Positive associations between AR activity and ERVs/anti-viral pathways were evident in patient transcriptomic data, supporting the clinical relevance of our findings. Collectively, our study reveals that the potent androgen MeT can increase the immunogenicity of PCa cells via a viral mimicry response, a finding that has potential implications for the development of strategies to sensitize this cancer type to immunotherapies.

overall_design: RNA-seq following androgen treatment in LNCaP prostate cancer cells

first: L

middle: A

first: M

last: Alizadeh-Ghodsi

first: W

middle: D

last: Tilley


title: Blood gene differential expression of heart failure patients with systemic iron deficiency: pathways and impact on clinical outcomes

status: Public on Nov 17 2021

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

summary: Background: a considerable numeer of patients with heart failure (HF) present systemic iron deficiency (ID), which is related with worse prognosis and a significant decline in quality of life. The mechanisms that underlay the crosstatlk between myocardial performance, neurohormonal activation and heart metabolism are still to be uncovered. Nonetheless, previous experimental studies have already revealed the potential links between iron, mitochondrial metabolism and heart function. Objectives: The present research attempts to investigate the mechanisms that link HF and ID and to identify potential biomarkers of disease prognosis by determning the gene expression pattern through mRNA transcriptome and PCR analyses. Results: The transcriptome of a first cohort of HF patients was analysed according to the presence of ID, underscoring 1128 overexpressed transcripts in patients with iron dysregulation, which permitted to identify 22 genes involved in biological pathways that could be related to HF and the cellular iron regulation and metabolism. From these 22 selected genes, 6 were found differentially expressed by PCR in a new wider cohort of patients, and comprehensive statistical studies identifying specific genetic patterns in three genes that correlate with prognostic outcomes. Briefly, a genetic expression pattern of the smal integral membrane protein 20 and the sirtuin 7 towards decreased expression (higher Δct) was significantly associated with an increased risk of death and the combined end-point of death and HF hospitalization and the composite. Similarly, the intermediate Δct gene expression pattern of mitochondrial ferritin was also associated of both of previous determined outcomes. Conclusions: Patients with HF present different standards of gene expression according to systemic iron status that involve paramount myocardial metabolic pathways implicated in myocardial function and correlate with prognosis. The study highlights the importance of iron regulation in the comprehensive approach to the treatment of myocardial disease.

overall_design: 14 samples were analyzed (7 controls- without iron deficiency and 7 cases- with iron deficiency, paired by gender, age (+-5), Hb (+-2), left ventricular ejection fraction (+-5), logarithm pro-BNP (+-1.5), ischemic etiology and Creatinine Clearance (+-7))

first: Josep

last: Comín

first: Marta

last: Tajes


title: Neuronal development in NEIL3-deficient mice (hippocampus) [CA3]

status: Public on Nov 25 2021

city: Trondheim

first: Jing

last: Ye

address: Høgskoleringen 1

department: Department of Clinical and Molecular Medicine (IKOM)

country: Norway

institute: Norwegian University of Science and Technology (NTNU)

summary: brain tissue from CA3 subregion of the hippocampal formation was isolated at postnatal day 8 and at an adult age (3-6months old animals) in wildtype and NEIL3-deficient mice (n=4 at p8 and n=3 at adult age). NEILs are DNA glycosylases potentially involved in transcription regulation and hippocampal neuronal maturation. RNA was extracted and sequenced.

overall_design: Wildtype (C57Bl6) and mice deficient in NEIL3 (C57Bl6-background) were used. Tissue was isolated exclusively at baseline, i.e. the animal was taken directly from its homecage without any behavioral intervention

first: Nicolas

last: Kunath

first: Tobias

last: Obermann

first: Anna

last: Bugaj

first: Marion

middle: S

last: Fernandez

first: Magnar

last: Bjørås


title: Post-GWAS functional analysis identifies CUX1 as a regulator of p16INK4a and cellular senescence

status: Public on Dec 05 2021

city: Raleigh

first: Xinxia

last: Peng

address: 1060 William Moore Drive

institute: North Carolina State University

summary: Accumulation of senescent cells with age is believed to be an important driver of aging and age-related diseases. However, the underlying mechanisms and the signaling pathways that regulate senescence remain elusive. In this report, we couple high throughput (HTP) mapping of disease-associated functional SNPs (fSNPs) with proteomics analysis of fSNP-binding regulatory proteins to dissect the CDKN2A/B locus, a locus known to be associated with multiple age-related diseases, as well as overall human longevity. We demonstrate that the homeodomain transcription factor CUX1 specifically binds to a fSNP (rs1537371) associated with atherosclerosis within the CDKN2A/B locus. Although it binds at a considerable distance (> 100 kb), CUX1 is shown to regulate the CDKN2A/B encoded genes p14ARF, p15INK4b, p16INK4a, and ANRIL in endothelial cells (ECs). In-depth analysis demonstrates that endothelial CUX1 expression correlates with telomeric length and is induced by both DNA-damaging agents and oxidative stress. Moreover, induction of CUX1 expression triggers both replicative and stress-induced premature senescence via activating p16INK4A expression. Consistent with these findings, we also detect elevated expression of CUX1 and p16INK4A in the plaques of patients with carotid artery disease. Our HTP strategy therefore identifies CUX1 as a regulator of p16INK4A expression and endothelial senescence and a potential therapeutic target for atherosclerosis and other age-related diseases.

overall_design: mRNA profiles from human endothelial cells treated with a scrambled siRNA control or a siRNA targeting human CUX1

first: Danli

last: Jiang

first: Wei

last: Sun

first: Ting

last: Wu

first: Meijuan

last: Zou

first: Sathish

middle: B

last: Vasamsetti

first: Xiaoyu

first: Yihan

last: Zhao

first: Julie

last: Phillippi

first: Amr

middle: H

last: Sawalha

first: Sina

last: Tavakoli

first: Partha

last: Dutta

first: Jonathan

last: Florentin

first: Stephen

middle: Y

last: Chan

first: Tammy

last: Tollison

first: Di

last: Cui

first: Ian

last: Huntress

first: Toren

last: Finkel

first: Gang


title: Expression data from monocytes and monocytic myeloid-derived suppressor cells from HNSCC patients and healthy donors [RNA-seq]

status: Public on Nov 11 2021

city: Nijmegen

first: Glenn

middle: van

last: Wigcheren

address: Geert Grooteplein Zuid 28

department: Tumor Immunology

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences

summary: A better understanding of the mechanisms that induce and drive human suppressive myeloid cells, such as myeloid-derived suppressor cells (MDSCs) and tolerogenic dendritic cells (TolDCs), stimulates therapeutic approaches that intent to restore the immune balance in patients. Here, we compared gene profiles of in vitro generated and isolated M-MDSCs derived from cancer patients to monocytes isolated from cancer patients and healthy donors.

overall_design: Human monocytes were isolated from healthy donor blood, M-MDSCs and monocytes were isolated from the peripheral blood of HNSCC patients and M-MDSCs were generated in vitro from patient derived monocytes. 14 samples from 5 patients were obtained plus 3 samples of monocytes from healthy donors for a total of 17 samples for which RNA was extracted and sequenced.

middle: F

last: van Wigcheren

first: Suzan

last: Stelloo

first: Carla

middle: M

last: van Herpen

first: Michiel

last: Vermeulen

first: I

middle: J

last: de Vries

first: Carl

middle: G

last: Figdor

first: Georgina

last: Flórez-Grau


title: Neuronal development in NEIL3-deficient mice (hippocampus)

first: Jing

last: Ye

summary: brain tissue from all subregions (CA1, CA3, dentate gyrus) of the hippocampal formation was isolated at postnatal day 8 and at an adult age (3-6months old animals) in wildtype and NEIL3-deficient mice (n=4 at p8 and n=3 at adult age). NEILs are DNA glycosylases potentially involved in transcription regulation and hippocampal neuronal maturation. RNA was extracted and sequenced.

first: Nicolas

last: Kunath

first: Tobias

last: Obermann

first: Anna

last: Bugaj

first: Marion

last: Fernandez

first: Magnar

last: Bjørås


title: Gene expression profiling of TNBC cells engineered to knock-down or overexpress PTX3

status: Public on Nov 06 2021

city: Brescia

first: Roberto

last: Ronca

address: viale Europa 11

country: Italy

institute: University of brescia

summary: The pattern recognition receptor long pentraxin-3 (PTX3) plays conflicting roles in cancer by acting as an oncosuppressor or as a pro-tumor mediator depending on tumor context. Triple negative breast cancer (TNBC) represents the most aggressive histotype of breast cancer, characterized by the lack of efficacious therapeutic targets/approaches and poor prognosis.  In this study, in silico data and experimental evidences indicate that PTX3 is produced by tumor parenchyma in TNBC and that its expression levels correlate with tumor stage. On this basis, the impact of PTX3 silencing or its overexpression on the tumorigenic potential of TNBC cell lines was analyzed. Gene expression and in vitro results demonstrate that high levels of PTX3 expression confer a high aggressive/proliferative phenotype, fosters stem-like features, and rewires the energy metabolism in TNBC cells. This results in a more tumorigenic potential in vivo when TNBC cells are grafted in immune-compromised and syngeneic animals. Mechanistically, our data reveal a strong positive correlation between PTX3 expression and the antitumor activity of Toll-like receptor 4 (TLR4) inhibition in TBNC, demonstrating for the first time that PTX3-driven TNBC aggressiveness is due to PTX3-mediated activation of TLR4 signaling.   Altogether, these data shed light on the role of tumor-produced PTX3 in TNBC and uncover the importance of the PTX3/TLR4 pathway for therapeutic and prognostic exploitation in TNBC.

overall_design: MDA-MB 231 cells were infected with lentiviral vector containing short-hairpin RNA (shRNA) targeting human PTX3 (TRCN0000436981) (MDA-MB 231 shPTX3) or a non-targeting/control sequence (SHC002V, Merck) (MDA-MB 231 shNT); MDA-MB 468 cells were infected with a pLentiPGK-Puro (Addgene Plasmid #19070) lentiviral vector harbouring (MDA-MB 468 PTX3) or not (MDA-MB 468 mock) the full length human PTX3 cDNA (GenBank accession n° X63613)

first: Arianna

last: Giacomini


title: Decoding the transcriptome of denervated muscle at single-nucleus resolution

status: Public on Nov 02 2021

city: Houston

first: Zhaoyong

last: Hu

state: Texas

address: One Baylor Plaza

department: Nephrology

institute: Baylor college of medicine

summary: Skeletal muscle exhibits remarkably plasticity under both physiological and pathological conditions. We used adult mice with sciatic denervation as model of muscle atrophy. SnRNA-seq was performed to generate single-nucleus transcriptome profiles of gastrocnemius from normal and denervation mice. Our results define the myonuclear transition, metabolic remodeling and gene regulation  networks associated with muscle atrophy induced by denervation and illustrated the molecular basis of heterogeneity and plasticity of muscle cells in response to muscle atrophy, thus providing a resource for exploring molecular mechanisms leading to muscle atrophy

overall_design: Single-nucleus RNA-seq in normal and denervated mice.

first: Hongchun

last: Lin

first: Xinxin

last: Ma

first: Yuxiang

last: Sun

first: Hui

last: Peng

first: Yanlin

last: Wang

first: Sandhya

last: Thomas


title: Neuronal development in NEIL3-deficient mice (hippocampus) [CA1]

summary: brain tissue from CA1 subregion of the hippocampal formation was isolated at postnatal day 8 and at an adult age (3-6months old animals) in wildtype and NEIL3-deficient mice (n=4 at p8 and n=3 at adult age). NEILs are DNA glycosylases potentially involved in transcription regulation and hippocampal neuronal maturation. RNA was extracted and sequenced.


title: Transcriptome after spatial exploration in CA1-specific brain tissue from wildtype and NEIL3-deficient mice

status: Public on Nov 01 2021

summary: CA1-specific brain tissue from the hippocampal formation was isolated at baseline (homecage condition) and after a spatial exploration paradigm ("open field") in wildtype and NEIL3-deficient mice. NEIL3 is a DNA glycosylase potentially involved in transcription regulation. RNA was extracted and sequenced. Subsequently, these results were correlated to an extracellular live recording of pyramidal cell activity ("place cell recording") in the same genotypes.

overall_design: Wildtype (C57Bl6) and NEIL3-deficient (Neil3-/-, C57Bl6-background) were used. At baseline, 2 wildtype and 2 mutant animals were included. After learning, 3 wildtype and 3 mutant animals were included. In both conditions, animals were exposed to the same housing conditions, food ad libitum and handled by the same experimenters.

first: Pegah

last: Bigonah


title: Epithelial-to-mesenchymal transition mediates resistance to maintenance therapy with vinflunine in advanced urothelial cell carcinoma patients

status: Public on Dec 28 2021

first: Júlia

last: Perera-Bel

summary:
Urothelial cell carcinoma (UCC) is the fifth most common type of cancer in developed countries. Vinflunine, a third-generation semi-synthetic anti-microtubule agent, was approved in 2009 by the EMA for the treatment of patients with advanced UCC (aUCC) who have progressed after initial treatment with a platinum-based chemotherapy regimen. However, nowadays with the incorporation of immune-checkpoint blockade in the management of aUCC, vinflunine is considered as a third line treatment after immunotherapy failure. In the randomized phase II MAJA trial we demonstrated that maintenance therapy with vinflunine in patients with controlled disease after first-line platinum-based chemotherapy resulted in significantly longer progression-free survival as compared to best supportive care. However, at present, the mechanisms that underlying vinflunine resistance in UCC remain unclear. Thus, the objective of this study is to perform a pre-planned gene expression analyses aimed to identify new resistance mechanisms as well as biomarkers to predict response to maintenance vinflunine.
We have compared the gene expression profiles of eight bad responders to vinflunine (<4 cycles) and nine good responders (>12 cycles). RNA was isolated from FFPE tumor tissue collected using the Covaris kit and gene expression levels were analyzed with Clariom S (Affymetrix). Differential expression, defined as p<0.05 and |FC|>1.5, was determined with linear models for microarray data included in the limma and sva packages. Pre-ranked Gene Set Enrichment Analysis (GSEA) was used for the functional classification of the differential expression genes. In vitro validation was performed using bladder cancer cell lines.
Hierarchical clustering of genes showed a differential expression pattern between good and bad responders. In good responders, GSEA revealed that “Epithelial-to-mesenchymal transition” (EMT) and “IL-6 – JAK – STAT3” pathways were the top enriched negatively hallmarks. Mechanistically, we showed that the downregulation of mesenchymal markers using the polyphenol curcumin, a well-known EMT inhibitor, significantly sensitized mesenchymal-like bladder cancer cells to vinflunine treatment.
In conclusion, our results demonstrated that EMT process mediates resistance to vinflunine and suggested that the combination of this anti-microtubule agent with an EMT inhibitor could be a good strategy of maintenance therapy in aUCC patients.

overall_design: 17 samples were analyzed: 9 good responders and 8 bad responders

first: Vicenç

middle: R

last: de Porras

first: Albert

last: Pous

first: Joaquim

last: Bellmunt


title: KIAA1429/VIRMA promotes breast cancer proliferation and migration by stabilizing m6A-modified HAS2 RNA expression in cytosol

city: La Jolla

last: Li

state: California

address: 9500 Gilman Dr

department: Pediatrics

institute: University of California, San Diego

type: Methylation profiling by high throughput sequencing

summary: N6-methyladenosine (m6A) is the most abundant internal RNA modification in mRNA molecules and plays important roles in multiple important biological processes including cancer development. KIAA1429/VIRMA is an important component of m6A methyltransferase complex to facilitate depositing m6A modification in RNA molecules. Here we found that KIAA1429/VIRMA was overexpressed in breast cancer patients among other m6A related enzymes. Breast cancer patients with higher KIAA1429 expression have worse survival compared with control group. In addition, KIAA1429/VIRMA protein mislocated in cytosol in breast cancer tissues and cell lines. KIAA1429/VIRMA depletion reduced breast cancer cell proliferation and migration. Mechanism studies showed that cytosolic expressed KIAA1429/VIRMA interacted with m6A reader protein IGF2BP3 and stabilized expression of m6A-modified HAS2 expression. HAS2 is downstream of KIAA1429/VIRMA to mediate breast cancer cell proliferation and migration and has positive correlation with KIAA1429/VIRMA expression in cancer patients.

overall_design: Control (NTC) MDA-MB-231 breast cancer cells, KIAA1429 KO MDA-MB-231 breast cancer cells, KIAA1429 KD MDA-MB-231 breast cancer cells, RNA-seq and MeRIP-Seq.

last: hui

first: Tariq

last: Rana


title: Sequencing of Mus musculus brain of 30 months old animals

status: Public on Oct 19 2021

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

summary: Comparison of gene expression profiles from Mus musculus brain at age 30 months. The RNA-seq data comprise 1 groups.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 5 samples: 30 months

first: Christiane

last: Frahm

first: Otto

middle: W

last: Witte

first: Madlen

last: Günther

first: Rolf

last: Hühne

first: Marco

last: Groth

first: Matthias

last: Platzer


title: Transcriptomics of human adenocarcinoma cell line HCT-8 infected with Cryptosporidium parvum treated with indole

status: Public on Oct 13 2021

city: St. Louis

first: Lisa

last: Funkhouser-Jones

state: MO

address: 660 Euclid Ave

institute: Washington University School of Medicine

summary:
Purpose: The goal of this study was to identify transcriptional changes in HCT-8 cells treated with indole for 4 or 12 hours.
Methods: Confluent HCT-8 monolayers were infected with excysted Cryptosporidium parvum sporozoites for 4 h, after which cells were washed to remove extracellular parasites. Cells were then treated with 1% DMSO in cell culture medium with or without 880 uM indole. RNA was collected in triplicate for each treatment type after 4 h and 12 h of treatment (8 and 16 hours post infection, respectively).
Results: When the two time points were combined, indole significantly upregulated 57 genes and downregulated 11 genes. Of the upregulated genes,16 genes were primarily upregulated in cells exposed to indole for 4 h and then went back down by 12 h of exposure. These genes were primarily involved in pathways related to ER stress and the unfolded protein response (UPR). Conversely, 41 genes had higher gene expression after 12 h of indole exposure and were predominantly involved in membrane transport of carboxylic acids and amino acids.
Conclusions: Indole treatment causes ER stress and upregulation of membrane transporters in a human adenocarcinoma cell line infected with Cryptosporidium parvum.

overall_design: mRNA profiles of HCT-8 cells infected with Cryptosporidium parvum treated with indole for 4 or 12 hours

first: L

last: Sibley


title: Single-cell Architecture and Functional Requirement of Alternative Splicing during Hematopoietic Stem Cell Emergence

status: Public on Oct 15 2021

city: Beijing

first: Jia

last: Yu

address: Dong Dan San Tiao 5, Dongcheng District

country: China

institute: Peking Union Medical College

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

overall_design: Refer to individual Series


title: The RNA-seq of knee joint cartilaginous tissues of  conditionally knockout Hbb or wildtype postnatal day 6 mice

status: Public on Sep 30 2021

city: Xi'an

first: Feng

last: Zhang

address: Changle west Road

department: Department of Pathology

institute: Fourth Military Medical University

summary: To investigate the gene expression difference between knee joint cartilaginous tissues of conditionally knockout Hbb or wildtype postnatal day 6 mice.

overall_design: 6 samples were investigated. Among these, 3 samples were control, another 3 samples were experiment group

first: Shuangping

last: Guo

first: Yuying

last: Wang


title: Regulation of intestinal immunity and tissue repair by enteric glia

status: Public on Oct 06 2021

city: London

first: Vassilis

last: Pachnis

state: London

address: 1 Midland Road

department: Development and Homeostasis of the Nervous System Laboratory

institute: The Francis Crick Institute


title: NR2F2 is an essential regulator of malignant tumor state by promoting tumor stemness, invasion and repressing differentiation I

status: Public on Sep 29 2021

city: Bruxelles

first: Yura

last: Song

address: 808, route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

summary: The non-genetic mechanisms required to sustain malignant tumor state are poorly understood. During the transition from benign tumors to malignant carcinoma, tumor cells need to repress differentiation and acquire invasive features. Using transcriptional profiling of cancer stem cells (CSC) from benign tumors and malignant skin squamous cell carcinoma (SCC), we identified the nuclear receptor NR2F2 as uniquely expressed in malignant SCC. Using genetic gain- and loss-of-function in vivo, we show that NR2F2 is essential for promoting the malignant tumor state by controlling tumor stemness and maintenance in mouse and human SCC. We demonstrate that NR2F2 promotes tumor cell proliferation, epithelial-mesenchymal transition (EMT) and invasive features, while repressing tumor differentiation and immune cell infiltration by regulating a common transcriptional program in mouse and human SCCs. Altogether, we identify NR2F2 as a key regulator of malignant CSC functions that promotes tumor renewal and restricts differentiation to sustain malignant tumor state.

overall_design: Sk-MES-1 human lung SCC cells (control) and respective CRISPR-generated NR2F2 KO cells.

first: Federico

last: Mauri

first: Cédric

last: Blanpain


title: Spec-seq data for ZNF140, ZNF10, ZFP3, ZNF675, ZNF382

status: Public on Dec 15 2021

city: Palo Alto

first: Zheng

last: Zuo

state: CA

address: Stanford

department: Genetics

institute: Stanford university

summary: This dataset consists of Spec-seq samples data for four tandem zinc finger proteins in human genome, each with two replicates. The Spec-seq is a medium throughput technique to characterize the binding specificity of a TF of interest to thousands of binding sites with resolution down to 0.2kT. Similar samples were deposited to NCBI GEO database before (GSE188166). The data analysis workflow for each ZFP can be accessed through https://github.com/zeropin/ZFPCookbook.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design:
For ZNF140, a truncated construct containing finger 1 to 6 (F1-F6) was fused to N-terminal Halo tag for protein expression and EMSA assay; For ZNF10, F1-F8 construct was used; For ZFP3, F1-F10 construct was used; For ZNF675, both F1-F11 and F1-F6 constructs were tested separately; The DNA library design and experimental workflow was described in a paper to be published in detail. The Spec-seq libraries for ZNF675 includes not only synthetic elements but also 500 endogeneous genomic elements from human genome (300 sites within repeat elements, 200 sites outside repeat elements).
For ZNF382, its DNA-binding domain including 9 fingers was fused to N-terminal HALO-Tag for experimental work. The DNA library design and experimental workflow was described in paper to be published in detail.


title: ARHGEF12 activates Rap1A and not RhoA in human capillary endothelial cells to reduce tumor necrosis factor-induced leak

status: Public on Dec 07 2021

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

summary: In acute critical illness the capillary barrier may break down resulting in hypovolemia, extracellular edema, tissue dysoxia and even death. Restoration of the tight junction dependent capillary barrier is regulated by small GTPases, the specific regulatory molecules most active in this setting are not well described. Transcriptional profiling of tight junction forming human dermal microvascular ECs (HDMECs) and adherens junctions forming human umbilical vein EC (HUVECs) demonstrate ARHGEF12 is significantly differentially regulated in HDMECs before and after stimulation with tumor necrosis factor (TNF). HDMEC depleted of ArhGEF12 demonstrate significantly exacerbated TNF-induced decrease in trans-endothelial electrical resistance and disruption of tight junction proteins claudin-5 and ZO-1. ArhGEF12 is a RhoA-GEF, an established finding which is inconsistent with our observed results. Pulldown activation assays from of HDMECs depleted of ArhGEF12 and treated with TNF show decreased Rap1A activity after four hours and paradoxically increased RhoA activity after 12 hours. In cell-free pulldown assays, immunoprecipitated ArhGEF12 effectively activates Rap1A and RhoA and not Rap2A-C, RhoB-C or even Rap1B which shares 95% sequence identity with Rap1A. We conclude that in tight junction forming EC, ArhGEF12 selectively activates Rap1A to promote capillary barrier restoration in a mechanism independent of traditionally described cAMP-mediated Epac1 activation. The unique dual in vitro specificity of ArhGEF12 for RhoA, Rap1A and not Rap1B cannot be explained by sequence identity and requires additional investigation.

overall_design: Whole transcriptome analysis of cultured human umbilical vein endothelial cells (HUVEC) with and without treatment with TNF with 3 replicates per condition

first: Alamzeb

last: Khan

first: Weiming

last: Ni

last: Lopez-Giraldez

first: Tania

last: Baltazar

first: Jordan

last: Pober

first: Richard

last: Pierce


title: neuronal development in NEIL3-deficient mice (hippocampus) [DG]

first: Jing

last: Ye

summary: brain tissue from Dentate Gyrus subregion of the hippocampal formation was isolated at postnatal day 8 and at an adult age (3-6months old animals) in wildtype and NEIL3-deficient mice (n=4 at p8 and n=3 at adult age). NEILs are DNA glycosylases potentially involved in transcription regulation and hippocampal neuronal maturation. RNA was extracted and sequenced.

first: Nicolas

last: Kunath

first: Tobias

last: Obermann

first: Anna

last: Bugaj

first: Marion

last: Fernandez

first: Magnar

last: Bjørås


title: High-throughput Ig and TCR repertoire single-cell sequencing analysis in rhesus macaques

status: Public on Nov 18 2021

first: Xinxia

last: Peng

summary: Recent advancements in microfluidics and high-throughput sequencing technologies have enabled recovery of paired heavy- and light- chain of immunoglobulins (Ig) and VDJ- and VJ- chains of T cell receptors (TCR) from thousands of single cells simultaneously. Due to the complexity of these polyclonal receptors, for many species single-cell immune repertoire sequencing assays are not yet commercially available. Rhesus macaques are one of the most well-studied model organisms of the human adaptive immune response; application of these new immune repertoire sequencing assays is highly relevant to vaccine and infectious disease studies. Here we use custom designed primers to target and enrich for every known Ig and TCR chain and isotype in the rhesus macaque animal model. We sequenced more than 110,000 cell barcodes from rhesus macaque repertoires using PBMC, splenocyte, and FACS-sorted T and B cell. We were able to recover every Ig and TCR isotype, measure clonal expansion in proliferating T cells, and pair repertoires with gene expression profiles of single cells. Our results establish the ability to perform single-cell based immune repertoire analysis in rhesus macaque.

overall_design: High-throughput single-cell sequencing of T and B cell receptor sequences from 6 samples (2 PBMC, splenocyte, stimulated B cells, and stimulated T cells divided into proliferating and non-proliferating fractions). In addition, 5' GEX profiles were also sequenced for all but one PBMC sample. This dataset includes the 5' GEM profiles.

first: Evan

last: Walsh

first: Tammy

last: Tollison

first: Hayden

middle: N

last: Brochu

first: Brian

middle: I

last: Shaw

first: Kayliegh

last: Dively

first: Hsuan

last: Chou

first: Lynn

last: Law

first: Allan

last: Kirk

first: Michael

last: Gale


title: NR2F2 controls malignant squamous cell carcinoma state by promoting stemness  and invasion and repressing differentiation II

status: Public on Sep 27 2021

first: Yura

last: Song

overall_design: FACS isolated CD34+Epcam+tumor cells from DMBA/TPA induced papillomas (benign skin SCC) and carcinomas (malignant skin SCC)

first: Federico

last: Mauri

first: Corentin

last: Schepkens

first: Cédric

last: Blanpain


title: RNA signatures of DMD urinary stem cells identify antisense effect and causative mutations in undiagnosed patients

status: Public on Nov 10 2021

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

summary: We have characterized the native urine derived stem cells (USCs) in order to understand if they could be an authologous, non-invasive, and cost effective in vitro model for research and diagnostic application in Duchenne muscular dystrophy disease

overall_design: We analyzed the gene expression levels of i) native USCs, derived from a pool of 3 healthy donors (C-n) and from the DMD patient IG (IG-n), ii) MyoD-transformed USCs from controls (C-m) and from the DMD patient IG (IG-m), and iii) MyoD-transformed USCs from the DMD patient IG transfected with AON to skip the exon 44 and reframe the DMD transcript (IG-m 44)

first: Maria

last: Falzarano

first: Andrea

last: Grilli

first: Silvia

last: Zia

first: Mingyan

last: Fang

first: Rachele

last: Rossi

first: Francesca

last: Gualandi

first: Paola

last: Rimessi

first: Reem

last: El Dani

first: Fabris

last: Marina

first: Zhiyuan

last: Lu

first: Wenyan

last: Li

first: Tiziana

last: Mongini

first: Federica

last: Ricci

first: Elena

last: Pegoraro

first: Luca

last: Bello

first: Valeria

last: Sansone

first: Hegde

last: Madhuri

first: Barbara

last: Roda

first: Pierluigi

last: Reschiglian

first: Rita

last: Selvatici

first: Alessandra

last: Ferlini


title: Epstein-Barr virus nuclear antigen 2 (EBNA2) extensively rewires the human chromatin landscape at autoimmune risk loci [ATAC-seq]

status: Public on Sep 23 2021

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The interplay between environmental and genetic factors plays a key role in the development of many autoimmune diseases. In particular, the Epstein-Barr virus (EBV) is an established contributor to multiple sclerosis, lupus, and other disorders. Previously, we demonstrated that the EBV nuclear antigen 2 (EBNA2) transactivating protein occupies up to half of the risk loci for a set of seven autoimmune disorders. To further examine the mechanistic roles played by EBNA2 at these loci on a genome-wide scale, we globally examined gene expression, chromatin accessibility, chromatin looping, and EBNA2 binding, in a B cell line that was 1) uninfected, 2) infected with a strain of EBV lacking EBNA2, or 3) infected with a strain that expresses EBNA2. We identified >400 EBNA2-dependent differentially expressed human genes and >5,000 EBNA2 binding events in the human genome. ATAC-seq analysis revealed >2,000 regions in the human genome with EBNA2-dependent chromatin accessibility, and HiChIP-seq data revealed >1,700 regions where EBNA2 altered chromatin looping interactions. Importantly, autoimmune genetic risk loci were highly enriched at the sites of these EBNA2-dependent chromatin-altering events.  We present examples of autoimmune risk genotype-dependent EBNA2 events, nominating genetic risk mechanisms for autoimmune risk loci such as ZMIZ1. Taken together, our results reveal important interactions between host genetic variation and EBNA2-driven disease mechanisms. Further, our study highlights a critical role for EBNA2 in rewiring human gene regulatory programs through rearrangement of the chromatin landscape and nominates these interactions as components of genetic mechanisms that influence the risk of multiple autoimmune diseases.

overall_design: ATAC-seq was performed in 2 biological replicates each from uninfected, EBNA2- (P3HR1) EBV infected, and EBNA2+ (B95.8) EBV infected Ramos B cells.

first: Leah

middle: C

last: Kottyan

middle: T


title: NR2F2 controls malignant squamous cell carcinoma state by promoting stemness  and invasion and repressing differentiation

first: Yura

last: Song

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Epstein-Barr virus nuclear antigen 2 (EBNA2) extensively rewires the human chromatin landscape at autoimmune risk loci [ChIP-seq]

overall_design: ChIP-seq was performed in 2 biological replicates from EBNA2+ (B95.8) EBV infected Ramos B cells and 2 biological replicates from GM12878 using EBNA2 antibody (Abcam; ab90543).


title: Expression data (HG-U133 Plus 2.0) from human monocyte-derived cell types (TolDC, M-MDSC, MoDC)

status: Public on Sep 20 2021

first: Glenn

last: Wigcheren

summary: A better understanding of the mechanisms that induce and drive human suppressive myeloid cells, such as myeloid-derived suppressor cells (MDSCs) and tolerogenic dendritic cells (TolDCs), stimulates therapeutic approaches that intent to restore the immune balance in patients. Here, we compared gene profiles of in vitro generated M-MDSCs to TolDCs in the context of monocytes and monocyte-derived DCs (MoDCs).

overall_design: Human M-MDSCs, TolDCs and MoDCs were generated in vitro from CD14+ purified Monocytes for 5 donors. Four cell types from 5 donors were used for RNA extraction and hybridization on Affymetrix microarrays. Three Monocyte samples failed QC leaving a total of 17 samples in this analysis.

last: van Wigcheren

first: Suzan

last: Stello

first: Yvonne

last: Wesseling

first: Anja

last: van de Stolpe

first: I

last: de Vries

first: Carl

last: Figdor

first: Georgina

last: Flórez-Grau


title: Epstein-Barr virus nuclear antigen 2 (EBNA2) extensively rewires the human chromatin landscape at autoimmune risk loci [RNA-seq]

overall_design: RNA-seq was performed in 2 biological replicates each from uninfected, EBNA2- EBV (P3HR1) infected, and EBNA2+ EBV (B95.8) infected Ramos B cells.


title: ATAC-seq of germinal center B cell-derived cell lines after POU2F2 or POU2AF1 knockdown

status: Public on Sep 11 2021

city: New York

first: Ashley

middle: Stephen

last: Doane

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: ATAC-seq in OCI-Ly7 and SUDHL4 cell lines after CRISPRi knockdown of OCT2 (POU2F2) or OCA-B (POU2AF1), or control non-targeting sgRNAs.

overall_design: Comparison of knockdown relative to control.


title: H3K27ac HiChIP of germinal center B cell-derived cells after POU2AF1 knockdown

summary: H3K27ac HiChIP of OCI-Ly7 cells following control or CRISPR-I knockdown of OCAB (POU2AF1).

overall_design: OCI-Ly7 control (n=3) and OCI-Ly7 with OCAB knockdown (n=2).


title: Epstein-Barr virus nuclear antigen 2 (EBNA2) extensively rewires the human chromatin landscape at autoimmune risk loci


title: A microRNA cluster controls fat cell differentiation and adipose tissue expansion by regulating SNCG

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

institute: Hospital del Mar Research Institute

summary: The H19X-encoded miR-424(322)/503 cluster regulates multiple cellular functions. Here we report for the first time that it is also a critical linchpin of fat mass expansion. Deletion of this miRNA cluster in mice results in obesity, while increasing the pool of early adipocyte progenitors and hypertrophied adipocytes. Complementary loss and gain of function experiments and RNA sequencing demonstrate that miR-424(322)/503 regulates a conserved genetic program involved in the differentiation and commitment of white adipocytes. Mechanistically, we demonstrate that miR-424(322)/503 targets γ-Synuclein (SNCG), a factor that mediates this program rearrangement by controlling metabolic functions in fat cells, allowing adipocyte differentiation and adipose tissue enlargement. Accordingly, diminished miR-424(322) in mice and obese humans co-segregates with increased SNCG in fat and peripheral blood as mutually exclusive features of obesity, being normalized upon weight loss. Our data unveil a previously unknown regulatory mechanism of fat mass expansion tightly controlled by the miR-424(322)/503 through SNCG.

overall_design: Mouse embryonic fibroblasts (MEFs) were isolated from wild-type (Wt) and miR-424(322)/503-/- (miR-KO) E14 embryos and differentiated into adipocytes. RNA sequencing was conducted in adipocyte precursor cells (PA) and in Wt and miR-KO fully-differentiated lipid-containing mature adipocytes (MA). Cryopreserved human subcutaneous preadipocytes carrying a doxycycline (Dox)-inducible pTRIPz lentiviral system were cultured and differentiated according to manufacturer’s instructions. RNA sequencing was conducted in differentiated adipocytes overexpressing (OE) the miR-424(322)/503 cluster during differentiation (14d) or for last 2 days of the adipogenic course (48h) vs respective non-targeting controls (NTC) under same conditions of cell culture and treatment.

first: Francisco

last: Ortega

first: David

last: Llobet-Navas


title: CD137 costimulation counteracts TGFβ inhibition of NK cell anti-tumor function and promotes the acquisition of tissue-resident Th9-like properties

status: Public on Sep 10 2021


title: ChIP-seq for OCT2 and OCA-B in human primary naïve and germinal center B cells and germinal center B cell-derived cell lines following POU2AF1 knock down

summary: ChIP-seq for OCT2 (POU2F2) and OCA-B (POU2AF1) in primary human tonsilar naïve and germinal center B cells, as well as germinal center B cell-derived cell lines following POU2AF1 knock down.

overall_design: Replicate experiments for cell lines representing independent experiments.


title: Epstein-Barr virus nuclear antigen 2 (EBNA2) extensively rewires the human chromatin landscape at autoimmune risk loci [HiChIP]

overall_design: We performed HiChIP-seq using anti-H3K27ac antibody (Abcam ab4729) on uninfected, EBNA2- (P3HR1) EBV infected, and EBNA2+ (B95.8) EBV infected Ramos B cells. There were two biological replicates for each condition.


title: NR2F2 controls malignant squamous cell carcinoma state by promoting stemness  and invasion and repressing differentiation IV

overall_design: NR2F2 inducible Gain-of-Function (GoF) was induced for 48h by Doxycycline (1µg/mL) on the human Skin SCC cell lines A431 before chromatin collection.

first: Federico

last: Mauri

first: Corentin

last: Schepkens

first: Cédric

last: Blanpain


title: RNA-seq of germinal center B cell-derived cell lines after POU2F2 or POU2AF1 knockdown

summary: RNA-seq in OCI-Ly7 and SUDHL4 cell lines after CRISPRi knockdown of OCT2 (POU2F2) or OCA-B (POU2AF1), or control non-targeting sgRNAs.


title: NR2F2 controls malignant squamous cell carcinoma state by promoting stemness  and invasion and repressing differentiation III

overall_design: FACS isolated Epcam+tumor cells from Ctrl vs NR2F2 overexpression (GOF) papillomas and Ctrl (Cre-) vs K5CreER;NR2F2fl/fl skin SCC


title: CD137 costimulation counteracts TGFβ inhibition of NK cell anti-tumor function and promotes the acquisition of tissue-resident Th9-like properties [2 treatments]

summary: Enhancing NK cell-based cancer immunotherapy by overcoming immunosuppression is an unmet goal. Here, we demonstrate the ability of the anti-CD137 agonist urelumab for overcoming TGF-β-mediated inhibition of human NK-cell proliferation and sustained anti-tumor function. Transcriptomic, immunophenotypic and functional analyses evidenced that CD137 costimulation modified the transcriptional program induced by TGF-β on activated NK cells by limiting SMAD4-dependent inhibition of pro-proliferative (CD25, cMyc), activating (NKG2D, CD16) and effector (Granzyme B, IFNγ) molecules while maintaining SMAD4-independent acquisition of tumor-retention features (CXCR3, CD103). Activated NK cells cultured in the presence of TGF-β1 and CD137 agonist showed preserved antibody-dependent cytotoxicity against cancer cells, recovered CCL5 and IFNγ secretion and gained the capacity for producing IL-9 upon restimulation. Treatment of breast tumor-derived multicellular cultures with trastuzumab and urelumab recapitulated CD137 induction and fostered tumor-infiltrating CD16+ NK cell persistence. Our data reveals CD137 as a targetable checkpoint for overturning TGF-β constrains on NK cell anti-tumor responses

overall_design: A total of 4 samples were analyzed: 2 different treatments in purified NK cells from 2 volunteer donors: 12h treatment with anti-CD16 coated plates and non-treated

first: Marcel

last: Costa

first: Aura

last: Muntasell


title: Chromatin architecture of B cell development during the humoral immune response

status: Public on Sep 09 2021

overall_design: Refer to individual Series


title: NR2F2 controls malignant squamous cell carcinoma state by promoting stemness  and invasion and repressing differentiation V

first: Yura

last: Song

overall_design: NR2F2 inducible Knockdown evaluation on human skin SCC (A431) cell lines, induced with Doxycycline (1µg/mL).


title: Regulation of intestinal immunity and tissue repair by enteric glia   (Single-cell expression analysis of  small intestinal glia cells in naïve and H. poly-infected mice.)

status: Public on Aug 31 2021

first: Vassilis

last: Pachnis

address: 1 Midland Rd

summary: Tissue maintenance and repair depend on the integrated activity of multiple cell types. Whereas the contributions of epithelial, immune and stromal cells in intestinal tissue integrity are well understood, the role of intrinsic neuroglia networks remains largely unknown. Here, we uncover pivotal roles of enteric glial cells (EGCs) in intestinal homeostasis, immunity and tissue repair. We demonstrate that infection of mice with Heligmosomoides polygyrus (H. poly) leads to enteric gliosis and upregulation of the interferon gamma (IFN-γ) gene signature. Single-cell transcriptomics of tunica muscularis (TM) showed that glia-specific abrogation of IFN-γ signaling leads to tissue-wide activation of pro-inflammatory transcriptional programs. In addition, disruption of the IFN-γ-EGC signaling axis enhanced the inflammatory and granulomatous response of TM to helminths. Mechanistically, we show that upregulation of Cxcl10 is an early immediate response of EGCs to IFN-γ signaling and provide evidence that this chemokine and the downstream amplification of IFN-γ signaling in the TM are required for a measured inflammatory response to helminths and resolution of granulomatous pathology. Our study demonstrates that IFN-γ signaling in enteric glia is central to intestinal homeostasis and reveals critical roles of the IFN-γ-EGC-Cxcl10 axis in immune response and tissue repair following infectious challenge.  To characterize the response of enteric glia to helminth infection at single cell resolution, we next performed scRNAseq (C1 Fluidigm platform) of tdT+ cells from the TM of naïve and H. poly-infected mice.

overall_design: To investigate how EGCs respond to pathogen invasion, tamoxifen-treated Sox10CreERT2;Rosa26tdTomato mice, which express the fluorescent reporter tdTomato (tdT) specifically in the intrinsic glia cell network of the gut, were infected with H. poly. At 7 days post, we isolated enteric glia cells (EGCs) from five biological samples (2x naïve and 3x H. poly infected animals (7 dpi)) from both male and female Sox10CreERT2;Rosa26tdTomato adult mice at 24 hours after tamoxifen induction.

first: Fränze

last: Progatzky

first: Michael

last: Shapiro

first: Song

last: Chng

first: Bethania

last: Garcia-Cassani

first: Cajsa

last: Classon

first: Selin

last: Sevgi

first: Anna

last: Laddach

first: Ana

last: Bon-Frauches

first: Reena

last: Lasrado

first: Maryam

last: Rahim

first: Eleni-Maria

last: Amaniti

first: Stefan

last: Boeing

first: Kathleen

last: Shah

first: Lewis

last: Entwistle

first: Alejandro

last: Suárez-Bonnet

first: Mark

last: Wilson

first: Brigitta

last: Stockinger


title: Characteristic evaluation of in vitro 3D cell culture model in a multi-dimensional way with high-throughput sequencing

status: Public on Aug 25 2021

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

summary: Organoids culture provides unique opportunities to study human diseases and to complement animal models. Several organs and tissues can be in vitro cultured in 3D structures resembling in vivo tissue organization. Organoids culture contains most of the cell types of the original tissue and are maintained by growth factors similar to the in vivo situation. However, the system is yet not fully understood, and specific in vivo features especially those driven by cell-extrinsic factors may be lost in culture. Here we show a comprehensive transcriptome-wide characterization of mouse gut organoids derived from different intestinal compartments and from mice of different gender and age. RNA-seq analysis showed that the in vitro culture strongly influences the global transcriptome of the intestinal epithelial cells (~60% of the total variance). Several compartment-, age- and gender-related transcriptional programs being lost after culturing suggest that they are driven by niche or systemic factors. However, some of the transcriptional programs proper of the cells of origin are kept in vitro indicating that compartment-, age- and gender-specific intrinsic features exist and can be studied in this system. Our study provides knowledge about the cell-extrinsic or cell-intrinsic origin of intestinal epithelial transcriptional programs. We anticipated that our characterization of this in vitro system is an important reference for scientists and clinicians using intestinal organoids as a research model.

overall_design: Bulk RNA sequencing on epithelial cells of small intestine of different compartments from mice of different gender and age in vivo (crypts) and in vitro (organoids)

first: Jing

last: Lu

last: Krepelova

first: Francesco

last: Neri


title: Global mapping of the macrophage-HIV-1 transcriptome reveals that productive infection induces remodeling of the host cell DNA and chromatin

status: Public on Jul 21 2021

city: Montreal

first: Eric

middle: A

last: Cohen

state: Quebec

address: 110 Ave des Pins Ouest

country: Canada

institute: IRCM

summary: It has been proposed that macrophages could serve as long-lived compartments for HIV-1 infection under in vivo situations because these cells are resistant to the virus-mediated cytopathic effect, produce progeny virus over extended periods of time and are localized in tissues that are often less accessible by treatment. Comprehensive experimental studies are thus needed to characterize the HIV-1-induced modulation of host genes in these myeloid lineage cells. To shed light on this important issue, we performed comparative analyses of mRNA expression levels of host genes in uninfected bystander and HIV-1-infected human macrophages using an infectious reporter virus construct coupled with a large-scale RNA sequencing approach. We observed a rapid differential expression of several host factors in the productively infected macrophage population including genes regulating DNA replication factors and chromatin remodeling. A siRNA-mediated screening study to functionally identify host determinants involved in HIV-1 biology has provided new information on the virus molecular regulation in macrophages.

overall_design: Human monocytes from healthy donors were differentiated in MØ by adherence for 3 days in the presence of RPMI-1640 culture medium supplemented with M-CSF (25 ng/mL) and 10% human AB serum. Cells were maintained in culture medium in absence of M-CSF for an additional 3 days, treated with Accutase™ (Stem Cell Technologies) for 60 to 90 min, and detached with a soft cell scraper (Sarstedt). Cells were plated at 2.5 x 10exp5 cells/mL for 24 (cell-culture coated dishes) or 72 h (Ultra-Low attachment dishes). MØ were infected with replication-competent NL/Bal-HSA (see A. Deshiere et al., Scientific Reports 2017) with multiplicities of infection (MOI) ranging from 0.004 to 2.5. HSApos and HSAneg MØ were isolated using biotinylated anti-HSA (clone M1/69; eBiosciences) and anti-Biotin Magnetic Beads (Miltenyi) in a MS separation column (Miltenyi). Purified MØ populations (HSAneg and HSApos) were resuspended and frozen in QIAzol lysis buffer. Total RNA was isolated from sorted cell populations using the miRNeasy Kit from QIAGEN (Valencia, CA).

first: Robert

last: Lodge

first: Alexandre

last: Deshiere

first: Corinne

last: Barat

first: Michel

last: Tremblay


title: Glyoxal as alternative fixative for single cell transcriptome experiments

status: Public on Jun 22 2021

city: Heidelberg

first: Erica

last: Valentini

address: Im Neuenheimer Feld 580

institute: DKFZ

summary: Within just a few years single cell RNA sequencing has become a frequently used standard method in many research fWithin just a few years single cell RNA sequencing has become a frequently used standard method in many research facilities worldwide. Declining sequencing costs and further refinements of the available protocols will pave the way for previously unimaginable prospects, up to single cell transcriptomic maps of entire organisms. The sample collection process can constitute a severe bottleneck in scRNA-seq experiments especially for solid tissues. Lengthy dissociation protocols are not uncommon to obtain sufficient amounts of starting material and can lead to significant changes in the gene expression profiles of cells. Preservation of the transcriptome prior to single cell dissociation can overcome this setback. Here we present an extensive performance analysis of glyoxal as an alternative fixative for scRNA-seq application. High numbers of transcripts and genes were recovered from glyoxal-fixed cells subjected to Drop-seq methodology with the best performance in Drosophila cells. While glyoxal fixation in Drosophila Kc167 and human HEK 293T cells revealed transcriptome data similar to the unfixed condition, reduced library complexity was observed for the human sample. We found the integrity of Drosophila intestinal tissue maintained following glyoxal fixation, while dissociation of the fixed tissue allowed sufficient cell isolation. In conclusion, we present glyoxal as a well-suited fixative for Drosophila samples that allows high-quality single cell transcriptomic analysis and successful intestinal tissue disaggregationcilities worldwide. Declining sequencing costs and further refinements of the available protocols will pave the way for previously unimaginable prospects, up to single cell transcriptomic maps of entire organisms. The sample collection process can constitute a severe bottleneck in scRNA-seq experiments especially for solid tissues. Lengthy dissociation protocols are not uncommon to obtain sufficient amounts of starting material and can lead to significant changes in the gene expression profiles of cells. Preservation of the transcriptome prior to single cell dissociation can overcome this setback. Here we present an extensive performance analysis of glyoxal as an alternative fixative for scRNA-seq application. High numbers of transcripts and genes were recovered from glyoxal-fixed cells subjected to Drop-seq methodology with the best performance in Drosophila cells. While glyoxal fixation in Drosophila and human cells revealed transcriptome data similar to the unfixed condition, reduced library complexity was observed for the human sample and might require further protocol optimization. We found the integrity of Drosophila intestinal tissue maintained following glyoxal fixation, while dissociation of the fixed tissue allowed sufficient cell isolation. In conclusion, we present glyoxal as a well-suited fixative for Drosophila samples that allows high-quality single cell transcriptomic analysis and successful intestinal tissue disaggregation.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design:
Experiments were performed in two biological replicates, with technical PCR replicates included in the first experiment (DS27) and Dropseq run replicates in the second experiment (DS34). In total, 7 libraries have been generated and analysed.

*** Raw data could not be provided due to institutional restrictions concerning human sequence data ***

first: Josephine

last: Bageritz

first: Niklas

last: Krausse

first: Schayan

last: Yousefian

first: Svenja

last: Leible

first: Michael

last: Boutros


title: Immunosuppression by myeloid cells_Van Wigcheren et al.

city: Nijmegen

first: Glenn

last: Wigcheren

address: Geert Grooteplein Zuid 28

institute: Radboud Institute for Molecular Life Sciences

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


title: Effects of Long-term Culture on the Biological Characteristics and ceRNA Network-associated RNA Profiles of Human Bone Marrow-derived Mesenchymal Stem Cells

status: Public on Jun 21 2021

city: Shenzhen

first: Ziming

last: Wang

state: Guangdong

address: 3025 Shennan Zhong Lu

department: Department of Orthopedics

institute: the eighth affiliated hospital of Sun Yat-sen University

summary: Expansion in vitro prior to mesenchymal stem cells (MSCs) application is a necessary process. Functional and genomic stability has a crucial role in stem cell-based therapies. Long non-coding RNAs (lncRNAs), circular RNAs (circRNAs) and messenger RNAs (mRNAs) play an important role in human bone marrow (BM)-derived MSCs, however, the exact expression and co-expressed profiles in human BM-MSCs in vitro ageing are still lacking. The decreased capacity of proliferation, differentiation and immunoregulation of MSCs at passage (P) 4, P6, P8, P10 and P12 was investigated, and RNA-sequencing identified 439 mRNAs, 65 lncRNAs, 59 miRNAs and 229 circRNAs were differentially expressed (DE) in P12 compared to P4, with a similar trend in P6. GO and KEGG analyses identified several significant biological processes and regulatory pathways, including binding, ossification, and Wnt and PPAR signalling pathways. Interaction and co- expression/co-localization analyses were performed for DE mRNAs and lncRNAs, and several key lncRNAs, circRNAs and important pathway like autophagy and mitophagy were identified in the competing endogenous RNA (ceRNA) network. Our studies indicate replicative senescence of MSC is a continuous process, including widespread alterations in phenotypic, proliferative, differentiation and immunoregulatory potential and global gene expression patterns that need to be considered before therapeutic applications of MSCs.

overall_design: Examination of changes in ceRNA Network-associated RNA profiles of human bone marrow-derived mesenchymal stem cells.

first: Shan


title: A Clock-Driven Neural Network Critical for Arousal

city: Baltimore

first: Mark

last: Wu

address: 855 N. Wolfe Street

institute: Johns Hopkins University

summary: Purpose: scRNA-Seq was performed to profile hypothalamic mWake+ cells of male at 7 weeks old

overall_design: The hypothalamus of mWake-tdTomato-Cre mice (male, 7 weeks old) were dissociated using modified Act-Seq protocol and flow-sorted to enrich tdTomato+ cells. A small aliquot of flow-sorted cells were labelled with DAPI and counted under the microscope (99% tdTomato+ cells). Cells were loaded into V3.0 10x Genomics Chromium Single Cell system, and 3 libraries (triplicates) were sequenced on Illumina NextSeq 500 with ~150 million reads per library. Sequencing results were processed with 10x Genomics pipeline. Seurat V3 was used in conjunction with Monocle3 to perform downstream analysis.

first: Benjamin

last: Bell

first: Dong

last: Kim

first: Seth

last: Blackshaw


title: RNA-seq analysis reveals significant transcriptome changes in huntingtin-null human neuroblastoma cells

status: Public on Jun 19 2021

city: Boca Raton

first: Jianning

last: Wei

state: FL

address: 777 GLADES RD

department: Biomedical Science

institute: Florida Atlantic University

summary: To investigate the transcriptional role of normal Htt, we first knocked out Htt in the human neuroblastoma SH-SY5Y cell line using the CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 (CRISPR-associated protein 9) gene editing approach. We then performed RNA-seq analysis on two indepedent Htt-null stable cell lines and wild type SH-SY5Y cells to probe the global transcriptome changes induced by Htt deletion. Conclusion: Htt has a widespread effect on gene transcription. Functional analysis of the differentially expressed genes (DEGs) using various bioinformatic tools revealed irregularities in pathways related to cell communication and signaling, and more specifically those related to neuron development, neurotransmission and synaptic signaling.

overall_design: RNA profiles of two independent HttKO cell lines and the parental wildtype SH-SY5Y cells


title: Identification of urinary exosomal non-coding RNAs biomarkers for high-grade prostate cancer using RNA-seq analysis

status: Public on Jul 28 2021

city: Guangzhou

first: wen

last: tao

address: Tianhe Road 600

institute: The Third Affiliated Hospital, Sun Yat-sen University

summary: Prostate cancer is one of the major cancers that seriously affect men's health. The low specificity of prostate-specific antigen (PSA) for prostate cancer has resulted in the overdiagnosis and subsequent overtreatment of clinically indolent tumors. There is an urgent need for noninvasive and easy diagnostic assays to help evaluate whether a prostate biopsy is warranted. Many non-coding RNAs (eg, microRNAs, long non-coding RNAs, circular RNAs) have been reported to play key roles in prostate cancer progression, showing great potential to impact cancer diagnostics and therapies. Remarkably, exosomes secreted by cells into body fluids contain molecules that reflect the disease information, and urinary exosomes could be used to detect prostate cancer as a new type of liquid biopsies. Non-coding RNAs are enriched and stable in exosomes. We performed high-throughput sequencing on urine-derived exosomes of 11 patients with high-grade (Gleason score 7 or greater) prostate cancer and 11 patients with benign prostatic hyperplasia to screen differentially expressed non-coding RNAs.

overall_design: We performed deep RNA-sequencing on exosomal RNA extracted from urinary exosomes of 11 patients with high-grade prostate cancer and 11 patients with benign prostatic hyperplasia using HiseqX

first: Liao-Yuan

last: Li

first: Wen

last: Tao


title: CD137 costimulation counteracts TGFβ inhibition of NK cell anti-tumor function and promotes the acquisition of tissue-resident Th9-like properties [4 treatments]

first: Júlia

last: Perera-Bel

summary: Enhancing NK cell-based cancer immunotherapy by overcoming immunosuppression is an unmet goal. Here, we demonstrate the ability of the anti-CD137 agonist urelumab for overcoming TGF-β-mediated inhibition of human NK-cell proliferation and sustained anti-tumor function. Transcriptomic, immunophenotypic and functional analyses evidenced that CD137 costimulation modified the transcriptional program induced by TGF-β on activated NK cells by limiting SMAD4-dependent inhibition of pro-proliferative (CD25, cMyc), activating (NKG2D, CD16) and effector (Granzyme B, IFNγ) molecules while maintaining SMAD4-independent acquisition of tumor-retention features (CXCR3, CD103). Activated NK cells cultured in the presence of TGF-β1 and CD137 agonist showed preserved antibody-dependent cytotoxicity against cancer cells, recovered CCL5 and IFNγ secretion and gained the capacity for producing IL-9 upon restimulation. Treatment of breast tumor-derived multicellular cultures with trastuzumab and urelumab recapitulated CD137 induction and fostered tumor-infiltrating CD16+ NK cell persistence. Our data reveals CD137 as a targetable checkpoint for overturning TGF-β constrains on NK cell anti-tumor responses.

overall_design: A total of 12 samples were analyzed: 4 different treatments (KD1, KT, KTU and NT) in purified NK cells from 3 volunteer donors.

first: Mariona

last: Cabo

first: Aura

last: Muntasell


title: BCL11B enhancer hijacking defines a subtype of lineage ambiguous stem cell leukemia

status: Public on May 19 2021

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

department: Pathology

institute: St Jude Children's Research Institute


title: Modulation of TGF-B1 mediated fibroblast activation in human vocal fold fibroblast cells by Porcine-Derived Lamina Propria Extracellular Matrix Hydrogel

status: Public on May 25 2021

city: Raleigh

first: Xinxia

last: Peng

address: 1060 William Moore Drive

institute: North Carolina State University

summary: Vocal folds (VFs) are exposed to external and internal stimuli that may cause damage leading to structural alterations and compromised function. Extracellular matrix (ECM)-based biomaterials have been explored as bioactive scaffolds to tissue repair. An injectable form of the VF-ECM scaffold would be an ideal biomaterial for minimally invasive delivery to injured VFs. The goal of this study was to develop a hydrogel form of VF lamina propria ECM (VFLP-ECM) and to characterize its properties and in vitro cellular response.

overall_design: Four conditions with two replicates each total 8 samples. Collogen treated with TGF1-b is a control representing typical fibrosis response.

first: Camilo

last: Navarro

first: Donald

middle: O

last: Freytes


title: in situ HiC in Smchd1-GFP NSCs

status: Public on May 08 2021

city: Melbourne

first: Andres

last: Tapia del Fierro

state: Victoria

address: 1G Royal Parade

department: EDD

institute: WEHI

summary: in situ HiC to assess chromatin conformation in Smchd1-GFPMD43/MD43 and Smchd1-GFP+/+ neural stem cells.

overall_design: 3 independent cell lines for each genotype were derived from E14.5 embryos' cortices and cultured for less than 10 passages to be used as biological replicates. One cell line of each genotype was used for the whole cell extract samples.

first: Marnie

last: Blewitt


title: Single cell RNA sequencing analysis of mouse dorsal root ganglions (DRGs) with and without spared nerve injury.

status: Public on Sep 01 2021

city: Aarhus

first: Lin

last: Lin

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

country: Denmark

institute: Aarhus University

summary: We report here a systematic approach to characterize the transcriptional responses of different cells types in the dorsal root ganglion (DRG) to peripheral nerve injury using single cell RNA sequencing (scRNAseq). We compare scRNAseq datasets of lumbar DRGs form naïve mice with corresponding datasets from mice subjected to spared nerve injury (SNI) 7 or 14 days prior to analysis. SNI surgery was performed in the left and right hindleg and development of mechanical allodynia was monitored by von Frey testing relative to control mice and the baseline level. Mice were perfused with PBS prior to extraction of L3 and L4 DRGs and DRGs were enzymatically and mechanically dissociated to single cell suspension before scRNAseq. Analysis of transcriptional changes in this nerve injury-paradigm reveals a differential response at 7 days versus 14 days post injury, suggesting dynamic gene modulation over time.

overall_design:
DRG single cell mRNA profiles evaluating the transcriptional changes of 13 weeks old wild type male mice with and without introduction of spared nerve injury (SNI) in the left and right hindlegs. Three samples in total are analyzed each containing DRGs from 2 mice (8 DRGs/sample).

The 'Cell_SNI_data.rds' (Seurat object rds file for integration and analysis of the 3 samples) has been added on Nov 18, 2021.

first: Lone

last: Pallesen

first: Christian

middle: B

last: Vægter


title: BCL11B enhancer hijacking defines a subtype of lineage ambiguous stem cell leukemia [HiChIP]

summary: Hijacking of primitive hematopoietic enhancers, or generation of a neo-enhancer by genomic amplification, results in deregulation of BCL11B as the defining feature of a subset of T/myeloid leukemia.  We report H3K27ac and BCL11B binding in these Leukemias.

overall_design: Chromatin interactions in leukemia cells using H3K27ac HiChIP

first: Lindsey

last: Montefiori

first: Charles

last: Mullighan


title: RNAseq from Smchd1MommeD43/MommeD43 NSCs

summary: RNAseq from Smchd1MD43/MD43 and Smchd1+/+ neural stem cells to see genome-wide changes in gene expression caused by MommeD43

overall_design: Independent cell lines for each genotype were derived from E14.5 embryos' cortices and cultured for less than 10 passages to be used as biological replicates, as well as some cell lines used more than once as technical replicates that were used to correct for batch effects


title: H3K27me3 ChIP-seq in Smchd1-GFP NSCs

summary: ChIP-seq using an anti-H3K27me3 antibody to asses histone 3 lysine 27 tri-methylation modification in Smchd1-GFPMD43/MD43 and Smchd1-GFP+/+ neural stem cells.


title: RNAseq from 8 somite stage PSM

summary: RNAseq from somite-paired pre-somitic mesoderm from E8.5 embryo tailbuds at the 8-somite developmental stage

overall_design: Tailbuds containing the pre-somitic mesoderm from 3 embryos for each genotype (Smchd1+/+ and Smchd1MommeD43/MommeD43) were dissected from E8.5 embryos to be used as biological replicates. The somite number of the embryos is an accurate measure of the developmental stage of embryos. This tissue is the most relevant to look at Hox gene expression.


title: GFP ChIP-seq in Smchd1-GFP NSCs

summary: ChIP-seq using an anti-GFP antibody to check chromatin binding of Smchd1 in Smchd1-GFPMD43/MD43 and Smchd1-GFP+/+ neural stem cells.


title: Opioid withdrawal produces sex-specific effects on fentanyl-vs.-food choice and mesolimbic transcription

status: Public on May 06 2021

city: Richmond

first: Peter

last: Hamilton

state: VA

address: 1217 E Marshall St

department: Anatomy and Neurobiology

institute: Virginia Commonwealth University

summary: Background: Opioid withdrawal is a key driver of opioid addiction and an obstacle to  recovery. However, withdrawal effects on opioid reinforcement and mesolimbic  neuroadaptation are understudied and the role of sex is largely unknown.  Methods: Male (n=13) and female (n=12) rats responded under a fentanyl-vs.-food  “choice” procedure during daily 2h sessions. In addition to the daily choice sessions,  rats were provided extended access to fentanyl during 12h self-administration  sessions. After two weeks of this selfadministration  regimen, the nucleus accumbens (NAc) and ventral tegmental area  (VTA) of a subset of rats were subjected to RNA sequencing. In the remaining rats, a  third week of this self-administration regimen was conducted, during which methadone  effects on fentanyl-vs.-food choice were determined.  Results: Prior to opioid dependence, male and female rats similarly allocated  responding between fentanyl and food. Abstinence from extended fentanyl access  elicited similar increases in somatic withdrawal signs in both sexes. Despite similar  withdrawal signs and extended access fentanyl intake, opioid withdrawal was  accompanied by a maladaptive increase in fentanyl  choice in males, but not females. Behavioral sex differences corresponded with a  greater number of differentially expressed genes in the NAc and VTA of opioidwithdrawn  females relative to males. Methadone blocked withdrawal-associated  increases in fentanyl choice in males, but failed to further decrease fentanyl choice in  females.  Conclusions: These results provide foundational evidence of sex-specific  neuroadaptations to opioid withdrawal, which may be relevant to the female-specific  resilience to withdrawal-associated increases in opioid choice and aid in the  identification of novel therapeutic targets.

overall_design: Bulk RNA sequencing from microdissected rat nucleus accumbens and ventral tegmental area brain areas, drug treated group DEGs generated relative to saline treated controls.


title: spatial transcriptome

status: Public on Apr 30 2021

city: Trondheim

first: Jing

last: Ye

address: Høgskoleringen 1

department: Department of Clinical and Molecular Medicine (IKOM)

institute: Norwegian University of Science and Technology (NTNU)

summary: CA1-specific brain tissue from the hippocampal formation was isolated at baseline (homecage condition) in wildtype and NEIL1, NEIL2 or NEIL1&2-deficient mice. NEILs are DNA glycosylases potentially involved in transcription regulation. RNA was extracted and sequenced.

overall_design: Wildtype (C57Bl6) and mice deficient in either NEIL1, NEIL2 or NEIL1 and NEIL2 (C57Bl6-background) were used. Tissue was isolated exclusively at baseline, i.e. the animal was taken directly from its homecage without any behavioral intervention

first: Gunn

last: Hildrestrand

first: Veslemøy

last: Rolseth

first: Nicolas

last: Kunath

first: Rajikala

last: Suganthan

first: Vidar

last: Jensen

first: Anna

last: Bugaj

first: Marion

middle: S

last: Fernandez

first: Sunniva

last: Sikko

first: Susanne

last: Vetlesen

last: Kusnierczyk

first: Ann-Karin

last: Olsen

first: Kristine

last: Guetzkow

first: Alexander

middle: D

last: Rowe

first: Wei

last: Wang

first: Olve

last: Modestad

first: Monica

last: Bjørge

first: Geir

last: Slupphaug

first: Lars

last: Eide

first: Arne

last: Klungland

first: Pål

last: Sætrom

first: Luisa

last: Luna

first: Katja

last: Scheffler

first: Magnar

last: Bjørås


title: Next Generation Sequencing of DIO Liver steatosis DMSO vs NCT (HNF4a agonist)

status: Public on Apr 17 2021

city: San Diego

first: Brian

middle: Patrick

last: James

address: 10901 North Torrey Pines Road

department: Genomics

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Mice rendered obese with high fat diet were treated by IP injection with N-trans caffeoyltyramine (NCT) (200 mg/kg bid) for 14 days, followed by harvesting of the liver for analysis, including RNA isolation.

overall_design: High fat diet induced non-alcoholic fatty liver (NAFLD) treated with DMSO or NCT compound.

first: Fred

last: Levine


title: Identification of gene targets of mutant C/EBPα reveals a critical role for MSI2 in CEBPA-mutated AML

status: Public on Mar 22 2021

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

summary: We mapped p30-associated regulatory elements by ATAC-seq and ChIP-seq in a myeloid progenitor cell model for p30-driven AML that enables inducible RNAi-mediated knockdown of p30. Concomitant p30-dependent changes in gene expression were measured by RNA-seq. Integrative analysis identified 117 p30-dependent regulatory elements associated with 33 strongly down-regulated genes upon p30-knockdown.

overall_design: Examination of H3K27ac- and C/EBPα-ChIP-seq, ATAC-seq and RNA-seq in a myeloid progenitor cell model for p30-driven AML

first: Elizabeth

last: Heyes

last: Schmidt

first: Gabriele

last: Manhart

first: Ludovica

last: Proietti

first: Florian

last: Grebien


title: Genome-wide maps of chromatin state in human iPSC derived Cardiomyocytes with 2N and 4N DNA content.

city: New Haven

first: Jennifer

last: VanOudenhove

address: 300 George St RM 786

department: Internal Medicine - Section of Hematology

institute: Yale University

summary: ChIP-seq was performed for seven marks (H3K4me1, H3K4me2, H3K4me3, H3K27ac, H3K27me3, H3K9me3, and H3K36me3) with Inputs on iPSC derived Cardiomyocytes with either 2N or 4N DNA content (3 replicates). Replicates were combined and put into the ChromImpute and ChromHMM pipelines (Ernst and Kellis, 2015), and a 25 state chromatin profilefor each was developed.

overall_design:
Examination of 7 different histone modifications with Inputs, in 2 cell types with 3 replicates each.

Please note that all replicates and all marks were combined into an imputation to generate the processed data which is linked as Series supplementary files.

first: Justin

middle: L

last: Cotney

first: J

last: Hinson


title: The transcriptional and architectural resetting of pluripotent stem cell identity during G1 entry [RNA-Seq]

status: Public on Mar 01 2021

city: New York

first: Effie

last: Apostolou

address: 1161 York Avenue, Apt 8A

institute: Weill Cornell Medicine

summary: The molecular identity of dividing cells is temporarily challenged during mitosis, as transcription is halted and chromatin architecture is drastically altered. The principles and key players that ensure faithful propagation of cell identity upon G1 entry in daughter cells remain elusive. Here, we characterized at a genome-wide scale the dynamic transcriptional and architectural resetting of mouse pluripotent stem cells upon mitotic exit.

overall_design: RNA-seq analysis was performed in cells undergoing mitosis. RNA was collected from mitotic and asynchronous ESC and from cell in Early and Late G1 phase


title: Mitotic bookmarking by H3K27 acetylation is critical for rapid transcriptional, but not architectural, resetting of stem cell-related genes and enhancers upon G1 entry [ChIP-seq]

summary: The identity of dividing cells is challenged during mitosis, as transcription is halted and chromatin architecture drastically altered. How cell type-specific gene expression and genomic organization are faithfully reset upon G1 entry in daughter cells remains elusive. To address this issue, we characterized at a genome-wide scale the dynamic transcriptional and architectural resetting of mouse pluripotent stem cells (PSCs) upon mitotic exit. This revealed distinct patterns of transcriptional reactivation with rapid induction of stem cell genes and their enhancers, a more gradual recovery of metabolic and cell cycle genes, and a weak and transient activation of lineage-specific genes only during G1. Topological reorganization at different hierarchical levels also occurred in an asynchronous manner and showed an overall weak coordination with transcriptional reactivation. Chromatin interactions around active promoters and enhancers, and particularly super enhancers, reformed at a faster rate than CTCF/Cohesin-bound structural loops. Interestingly, although regions with mitotic retention of the active histone mark H3K27ac associated both with faster transcriptional and architectural resetting, depletion of this mark specifically during mitosis perturbed transcriptional reactivation of H3K27ac-bookmarked genes without affecting chromatin topology. Our study provides an integrative map of the topological and transcriptional changes that lead to the resetting of pluripotent stem cell identity during mitotic exit, and reveals distinct patterns and features that balance the dual requirements for self-renewal and differentiation.

overall_design: H3K27ac ChIP-seq of mouse iPSCs after p300 inhibition and recovery, both in asychronous and M-to-G1 cell cycle populations. DMSO treatment was used as a control, and two replicates per condition/time point were analyzed. Both H3K27ac ChIP and input samples are included.

first: Alexander

last: Polyzos


title: Mitotic bookmarking by H3K27 acetylation is critical for rapid transcriptional, but not architectural, resetting of stem cell-related genes and enhancers upon G1 entry [PRO-seq]

overall_design: PRO-seq of mouse iPSCs after p300 inhibition and recovery, both in asychronous and M-to-G1 cell cycle populations. DMSO treatment was used as a control, and three replicates per condition/time point were analyzed, except for mitotic time points which had only two replicates.


title: The transcriptional and architectural resetting of stem cell identity during G1 entry [ATAC-Seq]

summary: The molecular identity of dividing cells is temporarily challenged during mitosis, as transcription is halted and chromatin architecture is drastically altered. The principles and key players that ensure faithful propagation of cell identity upon G1 entry in the daughter cells remain elusive. Here, we used rapidly dividing mouse pluripotent stem cell (PSC) as a study model to characterize for the first time the dynamic transcriptional and architectural resetting of cell identity during mitotic exit, and assess the role of mitotic bookmarking by the active histone mark H3K27 acetylation (H3K27ac). Globally, compartments and topologically associating domains (TADs) were quickly reformed and gradually gained strength and activity throughout G1, while long-range chromatin interactions were reestablished at a slower rate. Binding of PSC-specific transcription factors (TFs) and transcriptional machinery associated with faster boundary insulation and contact formation, while CTCF, Cohesin and Polycomb-bound regions were characterized by a slower architectural resetting. Similarly, transcriptional reactivation of both PSC enhancers and their target genes occurred in early G1, while enhancers and genes involved in housekeeping/cell cycle or differentiation processes were activated in a gradual or transient manner, respectively. Mitotic bookmarking by H3K27ac promoted faster compartmentalization, boundary insulation, and loop formation, as well as rapid transcriptional reactivation. Interestingly, we identified a group of developmental genes and enhancers that were transiently activated in G1 and were marked by H3K27ac specifically during mitosis. This study provides insights into the relative kinetics of transcriptional and architectural rewiring after mitosis and establishes a unique role for H3K27ac bookmarking in the resetting of stem cell identity.

overall_design: Transcriptional and architectural changes of iPSCs after mitotic exit


title: The transcriptional and architectural resetting of stem cell identity during G1 entry [Hi-C]


title: The transcriptional and architectural resetting of stem cell identity during G1 entry [PRO-Seq]

overall_design: Ttranscriptional and architectural changes of iPSCs after mitotic exit


title: The transcriptional and architectural resetting of pluripotent stem cell identity during G1 entry [4C-Seq]

overall_design: 4C-seq analysis was performed in 11 genes with different kinetics of transcriptional resetting after mitotic exit at 0, 0.5, 1, 3 hours and in ESC

first: Polyzos

middle: P

last: Alexandros


title: TNF-induced ArhGEF10 activates RhoB in human endothelial cells and contributes to tight junction disruption and barrier breakdown

status: Public on May 10 2021

city: West Haven

first: Francesc

last: Lopez

summary: Rationale: Endothelial cells (ECs) line the inner surface of continuous capillaries and form a permselective barrier between blood and tissues to limit paracellular fluid and solute flux. The capillary barrier is maintained by intercellular tight junctions (TJs) which are regulated, in part, by differential activity of small GTPases. Tumor necrosis factor (TNF) causes TJ disassembly in a process dependent upon NF-κB-mediated gene expression. Activated (GTP-bound) RhoB has been identified as a downstream effector of TNF-induced leak both through Rho-associated coiled-coil kinase-mediated phosphorylation of RelA, enhancing TNF-induced NF-κB-mediated gene activation, and through sequestration of Rac1 away from the cell junction, preventing barrier restoration. To date, no TNF-induced, RhoB-selective GTP exchange factor (GEF) has been identified in ECs.   Objective: Identify a TNF-induced RhoB specific GEF in capillary ECs.  Method and Results: human dermal microvascular ECs (HDMECs) were used because they form TJs. Candidate GEFs were identified by whole transcriptome profiling of HDMECs with or without TNF stimulation. Fifty-seven of 73 known GEFs were expressed in HDMECs and 17 were significantly upregulated by TNF. Functional impact of each of the latter group was assessed by measuring the effects of depletion by short interfering RNA knockdown on TNF-induced reduction of trans-endothelial electrical resistance (TEER) of HDMEC monolayers. Depletions of ArhGEF10 or RhoB or double depletion of ArhGEF10/RhoB similarly decreased TNF-mediated reduction of TEER. ArhGEF10 knockdown prevented TNF-induced disruption of TJ proteins assessed by confocal microscopy. TNF-induced increases in the levels of activated RhoB in HDMEC lysates were markedly reduced with only minimal alterations in RhoA or RhoC activation. Finally, immunoisolated ArhGEF10 selectively catalyzed GTP exchange for GDP in RhoB, but not RhoA or RhoC, in vitro.   Conclusion: ArhGEF10 is a TNF-induced RhoB-selective GEF for RhoB in cultured human capillary ECs that contributes to TJ disruption.

overall_design: Whole transcriptome analysis of cultured HDMECs, with and without treatment with TNF with 3 replicates per condition

first: Alamzeb

last: Khan

first: Weiming

last: Ni

last: Lopez-Giraldez

first: Martin

last: Kluger

first: Jordan

last: Pober

first: Richard

last: Pierce


title: RNAseq from 29 somite stage FNP

first: Andres

last: Tapia del Fierro

summary: RNAseq from somite-matched frontonasal prominence (FNP) from E10.5 embryos at the 29-somite developmental stage

overall_design: Frontonasal prominence from 2 embryos for each genotype (Smchd1+/+ and Smchd1MommeD43/MommeD43) were dissected from E10.5 embryos at the 29 somite developmental stage to be used as biological replicates. The somite number of the embryos is an accurate measure of the developmental stage of embryos. This tissue is relevant to look at gene expression related to craniofacial development.

first: Marnie

last: Blewitt