summary: We performed scRNA-seq over multiple time points of heart development in WT C57Bl6/J embryos and in Tbx1 mutant mice (Tbx1 KO). We dissected primarily the cardiac region but also the regions dorsal to the heart and the pharyngeal arches to capture the progenitor cells that migrate into the heart and the neural crest cells. For time points E10.5 and E11.5, we primarily dissected the regions behind the heart and included less of the overall cardiac region. We included pharyngeal arches for all time points and, at E11.5, we excluded the first arch. For Tbx1 null embryos, we also generated scRNA-seq data for WT and mutant embryos from the same pool of dissociated cells used for scATAC-seq.

overall_design: For all embryos, we micro-dissected the tissue and dissociated using TryplE. For all samples, multiple replicates for WT and KO were used and we include all replicates below.


title: Epigenetic aberrations of gene expression in a rat model of hepatocellular carcinoma

status: Public on Oct 28 2022

city: Vancouver

first: Barbara

last: Stefanska

state: BC

address: 2205 East Mall

department: Land and Food Systems

country: Canada

institute: The University of British Columbia

type: Expression profiling by high throughput sequencing

summary: Hepatocellular carcinoma (HCC) is mostly triggered by environmental and life-style factors and may involve epigenetic aberrations. However, a comprehensive documentation of the link between the dysregulated epigenome, transcriptome, and liver carcinogenesis is lacking. In the present study, Fischer-344 rats were fed a choline-deficient (CDAA, cancer group) or choline-sufficient (CSAA, healthy group) L-amino acid-defined diet. At the end of 52 weeks, transcriptomic alterations in livers of rats with HCC tumors and healthy livers were investigated by RNA sequencing. DNA methylation and gene expression were assessed by pyrosequencing and quantitative reverse-transcription PCR (qRT-PCR), respectively. We discovered 1,848 genes that were significantly differentially expressed in livers of rats with HCC tumors (CDAA) as compared with healthy livers (CSAA). Upregulated genes in the CDAA group were associated with cancer-related functions, whereas macronutrient metabolic processes were enriched by downregulated genes. Changes of highest magnitude were detected in numerous upregulated genes that govern key oncogenic signaling pathways, including Notch, Wnt, Hedgehog, and extracellular matrix degradation. We further detected perturbations in DNA methylating and demethylating enzymes, which was reflected in decreased global DNA methylation and increased global DNA hydroxymethylation. Four selected upregulated candidates, Mmp12, Jag1, Wnt4, and Smo, demonstrated promoter hypomethylation with the most profound decrease in Mmp12. MMP12 was also strongly overexpressed and hypomethylated in human HCC HepG2 cells as compared with primary hepatocytes, which coincided with binding of Ten-eleven translocation 1 (TET1). Our findings provide comprehensive evidence for gene expression changes and dysregulated epigenome in HCC pathogenesis, potentially revealing novel targets for HCC prevention/treatment.

overall_design: Examination of transcriptome in livers of rats with hepatocellular carcinoma triggered by choline-deficient amino acid-defined diet (CDAA) as compared with livers of rats on healthy diet (choline-sufficient amino acid-defined diet, CSAA)

first: Cayla

last: Boycott

first: Megan

last: Beetch

first: Tony

last: Yang

first: Katarzyna

last: Lubecka

first: Yuexi

last: Ma

first: Jiaxi

last: Zhang

first: Lucinda

middle: K

last: Kendall

first: Melissa

last: Ullmer

first: Benjamin

middle: S

last: Ramsey

first: Sandra

last: Torregrosa-Allen

first: Bennett

middle: D

last: Elzey

first: Abigail

last: Cox

first: Nadia

middle: A

last: Lanman

first: Alisa

last: Hui

first: Nathaniel

last: Villanueva

first: Aline

last: de Conti

first: Tao

last: Huan

first: Igor

last: Pogribny


title: Transcriptional responses to maternal trichloroethylene and/or N-acetyl cysteine exposure in Wistar rat placental tissue

status: Public on Jun 01 2022

city: San Diego

first: Elana

middle: R

last: Elkin

state: CA

address: 5500 Campanile Drive

department: School of Public Health

country: USA

institute: San Diego State University

summary: Trichloroethylene (TCE) is a persistent and pervasive environmental contaminant. N-acetyl cysteine (NAC) is an antioxidant that may reduce TCE effects. Pregnant Wistar rats were exposed to 480 mg TCE mg/kg/day, 200 mg/kg/day NAC or co-exposure with both chemicals via ingestion (mini vanilla wafer) on gestation days 6-16 (tissue collection day). TCE- and/or NAC-induced changes to gene expression were evaluated in male and female rat placentae.

overall_design: Timed-pregnant Wistar rats were exposed to vehicle control (PBS), trichloroethylene (TCE), N-acetyl cysteine (NAC) or co-exposure with both chemicals via ingestion (treated mini vanilla wafer) on gestation days 6-16 (tissue collection day). The doses were as follows: 480 mg TCE mg/kg/day, 200 mg/kg/day NAC or both doses together. There were 6 batches of rats (N=6) with 4 rats in each batch and 1 rat assigned to each treatment group (total of 24 dams). RNA was isolated from one male and one female placenta from each respective dam and sequenced (24 male and 24 female placental tissue samples). Differential gene expression comparisons were made between each treatment group and control tissues stratified by sex.

first: Kelly

middle: M

last: Bakulski

first: Anthony

middle: L

last: Su

first: John

middle: F

last: Dou

first: Rita

last: Loch-Caruso


title: Mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance

status: Public on Jun 05 2022

city: Mainz

first: Julian

last: König

address: Ackermannweg 4

department: Biology

country: Germany

institute: Institute of Molecular Biology, Mainz

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

overall_design: Refer to individual Series


title: Mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance: PTBP1 iCLIP2 in NALM-6 cells

summary: We developed a massively parallel reporter assay to determine the splicing effects of all mutations in the region comprising CD19 exons 1-3. Despite the great success of CART-19 (chimeric antigen receptor-armed autologous T-cells) immunotherapy to treat B-cell acute lymphoblastic leukaemia (B-ALL), many patients relapse due to loss of the targeted CD19 epitope. Since epitope loss can be caused by CD19 exon 2 mis-splicing, we set out to learn the regulatory code that controls CD19 alternative splicing.

overall_design: iCLIP2 protocol performed in NALM-6 cell lines in two replicates under two different RNAse I dilution values

first: Mariela

last: Cortés-López

first: Laura

last: Schulz

first: Mihaela

last: Enculescu

first: Claudia

last: Paret

first: Bea

last: Spiekermann

first: Anke

last: Busch

first: Anna

last: Orekhova

first: Fridolin

last: Kielisch

first: Mathieu

last: Quesnel-Vallières

first: Manuel

last: Torres-Diz

first: Jörg

last: Faber

first: Yoseph

last: Barash

first: Andrei

last: Thomas-Tikhonenko

first: Kathi

last: Zarnack

first: Stefan

last: Legewie


title: Characterisation of the mouse alpha-globin sub-TAD 3' boundary in erythroid cells [NG Capture-C]

city: Headington

first: Jim

last: Hughes

address: MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine

department: MRC WIMM

country: United Kingdom

institute: University of Oxford

summary: Mammalian genomes are subdivided into large (50-2000 kb) regions of chromatin referred to as Topologically Associating Domains (TADs or sub-TADs). Chromatin within an individual TAD contacts itself more frequently than with regions in surrounding TADs thereby directing enhancer-promoter interactions. In many cases, the borders of TADs are defined by convergently orientated boundary elements associated with CCCTC-binding factor (CTCF), which stabilises the cohesin complex on chromatin and prevents its translocation. This delimits chromatin loop extrusion which is thought to underlie the formation of TADs. However, not all CTCF-bound sites act as boundaries and, importantly, not all TADs are flanked by convergent CTCF sites. Here, we examined the CTCF binding sites within a ~70 kb sub-TAD containing the duplicated mouse α-like globin genes and their five enhancers (5’-R1-R2-R3-Rm-R4-α1-α2-3’). The 5’ border of this sub-TAD is defined by a pair of CTCF sites. Surprisingly, we show that deletion of the CTCF binding sites within and downstream of the α-globin locus leaves the sub-TAD largely intact. The predominant 3’ border of the sub-TAD is defined by a steep reduction in contacts: this corresponds to the transcribed α2-globin gene rather than the CTCF sites at the 3’-end of the sub-TAD. Of interest, the almost identical α1- and α2-globin genes interact differently with the enhancers, resulting in preferential expression of the proximal α1-globin gene which behaves as a partial boundary between the enhancers and the distal α2-globin gene. Together, these observations provide direct evidence that actively transcribed genes can behave as boundary elements.

overall_design: NG Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments; in this case promoters, enhancers and CTCF binding sites in the mouse alpha-globin sub-TAD were used as viewpoints. The method was applied to wild type mouse erythroid cells and to in vivo models in which CTCF sites HS+44/+48 (∆44-48), or θ1 and/or θ2 (∆θ1, ∆θ2, ∆θ1θ2) were deleted. Experiments performed on biological triplicates.

first: Caroline

last: Harrold

first: Matthew

middle: E

last: Gosden

first: Jelena

last: Telenius

first: Douglas

last: Higgs


title: scATAC-seq and scRNA-seq over multiple time points of heart development in WT C57Bl6/J embryos and in Tbx1 mutant mice (Tbx1 KO)

status: Public on Jul 26 2022

city: San Francisco

first: Sanjeev

last: Ranade

address: 1650 Owens St

institute: Gladstone Institutes

type: Genome binding/occupancy profiling by high throughput sequencing


title: Characterisation of the mouse alpha-globin sub-TAD 3' boundary in erythroid cells [ChIP-seq]

overall_design: CTCF ChIP-seq on chromatin isolated from primary erythroid Ter119+ cells obtained from the spleens of phenylhydrazine treated mice containing deletions for HS+44/+48 (∆44-48), or θ1 and/or θ2 (∆θ1, ∆θ2, ∆θ1θ2) CTCF binding sites. Experiments performed on biological triplicates.

first: Rosa

last: Stolper


title: Deconvoluting sex-dependent dendritic cell-monocyte lineages in emphysematous lung tissue with bulk and single-cell RNA sequencing

status: Public on May 31 2022

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

summary: Emphysema is a unique type of chronic obstructive pulmonary disease, and sex may influence susceptibility.  After cigarette smoke exposure, murine males and ovariectomized females developed more severe emphysema.  Herein, we present divergent bulk and single-cell transcriptomic profiles between male and female murine lungs. Weighted Gene Co-Expression Network Analysis of the bulk lung RNA sequencing identified a Green gene module that correlated with male sex and ovariectomy. The Green gene module was enriched in common monocyte progenitors, classical monocytes, type 1 dendritic cells, and macrophages from 83,698 murine cells exposed to air or cigarette smoke for five months. Sexual dimorphism altered the compositions and transcriptome of the clusters enriched with the Green gene module.  This comprehensive transcriptomic analysis advances our understanding of dynamic cellular responses controlled by sexual dimorphism during the development of emphysematous pulmonary tissue remodeling and reveals potential targets for mechanistic studies in the future.

overall_design: Experiment 1: male and female C57B/6 mice were exposed to cigarette smoke or room air. Experiment 2: female C57B/6 mice undervent ovariectomie or sham surgery followed by exposure to cigarette smoke.Total RNA were isolated from lung tissues and subjected to RNA-seq assay.

first: Jiyoung

last: Shin

first: Paula

last: Czarnota

first: Premanand

last: Balraj

first: Marie

last: Burdick

first: Riley

last: Hannan

first: Chaojie

last: Yang

first: Chingyee

last: Tan

first: Zhi

middle: im

first: Jeffrey

last: Sturek

first: Mikell

last: Paige

first: Dawn

last: Demeo

first: Ani

last: Manichaikul

first: Yun

last: Shim


title: Characterisation of the mouse alpha-globin sub-TAD 3' boundary in erythroid cells [RNA-seq]

first: Jim

last: Hughes

overall_design: RNA-seq of globin-depleted polyA-isolated RNA libraries isolated from primary erythroid Ter119+ cells obtained from the spleens of phenylhydrazine treated mice. Wild-type C57BL/6 mice were compared with mice containing deletions for θ1 and/or θ2 (∆θ1, ∆θ2, ∆θ1θ2) CTCF binding sites. Experiments performed on biological triplicates.

first: Caroline

last: Harrold

first: Douglas


title: Changes in DNA Methylation Hallmark Alterations In Chromatin Accessibility And Gene Expression For Eye Lens Differentiation [RNA-seq]

status: Public on Mar 31 2022

city: Boca Raton

first: Marc

last: Kantorow

state: FL

address: 777 Glades Road

institute: Florida Atlantic University

summary: Methylation at cytosines (mCG) is a well-known regulator of gene expression but its requirements for cellular differentiation have yet to be fully elucidated. A well-studied cellular differentiation model system is the eye lens, consisting of a single anterior layer of epithelial cells that migrate laterally and differentiate into a core of fiber cells. Here, we explore the genome-wide relationships between mCG methylation, chromatin accessibility and gene expression during differentiation of eye lens epithelial cells into fiber cells.  Whole genome bisulfite sequencing identified 7621 genomic loci exhibiting significant differences in mCG levels between lens epithelial and fiber cells. Changes in mCG levels were inversely correlated with the differentiation state-specific expression of 1285 genes preferentially expressed in either lens fiber or lens epithelial cells (Pearson correlation r = -0.37, p < 1x10-42). mCG levels were inversely correlated with chromatin accessibility determined by Assay for transposase-accessible sequencing (ATAC-seq) (Pearson correlation r = -0.86, p < 1x10-300). Many of the genes exhibiting altered regions of DNA methylation, chromatin accessibility and gene expression levels in fiber cells relative to epithelial cells are associated with lens fiber cell structure, homeostasis and transparency. These include lens crystallins (CRYBA4, CRYBB1, CRYGN, CRYBB2), lens beaded filament proteins (BFSP1, BFSP2), transcription factors (HSF4, SOX2, HIF1A), and Notch signaling pathway members (NOTCH1, NOTCH2, HEY1, HES5). Analysis of regions exhibiting cell-type specific alterations in DNA methylation revealed an overrepresentation of consensus sequences of multiple transcription factors known to play key roles in lens cell differentiation including HIF1A, SOX2, and the MAF family of transcription factors. Collectively, these results link DNA methylation with control of chromatin accessibility and gene expression changes required for eye lens differentiation. The results also point to a role for DNA methylation in the regulation of transcription factors previously identified to be important for lens cell differentiation.

overall_design: Examination of differentially methylated mCG regions between 3 biological replicates of pooled lens epithelial cells and 3 biological replicates of pooled lens fiber cells obtained from embryonic day 13 chick lenses and correlating with differentially expressed genes.

first: Joshua

last: Disatham

first: Lisa

last: Brennan

first: Xiaodong

last: Jiao

first: Zhiwei

last: Ma

first: J

last: Hejtmancik


title: Changes in DNA Methylation Hallmark Alterations In Chromatin Accessibility And Gene Expression For Eye Lens Differentiation

type: Methylation profiling by high throughput sequencing


title: Characterisation of the mouse alpha-globin sub-TAD 3' boundary in erythroid cells


status: Public on Feb 12 2022

city: Amherst

first: Peter

last: Chien

state: MA

address: 240 Thatcher Rd, Life Science Laboratories Room N325

department: Biochemistry and Molecular Biology

institute: University of Massachusetts Amherst

summary:
Purpose: The goal of this study is to compare RNA-seq libraries of wildtype Caulobacter crescentus with two lon deletion strains (delta lon and delta lon clpX*).
Methods: See Methods section of "Plasticity in AAA+ proteases reveals substrate specificity niches" for information regarding methods or contact lead correspondence. Briefly, Samples for RNAseq were extracted from wt and lon deletion strains grown to stationary phase.
Conclusions: Our study represents the first detailed analysis of lon deletions (delta lon and delta lon clpX*) comparison to wt caulobacter transcriptomes, with biologic replicates, generated by RNA-seq technology in stationary phas

overall_design: RNA seq profiles for Caulobacter crescentus wildtype and lon deletion strains (delta lon and delta lon clpX*) in stationary phase

first: Samar

last: Mahmoud

first: Berent

last: Aldikacti


title: The BAMM Trial: BRAF, Autophagy and MEK inhibition in Metastatic Melanoma: A phase I/II trial of dabrafenib, trametinib and hydroxychloroquine in patients with advanced BRAF mutant melanoma

status: Public on Jan 07 2022

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Importance: Autophagy has been identified as a resistance mechanism to BRAF and MEK inhibition in BRAF mutant melanoma. In the BAMM trial, hydroxychloroquine (HCQ) was used to inhibit autophagy in combination with dabrafenib and trametenib in BRAF mutant melanoma patients.   Objective: To a) determine safety and maximal tolerated dose (MTD) of hydroxychloroquine when combined with dabrafenib and trametinib and b) determine antitumor activity of the combination.    Design: Open label non-randomized phase I/II clinical trial   Setting: Prospective  therapeutic clinical trial conducted in 4 centers   Participants: Unresectable Stage III or Stage IV BRAF mutant melanoma patients  Intrevention: HCQ twice daily,  dabrafenib 150 mg twice daily  and trametinib 2 mg daily (D+T)  Main Outcome: Primary outcomes were safety and 1-year progression-free survival (PFS) rate   Results: Between December 2014 and January 2020, 50 patients were screened, 38 patients were enrolled and evaluable for toxicity and 34 patients were evaluable for 1-year PFS rate. Patient demographics were: 29% were ECOG PS 1, 47% had elevated LDH,  52%  were Stage IV M1c or M1d and 53% had previously received therapy for advanced melanoma. In the phase I trial there was no dose limiting toxicity of  HCQ at either 400 (n=3)  or 600 (MTD) mg po bid combined with D+T. For the entire study population, the 1-year PFS rate was 41%   (95% CI =  ), median PFS was 11.9 months (95% CI =  ), overall response rate (ORR) was 85% (95% exact CI=64-95%)and complete response rate of 41% (95% exact CI=25-59%). In a prespecificed subgroup analysis in 18 patients with elevated LDH, the ORR was 88% and median PFS was 8 months   Conlusion and Relevance: The combination of HCQ, dabrafenib and trametinib was well tolerated and produced a high response rate but did not meet the prespecified criteria for success with respect to the 1-year PFS rate. In patients with elevated LDH , the response rate and PFS were encouraging. A randomized placebo controlled trial of dabrafenib and trametinib with/without HCQ in advanced BRAF mutant melanoma patients with elevated LDH and previously treated with immunotherapy is being conducted through the National Clinical Trial Network.

overall_design: RNA-seq of high and low progression free survival patients

first: Ravi

last: Amaravadi

first: Janice

last: Mehnert


title: Characterisation of the mouse alpha-globin sub-TAD 3' boundary in erythroid cells [ATAC-seq]

overall_design: ATAC-seq on chromatin isolated from primary erythroid Ter119+ cells obtained from the spleens of phenylhydrazine treated mice containing deletions for HS+44/+48 (∆44-48), or θ1 and/or θ2 (∆θ1, ∆θ2, ∆θ1θ2) CTCF binding sites. Experiments performed on biological triplicates.

first: Matthew

last: Gosden

first: Jelena

last: Telenius

last: Higgs


title: Cardiac lipidomic profiling and mechanistic exploration by transcriptome in murine model of dilated cardiomyopathy

status: Public on Sep 22 2022

city: Melbourne

first: Mark

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

summary: Dilated cardiomyopathy (DCM) and heart failure are associated with mitochondrial dysfunction and dysregulated lipid metabolism. Recent studies have implicated a pivotal role of Hippo pathway activation in the development of DCM with profound metabolic remodelling. However, alterations in the cardiac lipid profile and responsible molecular mechanisms, including upregulated galectin-3, remain unclear in the setting of DCM. Mice with DCM induced by Hippo pathway activation (Mst1 gene overexpression alone or with galectin-3 gene deletion) were studied by lipidomic profiling, transcriptomic profiling and immunoblotting for mRNA and protein expression. Profound alterations in cardiac lipid classes were observed, notably elevated sphingolipids, reduced triacylglycerol (TG) and ether lipids, alterations in phospholipid species, elevated lysophosphatidylcholine, and a profound reduction in mitochondria-specific cardiolipin and coenzyme Q10. Relative to adult mice with advanced DCM, reduced TG content was evident but sphingolipid accumulation was absent in young mice at early phase of DCM. Mechanistically, the lipidomic profile in DCM heart was in consistent with dysregulated expression of specific gene sets for biosynthesis of ceramides or TG, TG storage/hydrolysis, mitochondrial lipid metabolism, peroxisome biogenesis, and suppressed PPAR-alpha signaling. Furthermore, galectin-3 gene deletion resulted in changes in some lipid classes and numerous lipid species in settings of healthy and DCM. Multiple alterations in cardiac lipids were identified by lipidomics in a mouse model of DCM due to activation of the Hippo pathway. By employing transcriptome and galectin-3 gene deletion, we revealed underlying mechanisms for lipid abnormalities involving upregulated galectin-3, downregulated expression of specific gene sets of lipid metabolism, and attenuated PPAR-alpha signaling.

overall_design: C57BL6 mice with DCM induced by Hippo pathway activation were studied by lipidomic profiling, transcriptomic profiling and immunoblotting for mRNA and protein expression and comparisons were made to control mice. The files included in this submission relate to 3 week old mice. Adult mice (15 week old) were described in a previous submission (GSE106201).

first: Wei

last: Wu

first: Kevin

last: Huynh

first: Thy

last: Duong

first: Jin-Chan

last: Du

first: Gang

last: She

first: Wei-Bo

last: Zhao

first: Xiu-Ling

last: Deng

first: Xiao-Jun


title: Spatial transcriptome analysis (Slide-seq2) of mouse main olfactory bulb

status: Public on Jan 31 2022

city: Worcester

first: I-Hao

last: Wang

address: 370 Sunderland Rd, Unit D24

department: PMM

institute: UMMS

summary: The goal of spatial transcriptome analysis is to profile the glomeruli position representing different olfactory receptors. 20 OB sections were obtained with equal spacing (130 μm) along the anterior-posterior axis. In total, two sets of 20 slides were obtained from different animals. All of the Slide-seqV2 procedures were performed as previously described

overall_design: Olfactory epithelial single cell suspensions made from 3 male and 3 female adult mice. Single-cell sequencing libraries were prepared using Chromium Single Cell 3’ Reagent Kit V3 (10X Genomics) according to the manufacturer’s guidelines. Libraries were sequenced using 150 cycles of paired end reads on Illumina Hiseq4000 and Novaseq6000 instruments (Novogene)

first: Evan

last: Murray

first: Fei

last: Chen

middle: Z

last: Macosko

first: Paul

last: Liberman Greer


title: Crosstalk between the diseased atherosclerotic aorta and the peripheral nervous system

status: Public on Feb 27 2022

city: Munich

first: Andreas

middle: Johann Richard

last: Habenicht

state: Bavaria

address: Pettenkoferstraße 9a

institute: Ludwig Maximilians Universität München


title: Mouse olfactory sensory neurons, main olfactory epithelium and main olfactory bulb


title: Transcriptome analysis of mouse olfactory sensory neurons expressing 3 different types of olfactory receptor

summary: The goal of RNA-seq is to explore whether olfactory sensory neurons (OSNs) that display a specific olfactory receptor (OR) express a distinct transcriptional program from OSNs that display a different OR. The GFP knockin mice (Olfr73-IRES-GFP, Olfr1507-IRES-GFP, and Olfr160-IRES-mCherry) was used to label the OSN expressing specific OR. These cells was then isolate with fluorescence activated cell sorting. For each sample, at least 5000 cells are collected, there biological replicates were collected for each genotype and in total 9 samples were prepared for RNA-seq libraries with using NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB) following the manufacturer’s guidelines with one alteration, which was to increase the insert length to ~300 base pair. Libraries were sequenced using paired end 150 cycle reads on an Illumina Hiseq4000 (Novogene). The sequencing reads were processed using the DolphinNext RNAseq pipeline (https://dolphinnext.umassmed.edu/index.php?np=1&id=732). The default settings were employed except STAR v2.6.1 and RSEM v1.3.1 were used for alignment and quantification, respectively. Differential analysis were conducted in DESeq2. The significant genes were deducted by computing Wald test with corrected p < 0.05. Our results shows that different types of OSNs express significantly different patterns of genes, especially the genes involved in axonal guidance.

overall_design: Messenger RNA from olfactory sensory neuron expressing different olfactory receptor (Olfr73, Olfr1507, or Olfr160) were extacted and cDNA libraries were generated for deep sequencing, in duplicate, using Hiseq4000

first: Hao-Ching

last: Jiang

first: Sung

last: Park


title: Genome-wide mapping of eIF3-RNA interactions in Jurkat cells using PAR-CLIP

status: Public on Dec 23 2021

city: Berkeley

first: Jamie

middle: H D

last: Cate

address: 2151 Berkeley Way

department: Molecular and Cell Biology/Chemistry

institute: University of California

summary: The goal of this study was to determine the RNAs that directly bind eukaryotic translation initiation factor eIF3 in activated and non-activated Jurkat cells.

overall_design:
Jurkat cells labeled with 4-thiouridine were treated were treated +/- phorbol 12-myristate 13-acetate (PMA) and ionomycin (IONO) for 5 hours, then crosslinked using 364 nm light, followed by isolation of RNAs crosslinked to eIF3, which were then prepared for DNA deep sequencing.

UPDATE: [Dec-02-2025] The titles, source names, and descriptions were swapped between the following Samples:
GSM5743374 and GSM5743376
GSM5743375 and GSM5743377

first: Dasmanthie

last: De Silva

middle: H

first: Grant

last: Chin


title: Single-cell Transcriptomic Atlas of Gingival Mucosa in Type 2 Diabetes

status: Public on Jan 01 2022

city: chengdu

first: qian

last: wang

address: renmin road south

country: China

institute: sichuan university

summary: The oral gingival barrier is a constantly stimulated and dynamic environment where homeostasis is often disrupted, resulting in inflammatory periodontal diseases. Type 2 diabetes (T2D), a risk factor for periodontitis, has been reported to be associated with barrier dysfunction, but the effect and underlying mechanism are inconclusive. Herein, we performed single-cell RNA sequencing (scRNA-seq) of gingiva from leptin receptor-deficient (db/db) mice to understand the heterogeneity of gingival barrier in the context of T2D. Periodontal health of control mice is characterized by populations of Krt14+-expressing epithelial cells and Col1a1+-fibroblasts mediating immune homeostasis primarily through the enrichment of innate lymphoid cells. The db/db mice exhibit an impaired gingival barrier with spontaneous periodontal bone loss, and a decreased proportion of epithelial/stromal cells. We further observed stromal, particularly fibroblast immune hyperresponsiveness linked to recruitment of myeloid cell populations in gingiva from T2D mice. Analysis of ligand-receptor interaction pairs suggested inflammatory signaling between fibroblasts and myeloid cells, a main driver of diabetes-induced periodontal damage. Moreover, the “Immune-like” stromal cells contributed to gingival Th17/IL-17 hyperresponsiveness in T2D. Our work reveals transcriptional diversity of stromal cells and interaction with innate immune cells in T2D, and uncovers the “immune-like” fibroblast subsets participating in barrier homeostasis at the diabetic gingiva.

overall_design: Gingival single-cell transcriptomic profile of 16-wk-old db/db mice and control mice were generated by sc-RNA sequencing.

first: Qian

first: Weimin

last: Lin

first: Quan

last: Yuan


title: Single-cell transcriptome analysis of mouse main olfactory epithelium

summary: The goal of scRNA-seq is to explore whether olfactory sensory neurons (OSNs) that display a specific olfactory receptor (OR) express a distinct transcriptional program from OSNs that display a different OR in a large and unbias scale. Olfactory epithelial single cell suspensions were made using 3 male and 3 female mice. Single-cell sequencing libraries were prepared using Chromium Single Cell 3’ Reagent Kit V3 (10X Genomics) according to the manufacturer’s guidelines. Libraries were sequenced using 150 cycles of paired end reads on Illumina Hiseq4000 and Novaseq6000 instruments (Novogene). The sequencing reads were processed using the DolphinNext Single Cell-10X Genomics pipeline (https://dolphinnext.umassmed.edu/index.php?np=1&id=420, default settings except STAR v2.6.1 was used for alignment).


title: Single-cell RNA sequencing of airway submucosal glands in wild-type and cystic fibrosis Pigs

status: Public on Nov 16 2021

city: Iowa city

first: Wenjie

last: Yu

state: IA

address: 200 Hawkins Dr, 6330 PBDB

institute: The University of Iowa

summary: Submucosal glands (SMGs) in the upper respiratory system of mammals play important roles in fluid secretion, mucociliary transport, and host defense. In people with cystic fibrosis (CF), airway mucus obstruction and SMG duct occlusion are hallmark features. Although intensive investigations have focused on airway surface epithelium in normal and diseased lungs, our knowledge of SMGs is limited in terms of cell biology and physiology. Here, we conducted single cell RNA sequencing (scRNA-seq) of airway SMGs in newborn piglets. First, we dissected individual SMGs and surrounding non-epithelial tissues from newborn non-CF (n = 4) and CF (n = 4) pig trachea. Second, we did scRNA-seq using 10x genomics chromium platform. Third, we processed the raw sequencing data using an improved RefSeq pig genome reference. Last, we integrated all samples together and clustered cells into 14 major cell clusters using Seurat R toolkit (Stuart et al., 2019). These data allowed us to elucidate airway SMGs at single cell resolution. Moreover, we found that cell-types and gene expression were the same in non-CF and CF SMGs, suggesting that loss of epithelial anion secretion rather than an intrinsic cell defect causes CF mucus abnormalities.

overall_design: We dissected and collected individual tracheal SMGs from 4 wild-type (WT) and 4 CFTR-/- (CF) newborn pigs.To eliminate contamination of airway surface epithelial cells, we brushed off airway surface epithelial cells as much as possible. To explore the SMGs before dissection, we peeled the epithelial layer away from the cartilage layer of the trachea. Single cells were processed using the 10X Genomics Chromium controller. cDNA libraries were generated using the Chromium Single cell 3’ V2 kit. Sequencing was conducted on a HiSeq 4000 system from Illumina.

first: Michael

last: Welsh


title: Gene expression analysis of whole blood obtained from COVID-19 in the Osaka cohort

status: Public on Jun 22 2022

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary: To obtain a detailed view of genes and pathways regulated in whole blood obtained from COVID-19 patients in the Osaka cohort, we carried out global RNA sequencing.

overall_design: We performed RNA-sequencing analysis using samples of leukocyte samples from 31 COVID-19 patients and 16 healthy controls.

first: Takeshi

last: Ebihara

first: Hisatake

last: Matsumoto


title: Single cell analysis of innate lymphoid cells in the context of TNF challenge in the intestine

status: Public on Nov 04 2021

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

summary: In the gastrointestinal tract, excessive TNF drives cell death in the intestinal epithelium, and blockade of TNF has provided substantial therapeutic benefit to individuals with inflammatory bowel disease. However, the cellular and molecular pathways that control the beneficial versus detrimental impacts of TNF in the gut remain poorly understood. To understand the role of ILCs in regulation of TNF outcome in the intestine, we performed single-cell RNA-sequencing on 11,556 sort-purified ILCs from the small intestine of mice treated with PBS or TNF, identified and classified nine distinct clusters of cells based on expression of signature genes.

overall_design: For each sample, two mice were pooled together, and ILCs (CD45+CD3-epsilon-CD5-CD8-alpha-ΝΚ1.1-ΤCR-gamma-delta-CD11b-CD11c-B220-CD127+) were sort-purified lamina propria of small intestine.

first: Lei

last: Zhou

last: Sonnenberg


title: Hepatitis C virus scarring of the epigenome and creates targetable vulnerabilities following viral clearance

status: Public on Sep 23 2021

city: Rochester

first: Keith

middle: Darrell

last: Robertson

state: MN

address: 200 First Street SW, Stabile 12-70

department: Pharmacology

institute: Mayo Clinic

type: Methylation profiling by genome tiling array

overall_design: Refer to individual Series


title: Sex-specific multi-level 3D genome dynamics in the mouse brain

status: Public on May 06 2022

city: Bronx

first: Marija

last: Kundakovic

address: 441 E. Fordham Road

department: Biological Sciences

institute: Fordham University

summary: Female mammalian brains exhibit sex-hormone-driven plasticity during the reproductive period. Evidence implicates the role of chromatin dynamics in gene regulation underlying this plasticity. However, whether ovarian hormones impact higher-order chromatin organization in post-mitotic neurons in vivo is unknown. Here, we mapped 3D genome of ventral hippocampal neurons across the estrous cycle and by sex in mice. In females, we found cycle-driven dynamism in 3D chromatin organization, including in estrogen-response-elements-enriched X-chromosome compartments, autosomal CTCF loops, and enhancer-promoter interactions. With rising estrogen levels, the female 3D genome becomes more similar to males. Cyclical enhancer-promoter interactions are partially associated with gene expression and enriched for brain disorder-relevant genes. Our study reveals unique 3D genome dynamics in the female brain relevant to female-specific gene regulation, neuroplasticity, and disease risk.

overall_design: To understand how biological sex and fluctuating sex hormones in females influence 3D genome organization and transcriptional regulation.

first: Devin

last: Rocks

first: Mamta

last: Shukla

first: Silvia

middle: C

last: Finnemann

first: Achyuth

last: Kalluchi

first: Jordan

last: Rowley


title: Single-cell RNA-seq of lung cells following bacterial pneumonia with or without LIF blockade

status: Public on Feb 17 2022

city: Boston

first: Single Cell

last: Sequencing Core

address: 72 E. Concord St

institute: BU Single Cell Sequencing Core

summary: C57BL/6 mice were intratracheally challenged for 24 hours with saline or E. coli (1 x 10^6 CFU) with or without LIF neutralization. Left lobes were collected and digested into single-cell suspensions for FACS. Equal ratios of CD45+ (leukocytes), CD45-EpCAM+ (epithelium), and CD45-EpCAM- (other) cells were pooled from a mouse undergoing each condition.

overall_design: Sorted whole lung C57BL/6 mouse cells 24 hours after IgG saline, IgG E. coli, or anti-LIF E. coli

first: Xaralabos

last: Varelas

first: Elim

first: Lee

last: Quinton


title: Clearance of chronic hepatitis C virus infection leaves scars on the epigenome driven by an interferon response and creates targetable vulnerabilities [seq]

summary: Background & aims: Chronic hepatitis C viral (HCV) infection is a leading etiologic driver of cirrhosis and ultimately hepatocellular carcinoma (HCC). Of the approximately ~71 million individuals chronically infected with HCV, 10-20% are expected to develop severe liver complications in their lifetime. Epigenetic mechanisms including DNA methylation and histone modifications become profoundly disrupted in disease processes including liver disease.   Methods: To understand how HCV infection influences the epigenome and whether these events remain as ‘scars’ following cure of chronic HCV infection, we mapped genome-wide DNA methylation, four key regulatory histone modifications (H3K4me3, H3K4me1, H3K27ac, and H3K27me3) and open chromatin by ATAC-seq in parental and HCV-infected immortalized hepatocytes and the Huh7.5 HCC cell line, along with DNA methylation and gene expression analyses following elimination of HCV in these models through treatment with interferon-α or a direct-acting antiviral (DAA).   Results: Our data demonstrate that HCV infection profoundly impacts the epigenome (particularly enhancers), HCV shares epigenetic targets with interferon-α targets, an overwhelming majority of epigenetic changes induced by HCV remain as ‘scars’ on the epigenome following cured infection, and similar findings are observed in primary human patient samples cured of chronic HCV infection. Supplementation of interferon-α/DAA antiviral regimens with DNA methyltransferase inhibitor 5-aza-2’deoxycytidine synergizes in reverting aberrant DNA methylation changes induced by HCV. Finally, both HCV-infected and cured cells displayed a blunted immune response, demonstrating a functional effect of epigenetic scarring.   Conclusions: Integration of epigenetic and transcriptional data elucidates key gene deregulation events driven by HCV infection and how this may underpin the long-term elevated risk for HCC in patients cured of HCV due to epigenome scarring.

overall_design: Hu1545 surrogate normal and Huh7.5 HCC cell lines profiled for gene expression, histone modifications, DNA methylation, and chromatin occupancy with and without HCV and drugs (interferon, Telaprevir, 5-azadC)

first: Ryan

last: Hlady


title: Integrated methylomic and transcriptomic characterisation of postoperative systemic inflammatory dysregulation (METHYLATION)

status: Public on Sep 17 2021

first: Mark

last: Ziemann

summary: The inflammatory response to surgery is essential for healing and recovery, however hyperinflammation and altered immune competence increases the risk of inflammation mediated complications. We hypothesised that, in some patients, a state of postoperative systemic inflammatory dysregulation (PSID) exists increasing the risk or infection and sepsis, and that this will be associated with, and potentially predicted by, altered patterns of genome-wide peripheral blood mononuclear cell differential DNA methylation and gene expression. In this study we utilised phenotypic extremes of postoperative plasma C-reactive protein levels to define PSID, which manifested clinically in significantly higher rates of sepsis, complications and longer hospital stays following major abdominal surgery. We identified altered DNA methylation and differential gene expression in specific immune and metabolic pathways during PSID. Our findings suggest that dysregulation results in, or from, dramatic changes in differential DNA methylation and highlights potential targets for early detection and treatment. The combination of altered DNA methylation and gene expression confirms that dysregulation is mediated at multiple levels within specific gene sets and hence, non-specific anti-inflammatory treatments such as corticosteroids alone are unlikely to represent an effective therapeutic strategy.

overall_design: In this study we have matched RNA-seq expression and EPIC methylation array data from patients before and after major abdominal surgery. There  are two patient groups, those with low CRP after surgery (n= 25) and those with elevated CRP after surgery (n=21). The purpose is to understand the gene regulatory events that occur in patients with high CRP levels, as these patients are at a higher risk of adverse outcomes after surgery.

first: Chris

last: Bain

first: Paul

last: Myles

first: Rachael

last: Taylor

first: Hugh

last: Trahair

first: Yin

middle: P

last: Lee

first: Larry

last: Croft

first: Phillip

last: Peyton

first: Matthew

last: Chan

first: Sophie

last: Wallace

first: Tomas

last: Corcoran

first: Andrew

last: Shaw

first: Eldho

last: Paul

first: Kiymet

last: Bozoaglu


title: Integrated methylomic and transcriptomic characterisation of postoperative systemic inflammatory dysregulation (RNA EXPRESSION)

overall_design: In this study we have matched RNA-seq expression and EPIC methylation array data from patients before and after major abdominal surgery. There are two patient groups, those with low CRP after surgery (n= 25) and those with elevated CRP after surgery (n=21). The purpose is to understand the gene regulatory events that occur in patients with high CRP levels, as these patients are at a higher risk of adverse outcomes after surgery.

middle: S


title: Interferon drives hepatitis C virus scarring of the epigenome and creates targetable vulnerabilities following viral clearance [array]

first: Keith

last: Robertson

summary: Background & aims: Chronic hepatitis C viral (HCV) infection is a leading etiologic driver of cirrhosis and ultimately hepatocellular carcinoma (HCC). Of the approximately ~71 million individuals chronically infected with HCV, 10-20% are expected to develop severe liver complications in their lifetime. Epigenetic mechanisms including DNA methylation and histone modifications become profoundly disrupted in disease processes including liver disease.   Methods: To understand how HCV infection influences the epigenome and whether these events remain as ‘scars’ following cure of chronic HCV infection, we mapped genome-wide DNA methylation, four key regulatory histone modifications (H3K4me3, H3K4me1, H3K27ac, and H3K27me3) and open chromatin by ATAC-seq in parental and HCV-infected immortalized hepatocytes and the Huh7.5 HCC cell line, along with DNA methylation and gene expression analyses following elimination of HCV in these models through treatment with interferon-α or a direct-acting antiviral (DAA).   Results: Our data demonstrate that HCV infection profoundly impacts the epigenome (particularly enhancers), HCV shares epigenetic targets with interferon-α targets, an overwhelming majority of epigenetic changes induced by HCV remain as ‘scars’ on the epigenome following cured infection, and similar findings are observed in primary human patient samples cured of chronic HCV infection. Supplementation of interferon-α/DAA antiviral regimens with DNA methyltransferase inhibitor 5-aza-2’deoxycytidine synergizes in reverting aberrant DNA methylation changes induced by HCV. Finally, both HCV-infected and cured cells displayed a blunted immune response, demonstrating a functional effect of epigenetic scarring.   Conclusions: Integration of epigenetic and transcriptional data elucidates key gene deregulation events driven by HCV infection and how this may underpin the long-term elevated risk for HCC in patients cured of HCV due to epigenome scarring.    Lay summary: Despite cure of hepatitis C viral (HCV) infection, patients remain at increased long-term risk for liver cancer. This study aimed to discover whether this effect was mediated through the epigenome. Using a novel cell culture system, we find that normal epigenetic marks and gene expression are disrupted by chronic HCV infection, and that these disrupted patterns are not restored following HCV cure. Moreover, the epigenetic disruptions caused by HCV are very similar to the natural interferon response that is typically key to clearing viral infections. Epigenetically disrupted pathways therefore contribute to suppression of innate immunity and increased risk for liver cancer in patients cured of HCV, but also reveal potential vulnerabilities that could be targeted pharmacologically.

overall_design: Hu1545 surrogate normal and Huh7.5 HCC cell lines profiled for gene expression, histone modifications, and chromatin occupancy with and without HCV and drugs (interferon, Telaprevir, 5-azadC)


title: De novo modeling of chromoplectic Ewing sarcoma tumors from patient-derived mesenchymal stem cells

status: Public on Aug 18 2021

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'ulm

country: France

institute: Institut Curie

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


title: Targeting mesenchymal stromal cells plasticity to reroute acute myeloid leukemia course

status: Public on Jul 01 2021

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

summary:
MSC and AML dual targeting to treat pediatric AML
Bone marrow (BM) microenvironment supports the regulation of normal hematopoiesis through a finely tuned balance of self-renewal and differentiation processes, cell-cell interaction and secretion of cytokines that during leukemogenesis are severely compromised and favor tumor cell growth. In pediatric acute myeloid leukemia (AML), chemotherapy is the standard of care, but still >30% of patients relapse. The need to accelerate the evaluation of innovative medicines prompted us to investigate the mesenchymal stromal cell (MSCs) role in the leukemic niche to define its contribution to the mechanisms of leukemia escape. We generated humanized three-dimensional (3D) niche with AML cells and MSCs derived from patients (AML-MSCs) or healthy donors. We observed that AML cells establish physical connections with MSCs, mediating a reprogrammed transcriptome inducing aberrant cell proliferation and differentiation, and severely compromising their immunomodulatory capability. We confirmed AML cells endow h-MSCs with a pro-oncogenic transcriptional profile and functions similar to the AML-MSCs when co-cultured in vitro. Conversely, MSCs derived from BM of patients at time of disease remission showed recovered healthy features, at transcriptional and functional levels, including the secretome. We sustained AML blasts altering MSC cell activities in the BM niche in order to favor disease development and progression, becoming a pharmacological target. We discovered that a novel AML-MSCs selective CaV1.2 channel blocker drug, Lercanidipine, is able to impair leukemia progression in 3D both, in vitro and when implanted in vivo, if used in combination with chemotherapy, supporting the hypothesis that synergistic effects can be obtained by dual targeting approaches.

overall_design: Gene expression was measured using  Affymetrix platform in 21 MSCs derived from bone marrow of pediatric AML patients at diagnosis

first: Silvia

last: Bresolin

first: Martina

last: Pigazzi


title: Identification of rare, transient post-mitotic cell states that are induced by injury and required for whole-body regeneration in Schmidtea mediterranea

status: Public on Jun 11 2021

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

summary: Regeneration requires the coordination of stem cells, their progeny and distant differentiated tissues. Here, we present a comprehensive atlas of whole-body regeneration in Schmidtea mediterranea and identify wound-induced cell states. An analysis of 299,998 single-cell transcriptomes captured from regeneration-competent and regeneration-incompetent fragments identified transient regeneration-activated cell states (TRACS) in the muscle, epidermis and intestine. TRACS were independent of stem cell division with distinct spatiotemporal distributions, and RNAi depletion of TRACS-enriched genes produced regeneration defects. Muscle expression of notum, follistatin, evi/wls, glypican-1 and junctophilin-1 was required for tissue polarity. Epidermal expression of agat-1/2/3, cyp3142a1, zfhx3 and atp1a1 was important for stem cell proliferation. Finally, expression of spectrinβ and atp12a in intestinal basal cells, and lrrk2, cathepsinB, myosin1e, polybromo-1 and talin-1 in intestinal enterocytes regulated stem cell proliferation and tissue remodelling, respectively. Our results identify cell types and molecules that are important for regeneration, indicating that regenerative ability can emerge from coordinated transcriptional plasticity across all three germ layers.

overall_design: For each time course, 100-150 biopsies were dissociated and fixed from each sample, then ~500,000 cells from each sample were sorted, barcoded and pooled into 8 sub-libraries for sequencing. Each sub-library contained 15,000-20,000 individual cells pooled from all timepoint within the timecourse.  Each timecourse was split into 8 sub-libraries, resulting in a total of 24 sub-libraries across the three timecourses. The read barcode structure is as follows for the demultiplexed fastq files: UMI: 1-10bp CellBarcode: 11-34bp. Note: SRA fixed an internal database issue about the samples on September 22, 2022. Please redownload the data if needed.

first: Blair

last: Benham-Pyle

first: Alejandro

last: Sánchez Alvarado


title: G3BP1 Binds to Guanine Quadruplexes in mRNAs

status: Public on Mar 16 2021

city: Riverside

first: Yinsheng

last: Wang

state: California

address: 501 Big Springs Road

institute: UC-Riverside

summary: we identify G3BP1 as a novel rG4-binding protein, and reveal that G3BP1 can modulate mRNA stability through its binding with rG4 structures

overall_design: Examination of G3BP1 mRNA binding sites in HEK293T cells with or without PDS treatment

first: Xiaomei

last: He


title: RNA-seq data in hMPC, MSC_Pat and EWIma1

status: Public on Sep 08 2021

summary: Ewing sarcoma is characterized by pathognomonic translocations fusing most frequently EWSR1 with FLI1 (EF1). In addition, Ewing sarcoma can also display alterations in STAG2, TP53 and CDKN2A (SPC). Starting from Ewing sarcoma derived human mesenchymal stem cells (MSCpat), we recapitulated this translocation and SPC alterations using a CRISPR/cas9 approach and generated a bona fide Ewing sarcoma model (EWIma1) displaying transcriptomic and epigenetic hallmarks of EwS.

overall_design:
RNA-seq were performed in hMPC (WT and derived clones) and MSC_Pat (WT and derived clones and tumors).
*****************************************
Raw data have been uploaded to the EGA database under accession EGAS50000001173: https://ega-archive.org/studies/EGAS50000001173

first: Anna

last: Sole

first: Sandrine

last: Grossetête

first: Sakina

last: Zaidi

first: Didier

last: Surdez

first: Erika

last: Brunet


title: Cell type-specific Chromatin Accessibility Analysis in the Mouse and Human Brain

status: Public on Mar 10 2021

first: Marija

last: Kundakovic

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: African American-specific APOL1  risk variants in endothelial cells exacerbate sepsis and COVID19 severity

status: Public on Aug 12 2021

first: Junnan

last: Wu

state: Pennsylvania

address: 12-188Smilow Center for Translational Research 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: To understand molecular changes in endothelial cells in vivo in EC/G2APOL1 mice, we performed droplet-based single-cell RNA sequencing (scRNA-seq) on kidney samples from WT and EC/G2APOL1 mice

overall_design: we compared WT and G2APOL1 mice endothelial cell gene expression

first: Katalin

last: Susztak


title: Cell type-specific Chromatin Accessibility Analysis in the Mouse and Human Brain (Mouse ATAC-seq experiments)

summary: The Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) is becoming increasing popular in the neuroscience field where chromatin regulation is thought to be involved in neurodevelopment, activity-dependent gene regulation, hormonal and environmental responses, and pathophysiology of neuropsychiatric disorders. The advantages of using this assay include a small amount of material needed, relatively simple and fast protocol, and the ability to capture a range of gene regulatory elements with a single assay. However, with increasing interest in chromatin research, it is an imperative to have feasible, reliable assays that are compatible with a range of neuroscience study designs in both animals and humans. Here we tested three different protocols for neuronal chromatin accessibility analysis, including a varying brain tissue freezing method followed by fluorescent-activated nuclei sorting (FANS) and the ATAC-seq analysis. Our study shows that the cryopreservation method impacts the number of open chromatin regions that can be identified from frozen brain tissue using the cell-type specific ATAC-seq assay. However, we show that all three protocols generate consistent and robust data and enable the identification of functional regulatory elements, promoters and enhancers, in neuronal cells. Our study also implies that the broad biological interpretation of chromatin accessibility data is not significantly affected by the freezing condition. In comparison to the mouse brain analysis, we reveal the additional challenges of doing chromatin analysis on postmortem human brain tissue. However, we also show that these studies are revealing important cell type-specific information about gene regulation in the human brain. Overall, the ATAC-seq coupled with FANS is a powerful method to capture cell-type specific chromatin accessibility information in the mouse and human brain. Our study provides alternative brain preservation methods that generate high quality ATAC-seq data while fitting in different study designs, and further encourages the use of this method to uncover the role of epigenetic (dys)regulation in healthy and malfunctioning brain.

overall_design: Mouse ATAC-seq experiments were designed to determine the effects of of the brain tissue cryopreservation method on the quality of chromatin accessibility data derived from frontal cortical tissue. The following three freezing conditions were included: 1) flash freezing in liquid nitrogen (LN2); 2) flash freezing in dry ice cooled hexane (HEX); and 3) slow freezing in a cryprotective medium (MED). Two biological replicates were tested per group.

first: Devin

last: Rocks

first: Ivana

last: Jaric

first: Lydia

last: Tesfa

first: John

last: Greally

first: Masako

last: Suzuki


title: IL11 is elevated in systemic sclerosis and IL11-dependent ERK signaling is needed for the profibrotic activity of TGFβ in dermal fibroblasts

status: Public on Feb 22 2021

city: Singapore

first: Eleonora

last: Adami

address: 8 College Road

department: CVMD

country: Singapore

institute: Duke-NUS Medical School

summary:
Objectives: Interleukin 11 (IL11) is highly upregulated in skin and lung fibroblasts from patients with systemic sclerosis (SSc). Here we tested whether IL11 is mechanistically linked with human dermal fibroblast (HDF) activation.
Methods: We measured serum IL11 levels in healthy volunteers and patients with early diffuse SSc and manipulated IL11 signalling in HDFs using gain- and loss-of-function approaches.
Results: In patients with SSc, serum IL11 levels are elevated as compared to healthy controls. Transforming growth factor beta (TGFβ) isoforms 1, 2 or 3 induced IL11 secretion from HDFs, which highly express IL11RA and the gp130 co-receptor, suggestive of an autocrine loop of IL11 activity in HDFs. IL11 consistently and robustly stimulated ERK activation in HDFs and resulted in HDF-to-myofibroblast transformation. IL11 induced STAT phosphorylation to a lesser extent than ERK and only at high IL11 concentrations. IL11-stimulated ERK activation and fibrosis phenotypes were absent in skin fibroblasts from patients with homozygous loss-of-function mutation in IL11RA. Inhibition of IL11 signaling using either a neutralizing antibody against IL11 or siRNA against IL11RA reduced TGFβ-induced HDF proliferation, matrix production and cell migration, which was phenocopied by pharmacologic inhibition of ERK activity.
Conclusions: These data reveal an important contribution of IL11-related ERK activity for TGFβ-stimulated fibrosis phenotypes in HDFs and suggest IL11 as a potential therapeutic target in SSc.

overall_design: We sequenced the transcriptome of human dermal fibroblasts (n=4) from a healthy donor.

first: Sivakumar

last: Viswanathan

first: Anissa

last: Widjaja

first: Ben

last: Ng

first: Sonia

last: Chothani

first: Nevin

last: Zhihao

first: Jessie

last: Tan

first: Pei

last: Lio

first: Umut

last: Altunoglu

first: Kakaly

last: Ghosh

first: Bhairav

last: Paleja

first: Sebastian

last: Schafer

first: Bruno

last: Reversade

first: Salvatore

last: Albani

first: Andrea

last: Low

first: Steven

last: O'Reilly

first: Stuart

last: Cook


title: Cell type-specific Chromatin Accessibility Analysis in the Mouse and Human Brain (Human ATAC-seq experiments)

first: Marija

last: Kundakovic

overall_design: Human ATAC-seq experiments were designed to evaluate the suitability of the ATAC-seq assay for profiling chromatin accessibility in neuronal and non-neuronal nuclei isolated from post-mortem human brain tissues, in comparison to the mouse neuronal ATAC-seq analysis.

first: Devin

last: Rocks

first: Ivana

last: Jaric

first: Lydia

last: Tesfa

first: John

last: Greally

first: Masako

last: Suzuki


title: ChIP-seq data in MSC_Pat and EWIma1 (FLI1 & H3K27ac)

first: Olivier

last: Delattre

overall_design:
ChIP-seq (FLI1 and H3K27ac) were performed in MSC_Pat and EWIma1 cells. Respective inputs were used as normalization controls.
*****************************************
Raw data have been uploaded to the EGA database under accession EGAS50000001172: https://ega-archive.org/studies/EGAS50000001172

first: Anna

last: Sole

first: Sandrine

last: Grossetête

first: Sakina

last: Zaidi

first: Didier

last: Surdez

first: Erika

last: Brunet


title: Dynamic changes in human single cell transcriptional signatures during fatal sepsis

status: Public on Mar 03 2021

city: RIVERSIDE

first: Xinru

last: Qiu

address: 109 Picnic Hill Rd

department: School of Medicine

institute: University of California, Riverside

summary: Systemic infections, especially in patients with chronic diseases, result in sepsis: an explosive, uncoordinated immune response that can lead to multisystem organ failure with a high mortality rate. Sepsis survivors and non-survivors oftentimes have similar clinical phenotypes or sepsis biomarker expression upon diagnosis, suggesting that the dynamics of sepsis in the critical early stage may have an impact on these opposite outcomes. To investigate this, we designed a within-subject study of patients with systemic gram-negative bacterial sepsis with surviving and fatal outcomes and performed single-cell transcriptomic analyses of peripheral blood mononuclear cells (PBMC) collected during the critical period between sepsis recognition and 6 hours. We observed that the largest sepsis-induced expression changes over time in surviving versus fatal sepsis were in CD14+ monocytes, including gene signatures previously reported for sepsis outcomes. We further identify changes in the metabolic pathways of both monocytes and platelets, the emergence of erythroid precursors, and T cell exhaustion signatures, with the most extreme differences occurring between the non-sepsis control and the sepsis non-survivor. Our single-cell observations are consistent with trends from public datasets but also reveal specific effects in individual immune cell populations, which change within hours. In conclusion, this pilot study provides the first single-cell results with a repeated measures design in sepsis to analyze the temporal changes in the immune cell population behavior in surviving or fatal sepsis. These findings indicate that tracking temporal expression changes in specific cell-types could lead to more accurate predictions of sepsis outcomes. We also identify molecular pathways that could be therapeutically controlled to improve the sepsis trajectory toward better outcomes.

overall_design:
Single-cell RNA-sequencing of human peripheral blood mononuclear cells from heathy controls, survivor and non-survivor of gram-negative sepsis patients.

When using datasets from GEO, please ensure to cite the corresponding peer-reviewed publications, as they provide vital context and methodology essential for accurate data application and scientific integrity. Proper acknowledgment through citation respects authors' contributions and upholds the standards of research excellence.

first: Jiang

last: Li

first: Jeff

last: Bonenfant

first: Lukasz

last: Jaroszewski

first: Walter

last: Klein

first: Adam

last: Godzik

first: Meera

middle: G

last: Nair


title: Single Cell RNA-sequencing analysis of the juvenile and embryonic mouse enteric nervous system (ENS) of the small intestine

status: Public on Sep 18 2020

city: Stockholm

first: Ulrika

last: Marklund

state: - If in U.S, Select a State -

address: Tomtebodavägen 16

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: The study aimed to make a molecular definition of myenteric neuron classes in the mouse small intestine and describe their differentiation from enteric stem cells during embryogenesis. Method: We performed single cell RNA-sequencing of enteric neurons from small intestine at the juvenile stage (postnatal day (P)21) and ENS cells from the small intestine at embryonic day (E)15.5 and E18.5. We confirmed novel marker genes for all classes using immunohistochemistry and characterised the morphology/axons of three of newly discovered ENS neuron types. Results: 12 unique enteric neuron classes (ENC1-12) were identified and confirmed in native tissue by histochemical methods. The communication machinery (ligand, receptors, adhesion molecules), axonal patterns and morphologies were presented to infer functional roles of the ENCs. Analysis of embryonic transcriptomes revealed that enteric stem cells differentiate into two neuronal branches, that successively diversify into ENC1-7 and ENC8-12, respectively. Conclusion: Utilizing single cell RNA-sequencing we conclude that murine small intestine consists of 12 major myenteric classes that emerge through a step-wise fashion during embryonic development. Reference: Morarach, Mikhailova et al., 2020. BioRxiv 2020.03.02.955757

overall_design: We isolated single myenteric neurons from pan-neuronal Baf53bCre;R26R-Tomato mice (P21) and single ENS cells (including enteric stem cells, glia and neurons) from Wnt1-Cre;R26R-Tomato embryos (E15.5 and E18.5) using flow cytometry and obtained transcriptomes by single cell RNA-sequencing (10xGenomics).


title: Genome-wide chromatin accessibility and DNA methylation of wildtype zebrafish livers at 120 hpf

status: Public on Jul 07 2021

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: The goal of this study is genomic chromatin accessibility of 120 hpf zebrafish livers by ATAC-Seq. ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) and the DNA methylation profile using reduced representation bisulfite sequencing (RRBS).

overall_design:
"To perform ATAC-seq on pools of zebrafish larvael livers collected at 120 hpf, we microdissected between 10-20 livers from 3 independent clutches of Tg(fabp10a:CAAX-EGFP) following immobilization using tricaine. ATAC-seq was performed using the protocol described in Buenrostro et al (2015): doi:10.1002/0471142727.mb2129s109, with the exception of dissociating the livers for cell suspension was obtained by treatment with trypsin at 37 degree for 30 minutes.  ATAC-seq: Protocol as described in Buenrostro et al (2015): doi:10.1002/0471142727.mb2129s109, using illumina barcoded primers for sequencing.

To perform RRBS on WT zebrafish livers to determine which genomic regions are methylated/unmethylated specifically in this tissue. We dissected 40 livers from a different set of larvae tahn were used for ATACseq.  These were WT siblings of a transgenic line following immobilization using tricaine at 5 days post fertilizaion (dpf). Livers were pooled and high molecular weight DNA from larvae was extracted by using a DNA extraction buffer as previously described (Chernyavskaya et al., 2017). DNA was used to perform RRBS library prep according to Garrett-Bakelman et al., 2015, with some modification. To avoid loss of gDNA, after MspI digestion, end repair, and Atailing, the reactions were stopped by heat inactivation. The adaptors used for multiplexing were purchased separately (Next Multiplex
Methylated Adaptors–New England Biolabs) and libraries were size selected by dual-step purification with Ampure XP Magnetic Beads (Beckman Coulter, Agencourt).

first: Bhavani

last: Madakashira

first: Filippo

last: Macchi

last: Sadler (Edepli)


title: Fast skeletal myosin binding protein-C regulates fast skeletal muscle contraction

status: Public on Nov 30 2020

city: Cincinnati

first: Taejeong

last: Song

state: OH

address: 231 Albert Sabin Way, CVC Building Room 4978

department: Internal Medicine

institute: University of Cincinnati

summary: Fast skeletal myosin binding protein-C (fMyBP-C) is one of three MyBP-C paralogs and is predominantly expressed in fast skeletal muscle. Mutations in the gene that encodes fMyBP-C, MYBPC2, is associated with distal arthrogryposis, while fMyBP-C protein is reduced in diseased muscle. However, the functional and structural roles of fMyBP-C in skeletal muscle remain unclear. To address this gap, we generated a homozygous fMyBP-C knockout mouse (C2-/-) and characterized it, both in vivo and in vitro. Ablation of fMyBP-C was benign in terms of muscle weight, fiber type, cross-sectional area, and sarcomere ultrastructure. However, grip strength and plantar-flexor muscle strength were significantly decreased in C2-/- compared to WT. Peak isometric tetanic force (Po) and isotonic speed of contraction were significantly reduced in isolated extensor digitorum longus (EDL) from C2-/- mice. In EDL muscles of C2-/- mice, small-angle X-ray diffraction revealed significant increase in equatorial intensity ratio (I1.1/I1.0) during contraction, indicating a greater degree of myosin head shift towards actin while MLL4 layer-line intensity was decreased at rest, indicating less ordered myosin heads at rest. Interfilament lattice spacing was also significantly increased in C2-/- EDL muscle compared to WT. Consistent with these findings, we observed a significant reduction of steady-state isometric force during Ca2+ activations, myofilament calcium sensitivity, sinusoidal stiffness in skinned EDL muscle fibers from C2-/- mice. Finally, C2-/- muscles displayed disruption of inflammatory and regenerative genes and increased muscle damage upon mechanical overload. Together, our data suggest that fMyBP-C is essential for maximal speed and force of contraction, sarcomere integrity, and calcium sensitivity in fast twitch muscle.

overall_design: Comparision of RNA sequence between wild type (WT ) and C2-/- EDL fiber

first: Sakthivel

last: Sadayappan


title: Identification of DNA methylation signatures associated with poor outcome in lower-risk Stage, Size, Grade and Necrosis (SSIGN) score clear cell renal cell cancer

status: Public on Jan 19 2021

first: Keith

last: Robertson

summary: DNA methylation from LTS (long term survivor) and STS (short term survivor) kidney tumors

overall_design: 94 total samples (51 LTS, 41 STS, 2 CON) from unique patients

first: Louis

middle: Y

last: El Khoury

middle: D


title: Ultra-Processed Foods drive Intestinal Barrier permeability increasing Microvascular Disease risk

status: Public on Dec 18 2020

city: Melbourne

first: Mark

last: Ziemann

address: 85 Commercial Rd

institute: Burnet Institute

summary: Abstract: Our intake of ultra-processed foods has dramatically increased over the past few decades in line with the prevalence of obesity and diabetes, key risk factors for microvascular diseases such as chronic kidney disease (CKD). The extent to which long-term intake of highly processed food influences CKD outcome is unclear. Here, we show in rodent models that a highly processed diet drives intestinal barrier permeability and an increased risk of CKD. Inhibition of the advanced glycation pathway, which generates Maillard reaction products within foods upon thermal processing, reversed kidney injury. Consequently, a highly processed diet leads to innate immune complement activation and local kidney inflammation via the potent proinflammatory effector molecule complement 5a (C5a). C5a receptor inhibition ameliorated albuminuria. In a mouse model of diabetes, a high resistant starch fiber diet led to a redistribution of the gut commensal consortium, prevented impaired gut barrier function and decreased the severity of kidney injury via suppression of complement. These results provide mechanistic insight into the role of highly processed foods on inflammation and chronic disease risk. One Sentence Summary: Ultra-processed diets promote chronic kidney disease

overall_design: The db/db mouse model of obesity was used to test the effect of different diets on renal transcriptomes. There were three diet groups (1) a standard chow diet, (2) heat-treated diet, and (3) heat-treated with added resistant starch. There were n=5 animal in each group. RNA was extracted from renal cortex for RNA-seq using a ribosomal RNA depletion library preparation.

first: Matthew

last: Snelson

first: Sih

middle: M

last: Tan

first: Rachel

last: Clarke

first: Vicki

last: Thallas-Bonke

first: Tuong-Vi

last: Nguyen

first: Sally

middle: A

last: Penfold

first: Brooke

last: Harcourt

first: Karly

last: Souris

first: Runa

last: Lindblom

first: David

last: Steer

first: Assam

last: El-Osta

first: Michael

last: Davies

first: Permal

last: Deo

first: Kerin

last: O’Dea

first: Catherine

last: Itsiopoulos

last: Cooper

first: Trent

last: Woodruff

first: Charles

middle: R

last: Mackay

first: Josephine

last: Forbes

first: Melinda

middle: T

last: Coughlan


title: Gene expression profiling in endometriosis and ovarian cancer

status: Public on Apr 01 2021

city: Seoul

first: Ha-Yeon

last: Shin

address: 237, Dogok-ro

department: Obstetrics and Gynecology

country: South Korea

institute: Yonsei University

summary: This study aimed to identify an essential gene in the malignant transformation of endometriosis to clear cell ovarian carcinoma and endometrioid ovarian carcinoma.

overall_design: Endometriosis, atypical endometriosis, adjacent endometriosis to clear cell ovarian carcinoma, adjacent endometriosis to endometrioid ovarian carcinoma, clear cell ovarian carcinoma, endometrioid ovarian carcinoma.

first: Ha

first: Jae

last: Kim

first: Woo

middle: K

last: Yang

first: Doo

middle: B

last: Chay


title: Transcriptomic maps of pharmacological LSD1 inhibition in MCC [SLAMseq]

status: Public on Sep 04 2020

city: Vienna

first: Anna

middle: Christina

last: Obenauf

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology

summary: Merkel cell carcinoma (MCC) is a highly aggressive, neuroendocrine skin cancer that lacks actionable mutations, which could be utilized for targeted therapies. Epigenetic regulators governing cell identity may represent unexplored therapeutic entry points. Here, we targeted epigenetic regulators in a pharmacological screen and discovered that the lysine-specific histone demethylase 1A (LSD1/KDM1A) is required for MCC growth in vitro and in vivo. We show that LSD1 inhibition in MCC disrupts the LSD1-CoREST complex leading to displacement and degradation of HMG20B (BRAF35), a poorly characterized complex member that is essential for MCC proliferation. Inhibition of LSD1 causes derepression of transcriptional master regulators of the neuronal lineage, activates a gene expression signature resembling normal Merkel cells, and induces cell cycle arrest and cell death. Our study unveils the importance of LSD1 for proliferation and maintaining cell identity in MCC. There is growing evidence that cancer cells exploit cellular plasticity and dedifferentiation programs to evade destruction by the immune system. The combination of LSD1 inhibitors with checkpoint inhibitors may thus represent a promising treatment strategy for MCC patients.

overall_design: Gene expression profiling of PeTa cell line upon pharmacological LSD1 inhibitor treatment by 3'-mRNA sequencing. PeTa cells were pre-treated for 30min with 100nM GSK-LSD1 and newly synthesized transcripts were labeled with 500uM 4-thiouridine for 1 or 6h.

first: Lukas

last: Leiendecker

first: Pauline

last: Jung

first: Izabela

last: Krecioch

first: Tobias

last: Neumann

first: Alexander

last: Schleiffer

first: Karl

last: Mechtler

first: Thomas

last: Wiesner


title: Transcriptomic maps of pharmacological LSD1 inhibition in MCC [QUANTseq]

overall_design: Gene expression profiling of PeTa cell line upon pharmacological LSD1 inhibitor treatment by 3'-mRNA sequencing. PeTa cells were treated for 24h or 6d with 100nM GSK-LSD1 or DMSO. Libraries were prepped with the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina.


title: Pharmacological LSD1 inhibition in MCC

overall_design: Refer to individual Series


title: Genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq) during female mouse ES differentiation

status: Public on Jun 25 2020

first: Eric

last: Aeby

state: Massachusetts

address: 185 Cambridge Street

department: Department of Molecular Biology and Department of Genetics

institute: Howard Hughes Medical Institute, Massachusetts General HospitalMassachusetts General Hospital, Harvard Medical School

summary: We analyzed the effect of developmental differentiation on nascent transcripts population in female mouse embryonic stem cells.

overall_design: Hybrid female mouse ES cells carrying a deletion of Tsix promoter on the mus allele were followed during differentiation

first: Hungoo

last: Lee

first: Jeannie


title: Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression

status: Public on May 27 2020

city: St. Louis

first: Jennifer

middle: E.

last: Phillips-Cremins

address: 4515 McKinley Ave

department: Bioengineering

institute: Washington University in St. Louis

summary: Post-mitotic neurons in the mammalian brain form synapses that dynamically remodel throughout an individual’s lifetime to encode learning and memory.  Here, we create high-resolution genome folding maps in >12 Megabases around IEGs and synaptic genes and find that 12% of long-range looping interactions are induced de novo during cortical neuron activation.

overall_design: Gene expression, enhancer activity, and looping status across 3 neuronal activity states quantified by RNA-seq, H3K27ac ChIP-seq, and 5C.

first: Jonathan

last: Beagan

first: Jason

last: Shepherd


title: DCP1A knockout: transcriptome-wide characterization

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


title: Genome-wide maps of chromatin state in folate deficiency mESCs

status: Public on May 01 2020

city: Beijing

first: Qiu

last: Xie

state: Beijing

address: No.1 Shuaifuyuan Wangfujing Dongcheng District

institute: Peking Union Medical College Hospital

summary: Folate deficiency causes widespread DNA breakages and is responsible for neural tube defect (NTD). However, little is known about the implications and mechanisms of these DNA instability to NTD. Here, by performing high-throughput sequencing, we generate genome-wide epigenetic profiles and map the distribution of DNA double-strands breaks (DSBs) in folate-antagonist treated embryonic stem cells. We find that DSBs exhibit distinct preference in active promoters and inhibit the interaction between enhancers and promoters. We uncover DSBs affected CTCF binding as a causal link for the abnormal expression of NTD susceptible genes. Finally, we propose a two-ways model for screening NTD susceptible genes and verifying 7 candidate genes in NTD fetuses with low folate level. In summary, our work demonstrate that folate deficiency induced DSBs trigger the dysregulation of NTD susceptible genes through impacting epigenetic regulation.

overall_design: Examination of gene expression, chromatin accessibility, 4 histone modifications, CTCF and gH2AX in normal mESC and  folate deficiency mESCs.

first: Hao

last: Li


title: Inadequate control of thyroid hormones sensitizes to hepatocarcinogenesis and unhealthy aging.

status: Public on Apr 13 2020

city: Seville

first: Alejandro

last: Martin-Montalvo

address: Av/ Américo Vespucio 24

country: Spain

institute: CABIMER

summary: An inverse correlation between circulating thyroid hormone levels and longevity has been reported in several species and reduced thyroid hormone levels have been proposed as a biomarker for healthy aging and metabolic fitness in humans. However, hypothyroidism is a serious medical condition associated with reduced health and life expectancy. In this report, we show that severe and even subtle modulations on thyroid hormone levels leading to different forms of hyperthyroidism and hypothyroidism produce an overall unhealthy status and reduced lifespan in mice. A mild reduction in circulating T4 levels (~10%) resulted in hepatic mitochondrial dysfunction, increased ROS production and oxidative damage accumulation. These actions may contribute to the development of metabolic disorders, increased prevalence of hepatocellular carcinomas and early mortality in mice. Our findings raise concerns regarding the development of interventions aiming to modulate thyroid hormones to promote healthy aging or lifespan extension in mammals.

overall_design: Murine pancreatic islets for mWt and Pax8+/- mice were isolated. RNA was extracted and hybridized on Affymetrix microarrays. We sought to obtain the  transcriptional profile of pancreatic islets of Wt and Pax8 +/- mice .

first: Livia

last: López-Noriega

first: Vivian

last: Capilla González

first: Nadia

last: Cobo-Vuilleumier

first: Enrique

last: Martinez-Force

first: Mario

last: Soriano-Navarro

first: María

last: García-Fernández

first: Silvana

last: Yanina Romero-Zerbo

first: Francisco

middle: J

last: Bermúdez-Silva

first: Ana

last: Sánchez-Cuesta

first: Carlos

last: Santos-Ocaña

first: Abdelkrim

last: Hmadcha

first: Bernat

last: Soria

first: Franz

last: Martín

first: Benoit

last: Gauthier

last: Martín-Montalvo


title: MiR-1253 exerts tumor-suppressive effects in medulloblastoma via inhibition of CDK6 and CD276 (B7-H3) (Infinium MethylationEPIC dataset)

status: Public on Apr 10 2020

city: Omaha

first: Pranita

last: Atri

state: NE

address: S 42nd and Emile St

department: Biochemistry

institute: UNIVERSITY OF NEBRASKA MEDICAL CENTER

summary: Of the four primary subgroups of medulloblastoma, the most frequent cytogenetic abnormality, i17q, distinguishes Groups 3 and 4 which carry the highest mortality; haploinsufficiency of 17p13.3 is a marker for particularly poor prognosis. At the terminal end of this locus lies miR-1253, a brain-enriched microR that regulates bone morphogenic proteins during cerebellar development. We hypothesized miR-1253 confers novel tumor-suppressive properties in medulloblastoma. Using two different cohorts of medulloblastoma samples, we first studied the expression and methylation profiles of miR-1253. We then explored the anti-tumorigenic properties of miR-1253, in parallel with a biochemical analysis of apoptosis and proliferation, and isolated oncogenic targets using high-throughput screening. Deregulation of miR-1253 expression was noted, both in medulloblastoma clinical samples and cell lines, by epigenetic silencing via hypermethylation; specific de-methylation of miR-1253 not only resulted in rapid recovery of expression but also a sharp decline in tumor cell proliferation and target gene expression. Expression restoration also led to a reduction in tumor cell virulence, concomitant with activation of apoptotic pathways, cell cycle arrest and reduction of markers of proliferation. We identified two oncogenic targets of miR-1253, CDK6 and CD276, whose silencing replicated the negative trophic effects of miR-1253. These data reveal novel tumor-suppressive properties for miR-1253, i.e., (i) loss of expression via epigenetic silencing; (ii) negative trophic effects on tumor aggressiveness; and (iii) downregulation of oncogenic targets.

overall_design: 3 normal cell lines, 7 MB cell lines, 15 normal brain control samples, 31 MB tumors samples with subgroup classification

first: Mahapatra

last: Sidharth


title: Transient PAX8 Expression in Islets During Pregnancy Correlates With β-Cell Survival, Revealing a Novel Candidate Gene in Gestational Diabetes Mellitus.

status: Public on Dec 31 2019

first: Alejandro

last: Martin-Montalvo

summary: Transient Pax8 expression was reported in mouse islets during gestation, whereas a genome-wide linkage and admixture mapping study highlighted PAX8 as a candidate gene for diabetes mellitus (DM). We sought the significance of PAX8 expression in mouse and human islet biology. PAX8 was induced in gestating mouse islets and in human islets treated with recombinant prolactin. Global gene expression profiling of human and mouse islets overexpressing the corresponding species-specific PAX8 revealed the modulation of distinct genetic pathways that converge on cell survival. Accordingly, apoptosis was reduced in PAX8-overexpressing islets. These findings support that PAX8 could be a candidate gene for the study of gestational DM (GDM). PAX8 was genotyped in patients with GDM and gestational thyroid dysfunction (GTD), a pathology commonly found in patients with mutations on PAX8 A novel missense PAX8 mutation (p.T356M, c.1067C>T) was identified in a female diagnosed with GDM and GTD as well as in her father with type 2 DM but was absent in control patients. The p.T356M variant did not alter protein stability or cellular localization, whereas its transactivation activity was hindered. In parallel, a retrospective clinical analysis uncovered that a pregnant female harboring a second PAX8 mutation (p.P25R, c.74C>G) previously reported to cause congenital hypothyroidism also developed GDM. These data indicate that increased expression of PAX8 affects islet viability and that PAX8 could be considered as a candidate gene for the study of GDM.

overall_design: Human or murine pancreatic islets from healthy individuals were transduced with control lentiviruses or lentiviruses allowing the over-expression of the murine or human PAX8 gene. RNA was extracted and hybridized on Affymetrix microarrays. We sought to obtain the  transcriptional profile of pancreatic islets overexpressing PAX8.

last: López-Noriega

first: Carmen

last: Jiménez-Moreno

first: Amanda

last: Herranz

first: Petra

middle: I

last: Lorenzo

first: Alejandra

last: Tamayo

first: Christian

last: González-Guerrero

first: Jonathan

last: Hofsteede

first: Fanny

last: Lebreton

first: Domenico

last: Bosco

first: Miguel

last: Garcia Toscano

first: Lucrecia

first: Joao

last: Anselmo

first: José

last: Moreno


title: MiR-1253 exerts tumor-suppressive effects in medulloblastoma via inhibition of CDK6 and CD276 (B7-H3)


title: High copy number variation burdens in cranial meningiomas from patients with diverse clinical phenotypes characterized by hot genomic structure changes

status: Public on Mar 28 2020

first: Dake

last: Zhang

address: NO.1 Beichen West Road, Chaoyang District

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: Meningiomas, as the most common primary tumor of the central nervous system, are known to harbor genomic aberrations that associate with clinical phenotypes. Here we performed genome-wide genotyping for cranial meningiomas in 383 Chinese patients and identified 9,821 copy number variations (CNVs).

overall_design: Genome-wide genotyping was performed for cranial meningiomas in 383 Chinese patients and identified 9,821 copy number variations (CNVs).

first: Liang

last: Wang

first: Zhen

last: Wu


title: Role of myeloid cells in heterotopic ossification (HO) in a burn and incision-induced mouse model

status: Public on Oct 23 2019

city: Ann Arbor

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

institute: University of Michigan

summary: Despite the high frequency of musculoskeletal extremity trauma, little is known about the dynamics of the initial inflammatory response that can result in pathologic healing. Here, we assess the circulatory monocyte/macrophage recruitment to sites of pathologic extremity wound healing as seen with heterotopic ossification (HO). Using single cell transcriptome analyses at key time points, we identify distinct monocyte/macrophage subpopulations that are recruited to the site of HO formation and contribute to ectopic bone development through varied transforming growth factor-1 (Tgfb1) expression. Monocyte/macrophage specific deletion of Tgfb1 leads to altered function of macrophages and reduced HO. We further identify CD47 as a novel target for Tgfb1 regulation on monocytes/macrophages as CD47 activation leads to decreased expression of Tgfb1 in macrophages and systemic treatment with CD47 activating peptide results in attenuation of canonical TGFB1 signaling and HO. These findings elucidate the critical role of monocytes/macrophage subpopulations in aberrant wound healing and provide a novel therapeutic avenue.

overall_design: We have used 10x Genomics to perform single cell sequencing on HO cells

first: Benjamin

last: Levi

last: Huber

first: Michael

last: Sorkin

first: Simone

last: Marini


title: Genome-wide discovery and validation of diagnostic DNA methylation-based biomarkers for hepatocellular cancer detection in circulating cell free DNA

status: Public on Aug 16 2019

city: Rochester

first: Keith

middle: Darrell

last: Robertson

address: 200 First Street SW, Stabile 12-70

institute: Mayo Clinic

summary:
Background & Aims. Hepatocellular carcinoma (HCC), the most prevalent form of liver cancer, is growing in incidence but treatment options remain limited, particularly for late stage disease. As liver cirrhosis is the principal risk state for HCC development, markers to detect early HCC within this patient population are urgently needed. Perturbation of epigenetic marks, such as DNA methylation (5mC), is a hallmark of human cancers, including HCC. Identification of regions with consistently altered 5mC levels in circulating cell free DNA (cfDNA) during progression from cirrhosis to HCC could therefore serve as markers for development of minimally-invasive screens of early HCC diagnosis and surveillance.
Methods. To discover DNA methylation derived biomarkers of HCC in the background of liver cirrhosis, we profiled genome-wide 5mC landscapes in patient cfDNA using the Infinium HumanMethylation450k BeadChip Array. We further linked these findings to primary tissue data available from TCGA and other public sources. Using biological and statistical frameworks, we selected CpGs that robustly differentiated cirrhosis from HCC in primary tissue and cfDNA followed by validation in an additional independent cohort.
Results. We identified CpGs that segregate patients with cirrhosis, from patients with HCC within a cirrhotic liver background, through genome-wide analysis of cfDNA 5mC landscapes. Lasso regression analysis pinpointed a panel of probes in our discovery cohort that were validated in two independent datasets. A panel of five CpGs (cg04645914, cg06215569, cg23663760, cg13781744, and cg07610777) yielded AUROCs of 0.9525, 0.9714, and 0.9528 in cfDNA discovery and tissue validation cohorts 1 and 2, respectively.
Conclusions. 5mC markers derived from cfDNA robustly identify HCC within a cirrhotic liver background indicating that further validation is warranted. Our finding that 5mC markers derived from primary tissue did not perform well in cfDNA, compared to those identified directly from cfDNA, reveals potential advantages of starting with cfDNA to discover high performing markers for liquid biopsy development.

overall_design: Infinium 450k profiling of cfDNA for DNA methylation-based biomarkers of HCC in cirrhotic patients

first: Ryan

last: Hlady


title: Transcriptome analysis of U1 snRNA overexpression in human neurons

status: Public on Jan 01 2020

city: Tianjin

first: Sha

last: Zhou

address: Nankai University

department: The State Key Laboratory of Medicinal Chemical Biology

institute: Nankai University

summary: U1 snRNA is the small nuclear RNA that services as the backbone of U1 snRNP. Removing intron from pre-mRNA to produce mature mRNA is the core function of the U1 snRNA. As one of the most abundant small noncoding RNA in human cells – estimated to be in the region of 1x10^6 copies per human neuron cell– U1 snRNA level is much more abundant than the other snRNAs. However, the potential role of the different amounts of the snRNAs is still unknown. To study the function of U1 snRNA in human neurons, we used lentivirus vector to overexpression U1 snRNA. We analyzed the gene expression change and identified target genes of U1 snRNA overexpression. We uncovered a novel role of U1 snRNA in regulating gene expression in human neurons.

overall_design: The transcriptome of U1 snRNA overexpression neurons and empty vector control neurons were analyzed by RNA-seq. The expression change of genes and transposable elements were analyzed to study the role of U1 snRNA in human neurons.

first: Zhi

last: Cheng

first: Yongwang

first: Xinyi

last: Lu

first: Tao


title: Chromatin organization in the female brain fluctuates across the estrous cycle

status: Public on May 03 2019

city: Bronx

first: Marija

last: Kundakovic

address: 441 E. Fordham Road

institute: Fordham University

summary: Brain structure and function are sexually dimorphic. As neuroscience research has largely focused on the male brain and behavior, the female brain and, in particular, its inherent dynamics have been left underexplored. During the mammalian reproductive period, the female brain is exposed to fluctuating hormone levels over the cycles known as menstrual (in humans) or estrous (in rodents). Variation in estradiol levels has been shown to affect synaptic plasticity in the female brain, including changes in dendritic spine density systematically across the estrous cycle. Female emotionality and cognitive function vary with physiologically fluctuating sex hormone levels. However, the molecular mechanisms underlying the dynamic nature of the female brain structure and function are currently unknown. Here we show that neuronal chromatin organization in the female ventral hippocampus of mouse is dynamic and fluctuates across the estrous cycle. We find changes in chromatin organization associated with the transcriptional activity of nearby genes important for neuronal function, neurotransmission, synapse formation, and behavior. We also link these chromatin dynamics to variation in anxiety-like behavior and to fluctuations in dendritic spine and synaptic density in the ventral hippocampus. In terms of chromatin structure, within-female and between-sex variation are of similar magnitudes, emphasizing the importance of accounting for fluctuating sex-hormone levels in females in the studies of the brain epigenome and behavior. These results provide critical insights into the mechanisms underlying sex-hormone and sex-dependent variation in adult brain structure and function. The study also has implications for better understanding of sex-biased disorders such as depression and anxiety which are strongly associated with sex-hormone status in females and are twice as prevalent in women than in men. This study establishes a foundation for the development of sex-specific approaches to treat sex-biased neuropsychiatric disorders including depression and anxiety disorders.

overall_design:
ATAC-seq experiments were designed to determine chromatin accessibility profiles of ventral hippocampal neurons in young adult females in two different stages of the estrous cycle  (preostrus and diestrus) and in age-matched males. Three biological replicates (each pooled from two animals) were tested per group.

nucRNA-seq experiments were designed to determine differential nuclear RNA expression in ventral hippocampal neurons in young adult females in two different stages of the estrous cycle  (preostrus and diestrus) and in age-matched males. Three biological replicates (each pooled from two animals) were tested per group.

first: Ivana

last: Jaric

first: Devin

last: Rocks

first: John

last: Greally

first: Masako

last: Suzuki


title: Integrating the Epigenome to Identify Novel Drivers of Hepatocellular Carcinoma

status: Public on Sep 09 2018

summary: Gene expression, histone modification, DNA methylation, and DNA hydroxymethylation from normal, cirrhotic, and HCC livers

overall_design: 10 total samples (2 normal, 4 cirrhosis, 4 HCC). Cirrhosis and HCC are from the same four patients.


title: Short tandem repeats susceptible to pathogenic instability linked to chromatin domain disruption

status: Public on Aug 29 2018

first: Jennifer

last: Phillips-Cremins

summary: More than 25 inherited human disorders are caused by the unstable expansion of repetitive DNA sequences termed short tandem repeats (STRs). A fundamental unresolved question is why some STRs are susceptible to pathologic expansion, whereas thousands of repeat tracts across the human genome are relatively stable. Here, we discover that nearly all disease-associated STRs (daSTRs) are located at boundaries demarcating 3D chromatin domains. We identify a subset of boundaries with markedly higher CpG island density compared to the rest of the genome. daSTRs specifically localize to ultra-high-density CpG island boundaries, suggesting they might be hotspots for epigenetic misregulation or topological disruption upon STR expansion. Fragile X Syndrome (FXS) patients exhibit severe boundary disruption in a manner that correlates with local loss of CTCF occupancy and the degree of FMR1 silencing. Our data uncover higher-order chromatin architecture as a new dimension in understanding repeat expansion disorders.

overall_design: Chromosome-Conformation-Capture-Carbon-Copy (5C) was used to interrogate the three-dimensional structure of the genome at the FMR1 locus in 2 normal and 3 FXS B-lymphocyte samples, 1 normal and 1 FXS fibroblast samples, and 2 normal and 2 FXS postmortem cerebellum tissue samples.     CTCF ChIP-seq was used to map the binding profile of CTCF genome-wide in 1 normal and 2 FXS B-lymphocyte samples. Two biological replicates of each sample are included.

first: James

last: Sun

first: Linda

middle: E


title: LADL: Light-activated dynamic looping for endogenous gene expression control

status: Public on Jun 24 2019

summary: Mammalian genomes are folded into tens of thousands of long-range looping interactions1,2. The cause and effect relationship between looping and genome function is poorly understood, and the extent to which chromatin loops are dynamic on short time scales remains a fundamental unanswered question. Currently available strategies for loop engineering involve synthetic transcription factors tethered to dCas93,4or zinc fingers5,6, which are constitutively expressed5,6or induced on long time scales by the presence of a small molecule3.Here we report a new class of 3D optoepigenetic toolsfor the directed rearrangement of 3D chromatin looping on short time scales using blue light. We create synthetic architectural proteins by fusing the CIBN protein subunit from Arabidopsis thaliana with enzymatically dead Cas9 (dCas9). We target our light-activated dynamic looping system (LADL) to two genomic anchors with CRISPR guide RNAs and engineer their spatial co-localization via light-induced heterodimerization of the cryptochrome 2 (CRY2) protein with dCas9-CIBN. We apply LADL to redirect a stretch enhancer(SE)away from its endogenous Klf4target gene and to the Zfp462promoter. Looping changes occur as early as four hours after light induction. Using single molecule RNA FISH, we observe a LADL-induced increase in the total nascent Zfp462transcripts and the number of Zfp462 alleles expressing simultaneously per cell.Moreover, LADL also increased synchronous Sox2 expression after reinforcement of a known Sox2-SElooping interaction. LADL facilitates loop synchronization across a large population of cells without exogenous chemical cofactors and can enable future efforts to engineer reversible and oscillatory looping on short time scales.

overall_design: Total of 20 5C samples from 5 independent replicate experiments on LADL-engineered mES cells and negative controls after blue light illumination or in dark.

first: Ji Hun

middle: H

last: Kim

first: Mayuri

last: Rege

first: Jacqueline

last: Valeri