title: FOXQ1 is a critical regulator of the mammary epithelial to mesenchymal transcription program

status: Public on Dec 01 2020

city: Detroit

first: Allison

last: Mitchell

state: MI

address: 4100 John R Rd

department: Oncology

institute: Wayne State University

summary: Purpose: The goals of this study were to uncover the epithelial to mesenchymal transcription program under direct regulation by FOXQ1 and to characterize the KMT2/MLL histone methyl transferase complex as a transcriptional co-activator for the FOXQ1 EMT program.

overall_design: We compare the transcription program of human mammary luminal epithelial cells (HMLE) with stable overexpression of FOXQ1 to a vector control (HMLE/LACZ) by RNA-seq. We also preform ChIP-seq of FOXQ1 (V5-epitotpe tage), RbBP5 and H3K4me3 in HMLE/FOXQ1 cells to identify direct gene targets.

first: Guojun

last: Wu


title: Whole blood transcriptome analysis of feedlot cattle with and without bovine respiratory disease

status: Public on Nov 26 2020

city: Edmonton

first: Graham

last: Plastow

state: Alberta

address: 1400 College Plaza, 8215 - 112 Street

department: Agricultural, Food & Nutritional Science

country: Canada

institute: University of Alberta

type: Expression profiling by high throughput sequencing

summary: In this study we aimed to identify differentially expressed (DE) genes involved in the host immune response to BRD using whole blood and RNA sequencing. Samples were collected from heifers (average arrival weight = 215.0 ± 5.3 kg) with (n = 25) and without (n = 18) BRD at a commercial feedlot in Western Canada. RNAseq analysis showed a distinct whole blood transcriptomic profile between BRD and non-BRD heifers. Further examination of the DE genes revealed that those involved in the host inflammatory response and infectious diseases pathways were enriched in BRD animals, while gene networks associated with metabolism and cell growth and maintenance were downregulated.  Overall, the transcriptome profile derived from whole blood provided evidence that a distinct antimicrobial peptide driven host immune response was occurring in the animals with BRD.

overall_design: 43 samples were collected from 25 cattle diagnosed with BRD and 18 pen matched controls at one time point.

middle: S

first: Edouard

middle: F

last: Timsit

first: Leluo

last: Guan

first: Karin

last: Orsel

first: Frank

last: vanderMeer


title: A Pilot Study for Protective Roles of tRNA-Derived Small RNA tRF-Ile-AAT-019 in Pathological Progression of Psoriasis

status: Public on Feb 19 2021

city: Changsha

first: Zeng

last: Jinrong

address: No.138 Tongzipo Rd, Yuelu District, Changsha, Hunan, China, 410013

country: China

institute: the Third Xiangya Hospital, Central South University

type: Non-coding RNA profiling by high throughput sequencing

summary: Psoriasis is a chronic recurrent inflammatory skin disease that is characterized by abnormal proliferation and differentiation of keratinocytes (KCs), angiogenesis and skin inflammation. tRNA-derived small RNA (tsRNA), including tRNA halves and tRNA fragments (tRFs), is a novel class of short non-coding RNA, possessing regulatory functions in many diseases. However, its role in the pathological development of psoriasis has been unknown. In this pilot study, we conducted small RNA sequencing to screen differentially expressed tRFs in psoriatic skin lesions as compared with normal controls. We found 130 upregulated and 104 downregulated tRFs, among which downregulation of tRF-Ile-AAT-019 in psoriatic skin lesions was further confirmed. Bioinformatics analysis by TargetScan and Miranda algorithms revealed that tRF-Ile-AAT-019 might target SERPINE1, thus regulating HIF-1α signaling pathway. We next showed that increased tRF-Ile-AAT-019 could downregulate expressions of SERPINE1, HIF-1α and vascular proliferative markers such as CD34, CD31, Factor VIII, and VEGF, but upregulate expressions of KCs differentiation markers including Keratin1 and Involucrin. Our data suggest that tRF-Ile-AAT-019 plays a protective role in the pathological progression of psoriasis via targeting SERPINE1 and blocking HIF-1α signaling pathway, leading to control KCs differentiation and vascular proliferation. This data provides a potential novel targeting pathway for the disease treatment.

overall_design: The tRF/tiRNAs-Seq analysis was used to assess the expression levels of tRF/tiRNAs in skin lesions of 3 psoriasis patients (P) and 3 normal volunteers (N).

first: Jinrong

last: Zeng

first: Zhibing

last: Fu

first: Yuezhong

last: Zhang

first: Hanyi

first: Lihua

last: Gao

first: Jianyun

last: Lu

first: Yue

first: Qian

last: Hu

first: Yajie

last: Xie

first: Wenbin

last: Tan

first: Xiaoliang

last: Tong


title: Network preservation reveals shared and unique biological processes associated with chronic alcohol abuse in the NAc and PFC [mRNA]

status: Public on Nov 24 2020

city: New York

first: Eric

last: Vornholt

state: NY

address: 800 E. Leigh St. Box 980126

country: USA

institute: Icahn School of Medicine

summary: Chronic alcohol abuse has been linked to the disruption of executive function and allostatic conditioning of reward response dysregulation in the mesocorticolimbic pathway (MCL). Here, we analyzed genome-wide mRNA and miRNA expression from matched cases with alcohol dependence (AD) and controls (n=35) via gene network analysis to identify unique and shared biological processes dysregulated in the prefrontal cortex (PFC) and nucleus accumbens (NAc). We further investigated potential mRNA/miRNA interactions at the network and individual gene expression levels to identify the neurobiological mechanisms underlying AD in the brain. By using genotyped and imputed SNP data, we identified expression quantitative trait loci (eQTL) uncovering potential genetic regulatory elements for gene networks associated with AD. At a Bonferroni corrected p≤0.05, we identified significant mRNA (NAc=6; PFC=3) and miRNA (NAc=3; PFC=2) AD modules. The gene-set enrichment analyses revealed modules preserved between PFC and NAc to be enriched for immune response processes, whereas genes involved in cellular morphogenesis/localization and cilia-based cell projection were enriched in NAc modules only. At a Bonferroni corrected p≤0.05, we identified significant mRNA/miRNA network module correlations (NAc=6; PFC=4), which at an individual transcript level implicated miR-449a/b as potential regulators for cellular morphogenesis/localization in NAc. Finally, we identified eQTLs (NAc: mRNA=37, miRNA=9; PFC: mRNA=17, miRNA=16) which potentially mediate alcohol’s effect in a brain region-specific manner. Our study highlights the neurotoxic effects of chronic alcohol abuse as well as brain region specific molecular changes that may impact the development of alcohol addiction.

overall_design: Postmortem brain tissue was provided by the Australian Brain Donor Programs of New South Wales Tissue Resource Centre (NSW TRC) under the support of The University of Sydney, National Health and Medical Research Council of Australia, Schizophrenia Research Institute, National Institute of Alcohol Abuse and Alcoholism, and the New South Wales Department of Health. Samples were excluded based on: (1) history of infectious disease, (2) circumstances surrounding death, (3) substantial brain damage, and (4) post-mortem interval > 48 hours. Total RNA was isolated from PFC (the superior frontal gyrus) and NAc tissue using the mirVANA-PARIS kit (Life Technologies, Carlsbad, CA) following the manufacturer’s suggested protocol. RNA concentrations and integrity (RIN) were assessed via Quant-iT Broad Range RNA Assay kit (Life Technologies) and Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA) respectively. Samples were matched for RIN, age, sex (all male), ethnicity, brain pH, and PMI as part of a previous study yielding a total of 18 case-control matched pairs (n=36). Due to our matching, the RINs in PFC were slightly lower (mean=4.5, ±2.04) compared to NAc (mean=6.9, ±0.84).

first: Vladimir

middle: I

last: Vladimirov


title: CRISPR genome-wide synthetic lethality screens of KRAS-driven mouse pancreatic ductal adenocarcinoma cells

status: Public on Nov 25 2020

city: Houston

first: Yulin

last: Li

state: Texas

address: 6670 Bertner Avenue

institute: Houston Methodist Research Institute

summary: We performed CRISPR genome-wide synthetic lethality screens to identify genetic vulnerabilities and chemogenetic interactions in KRAS-driven pancreatic cancer. We identify ERAD as a genetic target that synergizes with FTS treatment and we show that FTS treatment induces ER stress, which was further enhanced by inhibition of ERAD, leading to synergistic induction of apoptosis in pancreatic tumor cells. Altogether, our screens enable us to identify combination therapies for cancer treatment.

overall_design:
Screens were performed using the 4292 doxycycline-inducible Kras-G12D pancreatic ductal adenocarcinoma cell line in duplicate with two independent viral infections.

Please note that, on Nov 29, 2021,
1) The fastq files (for samples RA, RB, FA, FB) have been replaced as they were trimmed via cutadapt. The updated files are raw files before any processing
2) The *counts.txt files (for samples RA, RB, FA, FB) have been replaced as the original ones had some minor formatting issues with line breaks
3) Additional samples (samples GA, GB, KA, KB) have been added.

first: Nancy

middle: G

last: Azizian

first: Delaney

middle: K

last: Sullivan


title: Global transcriptome analysis of Rhizobium favelukesii LPU83 in response to acid stress.

status: Public on Nov 12 2020

city: La Plata

first: Gonzalo

middle: A

last: Torres Tejerizo

state: Buenos Aires

address: Calle 49 y 115

country: Argentina

institute: Instituto de Biotecnología y Biología Molecular

summary: Acid environments are worldwide distributed due to their natural conditions or by the inappropriate use of the intensive agriculture. The moderately low pHs from the soils are an important barrier in the plant-rhizobia interaction. These low pHs affect the establishment of the efficient rhizobia usually used as biofertilizer. This negative effect in the rhizobia-legume is mainly due the low acid-tolerance of the bacteria. Here, we described and identified relevant factors in the acid tolerance of Rhizobium. favelukesii, using RNA-Seq. A total of 1924 genes were differentially expressed under acidic condition, with ca. 60% underexpressed. Remarkably, 60% of the CDS of the symbiotic plasmid were also underexpressed. The in silico functional analysis showed that R. favelukesii acid response involves both general and specific response. Regarding the general response, it includes mainly changes in energetic metabolism and protein turnover, while the specific response is a combination of mechanisms that would contribute to the general phenotype of acid-tolerant in R. favelukesii. GABA and Histidine metabolism, cell envelope changes and reverse proton efflux were significant. Moreover, we confirmed a phenotype acid sensible of a mutant in braD, this gene showed a higher expression under acid stress. Remarkably, we evidenced that a strain without pSym presented an improved performance in acidic condition. Hence, this work supply relevant information in the characterization of genes associated with tolerance or adaptation to abiotic stresses of R. favelukesii LPU83 using transcriptomic tools.

overall_design: Examination of 2 different growing conditions of a bacteria strain

middle: T

last: Tejerizo

first: Juliet

last: Nilsson

first: Mariano

last: Pistorio


title: Network preservation reveals shared and unique biological processes associated with chronic alcohol abuse in the NAc and PFC [miRNA]


title: Network preservation reveals shared and unique biological processes associated with chronic alcohol abuse in the NAc and PFC

type: Genome binding/occupancy profiling by high throughput sequencing

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: LncRNA and mRNA profiling of the ischemia zone, the border zone and the remote non-ischemia zone of murine myocardial ischemia/reperfusion (MI/R) hearts

status: Public on Nov 11 2020

city: harbin

first: yang

last: zhang

address: baojian road #157

institute: harbin medical university

summary:
Purpose：Detection of differentially expressed lncRNA in the infarct zone and the control group in myocardial ischemia-reperfusion injury model tissue.
Method: Use 8 weeks of C57BL/6 mice to establish a myocardial ischemia-reperfusion injury model, 45 minutes of ischemia, and 24 hours after reperfusion, the mice were sacrificed to obtain materials.
Result: The expression of lncRNAs in the infarct area of myocardial ischemia-reperfusion injury model mice was detected, and it was found that a total of 43 lncRNAs related to myocardial ischemia-reperfusion injury changed in expression, of which 17 were up-regulated (fold change >1.5). 26 expressions are down-regulated (fold change <0.8)

overall_design: Three C57BL/6 mice (8 weeks old) were subjected to the 45 mins ligation of left anterior descending coronary artery followed 24h reperfusion. Then The heart were removed after the mice were euthanized and the left ventricle tissue were separated into normal zone, ischemia zone and ischemia border zone. Total RNA was isolated with TRIzol (Invitrogen) from heart tissue according to manufacturer’s instructions.LncRNA and mRNA expression profiling was performed using Affymetrix GeneChip Mouse Transcriptome Assay 1.0 according to the manufacturer’s instructions (Affymetrix, Inc., Santa Clara, CA).

first: Yang

first: Zhenwei

last: Pan


title: Genome-wide enhancer identification by massively parallel reporter assay in Arabidopsis

status: Public on Oct 13 2020

city: Shenzhen

first: Chunhui

last: Hou

state: Guangdong

address: Nanshan distinct

institute: Southern University of Science and Technology

summary: Enhancers are critical cis-regulatory elements controlling gene expression during cell development and differentiation. However, genome-wide enhancer characterization has been challenging due to the lack of a well-defined relationship between enhancers and genes. Here, we applied a massively parallel reporter assay on Arabidopsis to measure enhancer activities across the genome. We identified 4327 enhancers with various combinations of epigenetic modifications distinctively different from animal enhancers. Furthermore, we showed that enhancers differ from promoters in their preference for transcription factors. Although some enhancers are not conserved and overlap with transposable elements forming clusters, enhancers are generally conserved across thousand Arabidopsis species, suggesting they are selected under evolution pressure and could play critical roles in the regulation of important genes. Moreover, comparison analysis reveals that enhancers identified by different strategies do not overlap, suggesting these methods are complementary in nature. In sum, our work provides an additional catalog of enhancers and lays the foundation for further investigation into enhancers’ functional mechanisms in plants.

overall_design: 2 STARR-seq cDNA replicates and 2 STARR-seq plasmid replicates, in Arabidopsis 2-week seedlings

first: Yongjun

first: Longjian

last: Niu

first: Xiaohao

last: Yan

first: Jing

last: Wan

first: Xinxin

first: Jialei

last: Sun

first: Yingzhang

last: Huang

first: Li


title: Transcriptomic response of LSD1-UTX inhibitor on human breast cancer MCF7 cells

status: Public on Oct 15 2020

city: Rotterdam

first: Ning Qing

last: Liu

address: Wytemaweg 80

department: Hematology

country: Netherlands

institute: Erasmus University Medical Center Rotterdam

summary: In many human cancers, including breast and prostate cancers, LSD1 and other lysine demethylases (KDMs), such as UTX, are co-expressed and co-localize with androgen receptors (AR) and estrogen receptors (ER), suggesting the potential use of hybrid molecules to target histone methylation and therefore to regulate/redirect hormone receptor signaling.   Here, we report on the action of a pan-KDM inhibitor (3324), obtained by coupling the chemical properties of tranylcypromine, a known LSD1 inhibitor, with the 2OG competitive moiety developed for JmjC inhibition.   The 3324 hybrid molecule displays unique features not exhibited by moieties and well-characterized single inhibitors. The compound efficiently inhibits LSD1 as well as UTX enzymes, inducing significant growth arrest and apoptosis in hormone-responsive cells accompanied by a robust increase in H3K4me2 and H3K27me3. Treatment with 3324 reduces the level of ERα in breast and AR in prostate cancer cells at both transcriptional and non-transcriptional levels, acting as a selective endocrine receptor disruptor (SERD). Treatment with 3324 alters the methylation status of ER-regulated promoter regions, thereby affecting the transcription of genes involved in cell surveillance, death, and immune response. 3324 reduces cell proliferation in ex vivo breast cancers by interfering with hormone receptor signaling and/or receptor stability, as well as in cell models with acquired resistance to endocrine therapies (BT474, C4-2 and C4-2b). Similarly, 3324 displays tumor-selective potential in vivo, in both xenograft and chicken embryo models, with no toxicity and good oral efficacy.   This multi-target approach may overcome potential mechanism(s) of resistance caused in part by redundancy and robustness of biological pathways, and find potential application in the treatment of resistant-to-therapy cancers such as those with acquired tamoxifen/enzalutamide resistance.

overall_design: Examine expression changes between control and pan-KDM inhibitor 3324 treated MCF7 cells

first: Rosaria

last: Benedett

first: Ning

middle: Q

first: Lucia

last: Altucci


title: Transcription profiling of intestinal changes in APC deficient intestines following oncogenic Kras activation

status: Public on Oct 23 2020

city: GLASGOW

first: Karen

last: Pickering

state: Scotland

address: Garscube Estate, Switchback Road, Bearsden

country: United Kingdom

institute: CRUK Beatson institute

summary: Loss of APC with or without KRAS activation under the control of VilCreER

overall_design: RNA-seq expression data from murine intestine comparing VilCreER Apcfl/fl vs VilCreER Apcfl/fl KrasG12D/+

first: Owen

middle: J

last: Sansom


title: Plasma small RNA-Seq profile of healthy subjects with different dietary habits

status: Public on Nov 17 2020

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

summary: Small RNA-Seq analysis of circulating small RNAs performed on plasma samples from an Italian  cohort of 120 healthy individuals with three dietary habits. The cohort includes 72 women and 48 men included an equal proportion of vegetarians, vegans and omnivores.

overall_design: Plasma small RNA-Seq profile 120 healthy subjects with three dietary habits: omnivorous, vegetarian, and vegan

first: Sonia

last: Tarallo

first: Alessio

last: Naccarati

first: Barbara

last: Pardini

first: Sara

last: Carpi

first: Beatrice

last: Pollini

first: Paola

last: Nieri

first: Alessia

last: Impeduglia

last: Grioni


title: Augmented murine hematopoietic stem and progenitor cell reconstruction through conventional co-housing

status: Public on Oct 02 2020

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: National Institutes of Health

summary:
Background and methods: The effects of microbiota toward hematopoietic stem and progenitor cells (HSPCs) were very much complicated based on previous reports. In the current study, normal inbred C57BL6 (B6) mice from the Jackson Laboratory were maintained in the SPF environment for three weeks. Baseline complete blood counts were normal, and animals were then separated into two groups: 1) SPF mice stayed in the SPF facility, and 2) SPF mice being transferred to a conventional facility for co-housing (CVT). At one month of co-housing, we bled and euthanized animals, sorted lineage-CD117+ cells from bone marrow of SPF and CVT mice respectively, and performed single cell RNA sequencing on sorted hematopoietic stem and progenitor cells using 10XGenomics Chromium Single Cell 3' Solution and sequenced with Illumina HiSeq 3000 Systems.
Results: We characterized heterogeneity of HSPCs, defined differential gene expression and performed pathway analysis. Proportion of LTHSC was lower and the proportion of GMP was higher from CVT mice than those from SPF mice. Pathway analyses of differentially-expressed genes in HSPCs we found down-regulation of genes related to immune responses and cell proliferation and activation, and up-regulation of genes associated with cellular metabolism, including protein, ribosome, and energy metabolic processes, in cells from CVT mice.
Conclusion: Observations from our study demonstrated a positive effect in co-housed CVT mice that promotes HSPC reconstitution through modulation of molecular elements involving multiple signaling pathways.

overall_design:
mRNA profiles of single bone marrow hematopoietic stem and progenitor cells of ten B6 mice maintained in a SPF facility and ten B6 mice maintained in conventioanl facility were generated by deep sequencing using quencing using Illumina HiSeq 3000
FACS sorted bone marrow hematopoietic stem and progenitor cells from ten mice maintained in SPF facility were pooled into four samples, and sorted cells from ten mice maintained in conventional facility for one month were pooled into four samples.

first: Zhijie

last: Wu


title: Next Generation Sequencing  of Wild Type (Col-0) , LNJ overexpressor and jazD Transcriptomes in Arabidopsis thaliana

status: Public on Sep 25 2020

city: Frederiksberg C

first: Bin

last: Sun

address: Thorvaldsensvej 40

department: Department of Plant and Environmental Sciences

country: Denmark

institute: Copenhagen Plant Science Centre – University of Copenhagen

summary: Plants were grown for 21 days under LD conditions and RNA was extracted and sequenced

overall_design: Examination of three genotypes (wild type/ LNJ-OX / jazD) and one condition with two replicates each

first: Stephan

last: Wenkel


title: Single cell RNA seq of hepatic and renal p16 positive cells

status: Public on Sep 16 2020

city: Minato ku

first: Satotaka

last: Omori

state: tokyo

address: shirokanedai, 4-6-1

country: Japan

institute: the university of Tokyo

summary: We performed the single cell RNA sequencing of mouse normal kidney, normal liver, and NASH-induced liver from p16-tdTomato mice. In order to enrich p16 positive cells, we independently sorted the non-separated cells (including both of p16 positive and negative cells) and p16 positive cells alone through tdTomato intensity by FACS. By obtaining 13,876 single cell transcripts, after the graph-based clustering and marker genes defined cell type classification, we identified the heterogeneity of in vivo p16-positive cells which dispersedly existed in renal cells and non-parenchymal hepatic cells. Differential expressing genes (DEGs) comparisons for each cell type were feasible to study the in vivo p16 dependent transcriptomic pattern change. Finally, we verified several cell type specific senescence-like phenotypes which were previously found on in vitro cellular senescence, and also identified the p16-related subpopulation which might involve in NASH progression and renal damage response.

overall_design: single cell transcriptome of normal kidney, normal liver, and NASH liver with enriched p16 positive cells

first: Teh-Wei

last: Wang


title: The mole genome reveals regulatory rearrangements associated with adaptive intersexuality (ChIP-Seq)

status: Public on Oct 09 2020

city: Berlin

first: Francisca

last: Martinez Real

address: Ihnestrasse 73

country: Germany

institute: Max Planck Institute for Molecular Genetics

summary: Linking genomic variation to phenotypical traits remains a major challenge in evolutionary genetics. In this study, we use phylogenomic strategies to investigate a distinctive trait among mammals: the development of masculinizing ovotestes in female moles. By combining a chromosome-scale genome assembly of the Iberian mole, Talpa occidentalis, with transcriptomic, epigenetic, and chromatin interaction datasets, we identify rearrangements altering the regulatory landscape of genes with distinct gonadal expression patterns. These include a tandem triplication involving CYP17A1, a gene controlling androgen synthesis, and an intrachromosomal inversion involving the pro-testicular growth factor FGF9, which is heterochronically expressed in mole ovotestes. Transgenic mice with a knock-in mole CYP17A1 enhancer or overexpressing FGF9 showed phenotypes recapitulating mole sexual features. Our results highlight how integrative genomic approaches can reveal the phenotypic impact of noncoding sequence changes.

overall_design: We used ChIP-seq for a combination of histone modifications to identify regulatory elements involved in the ovotestis development of moles. We have performed ChIP-seq experiments in gonads from mole and mouse for comparisions to find the common and unique regulatory elements.


title: Bulk and single cell sequencing (bc-Smart-seq2  and 10XGenomics) of  human microglia from post mortem AD CNS tissue

status: Public on Sep 10 2020

city: Groningen

first: Bart

last: Eggen

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences

institute: UMCG Groningen

summary: Microglia are the tissue-resident macrophages of the central nervous system (CNS). Recent studies based on bulk and single-cell RNA sequencing in mice indicate high relevance of microglia with respect to risk genes and neuro-inflammation in Alzheimer’s disease. Here, we investigated microglia transcriptomes at bulk and single cell level in non-demented elderly and AD donors using acute human post-mortem cortical brain samples. We identified 7 human microglial subpopulations with heterogeneity in gene expression. Notably, gene expression profiles and subcluster composition of microglia did not differ between AD donors and non-demented elderly in bulk RNA sequencing nor in single-cell sequencing.

overall_design: To investigate transcriptomic changes in microglia during AD, bulk and single-cell RNA sequencing (scRNAseq) were performed. Post-mortem tissue samples of the superior parietal lobe (LPS) and superior frontal gyrus (GFS) were obtained from 27 donors. The samples were classified into 3 experimental groups based on a clinical diagnostic report provided by the Netherlands Brain Bank/ NeuroBiobank Born-Bunge and immunohistochemical analysis of Aβ and hyperphosphorylated tau (PHF-tau): CTR (no dementia, absence of Aβ plaques and PHF-tau), CTR with plaques (CTR+, no dementia, presence of Aβ plaques and/or PHF-tau) and AD (dementia, AD diagnosis, presence of Aβ plaques and/or PHF-tau). One donor diagnosed with mild cognitive impairment (MCI) and presence of Aβ and PHF-tau plaques was included in the single-cell studies. The stratification of CTR and CTR+ donors ensured that the CTR group was free of undiagnosed AD donors. Microglia were isolated from mechanically dissociated tissue using fluorescence-activated cell sorting (FACS) of single, viable CD11B and CD45 positive cells. Twenty-five microglia samples (13 LPS and 12 GFS) from 17 donors were sequenced as bulk samples, and 14 LPS samples from 14 donors were single-cell sequenced. Two donors were sequenced with both the 10X Genomics platform and the barcoded-SmartSeq2 protocol. Four donors (1 CTR, 3 CTR+) were included in both single-cell and bulk cohorts.

first: E

middle: W

last: Boddeke


title: Revealing the Key Regulators of Cell Identity in the Human Adult Pancreas [scRNA-seq]

status: Public on Sep 23 2020

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

country: Belgium

institute: KU Leuven

summary: Cellular identity during development is under the control of transcription factors that form gene regulatory networks. However, the transcription factors and gene regulatory networks underlying cellular identity in the human adult pancreas remain largely unexplored. Here, we integrate multiple single-cell RNA-sequencing datasets of the human adult pancreas, totaling 7393 cells, and comprehensively reconstruct gene regulatory networks. We show that a network of 142 transcription factors forms distinct regulatory modules that characterize pancreatic cell types. We present evidence that our approach identifies key regulators of cell identity in the human adult pancreas. We predict that HEYL, BHLHE41 and JUND are active in acinar, beta and alpha cells, respectively, and show that these proteins are present in the human adult pancreas as well as in human induced pluripotent stem cell (hiPSC)-derived islet cells. Using single cell transcriptomics, we found that JUND represses beta cell genes in hiPSC-alpha cells. Both BHLHE41 and JUND depletion seemed to increase the number of sc-enterochromaffin cells in hiPSC-derived islets. The comprehensive gene regulatory network atlas can be explored interactively online. We anticipate our analysis to be the starting point for a more sophisticated dissection of how transcription factors regulate cell identity in the human adult pancreas. Furthermore, given that transcription factors are major regulators of embryo development and are often perturbed in diseases, a comprehensive understanding of how transcription factors work will be relevant in development and disease.

overall_design:
Raw reads for five publicly available scRNA-seq datasets (GEO: GSE86469, GEO: GSE81608, GEO: GSE83139, GEO: GSE81547, ArrayExpress: E-MTAB-5061) were downloaded from SRA using SRA toolkit (v2.9.4). Afterwards, reads were aligned to the human reference genome GRCh38.95 using STAR (v2.5.3a) with default parameters followed by the conversion to the coordinate sorted BAM format. Next, the featureCounts command from the “Rsubread” (v1.5.2) package in R (v3.6.1) was used to assign mapped reads to genomic features. Low quality transcriptomes with a mitochondrial contamination greater than 5% and less than 200 expressed genes per cell were excluded from subsequent analyses. The resulting raw count matrix was batch corrected using the FindIntegrationAnchors and IntegrateData functions from the “Seurat” package (v3.1.1). The integrated single-cell RNA-seq data and pySCENIC results were used to create a loom file which can be uploaded to SCope. The embedding of the regulon and integrated gene expression based UMAP clustering were added to the loom file.
Gene regulatory networks were inferred using pySCENIC (python implementation of SCENIC, v0.9.15) in Python version 3.6.9. Integrated read counts were used as input to run GENIE3 which is part of arboreto (v0.1.5). GRNs were subsequently inferred using pySCENIC with the hg38_refseq-r80 motif database and default settings. To control for the stochasticity, which is inherent to pySCENIC, a consensus GRN was generated by merging results from five repeat pySCENIC runs. If regulons were identified in multiple pySCENIC runs, only the regulon with the highest AUC value was retained.

first: Lotte

last: Vanheer

first: Federica

last: Fantuzzi

first: San

last: To

first: Andrea

last: Schiavo

first: Matthias

last: Van Haele

first: Tine

last: Haesen

first: Xiaoyan

last: Yi

first: Adrian

last: Janiszewski

first: Joel

last: Chappell

first: Adrien

last: Rihoux

first: Toshiaki

last: Sawatani

first: Tania

last: Roskams

first: François

last: Pattou

first: Julie

last: Kerr-Conte

first: Miriam

last: Cnop


title: The mole genome reveals regulatory rearrangements associated with adaptive intersexuality

first: Francisca

last: Martinez Real

sample_organism:
Mus musculus
Talpa occidentalis

platform_organism:
Mus musculus
Talpa occidentalis


title: Sialyl-Lewis-X Glyco-antigen Is Enriched on Cells with Persistent HIV Transcription During Therapy

status: Public on Aug 24 2020

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: A comprehensive understanding of the phenotype of persistent HIV-infected cells, both transcriptionally-active and/or -inactive, is imperative for developing a cure. The relevance of cell-surface glycosylation to HIV persistence has never been explored. We characterized the relationship between cell-surface glycomic signatures and persistent HIV transcription in vivo. We found that the cell-surface of CD4+ T cells actively transcribing HIV, despite suppressive therapy, harbors high levels of fucosylated carbohydrate ligands, including the cell extravasation mediator Sialyl-Lewis-X (SLeX), compared to HIV-infected transcriptionally-inactive cells. These high levels of SLeX are induced by HIV transcription in vitro and are maintained after therapy in vivo. Cells with high SLeX are enriched with markers associated with HIV susceptibility, signaling pathways that drive HIV transcription, and pathways involved in leukocyte extravasation. Together, we describe a novel glycomic signature of HIV-infected transcriptionally-active cells that not only differentiates them from their transcriptionally-inactive counterparts, but also can impact their trafficking abilities.

overall_design: RNA-seq of high and low SLEX cells

first: Abdel-Mohsen

last: Mohamed

first: Colomb

last: Florent


title: Osteopontin expression identifies a subset of recruited macrophages distinct from Kupffer cells in the fatty liver. [Single cell RNA Seq]

status: Public on Aug 18 2020

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

institute: VIB-University of Ghent

summary: CITE-seq analysis on total CD45+ cells isolated from the livers of mice fed a standard diet (SD) or western diet (WD; fat, cholesterol and sugar) for 12, 24 and 36 weeks. We also performed single cell RNA sequencing analysis of the CD45- cells isolated from the livers of the mice fed the SD or WD for 24 and 36 weeks.

overall_design:
Single cell RNA Seq = Liver CD45+ and CD45- cells derived from mice fed a standard diet (SD) or western diet (WD; fat, cholesterol and sugar) for 12, 24 and 36 weeks.
Bulk RNA Seq = Kupffer cells, moKCs and Clec4f- macrophages derived from mice fed a standard diet (SD) or western diet (WD; fat, cholesterol and sugar) for 12 and 24 weeks.

first: Anneleen

last: Remmerie

first: Tinne

last: Thone

first: Angela

last: Castoldi

first: Ruth

last: Seurnick

first: Benjamin

last: Pavie

first: Joris

last: Roels

first: Bavo

last: Vanneste

first: Sofie

last: De Prijck

first: Mathias

last: Vanhockerhout

first: Mushida

middle: B

last: Latib

first: Lindsey

last: Devisscher

first: Anne

last: Hoorens

first: Johnny

last: Bonnardel

first: Niels

last: Vandamme

first: Anna

last: Kremer

first: Peter

last: Borghgraef

first: Hans

last: Van Vlierberghe

first: Saskia

last: Lippens

first: Edward

last: Pearce

first: Yvan

last: Saeys

first: Charlotte

last: Scott


title: Gene expression profiles for porcine alveolar macrophage isolated from piglets injected with Mab followed by challenge with two PRRSV strains: PRRSV-JXA1 and PRRSV-HNhx

status: Public on Aug 20 2020

city: Yangling

first: Yuchen

state: Shaanxi

address: No.22 XinongLu

institute: Northwest A&F University

summary: An PRRSV specific IgG-type Mab-PN9cx3, demonstrated broad recognition and neutralization activity against both PRRSV-1 and PRRSV-2 isolates in vitro, was tested for in vivo protection experiments. Administration of Mab-PN9cx3 20mg in piglets significantly alleviated the pathological changes in lungs and decreased virus loads in PAMs after challenging with two heterogenous PRRSV isolates: HP-PRRSV-JXA1 and PRRSV NADC-30 like HNhx when compared with piglets inoculated virus .  Transcriptome profile for  porcine alveolar macrophage  of different groups were analyzed via RNA-sequencing.

overall_design: PAMs isolated from different groups (n=3) were harvested by TRIzol for RNA extraction and subjected to RNA-sequencing

first: Chunyan

last: Wu

first: Jingrui

last: Li

first: Zhigang

last: Zhang


title: Multisite methylation profiling of primary human meningioma [RNA-seq]

status: Public on Aug 12 2020

city: San Francisco

first: Harish

last: Vasudevan

state: CA

address: 555 Mission Bay Blvd South, Room 452H

department: Radiation Oncology

institute: University of California San Francisco

summary: Multiple stereotatically separate sites from human meningioma were processed for methlyation profiling

overall_design:
Meningiomas are the most common primary intracranial tumors, but the molecular drivers of meningioma tumorigenesis are poorly understood. We hypothesized that investigating intratumor heterogeneity in meningiomas would elucidate biologic drivers and reveal new targets for molecular therapy. To test this hypothesis, we performed multiplatform molecular profiling of 86 spatially-distinct samples from 13 human meningiomas. Our data reveal that regional alterations in chromosome structure underlie clonal transcriptomic, epigenomic, and histopathologic signatures in meningioma. Stereotactic co-registration of sample coordinates to preoperative magnetic resonance images further demonstrated that high apparent diffusion coefficient (ADC) distinguished meningioma regions with proliferating cells enriched for developmental gene expression programs. To understand the function of these genes in meningioma, we developed a human cerebral organoid model of meningioma and validated the high ADC marker genes CDH2 and PTPRZ1 as potential targets for meningioma therapy using live imaging, single cell RNA sequencing, CRISPR interference, and pharmacology.
A total of 88 spatially-distinct samples from 13 human meningiomas were profiled

middle: N

first: David

middle: R

last: Raleigh


title: Osteopontin expression identifies a subset of recruited macrophages distinct from Kupffer cells in the fatty liver.

first: Liesbet

last: Martens


title: Dietary selenium-methionine affects the levels and toxicity of methylmercury in Balb-C mice

status: Public on Aug 29 2020

city: Bergen

first: Kai

middle: Kristoffer

last: Lie

state: Hordaland

address: Pobox 2029 Nordnes

department: Feed Safety

country: Norway

institute: Institute of Marine research

summary: Methylmercury (MeHg) is a well-known neurotoxicant, particularly harmful for the developing brain. Selenium is a nutrient previously shown to interact with MeHg, however the molecular mechanisms behind these interaction is not fully described. To explore the effect of selenium on MeHg, mice were exposed to selenomethionine (SeMet) and MeHg in a 2 x 3 full factorial design for 12 weeks. After termination, organs, including the brain, were collected for Hg and Se analysis. The hippocampus was collected and analysed using gel free proteomics and RNA sequencing (RNA-seq).  The presence of SeMet reduced the amount of Hg in several organs, including the brain, while the level of Hg were increased in the feces. The presence of Hg also increased the concentration of selenium in liver and cortex. Proteomic and RNA-seq analyses showed that several known pathways of MeHg toxicity, such as oxidative stress, altered metabolism and calcium disruption were alleviated when SeMet were present. Our results suggest that SeMet can to a certain extent ameliorate the neurotoxic effects of MeHg in a mouse model. Although, whether this is due to decrease of body burden of Hg or through direct interactions with selenium in vivo remains unclear.

overall_design: Mice were orally exposed to selenium and two different doses of mercury in a full factorial design. Exposure groups; no selenium and no mercury (Ctr), selenium (Se_Ctr), high dose mercury (HD), low dose mercury (LD), selenium and high dose mercury (Se_HD), selenium and low dose mercury (Se_LD).

first: Ragnhild

middle: M

last: Mellingen

first: Ole

last: Nøstbakken

first: Josef

middle: D

last: Rasinger

first: Lene

last: Myrmel

first: Lise

last: Madsen


title: Osteopontin expression identifies a subset of recruited macrophages distinct from Kupffer cells in the fatty liver. [Bulk RNA Seq]

first: Anneleen

last: Remmerie

first: Tinne

last: Thone

first: Angela

last: Castoldi

first: Ruth

last: Seurnick

first: Benjamin

last: Pavie

first: Joris

last: Roels

first: Bavo

last: Vanneste

first: Sofie

last: De Prijck

first: Mathias

last: Vanhockerhout

first: Mushida

last: Latib

first: Lindsey

last: Devisscher

first: Anne

last: Hoorens

first: Johnny

last: Bonnardel

first: Niels

last: Vandamme

first: Anna

last: Kremer

first: Peter

last: Borghgraef

first: Hans

last: Van Vlierberghe

first: Saskia


title: Pioneer factor GAF cooperates with PBAP and NURF to regulate transcription [GAF ChIP-seq]

status: Public on Sep 01 2020

city: Ithaca

first: Julius

last: Judd

address: 417 Biotechnology Bldg; 215 Tower Road

department: Molecular Biology and Genetics

institute: Cornell University

summary: The Drosophila pioneer factor GAF is known to be essential for RNA Pol II promoter-proximal pausing and the removal of nucleosomes from a set of target promoters with GAGAG motifs. We and others have speculated that GAF recruits the ISWI family ATP-dependent chromatin remodeling complex NURF, on the basis that NURF and GAF are both required to remodel nucleosomes on an hsp70 promoter in vitro and that GAF interacts physically with NURF. However, GAF was also recently shown to interact with PBAP, a SWI/SNF family remodeler. To test which of these remodeling complexes GAF works with, we depleted GAF, NURF301, BAP170, and NURF301+BAP170 in Drosophila S2 cells using RNAi. We used a combination of PRO-seq, ATAC-seq, 3'RNA-seq, and CUT&RUN to demonstrate that while GAF and PBAP synergistically open chromatin at target promtoers which allows Pol II recruitment and pausing to proceed, GAF and NURF also synergistically position the +1 nucleosome to ensure efficient pause release and transition to productive elongation.

overall_design:
We treated two independent replicates of Drosophila S2 cells with dsRNA to LACZ (control), GAF, NURF301, BAP170 (the unique subunits of the NURF and PBAP complexes, respectively), and NURF301+BAP170. After 5 days, we harvested cells, validated knockdowns, and performed PRO-seq, ATAC-seq and 3'RNA-seq. We also performed CUT&RUN for both GAF and NURF301 in untreated S2 cells.
Please note that each merged normalized (reads per million) bigwig file was generated from both replicates and is linked to the corresponding *Rep1 sample records.

first: Fabiana

last: Duarte

first: John

last: Lis


title: Molecular signatures underlying neurofibrillary tangle susceptibility in Alzheimer’s disease

status: Public on Aug 05 2020

city: Stanford

first: Inma

last: Cobos

state: California

address: 300 Pasteur Drive, Lane Building, L235

institute: STANFORD UNIVERSITY MEDICAL SCHOOL

summary: Tau aggregation in neurofibrillary tangles (NFTs) is closely associated with neurodegeneration and cognitive decline in Alzheimer’s disease (AD). However, the molecular signatures that distinguish between aggregation-prone and aggregation-resistant cell states are unknown. We developed methods for the high-throughput isolation and transcriptome profiling of single somas with NFTs fro¬m human AD brain, quantified the susceptibility of 20 neocortical subtypes for NFT formation and death, and identified both shared and cell-type-specific signatures. NFT-bearing neurons shared a marked upregulation of synaptic transmission-related genes, including a core set of 63 genes enriched for synaptic vesicle cycling. Oxidative phosphorylation and mitochondrial dysfunction were highly cell-type dependent. Apoptosis was only modestly enriched, and the susceptibilities of NFT-bearing and NFT-free neurons for death were highly similar. Our analysis suggests that NFTs represent cell-type-specific responses to stress and synaptic dysfunction. We provide a resource for biomarker discovery and the investigation of tau-dependent and tau-independent mechanisms of neurodegeneration.

overall_design: Fresh frozen brain tissue from the prefrontal cortex (BA9) of eight Braak stage VI AD and eight age-matched healthy control donors was micro-dissected and dissociated without detergents or enzymatic digestion. Immunostaining and FACS using an antibody to detect pathological tau aggregates (AT8) and the pan-neuronal marker MAP2 was used to isolate somas with NFTs (n = 24,660) and neighboring NFT-free neurons (n = 38,465) from AD donors and control NFT-free somas (n = 63,110). RNA capture and library preparation was performed using the 10× Genomics Chromium Single Cell 3’ v2 or v3 assay. The generated paired-end libraries were sequenced on Illumina Novaseq 6000. Paired-end sequence reads were processed using the 10× Genomics software package Cell Ranger and the R-based Seurat package. Raw data is available in SRA with Study accession SRP189891 and Bioproject accession PRJNA528824.

first: Marcos

last: Otero-Garcia

first: Yueqiang

last: Xue

first: Tamara

last: Shakouri

first: Yongning

last: Deng

first: Samuel

last: Morabito

first: Riki

last: Kawaguchi

first: Vivek

last: Swarup


title: Decoding the transcriptome of calcified atherosclerotic plaque at single-cell resolution

status: Public on Oct 21 2020

city: La Jolla

first: Ali

last: Torkamani

address: 3344 North Torrey Pines Court, Suite 300

department: Scripps Research Translational Institute

institute: Scripps Research

summary: Atherogenesis involves an interplay of inflammation, tissue remodeling and cellular transdifferentiation (CTD), making it especially difficult to precisely delineate its pathophysiology. Here we examine the single-cell transcriptome of entire calcified atherosclerotic core (AC) plaques and patient-matched proximal adjacent (PA) portions of carotid artery tissue from patients undergoing carotid endarterectomy. We use a novel tissue dissociation strategy, single-cell RNA sequencing, and systems-biology approaches to analyze the transcriptional profiles of six main cell populations and identify key gene drivers of pathogenic biological processes in vascular smooth muscle cells (VSMCs) and endothelial cells (ECs).

overall_design: Calcified atherosclerotic core (AC) plaques and patient-matched proximal adjacent (PA) portions of carotid artery were collected from three patients undergoing carotid endarterectomy and were assessed using single cell RNA-seq

first: Tom

last: Alsaigh

first: Doug

last: Evans

first: David

last: Frankel


title: Characterizing phenotypically distinct T cell populations

status: Public on Jul 25 2020

city: Zuerich

first: Yannik

last: Severin

state: ZH

address: Otto-Stern-Weg 3

department: Biology

country: Switzerland

institute: ETH Zurich

summary: We developed a novel multiplexed immunofluorescence approach, allowing for fast in-depth phenotypic characterization of immune blood cells. Utilizing this method allowed us to quantify immune cell plasticity and revealed identifiable phenotypic fingerprints across T-cells of ten tested donors. The goal of the requested project is to gain mechanistic insight into the described phenotypic variability by using transcriptomic analysis of T-cells obtained from the same 10 selected donors.

overall_design: T-cell mRNA profiles of ten healthy blood donor

first: Julien

last: Mena

first: Benjamin

last: Hale

last: Goslings

first: Beat

last: Frey

first: Berend

last: Snijder


title: Epigenome-Wide DNA Methylation Analysis of Small Cell Lung Cancer Cell Lines Suggests Potential Chemotherapy Targets

status: Public on Jun 24 2020

city: Princeton

first: Sudhir

last: Varma

state: NJ

address: 1215 Wessex Pl

institute: HiThru Analytics

type: Methylation profiling by genome tiling array

summary: Small cell lung cancer (SCLC) is an aggressive neuroendocrine lung cancer. SCLC progression and treatment resistance involve epigenetic processes. However, links between SCLC DNA methylation and drug response remain unclear. We performed an epigenome-wide study of 66 human SCLC cell lines using the Illumina Infinium MethylationEPIC BeadChip array. Correlations of SCLC DNA methylation and gene expression with in-vitro  response to 526 antitumor agents were examined. Results:We found multiple significant correlations between DNA methylation and chemosensitivity. A potentially important association was observed for TREX1,  which encodes the 3’ exonuclease I that serves as a STING antagonist in the regulation of a cytosolic DNA-sensing pathway. Increased methylation and low expression of   TREX1   were associated with the sensitivity to Aurora kinase inhibitors AZD-1152, SCH-1473759, SNS-314, and TAK-901, the CDK inhibitor R-547, the Vertex ATR inhibitor Cpd 45 and the mitotic spindle disruptor vinorelbine. Compared with cell lines of other cancer types, TREX1   had low mRNA expression and increased upstream region methylation in SCLC, suggesting a possible relationship with SCLC sensitivity to Aurora kinase inhibitors.  We also identified multiple additional correlations indicative of potential mechanisms of chemosensitivity. Methylation of the 3’UTR of   CEP350   and   MLPH  , involved in centrosome machinery and microtubule tracking, respectively, was associated with response to Aurora kinase inhibitors and other agents.   EPAS1   methylation was associated with response to Aurora kinase inhibitors, a PLK-1 inhibitor and a Bcl-2 inhibitor.  KDM1A methylation was associated with PLK-1 inhibitors and a KSP inhibitor. Increased promoter methylation of   SLFN11   was correlated with resistance to DNA damaging agents, as a result of low or no   SLFN11   expression. The 5’ UTR of the epigenetic modifier   EZH2   was associated with response to Aurora kinase inhibitors and a FGFR inhibitor. Methylation and expression of YAP1   were correlated with response to an mTOR inhibitor. Among non-neuroendocrine markers,   EPHA2  was associated with response to Aurora kinase inhibitors and a PLK-1 inhibitor, and  CD151   with Bcl-2 inhibitors. Conclusions Multiple associations indicate potential epigenetic mechanisms affecting SCLC response to chemotherapy and suggest targets for combination therapies. While many correlations were not specific to SCLC lineages, several lineage markers were associated with specific agents.

overall_design: Methylation measurements for all cell lines were generated in a single batch using Illumina Infinium MethylationEPIC BeadChip (Illumina, Inc).

first: Julia

last: Krushkal

first: Thomas

last: Silvers

first: William

middle: C

last: Reinhold

first: Dmitriy

last: Sonkin

first: Suleyman

last: Vural

first: John

last: Connelly

first: Paul

last: Meltzer

first: Mark

last: Kunkel

first: Annamaria

last: Rapisarda

first: Yves

last: Pommier

first: Beverly

last: Teicher


title: The neuromuscular junction is a focal point of mTORC1 signaling in sarcopenia [TSCmKO data set].

status: Public on Jun 19 2020

city: Basel

first: Anastasiya

last: Boersch

address: Klingelbergstrasse 50 / 70

department: Biozentrum

institute: University of Basel

summary:
Purpose: Sustained muscle fiber-specific mTORC1 activity, through deletion of the mTORC1 upstream inhibitor Tsc1, drives progressive muscle wasting and weakness reminiscent of sarcopenia. We aimed to characterise gene expression changes coinciding with the development of sarcopenia-like features in TSCmKO mice.
Methods: Extensorum digitorum longus (EDL) muscles from 3- (weak phenotype) and 9-month-old (severe phenotype) TSCmKO and littermate control mice (Tsc1 floxed, HSA-Cre negative) treated with either vehicle or rapamycin (8 mg.kg.min-1) for 3 days were processed and sequenced.
Results: The principal component analysis showed two major gene expression patterns. The first pattern represents an aging-like pattern with gene expression remaining stable between 3 and 9 months in wild type mice, but changing between 3 and 9 months in TSCmKO mice. The second pattern seems to represent early alterations in TSCmKO mice compared to WT, which subside between 3 and 9 months in TSCmKO. Importantly, when comparing changes in the gene expression in TSCmKO mice with natural aging gene expression profiles, there was a significant overrepresentation of commonly increasing and decreasing genes and an underrepresentation of oppositely regulated genes. Likewise, many of the top enriched GO terms for natural aging gene expression profiles were also enriched for genes changing the expression in the premature aging TSCmKO mice.
Conclusions: Sustained, muscle fiber-specific mTORC1 activity drives sarcopenia-like gene expression programs, and the hyperactive mTORC1 seen in sarcopenic muscle may therefore contribute to sarcopenia.

overall_design: Skeletal muscle mRNA profiles of 3 and 9 months old wild type mice and Tsc1 knockout (TSCmKO) mice untreated and treated with rapamycin for 3 days were generated by next-generation sequencing.

first: Lionel

last: Tintignac

first: Nitish

last: Mittal

first: Maitea

last: Guridi

last: Börsch

first: Daniel

last: Ham

first: Mihaela

last: Zavolan

first: Markus

last: Rüegg


title: The neuromuscular junction is a focal point of mTORC1 signaling in sarcopenia [Aging-Rapamycin data set].

summary:
Purpose: Despite demonstrating that the overall effect of long-term rapamycin-treatment is overwhelmingly positive in aging skeletal muscle, we observed muscle-specificity in the responsiveness to rapamycin, leading us to hypothesize that the primary drivers of age-related muscle loss and therefore effective intervention strategies may differ between muscles. To address this question and dissect the key signaling nodes associated with mTORC1-driven muscle aging, we created a comprehensive multi-muscle gene expression atlas in adult, sarcopenic and rapamycin-treated mice using RNA-seq.
Methods: To examine the impact of long-term rapamycin treatment, male C57BL/6 mice were fed encapsulated rapamycin incorporated into a standardized AIN93M diet at 42 ppm (i.e. mg per kg of food), corresponding to a dose of ~4 mg·kg-1·day-1, from 15- to 30-months of age. This dose of rapamycin has been shown to extend lifespan maximally in male C57BL/6 mice. We performed RNA-seq on gastrocnemius (GAS), tibialis anterior (TA), triceps brachii (TRI) and soleus (SOL) muscles from each of six mice for 10m, 30m and 30mRM groups. The four muscle types were chosen to encompass fore- and hindlimb locations (e.g. TRI and GAS); slow and fast contraction properties (e.g. SOL and GAS); anterior and posterior positioning (e.g. TA and GAS) and the extent of protection by rapamycin (TA and TRI: protected; SOL: partiallly protected; GAS: not protected).
Results: Age-related gene expression changes were remarkably consistent across the four different muscles, varying only in magnitude. Despite having the smallest age-related muscle loss of the four muscles, TA had the strongest age-related gene expression response which was associated with an increased reinnervation response. Despite the strong between-muscle commonality of age-related changes, gene expression responses to prolonged rapamycin treatment differed substantially between muscles. Rapamycin partially reversed many age-related changes in mRNA expression in the TA and TRI, but not in SOL or GAS muscle. Principle component analysis (PCA) showed that rapamycin had common 'anti-aging' effects on all muscles, while also exerting muscle-specific pro-aging effects on muscles not protected by rapamycin.
Conclusions: Sustained, muscle fiber-specific mTORC1 activity drives sarcopenia-like gene expression programs, and the hyperactive mTORC1 seen in sarcopenic muscle may therefore contribute to sarcopenia.

overall_design: Skeletal muscle mRNA profiles of 10 and 30 months old wild type mice and mice daily treated with rapamycin for 15 months from the age of 15 months were generated by next-generation sequencing.


title: CD28 regulation of global alternative splicing changes in activated human CD4+ T cells

status: Public on Jun 13 2020

first: Kristen

last: Lynch

state: Pennsylvania

address: 906 Stellar Chance Labs 422 Curie Blvd

department: Biochemistry and Molecular Biophysics

institute: University of Pennsylvania

summary:
Alternative splicing consists of exons that are selectively either included or excluded from the mature mRNA transcript. Previous studies have demonstrated that ~10-15% of alternatively spliced genes undergo signal-induced changes in isoform abundance in activated primary human CD4+ T cells. In the past, signal-induced alternative splicing changes in T cells have been characterized in the context of CD3 and CD28 activation. CD3 is a component of the T Cell Receptor (TCR) which is responsible for recognizing foreign peptides presented on antigen presenting cells. CD28 enhances various signaling events downstream of the TCR to boost the survival of T cells and is required for full T cell stimulation.  The contribution of CD28 signaling to transcriptional changes has been well documented, but the impact on splicing has not been investigated.
Here we test the hypothesis that CD28 exerts some of its functional impact through the enhancement of splicing changes in stimulated T cells. We utilized poly(A) RNA-seq and the MAJIQ alternative splicing algorithm to analyze splicing events of human CD4+ T cells stimulated with through CD3 in the presence and absence of co-stimulation with CD28. Consistent with previous studies, we identified approximately 400 and 1,000 significant splicing events induced by CD3/CD28 stimulation at 8 and 48 hours of culture, respectively. Alternative splicing changes induced by CD3 and CD3/CD28 stimuli are highly correlative, however, approximately 23% of alternative splicing changes are further enhanced with additional CD28 costimulation at 8 hours of culture.  This enhancement drops to 8% of alternative splicing events by 48 hours. Therefore, we conclude that CD28 costimulation increases the magnitude of splicing during T cell activation, in a manner that is eventually compensated for over time with CD3 stimulation alone.

overall_design: From 2 female and 1 male donors, naïve CD4+ T cells were isolated with magnetic beads, then stimulated with aCD3, aCD28, or both for 0, 8 or 48 hours

first: Blake

last: Davia

first: Mallory

last: Michael

first: Radens

last: Caleb

first: Lynch

last: Kristen


title: Gene expression profiles of MLL-AF4 acute lymphoblastic leukaemia blasts retrieved from central nervous system and spleen

status: Public on Jul 08 2020

city: Bearsden

first: Pawel

last: Herzyk

address: Wolfson Wohl Cancer Research Centre, Garscube Estate

department: College of Medical, Veterinary and Life Sciences

institute: University of Glasgow

summary:
Purpose: To investigate metabolic adaptation of leukaemia in two different microenvironments: central nervous system and spleen
Methods: The SEM (MLL-AF4) cell-line representing a high-risk subtype was used. Cells were transplanted into immunodeficient mice. CNS tropism was demonstrated and blasts invaded the leptomeninges in a timeframe ranging from 4 to 5 weeks. At experimental endpoint, blasts were retrieved from the CNS and periphery (spleen), and their gene expression profiles were compared using RNA-sequencing. The raw reads were pre-processed with Cutadapt v.1.5 and Sickle v.0.940 software. Transcript expression quantification was performed using Kallisto v.0.42.4 software against combined human and mouse transcriptomes, Ensembl GRCh38.79 and GRCm38.78, respectively. Read counts related to human transcripts were collected, rounded, and summarized into gene specific read counts. Gene-based differential expression analysis was done with DESeq2 R-package. Preprocessed RNA expression data from RNA sequencing was analysed further using single sample gene set enrichment analysis (ssGSEA).
Results: The human SEM cells’ gene expression profiles clustered according to site of colonization in the transplanted mice; CNS versus spleen. The top differentially expressed genes were associated with cellular metabolism or stress responses. ssGSEA analysis identified positive correlation of lipid and lipoprotein metabolism signatures in CNS-derived cells, with particular propensity towards fatty acid synthesis. On the other hand, oxidative phosphorylation processes, linked to fatty acid degradation, were negatively correlated with CNS involvement and enriched in SEM cells from the spleen of transplanted mice.
Conclusions: We demonstrate that leukaemic cells undergo widespread dynamic rewiring of metabolism when switching from bone marrow to CNS microenvironments, resulting in altered therapeutic vulnerabilities. We observed a strong fatty-acid synthesis signature in CNS leukaemia, highlighting Stearoyl-CoA desaturase (SCD1) as a key player.

overall_design: Gene Expression profiles of human leukaemic cells retrieved from CNS and spleen after cell transplantaton into immunodeficient mice, were generated by RNAseq using Illumina NextSeq 500 sequencer.

first: Orianne

last: Olivares

first: Antony

last: Cousins

first: Elke

last: Markert

first: Eyal

last: Gottlieb

first: Christina

last: Halsey


title: CD4+ T cell transcriptional reprogramming by small compounds

status: Public on Jul 30 2020

city: Dallas

first: Ivan

last: D'Orso

state: TX

address: 5323 Harry Hines

department: Microbiology

institute: UT Southwestern Medical Center

summary: A major obstacle for HIV eradication is the persistence of latent reservoirs, cells harboring replication competent yet transcriptionally silent proviruses. These reservoirs, composed primarily of CD4+ T cells, cannot be targeted by the host immune system or by combination anti-retroviral therapy (cART). Upon cessation of cART, a rapid viral rebound occurs. In order to develop effective HIV cure therapies, a better understanding of the factors and host programd governing latency establishment and/or maintenance must be obtained. To achieve this goal, we treated a CD4+T cell-based model of latency (J-Lat 10.6) with Latency Reversing Agents (LRAs) and performed bulk RNA-seq to predict host transcriptional programs activated, and potentially involved, in latent HIV reactivation. Our findings suggest that a novel small molecule (EPH-334) reactivates latent HIV by activating an oxidative stress transcriptional program linked to activation of MAPKs and downstream master regulators. Interestingly, the pan histone deacetylase inhibitor SAHA also induces oxidative stress programs potentially linking sensing of redox state aletartions with activation of cell signaling and transcriptioonal programs culminating on latent HIV reactivation.

overall_design: Steady-state RNA levels were compared between untreated (0hr) and time-course LRA treated J-Lat 10.6 cells. Each data set consists of twelve samples, which are four timepoints each in triplicates. Type of library preparation: Strand Specific Whole Transcriptome.

first: Emily

last: Cruz-Lorenzo

first: Jeon

last: Lee


title: Multisite methylation profiling of primary human meningioma

status: Public on Jun 17 2020

first: Harish

last: Vasudevan

summary:
Multiple stereotatically separate sites from human meningioma were processed for methlyation profiling
Meningiomas are the most common primary intracranial tumors, but the molecular drivers of meningioma tumorigenesis are poorly understood. We hypothesized that investigating intratumor heterogeneity in meningiomas would elucidate biologic drivers and reveal new targets for molecular therapy. To test this hypothesis, we performed multiplatform molecular profiling of 86 spatially-distinct samples from 13 human meningiomas. Our data reveal that regional alterations in chromosome structure underlie clonal transcriptomic, epigenomic, and histopathologic signatures in meningioma. Stereotactic co-registration of sample coordinates to preoperative magnetic resonance images further demonstrated that high apparent diffusion coefficient (ADC) distinguished meningioma regions with proliferating cells enriched for developmental gene expression programs. To understand the function of these genes in meningioma, we developed a human cerebral organoid model of meningioma and validated the high ADC marker genes CDH2 and PTPRZ1 as potential targets for meningioma therapy using live imaging, single cell RNA sequencing, CRISPR interference, and pharmacology.

overall_design: A total of 88 spatially-distinct samples from 13 human meningiomas were profiled

first: David

last: Raleigh


title: The neuromuscular junction is a focal point of mTORC1 signaling in sarcopenia [NMJ data set].

first: Anastasiya

last: Boersch

summary:
Purpose: To investigate whether our signatures of mTORC1-driven sarcopenia originate from cells residing at the neuromuscular junction (NMJ), we followed laser-capture microdissection with RNA-seq from adult and sarcopenic tibialis anterior (TA) muscles.
Methods: TA muscles were incubated in solution containing fluorescently-labeled bungarotoxin, which binds to post-synaptic AChRs and thereby marks NMJ regions. Approximately 300 synaptic regions (NMJ) and a comparable number of extra-synaptic (xNMJ) regions were collected from 30µM thick sections using laser-capture microdissection (LCM) and processed for RNA-seq.
Results: As compared to xNMJ regions, NMJ regions were highly enriched for genes known to be specifically expressed at the NMJ. The analysis demonstrated that genes associated with sarcopenia are significantly enriched at the NMJ in young (10 months) and old (30 months) mice. Furthermore, the age-related reduction in expression of genes associated with extracellular matrix (ECM) remodelling was particularly prominent in NMJ regions but not in xNMJ regions.
Conclusions: Diminished expression of ECM genes at the NMJ may impact the stability of the NMJ and its ability to remodel following common age-related remodelling events such as muscle fiber degeneration/regeneration and motor unit loss.

overall_design: mRNA profiles of synaptic and extra-synaptic regions of skeletal muscles of 10 and 30 months old wild type mice by next-generation sequencing.

first: Martin

last: Weihrauch

last: Börsch

first: Daniel

last: Ham

first: Markus

last: Rüegg

first: Mihaela

last: Zavolan

first: Christoph

last: Handschin


title: A genome-wide CRISPR screen reveals a role for the non-canonical nucleosome remodeling BAF complex in Foxp3 expression and regulatory T cell function

status: Public on Jul 07 2020

city: San Diego

first: Diana

middle: C.

last: Hargreaves

address: 10010 North Torrey Pines Road

institute: The Salk Institute for Biological Studies

summary: Regulatory T cells (Treg) play a pivotal role in suppressing auto-reactive T cells and maintaining immune homeostasis. Treg development and function are dependent on the transcription factor Foxp3. Here we performed a genome-wide CRISPR loss-of-function screen to identify Foxp3 regulators in mouse primary Treg cells. Foxp3 regulators were enriched in genes encoding subunits of the SWI/SNF nucleosome remodeling and SAGA chromatin modifying complexes. Among the three SWI/SNF-related complexes, the Brd9-containing non-canonical (nc)BAF complex promoted Foxp3 expression, whereas the PBAF complex was repressive. Chemical-induced degradation of Brd9 led to reduced Foxp3 expression and reduced Treg function in vitro. Brd9 ablation compromised Treg function in inflammatory disease and tumor immunity in vivo. Furthermore, Brd9 promoted Foxp3 binding and expression of a subset of Foxp3 target genes. Our findings provide an unbiased analysis of the genetic networks regulating Foxp3 and reveal ncBAF as a target for therapeutic manipulation of Treg function.

overall_design:
ChIP-seq for Foxp3, BRG1, BRD9 and PHF10 in natural T regulatory cells (nTregs) from Foxp3Thy1.1/Rosa-Cas9 mice to assess their genomic localization; replicates are indicated. ChIP-seq for Foxp3 and H3K27ac in nTregs either transduced with sgNT, sgFoxp3, sgBrd9, sgPbrm or treated with DMSO vehicle or dBRD9 to determine the role of Brd9 and Pbrm1 in regulating Foxp3 binding and H3K27ac levels. ChIP-seq for Foxp3 in nTregs exogenously expressing either MIGR empty vector or Foxp3 construct, with transduction of either sgNT or sgBrd9.

ATAC-seq in nTregs transduced with sgNT (non-targeting) or sgBrd9 to assess changes in chromatin accessibility after loss of Brd9. Two replicates per sample.

RNA-seq in nTregs treated with DMSO vehicle or dBRD9. RNA-seq in nTregs transduced with sgNT, sgFoxp3 or guides targeting different SWI/SNF subunits. Two to three replicates per sample.

first: Jovylyn

last: Gatchalian

first: Eric

last: Loo

first: Ye

last: Zheng


title: Muscle response to aging and aging-modulating interventions.

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

overall_design: Refer to individual Series


title: Retention of CD19 intron 2 contributes to CART-19 resistance in leukemias with subclonal frameshift mutations in CD19

status: Public on May 19 2020

first: Andrei

last: Thomas-Tikhonenko

address: 3501 Civic Center Blvd, CTRB 4056

department: Children's Hospital of Philadelphia

institute: Perelman School of Medicine at the University of Pennsylvania

summary: We report that retention of intron 2 which affects expression of CD19 in CART-19 relapsed leukemia occurs in the context of full length CD19 transcript using Oxford Nanopore sequencing technology. By performing Direct RNA sequencing on Reh leukemia cell lines, we showed that intron 2 retention is functionally equivalent to nonsense mutations.

overall_design: Characterizing CD19 intron 2 retention in leukemia cell lines and CART-19 relapsed samples

first: Mukta

last: Asnani


title: Gene expression profiles of TEL-AML1 acute lymphoblastic leukaemia blasts retrieved from central nervous system and spleen

first: Pawel

last: Herzyk

summary:
Purpose: To investigate metabolic adaptation of leukaemia in two different microenvironments: central nervous system and spleen
Methods: The REH (TEL-AML1) cell line representing a standard-risk subtype was used. Cells were transplanted into immunodeficient mice. CNS tropism was demonstrated and ALL blasts invaded the leptomeninges in a timeframe ranging from 4 to 5 weeks. At experimental endpoint, blasts were retrieved from the CNS and periphery (spleen), and their gene expression profiles were compared using RNA-sequencing. The raw reads were pre-processed with Cutadapt v.1.5 and Sickle v.0.940 software. Transcript expression quantification was performed using Kallisto v.0.42.4 software against combined human and mouse transcriptomes, Ensembl GRCh38.79 and GRCm38.78, respectively. Read counts related to human transcripts were collected, rounded, and summarized into gene specific read counts. Gene-based differential expression analysis was done with DESeq2 R-package. Preprocessed RNA expression data from RNA sequencing was analysed further using single sample gene set enrichment analysis (ssGSEA).
Results: The human REH cells’ gene expression profiles clustered according to site of colonization in the transplanted mice; CNS versus spleen. Top differentially expressed genes were associated with cellular metabolism or stress responses. ssGSEA analysis identified positive correlation of lipid and lipoprotein metabolism signatures in CNS-derived cells, with particular propensity towards fatty acid synthesis. On the other hand, oxidative phosphorylation processes, linked to fatty acid degradation, were negatively correlated with CNS involvement and enriched in REH cells from the spleen of transplanted mice.
Conclusions: We demonstrate that leukaemic cells undergo widespread dynamic rewiring of metabolism when switching from bone marrow to CNS microenvironments, resulting in altered therapeutic vulnerabilities. We observed a strong fatty-acid synthesis signature in CNS leukaemia, highlighting Stearoyl-CoA desaturase (SCD1) as a key player.

first: Orianne

last: Olivares

first: Antony

last: Cousins

first: Elke

last: Markert

first: Eyal

last: Gottlieb

first: Christina

last: Halsey


title: Gene expression profiles of MLL-AF4 and TEL-AML1 acute lymphoblastic leukaemia blasts retrieved from central nervous system and spleen


title: Single-cell RNA-seq reveals a distinct transcriptome signature of hematopoiesis in GATA2 deficiency

status: Public on Jun 06 2020

city: Bethesda

first: Shouguo

last: Gao

address: 9000 Rockville Pike

institute: National Institutes of Health

summary:
Background and Purpose: Constitutional GATA2 deficiency caused by heterozygous germline GATA2 mutation has a broad spectrum of clinical phenotypes including systemic infections, lymphedema, cytopenias, MDS and AML. A comprehensive profiling of transcriptome of hematopoiesis in GATA2 deficiency is currently lacking.
Methods: We performed single-cell RNA sequencing of sorted bone marrow CD34+ hematopoietic stem and progenitor cells (HSPCs) from eight GATA2 deficiency patients, who had various well characterized GATA2 mutations and clinically manifest myelodysplasia. We characterized transcriptomes in lineages, computationally defined cells with chromosomal abnormalities, and described gene expression of these cells.
Results: Mapping patients’ cells onto normal hematopoiesis, we observed preferred deficiency in lymphoid and myeloid progenitors, which also was evidenced in loss of heterogeneity in gene correlations. HSPCs in patients exhibited distinct gene expression pattern and gene coexpression pattern compared with its counterparts in healthy donors. Distinct lineages show different transcriptional profiles resulting from GATA2 mutations. HSCs in patients exhibited dysregulated genes in apoptosis, cell cycle and quiescence, and had increased expression of erythroid/megakaryocytic priming programs and decreased lymphoid priming programs. Thus, the prominent deficiency in myeloid/lymphoid lineages in GATA2 deficiency was partly due to expression of aberrant gene programs in HSCs prior to lineage commitment. We computationally defined cells with chromosomal abnormalities and described gene expression of these cells. DNA repair genes were downregulated in trisomy 8 cells, possibly rendering these cells vulnerable to second-hit somatic mutations and additional chromosomal abnormalities. Cells with complex cytogenetics had defects in multi-lineage differentiation and cell cycle.
Conclusion: Germline GATA2 mutations modulate gene expression and change gene coexpression patterns. Distinct lineages show different transcriptional profiles resulting from GATA2 mutations. The prominent deficiency in myeloid/lymphoid lineages in GATA2 deficiency was partly due to expression of aberrant gene programs in HSCs prior to lineage commitment.

overall_design: mRNA profiles of single bone marrow CD34+ cells of eight GATA2 deficiency patients and four healthy donors were generated by deep sequencing using Illumina HiSeq 3000

first: Zhijie

last: Wu


title: Non-Small Cell Lung Cancer, Peripheral Immunity, Extending the Tumor Macroenvironment

status: Public on Aug 02 2020

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

institute: The Wistar Institute

summary: We recently established that gene expression in PAXgene stabilized blood RNA distinguishes benign (BN) from malignant (MN) pulmonary nodules in high risk candidates with an AUC of 0.84.  We now expand our studies to include incidental nodules identified in routine clinical settings using data from 603 patients analyzed on Illumina microarrays. We identify 300 gene probes achieving an AUC of 0.84 for Indeterminate Pulmonary Nodules (IPN) from 6-25 mm and 0.824 for IPN from 8-20 mm, outperforming 3 prominent clinical models that achieve AUCs of 0.60-0.689.  We address the basis for these differences by in silico flow cytometry using CIBERSORT and identify significant differences between MN and BN patients including proportions of T-cells, M0 macrophages, NK cells, B cells and exhausted CD8 T-cells. We identify major increases in expression of genes promoting cell death and strong decreases in functions promoting transcription, lymphogenesis and cell viability. A preferential use of oxidative phosphorylation and a signature of mitochondrial dysfunction are also associated with the presence of a MN.

overall_design: Whole blood gene expression from patients with malignant (MN), benign (BN) nodules and patients with no nodules (NN)

first: Louise

last: Showe

first: Rehman

last: Qureshi


title: High dimensional association detection in large-scale genomic data

status: Public on Nov 18 2020

city: University Park

first: Ross

last: Hardison

address: 303 Wartik Lab

institute: Pennsylvania State University

summary: Joint analyses of genomic datasets obtained in multiple different conditions are essential for understanding the biological mechanism that drives tissue-specificity and cell differentiation, but they still remain computationally challenging. To address this we introduce CLIMB (Composite LIkelihood eMpirical Bayes), a statistical methodology that learns patterns of condition-specificity present in genomic data. CLIMB provides a generic framework facilitating a host of analyses, such as clustering genomic features sharing similar condition-specific patterns and identifying which of these features are involved in cell fate commitment. Our approach improves upon existing methods by boosting statistical power to identify meaningful signals while retaining interpretability and computational tractability. We illustrate CLIMB's value on two sets of hematopoietic data: one studying CTCF ChIP-seq measured in 17 different cell populations, and another examining RNA-seq measured across constituent cell populations in three committed lineages. These analyses demonstrate that CLIMB captures biologically relevant clusters in the data and improves upon commonly-used pairwise comparisons and unsupervised clusterings typical of genomic analyses.

sample_organism:
Homo sapiens
Mus musculus

overall_design: CTCF ChIP-seq from 17 cell populations were jointly analyzed; obtained clusters of genomic loci were compared against ATAC-seq, H3K4me1 ChIP- and H3K4me3 ChIP-seq at matching loci. RNA-seq reads were compared across differentiated states in the erythroid, myeloid, and megakaryocytic cell lineages. DNase-seq of 38 biosamples across all autosomes were jointly reanalyzed using CLIMB and non-negative matrix factorization (see GSE156074_DNase-seq_README.txt for details).

first: Hillary

last: Koch

first: Cheryl

last: Keller

first: Belinda

last: Giardine

first: Guanjue

last: Xiang

first: Feipeng

last: Zhang

first: Hardison

last: Ross

first: Qunhua

last: Li


title: Developing a translational polygenic score of biological sensitivity to context

status: Public on May 20 2020

city: Verdun

first: Nicholas

last: O'Toole

state: QC

address: 6875 Boulevard Lasalle

institute: Douglas Mental Health University Institute

summary: This study builds the first translational model of biological sensitivity to context. In order to determine gene expression patterns that underlie environmental responsivity, we conduct RNA sequencing of ventral dentate gyrus in C57BL6/J mice exposed to two distinctly divergent contexts: environmental enrichment or chronic social defeat stress. Differential expression analysis revealed 18 genes that were commonly regulated in response to these contexts compared to control and were thus considered environmentally responsive irrespective of the valance of the environment. Using the human orthologs, we build a polygenic score of environmental responsivity (ER-ePRS). We then tested whether this ER-ePRS moderated the relationship between the quality of the prevailing environment and anxiety-like or depression problems in four culturally distinctive human cohorts. Results reveal that the molecular underpinnings responsible for environmental responsivity in mice predict a greater propensity to develop psychopathological symptoms in humans in a context and sex dependent manner.

overall_design: RNA sequencing of the ventral dentate gyrus of mice exposed to social defeat and environmental enrichment

last: O’Toole

first: Tieyuan


title: Whole blood transcriptional profiling by RNA sequencing in patients with ST-elevation and non-ST elevation myocardial infarction

status: Public on May 27 2020

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

institute: Centro Cardiologico Monzino IRCCS

summary:
Aims. We sought for peripheral blood gene expression signatures at presentation that distinguish the ST elevation (STEMI) and non-ST elevation myocardial infarction (NSTEMI)  conditions, to define a precise map of differentially regulated biological processes, unveil new distinctive traits, and help predict markers of outcome.
Methods and results. Total RNA from whole blood of STEMI and NSTEMI patients was used to prepare poly(A)+ enriched libraries for paired-end RNA-Seq. Transcriptomes were reconstructed and, after adjustment for unwanted variation, we performed differential expression analysis. Enrichment analyses was performed to infer differentiating functional networks. We identified 153 differentially expressed genes, which stood correction for TnI levels at admission and included 32 putative novel genes (false discovery rate-adjusted P<0.05). We found a divergent modulation of inflammatory, immune-response, angiogenic, and mitochondrial dynamics pathways. Finally, we showed that specific gene expression patterns at admission predict troponin I (TnI) peak levels and/or GRACE risk score.
Conclusions. RNA-Seq allowed identifying novel differentially expressed genes in STEMI vs. NSTEMI, which might uncover unappreciated mechanisms underlying acute MI. Overall, our results depicted a scenario characterizing different pathological traits of these two types of acute MI that could pave the way for the identification of novel, specific biomarkers for early diagnosis, risk stratification, and therapeutic decision-making.

overall_design: Whole blood poly(A)+ RNA profiles of 15 STEMI and 15 NSTEMI patients were generated through RNA-Seq using the SOLiD 5500xl system.

first: Luca

last: Piacentini

first: Mattia

last: Chiesa

first: Elisa

last: Bono


title: Transcriptome profiling and genome-wide DNA-binding analysis for understanding the impact of Sox100B level on global gene expression and identifying target genes of Sox100B in intestinal epithelium in Drosophila

status: Public on May 18 2020

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS


title: Transcriptome profiling of different celltype of cells (Progenitor cells/Enteroendocrine cells/Enteroblast cells) and Sox100B depleted/overexpressed progenitor cells in Drosophila intestine

summary:
Purpose: 1)To compare transcriptome profiling (RNA-seq) of intestinal progenitor cells in Drosophila wild type and Sox100B depleted/overexpressed midgut.
2)To identify cell-type enriched genes and early-transcribed EC/EE genes by comparing transcriptome profiling (RNA-seq) of different celltype of cells
Results: Each sequencing experiment generated more than 20 million raw reads, and 92.5% was uniquely mapped for each experiment. 2310 genes of the transcripts showed significantly differential expression between the WT and Sox100B-OE progenitor cells, and 2181 genes of the transcripts showed significantly differential expression between the WT and Sox100B-IR progenitor cells, with a fold change ≥2.0 and p value <0.05. Genes that showed low level in progenitor cells while significantly higher level in terminally differentiated EC/EE cells were identified as early transcribed EC/EE genes. 169 genes were identified as early-transcribed EC genes and 452 genes were identified as early-transcribed EE genes.

overall_design: mRNA profiles of intestinal progenitor cells isolated from 3-day-old wild-type (Ctrl) and Sox100B depleted/overexpressed Drosophila midgut were generated by deep sequencing using Illumina HiSeq 4000.

first: Zhen

last: Jin

first: Xingting

last: Guo

first: Rongwen

last: Xi


title: Genome-wide DNA-binding analysis for Sox100B in intestinal stem cells by DamID

summary:
Purpose:  Genome-wide DNA-binding analysis for Sox100B in intestinal stem cells in Drosophila midgut by DNA adenine methyltransferase identification(DamID)
Methods: DNA adenine methyltransferase identification (DamID) on Sox100B driven by ESG-Gal4
Results: 5046 significant genomic binding sites, corresponding to 3182 genes were identified via iDamID following Sox100B overexpression in progenitor cells compared to WT. About a third of these genes were in the list of significantly altered genes following Sox100B overexpression and/or depletion.

overall_design: Dam(Ctrl) or Dam-Sox100B transgenes were expressed in intestinal stem cells by ESG-Gal4.The guts with 2 days after transgene expression were used for DamID-seq, followed by deep sequencing analysis.


title: Intergrated analysis of array-miRNAs and matched Affymetrix gene

status: Public on May 12 2020

first: Howard

last: Yang

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

summary:
MicroRNAs are considered to be essential regulators during
post-transcription in gene expression that mainly through repression mechanism to regulate target mRNAs. We generate expression data from profiling of 664 miRNA in 113 paired tumors and non-tumors of esophageal squamous carcinoma (ESCC), along with matched genome-wide mRNA gene expression data and extensive analysis association study with clinical viable. We identified an expanded list of miRNA dysregulated with Bonferroni correction at 0.05 and genes expression over 2 fold changes in esophageal squamous cell carcinoma. We also found of sixteen miRNAs significant associated with 195 genes. Further analysis show a group of miRNAs correlated with clinical variables including tumor metastasis, tumor stage, grade, and location, family history of UGI cancer, tobacco or alcohol use and pickled vegetable consumption. Survival correlation with either miRNAs or mRNAs was done. Finally, intersect genes correlated with survival and regulated by miRNAs are pulled out. This study provides a comprehensive dataset that can be used as groundwork for further studies of the involvement of miRNA and targeted mRNAs in ESCC and a group of genes may potential serve as biomarkers for prognosis.

overall_design:
miRNA profiling from 113 paired tumor and non-tumor frozen
tissues of esophageal squamous carcinoma was performed. TaqMan® Low Density Array was used for MicroRNA expression study that containing a two-card set of TaqMan® Array MicroRNA Cards (Cards A and B) for a total of 754 assays specific to unique 664 human miRNAs. It was using 9700HT fast real-time PCR system from ABI. Expression level (fold changes) was calculated when both tumor and normal sample giving signals in the assays using DataAssist software v2.0 (Life Technologies, http://www.lifetechnologies.com/about-life-technologies.html).
In the present study, the data are presented as the fold change.

mRNA profiling from 113 paired ESCC samples same as above was performed. Affymetrix Human Genome U133 Chip were used, and of the 113 paired ESCC samples, 34 pairs were using Human U133A chips, 73 pairs using U133A_2 chips, and 6 pairs using U133Plus_2 chips. All the Affymetrix array data (CEL files on all samples) were normalized by the RMA method using the software
Affymetrix Expression Console, version 1.2.1.

middle: H

first: Hua

last: Su

first: Philip

last: Taylor


title: Pioneer factor GAF cooperates with PBAP and NURF to regulate transcription [CUT&RUN]

status: Public on May 10 2020

first: Julius

last: Judd

state: NY

address: 417 Biotechnology Bldg; 215 Tower Road

institute: Cornell University

summary: The Drosophila pioneer factor GAF is known to be essential for RNA Pol II promoter-proximal pausing and the removal of nucleosomes from a set of target promoters with GAGAG motifs. We and others have speculated that GAF recruits the ISWI family ATP-dependent chromatin remodeling complex NURF, on the basis that NURF and GAF are both required to remodel nucleosomes on an hsp70 promoter in vitro and that GAF interacts physically with NURF. However, GAF was also recently shown to interact with PBAP, a SWI/SNF family remodeler. To test which of these remodeling complexes GAF works with, we depleted GAF, NURF301, BAP170, and NURF301+BAP170 in Drosophila S2 cells using RNAi. We used a combination of PRO-seq, ATAC-seq, 3'RNA-seq, and CUT&RUN to demonstrate that while GAF and PBAP synergistically open chromatin at target promoters which allows Pol II recruitment and pausing to proceed, GAF and NURF also synergistically position the +1 nucleosome to ensure efficient pause release and transition to productive elongation.

overall_design: We treated two independent replicates of Drosophila S2 cells with dsRNA to LACZ (control), GAF, NURF301, BAP170 (the unique subunits of the NURF and PBAP complexes, respectively), and NURF301+BAP170. After 5 days, we harvested cells, validated knockdowns, and performed PRO-seq, ATAC-seq and 3'RNA-seq. We also performed CUT&RUN for both GAF and NURF301 in untreated S2 cells.

first: Fabiana

last: Duarte

first: John

last: Lis


title: Integrative analysis of miRNAs and matched gene expression in ESCC


title: Integrative analysis of array-miRNAs and matched Affymetrix gene expression in esophageal squamous cell carcinoma

summary: ESCC is an aggressive tumor with about less than 20% 5-year survival rate, which is fourth worst among all cancers in the USA and the sixth leading cause of cancer mortality worldwide. miRNAs is an important layer of gene regulation that is able to integrate multiple genes into biologically networks.We previously characterized the profile of mRNA expression in ESCC [GSE44021]. In current study, we focused on the relationship of mRNA and miRNA using results from arrays in 113 cases from a high-risk region of China.

overall_design: In order to study a) differential expressed miRNAs and mRNA involved in the pathogenesis of ESCC; b) miRNA significantly correlates with mRNA expressed within the same ESCC set; c) significant miRNA expressions associate with patients’ clinical parameters including patients survival as a potential prognostic biomarker, we did mRNA arrays and miRNA arrays by using 113 ESCC cases with tumor and matched normal tissues.


title: Pioneer factor GAF cooperates with PBAP and NURF to regulate transcription [ATAC-seq]


title: Pioneer factor GAF cooperates with PBAP and NURF to regulate transcription [RNA-seq]


title: Pioneer factor GAF cooperates with PBAP and NURF to regulate transcription [PRO-seq]


title: BRD4 promotes metastatic potential in oral squamous cell carcinoma through the epigenetic  regulation of the MMP2 gene

status: Public on May 08 2020

city: Kumamoto-si

first: Akiyuki

last: Hirosue

state: Kumamoto

address: 1-1-1 Honjo,Chuo-ku

department: Faculty of Life Science

institute: Kumamoto University

summary: Oral squamous cell carcinoma (OSCC) has increased morbidity, and its high malignant potential, including metastasis, affects patient survival. Bromodomain containing 4 (BRD4) is a chromatin protein that recognizes and associates with acetylated histone lysines, and facilitates transcriptional activation. BRD4 has been implicated in cell proliferation, metastasis, and prognosis in several types of cancer. However, the role of BRD4 in OSCC remains to be elucidated. Herein, we investigated the role of BRD4 and the potential utility of BRD4 as a therapeutic target in OSCC. JQ1, which inhibits the interaction between BRD4 and acetylated histones, suppressed the proliferation, migration, and invasion of OSCC cell lines. JQ1 reduced the expression levels of 15 metastasis genes in OSCC, including the Matrix Metallopeptidase 2 (MMP2) gene. Interestingly, our chromatin immunoprecipitation assay showed that JQ1 reduced the BRD4 binding to the histone H3 lysine 27 acetylation-enriched sites in the MMP2 locus. Finally, qRT-PCR analyses of biopsy specimens from OSCC patients revealed that the BRD4 and MMP2 expression levels were correlated in the cancerous regions, and both were highly expressed in lymph node metastasis cases, including delayed metastasis. These results suggest that BRD4 contributes to metastasis in OSCC, through the epigenetic regulation of the MMP2 gene, and thus BRD4 may represent a therapeutic target and a novel prediction indicator for metastasis.

overall_design: The gene expression in HOC313 cells was measured at 48 hours treated with JQ1 (1.0 μM) or vehicle.

first: Tatsuro

last: Yamamoto

first: Masafumi

last: Nakamoto

first: Ryoji

last: Yoshida

first: Junki

last: Sakata

first: Yuichiro

last: Matsuoka

first: Kenta

last: Kawahara

first: Yuka

last: Nagao

first: Masashi

last: Nagata

first: Nozomu

last: Takahashi

first: Akimitsu

last: Hirakaki

first: Masanori

last: Shinohara

first: Mitsuyoshi

last: Nakao

first: Noriko

last: Saitoh

first: Hideki

last: Nakayama


title: Multiplexed relative and absolute quantitative immunpeptidomics reveals MHC I repertoire alterations induced by CDK4/6 inhibition [I]

status: Public on Apr 29 2020

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: Major histocompatibility complex (MHC) class I peptides play a critical role in immune cell recognition. Cancer cells modulate surface MHC levels in response to therapy, thereby affecting antitumor immunity. However, understanding the peptide repertoire response to treatment remains challenging and is limited by quantitative mass spectrometry-based strategies lacking robust normalization controls.  We describe a novel approach that leverages recombinant heavy isotope-coded peptide MHCs (hipMHCs) and multiplex isotope tagging for quantitation of peptide repertoires using low sample input. HipMHCs improve quantitative accuracy by normalizing for variation across analyses, and enable absolute quantification using internal calibrants to determine copies per cell of MHC antigens. Application of this platform to profile the immunopeptidome response to CDK4/6 inhibition and Interferon gamma, known modulators of antigen presentation, uncovered treatment-specific alterations that connect the intracellular response to extracellular immune presentation. This method quantifies repertoire changes that can inform targeted and combination immunotherapy design.

overall_design: 3 replicates each of DMSO-treated and Palbociclib-treated SKMEL5 cells

first: Lauren

middle: E

last: Stopfer

first: Joshua

last: Mesfin

first: Brian

last: Joughin

first: Forest

last: White


title: Cell Specific Transcriptional Responses to Heat Shock in the Mouse Utricle Epithelium

status: Public on May 05 2020

first: Robert

last: Morell

address: 35A Convent Drive, Room 1F-103

institute: National Institute on Deafness and Other Communication Disorders

summary: To determine the transcriptional responses to heat shock of inner ear sensory hair cells and supporting cells, we performed cell-type-specific transcriptional profiling using the RiboTag method, which allows for immunoprecipitation of actively translating mRNAs from specific cell types. RNA-Seq differential gene expression analyses demonstrated that RiboTag identified known cell type-specific markers as well as new markers for hair cells and supporting cells.  Gene expression differences suggest that both hair cells and supporting cells exhibit a transcriptional heat shock response. However, hair cells and supporting cells expressed different members of the heat shock protein family in response to heat stress, and supporting cells expressed a larger number of HSPs. Only one HSP, Chaperonin Containing T-Complex Polypeptide 1 Subunit 8, (CCT8) was uniquely induced in hair cells.  Together our data indicate that hair cells exhibit a limited but unique heat shock response, and supporting cells exhibit a broader and more robust transcriptional response to protective heat stress.

overall_design: RNA-seq comparisons of control (CON) versus Heat-shock treated cultured utricles. The RNA was isolated fom ribotag-enriched immunoprecipates (IP) and compared to RNA isolated from input to identify genes enriched in the IP. Two cre-expressing mouse lines were used to obtain either hair-cell enriched IP samples (Gfi1-Cre) or supporting cell enrich IP samples (GLAST-CreER).

first: Erica

last: Sadler

first: Matthew

last: Ryals

first: Lindsey

middle: A

last: May

first: Daniel

last: Martin

first: Nora

last: Welsh

first: Erich

last: Boger

first: Ronna

middle: P

last: Hertzano

first: Lisa

middle: L

last: Cunningham


title: The impact of progesterone levels and timing of progesterone exposure on human endometrial receptivity

status: Public on Mar 12 2020

city: nottingham

first: Sutham

last: Suthaporn

state: UK

address: Derby road

department: Ob&Gyn

institute: University of Nottingham

summary: Different progesterone levels and timing of exposure results in different endometrial gene expression and implantation potential. Sufficient progesterone level is important to induce endometrial receptivity and endometrial expressed the most receptive stage after exposure to progesterone for 7 days based on decidualisation marker expression.

overall_design: The human endometrial stromal cells were treated with different progesterone concentrations and different timing of exposure.  Global endometrial gene expression  between different progesterone concentrations and different timing of exposure were compared by microarray technique

first: S

first: K

last: Jayaprakasan

first: J

middle: G

last: Thornton

middle: F

last: Walker

last: Hernandez-medrano

first: M

last: Castellanos

middle: T

first: I

last: Khanc

first: W

last: Maalouf


title: RNA-seq analyses of cochleae from a mouse model of DFNB39

status: Public on Mar 25 2020

last: Morell

state: MD

summary: Noncoding microdeletion in mouse Hgf disrupts neural crest migration into the stria vascularis, reduces the endocochlear potential and suggests the neuropathology for human nonsyndromic deafness DFNB39

overall_design: Cochleae from 3 mice homozygous for a 10bp deletion in intron 5 of the Hgf gene and 3 wild-type littermates. Total RNA extracted, converted to cDNA, fragmented to make Illumina libraries and sequenced (93x93 PE) on an Illumina HiSeq1500. Reads were mapped to the mouse genome (GRCm38.vM11) with STAR, and differential gene expression analyzed with DeSeq2.

middle: J