title: DNA polymerase α interacts with H3-H4 and facilitates the transfer to parental histones to lagging strand

status: Public on Sep 02 2020

first: zhiguo

last: zhang

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

summary: How parental histones, the carriers of epigenetic modifications, are deposited onto replicating DNA remains poorly understood. Here, we develop the eSPAN method (enrichment and sequencing of protein associated nascent DNA) in mouse embryonic stem (ES) cells, which detects the distribution of histones with distinct modifications on leading and lagging strands in a relatively small number of cells. We show that DNA polymerase α (Pol α), which synthesizes primers used for synthesis of both leading and lagging strands, binds histone H3-H4 preferentially. The Pol α mutant defective in histone binding in vitro impairs the transfer of parental H3-H4 to lagging strand in both yeast and mouse ES cells. Finally, dysregulation of both coding genes and non-coding endogenous retroviruses (ERVs) is detected in mutant ES cells defective in parental histone transfer. Together, we report an efficient eSPAN method for analysis of DNA replication coupled processes in mouse ES cells and reveal the mechanism of Pol α in parental histone transfer.

sample_organism:
Saccharomyces cerevisiae
Mus musculus

platform_organism:
Saccharomyces cerevisiae
Mus musculus

overall_design: OK-Seq were performed in mouse ES (mES) cells  to identify replication zones. The CUT&TAG and eSPAN experiments were conducted in WT, POLA1-2A mutant, MCM2-2A mutant, POLE3 KO and POLE4 KO mES cells. The histone markers performed by CUT&TAG and eSPAN methods in mES cells included H4K20me2, H4K12ac, H3K36me3. In Saccharomyces cerevisiae yeast, we also performed ChIP and eSPAN expriments for H3K4me3 and H3K56ac in WT and pol1-2A2 mutant yeast cells. For the regulation of gene expression, we performed  total RNA-seq and H3K9me3 CUT&TAG experiments in WT, POLA1-2A mutant and MCM2-2A mutant mES cells.

first: Zhiming

first: Xu

last: Hua

first: Albert

last: Serra-Cardona

first: Xiaowei

last: Xu

first: Hui

last: Zhou

first: Chun-long

last: Chen

first: Ruiming

first: Zhiguo


title: Neuronal Defects in a Human Cellular Model of 22q11.2 Deletion Syndrome

status: Public on Jul 08 2020

city: Palo Alto

first: Themasap

middle: Ahmad

last: Khan

state: CA

address: 318 Campus Drive

department: Psychiatry

country: USA

institute: Stanford University

type: Expression profiling by high throughput sequencing

summary: 22q11.2 deletion syndrome (22q11DS) is a common cause of developmental neuropsychiatric disorders, including psychosis, autism and epilepsy. This highly penetrant genetic syndrome provides a unique opportunity to mitigate the challenges raised by the heterogeneity of complex mental disorders and to identify specific neuronal phenotypes. Here, we generated induced pluripotent stem cells from subjects carrying a 3 Mb deletion at the 22q11.2 locus and from controls and differentiated these cells in vitro into three-dimensional organoid resembling the developing cerebral cortex. We performed single-cell RNA-sequencing to establish the reliability and reproducibility of cortical organoid differentiation in 22q11DS.

overall_design:
RNA sequencing of iPS cell-derived cortical spheroids from four human cell lines: two derived from subjects with 22q11.2 Deletion Syndrome and two control subjects.

**Submitter declares that raw data were not provided due to confidentiality concerns.**

first: Sergiu

last: Pasca


title: Prognostic Molecular Signatures for Metastatic Potential in Clinically Low-Risk Stage I and II Clear Cell Renal Cell Carcinomas

status: Public on Jul 27 2020

city: Mahasset

first: Andrew

last: Shih

state: NY

address: 350 Community Dirive

institute: Feinstein Institute - Northwell Health

summary: Presented is the differential expression of mRNA and miRNA in 44 Stage I and Stage II patients who developed metastasis within 5 years of nephrectomy, compared to 21 patients who remained disease free. Extracted RNA from nephrectomy specimens preserved in FFPE blocks was sequenced using RNAseq. MiRNA expression was done using the TaqMan OpenArray qPCR protocol.

overall_design: Examination of molecular differences between metatstatic versus non-metatstatic in stage I and stage II

middle: J

first: Xin-Hua

last: Zhu


title: Single-cell RNA-seq of the developing C57BL/6 mouse ovary from E11.5 to E14.5

status: Public on Jun 30 2020

city: Qingdao

first: Wei

last: Ge

state: Shandong Province

address: Changcheng Road

department: College of life sciences

country: China

institute: Qingdao Agricultural University

summary: We profiled a time-course single-cell RNA-seq on C57BL/6 mouse ovary from E11.5 to E14.5 to study the cell population heterogeneity and regulation of meiosis initiation. We collected single cell from XX gonads at E11.5, E12.5, E13.5 and E14.5, and were further captured with 10x Genomics based single-cell system. By using single-cell RNA seq, we recapitulated the progression of meiosis using pseudotime ordering of all germ cells and delineated key molecular network among all germ cell clusters. Besides, we provide candidate meiosis stage-specific master regulons along the progression of meiosis and provide detailed transcriptome profile information for controversial Xist+ PGCs. Our data here offers the opportunity for exploring mechanisms underlying germ cell meiosis progression at single cell resolution.

overall_design: We totally analyzed ~20,000 single cell transcriptome profile from E11.5 to E14.5 XX gonads to reveal cellular heterogeneity during meiosis initiation stage.

first: W

first: R

middle: Q

last: Zhang

last: Shen


title: RNA sequencing for human induced pluripotent derived cerebral organoids

status: Public on Jun 22 2020

city: Boston

first: Annie

last: Kathuria

state: MA

address: 185 cambridge street

institute: Mass Gen Hospital

summary: Total RNA sequecing for human induced pluripotent derived cerebral organoids from healthy controls and schizophrenia (SCZ) patients

overall_design: Comparing the disease state (SCZ) versus healthy control

first: Rakesh

last: Karmacharya


title: Influence of G. lamblia infection on the transcriptional profile in intestinal and liver tissue [intestinal epithelial cells]

status: Public on Jun 01 2020

city: Aachen

first: Mathias

middle: W.

last: Hornef

address: Steppenbergallee 203

department: Medical Microbiology

country: Germany

institute: RWTH Áachen University

summary: G. lamblia is a fecal-oral transmitted human enteropathogenic protozoan with extremely high incidence in endemic areas in Africa and Asia particularly in the infant population.  It homes to the proximal small intestine and induced diarrhea and malabsoption. Here we established a novel murine G. lamblia infection model and analyzed the tissue response and downstream microbial and metabolic effects in the host.

overall_design: Neonate mice at the age of 3-4 days were orally infected by gavage with 2x105 G. lamblia ATCC 5058 (assemblage B, strain GS, clone H7) trophozoites. The infection was monitored by antigen ELISA and quantitative PCR using weekly fecal samples as well as histology, transcriptional analysis of total gut tissue, isolated intestinal epithelial cells (Lotz et al., JEM, 2006) and total liver tissue as well as metabolic analysis in blood, intestinal content and liver tissue.

middle: W

first: Ambre

middle: L

last: Riba

first: Kasra

last: Hassani


title: Influence of G. lamblia infection on the transcriptional profile in intestinal and liver tissue [liver]

overall_design: Neonate mice at the age of 3-4 days were orally infected by gavage with 2x10^5 G. lamblia ATCC 5058 (assemblage B, strain GS, clone H7) trophozoites. The infection was monitored by antigen ELISA and quantitative PCR using weekly fecal samples as well as histology, transcriptional analysis of total gut tissue, isolated intestinal epithelial cells (Lotz et al., JEM, 2006) and total liver tissue as well as metabolic analysis in blood, intestinal content and liver tissue.


title: Heterogeneous mesenchymal cell types modulate neonatal lung development and its response to hyperoxia

status: Public on May 27 2021

city: Kensington

first: Fabio

last: Zanini

state: NSW

address: High and Botany St

country: Australia

institute: University of New South Wales

summary: During the first days of life, the lung surface area increases explosively to enable efficient oxygen exchange. Alveolarization and angiogenesis involve profound changes within the lung mesenchyme to modulate extracellular matrix composition, tissue elasticity, and coordination with the lung epithelium and endothelium. To define the cell types and states populating the perinatal lung mesenchyme, we performed single cell transcriptomics and in-situ imaging in mice and discovered an extremely heterogeneous and dynamic landscape of fibroblasts, airway smooth muscle-like, and mural cells spanning fourteen distinct populations. In the fibroblast and airway smooth muscle-like compartments, bipotent progenitors differentiate rapidly within one day of birth and then again towards the end of alveolarization, while mural cell types are characterized by slow, gradual changes. Glucocorticoid release, retinoic acid inactivation, and oxygen sensing are controlled by specific stromal progenitors. A population of myofibroblasts arises postnatally, peaks at the onset of alveolarization and disappears before three weeks of age. Paracrine signaling with dozens of lung cell types decreases after birth and especially during alveolarization. Nonetheless, alveolarization is the most proliferative developmental stage, followed by a shift towards cell quiescence. Exposure to hyperoxia during the first week of life delayed the transcriptomic changes of normal development, mirroring the arrested development observed in human neonatal bronchopulmonary dysplasia (BDP). Hyperoxia also caused a severe loss of pericytes and myofibroblasts and reduced their proliferation, decreased mesenchymal-endothelial communications, gave rise to a small novel population of contractile alveolar fibroblasts and increased matrix adhesion and contractility across the mesenchyme.

overall_design: scRNA-Seq on FACS sorted cells

first: Xibing

last: Che

first: Nina

last: Suresh

first: Carsten

last: Knutsen

first: Min

last: Liu

first: Racquel

last: Domingo-Gonzales

first: Robert

middle: C

last: Jones

first: Paula

last: Klavina

first: Yike

last: Xie

first: Stephen

middle: R

last: Quake

first: Cristina

middle: M

last: Alvira

first: David

middle: N

last: Cornfield


title: Time series of Escherichia coli BL21(DE3) after temperature upshift from 37°C to 42°C, tiling arrays

status: Public on Apr 12 2020

city: Seoul

first: Sung Ho

last: Yoon

address: 120 Neungdong-ro, Gwangjin-gu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Konkuk University

type: Expression profiling by genome tiling array

summary:
Heat-responsive and time-resolved changes in transcriptome of E. coli BL21(DE3)
Experimentally mapped transcriptome structure of Escherichia coli BL21(DE3) by hybridizing total RNA (including RNA species <200 nt) to genome-wide high-density tiling arrays (60 mer probes tiled every 10 nt).

overall_design: One sample was taken from chemostat at 37°C (time point of -30min) and eight time-series samples were taken from chemostat at 42°C (time points of 2min, 10min, 30min, 1h, 2h, 4h, 8h, and 40h)

first: Sung

middle: H

first: Sinyeon

last: Kim


title: Influence of G. lamblia infection on the transcriptional profile in adult small intestinal tissue and isolated intestinal epithelial cells

status: Public on Apr 03 2020

first: Mathias

last: Hornef

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

overall_design: Refer to individual Series


title: Influence of G. lamblia infection on the transcriptional profile in intestinal and liver tissue


title: Transcriptional analysis of total small intestinal tissue from adult infected and age-matched control animals

summary: G. lamblia is a fecal-oral transmitted human enteropathogenic protozoan with extremely high incidence in endemic areas in Africa and Asia particularly in the infant population. It homes to the proximal small intestine and induceses diarrhea and malabsoption. Here we established a novel murine G. lamblia infection model and analyzed the tissue and epithelial response and downstream microbial and metabolic effects in the adult host.

overall_design: Neonate mice at the age of 3-4 days were orally infected by gavage with 2x10e5 G. lamblia ATCC 5058 (assemblage B, strain GS, clone H7) trophozoites. The infection was monitored by antigen ELISA and quantitative PCR using weekly fecal samples as well as histology. Transcriptional analysis of total gut tissue and isolated intestinal epithelial cells (Lotz et al., JEM, 2006) as well as metabolic analysis in blood, intestinal content and liver tissue were performed in adult animals.

first: Ambre

last: Riba

first: Kasra


title: Influence of G. lamblia infection on the transcriptional profile in intestinal and liver tissue [small intestinal tissue]

last: Hassani


title: Transcriptional analysis of isolated intestinal epithelial cells (IEC) from adult infected and age-matched control animals


title: Responses of retinal and brain microvasculature to diabetes revealed by global expression profiling

status: Public on Mar 31 2020

city: Groningen

first: Youhai

last: Li

state: Groningen

address: Hanzeplein 1

department: Dept. Pathology and Medical Biology

country: Netherlands

institute: University Medical Center Groningen (UMCG)

summary:
Retinal microvessels (RMVs) and brain microvessels (BMVs) were isolated from diabetic and nondiabetic rats.  RNA were extracted, amplified and processed on Affymetrix rat 2.0 microarray Chips. Differently expressed genes (DEGs) between diabetic RMVs and nondiabetic RMVs, and between diabetic BMVs and nondiabetic BMVs were analyzed.
Using these DEGs, we analyzed and compared the diabetic effects on the gene expression profiles in retinal microvasculature and brain microvasculature. In the brain microvasculature multiple compensatory mechanisms exists, serving to protect brain tissue from diabetic insults, whereas these mechanisms are not activated in the retinal microvasculature.

overall_design: Totally, we analyzed four groups: diabetic_BMVs, nondiabetic_BMVs, diabetic_RMVs, nondidabetic_RMVs. Each group contains 6 biological replicates. The nondiabetic simples were used as controls.

first: Alen

last: Faiz

first: Han

last: Moshage

first: Lothar

last: Schilling

first: J

middle: A

last: Kamps


title: Transcriptome of human macrophages infected with Aspergillus fumigatus

city: Braga

first: Nuno

middle: S.

last: Osório

address: Campus de Gualtar

country: Portugal

institute: ICVS

summary: RNA sequencing data from human monocyte-derived macrophages after infection with Aspergillus fumigatus.

overall_design: MDMs (5×105/well in 24-well plates) were infected with A. fumigatus conidia at a 1:2 effector-to-target ratio, and samples were collected after 2 and 6 hr. Uninfected MDMs were cultured in parallel as controls.

first: Samuel

last: Gonçalves

first: Cláudio

last: Duarte-Oliveira

first: Cláudia

middle: F

last: Campos

first: Vishukumar

last: Aimanianda

first: Rob

last: ter Horst

first: Luis

last: Leite

first: Toine

last: Mercier

first: Paulo

last: Pereira

first: Miguel

last: Fernández-García

first: Daniela

last: Antunes

middle: S

last: Rodrigues

first: Catarina

last: Barbosa-Matos

first: Joana

last: Gaifem

first: Inês

last: Mesquita

first: António

last: Marques

first: Egídio

last: Torrado

first: Fernando

first: Sandra

last: Costa

first: Leo

last: B Joosten

first: Katrien

last: Lagrou

first: Johan

last: Maertens

first: João

last: Lacerda

last: Campos Jr.

first: Gordon

middle: D

last: Brown

first: Axel

last: Brakhage

first: Coral

last: Barbas

first: Ricardo

last: Silvestre

first: Frank

last: van de Veerdonk

first: Georgios

last: Chamilos

first: Mihai

middle: G

last: Netea

first: Jean-Paul

last: Latgé

last: Cunha

first: Agostinho

last: Carvalho


title: Combined deletion of Bap1, Nf2, and Cdkn2ab causes rapid onset of malignant mesothelioma in mice

status: Public on Apr 04 2020

city: Amsterdam

first: Jitendra

last: Badhai

address: Plesmanlaan 121

department: Division Molecular Genetics

institute: Netherlands Cancer Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Here we describe a mouse model of mesothelioma with combined deletion of Bap1, Nf2, and Cdkn2ab that shows rapid onset and recapitulates human mesothelioma including its response to the standard treatment. This autochthonous model should be attractive for testing cancer immunotherapies.

overall_design: mRNA profiles of BNC and NC mesothelioma

first: J


title: RNA-Seq of resting and activated Jurkat E6.1 cells

status: Public on Feb 19 2020

city: Oxford

first: Ling

last: Felce

state: Select State

address: Botnar Research Centre, Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

summary: Purpose: to examine the early transcriptional responses to stimulation in Jurkat E6.1 cells, and the effects thereon of chemokine signaling

overall_design: The mRNA fraction of total RNA from resting Jurkat E6.1 cells, and Jurkat E6.1 activated in the presence or absence of CXCL12 and CCL19 was sequenced in duplicate using Illumina HiSeq4000

first: Suet

first: Gillian

last: Farnie

first: Michael

last: Dustin

first: James


title: The molecular and stromal landscape of salivary duct carcinoma reveals new therapeutic opportunities

status: Public on Feb 12 2020

city: Montpellier

first: Jacques

last: Colinge

address: 208, avenue des Apothicaires

country: France

institute: Inserm

summary: Purpose: RNA-sequencing data was used to determine the main molecular pathways invovled in SDC and describe the tumoral microenvironment composition with key cellular networks within the latter.

overall_design:
mRNA profiles were generated on HiSeq4000 using 2 x 75pb cycles, generating 130 millions of reads.

Third-party reanalyzed SRR data accessions:
SDC1 SRR5173683
SDC2 SRR5173684
SDC3 SRR5173685
SDC4 SRR5173686
SDC5 SRR5173687
SDC6 SRR5173688
SDC7 SRR5173689
SDC8 SRR5173690
SDC9 SRR5173691
SDC10 SRR5173692
SDC11 SRR5173693
SDC12 SRR5173694
SDC13 SRR5173695
SDC14 SRR5173696
SDC15 SRR5173697
SDC16 SRR5173698

first: Melissa

last: Alame

first: Emmanuel

last: Cornillot

first: Valère

last: Cacheux

first: Guillaume

last: Tosato

first: Marion

last: Four

first: Laura

last: De Oliveira

first: Stéphanie

last: Gofflot

first: Philippe

last: Delvenne

first: Evgenia

last: Turtoï

first: Simon

last: Cabello-Aguilar

first: Hideru

last: Obinata

first: Masahiko

last: Nishiyama

first: Andreï

first: Valérie

last: Costes-Martineau


title: RNA-seq on miRNA induced mouse keratinocytes. miR-200b cluster and miR-205.

status: Public on Feb 26 2020

city: Boulder

first: Glen

last: Bjerke

state: CO

address: 347 UCB

department: MCDB

institute: University of Colorado

summary: Vehicle versus Doxycycline miRNA induction.

overall_design:
miR-200 cells are K14rtTA/pTRE2-miR-200b cluster
miR-205 cells are K14rtTA/pTRE2-miR-205
For miR-200 induction, samples were sequenced on a Miseq and a Hiseq machine. Counts were then combined at the step of Htseq counts. This gave the most consistent results.
miR-200 experiments were done in duplicate and miR-205 were done in triplicates

first: Rui

last: Yi


title: Transcriptional Alterations of Genes Related to Fertility Decline in Male rats Induced by Chronic Sleep Restriction

status: Public on Dec 16 2019

city: zhangjiakou

first: wenyang

last: chen

address: zuanshi south street

institute: Hebei North University

type: Methylation profiling by high throughput sequencing

summary: The adverse effects of sleep disorders on male fertility are increasingly concerning. In this study, a rat model of chronic sleep restriction (CSR) was established using the modified multiplatform method. The effects of CSR on the fertility of male rats were evaluated first based on sexual behavior. Serum hormones, including testosterone (T), prolactin (PRL), luteinizing hormone (LH) and follicle-stimulating hormone (FSH), and sperm parameters (concentration, viability, motility, deformation rate) were measured, and testicular histology was analysed by hematoxylin and eosin staining. The transcriptional differences between CSR rats and control rats were detected by RNA sequencing (RNA-Seq), and DNA methylation was then detected by bisulfite sequencing. After the differently expressed genes of CSR rats were sequenced and screened, some representative up- and down-regulated genes were randomly sampled to verify the sequencing results by real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). Finally, functional annotations were completed, including gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomic (KEGG) pathway analyses. The results showed that the sexual behavior of CSR rats did not change when compared with control group rats. The sperm concentration, viability and motility of the CSR rats decreased significantly, while the sperm malformation rate increased significantly. In the KEGG pathway analysis database, some specific differentially expressed genes were screened, which are involved in metabolic pathways, inflammation-related pathways, the renin-angiotensin system, etc. However, the aforesaid differentially expressed genes in the testes were not related to their DNA methylation status. CSR could significantly reduce the fertility of male rats, and one of its mechanisms occurs by altering gene expression in the testes, which has nothing to do with their DNA methylation. It was suggested that CSR could cause male infertility by significantly altering the testicular transcriptome.

overall_design: There were total two groups, including chronic sleep restriction group and control group, each group had 6 samples for detecting.

first: Wenyang

last: Chen

first: Xingdao

last: Guo

first: Zhiping

last: Jin

first: Runan

last: Li

first: Lixia

last: Shen

first: Wei

first: Wangting

last: Cai

first: Guirong

last: Zhang


title: Analysis of the turkey reproductive tract transcriptome

status: Public on Dec 21 2019

city: Olsztyn

first: Jan

middle: Pawel

last: Jastrzebski

state: Wa-Ma

address: ul. Oczapowskiego 1A

department: Biology and Biotechnology

country: Poland

institute: University of Warmia and Mazury in Olsztyn

summary:
The male reproductive tract tissue samples were obtained from six 38-wk-old turkeys. The gene expression pattern in turkey testis, epididymis and ductus deferens were determined by high-throughput transcriptome sequencing. The obtained sequence reads were mapped to the turkey genome, and relative expression values were calculated for the analysis of differential expressed genes.
Bioinformatics analysis revealed several candidate genes potentially involved in spermatogenesis, spermiogenesis and flagella formation in testis and post-testicular sperm maturation in epididymis and ductus deferens.
The achievement of spermatozoa motility during post-testicular maturation were found to be linked with development of flagellum actin filaments and biochemical processes including Ca2+ influx and protein phosphorylation/dephosphorylation. Finally, genes involved in reproductive system development and morphogenesis were identified.

overall_design: The purpose of project was to profile testis, epididymis and ductus deferens transcriptome and identify the key genes and pathways associated with specificity of turkey reproductive tract. Novel candidate genes and pathways were identified as playing roles in spermatogenesis, spermiogenesis and flagella formation in testis and post-testicular sperm maturation in epididymis and ductus deferens.

first: Mariola

last: Slowinska

first: Lukasz

last: Paukszto

middle: P

last: Jastrebski


title: MUC1-C Drives Lineage Plasticity in Progression to Neuroendocrine Prostate Cancer

status: Public on Dec 02 2019

city: Buffalo

first: Qiang

last: Hu

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

summary: Neuroendocrine prostate cancer (NEPC) is a highly aggressive malignancy of increasing prevalence with an unmet need for targeted therapeutic approaches. The oncogenic MUC1-C protein is overexpressed in castration-resistant prostate cancer (CRPC) and NEPC; however, there is no known role for MUC1-C in driving lineage plasticity to these advanced PC phenotypes. The present studies demonstrate that upregulation of MUC1-C in androgen-independent (AI) PC cells suppresses androgen receptor (AR) axis signaling and induces the neural BRN2 transcription factor by a previously unrecognized MYC-mediated mechanism. MUC1-C activates the BRN2 pathway in association with induction of MYCN, EZH2 and NE differentiation markers (ASCL1, AURKA and SYP), which are linked to NEPC progression. We also show that MUC1-C suppresses the p53 pathway, induces the Yamanaka pluripotency factors (OCT4, SOX2, KLF4 and MYC) and drives stemness. Of potential clinical relevance, targeting MUC1-C decreases PC self-renewal capacity and tumorigenicity, supporting the treatment of CRPC and NEPC with agents directed against this oncoprotein. These findings and the demonstration that MUC1-C is upregulated and associated with suppression of AR signaling, and increases in BRN2 expression and the NEPC score in PC tissues highlight the unanticipated importance of MUC1-C as a master effector of lineage plasticity in progression to advanced PC with NE features.

overall_design: LNCaP-AI and DU-145 cells stably expressing a tet-MUCshRNA vector were treated with vehicle control or doxycycline. Total RNA from cells cultured in triplicates was isolated and used for library preparation.

first: Rajabi

last: Kufe D

first: Long

last: Mark

first: Hu

last: Qiang


title: Senescence-induced vascular remodeling creates therapeutic vulnerabilities in pancreas cancer

status: Public on Feb 03 2020

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: KRAS mutant pancreatic ductal adenocarcinoma (PDAC) is characterized by a desmoplastic response that promotes hypovascularity, immunosuppression, and resistance to chemo- and immunotherapies. We show that a combination of MEK and CDK4/6 inhibitors that target KRAS-directed oncogenic signaling can suppress PDAC proliferation through induction of retinoblastoma (RB) protein-mediated senescence. In preclinical mouse models of PDAC, this senescence-inducing therapy produces a senescence-associated secretory phenotype (SASP) that includes pro-angiogenic factors that promote tumor vascularization, which in turn enhances drug delivery and efficacy of cytotoxic gemcitabine chemotherapy. In addition, SASP-mediated endothelial cell activation stimulates the accumulation of CD8+ T cells into otherwise immunologically “cold” tumors, sensitizing tumors to PD-1 checkpoint blockade. Therefore, in PDAC models, therapy-induced senescence can establish emergent susceptibilities to otherwise ineffective chemo- and immunotherapies through SASP-dependent effects on the tumor vasculature and immune system.

overall_design: For RNA-seq analysis of the transcriptional profiles of tumor cells from KPCmut transplant PDAC tumors treated for 10 days with vehicle or combined trametinib (1 mg/kg body weight), and palbociclib (100 mg/kg), total RNA was extracted from GFP+ tumor cells (sorted on a FACSAria (BD Biosciences)) using the RNeasy Mini Kit (Qiagen). Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation. For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (Bolger et al., 2014), aligning sequencing data to GRCh37.75(hg19) with STAR (Dobin et al., 2013), and genome wide transcript counting using HTSeq (Anders et al., 2015) to generate a RPKM matrix of transcript counts. Genes were identified as differentially expressed using R package DESeq2 with a cutoff of absolute log2FoldChange ≥ 1 and adjusted p-value < 0.05 between experimental conditions (Love et al., 2014). Functional enrichments of these differential expressed genes were performed with enrichment analysis tool Enrichr (Kuleshov et al., 2016) and the retrieved combined score (log(p-value) * z-score) was displayed.

first: Marcus

last: Ruscetti

first: John

last: Morris IV

first: Riccardo

last: Mezzadra

first: James

last: Russell

first: Josef

last: Leibold

first: Paul

middle: B

last: Romesser

first: Janelle

last: Simon

first: Amanda

last: Kulick

first: Myles

last: Fennell

first: Jinyang

first: Robert

middle: J

last: Norgard

middle: E

last: Wilkinson

first: Direna

last: Alonso-Curbelo

first: Ramya

last: Sridharan

first: Daniel

last: Heller

first: Elisa

last: de Stanchina

first: Ben

middle: Z

last: Stanger

first: Charles

last: Sherr

first: Scott

last: Lowe


status: Public on Apr 01 2020

first: Annie

last: Kathuria

summary: Total RNA sequecing for human induced pluripotent derived cerebral organoids from healthy controls and Bipolar disorder

overall_design: Comparing the disease state BPI versus healthy control

first: Rakesh

last: Karmacharya


title: CD4 help is required for the generation of a transcriptionally distinct cytolytic CD8 T cell subset that arises during chronic viral infection

status: Public on Dec 05 2019

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

summary: CD4 help is crucial to sustain the function of exhausted CD8 T cells, yet the detailed mechanisms by which CD4 help regulates CD8 T cell differentiation and function during chronic viral infection remain elusive. Here, using single cell RNA-sequencing (scRNA-seq) we show that CD8 T cells responding to chronic viral infection are more heterogeneous than previously appreciated, with three transcriptionally distinct subsets dominating the late phase of the antiviral response. Importantly, our findings uncover the formation of a previously unrecognized CD8 T cell subset that exhibits potent cytolytic function. This subset is characterized by high expression of killer cell lectin-like receptors Klre1 and Klra9, the chemokine receptor CX3CR1, and the transcription factors T-bet and Zeb2. Notably, our data further demonstrate that the formation of this cytotoxic subset is critically dependent on CD4 help and that exploitation of this developmental pathway may be used therapeutically to enhance the killer function of CD8 T cells infiltrated into the tumor. These findings uncover novel cellular and molecular mechanisms of how CD4 help regulates CD8 T cell differentiation during persistent infection and have implications towards optimizing the generation of protective CD8 T cells in immunotherapy.

overall_design: Two samples (day 8 and day 30) prepared using 10x Genomics Chromium platform

first: David

last: Schauder


title: β-Caryophyllene Enhances the Transcriptional Upregulation of SREBP-dependent Lipid Biosynthesis in Breast Cancer Cells

status: Public on Dec 01 2019

city: Louisville

first: Christopher

last: Frost

state: KY

address: 139 LSB

department: Biology

institute: University of Louisville

summary: β-caryophyllene (BCP) exhibits anti-proliferative properties in cancer cells.  Here, we examine the hypothesis that BCP induces membrane remodeling.  Our data show that high concentrations of BCP increase membrane permeability of human breast cells (hBrC) causing detachment and cell death.  At a “sub-lethal” concentration of BCP, we show that BCP induces a striking upregulation of genes involved in cholesterol biosynthesis, including the gene that encodes for HMGCoA reductase (HMGCR), the rate-determining step in cholesterol biosynthesis. In addition, stearoyl-CoA desaturase (SCD) is also upregulated which would lead to the enhanced formation of monounsaturated fatty acids, specifically oleate and palmitoleate from stearoyl CoA and palmitoyl CoA, respectively.  These fatty acids are major components of membrane phospholipids and cholesterol esters. Together, these data suggest that cells respond to BCP by increasing the synthesis of components found in membranes.  These responses could be viewed as a repair mechanism and/or as a mechanism to mount resistance to the cytotoxic effect of BCP.  Blocking HMGCR enhances the cytotoxicity of BCP, suggesting that this may provide an additional therapeutic tool in controlling breast cancer cell growth, assuming that targeted specificity could be established.

overall_design: Examination of UFH-001 Triple Negative Breast Cancer cell line under hypoxic conditions (control) or in the presence of either 20uM or 200uM beta-caryophyllene (NOTE: The 3 hypoxia controls are duplicates of data submitted to GEO previously as part of another project - GSE123856)

first: Susan

middle: C


title: ssDNA aptamers against amyloid-β peptide as biomarker and inhibtor [SELEX]

status: Public on Sep 30 2019

city: Coimbatore

first: Nikhil

last: Maroli

state: TAMIL NADU

address: Bharathiar University

department: Physics

country: India

institute: DRDO BU CLS

summary: We report high-affinity ssDNA aptamers as biomarkers and antagonists of amyloid-β peptide. We generated three novel aptamer sequences from the pool of aptamers through the SELEX process, and evaluated their affinity and sensitivity using enzyme-linked immunosorbent assay (ELISA). (The forward primer: ATTAGTCAAGAGGTAGACGCACATA, reverse primer TTCTGGTCGTCGTGACTCCTAT) The ssDNA aptamers modeled into a three-dimensional structure; interaction and mechanism of action derived through molecular dynamics simulations (MD). MD simulations revealed the nature of binding and inhibition of aggregation by binding with amyloid-β peptide monomers, dimers, and other oligomers. The presence of high non-bonded interaction energy along with hydrogen bonds constitutes the complex structure of the aptamer-amyloid-β peptide. Furthermore, the changes in the secondary structure induced by aptamers may help remove the peptide through the blood-brain barrier. This study provided a framework for the application of aptamers against amyloid-β peptides as biomarkers and antagonists.

overall_design:
generationa and modeling of aptamers against  amyloid-β peptide and its mechanism of action.
Please note that the raw data corresponding for the aptamers were submitted which is required for the study (rest of the readings/files are discarded) and since the resulting raw data contains only 4 lines with 23 or 64 bp reads, they are included as GEO sample supplementary files.


title: Lung endothelial cells (MLECs) from knock-in  mouse model with or without the causative HGPS LmnaG609G mutation

status: Public on Oct 17 2019

city: Shenzhen

first: yuan

last: meng

address: College avenue 1066#

department: Department of Medicine

institute: Shenzhen University

summary: Vascular dysfunction is one of the typical characteristics of aging, but its contributing roles to systemic aging and the therapeutic potential is lacking experimental evidence. Accumulating data suggest that the mechanisms underlying aging are similar to those governing Hutchinson-Gilford progeria syndrome (HGPS), a premature aging disease, in which affected patients succumb to cardiovascular diseases (CVDs). Here, we generated a knock-in mouse model with the causative HGPS LmnaG609G mutation, called progerin. We crossed Lmnaf/f mice with a Tie2-Cre line to get Lmnaf/f;TC mice, which exhibit defective microvasculature and neovascularization, accelerated aging and shortened lifespan. Single-cell transcriptomic analysis of murine lung endothelial cells (MLECs) revealed a significant upregulation of inflammatory response. These data support endothelial dysfunction as a primary trigger of systemic aging and highlight gene therapy as a potential strategy for the clinical treatment of HGPS and age-related vascular dysfunction.

overall_design: We isolated CD31+ MLECs from three pairs of LmnaG609G/G609G (G609G) and Lmnaf/f (Flox) mice by FACS

first: Yuan

first: Baohua

last: Liu


title: ssDNA aptamers targeting Salmonella paratyphi A [SELEX]

status: Public on Dec 31 2019

summary: Here, we report an ssDNA aptamer with high specificity and affinity towards Salmonella paratyphi A generated using the whole-cell SELEX process. The aptamers generated against an organism show salient features, such as higher affinity than existing antibodies, and are highly specific towards the targeted organism. Thus, the generated aptamer sequences can serve as potential biomarkers for the onsite detection of pathogens with high specificity and sensitivity. Molecular dynamics simulation was used to model the linear chain of the aptamers to a three-dimensional conformation, and the binding mechanism against DNA gyrase was established.

sample_organism: Salmonella enterica subsp. enterica serovar Paratyphi A

overall_design: Salmonella paratyphi A specifc ssDNA bioligands for POC diagnostics

first: Maroli

last: Nikhil


title: Long range inter-chromosomal interaction of Oct4 distal enhancer loci regulates ESCs pluripotency

status: Public on Nov 30 2019

city: Los Angeles

first: Byoung San

last: Moon

state: California

address: 1425 San Pablo St. 409B

institute: University of Southern California

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

overall_design: Refer to individual Series


title: Long range inter-chromosomal interaction of Oct4 distal enhancer loci regulates ESCs pluripotency [RNA-seq]

summary: Nuclear architecture underlies the transcriptional programs within the cell to establish cell identity. As previously demonstrated, long-range chromatin interactions of the Oct4 distal enhancer (DE) are correlated with active transcription in naïve state embryonic stem cells. Here, we identify and characterize extreme long range interactions of the Oct4 DE through a novel CRISPR labeling technique we developed and chromosome conformation capture to identify lethal giant larvae 2 (Llgl2) and growth factor receptor-bound protein 7 (Grb7) as putative functional interacting target genes in different chromosomes. We show that the Oct4 DE directly regulates expression of Llgl2 and Grb7 in addition to Oct4. Expression of Llgl2 and Grb7 closely correlates with the pluripotent state, where knock down of either result in loss of pluripotency, and overexpression enhances somatic cell reprogramming. We demonstrated that biologically important interactions of the Oct4 DE can occur at extreme distances that are necessary for the maintenance of the pluripotent state.

overall_design: Stranded mRNA-seq of mouse ESCs with Oct4 DE deletion via treatment with tamoxifen inducible Cre and/or treated with doxycycline for inducible transgenic mOct4 expression

last: Huang

first: Byoung-San

first: Fan

last: Gao

first: Wange

last: Lu


title: Synthetic lethal and resistance interactions with BET bromodomain inhibitors

status: Public on Mar 30 2020

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute


title: Towards understanding the genetic basis of high-elevation adaptation in Himalayan giant honey bee

status: Public on Nov 07 2019

city: Beijing

first: long

last: su

state: Beijing

address: Xiangshan Street

institute: sulong

summary: Apis laboriosa, the Himalayan giant honey bee, is a species of honey bees (genus Apis), which is highly adapted to highland habitats and mainly occurs in mountainous regions, particularly the Himalayas. Up to data, the genetic basis of its high-elevation adaptation remains a mystery. In the present study, we generated transcriptomes for A. laboriosa and its closely related species A. dorsata, we then characterized the transcriptomes and did comparative and evolutionary analysis between them to understand the genetic basis of high-altitude adaptation in A. laboriosa. We identified 1,605 genes that are absent in A. dorsata but present in A. laboriosa. Those A. laboriosa-specific genes were involved in DNA damage repair, low temperature tolerance and oxidative stress response. In addition, for genes shared by the two species, genes related to anoxia tolerance, freeze tolerance and UV irradiation were positively selected in A. laboriosa. Taken together, our results suggest that both the increased copy number and the accelerated protein sequence evolution of genes related to high-elevation adaptation made a difference between A. laboriosa and A. dorsata, which should contribute to the adaptation of A. laboriosa to challenging environments in Himalayas.

sample_organism:
Apis dorsata
Apis laboriosa

platform_organism:
Apis dorsata
Apis laboriosa

overall_design: Three alive worker bees of A. laboriosa and three alive worker bees of A. dorsata are collected in different places. A single pooled RNA sample was prepared for each species by mixing equal amount of the RNA (1 μg) extracted from each of the three samples. The pooled 3 μg of RNA sample was used as input material for the species to construct sequencing libraries, which were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. The obtained libraries were sequenced on an Illumina Hiseq 2500 platform and paired-end reads were produced, with a read length of 150 nt.

first: Cheng

last: Sun

first: Lianfei

last: Cao

first: Long

last: Su


title: Long non-coding RNAs and mRNAs expression profilling in human nasopharyngeal carcinoma

city: Guangzhou

first: Ying

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Long non-coding RNAs (lncRNAs) play important roles in the tumorigenesis and progression of cancers. However, the clinical significance of lncRNAs and their regulatory mechanisms in nasopharyngeal carcinogenesis (NPC) are largely unknown. In this study, we used the microarray analysis to study the different expression profiles of lncRNAs and mRNAs in human nasopharyngeal carcinoma tissues. We performed genome-wide lncRNAs expression in 3 pairs of NPC and normal nasopharynx tissues and identified 384 dysregulated lncRNAs (fold change ≥2 and P <0.05).

overall_design: Total RNA recovered from 3 pairs of NPC and normal nasopharynx tissues were used to acquire different expression profiles of mRNAs and lncRNAs. In this way, this study provided the basis for identifying novel NPC biomarkers and further studying the roles and functions of differentially expressed lncRNA/mRNA in NPC.

first: Zi-Qi

last: Zheng


title: KCNH2-3.1 mediates aberrant complement activation to impair hippocampal-medial prefrontal pathway associated with schizophrenia

status: Public on Aug 23 2019

city: Baltimore

first: Gabsang

last: Lee

state: MD

address: 733 North Broadway, Suite 747

department: Department of Neurology and Neuroscience

institute: Institute for Cell Engineering, Johns Hopkins University

summary: Although elevated KCNH2-3.1 potassium channel expression is associated with cognitive dysfunctions and with schizophrenia, little is known about the pathophysiology of synapses in patient neurons and how elevated levels of KCNH2-3.1 potassium channel could lead to synaptic deficits in humans. Here, we identified specific and delayed disruption of hippocampal-mPFC synaptic transmission and connection unexpectedly associated with age-dependent reduction of SERPING1, CFH and CD74 in the KCNH2-3.1 overexpression transgenic mice, and dysfunctional interactions between hippocampus and prefrontal cortex in the fMRI coupling signal during working memory encoding in healthy subjects carrying schizophrenia-associated risk alleles of KCNH2 potassium channel. These three genes are enriched in neurons or microglia, and reduced expression of these genes dysregulates the complement cascade activation underlying impaired synaptic connectivity of hippocampal-mPFC projections. Knockdown of these genes’ expression impairs synapse formation, and replenishing reduced CFH gene expression rescues KCNH2-3.1-induced impaired synaptogenesis. Our results uncover a previously unrecognized role of truncated KCNH2-3.1 potassium channel mediating reduced expression of three genes mentioned above, which enhances aberrant complement cascade activation during development. These results direct an important conceptual advance that truncated KCNH2-3.1 causes synapse loss mediated by abnormally activated complement system, rather than aberrant neuronal firing, may represent the therapeutic targets for a number of patients with schizophrenia.

overall_design: In this study, we employed multifaceted approaches to investigate whether there are impaired functional or/and structural connectivity between the hippocampus and the PFC with schizophrenia-like behavior deficits in a transgenic KCNH2-3.1 mouse model and human subjects with schizophrenia-associated risk-alleles in KCNH2, and what molecular mechanisms of hippocampus-PFC disruption are in the transgenic KCNH2-3.1 mice.

first: Ming

last: Ren

first: Zhonghua

last: Hu

first: Qiang

last: Chen

first: Andrew

last: Jaffe

first: Yingbo

last: Li

first: Vijay

last: Sadashivaiah

first: Shujuan

last: Zhu

first: Nina

last: Rajpurohit

first: Joo-Heon

last: Shin

first: Wei

last: Xia

first: Yankai

last: Jia

first: Jingxian

last: Wu

first: Sunny

middle: L

last: Qin

first: Xinjian

first: Jian

first: Qingjun

last: Tian

first: Daniel

last: Parades

first: Fengyu

last: Zhang

first: Kuan

last: Wang

first: S

middle: V

last: Mattay

first: H

last: Callicott

first: Karen

last: Berman

middle: R

last: Weinberger

first: Feng

last: Yang


title: Diverse homeostatic and immunomodulatory roles of immune cells in the developing mouse lung revealed at single cell resolution

status: Public on Mar 28 2020

city: Kensington

first: Fabio

last: Zanini

address: High and Botany St

institute: University of New South Wales

summary: At birth, the lungs experience a sudden transition from a pathogen-free, hypoxic, fluid-filled environment to a pathogen-rich, rhythmically distended air-liquid interface. While many studies focus on adult tissue, the heterogeneity of immune cells in the perinatal lung remains unexplored. Here, we combine single cell transcriptomics with in situ hybridization to present an atlas of the murine lung immune compartment during a critical period of lung development. We show that the late embryonic lung is dominated by specialized proliferative macrophages with a surprising physical interaction with the developing vasculature. These macrophages disappear after birth and are replaced by a complex and dynamic mixture of macrophage subtypes, dendritic cells, granulocytes, and lymphocytes. Detailed characterization of macrophage diversity revealed a precise orchestration of five distinct subpopulations across postnatal development to fill context-specific functions in tissue remodeling, angiogenesis, and immunity. These data both broaden the putative roles for immune cells in the developing lung and provide a framework for understanding how external insults alter immune cell phenotype during a period of rapid lung growth and heightened vulnerability.

overall_design: scRNA-Seq on FACS sorted cells

first: Racquel

last: Domingo-Gonzales

first: Xibing

last: Che

first: Min

last: Liu

first: Robert

last: Jones

first: Michael

last: Swift

first: Stephen

last: Quake

first: David

middle: N

last: Cornfield

first: Cristina

middle: M

last: Alvira


title: Representation and relative abundance of cell-type selective markers in whole-kidney RNA-Seq data

status: Public on Jan 17 2019

city: Bethesda

first: Lihe

last: Chen

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

summary:
Purpose:  We used RNA-seq to determine the mRNA species and cell types presented in the whole kidney tissue.
Methods: We extracted RNA from the whole kidney tissue and microdissected proximal tubules. cDNA libraries were constructed for paired-end sequencing and sequenced on Illumina HiSeq3000 platform.Reads were mapped to mouse Ensembl Genome by STAR and transcript abundances were calculated in the units of transcripts per million (TPM) using RSEM (https://github.com/deweylab/RSEM).
Results and conclusion:  Based on a variety of data types we curated a list of 43 cell types that are thought to exist in the kidney. Our data indicated that, If mRNA levels parallel protein levels, the contribution of proximal tubules to total mRNA in the renal tubule is also likely to be in the vicinity of 66%.

overall_design: cDNAs from whole kidney tissue and microdissected proximal tubules were generated and sequenced using Illumina HiSeq 3000.

first: Jevin

last: Clark

first: Chung-Lin

last: Chou

first: Hyun Jun

last: Jung

first: Jae Wook

last: Lee

first: Mark

middle: A

last: Knepper


title: Tracing the first hematopoietic stem cell generation in human embryo by single-cell RNA sequencing

status: Public on Sep 09 2019

first: Jian

last: He

address: DongDaJie #8

institute: the Fifth Medical Center of the PLA General Hospital

summary: Tracing the emergence of the first hematopoietic stem cells (HSCs) in human embryos, particularly the scarce and transient precursors thereof, is so far challenging, largely due to technical limitations and material rarity. Here, using single-cell RNA sequencing, we constructed the first genome-scale gene expression landscape covering the entire course of endothelial-to-HSC transition during human embryogenesis. The transcriptomically defined HSC-primed hemogenic endothelial cells (ECs) were captured at Carnegie stage 12-14 in an unbiased way, showing an unambiguous arterial EC feature with the up-regulation of RUNX1, MYB and ANGPT1. Importantly, subcategorizing CD34+CD45- ECs into CD44+ population strikingly enriched hemogenic ECs by over 10-fold. We further mapped the developmental path from arterial ECs via HSC-primed hemogenic ECs to hematopoietic stem progenitor cells, and revealed a distinct expression pattern of genes that were transiently over-represented upon the hemogenic fate choice of arterial ECs, including EMCN, PROCR and RUNX1T1. We also uncovered another temporally and molecularly distinct intra-embryonic hemogenic EC population, which was detected mainly at earlier CS 10 and lacked the arterial feature. Finally, we revealed the cellular components of the putative aortic niche and potential cellular interactions acting on the HSC-primed hemogenic ECs. The cellular and molecular programs and interactions that underlie the generation of the first HSCs from hemogenic ECs in human embryos, together with distinguishing HSC-primed hemogenic ECs from others, will shed light on the strategies for the production of clinically useful HSCs from pluripotent stem cells.

overall_design: Here, we performed both well-based single-cell RNA-sequencing (scRNA-seq) of 528 cells and droplet-based scRNA-seq of 11,440 cells to firstly construct a molecular landscape of HSC generation in human embryos

first: Yang

last: Zeng

first: Zhijie

last: Bai

first: Zongcheng

last: Li

first: Yu

last: Lan

first: Bing


title: Macrophage reprogramming by negatively-charged membrane phospholipids controls infection

status: Public on Nov 02 2018

city: La Jolla

middle: Mario

last: Cauvi

address: 9500 Gilman Dr.

department: Surgery

institute: University of California, San Diego

summary: Extracellular vesicles (ECV) are heterogeneous membrane-enclosed structures containing proteins, nucleic acids and lipids that participate in intercellular communication by transferring their content to recipient cells. Although most of the attention has been directed at the biological effect of proteins and microRNA, the contribution of phospholipids present in ECV on cellular activation has not been extensively addressed. Here we investigated the biological effect of phosphatidylserine (PS) and phosphatidylcholine (PC), two phospholipids highly abundant in ECV. A transcriptomic analysis revealed that about 4,700 genes were specifically modified by exposing peritoneal macrophages to PS or PC liposomes in vivo. Among them, the expression of several chemokines and cytokines was highly upregulated by PS liposome treatment, translating into a massive neutrophil infiltration into the peritoneum capable of neutralizing a septic polymicrobial insult. Both the L and D stereoisomers of PS induced the same response, suggesting that the effect was related to the negative charge of the phospholipid head. We concluded that an increase in the internal negative charge of the cell triggers a signaling cascade activating an innate immune response capable of controlling infection.

overall_design: Total RNA isolated from peritoneal cells obtained by lavage from CD-1 mice intraperitoneally injected for 1 hour with POPC liposomes (400 µg at 1 mg/ml, n=3 mice), POPS liposomes (400 µg at 1 mg/ml, n=3 mice), or PBS (400 µl, controls n=3 mice)

first: Antonio

last: De Maio


title: Identification of a PDEF regulatory network that inhibits prostate cancer metastasis

status: Public on Jan 24 2020

city: New Orleans

first: HARI

last: KOUL

state: LA

address: 1700 Tulane Avenue 9th Flor

institute: LSUHSC-NEW ORLEANS-LA

summary: To investigate the role of PDEF in prostate cancer metastasis, we employed microarray analysis of PC3 cells ectopically expressing a pBABE vector control (PC3-SCR) or PDEF-containing vector (PC3-PDEF).

overall_design: Total RNA obtained from PC3-SCR and PC3-PDEF was harvested. RNA was extracted using RNeasy Mini Kit (Qiagen, Chatsworth, CA). cDNA was hybridized to Affymetrix GeneChip (HuGene-1.0-st-v1).

first: Sweaty

last: Koul

first: Fengtian

last: Wang

first: Hari

middle: K


title: Genome-wide analysis of glucocorticoid-responsive transcripts in the hypothalamic paraventricular region of male rats

status: Public on Sep 15 2018

city: Sendai

first: Ikuko

last: Motoike

state: Miyagi

address: 2-1 Seiryo-cho Aoba-ku

department: Tohoku Medical Meagabank Organizataion

country: Japan

institute: Tohoku Univertisy

summary:
Purpose: we sought to search for genes that are transcribed or repressed in a glucocorticoid (GC)-dependent manner in a hypothalamic region containing the paraventricular nucleus of the hypothalamus (PVH), thereby unraveling mechanisms underlying GC-induced neuroendocrine and autonomic regulation.
Methods: we employed unbiased quantification of the abundance of DNA transcripts provided by RNA-seq in the PVH region of male rats and identified genes whose expression is enhanced or suppressed by the 12-day exposure to a high dose of corticosterone (Cort) by Cort implant (12-day high Cort) or deprivation of corticoids for 7 days [7-day adrenalectomy (ADX)] (Experiment 1), as well as by acute Cort increase (Experiment 2). Sham-ADX animals served as controls in Experiment 1. In Experiment 2, rats underwent ADX and supplemented with Cort in drinking water. The animals were decapitated at 1 h [acute Cort (1) 1 h] or 3 h [acute Cort (1) 3 h] following injection of HBC Cort (1 mg), a dose shown to elicit plasma Cort surge comparable to that during acute stress. A group of rats without Cort injection served as controls (ADX + Cort suppl). Differential expression was calculated as fold-changes in gene expression [measured as fragments per kilobase of exon per million reads mapped (FPKM)]. The Benjamini & Hochberg method was applied to correct the unavoidable false positive data ensued from the multiple tests, and a q-value was calculated as the false discovery rate-adjusted p-value. The q-value < 0.05 was used as the cut-off criterion. Pearson’s correlation analysis was carried out for grouping genes that showed similar expression patterns. qRT–PCR validation was performed using Power SYBR Green PCR mix. Semi-quantitative in situ hybridization was carried out using 35S-labeled cRNA probes.
Results: some canonical GC target genes, among others of a broad functional spectrum, were upregulated prominently by 12-day high Cort. Crh was upregulated or downregulated most prominently by either 7-day ADX or 12-day high Cort, emphasizing the recognized feedback effects of GC on the hypothalamic-pituitary-adrenal (HPA) axis. Concomitant changes in Avp and Aplnr expression are likely to contribute to HPA repression. In keeping with the pleotropic cellular actions of GCs, 7-day ADX downregulated numerous genes of a broad functional spectrum. The transcriptome response signature differed markedly between acute Cort injection and 12-day high Cort. Remarkably, 6 immediate early genes, Bsx, Egr1, Fos, Fosb, Junb, and Nr4a3, were upregulated at 1 h after Cort injection, and the changes were confirmed by qRTPCR and semi-quantitative in situ hybridization.
Conclusions: the present study uncovered a broad spectrum of Cort-responsive genes, potentially involved in the regulation of the HPA-axis, as well as other neuroendocrine and pre-autonomic functions of the PVH.

overall_design: Transcriptome profiles of the hypothalamic region containing the PVH were generated by deep sequencing, in duplicate, using Illumina HiSeq2000.

first: Keiichi

last: Itoi

first: Ying

last: Liu

first: Sam

last: Clokie

first: Yasumasa

last: Iwasaki

first: Katsuya

last: Uchida

first: Tatsuya

last: Sato

first: Greti

last: Aguilera


title: Diagnosis of Kawasaki Disease in children using host RNA expression [Discovery_Dataset]

status: Public on Aug 09 2018

city: London

first: Michael

last: Levin

address: South Kensington Campus

department: Paediatrics

institute: Imperial College London

summary: Genome-wide analysis of transcriptional profiles in children <17 years of age with inflammatory diseases, bacterial or viral infections or with clinical features suggestive of infection.

overall_design: Patients were recruited at or after presentation to hospital. Main inclusion criteria were presence of illness of sufficient severity to warrant blood tests for clinical reasons, in child aged <17 years. Blood was collected into PAX gene tubes (PreAnalytiX). Total RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Labeled cRNA was hybridized to Illumina Human HT-12 V4 Beadchips (Discovery set). Numbers of arrays analysed in the discovery set were as follows: Kawasaki Disease (n=78), Healthy controls (n=55), Definite Bacterial infection (n=52), Definite Viral infection (n=94), Inflammatory diseases (n=84), infections of uncertain bacterial or viral aetiology (n=96).


title: Comparison of gene expression profiling of human non-muscle invasive bladder cancer and  muscle invasive bladder cancer

status: Public on Dec 01 2018

first: HUANG

last: CHEN

address: Yinghuadongjie 2#, Chaoyang District, Beijing

department: Department of Etiology and Carcinogenesis

institute: China-Japan Friendship Hospital

summary: The biological behaviors, clinical treatment, prognosis of nonmuscle-invasive bladder cancers (NMIBCs) and muscle-invasive bladder cancers (MIBCs) are distinct. Therefore, we performed high-through microarray screening of mRNA expression in 30 bladder tumors, to filter out some of the differential expression genes in NMIBCs and MIBCs.A total of 11 Genes in MIBCs versus in NMIBCs were considered differentially transcribed if they were transcribed ≤2.0 fold change and p<0.001 by unpaired T-test, including 9 up-regulated genes and 2 down-regulated genes in MIBCs (NR4A2, PLK3, CYR61, APOLD1, C13ORF33, LIG4, RBMS3, PCK2, AK098422, HSD17B3, RTN4). These candidate genes were validated in further and provide further insight into the discovery of new putative markers to identify MIBCs preoperatively.

overall_design: Newly diagnosed bladder cancer patients with the greatest tumor diameter >2.5 cm and without tumor peduncle preoperatively observed by cystoscopy were selected.  All fresh frozen tissue including in this study were from bladder cancer patients underwent radical or partial cystectomy and were bladder urothelial carcinoma confirmed by pathologist.  Cystectomy specimens from the maximal tumor were immediately reviewed by the pathologist, who visually selected the tumor zone to be immediately stored in RNA later (Ambion Austin, TX, USA) overnight and then stored at -80℃. Sixteen NMIBCs and fourteen MIBCs  were examined with Agilent 4×44K Whole Human Genome Oligo Microarrays (G4112F) according to the manufacturer’s protocol.

first: Huang

last: Chen

first: Yang

last: Zheng

first: Wei

first: Jingqiao

last: Bai

first: Jianzhong

last: Shou

first: Yanning

last: Gao


title: TH2BS11ph histone mark is enriched in the unsynapsed axes of the XY body and predominantly associates with H3K4me3-containing genomic regions in mammalian spermatocytes

status: Public on Sep 15 2019

city: Bangalore

first: Manchanahalli

middle: Rangaswamy

last: Satyanarayana Rao

state: Karnataka

address: Jakkur, Bengaluru, Karnataka

department: Molecular Biology and Genetics Unit (MBGU)

institute: Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)

summary: We report the localisation of TH2BS11ph histone mark in leptotene and pachytene cells determined by ChIP sequencing analysis

overall_design: Genome-wide occupancy of TH2BS11ph histone mark in mouse P12 and P20 testicular cells

first: Aditya

last: Iyer

first: Satyakrishna

last: Pentakota

first: Raktim

last: Roy

first: Utsa

last: Bhaduri

first: M

middle: S

last: Rao


title: Diagnosis of Kawasaki Disease in children using host RNA expression


title: SAKE (Single-cell RNA-Seq Analysis and Klustering Evaluation) Identifies Markers of Resistance to Targeted BRAF Inhibitors in Melanoma Cell Populations [10x]

status: Public on Jul 01 2018

city: Cold Spring Harbor

first: Molly

last: Hammell

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

summary: The goal of this study is to apply the SAKE algorithms to identify drug-resistant cellular populations as human melanoma cells respond to targeted BRAF inhibitors. Single-cell RNA-Seq data from 10x Genomics platform was analyzed to dissect this problem at multiple scales. Data indicates that BRAF inhibitor resistant cells can emerge from rare populations already present before drug application, with SAKE identifying both novel and known markers of resistance

overall_design:
Two Melanoma cell lines were treated with BRAF inhibitor for 6 weeks to derived a parental and resistant cell states. Bulk and single-cell RNA-Seq were generated using Illumina NextSeq to study cell response after drug treatment.

UPDATE: [06-01-2023] The processed data files were replaced because the previous processed data files contained GEM barcodes that likely corresponded to background noise (e.g., GEMs with free-floating mRNA from lysed or dead cells). The updated processed data files now contain only barcodes that pass the filtering for missing cells/empty drops, and thus correspond to detected cell and feature counts that should be used for downstream analysis.

first: Yu-Jui

last: Ho


title: SAKE (Single-cell RNA-Seq Analysis and Klustering Evaluation) Identifies Markers of Resistance to Targeted BRAF Inhibitors in Melanoma Cell Populations


title: Patients with a Kabuki syndrome phenotype demonstrate DNA methylation abnormalities.

status: Public on Jun 27 2018

first: Hans

middle: Tomas

last: Bjornsson

state: Maryland

address: 733 N. Broadway

department: McKusick-Nathans Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

type: Methylation profiling by genome tiling array

summary: Kabuki syndrome is a monogenic disorder caused by loss of function variants in either of two genes encoding histone-modifying enzymes. We performed targeted sequencing in a cohort of 27 probands with a clinical diagnosis of Kabuki syndrome. Of these, 12 had causative variants in the two known Kabuki syndrome genes. In 2, we identified presumptive loss of function de novo variants in KMT2A (missense and splice site variants), a gene that encodes another histone modifying enzyme previously exclusively associated with Wiedermann-Steiner syndrome. Although Kabuki syndrome is a disorder of histone modification, we also find alterations in DNA methylation among individuals with a Kabuki syndrome diagnosis relative to matched normal controls, regardless of whether they carry a variant in KMT2A or KMT2D or not. Furthermore, we observed characteristic global abnormalities of DNA methylation that distinguished patients with a loss of function variant in KMT2D or missense or splice site variants in either KMT2D or KMT2A from normal controls. Our results provide new insights into the relationship of genotype to epigenotype and phenotype and indicate cross-talk between histone and DNA methylation machineries exposed by inborn errors of the epigenetic apparatus.

overall_design: Case-control design. 48 total samples (randomized across four 12-well BeadChips): 4 synthetic methylation controls, 6 parental controls, 9 age-matched controls, 27 probands with a Kabuki Syndrome phenotype, and 2 patients originally recruited from the same clinic but dropped from further analysis when they were found to not have KS

first: Martha

middle: F

last: Brucato

first: Nara

last: Sobreira

first: Li

last: Zhang

first: Christine

last: Ladd-Acosta

first: Chrissie

last: Ongaco

first: Jane

last: Romm

first: Kimberly

last: Doheny

first: Regina

last: Mingroni-Netto

first: Debora

last: Bertola

first: Chong

last: Kim

first: Ana

last: Perez

first: Maria

middle: I

last: Melaragno

first: David

last: Valle

first: Vera

last: Meloni

middle: T


title: Response of the Drosophila Schneider cells to the 20-hydroxyecdysone

status: Public on Feb 19 2018

city: Moscow

first: Nadezhda

middle: E

last: Vorobyeva

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

summary: The subject of the current study was the response of the Drosophila Schneider cells to the developmental hormone 20-hydroxyecdysone. The whole-genome experiments revealed that ecdysone-dependent genes are at high level of readiness to the upcoming transcription. Their promoters in the inactive state are associated with significant amounts of the RNA polymerase II. The induction of transcription by 20-hydroxyecdysone results both in the recruitment of the additional portion of the RNA polymerase II and in the increase in its phosphorylation level. The primary events in the course of the transcriptional activation of the two ecdysone-dependent genes have been investigated to detail.

overall_design: ChIP-Seq of RNA polymerase II states (total, Ser2Phospho and Ser5Phospho), coregulators (Brm, KisL, CHD1, dSet1, lid/Kdm5, Gcn5, DART1, Spt5, cdk8 and PAF1) and ChIP H3-Mnase assay (with antibodies against Histone H3 and Histone H3K27Ac) were performed in S2 Scheider cell after 20-hydroxyecdysone treatment and in sham-treated cells (DMSO-treated)

first: N

first: A

last: Krasnov


title: H1609088 Human RNA-Sequencing

status: Public on Dec 12 2018

city: Luoyang

first: liu

last: Ke

state: Henan

address: 24 Jinghua Road, Jianxi Qu

department: Cancer Hospital

institute: The First Affiliated Hospital, College of Clinical Medicine, Medical College of Henan University of Science and Technology

summary: Transcriptome profiling of KYSE30 cells after intracellular invasion by Porphyromonas gingivalis  Purpose: Overabundance of Porphyromonas gingivalis (P. gingivalis) plays oncogenic roles in development and progression of esophageal squamous cell carcinoma (ESCC). To unveil the molecular mechanisms underlying the tumor-promoting role, RNAseq was used to identify differentially expressed genes in response to P. gingivalis in KYSE30 cells.  Methods: mRNA profiles were generated by deep sequencing for P. gingivalis-treated KYSE30 cells and PBS-treated control cells in triplicate. RNAseq data were mapped to human genome (hg19) using Hisat2. Differentially expressed genes were identified using StringTiel and Ballgown.  Results: A total of 10 239 genes and a total of 10 297 genes were identified in KYSE30 cells treated with P. gingivalis and PBS, respectively. After expression quantification using Ballgown, 124 up-regulated genes and 122 down-regulated genes were identified in P. gingivalis-treated KYSE30 cells compared with PBS-treated cells. Enrichment analysis of GO and KEGG pathway showed response to virus, innate immune response, Herpes simplex infection, metabolism of xenobiotics by cytochrome P450 and tyrosine metabolism were enriched in P. gingivalis-treated KYSE30 cells.  Conclusions: This study reveals that P. gingivalis infection in ESCC triggers immune response and may cause deregulation of signal transduction through tyrosine metabolism.

first: Ke

last: Liu

first: She-Gan

last: Gao

first: Yi-Jun

last: Qi


title: Genome-wide Mapping of 5-Hydroxymethylcytosines in Circulating Cell-free DNA as a Non-invasive Approach for Early Detection of Hepatocellular Carcinoma

status: Public on Aug 07 2019

city: Chicago

first: Zhou

last: Zhang

address: 680 North Lake Shore Drive, Suite 1400

department: Preventive Medicine

institute: Northwestern University

summary:
Background: The lack of highly sensitive and specific diagnostic biomarkers is a major contributor to the poor outcomes of patients with hepatocellular carcinoma (HCC). We sought to develop a non-invasive diagnostic approach using circulating cell-free DNA (cfDNA) for the early detection of HCC.

Methods: Applying the 5hmC-Seal technique, we obtained genome-wide 5-hydroxymethylcytosines (5hmC) in cfDNA samples from 2,554 Chinese subjects: 1,204 HCC patients, 392 patients with chronic hepatitis B virus infection (CHB) or liver cirrhosis (LC), and 958 healthy individuals and patients with benign liver lesions. A diagnostic model for early HCC was developed through case-control analyses using the elastic net regularization for feature selection.

Results: The 5hmC-Seal data from HCC patients showed a genome-wide distribution enriched with liver-derived enhancer marks. We developed a 32-gene diagnostic model that accurately distinguished early HCC (stage 0/A) based on the Barcelona Clinic Liver Cancer (BCLC) staging system from non-HCC (validation set: AUC = 88.4%; 95% CI, 85.8-91.1%), showing superior performance over α-fetoprotein (AFP). Besides detecting patients with early stage or small tumors (e.g., ≤ 2.0 cm) from non-HCC, the 5hmC model showed high capacity for distinguishing early HCC from high risk subjects with CHB or LC history (validation set: AUC = 84.6%; 95% CI, 80.6-88.7%), also significantly outperforming AFP. Furthermore, the 5hmC diagnostic model appeared to be independent from potential confounders (e.g., smoking/alcohol intake history).

Conclusions: We have developed and validated a non-invasive approach with clinical application potential for the early detection of HCC that are still surgically resectable in high risk individuals.

overall_design:
Applying the 5hmC-Seal technique, we obtained genome-wide 5-hydroxymethylcytosines (5hmC) in cfDNA samples from 2,554 Chinese subjects: 1,204 HCC patients, 392 patients with chronic hepatitis B virus infection (CHB) or liver cirrhosis (LC), and 958 healthy individuals and patients with benign liver lesions. A diagnostic model for early HCC was developed through case-control analyses using the elastic net regularization for feature selection.

UPDATE: [06-05-2023] The submitter reports that there is a potential sample mixup leading to inaccuracies in the "diagnosis" and "BCLC stage" characteristics. Therefore, the "diagnosis" and "BCLC stage" characteritics have been removed from the Sample records. The submitter declares that they are currently in the process of rectifying and updating the clinical information.

first: Jiabin

last: Cai

first: Lei

last: Chen

first: Xinyu

first: Xingyu

last: Lu

first: Weiwei

first: Guoming

last: Shi

first: Ge

last: Yang

first: Pingting

first: Yuan

first: Aiwu

first: LinLin

last: Xiao

first: Ruizhao

last: Dong

first: YanJing

last: Zhu

first: Xuan

first: Jiefei

last: Wang

first: Tongyu

first: DePing

first: Xiaowu

last: Huang

first: Chengjun

last: Sui

first: Shuangjian

last: Qiu

first: Feng

last: Shen

first: Huichuan

last: Sun

first: WeiPing

last: Zhou

first: Jian

first: Ji

last: Nie

first: Zeng

last: Chang

first: Emily

last: Stroup

first: Xu

first: Chiu

last: Brian

first: Lau

last: Wan Yee

first: Chuan

last: He

first: Hongyang

first: Wei

first: Jia

last: Fan


title: Gene regulatory network architecture in different developmental contexts influences the genetic basis of morphological evolution

status: Public on Apr 18 2018

city: Oxford

first: Sebastian

last: Kittelmann

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

summary: Convergent phenotypic evolution is often caused by recurrent changes at particular nodes in the underlying gene regulatory networks (GRNs). The genes at such evolutionary 'hotspots' are thought to maximally affect the phenotype with minimal pleiotropic consequences. This has led to the suggestion that if a GRN is understood in sufficient detail, the path of evolution may be predictable. The repeated evolutionary loss of larval trichomes among Drosophila species is caused by the loss of shavenbaby (svb) expression. svb is also required for development of leg trichomes, but the evolutionary gain of trichomes in the 'naked valley' on T2 femurs in Drosophila melanogaster is caused by the loss of microRNA-92a (miR-92a) expression rather than changes in svb. We used RNAseq of second (T2) pupal legs (20-28 h after puparium formation) to compare the expression of trichome GRN genes between strains with a large and a small naked valley. We also compared the function of components between the larval and leg trichome GRNs to investigate why the genetic basis of trichome pattern evolution differs in these developmental contexts. Moreover, we used ATAC-seq of second (T2) pupal legs (20-28 h after puparium formation) to identify the pupal leg enhancers of svb. We found key differences between the two networks in both the genes employed, and in the regulation and function of common genes. These differences in the GRNs reveal why mutations in svb are unlikely to contribute to leg trichome evolution and how instead miR-92a represents the key evolutionary switch in this context. Our work shows that variability in GRNs across different developmental contexts, as well as whether a morphological feature is lost versus gained, influence the nodes at which a GRN evolves to cause morphological change. Therefore, our findings have important implications for understanding the pathways and predictability of evolution.

overall_design: We used RNAseq to compare gene expression in second legs between two Drosophila melanogaster strains and ATAC-Seq to identify enhancers of certain genes. We used three replicates each of ca. 80 second (T2) pupal legs (20-28 h after puparium formation) of two different Drosophila melanogaster strains (ebony[4],white ocelli[1], rough[1] and Oregon R) and extracted RNA or chromatin from them. Library preparation for RNAseq and paired end (75 bp) seqencing with an Illumina HiSeq 4000 were done by Edinburgh Genomics. For ATAC-Seq Chromatin was tagmented using Tn5 transposase and library preparation was performed using a protocol modified after Buenrostro et al. (2013) DOI:10.1038/NMETH.2688. Paired end (50 bp) seqencing with an Illumina HiSeq 2500 was done by the Transcriptome and Genome Analysis Laboratory Goettingen.

first: Alexandra

middle: D

last: Buffry

first: Franziska

last: Franke

first: Isabel

last: Almudi

first: Marianne

last: Yoth

first: Gonzalo

last: Sabaris

first: Juan

middle: P

last: Couso

first: Maria

last: Santos Nunes

first: Nicolás

last: Frankel

first: José

last: Gómez-Skarmeta

first: Jose

last: Pueyo-Marques

first: Saad

last: Arif

first: Alistair

last: McGregor


title: Minor spliceosome inactivation in the developing mouse cortex causes self-amplifying radial glial cell death and microcephaly.

status: Public on Jun 05 2018

city: Storrs

first: Rahul

last: Kanadia

state: CT

address: 75 N. Eagleville Road

department: Physiology and Neurobiology

institute: University of Connecticut

summary: Inactivation of the minor spliceosome has been linked to microcephalic osteodysplastic primordial dwarfism type 1 (MOPD1). To interrogate how minor intron splicing regulates cortical development, we employed Emx1-Cre to ablate Rnu11, which encodes the minor spliceosome-specific U11 small nuclear RNA (snRNA), in the developing cortex (pallium). Rnu11 cKO mice were born with microcephaly, caused by death of self-amplifying radial glial cells (RGCs). However, both intermediate progenitor cells (IPCs) and neurons were produced in the U11-null pallium. RNAseq of the pallium revealed elevated minor intron retention in the mutant, particularly in genes regulating cell cycle. Moreover, the only downregulated minor intron-containing gene (MIG) was Spc24, which regulates kinetochore assembly. These findings were consistent with the observation of fewer RGCs entering cytokinesis prior to RGC loss, underscoring the requirement of minor splicing for cell cycle progression in RGCs. Overall, we provide a potential explanation of how disruption of minor splicing might cause microcephaly in MOPD1.

overall_design: RNA-seq on 5 control and 5 U11 mutant E12 dorsal telencephalon.


title: Differential response of polarized gut epithelial cells to type I and III interferon

status: Public on Dec 22 2017

city: Aachen

first: Mathias

middle: W.

last: Hornef

address: Steppenbergallee 203

department: Medical Microbiology

institute: RWTH Áachen University

summary: Whereas most body cells respond to stimulation with type I (alpha and beta) interferon, type III (lambda) interferon was shown to specifically stimulate epithelial cells in the gastrointestinal and respiratory tract.  Although both cytokines activate different receptor molecules (IFNAR versus IL-28R/IL-10R, respectively) the downstream signalling pathways and the ultimate response have been reported to be very similar. Here we examined the response of polarized gut intestinal epithelial cells to type I versus type III interferon in order to study potential differences in the transcriptional response.

overall_design: Comparative transcriptional analysis of polarized intestinal epithelial cells to type I interferon or type III interferon (versus unstimulated controls).

first: Tharini

last: Selvakumar

first: Hansjörg

last: Hauser

first: Mario

last: Köster

middle: W


title: Chip-seq analysis of H3K4me3, H3K27me3, DNMT1 and EZH2 binding to chromatin following acute (10 days) and chronic (10 months) treatment of human bronchial epithelial cells (HBEC3KT) cells with 10 µg/ml cigarette smoke condensate (CSC).

status: Public on Oct 21 2017

first: Hariharan

last: Easwaran

address: 1650 Orleans St #544, Baltimore, MD 21205

department: SOM Onc Cancer Biology

institute: Johns Hopkins Medicine

summary: We define how chronic cigarette smoke-induced time-dependent epigenetic alterations can sensitize human bronchial epithelial cells (HBEC) for transformation by a single oncogene. The smoke-induced, chromatin changes include initial repressive polycomb marking of genes later manifesting abnormal DNA methylation by 10 months. At this time, cells manifest epithelial to mesenchymal changes, anchorage-independent growth and upregulated RAS/MAPK signaling with silencing of hyper-methylated genes normally inhibiting these pathways and which are associated with smoking related NSCLC. These cells, in the absence of any driver gene mutations, now transform by introducing a single KRAS mutation and form adeno-squamous lung carcinomas in mice. Thus, epigenetic abnormalities may prime for changing oncogene senescence to addiction for a single key oncogene involved in lung cancer initiation.

overall_design: HBEC cells treated with 10 µg/ml CSC for 10 months. Control (DMSO treated) and CSC treated cells were harvested at 10 days (acute exposure) and 10 months (chronic exposure) and processed for ChIP to examine genome wide enrichment of H3K4me3, H3k27me3 and binding of DNMT1 and EZH2. ChIPed DNA was analyzed by ChIP-seq.

first: M

last: Vaz

first: S

middle: B

last: Baylin

first: H


title: Genes expression in xenografts obtained from 15 months cigarette smoke condensate (CSC)-exposed HBEC cells following expression of KRASV12

overall_design: Gene expression in xenografts obtained from two biological replicates (rep 1 and rep2) of 15 months cigarette smoke condensate (CSC)-exposed HBEC cells following expression of KRASV12.  Gene expression in Control cells  at the same time point and expressing KRASV12 was used for comparison in final analysis.


title: Exome-seq analysis of human bronchial epithelial cells (HBEC3KT) cells pre and post treatment with DMSO (Control) or 10 µg/ml cigarette smoke condensate (CSC) for 15 months and tumor xenografts obtained with 15 month CSC treated cells expressing KRASV12

overall_design: HBEC cells treated with DMSO (Control) or 10 µg/ml CSC for 15 months. Xenografts were obtained by subcutaneously injecting 15 month CSC treated cells expressing KRASV12 in NSG mice.


title: Oncogenic activation of the RNA binding protein RDBP and c-Myc signaling in hepatocellular carcinoma

status: Public on Aug 31 2017

city: Toronto

first: Timothy

last: Hughes

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

summary: Here, we analyze the RNA-binding preferences of the human RDBP protein using RNAcompete.

overall_design:
In the RNAcompete assay, purified GST-tagged RDBP (contains the RRM and 50 amino acids of flanking sequence) is incubated with an excess of RNA pool and bound RNA from individual pulldown experiments are directly labeled and hybridized to a custom Agilent 244K microarray.

Please note that raw data in channel 2 of file A199_2.D.txt


title: Gene Expression of HBEC-3KT cells exposed to cigarette smoke condensate (CSC) over a period of 15 months

overall_design: Gene expression in CSC treated cells from two biological replicates (rep 1 and rep2) over a period of 15 months. Gene expression in Control and CSC treated at 15 months expressing empty vector (EV) or KRASV12. Data is represented as fold change in CSC treated cells over control (DMSO treated) cells.


title: A RRM1-ZnF RNA recognition module targets RBM10 to exonic sequences to promote exon exclusion

status: Public on Aug 15 2017

summary: RBM10 is an RNA-binding protein that plays an essential role in development and is frequently mutated in the context of human disease. RBM10 recognizes a diverse set of RNA motifs in introns and exons and regulates alternative splicing. However, the molecular mechanisms underlying this seemingly relaxed sequence specificity are not understood and functional studies have focused on 3’ intronic sites only. Here we dissect the RNA code recognized by RBM10 and relate it to the splicing regulatory function of this protein. We show that a two-domain RRM1-ZnF unit recognises a GGA-centred motif enriched in RBM10 exonic sites with high affinity and specificity and test that the interaction with these exonic sequences promotes exon skipping. Importantly, a second RRM domain (RRM2) of RBM10 recognises a C-rich sequence, which explains its known interaction with the intronic 3’ site of NUMB exon 9 contributing to regulation of the Notch pathway in cancer. Together, these findings explain RBM10’s broad RNA specificity and suggest that RBM10 functions as a splicing regulator using two RNA-binding units with different specificities to promote exon skipping.

overall_design: In the RNAcompete assay, purified GST-tagged RBM10 proteins (RRM1-ZnF and RRM1-ZnF-RRM2) are incubated with an excess of RNA pool and bound RNA from individual pulldown experiments are directly labeled and hybridized to a custom Agilent 244K microarray.

first: Debashish

last: Ray


title: Systemic Lupus Erythematosus patient blood with controls

status: Public on Mar 21 2018

city: Parkville

first: CSL

last: Research

state: VIC

address: 30 Flemington Rd

institute: CSL Limited / bio21 Institute

summary: The experiment consists of 31 Systemic Lupus Erythematosus patient blood samples and 29 healthy donor blood samples.

overall_design: Whole blood was collected in PaxGene tubes from 31 SLE and 29 healthy donors.

first: Shereen

last: Oon

first: Katherine

last: Monaghan

first: Milica

last: Ng

first: Alberta

last: Hoi

first: Eric

last: Morand

first: Gino

last: Vairo

first: Eugene

last: Maraskovsky

first: Andrew

last: Nash

first: Ian

last: Wicks

first: Nicholas

middle: J

last: Wilson


title: Chronic Cigarette Smoke-Induced Epigenomic, gene expression and  chromatin changes in Bronchial Epithelial Cells

city: Baltimore

first: Hariharan

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

overall_design: Refer to individual Series


title: Methylation analysis of HBEC cells exposed to cigarette smoke condensate (CSC) over a period of 15 months

overall_design: Bisulphite converted DNA from control and CSC treated cells from two biological replicates (rep 1 and rep2) over a period of 15 months. Additionally methylation analysis of 15 month Control and CSC cells from both replicates expressing empty vector (EV) or mutant KRAS (KRASV12) and tumor xenografts obtained from CSC cells with KRASV12 from both replicates. DNA was hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: M


title: Mll3 suppresses tumorigenesis by activating the Ink4a/Arf locus

status: Public on Aug 01 2017

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center


title: The spectrum of mild-to-severe psoriasis vulgaris is defined by a common activation of IL-17 pathway genes, but with key differences in immune regulatory genes

status: Public on Feb 19 2017

city: Sacramento

first: JAEHWAN

last: KIM

state: CA

address: 10535 Hospital Way

department: Dermatology

institute: University of California, Davis

summary: Mild vs. severe psoriasis vulgaris is often distinguished by the Psoriasis Area and Severity Index. It is widely assumed that severe psoriasis involves higher levels of skin inflammation, but comparative molecular profiles of mild vs. severe disease have not been previously performed. In this study, we used gene arrays to phenotype North American patients with mild psoriasis vs. severe psoriasis.

overall_design: 14 mild plaque psoriasis lesional skin biopsy tissues, 13 severe plaque psoriasis lesional skin biopsy tissues, and 6 normal skin tissues

first: James

middle: G

last: Krueger

first: Mayte

last: Suárez-Fariñas

first: Jaehwan

last: Kim


title: Swarm intelligence-enhanced detection of non-small cell lung cancer using tumor-educated platelets

city: Amsterdam

first: Myron

last: Best

address: De Boelelaan 1117

department: Neurosurgery

institute: VU University Medical Center

summary: We report RNA-sequencing data of 779 blood platelet samples, including 402 tumor-educated platelet (TEP) samples collected from patients with non-small cell lung cancer (NSCLC). In addition, we report RNA-sequencing data of blood platelets isolated from 377 individuals without reported cancer, but not excluding individuals with inflammatory conditions. This dataset highlights the ability of TEP RNA-based 'liquid biopsy' diagnostics in patients with NSCLC.

overall_design: Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing EDTA anti-coagulant by standard centrifugation. Total RNA was extracted from the platelet pellet, subjected to cDNA synthesis and SMARTer amplification, fragmented by Covaris shearing, and prepared for sequencing using the Truseq Nano DNA Sample Preparation Kit. Subsequently, pooled sample libraries were sequenced on the Illumina Hiseq 2500 platform. All steps were quality-controlled using Bioanalyzer 2100 with RNA 6000 Picochip, DNA 7500 and DNA High Sensitivity chips measurements. For further downstream analyses, reads were quality-controlled using Trimmomatic, mapped to the humane reference genome using STAR, and intron-spanning reads were summarized using HTseq.

first: Thomas

last: Wurdinger


title: Mll3 suppresses tumorigenesis by activating the Ink4a/Arf locus [ChIP-seq]

summary: Mutations in genes encoding epigenetic regulators are among the most frequent somatic events in human cancers. For example, missense and truncating mutations in the MLL3 (KTM2C) histone H3K4-methyltransferase gene can be found in several tumor types. MLL3 is a member of the mixed lineage leukemia gene family and component of the mammalian COMPASS/like complex that promotes gene expression by establishing chromatin modifications favoring gene activation. While Mll3 loss of function promotes tumorigenesis in mice, the molecular targets and biological processes underlying its anti-neoplastic effects remain unknown. Here we combine powerful genetic, genomic, and animal modeling approaches to demonstrate that Mll3 suppresses hepatocellular carcinoma (HCC) by promoting activation of the Cdkn2a (Ink4a/Arf) locus. Hence, disruption of Mll3 using CRISPR/Cas9-mediated genome editing or by RNA interference using short hairpin RNAs cooperates with the Myc oncogene to drive tumorigenesis, producing tumors with reduced H3K4 methylation at multiple gene regulatory elements and low levels of p16Ink4a and p19Arf expression. These results place MLL3 in an established tumor suppressor network and reveal how disruption of a conserved mechanism of epigenetic regulation can alter CDKN2A action and cancer development.

overall_design: Analysis of genome-wide histone marks modification from liver tumor-derived Myc;sgp53/Cas9 and Myc;sgMll3/Cas9 cell lines.

first: Darjus

last: Tschaharganeh

first: Chun

middle: H

last: Huang

first: John

last: Morris 4th

first: Scott

last: Lowe


title: Mll3 suppresses tumorigenesis by activating the Ink4a/Arf locus [RNA-seq]

overall_design: Analysis of RNA isolated from liver tumor-derived Myc;sgp53/Cas9 and Myc;sgMll3/Cas9 cell lines.


title: mRNA state  in normal and irradiated skin of  rattus

status: Public on Dec 31 2016

city: Shanghai

first: Tienan

last: Feng

state: Shanghai

address: Siping Road No. 1239

institute: Tongji University

summary: We report the difference of mRNA and Long-non-coding  RNA state between normal and irradiated skin of rattus

overall_design: Examination of mRNA and Long-non-coding  RNA state between normal and irradiated skin ragion from three rattus

first: Shuyu

last: Zhang


title: RNA-seq profiling of glomeruli, S1 proximal tubule, and the whole kidney of uninephrecomized rats

status: Public on Jun 17 2017

city: Bethesda

first: Jae Wook

last: Lee

address: 10 Center Drive, 6N314

institute: National Institutes of Health

summary: We sequenced mRNAs in microdissected glomeruli and S1 proximal tubule segments and the whole remnant kidney of uninephrectomized rats.

overall_design: Male Sprague-Dawley rats received either right nephrectomy or sham surgery. Rats were sacrificed 24h, 48h, and 72h after surgery. Total RNAs were isolated from microdissected glomeruli, S1 proximal tubules, and the whole left kidney for RNA sequencing.

first: Jae

first: Mark

middle: A

last: Knepper


title: The Transcriptome of HIV-1 Infected Intestinal CD4+ T cells Exposed to Enteric Bacteria

status: Public on Feb 08 2017

city: Aurora

first: Kejun

last: Guo

state: Colorado

department: Division of Infectious Diseases

institute: University of Colorado Anschutz Medical Campus

summary:
The gastrointestinal tract is a major site of early HIV-1 replication and death of CD4+ T cells. As HIV-1 replicates in the gut, the protective epithelial barrier gets disrupted, leading to the entry of bacteria into the underlying tissue and the bloodstream, leading to inflammation and clinical complications even in HIV-1-infected patients taking antiviral drugs. Counteracting these pathogenic processes may require in-depth understanding of the molecular pathways that HIV-1 and microbes utilize to infect, functionally alter and/or kill CD4+ T cells. However, to date, the nature of the genes altered by relevant HIV-1 strains and bacteria in intestinal CD4+ T cells remains unclear.
Here, we obtained the first gene expression profiles of transmitted/founder (TF) HIV-1 (CH40-T2A-eGFP) infected gut CD4+ T cells infected with HIV-1 in the context of microbes found in the GI tract of HIV-1 infected patients. Our findings reveal common and distinct signaling pathways altered by HIV-1 depending on the presence of microbes that may shed light on infection, inflammation and CD4+ T cell depletion in HIV-1 infected individuals. In-depth understanding of these molecular programs may inform potential ways to counteract pathogenic outcomes initiated and/or sustained by HIV-1 infection in the GI tract.

overall_design: Transcriptomes from transmitted/founder HIV-1 infected (GFP+) human LPMC with or without exposure to Prevotella stercorea and mock infected LPMC were analyzed using Affemetrix GeneChip Human Gene 2.0 ST array.

first: Alyson

middle: M

last: Yoder

first: Tzu

last: Phang

first: Cara

middle: C

first: Mario

middle: L

last: Santiago


title: Genetic Variation amongst NHBE donor cells containing various TRPV1 SNPs with and without particulate matter treatments

status: Public on Oct 11 2016

city: Salt Lake City

first: Christopher

last: Reilly

state: UT

address: 30 S 2000 E, Room 201 Skaggs Hall

department: Pharmacology and Toxicology

institute: University of Utah

summary: The goal of our study was to determine the effect the TRPV1 I585V SNP has on lung cells.  NHBE cells, obtained from 4 different donor (Lonza), were genotyped to identify the presence of the TRPV1 SNP I585V.  Of the 4 patient samples, 2 were heterozygous for the I585V SNP and 2 expressed WT TRPV1.  These cells were plated in 12 well plates and treated with Coal Fly Ash (CFA) at multiple concentrations and capsasian.  Differences between the patient samples were assessed.

overall_design: NHBE cells from 4 different donors, (2 WT, 2 I585V HETS) were compared

first: Cassandra

last: Rice


title: Conserved functional antagonism between CELF and MBNL proteins regulates stem cell-specific alternative splicing and regeneration in planarians (dataset 2)

status: Public on Aug 01 2016

first: Timothy

last: Hughes

summary: Here, we analyze the RNA-binding preferences of the planarian smed-mbnl-like-2, smed-mbnl-1 (isoform X1), smed-bruli, smed-mbnl-1 (isoform Xins), and smed-mbnl-like-1 protein using RNAcompete.

overall_design: In the RNAcompete assay, a purified GST-tagged protein is incubated with an excess of RNA pool and bound RNA from individual pulldown experiments are directly labeled and hybridized to a custom Agilent 244K microarray.

first: Jordi

last: Solana

first: Manuel

last: Irimia

first: Salah

last: Ayoub

first: Marta

middle: R

last: Orejuela

first: Vera

last: Zywitza

first: Marvin

last: Jens

first: Debashish

last: Ray

first: Quaid

last: Morris

first: Benjamin

last: Blencowe

first: Nikolaus

last: Rajewsky


title: Microarray analysis of whole-blood in HIV-infected Viremic Non Progressor patients

status: Public on May 15 2016

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: We assessed correlates of protection from disease progression in a rare subset of HIV-infected individuals, viremic non-progressors (VNPs). These individuals have high viral load for several years, but in contrast to the majority of infected individuals, they do not progress to AIDS. Here we found this lack of progression was associated with selective preservation of two essential subsets of memory CD4+ T cells, central memory (TCM) and stem-cell memory (TSCM) cells. Compared to HIV-infected putative progressors, VNPs had higher proliferation of these indispensable subsets of memory cells, which was associated with the number of TCM. In addition, the long-lived CD4+ TCM and TSCM cells in VNPs had decreased HIV infection compared to the less critical effector memory CD4+ T cells, which indicates a possible mechanism by which VNPs maintain their CD4+ T cell pool after several years of infection, and remain free from AIDS progression.

overall_design:
6 HIV-infected patients fitting the clinical criteria of Viremic Non-Progressors were identified. VNPs were defined as having confirmed HIV-1 infection for at least 9 years with sustained plasma HIV RNA levels >10,000 copies/ml and maintenance of peripheral blood CD4+ T cell counts >500 cells/mm3 and a CD4% (of all lymphocytes) >15%. As controls, 7 HIV-infected Putative Progressors were identified. PPs were defined as having plasma HIV RNA levels >10,000 copies/mL, CD4+ T cell counts >400 cells/mm3 and having been initially infected with HIV 2-24 months prior to the index visit. The estimated date of initial HIV infection was calculated according to published algorithms that incorporate “de-tuned” anti-HIV-1 antibody ELISA results or by a documented sero-conversion window of <6 months. All participants were required to be antiretroviral therapy (ART)-naïve.
RNA from 6 VNP and 7 PPs was purified from PAXgene whole blood tubes and hybridized to Affymetrix U133 Plus 2.0 arrays. During data analysis, one VNP patient (PID 4015) was determined to be an outlier and removed from further analysis.  Thus, 5 VNPs and 7 PPs are represented in this Series.

first: Nichole

last: Klatt

first: Guido

last: Silvestri

first: Steven

last: Bosinger