title: Next-generation Sequencing (NGS) identified genome-wide profiles of piwi-interacting RNAs (piRNAs) in human Epithelial Ovarian Cancers (EOCa)

city: Rourkela

first: Dr. Bibekanand

last: Mallick

state: Odisha

address: NIT Rourkela

department: Department of Life Science

institute: National Institute of Technology

summary:
Purpose: The aim of this study is to identify known and novel small RNAs (Piwi-interacting RNAs and microRNAs) in normal ovary and epithelial ovarian malignancies by adopting high-throughput RNA sequencing (RNA-Seq) and unveil their possible functions in neoplastic pathways of the two most frequently observed and highly lethal subtypes of epithelial ovarian cancers, endometrioid ovarian cancer (ENOCa) and serous ovarian cancer (SOCa). The study has been performed in normal ovarian tissues as well as malignant tissues of these cancer subtypes.
Methods: 1 µg of total RNA was used as the starting material for library preparation as prescribed by Illumina Truseq small RNA library protocol. Small RNA sequencing was carried out by Genotypic Technology, Bangalore, India on Illumina Next-Seq 500 platform. Library preparation was done by performing 3' and 5' adapter ligation followed by reverse transcription of cDNA and amplification of the library. The construct of the library was fractionated to select 16-40 nucleotide insert of small RNAs using PAGE. The quality check of the library was done in Agilent Technologies 2100 Bioanalyzer using a DNA-specific chip, such as High Sensitivity DNA. The sequence reads that passed through Quality Check by FastQC and aligned to the human genome (hg19) were further analysed using in-house pipelines and set of known and novel piRNAs and miRNAs were identified. The sets of known piRNAs and miRNAs identified were assessed for their involvement in neoplastic processes of ovarian cancer subtypes by performing target analysis and GO enrichment studies.
Results: Using an in-house prediction pipeline, we mapped about 10-15 million sequence reads per sample to the human genome (hg19) and detected 256, 234 and 219 annotated piRNAs in ENOCa, SOCa, and normal ovary respectively; whereas the average number of known miRNAs present in each sample was estimated to be 480. The annotated piRNAs obtained from each sample exhibited varied length distribution between 26-32 nts.
Conclusions: For the first time, our study reported the presence of piRNAs in ENOCa, SOCa and normal ovarian tissue from the next-gen sequencing of small RNAs of 16-40 nts length. The extensive catalogue of human EOCa small RNAs (both piRNAs and miRNAs) detected in this study provides a useful resource to dissect complex neoplastic events that are possibly mediated by these ncRNAs, especially by piRNAs. Moreover, these piRNAs could be used as probable small RNA biomarkers for the EOCa.

overall_design: Small RNA profile of human epithelial ovarian cancer and normal epithelial ovarian tissue was generated by deep sequencing using Illumina Next-Seq 500

first: G

last: Singh

first: B


title: A cytoplasmic COMPASS is necessary for cell survival and triple-negative breast cancer pathogenesis by regulating metabolism

status: Public on Jan 10 2018

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University Feinberg School of Medicine

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mutations and translocations within the COMPASS (complex of proteins associated with Set1) family of histone lysine methyltransferases are associated with a large number of human diseases, including cancer. Here we report that SET1B/COMPASS, which is essential for cell survival, surprisingly has a cytoplasmic variant. SET1B, but not its SET domain, is critical for maintaining cell viability, indicating a novel catalytic-independent role of SET1B/COMPASS. Loss of SET1B or its unique cytoplasmic-interacting protein, BOD1, leads to up-regulation of expression of numerous genes modulating fatty acid metabolism, including ADIPOR1 (adiponectin receptor 1), COX7C, SDC4, and COQ7 Our detailed molecular studies identify ADIPOR1 signaling, which is inactivated in both obesity and human cancers, as a key target of SET1B/COMPASS. Collectively, our study reveals a cytoplasmic function for a member of the COMPASS family, which could be harnessed for therapeutic regulation of signaling in human diseases, including cancer.

overall_design: To examine changes in histone modification and gene expression after depletion/over expression of SET1B or knockout of ADIPOR1 in the human breast cancer cell line MDA-MB-231. We also examine changes of gene expression in BOD1 depleted cells.

first: Lu

last: Wang

first: Clayton

middle: K

last: Collings


title: Small RNA Sequencing of Sporadic Amyotrophic Lateral Sclerosis Cerebrospinal Fluid Reveals Differentially Expressed miRNAs Related to Neural and Glial Activity

status: Public on Jan 09 2018

city: Sheffield

first: Rachel

last: Waller

state: Outside U.S. & Canada

address: SITraN, The University of Sheffield, 385A Glossop Road

country: United Kingdom

institute: University of Sheffield

type: Non-coding RNA profiling by high throughput sequencing

summary: Amyotrophic lateral sclerosis (ALS) is a clinical subtype of motor neurone disease (MND), a fatal neurodegenerative disease involving the loss of both the upper and lower motor neurones from the motor cortex, brainstem, and spinal cord. Identifying specific disease biomarkers would help to not only improve diagnostic delay but also to classify disease subtypes, monitor response to therapeutic drugs and track disease progression. miRNAs are small non-coding RNA responsible for regulating gene expression and ultimately protein expression and have been used as biomarkers for many cancers and neurodegenerative disorders. Investigating the detection of miRNAs in cerebrospinal fluid (CSF), the fluid that bathes the central nervous system (CNS) is a prime target for identifying potential biomarkers for ALS. This is the first study to investigate the expression of miRNAs in the CSF of ALS patients using small RNA sequencing. We detected differentially expressed miRNAs in the CSF of sporadic ALS (sALS) patients related to neural and glial activity. Additionally, miRNAs involved in glucose metabolism and the regulation of oxidative stress were also identified. Detecting the presence of potential CSF derived miRNA biomarkers in sALS could open up a whole new area of knowledge to help gain a better understanding of disease pathophysiology.

overall_design: miRNAs are small non-coding RNA responsible for regulating gene expression and ultimately protein expression and have been used as biomarkers for many cancers and neurodegenerative disorders. Investigating the detection of miRNAs in cerebrospinal fluid (CSF), the fluid that bathes the central nervous system (CNS) is a prime target for identifying potential biomarkers for ALS. This is the first study to investigate the expression of miRNAs in the CSF of ALS patients using small RNA sequencing. We detected differentially expressed miRNAs in the CSF of sporadic ALS (sALS) patients related to neural and glial activity. Additionally, miRNAs involved in glucose metabolism and the regulation of oxidative stress were also identified. Detecting the presence of potential CSF derived miRNA biomarkers in sALS could open up a whole new area of knowledge to help gain a better understanding of disease pathophysiology. Additionally, with further investigation, the tracking of CSF miRNA over the disease course could be used to follow the disease progression and monitor the effect of novel therapeutics that could be personalised to an individual disease phenotype.

first: Matthew

last: Wyles

first: Paul

middle: R

last: Heath

first: Mbombe

last: Kazoka

first: Helen

last: Wollff

first: Pamela

middle: J

last: Shaw

first: Janine

last: Kirby


title: Abnormal RNA splicing and genomic instability after induction of DNMT3A mutations by CRISPR/Cas9 gene editing [Exome-Seq]

city: Bethesda

first: Valentina

last: Giudice

state: MD

address: 10 Center Drive

department: Hematology Branch

institute: NHLBI

summary:
Purpose: DNA methyltransferase 3A (DNMT3A) mediates de novo DNA methylation. Mutations in DNMT3A are associated with hematological malignancies, most frequently acute myeloid leukemia. DNMT3A mutations are hypothesized to establish a pre-leukemic state, rendering cells vulnerable to secondary oncogenic mutations and malignant transformation. However, the mechanisms by which DNMT3A mutations contribute to leukemogenesis are not well-defined.
Methods: Whole-exome sequencing of extracted DNA was performed to confirm DNMT3A mutations. Library construction, exon capture, and sequencing was performed by Otogenetics (Atlanta, GA, USA). In brief, paired-end libraries were generated using the Illumina TruSeq DNA sample preparation kit. Exons were enriched using the Agilent Human All Exon V5 (51 Mb) capture system. Illumina HiSeq2500 was used for sequencing with a paired-end sequencing length of 100-125 bp and approximately 70 million reads per sample.
Results: the DNMT3A mutations induced by K562 cells were transfected with a plasmid encoding Cas9, a CRISPR guide-RNA (gRNA) targeting the DNMT3A gene, and green fluorescent protein (GFP) followed by single-cell sorting. GFP-positive single cell clones were genotyped to confirm the presence of DNMT3A mutations. MT2-MT5 were verified by analysis of whole-exome sequencing data, and WTblk and WT1 were again confirmed to have no mutations in the DNMT3A gene.
Conclusions: CRISPR/Cas9 gene editing allowed the generation of DNMT3A-mutated K562 cells that may be used to model effects of DNMT3A mutations in human cells. Our findings implicate aberrant splicing and induction of genomic instability as potential mechanisms by which DNMT3A mutations might predispose to malignancy.

overall_design: whole-exome sequencing of wild type (WT) and DNMT3A mutated K562 cell lines were generated by deep sequencing using Illumina HiSeq2500

first: Lauren

middle: G

last: Banaszak


title: Abnormal RNA splicing and genomic instability after induction of DNMT3A mutations by CRISPR/Cas9 gene editing [MeDIP-Seq]

type: Methylation profiling by high throughput sequencing

summary:
Purpose: DNA methyltransferase 3A (DNMT3A) mediates de novo DNA methylation. Mutations in DNMT3A are associated with hematological malignancies, most frequently acute myeloid leukemia. DNMT3A mutations are hypothesized to establish a pre-leukemic state, rendering cells vulnerable to secondary oncogenic mutations and malignant transformation. However, the mechanisms by which DNMT3A mutations contribute to leukemogenesis are not well-defined.
Methods: Methylated DNA immunoprecipitation (MeDIP) was used to detect regional differences in DNA methylation between DNMT3A WT and MT clones. DNA extraction of WTblk, WT1, MT1, MT2, and MT4 cell lines was performed as previously described. 5-mC profiling, fragmentation, library preparation and sequencing were performed by Otogenetics (Atlanta, GA, USA). In brief, paired-end libraries were generated using the Illumina TruSeq DNA sample preparation kit. Illumina HiSeq2500 was used for sequencing with a paired-end sequencing length of 100-125 bp and approximately 40 million reads per sample.
Results: We attempted to identify differentially methylated genes based on DNMT3A mutation status and found very few regions of differential methylation between WT and MT cell lines (Figure 3C), which did not exceed the number of regions expected to exhibit differential methylation by chance alone. These data suggest that regional methylation patterns do not differ between DNMT3A MT and WT cell lines in our gene-edited K562 cells.
Conclusions: CRISPR/Cas9-mediated DNMT3A-mutated K562 cells may be used to model effects of DNMT3A mutations in human cells. Our findings implicate aberrant splicing and induction of genomic instability as potential mechanisms by which DNMT3A mutations might predispose to malignancy.

overall_design: methylation profiles of wild type (WT) and DNMT3A mutated K562 cell lines were generated by deep sequencing using Illumina HiSeq2500


title: Abnormal RNA splicing and genomic instability after induction of DNMT3A mutations by CRISPR/Cas9 gene editing

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

overall_design: Refer to individual Series


title: Expression data and HIRA ChIP-seq data from interferon treated IMR90 cells

city: Glasgow

first: Peter

last: Adams

address: Switchback Rd, Bearsden

institute: University of Glasgow, Beatson Institute for Cancer Research

summary: IMR90 cells treated with IFN and without IFN, with and without a lentivirus knockdown of HIRA

overall_design: We used RNA-Seq and ChIP-seq to detail the global programme of gene expression and HIRA binding in cells treated with and without IFN

first: Taranjit

middle: S

last: Rai

first: Mandy

last: Glass

first: John

last: Cole

middle: D


title: Transcriptomic and proteomic analyses of Anopheles gambiae (Ag55) cells: a potential model to study mosquito-pathogen interaction

city: Athens

first: Ruchir

last: Mishra

state: Georgia

address: 103 college station road, B108

department: Entomology

institute: University of Georgia

summary:
The goal of this study is to analyze the gene expression profile of Anopheles gambiae Ag55 cells and compare it with gene expression profile of blood fed female Anopheles gambiae adult to establish Ag55 cells as a potential model to study mosquito-pathogen interactions
Methods: The transcript profiles of Ag55 cells were generated by RNA-sequencing, in triplicate, using Illumina HiSeq 2000 v3 platform. The 7 samples (paired-end reads, including replicates ( 3 samples from Ag55 cells and 4 samples from blood-fed female adults downloaded from NCBI GEO (Series GSE55453, SRA id : SRP039058))) were independently mapped on to A. gambiae genome (Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.gz) downloaded from vectorbase by using TopHat followed by Cufflinks to estimate the expression values of the transcripts in FPKM (Fragments Per Kilobase per Million mapped reads) with the cuffdiff2 default geometric normalization. Differentially expressed genes (FDR<0.05 after Benjamini-Hochberg correction for multiple-testing) were identified for Ag55 cells relative to Blood fed female adults
Results: We provide detailed gene expression and proteome profiles of Ag55 cells. We further compare the gene expression profiles of Ag55 cells and blood fed female adults. Gene Ontology enrichment analysis of our transcriptomic data suggested that Ag55 cells have phagocytic properties, a hypothesis which we confirmed using confocal imaging. Transcriptomic data further backed by proteomic data suggest that Ag55 cells express hemocyte like properties, and are immune competent.
Conclusion: As Ag55 cells are immune competent and express hemocyte like properties they can be used as a model to study vector-pathogen immune response. Furthermore, the availability of transcriptomic and proteomic data of Ag55 cells will help researchers use and engineer the Ag55 cell line in an efficient way, for example by developing strategies to make it more suitable for studies of interactions with Plasmodium and other microbes.

overall_design: Gene expression profile of Ag55 cell line was generated by RNA sequencing, in triplicate, using  Illumina HiSeq 2000 v3 platform

first: Robert

middle: L

last: Bridger

first: Ujwal

last: Bagal

first: Gang

last: Hua

first: Lance

last: Wells

first: Donald

middle: E

last: Champagne

first: Michael

last: Adang


title: Histone H3 lysine 4 monomethylation modulates longrange chromatin interactions at enhancers

city: Kowloon

first: Jian

last: Yan

address: 83 Tat Chee Ave

department: Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

summary: Long-range chromatin interactions between enhancers and promoters are essential for transcription of many developmentally controlled genes in mammals and other metazoans. Currently, the exact mechanisms that connect distal enhancers to their specific target promoters remain to be fully elucidated. Here, we show that the enhancer-specific histone H3 lysine 4 monomethylation (H3K4me1) and the histone methyltransferases MLL3 and MLL4 (MLL3/4) play an active role in this process. We demonstrate that in differentiating mouse embryonic stem cells, MLL3/4-dependent deposition of H3K4me1 at enhancers correlates with increased levels of chromatin interactions, whereas loss of this histone modification leads to reduced levels of chromatin interactions and defects in gene activation during differentiation. H3K4me1 facilitates recruitment of the Cohesin complex, a known regulator of chromatin organization, to chromatin in vitro and in vivo, providing a potential mechanism for MLL3/4 to promote chromatin interactions between enhancers and promoters. Taken together, our results support a role for MLL3/4-dependent H3K4me1 in orchestrating long-range chromatin interactions at enhancers in mammalian cells.

overall_design: Examination of chromatin loop interactions in 3 cell types.

first: Bing

last: Ren


title: Analyzing differential gene expression pattern upon BRUCE knockdown in full medium and starvation conditions

status: Public on Jan 08 2018

city: Wien

first: Fumiyo

last: Ikeda

address: Dr. Bohr-Gasse 3

country: Austria

institute: Institute of Molecular Biotechnology

summary: BRUCE was identified as a novel positive regulator of autophagy. By analyzing changes in mRNA levels, we wanted to determine whether BRUCE regulates autopahgy on a trancscriptional level.

overall_design: Examination of changes in total mRNA levels comparing control (shRenilla) and BRUCE knockdown (shBruce) cells in full medium (FM) and starvation medium (Starv)

first: Petra

last: Ebner


title: DNA Double-strand Break Response Factors Influence End-joining Features of IgH Class Switch and General Translocation junctions

city: Boston

first: Rohit

middle: A

last: Panchakshari

state: MA

address: One Blackfan Circle, KARP building

department: PCMM

institute: Children's Hospital Boston

summary: IgH class switch recombination (CSR) in B lymphocytes switches IgH constant regions to change antibody functions. CSR is initiated by DNA double strand breaks (DSBs) within a donor IgH switch (S) region and a downstream acceptor S region. CSR is completed by fusing donor and acceptor S region DSB ends by classical non-homologous end-joining (C-NHEJ) and, in its absence, by alternative end-joining (A-EJ) that is more biased to use longer junctional micro-homologies (MHs). Deficiency for DSB response (DSBR) factors, including ATM and 53BP1, variably impair CSR end-joining, with 53BP1 deficiency having the greatest impact.  However, studies of potential impact of DSBR factor deficiencies on MH-mediated CSR end-joining have been technically limited. We now use a robust DSB joining assay to elucidate impacts of deficiencies for DSBR factors on CSR and chromosomal translocation junctions in primary mouse B cells and CH12F3 B lymphoma cells. Compared to wild-type, CSR and c-Myc to S region translocation junctions in the absence of 53BP1, and to a lesser extent other DSBR factors, have increased MH-utilization; indeed, 53BP1-deficient MH-profiles resemble those associated with C-NHEJ deficiency. Yet, translocation junctions between c-Myc DSB and general DSBs genome-wide are not MH-biased in ATM-deficient versus wild-type CH12F3 cells and less biased in 53BP1- and C-NHEJ-deficient cells than CSR junctions or c-Myc to S region translocation junctions. We discuss potential roles of DSBR factors in suppressing increased MH-mediated DSB end-joining and features of S regions that may render their DSBs prone to MH-biased end-joining in the absence of DSBR factors.

overall_design: We performed HTGTS with different B cells and CH12F3 cells genotypes which utilizes AID-initiated 5'Smu DSBs as bait to study their junction features to other AID-initiated S region breaks. We also examine junction features of Cas9-induced c-myc locus DSB translocations to general genome-wide DSBs and S region DSBs.

first: Xuefei

last: Zhang

first: Junchao

last: Dong

first: Frederick

middle: W

last: Alt


title: A Major Chromatin Regulator Determines Resistance of Tumor Cells to T cell Mediated Killing

city: Beijing

first: Deng

last: Pan

address: Tsinghua University Medical Science Building

department: School of Basic Medical Sciences

country: China

institute: Tsinghua University

summary: Many human cancers are resistant to immunotherapy for reasons that are poorly understood.  We used a genome-scale CRISPR/Cas9 screen to identify mechanisms of tumor cell resistance to killing by cytotoxic T cells, the central effectors of anti-tumor immunity.  Inactivation of >100 genes sensitized mouse B16F10 melanoma cells to killing by T cells, including Pbrm1, Arid2 and Brd7, which encode components of the PBAF form of the SWI/SNF chromatin remodeling complex. Loss of PBAF function increased tumor cell sensitivity to interferon-gamma, resulting in enhanced secretion of chemokines that recruit effector T cells.  Treatment-resistant tumors became responsive to immunotherapy when Pbrm1 was inactivated.  In many human cancers, expression of PBRM1 and ARID2  inversely correlated with expression of T cell cytotoxicity genes, and Pbrm1-deficient murine melanomas  were more strongly infiltrated by cytotoxic T cells.

overall_design: Contro, Arid2, Brd7 and Pbrm1 deficient B16F10 cells were either left untreated or treated with IFNg for 24 hours.

first: Aya

last: Kobayashi

first: Peng

last: Jiang

first: Kai

last: Wucherpfennig


title: Regeneration of the lung alveolus by an evolutionarily conserved epithelial progenitor [human RNA-seq]

city: Philadelphia

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: The lung alveolus is the primary site of gas exchange in mammals. Within the alveolus, the alveolar type 2 (AT2) epithelial cell population generates surfactant to maintain alveolar structure and harbors a regenerative capacity to repair the alveolus after injury. We show that a Wnt-responsive alveolar epithelial progenitor (AEP) lineage within the AT2 cell population is critical for regenerating the alveolar niche. AEPs are a stable lineage during alveolar homeostasis but expand rapidly to regenerate a majority of the alveolar epithelium after acute lung injury. AEPs exhibit a distinct transcriptome, epigenome, and functional phenotype with specific responsiveness to Wnt and FGF signaling that modulates differentiation and self-renewal, respectively. Importantly, human AEPs (hAEPs) can be isolated and characterized through a conserved surface marker and are required for human alveolar self-renewal and differentiation using alveolar organoid assays. Together, our findings show that AEPs are an evolutionarily conserved alveolar progenitor lineage essential for regenerating the alveolar niche in the mammalian lung.

overall_design: Examination of open chromatin in 2 subtypes of alveolar epithelial cell populations

first: William

last: Zacharias

first: David

middle: B

last: Frank

first: Jarod

last: Zepp

first: Micheal

middle: P

first: Farrah

last: Alkahleel

first: Edward

last: Cantu

last: Morrisey


title: Dermal endothelial cells of type 2 diabetic patients

city: Vienna

first: Reiner

last: Wimmer

address: Dr. Bohrgasse 3

institute: IMBA

summary: The prevalence of type 2 diabetes mellitus (T2D) is increasing constantly and various risk factors such as obesity, aging, nutritional states and physical inactivity, in addition to genetic pre-dispositions in different populations has been identified. The consequences of high blood glucose include damaged blood vessels, leading to arteriosclerosis and chronic diabetic microangiopathies. These changes lead to occlusive angiopathy, altered vascular permeability, or tissue hypoxia, resulting in complications such as heart disease, strokes, kidney disease, blindness, impaired wound healing, chronic skin ulcers, or amputations. We isolated dermal endothelial cells from diabetic patients (Pat) and control individuals (Ctrl) and performed RNASeq to compare differentially expressed genes.

overall_design: Surgical samples of human skin were taken from Type 2 diabetic patients and non-diabetic patients. The study was approved by the local ethics committee and all included patients gave their informed consent (no. 449/2001; 81/2008). Endothelial cells (CD31+, CD45-, Podoplanin-) from 4 diabetic patients (Pat) and 6 controls (Ctrl) were FACS sorted and processed for RNA Seq.

first: Nikolaus

last: Wick

first: Brigitte

last: Hantusch

first: Alexandra

last: Leopoldi

first: Martin

last: Aichinger

first: Monika

last: Hämmerle

first: Guibin

last: Chen

first: Manfred

last: Boehm

first: Johannes

last: Zuber

first: Dontscho

last: Kerjaschki

first: Josef

middle: M

last: Penninger


title: Regeneration of the lung alveolus by an evolutionarily conserved epithelial progenitor [ATAC-seq]

first: Michael

last: Morley

first: William

last: Zacharias


title: Abnormal RNA splicing and genomic instability after induction of DNMT3A mutations by CRISPR/Cas9 gene editing [RNA-Seq]

first: Valentina

last: Giudice

summary:
Purpose: DNA methyltransferase 3A (DNMT3A) mediates de novo DNA methylation. Mutations in DNMT3A are associated with hematological malignancies, most frequently acute myeloid leukemia. DNMT3A mutations are hypothesized to establish a pre-leukemic state, rendering cells vulnerable to secondary oncogenic mutations and malignant transformation. However, the mechanisms by which DNMT3A mutations contribute to leukemogenesis are not well-defined.
Methods: mRNA profiles of wild-type (WT) and DNMT3A mutated k562 cell lines were generated by deep sequencing, using Illumina HiSeq2500. Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality at the ends. Remaining sequence reads were then aligned to the human reference genome (hg19) using Tophat2. Gene read counts were measured using FeatureCounts and FPKM values were calculated with cufflinks. edgeR was used to identify differentially expressed genes between conditions, and topGO was used for annotation (Alexa, Rahnenfuhrer, and Lengauer, 2006). Sample comparison for differential gene expression was as follows: WTblk and WT1 versus MT2, MT3, MT4, and MT5. Gene enrichment set analysis (GSEA) was conducted with KEGG, Biocarta, and Reactome pathway datasets (Subramanian et al., 2005).
Results: DNMT3A-mutated cells displayed impaired differentiation capacity. RNA-seq was used to compare transcriptomes of DNMT3A-mutated and WT cells; DNMT3A ablation resulted in downregulation of genes involved in spliceosome function, causing dysfunction of RNA splicing. Unexpectedly, we observed DNMT3A-mutated cells to exhibit marked genomic instability and an impaired DNA damage response compared to WT.
Conclusions: CRISPR/Cas9-mediated DNMT3A-mutated K562 cells may be used to model effects of DNMT3A mutations in human cells. Our findings implicate aberrant splicing and induction of genomic instability as potential mechanisms by which DNMT3A mutations might predispose to malignancy.

overall_design: mRNA profiles of wild type (WT) and DNMT3A mutated K562 cell lines were generated by deep sequencing using Illumina HiSeq2500

first: Lauren

last: Banaszak


title: Genome-wide maps of metabolic labeled RNA in Drosophila S2 cells.

first: Karen

last: Adelman

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

summary: We report the application of ultrashort metabolic labeling of RNA for high-throughput profiling of RNA processing in Drosophila S2 cells.

overall_design: Examination of 3 different labeling timepoints in Drosophila S2 cells.

first: T

last: Henriques

first: A

last: Burkholder

first: K

last: Pai

first: J

last: Paggi

first: C

last: Burge


title: Alternative RNA Splicing in the Endothelium Mediated in Part by Rbfox2 Regulates the Arterial Response to Low Flow

city: Farmington

first: Patrick

last: Murphy

state: CT

address: 263 Farmington Ave

department: Center for Vascular Biology

institute: University of Connecticut Health Center

summary: Low and disturbed blood flow drives the progression of arterial diseases including atherosclerosis and aneurysms. The endothelial response to flow and its interactions with recruited platelets and leukocytes determine disease progression.  Here, we report widespread changes in alternative splicing of pre-mRNA in the flow-activated murine arterial endothelium in vivo.  Alternative splicing was suppressed by depletion of platelets and macrophages recruited to the arterial endothelium under low and disturbed flow.  Binding motifs for the Rbfox-family are enriched adjacent to many of the regulated exons. Endothelial deletion of Rbfox2, the only family member expressed in arterial endothelium, suppresses a subset of the changes in transcription and RNA splicing induced by low flow.  Our data reveal an alternative splicing program activated by Rbfox2 in the endothelium on recruitment of platelets and macrophages and demonstrate its relevance in transcriptional responses during flow-driven vascular inflammation.

overall_design: Samples include arterial intima from carotid artery in vivo, and isolated aortic endothelial cells under various flow conditions, and with or without depletion of specific splice factors or recruited innate immune cells.

first: Vincent

last: Butty

first: Paul

last: Boutz

first: Shahinoor

last: Begum

first: Philip

last: Sharp

first: Christopher

first: Richard

middle: O

last: Hynes


title: D. melanogaster eye-antennal imaginal discs developmental transcriptome

city: Göttingen

first: Nico

last: Posnien

address: Justus-von-Liebig-Weg 11

department: Department of Developmental Biology

country: Germany

institute: University of Göttingen

summary: Transcriptomes of Drosophila melanogaster eye-antennal imaginal discs at three sequential larval stages: late 2nd instar (72h after egg laying (AEL)), mid 3rd instar (96h AEL) and late 3rd instar (120h AEL).

overall_design: mRNA profiles of larval eye-antennal imaginal discs were generated by deep sequencing using Illumina HiSeq 2000. 3 biological replicates were generated for each stage and sequenced in 50 bp single-end reads.

first: Montserrat

last: Torres-Oliva


title: Regeneration of the lung alveolus by an evolutionarily conserved epithelial progenitor.

first: Michael

last: Morley

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Prmt1-mediated translation regulation is a crucial vulnerability of cancer

status: Public on Jan 06 2018

first: Jialiang

last: Huang

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

summary: Through an shRNA screen we have identified Prmt1 as a genetic vulnerability of p53/Rb-null murine osteosarcoma cells. Depletion of Prmt1 in p53-deficient cells impairs tumor initiation and maintenance in vitro and in vivo. Mechanistic studies reveal that translation-associated pathways are enriched for Prmt1 downstream targets, implicating a role of Prmt1 in translation control. In particular, we have shown that loss of Prmt1 leads to a the decrease in arginine methylation of the translation initiation complex, thereby disrupting its assembly and inhibiting translation. We also observed that p53/Rb-null cells are sensitive to p53-induced translation stress. Analysis of the human tumor cell Achilles data set further reveals that Prmt1 and translation-associated pathways converge on the same functional networks. We propose that targeted therapy directed to inhibition of Prmt1 and its associated translation-related pathways represents a novel and promising therapeutic strategy for p53-deficient cancer cells that exhibit dependencies on translation stress response.

overall_design: RNAs were extracted from Prmt1 control and conditional knockout murine osteosarcoma cell line.  In each group, RNAs from cytoplasmic, light (<3 ribosomes) polysome fractions (termed Light),  heavy (>3 ribosomes) polysome fractions (termed Heavy), as well as total cytoplasmic RNA (termed Total) were pooled and precipitated using Trizol-LS (Thermo Scientific). 500 ug of RNAs were used to prepare cDNA libraries using the illumina Truseq v2 kit. The libraries were quantified and sequenced using Illumina Nextseq sequencer.

first: Hao-Ru

last: Hsu

first: Stuart

middle: H

last: Orkin


title: Regeneration of the lung alveolus by an evolutionarily conserved epithelial progenitor [mouse RNA-seq]

first: William

last: Zacharias

first: David

last: Frank

first: Jarod

last: Zepp

first: Micheal

first: Farrah

last: Alkahleel

first: Edward

last: Cantu

last: Morrisey


title: Roquin suppresses PI3K-mTOR signaling to control T cell differentiation and Treg effector function

city: Basel

first: Joao

middle: C

last: Guimaraes

address: Klingelbergstrasse 50 / 70

department: Biozentrum

country: Switzerland

institute: University of Basel

summary: Roquin proteins are required to preclude spontaneous T cell activation and aberrant T follicular helper (Tfh) or T helper 17 (Th17) differentiation. Here, we show that deletion of Roquin encoding alleles in regulatory T cells (Tregs) also caused the activation of conventional T cells. These Tregs exhibited a follicular Treg phenotype, CD25 downregulation and could not protect from colitis. Mechanistically, Roquin was required for full expression and activity of Pten and Foxo1, two essential signaling molecules in Tregs and effector T cells. Roquin upregulated Pten by interfering with miR-17~92 binding to an overlapping cis-element in the Pten 3' UTR and downregulated the Foxo1-specific E3 ubiquitin ligase Itch. Loss of Roquin enhanced mTOR signaling and global protein synthesis, while inhibition of PI3K or mTOR in Roquin-deficient CD4+ T cells corrected increased Tfh and Th17 differentiation. Thereby, the control of PI3K-mTOR signaling by Roquin prevents autoimmunity through T cell-intrinsic and Treg-mediated regulation.

overall_design: Examination of transcriptome and ribosome occupancy in MEF and T cells upon Roquin expression and inhibition. Examination of Roquin binding sites in the mouse transcriptome of MEF cells. Examination of transcriptome in CD25+ and CD25- Treg cells from WT and Roquin DKO mice.

first: Katharina

last: Essig

first: Vigo

last: Heissmeyer


title: Small RNA profiling reveals deregulated PTEN/PI3K/Akt pathway in asthmatic bronchial smooth muscle cells

status: Public on Jan 07 2018

city: Portici

first: Elena

last: Alexandrova

state: Napoli

address: Viale Stazione, 22

department: Faculty of Medicine and Surgery

country: Italy

institute: University of Salerno

summary:
Background: Aberrant expression of small non-coding RNAs (sncRNAs), in particular microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs) define several pathological processes. Asthma is characterized by airway hyper-reactivity, chronic inflammation and airway wall remodeling. Asthma-specific miRNA profiles were reported for bronchial epithelial cells, but no information on sncRNA expression in asthmatic bronchial smooth muscle (BSM) cells is available.
Objective: To determine whether primary BSM sncRNA expression profile is altered in asthma and identify targets of differentially expressed sncRNAs.
Methods: SmallRNA sequencing was used for sncRNA profiling in BSM cells (8 asthma, 6 non-asthma). sncRNA identification and differential expression analysis was performed with iMir, . experimentally validated miRNA targets were identified with Ingenuity Pathway Analysis and putative piRNA targets with miRanda.
Results: Asthmatic BSM cells showed abnormal expression of 32 sncRNAs (26 miRNAs, 5 piRNAs, and 1 snoRNA). Target prediction for deregulated miRNAs and piRNAs revealed experimentally validated and predicted mRNA targets expressed in the BSM cells. 38 of these mRNAs represent major targets for deregulated miRNAs and may play important roles in the pathophysiology of asthma. Interestingly, 6 such miRNAs were previously associated with asthma and/or considered as novel therapeutic targets for treatment of this disease. Signaling pathway analysis revealed involvement of these sncRNAs in increased cell proliferation via PTEN and PI3K/Akt signaling pathways.
Conclusions: BSM cells from asthma patients are characterized by aberrant sncRNA expression that recapitulates multiple pathological phenotypes of these cells.
Implications: sncRNA expression profiling performed in this study further improve our understanding of the molecular mechanisms underlying asthma-associated processes in lungs.

overall_design: SmallRNA and mRNA profiles of primary bronchial smooth muscle cells from 8 asthmatic and 6 healthy donors were generated by deep sequencing using Illumina HiSeq1500 and NextSeq respectively.


title: Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues (brain, liver, skin)

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

summary:
Comparison of temporal gene expression profiles

Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 75 samples in sum; 5 age groups (6, 12, 24, 36, 42 months); 3 tissues (brain, liver, skin); 5 samples per group

first: Nils

last: Hartmann

first: Christoph

last: Englert

first: Steffen

last: Priebe

first: Marco

last: Groth

first: Matthias

last: Platzer


title: The Roc10, a Rice Homeodomain-leucine Zipper Transcription Factor, Modulates Lignin Biosynthesis that Confers Drought Tolerance

city: Pyeongchang

first: Pil Joong

last: Chung

state: Gangwondo

address: Pyeongchang daero 1447

department: Crop Biotechnology Institute

country: South Korea

institute: Seoul National University

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

overall_design: Refer to individual Series


title: The Roc10, a Rice Homeodomain-leucine Zipper Transcription Factor, Modulates Lignin Biosynthesis that Confers Drought Tolerance [RNA-seq]

summary: Drought is a major environmental constraint affecting physiological, biochemical and molecular changes of crops, causing loss in crop productivities. Understanding the molecular mechanisms of drought tolerance is important for crop biotechnology. Here, we report that the rice (Oryza sativa) homeodomain-leucine zipper class IV transcription factor gene, Rice outermost cell-specific gene 10 (Roc10), improves drought tolerance and grain yield by increasing lignin accumulation in ground tissues of rice plants. Overexpression of Roc10 significantly enhanced drought tolerance of transgenic rice plants at the vegetative stages of growth with highly effective photosystem and reduction of water loss rate as compared with non-transgenic control and RNAi plants. More importantly, Roc10 overexpression plants had higher drought tolerance at the reproductive stage of growth with higher grain yield over controls under field-drought conditions. We identified downstream and putative target genes of Roc10 by using RNA-seq and ChIP-seq data of rice shoots. Roc10 overexpression elevated the expression levels of lignin biosynthetic genes in shoots with a concomitant increase in accumulation of lignin. The overexpression and RNAi lines showed opposite patterns of lignin accumulation. The Roc10 is mainly expressed in the outer cell layers including epidermis and vasculature of shoots that coincides with areas of increased lignification. Furthermore, the Roc10 was found to directly bind to the promoter of PEROXIDASEN/PEROXIDASE38, a key gene in lignin biosynthesis. Together, our findings suggested that the Roc10 confers drought stress tolerance by enhancing lignin biosynthesis in ground tissues of rice plants.

overall_design: RNA-seq using leaves of NT and Roc10 transgenic plants.

first: Seung

last: Bang

first: Ju

middle: K

last: Kim


title: Intracranial aneurysm associated single-nucleotide polymorphisms alter regulatory DNA in the human circle of Willis

status: Public on Jan 04 2018

city: Utrecht

first: Ynte

last: Ruigrok

address: Heidelberglaan 100

country: Netherlands

institute: UMC Utrecht

summary:
Background and Purpose: Genome-wide association studies significantly link intracranial aneurysm (IA) to single-nucleotide polymorphisms (SNPs) in six genomic loci. To gain insight into the relevance of these IA associated SNPs, we aimed to identify regulatory regions and analyze overall gene expression in the human circle of Willis (CoW), on which these aneurysms develop.
Methods: We performed chromatin immunoprecipitation and sequencing for histone modifications H3K4me1 and H3K27ac to identify regulatory regions, including distal enhancers and active promoters, in post mortem specimens of the human CoW. These experiments were complemented with RNA sequencing on the same specimens. We determined whether these regulatory regions overlap with IA associated SNPs, using computational methods. By combining our results with publicly available data, we investigated the effect of IA associated SNPs on the newly identified regulatory regions and linked them to potential target genes.
Results: We find that IA associated SNPs are significantly enriched in CoW regulatory regions. Some of the IA associated SNPs that overlap with a regulatory region are likely to alter transcription factor binding, and in proximity to these regulatory regions are 102 genes that are expressed in the CoW. In addition, gene expression in the CoW is enriched for genes related to cell adhesion and the extracellular matrix.
Conclusions: CoW regulatory regions link IA associated SNPs to genes with a potential role in the development of IAs. Our data refine previous predictions on SNPs associated with IA and provide a substantial resource from which candidates for follow-up studies can be prioritized.

overall_design: 4 human circle of Willis samples (biological replicates) were used for both ChIP sequencing (H3K27ac and H3K4me1) and for RNA sequencing.

first: Melanie

last: Laarman

first: Marit

last: Vermunt

first: Rachel

last: Kleinloog

first: Jelkje

last: de Boer-Bergsma

first: Gabriel

last: Rinkel

first: Menno

last: Creyghton

first: Michal

last: Mokry

first: Jeroen

last: Bakkers


title: A unique ISR Program Determines Cellular Responses to Chronic Stress

status: Public on Jan 05 2018

city: Solna

first: Ola

last: Larsson

address: Tomtebodavägen 23

country: Sweden

institute: Karolinska Institutet

summary: Integrated Stress Response (ISR) is a homeostatic mechanism induced by endoplasmic reticulum (ER) stress. With acute/transient ER stress, decreased global protein synthesis and increased uORF mRNA translation are followed by translation normalization. Here, we report a dramatically different response during more physiologically relevant chronic ER stress. This unique ISR program is characterized by persistently elevated uORF mRNA translation and concurrent gene expression reprogramming, which permits simultaneous stress sensing and proteostasis. PERK-dependent switching from eIF4F/eIF2B- to eIF3D/GADD34-regulated translation initiation results in partial but not complete translation recovery, and together with transcriptional reprogramming, selectively bolsters expression of proteins with ER functions. Coordination of these transcriptional and translational changes prevents ER dysfunction and inhibits “foamy cell” development, thus establishing a molecular basis for understanding human diseases associated with ER dysfunction.

overall_design: Four replicates were used for each condition (Control, Tg 1h, Tg 16h and Tg 16h + PERKi). The RNA of every sample was seperated into Input (total RNA) and polysome-associated RNA (resulting in 32 samples) before sequencing.

first: Bo-Jhih

last: Guan

first: Vincent

last: van Hoef

first: Marie

last: Cargnello

first: Orna

last: Elroy-Stein

first: Raul

last: Jobava

first: Xing-Huang

last: Gao

first: Dawid

last: Krokowski

first: William

last: Merrick

first: Scot

middle: R

last: Kimball

first: Anton

last: Komar

first: Antonis

last: Koromilas

first: Anthony

last: Wynshaw-Boris

first: Ivan

last: Topisirovic

first: Maria

last: Hatzoglou


title: Dynamic reorganization of nuclear architecture during human cardiogenesis [HiC-seq]

city: Seattle

first: Charles

last: Murry

state: WA

address: 850 Republican St

department: Institute for Stem Cell and Regenerative Medicine

institute: University of Washington

summary: While chromosomal architecture varies among cell types, little is known about how this organization is established or its role in development. We integrated Hi-C, RNA-seq and ATAC-seq during cardiac differentiation from human pluripotent stem cells to generate a comprehensive profile of chromosomal architecture. We identified active and repressive domains that are dynamic during cardiogenesis and recapitulate in vivo cardiomyocytes. During differentiation, heterochromatic regions condense in cis. In contrast, many cardiac-specific genes, such as TTN (titin), transition to an active compartment coincident with upregulation. Moreover, we identify a network of genes, including TTN, that share the heart-specific splicing factor, RBM20, and become associated in trans during differentiation, suggesting the existence of a 3D nuclear splicing factory. Our results demonstrate both the dynamic nature in nuclear architecture and provide insights into how developmental genes are coordinately regulated.

overall_design: Hi-C, RNA-seq and ATAC-seq analysis of four stages of human pluripotent stem cell differentiation to cardiomyocytes, including stem cell, mesoderm, cardiac progenitor, and cardiomyocyte, with two biological replicates of each condition. Hi-C and RNA-seq analysis of two biological replicates fetal heart samples.

first: Paul

last: Fields


title: Dynamic reorganization of nuclear architecture during human cardiogenesis [ATAC-seq]


title: The Roc10, a Rice Homeodomain-leucine Zipper Transcription Factor, Modulates Lignin Biosynthesis that Confers Drought Tolerance [ChIP-seq]

first: Pil Joong

last: Chung

overall_design: ChIP-seq using leaves of NT and PGD1::6xmyc-Roc10 plants.

first: Seung

last: Bang

first: Ju

last: Kim


title: Dynamic reorganization of nuclear architecture during human cardiogenesis [RNA-seq]


title: BRD4 promotes DNA repair and mediates the formation of TMPRSS2-ERG gene rearrangements in prostate cancer

city: Dallas

first: Ram

last: Mani

state: Texas

address: 5323 Harry Hines Blvd NB6.444

department: Pathology

institute: UT Southwestern Medical Center

summary: We employ ChIP- seq methodology to study the effect of ionizing radiation on genome-wide localization of acetylated histone H4

overall_design: Antibody used for Acetylated histone H4 bound DNA in radiated and non-radiated LNCaP cells

first: Susmita

last: Ramanand

first: Yunpeng

first: Adam

last: Aslam

first: Mohammed

last: Kanchwala

first: Chao

last: Xing


title: Dynamic reorganization of nuclear architecture during human cardiogenesis


title: Deep sequencing of mRNA from mouse at five different timepoints in three different tissues (brain, liver, skin)

first: JenAge

last: Project

overall_design: 115 samples in sum; 5 age groups (2, 9, 15, 24, 30 months); 4 tissues (brain, liver, skin, blood); 5-8 samples per group

first: Otto

last: Witte

first: Christiane

last: Frahm

first: Steffen

last: Priebe

first: Marco

last: Groth

first: Matthias

last: Platzer


title: Angiogenic factor imbalance precedes complement deposition in the placenta of preeclamptic-like BPH/5 mice

city: Ithaca

first: Jennifer

last: Grenier

state: NY

address: 526 Campus Rd

institute: Cornell University

summary: BPH/5 mice are an inbred strain with “borderline hypertension” that spontaneously develops both maternal and fetal hallmarks of preeclampsia. RNA-Seq analysis of BPH/5 uterine implantation sites at embryonic day 7.5, the peak of decidualization, identifies differential expression of inflammatory response genes, including members of the complement family, compared to C57 controls.

overall_design: RNA-Seq was performed on RNA isolated from E7.5 BPH/5 and C57 implantation sites (n=4).

last: Sones


title: RNA-seq identifies a diminished differentiation gene signature in primary monolayer keratinocytes grown from lesional and uninvolved psoriatic skin

status: Public on Jan 03 2018

city: Ann Arbor

first: William

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

summary: Keratinocyte (KC) hyper-proliferation and epidermal thickening are characteristic features of psoriasis lesions, but the specific contributions of KCs to plaque formation are not fully understood. This study used RNA-seq to investigate the transcriptome of primary monolayer KC cultures grown from lesional (PP) and non-lesional (PN) biopsies of psoriasis patients and control subjects (NN). Whole skin biopsies from the same subjects were evaluated concurrently. RNA-seq analysis of whole skin identified a larger number of psoriasis-increased differentially expressed genes (DEGs), but analysis of KC cultures identified more PP- and PN-decreased DEGs. These latter DEG sets overlapped more strongly with genes near loci identified by psoriasis genome-wide association studies and were enriched for genes associated with epidermal differentiation. Consistent with this, the frequency of AP-1 motifs was elevated in regions upstream of PN-KC-decreased DEGs. A subset of these genes belonged to the same co-expression module, mapped to the epidermal differentiation complex, and exhibited differentiation-dependent expression. These findings demonstrate a decreased differentiation gene signature in PP/PN-KCs that had not been identified by pre-genomic studies of patient-derived monolayers. This may reflect intrinsic defects limiting psoriatic KC differentiation capacity, which may contribute to compromised barrier function in normal-appearing uninvolved psoriatic skin.

overall_design: Samples were obtained from lesional skin of psoriasis patients (PP), uninvolved skin of psoriasis patients (PN), and normal skin from control individuals (NN). RNA was extracted from full-thickness skin biopsies of keratinocytes (KCs) grown as monolayer cutures. Samples were obtained from 4 psoriasis patients (individuals 1 - 4) and 4 control subjects (individuals 5 - 8).

first: Johann

last: Gudjonsson


title: Xi-reactivation: A mixed modality approach to MECP2 restoration for Rett Syndrome and other X-linked disorders

first: Chen-Yu

last: Wang

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

summary: The X-chromosome harbors hundreds of disease genes whose associated diseases predominantly affect males. However, a subset — including neurodevelopmental disorders, Rett, Fragile X, and CDKL5 Syndromes — also affects females. These disorders lack disease-specific treatment. Because female cells carry two X-chromosomes, an emerging treatment strategy has been to reawaken the healthy allele on the inactive X (Xi). Here we focus on MECP2 restoration for Rett Syndrome and combinatorially target factors in the interactome of Xist, the noncoding RNA responsible for X-inactivation. We identify a mixed modality approach combining an Xist antisense oligonucleotide and a small molecule inhibitor of DNA methylation, which together achieve 30,000-fold MECP2 upregulation from the Xi in cultured cells. Combining a brain-specific genetic Xist ablation with short-term Aza treatment models the synergy in vivo without evident toxicity. The Xi is selectively reactivated. These experiments provide proof of concept for a mixed modality approach for treating X-linked disorders in females.

overall_design: Examination of transcriptome profiles of mouse tissues and embyronic fibroblasts undergone X-reactivation treatment

first: Lieselot

last: Carrette

first: Jeannie

middle: T

last: Lee


title: DRUID: A pipeline for reproducible transcriptome-wide measurements of mRNA stability

city: Toronto

first: Olivia

last: Rissland

address: 686 Bay Street

country: Canada

institute: The Hospital for Sick Children

summary: We present DRUID (for Determination of Rates Using Intron Dynamics), a computational pipeline, for determining mRNA stability transcriptome-wide uses metabolic labeling and approach-to-equilibrium kinetics. Our pipeline uses endogenous introns to normalize time course data and yields more reproducible half-lives than other methods, even with datasets that were otherwise unusable. DRUID can handle datasets from a variety of organisms, spanning yeast to humans.

sample_organism:
Saccharomyces cerevisiae
Caenorhabditis elegans
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design: Transcription inhibition time courses  (0, 1, 2, 4, 8, 12, 24 hr) using Actinomycin D or ⍺-amanitin were performed in HEK293 cells. Metabolic labeling time courses (1, 2, 4, 8, 12, 24 hr) using 4SU were performed in HEK293 and NIH3T3 cells. All experiments were performed in duplicate.

first: Andrew

last: Lugowski

first: Nicholson

last: Beth


title: RNA-Seq of CD8+ T cells expressing different levels of Runx3 in a cell culture model of CTL differentiation

city: Jupiter

first: Adam

last: Getzler

state: FL

address: 130 Scripps Way

institute: TSRI-FL

summary: Tissue-resident memory CD8+ T cells (Trm) are positioned at common sites of pathogen exposure where they elicit rapid and robust protective immune responses. However, the molecular signals controlling Trm differentiation and homeostasis are not fully understood. Here we show that mouse Trm precursor cells represent a unique CD8+ T cell subset that is distinct from the precursors of circulating memory populations at the levels of gene expression and chromatin accessibility. Exploiting computational and functional RNAi in vivo screens, we identified the transcription factor (TF) Runx3 as a key regulator of Trm differentiation and homeostasis. Runx3 was required to establish Trm populations in diverse tissue environments and supported expression of critical tissue-residency genes while suppressing genes associated with tissue egress and recirculation. Analysis of the accessibility of Runx3 target genes in Trm-precursor cells revealed a distinct regulatory role for Runx3 in controlling Trm differentiation despite relatively widespread and uniform expression among all CD8+ T cell subsets. Further, we show that human and murine tumor-infiltrating lymphocytes (TIL) share a core tissue-residency gene-expression signature with Trm. In a mouse model of adoptive T cell therapy for melanoma, Runx3-deficient CD8+ TIL failed to accumulate in tumors, resulting in greater rates of tumor growth and mortality. Conversely, overexpression of Runx3 enhanced TIL abundance, delayed tumor growth, and prolonged survival. In addition to establishing Runx3 as a central regulator of Trm differentiation, these results provide novel insight into the signals that promote T cell residency in tissues, which could be leveraged to enhance vaccine efficacy or adoptive cell therapy treatments that target cancer.

overall_design: 6 samples, 2 replicates each, 2 wildtype controls.

first: A

middle: J

first: D

first: M

last: Pipkin


title: RNA-Seq of different Clytia female gonad tissues and oocytes at different growth stage

city: Villefranche-sur-mer

first: Evelyn

last: Houliston

address: chemin du Lazaret

country: France

institute: Sorbonne Universités, UPMC Univ. Paris 06, CNRS

summary: We aimed to quantify in silico the expression level of candidate genes in different Clytia gonad tissues and oocytes at different growth stage

overall_design: A total of 8 samples were analysed: 4 different gonad samples; 2 biological replicates for each. In order to obtain a high enough RNA concentration for each sample we pooled tissues and oocytes that had been dissected in different days, under the same conditions and same jellyfish age.

first: Gonzalo

last: Quiroga Artigas

first: Pascal

last: Lapébie

first: Lucas

last: Leclère


title: Kinetics and molecular hallmarks of the acquisition of developmental pluripotency during cellular reprogramming

city: New York

first: Matthias

last: Stadtfeld

address: 540 First Avenue Skirball Lab 4-1

institute: NYU School of Medicine


title: Transitory accumulation of myeloid-derived suppressor cells in neonates is critical for maintenance of homeostasis

city: Philadelphia

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Myeloid-derived suppressor cells (MDSC) are potent negative regulators of immune responses at many pathological conditions. It is widely accepted that these cells are not present under steady state condition. Here, we report that MDSC with highly potent ability to suppress T cells accumulate during first two weeks of life in mice. MDSC suppressive activity in neonates was triggered by lactoferrin, a component of milk, and mediated by nitric oxide and up-regulation of PGE2 regulated by S100A9/A8 proteins. Newborn MDSC had transcriptome similar to that of tumor MDSC. However, they had strong up-regulation of antimicrobial gene network. This was associated with enhanced antimicrobial activity of these cells. MDSC played a critical role in control of experimental necrotizing enterocolitis in newborn mice. In humans, MDSC in cord blood of low-weight preterm infants prone to the development of NEC had significantly lower suppressive activity than the cells from cord blood of infants with normal weight. Thus, transitory presence of MDSC after birth is critical for the maintenance of immune homeostasis.

overall_design: RNA-seq on PMN-MDSC and M-MDSC cells from adult and neonate mice

first: Dmitry

last: Gabrilovich

first: Yu-Mei

last: He


title: Kinetics and molecular hallmarks of the acquisition of developmental pluripotency during cellular reprogramming [ATAC-Seq]

summary: The ability of induced pluripotent stem cells (iPSCs) to differentiate into all adult cell types makes them attractive for basic research and regenerative medicine applications, but it remains unknown when and how this hallmark of the pluripotent state is established. Here, we pinpoint the acquisition of developmental pluripotency in a suitable reprogramming system and show that nascent iPSCs abruptly and without extensive maturation period in culture become capable of generating all tissues upon injection into preimplantation embryos. Strikingly, the developmental potential of nascent iPSCs is comparable to or even surpasses that of high-quality established pluripotent cells. Further functional assays as well as genome-wide transcriptional and chromatin analyses suggest that cells acquiring developmental pluripotency exhibit a unique combination of molecular and functional properties that distinguish them from canonical pluripotency states. These include reduced clonal self-renewal potential and the elevated expression of transcriptional regulators of postimplantation development. Our observations close an important gap in our understanding of induced pluripotency and provide an improved roadmap of cellular reprogramming with ramifications for the biomedical use of iPSCs.

overall_design: ATAC-seq cells at four stages (MEF, Stage 1 or day 6, Stage 2 or day 6+4 and established iPSCs) in triplicate. Cells (except MEFs) were sorted for Oct4-GFP+

first: Bhishma

last: Amlani


title: Full-coverage landscape of extracellular RNAs, coding and non-coding, secreted by human glioma stem cells

city: Boston

first: Zhiyun

last: Wei

state: Massachusetts

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

summary: Communication between glioblastoma brain tumor (GBM) and its microenvironment alters the parameters of tumor growth and host responses, and may be mediated in part by tumor-secreted RNA. The global repertoire of extracellular RNAs (exRNAs) released by GBM, however, has not been investigated. We have developed a protocol enabling quantitative, minimally biased analysis of vesicular and non-vesicular exRNA complexes, including microvesicles (MVs) and exosomes (collectively called extracelluar vesicles; EVs), as well as ribonucleoproteins (RNPs) and applied it to study exRNA in patient-derived glioma stem-like cultures (GSC). Despite the intertumoral heterogeneity, further exacerbated at the exRNA level, the extracellular complexes exhibit distinct RNA composition, with microvesicles most closely reflecting the cellular transcriptome, and exRNPs exhibiting the most discrete repertoire. Up to 90% of exRNA reads represent fragmented rRNA; the remaining content is enriched in small ncRNA species, such as miRNAs in exosomes, and precisely processed tRNA and Y RNA fragments in both EVs and exRNPs. EV-enclosed mRNAs are mostly fragmented, and UTRs are more abundant than ORF regions; nevertheless, some full-length transcripts are present. Overall, there is less than one copy of non-rRNA per EV. Our results suggest that massive EV/exRNA uptake would be required to ensure functional impact of transferred information to the normal recipient cells of the brain and predict the most impactful miRNAs in such conditions. This study also provides a catalog of diverse vesicular and non-vesicular exRNA species useful for biomarker discovery.

sample_organism:
Homo sapiens
Mus musculus
other sequences

overall_design: Four low-passage patient-derived glioblastoma stem cell cultures were grown as neurospheres in serum-free media. Microvesicles (MVs), exosomes, and ribonucleoproteins (RNPs) were separated from conditioned media using sequential filtration, and RNA was isolated from each fraction. Cellular RNA was isolated from cultures in parallel. RNA was also isolated from MVs, exosomes, and RNPs from fresh media. Both long RNA library and small RNA libraries were prepared for each RNA sample, and sequenced on HiSeq2000. Cellular RNA of human or mouse primary normal brain cells (neurons, astrocytes, microglia, and endothelial cells) were also sequenced for small RNA libraries.

first: Wei

last: Zhiyun

first: Krichevsky

last: Anna


title: Kinetics and molecular hallmarks of the acquisition of developmental pluripotency during cellular reprogramming [RNA-Seq]

overall_design: RNA-seq cells at four stages of reprogramming (MEF, Stage 1 or day 6, Stage 2 or day 6+4 and established iPSCs) in triplicate. Cells (except MEFs) were sorted for Oct4-GFP+


title: Adaptive and reversible resistance to Kras inhibition in pancreatic cancer cells

city: Cambridge

last: Bhutkar

address: 77 Massachusetts Avenue

institute: MIT

summary: Activating Kras mutations are the hallmark genetic alterations in pancreatic ductal adenocarcinoma (PDAC) and key drivers of PDAC initiation and progression.  Despite increased efforts to develop novel Kras inhibitors, the degree of Kras oncogene addiction in PDAC cells remains unclear.  Here, we analyzed the requirement of endogenous Kras for the maintenance of murine PDAC cells using an inducible shRNA-based system that enables temporal control of endogenous Kras expression.  Surprisingly, the majority of murine PDAC cells analyzed tolerated acute and sustained Kras knockdown by adapting to a reversible cell state, characterized by differences in cell morphology, proliferative kinetics, and tumor-initiating capacity.  While significant mutational or transcriptional changes were not observed in the Kras-inhibited state, global phosphoproteomic profiling revealed alterations in cell signaling, including increased phosphorylation of focal adhesion pathway components.  Accordingly, Kras-inhibited cells displayed prominent focal adhesion plaque structures, enhanced adherence properties, and increased dependency on adhesion for viability in vitro.  Our analyses highlight the possibility of adaptive non-genetic and non-transcriptional mechanisms of resistance to Kras inhibition.  Furthermore, we have identified candidate proteins whose signaling activities are altered in the Kras-inhibited state, providing a basis for the rational design of combination therapeutic strategies with novel Kras inhibitors.

overall_design: 6 DOX-inducible shKras-expressing clones derived from 3 parental pancreatic tumor cell lines (A, B, and D; 2 clones per cell line) were treated with doxycycline (DOX) to induce Kras knockdown. One control DOX-inducible shLuc-expressing line was used as a control. RNA-sequencing was performed on long-term DOX-treated (LT DOX) or untreated (No DOX) cells. Technical replicates for specific samples are noted.

first: Pan-Yu

last: Chen

first: Mandar

last: Muzumdar

first: Kimberly

last: Dorans

first: Rebecca

last: Robbins

first: Arjun

first: Amanda

last: del Rosario

first: Philipp

last: Mertins

first: Jana

last: Qiao

first: Anette

last: Schafer

first: Frank

last: Gertler

first: Steven

last: Carr

first: Tyler

last: Jacks


title: TADs are 3D structural units of higher-order chromosome organization in Drosophila

city: Taipei

first: Jia-Ming

last: Chang

address: NO.64, Sec. 2, ZhiNan Rd., Wenshan District

department: Department of Computer Science

country: Taiwan

institute: National Chengchi University

overall_design: Refer to individual Series


title: Augmented R-loop is a Unifying Mechanism for Myelodysplastic Syndromes Induced by High Risk Splicing Factor Mutations

city: Nanjing

first: Jia-Yu

state: CA

address: No 163 of XianlinAvenue, Qixia District

department: School of Life Sciences

institute: Nanjing University

summary: Mutations in several general pre-mRNA splicing factors have been linked to Myelodysplastic Syndromes (MDS) and solid tumors. These mutations have generally been assumed to cause disease by resultant splicing defects, but different mutations appear to induce distinct splicing defects, raising a possibility for an alternative common mechanism involved. Here, we report a chain of events triggered by multiple splicing factor mutations, especially high-risk alleles in SRSF2 and U2AF1, including elevated R-loops, replication stress, and activation of the ATR-Chk1 pathway. We further demonstrate that enhanced R-loops, opposite to the expectation from gained RNA binding with mutant SRSF2, result from impaired transcription pause-release because the mutant protein lost its ability to extract the RNAPII CTD kinase P-TEFb from the 7SK complex. Enhanced R-loops are linked to compromised proliferation of bone marrow-derived blood progenitors, which can be partially rescued by RNase H overexpression, suggesting a direct contribution of augmented R-loops to MDS phenotype.

overall_design: To profile the R-loop dyanmics for comparison between cells with and without expression of mutant splicing factors (SRSF2 and U2AF1) identified in patients with myelodysplastic syndromes (MDS), We performed R-ChIP experiments, a new RNaseH1-based technique recently developped in the lab to specifically capture R-loop in vivo. We established an inducible cell system to control the expression of wild-type (SRSF2 or U2AF1) or mutant [SRSF2(P95H), U2AF1(S34F), U2AF1(Q157P)] splicing factors by Dox treatment in HEK293T cells expressing mutant RNASEH1(D210N) for R-loop capture by R-ChIP. R-ChIP experiments were done for cells under two Dox treatment conditions (0 hr and 5 hr). Standard GRO-seq experiments to monitor the nascent transcription activity in wild-type and mutant cells were performed to illucidate the correlation of transcription activity with R-loop dynamics. All sequencing data were obtained from experiemnts in duplicates.

first: Liang

first: Yi-Jou

last: Huang

first: Xiang-Dong

last: Fu


title: Multifaceted Functional Implications of an Endogenously Expressed tRNA Fragment in Vector Mosquito Aedes aegypti

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

summary: We performed small RNA sequencing (Illumina MiSeq) of mosquito Aedes aegypti to profile expression of tRNA derived fragments.

overall_design: We sequenced small RNA libraries from different biological samples such as males and females from 5 Aedes aegypti lab strains, developmental stages of Moyo-S and Moyo-R strains,and Moyo-S and Moyo-R females after blood feeding.

first: Matthew

last: Eng

first: Anthony

last: Clemons

first: Casey

last: Hill

first: Roberta

last: Engel

first: David

last: Severson


title: TADs are 3D structural units of higher-order chromosome organization in Drosophila [ph]

summary: Deciphering the rules of genome folding in the cell nucleus is essential in order to understand its functions. Recent Hi-C studies have revealed that the genome is partitioned into topologically associating domains (TADs), which demarcate functional epigenetic domains defined by combinations of specific chromatin marks. However, whether TADs are true physical units in each cell nucleus, or whether they reflect statistical frequencies of measured interactions within cell populations is unclear. Here, using a combination of Hi-C, 3D-Fluorescent In Situ Hybridization (3D-FISH), super-resolution microscopy and polymer modeling, we provide an integrative view of chromatin folding in Drosophila. We observed that repressed TADs form a succession of discrete nano-compartments, interspersed by less condensed active regions. Single-cell analysis revealed a consistent TAD-based physical compartmentalization of the chromatin fiber, with some degree of heterogeneity in intra-TAD conformations and in cis and trans inter-TAD contact events. These results indicate that TADs are fundamental 3D genome units that engage in dynamic higher-order inter-TAD connections. This domain-based architecture is likely to play a major role in regulatory transactions during DNA-dependent processes.

overall_design: HiC experiments in ph mutant drosophila embryos

first: Quentin

last: Szabo

first: Daniel

last: Jost

first: Diego

last: Cattoni

first: Giorgio

last: Papadopoulos

first: Boyan

last: Bonev

first: Tom

last: Sexton

first: Julian

last: Gurgo

first: Caroline

last: Jacquier

first: Marcello

last: Nollmann

first: Frédéric

last: Bantignies

first: Giacomo

last: Cavalli


title: TADs are 3D structural units of higher-order chromosome organization in Drosophila [male]

first: Jia-Ming

last: Chang

overall_design: HiC experiments in drosophila male embryos


title: TADs are 3D structural units of higher-order chromosome organization in Drosophila [S2R+]

overall_design: HiC experiments in drosophila S2R+ cells


title: Next-Generation Antimicrobial Discovery through Bacterial Self-Screening of Surface-Displayed Peptide Libraries

city: Austin

first: Bryan

last: Davies

state: TX

address: 2506 Speedway

institute: University of Texas at Austin

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

sample_organism: Escherichia coli str. K-12 substr. W3110


title: Relaxin reverses inflammatory and immune signals in aged hearts

city: Pittsburgh

first: Brian

last: Martin

state: Pennsylvania

address: 3550 Terrace St

department: Bioengineering

institute: University of Pittsburgh

summary:
Background: ‘Healthy’ aging drives structural and functional changes in the heart including maladaptive electrical remodeling, fibrosis and inflammation, which lower the threshold for cardiovascular diseases such as heart failure (HF) and atrial fibrillation (AF). Despite mixed results in recent clinical trials, Relaxin-therapy for 2-days could reduce mortality by 37% at 180-days post-treatment, in patients with acute decompensated HF. Relaxin’s short life-span (hours) but long-lasting protective actions led us to test the hypothesis that relaxin acts at a genomic level to reverse maladaptive remodeling in aging and HF.
Methods and Results: Young (9-month) and aged (24-month), male and female F-344/Brown Norway rats were treated with relaxin (0.4 mg/kg/day) for 2-weeks delivered by subcutaneous osmotic mini-pumps or with sodium acetate (controls).  The genomic effects of aging and relaxin were evaluated by extracting RNA from the left ventricles and analyzing genomic changes by RNA-sequencing, Ingenuity Pathway Analysis, MetaCore and tissue immunohistochemistry. We found that aging promotes a native inflammatory response with distinct sex-differences and relaxin suppresses transcription of multiple genes and signaling pathways associated with inflammation and HF in both genders. In addition, aging significantly increased macrophage infiltration in the ventricles and activation of the complement cascade, and relaxin reversed these age-related effects.
Conclusion: These data support the hypothesis that relaxin alters gene transcription and suppresses inflammatory pathways and genes associated with HF and aging. Relaxin’s suppression of inflammation and fibrosis supports its potential as a therapy for cardiovascular and inflammation-related diseases, such as HF, AF and diabetes.

overall_design: There were 12 Males Samples (3/group) with 4 technical replicants and 16 Female Samples (4/group) with 4 techincal replicants.

first: Beth

last: Gabris-Weber

first: Guillermo

last: Romero

first: Ansuman

last: Chattophadhyay

first: Guy

last: Salama


title: Next-Generation Antimicrobial Discovery through Bacterial Self-Screening of Surface-Displayed Peptide Libraries [HiSeq]

summary: Peptides have great potential to combat antibiotic resistance. While many platforms can screen peptides for their ability to bind to target cells, there are virtually no platforms that directly assess the functionality of peptides. This limitation is exacerbated when identifying antimicrobial peptides, since the phenotype, death, selects against itself, and has caused a scientific bottleneck confining research to only a few naturally occurring classes of antimicrobial peptides. We have used this seeming dissonance to develop Surface Localized Antimicrobial displaY (SLAY); a platform that allows screening of unlimited numbers of peptides of any length, composition, and structure in a single tube for antimicrobial activity. Using SLAY, we screened ~800,000 random peptide sequences for antimicrobial function and identified thousands of active sequences doubling the number of known antimicrobial sequences. SLAY hits present with different potential mechanisms of peptide action and access to areas of antimicrobial physicochemical space beyond what nature has evolved.

platform_organism: Escherichia coli str. K-12 substr. W3110

overall_design:
An 800,000 random peptide library was genetically encoded into our surface display system.We used high-throughput sequencing (Hi-seq) to identify surface expressed peptides with antimicrobial activity against E. coli. Samples include a non-induced and an induced (4- hours post-induction) in duplicate.
Please note that the Miseq run was a much smaller set of peptides than the Hiseq run. Also the miseq run had samplings at 0, 2, 3 and 4 hours rather than just 0 and 4 hours in the Hiseq. Downstream analysis was the same.

first: A

last: Tucker

first: D


title: Next-Generation Antimicrobial Discovery through Bacterial Self-Screening of Surface-Displayed Peptide Libraries [MiSeq]

overall_design:
As proof of concept, we used high-throughput sequencing (mi-seq) to identify a defined subset of surface expressed peptides with antimicrobial activity against E. coli. Samples include a non-induced and an 3 induced samples taken at 2, 3, and 4 hours post-induction in duplicate.
Please note that the Miseq run was a much smaller set of peptides than the Hiseq run. Also the miseq run had samplings at 0, 2, 3 and 4 hours rather than just 0 and 4 hours in the Hiseq. Downstream analysis was the same.


title: MS2-affinity purification coupled with RNA sequencing (MAPS) reveals RprA sRNA targetome.

city: SHERBROOKE

first: Eric

last: Massé

state: Québec

address: 3201, Jean Mignault

department: Biochemistry

institute: University of Sherbrooke

summary: Recently, we developed an in vivo technology to draw the interacting map of a specific small regulatory RNA (sRNA). We called it MAPS for MS2-affinity purification coupled with RNA sequencing. Using this technology, we already revealed the targetome of RyhB, RybB and DsrA, three well-characterized sRNAs in Escherichia coli. In this study, we perform MAPS with RprA sRNA.

overall_design: Identification of RNAs co-purified with MS2-RprA in a rne131 ΔrprA strain. RprA (without MS2) was used as control.

first: David

last: Lalaouna


title: MS2-affinity purification coupled with RNA sequencing (MAPS) reveals CyaR sRNA targetome in Escherichia coli.

summary: Recently, we developed an in vivo technology to draw the interacting map of a specific small regulatory RNA (sRNA). We called it MAPS for MS2-affinity purification coupled with RNA sequencing. Using this technology, we already revealed the targetome of RyhB, RybB and DsrA, three well-characterized sRNAs in Escherichia coli. In this study, we performed MAPS with CyaR sRNA.

overall_design: Identification of RNAs co-purified with MS2-CyaR in a rne131 ΔcyaR strain. CyaR (without MS2) was used as control.


title: Transcriptome sequencing (RNA-Seq) of non-tumor kidney tissues from 36 patients undergoing nephrectomy for exploring the metabolic mechanism of sorafenib and identifying the major transcriptional regulation factors in sorafenib metabolism in kidney

city: Guangzhou

first: Lan

last: Tang

state: Guangdong

address: 1838  Guangzhou North Ave,

department: School of Pharmaceutical Science

institute: Southern Medical University

summary: The multi-kinase inhibitor drug sorafenib is used as first line treatment for hepatocellular carcinoma and advanced renal cell carcinoma. Sorafenib mainly undergos cytochrome P450 (CYP) 3A4-mediated oxidation and uridine diphosphate glucuronosyl transferase (UGT) 1A9-mediated glucuronidation in liver, but the biotransformation of sorafenib in kidney remains unclear. Therefore, we integrated the mRNA expression data of 36 kidney samples and the corresponding metabolic activities for sorafenib to study the metabolic mechanism of sorafenib in kidney.

overall_design: Kidney mRNA profiles of 36 patients undergoing nephrectomy were generated by deep sequencing, using Illumina HiSeqTM 4000


title: RNA-seq transcriptome analysis in naïve and TNF-a-treated Sirt6-silenced YAMC cells to enrich for direct Sirt6 targets associated with inflammatory stimulation.

city: Chicago

first: Fangyi

last: Liu

state: IL

address: 2430 N Halsted St

department: Center for Intestinal and Liver inflammation Research

institute: Stanley Manne Children's Research Institute

summary: By comparing Sirt6-silenced YAMC cells to siControl-transfected YAMC cells, we found that there were 916 and 1,026 differentially expressed genes in the naïve and TNF-a treatment conditions respectively.  We also found that there were 302 genes that were co-expressed differentially in both naïve and TNF-a treatment conditions between Sirt6-silenced and siControl-transfected YAMC cells.

overall_design: YAMC cells were transfected with Sirt6 siRNA (siSirt6, 50 nM) and negative control siRNA (siControl, 50 nM) respectively using lipofectamine 2000. Forty-eight hours after transfections, the cells were cultured with medium containing TNFa (100 ng/mL) and medium alone respectively for additional 24 h.  At the end of treatments, cells were harvested for RNA extraction followed by RNA-seq transcriptome analysis.

first: Xiao-Di

last: Tan


title: Loss of microRNA-128 promotes cardiomyocyte proliferation and heart regeneration [miRNA-seq]

status: Public on Jan 02 2018

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: To identify the potential microRNAs (miRNAs) involved in the regulation of cardiomyocyte (CM) proliferation during homeostasis and injury, RNA sequencing (RNA-seq) in mouse cardiac ventricles was performed on postnatal day 1, 7, and 28 (P1, P7, and P28). Significant upregulation of MiR-128 was found in P7 hearts as compared to P1. To further specify the effect of miR-128 in the heart, RNA-Seq was performed in control mice (Ctrl) and miR-128 overexpression mice (miR-128OE) on P7. These data provide novel insights into the mechanisms by which adult CMs exit the cell cycle arrest and is fundamental for therapeutic manipulation to stimulate endogenous CM proliferate in cardiac regeneration.

overall_design: RNA-seq profilig of heart tissues from wild type mice on postanatal day 1, 7, and 28 (P1, P7, and P28), RNA-seq of hearts from control (Ctrl) and miR-128 overexpression transgenic mice (miR-128OE) at P7.

first: Wei

last: Huang

first: Yuliang

last: Feng

first: Yigang

last: Wang


title: Loss of microRNA-128 promotes cardiomyocyte proliferation and heart regeneration


title: Differential RNASeq of human nasal epithelial cells stimulated with RIG-I ligand SLR14

city: New Haven

first: Ellen

middle: Flescher

last: Foxman

state: CT

address: 330 Cedar St.

department: Laboratory Medicine

institute: Yale University

summary: The purpose of this study was to assess transcriptome changes in primary human airway epithelial cells following stimulation with RIG-I ligand.

overall_design: MRNA profiles were generated from primary human airway epithelial cells at rest or following stimulation with RIG-I ligand SLR-14.

first: Yong

last: Kong

first: Akiko

last: Iwasaki


title: ChIP-Seq analysis of Histone H3 acetylation (K27) changes in response to vasopressin in mouse renal collecting duct mpkCCD cells

city: Baltimore

first: Hyun Jun

last: Jung

state: MD

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

institute: Johns Hopkins University School of Medicine

summary: In mammals, the peptide hormone vasopressin controls renal water excretion, largely through regulation of the molecular water channel aquaporin-2 (AQP2) in the renal collecting duct. Regulatory mechanisms of AQP2 show:  1) short-term regulation by membrane trafficking; and 2) long-term regulation involving vasopressin-induced changes in the abundance of the aquaporin-2 protein. Vasopressin activates a G protein-coupled receptor (V2R) increasing cyclic AMP  and activating protein kinase PKA. Crebbp and Ep300 are known targets of PKA. They are histone acetyltransferases that acetylate histone H3 lysine-27, a histone mark associated with open chromatin and increased transcription (Tie F et al. Development 2009). The translocation of CREBBP and Ep300 into the nucleus in response to vasopressin in the collecting duct cells, predicts that vasopressin, working through PKA, may increase histone H3K27 acetylation of some genes. We tested this by performing ChIP-Seq for this modification.

overall_design: To identify changes of Histone modification (acetylation) in response to vasopressin in cultured mouse collecting duct cells (mpkCCD), we carried out ChIP-seq for genome-wide distribution of histone 3 acetylation (H3K27ac) (n=2). Observations were made both after 24-hr treatment with the vasopressin analog dDAVP and with vehicle.

first: J'Neka

middle: S

last: Claxton

first: Pablo

last: Sandoval

first: Hyun-Jun

first: Mark

last: Knepper


title: Wound regeneration deficit in rats correlates with low morphogenetic potential and distinct transcriptome profile of epidermis

city: Irvine

first: Maksim

middle: V

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

institute: University of California, Irvine

summary: We report whole tissue transcriptomes from rat and mouse wounds, as well as rat inter-follicular epidermis

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Total RNA was isolated from adult rat and mouse whole tissues. Tissues included rat and mouse wound dermis and wound epidermis collected one day after scab detachment, the time point that coincides with hair follicle regeneration in mice, and vaccum-suction isolated rat inter-follicular epidermis.

first: Christian

middle: F

last: Guerrero-Juarez


title: RNA sequence of ISL1-MSCs and Ctrl-MSCs

status: Public on Jan 01 2018

first: Minghui

last: He

address: International Biotech Island

department: Bioinformatics Department

institute: Forevergen Biosciences Co., Ltd

summary: The LIM-homeobox transcription factor islet-1 (ISL1) has been proposed as a marker of cardiovascular progenitor cells. This study investigated whether forced expression of ISL1 in human mesenchymal stem cells (hMSCs) improves myocardial infarction (MI) treatment outcomes. The lentiviral vector EF1α-ISL1 was constructed using the Multisite Gateway System, and used to transduce hMSCs.

overall_design: Examination of  mRNA in ISL1-MSCs and Ctrl-MSCs

first: Qiuling

last: Xiang


title: Expression data of intestinal epithelial isolates from rectosigmoid tissue in HIV-infected and control patients.

city: San Francisco

first: Charlie

last: Kim

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

summary:
Background: Prior analyses of mRNA expression in intestinal tissue as related to HIV cohorts has been on whole biopsies. More targeted isolation and enrichment of intestinal epithelial cells is needed to identify pathways specifically altered in the epithelium that may not be picked up at a global tissue scale.
Results: Analysis of intestinal epithelial cells isolated from primary human tissues taken from HIV-infected cohorts as well as uninfected controls. Results demonstrate key genes differentially expressed in HIV in the absence or presence of ART-therapy.

overall_design: Cross-sectional sampling and comparison of epithelial isolates from 9 uninfected, 6 viremic untreated, and 19 HIV-infected ART-treated patients. Whole biopsy RNA from 5 uninfected, 6 viremic untreated, and 5 HIV-infected ART-treated patients.

first: Charles

first: Avantika

last: Chitre


title: RNA sequencing of dendritic cells undergoing interaction with T cells in vivo

first: Ang

last: Cui

state: MA

address: 415 Main St.

institute: Broad Institute

summary: We used RNA sequencing to characterize gene expression of dendritic cells from mouse lymph node that, based on LIPSTIC labeling, underwent interaction with CD4+ T cells.

overall_design: Antigen pulsed dendritic cells (DCs) were transferred into recipient mice, followed by antigen specific CD4+ T cells. Forty-eight hours after T cell transfer, endogenous dendritic cells were isolated by facs sorting from mouse lymph node and analyzed based on their in vivo LIPSTIC labeling.

first: Giulia

last: Pasqual

first: Lawrence

middle: D

last: Schweitzer

first: Nir

last: Hacohen

first: Gabriel

last: Victora


title: Tumor-associated macrophages derived from circulating inflammatory monocytes degrade collagen through cellular uptake

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Physiologic turnover of interstitial collagen is mediated by a sequential pathway, in which collagen is fragmented by pericellular collagenases, endocytosed by specific collagen receptors, and routed to lysosomes for degradation by lysosomal cathepsins. Here, we used intravital microscopy to investigate if malignant tumors, which are characterized by high rates of extracellular matrix turnover, utilize a similar collagen degradation pathway. Tumors of epithelial, mesenchymal, or neural crest origin all displayed vigorous endocytic collagen degradation with an abundance of cells engaged in this process. These cells were identified as tumor-associated macrophage (TAM)-like cells that degraded collagen in a mannose receptor-dependent manner. Accordingly, increased intra-tumoral collagen was observed in mannose receptor-deficient mice. Whole transcriptome profiling uncovered a distinct extracellular matrix-catabolic signature of these collagen-degrading TAMs. Lineage-ablation studies revealed that collagen-degrading TAMs originated from circulating CCR2+ monocytes. The study identifies a novel function of TAMs in altering the tumor microenvironment through endocytic collagen turnover and establishes macrophages as centrally engaged in tumor-associated collagen degradation.

overall_design: Quantification of RNA expression in whole Lewis lung carcinomas (total tumor) and in three different cell types isolated from Lewis lung carcinomas. Lewis lung carcinoma cells (LLC), Fibroblasts and M2 tumor-associated macrophages (TAM).

first: Daniel

last: Madsen

first: Thomas

last: Bugge

first: Majken

last: Siersbæk


title: The human blood-nerve barrier transcriptome

city: Birmingham

first: Eroboghene

last: Ubogu

state: AL

address: 1720 7th Avenue South, SC200

institute: University of Alabama at Birmingham

summary: We report the application of whole exome sequencing to comprehensively deduce the normally conserved transcript profile of endoneurial endothelial cells that form the adult human blood-nerve barrier by combining in vitro and in situ analyses

overall_design: Examination of early and late passage primary human endoneurial endothelial cells combined with laser capture microdissected endoneurial microvessels from 4 histologically normal cryopreserved adult sural nerve biopsies

first: David

last: Crossman


title: Protein kinase A-dependent signaling network revealed by multi-omic analysis

first: Hyun Jun

last: Jung

overall_design: Refer to individual Series


title: Epithelial-to-mesenchymal transition antagonizes response to targeted therapies in lung cancer by suppressing BIM

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

summary:
Purpose: Epithelial-to-mesenchymal transition (EMT) confers resistance to a number of targeted therapies and chemotherapies. However, it has been unclear why EMT promotes resistance, thereby impairing progress to overcome it.
Experimental Design: We have developed several models of EMT-mediated resistance to EGFR inhibitors (EGFRi) in EGFR mutant lung cancers to evaluate a novel mechanism of EMT-mediated resistance.
Results: We observed that mesenchymal EGFR mutant lung cancers are resistant to EGFRi-induced apoptosis via insufficient expression of BIM, preventing cell death despite potent suppression of oncogenic signaling following EGFRi treatment. Mechanistically, we observed that the EMT transcription factor ZEB1 inhibits BIM expression by binding directly to the BIM promoter and repressing transcription. De-repression of BIM expression by depletion of ZEB1 or treatment with the BH3 mimetic ABT-263 to enhance “free” cellular BIM levels both led to re-sensitization of mesenchymal EGFR mutant cancers to EGFR inhibitors. This relationship between EMT and loss of BIM is not restricted to EGFR mutant lung cancers as it was also observed in KRAS mutant lung cancers and large datasets including different cancer subtypes.
Conclusions: Altogether, these data reveal a novel mechanistic link between EMT and resistance to lung cancer targeted therapies.

overall_design: Libraries from H1975 and H1975 R2 were sequenced as 40-bp paired-end reads on an Illumina NextSeq500 instrument.

first: Yotam

last: Drier


title: IL-7-dependent STAT1 activation limits homeostatic CD4+ T cell expansion

city: Bethesda

first: Timothy

middle: G

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

summary: IL-7 regulates homeostatic mechanisms that maintain the overall size of the T cell pool throughout life. We show that, under steady-state conditions, IL-7 signaling is principally mediated by activation of signal transducers and activators of transcription 5 (STAT5). In contrast, under lymphopenic conditions, there is a modulation of STAT1 expression resulting in an IL-7-dependent STAT1 and STAT5 activation. Consequently, the IL-7-induced transcriptome is altered with enrichment of IFN-stimulated genes (ISGs). Moreover, STAT1 overexpression was associated with reduced survival in CD4+ T cells undergoing lymphopenia-induced proliferation (LIP). We propose a model in which T cells undergoing LIP upregulate STAT1 protein, "switching on" an alternate IL-7-dependent program. This mechanism could be a physiological process to regulate the expansion and size of the CD4+ T cell pool. During HIV infection, the virus could exploit this pathway, leading to the homeostatic dysregulation of the T cell pools observed in these patients.

overall_design: Sorted naive CD4 T and CD8 T cells from WT or STAT1 transgenic mice were stimulated for 90 minutes with IL-7 or IFNg. Additonally CD4 T cells from WT or STAT1 trangenic or IL7Ra449F transgenic mice were stimulated for overnight with IL-7 or IFNg or IFNa4. Up to four biological replicates tested for each condition.

first: Cecile

last: Le Saout

first: Megan

middle: A

last: Luckey

first: Alejandro

last: Villarino

first: Mindy

last: Smith

first: Rebecca

last: Hasley

first: Jung-Hyun

last: Park

first: J

last: O’Shea

first: H

last: Lane

first: Marta

last: Catalfamo


title: DNA Damage Response in Elephant Cells

city: Salt Lake City

first: Chris

last: Gregg

state: UT

address: 20 South 2030 East

department: Neurobiology and Anatomy

institute: University of Utah

summary: The identity of most functional elements in the mammalian genome and the phenotypes they impact are unclear. Here, we perform a genome-wide comparative analysis of patterns of accelerated evolution in species with highly distinctive traits to discover candidate functional elements for clinically important phenotypes. We identify accelerated regions (ARs) in the elephant, hibernating bat, orca, dolphin, naked mole rat and thirteen-lined ground squirrel lineages in mammalian conserved regions, uncovering ~33,000 elements that bind hundreds of different regulatory proteins in humans and mice. ARs in the elephant, the largest land mammal, are uniquely enriched at elephant DNA damage response genes and changed conserved regulatory sites. The genomic hotspot for elephant ARs is the E3 ligase subunit of the Fanconi Anemia Complex, a master regulator of DNA repair. Additionally, ARs in the six species are associated with specific human clinical phenotypes that have apparent concordance with overt traits in each species.

overall_design: Perfrom RNA-seq to identgy genes differentially expressed in irradiated and untreated cells

first: Lisa

last: Abegglen

first: Joshua

last: Schiffman

first: Elliott

last: Ferris


title: RNA-sequencing of the Math1-Cre SmoM2 mouse genetic model of medulloblastoma

first: David

last: Raleigh

address: 555 Mission Bay Blvd South

institute: UCSF

summary: We investigated how misactivation of the Hedgehog (Hh) pathway causes medulloblastoma, and found that Hh signaling induces its transcriptional effector GLI2 to bind the Cdk6 promoter, activate gene expression, and drive uncontrolled cell proliferation. Genetic or pharmacological inhibition of CDK6 repressed the growth of Hh-associated medulloblastoma and prolonged survival in vivo through inhibition of cell proliferation. These findings suggest that CDK6 antagonists may be effective therapies for Hh-associated cancers in humans.

overall_design: RNA-sequencing of Math1-Cre Smo2 tumors and SmoM2 controls with transcriptomic analysis of age- and sex-matched littermate controls

first: Jeremy

last: Reiter


title: XIST derepression in active X chromosome hinders pig somatic cell nuclear transfer

first: Lihui

last: Lin

address: No.190, Kaiyuan Street

department: Stem cell

institute: Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science

summary: Pig cloning by somatic cell nuclear transfer (SCNT) remains extremely inefficient and many cloned embryos undergo abnormal development. Here by profiling transcriptome expression, we observed dysregulated chromosome-wide gene expression in every chromosome and identified a considerable number of genes that are aberrantly expressed in the abnormal cloned embryos. In particular, XIST, a long noncoding RNA gene, showed highly ectopic expression in abnormal embryos. We also proved that nullification of the XIST gene in donor cells can correct aberrant gene expression in cloned embryos and enhance long term development capacity of the embryos. Furthermore, the increased quality of XIST-deficient embryos was associated with the global H3K9me3 reduction. Injection of H3K9me demethylase Kdm4A into NT embryos could improve the development of preimplantation stage embryos. However, Kdm4A addition also induced XIST derepression in the active X chromosome, thus was not able to enhance the in vivo long term developmental capacity of porcine NT embryos.

overall_design: Fetuses original tissue mRNA profiles of 30-day and 35-day cloned and naturally fertilized (NF) were generated by deep sequencing, in triplicate or two replicates. Embryos mRNA profiles of in vitro 6-day cloned and fertilized were generated by deep sequencing, in two replicates.

first: Liangxue

last: Lai

first: Kepin

last: Wang

first: Xiaoping

last: Li


title: Genome-wide analysis of STAT3 in diffuse large B-cell lymphoma

city: Madison

first: Lixin

last: Rui

state: WI

address: 1111 Highland ave, Room 4053

institute: Wisconsin Ins for Medical Res

summary: By genome-wide ChIP-seq analysis in ABC DLBCL cell lines, we identified 2,251 STAT3 direct target genes, which involve B cell activation, survival, proliferation, differentiation and migration. Whole transcriptome profiling revealed that STAT3 acts as both a transcriptional activator and suppressor.

overall_design:
TMD8 and OCI-LY10 cells were treated by eithor DMSO or AZD1480 (JAK inhibitor) for 4hrs, ChIP-seq experiments were performed by STAT3 antibody (sc-482X, Santa Cruz Biotechnology).
Cells transduced with control shRNA, shSTAT3#10 or shSTAT3#16 in TMD8 and OCI-LY10 cells were induced with 20 ng/ml doxycycline for 2 days. Total RNA from these cells was then used for RNA-seq analysis.

first: Li

last: Lu