title: Oncogenic gene expression programs in leiomyosarcoma and characterization of conventional, inflammatory and uterogenic subtypes

status: Public on Jun 09 2020

city: Worcester

first: Matthew

last: Hemming

state: MA

address: 364 Plantation Street

institute: UMass Medical School

summary: Leiomyosarcoma (LMS) is a mesenchymal neoplasm with complex copy number alterations and characteristic loss of tumor suppressor genes without known recurrent activating mutations. Clinical management of advanced LMS relies on chemotherapy and complementary palliative approaches, and research efforts to date have had limited success identifying clinically actionable biomarkers or targeted therapeutic vulnerabilities. To explore the biological underpinning of LMS, we evaluated gene expression patterns of this disease in comparison to diverse sarcomas, non-mesenchymal neoplasms and normal myogenic tissues. We identified a recurrent gene expression program in LMS, with evidence of oncogenic evolution of an underlying smooth muscle lineage-derived program characterized by activation of E2F1 and downstream effectors. Recurrently amplified or highly expressed genes in LMS were identified that may represent therapeutic vulnerabilities, including targeting of IGF1R and retinoid signaling pathways. Though the majority of expressed transcripts were conserved across LMS samples, three separate subtypes were identified that were enriched for muscle-associated transcripts (conventional-LMS), immune markers (inflammatory-LMS) or a uterine-like gene expression program (uterogenic-LMS). Each of these subtypes express a unique subset of genes that may be useful in the managemeny of LMS: IGF1R was enriched in conventional LMS with prognostic implications, worse disease-specific survival was observed in inflammatory LMS, and prolactin was elaborated by uterogenic LMS and may represent a disease biomarker. These results extend our understanding of LMS biology and identify several strategies and challenges for further translational investigation.

overall_design: RNA-seq from leiomyosarcoma tumors and cell line


title: Endothelial to Mesenchymal Transition compromises vascular integrity to induce hypoxia and Myc mediated metabolic reprogramming of tubular epithelial cells in kidney fibrosis

city: Houston

first: Sara

last: Lovisa

state: TX

address: 1901 East Road

department: Cancer Biology

country: USA

institute: MD Anderson Cancer Center

type: Expression profiling by high throughput sequencing

summary: The aim of this study was to identify the functional impact of Endothelial-to-Mesenchymal Transition (EndMT) in kidney fibrosis. For this purpose EndMT has been conditionally deleted in endothelial cells by the genetic deletion of Twist and Snail in the endothelial cells, using the tamoxifen inducible Cdh5-ERT2 Cre model. Twist EndMT–cKO and Snail EndMT–cKO mice, together with WT mice, were challanged with the unilateral ureteral obstruction model (UUO) to induce kidney fibrosis. Mice were euthanized 10 days after surgery. In addition, since we found that EndMT-induced vascular damage and hypoxia induces Myc upregulation in tubular epithelial cells (TECs), we deleted Myc in TECs (using the GGT-Cre model). Myc GGT–cKO mice were also challenged with the UUO model and euthanized 10 days after surgery.

overall_design: Transcriptional profile of fibrotic (UUO), healthy or contralateral kidneys from Twist, Snail and Myc conditional knock-out mice (triplicate for each experimental condition) was generated by whole transcriptome RNA-Seq using the Illumina platform.

first: Raghu

last: Kalluri

first: Wu

last: Chang-Jiun


title: BET Bromodomain Proteins Regulate Transcriptional Reprogramming in Genetic Dilated Cardiomyopathy

city: Atlanta

first: Andrew

last: Antolic

state: Ga

address: 100 Woodruff Circle

department: School of Medicine Department of Cardiology

institute: Emory University

summary: In a model of chronic heart failure, BET bromodomain inhibition delayed cardiac remodeling and fibrosis by halting pathologic inflammatory gene networks in an NFkB-dependent manner.

overall_design: RNA-seq of mice treated with either JQ1 or vehicle; n=3 individual biologic replicates sequenced in each experiment

first: Michael

middle: A

last: Burke


title: Comparison of transcriptomic responses to individual and combinatorial copper and iron deficiencies in Arabidopsis thaliana rosettes.

status: Public on Jun 11 2020

city: Cerdanyola del Vallès

first: ANTONI

last: GARCIA-MOLINA

state: Barcelona

address: Campus UAB - CRAG Building

department: Plant Development and Signal Transduction

country: Spain

institute: Centre for Research in Agrigenomics

summary:
Purpose: plants exposed to multiple simultaneous adverse growth conditions trigger molecular responses that differ from the sum of those to individual stressors. Copper and iron are fundamental elements required for proper photosynthesis, energy production, DNA metabolism and hormone sensing, among all. Therefore, copper and iron deprivation limits plant yield. In natural environments, simultaneous deficiency to copper and iron can occur. As part of a multiple high-throughput study to identify combinatorial responses to both copper and iron deficiency, RNA-Seq profiling of Arabidopsis thaliana rosette leaves exposed to copper and/or iron deficiencies have been conducted.
Methods: RNA-Seq libraries were prepared from total RNA of whole rosettes of 20-d-old plants treated for control conditions, copper deficiency, iron deficiency or simultaneous deficiency to both copper and iron for 10 d and sequenced using Illumina protocols. 2 independent plants were RNA-Seq-sequenced per treatment. Adaptor sequences were removed with Trimmomatic and the resulting reads mapped to the Arabidopsis genome (Araport11) with Tophat 2.1.1. Read counts and differential expression analysis were conducted with Cufflinks/Cuffdiff.
Results: for RNA-Seq analysis a Tophat/Cuffdiff pipeline was designed. Each sample provided app. 9 million reads. After applying a cut-off of absolute log2(FC) ≥ 1 to controls and a FDR ≤ 0.05, copper deficiency led to 83 differentially expressed genes, followed by 1708 during iron deficiency, while the combinatorial treatment altered 2056 transcripts. Comparison of differential expressed genes among treatments indicated that double deficiency led to app. 45% rewiring of all detected transcriptional changes.
Conclusions: our data support that combinatorial copper and iron deficiency treatments in plants triggers transcriptional responses that differ from those to single deficiencies.

overall_design: Transcriptome profiling of 20-d-old rosette leaves from Arabidopsis grown under standard conditions, copper deficiency, iron deficiency and the double deficiency during 10 d were sequenced using Illumina Sequencing protocols in duplicates.

first: Antoni

last: Garcia-Molina


title: Transcriptome data of uncultured and HGFs along with 0.1% DMSO or LY plus Rapa or SR1-treated hUCB CD34+ cells

status: Public on Jun 08 2020

city: Wuhan

first: ying

last: chen

address: 1277 Jiefang Avenue, Wuhan, Hubei Province

department: Institute of Hematology

country: China

institute: Union Hospital，Tongji Medical College, Huazhong University of Science and Technology

overall_design: mRNA profiling of uncultured and HGFs along with 0.1% DMSO (HGFs) or LY plus Rapa (LR) or SR1-treated hUCB CD34+ cells for 4 days were generated by deep sequencing

first: Lingbo

last: Liu

first: Ying

last: Chen

first: Xiao

last: Ma

first: Xiaoyi

last: Li


title: Single cell RNAseq analysis revealed long-lasting adverse effects of prenatal tamoxifen administration on neurogenesis

status: Public on Jun 10 2020

city: Los Angeles

first: Quan

last: Lin

address: 635 Charles E Young Drive South

department: Department of Psychiatry and Behavioral Sciences, Intellectual Development and Disabilities Research Center

institute: University of California, Los Angeles

summary: We report that administration of tamoxifen (TAM) during early stages of cortical neurogenesis promoted precocious neural differentiation, while it inhibited neural progenitor cell (NPC) proliferation. The TAM-induced inhibition of NPC proliferation led to deficits in cortical neurogenesis, dendritic morphogenesis, synaptic formation, and cortical patterning in neonatal and postnatal offspring. Mechanistically, by employing single cell RNA sequencing (scRNA-seq) analysis combined with in vivo and in vitro assays, we showed TAM could exert these drastic effects mainly through dysregulating Wnt-Dmrta2 signaling pathway.

overall_design: Single cell mRNA profiles of embryonic day 12 (E12) control and tamoxifen treated C57BL/6 mouse forebrains

first: Liqiang

last: Zhou

first: Jiping

first: Yanan

last: Geng

first: Junbang

last: Wang


title: RNASeq analysis of offspring ileum tissue following Prenatal stress

city: Birmingham

first: Colin

last: Martin

state: AL

address: 1600 7th Ave S Lowder Bldg S300

department: Surgery

institute: University of Alabama at Birmingham

summary: Following a prenatal stress model, we collected RNA from ileum of offspring at 2 weeks of age. We sequenced the RNA  to identify genes that are differentially expressed compared to offspring from unstressed controls. We identified DEGs and a number of biological and signaling pathways in the offsping in response to gesstational stress. We discuss the implications of these stress-induced genes on the development of inflammatory diseases in the gut of the offsping.

overall_design:
Pregnant C57BL6 mice were subject to restraint stress (two hours everyday) during embyonic (E) days E7-19. After stress, the dams and litters were housed separately in different cages until the pups were 2 weeks of age. Ileum tissues were harvested for RNAseq analysis.
3 dams were stressed (identified as SD1, SD2, SD3) and tissues from one Male (M1) and one female (F1) offsping from each dams were collected. Therefore samples were labeled as SD1M1 and SD1F1 etc to identify each samples. Control dams were identified as CD1, CD2, and CD3.

first: Venkata

last: Yeramilli


title: Parallel Bimodal Single-cell Sequencing of Transcriptome and Chromatin Accessibility (Mouse single cell RNA-Seq mESCs)

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: We report a new technology for the parallel bimodal analysis of RNA-seq and ATAC-seq within a single-cell, known as ASTAR (Assay for Single-cell Transcriptome and Accessibility Regions).

overall_design: ASTAR-RNAseq libraries were prepared from mESCs with inducible DUX ORF and 2c-GFP constructs

first: Q

last: Xing

first: C

first: Y

middle: Y

last: Zeng

last: Yi

first: H

last: Loh


title: Parallel Bimodal Single-cell Sequencing of Transcriptome and Chromatin Accessibility (Mouse single cell ATAC-Seq mESCs)

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ASTAR-ATACseq libraries were prepared from mESCs with inducible DUX ORF and 2c-GFP constructs


title: LncRNA Malat1 inhibition of TDP43 cleavage suppresses IRF3-initiated antiviral innate immunity

city: Beijing

first: Wei

address: 5 Dongdan Santiao Road

institute: Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

summary: In this study, we performed RNA-seq to seek lncRNAs which changed significantly on expression in RAW264.7 cells before and after vesicular stomatitis virus (VSV) infection. For further investigation, we used iCLIP-seq technologies to identify the exact interaction sites between TDP43 protein and long non-coding RNA malat1 in mouse macrophages.

overall_design: Two RNA-Seq experiments were performed in nucleus of RAW264.7 cells infected with or without VSV for 8 hours, then purified RNAs were analyzed using Illumina Xten. iCLIP experiment was performed using anti-TDP43 antibody in RAW264.7 cells infected with or without VSV for 8 hours and then was analyzed by Illumina HiSeq2500 SE50 sequencing.

first: Ziqiao

first: Lun

first: Zongheng

last: Yang

first: Shuo

first: Zhongfei

first: Yin

first: Yuanwu

first: Lianfeng

last: Zhang

first: Xuan

first: Minghong

last: Jiang

first: Xuetao

last: Cao


title: The impact of cold priming on the light and cold regulation of gene expression in Arabidopsis thaliana

city: Berlin

first: Margarete

last: Baier

address: Königin-Luise-Straße 12-16

department: Institute of Biology

country: Germany

institute: Freie Universität Berlin

summary: We analysed the effect of cold priming on cold and high light regulation of gene expression. 5 days after the first cold treatment the primary stress response was widely reset. Then, a second (triggering) cold stimulus (24 h 4 °C) and a triggering high-light stimulus (2 h 800 µmol quanta m-2 s-1), which regulate many stress responsive genes in the same direction in naïve plants, caused widely specific and even inverse regulation of priming-responsive genes.

overall_design: Transcript levels were assessed in a transcriptome wide scale by single end next generation sequencing (Illumina High-Seq4000). Half of the 4-week old Arabidopsis thaliana Col-0 plants were primed for 24 hours at 4 °C. 5 days after priming, 1/3 of the non-primed and 1/3 of the cold-primed plants were harvested before triggering (non-primed control plants = C, primed plants = P). Half of the remaining primed and half of the remaining cold-primed plants were cold triggering for 24 hours at 4 °C (cold primed + cold triggered = PT-C; only cold trigger = T-C). The other plants were exposed for two hours at 800 μmol quanta*m−2 s−1 (cold primed + light triggered = PT-L ; only light trigger = T-L), which similarly induces the cold-primable gene ZAT10 in naïve plants. Triggered plants were harvested 2 h after the end of the triggering treatment.

first: Andras

last: Bittner

first: Joern

last: van Buer


title: Parallel Bimodal Single-cell Sequencing of Transcriptome and Chromatin Accessibility (Mouse single cell RNA-seq)

first: Chadi

summary: We report a new technology for the parallel bimodal analysis of  RNA-seq and ATAC-seq within a single-cell, known as STAR (Single-cell Transcriptome  and Accessibility Regions).

overall_design: Single-cell RNA-Seq libraries prepared from 96 E14 mES Cells and 96 2i mouse ES cells.

first: Qiaorui

first: C

last: EL Farran

first: Hu

last: Li

first: Yuin-Han


title: Estrogen induces dynamic ERa and RING1B recruitment to control gene and enhancer activities in luminal breast cancer

city: Miami

first: Lluis

last: Morey

state: FL

department: Sylvester Comprehensive Cancer Center

institute: University of Miami Miller School of Medicine

summary: We have previously shown that RING1B, a core Polycomb Repressive Complex 1 subunit, is amplified in 22% of breast cancer patients. In ER+ breast cancer, RING1B functionally interacts and co-localizes with ERa at enhancers and actively transcibed genes to modulate oncogenic transcriptional programs. However, the molecular mechanisms underlying this interaction is unclear. Here we demonstrate that in ER+ breast cancer cells, prolonged estrogen (E2) administration induces fluctuations in transcriptional output and chromatin landscape. RING1B loss impairs full E2-mediated gene expression and chromatin accessibility at genomic loci where key breast cancer transcription factors bind. RING1B mediates E2-induced gene expression and chromatin architectural changes both dependently and independently of its enzymatic activity and nucleosomal binding ability. We found that RING1B is recruited to ER, FOXA1, and GRHL2 co-bound sites in a cyclic manner during E2 administration and regulates E2-induced enhancers and ER recruitment. Finally, we characterized the spacial organization pattern between ER, FOXA1, GRHL2, and RING1B on the chromatin at single-nucleotide resolution genome-wide.

overall_design: ChIP-seq of H3K27Ac, RING1B, ERa, and FOXA1 in T47D shCtrl and shRING1B cells in HD and after 45', 8h, and 24h of E2 treatment. Pair-end ATAC-seq of T47D shCtrl and shRING1B cells in HD and after 4h, 8h, 12h, and 24h of E2 in duplicates. RNA-seq of T47D shCtrl and shRING1B cells (same cells as the ATAC-seq) in HD and after 4h, 8h, 12h, and 24h of E2 in duplicates. RNA-seq of T47D cells expressing RING1B wild type, RING1B R98A, and RING1B I53A in HD and after 24h of E2 in duplicates. ChIP-exo of RING1B, ERa, FOXA1, and GRHL2 in T47D parental cells in HD and after 45' of E2 treatment. RNA-seq of T47D shRING1B cells rescued with exogenous RING1B wild type in HD and after 24h of E2 in duplicates.

first: Yusheng

first: Ho

middle: L

last: Chan

first: Liliana

last: Garcia-Martinez

first: Daniel

last: Karl

first: Natalia

last: Weich

first: Joyce

middle: M

last: Slingerland

first: Ramiro

middle: E

last: Verdun


title: Expression profiling by RNA-Seq of adipose tissue in mice after partial nephrectomy and administration of pNaKtide

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

summary: We performed expression profiling by RNA-Seq on C57BL6 mice at 10 weeks of age. Mice were divided into four groups and either underwent partial nephrectomy (PNx) or sham (CTR) operation, and were adminstered either pNaKtide (NaK) or GFP.

overall_design: RNA was extracted from adipose tissue from six 10-week old mice in each group; PNx-GFP, CTR-GFP, PNx-GFP, or PNx-NaK, and sequenced in a 2x50 base-pair design on an Illumina 1500 sequencer.

first: Komal

last: Sodhi

first: M

last: Chaudhary

first: Xioliang

last: Wang

first: Hari

middle: V

last: Lakhani

first: Athar

last: Nawab

first: Mishghan

last: Zehra

first: Rebecca

last: Pratt

first: Cameron

last: Cottrill

first: Brian

last: Snoad

first: Jun

last: Fan

first: Jiang

last: Liu

first: Zijian

last: Xie

first: Nader

middle: G

last: Abraham

first: Joseph

middle: I

last: Shapiro


title: SMARCB1 loss induces druggable cyclin D1 deficiency via upregulation of MIR17HG in atypical teratoid rhabdoid tumors

city: Montreal

first: Sidong

last: Huang

state: Quebec

address: 3655 promenade Sir-William-Osler

department: Biochemistry

country: Canada

institute: McGill University

summary: Atypical teratoid rhabdoid tumor (ATRT) is a fatal pediatric malignancy of the central neural system lacking effective treatment options. It belongs to rhabdoid tumor family usually caused by biallelic inactivation of SMARCB1, encoding a key subunit of SWI/SNF chromatin remodelling complexes. Previous studies proposed that SMARCB1 loss drives rhabdoid tumor by promoting cell cycle through activating transcription of cyclin D1 while suppressing p16. However, low cyclin D1 protein expression is observed in most ATRT patient tumors. The underlying mechanism and therapeutic implication of this molecular trait remain unknown. Here, we show that SMARCB1 loss in ATRT leads to the reduction of cyclin D1 expression by upregulating MIR17HG, a microRNA (miRNA) cluster known to generate multiple miRNAs targeting CCND1. Furthermore, we find that this cyclin D1 deficiency in ATRT results in marked in vitro and in vivo sensitivity to the CDK4/6 inhibitor palbociclib as a single agent. Our study identifies a novel genetic interaction between SMARCB1 and MIR17HG in regulating cyclin D1 in ATRT and suggests a rationale to treat ATRT patients with FDA-approved CDK4/6 inhibitors.

overall_design: Two ATRT cell lines (BT12 and CHLA-06) with forced expression of vector control and SMARCB1 in triplicates

first: Yibo

last: Xue


title: Parallel Bimodal Single-cell Sequencing of Transcriptome and Chromatin Accessibility (Human single cell RNA-seq)

first: Chadi

last: El Farran

overall_design: ASTAR scRNA libraries prepared from BJ, K562, JK1 and Jurkat Human Cell Lines

first: Qiaorui

last: Xing

first: C

last: EL Farran

first: Hu

last: Li

first: Yuin-Han

last: Loh


title: RNA-Seq of whole kidneys of inducible TFAP2B KO mice (b-actinCreERT2+TFAP2Bfl/fl) mice and control littermates

city: Charlestown

first: Alexander

last: Marneros

address: 13th Street

institute: Massachusetts General Hospital

summary: RNA-Seq of kidneys lacking the gene TFAP2B in the nephron; knockdown at 6 weeks of age; assessed at 4-5 months of age

overall_design: 4 whole kidneys of b-actinCreERT2+TFAP2Bfl/fl mice and control littermates were used for RNA-Seq


title: Characterization of Alveolar macrophage subsets infected by Cryptococcus neoformans [ATAC-seq]

city: Durham

first: Mari

last: Shinohara

state: NC

department: Immunology

institute: Duke University School of Medicine

summary: We examined two subpopulations of alveolar macrophages differentiated by CXCL2 expression stimulated by Cryptococcus neoformans. The two subpopulations have distinct mRNA expression pattern indicating the heterogenity within alveolar macrophages.

overall_design: ATAC sequencing library was prepared from alveolar macrophages subpopulation from naïve and infected lung. The prepared library was sequenced on Illumnia NextSeq500.

first: Shengjie

last: Xu-Vanpala

first: Joshua

last: Wheaton

first: Morgan

last: Parker

first: Maria

last: Ciofani


title: A commensal Clostridium bacteria restricts alphavirus dissemination through a bile acid-type I IFN signaling axis

city: Saint Louis

first: Emma

middle: Suening

last: Winkler

state: Missouri

address: 660 S. Euclid Ave, Campus Box 8051

department: DOM-ID

institute: Washington University in St. Louis

summary:
The emerging alphavirus chikungunya virus (CHIKV) has infected millions of people. However, the factors modulating disease outcome remain poorly understood. We show that depletion of the gut microbiota in oral antibiotic-treated or germ-free mice leads to greater CHIKV infection and spread within one day of virus inoculation. Perturbation of the gut microbiota alters TLR7-MyD88 signaling in plasmacytoid dendritic cells (pDCs) and blunts systemic production of type I interferon (IFN). Consequently, circulating monocytes express fewer IFN-stimulated genes and become permissive for CHIKV infection. Reconstitution with a single commensal bacterial species, Clostridium scindens, or its derived metabolite, the bile acid deoxycholic acid, can restore pDC- and MyD88-dependent type I IFN responses to restrict systemic CHIKV infection and transmission back to vector mosquitoes. Thus, commensal gut bacteria modulate antiviral immunity and levels of circulating alphaviruses within hours of infection through a bile acid-pDC-IFN signaling axis, which affects virus dissemination and potentially, epidemic spread
3 biological replicates were processed per time point and group

overall_design: RNA was isolated from sorted splenic plasmacytoid dendritic cells using the MagMAX™ mirVana™ Total RNA Isolation Kit as per manufacturer’s instructions. For RNA analysis, 100 ng total RNA was hybridized to a nCounter® Mouse Immunology Panel (XT-CSO-MIM1-12) according to the manufacturer’s protocol (NanoString Technologies Inc.).

middle: S

first: Swathi

last: Shrihari

first: Barry

last: Hykes Jr

first: Scott

last: Handley

first: Prabhakar

last: Andhey

first: Yan-Jang

first: Amanda

last: Swain

first: Lindsay

last: Droit

first: Kranthi

middle: K

last: Chebrolu

first: Matthias

last: Mack

first: Dana

last: Vanlandingham

first: Larissa

middle: B

last: Thackray

first: Marina

last: Cella

first: Marco

last: Colonna

first: Maxim

middle: N

last: Artyomov

first: Thaddeus

last: Stappenbeck

first: Michael

last: Diamond


title: LIN28A binds to meiotic gene transcripts and modulates their translation in male germ cells

city: Nanjing

first: Mei

last: Wang

address: Nanjing Medical University, 101 Longmian Ave., Nanjing, Jiangsu

institute: Nanjing Medical University

summary: The RNA-binding protein LIN28A is required for maintaining tissue homeostasis, including in the reproductive system, but the underlying mechanisms on how LIN28A regulates germline progenitors remain unclear. Here, we dissected LIN28A-binding targets using high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) in the mouse testes. LIN28A preferentially binds to mRNA coding sequence (CDS) or 3'UTR regions at sites enriched wiGAG(A) sequences. Further investigation of Lin28a null mouse testes indicated that meiosis-associated mRNAs bound by LIN28A were differentially expressed. Next, ribosome profiling revealed that the mRNA levels of these targets were significantly reduced in polysome fractions, and their protein expression levels decreased in the Lin28a null mouse testes, even when meiotic arrest in the null mouse testes was not apparent. Collectively, these findings provide a set of LIN28A-regulated target mRNAs, and show that LIN28A binding might be mechanism through which LIN28A acts to regulate undifferentiated spermatogonia fates and male fertility in mammals.

overall_design: Triplicate identification of transcripts associated with LIN28A in mice testes, triplicate mRNA profiles profile of Lin28a knockout and control in 10dpp mouse testes were generated by deep sequencing.

first: Luping

last: Yu

first: Shu

first: Fan

last: Yang

first: Min

first: Lufan

last: Li

first: Xin

last: Wu


title: Gene expression analysis of mouse alveolar macrophages and whole-blood from mice with contained Mycobacterium tuberculosis infection

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

summary: The aim of this study was to measure the impact of contained infection with Mycobacterium tuberculosis (CMTB) on the immune response of alveolar macrophages (AMs) to intracellular Mtb infection in vivo and on the circulatory cellularity. We characterized the transcriptional profile of murine AMs in CMTB and control mice by sorting cells from whole-lung lysates and performing RNA-sequencing (samples 1-6). We also characterized the transcriptional profile of murine Mtb-infected AMs after aerosol infection by sorting cells from bronchoalveolar lavage fluid and performing low-input RNA-sequencing (samples 7-12). In order to characterize changes in chromatin accessibility induced by CMTB, we performed ATAC-seq on AMs isolated from control and CMTB mice by BAL (samples 13-18). We also generated whole-blood transcriptomes from mice prior to and following the establishment of CMTB (samples 19-28) in order to characterize the circulatory cellularity.

overall_design: To establish the model of CMTB, we infected mice intradermally in the ear with 10,000 CFU of a commonly used virulent strain of Mtb, H37Rv. Within 5 days the bacteria trafficked to the ipsilateral superficial cervical lymph nodes where the bacterial burden was relatively stable for at least one year with minimal dissemination to the spleen and no dissemination to the lung. We characterized the effect of CMTB on the basal state of AMs by performing RNA-seq and ATAC-seq analyses on AMs from CMTB and control mice prior to aerosol challenge. In addition, we performed whole-blood RNA-seq analysis of mice prior to and following the establishment of CMTB (day 42) in order to search for changes in the circulatory cellularity. To characterize the impact of CMTB on the early macrophage transcriptional response to Mtb infection, we infected mice with ~3000 CFU of mEmerald-H37Rv, and isolated AMs (CD45+, Zombie Violet-, CD3-/CD19-, Siglec-F+, CD11bmid, and CD64+) from BAL by fluorescence activated cell sorting at 24 hours following infection. Three populations were sorted for analysis by RNA-seq: Mtb-infected AMs (mEmerald+), bystander AMs (mEmerald-), and AMs from naïve mice.

first: Johannes

last: Nemeth

first: Alan

middle: H

last: Diercks

last: Aderem


title: Chromatin Accessibility and Transcription Dynamics During In Vitro Astrocyte Differentiation of Huntington’s Disease Monkey Pluripotent Stem Cells.

first: Isaac

last: Kremsky

state: GA

address: 1510 Clifton Rd

department: Biology

summary: Huntington’s Disease (HD) is a fatal, neurodegenerative disorder caused by a CAG repeat expansion, resulting in a mutant huntingtin protein. While it is now clear that astrocytes are affected by HD and significantly contribute to neuronal dysfunction and pathogenesis, the alterations in the transcriptional and epigenetic profiles in HD astrocytes have yet to be characterized. Here, we examined global transcription and chromatin accessibility dynamics during in vitro astrocyte differentiation in a transgenic non-human primate model of HD. We found global changed in accessibility and transcription across different stages of HD pluripotent stem cell differentiation, with distinct trends first observed in neural progenitor cells (NPCs), once cells have committed to a neural lineage. Transcription of p53 signaling and cell cycle pathway genes was highly impacted during differentiation, with depletion in HD NPCs and upregulation in HD astrocytes. E2F target genes also displayed this inverse expression pattern, and strong associations between E2F target gene expression and accessibility at nearby putative enhancers were observed. The results suggest that chromatin accessibility and transcription are altered throughout in vitro HD astrocyte differentiation and provide evidence that E2F dysregulation contributes to aberrant cell cycle reentry and apoptosis throughout the progression from NPCs to astrocytes.

overall_design: RNA-seq and ATAC-seq was taken from in vitro samples of pluripotent stem cells (PSCs), neural progenitor cells, developing astrocytes, and astrocytes, all of which were derived in vitro from PSCs.  PSCs were taken from macaques containing a transgene with exon 1 of the human mutant huntingtin gene (HD samples) as well as from control macaques.

first: Alexandra

last: Goodnight

first: Sujittra

last: Khampang

first: Yoon-Hee

last: Jung

first: James

last: Billingsley

first: Steven

last: Bosinger

first: Victor

last: Corces

first: Anthony

middle: W

last: Chan


title: Promoter proximal pausing limits Yki-induced tumorous growth in Drosophila

status: Public on Jun 07 2020

city: Pune

first: Sanket

last: Nagarkar

state: Maharashtra

address: Dr Homi bhabha Road, Pashan

country: India

institute: Indian Institute of Science education and Research

summary: Promoter proximal pausing (PPP) of RNA Polymerase II has emerged as a crucial rate-limiting-step in the regulation of gene expression. Regulation of PPP is brought about by complexes 7SK snRNP, P-TEFb (Cdk9/cycT) and the Negative Elongation Factor (NELF) which are highly conserved from Drosophila to humans. Here we show that RNAi-mediated depletion of bin3 or Hexim of the 7SK snRNP complex or depletion of individual components of the NELF complex enhance Yki-driven growth leading to neoplastic transformation of Drosophila wing imaginal discs. We also show that increased CDK9 expression cooperates with Yki, in driving neoplastic growth. Interestingly, over-expression of CDK9 on its own or in the background of depletion of one of the components of 7SK snRNP or the NELF complex necessarily and specifically needed Yki over-expression to cause tumorous growth. Genome-wide gene expression analyses suggested that deregulation of protein homeostasis is associated with tumorous growth of wing imaginal discs. As both Fat/Hippo/Yki pathway and PPP are highly conserved, our observations may provide insights into mechanisms of oncogenic function of YAP, the orthologue of Yki in human.

overall_design: Transcriptome of tumor tissue (over-expressing Yki in the background of knockdown of NELFA) was compared with non-tumorous tissues over-expressing Yki alone or only depleted for NELFA. GFP expressing wildtype wing imaginal disc tissue was used as a control genotype. We used two biological replicates of all tissue samples.

first: L

last: Shashidhara


title: Regulation of bacterial cell cycle progression by redundant phosphatases

city: Namur

first: Regis

last: Hallez

address: 61 Rue de Bruxelles

country: Belgium

institute: UNamur

summary: In the model organism Caulobacter crescentus, a network of two-component systems involving the response regulators CtrA, DivK and PleD coordinate cell cycle progression with differentiation. Active phosphorylated CtrA prevents chromosome replication in G1 cells while simultaneously regulating expression of genes required for morphogenesis and development. At the G1-S transition, phosphorylated DivK (DivK~P) and PleD (PleD~P) accumulate to indirectly inactivate CtrA, which triggers DNA replication initiation and concomitant cellular differentiation. The phosphatase PleC plays a pivotal role in this developmental program by keeping DivK and PleD phosphorylation levels low during G1, thereby preventing premature CtrA inactivation. Here, we describe CckN as a second phosphatase akin to PleC that dephosphorylates DivK~P and PleD~P in G1 cells. However, in contrast to PleC, we do not detect kinase activity with CckN. The effects of CckN inactivation are largely masked when PleC is present, but become evident when PleC and DivJ, the major kinase for DivK and PleD, are absent. Accordingly, mild overexpression of cckN restores most phenotypic defects of a pleC null mutant. We also show that CckN and PleC are proteolytically degraded in a ClpXP-dependent way well before the onset of the S phase. Surprisingly, known ClpX adaptors are dispensable for PleC and CckN proteolysis, suggesting the existence of adaptors specifically involved in proteolytic removal of cell cycle regulators. Since cckN expression is induced in stationary phase, depending on the stress alarmone (p)ppGpp, we propose that CckN acts as an auxiliary factor responding to environmental stimuli to modulate CtrA activity under suboptimal conditions.

overall_design: Examination of CtrA whole genome binding/occupancy (ChIP-Seq) in WT and 2 mutant strains of Caulobacter crescentus

first: Jérôme

last: Coppine

first: Andreas

last: Kaczmarczyk

first: Kenny

last: Petit

first: Thomas

last: Brochier

first: Urs

last: Jenal

first: Régis


title: Replacing the Calvin cycle with the reductive glycine pathway in Cupriavidus necator

status: Public on Jun 06 2020

city: Wageningen

first: Nico

middle: J

last: Claassens

address: Stippeneng 4

department: Laboratory of Microbiology

country: Netherlands

institute: Wageningen University

summary: These data belong to a metabolic engineering project that introduces the reductive glycine pathway for formate assimilation in Cupriavidus necator. As part of this project we performed short-term evolution of the bacterium Cupriavidus necator H16 to grow on glycine as sole carbon and energy source. Some mutations in a putiative glycine transporting systems facilitated growth, and we performed transcriptomics on the evolved strain growing on glycine. Analysis of these transcriptomic data lead us to the discovery of a glycine oxidase (DadA6), which we experimentally demonstrated to play a key role in the glycine assimilation pathay in C. necator.

overall_design: Transcriptomes are performed for the evolved strain growing on glyine (in triplicate).

first: Arren

last: Bar-Even


title: Analysis of gene expression in primary human foreskin keratinocytes (HFK) +/- HPV18 E7

city: Philadelphia

first: Elizabeth

last: White

state: PA

address: 3610 Hamilton Walk, 203C Johnson Pavilion, Mail Code 6114

department: Otorhinolaryngology

institute: University of Pennsylvania

summary: This RNA-seq study in primary human forekin keratinocytes was to define genes that are differetially expressed in the presence or absence of HPV18 E7 or the HPV18 E7 R84S variant.

overall_design: mRNA profiles in primary HFK were generated for the following samples (# of replicates): empty vector (3), HPV18 E7 (3), HPV18 E7 R84S (3)


title: Type V collagen in scar tissue regulates the size of scar after heart injury

status: Public on Jun 05 2020

city: Los Angeles

first: Yerbol

middle: Z.

last: Kurmangaliyev

state: CA

address: 675 Charles E. Young Drive South

institute: University of California, Los Angeles

summary: The mammalian heart possesses a poor ability to regenerate after acute ischemic cardiac injury and lost cardiac muscle is replaced by scar tissue. Multiple clinical studies demonstrate that the size of scar tissue following myocardial infarction is an independent predictor of cardiovascular outcomes, yet little is known about factors that regulate the size of scar after ischemic cardiac injury. In this report, we demonstrate that collagen V, a fibrillar collagen and a minor constituent of heart scars regulates the size of heart scars after ischemic cardiac injury. Depletion of collagen V in heart scars in two independent animal models led to a significant and paradoxical increase in post infarction scar tissue size with worsening of heart function. A systems genetics approach analyzing genes versus traits across 100 in-bred strains of mice independently demonstrated that collagen V is a critical driver of post injury heart function. We show that collagen V deficiency alters the ultra-structure and mechanical properties of scar tissue that make it more vulnerable to expansion. There is altered reciprocal feedback between matrix and cells that induce expression of specific mechanosensitive integrins which drive fibroblast activation and increased ECM gene expression. Scar size increases. Administration of cilengitide, an inhibitor of specific integrins, completely rescues the phenotype of increased post injury scarring, myofibroblast formation and cardiac dysfunction in collagen V deficient mice. These observations demonstrate that collagen V, a structural constituent of heart scar tissue regulates scar size in an integrin dependent manner.

overall_design: We subjected adult C57BL/6 mice to ischemic cardiac injury by permanent ligation of the left anterior descending coronary artery that supplies bulk of the blood flow to the left ventricular myocardium. Hearts were harvested at 3,7,14, 21 and 42 days after ischemic injury and the fibrotic scar tissue in the injured region and region remote to the area of injury (uninjured region) were dissected from the same heart for RNA sequencing (RNA-seq) to quantify temporal changes in gene expression.

first: Yokota

last: Tomohiro

first: Deb

last: Arjun


title: Multi-phenotype CRISPR-Cas9 screen identifies p38 kinase as a target for adoptive immunotherapies

city: Bethesda

first: Li

last: Jia

state: MD

address: 10 Clinic center

institute: NCI/NIH

summary: T cells are central to all currently effective cancer immunotherapies, but the characteristics defining therapeutically effective anti-tumor T cells have not been comprehensively elucidated.  Here we delineate four phenotypic qualities of effective anti-tumor T cells: cell expansion, differentiation, oxidative stress, and genomic stress. Using a CRISPR-Cas9-based genetic screen of primary T cells we measured the multi-phenotypic impact of disrupting 25 T cell receptor driven kinases. We identified p38 kinase as a central regulator of all four phenotypes and uncovered transcriptional and antioxidant pathways regulated by p38 in T cells. Pharmacological inhibition of p38 improved the efficacy of mouse anti-tumor T cells and enhanced the functionalities of human tumor-reactive and gene-engineered T cells, paving the way for clinically relevant interventions.

overall_design: RNA expression profiles of Pmel CD8+ T cells expanded in the presence of Vehicle or p38i (BIRB 796) for 5 or 10 days. Briefly, Pmel T cells received a primary stimulation with its cognate antigen hgp100 in the presence or absence of the p38 inhibitor (BIRB 796). The stimulated cells were expanded for 5 days, and the samples were processed for RNA sequencing. For day 10 RNA sequencing, day 5 cultured cells received a secondary stimulation with plate-bound anti-CD3 and soluble anti-CD28 antibodies in the presence or absence of p38i. The cells were expanded for an additional 5 days in the presence or absence of p38i (BIRB 796) and processed for RNA sequencing.

first: Nicholas

middle: P

last: Restifo

first: Shashank

last: Patel

first: Devikala

last: Gurusamy


title: GDNF drives rapid tubule morphogenesis in novel 3D in vitro model for ADPKD [GDNF RNAseq]

first: Eryn

last: Dixon

state: MO

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

summary: We report a significant change in epithelial differentiation pathways and principal cell specific transcription factors in tubuloids with a GDNF pulse, when compared to control tubuloid cultures.

overall_design: RNA-sequencing for GDNF pulsed (n=4) and control (n=4) tubuloids was generated by Illumina sequencing and analyzed for Expression Count (Star) and Differential Expression (DESeq2) analyses on BasePair.

first: Demetri

last: Maxim

first: Victoria

last: Halperin Kuhns

first: Allison

middle: C

last: Lane-Harris

first: Patricia

last: Outeda

first: Andrew

last: Ewald

first: Terry

last: Watnick

first: Paul

middle: A

last: Welling

first: Owen

last: Woodward


title: GDNF drives rapid tubule morphogenesis in novel 3D in vitro model for ADPKD [Pkd2- RNAseq]

summary: We report a profile of 35 genes that are differentially expressed in Pkd2- tubuloids compared to controls.

overall_design: RNA-sequencing for DOX (n=4) and DMSO (n=4) treated tubuloids was generated by Illumina sequencing and analyzed for Expression Count (Star) and Differential Expression (DESeq2) analyses on BasePair.

middle: L

middle: M


title: RNA-seq analysis of mouse retinas from animals treated with 140mg/kg/day Vigabatrin

city: Spokane

first: Mike

last: Gibson

state: Washington

address: 412 E Spokane Falls Blvd

department: Pharmacotherapy

institute: Washington State University

summary:
The goal of this study was to look at the effects of the anti epeleptic drug Vigabatrin on retinal transcripts.
Vigabatrin altered transcripts related to phototransduction, neuronal function and synaptic plasticity.
This is the first study showing that vigabatrin has an effect on the retinal transcriptome

overall_design:
Methods: C57/Bl6 (Week 10-12) Mice were treated with Vigabatrin via subcutaneous osmotic pump for 11 days. At DOL 11, mice were sacrificed and retinas were extracted, flash frozen and stored at -80 prior to RNA extraction.
[contributor] Novogene Inc.

first: Dana

last: Walters

first: Jean-Baptiste

last: Roullet


title: Whole transcriptomes analyses of gastric cancer HGC-27 cell line treated with SHAP or control peptide

city: shanghai

first: yang

last: tang

address: Yueyang Road 320

institute: Shanghai Institute of Biochemistry and Cell Biology

summary:
Purpose: To explore the molecular mechanisms of SHAP peptide (also termed as SOS) regulating gastic cancer tumorigenesis, RNA sequencing was performed to analyze the geome-wide change of SHAP treated HGC-27 cells compared to those of control peptide cells.
Methods: Total mRNA was extracted from HGC-27 cells. Then RNA quality was assessed using an Agilent Bioanalyzer 2100 and the sample reads were sequenced using Illumina Hiseq 4000 platform. As a reasult, we got the transcript data using Hisat2 followed by Stringtie. qRT–PCR validation was performed using TaqMan and SYBR Green assays.
Results: We mapped about 60 million sequence reads per sample to the human genome and identified about 58,000 transcripts in HGC-27 cells. Apprioximately 1,000 transcripts showed different expression between siSTRN3 and n.c. HGC-27 cells, with a fold change ≥2 and p value <0.05. Gene set enrichment analysis (GSEA) showed a significantly negative enrichment of Hippo target genes.
Conclusion: Our study present the datiled transcripts analysis of  HGC-27 cells, with biologic replicates. Based on RNA-seq transcriptome characterization , we conclude a molecular mechanism of SHAP regulating Hippo pathway in gastric cancer.

overall_design: Total mRNA was extracted from  HGC-27 cells treated with SHAP or control peptide. The quality was assessed using Agilent 2100, and the profiles were sequenced on the Illumina NovaSeq 6000.

first: Yang

last: Tang

first: Shi

last: Jiao


title: Asymmetrically-substituted quadruplex-binding napththalene diimides showing potent activity in models for pancreatic cancer

status: Public on Jun 04 2020

city: London

first: Stephen

last: Neidle

address: Brunswick Square

department: School of Pharmacy

country: United Kingdom

institute: UCL

summary: Targeting quadruplexes in cancer genes and pathways by a novel class of asymmetrically-substituted napththalene diimides (SOP1812) with potent cellular and antitumour activity in models for pancreatic cancer.

overall_design: Differential gene expression between treated and untreated MIA PaCa-2 cells after 6 h and 24 h treatment with a novel class of napththalene diimides (SOP1812), which were evaluated with RNA-seq.

first: Ahmed

last: Ahmed


first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

overall_design: Examination of mouse heart cell expression changes after Col5a1 knock out and treatment with cilengitide

first: Tomohiro

last: Yokota

first: Arjun

last: Deb

first: Matteo

last: Pellegrini


title: Mapping the effects of developmental lead (Pb) exposure on the hippocampus with single cell analysis

city: Ann Arbor

first: Kelly

last: Bakulski

state: MI

address: 1415 Washington Heights

department: Department of Epidemiology

institute: University of Michigan

summary: Lead (Pb) exposure is ubiquitous with permanent neurodevelopmental effects. The hippocampus brain region is involved in learning and memory with heterogeneous cellular composition. The hippocampus cell type-specific responses to Pb are unknown. This experiement sought to examine perinatal Pb treatment effects on adult hippocampus gene expression, at the level of individual cells. In mice perinatally exposed to control water or a human physiologically-relevant level (32 ppm in maternal drinking water) of Pb, two weeks prior to mating through weaning, we tested for hippocampus gene expression and cellular differences at 5-months of age.

overall_design: 8 mice, 4 perinatally exposed to control diet and 4 to a human physiologically relevant level (32 ppm in maternal drinking water) of lead, two weeks prior to mating through lactation

first: John

middle: F

last: Dou

first: Robert

last: Thompson

first: Christopher

last: Lee

first: Lauren

middle: Y

last: Middleton

first: Perera

last: Bambarendage

first: Sean

last: Ferris

first: Tamara

middle: R

last: Jones

first: Kari

last: Neier

first: Xiang

last: Zhou

first: Maureen

last: Sartor

first: Saher

last: Hammoud

last: Dolinoy

first: Justin

last: Colacino


title: Microarray data from uterine CD122+ macrophages

first: Scott

middle: Michael

last: Gordon

address: 3615 Civic Center Blvd

department: Neonatology

institute: Children's Hospital of Philadelphia

summary:
IL-15-responsive CD122+ macrophages (CD122+Macs) develop in the uterus during normal pregnancy.  We aimed to understand the signals driving macrophages to adopt this fate.
We aimed to determine how CD122+Macs and conventional uterine macrophages differ transcriptionally.

overall_design: Conventional macrophages (cMacs, F4/80bright, CD122-), CD122+Macs (F4/80bright, CD122+), and NK cells (F4/80-CD122+) were FACS-sorted from E7.5 mouse uterine deciduae

first: Edward

last: Behrens


title: In vitro modeling of hepatic aging using AML12 cells

city: Singapore

first: Brijesh

middle: Kumar

last: Singh

address: CVMD Level-8, 8 College Road

department: Cardiovascular and Metabolic Disorders Program

institute: Duke-NUS Gradiate Medical School

summary: RNAseq analysis of pooled samples from control (young) and senescent (old) AML12 cells.

overall_design: Senescence was induced in AML12 cells using multiple treatments of sublethal desage of hydrogen peroxide and total RNA was extracted from three replicates. RNAseq analysis was performed on pooled samples.

first: Paul

last: Yen

first: Madhulika

last: Tripathi


title: Identification of the human DPR core promoter element using machine learning

city: La Jolla

first: Long

last: Vo ngoc

state: California

address: 9500 Gilman Dr

institute: UCSD

summary: The RNA polymerase II (Pol II) core promoter is the strategic site of convergence of the signals that lead to the initiation of DNA transcription, but the downstream core promoter in humans has been difficult to understand. Here we analyse the human Pol II core promoter and use machine learning to generate predictive models for the downstream core promoter region (DPR) and the TATA box. We developed a method termed HARPE (high-throughput analysis of randomized promoter elements) to create hundreds of thousands of DPR (or TATA box) variants, each with known transcriptional strength. We then analysed the HARPE data by support vector regression (SVR) to provide comprehensive models for the sequence motifs, and found that the SVR-based approach is more effective than a consensus-based method for predicting transcriptional activity. These results show that the DPR is a functionally important core promoter element that is widely used in human promoters. Notably, there appears to be a duality between the DPR and the TATA box, as many promoters contain one or the other element. More broadly, these findings show that functional DNA motifs can be identified by machine learning analysis of a comprehensive set of sequence variants.

overall_design: Analysis of human core promoters using HARPE, applied to the Downstream core Promoter Region and TATA-box.

first: James

middle: T

last: Kadonaga


title: Characterization of Alveolar macrophage subsets infected by Cryptococcus neoformans

first: Mari

last: Shinohara

institute: Duke University School of Medicine

summary: We examined four subsets of alveolar macrophages differentiated by CXCL2 expression and FLT3 fate mapping induced by Cryptococcus neoformans infection. These four subpopulations have distinct mRNA expression pattern indicating the heterogenity within alveolar macrophages.

overall_design: We isolated mRNA from alveolar macrophages subsets from infected lung and run sequencing of total mRNA to detect the level of expression

first: Shengjie

last: Xu-Vanpala


title: Glucocorticoid Regulates Mesenchymal Cell Differentiation Required for Perinatal Lung Morphogenesis and Function

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: We integrated genome-wide gene expression profiling, ATAC-seq, and single cell RNA-seq data in mice in which GR was deleted or activated to identify the cellular and molecular mechanisms by which glucocorticoids control prenatal lung maturation.  GR activated differentiation of a newly defined proliferative mesenchymal progenitor cell (PMP) into matrix fibroblasts (MFB), in part by directly activating extracellular matrix-associated target genes, including Fn1, Col16a4, and Eln and modulating FGF, VEGF, JAK-STAT and WNT signaling. Loss of mesenchymal GR signaling blocked PMP differentiation into mature MFB, which in turn caused proliferation of SOX9+ alveolar epithelial progenitor cells and inhibited differentiation of more mature AT2 and AT1 cells. GR signaling controls genes required for differentiation of a subset of proliferative mesenchymal progenitors into matrix fibroblasts in turn, regulating signals controlling AT2/AT1 progenitor cell proliferation and differentiation, identifying cells and processes by which glucocorticoid signaling regulates fetal lung function.

overall_design: Using system biology approch we integrated genome-wide gene expression profiling, ATAC-seq and single cell RNA-seq data in mice in which GR was deleted or activated to identify the cellular and molecular mechanisms by which glucocorticoids control prenatal lung maturation.

first: J

last: Bridges

first: P

last: Sudha

first: M

last: Guo

first: Y

last: Du

last: Whitsett


title: Transcriptome Kuenenia stuttgartiensis bioreactor

city: Nijmegen

first: Stijn

last: Peeters

state: Gelderland

address: Heyendaalseweg 135

institute: Radboud University

summary: Anaerobic ammonium-oxidising (anammox) bacteria, members of the ‘Candidatus Brocadiaceae’ family, play an important role in the nitrogen cycle and are estimated to be responsible for about half of the oceanic nitrogen loss to the atmosphere. Anammox bacteria combine ammonium with nitrite and produce dinitrogen gas via the intermediates nitric oxide and hydrazine (anammox reaction) while nitrate is formed as a by-product. These reactions take place in a specialized, membrane-bound compartment called the anammoxosome. Therefore, the substrates ammonium, nitrite and product nitrate have to cross the outer-, cytoplasmic- and anammoxosome membranes to enter or exit the anammoxosome. The genomes of all anammox species harbour multiple copies of ammonium-, nitrite- and nitrate transporter genes. Here we investigated how the distinct genes for ammonium-, nitrite- and nitrate- transport were expressed during substrate limitation in membrane bioreactors. Transcriptome analysis of Kuenenia stuttgartiensis planktonic cells under ammonium-limitation showed that three of the seven ammonium transporter genes and one of the six nitrite transporter genes were significantly upregulated, while another ammonium and nitrite transporter gene were downregulated in nitrite limited growth conditions. The two nitrate transporters were expressed to similar levels in both conditions. In addition, genes encoding enzymes involved in the anammox reaction were differentially expressed, with those using nitrite as a substrate being upregulated under nitrite limited growth and those using ammonium as a substrate being upregulated during ammonium limitation. Taken together, these results give a first insight in the potential role of the multiple nutrient transporters in regulating transport of substrates and products in and out of the compartmentalized anammox cell.

overall_design: triplicate samples, two conditions.

first: Marjan

last: Smeulders

first: Theo

last: van Alen

first: Daan

last: de Bruijckere

first: Guylaine

last: Nuijten

first: Huub

last: Op den Camp

first: Mike

middle: S

last: Jetten

first: Laura

last: van Niftrik


title: Ythdf m6A readers compensate each other in a context dependent manner

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

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

overall_design: Refer to individual Series


title: RNA-Seq of whole kidneys of P8 Six2Cre+KCTD1fl/fl mice and control littermates

city: Charlestown

first: Alexander

last: Marneros

state: MA

address: 13th Street

institute: Massachusetts General Hospital

summary: RNA-Seq of kidneys lacking the gene KCTD1 in the nephron

overall_design: 4 whole kidneys of P8 Six2Cre+KCTD1fl/fl mice and control littermates were used for RNA-Seq

middle: G

first: John

last: Hutchinson


title: Angioimmunoblastic T-cell lymphoma-like lymphadenopathy in mice transgenic for human RHOA with p.Gly17Val mutation

city: Daejeon

first: Yukyung

last: Jun

address: 245 Daehak-ro, Yuseong-gu

department: Center for Supercomputing Applications

country: South Korea

institute: Korea Institute of Science and Technology Information

summary: A missense mutation in RHOA encoding p.Gly17Val has been reported to occur frequently in angioimmunoblastic T-cell lymphoma (AITL). Here, we describe a murine model which expresses the human RHOA mutant gene product in a T-cell specific manner and develops AITL-like symptoms. Most transgenic mice feature with latency one or two enlarged lymph nodes characterized by aberrant lymph node architecture, extensive lymphocytic infiltration, extrafollicular meshwork of follicular dendritic cells (FDC) and arborized endothelial venules. We also provide evidence for presence of dominant T cell clonal populations and expansion of B-cells leading to hypergammaglobulinemia. Transcriptomic profiling revealed that the gene expression pattern within affected lymph nodes of the mice most closely resembles that of AITL patients with the identical p.Gly17Val mutation. The murine model should therefore be useful in dissecting pathogenesis of AITL at the molecular level and in preclinical trials of various therapeutic agents, particularly for the cases with the highly prevalent p.Gly17Val mutation.

overall_design:
9 lymph nodes, including 4 tumor samples (enlarged lymph nodes from RHOA p.Gly17Val transgenic mice), 3 control samples (lymph nodes from litter mates), and 2 seemingly normal (i.e. not enlarged) lymph nodes from RHOA p.Gly17Val transgenic mice
CD4+lymphocytes from RHOA transgenic mice and from litter mates.

first: Gyu

last: Lee

first: Hae

last: Yoo

first: Yoon

middle: K

last: Jeon

first: Daekee

first: Sanghyuk

first: Jaesang

last: Kim


title: Effects of endogenous GDF11 on the odontogenic differentiation of dental pulp stem cells

status: Public on Jun 03 2020

city: Chengdu

first: Weiqing

last: Liu

address: No.14, Third section, Renmin Nan Road

institute: West China Hospital of Stomatology, Sichuan University

summary: Knockdown of endogenous GDF11 downregulated the odontogenic differentiation of human dental pulp stem cells (hDPSCs). We performed RNA-seq analysis on hDPSCs transfected with GDF11 small interfering RNA (siRNA) and control siRNA after 7 days of odontogenic induction, in order to investigate the underlying mechanisms of endogenous GDF11 regulating odontogenic differentiation in hDPSC.

overall_design: Comparison of gene expression between hDPSCs pretreated with GDF11 small interfering RNA (siRNA) and control siRNA after 7 days of odontogenic differentiation.

first: Xingying

last: Qi


title: Determinants for efficient editing with Cas9-mediated recombineering in Escherichia coli

city: Paris

first: Alaksh

last: Choudhury

address: 16 Rue Henri Huchard

department: IAME

country: France

institute: INSERM

type: Genome variation profiling by high throughput sequencing

summary: In E. coli, editing efficiency (EE) with Cas9-mediated recombineering varies across targets due to differences in the level of Cas9:gRNA DNA double-strand break (DSB)-induced cell death. We found that EE with the same gRNA and repair template can also change with target position, cas9 promoter strength, and growth conditions. Incomplete editing, off-target activity, non-targeted mutations, and failure to cleave target DNA even if Cas9 is bound also compromise EE. These effects on EE were gRNA-specific. We propose that differences in the efficiency of Cas9:gRNA-mediated DNA DSBs and differences in rates of dissociation of Cas9:gRNA complexes from target sites account for the observed variations in EE between gRNAs. We show that editing behavior using the same gRNA can be modified by mutating the gRNA spacer, which changes the DNA DSB activity. Finally, we discuss how variable editing with different gRNAs could limit high-throughput applications and provide strategies to overcome these limitations.

overall_design: Examination of edited genomic loci for 8 different editing cassettes each with a unique gRNA and homology repair template targeting galK by placing galK at different loci and Cas9 under different promoters. A 20 bp sequence homologous to the sequence upstream of the PAM was used as the gRNA spacer. In our editing cassettes for point mutations, we designed 150 bp homology repair templates (HRTs) centered around the NGG PAM. This template consisted a synonymous mutation to mutate the G in the NGG PAM to provide immunity to subsequent cleavage by Cas9 after editing as well as targeted mutation(s) within 20 bp of the synonymous PAM mutation. This repair homology template was placed in cis with the gRNA, which was expressed under control of the J23119 promoter.

first: Emily

last: Freed


title: TEAD1 ChIP-seq on on MDA-MB-231 and Detroit X1 562 cells

city: South San Francisco

first: Rohit

last: Reja

address: 1 DNA Way

institute: Genentech

summary: The Hippo Pathway is a critical signaling network that regulates organ size and cellular proliferation in metazoans. The transcriptional enhanced associate domain (TEAD) family of transcription factors serve as the receptors for the downstream effectors of the Hippo pathway, YAP and TAZ, to upregulate expression of multiple genes involved in proliferation, cell-fate determination, polarity, and survival1. Recent work revealed that TEAD proteins are palmitoylated at a conserved cysteine with the lipid tail extending into the hydrophobic core of the protein2. Mutagenic and covalent modulation of the palmitoylation site disrupts Hippo signaling2,3; however, an understanding of why TEAD proteins require this seemingly essential modification and the therapeutic implications of modulating TEAD palmitoylation has remained elusive. Here we report the identification and optimization of a potent pan-TEAD small molecule that binds the TEAD lipid pocket (LP), blocks palmitoylation, and dysregulates TEAD activity in multiple cancer cell lines. Cellular and biochemical data interrogating the mechanism of action for our compound reveal TEAD palmitoylation to function as a checkpoint that regulates TEAD homeostasis. We show that bypassing this checkpoint with a small molecule increases TEAD protein levels thereby decreasing the ability of YAP/TAZ to activate downstream target gene transcription in a dominant-negative manner.  Our study demonstrates a new role for lipidation in protein signaling and establishes the TEAD LP as a bona fide therapeutic site for modulation of the Hippo Pathway.

overall_design: ChIP-seq of TEAD1 was performed on the following cells in two replicates: MDA-MB-231 and Detroit X1 562 cells. We had one input sample as control for each cell type.

first: J

last: Holden

first: R


title: Cell type prioritization in single-cell data

city: Vancouver

first: Jordan

middle: W

last: Squair

state: BC

address: 818 West 10th Avenue

institute: University of British Columbia

summary: We present a machine-learning method to prioritize the cell types most responsive to biological perturbations within high-dimensional single-cell data. We validate our method, Augur (https://github.com/neurorestore/Augur), on a compendium of single-cell RNA-seq, chromatin accessibility, and imaging transcriptomics datasets. We apply Augur to expose the neural circuits that enable walking after paralysis in response to spinal cord neurostimulation.

overall_design: We devised an experiment to expose the neuron subtypes recruited by TESS using single-cell transcriptomics. Mice received a severe contusion of the thoracic spinal cord that led to permanent paralysis of both legs. In the presence of 5-HT1a and D1 agonists, TESS immediately enabled walking in paralyzed mice. We performed single-nucleus RNA-seq of 20,484 nuclei from mice placed on the treadmill for 30 min with or without TESS, identifying all the major cell types of the lumbar spinal cord. We then subjected the 6,171 identified neurons to an additional round of clustering, revealing the presence of 38 neuron subtypes that expressed classical marker genes and were detected across experimental conditions.

first: Michael

last: Skinnider

first: Claudia

last: Kathe

first: Mark

last: Anderson

first: Matthieu

last: Gautier

first: Kaya

last: Matson

first: Marco

last: Milano

first: Quentin

last: Barraud

first: Aaron

last: Phillips

first: Leonard

last: Foster

first: Gioele

last: La Manno

first: Ariel

last: Levine

first: Gregoire

last: Courtine


title: IMMUNE LANDSCAPES PREDICT CHEMOTHERAPY RESISTANCE AND IMMUNOTHERAPY RESPONSE IN ACUTE MYELOID LEUKAEMIA

city: Nottingham

first: Sergio

last: Rutella

address: Clifton Campus

department: John van Geest Cancer Research Centre

institute: Nottingham Trent University

summary: Immunological classifiers that predict patient outcome and therapeutic responses have been constructed through targeted immune gene expression profiling of diagnostic bone marrow samples from patients with acute myeloid leukaemia.

overall_design: In the study presented here, well annotated cohorts of children and adults with newly diagnosed acute myeloid leukaemia were used to acquire immune gene expression data.

first: Jayakumar

last: Vadakekolathu


title: Gene expression analysis by RNAseq in Fusarium graminearum WT, TRI6 mutant (∆tri6) and a mutant constitutively expressing TRI6 (∆tri6/TRI6).

city: Ottawa

first: Kristina

last: Shostak

address: 960 Carling Avenue

institute: Agriculture and Agri-Food Canada

summary: Identifying the role of TRI6 in Fusarium graminearum isolate NRRL29169 by high-throughput RNA sequencing under two environemental conditions.

overall_design: F. graminearum strains (wildtype, ∆tri6, ∆tri6/TRI6) were cultured in PN medium for 24 hours (PN conditions); also cultured in PN medium for 24 hrs followed by NPN medium for 24 hrs (NPN conditions). Total RNA was extracted and sequenced using Ilumina NextSeq platform.

first: Gopal

last: Subramaniam


title: Altered glucose metabolism in proximal tubule cells responding to acute kidney injury is associated with patient mortality

status: Public on Jun 02 2020

city: Los Angeles

first: Kari

middle: Ann

last: Koppitch

address: 1425 San Pablo Street, BCC 312

department: Stem Cell

institute: USC

summary: Single-cell transcriptomics revealed that gluconeogenesis is impaired in proximal tubule cells during AKI in mice.

overall_design: To investigate single cell transcriptomics on renal tubule cells, we generated a reporter mouse expressing GFP linked to the histone protein H2B in all nephron cells by combining 3 transgenes Six2-TGC; Rosa26rtTA ; pTRE-H2BeGFP. IRI and Sham surgeries were performed, and kidney tissue was harvested at different timepoints, followed by nuclei isolation, FACs sorting, and 10X Genomics Chromium Drop-Seq and library construction. Illumina Next-Seq sequencing of barcoded single nuclei libraries was performed and aligned to a pre-mrna genome with STAR/CellRanger. Gene/barcode matrices were merged and processed with the Seurat R package.

first: David

last: Legouis

first: Pietro

middle: E

last: Cippà

first: Sophie

last: de Seigneux

first: Andrew

last: McMahon

first: Sven-Erick

last: Ricksten

first: Anna

last: Faivre

first: Thomas

last: Verissimo

first: Karim

last: Gariani

first: Charles

last: Verney

first: Pierre

last: Galichon

first: Lena

last: Berchtold

first: Eric

last: Feraille

first: Marylise

last: Fernandez

first: Sandrine

last: Placier

first: Alexandre

last: Hertig

first: Pierre-Yves

last: Martin

first: Maarten

last: Naesens

first: Jérôme

last: Pugin


title: Hippocampal Gene Expression in bred High Responder (bHR) vs. bred Low Responder (bLR) Rats: Affymetrix Microarray Data from Generation F15

first: Megan

middle: Hastings

last: Hagenauer

address: 205 Zina Pitcher Pl.

department: MBNI

institute: University of Michigan

summary: The strong pattern of comorbidity amongst psychiatric disorders is believed to be generated by a spectrum of latent liability, arising from a complex interplay of genetic risk and environmental factors, such as stress and childhood adversity. At one end of this spectrum are internalizing disorders, which are associated with neuroticism, anxiety, and depression. At the other end of the spectrum are externalizing disorders, which are associated with risk-taking and novelty-seeking, as seen in mania, substance abuse, and impulse-control disorders. We model the genetic contributions underlying both extremes of this spectrum by selectively breeding rats that react differently to a novel environment. “Bred high responder” (bHR) rats are highly exploratory with a disinhibited, novelty-seeking temperament, including hyperactivity, aggression, and drug-seeking. “Bred low responder” (bLR) rats are highly-inhibited, exhibiting reduced locomotor activity and anxious and depressive-like behavior. These behavioral propensities are robust and stable, beginning early in development similar to temperament in humans.   This Affymetrix (Rat Expression Set 230 A) microarray study examined gene expression in the hippocampus in generation F15 male bHR rats and bLR rats at age postnatal day 14 (P14, n=6 per group).

overall_design: Overall Design: This microarray study examined gene expression in the hippocampus in generation F15 male bHR rats and bLR rats at age postnatal day 14 (P14, n=6 per group).  Sacrifice & RNA Extraction: The rats were sacrificed at postnatal day 14 (P14) via rapid decapitation followed by immediate brain extraction. The whole hippocampus was rapidly dissected on ice, fast-frozen at –40°C, and stored at –80°C before processing. TRIzol reagent (Invitrogen, Calsbad, CA) was used to extract total RNA, followed by purification using RNeasy RNA purification columns (Qiagen, Valencia, CA). The RNA was divided into two aliquots earmarked for transcriptional profiling using different microarray platforms. The quality and concentration of the RNA was determined using an Agilent bioanalyzer (Palo Alto, CA) and wavelength absorbance (260/280 nm ratio) by Nanodrop.  Microarray: One aliquot from each sample was transcriptionally profiled using Affymetrix Rat Expression Set 230 (RAE230A) microarray according to standard manufacturer’s procedures.   Microarray Data Preprocessing: For our current analyses, the ReadAffy() function (from R package affy version 1.54.0; Gautier et al. 2004, Bioinformatics. 20: 307–315) was used to read the data from the hippocampal Affymetrix .CEL files into R studio (R Studio v.1.0.153, R v.3.2.2). An expression set was generated using the Robust Multi-Array Average method (RMA: Irizarry et al. 2003, Biostatistics. 4: 249–264). Using a custom .cdf (Dai et al. 2005, Nucleic Acids Res. 33: e175) we summarized the probe signals into probesets for the RAE230A chip (“rae230arnentrezgcdf_19.0.0”) which mapped the probe sequences to Entrez Gene IDs (downloaded from http://nmg-r.bioinformatics.nl/NuGO_R.html on Jan 2017, release date Nov 2015). We re-annotated the data according to Official Gene Symbol using the function org.Rn.egSYMBOL() from the R package org.Rn.eg.db (version 3.4.1; Carlson 2017, http://bioconductor.org/packages/org.Rn.eg.db/), and then removed rows lacking annotation. During quality control, we found consistent irregularity associated with one subject (bLR subject X6_RN230_HC_P14_F15_L03.CEL) and it was removed prior to further analyses. The full analysis code is available at: https://github.com/isabellie4/PhenotypeProject and https://github.com/hagenaue/bHRbLR_MetaAnalysisProject.

middle: H

first: Sarah

last: Clinton

first: Isabelle

last: Birt

first: Stanley

middle: J

last: Watson Jr

first: Huda

last: Akil


title: Hippocampal Gene Expression in bred High Responder (bHR) vs. bred Low Responder (bLR) Rats: RNA-Seq Data from Generation F37

summary: The strong pattern of comorbidity amongst psychiatric disorders is believed to be generated by a spectrum of latent liability, arising from a complex interplay of genetic risk and environmental factors, such as stress and childhood adversity. At one end of this spectrum are internalizing disorders, which are associated with neuroticism, anxiety, and depression. At the other end of the spectrum are externalizing disorders, which are associated with risk-taking and novelty-seeking, as seen in mania, substance abuse, and impulse-control disorders. We model the genetic contributions underlying both extremes of this spectrum by selectively breeding rats that react differently to a novel environment. “Bred high responder” (bHR) rats are highly exploratory with a disinhibited, novelty-seeking temperament, including hyperactivity, aggression, and drug-seeking. “Bred low responder” (bLR) rats are highly-inhibited, exhibiting reduced locomotor activity and anxious and depressive-like behavior. These behavioral propensities are robust and stable, beginning early in development similar to temperament in humans.   This RNA-sequencing study examined gene expression in the hippocampus, a region critical for emotional regulation, in generation F37 adult male bHR rats and bLR rats (n=6/group), as well as in rats that showed an intermediate locomotor response to a novel field (“bred Intermediate Responder” or bIR rats, n=6), which were obtained by cross-breeding F37 bHR and bLR rats. Prior to sacrifice, the animals experienced behavioral testing. Locomotor response to a novel environment was assessed between age P50–75 as part of our selective breeding paradigm. We also measured anxiety-like behavior in adulthood (bHR/bLR: P160-P167; bIR: P65-75) using the percent time spent in the open arms of an Elevated Plus Maze (EPM; 5 min test). These behavioral testing results are provided here along with the gene expression data.

overall_design: Overall Design: This RNA-sequencing study examined gene expression in the hippocampus in generation F37 adult male bHR rats and bLR rats (n=6/group), as well as in adult male rats that showed an intermediate locomotor response to a novel environment (“bred Intermediate Responder” or bIR rats, n=6), which were obtained by cross-breeding F37 bHR and bLR rats.    Behavioral Testing: Locomotor response to a novel environment was assessed between age P50–75 as part of our selective breeding paradigm (protocol: Stead et al., 2006, Behav Genet. 36: 697–712). We measured anxiety-like behavior in adulthood (bHR/bLR: P160-P167; bIR: P65-75) using the percent time spent in the open arms of an Elevated Plus Maze (EPM; 5 min test, protocol: Aurbach et al. 2015, Proc Natl Acad Sci USA. 112: 11953–11958).    Sacrifice & RNA Extraction: The rats were sacrificed in adulthood (bHR/bLR=P160-P167, bIR=P126-134) by rapid decapitation and the whole hippocampus was extracted on ice, rapidly frozen, and stored at -80 degrees C.  Nucleotides were extracted using Qiagen AllPrep DNA RNA miRNA Universal Kit 50. Extracted RNA was evaluated for total concentration and quality using a Nanodrop spectrophotometer (concentration range 285-432 ng/ul, 260/280 ratio range 1.61-1.80) and then sent to the University of Michigan DNA Sequencing Core (https://seqcore.brcf.med.umich.edu).   RNA Sequencing: At the sequencing core, the RNA was re-assessed for quality using the TapeStation automated sample processing system (Agilent, Santa Clara, CA) and only samples with RNA integrity numbers (RINs) of  >8 were included in the analysis. The cDNA library was constructed using 0.1-3ug of total RNA and the Illumina TruSeq Stranded mRNA Library Preparation kit (Catalog #s RS-122-2101, RS-122-2102) (Illumina, San Diego, CA).   The final cDNA libraries were checked for quality once again by TapeStation (Agilent) as well as qPCR through the use of Kapa’s library quantification kit for Illumina Sequencing platforms (catalog # KK4835, Kapa Biosystems,Wilmington MA). The samples were clustered on a cBot automated cluster generation system (Illumina) for clonal amplification. The samples were then hybridized to the slide (“flow cell”) of a HiSeq 2000 (Illumina) with 6.66 samples per lane and underwent a 100 cycle paired end run in High Output mode using version 3 reagents.   RNA-Seq Data Preprocessing: Following sequencing and demultiplexing, the RNA-Seq reads were aligned to the rat genome (Rnor_6.0) using the SubRead aligner (Liao et al. 2014, Bioinformatics. 30: 923–930) using default parameters with the exception of indel detection (maximum length of indel that could be detected=0). The featureCounts program (Liao et al. 2014, Bioinformatics. 30: 923–930) then generated the gene-level RNA-Seq count summaries for each sample based on ENSEMBL annotation (Ensembl v.81). This count summary dataset was then filtered to exclude rows of data from genes that did not meet a minimum threshold of 4 samples with greater than or equal to 10 counts. Rows that lacked official gene symbol annotation were also excluded.  Our current analysis used the log2 fragments per million gene-level summary output for each sample provided by the voom() function (R package limma; Ritchie et al. 2015, Nucleic Acids Res. 43: e47). Quality control included 1) visualization of the overall log (base2) transformed transcript expression across all subjects via boxplot, 2) examination of the overall reads (mean and standard deviation) per subject, 3) visualization of a subject/subject correlation matrix to identify particularly atypical samples (R<.95). No outlier samples were identified.

first: Peter

last: Blandino Jr

first: Fan

last: Meng

middle: A


title: Whole transcriptomes analyses of gastric cancer HGC-27 cell line treated with siSTRN3 mixture or negative control siRNA

city: shanghai

first: yang

last: tang

address: Yueyang Road 320

institute: Shanghai Institute of Biochemistry and Cell Biology

summary:
Purpose: To explore the molecular mechanisms of STRN3 regulating gastic cancer tumorigenesis, RNA sequencing was performed to analyze the geome-wide change of siSTRN3 treated HGC-27 cells compared to those of control cells.
Methods: Total mRNA was extracted from HGC-27 cells in triplicate respectively. Then RNA quality was assessed using an Agilent Bioanalyzer 2100 and the sample reads were sequenced using Illumina Hiseq 4000 platform. As a reasult, we got the transcript data using Hisat2 followed by Stringtie. qRT–PCR validation was performed using TaqMan and SYBR Green assays.
Results: We mapped about 60 million sequence reads per sample to the human genome and identified about 58,000 transcripts in HGC-27 cells. Apprioximately 1,000 transcripts showed different expression between siSTRN3 and n.c. HGC-27 cells, with a fold change ≥2 and p value <0.05. Gene set enrichment analysis (GSEA) showed a significantly negative enrichment of Hippo target genes.
Conclusion: Our study present the datiled transcripts analysis of  HGC-27 cells, with biologic replicates. Based on RNA-seq transcriptome characterization , we conclude a molecular mechanism of STRN3 regulating Hippo pathway in gastric cancer.

overall_design: Total mRNA was extracted from  HGC-27 cells treated with siSTRN3 mixture or negative control siRNA in triplicate. The quality was assessed using Agilent 2100, and the profiles were sequenced on the Illumina NovaSeq 6000.

first: Yang

last: Tang

first: Shi

last: Jiao


title: Multi-species tomo-sequencing identifies new major hematopoietic stem cell regulators in the microenvironment of the embryonic aorta

city: Utrecht

first: Catherine

last: Robin

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: The behavior of (stem) cells is regulated by their local microenvironment through biochemical and biophysical interactions. To advance our understanding of the molecular characteristics and key components of the microenvironment, we applied a genome-wide RNA tomography sequencing approach in zebrafish, chicken, mouse and human embryos. The resulting anterior-posterior and/or dorsal-ventral transcriptional maps provide a powerful resource for identifying and comparing expression patterns in a given tissue or microenvironment along the embryonic axes of multiple species. We used these maps to explore the regulatory function of the aortic microenvironment, where the first hematopoietic stem cells are generated during embryonic development. By performing inter-species comparative analyses, we identified and functionally validated new conserved regulators of hematopoietic stem cell generation. Further analysis of spatial transcriptomics will elucidate the regulatory functions of the local microenvironment in vivo, paving the way for improved (stem) cell production in vitro and clinical cell therapy.

sample_organism:
Danio rerio
Gallus gallus
Homo sapiens
Mus musculus

overall_design: Spatial transcriptomics by RNA-tomography (Tomo-seq) on whole or sub-dissected embryos (processed along the anterior-to-posterior axis) and on transversal thick slices (processed along the dorsal-to-ventral axis).

first: Laurent

last: Yvernogeau

first: Ismaël

last: Morin-Poulard

first: Anna

last: Klaus

first: Joris

last: Maas

first: Stefan

last: Schulte-Merker

first: Eugene

last: Berezikov

first: Jan

middle: P

last: Junker


title: Multiple chromoanasynthesis in a rare case of sporadic renal leiomyosarcoma: case report

city: Moscow

first: Alexey

middle: Igorevich

last: Kalinkin

state: Russia

address: Moskvorechie st., 1

department: Epigenetics

country: Russia

institute: RCMG

type: Genome variation profiling by genome tiling array

summary:
Renal leiomyosarcomas (LMS) are extremely rare neoplasms with aggressive behaviour and poor survival prognosis. The most frequent somatic events in leiomyosarcomas are mutations in TP53, RB1, ATRX and PTEN genes, chromosomal instability and chromoanagenesis.
By using chromosomal microarray analysis we identified monosomy of chromosomes 3 and 11, gain of Xp (ATRX) arm and three chromoanasynthesis regions (6q21-q27, 7p22.3-p12.1 and 12q13.11-q21.2), with MDM2 and CDK4 oncogenes copy number gains, whereas no CNVs or tumor specific SNVs in TP53, RB1 and PTEN genes were observed.

overall_design: We analyzed FFPE tumor tissue of renal leiomyosarcoma from one patient using SNP-array CytoScan HD (ThermoFisher, USA) on GeneChip Scanner 3000 7G System (Applied Biosystems, USA). No technical replicates were performed.

middle: I

first: Kirill

last: Anoshkin


title: Expression of the neuronal tRNA n-Tr20 regulates synaptic transmission and seizure susceptibility

city: Farmington

first: Scott

last: Adamson

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

summary: Loss of the nuclear-encoded brain-specific arginine UCU tRNA, n-Tr20, gene increases seizure threshold in mice, and alters inhibitory neurotransmission in the hippocampus. We investigated the molecular impact of loss of n-Tr20 expression on the trancriptome and translatome in the forebrain and hippocampus of multiple n-Tr20 mutant and control strains. Loss of n-Tr20 altered translation initiation by activating the integrated stress response and suppressing mTOR signaling, the latter of which contributes to the enhanced GABAergic transmission.

overall_design: 33 samples are analyzed in this study from n-Tr20 tRNA knockouts and transgenes in the context of C57BL/6J (B6J) and C57BL6/NJ (B6N) forebrain and hippocampus. The design includes 4 replicates each of forebrain RNA-seq from B6N, B6N-nTr20-/-, B6J-nTr20-/-, B6J, and B6J with the B6N n-Tr20 transgene (B6J-Tg(nTr20N/N) or B6J-Tgwt) mice; one sample was sequenced twice to account for batch effects. Additionally, this study includes hippocampus RNA-seq and ribosome profiling with 3 replicates each from B6N and B6N-nTr20-/- hippocampi.

first: Mridu

last: Kapur

first: Archan

last: Ganguly

first: Gabor

last: Nagy

first: Jeffrey

last: Chuang

first: Wayne

middle: N

last: Frankel

first: Susan

middle: L

last: Ackerman


title: E proteins orchestrate dynamic transcriptional cascades implicated in the suppression of the differentiation of group 2 innate lymphoid cells

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF


title: E proteins orchestrate dynamic transcriptional cascades implicated in the suppression of the differentiation of group 2 innate lymphoid cells [ATAC-Seq]

summary: Group 2 innate lymphoid cells (ILC2s) represent a subset of newly discovered immune cells that are involved in immune reactions against microbial pathogens, host allergic reactions as well as tissue repair.  The basic helix-loop-helix transcription factors collectively called E proteins powerfully suppress the differentiation of ILC2s from bone marrow and thymic progenitors while promoting the development of B and T lymphocytes.  How E proteins exert the suppression is not well understood.  Here we investigated the underlying molecular mechanisms using inducible gain and loss of function approaches in ILC2s and their precursors, respectively.  Cross-examination of RNA sequencing and ATAC sequencing data obtained at different time points reveals a set of genes which are likely direct targets of E proteins.  Consequently, a widespread down-regulation of chromatin accessibility occurs at a later time point, possibly due to the activation of transcriptional repressor genes such as Cbfa2t3 and Jdp2.  The large number of genes repressed by gain of E protein function leads to the down-regulation of a transcriptional network important for ILC2 differentiation.

overall_design: ATAC-seq was performed on thymic ILC2 cells isolated from Id1 transgenic mice, which were transduced with retroviruses expressing either GFP alone or together with an E47-ER fusion protein after stimulation with ILC2, IL-7, IL-25 and IL-33.  Transduced cells were sorted for GFP and expanded in ILC2, IL-7, IL-25 and IL-33.  The cells were then treated with 4-hydroxy-Tamoxifen for 4 or 16 hours before harvesting for DNA isolation.

first: Xiao-Hong

last: Sun

first: Vincent

last: Peng


title: Transcriptional Analysis of Type II Alveolar Epithelial Cells in the Presence or Absence of Foxp3+ Regulatory T Cells during Experimental Acute Lung Injury Resolution

city: Chapel Hill

first: Jason

middle: Robert

last: Mock

state: North Carolina

address: 125 Mason Farm Rd, Marsico Hall 7229G

department: Internal Medicine

institute: University of North Carolina

summary:
These studies profiled the expression of mRNA in lung type II alveolar epithelial cells during lipopolysacchride induced lung injury in the presence or absence of Foxp3+ Regulatory T Cells
Baseline, uninjured lung type II alveolar epithelial (AT2) cells or resolving AT2 cells, in the presence or absence of Foxp3+ regulatory T cells (Tregs), were sorted (7 days after intratracheal instillation of LPS for resolving conditions) and mRNAs differentially expressed (DE) between control AT2 cells, resolving AT2 cells with Tregs present, or resolving AT2 cells in mice depleted of Tregs were identified using microarrays.

overall_design: Control lung type II alveolar epithelial (AT2) cells or two sets of AT2 cells obtained during a time point of lung injury resolution either in the presence or absence of regulatory T cells were sorted for mRNA analysis.  mRNA expression was profiled using Mouse Gene 2.1 ST arrays (Affymetrix, Santa Clara, CA) which cover over 28,000 RefSeq transcripts

middle: R

first: Hong

last: Dang

first: Claire

middle: M

last: Doerschuk


title: Gene expression profiling of human DLD-1 cells after instant depletion of basket nucleoporins

city: Bethesda

first: Alexei

last: Arnaoutov

address: 49 Convent Dr, Bldg 49 Room 5A10

department: PCRM

institute: NICHD

summary: We used RNA-seq approach to distinguish roles of basket nucleoporins Nup153, Nup50, and Tpr in transcription and nucleocytoplasmic trafficking. AID-mediated depletion of BSK-NUPs caused rapid and drastic changes in transcriptomic profiles within two hours of auxin addition. Changes upon Tpr nucleoporin loss were distinct from Nup153 and Nup50, but similar to changes upon loss of export factor NXF1 and GANP subunit of the TREX-2 mRNA export complex. Altogether, we demonstrated a unique role of Tpr nucleoporin in regulating genes expression through mRNA export.

overall_design: We performed RNA-Seq analyses on human DLD-1 cells that we specifically depleted of the basket nucleoporins using Auxin-Inducible Degron system.

first: H

last: Lee

first: V

last: Aksenova

first: J

last: Iben

first: S

last: Chen

first: C

last: Echeverria

first: A

first: M

last: Dasso


title: Hippocampal Gene Expression in bred High Responder (bHR) vs. bred Low Responder (bLR) Rats: RNA-Seq Data from Generation F43

city: Ann Arbor

first: Megan

last: Hagenauer

summary: The strong pattern of comorbidity amongst psychiatric disorders is believed to be generated by a spectrum of latent liability, arising from a complex interplay of genetic risk and environmental factors, such as stress and childhood adversity. At one end of this spectrum are internalizing disorders, which are associated with neuroticism, anxiety, and depression. At the other end of the spectrum are externalizing disorders, which are associated with risk-taking and novelty-seeking, as seen in mania, substance abuse, and impulse-control disorders. We model the genetic contributions underlying both extremes of this spectrum by selectively breeding rats that react differently to a novel environment. “Bred high responder” (bHR) rats are highly exploratory with a disinhibited, novelty-seeking temperament, including hyperactivity, aggression, and drug-seeking. “Bred low responder” (bLR) rats are highly-inhibited, exhibiting reduced locomotor activity and anxious and depressive-like behavior. These behavioral propensities are robust and stable, beginning early in development similar to temperament in humans.   This dataset was part of a larger RNA-Sequencing study examining gene expression in the bHR/bLR hippocampus, a region critical for emotional regulation. The original study compared repeated injections of either antidepressant medication (fluoxetine or desipramine) or vehicle (VEH=1:1 saline and water) solution in bHR and bLR rats (14 days of intraperitoneal injections - P78-P92, 1 per day) under either standard laboratory housing conditions or chronic variable stress. This upload includes only the data from the control subjects: generation F43 adult male bHR VEH rats and bLR VEH rats housed in standard conditions (n=5/group). Prior to sacrifice, at age P92, the rats underwent social interaction testing after 15 minutes of exposure to an anxiogenic environment (the elevated plus maze). The results from the social interaction testing are provided here along with the gene expression data.

overall_design: Overall Design: This dataset was part of a larger RNA-Sequencing study examining gene expression in the bHR/bLR hippocampus. The original study compared repeated injections of either antidepressant medication (fluoxetine or desipramine) or vehicle (VEH=1:1 saline and water) solution in bHR and bLR rats (14 days of intraperitoneal injections - P78-P92, 1 per day) under either standard laboratory housing conditions or chronic variable stress. This upload only includes the data from the control subjects: generation F43 adult male bHR VEH rats and bLR VEH rats housed in standard conditions (n=5 rats/group).   Behavioral Testing: At age P92, the rats underwent social interaction testing (protocol: Aydin et al. 2015, Behav Neurosci. 129: 679–682) after 15 minutes of exposure to an anxiogenic environment (the elevated plus maze, protocol: Isgor et al. 2004, Hippocampus. 14: 636–648).   Sacrifice & RNA Extraction: One hour after undergoing testing on the elevated plus maze, the animals were sacrificed by rapid decapitation and the brains were flash frozen in isopentane cooled on dry ice. The whole hippocampus was dissected from each brain on a dry ice and wet ice mixture and immediately put in TRIzol™. RNA was extracted using the Zymo RNA isolation Kit and shipped to the University of Michigan DNA Sequencing Core (https://seqcore.brcf.med.umich.edu).   RNA Sequencing: At the sequencing core, the RNA was re-assessed for quality using the TapeStation automated sample processing system (Agilent, Santa Clara, CA) and only samples with RNA integrity numbers (RINs) of  >8 were included in the analysis. The cDNA library was constructed using 0.1-3ug of total RNA and the Illumina TruSeq Stranded mRNA Library Preparation kit (Catalog #s RS-122-2101, RS-122-2102) (Illumina, San Diego, CA).   The final cDNA libraries were checked for quality once again by TapeStation (Agilent) as well as qPCR through the use of Kapa’s library quantification kit for Illumina Sequencing platforms (catalog # KK4835, Kapa Biosystems,Wilmington MA). The samples were clustered on a cBot automated cluster generation system (Illumina) for clonal amplification. The samples were then hybridized to the slide (“flow cell”) of a HiSeq 2000 (Illumina) and underwent non-stranded short read (50-bp length) single-end sequencing in High Output mode using version 3 reagents.   RNA-Seq Data Preprocessing: Following sequencing and demultiplexing, the RNA-Seq reads were aligned to the rat genome (Rnor_6.0) using the SubRead aligner (Liao et al. 2014, Bioinformatics. 30: 923–930) using default parameters with the exception of indel detection (maximum length of indel that can be detected=0).  The featureCounts program (Liao et al. 2014, Bioinformatics. 30: 923–930) then generated the gene-level RNA-Seq count summaries for each sample based on ENSEMBL annotation (Ensembl v.85).  This RNA-Seq count summary dataset was then filtered to exclude rows of data from genes that did not meet a minimum threshold of 5 samples with greater than or equal to 16 counts. Our current analysis used the log2 fragments per million gene-level summary output for each sample provided by the voom() function (R package limma; Ritchie et al. 2015, Nucleic Acids Res. 43: e47). Quality control included 1) visualization of the overall log (base2) transformed transcript expression across all subjects via boxplot, 2) examination of the overall reads (mean and standard deviation) per subject, 3) visualization of a subject/subject correlation matrix to identify particularly atypical samples (R<.95). No outlier samples were identified.

first: Cigdem

last: Aydin

first: Fan

last: Meng

first: Isabelle

last: Birt

first: Stanley

last: Watson

first: Huda

last: Akil


title: Geminin is required for Hox gene regulation to pattern the developing limb

city: Saint Louis

first: Kristen

last: Kroll

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

summary: Development of the complex structure of the vertebrate limb requires carefully orchestrated interactions between multiple regulatory pathways and proteins. Among these, precise regulation of 5’ Hox transcription factor expression is essential for proper limb bud patterning and development. Here, we identified Geminin (Gmnn) as a novel regulator of this process. A conditional model of Gmnn deficiency resulted in loss or severe reduction of forelimb skeletal elements, while both the forelimb autopod and hindlimb were unaffected. 5’ Hox gene expression expanded into more proximal and anterior regions of embryonic forelimb buds in this Gmnn-deficient model. A second conditional model of Gmnn deficiency instead caused a similar but less severe reduction of hindlimb skeletal elements and hindlimb polydactyly, while not affecting the forelimb. An ectopic posterior Shh signaling center was evident in the anterior hindlimb bud of Gmnn-deficient embryos in this model. This center ectopically expressed Hoxd13, the Hoxd13 target Shh, and the Shh target Ptch1, while these mutant hindlimb buds also had reduced levels of the cleaved, repressor form of Gli3, a Shh pathway antagonist. Together, this work delineates a new role for Gmnn in modulating Hox expression to pattern the vertebrate limb.

overall_design: Six litter and somite-matched pairs of Gmnnf/f; Prx-Cre (mutant) and Gmnn+/f; Prx-Cre (control) E10.5 embryos were used to prepare RNA. Batch correction was used to identify genes that were reproducibly differentially expressed genes (DEGs) across comparisons of paired mutant versus control samples.

first: EMA

last: Lewis

last: Sankar

last: Tong

first: E

last: Patterson

first: L

last: Waller

first: P

last: Gontarz

first: B

last: Zhang

first: D

last: Ornitz

first: K


title: HbtR, a heterofunctional homolog of the virulence regulator TcpP, facilitates the transition between symbiotic and planktonic lifestyles in Vibrio fischeri.

city: Honolulu

first: Brittany

middle: Dawn

last: Bennett

state: HI

address: 41 Ahui St.

department: Pacific Biosciences Research Center

institute: University of Hawaii

summary: The bioluminescent bacterium Vibrio fischeri forms a mutually beneficial symbiosis with the Hawaiian bobtail squid, Euprymna scolopes, in which the bacteria, housed inside a specialized light organ, produce light used by the squid in its nocturnal activities. Upon hatching, E. scolopes juveniles acquire V. fischeri from the seawater through a complex process that requires, among other factors, chemotaxis by the bacteria along a gradient of N-acetylated sugars into the crypts of the light organ, the niche in which the bacteria reside. Once inside the light organ, V. fischeri transitions into a symbiotic, sessile state in which the quorum-signaling regulator LitR induces luminescence. In this work we show that expression of litR and luminescence are repressed by a homolog of the V. cholerae virulence factor TcpP, which we have named HbtR. Further, we demonstrate that LitR represses genes involved in motility and chemotaxis into the light organ and activates genes required for exopolysaccharide production. Importance:  TcpP homologs are widespread throughout the Vibrio genus; however, the only protein in this family described thus far is a V. cholerae virulence regulator. Here we show that HbtR, the TcpP homolog in V. fischeri, has both a biological role and regulatory pathway completely unlike that in V. cholerae. Through its repression of the quorum-signaling regulator LitR, HbtR affects the expression of genes important for colonization of the E. scolopes light organ. While LitR becomes activated within the crypts, and upregulates luminescence and exopolysaccharide genes and downregulates chemotaxis and motility genes, it appears that HbtR, upon expulsion of V. fischeri cells into seawater, reverses this process to aid the switch from a symbiotic to a planktonic state. The possible importance of HbtR to the survival of V. fischeri outside of its animal host may have broader implications for the ways in which bacteria transition between often vastly different environmental niches.

overall_design: RNA-seq comparing transcription of each gene in the V. fischeri genome between two strains: ΔhbtRC carrying empty vector and ΔhbtRC overexpressing hbtRC.

middle: D

first: Tara

last: Essock-Burns

first: Edward

middle: G

last: Ruby