title: Physiological and Transcriptomic Changes in the Hypothalamic-Neurohypophysial System after 24 H of Furosemide-Induced Sodium Depletion

city: SAO PAULO

first: André

middle: Souza

last: Mecawi

state: SÃO PAULO

address: Rua Botucatu, 862 - Vila Clementino,, Edifício de Ciências Biomédicas

department: Department of Biophysics

institute: Federal University of Sao Paulo

summary:
Background/Aims: Furosemide is a loop diuretic widely used in clinical practice for the treatment of oedema and hypertension. The aim of this study was to determine physiological and molecular changes in the hypothalamic-neurohypophysial system as a consequence of furosemide-induced sodium depletion.
Methods: Male rats were sodium depleted by acute furosemide injection (10 and 30 mg/kg) followed by access to low sodium diet and distilled water for 24 h. The renal and behavioural consequences were evaluated, while blood and brains were collected to evaluate the neuroendocrine and gene expression responses.
Results: Furosemide treatment acutely increases urinary sodium and water excretion. After 24 h, water and food intake were reduced, while plasma angiotensin II and corticosterone were increased. After hypertonic saline presentation, sodium-depleted rats showed higher preference for salt. Interrogation using RNA sequencing revealed the expression of 94 genes significantly altered in the hypothalamic paraventricular nucleus (PVN) of sodium-depleted rats (31 upregulated and 63 downregulated). Out of 9 genes chosen, 5 were validated by quantitative PCR in the PVN (upregulated: Ephx2, Ndnf and Vwf; downregulated: Caprin2 and Opn3). The same genes were also assessed in the supraoptic nucleus (SON, upregulated: Tnnt1, Mis18a, Nr1d1 and Dbp; downregulated: Caprin2 and Opn3). As a result of these plastic transcriptome changes, vasopressin expression was decreased in PVN and SON, whilst vasopressin and oxytocin levels were reduced in plasma.
Conclusions: We thus have identified novel genes that might regulate vasopressin gene expression in the hypothalamus controlling the magnocellular neurons secretory response to body sodium depletion and consequently hypotonic stress.

overall_design: Male rats were sodium depleted by acute furosemide injection (10mg/kg) followed by access to low sodium diet and distilled water for 24 h. The PVN  region of the brain  was collected from 9 animals per group, and 3 animals were pooled per sequencing replicate to give a final n=3 for assessing  gene expression responses via RNAseq technology.

first: Alex

last: Paterson

first: Sabrina

middle: G

last: Dutra

first: Livia

middle: R

last: Monteiro

first: Michael

last: Greenwood

first: Mingkwan

first: Ludimila

middle: S

last: Amaral

first: Mariana

last: Melo

first: Débora

last: Colombari

first: Eduardo

first: Luís

last: Reis

first: Charles

last: Hindmarch

first: Lucila

last: Elias

first: José

last: Antunes-Rodrigues

first: David

last: Murphy

first: Andre


title: Regulating lineage progression of cortical neural stem cells by extrinsic signaling molecule SHH [single-cell RNA-seq]

status: Public on Feb 19 2020

city: Shanghai

first: Guoping

last: Liu

address: 138 Yi Xue Yuan Road

country: China

institute: Fudan University

type: Expression profiling by high throughput sequencing

summary:
Purpose:To asses changes in gene expression profiles of single cell from the E16.5 wild type littermate controls cortex, and ShhN IUE (ShhN palsmid were electroporated to wild type mice cortex at E13.5 and the cortex were dissected at E16.5) mice.
Methords: E16.5 wild type and ShhN-IUE cortices were carefully dissected under a fluorescent stereoscope, and incubated in 4 ml of papain solution for 20 min at 37℃, The cortical tissues were gently triturated, filtered through a 40 mm strainer, and washed with HBSS to obtain the single cell suspension. The Chromium droplet-based sequencing platform (10X Genomics) was used to generate scRNA-seq libraries, following the manufacturer’s instructions. The cDNA libraries were purified, quantified using Agilent 2100 Bioanalyzer, and sequenced on the Illumina Hiseq4000
Results: 7834 cells (2368 median genes per cell) captured for the Control cortex. And 8538 cells with 2422 median genes per cell captured for Shh-IUE mice.

overall_design: scRNA-seq: Individual cells were sampled from mice cortices of E16.5 wild type mice and ShhN IUE mice.

first: Yue

last: Zhang

first: Teng

last: Guo

first: Xiaoyi

last: Liang

first: Heng

last: Du

first: Lin

last: Yang

first: Aparna

last: Bhaduri

first: Xiaosu

last: Li

first: Zhejun

last: Xu

first: Zhuangzhi

first: Zhenmeiyu

first: Miao

last: He

first: Jeremiah

last: Tsyporin

first: Arnold

last: Kriegstein

first: John

middle: L

last: Rubenstein

first: Zhengang

first: Bin

last: Chen


title: Species-specific processing of long noncoding RNAs contributes to non-conserved functions in human and mouse stem cells

first: Li

address: 131 Dong-An Road

department: Institutes of Biological Sciences

summary: Subcellular RNA-seq datasets are used for genome-wide RNA localization analysis. We find different subcellular localization of lncRNAs in human and mouse stem cells. FAST, one of conserved lncRNAs with different localizations, is validated to be important for stem cell pluripotency. Futher, splicing factor PPIE is revealed to  regulate RNA processing and localization.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Total RNAs, cytoplasmic RNAs and nuclear RNAs of H9 and R1 cells are extracted and sequenced for downstream RNA subcellular localization analysis. Poly(A)+ RNA-seq of H9 FAST KD cells are used for FAST function anlaysis.

first: Ling-Ling

first: Chun-Jie

first: Xu-Kai

last: Ma

first: Yu-Hang

last: Xing

first: Chuan-Chuan

last: Zheng

last: Shan

first: Yi-Feng


title: Pbx4 limits vertebrate heart size and promotes pharyngeal arch artery development through partitioning progenitor fates within the second heart field and restricting proliferation

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

country: USA

institute: Cincinnati Children's Hospital

summary: Development of the vertebrate heart requires the appropriate integration of temporally-distinct differentiating progenitor populations. While factors that promote accrual of later-differentiating second heart field (SHF)-derived cells to the outflow tract (OFT) have been intensively investigated, few signals are understood that specifically restrict the size of the vertebrate OFT. Here, we show that improper specification and proliferation of SHF progenitors in zebrafish lazarus (lzr) mutants, which lack the transcription factor Pbx4, produces enlarged hearts with a specific increase in ventricular cardiomyocytes and smooth muscle cells within the OFT. Specifically, optogenetic lineage-tracing demonstrates Pbx4 initially promotes the proper partitioning of the SHF into anterior progenitors, which contribute to the OFT, and adjacent endothelial cell progenitors, which contribute to posterior pharyngeal arch arteries. Subsequently, Pbx4 also limits the size of the SHF through repressing SHF progenitor proliferation. Single-cell RNA sequencing of nkx2.5+ cells revealed that the enlarged SHF progenitor population within Pbx4-deficient embryos assimilates characteristics of normally distinct proliferative and more anterior, differentiated cardiomyocyte populations. Therefore, the generation of proper OFT size and great arteries in vertebrates requires Pbx-dependent stratification of unique progenitor differentiation states to facilitate homeotic-like transformations and limit progenitor production within the SHF.

overall_design: To determine the effects of Pbx4 loss on cardiac progenitors and differentiated cardiomyocytes, we utilized  single-cell RNA-Seq (scRNA-Seq) data sets collected from  control and Pbx4-depleted embryos nkx2.5:ZsYellow+ cells at 28 hours post-ferlilization. The 10x Genomics platform was used for these studies (version 2 library chemistry).

first: Andrew

last: Holowiecki

first: Kelsey

last: Linstrum

first: Padmapriyadarshini

last: Ravisankar

first: Kashish

last: Chetal

first: Joshua

last: Waxman


title: PanCancer pathway anaysis of RH41 Human Alveolar Rhabdomyosarcoma (ARMS) cell line

city: Singapore

first: Reshma

last: Taneja

state: Singapore

address: 2 Medical Drive, MD9, National University of Singapore

department: Department of Physiology

country: Singapore

institute: National University of Singapore

summary: multiplex gene expression analysis with 770 genes from 13 cancer-associated canonical pathways including: MAPK, STAT, PI3K, RAS, Cell Cycle, Apoptosis, Hedgehog, Wnt, DNA Damage Control, Transcriptional Regulation, Chromatin Modification, and TGF-ẞ.

overall_design: 770 including up to 40 PanCancer reference genes were probed for differntiatl regulation using from nSolver™ Analysis software from Nanostring Technologies, Inc.

first: R


title: Mouse Digits Regeneration RNA-seq Data

city: Cleveland

first: Peng

last: Jiang

address: 2121 Euclid Ave

institute: Cleveland State University

summary: Mice were subjected to hindlimb distal phalanx (P3) amputation to digit 3. For each amputation, mice were anesthetized, the hindlimb claw was extended, and the distal phalanx and footpad was sharply dissected.  A regenerating distal phalanx was generated by amputating ≤33% of the P3. Skin wounds were allowed to heal without suturing. Mice were subjected to micro-computed tomography (microCT) one day prior to surgery and immediately after amputation to confirm ≤ 33% removal of the P3. Any digit that did not fall within the ≤ 33% amputation guideline was omitted from the study. Based on our criteria, 17 animals were removed from the study resulting in a final total of 30 mice.  P3 mice were collected at hours (0h, 3h, 6h ,12h, and 24h), and days (3d, 7d, 14d, and 21d). Each time point contained 3 mice, except day 7 (6 mice). At the time of P3 collection, samples were immediately immersed in RNAlater for 24h at 4C. The digits were then removed from RNAlater and stored at -80C until performing RNA sequencing.

overall_design: 30 mice with digits amputation. We performed time course RNA-seq on these amputated digits to characterize transcriptome dynamics of regeneration

first: Connie

last: Chamberlain

first: Ray

last: Vanderby

first: James

middle: A

last: Thomson

first: Ron

last: Stewart


title: Regulating lineage progression of cortical neural stem cells by extrinsic signaling molecule SHH [bulk RNA-seq]

first: Guoping

last: Liu

summary:
Purpose:To asses changes in gene expression profiles from the P0 wild type littermate controls cortex, hGFAP-Cre, SmoM2f/+ mice cortex and ShhN IUE (ShhN palsmid were electroporated to wild type mice cortex at E13.5 and the cortex were dissected at P0) mice.
Methords:Total RNA was isolated and sequenced using an illumina high-seq 2500. Raw data was analyzed using TopHat. Genes were considered significantly changed whicn perform fold-change>=2 and P value <= 0.05
Results: Compared to controls, 2466 genes were significantly down-regulated, and 5289 genes were up regulated in the RNA expression level of the SmoM2 mice; 3492 genes were significantly down-regulated, and 3577 genes were up regulated in the RNA expression level of the cortex of ShhN IUE mice.

overall_design: Cortex RNA profiles of P0 Wild type mice brain, ShhN IUE mice brain and hGFAP-Cre, SmoM2f/+ mice brain

first: Yue

last: Zhang

first: Teng

last: Guo

first: Xiaoyi

last: Liang

first: Heng

last: Du

first: Lin

last: Yang

first: Aparna

last: Bhaduri

first: Xiaosu

last: Li

first: Zhejun

last: Xu

first: Zhuangzhi

first: Zhenmeiyu

first: Miao

last: He

first: Jeremiah

last: Tsyporin

first: Arnold

last: Kriegstein

first: John

last: Rubenstein

first: Zhengang

first: Bin

last: Chen


title: Expression profiles of hepatocellular carcinomas derived from ductular progenitor cells

city: Suita

first: Tomonori

last: Matsumoto

state: Osaka

address: 3-1 Yamadaoka

country: Japan

institute: Osaka University

summary:
Hepatocellular carcinoma (HCC) generally arises in chronically inflamed liver and is thought to originate from regenerating liver cells that acquired genetic alterations. Both hepatocytes and ductular progenitor cells (DPCs) contribute to liver regeneration and are candidate cellular origins of HCCs. In the current study, we used lineage-tracing analysis to show that Epcam-expressing DPCs give rise to HCCs in inflamed liver. Under conditions in which proliferating DPCs differentiate into cholangiocytes but not into hepatocytes, the accumulation of genetic alterations in Epcam-expressing DPCs resulted in the development of HCCs with histologic features of concomitant ductule-like structures resembling human cholangiolocellular carcinoma (CLC).
To elucidate the characteristics of DPC-derived HCC, gene expression of HCCs derived from Epcam-expressing DPCs were evaluated using Agilent SurePrint G3 Mouse Gene Expression 8x60K v2. Two DPC-derived HCCs with CLC components, two DPC-derived HCCs without CLC, and two HCCs derived from albumin-expressing cells were analyzed.

first: Hiroyuki

last: Marusawa


title: ATAC-seq identifies thousands of extrachromosomal circular DNA in cancers and cell lines

status: Public on Feb 18 2020

city: Charlottesville

first: Pankaj

last: Kumar

state: VA

address: JPA, 1312A Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Extrachromosomal circular DNAs (eccDNAs) are usually somatically mosaic and a source of intercellular heterogeneity in normal and tumor cells. Because short eccDNAs are poorly chromatinized, we hypothesized that they are sequenced by tagmentation in ATAC-seq experiments, without any enrichment of circular DNA, and thus identified thousands of eccDNAs. The eccDNAs identified in cell lines were validated by inverse PCR on DNA that survives exonuclease digestion of linear DNA, and by metaphase FISH. ATAC-seq in Gliomas and Glioblastomas identify hundreds of eccDNAs, including one containing the well-known EGFR gene amplicon from chr7.  Over 18,000 eccDNAs, many carrying known cancer driver genes, are identified in a pan-cancer analysis of 360 ATAC-seq libraries from 23 tumor types. Because of somatic mosaicism, eccDNAs are identified by ATAC-seq even before amplification of the locus is recognized by genome-wide copy number variation measurements. Thus, standard ATAC-seq is a sensitive method to detect eccDNA present in a subset of tumor cells, ready to be amplified under appropriate selection, as during therapy.

overall_design: Identification of extrachromsomal circular DNA from ATAC-Seq sequencing libraries

first: Zhangli

last: Su

first: Anindya

last: Dutta


title: The role of acid adaptation on transcriptome of breast cancer MCF7 cell line

city: Tampa

first: Mehdi

last: Damaghi

state: Fl

address: 12906 magnolia dr

institute: Moffitt Cancer Center

summary: Acid adaptation is a prominent event in solid tumor evolution and progression. Using RNA sequencing we studied the effect of acid adaptation on breast cancer cell line (MCF7)

overall_design: RNA profile of MCF7 breast cancer cell line was compared to acid adapted MCF7 cells


title: Activation of an endogenous pararetrovirus, petunia vein clearing virus, during long-term cultivation of host plants is associated with disturbance of star-type floral color pattern in Petunia hybrida

city: Kusatsu, Shiga

first: Midori

last: Tabara

address: 1-1-1, Noji-Higashi

institute: Ritsumeikan University

summary: White areas of star-type bicolor petals of petunia (Petunia hybrida) are caused by post-transcriptional gene silencing (PTGS) of the key enzyme of anthocyanin biosynthesis. We observed blotched flowers and vein-clearing symptom in leaves in 3- to 4-month-old petunia plants. In order to determine the cause of blotched flowers, we examined an endogenous pararetrovirus, petunia vein clearing virus (PVCV), because this virus causes vein-clearing symptom and may have a suppressor of PTGS. Transcripts and episomal DNA derived from proviral PVCV loci highly accumulated in 3- to 4-month-old plants, indicating that PVCV was activated as the host plant ages. Furthermore, CG and CHG sites of the promoter region of PVCV were highly methylated in 1-month-old plants but these cytosines were not methylated in 3- to 4-month-old plants, suggesting that poor maintenance of DNA methylation activates propagation of PVCV. In parallel, de novo methylation at CHH sites and 24-nt small RNAs were detected on the promoter region of PVCV, indicating that RNA-directed DNA methylation was induced by PVCV activation. Detections of transcripts and episomal DNA of PVCV in blotched regions and suppressor activity of PTGS support the mechanism that suppression of PTGS by activated PVCV causes blotched flowers.

overall_design: RNA-seq is perfomed using three 2-month-old and three 4-month-old petunia leaves.

first: Kazunori

last: Kuriyama

first: Hiromitsu

last: Moriyama

first: Akira

last: Kanazawa

first: Hisashi

last: Koiwa

first: Hideki

last: Takahashi

first: Toshiyuki

last: Fukuhara


title: A novel population of pro-inflammatory T cells that co-express αβ and γδ T cell receptors

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

summary: To understand these pro-inflammatory effects of hybrid αβ-γδ T cells in detail, we carried out a transcriptomic analysis of hybrid αβ-γδ T cells and conventional γδ T cells isolated from the LNs of WT mice at rest and during EAE.

overall_design: 20 samples analysed, 5 mice per group no pooling of samples. Control samples were Vy4 T cells from 5 naïve mice and hybrid Vy4 T cells from 5 naïve mice. Experimental samples were Vy4 T cells from 5 mice with EAE and hybrid Vy4 T cells from 5 mice with EAE

first: Kingston

last: Mills

first: Sarah

last: Edwards

first: Fiona

last: Roche

first: Caroline

last: Sutton

first: Valerie

last: Pivorunas

first: Lori

last: Dowding

first: Michael

last: Macoritto

first: Jesus

last: Paez-Cortez

first: Anthony

last: Slavin


title: Liver mRNA expression in high fat diet fed mice with hepatic specific Slug knockout

city: Ann Arbor

first: Liangyou

last: Rui

state: Michigan

address: 1137 Catherine Street

department: Molecular and Integrative Physiology

institute: University of Michigan

summary:
Liver steatosis is a driving force for nonalcoholic fatty liver disease (NAFLD), alcoholic liver disease, insulin resistance, and type 2 diabetes. Slug (also called Snai2 or Snail2) is a transcriptional regulator that may play a critical role in the regulation of liver function.
To prove that, we used microarrays to detail the hepatic Slug regulated gene expression underlying liver steatosis and identified distinct pathways controlled by Slug during this process.

overall_design: C57BL/6J mice males with hepatic specific Slug knockout and their littermates were fed a high fat diet fed (HFD) for 11 weeks. Then RNA samples were extracted from the same parts of liver tissues and hybridizated on Affymetrix microarrays.

first: Yan

last: Liu


title: AB569, A Nontoxic Chemical Tandem That Kills Major Human Pathogenic Bacteria

city: Vancouver

first: Erin

last: Gill

state: British Columbia

address: 2259 Lower Mall

country: Canada

institute: University of British Columbia

summary: Antibiotic-resistant “super-bug” bacteria represent a global health problem with no imminent solutions. Here, we demonstrate that AB569 (acidified nitrite (A-NO2-) and Na2-EDTA) killed all Gram-negative and Gram-positive bacteria tested. AB569 was also efficacious at killing the model organism P. aeruginosa in biofilms and in a murine chronic lung infection model. AB569 was not toxic to human cell lines at bactericidal concentrations. RNA-Seq analyses upon treatment of P. aeruginosa with AB569 revealed a catastrophic loss of the ability to support core pathways encompassing DNA, RNA, protein, ATP biosynthesis, and iron metabolism. Electrochemical analyses elucidated that AB569 produced more stable SNO-proteins, potentially explaining one mechanism of bacterial killing.  Our data implicate that AB569 is a safe and effective means to kill pathogenic bacteria, suggesting that simple strategies could be applied with highly advantageous therapeutic/toxicity index ratios to pathogens associated with a myriad of peri-epithelial infections and related disease scenarios.

overall_design: 11 total samples. 3 treatment conditions and 1 control condition. 3 biological replicates for all conditions except for the first treatment condition (NaNO2), where there are only 2 biological replicates.

first: Cameron

last: McDaniel

first: Warunya

last: Panmanee

first: Geoffrey

last: Winsor

middle: E

first: Claire

last: Bertelli

middle: J

last: Schurr

first: Prateek

last: Dongare

first: Andrew

middle: T

last: Paul

first: Seung-Hyun

middle: B

last: Ko

first: Gee

middle: W

last: Lau

first: Nupur

last: Dasgupta

first: Amy

last: Bogue

first: William

last: Miller

first: Joel

last: Mortensen

first: David

last: Haslam

first: Philip

last: Dexheimer

first: Daniel

last: Muruve

first: Bruce

last: Aronow

first: Malcolm

last: Forbes

first: Marek

last: Danilczuk

last: Brinkman

first: Robert

last: Hancock

first: Thomas

last: Meyer

last: Hassett


title: LncRNA AK036396 inhibits maturation and accelerates immunosuppression of polymorphonuclear myeloid-derived suppressor cells by enhancing the stability of ficolin B

status: Public on Feb 17 2020

city: Nanjing

first: Xinyu

last: Tian

email: jipinxinyu@163.com, sjwjs@ujs.edu.cn

state: Please select a state below

address: 321 Zhongshan Road, Nanjing Drum Tower Hospital

institute: The Affiliated Hospital of Nanjing University Medical School

summary: To identify lncRNAs involved in regulating PMN-MDSCs, an Arraystar lncRNA microarray was performed to determine the lncRNA expression profile in PMN-MDSCs. Compared to those in CD11b+Ly6G+ cells under physiological conditions, the expression of abundant lncRNAs was significantly higher in PMN-MDSCs from the tumor microenvironment. In these lncRNAs, lncRNA AK036396, whose sequencing information has been identified in the UCSC database, was one of the most significantly upregulated lncRNAs and  its expression was confirmed by quantitative real-time PCR (qRT-PCR). In addition, microarray data indicated that Fcnb expression, which can be used to identify immature granuloctyes and is closely associated with granulocyte maturation, was one of the highest potential target molecules of lncRNA AK036396 in PMN-MDSCs.

overall_design: PMN-MDSCs used for microarray analysis were first isolated from the spleens of wild-type mice and tumor tissue of tumor-bearing mice using a mouse MDSC isolation kit (Miltenyi Biotec, Auburn, CA) following the manufacturer’s protocol. Then, the enriched cells were stained with anti-mouse CD11b-PE/Cy5.5 (0.25 μg for 1×10^6 cells) (clone: M1/70) (eBioscience, San Diego, CA) and anti-mouse Ly6G-PE (0.25 μg for 1×10^6 cells) (clone: RB6-8C5) (eBioscience, San Diego, CA) for 30 minutes at 4°C. Stained cells were collected and further sorted with FACS (FACSAriaII, BD Biosciences) to eliminate interference from other cells. An Arraystar lncRNA microarray was conducted by KangChen Bio-tech.

first: Jie

last: Ma


title: Differentially expressed lncRNA in biological premature ovarian insufficiency (bPOI)

city: Jinan

first: Yingying

last: Qin

state: Shandong

institute: Shandong University

summary: Our study is designed to demonstrate altered profiles of lncRNAs in the granulosa cells from patients with bPOI. Functional studies will be further confirmed. This study will provide new viewpoint for understanding the roles of non-coding RNA for GCs function, as well as potential etiologic mechanism for POI.

overall_design: We have completed the human LncRNA microarray analysis of the 20 samples.

first: Xiaoyan

last: Wang


title: Effects of increased YY2 expression on heart development

status: Public on Feb 25 2020

city: Missouri City

first: Jun

address: 6770 Bertner Ave.

institute: Texas Heart Institute

summary: Yin Yang 2 (YY2) is a member of the Yin Yang family of transcription factors. Although the bioactivity of YY2 has been previously studied, its role in cardiovascular diseases is not known. We observed the increased expression of YY2 in failing human hearts compared with control hearts, raising the question of whether YY2 is involved in the pathogenesis of cardiomyopathy. To investigate the potential contribution of YY2 to the development of cardiomyopathy, we crossed two transgenic (Tg) mouse lines, pCAG-YY2-Tg+ and -MHC-Cre, to generate two independent double transgenic (dTg) mouse lines in which the conditional cardiomyocyte-specific expression of YY2 driven by the -MHC promoter was mediated by Cre recombinase, starting at embryonic day 9.0. In dTg mice, we observed partial embryonic lethality and hearts with defective cardiomyocyte proliferation. Surviving dTg mice from both lines developed cardiomyopathy and heart failure that occurred with aging, showing different degrees of severity that were associated with the level of transgene expression. The development of cardiomyopathy was accompanied by increased levels of cardiac disease markers, apoptosis, and cardiac fibrosis. Our studies further revealed that the Cre-mediated cardiomyocyte-specific increase in YY2 expression led to increased levels of Beclin 1 and LC3II, indicating that YY2 is involved in mediating autophagic activity in mouse hearts in vivo. Also, compared with control hearts, dTG mouse hearts showed increased JNK activity. Because autophagy and JNK activity are important for maintaining cardiac homeostasis, the dysregulation of these signaling pathways may contribute to YY2-induced cardiomyopathy and heart failure in vivo.

overall_design: A total of four samples are included (Mut-#1, mut-#5, control -#7, control-#8), with each having triplicate.

first: Yi

last: Zhang

first: Ilimbek

last: Beketaeva


title: The embryonic linker histone dBigH1 compromises the functional epigenetic state of active chromatin [Affy]

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

summary: Expression data from S2 cells wild type and expressing dBigH1

overall_design: 6 samples; 2 * 3 replicates

first: Paula

last: Climent-Cantó

first: Albert

last: Carbonell

first: Milos

last: Tatarski

last: Reina

first: Jofre

last: Font-Mateu

first: Miguel

last: Beato

first: Azorín

last: Fernando


title: Proteasome inhibitor-induced modulation reveals the spliceosome as a specific therapeutic vulnerability in multiple myeloma

city: San Francisco

first: Hector

middle: Han-Li

last: Huang

state: CALIFORNIA

address: 185 Berry St, Ste 290/Rm 2410

department: Laboratory Medicine

institute: University of California San Francisco

type: Non-coding RNA profiling by high throughput sequencing

summary: Resistance to proteasome inhibitors (PIs) is a ubiquitous clinical concern in multiple myeloma (MM).  We proposed that signaling-level responses after PI would reveal new means to enhance efficacy.  Unbiased phosphoproteomics after the PI carfilzomib surprisingly demonstrated the most prominent phosphorylation changes on spliceosome components.  Spliceosome modulation was invisible to RNA or protein abundance alone.  Transcriptome analysis demonstrated broad-scale intron retention suggestive of PI-specific splicing interference.  Direct spliceosome inhibition synergized with carfilzomib and showed potent anti-myeloma activity.  Functional genomics and exome sequencing further supported the spliceosome as a specific vulnerabilityin myeloma.  Our results propose splicing interference as an unrecognized modality of PI mechanism, reveal additional modes of spliceosome modulation, and suggest spliceosome targeting as a promising therapeutic strategy in myeloma.

overall_design: We examine 1) gene expression of MM cells in response to PI and 2)alternative splicing in response to PI and comparator chemotherapeutic compound.  We further investigate splice factor mechanism in MM cells, by examining alternative splicing in MM with overexpression of wild type and mutant splice factor, SRSF1

middle: H

first: Ian

middle: D

last: Ferguson

first: Alexis

middle: M

last: Thornton

first: Prabhakar

last: Bastola

first: Christine

last: Lam

first: Yu-Hsiu

last: Lin

first: Priya

last: Choudhry

first: Margarette

middle: C

last: Mariano

first: Makeba

last: Marcoulis

first: Chin

middle: F

last: Teo

first: Julia

last: Malato

first: Paul

last: Phojanakong

last: Martin

first: Jeffrey

last: Wolf

first: Sandy

last: Wong

first: Nina

last: Shah

first: Byron

last: Hann

first: Angela

middle: N

last: Brooks

first: Arun

middle: P

last: Wiita


title: The embryonic linker histone dBigH1 compromises the functional epigenetic state of active chromatin [ChIP2]

first: Oscar

last: Reina Garcia

summary: Genome wide distribution of dBigH1 and dH1 in cells expressing dBigH1ΔED. Genome wide distribution of Rpb3 in wild type S2 cells, cells expressing dBigH1 and cells expressing dBigH1ΔED.

overall_design: 16 samples

first: Paula

last: Climent-Cantó

first: Albert

last: Carbonell

first: Milos

last: Tatarski

last: Reina

first: Jofre

last: Font-Mateu

first: Miguel

last: Beato

first: Azorín

last: Fernando


title: Genome-wide analysis of human monocytes cultured on wt- LX2 or CD44 ko LX2

city: München

first: sainitin

last: donakonda

state: Bavaria

address: Ismaningerstr. 22

department: Institute of Immunology

country: Germany

institute: TUM

summary: Analyis of the induction of myeloid derived suppressor cells using the LX2 model

overall_design: Monocytes were cultured for 18h on LX2 to induce MDSCs. As control, CD44 ko LX2 were used. Total RNA was obtained from reisolated CD14 expressing cells after 18 hours.

first: Bastian

last: Höchst

first: Sainitin

last: Donakonda

first: Percy

last: Knolle


title: Magnitude of modulation of gene expression in aneuploid maize depends on the extent of genomic imbalance

city: Columbia

first: James

last: Birchler

state: MO

address: 310 Tucker hall

institute: University of Missouri

summary: Aneuploidy has profound effects on an organism, typically more so than polyploidy, and the basis of this contrast is not fully understood. A dosage series of maize chromosome arm 1L was used to compare relative global gene expression in different types and degrees of aneuploidy to gain insight into how the magnitude of genomic imbalance as well as hypoploidy affect global gene expression. While previously available methods required a selective examination of specific genes, RNA sequencing provides a whole-genome view of gene expression in aneuploids. Most studies of global aneuploid effects have concentrated on trisomics because other types of aneuploids are difficult to produce in most model genetic organisms. The genetic toolkit of maize allows the examination of multiple ploidies and 1-4 doses of chromosome arms. Thus, a detailed examination of expression changes both on the varied chromosome arm and elsewhere in the genome is possible, in both hypoploids and hyperploids, compared with euploid controls. Previous studies observed the inverse trans effect, in which genes not varied in DNA dosage are expressed in a negative relationship to the varied chromosomal region. This response was also the major type of change found globally in this study. It was also found that the effects of aneuploidy are progressive, with more severe aneuploids producing effects of greater magnitude.

overall_design: RNA-seq was used to compare gene expression in 6 different ploidy states in maize, with 27 biological replicates in total. All aneuploids are varied in dosage for the long arm of chromosome 1. The first dosage series includes 17 biological replicates: 4 diploids (used as control), 5 trisomics, 3 tetrasomics, 3 haploids, and 2 disomic haploids. The second dosage series includes 10 biological replicates: 4 monosomics, 3 diploids (used as control), and 3 trisomics.

first: Adam

last: Johnson

first: Jie

last: Hou


title: Expression data from mouse plasmacytoid dendritic cells stimulated with CpG and treated with lif

city: Campinas

first: Renata

last: Sesti-Costa

state: SP

address: Rua Carlos Chagas 480

country: Brazil

institute: UNICAMP

summary:
pDCs selectively express the receptor for leukemia inhibitory factor (LIF) that signals through STAT3.
We performed microarray analysis of primary pDCs sorted from bone marrow of C57BL6 mice and incubated with a) medium; b) LIF; c) CpG; d) LIF plus CpG.

overall_design: Sorting of pDCs from bone marrow was performed by magnetic beads using negative selection kit (Miltenyi Biotec), followed by sorting of CD11cintB220+SiglecH+ cells by FACS. pDCs were treated with LIF (10ng/ml) for 1 or 24h and stimulated with CpG-A (2216) or CpG-B (1826), both 6ug/ml, for 18-24h.

first: Marina

last: Cella

first: Marco

last: Colonna


title: Differential scaling of gene expression with cell size may explain size control in budding yeast.

status: Public on Feb 16 2020

city: Redwood City

first: Yuping

last: Chen

state: CA

address: 309 Oak Ave

institute: Stanford University

summary: Yeast cells must grow to a critical size before committing to division. It is unknown how size is measured. We find that as cells grow, mRNAs for some cell cycle activators scale faster than size, increasing in concentration, while mRNAs for some inhibitors scale slower than size, decreasing in concentration. Size-scaled gene expression could cause an increasing ratio of activators to inhibitors with size, triggering cell cycle entry. Consistent with this, expression of the CLN2 activator from the promoter of the WHI5 inhibitor, or vice versa, interfered with cell size homeostasis, yielding a broader distribution of cell sizes. We suggest that size homeostasis comes from differential scaling of gene expression with size. Such regulation of gene expression as a function of cell size could affect many cellular processes.

overall_design: Arrest yeast cells in cell cycle by inhibiting CDK activity, allow them to grow large, and analyze transcript abundance by RNA-Seq as a function of size.

first: Bruce

last: Futcher


title: Homeostatic leukotrienes, IL-25, and IL-33 signals on intestinal ILC2 status

city: Seattle

first: Jakob

middle: Helmuth

last: von Moltke

state: Washington

address: 750 Republican Street

department: Immunology

institute: University of Washington

summary: We report the high-throughput profiling of murine intestinal type 2 innate lymphoid cells (ILC2) transcriptome. By obtaining over 8.7 million bases of sequence, we generated genome-wide expression maps of mouse ILC2 without the presense of known activation signals(IL-25, IL-33 receptor) and new non-redundant signal (leukotriene). We find that homeostatic signaling minimally contributes to intestinal ILC2 activation statu. 500 ILC2s were sorted as CD45+Lineage-IL-17RB+

overall_design: Transcriptome profiling of type 2 innate lymphoid cells in small intestine

first: Mario

middle: G

last: Rosasco

first: Hung-An

last: Ting

first: John

last: McGinty

last: Von Moltke


title: The embryonic linker histone dBigH1 compromises the functional epigenetic state of active chromatin [ChIP1]

first: Oscar

last: Reina Garcia

summary: Genome wide distribution of dBigH1 and dH1 in wild type cells and cells expressing dBigH1

overall_design: 12 samples

first: Paula

last: Climent-Cantó

first: Albert

last: Carbonell

first: Milos

last: Tatarski

last: Reina

first: Jofre

last: Font-Mateu

first: Miguel

last: Beato

first: Azorín

last: Fernando


title: Profiling chromatin accessible regions in Merkel cell carcinoma cells

city: ALLSTON

first: Donglim

last: Park

state: MA

address: 4 Price Rd, Apt11

department: Medical oncology

institute: Dana-Farber Cancer Institute

summary: Merkel cell carcinoma (MCC) is an aggressive neuroendocrine cancer of the skin, caused by either excessive UV damage or integration of the Merkel cell polyomavirus (MCV) genome. Here, we report that virally encoded MCV small T antigen (ST) establishes dependence on the LSD1 transcriptional repressor. Inhibition of LSD1 reduces growth of MCV-positive MCC and suppresses ST’s transformation capacity in vitro and in vivo. To define the mechanism of LSD1 inhibition in MCC, we performed a CRISPR loss-of-function library screen. We found that deletion of components of the non-canonical (ncBAF) chromatin remodeler complex confers resistance to LSD1 inhibitors and that LSD1 and ncBAF antagonistically regulate an overlapping set of genes involved in neuron differentiation. Our work provides mechanistic insight into the dependence of MCC on LSD1 and the role of ncBAF as a tumor suppressor in cancer.

overall_design: Two independent replicates of ATAC-seq in MKL-1 virus-positive Merkel cell carcinoma cells treated with LSD1 and BRD9 inhibitors


title: LSD1 and BRD9 transcriptome analysis in the MKL-1 Merkel cell carcinoma (MCC) cell line

overall_design: RNA-seq of MKL-1 MCC cells treated with an LSD1 inhibitor (GSK-LSD1), BRD9 inhibitor (dBRD9) or both inhibitors for 6 days.


title: LSD1 transcriptome analysis in Merkel cell carcinoma (MCC) cell lines

overall_design: RNA-seq of six virus-positive (MKL-1, MKL-2, MS-1, WaGa, BroLi and PeTa) and one virus-negative (UISO) MCC cell lines before and after the treatment of specific LSD1 inhibitors for 1 or 3 days.


title: LSD1-RCOR2 binding and LSD1 and BRD9 transcriptome analysis in Merkel cell carcinoma cells

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

overall_design: Refer to individual Series


title: Genome-wide maps of LSD1-RCOR2 binding in Merkel cell carcinoma cells

overall_design: Two independent replicates of ChIP-seq of LSD1, RCOR2, and ATOH1 in MKL-1 virus-positive Merkel cell carcinoma cells


title: ONECUT2 is a putative oncogene associated with CpG hypomethylation at promoter-proximal DNA in gastric cancer and triggers ACSL5, a member of the ACS family

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: To access methylation change during gastric carcinogenesis in this study, we performed RRBS analysis with LCM-derived normal gastric mucosa and gastric tumor tissue [GSE55159]. Among a set of genes hypomethylated and upregulated in GC, ONECUT2 was identified as a hypomethylated target in GC. Upregulated ONECUT2 expression significantly increased the proliferation, colony formation, migration and invasion in GC cells. To identify target genes regulated by ONECUT2, we performed ChIP-seq and RNA-seq.

overall_design: Two control GC cells and ONECUT2 overexpressed GC cells were used for ChIP-seq and RNA-seq analysis.

first: Eun-Hye

last: Seo

first: Jong-Hwan

first: Yong

middle: S


title: 19p loss is significantly enriched in older age neuroblastoma patients and correlates with poor prognosis (Agilent-014950)

status: Public on Feb 15 2020

city: Genova

first: Annalisa

last: Pezzolo

address: Via Gerolamo Gaslini, 3

country: Italy

institute: IRCCS Istituto Gaslini

summary:
Genomic aberrations of neuroblastoma occurring in late childhood and adolescence are uncommon and still underestimated.
Public DNA copy number profiles of 556 tumors (discovery set) and of 208 tumors obtained by array-CGH assay (validation set) were used to verify if 19p loss is significantly over-represented in children and adolescents. The 19p loss occurrence was separately tested within different age groups in the discovery and validation set and the resulting P values were combined and corrected by Bonferroni’s method.
In both sets, the lowest age group significantly associated with 19p loss (discovery set: 20%; validation set: 35%) was 6 years. The 19p loss was considered to be a significant marker for overall survival in patients over 6 years of age. Relevant tumor suppressor genes (KEAP1, DNM2, SMARCA4, SLC44A2 and CDKN2D) and microRNAs (miR-181c, miR-27a, and mirR-199a-1) were in 19p loss. Down-regulation of DNM2, SLC44A2 and CDKN2D associated with poor patient outcome and older age. Among the recurrent NB chromosomal aberrations, only 1q gain was enriched in patients older than 6 years and was mutually exclusive respect to 19p loss.
Our data demonstrate that 19p loss is a genomic biomarker of NBs diagnosed in older children that can predict clinical outcome.

overall_design:
This study includes 208 neuroblastoma tumors obtained by array-CGH assay  were used to verify if 19p loss is significantly over-represented in children and adolescents.
This subseries includes 103 neuroblastoma tumors analyzed on Agilent-014950.


title: 19p loss is significantly enriched in older age neuroblastoma patients and correlates with poor prognosis (Agilent-022060)

overall_design:
This study includes 208 neuroblastoma tumors obtained by array-CGH assay  were used to verify if 19p loss is significantly over-represented in children and adolescents.
This subseries includes 24 neuroblastoma tumors analyzed on Agilent-022060.


title: 19p loss is significantly enriched in older age neuroblastoma patients and correlates with poor prognosis (Agilent-030587)

overall_design:
This study includes 208 neuroblastoma tumors obtained by array-CGH assay  were used to verify if 19p loss is significantly over-represented in children and adolescents.
This subseries includes 62 neuroblastoma tumors analyzed on Agilent-030587.


title: 19p loss is significantly enriched in older age neuroblastoma patients and correlates with poor prognosis (Agilent-013282, dataset 2)

overall_design:
This study includes 208 neuroblastoma tumors obtained by array-CGH assay  were used to verify if 19p loss is significantly over-represented in children and adolescents.
This subseries includes 17 neuroblastoma tumors analyzed on Agilent-013282.


title: 19p loss is significantly enriched in older age neuroblastoma patients and correlates with poor prognosis (Agilent-013282, dataset 1)

overall_design:
This study includes 208 neuroblastoma tumors obtained by array-CGH assay  were used to verify if 19p loss is significantly over-represented in children and adolescents.
This subseries includes 2 neuroblastoma tumors analyzed on Agilent-013282.


title: Next generation sequencing transcriptome analysis of polarized colonic Caco-2 cells exposed to prebiotics GOS and FOS

city: Loughborough

first: Ian

middle: Frank

last: Connerton

state: Leicestershire

address: College Road, Sutton Bonington

department: School of Biosciences

country: United Kingdom

institute: University of Nottingham

summary:
Objective: The purpose of this study is to describe colonic cells differential transcriptomes and cellular pathways directly modulated by exposure to prebiotics. Prebiotic oligosaccharides are widely used as animal and human in-feed additives for their beneficial effects on the probiotic gut microbiota. A number of studies have revealed a protective effect of several oligosaccharides on dysfunctional or challenged intestinal cells models through microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods. However, thus far there was limited data assessing the direct effect of such functional foods on on whole-transcriptome of unchallenged intestinal epithelial cells.
Methods: Colonic mRNA profiles of confluent Caco-2 cells exposed for 24h to GOS or FOS and their respective mono- and di-saccharides mock treatments were generated for 3 biological replicates.  Library pool was sequenced on the Illlumina NextSeq500 over two NextSeq500 High Output 150 cycle kits (Illumina; FC-404-2002). Sequence reads were quality checked with FastQC (version 0.11.3). Using CLC Genomics Workbench 12.03, sequences were trimmed from adaptor, paired and good quality sequence read pairs were mapped to the Homo sapiens GRCh38 reference genome (Hg38). Transcripts counts were normalised and differential gene expression analysed using  the RNAseq Analysis Module of CLC Genomics Workbench 12.03. Gene ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) analysis were developed to investigate the statistically significant gene sets (|FC value ≥ 1.5, FDR p-adj. < 0.05) by implementing the NIPA Enrichment R script (v0.6.7.R, https://github.com/ADAC-UoN/NIPA). RNAseq results were validated by qRT–PCR assays.
Results: Sequencing generated between 45 to 134 million of 75-bp paired-end sequence reads per sample. An average of 58 million sequence reads per sample were paired and mapped to human genes (genome Homo sapiens GRCh38).  For GOS exposure, 89 genes were differentially expressed (fold-change ≥ 1.5 and q-value < 0.05) between GOS and mock-treated groups. Gene ontology functional analysis revealed that genes up-regulated in the presence of GOS were involved in digestion, absorption, transmembrane transport whereas genes involved in drug and xenobiotic metabolic processes were reduced. With FOS treatment, 12 genes were differentially expressed (fold-change ≥ 1.5 and q-value < 0.05) relative to the control group and functional analysis of enriched GO terms revealed up-regulated DEGs were associated with steroid metabolic process.
Conclusions: Our study details the first whole-transcriptome analysis of colonic epithelial cells exposed to the direct effect of prebiotics GOS and FOS. Our RNA-seq based characterization of distinctive or shared differentially expressed genes and enriched pathways generated for GOS and FOS would support further network analyses and enable the examination of intricate biological functions within more complex environments.

overall_design: Three biological replicates (passage 22 to 26) of confluent ATCC® HTB-37™ Caco-2 cells were independently exposed for 24h to 2% GOS or FOS syrup-containing media and their respective monosaccharides mock-treatments in absence of antibiotics and FCS. To assess the direct effect of oligosaccharides on the cells, the presence of mono- and di-saccharides contained in GOS and FOS treatment syrups was accounted for. Accordingly, we tailored mock-treatment media for "GOS" samples by incorporating galactose, glucose and lactose in "mock-GOS" and by inclusion of fructose, glucose and sucrose in "mock-FOS" for "FOS" samples. A total of 12 poly(A) mRNA enriched samples were sequenced using Illlumina NextSeq500 High Output to generate over 40 million pairs of 75-bp paired-end reads per sample.

first: Geraldine

last: Flaujac Lafontaine


title: Regulation of the error-prone DNA polymerase polκ by oncogenic signaling and its contribution to drug resistance

city: New York

first: Nathaniel

middle: R

last: Campbell

state: NY

institute: Memorial Sloan Kettering Cancer Center

summary: We report how the A375 melanoma cell line changes following CRISPR-Cas9 inactivation of POLK

overall_design: RNA-seq of A375 melanoma cells following CRISPR-Cas9 with either POLK sgRNA or non-targeting control sgRNA (N=3 replicate samples each)

first: Richard

last: White


title: RNA-seq on cells with or without pathogenic PAX1 variants at different stages of in vitro differentiation into thymic epithelial progenitor cells

city: Bethesda

first: Luigi

last: Notarangelo

state: MD

address: 10 center drive, 10CRC, 5W3840

department: NIAID

institute: NIH

summary: Bi-allelic, loss-of-function PAX1 variants underlie a syndromic form of severe combined immunodeficiency (SCID) by disrupting thymus development. To assess if bi-allelic PAX1 variants affect differentiation of thymic epithelial cells in vitro, we reprogrammed fibroblasts from a healthy control and two patients with bi-allelic pathogenic PAX1 variants to induced pluripotent stem cells (iPSCs), and subsequently differentiated these to thymic epithelial progenitor cells (TEP).

overall_design: The cells were differentiated in 24-well-plates, in triplicate according to a treatment protocol summarized below. The samples labeled Control_1 and Control_2 correspond to two separate differentiations of cells derived from the same iPSC clone. Individual iPSC clones were used for Patient_1 or Patient_4 samples. Each differentiation was carried out in technical triplicates, starting from the iPSC stage. The samples corresponding to each triplicate are labeled _Rep1 through _Rep3. Samples were collected at the iPSC stage (day 0), definitive endoderm stage (day 5, only for Control_1), or TEP stage (day 14) of differentiation. Control_1 and Patient_1 iPSC clones were simultaneously differentiated toward TEPs. Control_2 and Patient_4 iPSC clones were simultaneously differentiated toward TEPs.

first: Yasuhiro

last: Yamazaki

first: Luis

last: Franco

first: Timothy

last: Myers


title: GRO-seq reported in "Phosphorylated Lamin A/C in the nuclear interior binds active enhancers associated with abnormal transcription in progeria"

city: Cincinnati

first: Kohta

last: Ikegami

state: OH

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

summary: LMNA encodes nuclear Lamin A/C that tethers lamina-associated domains (LADs) to the nuclear periphery. Mutations in LMNA cause degenerative disorders including the premature aging disorder Hutchinson-Gilford progeria, but the mechanisms are unknown. We report that Ser22-phosphorylated (pS22) Lamin A/C was localized to the nuclear interior in human fibroblasts throughout the cell cycle. pS22-Lamin A/C interacted with a subset of putative active enhancers, not LADs, at locations co-bound by the transcriptional activator c-Jun. In progeria-patient fibroblasts, a subset of pS22-Lamin A/C-binding sites were lost whereas new pS22-Lamin A/C-binding sites emerged in normally quiescent loci. New pS22-Lamin A/C binding was accompanied by increased histone acetylation, increased c-Jun binding, and upregulation of nearby genes implicated in progeria pathophysiology. These results suggest that Lamin A/C regulates gene expression by enhancer binding. Disruption of the gene regulatory rather than LAD tethering function of Lamin A/C presents a novel mechanism for disorders caused by LMNA mutations.

overall_design: The aims of this project are to 1) identify the locations of the human genome associated with Ser22-phosphorylated LMNA by ChIP-seq in normal and progeria-patient cells; 2) define the chromatin characteristics of  Ser22-phosphorylated LMNA-associated sites by histone ChIP-seq and ATAC-seq; and 3) identify genes dysregulated in progeria-patient cells by RNA-seq.


title: RNA-seq reported in "Phosphorylated Lamin A/C in the nuclear interior binds active enhancers associated with abnormal transcription in progeria"

first: Stefano

last: Secchia


title: 19p loss is significantly enriched in older age neuroblastoma patients and correlates with poor prognosis

overall_design:
This study includes 208 neuroblastoma tumors obtained by array-CGH assay  were used to verify if 19p loss is significantly over-represented in children and adolescents.
Refer to individual Series


title: Gene expression data from ETMR cell line BT183

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

institute: German Cancer Research Center DKFZ

summary: Gene expression data from this ETMR cell line was compared with gene expression data from primary ETMR tumors to search for potential drug targets in ETMR tumors.

overall_design: Total RNA from ETMR cell line BT183 was hybridised to the Affymetrix HG U133 Plus 2.0 microarray.

first: Christin

last: Schmidt

first: Stefan

last: Pfister


title: ATAC-seq reported in "Phosphorylated Lamin A/C in the nuclear interior binds active enhancers associated with abnormal transcription in progeria"


title: In situ capture of global transcription dynamics and enhancer activity with high accuracy and sensitivity

city: Chicago

first: Ruitu

last: Lyu

state: IL

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

summary: Transcription is a highly dynamic process that generates the majority of single-stranded DNA in the genome as ‘transcription bubbles’. Here we describe a kethoxal-assisted single-stranded DNA sequencing (KAS-seq), which marks single-stranded DNA in situ for genome-wide capture and sequencing, based on the fast and specific reaction between N3-kethoxal and guanines in single-stranded DNA in live cells. KAS-seq enables rapid (within 5 min) and sensitive detection of the position, relative level, and dynamics of ssDNA, as a readout of transcriptionally engaged RNA polymerases, with 1,000 cells. KAS-seq defines a group of enhancers that are single-stranded, which confers higher transcription factor binding density, more enhancer-promotor interactions, and higher ability to activate transcription. Under protein condensation inhibition condition, KAS-seq reveals unprecedented, rapid release of RNA polymerase II (Pol II) from a group of promotors, and reveals gene sets with different extents of responses, which correlate with Pol II C-terminal domain (CTD) serine 5 phosphorylation (S5P) level at TSS under no treatment condition. KAS-seq thus facilitates fast, comprehensive, and accurate analysis of transcription dynamics and enhancer activities simultaneously in a low input and high-throughput manner.

overall_design:
Examination of N3-kethoxal labeling ssDNA pattern in 2 HEK293 and mESCs.

Examination of N3-kethoxal labeling ssDNA pattern in mouse liver tissue.

first: Tong

last: Wu


title: H3K27me3 and H3K4me3 profiles in chr4/pkr1 and WT [RNA-seq]

status: Public on Feb 14 2020

city: Cologne

first: Alice

last: Pajoro

address: Carl-von-Linné-Weg 10

institute: MPIPZ

summary: Several pathways conferring environmental flowering responses in Arabidopsis converge on developmental processes that act in the shoot apical meristem to mediate the floral transition. Many characterized mutations impair environmental flowering responses, however downstream developmental processes have been more refractory to mutagenesis. We constructed a quintuple mutant in which several environmental pathways are impaired and showed that its flowering responses to changes in photoperiod and ambient temperature are almost abolished. Analysis of the quintuple mutant by RNA-seq showed that expression of gibberellin biosynthetic genes and transcription factors that contribute to the age pathway correlate with flowering. Mutagenesis of the quintuple mutant recovered two late-flowering mutants, quintuple ems 1 (qem1) and qem2. The causal genes were identified by isogenic mapping and transgenic complementation. The qem1 mutation was an allele of ga20ox2, confirming the importance of gibberellin for flowering in the absence of environmental responses. By contrast, qem2 is in CHROMATIN REMODELING 4 (CHR4), which was not previously genetically implicated in floral induction. Using co-immunoprecipitation, RNA-seq and ChIP-seq, we show that CHR4 interacts with transcription factors involved in floral meristem identity and affects expression of key floral regulators. We conclude that CHR4 plays important roles in the inflorescence meristem to promote floral identity.

overall_design: Examination of differentially expressed genes in betweeen WT and  svp flc ft tsf soc1, svp flc ft tsf soc1 and qem2 and col and chr4-2 apices in a short day time course.

first: A

first: G

last: Coupland


title: RNAseq of laser captured spinal and oculomotor neurons in post mortem material of ALS patients

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Stockholm University

summary: Gene expression profiles of specific neuronal populations might explain differential vulnerability to neurodegeneration in the lethal disease amyotrophic lateral sclerosis (ALS). Using laser capture microscopy (LCM) and RNA sequencing (LCM-seq), we demonstrate that the molecular signature of degeneration-resistant oculomotor neurons (OMNs) is distinct from that of vulnerable spinal motor neurons (MNs).

overall_design: A total of 14 samples were analyzed. Each sample consists of approximately 120 laser-captured motor neurons from ALS patient post-mortem human tissue. Samples are divided over 2 groups; spinal motor neurons (n=10) and oculomotor neurons (n=4).

first: Julio

last: Aguila Benitez

first: Jik

last: Nijssen


title: Paired ChIP-Seq studies of Kasumi-1 t(8;21) AML cells

city: St. Louis

first: Jinsong

last: Zhang

address: 1402 South Grand Blvd.

department: Department of Pharmacology & Physiology

institute: Saint Louis University School of Medicine

summary: Nearly 10-15% of all acute myeloid leukemia (AML) cases are caused by a recurring chromosomal translocation between 8 and 21, t(8;21). The t(8;21) translocation generates the AML1-ETO leukemia fusion protein. AML1-ETO promotes leukemogenesis by transcriptionally dysregulating important cell-fate genes. Here, to better understand how AML1-ETO deregulates transcription, we performed paired ChIP-Seq analyses of sequence-specific transcription factors, coactivators, corepressors, HDACs, RNA Pol II and acetyl-histone marks in both control and AML1-ETO-depleted Kasumi-1 t(8;21) AML cells.

overall_design: Chromatin immunoprecipitation using specific antibodies followed by deep sequencing in Kasumi-1 t(8;21) AML cells.


title: H3K27me3 and H3K4me3 profiles in chr4/pkr1 and WT [ChIP-seq]

overall_design: Examination of 2 different histone modifications (H3K4me3 and H3K27me3) in chr4/pkr1 and WT


title: Transcriptomic profiling of small intestinal crypts upon MEX3A deletion

status: Public on Feb 13 2020

city: Porto

first: Bruno

last: Pereira

address: Rua Alfredo Allen, 208

country: Portugal

summary: The effort to better understand intestinal stem cell (ISC) identity and regulation remains a challenge.  We have been studying the RNA-binding protein MEX3A as a putative ISC marker. In that context, we have generated the first Mex3a knockout (KO) mouse model and show MEX3A is crucial for maintenance of the Lgr5+ ISC pool. As part of a phenotypic characterization pipeline, we have performed transcriptomic profiling (RNA-sequencing) of isolated Mex3a KO small intestinal crypts and compared it against small intestinal crypts isolated from age-matched wild-type controls.

overall_design: Given the effect of Mex3a deletion for crypt cell populations and overall crypt development, Mex3a KO animals were sacrificed before the peak of phenotypic onset in order to preserve the crypt cellular content to its maximum extent. For each biological replicate (n = 3 for each genotype at P16), small intestinal crypts were isolated by incubation of intestinal fragments with crypt chelating buffer, followed by mechanical dissociation. Freshly isolated crypts were used for total RNA extraction with Tri reagent (Sigma) and subsequent RNA-sequencing analysis.

first: Raquel

last: Almeida


title: Neurofibromin is an Estrogen Receptor alpha Transcriptional Co-repressor in Breast cancer

city: HOUSTON

first: Eric

middle: C.

last: Chang

state: TX

address: ONE BAYLOR PLZ

department: BREAST CENTER

institute: BAYLOR COLLEGE OF MEDICINE

summary: We report that neurofibromin, a tumor suppressor and Ras-GAP (GTPase Activating Protein), is also an estrogen receptor-alpha (ER) transcriptional co-repressor through leucine/isoleucine-rich motifs that are functionally independent of GAP activity.  GAP activity, in turn, does not impact ER binding. Consequently, neurofibromin-depletion causes estradiol hypersensitivity and tamoxifen agonism, explaining the poor prognosis associated with neurofibromin-loss in endocrine therapy-treated ER+ breast cancer.  Neurofibromin-deficient ER+ breast cancer cells initially retain sensitivity to selective estrogen receptor degraders (SERDs).  However, Ras activation does play a role in acquired SERD resistance, which can be reversed upon MEK inhibitor addition, and SERD/MEK inhibitor combinations induce tumor regression.  Thus, neurofibromin is a dual repressor for both Ras and ER signaling, and co-targeting may treat neurofibromin-deficient ER+ breast tumors.

overall_design: RNA-seq of doxycycline inducible knockdown of NF1 in hormone-deprived MCF7 cells -/+ E2, and RNA-seq of NF1 wildtype and mutant CRISPR knock-in hormone-deprived MCF7 cells.

first: Ze-Yi

last: Zheng

first: Jonathan

last: Lei

first: Meenakshi

last: Anurag


title: Pilot study of DNA methylation, molecular aging markers and measures of health and well-being in aging

city: Boston

first: Olivia

last: Okereke

state: MASSACHUSETTS

address: One bowdoin square, room no. 745

institute: Massachusetts General Hospital

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation assays was conducted using the Illumina Infinium MethylationEPIC BeadArray technology (Methyl850K chip) that allows genome-wide DNA methylation analysis of 866,836 CpG sites. Samples included 11 psychiatric cases and 12 healthy controls balanced by age decade and sex.

overall_design: Bisulfite conversion, or bisulfite treatment, whole genome amplification (WGA), hybridization and single base extension were carried out to get labeled nucleotide using standard protocol. Dual color (Cy3 and Cy5) staining was used for allowing the nucleotide to be detected by the iSCAN reader and is converted to genotype during the analysis.

middle: I

first: Aditi

last: Hazra

first: Chirag

last: Vyas


title: The effect of osa RNAi with and without infection

city: TAMPERE

first: Mika

last: Ramet

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: Transcriptome profiling of immune-responsive genes in Drosophila melanogaster during Gram-positive bacterial infection and upon silencing of osa was performed. The most highly induced gene in the control set (150071 Valanne I) by Micrococcus luteus infection was CR44404, and its expression is fully dependent on osa expression (as shown in this dataset, 150071 Valanne II). The full transcriptome analysis also indicated that Osa regulates the expression of immune genes by modifying the expression of the Drosophila NF-kappaB factors Relish and Dif.

overall_design: Three biological replicates (A,B&C) containing 5 flies each are analyzed per condition (non-infected vs. M.luteus infected for 24h)

first: Susanna

last: Valanne

first: Mirva

last: Järvelä-Stölting

last: Rämet


title: H3K27me3 and H3K4me3 profiles in chr4/pkr1 and WT

first: Alice

last: Pajoro

overall_design: Refer to individual Series


title: FLT3 inhibition upregulates HDAC8 via FOXO to inactivate p53 and promote maintenance of FLT3-ITD+ acute myeloid leukemia

city: Shanghai

first: Jun

last: Long

address: Xincun Road

department: Department of Hematology

institute: Tongji Hospital

summary: Internal tandem duplication (ITD) mutations within the FMS-like receptor tyrosine kinase-3 (FLT3) can be found in up to 25~30% of acute myeloid leukemia (AML) patients and confer a poor prognosis. Although FLT3 tyrosine kinase inhibitors (TKIs) have shown clinical responses, the overall outcome of FLT3-ITD+ AML patients remains poor, and most of them would relapse very shortly. TKIs can not eliminate primitive FLT3-ITD+ AML cells, which are potential sources of relapse. Therefore, elucidating the mechanisms underlying FLT3-ITD+ AML maintenance and drug resistance is essential to develop novel, effective treatment strategies. Here, we demonstrate that FLT3 inhibition induces histone deacetylase 8 (HDAC8) upregulation through FOXO1 and FOXO3-mediated transactivation in FLT3-ITD+ AML cells. Upregulated HDAC8 deacetylates and inactivates p53, leading to leukemia maintenance and drug resistance upon TKIs treatment. Genetic or pharmacological inhibition of HDAC8 re-activates p53, abrogates leukemia maintenance and significantly enhances TKI-mediated elimination of FLT3-ITD+ AML cells. Importantly, in FLT3-ITD+ AML patient-derived xenograft models, the combination of FLT3 TKI (AC220) with a HDAC8 inhibitor (22d) significantly inhibits leukemia progression and effectively reduces primitive FLT3-ITD+ AML cells. Moreover, we extend these findings to an AML subtype harboring another tyrosine kinase activating mutation. In conclusion, our study demonstrates that HDAC8 upregulation as an important mechanism to resist TKIs and promote leukemia maintenance, and suggests that combining HDAC8 inhibition with TKI treatment could be a promising strategy to treat FLT3-ITD+ AML and other tyrosine kinase mutation-harboring leukemias.

overall_design: Gene expression analysis by RNA-seq of FLT3-ITD+ cell line MV4-11 treated with 22d (10nM) v.s vehicle control

first: Ai-Bin

last: Liang

first: Jiong

last: Hu


title: Polyploid hepatocytes are protected from cancer but maintain regenerative capacity in chronic liver disease

status: Public on Feb 12 2020

city: Dallas

first: Tao

last: Wang

state: Texas

address: 5323 Harry Hines Blvd.

institute: University of Texas Southwestern Medical Center

summary:
BACKGROUND & AIMS: Thirty to ninety percent of hepatocytes contain whole genome duplications, making it imperative to understand the fates and functions of these polyploid cells and how they affect development of liver disease. An important question is how polyploid cells respond to chronic proliferative demands, which are characteristic of liver diseases, but a challenging situation for cells with multiple genomes.
METHODS:  To interrogate liver polyploidy, we employed a mouse with reversible ANLN (  Anillin  actin binding protein) knockdown that drives hepatocyte polyploidization in a doxycycline inducible fashion. Diethylnitrosamine (DEN) and carbon tetrachloride (CCl4) were used to induce chronic liver damage and hepatocellular carcinoma (HCC). We performed partial hepatectomies to test regeneration and RNA-seq to assess gene expression changes. Lineage tracing was used to rule out repopulation from non-hepatocyte sources. In vivo imaging of mitotic hepatocytes estimated the frequency of aneuploidy during regeneration, and exome sequencing of 54 human cirrhotic nodules was used to quantify aneuploidy.
RESULTS:  Hepatocytes from mice given chronic CCl4  alone showed significant increases in ploidy. Super-polyploid mice with 97% polyploid hepatocytes, due to induced knockdown of  Anln  , were almost completely protected from tumorigenesis induced by DEN and chronic CCl4  . The protection was not associated with differences in regenerative capacity, tissue fitness, gene regulation, or mitotic errors. Regenerative contributions from a non-hepatocyte population were ruled out using lineage tracing, confirming that polyploids can replenish tissues during chronic damage. No lagging chromosomes or micronuclei were found in mitotic polyploid cells and there was no evidence of chromosomal copy number variations in 54 nodules, suggesting that aneuploidy is not a common outcome of polyploid cell divisions.
CONCLUSION:  During chronic injury, polyploid hepatocytes readily divide and regenerate while being buffered from tumor suppressor loss and tumorigenesis. Therapeutic strategies to increase numbers of polypoid hepatocytes could prevent cancer while preserving regeneration.

overall_design: 24 RNA-Seq data was generated from mouse

first: Hao

last: Zhu


title: Identification and characterization of artery and vein enhancers in the human genome

city: Worcester

first: Nathan

middle: D.

last: Lawson

address: 364 Plantation Street

department: Molecular, Cell, and Cancer Biology

institute: University of Massachusetts Medical School

summary: Our goal was to identify artery- and vein-specific cis regulatory elements in the human genome and use these to determine novel mechanisms that regulate arteriovenous differentiation

overall_design: Artery and vein enhancers were identified using ChIP-Seq for K27ac and EP300 on HUAEC and HUVEC, performed in duplicate. Further analysis included RNAseq in triplicate from the same cell types. To assess binding of known transcription factors NR2F2 and ERG, we performed ChIP-Seq in duplicate samples. We assessed K27ac and K27me3 occupancy under different experimental conditions using triplicate samples from HUVEC


title: Gene expression data of different SSc subsets

first: Pia

last: Moinzadeh

address: Kerpener Str 62

institute: University of Cologne

summary: We here used whole blood gene expression profiling to differentiate SSc patients from healthy controls (HC) and to identify a specific gene expression and predictive genes for SSc-overlap syndromes.

overall_design: For each collection, 2,5ml of peripheral whole blood of 150 SSc patients and 40 HC was drawn into 2 PAXGene Blood RNA tubes of PreAnalytiX (Qiagen, BD Company, Hilden, Germany). Gene expression analysis was performed using the Affymetrix Human Genome U219 Chip.

first: P

last: Frommolt

first: M

last: Franitza

last: Toliat

first: K

last: Becker

last: Nürnberg

first: S

last: Nihtyanova

last: Ahrazoglu

first: D

last: Belz

first: N

last: Hunzelmann

last: Abraham

first: V

last: Ong

first: L

last: Mouthon

first: R

last: Hesselstrand

first: C

last: Denton

first: T

last: Krieg


title: mTORC1 controls a dynamic program of TOP mRNA translation via LARP1

city: New Haven

first: Carson

last: Thoreen

state: CT

address: 333 Cedar St. SHM B 145

department: Cellular and Molecular Physiology

institute: Yale School of Medicine

summary: LARP1 has been proposed to control the translation of TOP mRNAs downstrteam of mTORC1. Here we used ribosome profiling to analyze transcriptome-wide changes in translation following mTOR inhibition in wild-type HEK-293T cells and cells where LARP1 (sgLARP1) or LARP1 and its homologue LARP1B (sgLARP1/1B) have been deleted using CRISPR/Cas9.

overall_design:
Ribosome profiling and RNA-seq datasets from wild-type HEK-293T, sgLARP1, and sgLARP1/1B cells treated for 2 h with 250 nM of the mTOR inhibitor Torin 1.

Please note that the 'larp1dko_*_RPF_rep*' processed data (e.g. DKO_DMSOa_RPF_unique.htseqcounts.txt) was generated together with the corresponding *reseq sample (e.g. GSM3889093 and GSM4146393) and is linked to the LP* sample records (e.g. GSM3889093 LP: larp1dko_dmso_RPF_rep1).


title: Single residue in CD28-costimulated CAR-T cells limits long-term persistence and antitumor durability

status: Public on Feb 11 2020

city: Cambridge

first: Aviv

last: Madar

address: 250 Massachusetts Ave

institute: Novartis Institutes for Biomedical Research

summary: Chimeric antigen receptor–T (CAR-T) cell therapies can eliminate relapsed and refractory tumors, but the durability of antitumor activity requires in vivo persistence. Differential signaling through the CAR costimulatory domain can alter the T cell metabolism, memory differentiation, and influence long-term persistence. CAR-T cells costimulated with 4-1BB or ICOS persist in xenograft models but those constructed with CD28 exhibit rapid clearance. Here, we show that a single amino acid residue in CD28 drove T cell exhaustion and hindered the persistence of CD28-based CAR-T cells and changing this asparagine to phenylalanine (CD28-YMFM) promoted durable antitumor control. In addition, CD28-YMFM CAR-T cells exhibited reduced T cell differentiation and exhaustion as well as increased skewing toward Th17 cells. Reciprocal modification of ICOS-containing CAR-T cells abolished in vivo persistence and antitumor activity. This finding suggests modifications to the costimulatory domains of CAR-T cells can enable longer persistence and thereby improve antitumor response.

overall_design: T cells from two different normal donors were genetically modified to express CARs targeting mesothelin and containing different intracellular domains. At the end of the primary expansion, T cells were stimulated with its cognate antigen in vitro. CD8-T cells were isolated six days after stimulation and their transcriptional profile was analyzed by RNAseq.

first: Sonia

last: Guedan

first: Avery

last: Posey

first: Carl

last: June

first: Regina

last: Young

first: Anna

last: Wing

first: Carolyn

last: Shaw

first: Fang

last: Liu

first: Victoria

last: Casado-Medrano


title: Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells [RNA-seq]

city: Philadelphia

first: Naomi

last: Goldman

state: PA

address: 324 BRB II/III, 421 Curie Blvd

institute: University of Pennsylvania

summary: Despite overwhelming evidence supporting the role of genetics in susceptibility tocomplex diseases, such as autoimmune disorders, a fundamental unresolved questionis whether large numbers of sequence variants with small effect sizes can alter thespatial genome organization. Here, we provide the first report on the reconfiguration ofthe 3D genome due to nucleotide differences associated with type 1 diabetes, anautoimmune disorder. We show that the chromatin organization at T cell identity genesis identical between diabetes-susceptible and diabetes-resistant mouse strains despitethousands of sequence polymorphisms, suggesting that these loci are epigeneticallyresilient to genetic variation. However, molecular and optical mapping of genomefolding demonstrate that diabetes risk-conferring loci coalesce into close spatialproximity in T cells of diabetes-susceptible mice, forming regulatory cliques, andresulting in aberrant gene expression. Our data uncover 3D chromatin architecture asa new dimension in understanding complex diseases

overall_design: Libraries were prepared with SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara).

first: Maria

last: Fasolino

first: Wenliang

last: Wang

first: Benjamin

last: Cattau

first: Yeqiao

last: Zhou

first: Jelena

last: Petrovic

first: Verena

last: Link

first: Allison

last: Cote

first: Michael

last: Silverman

first: Eric

last: Joyce

first: Shawn

last: Little

first: Arjun

last: Raj

first: Jorge

last: Henao-Mejia

first: Robert

middle: B

last: Faryabi

first: Golnaz

last: Vahedi


title: DRIP-sequencing U2OS

city: Copenhagen

first: Ivan

last: Vogel

address: Blegdamsvej 3B

country: Denmark

institute: University of Copenhagen

summary: Here, we identify that a human DNA helicase RTEL1, which is known to play a role in the maintenance of telomeres by interacting with proteins in the shelterin complex by resolving G4 quadruplexes, is essential for prevention of R-loop accumulation during replication and for MiDAS in mitosis at both CFSs and telomeres. Our findings indicate that RTEL1 plays a genome-wide role in preventing the collapse of replication forks at sites of G-quadruplexes and R-loop formation. Considering cancer cells rely on RTEL1 function to resolve the elevated transcription-replication conflicts caused by oncogene activation, RTEL1 is a potential drug target for cancer therapy.

overall_design: U2OS cell lines under various treatments.

first: Ying

last: Liu


title: Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells [ChIP-seq]

first: Naomi

last: Goldman

overall_design: Cells were chemically cross-linked by 1% formaldehyde. Samples were sonicated and protein-DNA complexes were isolated with antibody.


title: Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells [HiChIP-seq]

overall_design: HiChIP was performed as described (Mumbach et al., 2016) using antibody against Smc1 (Bethyl, cat# A300-055A)

first: Maria

last: Fasolino


title: Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells [ATAC-seq]

overall_design: ATAC-seq was performed as previously described with minor modifications (Buenrostro et al., 2013).

first: Wenliang

last: Wang


title: DNA methylation disruption reshapes the hematopoietic differentiation landscape

city: New York

first: Franco

last: Izzo

address: 1470 Madison Avenue

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

type: Methylation profiling by high throughput sequencing

summary: Somatic mutations in genes implicated in DNA methylation (DNAme; e.g., TET2, DNMT3A and IDH2), are frequently observed in hematological malignancies, as well as in clonal hematopoiesis (CH). Yet, how these mutations disrupt the hematopoietic differentiation topology remains largely unknown.  By applying complementary single-cell sequencing approaches to murine bone marrow hematopoietic stem and progenitor cells, we observe that mutations in DNAme modifiers result in significantly altered differentiation topology. In particular, we find shifts in the frequencies of erythroid vs. myelo-monocytic progenitors, which can be traced back to fate-priming skews in the earliest uncommitted hematopoietic stem cells (HSCs). DNAme analysis both in open chromatin regions and at single-cell resolution, demonstrate that methylation changes resulting from DNAme modifier disruption are distributed stochastically across the genome. To reconcile the distributed nature of DNAme changes with the deterministic erythroid vs. myelo-monocytic topological skews, our data implicate differential sensitivity of key transcription factors to global methylation changes due to biases in CpG enrichment in their binding motifs. Finally, by coupling single-cell whole transcriptome analysis with targeted genotyping, we observe a similar skew in early transcriptional priming impact human CH bone marrow progenitors in an individual with DNMT3A-755S mutation. Thus, our results provide evidence that DNAme encodes topological information for hematopoietic differentiation.

overall_design:
We performed multiple single cell assays, including single cell RNA sequencing, single cell ATAC-seq and single cell RNA plus reduced representation bisufite for Mx1-Cre (WT), Mx1-Cre Tet2fl/fl, Mx1-Cre Dnmt3afl/fl and Mx1-Cre Idh2WT/R140Q bone marrow hematopoietic progenitors (Lineage negative or Lineage negative, c-Kit positive as indicated). To induce recombination of the conditional alleles, 16-20 week-old male Mx1-Cre, Mx1-Cre Tet2fl/fl, Mx1-Cre Dnmt3afl/fl and Mx1-Cre Idh2R140Q/+ mice were treated with three doses of polyinosinic-polycytadylic acid (pIpC; 12 mg/kg/day; GE Healthcare, Chicago, IL) every other day via intra-peritoneal injection. Primary mouse bone marrow (BM) cells were isolated into cold phosphate-buffered saline (PBS), without Ca2+ and Mg2+, and supplemented with 2% bovine serum albumin (BSA) to generate single cell suspensions. Red blood cells (RBCs) were removed using ammonium chloride-potassium bicarbonate (ACK) lysis buffer, resuspended in PBS/2% BSA, and filtered through a 40μm cell strainer. Cells were then stained with streptavidin-conjugated secondary antibody, and live (DAPI-negative) lineage-negative cells were purified by flow cytometry on a BD Aria (BD Bioscience, San Jose, CA). For single cell RNA sequencing assays, a total of 10 WT, 10 Tet2 KO, 4 Dnmt3a KO and 3 Idh2-R140Q mice were used.

GRANT: DP2-CA239065 awarded to Dan Landau
GRANT: R01HL145283-01 awarded to Dan Landau

first: Stanley

last: Lee

first: Asaf

last: Poran

first: Ronan

last: Chaligne

first: Federico

last: Gaiti

first: Baptiste

last: Gross

first: Rekha

last: Murali

first: Sunil

last: Deochand

first: Chelston

last: Ang

first: Phillipa

middle: A

last: Jones

first: Anna

last: Nam

first: Kyu-Tae

last: Kim

first: Steven

middle: K

last: Hill

first: Rafael

last: Schulman

first: Michelle

last: Ki

first: Priscillia

last: Lhoumaud

first: Jane

last: Skok

first: Aaron

last: Viny

first: Ross

middle: L

last: Levine

first: Omar

last: Abdel-Wahab

first: Keningsberg

last: Ephraim

first: Dan

last: Landau


title: Identification of FMRP targets in human neural progenitors and neurons

city: Madison

first: Xinyu

last: Zhao

state: Wisconsin

address: 1500 HIghland Ave, Wiasman Center North Tower T513

institute: University of Wisconsin Madison

summary: We identified FMRP-bound RNAs in hPSC (human pluripotent stem cells)-differentiated forebrain neuroprogenitors (NPCs) and neurons using crosslinking immunoprecipitation (CLIP) coupled to high-throughput sequencing. We examined transcriptomic and proteomic changes in FMRP-KO NPCs and neurons.

overall_design: FMRP targets in human NPCs and neurons were isolated by CLIP from three hPSC lines (H1, H13, and GM1) were sequenced on Illumina HiSeq platforms. Transcriptomic profiles of NPCs and neurons were generated by deep sequencing, in triplicate, using Illumina HiSeq.

first: Meng

last: Li

first: Anita

last: Bhattacharyya


title: Transcriptional characterization of major cellular compartments within muscle tissue at homeostasis and after acute injury in mice

status: Public on Feb 10 2020

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: A distinct population of Foxp3+CD4+ regulatory T (Treg) cells promotes repair of acutely or chronically injured skeletal muscle. The accumulation of these cells depends critically on interleukin (IL)-33 produced by local mesenchymal stromal cells (mSCs). An intriguing physical association between muscle nerves, IL-33+ mSCs and Tregs has been reported, and begs a deeper exploration of this cell triumvirate. Here we evidence a striking proximity between IL-33+ muscle mSCs and both large-fiber nerve bundles and small-fiber sensory neurons; report that muscle mSCs transcribe an array of genes encoding neuropeptides, neuropeptide receptors and other nerve-related proteins; define muscle mSC subtypes that express both IL-33 and the receptor for the calcitonin-gene-related peptide (CGRP); and demonstrate that up- or down- tuning of CGRP signals augments or diminishes, respectively, IL-33 production by muscle mSCs and later accumulation of muscle Tregs. Indeed, a single injection of CGRP induced much of the genetic program elicited in mSCs early after acute skeletal muscle injury. These findings highlight neural/stromal/immune-cell cross-talk in tissue repair, suggesting future therapeutic approaches.

overall_design: Gene expression profiles of hematopoietic cells (CD45+), endothelial cells (CD31+), mesenchymal stromal cells (CD45-CD31-Sca1+PDGFRa+, MSCs), and satellite cells (CD45-CD31-Sca1-Vcam1+, MuSCs) from uninjured hindlimb muscle and from cardiotoxin-injured hindlimb muscle (day 1 post-injury). 3 biological replicates were obtained per experimental group.

first: Kathy

last: Wang

last: Yaghi

first: Raul

last: Spallanzani

first: Xin

last: Chen

first: David

last: Zemmour

first: Nicole

last: Lai

first: Isaac

middle: M

last: Chiu

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: Transcriptional characterization of mesenchymal stromal cells isolated from muscle and lymph node at homeostasis in mice

overall_design: Gene expression profiles of mesenchymal stromal cells from skeletal muscle and lymph node (combination of inguinal, axillary, brachial and cervical). 3 biological replicates were obtained per experimental group.


title: Role of CGRP on muscle mesenchymal stromal cells in mice

overall_design: Gene expression profiles of muscle mesenchymal stromal cells from mice injected IP with CGRP or PBS (isolated at 4 or 8 hours post-injection). 4 biological replicates were obtained per experimental group.


title: RNA-seq analysis of HD and MDS MSCs and MSC-conditioned monocytes

city: Minneapolis

first: Jeffrey S

last: Miller

state: MN

address: 420 Delaware St. SE

institute: University of Minnesota

summary: Altered bone marrow hematopoiesis and immune suppression is a hallmark of myelodysplastic syndrome (MDS). While the bone marrow microenvironment influences malignant hematopoiesis, the mechanism leading to MDS-associated immune suppression is unknown. We tested whether mesenchymal stromal cells (MSCs) contribute to this process. Here, we developed a model to study cultured MSCs from MDS patients compared to similar aged matched normal controls for regulation of immune function. MSCs from MDS patients (MDS-MSC) and healthy donor MSC (HD-MSC) exhibited a similar in vitro phenotype and neither had a direct effect on NK cell function. However, when MDS and HD-MSCs were cultured with monocytes, only the MDS-MSCs acquired phenotypic and metabolic properties of myeloid-derived suppressor cells (MDSCs), with resulting suppression of NK cell function, along with T cell proliferation. A unique MSC transcriptome was observed in MDS-MSCs compared to HD-MSCs, including increased expression of the reactive oxygen species (ROS) regulator, ENC1. High ENC1 expression in MDS-MSC induced suppressive monocytes with increased INHBA, a gene that encodes for a member of the TGF? superfamily of proteins. These monocytes also had reduced expression of the TGF? transcriptional repressor MAB21L2, further adding to their immune suppressive function. Silencing ENC1 or inhibiting ROS production in MDS-MSCs abrogated the suppressive function of MDS-MSC conditioned monocytes. In addition, silencing MAB21L2 in healthy MSC conditioned monocytes mimicked the MDS-MSC suppressive transformation of monocytes. Our data demonstrate that MDS-MSCs are responsible for inducing an immune suppressive microenvironment in MDS through an indirect mechanism involving monocytes.

overall_design:
We report our results of RNA-seq analysis on bone marrow-derived mesenchymal stem cells from  healthy donor or Myelodysplastic Syndrome patients. We also provide results from RNA-seq analysis on MSC-conditioned monocytes.
RNA was isolated from cultured MSCs or bead-isolated monocytes. Libraries were created using standard Illumina reagents and analyzed using a HiSeq2500.

first: Jeffrey

first: Dhifaf

last: Sarhan

first: Juan

middle: E

last: Abrahante


title: Axonal precursor miRNAs hitchhike on endosomes and locally regulate the development of neural circuits

city: Irapuato

first: Cei

last: Abreu-Goodger

state: Guanajuato

address: Km. 9.6 Libramiento Nte Carr Leon-Irapuato

country: Mexico

institute: Langebio - Cinvestav

summary: Various species of non-coding RNAs (ncRNAs) are enriched in subcellular compartments but the mechanisms orchestrating their localization and their local functions remain largely unknown. We investigated both aspects using the elongating retinal ganglion cell axon and its tip, the growth cone, as models. We reveal that specific endogenous precursor microRNAs (pre-miRNAs) are actively trafficked to distal axons by hitchhiking primarily on late endosomes / lysosomes. Upon exposure to Sema3A, pre-miRNAs are processed specifically within axons into newly generated miRNAs, one of which, in turn, silences the basal translation of tubulin beta 3 class III (TUBB3) but not amyloid beta precursor protein (APP). At the organismal level, these mature miRNAs are required for growth cone steering and a fully functional visual system. Overall, our results uncover a novel mode of ncRNA transport from one cytosolic compartment to another within polarized cells. They also reveal that newly generated miRNAs are critical components of a ncRNA-based signaling pathway that transduces environmental signals into the structural remodelling of subcellular compartments.

overall_design: Total RNA profile were obtained from isolated retinal ganglion cell axons from Xenopus laevis retinal eye cultures using RNA-sequencing

first: Eloina

last: Corradi

first: Irene

last: Dalla Costa

first: Antoneta

last: Gavoci

first: Archana

last: Iyer

first: Michela

last: Roccuzzo

first: Tegan

last: Otto

first: Eleonora

last: Oliani

first: Simone

last: Bridi

first: Stephanie

last: Strohbuecker

first: Gabriela

last: Santos-Rodriguez

first: Donatella

last: Valdembri

first: Guido

last: Serini

first: Marie-Laure

last: Baudet


title: Transcriptome profiling of murine liver from EndoV knock-out and wildtype mice

city: Oslo

first: Xiang Yi

last: Kong

address: Sognsvannsveien 20

country: Norway

institute: Oslo University Hospital

summary: We performed high-throughput RNA sequencing to characterize possible differences in the transcriptome of murine liver from both 12 months old EndoV and wildtype mice mice fed a regular diet.

overall_design: Sex- and age-matched EndoV and wildtype mice were fed standard rodent chow ad libitum for 12 months. Once terminated, the livers extracted and snap-frozen in liquid nitrogen until RNA extraction.

first: Ingrun

last: Alseth


title: Genome-wide transcriptome response of Streptomyces tsukubaensis to N-acetylglucosamine

status: Public on Feb 08 2020

city: León

first: Antonio

last: Rodríguez-García

address: Avenida Real 1

institute: INBIOTEC

summary: Chitin is the second most abundant biopolymer present in soils and is utilized by antibiotic-producing Streptomyces species. Its monomer, N-acetylglucosamine (NAG), regulates the developmental program of the model organism Streptomyces coelicolor. NAG blocks differentiation when growing on rich medium whilst it promotes development on poor culture media. We report here the negative effect of NAG on tacrolimus (FK506) production in Streptomyces tsukubaensis NRRL 18488 growing on a defined rich medium. Using microarrays technology, we found that GlcNAc represses the transcription of fkbN, encoding the main transcriptional activator of the tacrolimus biosynthetic cluster, and of ppt1, encoding a phosphopantheteinyltransferase involved in tacrolimus biosynthesis. On the contrary, NAG stimulated transcription of genes related to amino acid and nucleotide biosynthesis, DNA replication, RNA translation, glycolysis, pyruvate metabolism, and key gene members of the PHO regulon. The results obtained support those previously reported for S. coelicolor, but some important differences were observed

overall_design: The transcriptomic experiment is composed of 16 samples from two time series named NAG (culture medium containing N-acetylglucosamine) and CTL (control condition: the culture medium without addition). Each time series was replicated once. Streptomyces tsukubaensis spores (10e9) were inoculated into 0.5-L flasks containing 100 mL of MGm-2.5 medium (PMID 22990582) and cultivated at 28 ºC, 220 rpm. Samples for RNA extraction were taken from flask cultures at 70 h, 70.5 h, 71 h and 72 h (4 timepoints × 4 cultures = 16 samples). The final concentration of N-acetylglcuosamine was  22.6 mmol/L (i. e., 0.5 % w/v).

first: María

last: Ordóñez-Robles

first: Juan

middle: F

last: Martín


title: Effects of atmospheric ammonia on the production performance, serum biochemical indices, and liver RNA-seq data of laying ducks

city: Yangzhou

first: chunhong

last: zhu

address: Cangjie Rd.58

country: China

institute: Jiangsu Institute of Poultry Science

summary: The liver is the largest detoxification organ in the human body. RNA sequencing (RNA-seq) analyses of liver samples were performed to investigate the effects of high ammonia levels (ammonia exposure at 75 ± 5 ppm), a low ammonia level  (ammonia exposure at 5 ± 5 ppm) was set as control group, on the metabolism and detoxification capabilities of laying ducks.

overall_design: A total of 176 Shanma laying ducks (Fujian Longyan Shan Ma Duck Station, Longyan, China), aged 150 days, with comparable bodyweights were selected and randomly allocated to one of two groups: a high ammonia group (ammonia exposure at 75 ± 5 ppm) or a low ammonia group (ammonia exposure at 5 ± 5 ppm). The two groups were housed in separated atmospheric ammonia controlled rooms with free access to the same diet and water. Amnonia level was controlled by specialized equipment. The feeding experimental period was 30 days from day 200 to 230.

first: Chunhong

last: Zhu


title: Retinal astrocyte transcriptome reveals an important role for Cyp1b1 expression in modulation of cell adhesive and migratory properties

first: Nader

last: Sheibani

state: WI

address: 1111 Highland Ave, 9453 WIMR

department: Ophthalmology and Visual Sciences

country: USA

institute: University of Wisconsin_Madison

summary: Global genome-wide sequencing analysis of RNA prepared from Cyp1b1-/-AC and Cyp1b1+/+AC was perfomed to gain additional insight into the cellular regulatory mechanisms impacted by Cyp1b1 expression

overall_design: Transcriptome comapration between Cyp1b1-/- retina astrocytes vs Wt retina astrocytes

first: Juliana

last: Falero Perez


title: Proteogenomics uncovers a vast repertoire of shared tumor-specific antigens in ovarian cancer

city: Montréal

first: Claude

last: Perreault

state: Quebec

address: 2950, Chemin de Polytechnique

institute: Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal

summary: High-grade serous ovarian cancer (HGSC), the principal cause of death from gynecological malignancies in the world, has not significantly benefited from  advances in cancer immunotherapy. Although  HGSC infiltration by lymphocytes correlates with superior survival, the nature of antigens that can elicit anti-HGSC immune responses is unknown. The goal of this study was to establish the global landscape of HGSC tumor-specific antigens (TSAs) using a mass spectrometry pipeline that interrogated all reading frames of all genomic regions. In 23 HGSC tumors, we identified 103 TSAs. Classic TSA discovery approaches focusing only on mutated exonic sequences would have uncovered only three of these TSAs. Other mutated TSAs resulted from out-of-frame exonic translation (n=2) or from noncoding sequences (n=7).  One group of TSAs (n=91) derived from aberrantly expressed unmutated genomic sequences, which were not expressed in normal tissues. These aberrantly expressed TSAs (aeTSAs) originated primarily from non-exonic sequences, in particular intronic (29%) and intergenic (22%) sequences. Their expression was regulated at the transcriptional level by variations in gene copy number and DNA methylation. Although mutated TSAs were unique to individual tumors, aeTSAs were shared by a large proportion of HGSCs. Taking into account the frequency of aeTSA expression and HLA allele frequencies, we calculated that, in Caucasians, the median number of aeTSAs per tumor would be five. We conclude that, in view of their number and the fact that they are shared by many tumors, aeTSAs may be the most attractive targets for HGSC immunotherapy.

overall_design: mRNA sequencing was performed on primary HGSC tumors or CD45-negative ascites fluid cells.

first: Qingchuan

last: Zhao


title: Cleft lip and cleft palate (CL/P) in Esrp1 KO mice is associated with alterations in Wnt signaling and epithelial-mesenchymal crosstalk

status: Public on Feb 07 2020

city: Los Angeles

first: Zijun

last: Zhang

state: CA

address: 650 Charles E. Young Drive South

institute: UCLA

summary: To investigate the molecular mechanisms that lead to CL/P in Esrp1-/- mice, we performed RNA-Seq using RNAs collected from both epithelial cells and mesenchymal cells from control and Esrp1-/- embryos. We used a previously described method to separate facial ectoderm and mesenchyme from facial prominences at E12.0, a stage at which lip fusion is underway (Li and Williams, 2013). We collected pooled paired ectoderm and mesenchyme samples to obtain sufficient material for four replicates each of ectoderm and mesenchyme fractions from WT and Esrp1-/- embryos and prepared total RNA for RNA-Seq. We used paired end sequencing and obtained deep coverage with an average of 100 million read pairs per replicate. Preliminary analysis of transcripts per million (TPM) values in the RNA-Seq analysis from epithelial and mesenchymal control samples validated that they were derived from relatively pure populations of each cell type using a panel of standard epithelial and mesenchymal cell type-specific markers, including Esrp1

overall_design: RNA-Seq analysis of transcriptomic changes in ectoderm and mesenchyme of the facial prominences at E12 in wild-type and Esrp1 KO mouse embryos.

first: Russ

last: Carstens


title: Neuronal, stromal and T-regulatory cell cross-talk in murine skeletal muscle

city: Boston

first: CBDM

last: Lab

state: MA

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

overall_design: Refer to individual Series


title: RNA-Sequencing of 3rd-instar Spodoptera frugiperda post-infection with Spodoptera frugiperda ascovirus-1a (SfAV-1a), the ascovirus type species.

status: Public on Feb 09 2020

city: Riverside

first: Heba

middle: A. H. M.

last: Zaghloul

address: 900 University Ave

department: Entomology

institute: University of California, Riverside

summary: Purpose: We analyzed the 3rd-instar Spodoptera frugiperda response after SfAV-1a infection. Specifically, we targeted three gene types in the infected host namely, mitochondrial, cytoskeleton and innate immunity genes.

overall_design: Method: We used a wild type strain of the Spodoptera frugiperda ascovirus-1a (SfAV-1a), the type species for the family Ascoviridae. This strain was used to infect 3rd-instar caterpillars of Spodoptera frugiperda, and all transcriptome data were derived from this developmental stage. For sequencing the HiSeq2500 Illumina sequencer and NextSeq500 were used (Noll Core Facility at the UC Riverside Institute for Integrative Genome Biology), in triplicates.

first: Robert

last: Hice

first: Dennis

last: Bideshi

first: Peter

last: Arensburger

first: Brian

last: Federici