title: Optical stimulation of the FGF signaling pathway is sufficient to maintain human pluripotent stem cells

city: Baltimore

first: Gabsang

last: Lee

state: MD

address: 733 North Broadway, Suite 747

department: Department of Neurology and Neuroscience

institute: Institute for Cell Engineering, Johns Hopkins University

summary: Stem cell fate is largely determined by a cell-signaling network and can be controlled by the supplementation of exogenous recombinant proteins; this, however, may cause heterogeneous and unsynchronized signaling due to the uneven distribution of recombinant proteins. Such issues are closely associated with the spontaneous differentiation of human pluripotent stem cells (hPSC), which lead to a continuing loss of pluripotency. We report a novel optical control system to maintain the cellular fate of hPSCs without the daily supplementation of recombinant Fibroblast Growth Factor 2 (FGF2) protein, a key molecule for their stemness. Using blue light illumination, we mimick the activation of the FGF signaling pathway in hPSCs carrying the large light-oxygen-voltage (LOV)-sensing domain, an algae-/plant-derived photo-activable protein. The optically maintained hPSCs have similar cellular and molecular profiles to those cultured with FGF2 protein and display differentiation capabilities into three germ layers. These data provide proof-of-concept that the optical control of signaling pathways can be applied to human stem cells.

overall_design: We established an optical control system to maintain the characterization of hPSCs with blue light illumination. It was possible to maintain the status of undifferentiation with typical stemness abilities. Furthermore, we used RNA-seq for the comparison of protein treatment and blue light illumination groups to observe gene expression profiles in triplicate.

first: Lee

last: Gabsang

first: Kim

last: Hyesoo

first: Choi

last: In Young


title: Comparative analysis of skeletal muscle transcriptional signatures associated with aerobic exercise capacity or response to training in humans and rats

status: Public on Aug 30 2020

city: Stockholm

first: Jorge

last: Ruas

address: Solnavägen 9

department: Department of Physiology and Pharmacology

country: Sweden

institute: Karolinska Institute

type: Expression profiling by high throughput sequencing

summary: In this study, we set out to dissect the intrinsic and response components of aerobic exercise at the transcriptional level in the skeletal muscle.

overall_design: We employed the selectively bred rat models for divergent intrinsic aerobic capacity, high-capacity runners (HCR) and low-capacity runners (LCR) and for the adaptational aerobic capacity, low response trainers (LRT) and high response trainers (HRT). Using RNA-sequencing, we mapped out the transcriptional profiles of high exercise capacity and high response in skeletal muscle. Lastly, we utilized these signatures to explore molecular mediators of high capacity and response in human volunteers before and after exercise training.

first: Yildiz

last: Kelahmetoglu

first: Igor

last: Cervenka

first: Paulo

last: Jannig


title: DNA mismatches reveal conformational penalties in protein-DNA recognition VI

status: Public on Aug 29 2020

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

country: USA

institute: Duke University

summary: Transcription factors (TF) recognize specific genomic sequences to regulate complex gene expression programs. Although it is well established that TFs bind specific DNA sequences using a combination of base readout and shape recognition, some fundamental aspects of protein-DNA binding remain poorly understood. Many DNA-binding proteins induce changes in the DNA structure outside the intrinsic B-DNA envelope. However, how the energetic cost associated with distorting DNA contributes to recognition has proven difficult to study because the distorted DNA exists in low-abundance in the unbound ensemble. Here, we use a novel high-throughput assay called SaMBA (Saturation Mismatch-Binding Assay) to investigate the role of DNA conformational penalties in TF-DNA recognition. In SaMBA, mismatches are introduced to pre-induce DNA structural distortions much larger than those induced by changes in Watson-Crick sequence. Strikingly, approximately 10% of mismatches increased TF binding, and at least one mismatch was found that increased the binding affinity for each of 22 examined TFs. Mismatches also converted non-specific sites into high-affinity sites, and high-affinity sites into super-sites stronger than any known canonical binding site. Determination of high-resolution X-ray structures, combined with NMR measurements and structural analyses revealed that many of the mismatches that increase binding induce distortions similar to those induced by protein binding, thus pre-paying some of the energetic cost to deform the DNA. Our work indicates that conformational penalties are a major determinant of protein-DNA recognition, and reveals mechanisms by which mismatches can recruit TFs and thus modulate replication and repair activities in the cell.

overall_design: Saturation mismatch-binding assays (SaMBA) were performed for 22 eukaryotic transcription factors. Briefly, the SaMBA assays involved binding of tagged transcription factors to double-stranded Agilent microarrays in order to determine their binding specificity for putative DNA binding sites as well as sites containing all possible DNA mismatches (or mispairs). Each sequence of interest was represented on the array in 8-20 replicate spots. We report the signal intensity for each spot.


title: Transcriptome analysis of the circadian clock gene BMAL1 deletion with opposite carcinogenic effects

city: Istanbul

first: seref

last: gul

address: Yalikoy Mh., Beykoz

department: Institute of Life Sciences and Biotechnology

country: Turkey

institute: Bezmialem Vakif University

summary: We have previously reported that the deletion of BMAL1 gene has opposite effects in respect to its contribution to the pathways that are effective in the multistage carcinogenesis process. BMAL1 deletion sensitized nearly-normal breast epithelial (MCF10A) and invasive breast cancer cells (MDA-MB-231) to cisplatin and doxorubicin-induced apoptosis while this deletion also aggravated the invasive potential of MDA-MB-231 cells. However, the mechanistic relationship of the seemingly opposite contribution of BMAL1 deletion to carcinogenesis process is not known at genome-wide level. In this study, an RNA-seq approach was taken to uncover the differentially expressed genes (DEGs) and pathways after treating BMAL1 knockout (KO) or wild-type (WT) MDA-MB-231 cells with cisplatin and doxorubicin to initiate apoptosis. Gene Set Enrichment Analysis with the DEGs demonstrated enrichment in multiple genes/pathways contribute to sensitization to cisplatin or doxorubicin-induced apoptosis in BMAL1-dependent manner. Additionally, our DEG analysis suggested that non-coding transcripts RNA (such as lncRNA and processed pseudogenes) may have role in cisplatin or doxorubicin-induced apoptosis. Protein-protein interaction network obtained from common DEGs in cisplatin and doxorubicin treatments revealed that GSK3b, NACC1 and EGFR are the principal genes regulating the response of the KO cells. Moreover, the analysis of DEGs among untreated BMAL1 KO and WT cells revealed that epithelial-mesenchymal transition genes are upregulated in KO cells. As a negative control, we have also analyzed the DEGs following treatment with an endoplasmic reticulum (ER) stress-inducing agent, tunicamycin which was affected by BMAL1 deletion minimally. Collectively, the present study suggests BMAL1 regulates many genes/pathways of which the alteration in BMAL1 KO cells may shed light on pleotropic phenotype observed.

overall_design: We performed global transcriptome analysis of wild type (WT) and BMAL1 knock-out MDA-MB-231 cells treated with cisplatin and doxorubicin which initiate the apoptosis. To uncover the effect of apoptosis inducing agents, differentially expressed genes and pathways analyses were done. Additionally effect of tunicamycin, endoplasmic reticulum (ER) stress-inducing agent, which is affected minimally by BMAL1 deletion was analyzed as a negative control.  Deep sequencing technique was utilized via  illumina HiSeq4000 platfrom in two biological replicates for each condition.

first: S

last: Gul

first: O

last: Ozcan

first: I

middle: H

last: Kavakli

first: H

last: Emisoglu Kulahli

last: Morgil

first: N

last: Ozturk


title: RNA-sequencing analysis identifies BRLF1-dependent viral and cellular transcriptome during EBV primary infection in B lymphoma cells

city: guangzhou

first: Ersheng

last: Kuang

address: No. 74, 2nd Yat-Sen Road Yuexiu District, Guangzhou City, Guangdong Province, 510080, PRC

country: China

institute: Sun Yat-Sen University

summary:
Purpose: Immediate-early protein BRLF1 plays an important role in lytic infection of Epstein-Barr virus (EBV), it activates lytic viral transcription and viral DNA replication, affects cell cycle and suppresses inflammatory responses. However, the understanding of BRLF1 influence on cellular gene expression during early lytic cycle remains limited.
Methods:RNA-sequencing analysis identified the differentially expressed genes (DEGs) in B lymphoma cells undergoing wild type and BRLF1-deficient EBV primary infection. The libraries were sequenced on an Illumina HiSeq-Xten platform and 150 bp paired‐end reads were generated. An average read depth of 12G reads per sample was collected and analyzed. Data analysis was performed with Molecule Annotation System 3.0.
Results: A total of 159 unigenes were annotated and the major differentially enriched pathways were related to DNA replication and transcription, immune and inflammatory response, cytokine-receptor interaction and chemokine signaling, ECM-receptor interaction and focal adhesion. Further the mass spectrometry identified the BRLF1-binding proteins and showed that BRLF1 employed different strategies to influence RNA polymerase II-dependent viral and cellular transcription, by binding to a particular RREs motif and binding to unique transcription factors which binding to specific motifs.
Conclusions: Our study characterized the BRLF1-dependent cellular and viral transcriptional profile during primary infection and then revealed the important virus-cell interaction and alterations of cell activity for EBV primary infection and lytic replication.

overall_design: deep RNA sequencing profiles of wild type and BRLF1-deficient EBV primary infected B lymphoma cells

first: Xubing

last: Long


title: DNA mismatches reveal conformational penalties in protein-DNA recognition V


title: Real-time quantitative PCR analysis of TruB1 KD HEK-293FTcells

city: Yushima, Bunkyo-ku, Tokyo

first: Ryota

last: Kurimoto

state: Tokyo

department: Systems BioMedicine

country: Japan

institute: Tokyo Medical and Dental University

summary: Total RNA was purified from HEK-293FT cells treated with siRNA for TruB1 or scramble.

overall_design: qPCR gene expression profiling.  TruB1 KD cells were used(siRNA).


title: Expression of PIK3CA WT and mutant colon cancer cells grown with (+ Gln)or without glutamine (-Gln)

status: Public on Aug 28 2020

city: Cleveland

first: Zhenghe

last: Wang

state: OH

address: 2103 Cornell Rd, WRB 3204

institute: Case Western Reserve Univeristy

summary: We used human gene expression microarray to interrogate how glutamine deprivation differentially impact gene expession in isogenic PIK3CA mutant and WT cells.

overall_design: Two isogenic PIK3CA cell line pairs: DLD1 PIK3CA mut (with the WT allele knockout), DLD1 PIK3CA WT (with the mutant allele knockout), HCT116 PIK3CA mut (with the WT allele knockout), HCT116 PIK3CA WT (with the mutant allele knockoout), with or without glutamine (Gln) for 24 hours and total RNA were extracted for microarray analyses.

middle: J


title: DNA mismatches reveal conformational penalties in protein-DNA recognition IV


title: DNA mismatches reveal conformational penalties in protein-DNA recognition III


title: Endogenous TruB1 bound tRNA and other noncoding RNAs in HEK293FT cells. [HITS-CLIP]

summary: Purpose: We aimed to identify the targets of the RNA binding protein TruB1 in HEK293FT cells.  Methods: Total RNA from endogenous-Flag KI cells were treated with UV light to crosslink RNA and proteins, then RNA-protein complexes were pulled down with anti-Flag. RNA was extracted and used to make cDNS libraries that were then sequenced by MiSeq 150bp single-end read (Sample1).  Results: Reads were trimmed to remove any adaptor sequence and barcodes before mapping reads to genome hg38 using Bowtie2.   Conclusions: We identified TruB1 binding sites in tRNAs and noncodingRNAs.

overall_design: Highthrough-put crosslinking and immunoprecipitation (HITS-CLIP) was performed on Flag-KI HEK 293FT cells.


title: Transcriptomic profiles of Pseudomonas aeruginosa PA14 grown in the presence or absence of mucins or mucin-glycans

city: Cambridge

first: Katharina

last: Ribbeck

state: Massachusetts

address: 21 Ames St

department: Biological Engineering

institute: Massachusetts Institute of Technology

summary: We use high-throughput sequencing to profile the response of the opportunistic mucosal pathogen Pseudomonas aeruginosa to mucins and mucin-glycans from the mucosal niche. We find that P. aeruginosa undergoes a genome-wide phenotypic shift in response to mucins and their attached glycans. Specifically, nearly all virulence pathways are downregulated in response to these host-produced factors. This study provides a framework for understanding how the host environment regulates bacterial function.

overall_design: Examination of differential gene expression in Pseudomonas aeruginosa in response to mucin and mucin sugars

first: Kelsey

last: Wheeler

first: Benjamin


title: Cis-acting lnc-eRNA SEELA1/2 in leukemia progression

city: Guangzhou

first: Wen-Tao

state: Guangdong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: sun yat sen university

summary: Long non-coding enhancer RNAs (lnc-eRNAs) are a subset of stable eRNAs identified from the annotated lncRNAs. They might serve as enhancer activity-related therapeutic targets in cancer; however, the epigenetic activation mechanisms and the function of lnc-eRNAs in cancer initiation and progression remain largely unknown.Here, by genome-wide screening we firstly identified a set of lncRNAs as lnc-eRNAs according to the epigenetic signatures of enhancers.To demonstrate the functional roles of lnc-eRNAs, two newly identified lnc-eRNAs, SEELA1 and SEELA2, were chosen for further studies.Further studies showed that SEELA1/2-SERINC2 axis regulated cancer metabolism, such as sphingolipid synthesis, to affect the leukemia progression.

overall_design: si-NC,si-SEELA1,and si-SERINC2 MV4;11 cells used

first: Yue-Qin

last: Chen

first: Ke

last: Fang

first: Wei

last: Huang


title: To determine the differentially expressed genes in cancer associated fibroblasts upon ablation of the glutamatergic synapse protein NetrinG1.

city: philadelphia

first: suraj

last: peri

state: PA

address: 333 cottman ave

department: biostatistics and bioinformatics

institute: Fox chase cancer center

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

overall_design: Refer to individual Series


title: Hyaluronan Control of the Primary Vascular Barrier during Early Mouse Pregnancy is Mediated by Uterine NK Cells

city: Rehovot

first: Ron

last: Hadas

address: 234 Herzl st.

department: Department of Biological Regulation

country: Israel

institute: Weizmann Institute of Science

summary: The goals of this study are to the investigate how uterine NK cells mediate the role of hyaluronan as a vascular morphogen following embryo implantation in mice

overall_design: Lentiviral mediatedy genetic modification of hyaluronan metabolism, specifically targeted to embryonic trophoblast cells followed by embryo transfer to pseudo-pregnant mice

first: Bareket

last: Dassa

first: Nava

last: Dekel

first: Michal

last: Neeman


title: Discrete and continuous heterogeneity in the basolateral amygdala

city: Vancouver

first: Mark

middle: Steven

last: Cembrowski

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

country: Canada

institute: University of British Columbia

summary: Basolateral excitatory neurons constitute a prominent output neuron class of the amygdala. Here, we examined diversity in this cell type using single-cell RNA-seq.

overall_design: Examination of basolateral amygdala excitatory neuron transcriptomes.


title: To determine the differentially expressed genes in cancer associated fibroblasts upon ablation of the glutamatergic synapse protein NetrinG1. [Microarray]

summary:
Cancer associated fibroblast mRNA profiles were generated from Control and NetrinG1 KO fibroblast lines, with controls done in duplicate and KOs in triplicate.
Comparing the mRNA profiles of CON and NetrinG1 KO CAFs, we observed a reversion of many pro-tumor genes and associated pathways upon ablation of NetrinG1 in CAFs.

overall_design: Loss of NetrinG1 in CAFs results in normalization of CAF gene signatures.

first: Edna

last: Cukierman

first: Ralph

last: Francescone


title: To determine the differentially expressed genes in cancer associated fibroblasts upon ablation of the glutamatergic synapse protein NetrinG1. [RNA-Seq]

summary:
Purpose: To determine the differentially expressed genes in cancer associated fibroblasts upon ablation of the glutamatergic synapse protein NetrinG1.
Methods: Cancer associated fibroblast mRNA profiles were generated from Control and NetrinG1 KO fibroblast lines, with controls done in duplicate and KOs in triplicate.
Results: Comparing the mRNA profiles of CON and NetrinG1 KO CAFs, we observed a reversion of many pro-tumor genes and associated pathways upon ablation of NetrinG1 in CAFs.
Conclusions: Loss of NetrinG1 in CAFs results in normalization of CAF gene signatures.


title: RNA-seq Analysis of Pancreatic Epithelium and Mesenchyme from Wild Type and Pbx-mutant Embryos

city: London

first: Francesca

middle: M.

last: Spagnoli

address: Great Maze Pond

department: CGTRM

country: United Kingdom

institute: King's College London

summary: The surrounding microenvironment plays a crucial role in pancreas formation and differentiation. Nevertheless, its cellular composition has not been analyzed in depth and whether different cell populations exist within the mesenchyme of the developing pancreas is an open question. Similarly, the molecular mechanisms by which the mesenchyme coordinates and integrates various signaling pathways to stimulate epithelial pancreatic progenitor proliferation and differentiation remain elusive.   Here, we investigate the cell composition and molecular network in the pancreatic mesenchyme, which promote pancreas differentiation. Whole transcriptome analysis and functional experiments showed that PBX in the mesenchyme promotes endocrine differentiation non-cell autonomously, acting at two different levels in the epithelial-mesenchymal crosstalk: 1) the maintenance of BM integrity and ECM and 2) regulation of soluble molecules, including guidance cues.  In conclusion, this study has identified distinct pancreatic mesenchymal niches and dissected their different roles during pancreatic development. This knowledge will be useful to improve current differentiation strategies based on ECM and soluble factors to generate β-cell equivalents from pluripotent cells for future cell replacement therapies of diabetes.

overall_design: We performed sequencing-based expression profiling (RNA-Seq) of pancreatic epithelial and mesenchymal cells isolated from wild type (WT) and Pbx mutant mice at embryonic day (E) 12.5 and E14.5

first: Corinna

last: Cozzitorto

first: Laura

middle: M

last: Müller

first: Nancy

last: Mah

first: Julia

last: Kofent

first: Maurizio

last: Risolino

first: Licia

last: Selleri


title: Expression data from mice lung CD45-negative cells during fibrosis development

city: Suita

first: Kiyoharu

last: Fukushima

state: Osaka

department: Host defense

institute: Osaka university

summary:
We used microarrays to detail the global gene expression change and identified distinct classes of up-regulated genes during fibrosis development in lung non-hematopoietic cells.
Close interaction between nonhematopoietic and hematopoietic cells are critical for fibrosis development.

overall_design: Total RNA was isolated from mouse lung CD45-negative cells 10 days after PBS or BLM inoculation using an RNA isolation kit and subjected to microarray analysis

first: Takashi

last: Satoh


title: Epigenetic drugs selectively target a population of AML cells which are positive for CD123 cell surface markers and are chemoresistant II

city: Gainesville

first: Yi

last: Qiu

state: FL

address: 2033 Mowry Rd

institute: University of Florida

summary: Gene expression profiling was performed on OCI-AML2 R50 drug resistant leukemia cell line before or after Romidepsin treatment.

overall_design: mRNA profiles of OCI-AML2 R50 cells with or without Romidepsin treatment

first: Bowen

last: Yan


title: Epigenetic drugs selectively target a population of AML cells which are positive for CD123 cell surface markers and are chemoresistant


title: Fluidigm single-cell RNA-seq analysis for gene signatures associated with T-cell persistence

city: Bethesda

first: Li

last: Jia

address: 10 Clinic center

institute: NCI/NIH

summary: A patient (4095) with metastatic colorectal cancer was treated with polyclonal tumor infiltrating lymphocytes (TILs) targeting the KRAS(G12D) hotspot mutation. Three dominant clonotypes  specifically recognizing KRAS(G12D) epitopes were identified, but we found that only two clonotypes persisted 40 days after TIL treatment. Because of these findings, in this study, we performed single-cell RNA-seq analysis for the TILs isolated from this patient. This single-cell dataset is generated using a Fluidigm C1 system, followed by a Illumina HiSeq2500 sequencer.

overall_design: Single-cell RNA-Seq analysis on tumor infiltrating lymphocytes (TILs)  was perform on a Fluidigm C1 instrument, followed by an Illumina HiSeq2500 sequencer.

first: Yong-Chen

last: Lu


title: YTHDF2 regulates maternal transcriptome degradation and embryo development in goat

status: Public on Aug 27 2020

city: Nanjing

first: Mingtian

last: Deng

state: Jiangsu

address: Weigang No.1

department: College of Animal Science and Technology

institute: Nanjing Agricultural University

summary: Little information is known regarding the maternal mRNA clearance and mechanisms behind it in farm animals. In the present study, we determined 3362 differentially expressed genes as the maternal mRNAs in goat using RNA-seq. We further reported that knockdown of YTHDF2 led to decreased blastocyst rate and impaired the maternal mRNAs clearance by downregulation of decapping enzymes DCP1A and DCP2, and the de-adenlyase CNOT1 and CNOT11.

overall_design: Analyze gene expression in oocyte and 4-and 8-cell stage embryos (3 replicates each) and compared transcriptome of YTHDF2 knockdown embryos with the WTs (2 replicates each)

first: BaoBao

last: Chen

first: Zifei

last: Liu

first: Feng

last: Wang


title: ChIP-seq profiling of pancreatic tumor cells

city: New York

first: Jinyang

last: Li

state: New York

address: 1230 York Ave

institute: The Rockefeller University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Compare epigentic features between WT and Kdm3a-KO tumor cells in two tumor cell lines (6419c5 and 6694c2) with two knockout tumor cell clones (KO1 and KO2). Although immunotherapy has revolutionized cancer care, patients with pancreatic ductal adenocarcinoma (PDA) rarely respond to these treatments, a failure that is attributed to poor infiltration and activation of T cells in the tumor microenvironment (TME). We performed an in vivo CRISPR screen and identified lysine demethylase 3A (KDM3A) as a potent epigenetic regulator of immunotherapy response in PDA. Mechanistically, KDM3A acts through Krueppel-like factor 5 (KLF5) and SMAD family member 4 (SMAD4) to regulate the expression of the epidermal growth factor receptor (EGFR). Ablation of KDM3A, KLF5, SMAD4, or EGFR in tumor cells altered the immune TME and sensitized tumors to combination immunotherapy, while treatment of established tumors with an EGFR inhibitor erlotinib prompted a dose-dependent increase in intratumoral T cells. This study defines an epigenetic-transcriptional mechanism by which tumor cells modulate their immune microenvironment and highlights the potential of EGFR inhibitors as immunotherapy sensitizers in PDA.

overall_design: ChIP-seq analysis of WT and Kdm3a-KO 6419c5 and 6694c2 mouse pancreatic tumor cells

first: Ben

last: Stanger


title: DNA methylome of Canis lupus dingo

city: Sydney

first: Ksenia

last: Skvortsova

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute

type: Methylation profiling by high throughput sequencing

summary: Using WGBS we investigated blood DNA methylation profiles of Canis lupus dingo and determined putative regulatory elements (unmethlated regions (UMRs) and lowly methylated regions (LMRs).

overall_design: Whole genome bisulphite sequencing of dingo's blood DNA

first: Ozren

last: Bogdanovic


title: The Antiviral Small-Interfering RNA Pathway Induces Zika Virus Resistance in Transgenic Aedes aegypti

status: Public on Aug 26 2020

city: Fort Collins

first: Ken

middle: E

last: Olson

state: CO

address: 3185 Rampart Road

department: Microbiology, Immunology, Pathology

institute: Colorado State University

type: Non-coding RNA profiling by high throughput sequencing

summary: We have generated transgenic Ae. aegypti that express a ZIKV-specific inverted repeat RNA intended to trigger the mosquito siRNA anti-viral immune pathway. To confirm that the transgene is expressed and processed, we performed small RNA sequencing on both Higgs White Eye (HWE) & anti-NS3/4A-ZIKV transgenic Ae. aegypti 24 hours post-bloodmeal

overall_design: small RNA profiling of 15 midguts from HWE & transgenic anti-NS3/4A-ZIKV Ae. aegypti 24 hours post-bloodmeal

first: Adeline

last: Williams

first: Irma

last: Sanchez-Vargas

first: Williams

middle: R

last: Reid

first: Jingyi

last: Lin

first: Alexander

middle: W

last: Franz


title: Ablation of S1PR4 triggers CD8+ T cell expansion to reduce tumor growth and improve therapy

city: Frankfurt

first: Andreas

last: Weigert

address: Theodor-Sern-Kai 7

department: Medicine

country: Germany

institute: Goethe-University

summary: We studied the role of S1PR4 on tumor progression using the PyMT mammary carcinoma mouse model and the AOM/DSS model for colitis-associated cancer. To gain insights of the underlying mechanism how S1PR4 ablation resulted in enhanced intratumoral CD8+ T cell abundance, we performed whole transcriptome profiling of total WT and S1PR4 KO colons subjected to the AOM/DSS model (day 84) as well as FACS-sorted CD8+ T cells from WT and S1PR4 KO tumors of PyMT mice. Next-generation mRNA sequencing, in triplicates, on a NextSeq 500 (PyMT CD8+ T cells) or a HiSeq 2000 (AOM/DSS model) high-throughput sequencer was used.

overall_design: mRNA profiles of total colons of WT and S1PR4 KO mice at day 84 of the AOM/DSS model and of FACS-sorted CD8+ T cells from WT and S1PR4 KO PyMT tumors at the experimental endpoint (when one tumor reached a diameter of about 1.5 cm) were generated in triplicates.

first: Catherine

last: Olesch


title: Epigenetic drugs selectively target a population of AML cells which are positive for CD123 cell surface markers and are chemoresistant I

first: Yi

last: Qiu

summary: Global gene expression profiling was performed on OCI-AML2 leukemia cell line, R3 and R50 drug resistant cell lines.

overall_design: mRNA profiles of OCI-AML2 cells and Ara-C resistant cell lines 3R and 50R

first: Bowen

last: Yan


title: Equal parental contribution to the transcriptome is not equal control of embryogenesis

city: Wuhan

first: Peng

last: Zhao

address: Luojia Hill

department: College of Life Sciences

institute: Wuhan University

summary: The goal of present study is to investigate parental contributions to the transcriptome of apical and basal cell lineages in early embryogenesis. We found equivalent parental genome derived reads in the transcriptome of apical and basal cell lineages of early proembryos. Hundreds of parent-of-origin genes were identified in both apical and basal cell lineages according to our allele- specific transcriptome data.

overall_design: To determine parental contributions to apical and basal cell lineages, the transcriptome of apical and basal cell lineages of early proembryos at 1-cell and 32-cell embryo stages derived from the crosses between the Col-0 and Ler were sequenced. To minimize the variance and avoid the influence of inherent allele-specific expression in the transcriptome, three independent biological replicates were performed for each hybrid cell type.

first: Mengxiang

last: Sun


title: IFN-I and CD8 T cells increase intestinal barrier permeability after chronic viral infection

city: La Jolla

first: Nicola

last: Allen

state: CA

address: 10010 N Torrey Pines Rd

department: Molecular Neurobiology

institute: Salk Institute for Biological Studies

summary: Intestinal barrier leakage constitutes a potential therapeutic target for many inflammatory diseases and represents a disease progression marker during chronic viral infections. The causes of altered gut barrier remain, however, mostly unknown. By using murine infection with lymphocytic choriomeningitis virus we demonstrated that, in contrast to an acute viral strain, a persistent viral isolate led to long-term viral replication in hematopoietic and mesenchymal, but not epithelial (IEC), cells in the intestine. Viral persistence drove sustained intestinal epithelial barrier leakage, which was characterized by increased paracellular flux of small molecules and was associated with enhanced colitis susceptibility. IFN-I signaling caused tight junction dysregulation in IEC, promoted gut microbiome shifts and enhanced intestinal CD8 T cell responses. Notably, both IFN-I receptor blockade and CD8 T cell depletion prevented infection-induced barrier leakage. Our study demonstrated that infection with a virus that persistently replicated in intestinal mucosa increased epithelial barrier permeability, and revealed IFN-I and CD8 T cells as causative factors of intestinal leakage during chronic infections.

overall_design: 6 to 10 week old C57BL/6 female mice were left uninfected or infected with 2x10^6 pfu of LCMV ARM or LCMV Cl13 intravenously. In a different set of experiments, mice were infected with 2x10^6 pfu of LCMV Cl13 and intraperitoneally injected with IFNAR neutralizing antibody (MAR1-5A3; BioXCell) or mouse IgG1 isotype control (MOPC-21; BioXcell) on days -1 and 0 p.i. (500 µg/mouse) as well as on days 2, 4 and 6 p.i. (250 µg/mouse) with Cl13. For both experimental set ups, intestinal epithelial cells (IEC) from the small intestine were obtained (from pools of 3 mice per group) after FACS sorting based on a CD45-EpCAM+ gate at day 9 post-infection. We performed 3 experimental repeats with uninfected, LCMV ARM-infected and LCMV Cl13-infected mice where the average IEC purity was 96.4%±4.4, and 2 experimental repeats with LCMV Cl13-infected mice treated with isotype or IFNAR neutralizing antibody where the average IEC purity was 96.5%±3.2. Total RNA was extracted from 50,000 IEC and downstream processing was performed by the UCSD Institute for Genomic Medicine. mRNA stranded libraries were constructed by using TruSeq RNA Library Prep Kit v2 (Illumina) followed by single-end sequencing of 75 base-pair fragments with a HiSeq 4000 (Illumina). Raw sequencing files were processed with CASAVA 1.8.2 (Illumina) to generate .fastq files.

first: Elina

middle: I

last: Zuniga


title: Genome-wide studies identify genes directly regulated by PML/RARα fusion protein

city: Shanghai

first: Yun

last: Tan

state: Shanghai

address: Room 1109, Building 11, 197 Ruijin Er Rd

department: Shanghai Institute of Hematology

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: Acute promyelocytic leukemia (APL) is characterized by a specific t(15;17) chromosome translocation that generates the promyelocytic leukemia/retinoic acid receptor-α (PML/RARα) fusion gene. However, the global association between PML/RARα and transcriptional co-regulators, and the rules of their association in governing the key processes during the leukemogenesis remain obscure. Here, we performed the genome-wide binding profiling of PML/RARα, HDAC1 and P300, in NB4, an APL patient-derived cell line. We found that PML/RARα targets could be classified into two classes. Moreover, we also performed ChIP-seq of H3K27ac to determine super-enhancers in NB4. We identified a novel function of PML/RARα in super-enhancer regulation during the leukemogenesis of APL.

overall_design: Genome-wide binding profiling of PML/RARa, HDAC1, P300 and H3K27ac in NB4 cells using ChIP-seq, and expression profiling of NB4 cells before and after PML/RARa knockdown using RNA-seq.

first: Kankan

last: Wang


title: RNA-seq for UV irradiated C. elegans

city: Cologne

first: Björn

last: Schumacher

address: Joseph-Stelzmann-Str. 26

institute: CECAD Research Center

summary: RNA-seq was applied for identifying the change of transcriptome 6h and 24h post UV irradiation.

overall_design: Examine the transcription of UV treated or mock treated L1 stage worms at 6h and 24h post-UV.

first: Siyao

first: David

last: Meyer

first: Bjoern


title: UV irradiated C. elegans

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

overall_design: Refer to individual Series


title: Loss of the nuclear protein RTF2 enhances influenza replication

city: Cambridge

first: Nir

last: Hacohen

state: MA

address: 415 Main St

institute: Broad Institute of MIT and Harvard

summary: While hundreds of genes are induced by Type I interferons, their roles in restricting the influenza life cycle remain mostly unknown. Using a loss-of-function CRISPR screen in cells pre-stimulated with Type I interferon, we identified a small number of factors required for restricting influenza A virus replication. In addition to the known components of the interferon signaling pathway, we found a new factor, Replication Termination Factor 2 (RTF2). RTF2 restricts influenza, at least, at the nuclear stage of the viral life cycle based on several lines of evidence. First, a deficiency in RTF2 leads to higher levels of viral primary transcription, even in the presence of cycloheximide to block genome replication and secondary transcription. Second, cells that lack RTF2 have enhanced activity of a viral reporter that depends solely on four viral proteins that carry out replication and transcription in the nucleus. Third, when RTF2 protein is mislocalized outside the nucleus, it is not able to restrict replication. Furthermore, the absence of RTF2 not only led to enhanced viral transcription but also to reduced expression of anti-viral factors in response to interferon. RTF2 thus inhibits primary influenza transcription, likely acts in the nucleus, and contributes to upregulation of antiviral effectors in response to Type I interferons

overall_design: 54 samples in total (18 different samples in triplicate). RNA was harvested from WT A549, RTF2-KO and RTF2-rescued cells that were mock-treated or pre-treated with 200U/ml IFNb for 24 hours, mock-infected or IAV-infected (PR8) at MOI 5 for 16 hours, or subjected to both treatments

first: Bing

middle: S

last: Chia

first: Ang

last: Cui

first: Thomas

last: Eisenhaure

last: Lieb


title: Type 2 diabetes risk gene Dusp8 regulates hypothalamic Jnk signaling and insulin sensitivity

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary: Recent genome-wide association studies (GWAS) identified DUSP8, a dual-specificity phosphatase targeting MAP kinases, as type 2 diabetes (T2D) risk gene. Here, we unravel Dusp8 as gatekeeper in the hypothalamic control of glucose homeostasis in mice and humans. Male but not female Dusp8 loss-of-function mice, either with global or CRH neuron-specific deletion, had impaired systemic glucose tolerance and insulin sensitivity when exposed to high-fat diet (HFD). Mechanistically, we found impaired hypothalamic-pituitary-adrenal (HPA) axis feedback, blunted sympathetic responsiveness, and chronically elevated corticosterone levels driven by hypothalamic hyperactivation of Jnk signaling. Accordingly, global Jnk1 ablation, AAV-mediated Dusp8 overexpression in the mediobasal hypothalamus, or metyrapone-induced chemical adrenalectomy rescued the impaired glucose homeostasis of obese male Dusp8 KO mice, respectively. The sex-specific role of murine Dusp8 in governing hypothalamic Jnk signaling, insulin sensitivity and systemic glucose tolerance was consistent with fMRI data in human volunteers that revealed an association of the DUSP8 rs2334499 risk variant with hypothalamic insulin resistance in men. Further, expression of DUSP8 was increased in the infundibular nucleus of T2D humans. In summary, our findings suggest the GWAS-identified gene Dusp8 as novel hypothalamic factor that plays a functional role in the etiology of T2D.

overall_design: Transcriptomics of arcuate nucleus tissue from high-fat diet-fed Dusp8-deficient mice and control animals

first: Sonja

middle: C

last: Schriever

first: Dhiraj

middle: G

last: Kabra

first: Katrin

last: Pfuhlmann

first: Hamimatunnisa

last: Johar

first: Joachim

last: Nagler

first: Luke

last: Harrison

first: Peter

last: Baumann

first: Chun-Xia

last: Yi

first: Martin

last: Irmler

first: Julien

last: Castel

first: Moya

last: Wu

first: Ruchi

last: Jain

first: Hannah

last: Schug

first: Stephanie

last: Kullmann

first: Hans-Ulrich

last: Häring

first: Timo

last: Müller

first: Kerstin

last: Stemmer

first: Jan

last: Rozman

first: Ruben

last: Nogueiras

first: Karl-Werner

last: Schramm

first: Christian

last: Gieger

first: Harald

last: Grallert

first: Mathias

last: Schmidt

first: Serge

last: Luquet

first: Karl-Heinz

last: Ladwig

last: Heni

first: Matthias

last: Tschöp

first: Paul

middle: T

last: Pfluger


title: Genome-epigenome interactions associated with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome

status: Public on Aug 25 2020

city: Toronto

first: Patrick

last: McGowan

state: Ontario

address: 1265 Military Trail

department: Biological Sciences

institute: University of Toronto Scarborough

summary: Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a complex disease of unknown etiology. Multiple studies point to disruptions in immune functioning in ME/CFS patients as well as specific genetic polymorphisms and alterations of the DNA methylome in lymphocytes. However, potential interactions between DNA methylation and genetic background in relation to ME/CFS have not been examined. In this study we explored this association by characterizing the epigenetic (~480 thousand CpG loci) and genetic (~4.3 million SNPs) variation between cohorts of ME/CFS patients and healthy controls. We found significant associations of DNA methylation states in T-lymphocytes at several CpG loci and regions with ME/CFS phenotype. These methylation anomalies are in close proximity to genes involved with immune function and cellular metabolism. Finally, we found significant correlations of genotypes with methylation modifications associated with ME/CFS. The findings from this study highlight the role of epigenetic and genetic interactions in complex diseases, and suggest several genetic and epigenetic elements potentially involved in the mechanisms of disease in ME/CFS.

overall_design: DNA methylation was assessed for 109 samples using the Illumina Infinium Human Methylation 450K Beadchip Array

first: Santiago

last: Herrera

first: Suzanne

middle: D

last: Vernon

middle: O


title: RNA sequencing of Octopus bimaculoides bulk tissues

first: Lena

last: van Giesen

address: 16 Divinity Avenue

department: MCB

institute: Harvard University

summary: We performed paired end Illumina Hiseq on bulk tissues of Octopus bimaculoides sensory tissues, Libaries were sequenced on two different Lanes

overall_design:
Tissues from octopus sensory organs and control tissues were collected and used for RNA sequencing
Trinity_obim_assembly.fa was used for protein sequence confirmation.

first: Nicholas

last: Bellono


title: ChIP-seq for UV-irradiated C. elegans

first: Björn

last: Schumacher

summary: ChIP-seq was applied for identifying the deposition of H3K4me2 on genome of UV-treated C. elegans. C.elegans larvae are sensitive to UV treatment, and it may due to the deposition of various histone modification during DNA damage response (DDR). In our study, we identified one of the histone marks, H3K4me2, as a positive regulator of DDR related transcription. This ChIP-seq experiment was used to identify the genes that have H3K4me2 deposition.

overall_design: Examine the H3K4me2 and its control H3 deposition in UV-treated or mock-treated L1 worms.

first: Siyao

last: Wang

first: David

last: Meyer

first: Bjoern


title: A single cell atlas of the human proximal epididymis reveals cell-type specific functions and distinct roles for CFTR

city: Cleveland

first: Ann

last: Harris

address: 10900 Euclid Ave

institute: Case Western Reserve Uni

summary: Spermatozoa released from the testis are unable to fertilize an egg without a coordinated process of maturation in the lumen of the epididymis.  Relatively little is known about the molecular events that integrate this critical progression along the male genital ducts in man. Here we use single cell RNA-sequencing to construct an atlas of the human proximal epididymis. We find that the cystic fibrosis transmembrane conductance regulator (CFTR), which is pivotal in normal epididymis fluid transport, is most abundant in surface epithelial cells in the efferent ducts and in rare clear cells in the caput epididymis, suggesting region-specific functional properties. We reveal transcriptional signatures for multiple cell clusters, which identify the individual roles of principal, apical, narrow, basal, clear, halo and stromal cells in the epididymis. A marked cell-type-specific distribution of function is seen along the duct with local specialization of individual cell types integrating processes of sperm maturation.

overall_design: using single-cell RNA sequencing to map cell-type-specific gene expression in the HEE tissues

first: Shih-Hsing

last: Leir

first: Shiyi

last: Yin

first: Jenny

middle: L

last: Kerschner


title: RNA squencing of human NK cells activated with IL-15 or IL-12, IL-15, and IL-18

city: Saint Louis

first: Todd

last: Fehniger

state: Missouri

address: 660 South Euclid Avenue, Campus Box 8007

institute: Washington University School of Medicine

summary: NK cells are an emerging cancer cellular therapy and potent mediators of anti-tumor immunity.  Cytokine-induced memory-like (ML) NK cellular therapy is safe and induces remissions in acute myeloid leukemia (AML) patients. However, the dynamic molecular changes that occur after memory-like differentiation in vitro are unclear. Here, control or ML NK cells purified from normal donor PBMC were generated in vitro. Briefly, RosetteSep-purified NK cells were incubated in IL-12, IL-15, and IL-18, or low-dose IL-15 as a control for 16-18 hours. Control or cytokine-activated NK cells were washed three times and cultured for 6 days in low-dose IL-15, which is required for NK cell survival. After 6 days, RNA was isolated from control and memory-like (ML) NK cells (IL12/15/18 activation) and RNA-sequencing performed. Because the transcription factor GATA-3 was increased specifically in ML NK cells, we hypothesized ML NK cells would exhibit a GATA-3 gene signature compared to control NK cells. Indeed, using GSEA, a significant gene signature was associated with ML NK cell differentiation. These data support the role for GATA-3 in regulating the ML NK cell molecular program.

overall_design: NK cells were isolated from 3 distinct human donors (CD56+ CD3-), incubated with low-dose IL-15 (1 ng/mL) or IL-12, IL-15, and IL-18 (IL-12 - 10ng/mL, IL-15 - 50 ng/mL, IL-18 50ng/mL) for 16 hours, washed, and cultured in 1ng/mL IL-15  for 6 days before isolation for sequencing analysis

middle: A


title: CRISPR repair in a preclinical model of Noonan syndrome associated cardiomyopathy I

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: We profiled RNA expression in human iPSC-derived cardiomyocytes from patients with LZTR1-associated Noonan syndrome

overall_design: 8 biological replicates of human iPSC-derived ventricular cardiomyocytes from 2 Noonan syndrome patients and 5 biological replicates of iPSC-derived ventricular cardiomyocytes from 3 healthy controls

first: Lukas

last: Cyganek


title: Inhibiting DDX3X triggers tumor-intrinsic type I interferon response and enhances anti-tumor immunity

status: Public on Sep 03 2020

city: Washington

first: Hyeongjwa

last: Choi

state: DC

address: 3970 Reservoir Road NW

department: Oncology

institute: Georgetown University

summary: Accumulating evidence has shown that cellular double-stranded RNAs (dsRNAs) induce antiviral innate immune responses in human normal and malignant cancer cells. However, it is not fully understood how endogenous ‘self’ dsRNA homeostasis is regulated in the cell. Here, we show that an RNA-binding protein, DEAD-box RNA helicase 3X (DDX3X), prevents the aberrant accumulation of cellular dsRNAs. Loss of DDX3X induces dsRNA sensor-mediated type I interferon signaling and innate immune response in breast cancer cells due to abnormal cytoplasmic accumulation of dsRNAs. Dual depletion of DDX3X and a dsRNA-editing protein, ADAR1 synergistically activates the cytosolic dsRNA pathway in breast cancer cell. Moreover, inhibiting DDX3X enhances the antitumor activity by increasing tumor intrinsic-type I interferon response, antigen presentation, and tumor-infiltration of cytotoxic T cells as well as dendritic cells in breast tumors, which may lead to the development of breast cancer therapy by targeting DDX3X in combination with immune checkpoint blockade. To assess the impact of DDX3X on the gene expression in the breast cancer, we stably depleted DDX3X in breast cancer MCF7 cells using a short hairpin RNA (shRNA)-mediated knockdown, and performed a genome-wide transcriptome analysis using a next-generation RNA deep sequencing.

overall_design: The analyses were perfomed on 4 samples of DDX3X-control (shNS) and 5 samples of DDX3X-knockdonwn (shDDX3X) MCF7 cells. Total RNA from cells was extracted and sequenced by the SOLiD sequencing with pair-ended whole transcriptome sequencing.

first: Cecil

last: Han

first: Juntae

last: Kwon


title: DNA Methylation Patterns of Chronic Explosive Breaching in U.S. Military Warfighters

status: Public on Aug 24 2020

first: Fatemeh

last: Haghighi

state: NY

address: 1425 Madison Ave, 9-20D

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

type: Methylation profiling by genome tiling array

summary: Epigenetic profiles in peripheral blood samples from 59 subjects (in two separate U.S. Military training sessions) were screened using Illumina Infinium MethylationEPIC BeadChips, session 2 (31 subjects) were also screened post-exposure to a controlled, low-level blast during a 3-day explosive breaching course. Participants had varying numbers of exposures to blast over their military careers (empirically defined as high ≥ 40, and conversely, low < 39 breaching exposures) at baseline. Daily self-reported physiological symptoms were recorded.

overall_design: Genomic DNA from 59 subjects (28 with only pre-blast exposure sample, 31 with both pre- and post- blast exposure samples) was bisulfite converted and CpG methylation determined using Illumina Infinium MethylationEPIC BeadChip microarrays

first: Zhaoyu


title: Blast-related mild TBI alters anxiety-like behavior and transcriptional signatures in the rat amygdala

summary: Male Long Evans rats aging 10-12 weeks were exposed to repeated blast overpressure and then went through behavioral tests for anxiety and fear conditioning. After 1-1.5 months (sub-acute) or 12-13 months (chronic), amygdala tissue specimens from all animals were collected. RNA-seq was used to measure transcriptome-wide gene expression of sham and blast animals at different timepoints. The study identified changes in the amygdalar transcriptome and associated anxiety-related phenotypic outcomes related to both blast exposure and aging, which may play a role in the long-term pathological consequences of mTBI.

overall_design: RNA-seq profiling of sham and blast-exposed rats at different time points distal to blast injury.

first: Jennifer

last: Blaze


title: IGF2BP1 is a targetable SRC/MAPK-dependent driver of invasive growth in ovarian cancer

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

institute: Martin Luther University Halle-Wittenberg

summary: We identified IGF2BP1 as a marker of the C5 molecular subtype of high-grade ovarian carcinoma (HG-SOC). IGF2BP1 promotes SRC activity and ERK2 expression enhancing the tolerance towards SRC- and MEK-directed inhibitors saracatinib and selumetib. Combination treatment overcomes IGF2BP1-promoted resistance.

overall_design: PolyA-RNA sequencing of tumor samples was performed to investigate correlation of IGF2BP1 to molecular signatures and identify the molecular subtypes of the respective tumor samples.

first: Nadine

last: Bley

first: Annekatrin

last: Schott

first: Simon

last: Müller

first: Marcell

last: Lederer

first: Tommy

last: Fuchs

first: Chris

last: Aßmann

first: Markus

last: Glaß

first: Christian

last: Ihling

first: Andrea

last: Sinz

first: Nikolaos

last: Pazaitis

first: Claudia

last: Wickenhauser

first: Martina

last: Vetter

first: Olga

last: Ungurs

first: Hans-Georg

last: Strauss

first: Christoph

last: Thomssen

first: Stefan

last: Hüttelmaier


title: Early programming of CD8+ T cell response by the orphan nuclear receptor NR4A3

city: Montreal

first: Nathalie

last: Labrecque

state: QC

address: 5415, boul. de l’Assomption Montréal (Québec)

department: Microbiology and Immunology

institute: Université de Montréal


title: Early programming of CD8+ T cell response by the orphan nuclear receptor NR4A3 [RNA-Seq]

summary: We analysed the transcriptomic gene signature of day 3 CD8+ T cell effectors in the absence of NR4A3 to determine the impact of this transcription factor on early transcriptomic programming of CD8 T cell memory and function

overall_design: We compared the transcriptome of Nr4a3 deficient and sufficient CD8+ T (OT-I) cells effectors at day 3 post Listeria monocytogenes infection (strain that express OVA peptide). These effectors were generated by an adoptive transfer of Nr4a3 deficient or sufficient OT-I (CD8 CD45.2+) into a congenic B6.SJL (CD45.1+) that was then infected with a sublethal dose of  Lm-OVA. The viable activated (CD44hi) cells were sorted directly in TRIzol reagent and used for RNA extraction.

first: Livia

last: Odagiu


title: AGO2 mutations impair RNA interference and human neurological development

city: Potsdam

first: Alexander

last: Bartholomaeus

address: Telegrafenberg C

department: Department 3 Geochemie

institute: Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences

summary: Argonaute-2 forms together with associated miRNAs the RNA induced silencing complex (RISC), which recognizes target mRNAs for translational silencing and degradation. Here, we identified thirteen heterozygous mutations in AGO2 in a cohort of 20 patients affected by mild to severe neurodevelopmental disorder. Each of the identified single amino acid mutations results in impaired shRNA-mediated silencing. Through biochemical and molecular dynamic analyses, we uncovered two mutation-specific functional consequences: one mutation (p.G733R) induces a loss-of-function, whereas the other exchanges lead to increased binding of AGO2 to mRNA targets. The latter is supported by decreased phosphorylation of a C-terminal cluster of serine residues known to be involved in mRNA target release, and by the increased formation of dendritic P-bodies in neurons. Our data highlight the complexity underlying AGO2 function, and underline the importance of tight gene expression regulation through the dynamic AGO2-RNA association for neuronal development.

overall_design: RNA sequencing and gene expression analysis of primary fibroblasts

first: Davor

last: Lessel

last: Bartholomäus

first: Zoya

last: Ignatova

first: Hans-Jürgen

last: Kreienkamp


title: Early programming of CD8+ T cell response by the orphan nuclear receptor NR4A3 [ATAC-Seq]

summary: We analysed the chromatin opening and accessibillity of transcription factor binding motifs of in vitro activated OT-I CD8+ T cells in the absence of NR4A3 to determine the early impact of NR4A3 in CD8 T cell differentiation

overall_design: We isolated naive OT-I CD8+ T cells and stimulated them in vitro for 12h with anti-CD3 and anti-CD28 antibodies. Immediately we isolated the nuclei of stimulated cells and did the tagmentation assay, the isolation of DNA, it's amplification and paired-end sequencing


title: Effects of TRP53 upregulation by nutlin 3a on the transcriptome of interstitial cell of Cajal (ICC) stem cells

city: Rochester

first: Tamas

last: Ordog

state: MN

address: 200 1st St SW

institute: Mayo Clinic

summary: Interstitial cells of Cajal (ICC) are electrical pacemakers and mediators of neuromuscular neurotransmission in the gastrointestinal tract. Studies in organotypic cultures of intact gastric muscular wall tissues identified Kit(low)Cd44(+)Cd34(+)Insr(+)Igf1r(+) cells as local ICC progenitors (Lorincz et al., Gastroenterology 2008;134:1083-1093). Subsequently, conditionally immortalized Kit(low)Cd34(+) cells were isolated by immunomagnetic and fluorescent cell sorting and serial cloning from the gastric muscular wall of homozygous, 14-day-old H-2Kb-tsA58 and 7-day-old wild-type C57BL/6J mice and shown to share other phenotypic characteristics with in-situ ICC precursors (Bardsley et al., Gastroenterology 2010;139:942-952). ICC and their precursors undergo age-related depletion in mice and humans. These changes are associated with increased protein levels for transformation-related protein 53 (TRP53). This study utilized total RNA-sequencing to investigate the effects of TRP53 upregulation by nutlin 3a treatment (control: nutlin 3b) on the transcriptome of the ICC precursor line D2211B maintained in the verified absence of the SV40 tsA58 large T antigen.

overall_design: Libraries were made from total RNA isolated from the ICC progenitor cell line D2211B treated with nutlin 3a or nutlin 3b (30 μM for 72 h) using the TruSeq Stranded Total RNA Sample Prep Kit (Illumina, San Diego, CA) and sequenced on Illumina HiSeq 4000 platform.

first: Yujiro

last: Hayashi

first: Pritha

last: Chanana


title: Evolution of the histone variant H2A.W reconstituted in fission yeast [RNA-seq]

status: Public on Aug 23 2020

city: Tübingen

first: Michael

last: Borg

address: Max Planck Ring 5

department: Algal Development & Evolution

institute: Max Planck Insititue for Biology

summary: Diversification of histone variants is marked by the acquisition of distinct motifs and features through convergent evolution. H2A variants tend to be associated with defined domains of the genome. Specific features distinguish H2A variants in eukaryotes but whether evolution of these features predated the evolution of deposition mechanisms or vice-versa has remained unclear.In flowering plants, the variant H2A.W is tightly associated with heterochromatin. H2A.W evolved in land plants through acquisition of an extended C-terminal tail enriched with basic residues and a KSPK motif. Here, we used a synthetic approach in fission yeast, which lacks H2A.W and its dedicated deposition mechanism, to recapitulate the evolutionary steps that led to H2A.W and to assess the impact of the KSPK motif on heterochromatin composition and its properties. In conclusion, the acquisition of the KSPK motif in yeast promotes chromatin properties that are comparable to the properties and function of H2A.W in plant heterochromatin. Hence, the KSPK motif could have been selected before the evolution of direct heterochromatin deposition mechanisms. We propose that the acquisition of functional histone variant motifs can confer properties which affect only specific chromatin states, thereby driving the evolution of specific deposition mechanisms.

overall_design: Gene expression profiling of WT and spH2A.W

first: Bingkun

last: Lei

first: Malgorzata

last: Goizer


title: RNA sequencing of small non-coding RNAs in murine subcutaneous adipose tissue

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: Mice overexpressing a kinase dead AMPKa2 subunit or control were exercised 6.5 weeks and sacrifised 24 hours after last exercise bout. Total RNA from subcutaneous adipose tissue were isolated and small RNAs were purifed from this.

overall_design: The effect of training on miRNA expression in subcutaneous adipose tissue

first: Jonas

last: Treebak

first: Søren

last: Madsen


title: Age-Associated Epigenetic Change in Chimpanzees and Humans

city: Durham

first: Elaine

last: Guevara

state: North Carolina

address: 130 Science Drive

department: Evolutionary Anthropology

institute: Duke University

summary:
Genome wide DNA methylation profiling of captive chimpanzees of ages spanning the chimpanzee lifespan (whole blood)
Methylation levels have been shown to change with age at sites across the human genome. Change at some of these sites is so consistent across individuals that it can be used as an “epigenetic clock” to predict an individual’s chronological age within a few years. Studies of age-related epigenetic change in other mammals, including mice, whales, and canids, show that some but not all of the same loci as in humans undergo age-associated methylation changes. An in-depth comparison of chimpanzees with humans is of interest because the two species are genetically similar but differ in lifespan. To this end, we profiled genome-wide blood methylation levels for 113 samples from 83 chimpanzees aged 1-58 years (26 chimpanzees were sampled at multiple ages during their lifespan). We used this data to build a chimpanzee-specific epigenetic clock model as well as to compare genome-wide patterns of change with age between humans and chimpanzees more generally.

overall_design:
Bisulfite convrted DNA for 113 individuals was profiled by the Illumina Infinium EPIC array

Please note that all the human data was previously published by others and accessioned to GEO (Accession numbers: GSE40279, GSE87571, GSE56105).

first: Guevara

last: Elaine


title: Roles of hsa-miR-12462 and SLC9A1 in acute myeloid leukemia

status: Public on Aug 22 2020

city: Changsha

first: Sia

last: Jiang

address: Xiangya Street

institute: Central South University

summary: In this study, we defined a novel miRNA, hsa-miR-12462, through small RNA sequencing of the bone marrow (BM) cells from 128 newly diagnosed subjects with AML

overall_design: Small  RNA Sequencing of AML-RR and AML-CR

first: Hui

last: Zeng

last: Liang

first: Wei

last: Liu


title: The Brazilian Initiative on Precision Medicine (BIPMed)

city: Campinas

first: Cristiane

middle: de Souza

last: Rocha

state: São Paulo

address: Av Tessália Vieira de Camargo, 126 Cidade Universitária "Zeferino Vaz"

department: Medical Genetics

country: Brazil

institute: Unicamp

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: The development of precision medicine strategies requires prior knowledge of the genetic background of the target population. However, despite the availability of data from admixed Americans within large reference population databases, we cannot use these data as a surrogate for that of the Brazilian population. This lack of transferability is mainly due to differences between ancestry proportions of Brazilian and other admixed American populations. To address the issue, a coalition of research centres created the Brazilian Initiative on Precision Medicine (BIPMed), an initiative of five Research Innovation and Dissemination Centers (RIDCs) supported by FAPESP.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples from 340 reference individual.
The Brazilian Research Institute for Neuroscience and Neurotechnology (BRAINN), Center for Computational Science and Engineering (CCES), Center for Research in Cell Therapy (CTC), Center for Research on Inflammatory Diseases (CRID), Obesity and Comorbidities Research Center (OCRC)

first: C

first: R

last: Secolin

first: M

last: Rodrigues

first: B

last: Carvalho

first: I

last: Lopes-Cendes


title: Targeting Piezo1 Unleashes Innate Immunity Against Cancer and Infectious Disease

status: Public on Aug 21 2020

city: New York City

first: Alireza

last: Khodadadi-Jamayran

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: Piezo1 is a mechanosensitive ion channel that has gained recognition for its role in regulating diverse physiological processes. However, the influence of Piezo1 in inflammatory disease, including infection and tumor-immunity, is not well-studied. We postulated that Piezo1 links physical forces to immune regulation in myeloid cells. We discovered signal transduction via Piezo1 in myeloid cells and established this channel as the primary sensor of mechanical stress in these cells. Global inhibition of Piezo1 was protective against both cancer and septic shock and resulted in a diminution in suppressive myeloid cells. Moreover, deletion of Piezo1 in myeloid cells protected against cancer and increased survival in poly-microbial sepsis. Mechanistically, we show that mechanical stimulation promotes Piezo1-dependent myeloid cell expansion by suppressing Rb. We further show Piezo1-mediated silencing of Rb is regulated via upregulation of HDAC2. Collectively, our work uncovers Piezo1 as a targetable immune checkpoint that drives immune-suppressive myelopoiesis in cancer and infectious disease.

overall_design: For single cell Seq and ChIP-Seq experiments, mouse Piezo1f/f;LyzMCre and Piezo1f/f bone marrow cells were negatively enriched for CD3-CD19-Ter119- cells using FACS-sorting.

first: Berk

last: Aykut

first: George

last: Miller


title: Evolution of the histone variant H2A.W reconstituted in fission yeast [ChIP-seq]

first: Michael

last: Borg

overall_design: Genome-wide maps of H2A, H2A.Z and H3K9me2 in WT,spH2A.W and spH2A.W.4A  yeast strains

first: Bingkun

last: Lei

first: Malgorzata

last: Goizer


title: Evolution of the histone variant H2A.W reconstituted in fission yeast [ATAC-seq]

overall_design: Genome-wide maps of chromatin accessibility in WT, spH2A.W and spH2A.W.4A yeast strains


title: Effect of the acute and chronic administration of Lupinus albus β-conglutin on glycaemia, circulating cholesterol, and liver gene expression profile

city: Guadalajara

first: Carmen

middle: Magdalena

last: Gurrola-Díaz

state: Jalisco

address: Sierra Mojada 950

department: Departamento de Biología Molecular y Genómica

country: Mexico

institute: Universidad de Guadalajara

summary: Constituents of lupin seeds, like γ-conglutin and lupanine, have gained attention as potential complementary treatments for the management of dysglycaemia. Notwithstanding, the effect of other lupin components on carbohydrate metabolism, including β-conglutin protein, has received little attention. Here, we investigated the influence of the acute and chronic administration of β-conglutin on glycaemia modulation in normal and streptozotocin induced-to-diabetes rats. To identify potential molecular targets and pathways involved in this biological response, we analysed the liver transcriptome modulation exerted by β-conglutin in diabetes-induced rats using DNA microarrays. The acute administration of β-conglutin reduced the incremental area under the curve of glycaemia in normal and diabetes-induced animals. In a seven-day study with diabetic animals, glycaemia increased significantly in non-treated animals but remained unchanged in animals treated with a daily dose of β-conglutin. Noteworthy, total cholesterol was significantly lower at the end of the experimental period (−21.8%, p = 0.039). Results of the microarray test and gene ontology analyses revealed several targets and pathways modulated after β-conglutin treatment, including a down-regulation of Jun kinase activity. Moreover, our data indicate that targets related to oxidative stress, inflammation, and estrogenic activity might orchestrate these metabolic effects. In conclusion, our findings show that β-conglutin may be useful to manage postprandial glycaemia and reduce cholesterol levels under the dysglycaemia stage. We identified and proposed new potential molecular targets for further research related to the mechanism of action of β-conglutin.

overall_design: A two-color microarray experiment was performed. We separately pooled equal amounts of high-quality RNA from diabetic rats of the treated (with β-conglutin, n = 6) and non-treated (without β-conglutin, n = 6) groups before carrying out the cDNA synthesis and hybridization.

first: Tereso

middle: J

last: Guzmán

first: Alma

last: Martínez-Ayala

first: Pedro

last: García-López

first: Irma

last: Soto-Luna


title: Gene expression profiling of MDA_MB_231 cell line in response to treatment with Dexamethasone and SH4-54

city: Salt Lake City

first: Katherine

last: Varley

state: UT

address: 2000 Cir of Hope Dr.

department: Oncological Sciences

institute: University of Utah

summary: To determine how the transcription factors GR and STAT3 cooperate to regulate gene expression, the MDA-MB-231 breast cancer cell line was treated with dexamethasone (1µM for 24 hours) and the STAT3 inhibitor SH4-54 (8µM for 24 hours) alone and in combination. A multivariate linear model with a GR:STAT3 interaction term was used to identify genes that are differentially expressed when both TFs are fully active in the nucleus.

overall_design: MDA-MB-231 cells were plated in 6-well plates at ~300,000 cells in 4ml of media per well and grown for 24 hours. Three replicates wells were treated for 24 hours with 1µM of Dexamethasone (DEX), 8µM SH4-54, no treatment, or a combination of DEX and SH4-54. The cells were lysed using Qiagen RLT buffer and 1% BME.

first: Megan

last: Conway


title: Genome wide mRNA sequencing of induced pluripotent stem cell (iPSC) diffrentiated neural stem cells (NSCs).

city: McAllen

first: Satish

last: Kumar

state: Texas

address: 5300 North L Street (MBMRF-2.219)

department: Division of Human Genetics & South Texas Diabetes and Obesity Institute, UTRGV School of Medicine

institute: University of Texas Rio Grande Valley

summary: The NSC differentiation of six validated iPSC lines were induced using commercially available PSC neural induction medium and following manufacturer method with minor modifications (Gibco). An extensive characterization of generated NSCs on day 14 (at passage P1) was performed using immunocytochemistry (ICC) analysis of the NSC specific markers and by genome wide mRNA sequencing. The iPSC differentiated NSCs expressed NSC specific markers Nestin, PAX6, SOX1 and SOX2 across all six samples. The average correlation coefficient at 95% CI between 6 NSC samples, calculated based on all expressed mRNAs, was 0.97 ± 0.008 suggesting a uniform differentiation of generated NSC lines. The generated NSC showed high expression of neuroepithelial genes/transcription factors (NES, SOX2, SOX1, PAX6, NOTCH1, MSI1,and CHD2) and genes/transcription factors of dorsal tube neuroepithelium (PAX3, GDF7, SOX9 and SNAI2) but lacked the expression of ventral tube neuroepithelial markers (NKX2-2, FOXA2 and SHH) suggesting a dorsal tube neuroepithelial transcriptomic and functional profile of the generated NSCs. A differential gene expression analysis of iPSC’s and NSC’s expressed transcription identified 4,033 mRNAs that were significantly differentially expressed (DE) between iPSCs and differentiated NSCs. The 2,006 DE mRNA were significantly upregulated in differentiated NSCs and were highly enriched in developmental functional categories such as embryonic development (572 mRNAs; FDR adjusted p-value range: 1.92x10-53 – 3.26x10-9), organism development (749 mRNAs; FDR adjusted p-value range: 1.92x10-53 – 4.30x10-9), nervous system development and function (629 mRNAs; FDR adjusted p-value range: 3.23x10-48 – 4.15x10-9), tissue development (655 mRNAs; FDR adjusted p-value range: 3.63x10-40 – 4.32x10-9) and organ development (406 mRNAs; FDR adjusted p-value range: 8.74x10-40 – 2.37x10-9).

overall_design: To better understand the functional profile and disease modeling potential of iPSC generated NSCs. A genome wide mRNA sequencing analysis of iPSC generated NSCs was performed.

first: Joanne

last: Curran

first: John

last: Blangero


title: Suppression of DDX39B sensitizes ovarian cancer cells to DNA-damaging chemotherapeutic agents via destabilizing BRCA1 mRNA

city: Beijing

first: Zelin

last: Liu

state: --- Select a state ---

address: 38 Xueyuan Road

institute: Peking University Health Science Center

summary: Multiple RNA processing events including transcription, mRNA splicing and export are delicately coordinated by the TREX complex. As one of the essential subunits, DDX39B couples the splicing and export machineries by recruiting ALYREF onto mRNA. In this study, we further explore the functions of DDX39B in handling damaged DNA, and unexpectedly find that DDX39B facilitates DNA repair by homologous recombination through upregulating BRCA1. Specifically, DDX39B binds to and stabilizes BRCA1 mRNA. DDX39B ensures ssDNA formation and RAD51 accumulation at DSB sites by maintaining BRCA1 levels. Without DDX39B being present, ovarian cancer cells exhibit hypersensitivity to DNA-damaging chemotherapeutic agents like platinum or PARPi. Moreover, DDX39B-deficient mice show embryonic lethality or developmental retardation, highly reminiscent of those lacking BRCA1. High DDX39B expression is correlated with worse survival in ovarian cancer patients. Thus, DDX39B suppression represents a rational approach for enhancing the efficacy of chemotherapy in BRCA1-proficient ovarian cancers.

overall_design:
Analysis of the differential gene expression profile between wild type and DDX39B knockout HeLa cell line. Each type was performed in three replicates

DDX39B knockout HeLa cells were selected as the screening model for the mRNA sequencing in the early stage of our project. Subsequently, we confirmed the result in ovarian cancer cells by qPCR (data not included).

first: Zhanzhan

last: Xu

first: Xiaoman

last: Li

first: Hanxiao

first: Chen

last: Nie

first: Wanchang

first: Shiwei

first: Weibin

last: Wang

first: Jiadong


title: Transcriptional response to embryonic PCB exposure in 8 killifish populations

status: Public on Aug 20 2020

city: Storrs

first: Noah

middle: M

last: Reid

state: CT

address: 67 North Eagleville Road

department: Ecology and Evolutionary Biology

institute: University of Connecticut

summary: Embryos from 8 populations of killifish, four with evolved tolerances, were exposed to PCB-126. Approximately 5 replicate embryos per treatment/control were sequenced. Desensitization of aryl hydrocarbon receptor signaling to PCB-126 is found in all four populations with evolved pollution tolerance, and represents the strongest transcriptional difference between tolerant and sensitive populations.

overall_design: 4 populations with evolved tolerance (Bridgeport, Elizabeth River, New Bedford Harbor, and Newark) paired with a nearby sensitive population. One PCB-126 dose and 1 DMSO control, 5 replicates per treatment. Embryos were exposed from 1 day post fertilization to 10 days post fertilization (developmental stage 35).

first: Andrew

last: Whitehead


title: TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma

city: Los Angeles

first: Daniel

middle: James

last: Mullen

state: CA

address: 1441 Eastlake Ave., Room NTT 6420

department: Biochemistry and Molecular Medicine, Surgery

institute: University of Southern California

summary: To better understand the transcriptional regulators involved in the development of lung cancer, we used H3K27ac and open chromatin data to define enhancer regions which may be affected by differential transcriptional regulator activity. Additionally, we performed siRNA knockdown of key transcriptional regulators identified by our study followed by RNA-seq to identify potential downstream target genes of these regulators

overall_design: ChIP-seq for active H3K27ac histone marks and ATAC-seq for regions of open chromatin in alveolar epithelial cells, along with RNA-seq in A549 lung adenocarcinoma cells after siRNA knockdown of transcriptional regulators FOXM1 and MYBL2

first: Chunli

last: Yan

first: Diane

last: Kang

first: Beiyun

last: Zhou

first: Zea

last: Borok

first: Crystal

middle: N

last: Marconett

first: Peggy

last: Farnham

first: Ite

last: Offringa

first: Suhn

middle: K

last: Rhie


title: RNA-seq time course of MSC during osteogenesis

city: Oxford

first: chao

last: jiang

address: Botnar Research Centre

department: NDORMS

institute: University of Oxford

overall_design: Examination of gene expression changes during osteogenesis

first: Chao

last: Jiang

first: Martin

last: Philpott

first: Udo

last: Oppermann


title: Genome-wide expression analysis in murine brain in E14.5 vs. 10.5m old mice

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

summary: NBS1 (Nbn in Mus musculus) is a critical component of the MRN (MRE11/RAD50/NBS1) complex, which regulates ATM- and ATR-mediated DNA damage response (DDR) pathways. NBS1 mutations cause the human genomic instability syndrome Nijmegen Breakage Syndrome (NBS), in which microcephaly and intellectual disability are marked neuronal deficits. NBS1 is essential for life, because of its function in the DDR to ensure proliferation and preventing the cell death of replicating cells. However, the function of NBS1 in postmitotic cells is unclear. To explore the possible role of Nbs1 in non-dividing cells and the effection of its deletion on gene expression, RNA-seq was carried out to compare the expression of Nbs1 and  other DDR molecules in developing and adult brain.

overall_design: In total, samples of murine cortical plate were analysed of which 4 are taken from E14.5 old mice and 3 from 10.5m old mice.

first: Zhongwei


title: Fungal oxylipins direct programmed developmental switches in filamentous fungi

city: Madison

first: Nancy

last: Keller

state: WI

address: 1550 Linden Drive

department: Medical Microbiology and Immunology

institute: University of Wisconsin-Madison

summary: We report gene expression in Aspergillus fumigatus mycelium in exposure to either 0.005% ethanol (control) or 5 µg/mL 5,8-dihydroxyoctadecadienoic acid (5,8-diHODE) for 30 min and 120 min

overall_design: Examination of A. fumigatus mycelial gene expression in response to treatment of the fungal oxylipin metabolite 5,8-diHODE

first: M

last: Niu

first: B

last: Steffan

first: J

last: Fischer

first: N

last: Venkatesh

last: Raffa

last: Wettstein

middle: W

last: Bok

first: C

last: Greco

last: Zhao

first: E

last: Berthier

last: Oliw

first: D

last: Beebe

last: Bromley

middle: P


title: Neonatal hematopoietic stem and progenitor cell ontogeny at single cell resolution (scRNA-seq)

city: St Louis

first: Jeffery

last: Magee

address: 660 S Euclid Ave.

department: Internal Medicine - Cardiovascular Division

institute: Washington University School of Medicine

summary: Single-cell RNA-seq analysis of HSCs and HPCs during fetal, neonatal and adult stages of development

overall_design:
HSCs and HPCs were isolated at the stated ages for single-cell sequencing
The strain background for all experiments is B6

first: Samantha

last: Morris


title: Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: The genomic sequences of diverse varieties of many crop species continue to be produced at a frenetic pace. However, it remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Here, we explore the potential to use DNA methylation profiles to develop more complete and refined annotations. Using leaf tissue in maize, we define ~100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs (1.3% of the genome) are found greater than 2 kilobase pairs from genes. UMRs are highly stable in multiple vegetative tissues and they capture the vast majority of accessible chromatin regions from leaf tissue. However, many UMRs are not accessible in leaf (leaf-iUMRs) and these represent a set of genomic regions with potential to become accessible in specific cell types or developmental stages. Leaf-iUMRs often occur near genes that are expressed in other tissues and are enriched for transcription factor (TF) binding sites of TFs that are also not expressed in leaf tissue. The leaf-iUMRs exhibit unique chromatin modification patterns and are enriched for chromatin interactions with nearby genes. The total UMRs space in four additional monocots ranges from 80-120 megabases, which is remarkably similar considering the range in genome size of 271 megabases to 4.8 gigabases. In summary, based on the profile from a single tissue, DNA methylation signatures pinpoint both accessible regions and regions poised to become accessible or expressed in other tissues. Thus, UMRs can provide powerful filters to distill large genomes down to the small fraction putative functional elements and facilitate the discovery of tens of thousands of novel candidate regulatory regions.

overall_design: ATAC–seq maize B73 root tissue, duplicate samples.


title: Neonatal hematopoietic stem and progenitor cell ontogeny at single cell resolution

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

overall_design: Refer to individual Series


title: Common schizophrenia risk variants are implicated in the function of glutamatergic neurons

city: New York

first: Panos

last: Roussos

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: The epigenome of human brain cells encompasses key information in understanding brain function in both healthy and diseased states. To further explore this, we used ATAC-seq to profile chromatin structure in four distinct populations of cells (glutamatergic neurons, GABAergic neurons, oligodendrocytes, and microglia/astrocytes), from three different regions of the brain. Chromatin accessibility was found to vary vastly by cell type and, more moderately, by brain region, with glutamatergic neurons showing the greatest regional variability. Transcription factor footprinting pointed to cell-specific transcriptional regulators and inferred cell-specific regulation of protein coding genes, long intergenic noncoding RNAs, and microRNAs. In vivo transgenic mouse experiments validated the cell type specificity of a number of human-derived regulatory sequences. Open chromatin regions in glutamatergic neurons were enriched for neuropsychiatric risk variants, particularly those associated with schizophrenia. Combining differential chromatin accessibility analysis using ATAC-seq data from bulk tissue increased our statistical power to confirm glutamatergic neurons as the cell type most affected in schizophrenia. Jointly, these findings illustrate the utility of studying the cell type specific epigenome in complex tissues such as the human brain and implicate an association among chromatin accessibility in glutamatergic neurons and genetic risk for schizophrenia.

overall_design: Open chromatin profiles in neuronal and non-neuronal nuclei from 3 brain regions, 4 cell types of 4 control samples

first: John

middle: F

last: Fullard

first: Mads

middle: E

last: Hauberg

first: Jaroslav

last: Bendl


title: Paneth cell-derived intestinal luminal lysozyme shapes mucolytic microbiota and controls mucosal inflammatory tone

status: Public on Aug 19 2020

city: Nutley

first: Kevin

last: Tong

state: NJ

address: 111 Ideation Way

department: CDI

institute: Hackensack Meridian Health

summary: Paneth cells are the primary, and possibly the sole, source of lysozyme in the intestinal lumen. Mice lacking the Paneth cell lysozyme gene, Lyz1, had diminished NLR signaling and basal inflammation, and were further protected from experimental colitis. Protection depended on an enhanced goblet and tuft cell program that was driven by IL13-IL4Ra-Stat6 signaling and required an expansion of lysozyme-sensitive mucolytic bacteria. Forced ectopic lysozyme production in colonic epithelium suppressed these bacteria and exacerbated colitis. Single cell RNA-seq of Lyz1 KO lamina propria revealed an activated ILC2 profile towards cytokine production. One lysozymesensitive species, Ruminococcus gnavus , when processed by lysozyme, induced a pro-inflammatory response, while non-processed R. gnavus stimulated IL13 production in lymphocytes. Consistent with a role of lysozyme for cell-wall processing in the inflammatory response, Lyz1 KO microbiota was anti-colitogenic in lysozymedeficient hosts but colitogenic in lysozyme-sufficient hosts. Thus, Paneth cell lysozyme regulates inflammatory tone by modulating mucosal response to specific bacterial groups.

overall_design: Mouse Ileum fragments (3-4 mice/genotype/treatment) were collected and subjected to RNA extraction. RNA samples were submitted for sequencing using BGISEQ500 (BGI-US). Sequenced files were aligned to mm9 genome index using Kallisto (v0.45.0) (Bray et al., 2016) with default settings and 1000 bootstraps. Reads were normalized in DESeq2 (Build 3.9) using default settings in R.

first: Shiyan

last: Yu

first: Iyshwarya

last: Balasubramanian

first: Daniel

last: Laubitz

first: Sheila

last: Bandyopadhyay

first: Xiang

last: Lin

first: Juan

last: Flores

first: Rajbir

last: Singh

first: Yue

last: Liu

first: Carlos

last: Macazana

first: Yanlin

first: Fabienne

last: Béguet-Crespel

first: Karuna

last: Patil

first: Monica

middle: T

last: Midura-Kiela

last: Wang

first: George

middle: S

last: Yap

first: Ronaldo

last: Ferraris

first: Zhi

last: Wei

first: Edward

last: Bonder

first: Max

last: Häggblom

first: Lanjing

last: Zhang

first: Veronique

last: Douard

first: Michael

last: Verzi

first: Ken

last: Cadwell

first: Pawel

middle: R

last: Kiela

last: Gao


title: Neonatal hematopoietic stem and progenitor cell ontogeny at single cell resolution (ChIP-seq)

first: Jeffery

last: Magee

state: Missouri

summary: ChIPmentation-seq analysis of HSCs and HPCs during fetal, neonatal and adult stages of development

overall_design:
HSCs and HPCs were isolated at the stated ages for ChIP-seq
The strain background for all experiments is B6

first: Jeffrey


title: Neonatal hematopoietic stem and progenitor cell ontogeny at single cell resolution (ATAC-seq)

summary: The goal of this study was to characterize the transcriptional changes that take place in hematopoietic stem and progenitor cells as they transit the neonatal period of development. These changes were observed at the single cell level and they are correlated with epigenome remodeling, as evidenced by the ATAC-seq and Chipmentation data (H3K4me1 and H3K27ac) in this data set.

overall_design:
(i)  ATAC-seq analysis of HSCs and HPCs during fetal, neonatal and adult stages of development
(ii)  ATAC-seq analysis of wild type and Ifnar-ko HSCs and HPCs at P7
The strain background for all experiments is B6


title: Gene expression profile of IL4I1 knockout CAS-1 glioblastoma cells

city: Heidelberg

first: Ahmed

last: Sadik

address: Im Neunheimer Feld 280

department: Metabolic Crosstalk in Cancer

institute: DKFZ

summary: Aryl hydrocarbon receptor (AHR) activation by tryptophan (Trp) catabolites enhances tumor malignancy and suppresses anti-tumor immunity. Hitherto, indoleamine-2,3-dioxygenase 1 (IDO1) or tryptophan- 2, 3-dioxygenase (TDO2) are recognized as the main Trp-catabolizing enzymes (TCEs) responsible for the generation of AHR agonists. Here, the ability of the aromatic L-amino acid oxidase, interleukin 4 induced 1 (IL4I1), to activate the AHR was investigated using IL4I1 knockout CAS-1 glioblastoma cells.

overall_design: Expression profile of IL4I1 knockout (KO, sgIL4I1-2.4) CAS-1 cells, was compared to the expression profile of non-targeting control (NTC, sgCtrl) or NTC.01 (sgCtrl.01) CAS-1 cells, cultured for 72 h (n = 6). n values represent independent experiments.

first: Luis

last: Somarribas Patterson

first: Christiane

last: Opitz


title: Gene expression profiling of IL4I1 KO and WT CD8+ T-cell subsets from TCL1-AT mice

summary: Analysis of the effect of IL4I1 on gene expression of CD8 T-cells in CLL

overall_design: WT or Il4i1 KO BM chimeric mice were transplanted with murine CLL cells from Eµ-TCL1 mice. CD44high CD127high memory and CD44+CD127- Effector CD8 T-cell subsets were FACS-sorted and total RNA was isolated after 5 weeks of transplantation

first: Selcen

last: Öztürk

first: Murat

last: Iskar

first: Martina

last: Seiffert


title: Integrating Next Generation Sequencing with Morphology Improves Prognostic and Biologic Classification of Spitz Neoplasms [DNA-Seq]

city: Chicago

first: Pedram

last: Gerami

state: Illinois

address: 420 E Superior St

institute: Northwestern University

type: Genome variation profiling by high throughput sequencing

summary: The newest WHO classification suggests eliminating cases with BRAF and NRAS mutations from the categories of Spitz tumors (ST) and Spitz melanoma (SM). We aimed to better characterize the genomics of Spitz neoplasms and assess whether integrating genomic data with morphologic diagnosis improves classification and prognostication. We performed DNA and RNA sequencing on 80 STs, 26 SMs, and 22 melanomas with Spitzoid features (MSF).  NGS data was used to reclassify tumors by moving BRAF/NRAS-mutated cases to MSF. Eighty-one percent of STs harbored kinase fusions/truncations. Of SMs, 77% had fusions/truncations, 8 involving MAP3K8. Novel fusions identified were MYO5A-FGFR1, MYO5A-ERBB4, and PRKDC-CTNNB1. The majority of MSFs (84%) had BRAF, NRAS, or NF1 mutations, and 62% had TERT promoter mutations.  Only after reclassification, the following was observed: 1) mRNA expression showed distinct clustering of MSF; 2) 6/7 cases with recurrence and all distant metastases were MSFs; 3) RFS was worse in MSF than ST and SM groups (p=0.0073); 4) classification incorporating genomic data was highly predictive of recurrence (OR 13.20, p=0.0197). The majority of STs and SMs have kinase fusions as primary initiating genomic events.  Eliminating BRAF/NRAS-mutated neoplasms from these categories results in improved classification and prognostication of melanocytic neoplasms with Spitzoid cytomorphology.

overall_design: We performed DNA sequencing on 71 Spitz Tumors, 26 Spitzoid Melanomas, and 22 melanomas with Spitzoid features (MSF) to better characterize the genomics of Spitz neoplasms and assess whether integrating genomic data with morphologic diagnosis improves classification and prognostication.

first: Victor

middle: L

last: Quan

first: Bin

first: Yongzhan

first: Lauren

last: Mohan

first: Katherine

last: Shi

first: Annette

last: Wagner

first: Lacey

last: Kruse

first: Timothy

last: Taxter

first: Nike

last: Beaubier

first: Kevin

last: White

first: Lihua

last: Zou


title: Genetic study on the Sexual Stage of Cochliopodium (Amoebozoa)

city: Atlanta

first: YONAS

last: TEKLE

address: 350 Spelman Ln SW

institute: Spelman College

summary: We used stage specific RNA-seq to investigate the mechanism of sexual development in Cochliopodium minus.

overall_design: Examination of the differentially expressed genes in different sexual development stages.

first: Yonas

middle: I

last: Tekle


title: Maternal DNMT3A-dependent de novo methylation of the zygotic paternal genome inhibits gene expression in the early embryo

city: Vancouver

first: Matthew

last: Lorincz

state: BC

address: 2350 Health Sciences Mall

institute: University of British Columbia

summary: De novo DNA methylation (DNAme) during mammalian spermatogenesis yields a densely methylated genome, with the exception of CpG islands (CGIs), which are hypomethylated in sperm. Following fertilization, the paternal genome undergoes widespread DNAme loss before the first S-phase. Paradoxically, recent mass spectrometry analysis revealed that a low level of de novo DNAme occurs exclusively on the zygotic paternal genome. However, the genomic loci involved and impact on genic transcription was not addressed. Here, we employ allele-specific analysis of whole-genome bisulphite sequencing (WGBS) data and show that a number of genomic loci, including several dozen CGI promoters, are de novo methylated on the paternal genome in 2-cell embryos. A subset of these promoters maintain DNAme through development to the blastocyst stage. Consistent with zygotic paternal DNAme acquisition (PDA), many of these loci are hypermethylated in androgenetic blastocysts but hypomethylated in parthenogenetic blastocysts. Strikingly, PDA is lost following maternal deletion of Dnmt3a. Furthermore, a subset of promoters showing PDA which are normally transcribed from the paternal allele in ICM cells show premature transcription at the 4C stage in maternal Dnmt3a knockout embryos. Taken together, these observations uncover an unexpected role for maternal DNMT3A activity in post-fertilization epigenetic reprogramming and transcriptional silencing of the paternal genome.

overall_design:
WGBS in Dnmt3a WT and maternal KO 2-cell F1 hybrid embryos. RNAseq in Dnmt3a WT and maternal KO 2-cell, 4-cell and blastocyst (ICM cells) F1 hybrid embryos. WGBS in androgenetic blastocysts.

Please note that each .bw file was generated from 2 replicates and is linked to the corresponding 'rep 1' sample records.

first: Julien

last: Richard Albert

first: Wan Kin

last: Au Yeung

first: Keisuke

last: Toriyama

first: Hisato

last: Kobayashi

first: Ryutaro

last: Hirasawa

first: Julie

last: Brind'Amour

first: Aaron

middle: B

last: Bogutz

first: Hiroyuki

last: Sasaki

middle: C


title: AHR activation in glioblastoma cells [IL4I1_shAHR_U87]

first: Ahmed

last: Sadik

summary: The objective of this study was to analyze AHR activation through aromatic amino acid metabolism. To this end, glioblastoma cells were exposed to aromatic amino acid derived metabolites and their ability to activate AHR was analysed. In addition, AHR activation was evaluated in glioblastoma cells expressing IL4I1, an aromatic amino acid degrading enzyme, with or without shRNA mediated knockdown of AHR.

overall_design: IL4I1_shAHR_U87: expression profile of shCtrl and shAHR U-87MG cells expressing IL4I1, was compared to expression profile of shCtrl U-87MG cells without IL4I1 expression (dashed line), cultured for 120 h (n = 3). n values represent independent experiments.

first: Luis

last: Somarribas

first: Soumya

last: Mohapatra

first: Christiane

middle: A

last: Opitz


title: Neonatal hematopoietic stem and progenitor cell ontogeny at single cell resolution (RNA-seq)

first: Jeffery

last: Magee

summary: RNA-seq analysis of HSCs and HPCs during fetal, neonatal and adult stages of development

overall_design:
HSCs and HPCs were isolated at the stated ages for RNA-seq
The strain background for all experiments is B6

first: Jeffrey


title: AHR activation in glioblastoma cells [I3P_HPP_PP_U87_U87]

overall_design: I3P_HPP_PP_U87_U87: expression profile of U-87MG cells treated with indole-3-pyruvic acid (I3P), hydroxyphenylpyruvic acid (HPP) or phenylpyruvic acid (PP) 40 μM for 24 h, was compared to expression profile of U-87MG cells treated with DMSO (n = 5).


title: RNA-seq of HEK293 cells overexpressing NOCT ∆(2-15)-3F with controls overexpressing GST-3F

city: Ann Arbor

first: P. Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr.

department: Biological Chemistry

institute: University of Michigan

summary: To investigated the effect of cytoplasmically localized human NOCT on transcriptome-wide RNA levels, we generated HEK293 cell lines that stably overexpress NOCT ∆(2-15)-3F construct, which lacks the MTS and is localized to the cytoplasm. As a negative control, we also generated cells that stably express glutathione S-transferase-3x FLAG (GST-3F). Three independent clonal cell lines were generated for each construct, and served as biological replicates. Total RNA was isolated from each cell line, ribosomal RNA was depleted, and then stranded, whole transcriptome RNA sequencing was performed.

overall_design: RNA-seq for each clonal cell line (3 lines expressing GST-3F and 3 lines expressing NOCT ∆(2-15)-3F), by Illumina HiSeq 2500

first: Elizabeth

last: Abshire

first: Kelsey

last: Hughes

first: Rucheng

last: Diao

first: Sarah

last: Pearce

first: Shreekara

last: Gopalakrishna

first: Ray

last: Trievel

first: Joanna

last: Rorbach

first: Peter

last: Goldstrohm


title: AHR activation in glioblastoma cells [I3CA_U87]

overall_design: I3CA_U87: expression profile of U-87MG cells treated with indole-3-carboxaldehyde (I3CA) 50 μM for 24 h, was compared to expression profile of U-87MG cells treated with DMSO (n = 4).


title: AHR activation in glioblastoma cells and gene expression analysis of T cells in TCL1-AT mice.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Methylation and chromatin abnormalities in chronic myelomonocytic leukemia.

status: Public on Aug 18 2020

city: London

first: Kurt

last: Berger

state: Ontario

address: 800 Commissioner's Road E.

institute: UWO

summary: In this study, institutional IRB approval was obtained and peripheral blood and bone marrow samples on patients with chronic myelomonocytic leukemia were collected.  On the samples, we performed chromatin immuno-precipitation and next generation sequencing to assess histone modifications and epigenetic changes associated with proliferative and dysplastic phenotypes.

overall_design: Samples were collected from the bone marrow after obtaining written informed consent.  This was approved by the Mayo Clinic IRB 15-003786

first: Mrinal

last: Patnaik


title: Elevation of JAML Promotes Diabetic Kidney Disease by Modulating Podocyte Lipid Metabolism

city: Jinan

first: Yi

last: Fu

address: West Wenhua Road

institute: Shandong University

summary: Podocytes, highly differentiated glomerular epithelial cells, are essential for the maintenance of glomerular filtration barrier. Lipid accumulation in podocytes is a major determinant of proteinuric kidney disease. By RNA-sequencing analysis, we observed the significant changes of genes important in regulating cellular lipid homeostasis in podocytes with HG treatment. We generated two mouse podocyte cell lines stably transduced with either a sh-NC lentiviral construct or a shRNA lentiviral construct designed to target JAML RNA to investigate the consequences on the gene expression profile of JAML knockdown in  mouse podocytes.

overall_design: The gene expression of 4 samples from a 24 h high glucose induced sh-NC or sh-JAML podocyte cell line was compared to 4 untreated samples by RNA sequencing.

first: Yu

last: Sun


title: Epigenome analysis of paragangliomas of the filum terminale/cauda equina

city: Stanford

first: David

middle: A.

last: Solomon

address: 300 Pasteur Dr, Lane L216

department: Pathology

institute: Stanford University School of Medicine

summary: Genome-wide DNA methylation profiling of 12 spinal paragangliomas of the filum terminale/cauda equina. The Illumina Infinium EPIC 850k Human DNA Methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpG sites of genomic DNA extracted from formalin-fixed, paraffin-embedded tumor tissue of 12 spinal paragangliomas.

overall_design: Bisulfite converted genomic DNA extracted from the 12 tumor samples was hybridized to Illumina Infinium EPIC 850k Human DNA Methylation Beadchip


title: Prp19 is an independent prognostic marker and promotes neuroblastoma metastasis by regulating the Hippo-YAP signaling pathway [SK-N-BE(2)]

city: Shanghai

first: Yuanxia

last: Cai

address: No.1665, Kongjiang Road, Yangpu District

institute: Xinhua Hospital

summary: This study first reveals that Prp19 is a potential oncogene in neuroblastoma, which is significantly correlated with poor prognosis and promote metastasis viaregulating Hippo-YAP pathway

overall_design: Prp19 knockdown was performed in neuroblastoma cell line SK-N-BE(2)

first: Zhixiang

last: Wu