title: Dynamic changes in genome-wide histone methylation and gene expression of soybean roots in response to salt stress (ChIP-seq dataset)

status: Public on Jul 22 2019

city: Beijing

first: guoweijun

last: guoweijun

address: No. 12, Zhongguancun South Street

department: Biotechnology Research  Institute

institute: Chinese Academy of Agricultural Sciences

summary: Soybean is an important economic crop for human diet, animal feeds and biodiesel due to high protein and oil content. Its productivity is significantly hampered by salt stress, which impairs plant growth and development by affecting gene expression, in part, through epigenetic modification of chromatin status. However, little is known about epigenetic regulation of stress response in soybean roots. Here, we used RNA-seq and ChIP-seq technologies to study the dynamics of genome-wide transcription and histone methylation patterns in soybean roots under salt stress. 8798 soybean genes changed their expression under salt stress treatment. Whole-genome ChIP-seq study of an epigenetic repressive mark,  histone H3 lysine 27 trimethylation (H3K27me3), revealed the changes in H3K27me3 deposition during the response to salt stress. Unexpectedly, we found that most of the inactivation of genes under salt stress is strongly correlated with the de novo establishment of H3K27me3 in various parts of the promoter or coding regions where there is no H3K27me3 in control plants. In addition, the soybean histone modifiers were identified which may contribute to de novo histone methylation and gene silencing under salt stress. Thus, dynamic chromatin regulation, switch between active and inactive modes, occur at target loci in order to respond to salt stress in soybean. Our analysis demonstrates histone methylation modifications are correlated with the activation or inactivation of salt-inducible genes in soybean roots.

overall_design: Examination of histone modifications in control and salt-treated soybean roots.

first: Lei

last: Sun

first: Guangshu

last: Song

first: Weijun

last: Guo

first: LI

last: PU


title: Gene expression profiling of developing murine Müller glia

status: Public on Jul 23 2019

city: Miami

first: Dmitry

last: Ivanov

state: FL

address: 1638 NW 10th Avenue

department: Ophthalmology

country: USA

institute: University of Miami Miller School of Medicine

summary: To study molecular changes during differentiation of retinal progenitor cells (RPCs) into Müller glia, we isolated Notch1+ cells (Notch1 is a marker of RPCs) from postnatal-day (P) 0, 3, 7, and 14 retinas,as well as Glast + cells (Glast/Slc1a3 is a marker of Müller glia precursors and Müller glia in the retina) from P7, P14, P21, and P28 retinas. We studied gene expression in these cells using MEEBO microarrays.

overall_design: To characterize and compare P0, P3, P7, and P14 Notch1+ cells (RPCs) as well as P7, P14, P21, and P28 Glast+ cells (Müller glia precursors and adult Müller glia), RNA extracted from these cells was used for microarray analysis. A total of two-three independent biological replicates at each time point were obtained for comparative profiling of purified cells.


title: Real-time quantitative PCR analysis of human gingiva epithelial cells exposed to microbial biofilms

city: Amsterdam

first: Susan

last: Gibbs

address: Gustav Mahlerlaan 3004

department: Oral Cell Biology

country: Netherlands

institute: Academic Centre for Dentistry Amsterdam

summary: An organotypic gingiva model RHG was constructed by immortalized human gingiva cell lines (keratinocytes and fibroblasts) in vitro. The RHG model was exposed to either control medium or one of the three multi-species oral biofilms (commensal, gingivitis and cariogenic) for 24 hours. We used Qiagen RT² Profiler PCR array to analyse the expression of genes which are related to Toll-like receptor signaling pathway from the unexposed (control) and differently exposed (test) keratinocyte layer of the RHG model. Reference for RHG model and oral biofilms culture: J. K. Buskermolen et al., J Dent Res 97 (2018): 201-208. doi: 10.1177/0022034517729998.

overall_design: qPCR gene expression profiling. For each exposure condition, three (commensal, gingivitis) or two (cariogenic) replicates of RHG samples were used. Equal amount total RNA from each sample was processed to gene expression analysis.


title: Dynamic changes in genome-wide histone methylation and gene expression of soybean roots in response to salt stress

country: China

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Dynamic changes in genome-wide histone methylation and gene expression of soybean roots in response to salt stress (RNA-seq dataset)

overall_design: Transcription profile of control and salt-treated soybean roots.


title: Vitamin C dependent KDM6 demethylation specifies a functional chromatin state for endothelial-to-hematopoietic transition [ChIP-Seq]

city: Guangzhou

first: Tian

last: Zhang

state: Guangdong

address: 190 Kaiyuan Avenue,Science Park

institute: GIBH

summary: Hematopoietic stem/progenitor cells (HSPCs) are generated from hemogenic endothelial cells (HECs) through endothelial-to-hematopoietic transition (EHT); however, the underlying mechanism remains poorly understood. Here, we report that HPC generation is significantly reduced in hPSC differentiatiation in a defined condition without vitamin C (Vc). Mechanistically, the endothelial cells generated in the absence of Vc fail to undergo EHT due to apparent failure in opening genomic loci essential for hematopoiesis. These loci exhibit abnormal accumulation of H3K27me3, a repressive histone modification due to lower activity of its demethylases. Consistently, deletion of H3K27me3 demethylases, JMJD3 and UTX, impaires HPC generation in the presence of Vc. Furthermore, Vc and jmjd3 are also important for HSC generation during zebrafish development. Together, we reveal an obligatory role of Vc underlying EHT process in hematopoisis and further support the important function of Vc during development.

overall_design: We compared the H3K4me3 and H3K27me3 binding of  the GATA2/eGFP+ and  GATA2/eGFP- endothelial cells by ChIP-Seq.

first: Ke

last: Huang

first: Guangjin

last: Pan


title: Vitamin C-dependent lysine demethylase 6 (KDM6)-mediated demethylation promotes a chromatin state that supports the endothelial-to-hematopoietic transition

summary: Hematopoietic stem cells (HSCs)/progenitor cells (HPCs) are generated from hemogenic endothelial cells (HECs) during the endothelial-to-hematopoietic transition (EHT); however, the underlying mechanism remains poorly understood. Here, using an array of approaches, including CRSPR/Cas9 gene knockouts, RNA-Seq, ChIP-Seq, ATAC-Seq etc., we report that vitamin C (Vc) is essential in HPC generation during human pluripotent stem cell (hPSC) differentiation in defined culture conditions. Mechanistically, we found that the endothelial cells generated in the absence of Vc fail to undergo the EHT because of an apparent failure in opening up genomic loci essential for hematopoiesis. Under Vc deficiency, these loci exhibited abnormal accumulation of histone H3 trimethylation at Lys-27 (H3K27me3), a repressive histone modification that arose because of lower activities of demethylases that target H3K27me3. Consistently, deletion of the two H3K27me3 demethylases, Jumonji domain-containing 3 (JMJD3 or KDM6B) and histone demethylase UTX (UTX or KDM6A), impaired HPC generation even in the presence of Vc. Furthermore, we noted that Vc and jmjd3 are also important for HSC generation during zebrafish development. Together, our findings reveal an essential role for Vc in the EHT for hematopoiesis, and identify KDM6-mediated chromatin demethylation as an important regulatory mechanism in hematopoietic cell differentiation.

overall_design: We compared the genomic chromosal accebility of the GATA2/eGFP+ and  GATA2/eGFP- endothelial cells by ATAC-Seq.


title: Vitamin C dependent KDM6 demethylation specifies a functional chromatin state for endothelial-to-hematopoietic transition [RNA-Seq]

overall_design: We compared the transcriptome of  the GATA2/eGFP+ and  GATA2/eGFP- endothelial cells by RNA-Seq; and we analysis the timecourse samples of the re-plated GATA2/eGFP+ and  GATA2/eGFP- endothelial cells at different time points.


title: Transcriptome analysis of differentially expressed genes in different pod dehiscence characteristics of soybean

city: Nanchang

first: Dong

last: Wang

state: JiangXi

address: Hong Gu Tan New Road, No. 999

institute: Nanchang University

summary: Pod dehiscence is an important agronomic trait. Pod dehiscence would cause huge yield losses before soybean maturity. Although some of soybean pod dehiscence associated genes have been identified, the underlying mechanism of pod dehiscence is still not comprehensively explained. In this study, we have identified differentially expressed genes (DEGs) between shattering-resistant and shattering-susceptible soybean accessions based on transcriptome analyses of 10 soybean accessions. Long non-coding RNAs (lncRNAs) that may be involved in soybean pod dehiscence were also identified, and we constructed co-expression networks between mRNAs and lncRNAs. RNA sequencing results were further verified by real-time PCR. Furthermore, DEGs were screened through analyzing positions of soybean pod dehiscence quantitative trait locus (QTLs) and phenotypes of soybean pod dehiscence for achieving pod-dehiscence candidate genes.

overall_design: High-depth paired-end RNA-seq from pods of soybeans

first: Xiang

last: Kang


title: Vitamin C–dependent lysine demethylase 6 (KDM6)-mediated demethylation promotes a chromatin state that supports the endothelial-to-hematopoietic transition


title: Transcription-dependent targeting of Hda1C to hyperactive genes mediates H4-specific deacetylation in yeast (ChIP-seq)

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

summary: Hda1C directly binds to actively transcribed regions likely via the interaction with elongating RNA PolII and/or with nascent RNA transcripts. The Arb2 domain of Hda1 is also critical for its binding to chromatin. Interestingly, Hda1C specifically deacetylates histone H4 but not H3 at active genes to suppress nucleosome instability and partially inhibit elongation. In contrast, Hda1C mainly deacetylates histone H3 at inactive genes to delay gene induction.

overall_design: The examination of the changes of histone acetylation upon hda1 knockout as well as the changes of Hda1C upon Arb2 domain deletion.

first: So

middle: D

last: Ha

first: Seokjin

last: Ham

first: Min

middle: Y

last: Kim

first: Insoon

last: Jang

first: TaeSoo


title: Transcription-dependent targeting of Hda1C to hyperactive genes mediates H4-specific deacetylation in yeast (RNA-seq)

overall_design: The examination of the changes of gene expression during carbon source shifts.


title: Effect on small molecule RBPJ inhibitor (RIN1) on gene expression in Jurkat cells compared to gamma secretase inhibition and siRNA knockdown of RBPJ

status: Public on Jul 18 2019

city: Palo Alto

first: Mark

last: Mercola

state: CA

address: 1651 Page Mill Road

department: Department of Medicine

institute: Stanford University School of Medicine

summary: We discovered a new class of small molecule inhibitor that disrupts the interaction between NOTCH and RBPJ, which is the main transcriptional effector of NOTCH signaling. RBPJ Inhibitor-1 (RIN1) also blocked the functional interaction of RBPJ with SHARP, a scaffold protein that forms a transcriptional repressor complex with RBPJ in the absence of NOTCH signaling. RIN1 induced changes in gene expression  resembled siRNA silencing of RBPJ rather than inhibition at the level of NOTCH itself. RIN1 inhibits RBPJ in its repressing and activating contexts.

overall_design: Analysis of gene expression on Jurkat cells treated with different inhibitors of the Notch pathway: DAPT (gamma secretase inhibitor), CB-103 (inhibitor works downstream activated receptor but with unknown target), RIN1 (novel inhibitor at the level of RBPJ) and RBPJ siRNA

first: Cecilia

last: Hurtado


title: Expression analysis of Wild-type and Yeats4-deficient a4b7+ ILC progenitors

first: Benyu

last: Liu

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of Biophysics, CAS

summary: Investigation of differentially expressed genes in  Yeats4-deficient a4b7+ ILC progenitors

overall_design: Gene expression profiling using Lin-CD127+c-KitintSca-1inta4b7 + ILC progenitors from Yeats4 deletion mice or WT littermates. Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray were performed in accordance with the Affymetrix Mouse Gene2.0 analysis protocol (Affymetrix).

first: Buqing

last: Ye

first: Zusen

last: Fan


title: PAX5 belongs to a functional transcription factor network commonly targeted in B-lineage leukemia (murine)

status: Public on Jul 19 2019

city: Lund

first: Mikael

last: Sigvardsson

address: Sölvegatan 19

country: Sweden

institute: Lund University

summary:
One of the most frequently mutated proteins in human B-lineage leukemia, mutated in about one third of all cases, is the transcription factor PAX5. While reduced function of PAX5 has a clear connection to human malignancy there is limited evidence of a direct impact on the development and function of B-cell progenitors. One possible explanation to this comes from the finding that PAX5 mutated B-ALL display complex karyotypes and additional mutations, indicating that PAX5 might be just one component of a larger transcription factor network targeted in B-ALL. To investigate the functional network associated with PAX5 we used BioID technology to identify associated proteins. This revealed 239 proteins out of which several could be found mutated in human B-ALL. Most prominently we identified IKZF1, commonly mutated, and RUNX1, involved in the formation of ETV6-AML1 fusion protein formation, among the interaction partners. ChIP-seq as well as PLAC-seq analysis supported the idea that these factors share regulatory elements in human B-ALL cells. Gene expression and mutation analysis of both mouse models and primary human leukemia suggested that these factors form a functional gene regulatory network targeted by multiple mutations in human B-ALL.

Keywords: Expression profiling by high throughput sequencing

overall_design: RNA-seq experimens were run on FL-WT or Pax5-heterozygout cells in triplicates. FL-WT, FL-Pax5-KO, FL-Ebf1-KO cells and 230-238 cells were also used for ChIP-seq analysis using singe samples. Sequence inputs were used as controls.

first: Kazuki

last: Okuyama

first: Tobias

last: Strid

first: Jacob

last: Kuruvilla

first: Susana

last: Cristobal

first: Emma

last: Smith

first: Thoas

last: Fioretos

first: Henrik

last: Lilljebjörn

first: Shamit

last: Soneji

first: Stefan

last: Lang

first: Jonas

last: Ungerbäck

first: Rajesh

last: Somasundaram

first: Mahadesh

middle: A

last: Prasad


title: Machine Learning Classifiers for Endometriosis Using Transcriptomics and Methylomics Data [Transcriptomics]

city: Columbia

first: Trupti

last: Joshi

state: Missouri

address: NW 502, One Hospital Drive

institute: University of Missouri

summary: We experimented how well various supervised machine learning methods such as decision tree, partial least squares discriminant analysis (PLSDA), support vector machine and random forest perform in classifying endometriosis from the control samples trained on both transcriptomics and methylomics data. The assessment was done from two different perspectives for improving classification performances: (a) implication of three different normalization techniques, and (b) implication of differential analysis using the generalized linear model (GLM). We concluded that an appropriate machine learning diagnostic pipeline for endometriosis should use TMM normalization for transcriptomics data, and quantile or voom normalization for methylomics data, GLM for feature space reduction and classification performance maximization.

overall_design:
Total 38 RNA-seq samples were analyzed where 22 were control and 16 were disease samples

Please note that the GSE134052 records represent the methylomics data.

first: Sadia

last: Akter

first: Dong

last: Xu

first: Susan

middle: C

last: Nagel

first: John

last: Bromfield

first: Katherine

last: Pelch

first: Gilbert

middle: B

last: Wilshire


title: STAT3β is a tumor suppressor in acute myeloid leukemia

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

summary: Signal transducer and activator of transcription 3 (STAT3), an important multifunctional regulator of transcription, is expressed in two alternatively spliced isoforms, STAT3α and truncated STAT3β. While STAT3β was postulated to act as a dominant negative form of STAT3α, it has been shown to have various STAT3α-independent regulatory functions. Recently, STAT3β gained attention as a powerful anti-tumorigenic molecule in cancer. Deregulated STAT3 signaling is frequently observed in hematological malignancies, however, the role of STAT3β in acute myeloid leukemia (AML) remains elusive. We analyzed a cohort of AML patients for the STAT3β/α mRNA expression ratio and observed that a higher STAT3β/α ratio correlated with a favorable prognosis and increased overall survival. To gain better understanding of the function of STAT3β in leukemia we engineered a transgenic mouse allowing for balanced Stat3β expression. Transgenic Stat3β expression resulted in enhanced disease latency in PTEN- and MLL-AF9-dependent mouse models of AML. In conclusion, we demonstrate that STAT3β plays an essential tumor suppressor role in AML and its mRNA expression acts as an important prognostic tool in AML patients.

overall_design: RNA-seq of sorted Venus + BM cells ( Stat3β TG ) and wt, 3 replicates each

first: Petra

last: Aigner

first: Dagmar

last: Stoiber


title: RNA-seq in SUNE-1 cells after downregulation of DANCR expression

status: Public on Jul 20 2019

first: Jun

last: Ma

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

summary: To explore whether DANCR plays a role in  nasopharyngeal carcinoma tumorigenesis, a RNA-seq analysis was performed to compare the gene expression profiles of DANCR siRNA and control groups.

overall_design: RNA-seq was performed in SUNE-1 NPC cells after DANCR siRNA and control siRNA transfection

first: Xin

last: Wen

last: Liu


title: Transcription-dependent targeting of Hda1C to hyperactive genes mediates H4-specific deacetylation in yeast

first: Tae-Young

last: Roh


title: Machine Learning Classifiers for Endometriosis Using Transcriptomics and Methylomics Data [Methylomics]

address: One Hospital Drive

type: Methylation profiling by high throughput sequencing

overall_design:
Total 77 MBD-seq samples were analyzed where 35 were control and 42 were disease samples

Please note that GSE134056 records represent the transcriptomics data.


title: Oral JAK/SYK-inhibition (ASN002) suppresses inflammation and improves epidermal barrier markers in atopic dermatitis

city: New York

first: Ana

last: Pavel

state: NY

address: One Gustave L. Levy Place

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

summary: We conducted a randomized, double-blind, placebo-controlled trial in adults with moderate-to-severe AD to test the efficacy of JAK/SYK-inhibitor ASN002. ASN002 significantly suppressed key AD inflammatory pathways, corresponding to clinical response, and may be an effective novel therapeutic agent for moderate-to-severe AD.

overall_design: Patients were randomized to dose escalation of ASN002 20mg, 40mg, 80mg, and placebo groups. Skin biopsies were performed at baseline, day15, and day29. Gene expression studies were conducted using microarray and qRT-PCR, and cellular infiltrates and protein expression were studied by immunohistochemistry.

first: Teresa

last: Song

first: Hyun

middle: J

last: Kim

first: Del

last: Ester

first: James

middle: G

last: Krueger

first: Celina

last: Dubin

first: Xiangyu

last: Peng

first: Hui

first: Ning

last: Zhang

first: Yeriel

last: Estrada

first: Louis

last: Denis

first: Niranjan

last: Rao

first: Sandeep

last: Gupta

first: David

last: Zammit

first: Robert

last: Bissonnette

first: Emma

last: Guttman-Yassky


title: A sensor kinase controls turgor-driven plant infection by the rice blast fungus Magnaporthe oryzae.

city: Exeter

first: Darren

middle: Mark

last: Soanes

address: RILD Building, RD&E Hospital Wonford, Barrack Road

department: College of Medicine and Health

country: United Kingdom

institute: University of Exeter

summary: Conidia from null mutants strains for the genes CDC42, RHO4, BUF1, SLN1 as well as the wild-type Guy11 were harvested and placed on an inductive surface. After 16 hours developing appressoria were harvested and transcript abundance analysed using RNA-seq, two biological replicates per sample.

overall_design: Global transcript abundance was profiled in four null mutants of Magnaporthe oryzae during appressorium development on an inductive surface (16 hours after condia were placed on surface).

first: Lauren

middle: S

last: Ryder

middle: M

first: Miriam

last: Oses-Ruiz

first: Nicholas

last: Talbot


title: Loss of CHD1 facilitates oncogenic hijacking of AR during cancer progression

first: Deli

last: Liu

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: FoxH1 represses miR-430 during early embryonic development of zebrafish via non-canonical regulation

city: Innsbruck

first: Dietmar

last: Rieder

address: Innrain 80

department: Biocenter

institute: Medical University of Innsbruck

summary: Using ChIP-Seq we examined the targets of FoxH1 in zebrafish embryos at the 6hpf epiboly-stage. The revealed reads could be mapped to more than 16,000 peaks included also the known targets like ndr1, lft2, pitx2, flh, foxa3 and lhx1a. Relevant for our study, we identify the conserved microRNA-430 family (miR-430) as a novel target of FoxH1.

overall_design: eGFP-tagged FoxH1 was used for the assay.

first: Patrick

last: Fischer

first: Dirk

last: Meyer


title: CHD1 functions as a prostate-specific tumor suppressor by modulating nuclear receptor specificity towards distinct, lineage-specific, enhancers

summary: Deregulation of chromatin architecture is emerging as a critical feature of carcinogenesis, and genomic alterations in nucleosome remodelers are common in human cancer. Recurrent deletion of the chromatin remodeler CHD1 is among the most common alterations in prostate cancer, but its role as a tumor suppressor and the reasons for the tissue-specific nature of CHD1 deletion remain undefined. Here, we show that deletion of CHD1 drives prostate tumorigenesis and fundamentally reprograms the transcriptional program of the androgen receptor (AR), diverting AR towards an oncogenic transcriptional program and away from a growth suppressive transcriptome.  Conditional deletion of Chd1 in mouse prostate resulted in prostate neoplasia in vivo, confirming CHD1 as a tumor suppressor in prostate tissue. In prostate cells, the interactome of chromatin-bound CHD1 was enriched for factors that regulate nuclear receptor function, and interrogation of the CHD1 cistrome revealed promoter-independent enrichment of CHD1 at sites specifically occupied by AR and its associated transcriptional regulators. Deletion of CHD1 resulted in a dramatic redistribution of AR across the genome, localizing AR to sites enriched for HOXB13, and depleting AR at AR-halfsite motifs, consistent with the AR cistrome and epigenetic marks in human prostate cancer samples. Furthermore, the CHD1 null AR cistrome was associated with a unique AR transcriptional signature, enriched for pro-oncogenic pathways and depleted for processes consistent with normal prostatic function. Collectively, these data implicate CHD1 as a prostate-specific tumor suppressor which constrains the oncogenic functions of AR though maintenance of a normal AR transcriptional program.

overall_design: LNCaP isogenic models of CHD1 loss cells were initally assessed for chromatin acessibility via ATAC seq. Briefly, Cells were starved of androgen for 72 hours, and the treated with either Vehicle (EtOH) or 10nM DHT for 4 hours.  Cells were then fixed with 4% PFA, and ATAC libraries and sequencing performed by the Center for Functional Cancer Epigenetics at Dana Farber research institute.  Samples were submitted in biological duplicate.

first: Michael

last: Augello

first: Chris

last: Barbieri


title: The Position Beta57 of IAg7 Controls the Early Anti-Insulin Response and Onset of Diabetes in NOD mice to Link MHC and Disease [RT-PCR]

city: La Jolla

first: Luc

last: Teyton

address: 10550 North Torrey Pines Road

institute: TSRI

summary: Abstract- The class II region of the Major Histocompatibility locus is the main contributor to the genetic susceptibility to type 1 diabetes (T1D). The loss of an aspartic acid at position 57 of diabetogenic HLA-DQ8 chains supports this association; it influences the recognition of peptides in the context of HLA-DQ8, and I-Ag7 using a mechanism termed the P9 switch. Here, we built register-specific insulin MHC tetramers, Ins12-20 and Ins13-21, to examine anti-insulin CD4 T cell responses during the early pre-diabetic phase of disease in mice. A single cell gene expression analysis and single cell T cell receptor (TCR) sequencing of anti-insulin CD4 T cells performed in 6 and 12-week-old NOD mice, revealed tissue-specific gene expression signatures.  TCR signaling and clonal expansion were found only in the islets of Langerhans. and produced either classical Th1 differentiation or an unusual Treg phenotype, independent of TCR usage. The early phase of the anti-insulin response was dominated by cells specific for Ins12-20, the register that supports a P9 switch mode of recognition. The presence of the switch was demonstrated by TCR sequencing, re-expression, mutagenesis, and functional testing of alpha/beta TCR pairs in vitro. The genetic correction of the beta57 mutation resulted in the disappearance of D/E residues in the CDR3beta of anti-Ins12-20 T cells, and inability of cells normally activated by a switch to recognize the Ins9-23 peptide. These results provide the first molecular mechanistic explanation that links the unique MHC class II polymorphism of T1D with the recognition of islet antigens and disease onset.

overall_design: Murine CD4+ T cells, isolated from different tissues, were stained with either IAg7-1220 or IAg7-1321; both tetramers were labelled with the fluorscent moiety PE. Cells stained with either tetramer were single cell sorted into single wells of 96 well plates. Single cell cDNA libraries were made according to the Fluidigm BioMark "Two Step Single Cell Gene Expression Using EvaGreen" protocol. Then gene expression of 96 genes was assessed utilizing the Fluidigm Dynamic Array 96x96 IFC and the "GE Fast 96x96 PCR+Melt v2.pcl" cycling conditions. Data was pre-processed via the SINGuLAR Analysis Toolset and then futhered analyzed using custom R scripts that incorporated tSNE, clustering via k.means and differential gene expression analysis.  The protocol can be found using PMID 29224077 (Holt et al).

last: Gioia

first: Marie

last: Holt

first: Anne

last: Costanzo

first: Siddhartha

last: Sharma

first: Brian

last: Abe

first: Lisa

last: Kain

first: Maki

last: Nakayama

first: Xiaoxiao

last: Wan

first: Andrew

last: Su

first: Clayton

last: Mathews

first: Yi-Guang

last: Chen

first: Emil

last: Unanue


title: CHD1 functions as a prostate-specific tumor suppressor by modulating nuclear receptor specificity towards distinct transcriptional programs [ChIP-seq]

first: Deli

last: Liu

summary: Deregulation of chromatin architecture is emerging as a critical feature of carcinogenesis, and genomic alterations in nucleosome remodelers are common in human cancer. Recurrent deletion of the chromatin remodeler CHD1 is among the most common alterations in prostate cancer, but its role as a tumor suppressor and the reasons for the tissue-specific nature of CHD1 deletion remain undefined. Here, we show that deletion of CHD1 drives prostate tumorigenesis and fundamentally reprograms the transcriptional program of the androgen receptor (AR), diverting AR towards an oncogenic transcriptional program and away from a growth suppressive transcriptome.  Conditional deletion of Chd1 in mouse prostate resulted in prostate neoplasia in vivo, confirming CHD1 as a tumor suppressor in prostate tissue. In prostate cells, the interactome of chromatin-bound CHD1 was enriched for factors that regulate nuclear receptor function, and interrogation of the CHD1 cistrome revealed promoter-independent enrichment of CHD1 at sites specifically occupied by AR and its associated transcriptional regulators. Deletion of CHD1 resulted in a dramatic redistribution of AR across the genome, localizing AR to sites enriched for HOXB13, and depleting AR at AR-halfsite motifs, consistent with the AR cistrome and epigenetic marks in human prostate cancer samples. Furthermore, the CHD1 null AR cistrome was associated with a unique AR transcriptional signature, enriched for pro-oncogenic pathways and depleted for processe consistent with normal prostatic function. Collectively, these data implicate CHD1 as a prostate-specific tumor suppressor which constrains the oncogenic functions of AR though maintenance of a normal AR transcriptional program.

overall_design: LNCaP cells were initally assessed for genomic distribution of AR, CHD1, H3K4me3, H3K27me3, and cMYC under androgren proficient conditions using ChiP Sequencing.  Each condtion/IP was conducted in biological duplicate and analyzed for tag enrichment as compared to input controls.  The AR cistrome was also analyzed in the presence or absence of CHD1 in cells expressing with a scrambled (sgCtrl) or CHD1 targeting (sgCHD1) sgRNA.  Tag enrichment was assessed for each biological replicate using sequneced input samples from each cell line as a control.

first: Christopher

middle: E


title: Arctigenin attenuates diabetic kidney disease through the activation of PP2A in podocytes

status: Public on Jul 17 2019

first: Chengguo

last: Wei

address: 1428 Madison Ave1468 Madison Ave

department: Medicine

summary: Arctigenin (ATG) is a major component of Fructus Arctii, which as a traditional herbal remedy reduced proteinuria in diabetic patients. However, whether ATG specifically provided renoprotection in DKD was not known. Here we report that ATG administration is sufficient to attenuate proteinuria and podocyte injury in mouse models of diabetes. Transcriptomic analysis of diabetic mouse glomeruli showed that cell adhesion and inflammation are two key pathways affected by ATG treatment, and mass spectrometry analysis identified protein phosphatase 2A (PP2A) as one of the top ATG-interacting proteins in renal cells. Enhanced PP2A activity by ATG reduces p65 NF-κB-mediated inflammatory response and high glucose-induced migration in cultured podocytes via its interaction with Drebrin-1. Importantly, podocyte-specific Pp2a deletion in mice exacerbates DKD injury and abrogates the ATG-mediated renoprotection. Collectively, our results clearly demonstrate a renoprotective mechanism of ATG via PP2A activation and establish PP2A as a potential target for DKD progression.

overall_design: To elucidate the underlying mechanism of renoprotection conferred by ATG in DKD, we performed the RNA sequencing of isolated glomeruli from the diabetic and control eNOS-/- mice treated with ATG or vehicle. Diabetes was induced in 8-week old mice with intraperitoneal administration of streptozotocin (STZ, Sigma S0130, dissolved in 0.1 M citrate buffer, PH 4.5) at 50mg/kg after 4-6 hours of food deprivation each day for 5 consecutive days. Citrate buffer-injected mice served as nondiabetic controls. 10 weeks after diabetes induction, mice were given ATG (Cayman Chemicals) dissolved in 5% DMSO by oral gavage at a dose of 40mg/kg body weight/day for 8 weeks. 5% DMSO vehicle-treated mice served as controls.

first: Yifei

last: Zhong

first: Kyung

last: Lee


title: Development of a chimeric model to study and manipulate human microglia in vivo (scRNA-seq dataset)

status: Public on Jul 30 2019

city: Irvine

first: Mathew

last: Blurton-Jones

address: 845 Health Sciences Road, Room 3200

department: Neurobiology and Behavior

institute: University of California, Irvine

summary: iPSC-derived microglia offer a powerful tool to study microglial homeostasis and disease-associated inflammatory responses. Yet, microglia are highly sensitive to their environment, exhibiting transcriptomic deficiencies when kept in isolation from the brain. Furthermore, species-specific genetic variations demonstrate that rodent microglia fail to fully recapitulate the human condition. To address this, we developed an approach to study human microglia within a surrogate brain environment. Transplantation of iPSC-derived hematopoietic-progenitors into the postnatal brain of humanized, immune-deficient mice results in context-dependent differentiation into microglia and other CNS macrophages, acquisition of an ex vivo human microglial gene signature, and responsiveness to both acute and chronic insults. Most notably, transplanted microglia exhibit robust transcriptional responses to Ab-plaques that only partially overlap with that of murine microglia, revealing new, human-specific Ab-responsive genes. We therefore have demonstrated that this chimeric model provides a powerful new system to examine the in vivo function of patient-derived and genetically-modified microglia.

overall_design: iHPCs were transplanted at P1 into male and female MITRG and 5X-MITRG mice then aged for up to 12 months. Whole brains were enzymatically digested and xMGs were isolated via negative MAC sorting from Male MITRG (n=1, 10.5mos), Female MITRG (n=1, 10.5 mos), Male 5X-MITRG (n=2, 11.5 and 12 mos.), and Female 5X-MITRG (n=2, 10.5 mos.). Single-cell RNA sequencing was then performed utilizing the 10X genomics platform..

first: Jonathan

last: Hasselmann


title: Determining gestational age using genome methylation profile

city: Jerusalem

first: Tal

last: Michaeli

address: Ein Kerem Campus

country: Israel

institute: The Hebrew University

summary: Background: Gestational age determination by traditional tools (last menstrual period, ultrasonography measurements and Ballard Maturational Assessment in newborns) have major limitations and therefore there is a need to find molecular marker approaches that can be used to determine the accurate gestational age of the newborn.  Methods: We performed RRBS (Reduced Representation Bisulfite Sequencing) on 41 cord blood and matching placenta samples.  Results: We identified a set of 316 Differentially Methylated Regions (DMRs) that undergo demethylation in late gestational age in cord blood cells and can predict the gestational age (r = -0.7, p value<0.0001). Once the set of 411 DMRs that undergo de novo methylation in late gestational age was used in combination with the first set it generated a more accurate clock (r=0.77, p value=1.87E-05).  Conclusion: Taken together, this study demonstrates that DNA methylation can accurately predict gestational age. The clinical use of this predictor should be further investigated.

overall_design: Cord blood and placenta samples were collected from 48 pregnancies that met the enrolment criteria. Samples with low quality DNA were removed. The methylation profile was determined for 40 whole blood samples and 41 placenta samples.

middle: F

first: Adam

last: Spiro

first: Ofra

last: Sabag

first: Gilad

last: Karavani

first: Simha

last: Yagel

first: Howard

last: Cedar

first: Yehudit

last: Bergman

first: Yuval

last: Gielchinsky


title: Loss of CHD1 facilitates oncogenic hijacking of AR during cancer progression [RNA-seq]

overall_design: Differentially expressed genes between LnCap CHD1 loss and ctrl under differen androgen stimulation for 0,3, and 8 hours and WT and CHD1 loss in mouse organoids

first: Michael

last: Augello

last: Barbieri


title: Transcriptomics of the Avian Immune Response in Hypothalamus, Spleen, and Red Blood Cells using RNA-seq

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: The goal of this research is to better understand the transcriptomic response in peripheral and neural tissue of zebra finch to lipopolysaccharide (LPS) challenge using RNASeq. The acute phase response (APR) is the initial reaction of the immune system to infection, and is triggered by pro-inflammatory cytokines or exposure to immunogens, such as bacterial LPS. The APR also inhibits reproduction and induces a number of physiological and behavioral symptoms, such as fever and sickness behavior. Through RNAseq, we can better understand the transcriptomic response of genes that are important for response to infection in a wild species such as the Zebra Finch. This has implications for disease surveillance programs that monitor the epidemiology of zoonotic diseases, like avian influenza and West Nile virus. We examine the transcriptomic response in Zebra Finch spleen and hypothalumus  to lipopolysaccharide (LPS) challenge; however, unlike mammals, with the exception of the camel, avian species have red blood cells that contain a nucleus, and will have gene regulation depending on the physiological needs of the organism. Therefore, we also took the opportunity to investigate the transcriptomic response of nucleated red blood cells to lipopolysaccharide (LPS) challenge.

overall_design: A comparison was made of the transcriptomic response to lipopolysccharide challenge (Escherishia Coli) of Zebra Finch hypothalamus, spleen, and red blood cells using birds injected with saline as experimental controls.

first: Noah

last: Ashley

first: Cassandra

last: Scalf

first: Julia

middle: H

last: Chariker


title: ATAC-seq profiling of control or Ptpn2-null P14 CD8+ T-cell subsets from mice chronically infected with LCMV clone 13

city: Boston

first: Brian

middle: Christopher

last: Miller

state: MA

address: 77 Avenue Louis Pasteur

department: Immunology

institute: Harvard Medical School

summary: Chromatin accessibility profiling of CD8+ T cells in chronic LCMV Clone 13 infected mice depleted of CD4+ T cells.

overall_design: ATAC-seq based profiling of subsets of transferred control or Ptpn2-null P14 CD8+ T-cells from mice chronically infected with LCMV Clone 13 (day 8 post-infection).

first: Martin

middle: W

last: LaFleur

first: Debattama

last: Sen


title: COMPASS Family Histone Methyltransferase ASH2L Mediates Corticogenesis via Transcriptional Regulation of Wnt Signaling [RNA-Seq 2]

status: Public on Jul 16 2019

city: Beijing

first: Xiaozhong

last: Peng

address: No.5, Dongdan Santiao, Dongcheng District

department: Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences

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

summary: We show that the COMPASS family histone methyltransferase co-factor ASH2L is required in NPCs proliferation and upper layer cortical projection neurons production and position. Deletion of ASH2L impairs trimethylation of H3K4 and transcriptional machinery specifically for subsets of Wnt-β-catenin signaling, disrupting their transcription and consequently inhibiting the proliferation ability of NPCs in late stages of neurogenesis.

overall_design: We generated D6-Cre Ash2l conditional knockout mice.Through RNA-seq and ChIPseq of dorsal cortex from Ash2l WT and cKO mice to identify the role of Ash2l during corticogenesis

first: Liang

last: Li


title: Ptpn2 regulates the generation of cytotoxic Tim-3+ CD8+ T cells and restrains anti-tumor immunity

summary: Cellular and transcriptional experiments demonstrate that deletion of Ptpn2 enhances CD8+ T cell responses to chronic viral infection and cancer.

overall_design:
Murine bone-marrow chimeras were generated by intravenous transfer of lineage- Sca-1+ Kit+ (LSK) cells, derived from a CD45.1+ Cas9+ expressing mouse and infected with either control or Ptpn2-targeting sgRNAs, into irradiated recipient CD45.2 mice. CD8+ cells derived from the reconstituted hematopoetic compartment of the recipient mice were then isolated for transfer to host mice. For LCMV co-transfer studies, cells were transferred (500:500 mix) to recipient mice on day -1, and mice were infected with LCMV Clone 13 on day 0. For tumor co-transfer studies, cells were transferred (1000:1000 mix) to recipient mice on day -1, and mice were injected with MC38-OVA or B16-OVA on day 0. Day 7 or 8 post tumor or virus injection respectively, co-transferred T cells were isolated from the tumor or spleen (LCMV) (as above) and replicates of 500 cells were FACS sorted for transcriptional profiling.

A file with detailed methods is included at the foot of this record.

first: Kathleen

last: Yates


title: PTPN2 regulates the generation of exhausted CD8+ T cell subpopulations and restrains tumor immunity

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


title: Metabolomics, Transcriptomic and Genetic - Integrative Analysis Reveals Important Roles of Adenosine Diphosphate in Haemostasis and Platelet Activation in Non-Small Cell Lung Cancer

city: London

first: Long

last: Hoang

address: Dovehouse Street

department: Genomic Medicine

institute: Imperial College London

summary: Transcriptomic and genetic profiles of tumours and matched normal tissues could help to identify important factors and potential therapeutic targets that contribute to tumorigenesis. We integrated omics profiles in tumours and matched adjacent normal tissues of patients with LUSC (N = 20) and LUAD (N = 17)

overall_design: Global gene expression of tumour samples from patients with LUAD and LUSC were compared with the matched normal tissues

middle: T

first: Clara

last: Domingo-Sabugo

first: Elizabeth

last: Starren

first: Saffron

last: Willis-Owen

first: Deborah

last: Morris-Rosendahl

first: Andrew

last: Nicholson

first: William

last: Cookson

first: Miriam

last: Moffatt


title: Single cell RNA‐seq in the sea urchin embryo show marked cell‐type specificity in the Delta/Notch pathway

city: Providence

first: Gary

last: Wessel

state: RI

address: 185 Meeting St

department: Molecular Biology, Cell Biology & Biochemistry

institute: Brown University

summary: Overall, we conclude that single cell RNA‐seq analysis in this embryo is revealing of the cell types present during development, of the changes in the gene regulatory network resulting from inhibition of various signaling pathways, and of the selectivity of these pathways in influencing developmental trajectories.

overall_design: Adult S. purpuratus were obtained from South Coast Bio‐Marine info@scbiomarine.com and were spawned using 0.5 M KCl injections intracoelomically. DAPT (Tocris) was added at fertilization to 8 μM, a concentration previously determined to effectively perturb Delta/Notch signaling without affecting overall development (Materna & Davidson, 2012). C59 (Cellagen) was added at 0.5 μM at fertilization as previously described (Cui et al., 2014). Embryos were cultured and, at appropriate developmental stages, were dissociated into single cells as described (McClay, 2004). We started with 50 ml cultures containing 0.25% of embryos (125 ul of embryos in 50 ml). The full volume was dissociated into single cells. We obtained 12 million single cells from which 5,000 were used for the DropSeq.The single‐cell RNA‐seq protocol was performed using the ChromiumTM Single Cell 3′ reagent kit v2 chemistry and cells were loaded on a GemCode Single Cell Instrument (10× Genomics, Pleasanton, CA).

first: Stephany

last: Foster


title: Primary Human B-cell Temporal Response to CD40L Stimulation

first: Benjamin

last: Gewurz

state: Massachusetts

address: 181 Longwood Ave

institute: Brigham and Women's Hospital

summary: RNAseq was used to identify primary human B-cell responses to CD40L stimulation.  Primary human peripheral blood B-cells were isolated by negative selection and then subjected to 0, 1 or 18 hours of mega-CD40L stimulation at 50 ng/ml.

overall_design: Primary human B cells were untreated or treated with CD40L for different lengths of time. RNA-seq was performed on these samples to conduct transcriptome profiling.

first: Yijie

last: Ma

first: Chang

last: Jiang


title: Defining an evolutionarily conserved role of GW182 in circular RNA degradation.

city: Chongqiing

first: Chuan

last: Huang

state: C

address: No.174 Shazhengjie

institute: Chongqing University, China

summary: By using dsRNA screening, we found that GW182 is critical for the degradation of circRNA in the Drosophila cells. To further confirm our finding genome widely, S2 cells were treated with either β-gal dsRNA (as a control) or GW182 dsRNA for 3 days and total RNA was extracted and sequenced after ribosome depletion. By comparing the expression level of both circRNAs and linear mRNAs between controls and GW182 depleted samples, we confirmed that GW182 depletion led to accumulation circRNAs but not their parental linear mRNAs, indicating that GW182 may play an import role in the degradation of circRNAs.

overall_design: Three biological replicates for both beta-gal dsRNA and GW182 dsRNA treated samples.

first: Meisheng

last: Xiao


title: COMPASS Family Histone Methyltransferase ASH2L Mediates Corticogenesis via Transcriptional Regulation of Wnt Signaling

first: Xiaozhong

last: Peng

summary:
This SuperSeries is composed of the SubSeries listed below
Histone methylation is essential for regulating gene expression during organogenesis to maintain stem cells and execute a proper differentiation program for their descendants. Here, we show that the COMPASS family histone methyltransferase co-factor ASH2L is required for maintaining neural progenitor cells (NPCs) and the production and positioning of projection neurons during neocortex development. Specifically, loss of ASH2L in NPCs results in malformation of the neocortex; the mutant neocortex shows fewer neurons that are also abnormal in composition and laminar position. Moreover, ASH2L loss impairs the trimethylation of H3K4 and the transcriptional machinery specific for Wnt-β-catenin signaling, inhibiting the proliferation ability of NPCs at late stages of neurogenesis by disrupting S phase entry to inhibit cell cycle progression. Overexpressing β-catenin after ASH2L elimination rescues the proliferation deficiency. Therefore, our findings demonstrate ASH2L is crucial for modulating Wnt signaling to maintain NPCs and generate a full complement of neurons during mammalian neocortex development.

overall_design:
Refer to individual Series
For RNA-seq, there are two databases and each of within  three biological replicates :
1) WT and Ash2l cKO dorsal cortices of E14.5 and 16.5;
2)Primary neurospheres derived from WT and Ash2l cKO dorsal cortices of E14.5, which cultured for 7 days.
For ChIP-seq, we test ASH2L and H3K4me3 binding peak in E14.5 WT dorsal cortices, and H3K4me3 binding peak in E14.5 KO dorsal cortices. ASH2L within two technical replicates.


title: A Novel Silent Mutation in the L1CAM Gene causing Fetal Hydrocephalus

city: hangzhou

first: yixi

last: sun

state: zhejiang

address: XUESHI ROAD 1

institute: Zhejiang University

summary:
To explore the genetic cause of a Chinese woman with fetal hydrocephalus
X-linked hydrocephalus (XLH), a genetic disorder, has an incidence of 1/30,000 male births. The great proportion of XLH is ascribed to loss of function mutations of L1 cell adhesion molecule gene (L1CAM), but silent mutations in L1CAM with pathogenic potential were rare, and were usually ignored especially in WES detection. In the present study, we describe a novel silent L1CAM mutation in a Chinese pregnant woman reporting continuous five times pregnancies with fetal hydrocephalus. After fetal blood sampling, we found c.453G>T (p.Gly151=) in L1CAM gene of the fetus by whole exome sequencing (WES), RT-PCR of the mRNA from cord blood mononuclear cells and subsequent sequence analysis identified the mutation created a potential 5' splice site consensus sequence, which would result in an in-frame deletion of 72 bp from exon 5 and 24 amino acids of the L1CAM protein. Heterozygous mutations were confirmed in analyzing DNA and mRNA from peripheral blood mononuclear cells of the woman, and, a severe L1 syndrome was confirmed by fetal ultrasound scan and MRI. Our study first indicated c.453G>T (p.Gly151=) in L1CAM could be disease causing for hydrocephalus, which would aid in genetic counseling for the prenatal diagnosis of hydrocephalus. Meanwhile, it suggested some silent mutations detected in WES should not be ignored, splicing predictions of these mutations were necessary.

overall_design: Fetal blood sampling was conducted at 26 weeks of gestational age,one sample was analyzed by Affymetrix CytoScan HD Array

first: Yixi

last: Sun

first: Minyue

last: Dong


title: ATAC-Seq examining the TFH and TEFF primed in Wild-type and IL6 KO mice

city: Birmingham

first: Andre

last: Ballesteros-Tato

state: Al

address: 1825 University Blvd Shelby building.  Office 413

department: Medicine, Division of Clinical Immunology and Rheumatology

institute: University of Alabama at Birmingham

summary: The goal of this study was to determine if there were differences in chromatin accessiblity between TFH and TEFF developing in Wild-type and IL6 KO mice

overall_design: OTII (CD45.1+) cells were adoptively transferred into WT (C57Bl/6) and Il6-/- recipient mice. One day later, recipient mice were infected with PR8-OTII. Seven days after infection, 30,000 donor-derived CD45.1+CXCR5hiSLAMloCD4+CD19- TFH and CD45.1+CXCR5loSLAMhi CD4+CD19- Teff cells were sorted from the mLN of WT and Il6-/- recipient mice

first: Amber

last: Papillion

first: Michael

middle: D

last: Powell

first: Danielle

last: Chislom

first: Holly

last: Bachus

last: Fuller

first: Amy

last: Weinmann

first: Alejandro

last: Villarino

first: John

last: O’Shea

first: Beatriz

last: León

first: Kenneth

last: Oestreich

first: André


title: Kdm6b is Required for Self-Renewal of Normal and Leukemic Stem Cells Under Proliferative Stress

city: St Louis

first: Grant

last: Challen

state: MO

address: 660 Euclid Avenue

institute: Washington University School of Medicine

summary: Recent studies have indicated that the histone 3 lysine 27 (H3K27me2/3) demethylase KDM6B (JMJD3) is frequently upregulated in a myriad of blood disorders including myelodysplastic syndrome (MDS), T-cell acute lymphoblastic leukemia (T-ALL), and multiple myeloma (MM) suggesting it may have important functions in the pathogenesis of hematopoietic cancers.  Here, we sought to determine the role of Kdm6b in hematopoietic stem cell (HSC) fate decisions under normal and malignant conditions to evaluate its potential as a therapeutic target. We show that loss of Kdm6b leads to a significant reduction in phenotypic and functional HSCs in adult mice, and that Kdm6b is necessary for HSC self-renewal in response to inflammatory, genotoxic and oncogenic stress.  Additionally, we show that loss of Kdm6b in HSCs leads to a stress-response gene expression signature in native HSCs that is independent of its demethylase activity.  Loss of Kdm6b lead to increased expression of a subset of genes implicated in HSC quiescence (e.g. Fos, Jun, Ier2, Dusp1, Zfp36). Upon inflammatory or replicative stress, HSCs deficient for Kdm6b are not able to efficiently resolve this gene expression program, leading to increased quiescence and a self-renewal block, forcing them to differentiate.  These findings show that Kdm6b is necessary for self-renewal of normal and leukemic stem cells, and suggest inhibiting Kdm6b in blood cancers in the presence of proliferative agents may force differentiation and eventual depletion of leukemic stem cells.

overall_design: Hematopoietic stem cells (HSCs) were sorted from Vav-CRE:Control and Vav-CRE:Kdm6b-KO mice for RNA-seq to determine gene expression and ChIPmentation for H3K27me3 and H3K4me3 chromatin markers

first: Cates

last: Mallaney

first: Elizabeth

middle: L

last: Ostrander

first: Hamza

last: Celik

first: Ashley

last: Kramer

first: Andrew

last: Martens

first: Alok

last: Kothari

first: Won

middle: K

last: Koh

first: Emily

last: Haussler


title: A novel spleen-resident immature NK cell subset and its maturation in a T-bet-dependent manner

status: Public on Jul 15 2019

city: hefei

first: baohui

last: wang

state: anhui

address: No.443 huangshan road

department: Institue of Immunology

institute: University of Science and Technology of China

summary: We identified a unique NK cell subset (DN NK) in the spleen. These cells displayed an immature phenotype and could develop into mature conventional NK (cNK) cells.

overall_design: DN NK and cNK mRNA profiles of wild type mice were generated by deep sequencing, in triplicate, using Illumina

first: Baohui

last: Wang

first: Hui

last: Peng

first: Zhigang

last: Tian


title: ATACSeq - human CAR-T cells treated with lenalidomide

city: Seattle

first: Timothy

middle: George

last: Johnstone

state: WA

address: 400 Dexter Ave N #605

department: Computational Genomics & Data Science

institute: Juno Therapeutics

summary: Genome-wide DNA accessibility maps of chromatin state in human CAR-T cells treated with lenalidomide in the presense or absense of Ag-specific restimulation

overall_design: Anti-BCMA CAR T cells were cultured in the presence or absence of BCMA beads for either 24 hours or 7 days with or without 1 µM lenalidomide and subjected to ATACSeq

first: David

last: Kugler

first: Melissa

last: Works


title: Ecdysone-induced 3D chromatin reorganization involves active enhancers bound by Pipsqueak and Polycomb

city: Omaha

first: M

middle: Jordan

last: Rowley

state: NE

address: 601 S Saddle Creek Rd

department: GCBA

institute: Univ of Nebraska Medical Center

summary: In Drosophila, Polycomb (Pc) has emerged as a loop-anchored associated protein, but further investigation of its directed chromatin architecture is needed. It is recruited to DNA by GAGA-binding factors GAF and Pipsqueak (Psq). psq encodes distinct isoforms that contain or lack a BTB oligomerization domain, but their contribution to the general epigenetic role of Psq in development and cancer is rarely considered. Here, we use HiChIP in Drosophila cells to characterize the Pc- and Psq-directed genome architecture. We show that PsqS isoforms lacking the BTB domain are consistently found at Pc loop anchors and at active enhancers, including those responsive to ecdysone. PsqS mediates ecdysone-induced enhancer-promoter interactions, coordinating expression of a selective set of genes by chromatin looping. BTB-Psq isoforms, on the other hand, bind at architectural protein binding sites. Our findings support a BTB-directed role of Psq at different types of regulatory elements, mediating selective responses to hormonal cues.

overall_design: HiChIP, ChIP-seq

first: Irene

last: Gutierrez-Perez

first: Jordan

first: Xiaowen

last: Lyu

first: Viviana

last: Valadez

first: Esther

last: Ballesta-Illan

first: Jose

middle: p

last: Lopez-Atalaya

first: Isaac

last: Kremsky

first: Diana

last: Vallejo

last: Caparros

first: Victor

last: Corces

first: Maria

last: Dominguez


title: COMPASS Family Histone Methyltransferase ASH2L Mediates Corticogenesis via Transcriptional Regulation of Wnt Signaling [RNA-seq]

first: Xiaozhong

first: Liang

last: Li


title: The mRNA degradation factor Xrn1 regulates transcription elongation in parallel to Ccr4

city: Burjassot

first: Antonio

last: Jordan

state: Valencia

address: Doctor Moliner 50

country: Spain

institute: Universitat de Valencia

summary: During the last decade several examples of coordination between gene transcription and mRNA degradation have been reported. mRNA imprinting by Rpb4 and 7 subunits of RNA polymerase II (RNAPII) and by the Ccr4-Not complex allows controlling its fate during transcription. Transcription regulation by mRNA degradation factors like Xrn1 constitutes a feedback loop that contributes to mRNA homeostasis. Mechanistic details of these phenomena are unclear. Most studies involve measurement of mRNA decay rates, usually  by stressing procedures such as transcriptional shut-off or incorporation of modified nucleotides that can lead to biased results. In this work we have used the easily repressible yeast GAL1 gene to perform a genetic analysis of mRNA synthesis and degradation under physiological conditions. We combined this experimental approach with computational multi-agent modelling, testing different possibilities of Xrn1 and Ccr4-Not action in gene transcription. This double strategy brought us to conclude that Xrn1 regulates RNAPII backtracking in a Ccr4-independent manner. We validated this conclusion measuring TFIIS genome-wide recruitment to elongating RNAPII molecules. We found that xrn1∆ and ccr4∆ exhibited very different patterns of TFIIS/RNPAII which confirmed their differential role in controlling transcription elongation.

overall_design: 18 ChIP-seq samples: 2 IP and 1 Input; 3 strains; 2 replicates each.

first: Victoria

last: Begley

first: Daniel

last: Corzo

last: Jordán-Pla

first: Abel

last: Cuevas-Bermúdez

last: Pérez-Aguado

first: Mercedes

last: Machuca-Ostos

first: Francisco

last: Navarro

first: María

middle: J

last: Chávez

first: José

last: Pérez-Ortín

first: Sebastián


title: RNASeq: lenalidomide-treated anti-BCMA CAR T cells

first: Timothy

last: Johnstone

summary: Transcriptom-wide RNA expression profilng in human CAR-T cells treated with lenalidomide in the presense or absense of Ag-specific restimulation

overall_design: Anti-BCMA CAR T cells were cultured in the presence or absence of BCMA beads for either 24 hours or 7 days with or without 1 µM lenalidomide and subjected to polyA RNASeq

middle: G

first: Christopher

last: Clouser

first: Melissa

last: Works


title: COMPASS Family Histone Methyltransferase ASH2L Mediates Corticogenesis via Transcriptional Regulation of Wnt Signaling [ChIP-seq]

last: Peng


title: Transcriptional analysis of HIV-specific CD4+ T cells in progressive disease and in spontaneously controlled infection.

city: Montreal

middle: Elias

last: Kaufmann

state: Quebec

address: 900 Rue St. Denis

country: Canada

institute: CRCHUM

summary:
The virus-specific CD4+ T cell dysfunction associated with failure to control chronic infections is poorly understood in humans.
In this study we sought to determine transcriptional signatures that link HIV-specific T cell help to viral control by performing genome wide transcriptional analysis on ex vivo stimulated HIV-specific CD4+ T cells from HIV-infected subjects with diverse viral loads, who were not on antiretroviral therapy at time of sampling.

overall_design: HIV-specific CD4 T cells were live-sorted after a 9-h stimulation of PBMCs with an HIV Gag peptide pool based on coupregulation of activation markers CD40L and CD69. The HIV-infected individuals were categorized in 3 groups: “Chronic progressors (CP) (n=11), defined as people with a viral load of more than 5,000 vRNA copies per ml of plasma; viremic controllers (VC) (n=9), defined as individuals with more than 50 and less than 5,000 vRNA per ml plasma; and elite controllers (EC) (n=12), defined as subjects who spontaneously controlled viremia to below 50 RNA copies per ml plasma in the absence of therapy.

first: Antigoni

last: Morou


title: Transcriptional analysis of HIV-specific CD4+ T cells after suppression of viremia by ART.

summary:
The virus-specific CD4+ T cell dysfunction associated with failure to control chronic infections is poorly understood in humans.  An issue of critical clinical relevance is the lack of restoration of effective anti-HIV immunity after suppressive ART: viral rebound is the rule after cessation of therapy. Whether persistent HIV-specific CD4+ T cell dysfunction on ART contribute to this failed response is an important, yet unresolved, question.
To decipher the consequences of ongoing viral antigen exposure, versus the results of durable cell-fate decision programs that would persist in former CP individuals after successful viral suppression on ART, we compared trancriptional profiles of chronic progressor before and after the initiation of ART, with the transcriptional profiles of elite controllers, HIV-infected individuals that spontaneously control viral load. Suppression of viremia by ART resulted in a distinct transcriptional landscape, with reduction in TFH gene expression but no correction of the TH1, TH17 and TH22 gene levels compared to the elite controller profile.

overall_design: HIV-specific CD4 T cells were live-sorted after a 9-h stimulation of PBMCs with an HIV Gag peptide pool based on coupregulation of activation markers CD40L and CD69. The HIV-infected individuals were categorized in 3 groups: “Chronic progressors before ART (CPpre) (n=8), untreated HIV-infected individuals with a viral load of more than 5,000 vRNA copies per ml of plasma; Chronic progressors after ART (CPpost) (n=8),   longitudinally followed CPs  for at least 6 months after initiation of ART therapy and suppression of viral load below 50 copies mL ; and elite controllers (EC) (n=12),  HIV-infected individuals who spontaneously controlled viremia to below 50 RNA copies per ml plasma in the absence of therapy.


title: Sebaceous gland progenitor cell RNAseq during morphogenesis and steady state homeostasis

city: Copenhagen

first: Svetlana

last: Ulyanchenko

address: Ole Maaløes Vej 5

country: Denmark

institute: Biotech Research and Innovation Centre

summary: Laser capture microdissection enriched for sebaceous gland basal cells at P4, P10, P30

overall_design: Examination of differences in gene expression during morphogenesis and steady state homeostasis in sebaceous gland progenitor cells

first: Kim

middle: B

last: Jensen


title: Transcriptional analysis of human peripheral CXCR5mem and CXCR5neg HIV-specific CD4 T cells in progressive disease

summary:
The virus-specific CD4+ T cell dysfunction associated with failure to control chronic infections is poorly understood in humans. A striking enrichment of a Tfh signature is observed in ex vivo stimulated HIV-specific CD4 T cells of Chronic progressors (CPs)  compared to Elite controls (ECs), which was not due to a higher fraction of CXCR5mem HIV-specific CD4 in CPs.
Here, we sought to define the cell subsets that contributed to the TFH transcriptional signature observed in CPs, applying microarray analysis to paired live-sorted subsets of CXCR5mem and CXCR5neg HIV-specific CD4+ T cells from CPs and ECs . The Tfh signature was not confined to TFH but also atypically enriched in CXCR5neg non-TFH cells and increased expression of key TFh molecules were enriched in the CXCR5neg HIV-specific CD4 T cells of CPs compared to ECs. Thus, altered differentiation is central to HIV-specific CD4+ T cell impairment and involves both gain and loss of functions.

overall_design: CXCR5mem and CXCR5neg HIV-specific CD4 T cells were live-sorted after a 9-h stimulation of PBMCs with an HIV Gag peptide pool. HIV-specific CD4 T cells were identified based on coupregulation of activation markers CD40L and CD69. The HIV-infected individuals were categorized in 2 groups: “Chronic progressors (CP) (n=5), defined as people with a viral load of more than 5,000 vRNA copies per ml of plasma; ; and elite controllers (EC) (n=4), defined as subjects who spontaneously controlled viremia to below 50 RNA copies per ml plasma in the absence of therapy.

middle: E


title: Associated bacteria affect sexual reproduction by altering gene expression and metabolic processes in a biofilm inhabiting diatom (Seminavis robusta)

city: Jena

first: Emilio

last: Cirri

address: Lessingstrasse 8

country: Germany

institute: Friedrich Schiller University Jena

summary: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of Seminavis robusta in presence and absence of associated bacterial spent medium (Maribacter sp. and Roseovarius sp.) in order to highlight the effect of bacterial exudates on diatom gene expression and metabolic processes.

overall_design: Transcriptomics of 6 different treatments of Seminavis robusta mating type - (MT-) treated with spent medium of associated bacteria (Roseovarius sp. and Maribacter sp.). In three treatments S. robusta was sexually induced (SIP, SIPM and SIPR), in other three treatments it was not sexually induced (C, M, R). Differential gene expression was employed to find genes influenced either by the induction fo sexuality, by the presence of bacteria or by both effects.

first: Sam

last: De Decker


title: Esrrb function in the extraembryonic ectoderm is required for proper primordial germ cell specification [RNA-seq]

city: Otsu

first: Eiichi

last: Okamura

state: Shiga

address: Seta, Tsukinowa-cho

department: Research Center for Animal Life Science

country: Japan

institute: Shiga University of Medical Science

summary: Estrogen related receptor beta (Esrrb) is an orphan nuclear receptor that is required for self-renewal and pluripotency in mouse embryonic stem (ES) cells. However, in the early post-implantation mouse embryo, Esrrb is specifically expressed in the extraembryonic ectoderm (ExE) and plays a crucial role in trophoblast development. In this study, to better understand the function of Esrrb in trophoblast lineage cells, we performed microarray analysis of Esrrb-null mutant versus wild-type mouse embryos. To further characterize the regulatory targets of Esrrb, we treated trophoblast stem (TS) cells with either Esrrb inhibitor DES or vehicle and compared their global gene expression profile via RNA-seq analysis. In addition, to ask whether these target genes are directly regulated by Esrrb, we performed Chromatin immunoprecipitation-sequencing (ChIP-seq) analysis of TS cells using anti-Esrrb antibody.

overall_design: Differential gene expression analysis was performed on trophoblast stem cells treated with diethylstilbestrol (Esrrb inhibitor) or ethanol (vehicle control)

first: Oliver

last: Tam

first: Eszter

last: Posfai

first: Lingyu

last: Li

first: Katie

last: Cockburn

first: Cheryl

middle: Q

last: Lee

first: Jodi

last: Garner

first: Janet

last: Rossant


title: Gene expression profiling  in RagC T89N germinal center B cells and RagC S74C murine B220+ lymphoma cells

city: Madrid

first: Kevin

last: Troulé

state: Madrid

address: Melchor Fernandez Almagro, 3

institute: SPANISH NATIONAL CANCER CENTER

summary:
Gene expression by RNAseq in murine germinal centers induced by SRBC in RagC T89N mice  (YRT codes) and RNAseq in murine B220+ from VavVPBcl2/RagC S74C and VavVPBcl2/RagC +/+ lymphomas

Follicular Lymphoma (FL) is an incurable B cell malignancy derived from germinal center (GC) B cells. The RRAGC gene, encoding a GTPase that links cellular nutrient sufficiency with the activation of mechanistic target of rapamycin complex 1 (mTORC1) is mutated in 15% of FL patients, but its impact in B cell functions and lymphomas is unexplored. Endogenous expression of Rragc mutant variants in B lymphocytes from novel knock-in strains of mice resulted in a partial insensitivity of mTORC1 to nutrient deprivation. A mild, but not a full-blown activation of the nutrient signaling pathway enhanced B cell activation and the GC response, suppressed apoptosis, and accelerated lymphomagenesis. Moreover, murine RRAGC mutant FL showed selective vulnerability to pharmacological inhibition of mTORC1. This moderate increase in nutrient signaling synergized with paracrine cues from the supportive T cell microenvironment that activate mTORC1 via the PI3K-Akt axis to promote B cell activation. Hence, RRAGC mutations sustained experimental GCs and murine and human FL in the presence of decreased T cell support. Moreover, mutations in RRAGC in human FLs are mutually-exclusive with mutations that result in increased abundance of T helper cells, consistent with functional redundancy between those pathways. Taken together, our results support a model in which activating mutations in the nutrient signaling pathway foster lymphomagenesis by corrupting a nutrient-dependent control of mTORC1-activating paracrine signals from the T cell microenvironment

overall_design: Using RNA-seq we profiled murine Germinal Centers (GCB cells) induced by SRBC in RagC T89N/+ (n=4) and RagC +/+ mice (n=4). We have also profiled murine B220+ purified cells from VavVPBcl2/RagC S74C (n=4)and VavVPBcl2/RagC +/+ lymphomas (n=7)

first: Ana

last: Ortega-Molina

first: Osvaldo

last: Graña

first: Alejo

last: Efeyan


title: Esrrb function in the extraembryonic ectoderm is required for proper primordial germ cell specification [ChIP-seq]

overall_design: Genome-wide binding of Esrrb in trophoblast stem cells was assessed by ChIP-Seq using anti-Esrrb antibody. An input control was generated concurrently


title: Gene expression profiling  in RagC S74C germinal center B cells

summary:
Gene expression by RNAseq in murine germinal center B cells induced by SRBC in RagC S74C mice

Follicular Lymphoma (FL) is an incurable B cell malignancy derived from germinal center (GC) B cells. The RRAGC gene, encoding a GTPase that links cellular nutrient sufficiency with the activation of mechanistic target of rapamycin complex 1 (mTORC1) is mutated in 15% of FL patients, but its impact in B cell functions and lymphomas is unexplored. Endogenous expression of Rragc mutant variants in B lymphocytes from novel knock-in strains of mice resulted in a partial insensitivity of mTORC1 to nutrient deprivation. A mild, but not a full-blown activation of the nutrient signaling pathway enhanced B cell activation and the GC response, suppressed apoptosis, and accelerated lymphomagenesis. Moreover, murine RRAGC mutant FL showed selective vulnerability to pharmacological inhibition of mTORC1. This moderate increase in nutrient signaling synergized with paracrine cues from the supportive T cell microenvironment that activate mTORC1 via the PI3K-Akt axis to promote B cell activation. Hence, RRAGC mutations sustained experimental GCs and murine and human FL in the presence of decreased T cell support. Moreover, mutations in RRAGC in human FLs are mutually-exclusive with mutations that result in increased abundance of T helper cells, consistent with functional redundancy between those pathways. Taken together, our results support a model in which activating mutations in the nutrient signaling pathway foster lymphomagenesis by corrupting a nutrient-dependent control of mTORC1-activating paracrine signals from the T cell microenvironment

overall_design: Using RNA-seq we profiled murine Germinal Center B cells (GC B cells) induced by SRBC in RagC S74C/+ (n=4) and RagC +/+ mice (n=4)


title: Esrrb function is required for proper primordial germ cell development in presomite stage mouse embryos

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

overall_design: Refer to individual Series


title: Transcriptional analysis of HIV-specific CD4+ T cells

first: Daniel

last: Kaufmann


title: The effects of U1 snRNA mutation in chronic lymphocytic leukemia cell lines

status: Public on Jul 13 2019

city: Toronto

first: Shimin

last: Shuai

state: ON

address: MaRS Centre, 661 University Avenue Suite 510

institute: ONTARIO INSTITUTE FOR CANCER RESEARCH

summary: Despite an intensive search for non-coding cancer drivers, only a few have been discovered to date and none have been found among the RNAs contributing to the spliceosome. Here we report a highly recurrent A>C somatic mutation at the third base of U1 spliceosomal RNA in several tumour types. This mutation changes the preferential A-U base-pairing between U1 and 5′ splice site to C-G base-pairing, thereby creating novel splice junctions and altering the splice pattern of multiple genes, including those related to cancer. Clinically, the A>C mutation is associated with alcohol consumption in hepatocellular carcinoma and the aggressive IGHV unmutated subtype of chronic lymphocytic leukaemia (CLL). The U1 hotspot mutation confers an adverse prognosis to CLL patients independently, and may represent a new target for treatment. Our study demonstrates one of the first non-coding drivers in spliceosomal RNAs and reveals a novel mechanism of aberrant splicing in human cancer.

overall_design: RNA-Seq of three CLL cell lines with or without the U1 g.3A>C mutation; each condition has two technical replicates


title: Identification and validation of GPD1 as an essential cancer stem cell specific target in glioblastoma

city: Heidelberg

first: Haikun

last: Liu

address: INF 581

institute: DKFZ


title: Esrrb function in the extraembryonic ectoderm is required for proper primordial germ cell specification [microarray]

overall_design: Extraembryonic ectoderm from WT and Esrrb mutant mice were pooled into 3 biological replicates each, and gene expression differences were assessed with Affymetrix microarray


title: KS-associated herpesvirus Rta and cellular POU proteins regulate DNA binding of the Notch signaling protein RBP-Jk/CSL broadly to the virus genome

status: Public on Jul 14 2019

city: Newark

first: David

middle: M.

last: Lukac

state: NJ

address: 225 Warren St.; ICPH E350C; PO Box 1709

department: Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers Univ./NJ Medical School

summary: Interaction of the Kaposi’s sarcoma-associated herpesvirus (KSHV) Rta protein with the cellular Notch signaling effector, Recombination Signaling Protein (RBP)-Jk (aka CSL and CBF-1), is essential for viral reactivation from latency.  We previously showed that Rta binds to a DNA motif repeated in the viral Mta promoter (called “CANT” or Rta-c) to stimulate RBP-Jk DNA binding, and distinguished Rta from the activated Notch-1 protein.  To determine whether Rta’s mechanism would apply generally to other viral promoters, we employed chromatin immunoprecipitation/deep sequencing (ChIP/Seq) to identify Rta and RBP-Jk binding sites across the KSHV genome.   We show that RBP-Jk binds nearly exclusively to unique genome sites during latency and reactivation.   Many, but not all, reactivation-specific RBP-Jk peaks were associated with Rta bound to single Rta-c motifs.   Other motifs that were over-represented with stimulated RBP-Jk DNA binding including those for the cellular DNA binding proteins BCL11A, MNT, MAF B, and TCF12.  Four of the top seven motifs that were most over-represented with inhibition of RBP-Jk DNA binding were putative binding sites for the Pit/Oct/Unc (POU) family of proteins, including POU3F3 (Oct-8) and POU5F1 (Oct-4).   Interestingly, two other POU motifs, including one for the POU2F1 (Oct-1) protein, are associated with inhibition of RBP-Jk DNA binding unless Rta bound to a nearby Rta-c motif.   The relative distances between the Rta-c, POU, and RBP-Jk motifs were conserved at reactivation-specific RBP-Jk peaks in three promoters that Rta transactivated, and the Rta-c and Oct-1 motifs overlapped in two of those.  The proximity of the Rta-c/Oct-1 motif to an RBP-Jk motif is critical for Rta transactivation of the ORF50AS/KbZIP promoter, and knockdown of Oct-1 protein debilitated reactivation and production of infectious virus.  Our data suggest a broad role for POU proteins in regulating DNA binding of RBP-Jk and its associated transactivators.

overall_design: ChIP/Seq using anti-Rta and anti-RBP-Jk antibodies on chromatin from B cells latently infected with KSHV or induced to reactivate by treating with valproic acid (VPA).  Rabbit total IGG is the control antibody.

middle: M

first: Olga

last: Gonzalez-Lopez


title: p53 binding and gene expression profiles in Drosophila postmitotic and embryonic tissue

city: Dallas

first: John

last: Abrams

state: TX

address: 6000 Harry Hines Blvd., NL7.110L

department: Cell Biology

institute: UT Southwestern Medical Center

summary: TP53 is the most frequently mutated gene in human cancers, and despite intensive research efforts, genome-scale studies of p53 function in whole animal models are rare. Yet the need for such in vivo studies is underscored by recent challenges to established models indicating that unappreciated p53 functions contribute to tumor suppression. Here we leveraged the Drosophila system to interrogate p53 function in a postmitotic context. In the developing fly, p53 robustly activates important apoptotic genes in response to radiation-induced DNA damage. We have recently shown that a p53 enhancer near the cell death gene reaper (p53RErpr), forms chromatin contacts and enables p53 target activation through long genomic distances. Interestingly, we found that this canonical p53 apoptotic program fails to activate in response to radiation in postmitotic tissue. Furthermore, the lack of apoptotic responses was not associated with altered chromatin contacts; instead we determined that p53 does not occupy the p53RErpr enhancer in postmitotic tissue. In addition, we conducted RNA-seq and ChIP-seq studies to directly compare the developing and postmitotic tissues, and we determined that p53 regulates distinct transcriptional programs in adult heads, which include DNA repair, metabolism and proteolysis genes. Strikingly, in the postmitotic context p53 binding landscapes were poorly correlated with nearby transcriptional effects, raising the possibility that p53 enhancers could be generally acting through long distances.

overall_design: We conducted RNA-seq and ChIP-seq studies to characterize and compare p53 function in Drosophila postmitotic and embryonic tissue in vivo.

first: Paula

last: Kurtz

first: Amanda

last: Jones


title: Illumina sequencing of PCR products derived from TBLV-induced tumors in the presence and absence of Rem

city: Austin

first: Dennis

middle: Cates

last: Wylie

state: Texas

address: 102 East 24th Street

department: Center for Biomedical Research Support

institute: University of Texas at Austin

summary: Sequencing of portions (polymerase, envelope, and part of the 3’ LTR) of the TBLV retroviral genome were recovered by PCR amplification from tumors induced with or without Rem expression.  PCR products from the mouse Gapdh gene were obtained as a control for acquisition of mutations during PCR and library preparation.

overall_design: PCR products and library preparation from several different parts of the TBLV genome were obtained for sequence analysis to determine if the loss of Rem gave hypermutation typical of Apobec cytidine deaminases.

first: Jaquelin

last: Dudley

first: Hyewon

last: Byun

first: Gurvani

last: Singh


title: TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation

status: Public on Jul 12 2019

city: Vancouver

first: Brad

last: Hoffman

state: BC

institute: University of British Columbia


title: TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation (E13.5 Dpy30∆P pancreas scRNA-Seq)

summary:
Purpose: To investigate whether pancreas progenitor specification may be altered, we performed single-cell RNA-sequencing (scRNA-seq) using E13.5 control and Dpy30∆P pancreas. To determine whether Dpy30∆P cells have a different developmental trajectory than control cells, we performed pseudo-temporal analysis (Trapnell et al., 2014).
Methods: Floxed Dpy30 mice were crossed to Pdx1-Cre driver mice to obtain conditional deletion of Dpy30 exon 4 in the pancreas. In all studies, knockout mice (Dpy30∆P, Pdx1-Cre; Dpy30flox/flox) were compared to littermate controls (Dpy30flox/flox or Dpy30flox/wt).
Results: In total, we sequenced 3,900 control and 3,044 Dpy30∆P cells from which 786 control and 477 Dpy30∆P epithelial cells were identified for further analysis. As expected, control progenitor cells gave rise to cells in two distinct branches corresponding to the acinar and endocrine lineages, with terminal markers upregulated in cells at the ends of these branches. Dpy30∆P progenitors differentiated along these same trajectories; however, relatively few Dpy30∆P cells were found at the ends of these branches, and acinar and endocrine terminal marker expression was reduced in Dpy30∆P cells. Interestingly, a higher fraction of Dpy30∆P cells were found within the MPC/BPC and acinar clusters, predominantly at the expense of endocrine cells. Analyzing the fraction of cells in G1 phase across pseudo-time showed that a higher fraction of Dpy30∆P acinar lineage cells were in G1 phase.
Conclusions: Overall, this suggests that MPC/BPCs and acinar cells may have a prolonged G1 phase due to a failure to appropriately induce genes essential for progression through G2M or S phase.

overall_design: Single-cell RNA-sequencing was performed using one E13.5 control and one E13.5 Dpy30∆P pancreas

first: Stephanie

middle: A

last: Campbell

first: Cassandra

last: McDonald

first: Nicole

last: Krentz

first: Francis

middle: C

last: Lynn


title: Notch1 enhances NF-κB activation to promote CD133+ Skin Cancer Stem Cells

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: Cancer stem-like cells are hypothesized to be the major tumor initiating cell (TIC) population of human cutaneous squamous cell carcinoma (hcSCC), but the molecular alterations underpinning their cellular phenotype remain undefined. Here, a small CD133+CD31-CD45-CD61-CD24- (CD133+) cell population enriched for self-renewing and TIC features was isolated by sorting from primary hcSCC tumors. CD133+ cells show enhanced spheroid formation in vitro and tumor generation in vivo. Gene expression profiling comparing CD133+ with CD133- cells revealed that CD133+ cells expressed enriched stem cell-like and cancer-related gene signatures. Eighty differentially expressed stem cell-related genes were identified in CD133+ cells, where the top pathways include Notch, Notch1-mediated NF-κB, and WNT signaling. Overexpression of growth factor receptors, PI3K/mTOR, and STAT pathway genes and inactivation of genes regulating epigenetic modification of chromatin implicated in cancer were also identified. Verification of these gene signatures was conducted with Nanostring in an independent tumor set. Pharmacologic or genetic modulation of Notch1, IKKα, RELA and RELB modulated NF-κB transactivation, the CD133+ population, and phenotype. Immunofluorescent staining confirmed co-localization of CD133+ and IKKα expression in SCC tumor specimens. Our data support the linkage and importance of non-canonical Notch1 and IKK-mediated NF-κB activation in promoting CD133+ population and TIC phenotype in hcSCC.

overall_design: Comparing Gene expression profiling for CD133+ with CD133- cells from the sorting from primary hcSCC tumors by 15 samples for both positive and neg in total 30 samples.

first: Xin

middle: X

last: Quan

first: Nga

last: Voong

first: Weiping

first: Jamie

last: Coupar

first: Steven

last: Lee

middle: W

last: Petersen

first: Daniel

last: Edelman

first: Paul

middle: S

last: Meltzer

first: Andrew

last: Montemarano

first: Marty

last: Braun

first: Jonathan

last: Vogel

first: Zhong

first: Carter

last: Van Waes


title: High-throughput sequencing of MiRNA

city: CHANGCHUN CITY

first: Tu

middle: zhong

last: zhong

address: LIUYING XILU 666

institute: CVRI

summary: We detected the differentially expressed miRNAs on CVS-11 infected BHK-21 cells at 48 h postinfection.

overall_design: Examination of different expression miRNAs in CVS-11 infected BHK-21 cells

first: zhongzhong

last: tu


title: Distinct tissue-specific roles for the disease-associated autophagy genes ATG16L2 and ATG16L1

city: Boston

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

summary: The clear role of autophagy in human inflammatory diseases such as Crohn’s disease was first identified by genome-wide association studies and subsequently dissected in multiple mechanistic studies. ATG16L1 has been particularly well studied in knockout and hypomorph settings as well as models recapitulating the Crohn’s disease-associated T300A polymorphism. Interestingly, ATG16L1 has a single homolog, ATG16L2, which is independently implicated in diseases including Crohn’s disease and systemic lupus erythematosus. However, the contribution of ATG16L2 to canonical autophagy pathways and other cellular functions is poorly understood.To better understand its role, we generate and analyze the first, to our knowledge, ATG16L2 knockout mouse. Our results show that ATG16L1 and ATG16L2 contribute very distinctly to autophagy and cellular ontogeny in myeloid, lymphoid and epithelial lineages. Dysregulation of any of these lineages could contribute to complex diseases like Crohn’s disease and systemic lupus erythematosus, highlighting the value of examining cell-specific effects. We also identify a novel genetic interaction between ATG16L2 and epithelial ATG16L1. These findings are discussed in the context of how these genes may contribute distinctly to human disease.

overall_design: Examination of the role of autophagy-related disease-associated genes using novel knock-out mouse model

first: Bernard

last: Khor

first: Kara

middle: L

last: Conway

first: Abdifatah

last: Omar

first: Moshe

last: Biton

first: Leigh

last: Baxt

first: Jakob

last: Begun

first: Petric

last: Kuballa

first: John

middle: D

last: Gagnon

last: Lassen

first: Aviv

last: Regev

first: Ramnik

last: Xavier


title: 10X single-cell RNASeq profiling of control or Ptpn2-null P14 CD8+ T-cells from mice chronically infected with LCMV Clone 13

first: Brian

middle: Christopher

last: Miller

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: 5 distinct populations of exhausted CD8+ T cells occur in chronic LCMV Clone 13 infected mice depleted of CD4+ T cells

overall_design: Single-cell RNA-sequencing based profiling of transferred control or Ptpn2-null P14 CD8+ T-cells from mice chronically infected with LCMV Clone 13 (day 30 post-infection)

first: Martin

last: LaFleur


title: Genome-wide methylation analysis of cancer-associated fibroblasts using Infinium HumanMethylation 450 BeadChip

city: Chuo-ku, Tokyo

first: Masahiro

last: Maeda

address: 5-1-1, Tsukiji

department: Division of Epigenomics

institute: National Cancer Center Research Institute

summary: DNA methylation in cancer-associated fibroblasts

overall_design: An epigenetic landscape of CAFs was characterized.

first: Hideyuki

last: Takeshima

first: Naoko

last: Iida

first: Satoshi

last: Yamashita

first: Toshikazu

last: Ushijima


title: TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation (shWdr5 lentivirus treated spheres )

first: Brad

last: Hoffman

summary:
Purpose: To determine the genome-wide effect of Wdr5 and Dpy30 suppression on acinar, duct and endocrine gene activation during pancreas spheroid differentiation
Methods: We adapted an ex vivo mouse E13.5 pancreas spheroid model of growth and differentiation (Sugiyama et al., 2013) and generated RNA-sequencing data from pooled shScramble, shWdr5 and shDpy30 spheroids.
Results: We identified 1,744 genes whose expression was substantially impaired and 693 genes with increased expression in shWdr5-treated spheres compared to shScramble controls. In shDpy30-treated spheres, we identified no genes with impaired expression and only 2 genes with increased expression compared to shScramble controls. Genes expressed in pancreas progenitors were largely not altered by either Wdr5 or Dpy30 suppression. However, genes expressed in the endocrine (Gcg, Ins1, Ins2 and Neurog3) and acinar (Cpa1, Cpa2 and Amy2) lineages had dramatically reduced expression in shWdr5-treated spheres, but were unaffected by Dpy30 suppression.
Conclusions: These data suggest that the co-activator activity of the TrxG complexes and not their methyltransferase activity, is required for acinar and endocrine cell gene activation in an ex vivo model of pancreas development.

overall_design: RNA-sequencing data was generated from combining > 4 sphere differentiations from Day 7 shScramble, shWdr5 and shDpy30 lentivirus treated spheres

first: Stephanie

last: Campbell

first: Cassandra

last: McDonald

first: Nicole

middle: J

last: Krentz

first: Francis

last: Lynn

middle: G


title: The RNA exosome nuclease complex regulates human embryonic stem cell differentiation [RNA-Seq SS]

status: Public on Jul 11 2019

city: Frederick

first: Sandra

last: Wolin

state: Maryland

address: 1050 Boyles Street, BLDG 560 Room 11-39

department: NCI

institute: NIH

summary: This work shows that the exosome modulates the levels of LINE-1 retrotransposons, miRNAs, lncRNAs and specific mRNAs that encode developmental regulators or affect their expression. The exosome restrains differentiation in part by degrading transcripts encoding FOXH1, a transcription factor crucial for mesendoderm formation.

overall_design: RNA profiles of hESCs expressing doxycycline-inducible shRNA against the RNA exosome subunit EXOSC3 (shEXOSC3) or a control non-silencing shRNA (shNS) after 5 or 7 days of doxycycline treatment

first: Cedric

last: Belair

first: Soyeong

last: Sim

first: Kun-Yong

last: Kim

first: Yoshiaki

last: Tanaka

first: In-Hyun

last: Park


title: TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation (shDpy30 lentivirus treated spheres)


title: PAX5 belongs to a functional transcription factor network commonly targeted in B-lineage leukemia

city: Lund

first: Jonas

last: Ungerback

address: Klinikgatan 26

department: Division of Molecular Hematology

institute: Lund University

summary:
One of the most frequently mutated proteins in human B-lineage leukemia is the transcription factor PAX5 mutated in about one third of all cases. While reduced function of PAX5 has a clear link to human malignancy there is limited evidence for that the this directly impact the development of function of B-cell progenitors. One possible explanation to this comes from the finding that PAX5 mutated B-ALL display complex karyotypes and additional mutations. This suggestsindicating that PAX5 might be one component of a larger transcription factor network targeted in B-ALL. To investigate the functional network associated with PAX5 we identified proteins associated with this transcription factor using BioID technology. This identified more than 239 proteins several of which could be found mutated in human B-ALL. Most prominently we identified IKZF1, commonly mutated, and RUNX1, involved in the formation of ETV6-AML1 fusion protein formation, among the interaction partners. CHIPChIP-seq as well as PLAC-seq analysis supported the idea that these factors share regulatory elements in human B-ALL cells. Gene expression and mutation analysis of both mouse models and primary human leukemia suggested that these factors form a functional gene regulatory network targeted by multiple mutations in human B-ALL.
In summary, we here present a model where a transcription factor can work through redeployment of other factors and not only through sites that it binds itself.

overall_design: ChIP-Seq, ATAC-seq, and PLAC-sequencing in NALM6 B-ALL cells

first: Kazuki

last: Okuyama

first: Tobias

last: Strid

first: Shamit

last: Soneji

first: Stefan

last: Lang

last: Ungerbäck


title: The RNA exosome nuclease complex regulates human embryonic stem cell differentiation [RNA-Seq rescue_SS]

overall_design: RNA profiles of shEXOSC3-expressing hESCs carrying an shRNA-resistant EXOSC3 transgene (EXOSC3r) or an empty vector (PB)


title: The RNA exosome nuclease complex regulates human embryonic stem cell differentiation


title: TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation (E18.5 Dpy30∆P pancreas scRNA-seq)

last: Hoffman

summary:
Purpose: To gain insight into why Dpy30∆P acinar cells fail to express terminal makers, we performed scRNA-seq using E18.5 control and Dpy30∆P pancreata.
Methods: Floxed Dpy30 mice were crossed to Pdx1-Cre driver mice to obtain conditional deletion of Dpy30 exon 4 in the pancreas. In all studies, knockout mice (Dpy30∆P, Pdx1-Cre; Dpy30flox/flox) were compared to littermate controls (Dpy30flox/flox or Dpy30flox/wt).
Results: In total, we sequenced 8,050 control and 7,858 Dpy30∆P cells that with the E13.5 scRNA-seq data allowed us to identify 2,207 control and 2,354 Dpy30∆P epithelial cells. We found a cluster that contained almost entirely Dpy30∆P cells, where the expression of acinar cell digestive enzymes was consistently low. The distribution of gene expression values for terminal acinar markers suggested an increased distribution in gene expression levels in the Dpy30∆P cells relative to control cells; however, this was not the case for terminal endocrine markers. Comparing the variance-to-mean ratios in the Dpy30∆P and control cells showed an increase in variance in the Dpy30∆P acinar cells but not in endocrine cells.
Conclusions: Overall, these data suggest increased variation in acinar cell transcript expression in the Dpy30∆P pancreas.

overall_design: Single-cell RNA-sequencing was performed using one E18.5 control and one E18.5 Dpy30∆P pancreas


title: TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation (E18.5 Dpy30∆P pancreas)

summary:
Purpose: To gain insight into why Dpy30∆P acinar cells fail to express terminal makers, we performed RNA-seq using E18.5 control and Dpy30∆P pancreata.
Methods: Floxed Dpy30 mice were crossed to Pdx1-Cre driver mice to obtain conditional deletion of Dpy30 exon 4 in the pancreas. In all studies, knockout mice (Dpy30∆P, Pdx1-Cre; Dpy30flox/flox) were compared to littermate controls (Dpy30flox/flox or Dpy30flox/wt).
Results: Differential gene expression analysis demonstrated that endocrine cell hormones such as Ins2 and acinar cell digestive enzymes were downregulated in the E18.5 Dpy30∆P pancreas compared to controls. GO term analysis indicated that genes involved in pancreatic secretion, digestion and proteolysis were reduced in Dpy30∆P cells. Notably, transcripts with very high expression levels (above 9000 FPKM) were more downregulated in the E18.5 Dpy30∆P pancreas compared to transcripts with lower expression levels.
Conclusions: Overall, these data suggest increased variation in acinar cell transcript expression in the Dpy30∆P pancreas.

last: Campbell


title: The RNA exosome nuclease complex regulates human embryonic stem cell differentiation [PAR-iCLIP]

overall_design: RNA exosome targets were identified in human embryonic stem cells by performing PAR-iCLIP using antibodies against EXOSC4, a core subunit of the exosome.


title: Pathophysiology and therapeutics of arrhythmogenic right ventricular cardiomyopathy 5

first: Enrique

last: Lara-Pezzi

institute: CNIC

summary: Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC) is an inherited cardiac disease characterized by fibro-fatty replacement of the myocardium that causes heart failure and sudden cardiac death. The most aggressive subtype of ARVC is ARVC type 5 (ARVC5), caused by a p.S358L mutation in TMEM43. The function and localization of TMEM43 and the mechanism by which the p.S358L mutation causes the disease, are unknown.

overall_design: RNA was isolated from the left ventricle of hearts from WT mice, mice overexpressing the human form of TMEM43 (TMEM43wt) and mice expressing the human p.S358L mutant form of TMEM43 (TMEM43mut) under Myosin Heavy Chain 6 (Myh6) promoter gene. Myh6:hTMEM constructs have been inserted randomly in the genome.

first: Laura

last: Padrón-Barthe

first: Pablo

last: García-Pavía


title: Histone Chaperone Paralogs Have Redundant, Co-operative and Divergent Functions in Yeast.

city: Victoria

first: Chris

last: Nelson

address: 3800 Finnerty Road

department: Dept. of Biochemistry & Microbiology, The University of Victoria

institute: University of Victoria

summary: We report the transcriptomes of wildtype and the indicated mutant yeast strains using RNAseq

overall_design: Yeast were grown to mid log phase in YEPD media, and ribo-minus RNAs sequenced on an Illlumina MiSeq platform

first: N

last: Savic

first: S

middle: P

last: Shortil

first: M

last: Bilenky

last: Hirst

first: Christopher