title: transcriptional reponse of yeast glucose sensing pathway mutants to glucose addition

city: Chapel Hill

first: Henrik

last: Dohlman

state: NC

address: 120 Mason Farm Rd, 4th Floor

department: Pharmacology

institute: University of North Carolina at Chapel Hill

summary: While much is known about glucose metabolism in yeast, less is known about the receptors and signaling pathways that indicate glucose availability. Here we compared  wildtype and 16 mutants in yeast glucose sensing pathway for their transcriptomics profiles in 0.05% glucose vs 10 min after glucose addition to 2% glucose. With these data, we were able to define various roles of glucose sensing pathway components. We demonstrated that the G protein-coupled receptor (Gpr1/Gpa2) directed early events in glucose utilization, the transceptors (SNF3/RGT2) regulated subsequent processes and downstream products of glucose metabolism. Whereas the large G protein transmits the signal from its cognate receptor, Ras2 (but not Ras1) integrates responses from both receptor pathways. We also determined the relative contributions of the Gα (Gpa2) and Gβ (Asc1) protein subunits to glucose-initiated processes in yeast. We determined that Gpa2 is primarily involved in regulating carbohydratesugar metabolism while Asc1 is primarily involved in amino acid metabolism. Both proteins are involved in regulating purine metabolism. Collectively, our analysis reveals the molecular basis for glucose detection and the earliest events of glucose-dependent signal transduction in yeast.

overall_design: wildtype and 16 yeast glucose sensing pathway mutants in 0.05% glucose vs. 10 min after glucose addition to 2% glucose, each in 2 replicates

first: Shuang

last: Li

first: Amy

last: Perou

first: Chris

last: Nagy

first: Donghui

last: Tan

first: Hemant

last: Kelkar

first: Stephanie

last: DeYoung

first: Blisse

last: Wiggins

first: Tristain

last: De Buysscher


title: Lens orientalis contributes quantitative trait loci and candidate genes associated with Ascochyta blight resistance in lentil

status: Public on Jun 09 2021

city: Nathan

first: Ido

last: Bar

state: QLD

address: 170 Kessels Road

department: School of Environment and Science

country: Australia

institute: Griffith University

type: Expression profiling by high throughput sequencing

type: Genome variation profiling by high throughput sequencing

summary:
Purpose: The goal of this study is to construct an interspecific genetic linkage map using SNP markers generated using a genotyping by sequencing transcript approach.
Methods: mRNA profiles of 14-day-old parents and 140 recombinant inbred lines were generated by high-throughput sequencing using Illumina HiSeq 3000 system. The sequence reads that passed filtering were mapped to lentil cultivar Cassab reference transcriptome using Burrows Wheeler Aligner and the SNPs generated were then clustered to linkage groups (LG) to construct a high-density linkage map using the ‘mstmap’ function from within the ASMap R package (v1.0-4) (Taylor and Butler, 2017).
Results: A total of 694,694,624 paired end reads (150-bp) were generated by sequencing multiplexed cDNA libraries on the Illumina HiSeq 3000 platform with an average of 4,997,803 reads per RIL progeny. Variant calling and sequential filtering led to identification of 2,363 SNP markers which were used to construct a genetic linkage map spanning 545.5 cM with 8 linkage groups.
Conclusions: The study has utilized a novel interspecific-derived RIL population to add an array of SNPs to the existing marker data for lentil, which will be of use in future genetic and genomic analyses.

sample_organism:
Lens culinaris
Lens orientalis
Lens culinaris x Lens orientalis

overall_design: mRNA profiles of 14-day-old Lens orientalis (ILWL 180) and Lens culinaris (ILL 6002) accessions and 140 recombinant inbred lines.

first: Ramaharinathreddy

last: Dadu

first: Sukhjiwan

last: Kaur

first: Shimna

last: Sudheesh

first: Rebecca

last: Ford

first: Dorin

last: Gupta


title: Tissue-resident macrophages promote multiple myeloma early dissemination and progression via IL-6 and TNFa

city: Bronx

first: Phillip

last: Galbo

state: New York

address: 1300 Morris Park

country: USA

institute: Albert Einstein College Of medicine

summary: Multiple myeloma (MM) is a plasma cell malignancy characterized by the presence of multiple foci in the skeleton. These distinct tumor foci indicate cycles of tumor growth and dissemination that seed new clusters and drives disease progression. Utilizing an intra-tibial Vk*MYC murine myeloma, we found that CD169 + radiation-resistant, tissue-resident macrophages (MPs) were critical for myeloma early dissemination and disease progression. While depletion of these MPs had no effect on tumor proliferation, it reduced myeloma BM egress and spreading to other bones, which improved overall survival as a single therapy and in combination with BM transplantation. Myeloma dissemination correlated with an increased inflammatory signature in BM MPs, as well as production of IL-6 and TNFα by tumor-associated MPs (TAMs). Exogenous i.v. IL-6 and TNFa could trigger myeloma intravasation in the BM by increasing vascular leakiness in the BM, and by enhancing myeloma motility by reducing CD138 adhesion. Moreover, mice lacking IL-6 had defects in myeloma dissemination as in MP-depleted recipients. While in TNFa or TNFaR deficient mice had defects in MM dissemination, engraftment was also impaired. These effects on myeloma dissemination required production of cytokines in the radiation-resistant compartment, containing these radiation-resistant BM MPs. Taken together, we propose BM egress of myeloma cells is regulated by localized inflammation in foci, driven in part by CD169 + MPs.

overall_design: To extend our analysis of Tumor associated macrophages (TAM) programming, we analyzed their transcriptome by RNA sequencing (RNA-seq). We FACS-purified TAMs (F4/80high, CD11blow) from bone marrow of myeloma bearing mice that both were in contact (TAM-IC) or not in contact (TAM-NIC) with myeloma, on the basis of GFP expression as well as BM macrophages from naïve mice as controls (Naive) for comparison. In addition, Vk*MYC myeloma (GFPhigh, CD138high) and polyclonal (GFP- CD138high B220low) BM PCs from naïve mice were also FACS-sorted and analyzed to investigate myeloma-macrophage interactions. Sorted MPs were clustered into distinct groups based on principal component analysis. Next, we performed pair-wise comparisons of the numbers of differentially expressed genes (DEGs) shared and uniquely expressed by the three MP subsets and found that a majority of DEGs were specific to each subset, even when comparing the two different TAM MPs.

first: David

last: Fooksman

first: Ilseyar

last: Azhmetzyanova

first: Deyou

last: Zheng


title: P23 acts as an RNA binding protein, which interacts differentially with specific mRNAs in response to LPS and modulates the macrophage inflammation response

city: Aachen

first: Antje

last: Ostareck-Lederer

address: Pauwelsstr. 30

department: Dept. of Intensive Care Medicine

country: Germany

institute: University Hospital RWTH Aachen

summary: We report the identification of RNAs bound by P23, which was previously uncovered as new poly(A+)-RNA interacting protein in murine RAW 264.7 macrophages (Liepelt, et al., 2016). RNAseq of RNAs immunoprecipitated with P23 revealed that specifc mRNAs were bound differentially in untreated and in LPS-activated RAW 264.7 cells.

overall_design: RNA profiles of P23 immunoprecipitations from untreated and 2hrs LPS-treated RAW 264.7 macrophages, performed in triplicates, LUC immunoprecipitation served as control. Input RNA at time point 0 and at 2hrs was analyzed as reference.

first: Sebastian

last: de Vries

first: Vladimir

last: Benes

first: Isabel

middle: S

last: Naarmann-de Vries

first: Cornelia

last: Rücklé

first: Katharina

last: Zarnack

first: Gernot

last: Marx

first: Dirk

middle: H

last: Ostareck


title: YAP1/TEAD1 ChIP in N/TERT2G human keratinocytes

city: Bethesda

first: Ramiro

last: Iglesias-Bartolome

address: 37 Convent Drive

department: LCMB

institute: NIH/NCI

type: Genome binding/occupancy profiling by high throughput sequencing

summary: YAP1/TEAD1 ChIP was performed in N/TERT2G human keratinocytes

overall_design: Keratinocytes were harvested during exponential growth and ChIP was performed with YAP1 antibody and TEAD1 antibodies.

first: Yao

last: Yuan


title: A randomised controlled trial of folic acid intervention in pregnancy highlights a putative methylation-regulated control element at ZFP57

status: Public on Jun 08 2021

city: Coleraine

first: Colum

middle: Patrick

last: Walsh

state: County Londonderry

address: Cromore Road

department: Life and Health Sciences

country: United Kingdom

institute: Ulster University

type: Methylation profiling by genome tiling array

summary:
Background: Maternal blood folate concentrations during pregnancy have been previously linked with DNA methylation patterns, but this has been done predominantly through observational studies. We showed recently in an epigenetic analysis of the first randomized controlled trial (RCT) of folic acid supplementation specifically in the second and third trimesters (the EpiFASSTT trial) that methylation at some imprinted genes was altered in cord blood samples in response to treatment. Here, we report on epigenome-wide screening using the Illumina EPIC array (~ 850,000 sites) in these same samples (n = 86).
Results: The top-ranked differentially methylated promoter region (DMR) showed a gain in methylation with folic acid (FA) and was located upstream of the imprint regulator ZFP57. Differences in methylation in cord blood between placebo and folic acid treatment groups at this DMR were verified using pyrosequencing. The DMR also gains methylation in maternal blood in response to FA supplementation. We also found evidence of differential methylation at this region in an independent RCT cohort, the AFAST trial. By altering methylation at this region in two model systems in vitro, we further demonstrated that it was associated with ZFP57 transcription levels.
Conclusions: These results strengthen the link between folic acid supplementation during later pregnancy and epigenetic changes and identify a novel mechanism for regulation of ZFP57.

This trial was registered 15 May 2013 at www.isrctn.com as ISRCTN19917787.

Ethics approval and consent to participate: The Office for Research and Ethics Committees Northern Ireland (ORECNI) granted ethical approval (reference 05/ Q2008/21) and each participant gave written informed consent upon recruitment.

overall_design: Pregnant women took folic acid in trimester 1 and then were randomised into two groups: 1) placebo - taking dummy pill (n= 45), 2) folic acid - continuation with folic acid supplementation for trimesters 2 and 3 (n=41). DNA was extracted from cord blood at birth and genome-wide methylation levels were assayed using the Illumina 850k EPIC Beadchip with subsequent analysis using bioinformatic approaches. Gene targets of relevant interest identified through bioinformatic mining were validated using wet lab approaches.

first: Rachelle

middle: E

last: Irwin

first: Sara

middle: J

last: Thursby

first: Miroslava

last: Ondičová

first: Kristina

last: Pentieva

first: Helene

last: McNulty

middle: C

last: Richmond

first: Aoife

last: Caffrey

first: Diane

last: Lees-Murdock

first: Marian

last: McLaughlin

first: Tony

last: Cassidy

first: Matthew

last: Suderman

first: Caroline

middle: L

last: Relton

middle: P


title: Harnessing Self-Labeling Enzymes for Selective and Concurrent A-to-I and C-to-U RNA Base Editing

city: Heidelberg

first: F. Nina

last: Papavasiliou

address: Im Neuenheimer Feld 280

department: Tumor Immunology Unit

institute: German Cancer Research Center (DKFZ)

summary: The SNAP-ADAR tool enables precise and efficient A-to-I RNA editing in a guideRNA-dependent  manner by applying the self-labeling SNAP-tag enzyme to generate RNA-guided  editases in cell culture. Here, we extend this platform by combining the SNAP-tagged tool with  further effectors steered by the orthogonal HALO-tag. Due to their small size (ca. 2 kb), both  effectors are readily integrated into one genomic locus. We demonstrate selective and  concurrent recruitment of ADAR1 and ADAR2 deaminase activity for optimal editing with  extended substrate scope and moderate global off-target effects. Furthermore, we combine the  recruitment of ADAR1 and APOBEC1 deaminase activity to achieve selective and concurrent  A-to-I and C-to-U RNA base editing of endogenous transcripts inside living cells again with moderate global off-target effects. The platform  should be readily transferable to further epitranscriptomic writers and erasers to manipulate  epitranscriptomic marks in a programmable way with high molecular precision.

overall_design: Identification of off-target editing events in a 293 Flp-In T-REx cell line stably expressing both HALO-ADAR1Q and mAPOBEC1-SNAP by RNA-Seq. Overall 4 samples × 2 independent experiments.

first: Anna

last: Stroppel

first: Ngadhnjim

last: Latifi

first: Alfred

last: Hanswillemenke

first: Rafail

middle: N

last: Tasakis

first: F

first: Thorsten

last: Stafforst


title: Next Generation Sequencing of Oocyte and Associated Cumulus Cells Pools from Preovualtory Follicles in Bovine

city: Knoxville

first: Sarah

last: Moorey

state: Tennessee

address: 2506 River Drive

department: Animal Science

institute: University of Tennessee

summary:
Purpose: Preovualtory follicle diameter influences embryo quality in beef cattle that rely on a gonadotropin releasing hormone (GnRH) injection to induce the preovualtory gonadotropin surge and subsequent ovualtion. The goals of this study are to compare transcriptome profiles of pools of four oocytes or associated cumulus cells collected from small (≤11.7mm) and large follicles (≥12.7 mm) exposed to a GnRH-induced gonadotropin surge and follicles (11.7-14.0 mm) exposed to an endogenous gonadotropin surge (spontaneous follicles).
Methods: Oocyte and cumulus cell  mRNA profiles of  pools of four oocytes or associated cumulus cells collected from small (≤11.7mm) and large follicles (≥12.7 mm) exposed to a GnRH-induced gonadotropin surge or spontaneous follicles (11.7-14.0 mm) which were exposed to an endogenous gonadotropin surge were generated by deep sequencing (n=6 small follicle oocyte, 6 small follicle cumulus, 6 large follicle oocyte, 6 large follicle cumulus, 4 spontaneous follcile oocyte, and 5 spontaneous follicle cumulus pools), using Illumina HiSeq 2000 . The sequence reads that passed quality filters were aligned to the Bos taurus reference genome UMD3.1 using Hisat2mapper.  FeatureCounts was used to quantify transcript abundance in each library using Bos taurus gene annotation from Ensembl. Differences in gene transcript expression were then analyzed amoung oocyte or cumulus cell follcile classifications using the packages edgeR and DESeq2 in R software.
Results: We mapped an average of 30 million sequence reads per sample to the Bos taurus reference genome UMD3.1 and identified 69, 94, and 83 differentially expressed gene transcripts (DEG) among oocyte libraries from small versus large, small versus spontaneous, and large versus spontaneous follicle classifications, respectively.  We also identified 128, 98, and 80 DEG among cumulus cell libraries from small versus large, small versus spontaneous, and large versus spontaneous follicles, respectively.
Conclusions: Our study represents detailed analysis of RNA-sequencing data generated from in vivo produced cumulus and oocyte samples collected from preovualtory follicles of varied physiological status after exposure to an endogenous or exogenously stimulated gonadotropin surge. The results of our study highlight key differences in the transcriptome of samples from small, large, or spontaneous follicles and provide insight into the reduced embryo quality observed when small follicles undergo a GnRH induced gonadotropin surge.

overall_design: Oocyte and cumulus cell mRNA profiles of pools of four oocytes or associated cumulus cells collected from small (≤11.7mm; GnRH induced gonadotropin surge), large follicles (≥12.7 mm; GnRH induced gonadotropin surge), and spontaneous follicles (11.7-14.0 mm; endogenous gonadotropin surge)

first: Jenna

middle: M

last: Monnig

first: Michael

middle: F

last: Smith

first: M

last: Ortega

first: Jonathan

middle: A

last: Green

first: Ky

middle: G

last: Pohler

first: G

last: Bridges

first: Susanta

middle: K

last: Behura

first: Thomas

middle: W

last: Geary


title: Revealing immune responses in the Mycobacterium avium subsp. paratuberculosis-infected THP-1 cells using single cell RNA-sequencing

city: Seoul

first: Hong-Tae

last: Park

address: 1, Gwanak-ro

country: South Korea

institute: Seoul National University

summary: To determine the initial responses of human THP-1 cells against MAP infection using single-cell RNA-seq analysis.

overall_design: Differentiation of THP-1 cells into macrophages was performed by stimulation with 50 ng/ml PMA. After 72 h of incubation, the cells were washed twice with FBS-free RPMI 1640 medium and incubated with 5% FBS-RPMI 1640 medium without antibiotics for 24 h before the experiments. Differentiated THP-1 cells (5 × 106 cells) were inoculated with MAP strain K-10 at a multiplicity of infection (MOI) of 10:1 and incubated for 3 h.

first: Han

last: Yoo

first: Jong-Sung

last: Lim

first: Gyoungju

last: Nah


title: Methylation of Q105 on histone H2A is part of a dynamic regulatory mechanism integrating metabolism with ribosome biogenesis through recruitment of Nhp2 [ChIP-Seq]

city: Cologne

first: Jennifer

last: Maßen

address: Joseph-Stelzmann-Straße 9B

institute: MPI Biology of Ageing

summary: Ribosome biogenesis is an essential cellular process that requires integration of extracellular cues, such as metabolic state, with intracellular signaling, transcriptional regulation and chromatin accessibility at the ribosomal DNA. Here, we demonstrate that the recently identified histone modification, methylation of H2AQ105, is an integral part of a dynamic chromatin network at the rDNA locus. Its deposition depends on a functional mTor signaling pathway as well as acetylation of histone H3 at position K56, thus integrating signals from cell cycle, metabolic and proliferative states. Furthermore, we identify a first epigenetic reader of this modification, the ribonucleoprotein Nhp2, which specifically recognizes the methylation on H2AQ105. Based on functional and proteomic data we suggest that Nhp2 functions as an adapter to bridge the rDNA chromatin with components of the small subunit processome to efficiently coordinate transcription of rRNA with its post-transcriptional processing. We support this by showing that an H2AQ105A mutant has a mild defect in early processing of the rRNA.

overall_design: Examination of Nhp2 binding to the DNA. For each genotype, two biological replicates were used. ChIP was performed using Nhp2 antibody. Input samples were taken before addition the antibody as reference.

first: Julia

last: Mawer

last: Massen

first: Christina

last: Reichert

first: Niklas

last: Grabenhorst

first: Constantine

last: Mylonas

first: Peter

last: Tessarz


title: Differential gene expression of DLD1 cells expressing oncogenic KRAS-S181, -S181A or -181D

city: Barcelona

first: Neus

last: Agell

address: C/Casanova 143

department: Biomedicina

country: Spain

institute: Universitat de Barcelona

summary: Oncogenic mutations of KRAS are found in the most aggressive human tumors, including colorectal cancer. It has been suggested that oncogenic KRAS phosphorylation at Ser181 modulates its activity and favors cell transformation. Using non-phosphorylatable (S181A), phosphomimetic (S181D) and phospho/dephosphorylatable (S181) oncogenic KRAS mutants, we analyzed the role of this phosphorylation to the maintenance of tumorigenic properties of colorectal cancer cells. Our data show that the presence of phospho/dephosphorylatable oncogenic KRAS is required for preserving the epithelial organization of colorectal cancer cells in 3D cultures, and for supporting subcutaneous tumor growth in mice. Interestingly, gene expression differed according to the phosphorylation status of KRAS. In DLD-1 cells, CTNNA1 was only expressed in phospho/dephosphorylatable oncogenic KRAS expressing cells, correlating with cell polarization. Moreover, lack of oncogenic KRAS phosphorylation leaded to changes in expression of genes related to cell invasion, such as SERPINE1, PRSS1,2,3 and NEO1, and expression of phosphomimetic oncogenic KRAS resulted in diminished expression of genes involved in enterocyte differentiation, such as HNF4G. Finally, the analysis, in a public data set of human colorectal cancer, of the gene expression signatures associated to phosphomimetic and non-phosphorylatable oncogenic KRAS suggests that this post-translational modification regulates tumor progression in patients

overall_design: DLD-1 colorectal cancer cell line knocked out for the oncogenic KRAS allele were stably transfected with HA-KRASG12V-S181,  HA-KRASG12V-S181A, HA-KRASG12V-S181D. Three clons for each phosphomutant with a expression of exogenous KRAS similar to the endogenous one were chosen

first: Debora

last: Cabot

first: Sònia

last: Brun

first: Noelia

last: Paco

first: Mireia

last: Ginesta

first: Nuria

last: Gendrau-Clemente

first: Baraa

last: Abuasaker

first: Triana

last: Ruiz-Fariña

first: Carles

last: Barceló

first: Miriam

last: Cuatrecasa

first: Marta

last: Bosch

last: Rentero

first: Gabriel

last: Pons

first: Josep

last: Estanyol

last: Capellà

first: Montserrat

last: Jaumot


title: Cellular fractionation reveals transcriptome responses of human fibroblasts to UV-C irradiation

city: Guangzhou

first: Yuming

last: Wang

state: Guangdong

address: Room 512, Anatomy Building

department: School of Basic Medical Science

country: China

institute: Guangzhou medical university

summary: The response to DNA damage intersects with many other physiological processes in the cells, including initiation of DNA repair, regulation of transcription and translation, chromatin remodeling, and the cell cycle regulation to contend with the challenge. Transcription shutdown is not simply a consequence of the physical arrest of RNA polymerase II by DNA lesions, but also could be elicited by signaling in trans. While to date many of the specific molecular events are not fully elucidated. What is the signal that operates in trans to slow transcriptional elongation globally? Which factors are required for transcription restart after DNA repair? How is TC-NER controlled by the multifaceted transcriptional response? In this study, we sought to map the transcription restart and isolate the set of lncRNAs that are likely to function at the chromatin interface by using biochemical fractionation of the cellular compartment coupled to RNA-seq.

overall_design: MRC5_VA cells were either left untreated as control or treated with 10 J/m2 of UV-C irradiation, followed by recovery for 30 minutes, 3 or 24 hours. Cellular fractionation was performed to isolate total RNA from cytoplasm and chromatin extracts.

first: Zhenzhen

last: Wu

first: Jiena

last: Liu

first: Jin

last: He

first: Zhaoya

last: Han

first: Fangkeng

last: Liang


title: Arabidopsis RPD3-type histone deacetylases form multiple plant-specific complexes that are required for preventing overexpression of stress-induced genes (RNA-Seq)

status: Public on Jun 10 2021

city: Beijing

first: xinjian

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

summary: Although the Arabidopsis thaliana RPD3-type histone deacetylases have been known to form SIN3 histone deacetylase complexes that are conserved in eukaryotes, it is unknown whether they also form other types of histone deacetylase complexes. Here, we performed affinity purification followed by mass spectrometry and demonstrated that the Arabidopsis RPD3-type histone deacetylases HDA6 and HDA19 can interact with several previously uncharacterized proteins and form three types of plant-specific histone deacetylase complexes, which we named SANT, ESANT, and ARID. RNA-seq indicated that HDA6 and HDA19 function together with other components of the histone deacetylase complexes and co-regulate the expression of a number of genes. HDA6 and HDA19 have been thought to repress gene transcription by histone deacetylation. We found that the histone deacetylase complexes can also repress gene expression via certain histone-deacetylation-independent mechanisms. In the mutants of the histone deacetylase complexes, the expression of a number of stress-induced genes was up-regulated. Several mutants of the histone deacetylase complexes showed severe retardation in growth. Considering that the growth retardation is thought to be a trade-off for the increase of stress tolerance, we predict that the histone deacetylase complexes identified in this study prevent overexpression of stress-induced genes and thereby ensure normal growth of plants under non-stress conditions.

overall_design: Examination of the mRNA expression of wild type and seven mutants grown under long day conditions.

first: Xin-Jian


title: RhoC modulates cell junctions and Type I interferon response in aggressive breast cancers

status: Public on Jun 07 2021

city: Ann Arbor

first: Sofia

middle: D

last: Merajver

state: MI

address: 1500 E. Medical Ct. Dr., 7314 CC

department: Int Med-Hematology/Oncology

institute: University of Michigan

summary: Metastases are the leading cause of death in cancer patients. RhoC, a member of the Rho GTPase family, has been shown to facilitate metastasis of aggressive breast cancer cells by influencing motility, invasion, and chemokine secretion, but as yet there is no integrated model of the precise mechanism of how RhoC promotes metastasis. A common phenotypic characteristic of metastatic cells influenced by these mechanisms is dysregulation of cell-cell junctions. Thus, we set out to study how RhoA- and RhoC-GTPase influence the cell-cell junctions in aggressive breast cancers. We demonstrate that CRISPR-Cas9 knockout of RhoC in SUM 149 and MDA 231 breast cancer cells results in increased normalization of junctional integrity denoted by junctional protein expression/colocalization. In functional assessments of junction stability, RhoC knockout cells have increased barrier integrity compared to wild-type cells as measured by the FITC-Dextran leakage assay, and increased cell-cell adhesion as measured by fluorimetric centrifugation assay. Whole transciptome RNA sequencing demonstrate decreased expression of Type I interferon-stimulated genes in RhoC knockout cells compared to wild-type, and subsequent treatment with interferon-alpha resulted in significant increases in adhesion and decreases in invasiveness of wild-type cells and a dampened response to interferon-alpha stimulation with respect to adhesion and invasiveness in RhoC knockout cells. We delineate a key role of RhoC-GTPase in modulation of junctions and response to interferon, which supports inhibition of RhoC as a potential anti-invasion therapeutic strategy.

overall_design: Bulk RNASeq of six Crispr-RhoC knockout breast cancer cell lines are compared to WT.

first: Hannah

last: Abraham

first: Peter

last: Ulintz


title: Transgenic mice for in vivo epigenome editing with CRISPR-based systems [foxp3_p300 ChIP-seq]

city: Durham

first: Charles

last: Gersbach

address: 101 Science Drive

department: Biomedical Engineering

institute: Duke University

summary: The discovery, characterization, and adaptation of the RNA-guided clustered regularly interspersed short palindromic repeat (CRISPR)-Cas9 system has greatly increased the ease with which genome and epigenome editing can be performed. Fusion of chromatin-modifying domains to the nuclease-deactivated form of Cas9 (dCas9) has enabled targeted gene activation or repression in both cultured cells and in vivo in animal models. However, delivery of the large dCas9 fusion proteins to target cell types and tissues is an obstacle to widespread adoption of these tools for in vivo studies. Here we describe the generation and validation of two transgenic mouse lines for targeted gene regulation, including Rosa26:LSL-dCas9-p300 for gene activation and Rosa26:LSL-dCas9-KRAB for gene repression. Using the dCas9p300 and dCas9KRAB transgenic mice we demonstrate activation or repression of genes in both the brain and liver in vivo, and T cells ex vivo. We show gene regulation with gRNAs targeting either transcriptional start sites (TSS) or distal enhancer elements, as well as corresponding changes to downstream phenotypes. These mouse lines are convenient and valuable tools for facile, temporally controlled, and tissue-restricted epigenome editing and manipulation of gene expression in vivo.

overall_design: Th0 cells from Rosa26-LSL-dCas9p300-Cd4Cre mice (with or without Cd4-Cre) were treated with retrovirus expressing gRNA (control or Foxp3 targeting) in vitro. Transduced cells were harvest three days after treatment

first: Matthew

last: Gemberling

first: Keith

last: Siklenka

first: Alejandro

last: Barrera


title: Transgenic mice for in vivo epigenome editing with CRISPR-based systems [foxp3_p300 RNA-seq]

overall_design: Th0 cells from Rosa26-LSL-dCas9p300 mice (with or without Cd4-Cre) were treated with retrovirus expressing gRNA (control or Foxp3 targeting) in vitro. Transduced cells were harvest three days after treatment


title: High migration and invasion ability of PGCCs and their daughter cells associated with the nuclear localization of S100A10 modified by SUMOylation

city: Tianjin

first: Zhang

middle: shi

last: wu

state: Tianjin

address: Tianjin Union Medical Center, JieYuan Street No.190, HongQiao District, Tianjin, China

department: Pathology

institute: Tianjin Union Medical Center

summary:
Purpose: S100A10 uesed to located in the cell membrane or cytoplasm. However nuclear-located S100A10 was observed in the polyploid tumor giant cells(PGCCs) with daughter cells induced by cobalt chloride(CoCl2). To study the function of nuclear-located S100A10, we performed ChIP-Seq.
Methods:LoVo and Hct116 cells were incubated in T25 flasks in RPMI-1640 medium until they reached 80-90% confluence. The cells were treated with 450 μM CoCl2 (Sigma-Aldrich, St. Louis, MO, USA) for 48-72h based on their resistance to hypoxia. After the treatment with CoCl2 was repeated for 3-4 times, there were 20-30% of PGCCs and 70-80% of small-sized daughter cells that originated from PGCCs among the total cells.ChIP assays were performed according to the instructions of the Pierce Magnetic ChIP Kit (Thermo Fisher Scientific, #26157) For data analysis of ChIP DNA, sequencing and library preparation were performed using Novogene Technology Co., Ltd. (Tianjin, China). Raw data (raw reads) of FASTQ format were first processed through in-house PERL scripts, and then reference genome and gene model annotation files were downloaded directly from the genome website. For a specific ChIP-seq binding site, individual reads were mapped to the plus or minus strand and presented significant enrichment. After mapping the reads to the reference genome, the MACS2 version 2.1.0 (model-based analysis of ChIP-seq) peak finding algorithm was used to identify regions of specific IP enrichment over background. A p-value threshold of enrichment of 0.05 was used for all data sets. The interaction between transcription factor or chromatin histone modification and DNA was not random, but they showed some specific sequence preference. MEME 52 and DREME 53 were used to detect the sequence motif, which was used to detect long and short consensus sequences. The position of peak summit around the transcript start sites of genes can predict the interaction sites of proteins and genes. Genes associated with different peaks were identified, and GO and KEGG enrichment analyses were performed.
Results:The results showed that 4148 significant ChIP-seq peaked in Hct116-derived PGCCs with daughter cells, and 1380 peaked in LoVo-derived PGCCs with daughter cells. Genes with overlapping peaks were then enriched by Gene Ontology [GO], which revealed that these genes participated in various processes including stimulus, cell migration, and cell motility.Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed the potential targets involved in metabolic pathways, axon guidance TGF-β signaling pathway, and so on.
Conclusions: S100A10 can be modified by SUMOylation in PGCCs and their daughter cells induced by either CoCl2 or chemotherapeutic drugs. SUMO1-modified S100A10 can translocate to the nucleus and regulate the expression of ARHGEF18, PTPRN2, and DEFA3 to promote the proliferation, migration, and invasion of PGCCs and their daughter cells, which may contribute to the poor prognosis in patients with cancer. The discovery of detailed mechanisms of the S100A10 SUMOylation, such as the specific lysine sites involved in SUMOylation and which SUMO E3 ligase regulates the SUMOylation of S100A10 requires further study.

overall_design: Examination of nuclear-located S100A10 in CoCl2-induced PGCCs with daughter cells of colorectal cancer cell lines HCT116 and LoVo.

first: Shiwu

last: Zhang

first: Qi

last: Zhao

first: Kexin


title: CTCF is a Barrier for Totipotent-like Reprogramming  [ChIPseq]

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

summary: Totipotent cells have the ability of generating embryonic and extra-embryonic tissues. Interestingly, a rare population of cells with totipotent-like potential was identified within ESC cultures. These cells, known as 2 cell (2C)-like cells, arise from ESC and display similar features to those found in the totipotent 2 cell embryo. However, the molecular determinants of 2C like conversion have not been completely elucidated. Here, we show that CTCF is a barrier for 2C-like reprogramming. Indeed, forced conversion to a 2C-like state by DUX expression was associated with DNA damage at a subset of CTCF binding sites. Endogenous or DUX-induced 2C-like ESC showed decreased CTCF enrichment at known binding sites, suggesting that acquisition of a totipotent-like state is associated with a highly dynamic chromatin architecture. Accordingly, depletion of CTCF in ESC efficiently promoted spontaneous and asynchronous conversion to a totipotent-like state. This phenotypic reprogramming was reversible upon restoration of CTCF levels. Furthermore, we showed that transcriptional activation of the ZSCAN4 cluster was necessary for successful 2C-like reprogramming. In summary, we revealed the intimate relation between CTCF and totipotent-like reprogramming.

overall_design: ChIP-seq experiments of RPA in untreated and DUX-overexpressing ESC lines for 16h or 24h.

first: Sergio

last: Ruiz

first: Teresa

last: Olbrich


title: CTCF is a Barrier for Totipotent-like Reprogramming [END-seq]

overall_design: ENDseq experiments in DUX-overexpressing ESC lines for 16h.

first: Wei

last: Wu

first: Andre

last: Nussenzweig


title: RNA-seq and small RNA-seq in fission yeast CPF mutants that enable small-RNA-mediated epigenetic gene silencing

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNAs are the common denominator of various RNA silencing pathways that regulate gene expression and protect the genome against mobile repetitive DNA sequences, retroelements, and transposons. In Schizosaccharomyces pombe, small interfering RNAs (siRNAs) are required for the faithful propagation of heterochromatin that is found at peri-centromeric repeats. In contrast to repetitive DNA, protein-coding genes are refractory to siRNA-mediated heterochromatin formation, unless siRNAs are expressed in mutant cells.  Different studies have shown that siRNAs become potent mediators of RNAi-mediated epigenetic gene silencing in S. pombe cells that are mutant for mlo3+, dss1+, mst2+, or genes encoding subunits of the Paf1 complex (Paf1C). In this study, we have combined chemical mutagenesis with whole-genome sequencing in a sensitized S. pombe reporter strain to obtain a more comprehensive list of putative suppressors of small-RNA-mediated epigenetic gene silencing. This revealed more than 20 novel silencing-enabling mutations in genes that are associated with RNA processing, regulation of transcription, or post-translational protein modification. Focusing on factors involved in pre-mRNA cleavage and polyadenylation, we for example show that single amino acid substitutions in Yth1, which is responsible for polyadenylation signal recognition, lead to nearly 100% effective de novo formation of silent heterochromatin.   In S. pombe, small RNA-mediated silencing relies on the continuous amplification of the siRNA pool through a positive feedback loop. The deposited data shows the generation of secondary small RNAs over the reporter gene exclusively in the presence of RNAi-enabling mutations in the pre-mRNA cleavage and polyadenylation machinery. Furthermore, the RNA-seq data show that overall transcriptome levels are not markedly changing in the mutations themselves.   Altogether, our work shows that epigenetic gene silencing can be enabled by the acquisition of a plethora of mutant alleles in fission yeast.

overall_design: In the course of this project, we have identified mutations in the pre-mRNA cleavage and polyadenylation machinery that enable RNAi-dependent heterochromatin formation. To show the direct effect of the mutants on siRNA generation and subsequent reporter gene silencing, we performed small RNA-seq and total RNA-seq experiments. To this end, total RNA from exponentially growing cultures was extracted with the MasterPure Yeast RNA Purification Kit (Epicenter). Small RNA libraries were prepared with the QIAseq miRNA Library Kit (QIAGEN) according to the manufacturer’s instructions and sequenced with an Illumina NextSeq500 (75bp single-end). Total RNA libraries were prepared with TruSeq Stranded Total RNA kit (Illumina) according to the manufacturer’s instructions and sequenced with an Illumina HiSeq2500 (50bp single-end).

first: Yukiko

last: Shimada

first: Sarah

last: Carl

first: Valentin

last: Flury

first: Tahsin

last: Kuzdere

first: Merle

last: Skribbe

first: Georg

last: Kempf

first: Marc

last: Bühler


title: CTCF is a Barrier for Totipotent-like Reprogramming  [Cut&Run]

overall_design: Cut&Run experiments of CTCF in untreated and DUX-overexpressing ESC lines for 16h or 24h. Cut&Run experiments of CTCF in a population of sorted spontaneously converted ESC into totipotent-like cells expressing LTR-sequences


title: CTCF is a Barrier for Totipotent-like Reprogramming

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

overall_design: Refer to individual Series


title: TEAD transcriptional inhibition in basal cell carcinoma

first: Ramiro

last: Iglesias-Bartolome

summary: RNA sequencing (RNAseq) of primary keratinocytes from mouse basal cell carcinoma mice (BCC) transduced with pooled siRNAs targeting YAP1 and TAZ (siYT) or non-targeting control siRNA (siCon), and with TEADi or GFP as control

overall_design: Primary keratinocytes were isolated from tail skin of K14-SmoM2 mice five weeks following tamoxifen induction and transduced with siRNAs or adenoviruses

first: Yao

last: Yuan


title: Expression profile in hepatocellular carcinoma patient paired tissues

city: Singapore

first: Caroline G.

last: Lee

address: MD7, Level 2, 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore


city: Bern

first: Kellie

last: Cotter

state: Bern

address: Murtenstrasse 35

department: Dept for BioMedical Research

institute: University of Bern

summary: Genomic and transcriptomic alterations are insufficient to explain the variance in protein expression seen in cancer. Recent evidence has highlighted the role of N6-methyladenosine (m6A) in the regulation of mRNA expression, stability and translation, supporting a potential role for post-transcriptional regulation mediated by m6A in cancer. Here we explore prostate cancer as an exemplar cancer and generate the first prostate m6A maps, and further examined how low levels of N6-adenosine-methyltransferase (METTL3) associates with advanced prostate cancer and results in altered expression at the level of transcription, translation, and protein. In particular extracellular matrix proteins have a high number of m6A sites and show significant changes in expression with METTL3 knock-down. We also discovered the upregulation of a hepatocyte nuclear factor-driven gene signature that is associated with therapy resistance in prostate cancer. Significantly, METTL3 knock-down rendered the cells resistant to androgen receptor antagonists, implicating changes in m6A as a mechanism for therapy resistance in metastatic prostate cancer.

overall_design: RNA-Seq and Ribo-Seq analysis of contol and  METTL3 inducible shRNA LNCaP lines with and without doxycycline induction.

first: John

last: Gallon

first: Mark

last: Rubin


title: Transgenic mice for in vivo epigenome editing with CRISPR-based systems [pcsk9 RNA-seq]

first: Charles

last: Gersbach

overall_design: Rosa26-LSL-dCas9-KRAB mice were treated with PBS or AAV expressing gRNA (control and pcsk9 targeting) by tail-vein injection. Eight weeks after treatment, we harvested livers from treated animals.

first: Matthew

last: Gemberling

first: Keith

last: Siklenka


title: Transgenic mice for in vivo epigenome editing with CRISPR-based systems [pdx1 ChIP-seq]

overall_design: Rosa26-LSL-dCas9p300 mice were treated with PBS or AAV expressing gRNA (control and pdx1 targeting) by tail-vein injection. Two weeks after treatment, we harvested livers from treated animals.


overall_design: RNA-Seq analysis of contol and METTL3 inducible shRNA LNCaP lines with and without enzalutamide treatment.


title: Transgenic mice for in vivo epigenome editing with CRISPR-based systems [pcsk9 ChIP-seq]

overall_design: Rosa26-LSL-dCas9-KRAB mice were treated with PBS or AAV expressing gRNA (control and pdx1 targeting) by tail-vein injection. Eight weeks after treatment, we harvested livers from treated animals.


title: Alterations in neuronal physiology, development, and function associated with a common duplication of chromosome 15 involving CHRNA7.

city: Saint Louis

first: Kristen

last: Kroll

state: MO

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

department: Developmental Biology

institute: Washington University School of Medicine

summary: Copy number variants at chromosome 15q13.3 contribute to liability for multiple intellectual and developmental disabilities (IDDs) including Autism Spectrum Disorder (ASD). Individuals with duplications of this interval, which includes the gene CHRNA7, have IDDs with variable penetrance. However, the basis of such differential affectation remains uncharacterized.Methods: Induced pluripotent stem cell (iPSC) models were generated from two first degree relatives with the same 15q13.3 duplication, a boy with distinct features of autism and emotional dysregulation (the affected proband, AP) and his clinically unaffected mother (the UM). These models were compared to unrelated control subjects lacking this duplication (UC, male and female). iPSC-derived neural progenitors and cortical neuroids consisting of cortical excitatory and inhibitory neurons were used to model potential contributors to neuropsychiatric impairment. Results: The AP-derived model uniquely exhibited disruptions of cellular physiology and neurodevelopment not observed in either the UM or in unrelated male and female controls. These included enhanced neural progenitor proliferation but impaired neuronal differentiation, maturation, and migration, and increased endoplasmic reticulum (ER) stress in neural progenitors. Both the AP’s neuronal migration deficit and elevated ER stress could be selectively rescued by different pharmacologic agents. Neuronal gene expression was also specifically dysregulated in the AP, including altered expression of genes related to behavior, psychological disorders, neuritogenesis, neuronal migration, and WNT signaling. By contrast with these AP-specific phenotypes, both the AP- and UM-derived neurons exhibited shared alterations of neuronal function, including elevated cholinergic activity consistent with increased homomeric CHRNA7 channel activity.Conclusion: Together, these data define both affectation-specific phenotypes seen only in the AP, as well as abnormalities observed in both individuals with CHRNA7 duplication, the AP and UM, but not in UC-derived neurons. This is, to our knowledge, the first study to use a human stem cell-based platform to study the basis of variable affectation in cases of 15q13.3 duplication at the cellular, molecular, and functional levels. This work suggests potential approaches for suppressing abnormal neurodevelopment or physiology that may contribute to severity of affectation in this proband. Some of these AP-specific neurodevelopmental anomalies, or the functional anomalies observed in both 15q13.3 duplication carriers (the AP and UM), could also contribute to the differential phenotypic penetrance seen in other individuals with 15q13.3 duplication.

overall_design: iPSC's were generated from patients with 15q13.3 duplication involving two first degree relatives (Affected Proband (AP), Unaffected Mother (UM)), with and without affectation. The Neural Progenitor Cells were generated from the iPSCs, and they are further matured for 15 days as a cortical neuroids. This study also includes two unrelated male (UC-M) and female (UC-F) control samples. Four independent biological experiments were performed and RNA was isolated from cortical neuroids after 15 days of differentiation. A batch correction was used to identify genes that were reproducibly differentially expressed genes (DEGs) across comparisons of paired mutant versus control samples.

first: K

last: Meganathan

first: R

last: Prakasam

first: D

last: Baldridge

first: P

last: Gontarz

first: B

last: Zhang

first: F

last: Urano

first: A

last: Bonni

first: J

last: Huettner

last: Constantino


title: Transgenic mice for in vivo epigenome editing with CRISPR-based systems


title: circRNA expression profile in hepatocellular carcinoma patient paired tissues

last: Lee

summary: This study aimed to identify differential expression of circRNAs in hepatocellular carcinoma patient tissues.

overall_design: Arraystar Human circRNA Array V2 microarray was performed on total RNA that was extracted from 49 hepatocellular carinoma patient tumor tissues and adjacent non-tumor tissues.

first: Jian

last: Han

first: Alexander

middle: Y

last: Chung

first: Brian

last: Goh

first: Pierce

last: Chow

first: CY

last: Chan

first: PC

last: Cheow

first: SY

first: Tony

last: Lim

first: London

last: Ooi

first: Caroline


title: ARID1A deficiency promotes pancreatic tumorigenesis by reducing KRAS-induced senescence (RNA-Seq I)

status: Public on Jun 06 2021

city: Houston

first: Chenghang

last: Zong

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: ARID1A  is one of the most frequently mutated epigenetic regulators in a wide spectrum of cancers. In this study, we identified the anti-senescence effect of ARID1A deficiency in the progression of pancreatic intraepithelial neoplasia (PanIN) by profiling the transcriptome of individual PanINs in the mouse model. Interestingly, we found that ARID1A deficiency activates the transcription of Aldehyde dehydrogenase 1 family, member A1 (ALDH1A1), which play essential roles in attenuating the senescence by significantly reducing reactive oxygen species (ROS) induced by oncogenic KRAS. Our findings further suggest that ALDH could be considered as a potential adjuvant target for prevention and treatment of pancreatic cancer.

overall_design: We performed RNA-seq on wild type HPNE cell line and ARID1A-KO HPNE cell line with and without KRAS overexpression. Three biological replicates per group.

first: Shou

last: Liu

first: Wenjian

last: Cao

first: Yichi

last: Niu


title: Durable Suppression of Acquired MEK Inhibitor Resistance in Cancer by Sequestering MEK from ERK and Promoting Anti-Tumor T-cell Immunity [single-cell RNA-seq]

city: LOS ANGELES

first: Sixue

state: California

address: 10833 Le Conte Avenue

department: Medicine

institute: UCLA

summary: Disruption of the MAPK pathway in cancer by kinase inhibition often fails due to pathway reactivation, causing clinical relapse. Among MAPK inhibitors, type I RAF inhibitors are only active against specific BRAF mutants; MEK inhibitor monotherapy is associated with limited clinical benefits but may serve as a foundation for combinatorial therapy. Here, we show that type II RAF plus allosteric MEK inhibitors durably blunt the development of acquired MEK inhibitor resistance among cancers with KRAS, NRAS, NF1, BRAFnon-V600 and BRAFV600 mutations, when compared to a combination of type II RAF plus ERK inhibitors. Type II RAF and MEK (versus ERK) inhibitors also display superior capacity to sequester MEK in RAF complexes and uncouple MEK and ERK interaction in acquired resistant tumor subpopulations. Systemically and intratumorally, type II RAF plus MEK inhibitors expand memory and activated/exhausted CD8+ T-cells. Whereas trametinib alone temporally reduces dominant intra-tumoral T-cell clones, type II RAF inhibitor co-treatment reverses this effect and promotes T-cell clonotypic expansion and convergence. Importantly, durably control of tumors by this combination requires CD8+ T-cells. Thus, the prolonged anti-tumor efficacy of type II RAF plus MEK inhibitors reveals exquisite MAPK addiction in common lethal cancer histologies, and the mechanisms include unexpected allosteric perturbation of the MAPK pathway and engagement of anti-tumor CD8+ T-cell immunity.

overall_design:
This dataset contains single cell transcriptomes of the murine melanoma cell line (Nras mutated) with/without combination treatment of Trametinib and BGB-283 using 10x Genomics single cell RNA-Seq.

The Nras mutated melanoma model was derived from a Nras Q61R murine syngeneic melanoma cell line NIL, and has been exposed to ultraviolet (UV) radiation to introduce mutational burden equivalent to human melanoma.

first: Aayoung

last: Hong

first: Marco

last: Piva

first: Willy

last: Hugo

first: Shirley

middle: H

last: Lomeli

first: Vincent

last: Zoete

first: Chris

last: Randolph

first: Zhentao

last: Yang

first: Yan

last: Wang

first: Lu

last: Sun

first: Agustin

last: Vega-Crespo

first: Alejandro

last: Garcia

first: David

last: Shackelford

first: Steven

last: Dubinett

first: Philip

middle: O

last: Scumpia

first: Alan

last: Tackett

first: Timothy

middle: R

last: Donahue

first: Olivier

last: Michielin

first: Sheri

last: Holmen

first: Antoni

last: Ribas

first: Gatien

last: Moriceau

first: Roger

middle: S

last: Lo


title: Transgenic mice for in vivo epigenome editing with CRISPR-based systems [pdx1 RNA-seq]

first: Charles

last: Gersbach

overall_design: Rosa26-LSL-dCas9p300 mice were treated with PBS or AAV expressing gRNA (control and pdx1 targeting) by tail-vein injection. Two weeks after treatment, we harvested livers from treated animals, isolated RNA, and performed RNA-sequencing.

first: Matthew

last: Gemberling

first: Keith

last: Siklenka


title: ARID1A deficiency promotes pancreatic tumorigenesis by reducing KRAS-induced senescence (ATAC-Seq)

first: Chenghang

last: Zong

overall_design: We performed ATAC-seq on wild type HPNE cell line and ARID1A-KO HPNE cell line. Three biological replicates per group.

first: Shou

last: Liu

first: Wenjian

last: Cao

first: Yichi

last: Niu


title: Genome-wide analysis of chromatin landscape in murine bone marrow derived eosinophils

city: Cincinnati

first: Jennifer

last: Felton

state: Ohio

address: 3333 Burnet Ave, ML7028

department: Department of Allergy and Immunology

institute: Cincinnati Children's Hospital Medical Center

summary: We applied a global approach using broad-range, next-generation sequecing to identify a repertoire of eosinophil-specific enhancers. H3K4me1, H3K4me3, H3K27ac and PU.1 ChIPseq data was paired with ATAC and gene expression data from bmEos. Transcription factor motif analysis revealed enrichment for PU.1 in eosinophil enhancers, and ChIP-seq confirmed PU.1 binding in enhancer of genes highly expressed in eosinophils. Comparison of identified PU.1-bound enhancers with 3 publically available myeloid datasets (neutrophils, bone marrow derived macrophages and immature granulocytes) revealed 25% of PU.1-bound enhancers were unique to eosinophils - an eosinophil-specific PU.1 regulome. GO analysis of eosinophil-specific PU.1-bound enhancers revealed enrichmend for genes involved in migration, proliferation, degranulation and survival.  Collectively, our data identify eosinophil-specific enhancers regulating key eosinophil genes through epigenetic mechanisms and TF binding. These findings are supportive of a dynamic, epigenetic eosinophil regulome underlying eosinophil function and diversity.

overall_design:
CHIP, ATAC and RNAseq datasets from day 14  culture derived bone marrow eosinophils (bmEos)

This series includes re-analyzed data from: GSE110861, GSE110863, GSE110864, GSE110865, GSE38371, GSE38377, GSE38379 and GSE42110.

first: Patricia

middle: C

last: Fulkerson


title: miRNA expression profile in hepatocellular carcinoma patient paired tissues

first: Caroline G.

last: Lee

summary: This study aimed to identify differential expression of miRNAs in hepatocellular carcinoma patient tissues and explore the function of miRNAs acting as sponge of circRNAs.

overall_design: Illumina NextSeq 500 was performed on total RNA that was extracted from 49 hepatocellular carinoma patient tumor tissues and adjacent non-tumor tissues.

first: Jian

last: Han

first: Alexander

last: Chung

first: Brian

last: Goh

first: Pierce

last: Chow

first: C

last: Chan

first: P

last: Cheow

first: S

first: Tony

last: Lim

first: London

middle: L

last: Ooi

first: Caroline


title: Durable Suppression of Acquired MEK Inhibitor Resistance in Cancer by Sequestering MEK from ERK and Promoting Anti-Tumor T-cell Immunity

first: Sixue

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Durable Suppression of Acquired MEK Inhibitor Resistance in Cancer by Sequestering MEK from ERK and Promoting Anti-Tumor T-cell Immunity [RNA-seq]

overall_design: This dataset contains the RNA-seq of human melanoma PDXs and cell lines sensitive/resistant to the MEK inhibitor

first: Aayoung

last: Hong

first: Marco

last: Piva

first: Willy

last: Hugo

first: Shirley

last: Lomeli

first: Vincent

last: Zoete

first: Chris

last: Randolph

first: Zhentao

last: Yang

first: Yan

last: Wang

first: Lu

last: Sun

first: Agustin

last: Vega-Crespo

first: Alejandro

middle: J

last: Garcia

first: David

last: Shackelford

first: Steven

last: Dubinett

first: Philip

last: Scumpia

first: Alan

last: Tackett

first: Timothy

last: Donahue

first: Olivier

last: Michielin

first: Sheri

last: Holmen

first: Antoni

last: Ribas

first: Gatien

last: Moriceau

first: Roger

last: Lo


title: Regulation of cold-induced thermogenesis by the stress granule protein FAM195A

status: Public on Jun 05 2021

city: Dallas

first: Jessica

last: Cannavino

address: 6000 Harry Hines

department: Molecular Biology

institute: UT Southwestern Medical center

summary: Homeothermic vertebrates are capable of surviving in cold environments by maintaining constant body temperature through thermogenesis, in which brown adipose tissue (BAT) produces heat by increasing mitochondrial oxidation along with the uncoupling of the electron transport chain and activation of uncoupling protein 1 (UCP1).  Although the transcription factors that control the expression of UCP1 and genes involved in nutrient oxidation, mitochondrial function, have been extensively studied, only a few other proteins essential for BAT function have been identified.  Here we describe the discovery of FAM195A, a disordered domain RNA-binding protein associated with stress granules that is required for cold-dependent thermogenesis in mice.  FAM195A expression is enriched in BAT and striated muscles, and mice lacking FAM195A display whitening of BAT and an inability to survive at cold temperatures.  In BAT of mice lacking FAM195A, key enzymes involved in branched chain amino acid (BCAA) metabolism, in particular leucine, and fatty acid (FA) oxidation are downregulated, impairing the physiological response to cold stress.  Moreover, in vitro knock down of FAM195A impairs expression of leucine oxidation enzymes, revealing a direct role of FAM195A in the regulation of BCAA metabolism during thermogenesis

overall_design: Discovery of FAM195A, a RNA-binding protein required for cold-dependent thermogenesis in mice and characterization of FAM195A KO animals

first: Jiwoong

last: Kim

first: Lin

last: Xu

first: Rhonda

last: Bassel-Duby

first: Eric

middle: N

last: Olson


title: ELMO1 is a promoter of osteoclast function and bone loss

city: New York

first: Justin

middle: Shaun Arnold

last: Perry

address: 408 East 69th Street, 408-15

department: Immunology Program

institute: Sloan Kettering Institute for Cancer Research

summary: Osteoporosis and bone fractures affect millions of men and women worldwide and are often due to increased bone resorption (bone loss) mediated by osteoclasts. Here, we identify a novel role for the cytoplasmic protein ELMO1 as an important ‘signaling node’ controlling the bone resorption function of osteoclasts. Initially, we noted association of ELMO1 SNPs with bone abnormalities and altered bone density in humans. Experimentally, ELMO1 emerged as a promoter of bone loss wherein deletion of ELMO1 reversed osteoporosis / bone erosions in four in vivo mouse models: osteoprotegerin deficiency, ovariectomy, and two types of inflammatory arthritis.  However, ELMO1 did not promote bone loss under homeostatic conditions. Mechanistic studies pointed to a larger ELMO1 signaling network that regulates osteoclast activity at several levels. First, transcriptomics coupled with CRISPR/Cas9 genetic deletion approaches identified new regulators of osteoclast function associated with Elmo1, including cathepsin G and myeloperoxidase. Second, defining the ‘ELMO1 interactome’ in osteoclasts via proteomics revealed membrane proteins and v-ATPases required for bone degradation. Third, ELMO1 affects the formation of the actin ring /sealing zone on bone-like surfaces and the distribution of osteoclast-specific proteases. Finally, a 3D structure-based inhibitory peptide targeting a highly conserved region of ELMO1 reduced bone resorption in wild type osteoclasts. Collectively, these data identify ELMO1 as a signaling hub that regulates osteoclast function and bone loss, with relevance to diseases such as osteoporosis and arthritis.

overall_design: The experiment consisted of two conditions - mature osteoclasts differentiated from the bone marrow of either Elmo1+/– or Elmo1–/– mice. Each condition consisted of four biological replicates.

first: Sanja

last: Arandjelovic

first: Ming

last: Zhou

first: Adam

last: Ceroi

first: Igor

last: Smirnov

first: Scott

last: Walk

first: Laura

last: Shankman

first: Isabelle

last: Cambre

first: Suna

last: Onengut-Gumuscu

first: Dirk

last: Elevaut

first: Thomas

middle: P

last: Conrads

first: Kodi

last: Ravichandran


first: Kellie

last: Cotter

overall_design: miCLIP analysis of m6A sites in LNCaP and RWPE cells.

middle: A

first: Kate

last: Meyer

first: Mark

last: Rubin


title: Genomic Analysis of Response to Bacillus Calmette-Guerin (BCG) Treatment in High-Grade Stage 1 Bladder Cancer Patients

city: Charlotte

first: Peter

middle: E

last: Clark

state: North Carolina

address: 1021 Morehead Medical Dr Suite 5201

department: Urology

institute: Atrium Health Levine Cancer Institute

summary:
Background: Intravesical bacillus Calmette-Guérin (BCG) therapy is standard treatment for high-risk non-muscle invasive bladder cancer (NMIBC) but overall efficacy is low, and no reliable predictive biomarkers currently exist to refine patient selection. We performed genomic analysis on high-grade (HG) T1 NMIBCs to determine if response to therapy is predicted by certain mutational and/or expressional changes.
Methods: Patients with HG T1 NMIBC treated with induction BCG were stratified by response into durable and non-durable responders. Tumor samples were subjected to whole-exome RNA sequencing. Gene expression and variant analysis were performed on RNA sequencing to identify changes between BCG durable responders and those that did not respond.
Results: Differentially expressed genes in durable responders were input into IPA and identified associated immune related pathways: MIF-mediated Glucocorticoid Regulation, MIF Regulation of Innate Immunity, and p38 MAPK Signaling. The differentially expressed genes were crossed with RNAseq variant analysis to identify genes that had significant changes in both. This analysis identified JCHAIN, S100A7, CLECB, and ANXA10 genes that had snps in non-durable responders vs durable responders and also had significant change in gene expression between these two groups.
Conclusions: Differences in the genomic profiles of HG T1 NMIBC tumors exist between those who show durable response to BCG and those who do not. Using pathway analysis, those differences imply upregulation of several interconnected inflammatory pathways among responders. Specific variants identified here are candidates for further study and, if clinically validated, may serve as useful biomarkers in the future.

overall_design: RNA sequencing of stage 1 bladder cancer tumor samples in patients treated with BCG treatment.

first: J

last: Sanders

first: Connor

last: Frasier

middle: T

last: Matulay

first: Nury

middle: M

last: Steuerwald

first: Jason

last: Zhu

first: Claud

last: Grigg

first: James

last: Kearns

first: Stephen

last: Riggs

first: Kris

last: Gaston

first: Cory

last: Brouwer

first: R

last: Burks

first: Aaron

last: Hartman

first: David

last: Foureau

first: Earle

middle: F

last: Burgess


title: H3 acetylation selectively promotes basal progenitor proliferation and neocortex expansion by activating TRNP1 expression

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: We performed RNA-Seq and H3K9ac ChIP-Seq from the whole embryonic cortex at E15.5 from BAF155 cKO mice treated either with vehicle or HDAC inhibitor (TSA).

first: Cemil

last: Kerimoglu


title: Dynamic landscape of chromatin accessibility and transcriptomic changes during differentiation of human embryonic stem cells into dopaminergic neurons

city: Monterrey

first: Raquel

last: Cuevas Diaz Duran

address: Av Morones Prieto No. 3000, Colonia Los Doctores

department: Escuela de Medicina y Ciencias de la Salud

country: Mexico

institute: Tecnologico de Monterrey

summary: We profiled chromatin accessibility and gene expression changes along the differentiation of human pluripotent stem cells to dopaminergic neurons. We integrated the epigenomic and transcriptomic profiles to infer the activity of transcription factors (TFs) and DNA regulatory regions such as enhancers and long non-coding RNAs.

overall_design: Time series gene expression profiles and chromatin accessibility genome-wide maps were obtained through ATAC-sequencing and RNA-sequencing of samples obtained during dopaminergic neural induction of human pluripotent stem cells. We used 3 induction time points: day 0, day 14, and day 28. H9 cells expressing GFP (WA09-GFP) were used as pluripotent stem cells. For RNA-seq we obtained 3, 4, and 2 replicates from induction time points D0, D14, and D28 respectively. For ATAC-seq we used one replicate for each time point.

first: Cesar

last: Melendez-Ramirez

last: Duran

first: Tonatiuh

last: Barrios-Garcia

first: Mayela

last: Giacoman

first: Adolfo

last: Lopez-Ornelas

first: Jessica

last: Herrera-Gamboa

first: Ivan

last: Velasco

first: Victor

last: Treviño


title: Deep and accurate detection of m6A RNA modifications in human and mouse cells using miCLIP2 and m6Aboost machine learning [c]

city: Würzburg

first: Kathi

last: Zarnack

address: Biocenter, Am Hubland

department: Theodor Boveri Institute

institute: University Würzburg

summary: N6-methyladenosine (m6A) is the most abundant internal RNA modification in eukaryotic mRNAs and influences many aspects of RNA processing, such as RNA stability and translation. miCLIP (m6A individual-nucleotide resolution UV crosslinking and immunoprecipitation) is an antibody-based approach to map m6A sites in the transcriptome with single-nucleotide resolution. However, due to broad antibody reactivity, reliable identification of m6A sites from miCLIP data remains challenging. Here, we present several experimental and computational innovations that significantly improve transcriptome-wide detection of m6A sites. Based on the recently developed iCLIP2 protocol, the optimised miCLIP2 results in high-complexity libraries using less input material, leading to a more comprehensive representation of m6A sites. Next, we established a robust computational pipeline to identify true m6A sites from our miCLIP2 data. The analyses are calibrated with data from Mettl3 knockout cells to learn the characteristics of m6A deposition, including a significant number of m6A sites outside of DRACH motifs. In order to make these results universally applicable, we trained a machine learning model, m6Aboost, based on the experimental and RNA sequence features. Importantly, m6Aboost allows prediction of genuine m6A sites in miCLIP data without filtering for DRACH motifs or the need for Mettl3 depletion. Using m6Aboost, we identify thousands of high-confidence m6A sites in different murine and human cell lines, which provide a rich resource for future analysis. Collectively, our combined experimental and computational methodology greatly improves m6A identification.

overall_design: miCLIP2 experiments were performed on polyA+ RNA from the human macrophage cell line RAW 264.7, with 3 biological replicates

first: Körtel

last: Nadine

first: Rücklé

last: Cornelia

first: Zhou

last: You

first: Busch

last: Anke

first: Ostareck-Lederer

last: Antje

first: Ostareck

last: Dirk

first: Zarnack

last: Kathi

first: König

last: Julian


title: Expression data of extracellular vesicles from bone metastatic breast cancer cell line

status: Public on Jun 04 2021

city: Winston-Salem

first: Kounosuke

last: Watabe

address: 1 Medical Center Blvd

institute: Wake Forest University School of Medicine

summary:
Bone metastasis is an incurable complication of breast cancer. In advanced stages, patients with estrogen-positive tumors experience significantly higher incidence of bone metastasis compared to estrogen-negative patients. To investigate how estrogen-positive breast cancer cells communicate with bone microenvironmental cells, extracellular vesicles from bone metastatic MCF7BoM2 were purified and analyzed.
We used GeneChip miRNA 4.1 Array to detail the miRNA expression in the extracellular vesicles from the bone metastatic MCF7BoM2 and its parental cell line MCF7, and identified the dysregulated miRNAs.

overall_design: Extracellular vesicles from cells were isolated by ultracentrifugation. Cells were grown in extracellular vesicles-depleted media for 48 h before conditioned media were collected for extracellular vesicles purification. To isolate total extracellular vesicles, conditioned media was centrifuged at 300g for 10 minutes to remove cells. Extracellular vesicles were collected by ultracentrifugation at 120,000g for 70 minutes, folloed by RNA extraction and hybridization on GeneChip miRNA 4.1 Array.

first: Kerui

last: Wu

first: Shih-Ying

first: Dan

last: Zhao

first: Abhishek

last: Tyagi

first: Ravindra

last: Pramod Deshpande


title: A Novel Single Cell RNA-seq Analysis of  Circulating Immune Cells in Late Sepsis

city: Gainesville

first: Rhonda

last: Bacher

state: FL

address: 2004 Mowry Rd.

institute: University of Florida

summary: With the successful implementation of guidelines from the Surviving Sepsis Campaign, in-hospital mortality to sepsis continues to decrease.  However, this is has not lead to completely improved outcomes after sepsis. Up to 1/3 of sepsis survivors continue to have dismal long-term outcomes and 1-year mortality.  Although the pathobiology of the dismal outcomes after sepsis remains undefined, it is thought that late after sepsis individuals enter a state of pathologic myeloid activation, inducing suboptimal lymphopoiesis and erythropoiesis, with many of the downstream immune cells being dysfunctional.  The goal of this study was to use single-cell RNA sequencing to perform a detailed transcriptomic analysis of non-myeloid cells to better understand the pathology of late sepsis. Our findings highlight the unique transcriptomic pattern that circulating non-myeloid cells display 14 days after sepsis.  Non-myeloid leukocytes in particular reveal an endotype of inflammation, immunosuppression and dysfunction. Immunomodulatory therapies at this late time point in sepsis may be feasible through precision medicine.

overall_design: A mixture of whole blood myeloid-enriched and Ficoll-enriched peripheral blood mononuclear cells from four late septic patients (post-sepsis day 14-21, RAP n=1 and CCI n=3) and five healthy subjects underwent Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq).

first: Phil

last: Efron

first: Dijoia

middle: B

last: Darden


title: Durable Suppression of Acquired MEK Inhibitor Resistance in Cancer by Sequestering MEK from ERK and Promoting Anti-Tumor T-cell Immunity [TCR-seq]

first: Sixue

last: Liu

overall_design:
This dataset contains the TCR-seq of the murine melanoma cell line (Nras mutated) under different treatment conditions

The Nras mutated melanoma model was derived from a Nras Q61R murine syngeneic melanoma cell line NIL, and has been exposed to ultraviolet (UV) radiation to introduce mutational burden equivalent to human melanoma.

first: Aayoung

last: Hong

first: Marco

last: Piva

first: Willy

last: Hugo

first: Shirley

last: Lomeli

first: Vincent

last: Zoete

first: Chris

last: Randolph

first: Zhentao

last: Yang

first: Yan

last: Wang

first: Lu

last: Sun

first: Agustin

last: Vega-Crespo

first: Alejandro

last: Garcia

first: David

last: Shackelford

first: Steven

last: Dubinett

first: Philip

last: Scumpia

first: Alan

last: Tackett

first: Timothy

last: Donahue

first: Olivier

last: Michielin

first: Sheri

last: Holmen

first: Antoni

last: Ribas

first: Gatien

last: Moriceau

first: Roger

last: Lo


title: ARID1A deficiency promotes pancreatic tumorigenesis by reducing KRAS-induced senescence (RNA-Seq II)

first: Chenghang

last: Zong

overall_design: We dissected and profiled the transcriptomes of 20 lesoins from 2 KC mice and 24 lesions from 2 AKC mice.

first: Shou

last: Liu

first: Wenjian

last: Cao

first: Yichi

last: Niu


title: Histone H4 lysine 20 mono-methylation directly facilitates chromatin ‘openness’ and promotes transcription of housekeeping genes (ATAC-seq_DRB)

city: Copenhagen N

first: Mads

last: Lerdrup

address: Blegdamsvej 3C

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary: To study the role of Histone H4 lysine 20 mono- and tri-methylation (H4K20me1, H4K20me3) in relationship to chromatin accessibility and gene expression, we report the application of high-throughput profiling of these marks in synchronized and asynchronous Human Osteosarcoma U2OS and asynchronous Mouse Fibroblast (MEF) cells with Set8 knockdown or control siRNA treatment. We find that H4K20me1 contributes to the open chromatin structure at active genes.

overall_design: siRNA knockdown of the H4K20 methyltransferase Set8 in humans cells followed by ATAC-seq of DRB-treated cells.

first: Muhammad

last: Shoaib

first: Qinming

last: Chen

first: Xiangyan

last: Shi

first: Nidhi

last: Nair

first: Chinmayi

last: Prasanna

first: Renliang

last: Yang

last: Walter

first: Klaus

last: Frederiksen

first: Einarsson

last: Hjorleifur

first: Peter

last: Svenson

first: Chuan-Fa

first: Karl

last: Ekwall

first: Lars

last: Nordenskiöld

first: Claus

last: Sørensen


title: Chamber-Enriched gene expression profiles in failing human hearts with reduced ejection fraction [snRNA-Seq]

city: South San Francisco

first: Xin

last: Luo

state: CA

address: 750 Gateway Blvd

department: Research and Development

institute: Amgen Inc

summary: To generate the reference for cell composition deconvolution and characterize the cellular expression landscape, we performed single nucleus RNA-Seq (snRNA-Seq) on left ventricles from four non-failing hearts and one failing heart.

overall_design: single nucleus RNA-Seq on left ventricles from 4 non-failing (Control) hearts and 1 failing (HF) heart.

first: Marina

last: Stolina


title: Hypermethylation and downregulation of UTP6 are associated with stemness properties, chemoradiotherapy resistance and prognosis in rectal cancer: A co-expression network analysis

city: Fuzhou

first: Guanxian

last: Guan

state: China

address: 20 Chazhong Road

department: Department of Colorectal Surgery

institute: The First Affiliated Hospital of Fujian Medical University

summary: To measure global gene expression in primary locally advanced rectal cancer patients who have undergone CRT and screen valuable biomarkers to predict the effects of CRT.Samples fromprimary locally advanced rectal cancer patients were collected. The effects of chemoradiotherapy were evaluated.

overall_design: All patients underwent standard CRT  after signing the chemoradiotherapy agreement; subsequently, they were evaluated in accordance with the AJCC tumor regression grade (TRG).Each samplewas collected before CRT. Each sample was stored in liquid nitrogen until total RNA extraction.

first: Qiao

last: Gao

first: Yiyi

last: Zhang


title: In vitro fibroblast gene expression - tissue comparison

status: Public on Jun 03 2021

city: MANCHESTER

first: Alexander

last: Kononov

address: Oglesby Building, 555 Wilmslow Rd,

institute: Cancer Research UK Manchester Institute

summary: Gene expression of in vitro CD105pos and CD105neg pancreatic fibroblasts (PaFs) and liver fibroblasts (LiFs)

overall_design: CD105pos and CD105neg fibroblasts were isolated from in vitro expanded cultures of pancreatic fibroblasts (PaFs) and liver fibroblasts (LiFs) and gene expression analysed at steady state (normal growth media with no additional stimualtions)

first: Colin

last: hutton

first: Alex

last: Jorgensen


title: Histone H4 lysine 20 mono-methylation directly facilitates chromatin ‘openness’ and promotes transcription of housekeeping genes

first: Mads

last: Lerdrup

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

overall_design: Refer to individual Series


title: Deep and accurate detection of m6A RNA modifications in human and mouse cells using miCLIP2 and m6Aboost machine learning [b]

first: Kathi

last: Zarnack

overall_design: miCLIP2 experiments were performed on polyA+ RNA from the human thyroid cancer cell line C643, with 3 biological replicates

first: Körtel

last: Nadine

first: Rücklé

last: Cornelia

first: Zhou

last: You

first: Busch

last: Anke

first: Hüttelmaier

last: Stefan

first: Haase

last: Jacob

first: Zarnack

last: Kathi

first: König

last: Julian


title: Chamber-Enriched gene expression profiles in failing human hearts with reduced ejection fraction [RNA-Seq]

first: Xin

last: Luo

summary: Heart failure with reduced ejection fraction (HFrEF) constitutes 50% of HF hospitalizations and is characterized by high rates of mortality. To explore the underlying mechanisms of HFrEF etiology and progression, we studied the molecular and cellular differences in four chambers of non-failing (NF, n=10) and HFrEF (n=12) human hearts.  This study contributes to a growing body of knowledge describing chamber-specific heart transcriptomics and revealed genes and pathways that are associated with heart failure pathophysiology, which may aid in therapeutic target discovery.

overall_design: mRNA profiles of 84 samples of four chambers of human hearts: 10 non-failing (NF) donors and 12 heart failure with reduced ejection fraction (HFrEF)

first: Marina

last: Stolina


title: Identifying subpopulation methylation profiles from sequencing of heterogeneous samples with DXM

city: St. Louis

first: Jerry

last: Fong

address: 4565 McKinley Ave

type: Methylation profiling by high throughput sequencing

summary:
Changes in epigenetic marks, such as DNA methylation, in cancer subclones may increase their fitness, leading to cancer progression, treatment resistance, and worse prognosis. We have developed DXM, a novel computational method to identify subpopulation methylation events from bisulfite sequencing data of a heterogeneous sample
DXM does not require prior knowledge of the number of cell types or what cell types to expect in the sample, and it outperforms existing methods.
To further validate our method, we conducted genomic bisulfite sequencing on four primary DLBCL samples, obtaining data from >4.9 million CpGs at 50x average coverage.
DXM predictions of subpopulation methylation profiles in these samples were confirmed in FACS-sorted CD4+ and CD19+ cells.
Thus, we have developed a method, DXM, that can identify subpopulation methylation profiles in heterogeneous samples

overall_design: Bisulfite Sequencing (Agilent Methyl-Seq) of four cryopreserved primary DLBCL samples


title: Using DMS-MaPseq to dissect structural differences of ribosomal RNA in different pre-40S intermediates

city: Jupiter

first: Haina

last: Huang

state: Florida

address: 130 scripps way c296

department: The integrative structural and computational biology

institute: The Scripps Research Institute

summary: Ribosomes are among the largest folded RNAs, whose function depends on their structure. Nonetheless, in vitro studies indicate a propensity of rRNAs to misfold. We use a combination of DMS-MaPseq, structural analyses, biochemical experiments, and yeast genetics to dissect the final RNA folding steps of the small ribosomal subunit head.

overall_design: Pre-40S are purified from WT or S15_YRR or Rio2_Δloop cells are purified via Rio2-TAP. Mature 40S are also tested. Each sample has DMS treated and its untreated control. There are 5 biological replicates for WT pre-40S, 4 biological replicates for Rio2_Δloop pre-40S and 3 biological replicates for  S15_YRR and mature 40S.

first: Katrin

last: Karbstein


title: Neuroinflammatory astrocyte subtypes in the mouse brain [bulk RNA-seq, Interferon_in_vitro]

first: Philip

last: Hasel

address: 435 E 30th St

institute: NYU Langone Medical Centre

summary: RNA-seq of primary astrocytes exposed to different cytokines

overall_design: Primary immunopanned astrocytes were treated with IFNg (3 ng/ml), IFNb (1000 U/ml), TNFa (30 ng/ml)+IL1a (3 ng/ml) +C1q (40 ng/ml) or combinations thereof for 24h, RNA collected and sequenced on a NovaSeq6000

first: Shane

last: Liddelow


title: Neuroinflammatory astrocyte subtypes in the mouse brain [scRNAseq]

summary: Single cell RNAseq of FACS-purified astrcoytes from saline- and LPS-injected Aldh1l1egfp mice at 24h and comparison male vs female

overall_design: Astrocytes were FACS-purified from LPS- or saline-treated (24h) Aldh1l1egfp mice, run on the 10xChromium system and sequenced on NovaSeq6000. 3 saline female, 3 saline male, 3 LPS female, 3 LPS male animals


title: Labile Iron Release Primes Pancreatic Cancer for Ferroptosis

city: Ann Arbor

first: Brian

last: Magnuson

address: 1500 East Medical Center Drive

institute: University of Michigan

summary: Cancers have unique metabolic adaptations in response to cell-intrinsic and environmental stressors, where identifying new strategies to target these adaptions is an area of active research. We previously described a dependency on a cytosolic aspartate aminotransaminase (GOT1)-dependent pathway for NADPH generation in pancreatic cancer. Here, we sought to identify metabolic dependencies following GOT1 inhibition to provide insight into the regulation of redox metabolism. Using pharmacological methods, we identified cysteine, glutathione, and lipid antioxidant function as metabolic vulnerabilities following GOT1 withdrawal. Targeting any of these pathways triggered ferroptosis, an oxidative, non-apoptotic, iron-dependent form of cell death in GOT1 knockdown cells. Mechanistically, GOT1 inhibition promoted a catabolic state and enhanced the availability of labile iron through autophagy and iron uptake. In sum, our study identifies a novel biochemical connection between GOT1, iron regulation, and ferroptosis, and suggests GOT1 plays a role in protecting PDA from metabolic stress.

overall_design: GOT1 was knocked down via doxycycline-inducible shRNA in two human pancreatic cancer cell lines, Tu8902 and MiaPaCa, and subject to RNA-seq.  For each cell line, three replicates each of control (-Dox, "mnsdox") and knockdown (+Dox, "plsdox") were sequenced.

first: Daniel

last: Kremer

first: Costas

last: Lyssiotis


title: Inflammation drives alternative first exon usage of critical immune genes including Aim2 [RNA-seq]

status: Public on Jun 02 2021

city: Santa Cruz

first: Sergio

last: Covarrubias

address: Thimann Receiving/Department Carpenter Lab/Biomed 125, 1156 High St., Thimann Labs

department: MCD

institute: UCSC

summary:
Macrophage cells are essential components of the innate immune system and contain toll-like receptors (TLRs) that intiate the immune response when pathogen-associated molecular pattern molecules (PAMPs) are recognized.
In this experiment, we stimulate TLR4 in bone marrow-derived macrophage cells with lipopolysaccharide (LPS) for 6 hours to simmulate inflammation and study the resulting differential splicing landscape and gene expression.

overall_design: Unstimulated or LPS stimulated Primary Bone Marrow Derived Macrophages (BMDMs) from WT mice were collected and placed in Trizol. RNA was isolated and sequenced using Illumina.

first: Susan

last: Carpenter

first: Angela

last: Brooks


title: Chamber-Enriched gene expression profiles in failing human hearts with reduced ejection fraction


title: Heart, skeletal muscle, and kidney total RNA sequencing in adult and aging mice

status: Public on Jun 01 2021

city: Aurora

first: Edward

last: Lau

state: CO

address: 12700 E19th Av RCII Rm 8004

department: Medicine/Cardiology

institute: University of Colorado

summary: Total ribosome-depleted RNA sequencing was performed on the left cardiac ventricle, skeletal muscle (quadriceps femoris), and kidney of young adult (16.5 wk) and early aging (86 wk) C57BL/6J mice.

overall_design: 4 mice (2 male, 2 female) at each age group were sequenced.


title: Comparing the whole genome methylation landscape of dairy calf blood cells revealed potential intergenerational inheritance of the maternal metabolic status

city: quebec

first: ying

last: zhang

address: 735 Ave.Neree tremblay

country: Canada

institute: UNIVERSITY LAVAL

summary: Whole genome methylation of the daughters’ blood cells was assessed by Whole Genome Bisulfite Sequencing (WGBS), revealed the whole epigenetic landscape of calf blood cells, suggesting that the maternal metabolic status can indeed affect the embryo's epigenetic status and metabolic related pathways in offspring, providing further evidence for epigenetic intergenerational inheritance of metabolic stress in domestic animals

overall_design: methylation profile of eight daughter descended from metabolic stessed cow

first: Ying

last: Zhang

first: Julien

last: Prunier

first: Catherine

last: Chaput

first: Eric

last: Fournier

first: Marc-André

last: Sirard


title: Early blood transcriptomic markers of necrotizing enterocolitis in preterm piglets

city: Frederiksberg

first: Xiaoyu

last: Pan

address: Dyrlægevej 68

department: Department of Veterinary and Animal Sciences

summary: Necrotizing enterocolitis (NEC), a severe gut disorder in preterm infants, is difficult to predict due to poor specificity and sensitivity of clinical signs and biomarkers. Using preterm piglets as a model, we hypothesized that early development of NEC affects blood gene expression, potentially related to early systemic immune responses. In this animal model, variable severity of gut NEC lesions were detected in 5d-old piglets with limited clinical signs. NEC (n=20) and control piglets (CON, n=19) were analyzed for whole blood transcriptome, revealing 344 differentially expressed genes (DEGs) between NEC and CON piglets. Co-expression network analyses and qPCR suggested AOAH, FKBP5, PAK2 as three NEC-specific genes associated with severe gut lesions. These results suggest that whole blood gene expressions are affected in preterm piglets when clinical symptoms of NEC are minimal. Blood transcriptome may be a novel tool to identify early biomarkers of NEC.

overall_design: A retrospective analysis of clinical data was performed on 129 formula fed piglets that had NEC diagnosis at necropsy on day 5. Subgroups of NEC (n=20) and control piglets (CON, n=19) were analyzed for whole blood transcriptome. Key genes were validated in whole blood and dried blood spots by qPCR.

first: Tik

last: Muk

first: Shuqiang

last: Ren

first: Duc

last: Nguyen

first: Rene

last: Shen

first: Fei

last: Gao

first: Per

last: Sangild


title: Identification of TIA1 mRNA targets during human neuronal development

city: Toronto

first: Marat

last: Mufteev

address: 686 Bay St.

department: Molecular Genetics

institute: University of Toronto

summary:
Background: Neuronal development is a tightly controlled process involving multi-layered regulatory mechanisms. While transcriptional pathways regulating neurodevelopment are well characterized, post-transcriptional programs are still poorly understood. TIA1 is an RNA-binding protein that can regulate splicing, stability, or translation of target mRNAs, and has been shown to play critical roles in neurodevelopment. However, the identity of mRNAs regulated by TIA1 during neurodevelopment is still unknown.
Methods and Results: To identify the mRNAs targeted by TIA1 during the first stages of human neurodevelopment, we performed RNA immunoprecipitation-sequencing (RIP-seq) on human embryonic stem cells (hESCs) and derived neural progenitor cells (NPCs), and cortical neurons. While there was no change in TIA1 protein levels, the number of TIA1 targeted mRNAs decreased from pluripotent cells to neurons. We identified 2400, 845, and 330 TIA1 mRNA targets in hESCs, NPC, and neurons, respectively. The vast majority of mRNA targets in hESC were genes associated with neurodevelopment and included autism spectrum disorder-risk genes that were not bound in neurons. Additionally, we found that most TIA1 mRNA targets have reduced ribosomal engagement levels.
Conclusion: Our results reveal TIA1 mRNA targets in hESCs and during human neurodevelopment, indicate that translation repression is a key process targeted by TIA1 binding and implicate TIA1 function in neuronal differentiation.

overall_design: Human ESC, ESC-derived NPCs and Neurons were subjected to RIP-seq and RNA-seq to characterize changes in TIA1 binding during human neurodevelopment.

first: L

last: Byres

first: M

first: D

last: Rodrigues

first: J

last: Ellis


title: CTCF chromatin residence time controls 3D genome organization, gene expression and DNA methylation in pluripotent cells [Hi-C]

city: Rotterdam

first: Niels

last: Galjart

department: Cell Biology

country: Netherlands

institute: Erasmus University Medical Centre

summary: The eleven zinc finger (ZF) protein CTCF regulates topologically associating domain (TAD) formation and transcription through selective binding to thousands of genomic sites. We replaced endogenous CTCF in mouse embryonic stem (ES) cells with GFP-tagged wildtype or mutant proteins lacking individual ZFs. We examined the various ES cell lines using next generation sequencing methods (ChIP-Seq, RNA-Seq, MedSeq, HiC) in order to identify additional determinants of CTCF positioning and function.

overall_design: 2) Hi-C derived from mouse ES cells expressing GFP-CTCF or a CTCF mutant protein lacking ZF8. Hi-C libraires were prepared from three biological replicates.


title: RNA-binding proteins regulate aldosterone homeostasis in human steroidogenic cells

city: NEW YORK

first: RUI

last: FU

state: NY

address: 101 6th Ave

department: Computational Biology

institute: New York Genome Center

summary: AngiotensinII (AngII) binds to the type I angiotensin receptor in the adrenal cortex to initiate a cascade of events leading to the production of aldosterone, a master regulator of blood pressure and volume. While the key signaling pathways, transcription factors, and steroidogenic enzymes necessary for adrenocortical production have been identified, surprisingly little is known about post-transcriptional regulation of this process. To investigate this question, we performed a high-resolution RNA-seq time course of the AngII stimulation response in a steroidogenic human cell line (H295R). We identified twelve temporally distinct groups of gene expression responses important for various steps of aldosterone production. AngII response kinetics for many of these mRNAs revealed a coordinated increase in both synthesis and decay. These findings were validated in primary human adrenocortical cells stimulated ex vivo with AngII or ACTH.

overall_design: RNA sequencing of AngII-treated H295R cells and AngII/ACTH-treated primary adrenocortical cells

first: Neelanjan

last: Mukherjee

first: Kent

last: Riemondy

first: Rui

last: Fu

first: Amber

last: Baldwin


title: RNA Sequencing profiling of cells from wild tpye mESC and differentiated cells derived from mESCs, and brains from Wild Type and Discn-/- mice

city: Kunming

first: Ping

last: Zheng

address: Qingsong Road 21

institute: Kunming Institute of Zoology, Chinease Academy of Sciences

summary: Aim: The goals of this study are to compare transcriptome profile of mESCs and differentiated cells, and transcriptome profile of brains from wild type and Discn-/- mice.

overall_design: mESCs and differentiated cells derived from mESCs were treated with 10 μM etoposide or 2 mM  Hydroxyurea for 4 hours. Brains were isolated from 5 weeks old wild type (WT) and Discn-/- mice. RNA was isolated and RNA-seq was performed.

first: Lin

last: Wang

first: Jingzheng

last: Li


title: Inflammation drives alternative first exon usage of critical immune genes including Aim2 [nanopore]

first: Sergio

last: Covarrubias

first: Susan

last: Carpenter

first: Angela

last: Brooks


title: In vivo co-transplant gene expression

first: Alexander

last: Kononov

summary: Gene expression of bulk subcutaneous tumors growing from either KPC PDA tumor cells co-transplanted with CD105pos Pancreatic Fibroblasts (PaFs) or CD105neg PaFs

overall_design: Tumor cells and CD105pos or CD105neg PaFs (tumor:fibroblasts 1:1) were injected in matrigel into the flank of syngeneic B6 hosts. After 10 days the tumors were collected and RNA isolated.

first: Colin

last: hutton

first: Alex

first: Claus

last: Jorgensen


title: A DNA Repair Pathway Can Regulate Transcriptional Noise to Promote Cell Fate Transitions

city: San Francisco

first: Xinyue

last: Chen

address: 1650 Owens St

institute: Gladstone Institutes

summary: Stochastic fluctuations in gene expression (‘noise’) are often considered detrimental but, in many disciplines, fluctuations are exploited for benefit (e.g., dither).  We show here that DNA base-excision repair amplifies transcriptional noise to facilitate cellular reprogramming.  Specifically, the DNA-repair protein Apex1, which recognizes both naturally occurring and unnatural base modifications, amplifies expression noise while homeostatically maintaining mean-expression levels.  This amplified expression noise originates from shorter duration, higher intensity, transcriptional bursts generated by Apex1-mediated DNA supercoiling.  The remodeling of DNA topology first impedes and then accelerates transcription to maintain mean levels and this mechanism, which we term Discordant Transcription through Repair (DiThR), potentiates cellular reprogramming and differentiation.  Our study reveals a potential functional role for transcriptional fluctuations mediated by DNA base modifications in embryonic development and disease.

overall_design: We set out to determine the effects of nucleotide base analogues on transcriptional noise and mean gene expression levels. Specifically, we tested a pyrimidine analogue, 5’-iodo-2’-deoxyuridine (IdU) in mouse embryonic stem cells (mESCs), and mouse embryonic fibroblasts (MEFs) during reprogramming.  We performed single-cell RNA-seq in mESCs treated with 10uM IdU or DMSO control to analyze gene expression noise.  And we also performed bulk RNA-seq in mESCs treated with 5uM IdU, 10uM IdU, and DMSO in triplicates to analyze gene expression changes in response to IdU.  Further we analyzed Day 2 and Day 5 reprogramming MEFs treated with 4uM IdU and DMSO in duplicates using bulk RNA-seq to assess the effects of noise enhancer (IdU) on cell-fate transitions.

first: Ravi

middle: V

last: Desai

first: Leor

last: Weinberger


title: Impairment of human terminal erythroid differentiation by histone deacetylase 5 deficiency

city: zhengzhou

first: huizhi

last: zhao

address: No.100 Science Avenue

institute: zhengzhou university

summary: Histone deacetylases (HDACs) are a group of enzymes catalyzing the removal of acetyl groups from histone and non-histone proteins. HDACs have been shown to play diverse functions in a wide range of biological processes. However, their roles in mammalian erythropoiesis remain to be fully defined. We show here that of the eleven classic HDAC family members, six of them (HDAC 1,2,3 and HDAC 5,6,7) are expressed in human erythroid cells with HDAC5 significantly up regulated during terminal erythroid differentiation. Knockdown of HDAC5 in human CD34+ cells followed by erythroid cell culture led to increased apoptosis, decreased chromatin condensation, and impaired enucleation of erythroblasts.

overall_design: ATAC-seq and RNA-seq analyses between normal erythropoiesis and  HDAC5 knockdown erythropoiesis

first: Xiuli

last: An


title: Mutational synergy coordinately remodels chromatin accessibility, enhancer landscape and 3-Dimensional DNA topology to alter gene expression during leukemia induction (RNA-seq)

city: Stuttgart

first: Haiyang

last: Yun

address: Auerbachstraße 112

institute: Robert Bosch Center for Tumor Diseases

summary: Altered transcription is a cardinal feature of acute myeloid leukemia (AML), however, exactly how mutations synergise to remodel the epigenetic landscape and rewire 3-Dimensional (3-D) DNA topology is unknown. We have utilized an allelic series of mice carrying the most common mutations in AML, namely Flt3-ITD and Npm1c. These model different “transition states” (normal: wild-type (WT); pre-malignant: single mutant (SM) with either Flt3-ITD or Npm1c; malignant: double mutant (DM)) during AML induction. We have analyzed hematopoietic stem and progenitor cells (HSPCs) from WT and mutant mice for gene expression (RNA-seq), chromatin activation states (ChIP-seq for H3K4me1, H3K4me3, H3K27ac), chromatin accessibility (ATAC-seq), and promoter-anchored 3-D chromatin interaction (promoter capture HiC, pCHiC) and have integrated these analyses to determine the transcriptional, epigenetic and DNA-topological evolution of AML. These findings allow the identification of long-range cis-regulatory circuits, as well as larger and more detailed gene-regulatory networks, whose importance we demonstrate through perturbation of network members.

overall_design: Global gene expression was profiled using RNA-seq in WT and mutant HSPCs, as well as in WT neutrophils. Two biological replicates were performed for each cellular state.

first: Shabana

last: Vohra

first: Brian

last: Huntly