title: Nascent transcriptomic landscape in bread wheat detected Pol II-dependent enhancer transcription

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

summary: Bread wheat is the major staple food of the world with a complex hexaploidy genome. The precise spatiotemporal gene expression is orchestrated by enhancers, which lack general sequence features and thus are difficult to be located, especially in large genomes. Epigenomic architecture, including chromatin openness and active chromatin marks, has been widely used to characterize enhancers. However, an active chromatin environment does not necessarily mean an active enhancer. Recently, enhancer RNAs (eRNAs), the hallmark for active enhancers, have been detected by nascent RNA sequencing in both Drosophila and mammalian. In order to answer whether plant enhancers could be transcribed, we investigated the transcriptome of bread wheat via two nascent RNA sequencing methods, GRO-seq and pNET-seq combining with epigenome profiling. Our study demonstrates the presence and wide distribution of transcription at intergenic enhancers, which accurately reflects high enhancer activity, shedding light on the complex gene expression regulation across subgenomes in bread wheat.

overall_design: To elucidate the general features and functional roles of enhancer transcription in bread wheat, we modified and applied global nuclear run-on sequencing (GRO-seq) and plant native elongating transcript sequencing (pNET-seq), both methods are competent for capturing nascent transcripts regardless of the stability, thus capable of mapping the exact position, amount and orientation of transcriptionally engaged RNA polymerase II in a more complete and precise manner.

first: Zhicheng

last: Dong

first: Yijing

last: Zhang


title: Probing in vivo RNA structure with optimized DMS-MaPseq in rice

status: Public on Apr 05 2022

city: Nanjing

first: Xiaorong

last: Fan

address: Nanjing city Wei Tong Road 6

department: 1State Key Laboratory of Crop Genetics and Germplasm Enhancement

country: China

institute: Nanjing Agricultural University

type: Expression profiling by high throughput sequencing

summary: Here, we use dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) to conduct a target-specific and genome-wide profile of in vivo RNA secondary structure in rice (Oryza sativa). Our study presents an optimized DMS-MaPseq for probing in vivo RNA structure in rice.

sample_organism:
Arabidopsis thaliana
Oryza sativa
Oryza sativa Japonica Group

overall_design: Use target-specific and genome-wide DMS-MaPseq to probe in vivo RNA structure.

first: Qiongli

last: Jin

first: Linqi

first: Saiyan

last: Hu

first: Guangbo

last: Wei

first: Zhiye

last: Wang


title: Two pathways drive meiotic chromosome axis assembly in Saccharomyces cerevisiae

status: Public on Apr 08 2022

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

country: USA

institute: New York University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Successful meiotic recombination, and thus fertility, depends on conserved axis proteins that organize chromosomes into arrays of anchored chromatin loops and provide a protected environment for DNA exchange. Here, we show that the stereotypic chromosomal distribution of axis proteins in S. cerevisiae is the additive result of two independent pathways: a cohesin-dependent pathway, which was previously identified and mediates focal enrichment of axis proteins at gene ends, and a parallel cohesin-independent pathway that recruits axis proteins to broad genomic islands with high gene density. These islands exhibit elevated markers of crossover recombination as well as increased nucleosome density, which we show is a direct consequence of the underlying DNA sequence. A predicted PHD domain in the center of the axis factor Hop1 specifically mediates cohesin-independent axis recruitment. Intriguingly, other chromosome organizers, including cohesin, condensin, and topoisomerases, are differentially depleted from the same regions even in non-meiotic cells, indicating that these DNA sequence-defined chromatin islands exert a general influence on the patterning of chromosome structure.

overall_design:
ChIP-seq analysis of binding dynamics of meiotic and nonmeiotic factors in S. cerevisiae during meiosis. Each bedgraph file is the results from paired Input and ChIP samples.

Spike in samples were spiked in with 20% SK288C yeast in order to normalize SK1 reads between genotypes.

first: Jonna

last: Heldrich

first: Carolyn

middle: R

last: Milano

first: Tovah

middle: E

last: Markowitz

first: Sarah

middle: N

last: Ur

first: Luis

middle: A

last: Vale-Silva

first: Kevin

middle: D

last: Corbett


title: mCRPC LuCaP PDXs ChIP-seq

status: Public on Apr 06 2022

city: Boston

first: Xintao

last: Qiu

state: MA

address: 440 brookline ave

institute: Dana Faber Cancer Institute

summary: Informed consent was obtained to collect human mCRPC tissues and generate the patient-derived xenograft tumors as described previously (Labrecque et al., 2019; Nguyen et al., 2017). The study was approved by the University of Washington Human Subjects Division institutional review board (no. 39053). All animal studies were approved by University of Washington IACUC and performed according to NIH guidelines. Molecular characterization of AR+ mCRPC LuCaP PDXs 70CR, 78CR, 81CR, 96CR, 105CR, 136CR and 147CR was previously described (Labrecque et al., 2019; Nguyen et al., 2017). LuCaP PDX 167CR was established from a liver metastasis of 77-year-old Caucasian male who died of abiraterone-, carboplatin- and docetaxel-resistant CRPC. LuCaP 167CR expresses AR, responds to castration and is negative for synaptophysin. PDX cellular morphology recapitulates the original liver metastasis (Supplementary Figure S8A).

overall_design: ChIP-seq for AR, FOXA1, H3K27Ac

first: Eva

last: Corey

first: Mark

middle: M

last: Pomerantz

first: Matthew

middle: L

last: Freedman

first: Henry

middle: W

last: Long


title: Cell-free RNA as a Novel Biomarker for Response to Therapy in Head & Neck Cancer

city: Vienna

first: Anela

last: Tosevska

address: Waehringer Guertel 18-20

department: Division of Rheumatology

country: Austria

institute: Medical Univrsity of Vienna

summary:
Liquid biopsies are gaining more traction as non-invasive tools for the diagnosis and monitoring of cancer. A new class of cancer therapeutics, synergistic botanical drug combinations (APG-157) can target multiple pathways and provide a durable response and safety. Monitoring the efficacy of such drugs involves assessing multiple molecules and cellular events simultaneously. We report a methodology using plasma cell-free RNA (cfRNA) as an indicator of patient response during drug treatment.
Plasma was collected from six patients with head and neck cancer (HNC) and four controls receiving APG-157 or placebo through an oral mucosal route, before treatment and on multiple points post-dosing. Circulating cfRNA was extracted from plasma at 0-, 3- and 24-hours post-treatment, followed by RNA sequencing.
Analysis of the circulating transcriptome pointed to significant perturbations following APG-157 treatment. Transcripts associated with inflammatory response and leukocyte activation were upregulated upon treatment with APG-157 in cancer patients, but not in controls or placebo-treated patients. A platelet-related transcriptional signature could be detected in patients but not in controls, indicating a platelet-centric pathway in HNC.
These results from a Phase 1 study are a proof of principle of the utility of cfRNAs as non-invasive biomarkers for monitoring the efficacy of APG-157 in HNC.

overall_design: Examining the potential of cfRNA liquid biopsies for diagnosis and treatment monitoring in Head and Neck cancer.

first: Matteo

last: Pellegrini


title: Long-lasting priming by β-amino butyric acid is marked by DNA hypomethylation

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

type: Methylation profiling by high throughput sequencing

summary: Exposure of plants to stress conditions or to certain chemical elicitors can establish a primed state, whereby responses to future stress encounters are enhanced. Stress priming can be long-lasting and likely involves epigenetic regulation of stress-responsive gene expression. However, the molecular events underlying priming are not well understood. Here, we characterise epigenetic changes in tomato plants primed for pathogen resistance by treatment with β-aminobutyric acid (BABA). We used whole genome bisulphite sequencing to construct tomato methylomes from control plants and plants treated with BABA at the seedling stage, and a parallel transcriptome analysis to identify genes primed for the response to inoculation by the fungal pathogen, Botrytis cinerea. Genomes of plants treated with BABA showed a significant reduction in global cytosine methylation, especially in CHH sequence contexts. Analysis of differentially methylated regions (DMRs) revealed that CHH DMRs were almost exclusively hypomethylated and were enriched in gene promoters and in DNA transposons located in the chromosome arms. Although there was some enrichment of stress response-related gene ontology terms in genes overlapping CHH DMRs, there was no significant enrichment of DMRs amongst a set of 747 primed defence genes, and nor was the pattern of methylation in these genes altered by BABA treatment. Hence, we conclude that whilst BABA treatment of tomato seedlings results in characteristic changes in genome-wide DNA methylation, CHH hypomethylation does not appear to directly target genes showing primed responses to pathogen infection. Instead, methylation may confer priming via in-trans regulation, acting at a distance from defence genes, and/or by targeting a smaller group of regulatory genes controlling stress responses.

overall_design: Examination of genome DNA methylation of Solanum licopersicum plants trated with  β-amino butyric acid (BABA), and mock-treated plants as control.

first: Michael

last: Roberts


title: Priming resistance of tomato to Botrytis cinerea infection by root drench treatment with beta-aminobutyric acid.

summary:
Induced resistance responses of plants to biotic stress can be enhanced by prior treatment by chemical priming agents such as beta-aminobutyric acid (BABA). Defence-related genes are typically not expressed following priming, but show faster and/or stronger induced expression following infection.
Here we test the transcriptome responses of control and BABA-primed plants to infection with the fungal pathogen Botrytis cinerea.

overall_design: Tomato leaves from control and primed plants were either mock inoculated or inolculated with Botrytis spores. Leaves were harvested immediately (time zero) and at 6, 9 and 12 hours following inoculation.

first: Dawn

last: Worrall


title: RNA-seq analysis of Mature (EMM) vs. Immature (baseline) iPSC-aCM compared to human atrial tissue (HAT) obtained from the same patient.

city: Chicago

first: Olivia

middle: Thao

last: Ly

state: Illinois

address: 768 W Jackson Blvd, 424

department: Medicine

institute: University of Illinois in Chicago College of Medicine

summary: The goal of this experiment is to identify gene ontology pathways and differentially expressed genes that distinguish mature iPSC-aCM, immature iPSC-aCM, and human atrial tissue derived from the same patient.

overall_design: Examination of 3 different iPSC-aCM lines at 4 different time points and 2 different culture conditions, as well as 2 different human atrial tissue samples. The first iPSC-aCM line (P1) and the second iPSC-aCM line (P2) are compared at baseline conditions vs. EMM conditions, and compared against human atrial tissue (P1-HAT and P2-HAT) from the same patient. The third iPSC-aCM line (L3) are compared at day 15 (3 samples), day 25 (3 samples), day 32 baseline (3 samples), and day 32 EMM (3 samples).

middle: T

first: Dawood

last: Darbar


title: Suppression of p53 response by blocking p53-Mediator binding with a stapled peptide

city: Boulder

first: Taylor

middle: K

last: Jones

state: CO

address: 3415 Colorado Ave

institute: University of Colorado Boulder

summary: DNA-binding transcription factors (TFs) have been challenging to target with molecular probes.  Many TFs function in part through interaction with Mediator; we sought to block p53 function by disrupting the p53-Mediator interaction.  Through rational design and activity-based screening, we characterized a stapled peptide, with functional mimics of both p53 activation domains, that selectively disrupted p53- and Mediator-dependent transcription in vitro. This “bivalent peptide” also suppressed p53 transcriptional response in human cancer cells.  Our strategy circumvents the TF and instead targets the TF-Mediator interface, with desired transcriptional outcomes.  Different TFs target Mediator through different subunits, suggesting this strategy could be generalizable.

overall_design: Examination of polII (pol II Ser5 3E8) TSS occupancy by ChIPseq with and without the inhibitory peptide in the presense of the p53 activator Nutlin3a.


title: Oral shedding of an oncogenic virus alters signatures of oral microbiome in HIV+ patients

city: Little Rock

first: Yong-Chen

middle: William

last: Lu

address: 4301 W Markham St

department: Pathology

institute: University of Arkansas for Medical Sciences

summary: Collectively, viruses are the principal cause of cancers arising in patients with immune dysfunction, including HIV+ patients. Kaposi’s Sarcoma (KS) etiologically linked to KSHV continues to be the most common AIDS-associated tumor. The involvement of oral cavity represents one of the most common clinical manifestations of this tumor. HIV infection incurs an increased risk for periodontal diseases and oral carriage from a variety of pathogenic bacteria. In the current study, by using 16S rRNA based pyrosequencing, we found that oral shedding of KSHV altered oral microbiota signature in HIV+ patients which may contribute to virus-associated malignancies development.

overall_design: We sequenced the hypervariable V4 region of the 16S rRNA gene present in saliva DNA from cohort of HIV+ patients by next generation sequencing at the Argonne National Laboratory.

first: Zhiqiang

last: Qin


title: Transcriptome profiling in swine macrophages infected with African swine fever virus at single-cell resolution

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

summary: African swine fever virus (ASFV) is the causative agent of African swine fever, a highly contagious and usually fatal disease in pigs. The pathogenesis of ASFV infection has not been clearly elucidated. Here, we used single-cell RNA-sequencing technology to survey the transcriptomic landscape of ASFV-infected primary porcine alveolar macrophages. The temporal dynamic analysis of viral genes revealed increased expression of viral transmembrane genes. Molecular characteristics in the ASFV-exposed cells exhibited the activation of antiviral signaling pathways with increased expression levels of interferon-stimulated genes and inflammatory- and cytokine-related genes. By comparing infected cells with unexposed cells, we showed that the unfolded protein response (UPR) pathway was activated in low viral load cells, while the expression level of UPR-related genes in high viral load cells was less than that in unexposed cells. Cells infected with various viral loads showed signature transcriptomic changes at the median progression of infection. Within the infected cells, differential expression analysis and coregulated virus–host analysis both demonstrated ASFV promoted metabolic pathways but inhibited interferon and UPR signaling, implying the regulation pathway of viral replication in host cells. Furthermore, our results revealed that the cell apoptosis pathway was activated upon ASFV infection. Mechanistically, the production of tumor necrosis factor alpha (TNF-α) induced by ASFV infection is necessary for cell apoptosis, highlighting the importance of TNF-α in ASFV pathogenesis. Collectively, the data provide insights into the comprehensive host responses and complex virus–host interactions during ASFV infection, which may instruct future research on antiviral strategies.

overall_design: This study performed 10× experiment for seven samples from the uninfected group with various time points (0, 2, 6, 10, 15, 24 and 36 hpi) and six samples from the infected group with various time points (2, 6, 10, 15, 24 and 36 hpi).

first: Su

last: Li

first: Shi-Hua

first: Shaoxiong

last: Yu

first: Qihui

last: Wang

first: Kehui

last: Zhang

first: Liang

last: Qu

first: Yuan

last: Sun

first: Yuhai

last: Bi

first: Fuchou

last: Tang

first: Hua-Ji

first: George

middle: F

last: Gao


title: Gene repression through epigenetic modulation by PPARA enhances hepatocellular proliferation

city: Bethesda

first: Frank

middle: J.

last: Gonzalez

state: MD

address: 37 Convent Drive. Bldg37/Rm3106

department: National Cancer Institute

institute: National Institutes of Health

summary:
Peroxisome proliferator-activated receptor α (PPARA) is a key mediator of lipid metabolism and inflammation. Activation of PPARA in rodents causes hepatocyte proliferation, but the underlying mechanism is poorly understood. This study focused on genes repressed by PPARA and analyzed the mechanism by which PPARA promotes hepatocyte proliferation in mice. Activation of PPARA by agonist treatment was autoregulated, and induced expression of the epigenetic regulator UHRF1 via activation of the newly described PPARA target gene E2f8, that in turn regulates Uhrf1. UHRF1 strongly repressed expression of CDH1 via methylation of the Cdh1 promoter marked with H3K9me3. Repression of CDH1 by PPARA activation was reversed by PPARA deficiency or knockdown of E2F8 or UHRF1. Furthermore, forced expression of CDH1 inhibited expression of the Wnt signaling target genes such as Myc after PPARA activation, and suppressed hepatocyte hyperproliferation. These results demonstrate that the PPARA-E2F8-UHRF1-CDH1 axis causes epigenetic regulation of hepatocyte proliferation.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
Refer to individual Series
RNA-seq: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE154275
ChIP-seq: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE154276


title: Genome-wide profiling of PPARA in PPARA agonist-treated mouse livers [ChIP-seq]

summary: To clarify mouse PPARA autoinduction and hepatocyte proliferation signaling pathways, genome-wide distribution of PPARA in the liver of PPARA agonist-treated mice compared to Vehicle was analyzed.

overall_design: ChIP was carried out to pull down PPARA bound chromatin from nuclei isolated from Vehicle (Control)- or PPARA agonist (Wy14,643)-treated C57BL/6 mouse livers. This chromatin fraction was then digested using micrococcal nuclease to release mononucleosomes. DNA fragments purified from nucleosomes were then used to generate libraries and sequenced.

first: Daisuke

last: Aibara

first: Tomoki

last: Yagai

first: Chad

last: Brocker

first: Shogo

last: Takahashi

middle: J


title: Oncogenic RAS sensitizes cells to drug-induced replication stress via transcriptional silencing of P53

city: Utrecht

last: Riemers

address: Uppsalalaan 8

country: Netherlands

institute: Utrecht University

summary: Since oncogenes induce DNA replication stress (RS), cancer cells rely on the intra S-phase checkpoint for survival. Consequently, RS inducing drugs and ATR and CHK1 inhibitors are exploited as anti-cancer therapy. However, drug resistance limits efficient use. This raises the question what determines sensitivity of individual cancer cells to RS. Here, we report that oncogenic RAS dampens the P53 checkpoint which confers sensitivity to RS. We demonstrate that inducible expression of HRASG12V leads to mild RS in RPE-hTERT cells and was sufficient to sensitize cells to ATR and CHK1 inhibitors. Using RNA-sequencing we discovered that P53 signaling is essential for the response to RS. However, oncogenic RAS attenuates transcription of P53 and its target genes. Accordingly, live cell imaging shows that HRASG12V exacerbates RS in S/G2-phase. Thus, our results suggest that hyperactivation of the MAPK pathway could predict durable responses to RS inducing drugs in cancer patients

overall_design: Retina-pigment epithelial (RPE-hTERT) cells with stable expression of the FUCCI4 system and inducible oncogenic HRAS (HRASG12V) under the control of a Tet repressor and bladder cancer cell line (UM-UC-3) cells with stable expression of Geminin-Clover (FUCCI4) were treated with the combination of CHK1 inhibitor Prexasertib (CHK1i) (10nM) and Gemcitabine (4uM) or vehicle, and harvested after 16 hours. S-phase (Geminin-positive/SLBP-positive) RPE and S/G2-phase (Geminin-postive) UM-UC-3 cells were collected using FACS sorting. For each sample three biological replicates were used, and 2 independent clones of RPE cells harboring the FUCCI4 reporter system were included.

first: F

first: H

last: Segeren

first: B

last: Westendorp


title: Inhibition of mitochondrial complex I reverses NOTCH1-driven metabolic reprogramming in T-cell acute lymphoblastic leukemia

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

summary: NOTCH1-mutated T-ALL is a feasible target for OxPhos inhibitors owing to its significantly upregulated mitochondrial machinery. Mitochondrial OxPhos can be effectively targeted by the novel inhibitor of mitochondrial complex I IACS-010759, which demonstrated preclinical activity in NOTCH1-mutated T-ALL

overall_design: We used RNAseq to compare gene expression of ICAS, CB839, ICAS_CB839 and Vehicle treated samples in Leukemia cell lines.

first: Natalia

last: Baran

first: Marina

last: Konopleva

first: Yogesh

last: Dhungana

first: Jiyang


title: Expression profiling in liver of wild type and Ppara-null mice treated with PPARA agonists [RNA-seq]

summary: To clarify the mechanism underlying the proliferation of hepatocytes induced by PPARA agonists, expression profiling in liver of wild type and Ppara-null mice treated with PPARA agonist was investigated.

overall_design: RNA was extracted from the liver of wild type (Ppara+/+), and Ppara-null (Ppara-/-) mice treated with the PPARA agonist (Wy14,643 or Fenofibrte). RNA purified were then used to generate libraries and sequenced.


title: Long-lasting priming by β-amino butyric acid is marked by DNA hypomethylation.

status: Public on Apr 04 2022

first: Marco

last: Catoni

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

overall_design: Refer to individual Series


title: The immune checkpoint B7x promotes tumor-infiltrating tregs and resistance to anti-CTLA-4 therapy.

status: Public on Apr 02 2022

city: NEW YORK

first: Phillip

last: Galbo

institute: Albert Einstein college of medicine

summary: Tumor cells inhibit the anti-tumor immune response by expressing immunomodulatory factors and recruiting immunosuppressive cells to their microenvironment. Regulatory T cells (Tregs) are a population of CD4+ T cells that are commonly found in tumors, promoting a tolerogenic microenvironment and aiding in tumor immune evasion. The immune checkpoint ligand B7x is widely expressed in a broad variety of tumor types and is often associated with greater Treg infiltration, but the mechanism by which B7x promotes tumor-infiltrating Tregs is unknown. Here, we recapitulate the B7x-mediated increase in Tregs in murine tumor models and show that B7x promotes conversion of conventional CD4+ T cells into potently suppressive Tregs. We found that B7x induces global transcriptomic changes in Tregs, driving these cells to adopt an activated and suppressive phenotype. Mechanistically, B7x increased Foxp3 transcriptional expression by modulating the Akt/Foxo signaling pathway. Further, we found that expression of B7x by tumor cells reduced the efficacy of anti-CTLA-4 in syngeneic murine models in a Treg-dependent manner, but this resistance phenotype was overcome by combination anti-B7x and anti-CTLA-4 treatment. Put together, B7x mediates a novel Treg-promoting pathway within tumors and is a promising candidate for combination immunotherapy.

overall_design: In vivo: Foxp3-GFP-DTR mice (strain C57BL6) were engrafted with MC38-B7x or MC38-Control tumors, and tumors were enzymatically dissociated with collagenase-dispase-DNase solution. 10,000 to 20,000 tumor-infiltrating Tregs, defined as CD45+ CD4+ GFP+ cells, were flow-sorted on the BD FACSAria directly into RNA lysis buffer. In vitro: splenic CD4+ T cells from Foxp3-GFP-DTR mice were differentiated into iTregs with either B7x-Ig or Control-Ig, and subsequently up to 10,000 GFP+ CD4+ cells were sorted directly intro RNA lysis buffer.

first: Peter

last: John

first: Xingxing

last: Zang

first: Deyou

last: Zheng


title: Study the differential gene expression of different  lung cancer EGFR mutants in NIH3T3 cells

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

summary: Oncogenic mutations in the EGFR gene account for 15-20% of lung adenocarcinoma (LUAD) cases. However, the mechanism for EGFR driven tumor development and growth is not fully understood. Here, using a mRNA expression profiling-based approach we identified betacellulin (BTC) as one the gene upregulated by oncogenic EGFR in a MAP kinase-dependent manner. BTC protein expression was markedly increased in LUAD patient samples compared to normal lung tissue, with higher expression in EGFR-mutant LUAD. BTC was sufficient to transform immortalized mouse cells, initiate tumor development in mice, and promote the survival of immortalized human lung epithelial cells. Conversely, knockdown of BTC inhibited the growth of EGFR-mutant human LUAD cells in culture and their tumor-forming ability in mice. Mechanistically, BTC knockdown resulted in attenuated EGFR signaling and apoptosis induction. Collectively, these results demonstrate a key role of BTC in EGFR-mutant LUAD, with potential therapeutic implications in LUAD and other EGFR-mutant cancers.

overall_design: The study evaluated the differential gene expression within different EGFR mutant cells compared to the empty vector expressed NIH3T3 cells. Briefly, mouse NIH3T3 cells were stably expressing either empty vector (pBABEpuro) or different EGFR mutants (EGFR Wild Type, EGFR Del1, EGFR L858R, EGFR L861Q). Total RNA was extracted from all the 5 transformed cells, followed by poly-A selection and RNA-sequencing using Illumina Hi-Seq 2500 platform, with three biological replicates for each transformed sample.

first: Suresh

last: Chava

last: Bugide

first: Xuchen

last: Zhang

first: Romi

last: Gupta


title: Integrative genome analysis reveals low T cell infiltration as the primary feature of tobacco use in HPV(+) oropharyngeal cancer

city: St Louis

first: Jose

middle: P

last: Zevallos

state: MO

address: 660 South Euclid Avenue, Campus Box 8115

department: Otolaryngology - Head and Neck Surgery

institute: Washington University School of Medicine

summary: Tobacco use is an independent adverse prognostic feature in human papillomavirus (HPV)-associated oropharyngeal squamous cell carcinoma (OPSCC). Despite this, the biologic features associated with tobacco use have not been systematically investigated in this population. We sought to characterize the genomic and immunologic features of HPV(+) OPSCC associated with tobacco use and adverse oncologic outcomes. Whole exome sequencing of 47 primary HPV(+) OPSCC tumors was performed to investigate mutational differences associated with tobacco exposure. To characterize the tumor immune microenvironment (TIME), targeted mRNA hybridization was performed. Low expression of transcripts in a T cell-inflamed gene expression profile (TGEP) was associated with tobacco use at the time of diagnosis and lower overall and disease-free survival. Tobacco use was associated with an increased proportion of T>C substitutions and a lower proportion of mutational signatures typically observed in HPV(+) OPSCC tumors, but was not associated with increases in mutational burden or the rate of recurrent oncogenic mutations. Our work suggests that rather than increased mutational burden, tobacco’s primary and clinically relevant association in HPV(+) OPSCC is immunosuppression of the tumor immune microenvironment.

overall_design: Cohort study

first: Benjamin

last: Wahle


title: B16-huCD20 tumors treated with 177Lu-TRT were subjected to multiplex analysis to study the tumor immune signature.

city: Jette

first: Thomas

last: Ertveldt

state: Brussels

address: Laarbeeklaan 103, E206

department: BMWE

country: Belgium

institute: Vrije Universiteit Brussel

summary: Targeted gene expression on 9 B16-huCD20 Melanoma tumor samples treated with 177Lu-radiolabed sdAbs using the murine panCancer Immune panel (NanoString Technologies)

overall_design: In the study presented here, 9 mice were inoculated s.c. with 100.000 B16-huCD20 tumorcells and were treated 3, 9 and 14 days after inoculation with 177Lu-labeled sdAbs (3 low dose TRT, 3 high dose TRT and 3 control conditions) were used to acquire expression profiles of a total of 770 genes, leading to assessment of alterations in the tumor microenvironment

first: Kirsten

last: De Ridder


title: Persistence of SARS-CoV-2 Antibodies in Vaccinated Health Care Workers Analyzed by Coronavirus Antigen Microarray

city: Irvine

first: Rafael

last: de Assis

state: CA

address: 3800 PARKVIEW LN APT 38A, Irvine, CA 92612

institute: University of California Irvine

summary:
Individualized  antibody reacitivty levels for SARS-CoV-2 antigens were successfully quantified and reactivity classification (Reactive non reactive) was performed based on a logistic regression model.
Individuals were tested at several time points including their reactivity before the mRNA vaccination (Pfizer and Moderna), soon after first and second doses and up to 6 months after immunization

platform_organism: Severe acute respiratory syndrome-related coronavirus

platform_organism: Middle East respiratory syndrome-related coronavirus

platform_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: This study follows a health care workers from the University of California Irvine medical center for a logitudinal evaluation of their antobody reactivity against SARS-CoV-2 antigen up to 6 months after immunization with mRNA vaccine. Contributor:   The Specimen Collection Group

first: Sina

last: Hosseinian

first: Kathleen

last: Powers

first: Milind

last: Vasudev

first: Anton

last: Palma

first: Aarti

last: Jain

last: Horvath

first: Paramveer

middle: S

last: Birring

first: Rana

last: Andary

first: Connie

last: Au

first: Brandon

last: Chin

first: Ghali

last: Khalil

first: Jenny

last: Ventura

first: Madeleine

last: Luu

first: Cesar

last: Figueroa

first: Joshua

last: Obiero

first: Emily

last: Silzel

first: Rie

last: Nakajima

first: William

last: Gombrich

first: Algis

last: Jasinskas

first: Frank

last: Zaldivar

first: Sebastian

last: Schubl

first: Philip

last: Felgner

first: Saahir

last: Khan


title: Differential gene expression in C. auris in presence of pyrvinium pamoate

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

department: Biomedicine Discovery Institute

country: Australia

institute: Monash University

summary: PAT-seq approach was utilised to determine the gene expression in the the transcriptome of C. auris treated with the vehicle DMSO or drug pyrvvinium pamoate (PP). Biological triplicates of C. auris cultures grown in RPMI medium with either DMSO or 1uM PP for 30 minutes at 37 Celsius were havested and total RNA was isolated using standard procedures (hot phenol method).

overall_design: Analysis of poly(A) dynamics in C. auris

first: Ana

last: Traven

first: Claudia

last: Simm

first: Paul

last: Harrrison

middle: H


title: SAM68 is a splicing regulator in triple negative breast cancer

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary: SAM68 is an RNA binding protein frequently up-regulated in several human cancers and its oncogenic activity has often been associated with its splicing activity. Nevertheless, the genome-wide impact of SAM68 on the transcriptome of cancer cells is still unknown. Herein,  by high-throughput RNA sequencing analysis of MDA-MB-231 SAM68-silenced cells, we uncover an extensive modulation of triple-negative breast cancer cell transcriptome by this splicing factor.

overall_design: RNA‐Seq data for MDA-MB-231 cells, transiently silenced for SAM68.

first: Chiara

last: Naro

last: de La Grange

first: Claudio

last: Sette


title: NHEJ-mediated insertional mutagenesis reveals a novel target for enhancing fatty alcohols production in Yarrowia lipolytica

status: Public on Apr 01 2022

city: Tianjin

first: Mengxu

last: Li

state: China

address: Tianjin University, School of Chemical Engineering and Technology, 321, 54 building, Tianjin Univ., Peiyang Park Campus: No.135 Yaguan Road, Haihe Education Park

institute: Tianjin University

summary: We employed omics analyses to identify the new target discovered, enabling us to systematically reveal changes in gene transcript levels resulting from the disruption of new targets that can be engineered to enhance fatty alcohols production in Yarrowia lipolytica. Transcriptomic results indicated that disruption of the new target A1 resulted in significantly increased transcript levels of genes involved in protein synthesis processes, which was strongly enhanced.

overall_design: Transcriptome analysis of strains A24 and C24, three parallel samples were carried out at each strain.

first: Jinla

last: Zhang

first: Qiuyan

last: Bai

first: Yingxiu

last: Cao

first: Hao

last: Song


title: RNA-seq analsis of control or two P-cadherin knockout HCA-7 cell lines

status: Public on Apr 03 2022

city: Cleveland

first: Pranab

last: Mukherjee

state: OH

address: 9500 Euclid Avenue

department: Infection and Immunity

institute: Cleveland Clinic

summary: The goal of this experiment was to determine the effect of P-cadherin knockout on transcriptional profile of cells

overall_design: RNA was isolated, cDNA libraries (paired end) were made at the University of Chicago Genomics Facility, and sequenced on an Illumina HiSeq4000, in four replicates, according to standard protocols.

first: Nayden

middle: G

last: Naydenov

first: Florian

last: Rieder

first: Andrei

middle: I

last: Ivanov


title: Functional reprogramming of monocytes in acute and convalescent severe COVID-19 patients [RNA-seq]

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

institute: Université Libre de Bruxelles

summary: Severe COVID-19 disease is associated with dysregulation of the myeloid compartment  during acute infection. Survivors frequently experience long-lasting sequelae but little is known  about the eventual persistence of this immune alteration. Herein, we evaluated Toll-like  receptor-induced cytokine responses in a cohort of mild to critical patients during acute or  convalescent phases (n=97). In the acute phase, we observed impaired cytokine production  by monocytes in the most severe patients. This capacity was globally restored in convalescent  patients. Yet, we observed increased responsiveness to TLR1/2 ligation in patients that  recovered from severe disease, indicating that these cells display distinct functional properties  at the different stages of the disease. We identified a specific transcriptomic and epigenomic  state in monocytes from acute severe patients that can account for their functional  refractoriness. The molecular profile of monocytes from recovering patients was distinct and  characterized by increased chromatin accessibility at AP-1 and MAF loci. These results  demonstrate that severe COVID-19 infection has a profound impact on the differentiation  status and function of circulating monocytes both during the acute and the convalescent  phases in a completely distinct manner. This could have important implications for our  understanding of short and long-term COVID19-related morbidity.

overall_design: RNA-seq

first: Elisa

last: Brauns

last: Azouz

first: David

last: Grimaldi

first: Hanxi

last: Xiao

first: Séverine

last: Thomas

first: Muriel

last: Nguyen

first: Véronique

last: Olislagers

first: Ines

last: Vu Duc

first: Carmen

last: Orte Cano

last: Del Marmol

first: Pieter

last: Pannus

first: Frédérick

last: Libert

first: Sven

last: Saussez

first: Nicolas

last: Dauby

first: Jishnu

last: Das

first: Arnaud

last: Marchant

first: Stanislas

last: Goriely


title: Functional reprogramming of monocytes in acute and convalescent severe COVID-19 patients [ATAC-seq]

last: AZOUZ

overall_design: ATAC-seq

last: Brauns


title: The nuclear receptor THRB facilitates differentiation of human PSCs into more mature hepatocytes

city: Cambridge

first: Haiting

last: Ma

address: 455 Main Street

institute: Whitehead Institute

summary: To understand the mechanisms regulating the in vitro maturation of hPSC-derived hepatocytes, we developed a 3D differentiation system and compared gene regulatory elements in human primary hepatocytes with those in hPSC-hepatocytes that were differentiated in 2D or 3D conditions by RNA-seq, ATAC-seq, and H3K27Ac ChIP-seq. Regulome comparisons showed a reduced enrichment of thyroid receptor THRB motifs in accessible chromatin and active enhancers without a reduced transcription of THRB. The addition of thyroid hormone T3 increased the binding of THRB to the CYP3A4 proximal enhancer, restored the super-enhancer status and gene expression of NFIC, and reduced the expression of AFP. The resultant hPSC-hepatocytes showed gene expression, epigenetic status, and super-enhancer landscape closer to primary hepatocytes and activated regulatory regions including non-coding SNPs associated with liver-related diseases. Transplanting the hPSC-hepatocytes resulted in the engraftment of human hepatocytes into the mouse liver without disrupting normal liver histology. This work implicates the environmental factor-nuclear receptor axis in regulating the maturation of hPSC-hepatocytes.

overall_design: Examination of gene expression of primary human non-cultured hepatocytes, human pluripostent stem cells differentiated hepatocyte-like cells under 2D condition, 3D spheroid condition, and 3D spheroid condition with T3 and without OSM.

first: Rudolf

last: Jaenisch


title: Functional reprogramming of monocytes in acute and convalescent severe COVID-19 patients

first: Abdulkader


title: MEOX2-mediated regulation of Cathepsin S promotes cell proliferation and motility in glioma.

city: suzhou

first: Ji

last: Wang

address: 1055 Sanxiang Road, Gusu District

institute: Soochow University

summary: Nuclear transcription factor Mesenchyme Homeobox 2 (MEOX2) is a homeobox gene that is originally discovered to suppress the growth of vascular smooth muscle and endothelial cells. However, whether or not it is connected to cancer is yet unknown. Here, we report that MEOX2 functions as a tumor-initiating element in glioma. Bioinformatic analyses of public databases and investigation of MEOX2 expression in patients with glioma demonstrated that MEOX2 was abundant at both mRNA and protein levels in glioma. MEOX2 expression was shown to be inversely linked with the prognosis of glioma patients. MEOX2 inhibition changed the morphology of glioma cells, inhibited cell proliferation and motility, whereas had no effect on cell apoptosis. Besides, silencing of MEOX2 also hampered the epithelial-mesenchymal transition (EMT), focal adhesion maturation, and F-actin assembly. Overexpression of MEOX2 exhibited opposite effects. Importantly, RNA-seq, ChIP assay, and luciferase reporter assay revealed Cathepsin S (CTSS) as a novel transcriptional target of MEOX2 in glioma cells. Consistently, MEOX2 causes glioma tumor development in mice and greatly lowers the survival period of tumor-bearing mice. Our findings indicate that MEOX2 promotes tumorigenesis and progression of glioma partially through the regulation of CTSS. Targeting the MEOX2-CTSS axis might be a promising alternative for the treatment of glioma.

overall_design: To test the effect of suppression of MEOX2 on the gene expression, SNB19 cells were transfected with MEOX2 Scramble siRNA (Control) or MEOX2 siRNA. MEOX2-knockdown SNB19 cells were compared to control cells. To test the effect of activation of MEOX2 on the gene expression, U87 cells were transfected with MEOX2 empty vector (EV) or MEOX2 overexpression lentivirals. MEOX2-overexpression U87 cells were compared to control cells.

first: Yanming

last: Chen

first: Qing

last: Lan


title: Maternal antagonism of Glp1 reverses the adverse outcomes of sleeve gastrectomy on mouse offspring

city: Jerusalem

first: Liron

last: Hefetz

address: Ein Kerem Campus

department: Developmental Biology and Cancer Research

country: Israel

institute: Hebrew University of Jerusalem

summary: Maternal sleeve gastrectomy in lean mice leads to small-for-gestational births and higher sensitivity of offspring to a high fat diet. These effects are reduced by maternal treatment with a Glp1 antagonist.

overall_design: Placental mRNA profiles of e18.5 fetuses of Sham- and SG-operated dams.

first: Rachel

last: Ben-Haroush Schyr

first: Michael

last: Bergel

first: Yhara

last: Arad

first: Doron

last: Kleiman

first: Hadar

last: Israeli

first: Itia

last: Magenheim

first: Shira

last: Azulai

first: Arnon

last: Haran

first: Yovel

last: Levi

first: Dana

last: Sender

first: Amihai

last: Rottenstreich

first: Danny

last: Ben-Zvi


title: addition of proteasome inhibitor to J774 cells

city: Tokushima

first: Yuki

last: Sasaki

address: 3-18-15 Kuramoto-cho

department: Department of Immunology and Parasitology

country: Japan

institute: Tokushima University Graduate school of Medicine

summary:
J774 cells were treated with MG132, epoxomicin and ONX-0912 for 4 hours, and gene expression was evaluated
In order to evaluate the molecular mechanism of inflammatory responses in PRAAS(Proteasome-Associated Autoinflammatory Syndromes ), we established Psmb8-KI mouse that harbors the same mutation in human patients. Psmb8-KI mice showed higher susceptibility to imiquimod-induced skin inflammation (IMS).  DNA microarray analysis showed that treatment of J774 cells with proteasome inhibitors increased the expression of the Cxcl9 and Cxcl10 genes, and the skins where imiquimod was painted also expressed both genes at higher levels in Psmb8-KI than control mice. Deficiency in Cxcr3, the gene encoding the receptor of CXCL9 and CXCL10, in wild-type mice did not change IMS susceptibility, while deficiency in Cxcr3 in Psmb8-KI mice ameliorated IMS.

overall_design: Blockade of the CXCR3-CXCL10 axis ameliorates inflammation caused by immunoproteasome dysfunction

first: Koji

last: Yasutomo


title: RNA-seq from CD4 T lymphocytes of cirrhotic patients with cognitive impairment

city: Paterna

first: Ana

last: Conesa

state: Valencia

address: Carrer del Catedràtic Agustín Escardino Benlloch

country: Spain

institute: CSIC

summary: Patients with liver cirrhosis may have minimal hepatic encephalopathy (MHE) with cognitive and motor impairments that reduce life quality and span. MHE onset is associated with a shift in peripheral inflammation in which CD4+ lymphocytes play a key role but the underlying mechanisms remain unclear. We aimed to identify in CD4+ lymphocytes from patients with and without MHE: (1) gene expression changes and associated biological pathways using RNA-seq; (2) alterations in miRNA levels using miRNA-seq; (3) miRNAs and transcription factors regulating key mRNAs and (4) signalling pathways contributing to the peripheral inflammation shift associated to MHE onset. Additionally, we recovered T-cell receptor (TCR) repertoires from RNA-seq dataset to understand the immune status of control patients and cirrhotic patients with or without MHE.

overall_design: Gene expression was measured using RNA-seq in CD4 T cells of control and cirrhotic patients with and without minimal hepatic encephalopathy.

first: Teresa

last: Rubio

first: Maria

last: Chernigovskaya

first: Cristina

last: Marti

first: Paula

last: Izquierdo-Altarejos

first: María-Pilar

last: Ballester

first: Juan

last: Gallego

first: Desamparados

last: Escudero-Garcia

first: Amparo

last: Urios

first: Carmina

last: Montoliu

first: Vicente

last: Felipo

first: Victor

last: Greiff

first: Sonia

last: Tarazona


title: Cotton (Gossypium hirsutum L.) root transcriptional response to the southern Root-Knot Nematode (RKN) Meloidogyne incognita infestation

city: Lubbock

first: Mauricio

last: Ulloa

state: Texas

address: 3810 4th Street

department: PA, CSRL

institute: USDA-ARS

summary: As an initial step to explore the cotton (Gossypium hirsutum L.) root transcriptional response to the southern Root-Knot Nematode (RKN) Meloidogyne incognita infestation, conventional heirloom G. hirsutum (Gh) cultivars [susceptible Acala SJ-2 (SJ2), moderately resistant Upland Wild Mexico Jack Jones (WMJJ), and resistant Acala NemX] that have been shown to be useful as an informative genetic model for detecting and introgressing RKN resistance genes into commercial Upland cotton were used to enlighten the molecular mechanisms and gene expression of RKN resistance. Using the next generation sequencing (NGS) Illumina MiSeq and HiSeq, we performed RNA-seq profiling in roots with disease progression of 10 days and collected from 23 days old plants of SJ2, WMJJ, and NemX. With three biological replicates of each treatment from each cultivar, plants were subjected to RKN-infestation and non-infested control developing a total of 18 RNA-seq libraries

overall_design: Three cotton genotypes (Acala SJ-2 (RKN-susceptible), Wild Mexico Jack Jones (WMJJ; moderately tolerant to RKN) and Acala NemX (RKN-resistant)) and 2 treatments (Control, RKN-infested) were tested. 3 biological replicates for each treatment and genotype.

first: Damar

last: López-Arredondo

first: Jonathan

middle: O

last: Ojeda-Rivera

first: Luis

last: Herrera-Estrella


title: The lymph node transcriptome of unicentric and idiopathic multicentric Castleman disease

city: Rochester

first: Tao

last: Ma

state: MN

address: 200 First St. SW

institute: Mayo Clinic

summary: Castleman disease is polyclonal lymphoproliferative disorder characterized by unicentric or multicentric lymphadenopathy with characteristic histomorphologic features, in addition to variable inflammatory symptomatology. The molecular mechanisms and etiologies of unicentric Castleman disease (UCD) and idiopathic multicentric Castleman disease (iMCD) are poorly understood, and identification of targetable disease mediators remains an unmet clinical need. We performed whole exome sequencing on lymph node biopsies from patients with UCD and iMCD; and compared the transcriptomic profile to that of benign control lymph nodes. We identified significantly upregulated genes in UCD (443), iMCD (316) or both disease subtypes (51); in addition to downregulated genes in UCD (321), iMCD (105) or both (10). The transcriptomes of UCD and iMCD showed enrichment and upregulation of elements of the complement cascade. By immunohistochemistry, C4d deposits indicative of complement activation were present in UCD and iMCD mostly within abnormally regressed germinal centers, but also in association with plasma cell clusters, endothelial cells and stroma cells proliferations. Other enriched gene sets included collagen organization, S1P3 pathway and VEGFR pathway in UCD; and humoral response, oxidative phosphorylation and proteosome in iMCD. Analysis of cytokine transcripts showed upregulation of CXCL13 but not IL-6 in UCD and iMCD. Among angiogenic mediators, the VEGFR1 ligand placental growth factor (PGF) was upregulated in both disease subtypes. We hereby report for the first time the whole lymph node transcriptome of UCD and iMCD, underscoring findings that could aid in the discovery of targetable disease mediators.

overall_design: Whole exome sequecing was performed on 24 fresh frozen lymph node samples from 22 patients with uncentric Castleman disease; 7 lymph nodes and 1 spleen sample from 8 patients with idiopathic multicentric Castleman disease; and 19 control lymph node samples consistent with unremarkable lymph node tissue.

first: Pedro

last: Horna


title: Epigenetic changes induced by in utero dietary challenge result in phenotypic variability in successive generations of mice.

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

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

overall_design: Refer to individual Series


title: Active endogenous retroviral elements in human pluripotent stem cells are functional in regulating host gene expression

city: Wuhan

first: Zhang

last: Tianzhe

address: Donghu Road 116, District Wuchang

department: Medical Research Institute

institute: Wuhan University

summary: Human endogenous retroviruses were also called LTR elements which can be bound by transcription factors and marked by different histone modifications. In previous studies, LTR had been considered harmful to genome stability, but recently individual LTR or certain subclasses of LTRs such as LTR7/HERVH and LTR5/HERVK families had been identified as functional elements which had acted as a cis-regulatory element, constructed topological domains and contributed to immunity. However, there were still many LTR elements with unknown functions, and the biological significance of LTR for the host was poorly understood. Overall, our study has not only provided a comprehensive regulatory map of LTRs in human ESCs, but also explored the regulatory models of MER57E3 and LTR5_Hs on host genes.

overall_design: RNA-seq of 2 replicates in hESCs and ffEPSCs by targeting LTR5_Hs or ZNF730-MER57E3 in CRISPRi system

first: Tianzhe

last: Zhang

first: Ran

last: Zheng

first: Wei

last: Jiang


title: Epigenetic changes induced by in utero dietary challenge result in phenotypic variability in successive generations of mice [BS-seq]

summary: Transmission of epigenetic information between generations occurs in nematodes, flies and plants, mediated by specialised small RNA pathways, modified histones and DNA methylation. In mammals, evidence supports similar trans- and inter-generational effects although the underlying mechanisms are incompletely understood. Here a luciferase knock-in reporter mouse for the imprinted Dlk1 locus was generated to visualise and track epigenetic fidelity across generations. Exposure to high-fat diet (HFD) in pregnancy provoked sustained re-expression of the normally silent maternal Dlk1 allele in offspring (a loss of imprinting) and increased DNA methylation at the sDMR. In the next generation heterogeneous Dlk1 mis-expression was seen exclusively among animals born to F1-exposed females. Oocytes from these females showed altered gene and miR expression without changes in DNA methylation, and correct imprinting was restored in subsequent generations. Our results illustrate how diet impacts the foetal epigenome, disturbing canonical and non-canonical imprinting mechanisms to modulate the properties of two successive generations of offspring.

overall_design: A total of 78 MII oocytes, 41 from F1 mat-CD mice and 37 from F1 mat-HFD mice.

first: Mathew

last: Van de Pette

first: Antonio

last: Galvao

first: Steven

last: Millership

first: Andrew

last: Dimond

first: Wilson

last: To

first: Chiara

last: Prodani

first: Grainne

last: McNamara

first: Ludovica

last: Bruno

first: Alessandro

last: Sardini

first: Zoe

last: Webster

first: James

last: McGinty

first: Paul

last: French

first: Anthony

last: Uren

first: Juan

last: Castillo-Fernandez

first: William

last: Watkinson

first: Rosalind

last: John

first: Anne

middle: C

last: Ferguson-Smith

first: Matthias

last: Merkenschlager

first: Gavin

last: Kelsey

first: Amanda

last: Fisher


title: Epigenetic changes induced by in utero dietary challenge result in phenotypic variability in successive generations of mice [RNA-seq]

first: Felix

last: Krueger

overall_design: A total of 79 MII oocytes, 42 from F1 mat-CD mice and 37 from F1 mat-HFD mice.

first: Mathew

last: Van de Pette

first: Antonio

last: Galvao

first: Steven

last: Millership

first: Andrew

last: Dimond

middle: M


title: HOXB13 inhibits lipid metabolism through HDAC3-mediated epigenetic reprogramming

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University


title: HOXB13 inhibits lipid metabolism through HDAC3-mediated epigenetic reprogramming [ChIP-Seq]

summary: HOXB13 is a homeodomain transcription factor with prostate-specific expression. It is essential for normal prostate epithelium differentiation during development and functions as a key regulator of androgen-dependent cell growth in adult and cancerous prostate. Previous studies have demonstrated that HOXB13 is a pioneer factor of the androgen receptor (AR) and also a critical cofactor of AR variant v7 in castration-resistant prostate cancer (PCa). However, the intrinsic function of HOXB13 as a DNA-binding protein in an AR-independent context has not been elucidated. Here, our data reveal HOXB13, but not G84E mutant, recruits HDAC3 to specific genomic regions to catalyze histone de-acetylation and chromatin remodeling. We demonstrate a predominant function of HOXB13 in transcriptional repression of lipogenic genes requiring HDAC3.

overall_design: ChIP-seq of HOXB13, HDAC3, and H3K27ac in prostate cancer cells

first: Xiaodong

last: Lu


title: HOXB13 inhibits lipid metabolism through HDAC3-mediated epigenetic reprogramming [RNA-Seq]

overall_design: RNA-seq of prostate cancer cells with HOXB13 and/or HDAC3 de-regulation


title: RNA splicing is a key mediator of tumour cell plasticity and a therapeutic vulnerability in colorectal cancer [wild-type and Apc mutant]

status: Public on Mar 31 2022

city: Edinburgh

first: Kevin

last: Myant

address: Crewe Road

institute: MRC Institute of Genetics and Molecular Medicine

summary: mRNAseq of wild-type and Apc mutant mouse small intestine.

overall_design: RNA was extracted from wild-type and Apc mutant mouse small intestines. mRNAseq was carried out to identify differentially expressed transcripts.

first: Adam

last: Hall

first: Sebastian

last: Other-Gee Pohl

first: Patrizia

last: Cammareri

first: Stuart

last: Aitken

first: Michela

last: Raponi

first: Caroline

last: Billard

first: Alfonso

last: Bolado Carrancio

first: Aslihan

last: Bastem

first: Paz

last: Freile

first: Fiona

last: Haward

first: Ian

last: Adams

first: Javier

last: Caceres

first: Nicholas

last: Younger

first: Alex

last: von Kriegsheim

first: Malcolm

last: Dunlop

first: Farhat

last: Din


title: Time-Course Transcriptome Analysis of Lungs From Mice Infected With Hypervirulent Klebsiella pneumoniae via Aerosolize Intratracheal Inoculation

city: Beijing

first: Xinying

last: Zheng

address: Feitai region Dongda road

institute: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology

summary:
Purpose:Investigated transcriptome profile changes in the lungs of infected mice at different time points, to increase our understanding of hvKp pulmonary infection and to screen for genes or targets of research value. microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods:  Animals were randomly divided into four infection groups and one control group (five mice per group), and the infected mice were euthanized at 12, 24, 48 and 60 h post-infection (hpi), respectively, while the control group mice were euthanized immediately after delivery of PBS at the 0 h time point. The lungs of the mice were isolated and divided into two parts for subsequent histopathologic examination or total RNA extraction.
Results: Using the control group (0 hpi) as a reference, 6247 DEGs were identified across four time points after hvKp infection. At 12 hpi, 939 upregulated DEGs and 439 downregulated DEGs were detected, and by 60 hpi, 2647 upregulated DEGs and 2806 downregulated DEGs were detected. Overall, the number of upregulated and downregulated DEGs increased over time and a total of 688 genes were upregulated and 240 genes downregulated in common for all time points.  And 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.9548. To get a more holistic view, DEGs were clustered into nine clusters according to their temporal expression patterns.WGCNA was performed with the detected DEGs. The dynamic tree cutting algorithm in the WGCNA package was used to process the hierarchical clustering tree, and a total of 28 different modules were finally obtained.
Conclusions: Our work both validates the results of previous studies on K. pneumoniae pulmonary infections and provides new additions and insights on hvKp pulmonary infections, which may contribute to the development of therapeutic approaches to reduce hvKp lung inflammation.

overall_design: Lung mRNA profiles of c57 mice at 0, 12, 24, 48 and 60 hours after infection with hvKp

first: Jianshu

last: Guo

first: Chaoyue

last: Cao

first: Tongtong

last: Qin


title: Single cell RNA-seq of brain macrophages and microglia in mice lacking Notch3

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

summary: In this single cell RNAseq analysis, we compared brain macrophage and microglia transcriptomes from Notch3 knock out and control.

overall_design: Brain single cells from Notch3 knockout and control were sorted into 384-well-plates and RNA-sequenced using the SmartSeq2 method

first: Francesca

last: Del Gaudio

first: Urban

last: Lendahl


title: MicroRNA 3'-compensatory pairing occurs through two binding modes, with affinity shaped by nucleotide identity and position

first: Sean

middle: E.

last: McGeary

address: 455 Main St.

department: Biology

institute: Whitehead Institute / MIT

type: Non-coding RNA profiling by high throughput sequencing

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct


title: H3K9 trimethylation in active compartments optimizes stimulus-regulated transcription by restricting usage of CTCF sites in SINE-B2 repeats [RNA-Seq]

city: Milan

first: Francesco

last: Gualdrini

address: Via Adamello, 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

summary: Six methyltransferases divide labor in establishing genomic profiles of histone H3 lysine 9 methylation (H3K9me), an epigenomic modification involved in the formation of constitutive heterochromatin, gene repression and silencing of retroelements. Among them, SETDB1 is recruited to active chromatin compartments to silence the expression of endogenous retroviruses. In the context of experiments aimed at determining the role of SETDB1 in stimulus-inducible gene expression in macrophages, we unexpectedly found that upon SETDB1 depletion, loss of H3K9me3 in active compartments was associated with increased recruitment of CTCF to >1,600 DNA-binding motifs contained within SINE-B2 repeats, a previously unidentified target of SETDB1-mediated repression. CTCF is an essential regulator of chromatin folding that restrains DNA looping by cohesin, thus creating boundaries among adjacent topological domains. Increased CTCF binding to SINE-B2 repeats generated novel boundaries within topological domains containing lipopolysaccharide-inducible genes, correlating with their impaired regulation in response to stimulation. These data indicate a role of H3K9me3 in restraining genomic distribution and activity of CTCF, with impact on chromatin organization and gene regulation.

overall_design: RNAseq of mouse bone marrow-derived macrophages (BMDM) were infected with purified lentiviruses expressing two non-targeting (NT) shRNAs or two distinct shRNAs specific for SETDB1.

first: Sara

last: Polletti

first: Marta

last: Simonatto

first: Elena

last: Prosperini

first: Gioacchino

last: Natoli


title: H3K9 trimethylation in active compartments optimizes stimulus-regulated transcription by restricting usage of CTCF sites in SINE-B2 repeats [ATAC-Seq]

overall_design: ATACseq of mouse bone marrow-derived macrophages (BMDM) were infected with purified lentiviruses expressing two non-targeting (NT) shRNAs or two distinct shRNAs specific for SETDB1.


title: H3K9 trimethylation in active compartments optimizes stimulus-regulated transcription by restricting usage of CTCF sites in SINE-B2 repeats [HiC]

overall_design: In situ HIC of mouse bone marrow-derived macrophages (BMDM) were infected with purified lentiviruses expressing two non-targeting (NT) shRNAs or two distinct shRNAs specific for SETDB1.


title: H3K9 trimethylation in active compartments optimizes stimulus-regulated transcription by restricting usage of CTCF sites in SINE-B2 repeats [ChIP-Seq]

overall_design: H3K27Ac, H3K9me3, PU.1 and CTCF Chip-seq of mouse bone marrow-derived macrophages (BMDM) were infected with purified lentiviruses expressing two non-targeting (NT) shRNAs or two distinct shRNAs specific for SETDB1.


title: Atlas of the aging mouse colon

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

summary: Colon cancer is one of the leading causes of death within the western world and is linked to the aging of the colon. The disease presents differently between men and women, developing in different parts of the colon and often with a different morphology. The colonic epithelium is a rapidly renewing tissue, tasked with absorption of water and nutrients, interacting with a wide array of intestinal microbes. The gut-associated lymphoid tissue houses the majority of all immune cells. These immune cells interact with and help regulate the activity of epithelial cells. However, not much is known whether compartment-specific changes occur during aging and how said changes could impact the epithelium. Here we show that both epithelial and immune cells differ significantly between colonic compartments and experience age-related changes, with the possible causal interactions. We found a shift in the absorptive-secretory cell balance, the decrease in colonocytes possibly linked to age-associated malabsorption and intestinal disturbances. We demonstrate marked changes in the aging of the immune cells with regard to populations and interactions with epithelial cells, linking aged immune cell produced cytokines (Ifn-γ, Il1B) and the aging of colonic epithelium, which lines up with observations of inflammation causing or exacerbating age-associated gut disfunctions, such as colon cancer. Our results provide new insights into the normal and age-associated states of the colon. We anticipate our work will provide a foundation for further inquiry not only into diseases of the colon (even outside the realm of aging research) but developmental research as well.

overall_design: Single-cell RNA seq on epithelial and immune cells from the mouse colon

first: Seyed

last: Mahdi Rasa

first: Omid

last: Omrani

first: Dovydas

last: Sirvinskas

first: Lisa

last: Adam

last: Neri


title: MicroRNA 3'-compensatory pairing occurs through two binding modes, with affinity shaped by nucleotide identity and position [2]

state: MA

summary: MicroRNAs (miRNAs), in association with Argonaute (AGO) proteins, direct repression by pairing to sites within mRNAs. Compared to pairing preferences of the miRNA seed region (nucleotides 2–8), preferences of the miRNA 3′ region are poorly understood, due to the sparsity of measured affinities for the many pairing possibilities. We used RNA bind-n-seq with purified AGO2–miRNA complexes to measure relative affinities of >1,000 3′-pairing architectures for each miRNA. In some cases, optimal 3′ pairing increased affinity by >500-fold. Some miRNAs had two high-affinity 3′-pairing modes—one of which included additional nucleotides bridging seed and 3′ pairing to enable high-affinity pairing to miRNA nucleotide 11. The affinity of binding and the position of optimal pairing both tracked with the occurrence of G or oligo(G/C) nucleotides within the miRNA. These and other results advance understanding of miRNA targeting, providing insight into how optimal 3′ pairing is determined for each miRNA.

overall_design: mRNA sequencing of F9 cells co-transfected with synthetic miRNA duplexes and a massively parallel reporter library. This study consists of 8 libraries with 4 transfection conditions (1 mock and 3 different miRNAs), each in replicate.

middle: E

first: Namita

last: Bisaria

first: David

last: Bartel


title: RNA splicing is a key mediator of tumour cell plasticity and a therapeutic vulnerability in colorectal cancer [Apc mutant and Apc Srsf1 double mutant]

first: Kevin

last: Myant

summary: mRNAseq of Apc mutant and Apc Srsf1 double mutant mouse small intestine.

overall_design: RNA was extracted from Apc mutant and Apc Srsf1 double mutant mouse small intestines. mRNAseq was carried out to identify differentially expressed transcripts.

first: Adam

last: Hall

first: Sebastian

last: Other-Gee Pohl

first: Patrizia

last: Cammareri

first: Stuart

last: Aitken

first: Michela

last: Raponi

first: Caroline

last: Billard

first: Alfonso

last: Bolado Carrancio

first: Aslihan

last: Bastem

first: Paz

last: Freile

first: Fiona

last: Haward

first: Ian

last: Adams

first: Javier

last: Caceres

first: Nicholas

last: Younger

first: Alex

last: von Kriegsheim

first: Malcolm

last: Dunlop

first: Farhat

last: Din


title: The histone variant macroH2A1.1 regulates RNA Polymerase II paused genes within defined chromatin interaction landscapes.

city: TOULOUSE

first: Ludmila

middle: Alexandra

last: Recoules

address: 69 avenue Marianne Grunberg-Manago, 31062 Toulouse Cedex 9, Toulouse

institute: CNRS

summary: The histone variant macroH2A1.1 plays a role in cancer development and metastasis. To determine the underlying molecular mechanisms, we mapped the genome-wide localization of endogenous macroH2A1.1 in the human breast cancer cell line MDA-MB 231. We demonstrate that macroH2A1.1 specifically binds to active promoters and enhancers in addition to facultative heterochromatin. Selective knock-down of macroH2A1.1 deregulates expression of hundreds of highly active genes. Depending on the chromatin landscape, macroH2A1.1 acts through two distinct molecular mechanisms. The first mitigates excessive transcription by binding over domains including the promoter and the gene body. The second stimulates expression of RNA Polymerase II (Pol II) paused genes, including genes regulating mammary tumor cell migration. In contrast to the first one, macroH2A1.1 specifically associates with the TSS of Pol II paused genes. These processes occur in a predefined local 3D genome organization but do not require rewiring of enhancer-promoter contacts. We thus propose that macroH2A1.1 serves as a transcriptional modulator with a potential role in assisting the conversion of promoter-locked into a productive and elongating Pol II.

overall_design: ChIP-seq data against mH2A1.1 and total mH2A1 in MDA-MB 231 cells, combined with RNA-seq and Promoter Capture HiC data in WT and mH2A1.1 KD conditions

first: Thomas

last: Sexton

first: Nezih

last: Karasu

first: Fatima

last: Mouthair

first: Anne-Claire

last: Lavigne

first: Kerstin

last: Bystricky


title: RNA splicing is a key mediator of tumour cell plasticity and a therapeutic vulnerability in colorectal cancer

first: Kevin

last: Myant

overall_design: Refer to individual Series


title: The deacetylase SIRT2 contributes to autoimmune disease pathogenesis by modulating IL-17A and IL-2 transcription

status: Public on Mar 30 2022

city: Sapporo

first: Ryo

last: Hisada

state: Hokkaido

address: 3-11, Miyanomori, Tyuouku, Sapporo

institute: BIDMC Rheumatology and Clinical Immunology

summary: Aberrant expression of IL-17A together with abated IL-2 production by effector CD4+ T cells contributes to the pathogenesis of systemic lupus erythematosus (SLE). Here we report that Sirtuin 2 (SIRT2), a member of the family of NAD+-dependent histone deacetylases, suppresses IL-2 production by CD4+ T cells while it promotes their differentiation into Th17 cells. Mechanistically, we show that SIRT2 is responsible for the deacetylation of p70S6K and the activation of the mTORC1/HIF-1α/RORγt pathway and the generation of Th17 cells differentiation. Additionally, SIRT2 is responsible for the deacetylation of c-Jun and histones on the Il-2 gene, resulting in decreased IL-2 production. We found that the transcription factor inducible cAMP early repressor (ICER), which is overexpressed in T cells from people with SLE and lupus-prone mice, binds directly to the Sirt2 promoter and promotes its transcription. AK-7, a SIRT2 inhibitor limited the ability of adoptively transferred antigen-specific CD4+ T cells to cause autoimmune encephalomyelitis and disease in the lupus-prone MRL/lpr mice. Finally, CD4+ T cells from SLE patients exhibited increased expression of SIRT2, and pharmacological inhibition of SIRT2 in primary CD4+ T cells from patients with SLE attenuated their ability to differentiate into Th17 cells and promoted IL-2–producing T cells. Collectively, these results suggest that SIRT2-mediated deacetylation is essential for the aberrant expression of IL-17A and IL-2 and that SIRT2 may be a promising molecular target for new therapies for SLE.

overall_design: mRNA profiles of CRIPSR/Cas9 enabled Sirt2 KO and control murine Th17 cells

first: George

last: Tsokos


title: Identification of different transcripts that favor the nuclear or cytoplasmic Poly(A) Binding Proteins (PABPs) through RNA immunoprecipitation

city: La Jolla

first: Amy

last: Pasquinelli

address: 9500 Gilman Drive

department: Biological Sciences

institute: University of California, San Diego

summary: The poly(A) tail appended to the 3’ end of many eukaryotic transcripts plays a key role in the stability, nuclear transport, and translation of the RNA. These roles are largely mediated by the Poly(A) Binding Proteins (PABPs) that coat the poly(A) tails and interact with various proteins involved in the biogenesis and function of the RNA. While it is well established that the nuclear PABP (PABPN) binds newly synthesized poly(A) tails and is apparently replaced by the cytoplasmic PABP (PABPC) on transcripts exported to the cytoplasm, the distribution of transcripts for different genes or isoforms of the same gene on these distinct PABPs has not been investigated on a genome-wide scale. Here, we analyzed the identity, splicing status, poly(A) tail size, and translation status of RNAs co-immunoprecipitated with endogenous PABPN or PABPC in human cells. At steady state, many protein coding and non-coding RNAs exhibit strong bias for association with PABPN or PABPC. While PABPN-enriched transcripts more often were incompletely spliced and harbored longer poly(A) tails and PABPC-enriched RNAs tended to have longer half-lives and higher translation efficiency, there are curious outliers. Overall, our study reveals the landscape of RNAs bound by PABPN and PABPC, providing new details that support and advance the current understanding of the roles these proteins play in poly(A) tail synthesis, maintenance and function.

overall_design: 3 biological replicates were crosslinked and collected; a single input sample was divided so as to immunoprecipitate PABPN or PABPC from a single lysate sample. Antibodies used for immunoprecipitation were anti-PABPC, ab21060 Abcam; anti-PABPN, [EP3000Y] ab75855 Abcam.

first: Angela

middle: L

last: Nicholson-Shaw


title: The TH1 cell lineage-determining transcription factor T-bet supresses TH2 gene expression by redistributing GATA3 away from TH2 genes [ChIP-seq series 2]

city: London

first: Arnulf

last: Hertweck

address: Gower Street

department: UCL Cancer Institute

institute: University College London

summary: Differentiation of progenitor cells into mature cell types is commonly associated with the expression of lineage-determining transcription factors (LD-TFs) specific to that lineage. In CD4+ T cells, T-bet dictates differentiation of the TH1 lineage, whereas GATA3 drives differentiation of the alternative TH2 lineage. LD-TFs, including T-bet and GATA3, are frequently co-expressed, both in vitro and in vivo. How co-expression of two mutually antagonistic LD-TFs affects their function and lineage determination is not known. By expressing T-bet and GATA3 separately or together, we show that T-bet sequesters GATA3 at its target sites, thereby removing GATA3 from TH2 genes. T-bet interacts with the GATA3 DNA binding domain, changing its DNA sequence binding preference. This mechanism allows T-bet to dominate and drive the TH1 gene expression program in the presence of the GATA3. We propose that redistribution of one LD-TF by another may be a common mechanism that could explain how specific cell fate choices can be made even in the presence of other TFs driving alternative differentiation pathways.

overall_design: ChIP-seq for FLAG-T-bet and HA-GATA3 in EL4 cells expressing HA-GATA3 and Doxycycline-inducible T-bet. Cells were treated with a range of doxycycline (0-10ug/ml) for 48 hours prior to harvesting, to induce T-bet expression.

first: Richard

last: Jenner


title: Ribo-STAMP reveals translation status of RNAs bound by PABPN and PABPC

overall_design: 3 biological replicates, each replicate consists of a Control-STAMP sample and a RPS2-STAMP sample. These were crosslinked and collected; each single input sample was divided so as to immunoprecipitate PABPN or PABPC from a single lysate sample. Antibodies used for immunoprecipitation were anti-PABPC, ab21060 Abcam; anti-PABPN, [EP3000Y] ab75855 Abcam.


title: Cytoplasmic and nuclear fractionation from HEK293T cells

overall_design: 2 biological replicates were crosslinked and collected; subcellular fractionation was performed to separate the cytoplasm from the nuclear fraction

first: Anglela


title: ASCL1 activates neuronal stem cell-like lineage programing through remodeling of the chromatin landscape in prostate cancer [RNA-Seq]

city: Vancouver

first: Amina

last: Zoubeidi

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

summary: Treatment with androgen receptor pathway inhibitors (ARPIs) in prostate cancer leads to the emergence of resistant tumors characterized by lineage plasticity and divergent differentiation toward neuroendocrine lineage. We found that ARPIs induce a rapid epigenetic alteration mediated by large-scale chromatin remodeling to support activation of stem/neuronal transcriptional programs. We identified motifs for the proneuronal transcription factor ASCL1 to be enriched in hyper-accessible regions. ASCL1 acts as a driver of the lineage plastic, neuronal transcriptional program to support treatment resistance and neuroendocrine phenotype. Targeting ASCL1 switches the neuroendocrine lineage back to the luminal epithelial state. This effect is modulated by disruption of the polycomb repressive complex-2 and change the chromatin architecture in favor of luminal phenotype. Our study provides insights into the epigenetic alterations induced by ARPI governed by ASCL1, provides a proof of principle of targeting ASCL1 to reverse the neuroendocrine phenotype, support luminal conversion and re-addiction to ARPIs.

overall_design: Deciphering enzalutamide dependent prostate cancer stage specific gene expression profile by RNAseq.

first: Shaghayegh

last: Nouruzi

first: Dwaipayan

last: Ganguli

first: Nakisa

last: Tabrizian

first: Maxim

last: Kobelev

first: Olena

last: Sivak

first: Takeshi

last: Namekawa

first: Adeleke

last: Aguda

first: Daksh

last: Thaper

first: Alastair

last: Davies


title: A preclinical platform for assessing anti-tumor effects and systemic toxicities of cancer drug targets

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: Anti-cancer drug development campaigns often fail due to an incomplete understanding of the therapeutic index differentiating the efficacy of the agent against the cancer and its on-target toxicities to the host. To address this issue, we established a versatile preclinical platform in which genetically defined cancers are produced using somatic tissue engineering in transgenic mice harboring a Doxycycline-inducible short hairpin RNA against the target of interest. In this system, target inhibition is achieved by addition of doxycycline, enabling simultaneous assessment of efficacy and toxicity in the same animal. As proof-of-concept, we focused on CDK9 — a cancer target whose clinical development has been hampered by compounds with poorly understood target specificity and unacceptable toxicities. We systematically compared phenotypes produced by genetic Cdk9 inhibition to those achieved using a recently developed highly specific small molecule CDK9 inhibitor and found that both perturbations led to robust anti-tumor responses. Remarkably, non-toxic levels of CDK9 inhibition could achieve significant treatment efficacy, and dose-dependent toxicities produced by prolonged CDK9 suppression were largely reversible upon Cdk9 restoration or drug withdrawal. Overall, these results validate a versatile in vivo target validation platform that can be employed for rapid triaging of therapeutic targets and lend support to efforts aimed at advancing CDK9 inhibitors for cancer therapy.

overall_design: For RNA-seq analysis of the transcriptional profiles of Myc;p53-/- liver tumors expressing shCdk9 or shRenilla (control) induced by doxycycline, as well as normal liver tissues with doxycycline-induced shRenilla expression, total RNA was extracted from bulk tissue using the RNeasy Mini Kit (Qiagen). Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.

first: Xiang

last: Li

first: Chun-Hao

last: Huang

first: Francisco

last: Sánchez-Rivera

first: Margaret

last: Kennedy

first: Darjus

last: Tschaharganeh

first: John

last: Morris IV

first: Antonella

last: Montinaro

first: Kevin

last: O'Rourke

first: Ana

last: Banito

last: Wilkinson

first: Chi-Chao

last: Chen

first: Lukas

last: Dow

first: Sha

last: Tian

first: Wei

last: Luan

first: Elisa

last: de Stanchina

first: Tinghu

last: Zhang

first: Nathanael

last: Gray

first: Henning

last: Walczak

first: Scott

middle: W

last: Lowe


title: ASCL1 activates neuronal stem cell-like lineage programing through remodeling of the chromatin landscape in prostate cancer [ChIP-Seq]

first: Amina

last: Zoubeidi

overall_design: ChIP-seq for AR, PRC2 subunits, and the histone marks H3K27Me3 and H3K27Ac, ATAC-seq for measuring chromatin accessibility, and RNA-seq for transcriptome profiling.

first: Shaghayegh

last: Nouruzi

first: Dwaipayan

last: Ganguli

first: Nakisa

last: Tabrizian

first: Maxim

last: Kobelev

first: Olena

last: Sivak

first: Takeshi

last: Namekawa

first: Adeleke

last: Aguda

first: Daksh

last: Thaper

first: Alastair

last: Davies


title: ASCL1 activates neuronal stem cell-like lineage programing through remodeling of the chromatin landscape in prostate cancer [ATAC-Seq]

overall_design: Deciphering enzalutamide dependent prostate cancer stage specific chromatin accessibility profile.


title: ASCL1 activates neuronal stem cell-like lineage programing through remodeling of the chromatin landscape in prostate cancer

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


title: The TH1 cell lineage-determining transcription factor T-bet supresses TH2 gene expression by redistributing GATA3 away from TH2 genes

first: Arnulf

last: Hertweck


title: The TH1 cell lineage-determining transcription factor T-bet supresses TH2 gene expression by redistributing GATA3 away from TH2 genes [RNA-seq]

overall_design: poly-A+ RNA-Seq in T-bet-expressing, GATA3-expressing and T-bet and GATA3 co-expressing EL4 cells  and EL4 cells expressing neither protein.

first: Richard

last: Jenner


title: The TH1 cell lineage-determining transcription factor T-bet supresses TH2 gene expression by redistributing GATA3 away from TH2 genes [ATAC-seq]

overall_design: ATAC-seq in unstimulated and stimulated in FLAG-T-bet expressing EL4 cells and control cells not expressing T-bet


title: The TH1 cell lineage-determining transcription factor T-bet supresses TH2 gene expression by redistributing GATA3 away from TH2 genes [ChIP-seq]

overall_design: ChIP-seq for FLAG-T-bet and HA-GATA3 in T-bet-expressing, GATA3-expressing and T-bet and GATA3 co-expressing EL4 cells. ChIP-seq for H3K27ac in T-bet-expressing, GATA3-expressing and T-bet and GATA3 co-expressing EL4 cells  and EL4 cells expressing neither protein.


title: H3K9 trimethylation in active compartments optimizes stimulus-regulated transcription by restricting usage of CTCF sites in SINE-B2 repeats

first: Francesco

last: Gualdrini


title: Next Generation Sequencing of HUVECs stimulated by conidia of Aspergillus fumigatus

status: Public on Mar 29 2022

city: Changchun

first: Dong

last: Li

address: 126 Xinmin Avenue

department: Department of Immunology

institute: Jilin University

summary:
Purpose: The goal of this study is to investigate the responses of HUVECs after the stimulation of conidia of A. fumigatus
Methods: HUVECs were stimulated with conidia of Aspergillus fumigatus for 2 and 6 hours. Three biological repeats of stimulated cells or un-stimulated controls were send for RNA sequencing.
Results: Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample to the human genome (build hg38) and identified round 80,000 transcripts in the HUVECs upon stimulation.
Conclusions: Our resutls showed the detailed analysis of HUVECs transcriptomes upton conidia of Aspergillus fumigatus stimulation.

overall_design: HUVEC cells were seeded in 6-well-plate (2x10^6 cells per well) overnight before the conidia of A. fumigatus were added to the wells at a cells:spores ratio of 1:2. The cell lysates were harvest 2 and 6 hours post stimulation.

first: Wenxin

last: Zhang

first: Li

last: Wang


title: Heterogeneity among hiPSC-MuPCs

status: Public on Mar 28 2022

city: Kyoto

first: Hidetoshi

last: Sakurai

address: 53 Shogoin-Kawahara-cho, Sakyo-ku

institute: Center for iPS Cell Research and Application

summary: To identify different populations of hiPSC-MuPCs and differentially expressed genes between these populations

overall_design: sc-RNA seq of hiPSC-MuPCS differentiated by a step wise protocol (Zhao et al, Stem Cell Reports, 2021)

first: M

last: Nalbandian

last: Zhao

first: H

last: Kato

first: T

last: Jonoguchi

last: Nakajima-Koyama

last: Yamamoto


title: ATAC-seq, histone-seq, and RNA-seq of mouse craniofacial tissues [RNA-seq]

city: Iowa City

first: Eric

last: Van Otterloo

state: Iowa

address: 801 Newton Rd

institute: University of Iowa

summary: To investigate the role of the transcription factor AP-2 in craniofacial development, we performed: ATAC-seq on E11.5 craniofacial surface ectoderm in control and Tfap2a/Tfap2b ectoderm knock-out embryos; RNA-seq on E10.5 craniofacial prominences from control and Tfap2a/Tfap2b ectoderm knock-out embryos; histone-seq (H3K4me3) in E10.5 and E11.5 wild-type craniofacial surface ectoderm.

first: Trevor

last: Williams


title: RNA-sequencing (RNAseq)  based transcriptomic profiling in primary human valve interstitial cells with depleted PALMD expression

city: Guangzhou

first: Dongxing

last: Zhu

state: Guangdong

address: Xinzao, Panyu District

department: School of Basic Medical Sciences

institute: Guangzhou Medical University

summary: We performed RNA sequencing (RNA-Seq) based transcriptomic profiling in hVICs with depleted PALMD expression by siRNA. Our RNA-Seq analysis revealed 751 altered genes (1.5 fold change, p<0.05), of which 380 genes were significantly down-regulated and 371 genes were significantly up-regulated in hVICs with depleted PALMD.Gene ontology and pathway analysis of the down-regulated genes indicated that PALMD regulated multiple biological processes such as responses to hypoxia and stress, and regulation of cell apoptosis, and several important pathways including glycolysis and TNFα signaling pathway. Gene ontology and pathway analysis showed that the up-regulated genes were associated with the biological processes such as extracellular matrix and structure organization, and multiple pathways including biosynthesis of amino acids, and carbon metabolism. These data suggest that PALMD may be a novel regulator of glycolysis and TNFα signaling in hVICs.

overall_design: Examination of differentially expressed genes in primary human valve interstial cells regulated by PALMD


title: ATAC-seq, histone-seq, and RNA-seq of mouse craniofacial tissues [ATAC-seq]

overall_design: To investigate the role of the transcription factor AP-2 in craniofacial development, we performed: ATAC-seq on E11.5 craniofacial surface ectoderm in control and Tfap2a/Tfap2b ectoderm knock-out embryos; RNA-seq on E10.5 craniofacial prominences from control and Tfap2a/Tfap2b ectoderm knock-out embryos; histone-seq (H3K4me3) in E10.5 and E11.5 wild-type craniofacial surface ectoderm.


title: Genome wide analysis of the effect of MMP13-ablation on mouse dental pulp tissue

city: Dublin

first: Henry

middle: Fergus

last: Duncan

address: Lincoln Place

department: Restorative Dentistry

country: Ireland

institute: Dublin Dental University Hospital, Trinity College Dublin

summary: Tissue form 3-month old mouse molar teeth was used to obtain mRNA profies in developing wild-type (WT) and matrix metalloproteinase-13 (Mmp13−/−) mice using high throuput RNA-seq.Ssamples were analysed in triplicate using Illumina HiSeq 2500 system. Sequence reads that passed stringent quality filters were analyzed at the transcript isoform level using after passing a t-test (P < 0.05), post-hoc test (Storey with Bootstrapping) with a corrected q value of 0.05. qRT–PCR validation was performed using SYBR Green assays. the effect of MMp13 on tooth development and mineralsiation processes was the focus of this work.

overall_design: Dental pulp mRNA profiles of 3-month old wild type (WT) and Mmp13-/- mice. 3 Biological replicates per genotype.

first: Emi

last: Shimizu


title: MYC drives aggressive prostate cancer by disrupting transcriptional pause release at androgen receptor targets at androgen receptor targets [ChIP-Seq]

city: Boston

first: Xintao

last: Qiu

address: 440 brookline ave

institute: Dana Faber Cancer Institute

summary: c-MYC (MYC) is a major driver of prostate cancer tumorigenesis and progression. Although MYC is overexpressed in both early and metastatic disease and associated with poor survival, its impact on prostate transcriptional reprogramming remains elusive. We demonstrate that MYC overexpression significantly diminishes the androgen receptor (AR) transcriptional program (the set of genes directly targeted by the AR protein) in luminal prostate cells without altering AR expression. Importantly, analyses of clinical specimens revealed that concurrent low AR and high MYC transcriptional programs accelerate prostate cancer progression toward a metastatic, castration-resistant disease. Data integration of single-cell transcriptomics together with chromatin immunoprecipitation followed by sequencing (ChIP-seq) revealed an increased RNA polymerase II (Pol II) promoter-proximal pausing at AR-dependent genes following MYC overexpression without an accompanying deactivation of AR-bound enhancers. Altogether, our findings suggest that MYC overexpression antagonizes the canonical AR transcriptional program and contributes to prostate tumor initiation and progression by disrupting transcriptional pause release at AR-regulated genes.

overall_design: ChIP-seq for AR, FOXA1, H3K27ac and RNA Pol2

first: Nadia

last: Boufaied

last: Long

first: David

last: Labbé


title: MYC drives aggressive prostate cancer by disrupting transcriptional pause release at androgen receptor targets at androgen receptor targets [RNA-Seq]

overall_design: Bulk RNA-seq


title: Characterising the molecular-physiological basis of pollen abortion upon prolonged high temperature stress.

status: Public on Mar 27 2022

city: Nijmegen

first: Ivo

last: Rieu

state: Gelderland

address: Heyendaalseweg 135

department: Plant Systems & Physiology

institute: Radboud University

summary: We compared the transcriptomic response of polarized microspore stage tomato anthers to long-term mild heat (LTMH-) stress of wild-type and three lines that display increased pollen thermo-tolerance. Our results indicated distinct differences between the thermo-tolerant lines and wild-type, suggesting a dampened response to LTMH in the tolerant lines than in wild-type.

overall_design: mRNA profiles of polarized microspore stage tomato anthers of wild-type, Never ripe mutant, 35S::nahG and 35S::asCCD7 transgenic lines after exposure to long-term mild heat stress

first: Stuart

last: Jansma

first: Wilco

last: Ligterink


title: RhoA-ROCK competes with YAP to regulate amoeboid breast cancer cell migration in response to lymphatic-like flow

city: Houston

first: Pamela

last: Wenzel

state: TX

address: 6431 Fannin St, MSB 4.130

department: Integrative Biology & Pharmacology

institute: University of Texas Health Science Center at Houston

summary: Lymphatic drainage generates force that induces prostate cancer cell motility via activation of Yes-associated protein (YAP), but whether this response to fluid force is conserved across cancer types is unclear. Here, we show that shear stress corresponding to fluid flow in the initial lymphatics modifies taxis in breast cancer. Whereas some cell lines employ rapid amoeboid migration behavior in response to fluid flow, a separate subset decrease movement. Positive responders displayed transcriptional profiles typical of an amoeboid cell state. Regulation of the HIPPO tumor suppressor pathway and YAP activity also differed between breast subsets and prostate cancer. Although subcellular localization of YAP to the nucleus positively correlated with overall velocity of locomotion, YAP gain- and loss-of-function demonstrates that YAP inhibits breast cancer motility but is outcompeted by other pro-taxis mediators in the context of flow. Specifically, we show that RhoA dictates response to flow. GTPase activity of RhoA, but not Rac1 or Cdc42 Rho family GTPases, is elevated in cells that positively respond to flow and is unchanged in cells that decelerate under flow. Disruption of RhoA or the RhoA effector, Rho-associated kinase (ROCK), blocked shear stress-induced motility. Collectively, these findings demonstrate stratification of breast cancer subsets by flow-sensing mechanotransduction pathways and point to a role for biophysical force in regulation of an amoeboid cell state.

overall_design: Breast cancer cell lines were cultured under static conditions or fluid wall shear stress (WSS) of 0.05 dyne cm-2 for 6 hr in collagen-coated microfluidic channels. Breast cancer cell lines examined included MCF-7, HCC1187, EFM-19, and MDA-MB-231. Three independent biological replicates were included for each cell line. MCF-7 and HCC1187 were classified as negatively responding to WSS by decreased migration; whereas, EFM-19 and MDA-MB-231 were classified as positive responders associated with induction of rapid amoeboid migration in response to fluid flow.


title: ATAC-seq, histone-seq, and RNA-seq of mouse craniofacial tissues

overall_design: Refer to individual Series


title: RNA-seq analysis of Vitamin K2 treated WT worms

status: Public on Mar 25 2022

city: Kaifeng

first: Shanqing

last: Zheng

address: 1 Jinming Avenue North, Longting District,  School of Basic Medical Sciences, Henan University

institute: Henan university

summary: We used RNA-seq analysis to identify changes in gene expression occurring in the worms treated with VK2, and based on these sequencing data, more than fifteen hundred genes were identified as up-regulated by as much as 1.5 times subsequent to VK2 treatment. These differentially expressed genes were analyzed for pathway and gene ontology (GO) enrichment, which indicated that the genes influenced by VK2 treatment were enriched in several significant signaling pathways, including longevity, stress resistance, peroxisome, and fat metabolism pathways.

overall_design: Synchronized young adults were cultured on NGM plates with or without 0.1 µM VK2 and incubated at 20°C for seven days. The worms were transferred to new NGM plates with or without VK2 every day to get rid of the progeny and then collected. Total RNA quality was measured using a NanoDrop ND-1000 (Agilent Technologies). Library preparation was performed using a KAPA Stranded RNA-Seq Library Prep Kit (Illumina), and the quality was confirmed using an Agilent 2100 Bioanalyzer (Agilent Technologies). Paired-end sequencing was performed on an Illumina NovaSeq 6000. Transcriptome alignment and quantification were performed using Hisat2 software. C. elegans genome version WBcel235 was used as the reference. Differentially expressed genes were identified using the Ballgown package of R project to calculate the Fragments Per Kilobase of gene/transcript model per million mapped fragments (RPKM). The newest version of KEGG pathway enrichment and Gene Ontology were performed using R project or Python developed by Aksomics Inc. The heat maps were generated using Group FPKM (The average of log scaled FPKM: log2(FPKM + 1) of the genes in the groups).


title: Single-cell transcriptomics reveal a unique memory-like NK cell subset that accumulates with aging and correlates with disease severity in COVID-19

city: Hefei

first: mingming

last: wu

address: University of Science and Technology of China, No.96, JinZhai Road Baohe District

summary: For the scRNA-seq analysis of human blood lymphocytes and NK cells, lymphocytes were sorted as CD45+ cells, and NK cells were sorted as CD3/CD19/CD20/CD14−CD7+ cells using FACS (SONY SH800S); the purity was above 95%. The cells from 4 elderly individuals were pooled in one tube and the cells from 4 young individuals were pooled in another tube. We then counted and resuspended the pooled cells at a concentration of 1000 cells/μL, aiming for an estimated 6000 cells per library, following the instructions of the single-cell 3ʹ solution v3 reagent kit (10X Genomics). Single-cell libraries were constructed strictly according to the manufacturer’s standard protocols. Each sequencing library was generated with a unique sample index. Libraries were sequenced on the Illumina NovaSeq 6000 system.

overall_design: Lymphocytes and sorted NK cells in peripheral blood from young (<=30 years) and elderly (>=65 years) healthy individuals were collected and subjected to single-cell sequencing.

first: Chuang

last: Guo

first: Mingming

last: Wu

first: Beibei

last: Huang

first: Rui

last: Zhao

first: Haiming

last: Wei

first: Kun

last: Qu

first: Fang

last: Ni


title: ATAC-seq, histone-seq, and RNA-seq of mouse craniofacial tissues [ChIP-seq]

first: Eric

last: Van Otterloo

first: Trevor

last: Williams


title: Cancer cells utilize self-inflicted DNA breaks to evade growth limits imposed by exogenous genotoxic stress

city: Solna

first: Simon

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

institute: Karolinska Institutet

summary: Exposure to genotoxic challenge activates cell cycle checkpoints to prevent progression and propagation of deleterious DNA damage. We identify the activity of a nuclease, Caspase-activated DNase (CAD), in promoting G2 checkpoint control in cancer cells via the infliction of DNA breaks. To appreciate the genomic context of these breaks, we performed    (genome wide ligation of 3’-hydroxy (OH) ends followed by sequencing), to map the endogenously inflicted DNA breaks following irradiation.

overall_design: GLOE-seq on HCT116 wildtype and CAD-/- cells: Untreated (UT), 20 min post-IR and 24 h post-IR. IR dosage: total of 8Gy given at a dosage rate of 1Gy/min.

first: Brian

middle: D

last: Larsen

first: Claus

last: Sørensen

first: Philip

middle: Y

last: Yung


title: MYC drives aggressive prostate cancer by disrupting transcriptional pause release at androgen receptor targets

first: Xintao

last: Qiu

overall_design: Single-cell RNA-seq.

first: Nadia

last: Boufaied

first: Henry

last: Long

first: David

last: Labbé