title: Identification of recurrent chromosome breaks underlying structural rearrangements in mammary cancer cell lines [Break-seq]

summary: Cancer genomes are characterized by accumulation of small-scale somatic mutations as well as large-scale chromosomal deletions, amplifications, and complex structural rearrangements.  This characteristic is at least partially dependent on the ability of cancer cells to undergo recurrent chromosome breakage.  In order to address to what extent chromosomal structural rearrangement breakpoints correlate with recurrent DNA double strand breaks (DSBs), we simultaneously mapped chromosome structural variation breakpoints by whole genome DNA-seq and spontaneous DSB formation by Break-seq in the breast cancer cell line MCF-7 and a non-cancer control cell line MCF-10A.  We identified concurrent DSBs and structural variation breakpoints almost exclusively in the pericentromeric region of chromosome 16q in MCF-7 cells.  We fine-tuned the identification of copy number variation breakpoints on 16q.  In addition, we detected recurrent DSBs that occurred in both MCF-7 and MCF-10A.  We propose a model for DSB-driven chromosome rearrangements that led to the translocation of 16q, likely with 10q, and the eventual 16q loss that does not involve the pericentromere of 16q.  We present evidence from RNA-seq data that select genes, including SHCBP1, ORC6 and MYLK3, which are immediately downstream from the 16q pericentromere show heightened expression in MCF-7 cell line compared to the control.  Data published by The Cancer Genome Atlas showed that all three genes have increased expression in breast tumor samples.  We suggest that these genes are potential oncogenes for breast cancer progression.  The search for tumor suppressor loss that accompanies the 16q loss ought to be augmented by the identification of potential oncogenes that gained expression during chromosomal rearrangements.

overall_design: Exponentially growing MCF-7 and MCF-10A mammary cell lines were subjected to genomic queries by Break-seq, DNA-seq, and RNA-seq.

first: Natalie

middle: C

last: Senter

first: Andrew

last: McCulley


title: Resistance of Scots pine seedlings against the root and stem rot conifer pathogen (Heterobasidion anosum)

status: Public on Jul 12 2022

city: Helsinki

first: Fred

last: Asiegbu

address: Latokartanonkaari 7

country: Finland

institute: University of Helsinki

type: Expression profiling by high throughput sequencing

summary: By exploring the large-scale transcriptome analysis, we aim to identify differentially expressed genes in the comparison between resistant and susceptible families.

overall_design: mRNA profiles of needles from resistant and susceptible 1-year old Scots pine families

first: Mengxia

last: Liu

first: Kai

last: Wang


title: High-resolution mapping of transcribing RNAPIII by CRAC upon depletion of Nrd1 [Experiment 2]

status: Public on Jul 13 2022

city: Paris

first: Odil

last: Porrua Fuerte

address: 15 rue Helene Brion

country: France

institute: Institut Jacques Monod-CNRS

summary: Here we report high-resolution analyses of transcribing RNAPIII in either a wild-type (WT) background or a Nrd1 auxin-inducible degron (AID) strain in which Nrd1 can be rapidly depleted upon addition of the auxin analogue Indole-3-acetic acid (IAA). Nrd1 functions together with Sen1 in transcription termination at RNAPII-dependent non-coding genes. Here we show that depletion of Nrd1 does not affect transcription termination at RNAPIII-dependent genes, indicating that Nrd1 is not an RNAPIII transcription termination factor.

overall_design: Analysis of the effect of the  depletion of Nrd1 on RNAPIII-dependent transcription genome-wide using CRAC

last: Porrua


title: Identification of recurrent chromosome breaks underlying structural rearrangements in mammary cancer cell lines [RNA-seq]

city: Syracuse

first: Wenyi

last: Feng

state: NY

address: 750 East Adams Street

department: Biochemistry and Molecular Biology

country: USA

institute: SUNY Upstate Medical University


title: seRNA PAM-1 interacts with Ddx5 to regulate skeletal muscle satellite cell activation and aging through trans regulation of Timp2 expression [4C-Seq]

city: Sha Tin

first: Yile

last: Huang

state: Hong Kong

address: Room 503, Li Ka Shing Health and Science Buiding, Prince of Wales Hospital, Sha Tin

department: Chemical Pathology

country: China

institute: The Chinese University of HongKong

summary: There is an absolute requirement of Pax7 for the normal function of MuSCs during regenerative myogenesis in skeletal muscle at any stage of life. Here using RNA-seq, H3K27ac and Pax7 ChIP-seq, we discover PAM-1 (Pax7 Associated Muscle lncRNA) that is enriched in activated skeletal muscle satellite cells (ASCs) 24 and 48 hours after activation. Knockdown of PAM-1 reduces proliferating Pax7+Myod+ ASCs number, while overexpression of PAM-1 increases ASCs number. Mechanistically, PAM-1 is located on ASCs and myoblast specific super-enhancer (SE), and we categorize it as seRNA. Through a series of multiomics analysis of PAM-1 interactome in myoblast including PAM-1-DNA interaction by ChIRP-seq, PAM-1 SE-DNA interaction by 4C-seq, PAM-1-protein interaction by mass spectrometry and ChIP-seq, we identify a novel class of transcriptional regulation that seRNA PAM-1 interacts with RNA binding protein Ddx5 and tethers PAM-1 SE to regulate inter-chromosomal targets Timp2. Altogether, our findings identify PAM-1 is driven by Pax7 in ASC and myoblast to regulate myogenic activation through binding with Ddx5 and targeting Timp2.

overall_design: 4C-seq of PAM-1 SE

first: Karl

middle: K

last: So

first: Hao

last: Sun

first: Huating


title: seRNA PAM-1 interacts with Ddx5 to regulate skeletal muscle satellite cell activation and aging through trans regulation of Timp2 expression [PAM-1 ChIRP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIRP-seq on PAM-1 seRNA


title: seRNA PAM-1 interacts with Ddx5 to regulate skeletal muscle satellite cell activation and aging through trans regulation of Timp2 expression [Ddx5 ChIP-seq]

overall_design: Ddx5 ChIP-seq


title: seRNA PAM-1 interacts with Ddx5 to regulate skeletal muscle satellite cell activation and aging through trans regulation of Timp2 expression [PAM-1 KO ChIP-seq]

overall_design: H3K27ac ChIP-seq on PAM-1 knockout


title: seRNA PAM-1 interacts with Ddx5 to regulate skeletal muscle satellite cell activation and aging through trans regulation of Timp2 expression

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

overall_design: Refer to individual Series


title: Pan-caspase inhibition during normothermic machine perfusion of discarded livers mitigates ischemia-reperfusion injury

status: Public on Jul 11 2022

city: Providence

first: Jennifer

middle: Ann

last: Sanders

state: RI

address: 593 Eddy Street

department: Pediatric Endocrinology

institute: Rhode Island Hospital

summary: Access to liver transplantation is limited by a significant organ shortage. The recent introduction of machine perfusion technology allows surgeons to monitor and assess ex situ liver function prior to transplantation. However, many donated organs are of inadequate quality for transplant, though opportunities exist to rehabilitate organ function with adjunct therapeutics during normothermic machine perfusion. In this preclinical study, we targeted the apoptosis pathway as a potential method of improving hepatocellular function. Treatment of discarded human livers during normothermic perfusion with an irreversible pan-caspase inhibitor, emricasan, resulted in significant mitigation of ischemia-reperfusion injury at both the transcriptional and protein level. This was evidenced by significantly decreased circulating levels of the pro-inflammatory cytokines, interleukin-6, interleukin-8, and interferon-gamma, compared to control livers. Untreated livers also demonstrated transcriptional changes notable for enrichment in pathways involved in innate immunity, leukocyte migration, and cytokine-mediated signaling. Targeting of unregulated apoptosis may represent a viable therapeutic intervention for rehabilitating liver hepatocellular function during machine perfusion.

overall_design: mRNA profiles of human livers subjected to 0, 3 or 6 hours of normothermic machine perfusion, with or without Emricasan treatment.

first: Siavash

last: Raigani

first: John

last: Santiago

first: Anders

last: Ohman

first: Megan

last: Heaney

first: Sofia

last: Baptista

first: Taylor

last: Coe

first: Reinier

last: de Vries

first: Ivy

last: Rosales

first: Angela

last: Shih

first: James

last: Markmann

first: Korkut

last: Uygun

first: Philip

last: Gruppuso

first: Heidi

last: Yeh


title: EZH2 T367 phosphorylation activates p38 signaling through lysine methylation to promote breast cancer progression [ChIP-seq]

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: To investigate the differential abundance of H3k27me3 mark on the promoters of  Breast Cancer cells  treated with P38i, EPZi, the combination and controls

overall_design: MDAMD231 cells were treated for 24 h with P38i, EZH2i , the combination and controls, 4 samples per condition were collected and submitted to Chip-seq analysis

first: Shilpa

middle: R

last: Tekula

first: Celina

middle: G

last: Kleer


title: Identification of recurrent chromosome breaks underlying structural rearrangements in mammary cancer cell lines [DNA-seq]

first: Wenyi

last: Feng

first: Natalie

last: Senter

first: Andrew

last: McCulley


title: PRC2-mediated repression is essential to maintain identity and function of differentiated dopaminergic and serotonergic neurons [bulk RNA-Seq]

city: Lund

first: Markus

last: Ringner

address: Sölvegatan 35

country: Sweden

institute: Lund University

summary: Neurons of the CNS must maintain their distinct identity over an entire lifespan. Apart from instructive information provided by transcription factors driving neuron specific genes, other gene programs need to be permanently silenced. The mechanisms governing enduring gene-silencing in neurons are largely unknown, as are the consequences if they fail. Here we show that loss of the Polycomb repressive complex 2 (PRC2) obligate unit Eed in differentiated murine midbrain dopamine (mDA) neurons resulted in progressive loss of the H3K27me3 histone modification followed by upregulation of PRC2 targets, also highly enriched for the constitutive heterochromatin H3K9me3 modification. This was followed by reduced expression of mDA neuron-identity genes, particularly evident in the Substantia nigra pars compacta. Consequently, mDA-neuronal function was severely disrupted, causing parkinsonian-like motor skill deficits. Deletion of Eed in differentiated serotonergic (5HT) neurons resulted in a similar upregulation of PRC2-targets and reduced expression of genes defining 5HT neurons, which promoted loss of serotonergic identity followed by loss of function and altered behaviour. Overall, our results reveal that PRC2 inactivation leads to a selective and progressive loss of mDA or 5HT neuronal identity and function, but not to any loss of cells. Thus, our study shows that PRC2-dependent maintenance of neuronal identity is essential and safeguards against expression of other non-relevant gene programs and loss of neuronal function.

overall_design: Evaluation of gene expression in dopaminergic and serotonergic neurons with and without functional Polycomb repressive complex 2 (PRC2).

first: Konstantinos

last: Toskas

first: Behzad

last: Yaghmaeian-Salmani

last: Ringnér

first: Thomas

last: Perlmann

first: Johan

last: Holmberg


title: The TAM receptor tyrosine kinases Axl and Mer drive the phagocytic differentiation of tissue-resident macrophages

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: Many apoptotic thymocytes are generated during the course of T cell selection in the thymus, yet the machinery through which these dead cells are recognized and phagocytically cleared is incompletely understood. We find that the TAM receptor tyrosine kinases Axl and Mer, which are co-expressed by a specialized set of phagocytic thymic macrophages, are essential components of this machinery. Axl-/-Mertk-/- double mutant mice exhibited a marked accumulation of apoptotic cells during the time that autoreactive and nonreactive thymocytes die. Unexpectedly, the double mutants also displayed a profound deficit in the total number of phagocytic macrophages in the thymus, and concomitantly exhibited diminished expression of key non-TAM engulfment systems in the macrophages that remain. These previously unrecognized deficits were not confined to the thymus, and were also evident in the bone marrow and spleen. They had pleiotropic metabolic consequences for the double mutants, which included severe dysregulation of hemoglobin turnover, iron metabolism, and erythropoiesis.

overall_design: stranded mRNA sequencing

first: Lidia

last: Jiménez-García

first: Christopher

last: Mayer

first: Patrick

last: Burrola

first: Youtong

last: Huang

first: Maxim

middle: N

last: Shokhirev

first: Greg

last: Lemke


title: PRC2-mediated repression is essential to maintain identity and function of differentiated dopaminergic and serotonergic neurons


title: PRC2-mediated repression is essential to maintain identity and function of differentiated dopaminergic and serotonergic neurons [ChIP-Seq]

overall_design: Evaluation of three different histone marks in dopaminergic neurons with and without functional Polycomb repressive complex 2 (PRC2)


title: Identification of differentially expressed miRNAs in Wild-type and IL-17KO asthmatic mice

status: Public on Jul 10 2022

city: Xi'an

first: Ying

last: Chang

address: Xianning West Road

institute: Xi'an Jiaotong University

summary:
To explore the roles of IL-17 in asthma and the relationship between IL-17 and miRNAs, we used a model of severe asthma driven by chronic respiratory exposure to house dust mite (HDM) exposure in wild type and IL-17KO mice, followed with miRNA profiling assays and analysis.
Male and female C57BL/6 mice (6-8 weeks old) and IL-17KO mice (C57BL/6 background) were exposed to purified HDM extract intranasally for 5 days/week for 5 consecutive weeks. Sterile saline was used as the control.

overall_design: 4 groups of samples were tested In this assay, and each group contains 3 samples.

first: Weijia

last: Wang


title: Integrative Genomic Analysis of Medulloblastoma Identiﬁes a Molecular Subgroup That Drives Poor Clinical Outcome [DNA copy number]

first: Jill

middle: P

last: Mesirov

state: CA

address: 9500 Gilman Drive

department: Medicine

institute: University of California, San Diego

summary:
Medulloblastomas are heterogeneous tumors that collectively represent the most common malignant brain tumor in children. To understand the molecular characteristics underlying their heterogeneity and to identify whether such characteristics represent risk factors for patients with this disease, we performed an integrated genomic analysis of a large series of primary tumors.
Identified are six molecular subgroups of medulloblastoma, each with a unique combination of numerical and structural chromosomal aberrations that globally influence mRNA and miRNA expression. We reveal the relative contribution of each subgroup to clinical outcome as a whole and show that a previously unidentified molecular subgroup, characterized genetically by c-MYC copy number gains and transcriptionally by enrichment of photoreceptor pathways and increased miR-183-96-182 expression, is associated with significantly lower rates of event-free and overall survivals. Our results detail the complex genomic heterogeneity of medulloblastomas and identify a previously unrecognized molecular subgroup with poor clinical outcome for which more effective therapeutic strategies should be developed.

overall_design:
We profiled the mRNA transcriptome of 194 medulloblastomas and performed high-density single nucleotide polymorphism array and miRNA analysis on 115 and 98 of these, respectively. Non-negative matrix factorization-based clustering of mRNA expression data was used to identify molecular subgroups of medulloblastoma; DNA copy number, miRNA profiles, and clinical outcomes were analyzed for each. We additionally validated our findings in three previously published independent medulloblastoma data sets. DNA copy number data was generated by using Affymetrix 250K Sty arrays or Affymetrix 6.0 arrays to obtain signal intensities and genotype calls.
The submitter-provided processed data (that forms the basis of the study's conclusion) is included in the MD_CN.cbs.

first: Yoon-Jae

last: Cho

first: Aviad

last: Tsherniak

first: Pablo

last: Tamayo

first: Sandro

last: Santagata

first: Azra

last: Ligon

first: Heidi

last: Creulich

first: Rameen

last: Berhoukim

first: Vladimir

last: Amani

first: Liliana

last: Goumnerova

first: Charles

last: Eberhart

first: Ching

last: Lau

first: James

middle: M

last: Olson

first: Richard

middle: J

last: Gilbertson

first: Amar

last: Gajjar

first: Olivier

last: Delattre

first: Marcel

last: Kool

first: Keith

first: Matthew

last: Meyerson

first: Scott

middle: L

last: Pomeroy


title: seRNA PAM-1 interacts with Ddx5 to regulate skeletal muscle satellite cell activation and aging through trans regulation of Timp2 expression [siPAM-1 ChIP-seq]

first: Yile

last: Huang

overall_design: H3K27ac ChIP-seq on PAM-1 knockdown

first: Karl

last: So

first: Hao

last: Sun

first: Huating

last: Wang


title: Counteraction of myocardial ferritin heavy chain deficiency by heme oxygenase-1

city: Birmingham

first: Abolfazl

last: Zarjou

state: AL

address: 618 Zeigler Research Building, 703 South 19th Street

institute: University of Alabama at Birmingham

summary:
To investigate the functional significance of myocardial ferritin heavy chain (FtH) in a model of acute myocardial infarction (MI). FtH was deleted using FtH floxed mice and Sm-22 Cre mice on a C57/bl6 background
At 3 hours following 45 minutes of ischemia induced via ligation of left ant. decsending coronary artery, ischemic regions were identified, dissected, and total RNA was isolated fand gene expression profiling analysis using data obtained from RNA-seq of 3 different animals.  RNA
Total RNA isolated from left ventricle under homeostatic (bseline conditions) served as negative ctr. (n=3/group)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for widltype and FtH KO myocardium at baseline and 3 hours post ischemia

first: Min

last: Xie


title: Genetic and functional analyses of archaeal ATP-dependent RNA Ligase

status: Public on Jul 09 2022

city: Tsukuba

first: Yancheng

last: Liu

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, we generated allelic knockouts of ATP-dependent RNA ligase (Rnl) in hyperthermophilic archaeon T. kodakarensis and analyze the small RNAs.

overall_design: T. kodakarensis gene encoding for RNA ligase TK1545 was knock-out by homologous recombination, and the RNA samples were analyzed by  RNA seq. The differentially expressed circular RNAs between the two strains were analyzed.

first: Yuko

last: Takagi

first: Kiong

last: Ho


title: Evaluation of the synergistic potential of simultaneous pan- or isoform specific BET and SYK inhibition in B-cell lymphoma (RNA-Seq)

status: Public on Jul 08 2022

city: Rostock

first: Sina

last: Sender

state: Mecklenburg Vorpommern

address: Schillingallee 70

department: Department of Medicine, Clinic III

country: Germany

institute: Rostock University Medical Center

summary: Background: Bromodomain and extra-terminal domain (BET) proteins and the spleen tyrosine kinase (SYK) represent promising targets in Diffuse large B-cell (DLBCL) and Burkitt’s lympho-ma (BL). We evaluated the anti-lymphoma activity of the isoform specific bivalent BET inhibitor AZD5153 (AZD) and the pan-BET inhibitor I-BET151 (I-BET) as single agents and in combination with SYK inhibitor Entospletinib in vitro.    Methods: Single agent exposures were evaluated on two DLBCL and two BL cell lines analyzing cell proliferation and metabolic activity. Proliferation, metabolic activity, apoptosis, cell cycle and morphology were investigated after combined AZD or I-BET and Ento exposure. RNAseq of combined AZD+Ento exposure was characterized in SU-DHL-4.   Results: Both BET inhibitors reduced cell proliferation/metabolic activity dose and time de-pendently. Combined BET and SYK inhibition enhanced the anti-proliferative effect and induc-ing a G0/G1 cell cycle arrest. SU-DHL-4 demonstrated a pronounced modulation of gene expres-sion by AZD, which was markedly increased by additional SYK inhibition. Functional enrich-ment analyses identified combination-specific GO terms related to cell division, transport and DNA replication. Genes such as PLEKHH3, MYB, SLC8A1, PARP9, HSPB1 and S100A4 were iden-tified as the presumable key regulators.   Conclusion: Simultaneous inhibition of BET and SYK enhanced the anti-proliferative effects, and especially the combination-specific gene expression signature.

overall_design: Comparative expression analyses of AZD+Ento exposed SU-DHL-4 cells compared to DMSO control and AZD or Ento single agents; all sample measured in three biological

first: Ahmad

middle: W

last: Sultan

first: Daniel

last: Palmer

first: Dirk

last: Koczan

first: Anett

last: Sekora

first: Julia

last: Beck

first: Ekkehard

last: Schuetz

first: Bertram

last: Brenig

first: Georg

last: Fuellen

first: Christian

last: Junghanss

first: Hugo

last: Escobar


title: RNA Binding Protein CELF6 Modulates Expression and Alternative Splicing of Genes associated with Tumorigenesis in Non-small Cell Lung Cancer Cells.

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: CELF6 (CUGBP Elav-Like Family Member 6), a typical RNA binding protein, can regulate alternative splicing of pre-mRNAs, and may also participate in mRNA editing and translation. As a tumor suppressor, CELF6 is abnormally low expressed in colon cancer, breast cancer and other tumors, and is closely related to proliferation, invasion, and migration. Recent studies have shown that CELF6 has abnormally low expression in lung cancer tissues, and is increased after ultra-hypoxia treatment in A549 cells, however, the functions and molecular mechanisms of CELF6 in lung cancer are still unclear. We overexpressed CELF6 in human non-small cell lung cancer cells (A549), and set up a control; after collecting cells, we used RNA sequencing to screen for genes with significant differential expression (DEGs) after CELF6 overexpression, and significantly alternative splicing events (ASEs). CELF6 overexpression widely regulates the expression of related genes in immune response，Inflammation response, Innate immune response，TNF signaling pathway, cell adhesion molecules (CAMs) and so on. We found that CELF6 can inhibit the expression many immune-related genes, such as TNFSF10、CCL5、JUNB、BIRC3、MLKL、PIK3R2、CCL20、STAT1、MYD88 and CFS1，which mainly function in promoting tumorigenesis in lung cancer. These DEGs were validated by reverse transcriptase quantitative polymerase chain reaction (RT-PCR). In addition, CELF6 regulates the alternative splicing of a large number of genes which were enriched in p53 signaling pathway and apoptosis，such as TP53 and CD44. This study is the first to analyze the transcriptome analysis of differential gene expression and alternative splicing of CELF6 overexpression. which will provide a new idea for the gene regulation mechanism mediated by CELF6 in the production and development of NSCLC.

overall_design: In the present study, We overexpressed CELF6 in A549 cells derived from human non-small cell lung cancer and set control; after collecting cells, we performed high_x001E_throughput RNA-seq sequencing to screen for differences expression genes and alternative splicing genes after CELF6 overexpression, by analyzing the functional pathways and classifications of these genes, The present results identified that CELF6 regulated the transcription and AS of genes associated to tumorigenesis, especially those involved in apoptosis, P53 signaling pathways. The present results may provide insight for the current understanding of CELF6 in regulating gene transcription and AS non-small cell lung cancer.

first: HuSai

last: Ma

first: GuoWei

first: Bin

last: Yu


title: PRC2-mediated repression is essential to maintain identity and function of differentiated dopaminergic and serotonergic neurons [snRNA-Seq]

first: Markus

last: Ringner

overall_design: Evaluation of single nuclei gene expression in dopaminergic neurons with and without functional Polycomb repressive complex 2 (PRC2).

first: Konstantinos

last: Toskas

first: Behzad

last: Yaghmaeian-Salmani

first: Thomas

last: Perlmann

first: Johan

last: Holmberg


title: Role of EXO1 nuclease activity in genome maintenance, the immune response and tumor suppression in Exo1D173A mice

city: Pamplona

first: SERGIO

last: ROA

address: Irunlarrea, 1

department: Biochemistry and Genetics

country: Spain

institute: University of Navarra

summary: DNA damage response pathways rely extensively on nuclease activity to process DNA intermediates. Exonuclease 1 (EXO1) is a pleiotropic evolutionary conserved DNA exonuclease. In mammals, it is involved in various DNA repair pathways, replication, antibody diversification, and meiosis. But, whether EXO1 facilitates these DNA metabolic processes through its enzymatic or scaffolding functions remains unclear. Here we dissect the contribution of EXO1 enzymatic versus scaffolding activity by comparing Exo1DA/DA mice expressing a proven nuclease-dead mutant form of EXO1 to entirely EXO1-deficient Exo1-/- and EXO1 wild type Exo1+/+ mice. We show that Exo1DA/DA and Exo1-/- mice are compromised in canonical DNA repair processing, suggesting that the EXO1 enzymatic role is important for error-free DNA mismatch and double-strand break repair pathways. However, in non-canonical repair pathways, EXO1 appears to have a more nuanced function. Next-generation sequencing of heavy chain V region in B cells showed the mutation spectra of Exo1DA/DA mice to be intermediate between Exo1+/+ and Exo1-/- mice, suggesting that both catalytic and scaffolding roles of EXO1 are important for somatic hypermutation. Similarly, while overall class switch recombination in Exo1DA/DA and Exo1-/- mice was comparably defective, switch-switch junction analysis suggests that EXO1 might fulfill an additional scaffolding function downstream of class switching. In contrast to Exo1-/- mice that are infertile,  meiosis progressed normally in Exo1DA/DA  and Exo1+/+ cohorts, indicating that a structural but not the nuclease function of EXO1 is critical for meiosis. However, both Exo1DA/DA and Exo1-/- mice displayed similar mortality and cancer predisposition profiles. Taken together, these data demonstrate that EXO1 has both scaffolding and enzymatic functions in distinct DNA repair processes and suggest a more composite and intricate role for EXO1 in DNA metabolic processes and disease.

overall_design: To delineate the precise contribution of EXO1 structural and/or catalytic functions during somatic hypermutation (SHM), we examined error-prone repair of the VH186.2 heavy chain region by RT-PCR-based sequencing of this region from splenocytes after primary immune responses in Exo1+/+ (n=7), Exo1DA/DA (n=8), and Exo1-/- (n=3) cohorts of mice.

first: Shanzhi

last: Wang

first: Kyeryoung

last: Lee

first: Stephen

last: Gray

first: Yongwei

last: Zhang

first: Catherine

last: Tang

first: Rikke

middle: B

last: Morrish

first: Elena

last: Tosti

first: Johanna

last: van Oers

first: Paula

middle: E

last: Cohen

last: MacCarthy

first: Sergio

last: Roa

first: Matthew

middle: D

last: Scharff

first: Winfried

last: Edelmann

first: Richard

last: Chahwan


title: Lymphatic-Preserving Treatment Sequencing with Immune Checkpoint Inhibition Unleashes cDC1-Dependent Antitumor Immunity in HNSCC

city: La Jolla

first: Robert

last: Saddawi-Konefka

address: 3855 Health Sciences Dr

institute: UC San Diego

summary: Despite the promise of immune checkpoint inhibition (ICI), therapeutic responses remain limited. This raises the possibility that standard of care treatments delivered in concert may compromise the tumor response. To address this, we employed tobacco-signature HNSCC murine models in which we mapped tumor-draining lymphatics and developed models for regional lymphablation with surgery or radiation. Remarkably, we found that lymphablation eliminates the tumor ICI response, significantly worsening overall survival and repolarizing the tumor- and peripheral- immune compartments. Mechanistically, within tumor-draining lymphatics, we observed an upregulation of cDC1 cells and IFN-I signaling and show that both are necessary for the ICI response and lost with lymphablation. Ultimately, we provide a mechanistic understanding of how standard oncologic therapies targeting regional lymphatics impact the tumor response to immune- oncology therapy in order to define rational, lymphatic-preserving treatment sequences that mobilize systemic antitumor immunity, achieve optimal tumor responses, control regional metastatic disease, and confer durable antitumor immunity.

overall_design: Comparisoin of peripheral blood after neoadjuvant ICI in tumor bearing animals receiving immediate or delayed neck dissection to ablate locoregional draining lymphatics.

first: Saddawi-Konefka

last: Robert

first: Gutkind

last: Silvio


title: Melanoma RBPome identification reveals PDIA6 as an unconventional RNA-binding protein involved in metastasis

city: Barcelona

first: Neus

last: Mestre-Farràs

state: Barcelona

address: C/ Doctor AIguader 88

institute: CRG

summary: RNA-binding proteins (RBPs) have been relatively overlooked in cancer research despite their contribution to virtually every cancer hallmark. Here, we use RNA interactome capture (RIC) to characterize the melanoma RBPome and uncover novel RBPs involved in melanoma progression. Comparison of RIC profiles of two melanoma cell lines with different aggressiveness revealed prevalent changes in RNA binding capacities that were not associated with changes in RBP levels. Extensive functional validation of a selected group of 24 RBPs using five different in vitro assays unveiled unanticipated roles of RBPs in melanoma malignancy. As proof-of-principle we focused on PDIA6, an ER-lumen chaperone that displayed a novel RNA-binding activity. We show that PDIA6 is involved in metastatic progression and map its RNA-binding domain, which we find to be required for PDIA6 tumorigenic properties. These results exemplify how RIC technologies can be harnessed to uncover novel vulnerabilities of cancer cells

overall_design: RNAseq, in duplicates, of immortalized melanocytes (Mel_ST) and metastatic melanoma cells (SK_MEL_147).

first: Fátima

last: Gebauer


title: Hepatic transcript modules are predictive of atherosclerotic lesion burden after a 2-year high cholesterol, high fat diet challenge in baboons [2 years HCHF]

city: Winston-Salem

first: Laura

middle: A

last: Cox

state: NC

address: Medical Center Boulevard

department: Internal medicine-Section of Molecular Medicine

institute: Wake Forest School of Medicine

summary:
Analysis of hepatic transcript data using unbiased Weighted Gene Correlation Network Analysis (WGCNA) to identify significant modules of genes correlated with lesion burden and performed pathway enrichment analysis of genes in significant modules. The hypothesis tested in the present study was that transcript modules are predictive of atherosclerotic lesion burden after a high cholesterol, high fat diet challenge.
results of the study provide an understanding of the key pathways and genes underlying atherosclerotic lesion burdenafter high cholesterol and high fat diet challenge in baboons .

overall_design:
Baboons (n=111; 47 Females, 64 males) were maintained on a two-year dietary challenge with a diet high in cholesterol and saturated fat (HCHF).  Liver biopsy samples were collected at the end of two-year period.
The sample number refers to the same animal across all time points.

first: Sobha

last: Puppala


title: The S. cerevisiae m6A reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts [CRAC]

city: Illkirch

first: Jérémy

last: Scutenaire

address: 1 rue Laurent Fries

institute: IGBMC

summary: We performed CRAC (UV-crosslinking and analysis of cDNA)  to identify Ime4-dependent mRNA targets of Pho92 during meiosis at 5 hr in SPO.

overall_design: Pho92 footprint on its RNA targets were obtained after exposing the cells to UV irradiation and purification of HTP-tagged Pho92 under stringent and denaturing conditions. Control samples includes cells expressing Pho92-HTP in ime4 mutant, Pho92-HTP cells with no UV irradiation and WT cells with no HTP-tag. Two biological replicates were performed for each sample and normalization between samples was achieved by addition, to each sample during the procedure, of an equal amount of UV-crosslinked cells of schyzosaccharomyces pombe expressing a HTP-tagged Luc7.

first: Damien

last: Plassard

first: Tommaso

last: Villa

first: Domenico

last: Libri


title: Genome-wide characterization of lncRNAs and mRNAs in muscles with differential meat quality

city: Harbin

first: lu

middle: yuan

last: sun

address: Heilongjiang

institute: Northeast Agricultural University

summary:
Meat quality is one of the most important traits in pig production. Long non-coding RNAs (lncRNAs) has been involved in diverse biological processes such as muscle development through regulating gene expression. However, studies on lncRNAs lag behind and a comparatively small number of lncRNAs have been identified in pigs. Also, effects of lncRNAs on meat quality remains to be characterized. Here, we analyzed lncRNAs in longissimus thoracis (LT) and semitendinosus (ST) muscles, being different in meat quality, with RNA-sequencing technology. A total of 500 differentially expressed lncRNAs (DELs) and 2094 protein-coding genes (DEGs) were identified. Through KEGG analysis on DELs we first made clear that fat deposition might be the main reason resulting in differential phenotype of LT and ST, on the basis of which 41 key DELs and 50 DEGs involved in differential fat deposition were characterized.
One of the key genes, cAMP-response element binding protein 1, was selected to confirm its role in porcine adipogenesis with molecular biology methods and found that it promotes the differentiation of porcine preadipocytes, consistent with its higher expression level and intramuscular fat contents in LT than that in ST muscle. Furthermore, through integrated analysis of DELs and DEGs, transcription factors important for differential fat deposition were characterized among which BCL6 have the most target DEGs while MEF2A was targeted by the most DELs. The results provide candidate genes crucial for meat quality, which will contribute to revealing the molecular mechanisms underlying meat quality

overall_design: we analyzed lncRNAs in longissimus thoracis (LT) and semitendinosus (ST) muscles, being different in meat quality, with RNA-sequencing technology to identifide differentially expressed lncRNAs and mRNAs

first: Yuanlu

last: Sun

first: Xu

last: Lin


title: Primary infection by E. multilocularis induces distinct patterns of crosstalk between hepatic Natural killer T and regulatory T cells in mice

city: Bern

first: Tural

last: Yarahmadov

address: Murtenstrasse 35

department: BioMedical Research

country: Switzerland

institute: University of Bern

summary: T cells are important in forming short- and long-term immunity. We used single cell RNA sequencing (scRNA-seq) to assess their dynamics over the course of E. multilocularis infection.

overall_design: CD3+ cells were extracted from regions surrounding lesions in livers of mice infected perorally by E. multilocularis eggs at 10, 21, and 48 days post infection, as well as from livers of control animals.

first: Junhua

last: Wang

first: Isabel

last: Büchi

first: Adrian

last: Keogh

first: Tess

last: Brodie


title: Hepatic transcript modules are predictive of atherosclerotic lesion burden after a 2-year high cholesterol, high fat diet challenge in baboons

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

overall_design: Refer to individual Series


title: Hepatic transcript modules are predictive of atherosclerotic lesion burden after a 2-year high cholesterol, high fat diet challenge in baboons [7weeks HCHF]

overall_design:
Baboons (n=111; 47 females, 64 males) were maintained on a 7wk dietary challenge with a diet high in cholesterol and saturated fat (HCHF).  Liver biopsy samples were collected  at the end of seven week period.
The sample number refers to the same animal across all time points.


title: BALANCED GENE DOSAGE CONTROL RATHER THAN PARENTAL ORIGIN UNDERPINS GENOMIC IMPRINTING

city: Rehovot

first: Yonatan

last: Stelzer

address: Herzl 234

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

summary: Mammalian parental imprinting represents an exquisite form of epigenetic control regulating the parent-specific monoallelic expression of genes in clusters. While imprinting perturbations are widely associated with developmental abnormalities, the intricate regional interplay between imprinted genes makes interpreting the contribution of gene dosage effects to phenotypes a challenging task. Using mouse models with distinct deletions in an intergenic region controlling imprinting across the Dlk1-Dio3 domain, we link changes in genetic and epigenetic states to allelic-expression and phenotypic outcome in vivo. This determined how hierarchical interactions between regulatory elements orchestrate robust parent-specific expression, with implications for non-imprinted gene regulation. Strikingly, flipping imprinting on the parental chromosomes by crossing genotypes of complete and partial intergenic element deletions, rescues the lethality of each deletion on its own. Our work indicates that parental origin of an epigenetic state is irrelevant as long as appropriate balanced gene expression is established and maintained at imprinted loci.

overall_design: Tail DNA was collected from E18.5 and E8.5 embryos. DNA was genotyped and embryos were divided into groups by genotype. WT littermates were used as controls. Each embryo was sequenced and analyzed separately. A total of 13 paternal deletion, 2 maternal deletion, 5 biallelic deletion and 3 WT controls were collected. We used the PBAT capture protocol combining PBAT and hybridization with an RNA probe library (capture), as described in detail in Meir Z. et al. Nature Genetics 2020. Final libraries were pooled and sequenced on an Illumina NextSeq system using the 150-bp high-output sequencing kit.

first: Ariella

last: Weinberg-Shukron

first: Raz

last: Ben-Yair

first: Nozomi

last: Takahashi

first: Marko

last: Dunjić

first: Alon

last: Shtrikman

first: Carol

last: Edwards

first: Anne

middle: C

last: Ferguson-Smith


title: Integrated Analysis of lncRNA and mRNA Expression Profiles in brown adipose tissue of obesity-prone and obesity-resistant mice

city: Hangzhou

first: Fei

last: Yang

address: 866 Yu-hang-tang Road

institute: Zhejiang University

summary: The expression profiles of lncRNAs in BAT were investigated by high-throughput RNA sequencing using HFD-induced C57BL/6J mice. Genes that play roles in thermogenesis and related pathways were identified.

overall_design: The expression profiles of lncRNAs in BAT by high-throughput RNA sequencing using HFD-induced C57BL/6J mice.

first: Congcong

first: Meng

last: Duan

first: Shankuan

last: Zhu

first: Jinhua


title: Hepatic transcript modules are predictive of atherosclerotic lesion burden after a 2-year high cholesterol, high fat diet challenge in baboons [LCLF]

first: Laura

last: Cox

summary:
Analysis of hepatic transcript data using unbiased Weighted Gene Correlation Network Analysis (WGCNA) to identify significant modules of genes correlated with lesion burden and performed pathway enrichment analysis of genes in significant modules. The hypothesis tested in the present study was that transcript modules are predictive of atherosclerotic lesion burden after a high cholesterol, high fat diet challenge.
Results of the study provide an understanding of the key pathways and genes underlying atherosclerotic lesion burdenafter high cholesterol and high fat diet challenge in baboons .

overall_design:
Baboons (n=111; 47 females, 64 males) were maintained a low cholesterol, low fat (LCLF) diet prior to beginning a two-year dietary challenge with a diet high in cholesterol and saturated fat (HCHF).  Liver biopsy samples were collected just prior to beginning the two-year HCHF diet challenge (while on LCLF diet).
The sample number refers to the same animal across all time points.

first: Sobha

last: Puppala


title: The S. cerevisiae m6A reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts.

first: Jérémy

last: Scutenaire


title: Natural history of a mouse model of X-linked myotubular myopathy

city: Toronto

first: James

last: Dowling

state: Ontario

address: 686 Bay Street

country: Canada

institute: Hospital for Sick Children

summary: X-linked myotubular myopathy (XLMTM) is a severe monogenetic disorder of the skeletal muscle. It is caused by loss-of-expression/function mutations in the myotubularin (MTM1) gene. Much of what is known about the disease, as well as the treatment strategies, has been uncovered through experimentation in pre-clinical models, particularly the Mtm1 gene knockout mouse line (Mtm1 KO). Despite this understanding, and the identification of potential therapies, much remains to be understood about XLMTM disease pathomechanisms, and about the normal functions of MTM1 in muscle development. To lay the groundwork for addressing these knowledge gaps, we performed a natural history study of Mtm1 KO mice. This included longitudinal comparative analyses of motor phenotype, transcriptome and proteome profiles, muscle structure and targeted molecular pathways.We identified age-associated changes in gene expression, mitochondrial function, myofiber size and key molecular markers, including DNM2. Importantly, some molecular and histopathologic changes preceded overt phenotypic changes, while others, such as triad structural alternations, occurred coincidentally with the presence of severe weakness. In total, this study provides a comprehensive longitudinal evaluation of the murine XLMTM disease process, and thus provides a critical framework for future investigations.

overall_design: Gene expression profiling analysis of RNA-seq data for skeletal muscle from WT and Mtm1 KO mice at 1, 14, 21 and 35 days of age.

first: Ege

last: Sarikaya

first: Nesrin

last: Sabha

first: Jonathan

last: Volpatti

first: Emanuela

last: Pannia

first: Nika

last: Maani

first: Hernan

last: D Gonorazky

first: Alper

last: Celik

first: Yijing

last: Liang

first: Paula

last: Onofre-Oliveira

last: J Dowling


title: Human alveolar progenitors generate dual lineage bronchioalveolar organoids

city: Berlin

first: Benedikt

last: Obermayer

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

summary: Mechanisms of epithelial renewal in the alveolar compartment remain incompletely understood. To this end, we aimed to characterize alveolar progenitors. Single-cell RNA-seq (scRNA-seq) analysis of the HTII-280 positive and  HTII-280+ /EpCAM+populations from total 6 donors from periferal tissue was performed, and analysis revealed subclusters enriched for stem cell signature genes. We found that these alveolar progenitors in organoid culture in vitro show phenotypic lineage plasticity as they can yield alveolar or bronchial cell type progeny. The direction of the differentiation is dependent on the presence of the GSK-3β inhibitor, CHIR99021. By RNA-seq analysis of GSK-3 βknockdown organoids, we identify additional functional candidate target genes and pathways which contribute to alveolar differentiation independent of Wnt signaling

overall_design:
Human peripheral lung tissue resident HTII-280+ ,  and HTII-280+/Epcam+cells were analyzed by single-cell RNA sequencing (scRNA-seq). Organoid forming and differentiation capacity was tested in different signaling environments, and phenotype was characterized by scRNA-seq, confocal imaging, electron microscopy, qPCR, and immunoblotting. ShGSK3β  organoids were generated by lentiviral tansduction of 2 different hairpins against GSK 3β and control vector The validity of organoids as an infection model for influenza virus (IAV) was established in comparison to human ex vivo lung tissue.

Analysis code is available from https://github.com/bihealth/hoffmann_et_al_bronchioalveolar_organoids

>>>Submitter states that raw data are unavailable due to patient privacy concerns<<<

first: Mirjana

last: Kessler

first: Karen

last: Hoffmann

first: Morris

last: Baumgardt

first: Maren

last: Mieth

first: Emanuel

last: Wyler

first: Zeynep

last: Demir


title: Evaluation of the synergistic potential of simultaneous pan- or isoform specific BET and SYK inhibition in B-cell lymphoma

first: Sina

last: Sender


title: RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development [5hmC-Seal]

status: Public on Jul 07 2022

first: Dengfeng

last: Ruan

state: China

address: 88 Jie Fang Road

department: Department of Orthopedic Surgery

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

summary: The Ten-eleven translocation (TET) family of dioxygenases can mediate cytosine demethylation by catalyzing the oxidation of 5-methylcytosine (5mC). TET-mediated DNA demethylation controls the proper differentiation of embryonic stem cells and TET proteins display functional redundancy during early gastrulation. However, it is unclear if TET proteins have functional significance in mammalian skeletal development. Here, we report that Tet deficiency in mesoderm mesenchymal stem cells results in severe defects of bone development. The existence of any single Tet gene allele can support early bone formation, suggesting a potential functional redundancy of TET proteins. Integrative analyses of RNA-seq, Whole Genome Bisulfite Sequencing (WGBS) and Assay for Transposase-Accessible Chromatin (ATAC-seq) demonstrate that TET-mediated demethylation increases the chromatin accessibility of target genes by RUNX2 and facilities RUNX2-regulated transcription. In addition, TET proteins interact with RUNX2 through their catalytic domain to regulate cytosine methylation around RUNX2 binding region. The catalytic domain is indispensable for TET proteins to regulate RUNX2 transcription activity on its target genes and to regulate bone development. These results demonstrate that TET proteins function redundantly to regulate RUNX2 activity via dual mechanisms and maintain skeletal homeostasis.

overall_design: The RNA-seq library constructions and sequencing were utilized 3 repeats per group in WT and TCKO osteoblasts. BS-seq library constructions and sequencing utilized one sample per group. ATAC-seq library constructions and sequencing utilized 2 sample per group.

first: Lijun

last: Wang

first: Xiuling

last: You

first: Rui

last: Shao

first: Haiqiang

last: Dai

first: Guo-Liang

last: Xu

first: Weiliang

last: Shen

first: Wanlu

last: Liu

first: Weiguo

last: Zou


title: Immunoprotective effects of two histone H2A variants in the grass carp against Flavobacterium columnare infection

first: cao

last: lu

address: 7 Donghu South Road

department: Chinese Academy   of Sciences

institute: Institute of Hydrobiology

summary: It is well established that histone derived antimicrobial peptides (AMPs) have anti-microbial properties in various invertebrate and vertebrate species.To reveal the possible immunoregulatory functions of the engineered S. cerevisiae expressing gcH2A-4(7t) and gcH2A-11(2t) on the grass carp, the intestines from the immunized grass carp were collected at the first immunization for 7 days and used for transcriptome sequencing. The results found that the activation of PRRs-related pathways including TLRs, NLRs and RLRs was revealed in the engineered S. cerevisiae expressing gcH2A-4(7t)  and gcH2A-11(2t)  on the grass carp intestines."

first: Yuan

middle: Y

last: Yang

first: Hong

last: Fang

first: Si

last: Zheng

first: Xiao

last: Wu

first: Lu

last: Cao

first: Jie

last: Zhang

first: Ming

middle: X

last: Chang


title: Evaluation of the synergistic potential of simultaneous pan- or isoform specific BET and SYK inhibition in B-cell lymphoma (microarray)

first: Sina

last: Sender

summary:
Background: Bromodomain and extra-terminal domain (BET) proteins and the spleen tyrosine kinase (SYK) represent promising targets in Diffuse large B-cell (DLBCL) and Burkitt’s lymphoma (BL). We evaluated the anti-lymphoma activity of the isoform specific bivalent BET inhibitor AZD5153 (AZD) and the pan-BET inhibitor I-BET151 (I-BET) as single agents and in combination with SYK inhibitor Entospletinib in vitro.  Methods: Single agent exposures were evaluated on two DLBCL and two BL cell lines analyzing cell proliferation and metabolic activity. Proliferation, metabolic activity, apoptosis, cell cycle and morphology were investigated after combined AZD or I-BET and Ento exposure. RNAseq of combined AZD+Ento exposure was characterized in SU-DHL-4.  Background: Bromodomain and extra-terminal domain (BET) proteins and the spleen tyrosine kinase (SYK) represent promising targets in Diffuse large B-cell (DLBCL) and Burkitt’s lymphoma (BL). We evaluated the anti-lymphoma activity of the isoform specific bivalent BET inhibitor AZD5153 (AZD) and the pan-BET inhibitor I-BET151 (I-BET) as single agents and in combination with SYK inhibitor Entospletinib in vitro.  Methods: Single agent exposures were evaluated on two DLBCL and two BL cell lines analyzing cell proliferation and metabolic activity. Proliferation, metabolic activity, apoptosis, cell cycle and morphology were investigated after combined AZD or I-BET and Ento exposure. RNAseq of combined AZD+Ento exposure was characterized in SU-DHL-4.
Results: Both BET inhibitors reduced cell proliferation/metabolic activity dose and time de-pendently. Combined BET and SYK inhibition enhanced the anti-proliferative effect and induc-ing a G0/G1 cell cycle arrest. SU-DHL-4 demonstrated a pronounced modulation of gene expres-sion by AZD, which was markedly increased by additional SYK inhibition. Functional enrich-ment analyses identified combination-specific GO terms related to cell division, transport and DNA replication. Genes such as PLEKHH3, MYB, SLC8A1, PARP9, HSPB1 and S100A4 were iden-tified as the presumable key regulators.  Conclusion: Simultaneous inhibition of BET and SYK enhanced the anti-proliferative effects, and especially the combination-specific gene expression signature.

overall_design: Comparative expression analyses of AZD+Ento exposed SU-DHL-4 and DG-75 cells compared to DMSO control and AZD or Ento single agents; all sample measured in three biological triplicates

first: Ahmad

last: Sultan

first: Daniel

last: Palmer

first: Dirk

last: Koczan

first: Anett

last: Sekora

first: Julia

last: Beck

first: Ekkehard

last: Schuetz

first: Bertram

last: Brenig

first: Georg

last: Fuellen

first: Christian

last: Junghanss

first: Hugo

last: Escobar


title: Type I interferons promote germinal centers through B cell intrinsic signaling and dendritic cell dependent Th1 and Tfh cell lineages

city: Lund

first: Bengt

last: Johansson-Lindbom

address: BMC D1421b

department: Adaptive Immunity

institute: Lund University

summary: Type I interferons (IFNs) play an essential role in antiviral immunity, correlate with severity of systemic autoimmune disease, and are likely to represent a key component of mRNA vaccine-adjuvanticity. Relevant to all, type I IFNs can enhance germinal center (GC) B cell responses but underlying signaling pathways are incompletely understood due to pleiotropic effects in multiple cell types. Here, we demonstrate that a succinct type I IFN response promotes GC formation and associated IgG subclass distribution primarily through signaling in cDCs and B cells. Type I IFN signaling in cDCs, distinct from cDC1, stimulates development of separable Tfh and Th1 cell subsets. However, Th cell-derived IFN-g induces T-bet expression and IgG2c isotype switching prior to this bifurcation and has no evident effects once GCs and bona fide Tfh cells developed. This pathway acts in synergy with early B cell-intrinsic type I IFN signaling, which reinforces T-bet expression in B cells and leads to a selective amplification of the IgG2c+ GC B cell response. Despite the strong Th1 polarizing effect of type I IFNs, the Tfh cell subset develops into IL-4 producing cells that control the overall magnitude of the GCs and promote generation of IgG1+ GC B cells. Thus, type I IFNs act on B cells and cDCs to drive GC formation and to coordinate IgG subclass distribution through parallel Th1 and Tfh cell-dependent pathways.

overall_design: mRNA sequencing of sorted IFNAR KO, IFNgR KO and WT splenic GC B cells at D8 after immunization with poly I:C and ovalbumin

first: Adam

last: Plumb


title: A novel CRISPR activation mouse enables modelling of aggressive lymphoma and interrogation of venetoclax resistance

city: Melbourne

first: Goknur

last: Giner

state: VIC

address: 1G Royal Parade

department: Blood Cells and Blood Cancer

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

summary: CRISPR technologies have advanced cancer modelling in mice, but CRISPR activation (CRISPRa) methods have not been exploited in this context. We establish a CRISPRa mouse (dCas9a-SAMKI/+ 38 ) for inducing gene expression in vivo and in vitro. Using dCas9a-SAMKI 39 primary lymphocytes, we induced B cell restricted genes in T cells and vice versa, demonstrating the power of this system. There are limited models of aggressive double hit lymphoma. Therefore, we transactivated pro-survival BCL-2 in Eµ-MycT/+;dCas9a-SAMKI/+ 42 haematopoietic stem and progenitor cells. Mice transplanted with these cells rapidly developed lymphomas expressing high BCL-2 and MYC. Unlike standard Eµ-Myc lymphomas, BCL-2 expressing lymphomas were highly sensitive to the BCL-2 inhibitor venetoclax. We performed genome-wide activation screens in these lymphoma cells and found a dominant role for the BCL-2 protein A1 in venetoclax resistance. Here we show the power of our CRISPRa model for mimicking disease and providing insights into resistance mechanisms towards targeted therapies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Mouse Embryonic Fibroblast (MEF) cell lines.

first: Ashley

last: Ng

first: Yexuan

last: Deng

first: Marco

last: Herold

first: Sarah

last: Diepstraten

first: Andrew

last: Kueh


title: [SHAPE-MaP_10_mM] U1 snRNP regulates recruitment of early spliceosomal components by disrupting SRSF1-pre-mRNA interactions

first: Kaushik

last: Saha

address: 9500 Gilman Drive

department: Chemistry and Biochemistry

institute: University of California San Diego

summary: Please refer to the summary of the Superseries.

overall_design: Estimation of in vitro SHAPE reactivity with 10 mM NMIA by SHAPE-MaP  Please note that each processed data file for SHAPE_MaP was generated from three raw data files (DMSO i.e. vehicle treated, NMIA i.e. reagent treated, and DC i.e. denatured control) and is linked to the corresponding NMIA sample records.

first: Gourisankar

last: Ghosh


title: [RNP-MaP] U1 snRNP regulates recruitment of early spliceosomal components by disrupting SRSF1-pre-mRNA interactions

overall_design:
Examination of in vitro protein binding sites by RNP-MaP
Please note that each processed datafile for RNP_MaP is obtained from two samples (reagent-treated and vehicle-treated) and is linked to the corresponding reagent-treated sample records.


title: The S. cerevisiae m6A reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts [RNA-seq]

first: Jérémy

last: Scutenaire

summary: We performed high-throughput mRNA sequencing during a meiotic time course (0, 2, 3, 5, 6, 7 and 9 hr) in WT, pho92 mutant and ime4 mutant cells.

overall_design: Meiosis was induced by resuspension of cells in SPO medium and high synchronicity was achieved thanks to the SK1 pCUP-IME1 background alowing inducible activation of IME1 after 2 hr in SPO by addition of 50 µM of copper (II) sulfate. PolyA RNAs were extracted from cells collected at 7 time points from 3 different strains (WT, pho92 mutant, ime4 mutant) and in 3 biological replicates, giving a total of 63 yeast mRNA-seq samples.

first: Damien

last: Plassard


title: PARP1-SNAI2 Transcription Axis Drives Resistance to PARP Inhibitor, Talazoparib (ATAC-Seq)

city: San Diego

first: Xia

last: Ding

address: 10724 Science Center Dr

institute: Pfizer, Inc.

summary: The synthetic lethal association between BRCA deficiency and poly (ADP-ribose) polymerase (PARP) inhibition supports PARP inhibitor (PARPi) clinical efficacy in BRCA-mutated tumors. PARPis also demonstrate activity in non-BRCA mutated tumors presumably through induction of PARP1-DNA trapping. Despite pronounced clinical response, therapeutic resistance to PARPis inevitably develops. An abundance of knowledge has been built around resistance mechanisms in BRCA-mutated tumors, however, parallel understanding in non-BRCA mutated settings remains insufficient. In this study, we find a strong correlation between the epithelial-mesenchymal transition (EMT) signature and resistance to a clinical PARPi, Talazoparib, in non-BRCA mutated tumor cells. Genetic profiling demonstrates that SNAI2, a master EMT transcription factor, is transcriptionally induced by Talazoparib treatment or PARP1 depletion and this induction is partially responsible for the emerging resistance. Mechanistically, we find that the PARP1 protein directly binds to SNAI2 gene promoter and suppresses its transcription. Talazoparib treatment or PARP1 depletion lifts PARP1-mediated suppression and increases chromatin accessibility around SNAI2 promoters, thus driving SNAI2 transcription and drug resistance. We also find that depletion of the chromatin remodeler CHD1L suppresses SNAI2 expression and reverts acquired resistance to Talazoparib. The PARP1/CHD1L/SNAI2 transcription axis might be therapeutically targeted to re-sensitize Talazoparib in non-BRCA mutated tumors.

overall_design: Human tumor cell lines treated with indicated compound or genetically modified were subjected to ATACseq. Triplicated samples were submitted for sequencing.

first: Zhou

last: Zhu

first: John

last: Lapek

first: Elizabeth

last: McMillan

first: Alexander

last: Zhang

first: Chi-Yeh

last: Chung

first: Sara

last: Dubbury

first: Jennifer

last: Lapira

last: Firdaus

first: Xiaolin

last: Kang

first: Jingjin

last: Gao

first: Jon

last: Oyer

last: Chionis

first: Robert

last: Rollins

first: Lianjie

last: Li

first: Sherry

last: Niessen

first: Shubha

last: Bagrodia

first: Lianglin

first: Todd

last: VanArsdale


title: PARP1-SNAI2 Transcription Axis Drives Resistance to PARP Inhibitor, Talazoparib (RNA-Seq)

first: Xia

last: Ding

overall_design: Human tumor cell lines treated with indicated compound or genetically modified were subjected to RNAseq. Triplicated samples were submitted for sequencing.

last: Zhu

first: Sarah


title: RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development

first: Dengfeng

last: Ruan

type: Methylation profiling by high throughput sequencing


title: PARP1-SNAI2 Transcription Axis Drives Resistance to PARP Inhibitor, Talazoparib (scRNA-Seq)

overall_design: Human tumor cell lines treated with indicated compound were subjected to single cells RNAseq.

first: Zhou

first: John

last: Lapek

first: Elizabeth

last: McMillan

last: Zhang


title: RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development (RNA-Seq)

overall_design: The RNA-seq library constructions and sequencing were utilized 3 repeats per group in WT and TCKO osteoblasts.BS-seq library constructions and sequencing utilized one sample per group.ATAC-seq library constructions and sequencing utilized 2 sample per group.

first: Lijun

last: Wang

first: Xiuling

last: You

first: Rui

last: Shao

first: Haiqiang

last: Dai

first: Guo-Liang

last: Xu

first: Weiliang

last: Shen

first: Wanlu

last: Liu

first: Weiguo

last: Zou


title: RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development (ATAC-Seq)


title: [SHAPE-MaP_4_mM] U1 snRNP regulates recruitment of early spliceosomal components by disrupting SRSF1-pre-mRNA interactions

first: Kaushik

last: Saha

overall_design:
Estimation of in vitro SHAPE reactivity with 4 mM NMIA by SHAPE-MaP:
Please note that each processed data file for SHAPE_MaP was generated from three raw data files (DMSO i.e. vehicle treated, NMIA i.e. reagent treated, and DC i.e. denatured control) and is linked to the corresponding NMIA sample records.

first: Gourisankar

last: Ghosh


title: Transcriptomic analysis of synovial cells derived from collagen-induced arthritis mice

status: Public on Jul 06 2022

city: Tokyo

first: Hiroshi

last: Takayanagi

address: 7-3-1, Hongo, Bunkyo-ku, Tokyo

department: Department of Immunology

institute: The University of Tokyo

summary: The destruction of bone and cartilage results in a loss of joint functionality, critically impairing the quality of life in arthritis patients. Synovial fibroblasts (SFs) critically contribute to the pathogenesis of rheumatoid arthritis (RA) by acquiring either a pro-inflammatory or tissue-destructive phenotype. To explore the molecular mechanisms underlying the pathogenic fibroblast phenotype in arthritis, we performed single-cell RNA sequencing (scRNA-seq) on the synovial cells which were isolated from collagen-induced arthritis (CIA) mice.

overall_design: scRNA-seq analysis was performed on synovial cells which were isolated from the knee joints of CIA mice (n=3) and healthy control mice (n=9). Alignment, quantitation and aggregation of the sample count matrices (CIA + control) were performed using the 10x Genomics Cell Ranger pipeline (v.3.0) according to the manufacturer’s protocol (GENEWIZ).

first: Yan

last: Minglu


title: Biallelic PAX5 mutations cause hypogammaglobulinemia,sensorimotor deficits and autism spectrum disorder

city: Vienna

first: Moritz

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

summary: To investigate the molecular basis for the B cell developmental arrest in Pax5R31Q/– mice, we performed RNA-sequencing (RNA-seq) with ex vivo sorted Pax5+/+ and Pax5R31Q/– pro-B cells. We identified Pax5-activated and Pax5-repressed genes that were no longer properly regulated by the Pax5-R31Q protein in Pax5R31Q/– pro-B cells. Notably, these genes were only a subset of the activated and repressed genes identified by comparing Pax5+/+ and Pax5–/– pro-B cells, which raised the question whether binding of the Pax5-R31Q protein may be selectively lost at the subset of deregulated genes in Pax5R31Q/– pro-B cells. By using a Pax5 paired domain antibody for chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) of short-term cultured Pax5+/+ and Pax5R31Q/– pro-B cells, we identified all associated Pax5 binding sites. Common Pax5 peaks had a similar Pax5-binding density in contrast to the strong binding difference observed at the unique peaks present in Pax5+/+ pro-B cells. To investigate a correlation between the loss of Pax5 binding and gene expression, we focused our analysis on Pax5 peaks in the TSS region of activated genes. We systematically investigated the correlation between loss of Pax5 binding at the TSS and down-regulation of gene expression in Pax5R31Q/– pro-B cells. The ratio of Pax5 binding between Pax5R31Q/– and Pax5+/+ pro-B cells at the TSS of these activated genes was significantly reduced compared to that of expressed non-regulated genes. We next explored whether the Pax5-binding difference at the TSS also correlated with the magnitude of gene expression difference. The loss of Pax5 binding at the TSS also correlated with the degree of expression change in Pax5R31Q/– pro-B cells compared to Pax5+/+ pro-B cells. We conclude therefore that the selective DNA-binding of Pax5-R31Q is responsible for the observed gene expression differences in Pax5R31Q/– pro-B cells.

overall_design: 8 RNA-Seq samples, 4 different conditions (A,B,C,D) two replicates each. A (wildtype): Pro-B cells Pax5(+/+)  111735 + 111736; B (R31Q mutant): Pro-B cells pax5(R31Q/-) 111739 + 111740; C (Pax5 knock out): Progenitor cells Pax5(fl/fl) VAV-cre 111726 + 111741; D (Pro-B cells Pax5 het): Pro-B cell Pax5(+/-) 111737 + 111738. 2 ChIP-Seq samples (65448 (wildtype) + 65449 (mutant)).

first: Fabian

last: Kaiser

first: Sarah

last: Grünbacher

first: Markus

last: Jaritz

first: Meinrad

last: Busslinger


title: Next generation sequencing analysis in Y-1 mouse adrenocortical cells after dexamethasone treatment

city: Auburn

first: Sophia

last: Zheng

address: 1130 Wire Road

department: Anatomy, Physiology 7 Pharmacology

institute: Auburn University

summary: RNA sequencing (RNA-seq) was used to identify early transcriptomic responses of Y-1 cells to the  dexamethasone treatment.

overall_design: Y-1 adrenocortical cells  were subcultured separately onto three groups. mRNA profiles of the control ,1h-dexamethasone treatment, and 24h-dexamethasone treatment were compared. Three replicated experiments were performed independently on different days starting from different cell passages.

first: Huifei

middle: S

first: Jeffery

last: Daniel

first: Julia

last: Salamat

first: Laci

last: Mackay

first: Chad

last: Foradori

first: Robert

last: Kemppainen

first: Satyanarayana

middle: R

last: Pondugula

first: Ya-xiong

last: Tao

first: Chen-che

last: Huang


title: Transcriptional and Translational Dynamics of Zika and Dengue Virus Infection

city: Bronx

first: Kamini

last: Singh

address: 1300 Morris Park Ave, Golding 203

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

summary: Zika virus (ZIKV) and dengue virus (DENV) are members of the Flaviviridae family of RNA viruses and cause severe disease in humans. ZIKV and DENV share over 90% of their genome sequences, however the clinical features of Zika and dengue infections are very different reflecting tropism and cellular effects. Here, we used simultaneous RNA sequencing and ribosome footprinting to define the transcriptional and translational dynamics of ZIKV and DENV infection in human neuronal progenitor cells (hNPCs). The gene expression data showed induction of aminoacyl tRNA synthetases (ARS) and the translation-activating PIM1 kinase indicating an increase in RNA translation capacity. The data also reveal activation of different cell stress reponses, with ZIKV triggering a BACH1/2 redox program, and DENV activating the ETF/CHOP endoplasmatic reticulum (ER) stress program. The RNA translation data highlight activation of polyamine metabolism through changes in key enzymes and their regulators. This pathway is needed for eIF5A hypusination and has been implicated viral translation and replication. Concerning the viral RNA genomes, ribosome occupancy readily identifies highly translated open reading frames and a novel upstream ORF (uORF) in the DENV genome. Together, our data highlight both the cellular stress response and also the activation of RNA translation and polyamine metabolism during DENV and ZIKV infection.

overall_design: We performed ribosome footprinting and RNA sequencing on human neuronal progenitor cells (hNPCs) cells either uninfected or infected with ZIKV or DENV  in two biological replicates that were collected 72 hours post infection. Unifected samples are indicated as A1 and B1, ZIKV infected samples are indicated as A2, B2 and DENV infected samples are indicated as A3 and B3.

first: Guadalupe

last: Martinez

first: Jianan

last: Lin

first: James

last: Gregory

first: Rawan

last: Abdelaal

first: Kristy

last: Kang

first: Kristen

last: Brennand

first: Arnold

last: Grunweller

first: Zhengqing

last: Ouyang

first: Hemali

last: Phatnani

first: Margaret

last: Kielian

first: Hans-Guido

last: Wendel


title: Histone H3K36me2 and H3K36me3 form a chromatin platform essential for DNMT3A-dependent DNA methylation in mouse oocytes

city: Fukuoka

first: Hiroyuki

last: Sasaki

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Molecular and Structural Biology

institute: Medical Institute of Bioregulation, Kyushu University

summary: Establishment of the DNA methylation landscape of mammalian oocytes, mediated by the DNMT3A-DNMT3L complex, is crucial for reproduction and development. In mouse oocytes, high levels of DNA methylation occur exclusively in the transcriptionally active regions, with moderate to low levels of methylation in other regions. Histone H3K36me3 mediates the high levels of methylation in the transcribed regions; however, it is unknown which histone mark guides the methylation in the other regions. Here, we show that, in mouse oocytes, H3K36me2 is highly enriched in the X chromosome and is broadly distributed across all autosomes. Upon H3K36me2 depletion, DNA methylation in moderately methylated regions is selectively affected, and a methylation pattern unique to the X chromosome is switched to an autosome-like pattern. Furthermore, we find that simultaneous depletion of H3K36me2 and H3K36me3 results in global hypomethylation, comparable to that of DNMT3A depletion. Therefore, the two histone marks jointly provide the chromatin platform essential for guiding DNMT3A-dependent DNA methylation in mouse oocytes.

overall_design: ChIP-seq, CUT&RUN, WGBS were performed with mouse oocytes. RNA-seq was performed with oocytes or late 2-cell embryos.

first: Seiichi

last: Yano

first: Takashi

last: Ishiuchi

first: Shusaku

last: Abe

first: Satoshi

middle: H

last: Namekawa

first: Gang

first: Yoshihiro

last: Ogawa


title: Nano-silica particles synergistically IgE-mediated mast cell activation

status: Public on Jul 05 2022

city: Beijing

first: Jinlyu

last: Sun

state: Beijing

address: No.1 Shuaifuyuan, Wangfujing, Dongcheng District

department: Department of Allergy

institute: Peking Union Medical College Hospital

summary: To deeply investigate the details of the nano-SiO2 effects, we examined the gene expression profile alterations after nano-SiO2 treatment in BMMCs. The difference analysis between the groups showed that 285 genes were significantly expressed after treatment with nano-SiO2. Compared with the blank group, both nano-SiO2 exposure and DNP-HSA stimulation increased the expression of genes related to the MAPK signaling pathway in mast cells to varying degrees.

overall_design: Mature BMMCs were collected after treatment with SiO2 solution for transcriptome sequencing analysis. The experiment was divided into four groups: blank control,DNP-HSA, SiO2, and SiO2+DNP-HSA. We performed 2×150 bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-BioTechnology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.  Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were used to analyze these differentially expressed genes. Bioinformatics analysis was performed using the OmicStudio tools at https://www.omicstudio.cn/tool.

first: Yongshi

last: Yang

first: MengDa

last: Cao

first: An

last: Wang

first: DianDou

last: Xu

first: JiFu

last: Wei

first: JinLyu


title: RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development (WGBS)

first: Dengfeng

last: Ruan

first: Lijun

first: Xiuling

last: You

first: Rui

last: Shao

first: Haiqiang

last: Dai

first: Guo-Liang

first: Weiliang

last: Shen

first: Wanlu

last: Liu

first: Weiguo

last: Zou


title: RNA-seq analysis of synovial fibroblasts isolated from Ets1-flox/flox and Col6a1-Cre-Ets1-flox/flox mice of serum transfer-induced arthritis (STIA)

first: Hiroshi

last: Takayanagi

summary: Synovial fibroblasts critically contribute to the pathogenesis of rheumatoid arthritis (RA) by acquiring either a pro-inflammatory or tissue-destructive phenotype. To explore the molecular mechanisms underlying the tissue-destructive fibroblast phenotype in arthritis, we performed bulk RNA-sequencing analysis on the synovial fibroblasts which were isolated from Col6a1-Cre-Ets1-flox/flox (Ets1ΔFib) and Ets1-flox/flox (Ets1flox) mice.

overall_design: RNA-seq analysis was performed on synovial fibroblasts (CD45-CD31-CD146-PDPN+) isolated from the ankle joints of Ets1flox and Ets1ΔFib mice under STIA condition (n=3 per group) . Data were acquired on an Ion Proton sequencer (Thermo Fisher Scientific) and CLC genomics Workbench v.12.

first: Minglu

last: Yan


title: A functional role of meningeal lymphatics in sex difference of stress susceptibility in mice

city: Guangzhou

first: Huang

last: Shuying

address: 中国广州市中山二路74号中山大学广州校区北校园

institute: Sun Yat-Sen University

summary: Major depressive disorder is one of the most common mental health conditions. Meningeal lymphatics are essential for drainage of molecules in the cerebrospinal fluid to the peripheral immune system. Their potential role in depression-like behaviour has not been investigated. Here, we show in mice, sub-chronic variable stress as a model of depression-like behaviour impairs meningeal lymphatics in females but not in males. Manipulations of meningeal lymphatics regulate the sex difference in the susceptibility to stress-induced depression- and anxiety-like behaviors in mice, as well as alterations of the medial prefrontal cortex and the ventral tegmental area, brain regions critical for emotional regulation. Together, our findings suggest meningeal lymphatic impairment contributes to susceptibility to stress in mice, and that restoration of the meningeal lymphatics might have potential for modulation of depression-like behaviour.

overall_design: Transcriptomic profiles of the meningeal lymphatic endothelial cells in female mice at 6 days after Sub-chronic variable stress

first: Weiping

first: Mengqian

first: Pei

last: Xia

first: Chuan

last: Xiao

first: Shuying

last: Huang

first: Zhan

last: Zhang

first: Xin

last: Cheng

first: Wenchang

last: Li

first: Jian

last: Jin

first: Jingyun

first: Binghuo

last: Wu

first: Yingying

first: Pei-hui

first: Yangyang

last: Lin

first: Wen

first: Hu

last: Zhao

first: Yan

first: Lin

first: Pei-hui Wu

last: Pei-hui Wu


title: PARP1-SNAI2 Transcription Axis Drives Resistance to PARP Inhibitor, Talazoparib

first: Xia

last: Ding

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

overall_design: Refer to individual Series


title: eIF1-eIF4G1 inhibitors uncover alternative translation activation of stress-response genes via enhanced ribosome loading and 5’UTR translation [Ribo-Seq and Ti-Seq]

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

institute: Weizmann Institute of Science

summary: The Ribo-seq and TI-seq analysis following i14G1s (eI1-eIF4G1 inhibitors) treatments uncover opposing roles of eIF1-eIF4G1 and eIF4E-eIF4G1 in scanning-dependent and independent translation. Furthermore, i14G1s inhibition of eIF4G1-eIF1 resulted in translation activation of ER/UPR stress-response genes via enhanced ribosome loading, elevated 5’UTR translation at near cognate AUGs, and unexpected concomitant upregulation of coding-region translation.

overall_design: Ribo-seq and TI-seq analysis was performed either in HEK293T cells treated with either DMSO (vehicle control), i14G1-10  or i14G1-12.

first: Urmila

last: Sehrawat

first: Ora

last: Haimov

first: Ana

middle: T

last: Harush

first: Alexander

last: Plotnikov

first: Rivka

last: Dikstein


title: Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses

city: Klosterneuburg

first: Sandra

last: Siegert

state: Lower Austria

address: Am Campus 1

institute: Institute of Science and Technology Austria

summary: G protein-coupled receptors (GPCRs) regulate processes ranging from immune responses to neuronal signaling. However, ligands for many GPCRs remain unknown, suffer from off-target effects or have poor bioavailability. Additionally, dissecting cell type-specific responses is challenging when the same GPCR is expressed on different cells within a tissue. Here, we overcome these limitations by engineering DREADD-based GPCR chimeras that bind their agonist clozapine-N-oxide (CNO) and mimic a GPCR-of-interest. We show that the chimeric DREADD-β2AR triggers responses comparable to levalbuterol-stimulated β2AR on second messenger and kinase activity, post-translational modifications, and protein-protein interactions. Moreover, we successfully recapitulate β2AR-mediated filopodia formation in primary microglia, an immune cell capable of driving central nervous system inflammation. When dissecting microglial inflammation, we utilized the microglia-like HMC3 cell line and included two additionally designed DREADD-based chimeras mimicking GPR65 and GPR109A. DREADD-β2AR and DREADD-GPR65 modulate the inflammatory response with high similarity to endogenous β2AR, while DREADD-GPR109A had no impact. Our DREADD-based approach allows investigation of cell type-dependent pathways without known endogenous ligands.

overall_design: We used lentiviral transduction and generated HMC3 cell lines with stable expression of DREADD-β2AR, DREADD-GPR65, or DREADD-GPR109A, respectively. Non-transduced cells represent unaltered (wild type) HMC3 cells, which endogenously express β2AR that can be stimulated with levalbuterol (LB). We induced inflammation in HMC3 cells through simultaneous challenge with the recombinant cytokines IFNγ and IL1β. Concomitantly, we applied levalbuterol or CNO to study how GPCR signaling can modulate inflammatory gene expression. In total, we sequenced 30 samples with three replicates for each of the following 10 experimental conditions: Non-transduced: Untreated; Non-transduced: IFNγ/IL1β; Non-transduced: IFNγ/IL1β+LB; Non-transduced: IFNγ/IL1β+CNO; DREADD-β2AR: IFNγ/IL1β; DREADD-β2AR: IFNγ/IL1β+CNO; DREADD-GPR65: IFNγ/IL1β; DREADD-GPR65: IFNγ/IL1β+CNO; DREADD-GPR109A: IFNγ/IL1β; DREADD-GPR109A: IFNγ/IL1β+CNO.

first: Rouven

last: Schulz

first: Medina

last: Korkut-Demirbaş

first: Alessandro

last: Venturino

first: Gloria

last: Colombo


title: Deletion of thioredoxin reductase disrupts redox homeostasis and impairs β-cell function

city: Charleston

first: Jennifer

last: Stancill

state: South Carolina

address: 173 Ashley Avenue, CR513

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

summary: Reactive oxygen species (ROS) have been implicated as mediators of pancreatic β-cell damage. While β-cells are thought to be vulnerable to oxidative damage, we have shown, using inhibitors and acute depletions, that thioredoxin reductase, thioredoxin, and peroxiredoxins are the primary mediators of antioxidant defense in β-cells. However, the role of this antioxidant cycle in maintaining redox homeostasis and β-cell survival in vivo remains unclear. Here, we generated mice with a β-cell specific knockout of thioredoxin reductase 1 (Txnrd1.fl/fl; Ins1.Cre/+, βKO). Despite blunted glucose-stimulated insulin secretion, knockout mice maintain normal whole body glucose homeostasis. Unlike pancreatic islets with acute Txnrd1 inhibition, βKO islets do not demonstrate increased sensitivity to continuous ROS. RNA-sequencing analysis revealed that Txnrd1-deficient β-cells have increased expression of Nuclear factor erythroid 2-related factor 2 (Nrf2)-regulated genes, and altered expression of genes involved in heme and glutathione metabolism, suggesting an adaptive response. Txnrd1-deficient β-cells also have decreased expression of factors controlling β-cell function and identity which may explain the mild functional impairment. Together, these results suggest that Txnrd1-knockout β-cells compensate for loss of this essential antioxidant pathway by increasing expression of Nrf2-regulated antioxidant genes, allowing for protection from excess ROS at the expense of normal β-cell function and identity.

overall_design: RNA-sequencing of FACS-purified islet beta-cells and islet non-beta cells from mice with a beta-cell specific knockout of the cytoplasmic thioredoxin reductase, Txnrd1, vs. control cells

first: John

last: Corbett


title: Next generation sequencing analysis of mouse adrenal glands after a one-hour dexamethasone treatment

first: Sophia

last: Zheng

summary: RNA sequencing (RNA-seq) was used to identify early transcriptomic responses of the adrenal gland to the 1-hour dexamethasone treatment in mice.

overall_design: Five male mice were IP injected with dexamethason (10 micro gram) and another five mice were IP injected with phosphate-buffered saline. Adrenal glands were collected one hour after the treatment. Adrenal glands were pooled (2 mice and 3 mice) and total RNAs were extracted to make two replicates for each treatment group. Paired-end RNA-seq (PE150) was performed using the Illumina platform.

first: Huifei

first: Jeffery

middle: G

last: Daniel

first: Julia

last: Salamat

first: Laci

last: Mackay

first: Chad

last: Foradori

first: Robert

last: Kemppainen

first: Satyanarayana

last: Pondugula

first: Ya-xiong

last: Tao

first: Chen-Che

last: Huang


title: RNA sequencing of Normal Human Fibroblasts and Patient Fibroblasts with Novel SCP2 Variant

city: Los Angeles

first: Melanie

last: Galano

address: 1985 Zonal Ave

institute: University of Southern California

summary: The purpose of this study was to identify differentially expressed genes beween normal and SCP2 mutant fibroblasts

overall_design: Gene expression profile of normal human fibroblasts and patient fibroblasts

first: Shereen

last: Ezzat

first: Vassilios

last: Papadopoulos


title: Archetype tasks link intratumoral heterogeneity to plasticity in recalcitrant small cell lung cancer

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: miRNA data from C8+ T cells exposed to DCMU or control vehicle (DMSO)

city: Nantes

first: Delphine

last: Fradin

address: 8 quai Moncousu

institute: CRCI2NA, Inserm UMR1307, CNRS UMR6075

summary: DCMU, or diuron, is a widely used herbicide, which can cause adverse effects on human. Here, we develop an approach that combines functional, miRNA and RNA sequencing data to evaluate the effects of DCMU exposure on the human immune system, notably on CD8+ T cells, as the main effectors of the organism’s defense against viruses or neoplastic cells. We found that DCMU reduces T cell abilities, in vitro but also in vivo in orthotopic mouse and zebrafish models, participating to the establishment of a suitable environment for the development of more serious diseases such as cancers. We identified several miRNAs, such as hsa-miR3135b and hsa-miR-21-5p, respectively induced and repressed by DCMU, which alters CD8+ T cell functions. The major advancement of our study is the description of the molecular mechanisms induced by DCMU that control human immune functions.

overall_design: We used microarray to identify miRNA induced or repressed by DCMU

first: Fradin

last: Delphine

first: Autin

last: Pierre


title: mRNA data from C8+ T cells exposed to DCMU or control vehicle (DMSO)

overall_design: We used this sequencing technology to identify mRNA induced or repressed by DCMU in huan CD8+ T cells

first: Pierre

last: Autin


title: G+C content of transcribed sequence modulates DSIF-assisted DNA occupancy by RNA polymerase II

city: Stanford

first: Stanley

middle: N.

last: Cohen

address: 300 Pasteur Drive, Lane Bldg, Rm L-314

department: Genetics

institute: Stanford University


title: Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice

status: Public on Jul 04 2022

city: Hamburg

first: Yu

last: Zhao

address: Falkenried 94

department: Institute of Medical Systems Biology

institute: University Medical Center Hamburg-Eppendorf

summary: Maternal immune cells (called 'Maternal microchimeric cells' (short: MMc)) seed fetal brain tissue during pregnancy. We used single cell RNA sequencing (scRNA-seq) to characterize the diversity of MMc in the fetal brain.

overall_design: C57BL/6 female mice were mated to CByJ.SJL(B6)-Ptprca/J male mice. MMc were isolated from 16 fetal brains from 4 litters by Fluorescence-activated cell sorting (FACS) according to CD45.2 and H-2Db/b expression and analyzed using scRNAseq.

first: Steven

last: Schepanski

first: Ting

last: Sun

first: Anna

last: Woestemeier

first: Stefan

last: Bonn

first: Nicola

last: Gagliani

first: Ileana

last: Hanganu-Opatz

first: Petra

last: Arck


title: G+C content of transcribed sequence modulates DSIF-assisted DNA occupancy by RNA polymerase II [ChIP-seq]

summary: The DSIF complex, which is composed of the Supt4h and Supt5h transcription elongation proteins, clamps RNA polymerase II (RNAPII) onto DNA templates—facilitating polymerase processivity. Lowering of DSIF components can differentially decrease expression of certain neurodegenerative disease-gene alleles containing nucleotide repeat expansions, suggesting that DSIF assists RNAPII progression through these alleles. To identify sequence features that globally affect the actions of DSIF in neuronal cells, we used ultra—deep ChIP-seq analyses  together with RNA-seq to investigate and quantify the genome-wide consequences  of reducing DSIF on template occupancy and transcription by RNAPII.  Our ChIP-seq analysis yielded an average of 378 million reads per sample, facilitating  precision in  identification of read end-points. The results indicate that DSIF is differentially utilized throughout the human genome by RNAPII in its occupancy of human DNA and that the G+C_composition of the template segment being transcribed determines the extent to which the polymerase relies on DSIF for template occupancy.  Additional analysis by us of previously published data obtained. We following knockdown of  the Supt5h component of DSIF  in  murine fibroblasts  showed similar effects.  We further observed  that DSIF reduction resulted in  progressively decreased RNAPII occupancy of template during transcript elongation in genes of  high G+C content, but  had little effect on genes low in G+C content. Our discovery that DSIF dependency varies in different template regions according to G+C content and transcript length suggest a biochemical basis for selective effects of deficiency of DSIF components on genes containing expansions of G+C-rich nucleotide repeats.

overall_design: Compare elongating RNAPII's DNA occupancy by ChIP-seq and RNA transcription by RNA-seq when Supt4 is present or absent in human neuronal progenitor cells

first: Ning

last: Deng

first: Yue

last: Zhang


title: G+C content of transcribed sequence modulates DSIF-assisted DNA occupancy by RNA polymerase II [RNA-seq]


title: METTL3 inhibits inflammation of retinal pigment epithelium cells by regulating NR2F1 in an m6A-dependent manner

status: Public on Jul 03 2022

city: Chongqing

first: 刘

middle: 先

last: 洋

address: Medical road

institute: The First Affiliated Hospital of Chongqing Medical University


title: Spermidine reduces neuroinflammation and soluble amyloid beta in an Alzheimer’s disease mouse model

city: Berlin

first: Benedikt

last: Obermayer

address: Chariteplatz 1

institute: Berlin Institute of Health

summary: Deposition of amyloid beta (Aβ) and hyperphosphorylated tau along with glial cell-mediated neuroinflammation are prominent pathogenic hallmarks of Alzheimer’s disease (AD). In recent years, impairment of autophagy has been found to be another important feature contributing to AD progression. Therefore, the potential of the autophagy activator spermidine, a small body-endogenous polyamine often used as dietary supplement, was assessed on Aβ pathology and glial cell-mediated neuroinflammation. Oral treatment of the amyloid prone AD-like APPPS1 mice with spermidine reduced neurotoxic soluble Aβ and decreased AD-associated neuroinflammation during disease progression. Mechanistically, single nuclei sequencing revealed AD-associated microglia to be the main target of spermidine. This microglia population was characterized by increased AXL levels and expression of genes implicated in cell migration and phagocytosis. Our data highlight that the autophagy activator spermidine holds the potential to enhance Aβ degradation and to counteract glia-mediated neuroinflammation in AD pathology.

overall_design: Cerebrum samples of spermidine-treated APPPS1 mice compared to H2O-control APPPS1 mice and wild type control mice, replicates are included

first: Kiara

last: Freitag

first: Frank

last: Heppner

first: Marina

last: Jendrach


title: Primary cilia control translation and the cell cycle in medulloblastoma

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: The primary cilium, a signaling organelle projecting from the surface of a cell, controls cellular physiology and behavior. The presence or absence of primary cilia is a distinctive feature of a given tumor type; however, whether and how the primary cilium contributes to tumorigenesis is unknown for most tumors. Medulloblastoma (MB) is a common pediatric brain cancer comprising four groups: SHH, WNT, group 3 (G3), and group 4 (G4). From 111 cases of MB, we show that primary cilia are abundant in SHH and WNT MBs but rare in G3 and G4 MBs. Using WNT and G3 MB mouse models, we show that primary cilia promote WNT MB by facilitating translation of mRNA encoding β-catenin, a major oncoprotein driving WNT MB, whereas cilium loss promotes G3 MB by disrupting cell cycle control and destabilizing the genome. Our findings reveal tumor type–specific ciliary functions and underlying molecular mechanisms. Moreover, we expand the function of primary cilia to translation control and reveal a molecular mechanism by which cilia regulate cell cycle progression, providing new frameworks for studying cilia function in normal and pathologic conditions.

overall_design: 3 WNT MB mouse models used for controls in experiments and 3 shIft88  knock down WNT MB used for comparison and data analysis

first: Yong

last: Youn

first: Shirui

last: Hou

first: Chang-Chih

last: Wu

first: Daisuke

last: Kawauchi

first: Brent

last: Orr

first: Giles

last: Robinson

first: Makoto

middle: M

last: Taketo

first: Richard

middle: J

last: Gilbertson

first: Martine

middle: F

last: Roussel

first: Young-Goo

last: Han


title: Wnt Signaling Regulates Hepatocyte Cell Division by a Transcriptional Repressor Cascade

status: Public on Jul 02 2022

city: Palo Alto

first: Roel

last: Nusse

address: 265 Campus Drive

department: Developmental biology

institute: Stanford University, School of Medicine

summary: Cell proliferation is tightly controlled by inhibitors that block cell cycle progression until growth signals relieve this inhibition, allowing cells to divide. In several tissues including the liver, cell proliferation is inhibited at mitosis by the transcriptional repressors E2F7 and E2F8, leading to formation of polyploid cells. Whether growth factors promote mitosis and cell cycle progression by relieving the E2F7/E2F8-mediated inhibition is unknown. We report here on a new mechanism of cell division control in the postnatal liver, in which Wnt/βcatenin signaling maintains active hepatocyte cell division through Tbx3, a Wnt target gene. Tbx3 directly represses transcription of E2F7 and E2F8, thereby promoting mitosis. This cascade of sequential transcriptional repressors, initiated by Wnt signals, provides a new paradigm for exploring how commonly active developmental signals impact cell cycle completion.

overall_design: Primary mouse hepatocytes that were overexpressing HA-tagged TBX3 protein were used for each chromatin IP reaction. Anti-HA antibody was used for chromatin immunoprecipitation (ChIP). Two biological replicates were generated for Input and ChIP DNA.

first: Yinhua

last: Jin

first: Wenyu

last: Zhou


title: METTL3 inhibits inflammation of retinal pigment epithelium cells by regulating NR2F1 in an m6A-dependent manner [meRIP-seq]

first: 刘

last: 洋

summary: To investigate the fuction of METTL3 in autoimmune uveitis, we established ARPE-19 cell lines in which target gene has been knocked down by shRNA.

overall_design: In this study, we explored the effects and underlying mechanisms of methyltransferase-like 3 (METTL3) in retinal pigment epithelium (RPE) cells, which are crucial for the pathogenesis of autoimmune uveitis. Our results showed that the expression of METTL3 was increased in both human RPE (hRPE) cells and ARPE19 cells after lipopolysaccharide (LPS) stimulation. Moreover, these two types of RPE cells exhibited inhibited proliferation and increased barrier destruction and inflammatory factor secretion after METTL3 silencing. Mechanistically, we found that NR2F1, as a METTL3-methylated target gene, promotes the inflammation of RPE cells in an m6A-dependent manner. Interestingly, NR2F1 deficiency reversed the increased inflammation in the METTL3-defective RPE cells. In conclusion, our study revealed that METTL3 attenuates RPE cell inflammation by methylating NR2F1, suggesting the critical role of METTL3 in RPE cells.

first: Jiayu

last: Meng

first: Xianyang

last: Liu


title: METTL3 inhibits inflammation of retinal pigment epithelium cells by regulating NR2F1 in an m6A-dependent manner [RNA-seq]

summary:
To investigate the fuction of METTL3 in autoimmune uveitis, we established ARPE-19 cell lines in which target gene has been knocked down by shRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq between sh-Control groups and sh-METTL3 groups.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ARPE-19 (sh-Control) cells and its KD derivatives(sh-METTL3).


title: A local neuronal clock regulates retinal angiogenesis and neovascularization

status: Public on Jul 01 2022

city: Cleveland

first: Sujata

last: Rao

state: OH

address: 2022 E 105th St i building

institute: Cole eye, Cleveland Clinic foundation

summary: Emerging evidence suggests a link between the circadian clock and retinopathies though the causality has not been established. Circadian clocks in the mammalian retina regulate a diverse range of retinal functions that allow the retina to adapt to the light-dark cycle. We report that clock genes are expressed in the embryonic retina, and the embryonic retina requires light cues to maintain robust circadian expression of the core clock gene, Bmal1. Deletion of Bmal1 and Per2 from the retinal neurons results in retinal angiogenic defects similar to when animals are maintained under constant light conditions. Using two different models to assess pathological neovascularization, we show that neuronal Bmal1 deletion reduces neovascularization with reduced vascular leakage, suggesting that a dysregulated circadian clock primarily drives neovascularization. Chromatin immunoprecipitation sequencing analysis suggests that semaphorin signaling is the dominant pathway regulated by Bmal1. Our data indicate that therapeutic silencing of the retinal clock could be a common approach for the treatment of certain retinopathies like diabetic retinopathy and retinopathy of prematurity.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Bmal1 occupancy in postnatal (P3) vs postnatal (P5) mouse retinal tissue.

first: Vijay

middle: K

last: Jidigam

first: Onkar

middle: B

last: sawant

first: Rebecca

last: Fuller

first: Kenya

last: Wilcots

first: Rupesh

last: Singh

last: Lang


title: High-throughput high-multiplexed screening for splicing factors

city: San Diego

first: Yajing

last: Hao

address: George Palade Laboratories 9500 Gilman Drive, Room 217

department: Dept. of Cellular and Molecular Medicine

institute: University of California, San Diego

summary: An arrayed library containing pooled siRNAs targeting 18,480 human genes (Dharmacon, Lafayette, CO) was screened as previously described (Roosing et al., 2015).Briefly, 384-well plates with optical bottom (Greiner Bio-One, Monroe, NC) were spotted with 1 μl of 0.5 μM siRNA. Reverse transfection was next performed using Lipofectamine RNAiMAX at the final siRNA concentration of 10 nM. Culture medium was replaced with DMEM 24 hrs after transfection and cells were incubated for additional 48 hrs before lysis in SDS buffer for downstream analysis. These siRNAs were distributed in 57 plates, and after screen, we pooled 4 bar-coded plates for sequencing per Illumina sequencing lane.

overall_design: Identification and characterization of splicing factors in human genome.

first: Changwei

last: Shao

first: Jinsong

last: Qiu

first: Bing

first: Xiang-Dong

last: Fu


title: MGE, CGE, LGE and cortical regions from mouse embryonic forebrain

city: Bethesda

first: Timothy

last: Petros

state: Maryland

address: 35 Convent Drive, Bg 35 Room 3B-1002

institute: NICHD

overall_design: Refer to individual Series