title: The transcriptional landscape of pericytes in acute ischemic stroke

city: Lund

first: Robert

last: Carlsson

address: Sölvegatan 17

department: IKVL

institute: Lund University

summary: The current treatment options for ischemic stroke aim to achieve reperfusion but are time critical. Novel therapeutic approaches that can be given beyond the limited time window of 3 - 4.5 hours are still an unmet need to be addressed to improve stroke outcome. The lack of oxygen and glucose in the area of ischemic injury initiates a pathological cascade leading to blood-brain barrier (BBB) breakdown, inflammation and neuronal cell death, a process that may be intercepted to limit stroke progression. Pericytes located at the blood/brain interface are one of the first responders to hypoxia in stroke and therefore a potential target cell for early stroke interventions. Using single-cell RNA sequencing in a mouse model of permanent middle cerebral artery occlusion, we investigated the temporal differences in transcriptomic signatures in pericytes at 1, 12, and 24 hours after stroke compared to the contralateral hemisphere. Our results reveal a stroke-specific subcluster of pericytes that is present at 12 and 24 hours and characterized by the upregulation of genes mainly related to cytokine signalling and immune response.   This study identifies temporal transcriptional changes in the acute phase of ischemic stroke that reflect the early response of pericytes to the ischemic insult and its secondary consequences and may constitute potential future therapeutic targets.

overall_design: Live non-neuronal single cells from ipsilateral or contralateral cortex of heterozygous RGS5::GFP mice were sequenced after 1h, 12h or 24h permanent middle cerebral artery occlusion.

first: Andreas

last: Enström

first: Carolina

last: Buizza

first: Gesine

last: Paul-Visse


title: Gene expression profile of T cells from Isocitrate Dehydrogenase (IDH) stratified human gliomas at single cell level

status: Public on Jun 29 2023

city: Houston

first: Jeffrey

middle: Andrew

last: How

state: TX

address: 1515 Holcombe Blvd. Unit 1362

department: Gyn Onc & Reproductive Med

country: USA

institute: The University of Texas MD Anderson Cancer Center

type: Expression profiling by high throughput sequencing

summary: The brain tumor immune microenvironment (TIME) continuously evolves during glioma progression, but only a limited view of a highly complex glioma associated immune contexture across isocitrate dehydrogenase mutation (IDH) classified gliomas is known. Herein, we present an unprecedentedly comprehensive view of T cells from brain TIME at single cell resolution, which served as part of our pan-cancer T cell atlas analysis.

overall_design:
The glioma associated CD45+ leukocyte were subjected to Fluorescence-activated cell sorting (FACS) from cryopreserved single cells. The leukocyte enriched single cell suspensions were obtained from freshly resected tumors of IDH-mutant primary (IMP; n=4), IDH-mutant recurrent (IMR; n=4), IDH-wild type primary (IWP; n=3), or IDH-wild type recurrent (IWR; n=4) glioma patients and quasi-normal non-glioma brain (NGB; n=2) from an epilepsy patient and a dysembryoplastic neuroepithelial tumor. T cells were digitally isolated from the single-cell RNA sequencing data based on the canonical lineage marker.

*** Raw data are not provided for this study. Raw data are protected by MD Anderson internal review board (IRB)-approved protocol numbers LAB03-0687, LAB04-0001 and 2012-0441 and Baylor College of Medicine IRB-approved protocol number H-13798 ***

first: Pravesh

last: Gupta

first: Minghao

last: Dang

first: Linghua

last: Wang

first: Krishna

last: Bhat


title: CDK4/6-MEK inhibition in MPNSTs causes plasma cell infiltration, sensitization to PD-L1 blockade, and tumor regression

city: Iowa City

first: Michael

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

summary: Malignant peripheral nerve sheath tumors (MPNSTs) are lethal, Ras-driven sarcomas that lack effective therapies. Ras effectors, CDK4/6 and MEK, were identified as rational targets for combination therapy from patient tumor analyses and preclinical drug studies. In MPNST cells, low-dose combinations of CDK4/6 and MEK inhibitors synergistically reactivated the retinoblastoma (RB1) tumor suppressor, induced cell death, and decreased clonogenic survival. In immune-deficient mice, dual CDK4/6-MEK inhibition slowed growth but did not shrink MPNSTs in 4 of 5 patient-derived xenografts (PDXs). By comparison, combination therapy of de novo MPNSTs in immunocompetent mice caused tumors to regress, delayed resistant tumor outgrowth, and improved survival relative to monotherapies. While drug-resistant tumors adopted an immunosuppressive microenvironment enriched with MHC II-low macrophages, drug-sensitive tumors that regressed contained plasma cells and increased T cell clustering. In other cancers, intratumoral plasma cells are associated with better response to immune checkpoint blockade (ICB). Impressively, CDK4/6-MEK inhibition sensitized MPNSTs to anti-PD-L1 ICB therapy with some mice displaying complete tumor ablation. These results reveal a novel plasma cell-associated immune response and extended antitumor activity of combined CDK4/6-MEK inhibition in MPNSTs, which dramatically enhanced the efficacy of ICB therapy. This work highlights promising, potentially curative treatment options for MPNSTs.

overall_design: We performed gene expression analysis of vehicle, combination-sensitive, and combination-resistant tumors.

first: Dawn

middle: E

last: Quelle

first: Jordan

middle: L

last: Kohlmeyer


title: Understanding Heterogeneity of Human Bone Marrow Plasma Cell Maturation and Survival Pathways by Single Cell Analyses [scVDJ-seq]

status: Public on Jun 28 2023

city: Atlanta

first: Frances

middle: Eun-Hyung

last: Lee

state: GA

address: 615 Michael Street, Suite 205

department: Department of Medicine

institute: Emory University

summary: Human bone marrow (BM) plasma cells are heterogeneous, ranging from newly arrived antibody-secreting cells (ASC) to long-lived plasma cells (LLPC). We provide single cell transcriptional resolution of 17,347 BM ASC from 5 healthy adults. Fifteen clusters were identified ranging from newly minted ASC (cluster 1) expressing MKI67 and high MHC Class II that progressed to late clusters 5-8 through intermediate clusters 2-4. Additional clusters included IgM-predominant ASC of likely extra-follicular origin; IFN-responsive; and high mitochondrial activity ASC. Late ASCs were distinguished by differences in G2M checkpoints, MTOR signaling, distinct metabolic pathways, CD38 expression, and utilization of TNF-receptor superfamily members. They mature through two distinct paths differentiated by the degree of TNF signaling through NFKB. This study provides the first single cell resolution atlas and molecular roadmap of LLPC maturation, thereby providing insight into differentiation trajectories and molecular regulation of these essential processes in the human BM microniche. This information enables investigation of the origin of protective and pathogenic antibodies in multiple diseases and development of new strategies targeted to the enhancement or depletion of the corresponding ASC.

overall_design: Expression profiling by high throughput sequencing


title: Peripheral blood cellular dynamics of Rheumatoid arthritis treatment informs about efficacy of response to disease modifying drugs.

city: Cambridge

first: Scott

last: Jelinsky

state: MA

address: 610 Main Street

department: Inflammation and Immunology

institute: Pfizer

summary: Samples from healthy blood donors, newly diagnosed RA patients, and established RA patients that had an inadequate response to MTX and were about to start tumor necrosis factor inhibitors (TNFi) treatment were collected before and after 3 months treatment.  We used in parallel a computational deconvolution approach based on RNA expression and flow cytometry to determine the relative cell-type frequencies

overall_design:
We included 53 DMARD treatment naïve early RA patients, 37 individuals who previously did not responded to MTX treatment and started TNFi treatment, and 30 age matched healthy controls at two timepoints separated by approximately 3 months.  Data was pooled into 10 groups into each cohort
***Submitter declares that European law does not allow the deposit of the raw data to GEO***

first: Leonid

last: Padyukov


title: Understanding Heterogeneity of Human Bone Marrow Plasma Cell Maturation and Survival Pathways by Single Cell Analyses [scRNA-Seq]


title: MBD2a-NuRD Binds to the Methylated γ-Globin Gene Promoter and Uniquely Forms a Complex Required for Silencing of HbF Expression

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: During human development, there is a switch in the erythroid compartment at birth that results in silencing of expression of fetal hemoglobin (HbF). Reversal of this silencing has been shown to be effective in overcoming the pathophysiologic defect in sickle cell anemia. Among the many transcription factors and epigenetic effectors that are known to mediate HbF silencing, two of the most potent are BCL11A and MBD2-NuRD. In this report we present direct evidence that MBD2- NuRD occupies the γ-globin gene promoter in adult erythroid cells and positions a nucleosome there that results in a closed chromatin conformation that prevents binding of the transcriptional activator, NF-Y. We show that the specific isoform, MBD2a, is required for the formation and stable occupancy of this repressor complex that includes BCL11A, MBD2a-NuRD and the arginine methyltransferase, PRMT5. The methyl cytosine binding preference and the arginine rich (GR) domain of MBD2a are required for high affinity binding to methylated γ-globin gene proximal promoter DNA sequences. Mutation of the methyl cytosine binding domain of MBD2 results in a variable but consistent loss of γ-globin gene silencing, in support of the importance of promoter methylation. The GR domain of MBD2a is also required for recruitment of PRMT5, which in turn results in placement of the repressive chromatin mark H3K8me2s at the promoter. These findings  2  support a unified model that integrates the respective roles of BCL11A, MBD2a-NuRD, PRMT5 and DNA methylation in HbF silencing.

overall_design: HUDEP-2 WT and MBD2KO groups

first: Shengzhe

last: Shang

first: Xia

last: Li

first: Alexander

last: Azzo

first: Tin

last: Truong

first: Charles

last: Lyons

first: Asit

middle: K

last: Manna

first: David

middle: C

last: Williams Jr.

first: Gordon

middle: D

last: Ginder


title: Understanding Heterogeneity of Human Bone Marrow Plasma Cell Maturation and Survival Pathways by Single Cell Analyses

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

overall_design: Refer to individual Series


title: Activating-transcription factor 3 stimulates follicle-stimulating hormone β transcription in vitro, but is dispensable for FSH production in murine gonadotropes in vivo

city: New York

first: Stuart

last: Sealfon

state: NY

address: One Gustave L. Levy Place

department: Department of Neurology

institute: Icahn School of Medicine at Mount Sinai

summary: Follicle-stimulating hormone (FSH), a dimeric glycoprotein produced by pituitary gonadotrope cells, regulates spermatogenesis in males and ovarian follicle growth in females. Hypothalamic gonadotropin-releasing hormone (GnRH) stimulates FSHβ subunit gene (Fshb) transcription, though the underlying mechanisms are poorly understood. To address this gap in knowledge, we examined changes in pituitary gene expression in GnRH-deficient mice (hpg) treated with a regimen of exogenous GnRH that increases pituitary Fshb but not luteinizing hormone β (Lhb) mRNA levels. Activating transcription factor 3 (Atf3) was among the most upregulated genes. ATF3 can heterodimerize with members of the AP-1 family to regulate gene transcription. Co-expression of ATF3 with JunB stimulated murine Fshb, but not Lhb, promoter-reporter activity in homologous LβT2 cells. ATF3 also synergized with a constitutively active activin type I receptor to increase endogenous Fshb expression in these cells. Nevertheless, FSH production was intact in gonadotrope-specific Atf3 knockout mice (cKO) and control littermates. Ovarian follicle development, ovulation, and litter sizes were also equivalent between genotypes. Testis weights and sperm counts did not differ between cKO and control males. Following gonadectomy, increases in LH secretion were enhanced in cKO animals. Though FSH levels did not differ between genotypes, post-gonadectomy increases in pituitary Fshb and gonadotropin α subunit expression were more pronounced in cKO mice.  These data indicate that ATF3 can selectively stimulate Fshb transcription in vitro but is not required for FSH production in vivo.

overall_design:
25 samples analyzed. 11 females, 14 males. 5-7 replicates per condition (sex/treatment)
*** Submitter declares access to the raw data was lost. ***

first: Carlos

middle: A

last: Alonso

first: Caroline

last: David

first: Chirine

last: Toufaily

first: Ying

last: Wang

first: Xiang

last: Zhou

first: German

last: Nudelman

first: Frederique

last: Ruf-Zamojski

first: Ulrich

last: Boehm

first: Daniel

middle: J

last: Bernard

first: Venugopalan

last: Nair


title: Immunoglobulin repertoires in mice carrying a knock-in human Cµ gene downstream of the IGH 3' regulatory region

city: Rennes

first: Delphine

last: Rossille

address: 2 avenue du Pr. Léon Bernard

country: France

institute: INSERM U1236-MOBIDIC

summary: To in-depth analyze the repertoire of B cells after the occurrence of recombination events joining SÙ to the IgH downstream regulatory region (3'RR)

overall_design: Spleen B cell RNA samples from knock-in mice, comparing the endogenous IgM µ heavy chain transcripts (VDJ spliced onto MmCµ), versus endogenous mouse spliced IgG2b gamma heavy chain transcripts (VDJ spliced to MmG2b), versus spliced VDJ-hCµ transcripts obtained after recombination close to the ectopic knock-in human Cµ gene

first: Michel

last: Cogné

last: ROSSILLE


title: RNA-seq and CUT&RUN of mouse prostate basal cell organoids

city: Beijing

first: wang

last: jiawen

address: 7 Science Park Road ZGC Life Science Park

country: China

institute: National institute of biological sciences


title: Reduced levels of ALS gene DCTN1 induce motor defects in Drosophila

city: Msida

first: Ruben

last: Cauchi

address: Biomedical Sciences Building

department: Physiology & Biochemistry

country: Malta

institute: University of Malta

summary: Amyotrophic lateral sclerosis (ALS) is a rapidly progressive neuromuscular disease that has a strong genetic component. Deleterious variants in the DCTN1 gene are known to be a cause of ALS in diverse populations. DCTN1 encodes the p150 subunit of the molecular motor dynactin which is a key player in the bidirectional transport of cargos within cells. Whether DCTN1 mutations lead to the disease through either a gain or loss of function mechanism remains unresolved. Moreover, the contribution of non neuronal cell types, especially muscle tissue, to ALS phenotypes in DCTN1 carriers is unknown. Here we show that gene silencing of Dctn1, the Drosophila main orthologue of DCTN1, either in neurons or muscles is sufficient to cause climbing and flight defects in adult flies. We also identify Dred, a protein with high homology to Drosophila Dctn1 and human DCTN1, that on loss of function also leads to motoric impairments. A global reduction of Dctn1 induced a significant reduction in the mobility of larvae and neuromuscular junction (NMJ) deficits prior to death at the pupal stage. RNA-seq and transcriptome profiling revealed splicing alterations in genes required for synapse organisation and function, which help explain the observed motor dysfunction and synaptic defects downstream of Dctn1 ablation. Our findings support the possibility that loss of DCTN1 function can lead to ALS and underscore an important requirement for DCTN1 in muscle in addition to neurons.

overall_design: RNA-seq of Drosophila melanogaster larvae (whole body) 96 hr after hatching from eggs for test (Dcnt1 whole body knockdown) and control genotypes in triplicates; the six samples were sequenced using a 100bp paired-end read Illumina HiSeq 2500 system.

first: Rebecca

last: Borg

first: Angie

last: Purkiss

last: Cacciottolo

first: Paul

last: Herrera


title: The angiogenic role of circRNA-007371 in liver fibrosis [RNA-Seq]

city: chengdu

first: shuaijie

last: qian

state: sichuan

address: NO. 1, 4th Keyuan Road, Chengdu,

institute: West China Hospital, Sichuan University

summary: Objective Circular RNAs (circRNAs) are covalently closed, endogenous non-coding RNAs. CircRNAs play a vital role in liver diseases, acting as microRNA (miRNA) sponges. However, the angiogenic role of circRNA remains unknown in liver fibrosis and is the focus of this study.  Methods Liver fibrosis was induced by thioacetamide (TAA), or carbon tetrachloride (CCl4) in mice. CircRNA-microarray, AGO2-RNA immunoprecipitation (RIP), and RNA-seq were utilized to explore the hepatic circRNAs profile. The qPCR and PCR-gel electrophoresis analysis were used to investigate the characterization of circRNA-007371. Liver tissues and EMOA murine endothelial cells were used to verify the angiogenic mechanism of circRNA-007371.  Results The increased collagen deposition, pseudolobule formation, and angiogenesis were observed in murine liver induced by TAA and CCl4. CircRNA-microarray in TAA-induced fibrotic murine liver indicated that the expression of circRNA-007371 was up-regulated. Moreover, AGO2-RIP and PCR analysis showed that circRNA-007371 had the characterization of circRNAs and played a role as competing endogenous RNAs (ceRNA) sponging miR-200a. In vitro, circRNA-007371 promoted the ability of migration, growth, and blood vessel formation in EMOA murine endothelial cells using wound healing and tube formation assay. The AGO2-RIP and RNA-sequencing analysis in overexpression circRNA-007371 EMOA murine endothelial cells demonstrated that circRNA-007371 upregulates the stromal antigen 1 (Stag1) via spouse of miR-200a and HIF-1 signaling pathway might participate in the angiogenesis.  Conclusions This study discovers that circRNA-007371, a novel ceRNA, is up-regulated, and enhances the angiogenesis via angiocrine role to regulate the STAG1-miR-200a-5p signaling pathway in liver fibrosis.

overall_design: 1. One liver fibrosis model was induced by intraperitoneal injection of thioacetamide (TAA) in C57BL/6J mice for 8 weeks. Control mice received the same volume of normal saline (NS). Another model was induced by intraperitoneal injection of carbon tetrachloride (CCl4) in C57BL/6J mice for 6 weeks. Control mice received the same volume of olive oil. 2. The mouse hemangioendothelioma endothelial cells (EOMA) were transfected with circRNA-007371 overexpression plasmid.

first: Chong

last: Zhao

first: Shuaijie

last: Qian

first: Yang

last: Tai

first: Chengwei

last: Tang

first: Zhiyin

last: Huang

first: Jinhang

last: Gao


title: MATR3-binding RNAs in ES cells [RIP-Seq]

city: Shanghai

first: Xuan

last: Cao

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health,  Chinese Academy of Sciences

summary: We performed RNA binding protein immunoprecipitation (RIP)  assay with anti-IgG/anti-MATR3 antibody. The  RNA libraries were constructed using rib-off and strand-specific kits. Next-generation sequencing (NGS) were performed to analyze MATR3-binding RNAs.

overall_design: Two replicates for each antibody (MATR3 and IgG)

first: Bo

last: Wen

first: Yuwen

last: Zhang


title: The transcriptome profile after antisense L1 ASO treatment  [ssRNA-Seq]

summary: We performed RNA-seq assay in Scramble ASO and antisense Mus1_L1 ASO treated AML12 cells to reveal the trscriptiome associated with MATR3 protein. The libraries were constructed by ribosome-depleted and strand-specific kits.

overall_design: Two replicates for each sample.


title: The angiogenic role of circRNA-007371 in liver fibrosis [circRNA Microarray]


title: The angiogenic role of circRNA-007371 in liver fibrosis

type: Non-coding RNA profiling by high throughput sequencing


title: MATR3 II


title: The angiogenic role of circRNA-007371 in liver fibrosis [RIP-Seq]


title: The nuclear matrix protein MATR3 maintains higher-order chromatin architecture II [Hi-C]

summary: The chromatin structure in eukaryotic nucleus is highly ordered and organized in hierarchical frameworks. We performed Hi-C assay in WT and MATR3-degradated mouse ES cells to reveal the MATR3's role in ES cells.


title: CUT&RUN of AR and beta-catenin for mouse prostate basal cell organoids

summary: To evaluated the chromatin binding of AR and beta-catenin in mouse prostate basal cell organoids

overall_design: CUT&RUN using AR and beta-catenin antibodies on mouse prostate basal cell organoids cultured under different conditions

first: Corrigan

last: Horton

first: Yueli

last: Liu

first: Jiawen

last: Wang

first: Zhu


title: Chemical inhibition of immune signaling rescues defects during heart development in Down syndrome via regulating canonical Wnt pathway

city: Aurora

first: Kunhua

last: Song

state: Colorado

institute: University of Colorado Anschutz Medical Campus

summary: Congenital heart defects (CHDs) are very frequent in children with Down syndrome (DS), the genetic condition caused by trisomy of chromosome 21 (T21). However, the mechanisms by which T21 causes susceptibility to CHDs are poorly understood. Here, using a combination of human induced pluripotent stem cell (iPSC)-based model and Dp(16)1Yey/+ (Dp16) a mouse model of DS, we identified downregulation of canonical Wnt signaling that is caused by increased dosage of interferon (IFN) receptors encoded on chromosome 21 (HSA21) as a causative factor of CHDs in DS. We differentiated human iPSCs derived from individuals with DS as well as CHDs (DS/CHD iPSCs), and controls (control iPSCs) into cardiac cells. We observed that T21 upregulates IFN signaling, downregulates the canonical WNT pathway, and impairs cardiac differentiation. Furthermore, genetic and pharmacological normalization of IFN pathways restored canonical WNT signaling and rescued defects during cardiac differentiation of DS/CHD iPSCs. Strikingly, treatment with an inhibitor of Janus kinase, which is activated by IFN receptor engagement normalized the canonical Wnt pathway and ameliorated CHDs in Dp16 embryos. Our findings provide new mechanisms underlying CHDs in DS, ultimately aiding the development of novel therapeutic strategies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Comparative gene expression profiling analysis of RNA-seq data for: 1) human cells derived from healty controls, patients with Down syndrome as well as congenital heart defects, with or without Wnt signaling activator (CHIR99021) and/or JAK inhibitor (JAKi, Tofacitinib) treatments by using the indicated dosage, harvested at different day points during cardiac differentiation as indicated; 2) E15.5 mouse hearts from WT, Dp16 with or without 10 mg/kg bodyweight/day of JAK inhibitor (JAKi, Tofacitinib) treatments from E6.5 to E14.5, low p-STAT1 indicated the p-STAT1 levels are comparable to WT without JAKi treatment, high p-STAT1 indicated the p-STAT1 levels are significantly higher than WT without JAKi treatment.

first: Congwu

last: Chi


title: RNA-seq of mouse prostate basal cell organoids treated under different androgen and Wnt signaling conditions

first: wang

last: jiawen

summary: To determine the role of Wnt and AR signaling pathway crosstalk on prostate basal stem cells, RNA-seq was performed for mouse prostate basal cell organoids treated under three conditions.

overall_design: Mouse prostate basal cells were flow-sorted and cultured as organoids under three treatment conditions, with three samples per condition. RNA-seq was performed for each sample.


title: More than a ligand: PD-L1 promotes oncolytic virus infection via a metabolic shift that inhibits the type I interferon pathway

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

country: Canada

institute: Ottawa Hospital Research Institute

summary: Targeting the PD-1/PD-L1 axis has transformed the field of immune-oncology. While conventional wisdom initially postulated that PD-L1 serves as the inert ligand for PD-1, an emerging body of literature suggests that PD-L1 has cell‑intrinsic functions in immune and cancer cells. In line with these studies, here we show that PD-L1 potently inhibits the type I interferon pathway in cancer cells. Hampered type I interferon responses in PD-L1-expressing cells resulted in enhanced infection with oncolytic viruses in cancer cells in vitro and in vivo. PD-L1 expression marks tumor explants from cancer patients that are best infected by oncolytic viruses. Agonistic antibodies targeting PD-L1 further reduced type I IFN responses and enhanced oncolytic virus infection. Mechanistically, PD-L1 suppressed type I interferon by promoting Warburg metabolism, characterized by enhanced glucose uptake and glycolysis rate. Lactate generated from glycolysis was the key metabolite responsible for inhibiting type I interferon responses and enhancing oncolytic virus infection in PD‑L1‑expressing cells. In addition to adding mechanistic insight into PD-L1 intrinsic function and showing that PD-L1 has a broader impact on immunity and cancer biology besides acting as a ligand for PD-1, our results will also help guide the numerous efforts currently ongoing to combine PD-L1 antibodies with oncolytic virotherapy in clinical trials.

overall_design: PolyA RNA-seq of wild-type and PD-L1-KO TRAMP2-C2 cells with and without infection with the oncolytic virus VSVdelta51-YFP at an MOI of 0.1 for 8 hours

middle: P

first: Jonathan

last: Hodgins

first: Michele

last: Ardolino


title: Genome-wide maps of chromatin state in AML12 cells [SAMMY-Seq]

summary: We performed SAMMY (Sequential Analysis of Macro-Molecules accessibilitY) chromatin fraction assay followed by next-generation sequencing in WT and MATR3-depleted AML12 cells to investigate the epigenetic landscape of AML12.

overall_design: SAMMY-seq analysis of WT and MATR3-depleted AML12 cells


title: The angiogenic role of circRNA-007371 in liver fibrosis [ncRNA-Seq]

first: shuaijie

last: qian

first: Chong

last: Zhao

first: Shuaijie

last: Qian

first: Yang


title: Effects of triiodothyronine and/or Irisin on human subcutaneous adipocytes: a global transcriptome analysis

city: Botucatu

first: Miriane

last: Oliveira

address: District of Rubião Jr

country: Brazil

institute: Botucatu Medical School, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.

summary: In order to investigate, at the mRNA level, the signaling pathways through which triiodothyronine (T3) and irisin (I) affects Human subcutaneous adipocytes function, human Cultured Human subcutaneous preadipocytes were differentiated into mature adipocytes, which were cultured with T3 and/or Irisin, the control group was without treatment. RNA-Seq was performed using Illumina platform, and differential gene expression was assessed with DESeq2. Among differentially expressed genes, enrichment analysis was performed for biological processes against the Gene Ontology Consortium database, using both ClusterProfiler R package and STRING. Grant 2016/03242-3, São Paulo Research Foundation (FAPESP). Grant 409438/2016, National Council for Scientific and Technological Development (CNPq).

overall_design: The study consists of four groups with three biological replicates each. Human subcutaneous adipocytes  cells were cultured for 24h with  T3 (10nM) or Irisin (20nM) and T3 plus Irisin (T3+Irisin), for the without treatment control group.

first: Célia

middle: R

last: Nogueira


title: Genome-wide maps of chromatin state in AML12 cells [ChIP-Seq]

first: Xuan

last: Cao

summary: We performed chromatin Immunoprecipitation (ChIP)  assay followed by next-generation sequencingwith H3K9me3 and H3K27ac antibodies in WT AML12 cells to investigate the epigenetic landscape of AML12. And we performed ChIP-seq using H3K27me3 antibody in WT and MATR3-depleted AML12 cells.

overall_design: Two replicates for each antibody and each sample.

first: Bo

first: Yuwen


title: Transcriptional alteration in malaria parasite after disruption of PfPRMT5 [Array]

city: Tampa

first: JUN

last: MIAO

state: Florida

address: 3720 Spectrum Boulevard, MDC84

department: Internal Medicine

institute: University of South Florida

summary:
Purpose: this study is to analyze the change of overall transctiption after disruption of Protein Arginine Methyltranferase 5 (PRMT5) in Plasmodium falciparum.
Methods: In this study, the transcriptomes of a PfPRMT5 gene knockout (KO) parasite line with its wildtype control were analyzed a custom-desinged Agilent microarray.Total RNA were harvested from the asexual parasites at four stages (ring, early trophozoite, late trophozoite, and schizont)(12h, 24h, 36h, and 46h post-invasion) using the Quick-RNA MiniPrep kit (Zymo Research).

overall_design: A three replicates of 8-chip study using total RNA recovered from a PfPRMT5 gene knockout (KO) parasite line with its wildtype control at ring (12h), early trophozoite (24h), late trophozoite (36) and schizont (46) stage.  The chip used in this stury was a custom designed microarray by agilent eArray (array name: MALARIAARRAY_JM, Design ID: 048532, Design format: 4 X 44K, Control grid: IS-45220-4-V1_4x44K_GX_EQC_V20060608)

first: Jun

last: Miao

first: Liwang

last: Cui


title: Transcriptome of ΔPfPRMT5 parasite during malaria parasite asexual development [PRMT5_RNAseq]

summary:
Purpose: this study is to analyze the change of RNA splicing events after disruption of Protein Arginine Methyltranferase 5 (PRMT5) in Plasmodium falciparum.
Methods: In this study, the transcriptomes of a PfPRMT5 gene knockout (KO) parasite line with its wildtype control were analyzed by RNAseq.Total RNA were harvested from the asexual parasites at four stages (ring, early trophozoite, late trophozoite, and schizont)(12h, 24h, 36h, and 46h post-invasion) using the Quick-RNA MiniPrep kit (Zymo Research). RNA sequencing libraries were prepared using the KAPA stranded RNA-seq library preparation kit (Roche) with 500 ng RNA from each sample. Illumina adapter sequence removal and quality trimming of reads were performed using Trimmomatic. Only reads that had a minimum length of 50 base pairs were retained. Reads were then mapped to the P. falciparum 3D7 strain reference genome with HISAT2.
Results: This RNAseq analysis with strand-specific mRNA libraries from both ΔPfPRMT5 and WT lines showed that >90% of sequencing reads were of high quality for mapping to the P. falciparum genome with nearly 40 times of coverage. This allows us to analyze the change of alternative splicing events (alternative 5' splice site, alternative 3' splice site, retained intron and skipped exon). 800, 1056, 479, and 1158 alternative splicing events (alternative 5' splice site, alternative 3' splice site, retained intron and skipped exon) were altered in the DPfPRMT5 parasite line as compared to the WT line at four development stages, respectively (unpublished data).
Conclusions: Collectively, this RNAseq provide a dataset for analysis of abnormal RNA splicing events in the ΔPfPRMT5 parasites.

overall_design: Transcriptome of ΔpfPRMT5 parasites at four developmental stages for in-depth RNA splicing analysis


title: Chromatin profiling of H3R2me2s in human malaria parasite

summary:
Purpose: this study is to analyze the chromatin landscape of H3R2mes in Plasmodium falciparum.
Methods: In this study, H3R2me2s enrichment in the chromatin of wildtype parasite at schizont stage was analyzed by Cleavage Under Targets and Tagmentation (CUT&Tag) coupled with next generation sequencing (CUT&Tag-seq). Synchronized WT 3D7 at 40–46 hpi schizonts were harvested and fixed with 1% formaldehyde for 1 min at room temperature, followed by lysis with 0.06% saponin. The parasite pellets were suspended in 100 μl nuclear extraction buffer (20 mM HEPES–KOH pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol, 0.5 mM Spermidine, 1x EDTA-free Protease Inhibitor cocktail). Ten μl of activated Concanavalin A-coated magnetic beads (EpiCypher # 21-1401) were added to each sample (~0.5 × 106 nuclei) and incubated for 10 min. The bead-bound nuclei were resuspended in 50 μl Antibody150 buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1× protease inhibitor cocktail, 0.01% digitonin, 2 mM EDTA) containing 0.5 μg of rabbit anti-H3R2me2s (Epigentek #A-3705-050) as the primary antibody or rabbit IgG (Cell Signaling Technology #2729S) serving as a control.  The primary antibody was then removed, and nuclei were then incubated with 0.5 μg of the secondary antibodies in 50 μl of Digitonin150 buffer (Antibody150, no EDTA) at room temperature for 30 min.  The secondary antibodies were mouse anti-rabbit IgG (Invitrogen #31213). The nuclei were washed thrice with 200 μl Digitonin150 Buffer for 5 min to remove unbound antibodies and finally resuspended in 50 μl Digitonin300 Buffer (Digitonin150 but with 300 mM NaCl). Then, 2.5 μl of CUTANA pAG-Tn5 (EpiCypher #15-1017) were added to each reaction at room temperature for 1 h. The nuclei were washed thrice for 5 min in 200 μl Digitonin300 Buffer to remove the unbound pA-Tn5. Next, the nuclei were resuspended in 50 μl Tagmentation buffer (10 mM MgCl2 in Digitonin300) and incubated at 37 °C for 1 h. The beads were washed with 50 µl TAPS buffer (10 mM TAPS, pH 8.5, 0.2 mM EDTA), mixed with 5 µL SDS release buffer (10 mM TAPS pH 8.5; 0.1% SDS) to quench tagmentation, and then incubated for 1 hr at 58ºC to release tagmented chromatin into solution. Finally, 15 µl of 0.67% Triton-X was added to each reaction to quench SDS. PCR with appropriate barcoded primers was performed using the CUTANA High Fidelity 2x PCR Master Mix (EpiCypher #15-1018) according to the manufacturer's recommendations. Amplified DNA libraries were captured by incubating with 1.3 × Kapa pure beads (Roche #KK8001) according to the manufacturer's recommendations, and next-generation sequencing was performed on the NextSeq 550 platform. The reads of CUT&Tag-seq from three biological replicates were mapped to the P. falciparum genome (PlasmoDB Release 39.0) by using BWA (Li and Durbin 2009) after FastQC quality control. The peak calling was finished by MACS2 version 2.2.7.1 with parameters ‘callpeak -f BAMPE’ and a q-value cutoff of 0.05.
Results: The three replicates of CUT&Tag-seq using nuclei from the schizont stage showed high reproducibility, with correlation coefficients of ~0.8. Peak calling using criteria of presence in at least two of three replicates with at least 50% overlap of the peaks identified 1629 H3R2me2s signals, distributed among the 14 chromosomes. Among these peaks, 57% (927) are localized at 5’ UTR regions of 791 genes, 35% (577) at coding regions of 470 genes, and 8% (125) at 3’ UTR regions of 115 genes. The peaks are ~17.44 bp wide and ~1265 bp from the ATG sites. Comparing the transcriptome data showed genes with H3R2me2s enrichment in the 5’ UTRs showed significantly higher expression than other genes in the genome, suggesting that H3R2me2s is associated with gene activation. In addition, H3R2me2s peaks were highly co-localized with the active mark H3K9Ac, H2A.Z, and H3K4me3, further implying H3R2me2s as a euchromatin mark. Gene ontology (GO) enrichment analysis revealed a multitude of cellular pathways, including merozoite invasion, transcription, translation, stress response, cell cycle, schizogony, cell adhesion, exit from RBC, vesicle transport, signal transduction, DNA repair, and telomere organization, which are potentially regulated by this euchromatic mark.
Conclusions: Collectively, H3R2me2s is a active chromatin mark and regulates invasion and other important processes in human malaria parasite.

overall_design: H3R2me2s chromatin profiles in 3D7 (WT)at schizont stage were generated by CUT&Tag-seq, in triplicate


title: Single cell RNA-Seq of mouse bone marrow-derived hematopoietic stem cells after 7-days in viro culture

city: Tianjin China

first: Miner

last: Xie

address: No.288, Nanjing Road

institute: State Key Laboratory of Experimental Hematology

summary: Hematopoietic stem cells (HSCs) are cells able to self-renew and differentiate into all blood lineages. We previously have performed serum-free single-cell culture for HSC1 (CD201+CD150+CD48-CD41-CD34-LSK) and competitive repopulation with cultured cells. Single highly purified HSC1 were cultured with stem cell factor (SCF), SCF + G-CSF, or SCF + thrombopoietin (TPO) for 7 days. SCF directly acted on HSC1 and maintained their long-term multilineage reconstitution after serial transplantation. Compared with SCF alone, SCF+G-CSF neither enhanced the number of divisions of HSC1 nor enhanced their levels of reconstitution after serial transplantation. SCF+TPO significantly increased the number of divisions of HSC1. The levels of reconstitution of each lineage in SCF + TPO culture were significantly increased at early months after primary transplantation, however, it gradually decreased after secondary transplantation. Therefore, we performed single-cell RNA-Seq to examine the gene expression of cells cultured with different cytokine combinations.

overall_design: scRNA-Seq were successfully performed on 43,48, and 48 HSC1 cells after cultured with SCF, SCF+G-CSF, and SCF+TPO, respecitvely

first: Peng

last: Wu

first: Fang

last: Dong

first: Caiying

last: Zhu

first: Chenchen


title: Gene expression in the hTSCs of si-NC and si-PR-SET7 KD hTSCs

city: Xiamen

first: Jinhua

last: Lu

address: No. 4221, Xiangan Road, Xiangan District, Xiamen city

institute: Xiamen University

summary: To detect the gene profiles in si-NC and si-PR-SET7 KD hTSCs,  hTSCs are collected and subjected to RNA-Seq. After aligned to mouse hg38 by HISAT2, RPKM value was calculated by Edger. Our results show that PR-SET7 as the key regulator for hTSCs. There are also some  genes differentially expressed after  PR-SET7 KD, some of the DEGs were further confirmed by qPCR,  the DEGs were associated with viral mimic inflammatory activities, antiviral innate immune response, genomic instability, and programmed cell death, indicating the essential role of PR-SET7. This RNA-Seq data provides fundamental information for our further physiological study of PR-SET7.

overall_design: Total RNAs in hTSCs from two independent experiments were extracted by TRIzol and  subjected to RNA-Seq by MGISEQ 2000. The expression of level of each gene is normalized to RPKM.


title: The transcriptome profile before and after knocking-down of nuclear matrix protein MATR3  [ssRNA-Seq]

summary: We performed RNA-seq assay in WT and MATR3-depleted AML12 cells to reveal the trscriptiome associated with MATR3 protein. The libraries were constructed by poly-A enriched and strand-specific kits.

last: Wen

last: Zhang


title: Transcriptome analysis of Aofus3 in nematode-trapping fungus Arthrobotrys oligospora

city: Yunnan Kunming

first: xie

middle: mei

last: hua

state: Yunnan

address: 121 street

institute: Yunnan university

summary: Transcriptomic analysis revealed that differentially expressed genes in the absence of Aofus3 were involved in cell fusion, repair, and cellcommunication during trap formation.

overall_design: WT and ΔAofus3 strains grown on cellophane-overlaid PDA plates at 28°C for 5 days. Approximately 600 nematodes were then added to each plate for 0, 12, 24, and 36 h of induction, three replicates were used for each sample. After collecting the samples, RNA was extracted with the AxyPrep Multisource RNA Miniprep Kit (Axygen, Jiangsu, China), and then sent to Majorbio Bio-Pharm Technology Co., Ltd. (Shanghai, China) to construct the transcriptome of WT and ΔAofus3 strains. The final cDNA library was sequenced on an Illumina Novaseq 6000 platform.

first: Meihua

last: Bai

first: Qianqian

last: Liu

first: Jingkui

last: Yang


title: MATR3-binding RNAs in AML12 cells [RIP-Seq]

summary: We performed RNA binding protein immunoprecipitation (RIP)  assay with anti-IgG/anti-MATR3 antibody. The  RNA libraries were constructed using rib-off and strand-specific kits. Next-generation sequencing (NGS) were performed to analyze MATR3-binding RNAs.


title: The nuclear matrix protein MATR3 maintains higher-order chromatin architecture [Hi-C]

summary: The chromatin structure in eukaryotic nucleus is highly ordered and organized in hierarchical frameworks. We performed Hi-C assay in WT and MATR3-depleted AML12 cells to reveal the MATR3's role in AML12 cells.


title: Analysis of HCV-induced miRNA expression

status: Public on Jun 27 2023

city: Kaohsiung

first: Shu-Chi

last: Wang

address: No.100 Shiquan Road

department: Medical Laborstory Science and Biotechnology

country: Taiwan

institute: Kaohsiung Medical University

summary: We performed miRNA array analysis for S-HCV (short-term HCV), L-HCV (long-term HCV) and control (uninfected Huh751), total for 3 samples to identify miRNA candidates in HCV-related HCC.

overall_design: To understand the effects of HCV infection on miRNA expression, we used miRNA array expression profiling as a discovery platform to identify HCV induced miRNA and their potential role in HCV related HCC. Huh751 cells were infected with HCV-JFH1 in vitro and differentially expressed (DE) miRNAs with a >3.2-fold change (p < 0.05) between samples (S-HCV, L-HCV) and control (Huh751). A total of 73 miRNA were identified  as DE. HCV induced miRNA expression in JFH1 infected Huh751 in S-HCV (5-days)  and L-HCV (30-days).


title: Aspirin Challenge–Induced Genome-Wide DNA Methylation Profile of Peripheral Blood Lymphocytes in Aspirin-Exacerbated Respiratory Disease

city: Bucheon

first: Jong Uk

last: Lee

address: 170, Jomaru-ro, Wonmi-gu

country: South Korea

institute: Soonchunhyang University Bucheon Hospital

type: Methylation profiling by genome tiling array

summary: Oral aspirin challenge may induce different global CpG methylation patterns between  aspirin-exacerbated respiratory disease (AERD) and aspirin-tolerant asthma (ATA), which may affect gene expression several hours later. Therefore, in the present study, we compared global CpG methylation profiles before and after an oral aspirin challenge in patients with asthma. In addition, we compared differences in methylation profiles between AERD and ATA using an Illumina 860K Infinium Methylation EPIC BeadChip array platform, which had greater coverage than in the previous study (26,485 CpGs) to discover new methylated CpGs in PBLs associated with aspirin-induced bronchospasm.

overall_design: Genomic DNA obtained from peripheral blood mononuclear cells from patients with AERD and ATA.

first: Jong-Uk

first: Choon-Sik

last: Park


title: Dendritic cells mediated by small extracellular vesicles derived from MSCs attenuated the ILC2 activity in patients with allergic rhinitis

city: GUANGZHOU

first: xiaoqing

state: Guangdong

address: 58 Zhongshan Road II, , Guangzhou

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: Mesenchymal stromal cells-derived small extracellular vesicles (MSC-sEVs) have recently attracted considerable attention because of their therapeutic potential in various immune diseases. We previously reported that MSC-sEVs could exert immunomodulatory roles in allergic airway inflammation by regulating group 2 innate lymphoid cell (ILC2) and dendritic cell (DC) functions. Therefore, this study aimed to investigate the therapeutic effects of MSC-sEVs on mature DC (mDC)-ILC2 interplay in allergic rhinitis (AR). Here, we isolated MSC-sEVs from induced pluripotent stem cells (iPSC)-MSCs using anion-exchange chromatography for the generation of sEV-mDCs. sEV-mDCs were co-cultured with peripheral blood mononuclear cells (PBMCs) from patients with AR or purified ILC2s. The levels of IL-13 and GATA3 in ILC2s were examined by flow cytometry. Bulk RNA-sequence for mDCs and sEV-mDCs was employed to further probe the potential mechanisms, which were then validated in the co-culture systems.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data for human mDC and MSC-sEV mediated sEV-mDC

first: Xiaoqing

first: Yaqi

last: Peng

first: Qingling

last: Fu


title: Small extracellular vesicles from spared nerve injury model and sham control mice differentially regulate gene expression in primary microglia

city: Philadelphia

first: Seena

last: Ajit

state: PA

department: Pharmacology & Physiology

institute: Drexel University

summary: Nerve injury outcomes might be predicted by examining small extracellular vesicles  (sEVs) in circulation, as their biomolecular cargo facilitates cellular communication and  can alter transcriptional state and behavior of recipient cells. We found that sEVs from  the serum of spared nerve injury (SNI) model male mice had seven differentially  expressed miRNAs compared to sEVs from sham-operated control mice four weeks  post-surgery. We investigated how these sEVs alter transcription in primary cortical  microglia, a crucial mediator of neuropathic pain, using RNA sequencing. While the  uptake of sEVs from both SNI model and sham groups changed gene expression in  microglia compared to PBS treatment, sEVs from the sham group induced a more  drastic change, particularly in genes involved in immune response. This was  recapitulated by increased levels of pro-inflammatory cytokines and chemokines in  microglia incubated with sEVs from sham control compared to sEVs from SNI model,  naïve mice, or PBS. However, treating microglia with sEVs from female mice showed  that serum sEVs derived from female SNI mice but not from female sham mice induced  a more pronounced microglial secretion of pro-inflammatory mediators. Our data  demonstrate that the molecular changes induced by sham surgery injuring skin and  muscles are reflected in circulating sEVs in male mice four weeks later. Thus, when  using sEVs from sham mice as control in comparative mechanistic studies after nerve  injury, sex of mice should be taken into consideration.

overall_design: Comparative expression profiling using RNA-seq in primary cortical microglia treated with serum-derived small extracellular vesicles (sEVs) from spared nerve injury model and sham control mice.

first: Xuan

last: Luo

first: Renee

last: Jean-Toussaint


title: Effects of Lithospermum erythrorhizon on gut health and growth performance of pearl gentian grouper based on Transcriptome

city: Qinzhou City

first: Xin

address: 12 Binhai Avenue, Qinnan District, Qinzhou City, Guangxi, China

institute: Beibu Gulf University

summary: The purpose of this study is to explore the effect of adding Lithospermum purpurea to the diet of soybean meal instead of 50% fish meal on the intestinal health of pearl gentian Grouper through Transcriptome

sample_organism: Epinephelus fuscoguttatus x Epinephelus lanceolatus

overall_design: Comparative gene expression profiling analysis of RNA-seg data for FM group, SBM group , and Drug group

first: Xiaohui

last: Cai

first: Yingrui

last: Wu

first: Yinhui


title: Dissecting aortic aneurysm in Marfan syndrome is associated with losartan-sensitive transcriptomic modulation of aortic cells

city: New York

first: Yifei

last: Sun

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: To improve our limited understanding of the pathogenesis of thoracic aortic aneurysm (TAA) leading to acute aortic dissection, we used single-cell RNA sequencing to profile disease-relevant transcriptomic changes of aortic cell populations in a well-characterized mouse model of the most commonly diagnosed form of Marfan syndrome (MFS). As result,MFSmod were identified only in the aorta of Fbn1mgR/mgR mice. In situ hybridizations of diagnostic transcripts located MFSmod cells to the intima of Fbn1mgR/mgR aortas.  Consistent with angiotensin II type I receptor (At1r) contribution to TAA development, MFSmod cells were absent in the aorta of Fbn1mgR/mgR mice treated with the At1r antagonist losartan. Altogether, our findings indicate that a discrete dynamic alteration of aortic cell identity is associated with dissecting TAA in MFS mice and increased risk of aortic dissection in MFS patients.

overall_design: Hypomorphic Fbn1mgR/mgR mice were routinely backcrossed for 10 generation on the C57BL/6J background. Mutant mice and WT littermates were euthanized to harvest aortic specimens spanning from immediately above the aortic root to immediately before the brachiocephalic artery.Aortic tissues of each genotype and treatment were pooled together, cleaned, minced and digested to make single-cell suspensions, then immediately processed according to manufacturer’s instructions.

first: Keiichi

last: Asano

first: Lauriane

last: Sedes

first: Anna

last: Cantalupo

first: Jens

last: Hansen

first: Ravi

last: Iyengar

first: Francesco

last: Ramirez


title: Single-cell transcriptomic analysis links non-myelinating Schwann cells to pro-inflammatory response in the lung

city: South San Francisco

first: Josh

last: Kaminker

state: CA

address: 1 DNA Way

department: OMNI Bx, gRED

institute: Genentech Inc

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

overall_design: Refer to individual Series


title: Gene expression in the mTSCs of WT and Pr-set7 KO mTSCs

first: Jinhua

last: Lu

summary: To detect the gene profiles in WT and Pr-set7 KO mTSCs, mTSCs are collected and subjected to RNA-Seq. After aligned to mouse mm10 by HISAT2, RPKM value was calculated by Edger. Our results show that Pr-set7 as the key regulator for mTSCs. There are also some  genes differentially expressed after Pr-set7 KO, some of the DEGs were further confirmed by qPCR, the DEGs were associated with viral mimic inflammatory activities, antiviral innate immune response, genomic instability, and programmed cell death,  indicating the essential role of Pr-set7. This RNA-Seq data provides fundamental information for our further physiological study of Pr-set7.

overall_design: Total RNAs in mTSCs from two independent experiments were extracted by TRIzol and  subjected to RNA-Seq by MGISEQ 2000. The expression of level of each gene is normalized to RPKM.


title: ChIP_Seq analysis in cultured mTSC cells with or without Dox

summary: To detect the direct target genes of H4K20me1, H4K20me3, and H3K4me3  in mTSCs, mTSCs with or without Dox are collected and subjected to ChIP-Seq. After aligned to mouse mm10 by HISAT2, peaks are called by MACS2. Our results show that methylation of H4K20 mediated by Pr-set7 as the key regulator of mTSCs, indicating the essential role of Pr-set7. This ChIP-Seq data provides fundamental information for our further physiological study of Pr-set7.

overall_design: ChIP was performed according to the reported previousl with slight modification. Briefly, about 2x106 TS cells were cross-linked with 1/15 volume of 16% formaldehyde (CST) at room temperature for 10 minutes and quenched with 1/10 volume of 1.25 M glycine for 15 minutes on ice. Cell lysate in lysis buffer III were sonicated using Bioruptor pico (Diagenode) and then incubated with 4 µg antibody overnight at 4℃ with rotation. Immunoprecipitated complexes were collected with 15 µl Protein A Dynabeads (Invitrogen, 10002D) for 1 hour at 4℃ with rotation. Subsequently, beads were washed sequentially once with low-salt buffer, twice with high-salt buffer, once with LiCl buffer, twice with TE, and then eluted in 400 µl of elution buffer for 30 min at 65℃. The eluates were incubation at 65℃ for 8 h to reverse the cross-linking. Next, eluates were treated with proteinase K for 1 h at 55℃ and then RNase A for 30 min at 37℃ before DNA was extracted and purified. The ChIP libraries were prepared using KAPA HyperPrep Kits (Roche, 07962347001) and then run on the Illumina sequencer Hiseq-Xten PE150.


title: Hepatic stellate cells maintain liver homeostasis through paracrine neurotrophin-3 signaling that induces hepatocyte proliferation

first: Kemal

middle: Marc

last: Akat

address: 1230 York Avenue

institute: The Rockefeller University

summary: Organ size is maintained by the controlled proliferation of distinct cell populations. In the mouse liver, hepatocytes in the midlobular zone that are positive for cyclin D1 (CCND1) repopulate the parenchyma at a constant rate to preserve liver mass. Here, we investigated how hepatocyte proliferation is supported by hepatic stellate cells (HSCs), pericytes that are in close proximity to hepatocytes. We used T cells to ablate nearly all HSCs in the murine liver, enabling the unbiased characterization of HSC functions. In the normal liver, complete loss of HSCs persisted for up to 10 weeks and caused a gradual reduction in liver mass and in the number of CCND1+ hepatocytes. We identified neurotrophin-3 (Ntf-3) as an HSC-produced factor that induced the proliferation of midlobular hepatocytes through the activation of tropomyosin receptor kinase B (TrkB). Treating HSC-depleted mice with Ntf-3 restored CCND1+ hepatocytes in the midlobular region and increased liver mass. These findings establish that HSCs form the mitogenic niche for midlobular hepatocytes and identify Ntf-3 as a hepatocyte growth factor.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data from whole liver of hepatic stellate cell depleted cells and controls.

Grant information:
ID: RSG-22-061-01-MM
Title: Hepatic Stellate Cells in Liver Cancer
Grantee: Youngmin Anna Lee
Funding source: American Cancer Society

middle: M

first: Youngmin

last: Lee


title: Anthocyanin transcriptional profile and pigmentation pattern in the purple tomato fruit in response to light

city: Rio de Janeiro

first: Luis

middle: Willian

last: Pacheco Arge

state: Rio de Janeiro

address: Av. Carlos Chagas Filho, 373

department: Genetica

institute: UFRJ

summary: Anthocyanins are specialized plant metabolites with significant dietary value due to their antioxidant and anti-inflammatory properties. Extensive research has indicated that dietary intake of these phenolic compounds contributes to preventing various chronic diseases. Consequently, incorporating anthocyanin-rich foods into one's diet, particularly from natural sources, is highly beneficial. The tomato (Solanum lycopersicum) is the most consumed vegetable worldwide, making it an excellent candidate for anthocyanin-enrichment strategies. The activation of anthocyanin biosynthesis is light-dependent in tomato, but this mechanism has not been entirely characterized. In this study, a purple tomato line in the cv. Micro-Tom (MT-Aft/atv/hp2) was utilized to investigate cyanic fruits developed under varying light conditions. This genotype is derived from natural genetic variation and exhibits anthocyanin accumulation starting early in fruit development. Transcriptional analyses of the fruit peel (exocarp or epicarp) and flesh (mesocarp) revealed that the bHLH transcription factor SlAN1 (Solyc09g065100) is the limiting factor for anthocyanin accumulation in both tissues. In this genotype, the absence of anthocyanin accumulation in the flesh results from the sun-blocking effect of the cyanic epicarp on the mesocarp, preventing light from penetrating deeper into the fruit during its development. This research enhances our comprehension of the genetic and environmental regulation of anthocyanin accumulation in fruit tissues, offering valuable insights for plant breeding and human nutrition.

overall_design: Gene expression analysis of tomato tissues (epicarp and mesocarp) developed under dark conditions followed by light exposition to evaluate the regulatory mechanism of anthocyanin accumulation in the tissues.

last: Arge


title: Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex

city: Seattle

first: John

middle: Kenneth

last: Mich

state: WA

address: 615 Westlake Ave N

institute: Allen Institute for Brain Science

summary: Viral genetictools that target specificbraincell types could transform basicneuroscienceand targeted gene therapy. Here, we use comparative open chromatin analysis to identify thousands of human-neocortical-subclass-specific putative enhancers from across the genome tocontrol gene expressionin adeno-associated virus (AAV) vectors. The cellular specificity of reporter expression from enhancer-AAVs is established by molecular profiling after systemic AAV delivery in mouse. Over 30% of enhancer-AAVs produce specific expression in the targeted subclass, including both excitatory and inhibitory subclasses. We present a collection ofParvalbumin(PVALB) enhancer-AAVs that show highly enriched expression not only in cortical PVALB cells but also in some subcortical PVALB populations. Five vectors maintain PVALB-enriched expression in primateneocortex. These results demonstrate how genome-wide open chromatin data mining and cross-species AAV validation can be used to create the next generation of non-species-restricted viral genetic tools.

overall_design:
Single-cell RNA-seq on flow-sorted enhancer-AAV-labeled transgene-expressing cells from 33 mouse brains.  From each mouse brain up to 48 individual cells were profiled by SMARTer single-cell RNA-seq.
These data are part of the study located at https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002292.v1.p1.

first: Lucas

middle: T

last: Graybuck

first: Erik

last: Hess

first: Joseph

last: Mahoney

first: Yoshiko

last: Kojima

first: Yi

last: Ding

first: Saroja

last: Somasundaram

first: Jeremy

last: Miller

first: Brian

last: Kalmbach

first: Cristina

last: Radaelli

first: Bryan

middle: B

last: Gore

first: Natalie

last: Weed

first: Victoria

last: Omstead

first: Yemeserach

last: Bishaw

first: Nadiya

middle: V

last: Shapovalova

first: Refugio

last: Martinez

first: Olivia

last: Fong

first: Shenqin

last: Yao

first: Marty

last: Mortrud

first: Peter

last: Chong

first: Luke

last: Loftus

first: Darren

last: Bertagnolli

first: Jeff

last: Goldy

first: Tamara

last: Casper

first: Nick

last: Dee

first: Ximena

last: Opitz-Araya

first: Ali

last: Cetin

first: Kimberly

last: Smith

first: Ryder

last: Gwinn

first: Charles

last: Cobbs

first: Andrew

last: Ko

first: Jeffrey

middle: G

last: Ojemann

first: C

last: Keene

first: Daniel

last: Silbergeld

first: Susan

last: Sunkin

first: Viviana

last: Gradinaru

first: Gregory

last: Horwitz


title: Several key elements in the pathogenesis of severe udder cleft dermatitis as revealed by RNA transcriptomics

city: Gent

first: Anne-Sofie

last: Vermeersch

address: Ottergemsesteenweg 46

country: Belgium

institute: Ghent University

summary: This study is the first to investigate the transcriptomic changes occurring in severe udder cleft dermatitis lesions (UCD) in Holstein-Friesian cows. An examination of the gene expression levels in natural UCD lesions and healthy udder skin through RNA Seq-Technology provided a deeper insight into the inflammatory pathways associated with this disease. A clear distinction between the gene expression patterns of UCD lesions and healthy skin was shown in the principal component analysis. Genes coding for inflammatory molecules were upregulated such as the chemokines C-X-C motif ligand 2 (CXCL2), 5 (CXCL5) and 8 (CXCL8), and C-C motif ligand 11 (CCL11). Moreover, the genes coding for the multifunctional molecules ADAM12 and SLPI were amongst the highest upregulated ones, whereas the most downregulated genes included the ones coding for keratins and keratin-associated molecules. Predominantly inflammatory pathways such as the chemokine signaling, cytokine receptor interaction and IL-17 signaling pathway were significantly upregulated in the pathway analysis. These results point towards a fulminant, dysregulated inflammatory response concomitant with a disruption of the skin barrier integrity and a hampered wound repair mechanism in severe UCD lesions.

overall_design: Ten samples of severe udder cleft dermatitis were compared with 5 healthy udder skin tissue samples with RNA sequencing of the host genome (DGE analysis).

first: Peter

last: Geldhof

first: Richard

last: Ducatelle

first: Mohsin

last: Ali

first: Yannick

last: Gansemans

first: Filip

last: van Nieuwerburgh

first: Dieter

last: Deforce

first: Geert

last: Opsomer

first: Jozefien

last: Callens


title: Effect of CXCL4 on TLR9-induced B cells

first: HSS Genomics

last: Research Center

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

summary: CXCL4 is a cationic peptide that binds to TLR9-ligand oligonucleotide, resulting in an inhibition of TLR9 response in B cells

overall_design: Examination of 2 different histone modifications in Neural progenitor cells.

first: M

last: Ah Kioon

first: D

last: Oliver

first: F

last: Barrat


title: Nitrogen-regulated antisense transcription in the adaptation to nitrogen deficiency in Nostoc sp. PCC 7120

city: Freiburg im Breisgau

first: Manuel

last: Brenes-Álvarez

address: Schänzlestraße 1

department: Genetics and Experimental Bioinformatics

country: Germany

institute: University of Freiburg

summary: Transcriptomic analyses using high-throughput methods have revealed abundant antisense transcription in bacteria. Most frequently, antisense transcription is due to the overlap of mRNAs with long 5’ regions or 3’ ends that extend beyond the coding sequence. In addition, antisense RNAs that do not contain any coding sequence are also observed. Nostoc sp. PCC 7120 is a filamentous cyanobacterium that, under nitrogen limitation, behaves as a multicellular organism with division of labor among two different cell types that depend on each other, the vegetative CO2-fixing cells and the nitrogen-fixing heterocysts. Differentiation of heterocysts depends on the global nitrogen regulator NtcA and requires the specific regulator HetR. To identify antisense RNAs potentially involved in heterocyst differentiation we performed an RNA-Seq analysis of cells subjected to nitrogen limitation (either at 9 or 24 hours after nitrogen removal) and analyzed the results in combination with a genome-wide set of nitrogen-regulated transcriptional start sites and a prediction of transcriptional terminators. Our analysis resulted in the definition of a transcriptional map including more than 4,000 transcripts, 65% of them in antisense orientation to other transcripts. In addition to overlapping mRNAs we identified nitrogen-regulated non-coding antisense RNAs transcribed from NtcA-dependent or HetR-dependent promoters.

overall_design: Transcriptional units prediction and comparative gene expression analysis of RNA-seq for Nostoc sp. PCC 7120 cells subjected to nitrogen deficiency for 9 and 24 hours.

first: Agustín

last: Vioque

first: Alicia

last: Muro-Pastor


title: The glomerular mRNA expression data from podocyte specific GC-A and p38MAPK double knockout mice

city: Kyoto

first: Sayaka

last: Sugioka

address: 54, Syogoin Kawahara-cho, Sakyo-ku

department: Nephrology

country: Japan

institute: Kyoto University

summary:
To study the role of GC-A and p38MAPK in podocytes, we used microarray analysis and compared gene expression profiles of the glomerulus of GC-A fl/fl p38 fl/fl Nephrin-Cre(Cre/+) mice and GC-A fl/fl p38 fl/fl Nephrin-Cre (+/+) mice.
GC-A: guanylyl cyclase-A

overall_design: We analyzed glomerular mRNA expressions of GC-A fl/fl p38 fl/fl Nephrin-Cre (Cre/+) mice and GC-A fl/fl p38 fl/fl Nephrin-Cre(+/+) mice at 2 months of age after high salt diet(6%NaCl) and aldosterone administration(0.2μg/kg body weight per minute) using osmotic minipump (ALZET2004, Cupertino, CA) for 3 weeks

first: Hideki

last: Yokoi


title: THe role of CXCL8 in the mesenchymal state of glioblastoma stem cells

city: Nanjing

first: Wei

last: Yuan

address: No. 101, Longmian Avenue, Jiangning District, Nanjing City, Jiangsu Province, China

institute: Nanjing Medical University

summary: To determine the functional significance of the expression of CXCL8 in mesenchymal GSCs, we examined the effect of CXCL8 disruption with two non-overlapping small hairpin RNAs (shRNA) on the mesenchymal GSC maintenance. Silencing CXCL8 with two independent shRNAs significantly reduced CXCL8 expression on in mesenchymal GSCs (839 and 2907) .

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells.

first: Qian

last: Zhang

first: Xiuxing

last: Wang

first: Jiancheng

last: Gao

first: Chenfei

last: Lu

first: Deobrat

last: Dixit

first: Ryan

last: Gimple

first: Yisu

first: Danling

last: Gu

first: Daqi

last: Li

first: Danyang

last: Shan

first: Lang

last: Hu

first: Lu

first: Yangqing

first: Shusheng

last: Ci

first: Hao

last: You

first: Linping

last: Yan

first: Kexin

last: Chen

first: Chuanhai

last: Xu

first: Jianyun

last: Lan

first: Dong

last: Liu

first: Junxia

first: Zhumei

last: Shi

first: Qiulian

last: Wu

first: Kailin

last: Yang

first: Linjie

last: Zhao

first: Zhixin

last: Qiu

first: Deguang

last: Lv

first: Hui

first: Fan

last: Lin

first: Qianghu

first: Jianghong

last: Man

first: Chaojun

first: Weiwei

last: Tao

first: Sameer

last: Agnihotri

first: Xu

last: Qian

first: Yu

first: Stephen

last: Mack

first: Nu

first: Yongping

first: Jeremy

middle: N

last: Rich

first: Guan

last: Sun


title: TMPRSS2-ERG and gain-of-function p53 mutants co-dictate pyrimidine synthesis and prostate cancer fitness [RNA-seq-2021 ERG-p53 project]

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

summary: TMPRSS2-ERG fusion is the most common genetic alteration in prostate cancer (PCa) and TP53 is the most frequently mutated gene in human cancers. However, their precise roles in PCa pathogenesis remain elusive. Here we showed that TMPRSS2-ERG fusion co-occurred with TP53 deletion/mutation in PCa patient specimens. ERG overexpression and Trp53 knockout/R172H mutant knockin induced pyrimidine synthesis gene (PSG) expression and prostate tumorigenesis in mice. Gain-of-function p53 mutants bound to the CTNNB1 promoter and upregulated β-Catenin. Overexpressed ERG and β-Catenin co-occupied PSG loci and mediated PSG expression, and high PSG expression associated with increased β-Catenin level and poor overall survival of PCa patients. β-Catenin inhibition by proteolysis-targeting chimeras (PROTACs) of its co-activator CBP and partner proteins LEF1/TCFs blocked ERG/p53-mutant PCa growth. Our study identifies CTNNB1 as a transcriptional target of p53 GOF-mutants, and reveals a druggable dependency on β-Catenin and pyrimidine synthesis in p53-mutated cancers with or without TMPRSS2-ERG fusion.

overall_design: To find the genes differentially expressed in Pb-ERG;Trp53pc-/- mice

first: Haojie

last: Huang

first: Liguo

last: Wang

first: Donglin

last: Ding

first: Alexandra

last: Blee


title: RNA-seq Series of Bladder carcinoma Cell lines associated with the Study "Epigenomic mapping identifies a super-enhancer repertoire that regulates cell identity in bladder cancers through distinct transcription factor networks"

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

institute: Institut Curie

summary: Background:  Muscle-invasive bladder cancer is a common aggressive disease with unmet clinical needs.  Recent work established a set of consensus bladder cancer transcriptomic subtypes that  distinguishes the cell identity of bladder cancers for improved diagnosis and treatment.  However, how these distinct subtypes are regulated remains unclear. Given the link between  super-enhancers and the regulation of cell identity, we hypothesized that epigenetic activation  of distinct super-enhancers could drive the transcriptional programs of the various bladder  cancer subtypes.    Results:  Through integrated RNA sequencing and epigenomic profiling of histone marks (H3K27ac,  H3K27me3, H3K9me3) in a diverse panel of 15 primary bladder tumours, seven bladder  cancer cell lines, and two primary cultures from normal human urothelia, we established the  first integrated epigenetic map of bladder cancer and demonstrate the link between bladder  cancer subtype and epigenetic control. Through H3K27ac analysis, we identify the repertoire  of activated super-enhancers in bladder cancer that distinguish molecular subtypes. Building  on these findings, we reveal the super-enhancer-regulated networks of candidate master  transcription factors for Luminal and Basal bladder cancer subgroups. We find that FOXA1, a  key pioneer factor in Luminal bladder cancers identified in our Luminal transcription factor  network, binds subgroup-specific bladder super-enhancers and correlates with their activation.  Furthermore, CRISPR-Cas9 inactivating mutation of FOXA1 triggers a shift from Luminal to  Basal cell identity. This shift is accompanied by an overexpression of ZBED2, one of the  newly identified transcriptional regulators in the Basal-specific transcription factor network.  5Finally, we show that both FOXA1 and ZBED2 play concordant roles in preventing  inflammatory response in bladder cancer cells through STAT2 inhibition and promote cancer  cell survival.    Conclusions:  Overall, our study provides new data for understanding epigenetic regulation of muscle-  invasive bladder cancer and identifies a coregulated network of super-enhancers and  associated transcription factors as new potential targets for the treatment of this aggressive  disease

first: Hélène

last: Neyret-Kahn

first: François

last: Radvanyi

first: Isabelle

last: Bernard-Pierrot

last: Chapeaublanc


title: TMPRSS2-ERG and gain-of-function p53 mutants co-dictate pyrimidine synthesis and prostate cancer fitness [RNA-seq-2018 ERG-p53 project]

overall_design: To find the genes differentially expressed in Pb-ERG;Trp53pcR172H/- mice


title: Polycomb suppresses a female gene regulatory network in Sertoli cells

city: Noda

first: Ryo

last: Sugiyama

state: Chiba

department: Applied Biological Science

institute: Tokyo University of Science

summary: To examine the function of PRC1 in postnatal Sertoli cells, we performed RNA-seq using PRC1 conditional KO and control mouse Sertoli cells.  We also analyzed the distribution of H2AK119ub, H3K27me3 and RNF2 by ChIP-seq.

overall_design: ChIP-seq and RNA-seq analyses using PRC1 conditional KO and control mouse Sertoli cells.

first: So

last: Maezawa

first: Artem

last: Barski

first: Satoshi

last: Namekawa


title: ADAM10 shapes myeloid antigen-presenting cell homeostasis in the splenic marginal zone

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

summary: The spleen contains phenotypically and functionally distinct cDC1 and cDC2 subpopulations, which each can be divided into several smaller and less-well characterized subsets. Despite advances in understanding the complexity of DC ontogeny and function by transcriptional programming, the significance of post-translational modifications in controlling tissue-specific cDC (subset) immunobiology remains elusive. Here, we identified the cell surface-expressed A-disintegrin-and-metalloproteinase 10 (ADAM10) as an essential regulator of cDC1 and cDC2 homeostasis in the splenic marginal zone (MZ). Mice with a CD11c-specific deletion of ADAM10 (ADAM10ΔCD11c) exhibited a complete loss of splenic ESAMhi cDC2A, because ADAM10 controlled their commitment, differentiation, survival, and EBI2-mediated localization within the MZ. Moreover, we discovered that ADAM10 is a molecular switch regulating cDC2 subset heterogeneity in the spleen, as this unbalanced cDC2A homeostasis in the absence of ADAM10 was compensated for by the emergence of a novel Clec12a+ cDC2B subset, closely resembling cDC2 generally found in peripheral lymph nodes. Moreover, in ADAM10ΔCD11c mice terminal differentiation of cDC1 was abrogated, resulting in reduced numbers of Langerin+ cDC1.

overall_design:
Whole Transcriptome Analysis (WTA) of splenic CD11c positive single cells from WT and ADAM10-deficient mice
The linked python script can be used to translate cell indexes to raw sequences found in the fastq files. See the linked readme file for further instructions.

first: Ronald

last: Backer

first: Jean-Fred

last: Fontaine

first: Tobias

last: Bopp

first: Björn

middle: E

last: Clausen


title: Single-cell sequencing of Epstein-Barr virus infected cells reveals constitutive lytic gene expression in latent cell populations

city: New Orleans

first: Erik

last: Flemington

state: LA

address: 1430 Tulane Ave

institute: Tulane University

summary: Single-cell RNA sequencing using the 10X Genomics 3' platform was performed to determine patterns of gene expression in EBV-positive lymphoma and gastric carcinoma cell lines.

overall_design: Single-cell RNA sequencing of Mutu (lymphoma) and SNU719 (gastric carcinoma) cells

first: Hani

last: Nakhoul

first: Zhen

last: Lin

first: Tina

last: O'Grady

first: Xia

last: Wang

first: Claire

last: Roberts

first: Nate

last: Ungerleider

first: David

last: Mohr

first: Yaozhong

last: Liu

first: Yan

last: Dong

first: Jovanny

last: Zabaleta


title: The pseudoenzyme ADPRHL1 affects cardiac function by regulating the ROCK pathway

status: Public on Jun 26 2023

city: beijing

first: Guo

last: Tianwei

address: No.167 North Lishi Road, Xicheng District, Beijing, China

institute: fuwai hospital

summary: Pseudoenzymes, catalytically deficient variants of active enzymes, have a wide range of regulatory functions. ADP-ribosylhydrolase like-1 (ADPRHL1), which belongs to a small group of ADP-ribosylhydrolase enzymes, lacks the amino acid residues required for catalytic activity, and is therefore considered a pseudoenzyme. Here, to investigate the role of ADPRHL1 in the heart, we established, for the first time, an in vitro ADPRHL1 knockout human myocardial cell culture model. These ADPRHL1 knockout cardiomyocytes adhered abnormally. However, the lack of ADPRHL1 disrupted the formation of focal adhesions in these cardiomyocytes by excessively upregulating the ROCK–myosin II pathway. Inhibitors of ROCK and myosin II effectively restored the focal adhesions in these ADPRHL1-deficient cardiomyocytes and improved electrical conduction and calcium activity. Our findings reveal that ADPRHL1 plays a major role in cardiac function by regulating the ROCK pathway, suggesting that it may serve as a potential drug target for the treatment of ADPRHL1-related diseases.

overall_design: To elucidate how ADPRHL1 deficiency prevents the formation of FAs, WT-CMs and KO-CMs were collected for global transcriptome analysis within 3 days after re-seeding.


title: Loss of endothelial cell heterogeneity in arteries after obesogenic diet [Bulk-seq]

city: Charlottesville

first: Brant

last: Isakson

state: Virginia

department: Cardiovascular Research Center

institute: University of Virginia

summary: Background: It is well recognized that obesity leads to arterial endothelial dysfunction and cardiovascular disease. However, the progression to endothelial dysfunction is not clear. Endothelial cells (ECs) adapt to the unique needs of their resident tissue and respond to systemic metabolic perturbations. We sought to better understand how obesity affects EC phenotypes in different tissues specifically focusing on mitochondrial gene expression.  Methods: We performed bulk RNA sequencing (RNA-seq) and single cell RNA-seq (scRNA-seq) on mesenteric and adipose ECs isolated from normal chow (NC) and high fat diet (HFD) fed mice. Differential gene expression, gene ontology pathway, and transcription factor analyses were performed. We further investigated our hypothesis in humans using published human adipose single nuclei RNA-seq (snRNA-seq) data.   Results: Bulk RNA-seq revealed higher mitochondrial gene expression in adipose ECs compared to mesenteric ECs in both NC and HFD mice. We then performed scRNA-seq and categorized EC clusters as arterial, capillary, venous, or lymphatic. HFD decreased the number of differentially expressed genes between mesenteric and adipose ECs in all subtypes, but the largest effect was seen in arterial ECs. Further analysis of arterial ECs revealed genes coding for mitochondrial oxidative phosphorylation proteins were enriched in adipose compared to mesentery under NC conditions. In HFD mice, these genes were decreased in adipose ECs becoming similar to mesenteric ECs. Transcription factor analysis revealed C/EBP and PPAR, both known to regulate lipid handling and metabolism, had high specificity scores in the NC adipose artery ECs. These findings were recapitulated in snRNA-seq data from human adipose.  Conclusions: These data suggest mesenteric and adipose arterial ECs metabolize lipids differently and the transcriptional phenotype of these two vascular beds converge in obesity, in part, due to downregulation of PPARand C/EBP in adipose artery ECs. This work lays the foundation for investigating vascular bed specific adaptations to obesity.

overall_design: Endothelial cells of ROSA26-eYFP+/+ Cdh5-CreERT2+ mice were isolated from the mesentery and adipose by fluorescence activated cell sorting (FACS) and analyzed using bulk RNA-seq.

first: Luke

middle: S

last: Dunaway

first: Melissa

last: Luse

first: Shruthi

last: Nyshadham

first: Gamze

last: Bulut

first: Nicholas

middle: W

last: Chavkin

first: Karen

middle: K

last: Hirschi

first: Gary

last: Owens


title: Single-cell ATAC-seq of mouse thymus iNKT cells

city: Detroit

first: Indra

last: Adrianto

state: MI

address: 1 Ford Place

department: Public Health Sciences

institute: Henry Ford Health System

summary: Invariant natural killer T (iNKT) cells are innate-like T cells.  Although remarkable advancements in the understanding of iNKT cell development have been made, the underlying molecular programs that guide iNKT cell lineages and the heterogeneity of iNKT subsets remain unclear.

overall_design: We profiled the chromatin accessibility patterns of individual mouse thymic iNKT cells across their developmental stages (stages 0 to 3) using a droplet-based single-cell ATAC-sequencing (scATAC-seq) approach.

first: Jie

first: Xiaojun

last: Wu

first: Li

last: Zhou

first: Qing-Sheng

last: Mi


title: Synthetic lethal and resistance interactions with BET bromodomain inhibitors

city: Brookline

first: Kornelia

last: Polyak

state: Massachusetts

address: 450 Brookline St

institute: Dana-Farber Cancer Institute

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

overall_design: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing


title: Effect of intranasal vaccination on transcriptome of mouse lung immune cells

city: Daejeon

first: Heung Kyu

last: Lee

address: 291 Daehak-ro, Yuseong-gu

department: Graduate School of Medical Science and Engineering

institute: Korea Advanced Institute of Science and Technology

summary: We used single-cell RNAseq to analyze transcriptional changes in lung cells following intranasal delivery of adenovirus vector-based recombinant SARS-CoV-2 vaccine.

overall_design: Isolate CD45.2+7-AAD- live lung cells from vaccinated BALB/c mice, then preform single cell RNA and TCR sequening (10x genomics).

first: Hi-Eun

last: Jung

first: Keun-Bon

last: Ku

first: Byeong-Hoon

last: Kang

first: Jang-Hyun

last: Park

first: Hyeon-Cheol

last: Kim

first: Kyun-Do

first: Heung-Kyu


title: Transcriptomic Response of Adult Fruit Flies to Arsenite Exposure

city: Bloomington

first: Jason

last: Tennessen

email: tennessenlab@gmail.com, tennlab@iu.edu, jtenness@iu.edu, tourigny@iu.edu

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University

summary: As part of our exploration into alternative model systems for toxicology, we exposed male and female adult D. melanogaster to varying concentratios of arsenite over the course of two days

overall_design: Male and female starved adult flies were exposed to zero (control), 0.25mM, or 1mM sodium arsenite in their food for the alotted time, before collection and proccessing for RNA-seq

first: Shannon

last: Smoot

last: Tourigny

first: Thomas

last: Kaufman

first: Brian

last: Oliver


title: Single-cell RNA sequencing reveals the ability to metastasize of tumor in human hypopharygeal squamous cell carcinoma and lymphatic metastasis

city: Jinan

first: Rui

last: Guan

state: Shandong

address: West Wenhua Road

institute: Shandong University

summary: Human hypopharygeal squamous cell carcinoma (HSCC) is a common head and neck cancer with a poor prognosis in advanced stages. Determining genes associated with transferring in HSCC could provide new targets and therapeutic strategies. We performed single-cell RNA sequencing of hypopharyngeal carcinoma and lymphoid metastases from five patients with hypopharyngeal squamous cell carcinoma.

overall_design: Examination of the expression of cells and genes of hypopharyngeal carcinoma and lymphoid metastases from five patients with hypopharyngeal squamous cell carcinoma

first: Ce

last: Li

first: Dapeng

last: Lei


title: Loss of endothelial cell heterogeneity in arteries after obesogenic diet [scRNA-seq]

first: Brant

last: Isakson

overall_design: Endothelial cells of ROSA26-eYFP+/+ Cdh5-CreERT2+ mice were isolated from the mesentery and adipose by fluorescence activated cell sorting (FACS) and analyzed using scRNA-seq.

first: Luke

last: Dunaway

first: Melissa

middle: A

last: Luse

first: Shruthi

last: Nyshadham

first: Gamze

last: Bulut

first: Nicholas

last: Chavkin

first: Karen

last: Hirschi

first: Gary

last: Owens


title: Enzymatic depletion ofl‐Met using an engineered human enzyme as a novel therapeutic strategy for melanoma

city: Austin

first: Anna

last: Battenhouse

state: TX

address: 100 East 24th St., Stop A5000

department: Center for Biomedical Research Support

institute: The University of Texas at Austin

summary: Many cancers, including melanoma, have a higher requirement forl‐methionine in comparison with noncancerous cells. In this study, we use a multiomics approach to show that administration of an engineered human methionine‐γ‐lyase (hMGL) significantly reduced the survival of both human and mouse melanoma cells in vitro.

overall_design: Six independent cell cultures of ATCC melanoma cell line A375 were prepared, three  treated with hMGL for 24 h ("Treated") and the other three left untreated ("Control").

first: Carly

last: Wilder

first: Jennifer

last: Chiou

first: Achinto

last: Saha

first: Zhao

last: Chen

first: Eunice

last: Kim

first: Mohamed

middle: I

last: Gadallah

first: Stefano

last: Tiziani

first: George

last: Georgiou

first: Everett

last: Stone

first: John

last: DiGiovanni


title: Effect of SERT LOF on Drosophila Kenyon Cell subtypes postsynaptic to serotonin [scRNA-seq]

city: Los Angeles

first: Shivan

middle: Luca

last: Bonanno

address: Gonda Rm3335, 695 Charles E. Young Dr.

department: Psychiatry

institute: UCLA

summary: to investigate the transcriptional effects on postsynaptic cells following SSRI-like SERT LOF, we used Drosophila mutants for SERT and compared to controls, isolating and profiling Kenyon Cells of the mushroom body

overall_design: Kenyon cells of SERT LOF or WT groups were isolated (FACS) according to the presence of nls.GFP signal and analyzed using scRNAseq.

first: David

last: Krantz


title: A cell therapy to restore Trem2 function in a mouse model of Alzheimer's disease

city: Stanford

first: Yongjin

last: Yoo

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

summary: Alzheimer’s disease (AD) remains one of the grand challenges facing human society. Much controversy exists around the complex and multifaceted pathogenesis of this prevalent disease. Given strong human genetic evidence, there is little doubt, however, that microglia play an important role in preventing degeneration of neurons. E.g., loss-of-function of the microglial gene Trem2 render microglia dysfunctional and causes an early-onset neurodegenerative syndrome and Trem2 variants are among the strongest genetic risk factors for AD. Thus, restoring microglial function represents a rational therapeutic approach. Here we show that systemic hematopoietic cell transplantation followed by enhancement of microglia replacement restores microglial function in a Trem2 mutant model of Alzheimer’s disease.

overall_design: Microglial replacement using bone-marrow cells combined with PLX5622 in Trem2 wildtype and Trem2 knockout mice.

first: Gernot

last: Neumayer

first: Yohei

last: Shibuya

first: Marius

last: Mader

last: Wernig


title: Hnf4 controls gut and liver gene programs in the thymus [scRNAseq]

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: We profiled medullary thymic epithelial cells by scRNA-seq to investigate mechanisms of T-cell tolerance.

overall_design: scRNA-seq of mTECs

first: Daniel

last: Michelson

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Hnf4 controls gut and liver gene programs in the thymus

overall_design: Refer to individual Series


title: Galectin-1 mediated chronic tumoral-STING activation promotes metastasis 1 through MDSC recruitment

first: Dhanya

last: Nambiar

address: 269 Campus Drive

summary:
To identify the differences in the MDSC population in the tumor verus pre-metastatic niche site, we performed RNA sequencing of isolated CD11b+ Ly6G+ MDSCs and analyzed the differentially expressed genes in PMN-MDSCs isolated from MOC2 tumors and corresponding lung tissues from the same mice
To compare the MDSC RNA-level expression with neutrophil expression, a public mouse neutrophil microarray dataset was used (GSE60336).  Our MDSC RNA-seq and the public mouse neutrophil data sets were merged using  COMBAT55. DEGs for three groups (MDSC lung, MDSC tumor and neutrophil) were calculated using SAM56 multiple class comparison with false discovery rate smaller than 0.05. A total of 5 samples were generated.

overall_design: RNA was isolated from a minimum of 2x10^6 sorted PMN-MDSCs from tumors or lungs using a RNeasy micro Kit (Qiagen). Library preparation and RNA sequencing were performed by Novogene via Illumina platforms based on mechanism of SBS (Sequencing by synthesis).Expression levels of RNA sequencing data were  quantified using a quasi-mapping two phase inference algorithm implemented in Salmon 635 (version 0.9.1). Transcript sequences for mouse M24 from Gencode  (https://www.gencodegenes.org) were used for reference transcriptome indexing. Transcript-per-million (TPM) value was used as normalized expression level unit.  Quantified gene expressions were then log transformed for downstream analysis. Differentially expressed gene (DEG) analysis between MDSC tumor group and MDSC lung group was performed on each gene expression and the p-values were corrected using false discovery rate. DEGs were defined by false discovery rate smaller than 0.05  and fold change higher than 1.5.


title: Wnt/β-catenin signaling activation induces differentiation in human limbal epithelial stem cells cultured ex vivo

city: OSLO

first: Agate

last: Noer

address: Kirkeveien 166

department: Ophthalmology

country: Norway

institute: Oslo University Hospital, Ullevaal

summary:
hLESC ex vivo cultures treated with GSK-3 inhibitor LY2090314 (small molecule) to activate Wnt/β-catenin signaling and further examine the impact of canonical Wnt/β-catenin signaling activation on hLESCs.
We used microarray to explore the changes in gene expression in GSK-3 inhibitor LY2090314 treated and untreated ex vivo cultures of hLESCs to examine gene expression changes upon Wnt/β-catenin signaling activation in hLESCs.

overall_design: hLESC ex vivo cultures untreated controls and treated with GSK-3 inhibitor LY2090314 (small molecule) to activate Wnt/β-catenin signaling, were selected for RNA isolation and hubridization to Affimetrix array to identify gene expression changes in hLESCs upon Wnt/β-catenin signaling activation.

first: Jovana

last: Bisevac

first: Kirankumar

last: Katta

first: Goran

last: Petrovski

first: Morten Carstens

last: Moe


title: Social network position is a major predictor of ant behaviour,  microbiota composition, and brain gene expression

city: Lausanne

first: Tomas

last: Kay

state: Vaud

address: Biophore building

country: Switzerland

institute: University of Lausanne

summary: RNA sequencing of individual whole brains from behaviorally tracked Camponotus fellah workers

overall_design: Colonies were behaviorally tracked for a week before all individuals were sacrificed for sequencing


title: Hnf4 controls gut and liver gene programs in the thymus [bulk_RNAseq]

summary: We profiled medullary thymic epithelial cells by bulk RNA-seq to investigate mechanisms of T-cell tolerance.

overall_design: Bulk RNA-seq of mTECs


title: Effect of SERT LOF on Drosophila Kenyon Cells postsynaptic to serotonin [bulkRNA-seq]

first: Shivan

last: Bonanno

overall_design: SMART-seq bulk RNA-seq on FACS-isolated Kenyon Cells, following SERT LOF

last: Krantz


title: Mouse DRG RNA-Seq

city: Aarhus

first: Marta

last: Diaz-delCastillo

address: Palle Juul-Jensens Boulevard 99

department: Department of Forensic Medicine

country: Denmark

institute: University of Aarhus

summary: Multiple myeloma (MM) is a neoplasia of B plasma cells that often induces bone pain. However, the mechanisms underlying myeloma-induced bone (MIBP) pain are mostly unknown. Using a localized MM mouse model, we investigated MM induced gene expression changes in the dorsal root ganglia (DRG) innervating the MM-bearing bone and found alterations in pathways associated with cell cycle, immune response and neuronal signalling. The MM transcriptional signature was consistent with metastatic MM infiltration to the DRG, a never-before described feature of the disease that we further demonstrated histologically. In the DRG, MM cells caused loss of vascularization and neuronal injury, which may contribute to late-stage MIBP.

overall_design: RNA-Seq of DRG tissue from 9 MM and 9 SHAM mice

first: Oana

last: Palasca

first: Anne-Marie

last: Heegaard


title: Regulatory variants in a novel distal enhancer regulate the expression of CYP3A4 and CYP3A5: ATAC-Seq and 4C data from human hepatocytes [4C]

city: Gainesville

first: Danxin

last: Wang

state: FL

address: 1345 Center Drive MSB PG-05B

department: Pharmacotherapy and Translational Research

institute: University of Florida

summary: The cytochrome P450 3As (CYP3As) are abundantly expressed in the liver and metabolize many commonly prescribed medications. Their expression is highly variable between individuals with little known genetic cause. Despite extensive investigation, cis-acting genetic elements that control the expression of CYP3As remain uncharacterized. Using chromatin conformation capture (4C assays), we detected reciprocal interaction between a distal regulatory region (DDR) and the CYP3A4 promoter. The DRR colocalizes with a variety of enhancer marks and was found to promote transcription in reporter assays. CRISPR-mediated knockout of the DRR decreased expression of CYP3A4, CYP3A5, and CYP3A7, supporting its role as a shared enhancer regulating the expression of three CYP3A genes. Here we provided data generated from circular chromatin confirmation capture followed by sequencing (4C-Seq) analysis of human primary hepatocytes originating from both black and white donors.

overall_design: 4C-Seq for human primary hepatocytes generated from both black and white donors targeting CYP3A promoters and the DRR.

first: Joseph

last: Collins


title: Transcriptional changes in specifc subsets of Drosophila neurons following inhibition of the serotonin transporter


title: Mesenchymal-like tumor cells and myofibroblastic cancer-associated fibroblasts are associated with progression and immunotherapy response of clear-cell renal cell carcinoma [scRNA-seq]

city: Illkirch-Graffenstaden

first: Guillaume

last: Davidson

address: 1 Rue Laurent Fries

institute: I.G.B.M.C. - Institut de génétique et de biologie moléculaire et cellulaire

summary: Immune checkpoint inhibitors (ICI) represent the cornerstone for treatment of patients with metastatic clear-cell renal cell carcinoma (ccRCC). Despite a favorable response for a subset of patients, others experience primary progressive disease highlighting the need to precisely understand plasticity of cancer cells and their crosstalk with the microenvironment to better predict therapeutic response and personalize treatment. Single-cell RNA sequencing of ccRCC at different disease stages and normal adjacent tissue (NAT) from patients identified 46 cell populations, including 5 tumor subpopulations, characterized by distinct transcriptional signatures representing an epithelial to mesenchymal transition gradient and a novel inflamed state. Deconvolution of the tumor and microenvironment signatures in public datasets and in data from the BIONIKK clinical trial (NCT02960906) revealed a strong correlation between mesenchymal-like ccRCC cells and myofibroblastic cancer-associated fibroblasts (myCAFs), which are both enriched in metastases and correlate with poor patient survival. Spatial transcriptomics and multiplex immune staining uncovered spatial proximity of mesenchymal-like ccRCC cells and myCAFs at the tumor-NAT interface. Moreover, enrichment in myCAFs was associated with primary resistance to ICI therapy in the BIONIKK clinical trial. This data highlights the epithelial-mesenchymal plasticity of ccRCC cancer cells and their relationship with myCAFs, a critical component of the microenvironment associated with poor outcome and ICI resistance.

overall_design: Seven tumoral and two normal adjacent tissue samples from patients presenting clear-cell Renal Cell Carcinoma were analyzed by single-cell RNA sequencing.

first: Alexandra

last: Helleux

first: Gabriel

last: Malouf

first: Irwin


title: Cross-activation of the FGF, TGF- and WNT pathways constrains BMP4-mediated induction of the Totipotent state in mouse embryonic stem cells.

city: Montreal

first: Thulaj

last: Meharwade

state: QC

address: 110 Pine Ave W,

department: Division of Systems Biology

institute: Montreal Clinical Research Institute

summary: Cell signaling induced cell fate determination is central to stem cell and developmental biology. Embryonic stem cells (ESC) are an attractive model for understanding the relationship between cell signaling and cell fates. Cultured mouse ESCs can exist in multiple cell states resembling distinct stages of early embryogenesis, such as Totipotent, Pluripotent, Primed and Primitive Endoderm. The signaling mechanisms regulating the Totipotent state acquisition and coexistence of these states are poorly understood. Here we identify BMP4 as an inducer of the Totipotent state. However, we discovered that BMP4-mediated induction of the Totipotent state is constrained by the cross-activation of FGF, TGF- and WNT pathways. We exploited this finding to enhance the proportion of Totipotent cells in ESCs by rationally inhibiting these cross-activated pathways using small molecules. Single-cell mRNA-sequencing further revealed that induction of the Totipotent state is accompanied by the suppression of both the Primed and Primitive Endoderm states. Furthermore, the reprogrammed Totipotent cells generated in culture have a molecular and functional resemblance to Totipotent cell stages of preimplantation embryos. Our findings reveal a novel BMP4 signaling mechanism in ESCs to regulate multiple cell states, potentially significant for managing stem cell heterogeneity in differentiation and reprogramming.

overall_design: Mouse ESCs grown in LB and LBPXRS were analyzed at 72hours using single cell RNAsequencing.

first: Loïck

last: Joumier

first: Maxime

last: Parisotto

first: Vivian

last: Huynh

first: Edroaldo

middle: L

last: da Rocha

first: Mohan

last: Malleshaiah


title: RNA-Seq of H8, SiHa and  KD HSPA9 SiHa cells

status: Public on Jun 25 2023

city: shenzhen

first: Keyi

last: Ao

address: Xinan

institute: shenzhen hospital of Southern medical school

summary: To investigate the different gens expression in the cervical immortalized cervical cells (H8 cells), cervical cancer cells (SiHa cells) and KD HSPA9 SiHa cells.

overall_design: To investigate the function of  HSPA9-knockdown in cervical cancer cells, we established KD HSPA9 SiHa cell line in which the gene HSPA9 has been knocked down by shRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells (H8, SiHa and KD HSPA9 SiHa cells). Comparative gene expression profling analysis of RNA-seq data for H8 cells, SiHa cells and KD HSPA9 SiHa cells were performed.

first: Xia

last: Guo

first: Minuo

last: Yin

first: Sheng

last: Zhong


title: A transcriptome comparison between pao5 vs NIP, ACC-treatment vs Mock (NIP) and H2O2-treatment vs Mock (NIP)

city: Hangzhou

first: lv

middle: yu

last: song

address: CNRRI

institute: CNRRI

summary: OsPAO5 mainly functions to oxidize spermine and produce H2O2,which finally affects mesocotyl elongation in rice. Meanwhile ethylene and polyamines synthesis  crosstalk has been reported in competing the common substrate. To further confirm the relationship between H2O2 and ethylene in contributing to the mesocotyl length, we conducted a transcriptome comparison between pao5-1 vs NIP, ACC-treatment vs Mock (NIP) and H2O2-treatment vs Mock (NIP).

overall_design: Generally, the sterile grains of pao5-1 and NIP were sowed on a 0.6% agar medium containing 10 μM ACC or 10 μM H2O2, and cultivated for 7 days under absolute darkness environment (at 30 ℃ and 75% humidity). The 7-day-old mesocotyl tissues of pao5, NIP (Mock), ACC-treatment of NIP and H2O2-treatment of NIP were gathered to perform a transcriptome comparison.

first: Yusong

last: Lyu


title: TMPRSS2-ERG and gain-of-function p53 mutants co-dictate pyrimidine synthesis and prostate cancer fitness

city: Rochester

first: LIGUO

last: WANG

address: 200 1st St SW

institute: Mayo Clinic

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