title: Gene expression profile at single cell level of goblet cells (GCs) from the distal colon (DC) and the 8th portion of the small intestine (Si8)

status: Public on Sep 09 2022

city: Shanghai

first: Sun

last: Jianming

address: PuDong

institute: Shanghai Seventh People's Hospital

summary: Objective: Benign prostatic hyperplasia (BPH) is a common disease in men over 50 years old, which seriously reduces the quality of life of patients. At present, the transcriptome changes of gene expression profile in benign prostatic hyperplasia have not been explored to a great extent.   Methods: In this study, single-cell RNA sequencing was performed on the isolated prostate tissue of BPH mice, and its cell types were identified and enriched. In addition, we constructed the cell communication network and sequence analysis, revealing its receptor-ligand pair and its transmission signals with other cells.   Results: The results revealed the changes in 11 cell subpopulations including B cells, DC, Endothelial cells, Epithelial cells, Fibroblast & Myofibroblast, Macrophage, Mast cells, Satellite cells, Schwann cells, Smooth Muscle cells, and T Cell  & NK & NKT in the microenvironment at various stages of the occurrence and development of benign prostatic hyperplasia, and updated the understanding of Epithelial cells, Fibroblast & Myofibroblast cell markers.   Conclusion: Our study promotes the understanding of cellular dynamic changes and potential molecular mechanisms in the development of BPH.

overall_design: ICR mice (5 weeks old, male)  were housed in specific pathogen-free conditions with free access to water and mice chow. The mice were anesthetized by intraperitoneal injection of pentobarbital sodium, and their bilateral testes were removed by aseptic operation through the scrotum. After 1 week of natural recovery, the mice were subcutaneously injected with 7.5 ml/kg of testosterone propionate every day. The control group was injected with 200 μl soybean oil every day. After 3 weeks, the mice were anesthetized and bled to death. The tissues around the prostate were stripped and single-cell sequencing was performed.

first: Peng

last: Liu

first: Jianmin

last: Mao

first: Wenjun

last: Han

first: Quanyao

last: Yu

first: Jun

last: Bo

first: Jianming

last: Sun


title: Multiomic Analysis of Adult Diapause in Drosophila melanogaster Identifies Hallmarks of Cellular Quiescence

status: Public on Sep 10 2022

city: Providence

first: Corinne

last: Hutfilz

state: Rhode Island

address: 171 Meeting St.

country: USA

institute: Brown University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Crosstalk between macrophages and fibro-adipogenic progenitors during muscle regeneration

status: Public on Sep 12 2022

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

country: Japan

institute: Chiba University

summary:
The purpose of this study is to investigate how immune cells (macrophages) are closely linked with fibro-adipogenic progenitors (FAPs) during recovery processe.
We report that the depletion of Mrc1+ (gene encoding CD206) M2-like macrophages promoted the recovery of muscle after injury. A total RNA sequence analysis of whole muscle or isolated FAPs revealed that the depletion of Mrc1+ M2-like macrophages resulted in the activation of FAPs. Activated FAPs secrete follistatin (Fst), a promyogenic factor, boosting the recovery process. We further determined that the knockdown of FAPs-derived Fst delayed the recovery process. Mechanistically, Mrc1+ M2-like macrophages-specific TGF-b1 inhibited the activation of FAPs, and the FAPs failed to secrete Fst.

overall_design: mRNA profiles of whole muscle 4,7,14 post-day injury (cardiotoxin [CTX]-induced muscle injury) and mRNA profile of isolated FAPs from 7 post-day injured muscle of  wild type (WT) and CD206DTR mice were generated by deep sequencing.

first: Oishi

last: Yumiko

first: Manabe

last: Ichiro


title: Genome-wide maps of chromatin state in human primary CAR-T cells [scRNA-seq]

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

institute: Stanford University

summary: We report the single-cell transcriptomic profile of human primary T cells specifc for NY-ESO-1.

overall_design: CRISPR gene editing was used to delete MED12 or the "safe harbor" control gene AAVS1. T cells were transduced with a lentiviral vector encoding alpha and beta chains of the NY-ESO-1 TCR, then cultured in vitro for 10 days and adoptively transferred into A375 tumor bearing mice. Tumors were harvest 6 days following adoptive transfer. Tumors were dissociated and antigen-specific T cells were isolated by FACS.

first: Katherine

last: Freitas


title: miRNA-seq analysis of human serum in different working schedules.

city: Guangzhou

first: Jinhu

last: Guo

address: No. 135, Xingang Xi Road

country: China

institute: Sun Yat-sen University

type: Non-coding RNA profiling by high throughput sequencing

summary: Analysis of genes differentially expressed of human serum in different working schedules

overall_design: Total RNA obtained from human serum in different working schedules

first: Guobin

last: Huang


title: Immune deconvolution and temporal mapping identifies stromal targets and developmental intervals for abrogating murine low-grade optic glioma formation

city: St Louis

first: David

last: Gutmann

state: MO

address: 660 S Euclid Ave

department: Neurology

institute: Washington University in St Louis

summary: Leveraging RNA sequencing deconvolution, single cell RNA sequencing and protein-based analyses of Nf1OPG, we define the stromal cell composition during mouse Nf1-OPG evolution, as well as in human pediatric low-grade gliomas (LGGs). We show that T cells and microglia are the main non-neoplastic immune cell populations in both murine and human LGGs.

overall_design: For single cell RNA sequencing, the optic nerves of 8 male 12 week-old Nf1OPG mice were pooled.  Mice were perfused using D-PBS with calcium, magnesium, glucose, pyruvate (ThermoFisher), and the adult brain dissociation kit (Miltenyi Biotec 130-107-677) was used to prepare single cell suspensions. Single-cell barcoding, cDNA amplification and Gene Expression Library Construction were then performed using Chromium Single Cell 3ʹ Reagent Kits v3, and10x Genomics® was used for sequencing. Nf1-OPG scRNAseq data were analyzed in Partek Flow using CPM normalization and graph-based clustering with the Louvain clustering algorithm.

first: Amanda

last: de Andrade Costa

first: Jit

last: Chatterjee

first: Olivia

last: Cobb

first: Elizabeth

last: Cordell

first: Astoria

last: Chao

first: Suzanne

last: Schaeffer

first: Andrea

last: Goldstein

first: Sonika

last: Dahiya

middle: H


title: Prediction of Golimumab Response in the PROgECT Phase 2a Open-Label Trial of Patients With Ulcerative Colitis

status: Public on Sep 08 2022

city: London

first: Nick

last: Powell

address: Du Cane Road

department: Department of Metabolism, Digestion and Reproduction

country: United Kingdom

institute: Imperial College London

summary: PROgECT (ClinicalTrials.gov Identifier: NCT01988961) was a multicenter, open-label study evaluating the accuracy of a probe-set panel in predicting response to golimumab treatment in participants with moderately to severely active ulcerative colitis (UC). Biopsy samples (collected 15 to 20 cm from the anal verge) were taken at screening from 84 patients and used for RNA extraction and profiling by microarrays. All patients enrolled in the study received the approved induction dose regimen of subcutaneous (SC) golimumab.

overall_design: A gene expression profiling study was conducted in which colon biopsy samples were collected for RNA extraction and hybridization to microarrays from patients (n=84) with moderate-to-severe ulcerative colitis.

first: Polychronis

last: Pavlidis

first: Anastasia

last: Tsakmaki

first: Eirini

last: Pantazi

last: Li

first: Domenico

last: Cozzetto

first: Jonathan

last: Digby-Bell

first: Feifei

last: Yang

last: Lo

first: Elena

last: Alberts

first: Ana

middle: C

last: Costa Sa

first: Umar

last: Niazi

first: Joshua

last: Friedman

first: Anna

last: Long

first: Yuchun

last: Ding

first: Christopher

last: Carey

last: Lamb

first: Mansoor

last: Saqi

first: Matthew

last: Madgwick

first: Leila

last: Gul

first: Agatha

last: Treveil

first: Tamas

last: Korcsmaros

first: Thomas

last: MacDonald

first: Graham

last: Lord

first: Gavin

last: Bewick


title: Functional E3 ligase hotspots and resistance mechanisms to small-molecule degraders [Saturating mutagenesis]

city: Vienna

first: Hana

last: Imrichova

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: CeMM, Vienna

summary: Targeted protein degradation is a novel pharmacology established by drugs that recruit target proteins to E3 ubiquitin ligases. Based on the structure of the degrader and the target, different E3 interfaces are critically involved, thus forming defined "functional hotspots". Understanding disruptive mutations in functional hotspots informs on the architecture of the assembly, and highlights residues susceptible to acquire resistance phenotypes. Here, deep mutational scanning revealed hotspots that are conserved or specific for chemically distinct degraders and targets and validated hotspots mutated in patients that relapse from degrader treatment.

overall_design:
CRBN/VHL deficient RKO cells were transduced with the respective mutational library. VHL screens were performed in two infection replicates, CRBN screens in triplicates. Cells were treated for 7 days with DMSO or small-molecule degraders.

Amplicon next-generation sequencing of the amplified CRBN and VHL cDNA harboring a mutation.

first: Alexander

last: Hanzl

first: Matthias

last: Brand

first: Georg

middle: E

last: Winter


title: Functional E3 ligase hotspots and resistance mechanisms to small-molecule degraders via chemical genetics [Hybrid capture]

summary: Targeted protein degradation is a novel pharmacology established by drugs that recruit target proteins to E3 ubiquitin ligases. Based on the structure of the degrader and the target, different E3 interfaces are critically involved, thus forming defined "functional hotspots". Understanding disruptive mutations in functional hotspots informs on the architecture of the assembly, and highlights residues susceptible to acquire resistance phenotypes. Here, we employ haploid genetics to show that hotspot mutations cluster in substrate receptors of hijacked ligases, where mutation type and frequency correlate with gene essentiality. A Hybrid capture assay reveals resistance-conferring mutations after degrader treatment. 29 putative target genes were selected to be sequenced. Target gene enrichment from gDNA of treated cells was performed, followed by amplification and sequencing to identify mutations.

overall_design:
Total of 7 samples of KBM7 cells treated with BET PROTAC degraders ARV-771 or dBET6 (concentrations: 25x, 50x, 25x-50x pool).

Amplicon next-generation sequencing of 29 genes after enrichment and amplification to detect genomic mutations.


title: Combined α- and β-adrenergic receptor activation triggers thermogenesis by the futile creatine cycle.

city: Montreal

first: Lawrence

last: Kazak

state: Quebec

address: 3655 Prom Sir-William-Osler

country: Canada

institute: McGill University

summary: Noradrenaline regulates cold-stimulated adipocyte thermogenesis. Aside from cAMP signaling downstream of β-adrenergic receptor (βAR) activation, how noradrenaline promotes thermogenic output is still not fully understood. Here, we show that coordinated α1-adrenergic receptor (α1AR) and β3AR signaling induces the expression of thermogenic genes of the futile creatine cycle, and that EBFs, ERRs, and PGC1α are required for this response in vivo. Noradrenaline triggers physical and functional coupling between the α1AR subtype (ADRA1A) to Gαq to promote adipocyte thermogenesis in a manner that is dependent on the effector proteins of the futile creatine cycle, creatine kinase b (CKB) and tissue-nonspecific alkaline phosphatase (TNAP). Combined Gαq and Gαs signaling selectively in adipocytes promotes a continual rise in whole-body energy expenditure, and CKB is required for this effect. Thus, the ADRA1A-Gαq-futile creatine cycle axis is a key regulator of facultative and adaptive thermogenesis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for brown adipose tissue (either 30°C or 6°C) with saline solution or PBZ injections.

first: Janane

middle: F

last: Rahbani


title: Mastication stimuli enhance the learning ability of weaning-stage rats

city: Bunkyo-ku

first: Tomiko

last: Asakura

state: Tokyo

department: Applied Biological Chemistry Graduate School of Agricultural and Life Sciences

institute: The University of Tokyo

summary:
The mastication stimuli during the weaning period can enhance the learning ability of rats by increasing the dendrite branches of hippocampal CA1 neurons and by regulating genes related to dendrite growth.
Using DNA microarray analysis, differentially expressed genes were enriched in functional terms related to dendrite growth and included the Igf2, RhoA, and Rho GEF genes, most of which were upregulated in the chow diet group.

overall_design: Three-week-old male Wistar rats were administered powdered (P-gloup) or solid (C-gloup) feed and water ad libitum for eight days, and the mRNA expression in the hippocampus was compared between the two groups.

first: Akihito

last: Yasuoka

first: Toshitada

last: Nagai

first: Seonmi

last: Lee

first: Hitonari

last: Miyaguchi

first: Yoshikazu

last: Saito

first: Keiko

last: Abe


title: Efficacy and safety of ustekinumab treatment in patients with Crohn's disease

first: Nick

last: Powell

summary: UNITI-2 was a phase 3 clinical trial (ClinicalTrials.gov Identifier: NCT01369342) comparing the effects (both positive and negative) of an initial treatment with ustekinumab to a placebo over 8 weeks in patients with moderately to severely active Crohn's disease.

overall_design: A gene expression profiling study was conducted in which rectum biopsy samples were collected for RNA extraction and hybridization to microarrays from patients (n=125) with moderate-to-severe Crohn's disease and from non-IBD subjects (n=23).

first: Polychronis

last: Pavlidis

first: Anastasia

last: Tsakmaki

first: Eirini

last: Pantazi

first: Katherine

last: Li

first: Domenico

last: Cozzetto

first: Jonathan

last: Digby-Bell

first: Feifei

last: Yang

last: Lo

first: Elena

last: Alberts

first: Ana

last: Costa Sa

first: Umar

last: Niazi

first: Joshua

last: Friedman

first: Anna

last: Long

first: Yuchun

last: Ding

first: Christopher

last: Carey

last: Lamb

first: Mansoor

last: Saqi

first: Matthew

last: Madgwick

first: Leila

last: Gul

first: Agatha

last: Treveil

first: Tamas

last: Korcsmaros


title: Efficacy-enhanced anti-CD7 universal chimeric antigen receptor-T cell therapy for relapsed/refractory CD7-positive hematological malignancies: A phase I clinical study

city: Hangzhou

first: He

last: Huang

address: 79 Qingchun Rd., Shangcheng District, Hangzhou

institute: the First Affiliated Hospital, Zhejiang University School of Medicine

summary: Chimeric antigen receptor-T cell (CAR-T) therapy in T cell malignancies faces fratricide, T cell aplasia, and product contamination. We developed an universal anti-CD7 CAR-T cells in which TRAC, CD7 and HLA-II were disrupted, while E-cadherin (a NK cell inhibitory molecule) was introduced, to mitigate graft versus host disease (GvHD), fratricide and rejection. Furthermore, we designed a subtle receptor, bbzg-CAR, comprising not only conventional domains (anti-CD7 scFv, 4-1BB co-stimulatory domain, and CD3ζ signaling domain), but also the intracellular domain of common γ chain. Bbzg-CAR-T exerted anti-tumor effects superior to those of conventional universal CAR-T cells. In adoptive therapy for relapsed/refractory (r/r) patients, no dose-limiting toxicity, GvHD, immune effector cell-associated neurotoxicity or severe cytokine release syndrome (grade≥3) was observed. Nine patients (82%) showed objective response with, complete response rates of 75% and 33.3% in r/r leukemia and lymphoma respectively. Preliminary safety and efficacy of this universal CAR-T product was achieved in CD7+ malignancies.

overall_design: Single-cell RNA analysis were performed in RD13-01 product (batch number C20201001) and PBMCs from patient 5 at day 14 and day 19 post RD13-01 infusion.

first: Yongxian

last: Hu

first: Jiangtao

last: Ren

first: Yali

last: Zhou


title: High affinity chromodomains engineered for improved detection of histone modifications and enhanced CRISPR-based gene repression

city: Toronto

first: Gianluca

last: Veggiani

address: 160 College Street

department: Banting and Best Department of Medical Research, University of Toronto

institute: Donnelly Centre for Cellular and Biomolecular Research

summary: Histone methylation is an important post-translational modification that plays a crucial role in regulating cellular functions, and its dysregulation is implicated in cancer and developmental defects. Therefore, systematic characterization of histone methylation is necessary to elucidate complex biological processes, identify biomarkers, and ultimately, enable drug discovery. Studying histone methylation relies on the use of antibodies, but these suffer from batch-to-batch variation, are costly, and cannot be used in live cells. Chromatin-modification reader domains are potential affinity reagents for methylated histones, but their application is limited by their modest affinities. We used phage display to identify key residues that greatly enhance the affinities of Cbx chromodomains for methylated histone marks and developed a general strategy for enhancing the affinity of most chromodomains of the human Cbx protein family. Our strategy allowed us to develop powerful probes for genome-wide binding analysis and live cell imaging. Furthermore, we used optimized chromodomains to develop extremely potent CRISPR-based repressors for tailored gene silencing. Our results highlight the power of engineered chromodomains for analyzing protein interaction networks involving chromatin and represent a modular platform for efficient gene silencing.

overall_design: Chromatin immunoprecipitation from crosslinked mouse embryonic stem cells expressing engineered chromodomains.

first: Sachdev

last: Sidhu

first: Rodrigo

last: Villaseñor


title: Knock-out of 5-lipoxygenase in overexpressing tumor cells – consequences on gene expression and cellular function

city: Frankfurt am Main

first: Astrid

middle: Stefanie

last: Kahnt

address: Max-von-Laue-Straße 9

department: Institute of Pharmaceutical Chemistry

country: Germany

institute: Goethe University

summary: In healthy human beings expression of 5-lipoxygenase (5-LO), the central enzyme in the biosynthesis of leukotrienes (LT) and 5-oxo-ETE, is restricted to leukocytes where 5-LO-derived lipid mediators shape the immune response upon an acute inflammation. Even though solid tissues do not express 5-LO under physiological conditions, 5-LO expression has been frequently found in many solid malignancies. There is still little knowledge on the functional consequences of 5-LO overexpression in solid tumor cells. We established a complete knock-out (KO) of 5-LO in HCT-116 and HT-29 colon cancer cells as well as the osteosarcoma cell line U2OS using the CRISPR/Cas technology.  Consequences on global gene expression in the three cell lines were studied employing next generation sequencing followed by pathway enrichment analysis and expression of the differentially expressed genes was verified using qPCR.

overall_design: mRNA profiling of  wildtype (WT) HCT-116, HT-29 and U2OS cells as well as  several 5-Lipoxygenase knockout cell clones (5-LO KO) derived from these cell lines and the corresponding vector controls (VC). Knockout of 5-Lipoxygenase was established using CRISPRCas technology. Three independent replicates from each cell line were measured.

first: Hannah

last: Weisser

first: Tamara

last: Göbel

first: Melissa

middle: G

last: Krishnathas

first: Marius

last: Kreiss

first: Carlo

last: Angioni

first: Duran

last: Sürün

first: Dominique

last: Thomas

first: Tobias

last: Schmid

first: Ann-Kathrin

last: Häfner

middle: S


title: Stress-induced multimerization of MYC shields stalled replication forks from RNA Polymerase

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

institute: Christian-Albrechts-University Kiel

summary: Oncoproteins of the MYC family drive the development of numerous human tumors1-4. In unperturbed cells, MYC proteins bind to virtually all active promoters and control transcription by RNA Polymerase II (RNAPII)2,3,5,6. MYC proteins can also coordinate transcription with DNA replication7-9 and promote the repair of transcription-associated DNA damage10, but how they exert these mechanistically diverse functions is unknown. Here we show that MYC dissociates from most of its binding sites in promoters and forms stable multimeric shell-like structures in response to perturbation of transcription elongation, mRNA splicing, or DNA replication. MYC multimers recruit interacting proteins that can promote transcription termination into their shells. Intriguingly, MYC multimers accumulate on chromatin immediately adjacent to stalled replication forks and surround the FANCD2, ATR and BRCA1 proteins, which are located at stalled forks11,12. MYC multimers accumulate ubiquitylated proteins and their formation depends on the HUWE1 ubiquitin ligase10,13. In response to replication stress, HUWE1 and MYC limit phosphorylation of the single-strand binding protein, RPA. We propose that localised multimerisation of MYC creates a transcription termination zone around stalled replication forks that limits checkpoint signalling in response to transcriptional and replication stress, allowing tumor cells to actively proliferate under stressful conditions

overall_design: Chromatin binding of MYC, FANCD2 and ATR alsong with gene expression data after variation chemical treatments

first: Daniel

last: Solvie

first: Apoorva

last: Baluapuri

first: Leonie

last: Uhl

first: Theresa

last: Endres

first: Martin

last: Eilers


title: Single-cell RNA sequencing of MCF-7, T-47D and ZR-75-1 breast cancer cell lines treated with estrogen and progesterone

city: Portland

first: Ellen

last: Langer

state: OR

address: 2720 SW Moody Ave

department: DOS (Department of Oncological Sciences)

institute: Oregon Health and Science University

summary: In order to study transcriptional heterogeneity in response to hormone stimulation in breast cancer, we performed high-throughput single-cell RNA sequencing (scRNA-seq) on 3 breast cancer cell lines that differ in their nuclear receptor expression levels. MCF-7, T-47D and ZR-75-1 cell lines were treated with estrogen and progesterone alone or in combination and collected at different time points. Hash-tagging antibodies were used to identify samples.

overall_design: High throughput single cell RNA sequencing (RNA-seq) for MCF-7 (27606 cells ), T-47D (25165 cells ) and ZR-75-1 (21397 cells) breast cancer cell lines treated with estrogen (E2) for 3, 6, 24, 48 and 72 hours (h) or progesterone (PG) for 3 and 48 h or a combination of estrogen and progesterone (E2 + PG) or 3 and 48 h. 2 clones were isolated from MCF-7 and subject to 24h and 48h estrogen treatments to assess for clonal derive effect in gene expression. Single cell RNA sequencing of TAMR (3750 cells), HCI003 (1615 cells) and HCI011 (13470 cells) organoids treated with estrogen. 10X multiomic (scRNA and scATAC) sequencing of MCF7 cells (6438 cells) treated with estrogen.

first: Aysegul

last: Ors

first: Aaron

last: Doe

first: Alex

last: Chitsazan

first: Hisham

last: Mohammed

first: Yahong

last: Wen

first: Ryan

last: Mulqueen


title: Human OA cartilages treated with ANGPTL3 mimetic LNA043 and placebo

city: Cambrdige

first: Yunyu

last: Zhang

state: MA

address: 22 Windsor Ave

institute: Novartis Institute for Biomedical Research

summary: Human OA patients subject to total knee replacement (TKR) were randomly selected and treated either LNA043 or placebo via intra-articular injection at 2hrs, 7days and 21days before surgery. The cartilage tissue were collected. Total RNA were extraced from both damaged and undamaged looking part of the tissue, and underwent gene expression profiling performed using next-generation sequencing on a Illumina platform.

overall_design:
Paired design of both damaged and undamaged carilage tissue each from 7 and 9 patients treated with placebo and LNA043 were used in this study
>>> Submitter declares that the raw data are unavailable for patient confidentiality reasons. <<<

first: Celeste

last: Scotti

first: Thomas

last: Peters

first: Sophie

last: Lemire

first: Nicole

last: Gerwin


title: The non-coding RNA miR-17∼92 is a central mediator of T cell costimulation [II]

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: To unravel the molecular mechanism underlying miR-17∼92 costimulatory function, we performed RNA-seq on CD4+ T cells from mice lacking miR-17∼92 in T cell, wildtype mice, mice overexpressing miR-17∼92 in T cells , mice with a constitutive knockout of CD28, and rescue mice, in naïve state or activated vitro for 24h.

overall_design: We compared mice from 5 genotypes: CD4cre.miR-17∼92lox/lox (designated T1792Δ/Δ hereafter); wildtype (designated wt hereafter); CD4cre.Rosa26loxSTOPloxCAG-miR-17∼92Tg (designated T1792tg/tg hereafter); B6.CD28-/- knockout (designated CD28-/- hereafter); and B6.CD28-/-.CD4cre.Rosa26loxSTOPloxCAG-miR-17∼92Tg (designated rescue hereafter). Naïve CD4+ T cells were stimulated in vitro for a duration of 24 hours.

first: Marianne

last: Doelz

first: Lukas

last: Jeker

first: Julien

last: Roux


title: The  non-coding RNA miR-17∼92 is a central mediator of T cell costimulation [I]

summary: To unravel the molecular mechanism underlying miR-17∼92 costimulatory function, we performed RNA-seq on CD4+ T cells from mice lacking miR-17∼92 in T cell, wildtype mice and mice overexpressing miR-17∼92 in T cells, in naïve state or activated vitro for 24h and 48h.

overall_design: We compared mice from 3 genotypes: CD4cre.miR-17∼92lox/lox (designated T1792Δ/Δ hereafter); wildtype (wt); and CD4cre.Rosa26loxSTOPloxCAG-miR-17∼92Tg (designated T1792tg/tg hereafter). Naïve CD4+ T cells were stimulated in vitro for a duration of 24 or 48hours.


title: Dementia with Lewy bodies post-mortem brains reveal differentially methylated CpG sites with biomarker potential

city: Royal Oak

first: Stewart

middle: F.

last: Graham

state: MI

address: 3811 W.13 Mile Road

department: Obstetrics and Gynecology

institute: Oakland University William Beaumont School of Medicine

type: Methylation profiling by genome tiling array

summary:
Dementia with Lewy bodies (DLB) is a common form of dementia with known genetic and environmental interactions. However, the underlying epigenetic mechanisms which reflect these gene-environment interactions are poorly studied.
Herein, we measured genome-wide DNA methylation profiles of post-mortem brain tissue (Broadmann area 7) from 15 pathologically confirmed DLB brains and compared them with 16 cognitively normal controls using Illumina MethylationEPIC arrays. We identified 17 significantly differentially methylated CpGs (DMCs) and 17 differentially methylated regions (DMRs) between the groups. The DMCs are mainly located at the CpG islands, promoter and first exon regions. Genes associated with the DMCs are linked to “Parkinson disease” and “metabolic pathway”, as well as the diseases of “severe intellectual disability” and “mood disorders”.
Overall, our study highlights previously unreported DMCs offering insights into DLB pathogenesis with the possibility that some of these could be used as biomarkers of DLB in the future.

overall_design: Bisulphite converted DNA from the 15 DLB brain samples and 16 normal brain samples were hybridised to the Illumina Infinium Human MethylationEPIC Beadchip

first: Xiaojian

last: Shao

first: Sangeetha

last: Vishweswaraiah


title: The non-coding RNA miR-17∼92 is a central mediator of T cell costimulation

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

overall_design: Refer to individual Series


title: 3D microengineered vascularized tumor spheroid for drug delivery and efficacy testing

status: Public on Sep 07 2022

city: Seoul

first: Da-Hyun

last: Kim

address: 1 Gwanakro

country: South Korea

institute: Seoul National University

summary: Tumor angiogenesis is regarded as a promising target for limiting cancer progression because tumor-associated vasculature supplies blood and provides a path for metastasis. Thus, in vitro recapitulation of vascularized tumors is critical to understand the pathology of cancer and identify the mechanisms by which tumor cells proliferate, metastasize, and respond to drugs. In this study, we microengineered a vascularized tumor spheroid (VTS) model to reproduce the pathological features of solid tumors. We first generated tumor cell-EC hybrid spheroids with self-assembled intratumoral vessels, which enhanced the uniformity of the spheroids and peritumoral angiogenic capacity compared to spheroids comprised only with cancer cells. Notably, the hybrid spheroid also exhibited expression profiles associated with aggressive behavior. The blood vessels sprouting around the hybrid spheroids on the VTS chip were interconnected with intratumoral vessels and displayed the distinctive characteristics of leaky tumor vessels. With the VTS chip showing a progressive tumor phenotype, we validated the suppressive effects of axitinib on tumor growth and angiogenesis, which depended on exposure dose and time, highlighting the significance of tumor vascularization to predict the efficacy of anticancer drugs. Ultimately, we effectively induced both lymphangiogenesis and angiogenesis around the tumor spheroid by promoting interstitial flow. Thus, our VTS model is a valuable platform with which to investigate the interactions between tumor microenvironments and explore therapeutic strategies in cancer.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tumor spheroids consisting of HepG2 cells and tumor-EC hybrid spheroids in a different ratio.

first: Jungho

last: Ahn

first: Dong-Jun

last: Koo

first: Sung-Yon

first: YongTae

first: NooLi

last: Jeon


title: Hepatic CYP2B10 is highly induced by binge ethanol and contributes to acute-on-chronic alcohol-induced liver injury

city: Rockville

first: Bryan

last: Mackowiak

state: MD

address: 5625 Fishers Lane, 2S12

institute: NIH

summary: We altered the NIAAA (Gao Binge Model) of 8 week chronic plus binge ethanol (E8G1) to have 3 total ethanol gavages (5 g/kg; 1 every 24h) of ethanol after 8 weeks of chronic ethanol feeding (E8G3) to determine how the liver responds to chronic plus consecutive binge ethanol. Surprisingly, E8G3 treatment induced lower levels of liver injury, steatosis, inflammation, and fibrosis as compared to mice after E8G1 treatment. Microarray analyses were performed, identifying several pathways that may contribute to the observed liver adaptation to binge ethanol. In addition, cytochrome P450 2B10 (Cyp2b10) was a top upregulated gene in the E8G1 group and further upregulated in the E8G3 group, but only moderately induced after chronic ethanol consumption, which was confirmed by RT-qPCR and western blot analyses. Genetic disruption of the Cyp2b10 gene worsened liver injury in E8G1 and E8G3 mice with higher blood ethanol levels compared to wild-type control mice, while in vitro experimentation revealed that CYP2b10 did not directly promote ethanol metabolism. Metabolomic analyses revealed significant differences in hepatic metabolites from E8G1-treated Cyp2b10 KO and WT mice, and these metabolic alterations may contribute to the reduced liver injury in Cyp2b10 KO mice.

overall_design: This experiment was conducted in parallel with GSE67546 - the E8w3B group is being uploaded in this dataset.

first: Mackowiak

last: Bryan

first: Xu

last: Ming-Jiang

first: Gao

last: Bin


title: Gut colonization by Proteobacteria alters host metabolism and modulates cocaine neurobehavioral responses

city: Madison

first: Santiago

last: Cuesta

state: Wisconsin

address: 3205 Microbial Sciences Building - 1550 Linden Drive

department: Department of Medical Microbiology and Immunology

institute: University of Wisconsin School of Medicine and Public Health

summary: Gut-microbiota membership is associated with diverse neuropsychological-diseases, including substance use disorders (SUDs). Unravelling mechanistic interactions between gut microbes and the host during psychostimulant use remains challenging. Here we show that cocaine exposure increases intestinal levels of norepinephrine, sensed through the bacterial adrenergic receptor QseC, promoting intestinal colonization of g-Proteobacteria. Gut colonization by g-Proteobacteria depletes the neuroactive metabolite glycine (used as a nitrogen source) both in the gut and cerebrospinal fluid, enhancing host cocaine-induced behaviors. Glycine repletion reversed this response, and intestinal colonization by g-Proteobacteria unable to uptake glycine did not alter the host response to cocaine. Transcriptomic profiling indicates a role of g-Proteobacteria modulated glycine levels in cocaine induced transcriptional plasticity in the nucleus accumbens through the glutamatergic transmission. Altogether, we introduce a mechanism by which intestinal bacteria alter the host’s brain responses to cocaine that could be exploited to modulate reward-related brain circuits that contribute to SUDs.

overall_design: RNA-Seq was performed on brain punches of the NAcc of mice collected 24 hs after the last injection of a repeated cocaine treatment. Three different groups were evaluated: mice microbiota-depleted reconstituted with a full microbiota (FMT, fecal microbiota transplant); mice microbiota-depleted reconstituted with a proteobacteria representative (Citrobacter rodentium DescN or Escherichia coli HS: Proteo animals). Cocaine treatment was administered once a day for 5 consecutive days using a dose of 15 mg/hg, i.p. The FMT groups was used as control. Each of the three conditions was performed in triplicate, resulting in a total of nine samples.

first: Paula

last: Burdisso

first: Amir

last: Segev

first: Said

last: Kourrich

first: Vanessa

last: Sperandio


title: Multimerization of MYC shields stalled replication forks from RNA polymerase [4sU-seq]

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

summary: Oncoproteins of the MYC family drive the development of numerous human tumors. In unperturbed cells, MYC proteins bind to virtually all active promoters and control transcription by RNA Polymerase II (RNAPII). MYC proteins can also coordinate transcription with DNA replication and promote the repair of transcription-associated DNA damage, but how they exert these mechanistically diverse functions is unknown. Here we show that MYC dissociates from many of its binding sites in active promoters and forms multimeric, often sphere-like structures in response to perturbation of transcription elongation, mRNA splicing or inhibition of the proteasome. Multimerization is accompanied by a global change in the MYC interactome towards proteins involved in transcription termination and RNA processing. MYC multimers accumulate on chromatin immediately adjacent to stalled replication forks and surround FANCD2, ATR and BRCA1 proteins, which are located at stalled forks. MYC multimerization is triggered in a HUWE1 and ubiquitylation-dependent manner. At active promoters, MYC multimers block antisense transcription and stabilize FANCD2 association with chromatin. This limits DNA double-strand break formation during S-phase and allows rapid recovery from replication stress, suggesting that multimerization of MYC enables tumor cells to proliferate under stressful conditions

overall_design: Nascent RNA profiling of cells upon rapid MYC degradation and rescue by either wtMYC or klessMYC

first: Danie

last: Solvie

first: Apoorva

last: Baluapuri

first: Leonie

last: Uhl

first: Theresa

last: Endres

first: Elmar

last: Wolf


title: Multimerization of MYC shields stalled replication forks from RNA polymerase [CUT&RUN, ChIP-seq]

overall_design: Chromatin binding of MYC, FANCD2, ATR, SPT5, RNAPII, pS4S8RPA, MAX, JUN and EXOSC10 along with gene expression data after variation chemical treatments

first: Daniel


title: Multimerization of MYC shields stalled replication forks from RNA polymerase

overall_design: Sequencing of double-strand breaks in cells exposed to HU, BI8626 in presence or absence of MYC induction


title: RNA-sequencing of human embryonic stem cell-derived retinal pigment epithelial cells (hESC-derived RPE) at different time points of culture.

city: Shanghai

first: Ting

last: Zhang

address: 100 Haining Road

department: Department of Ophthalmology

institute: Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine

summary: We report that the phase/stage of cell culture used for cryopreservation greatly affects the post-thaw outcomes. The goal of the study is to compare the transcriptome profiles between different time points and uncover the mechanism underlying RPE tolerace to freezing.

overall_design: In this study, hESC-derived RPE cells were collected and seeded at passage 1 day 35 (P1D35). After passage, these cells were labeled as passage 2 (P2).Three independent batches of hESC-derived RPE cells at P1D35, P2D5 and P2D11 (9 samples in total) were subjected to RNA sequencing.

first: Mei

last: Jiang


title: RNA-Seq siCtl vs siTMED2/10 in RPE1 cells

city: Lausanne

first: F.

last: van der Goot

state: Vaud

address: Bâtiment AI, Station 19

department: SV

institute: EPFL – École Polytechnique Fédérale de Lausanne

summary: Using the RNA seq data we show that Cholesterol synthesis pathway is upregulated upon siTMED2/10

overall_design: Total RNA was extracted from Ctl and TMED2/10 siRNA transfected RPE1 cells after 72 hr. Sequencing was performed using Illumina protocol.

first: Muhammad

middle: U

last: Anwar

first: Marion

last: Leleu


title: Tumor-associated macrophages expressing the transcription factor IRF8 promote T cell exhaustion in cancer

status: Public on Sep 06 2022

city: New York

first: Fengshen

last: Kuo

state: New York

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

summary: Tumor progression is associated with overstimulation of cytotoxic T lymphocytes (CTLs), resulting in a dysfunctional state of exhaustion. However, the identity of antigen-presenting cells that drive CTL exhaustion is poorly defined. Here we show that tumor-associated macrophages (TAMs) expressing the transcription factor interferon regulatory factor-8 (IRF8) promote CTL exhaustion in a murine model of breast cancer. While CTL priming in tumor-draining lymph nodes was enabled by IRF8-dependent type 1 dendritic cells, CTL exhaustion in tumor required TAM expression of IRF8 that supported the cancer cell antigen-presenting function of TAMs. Macrophage-specific ablation of IRF8 reversed exhaustion of cancer cell antigen-reactive CTLs, and suppressed tumor growth. Analysis of the immune-infiltrated human renal cell carcinoma tumors revealed abundant TAMs that expressed IRF8 and were enriched for an IRF8 gene expression signature. Furthermore, the TAM-IRF8 signature co-segregated with CTL exhaustion signatures across multiple cancer types. Thus, CTL exhaustion is promoted by TAMs via IRF8.

overall_design: Bulk RNAseq on antigen-presenting cells from mouse PyMT breast tumor, tumor-associated macrophages expressing or not the transcription factor IRF8, and scRNA-seq on CD8 T cells in PyMT breast tumor from IRF8FLPyMT or MafBiCreIRF8FLPyMT mice.

first: Briana

last: Nixon

first: LiangLiang

last: Ji

first: Ming

last: Liu

first: Kristelle

last: Capistrano

first: Mytrang

last: Do

first: Ruth

middle: A

last: Franklin

first: Xiaodi

last: Wu

first: Emily

middle: R

last: Kansler

first: Raghvendra

middle: M

last: Srivastava

first: Tanaya

last: Purohit

first: Alejandro

last: Sanchez

first: Lynda

last: Vuong

first: Chirag

last: Krishna

first: Xinxin

last: Wang

first: Herbert

last: Morse III

first: James

middle: J

last: Hsieh

first: Timonthy

last: Chan

first: Kenneth

last: Murphy

last: Moon

first: A

last: Hakimi

middle: O

last: Li


title: Analysis of 3D Chromatin Structure in Chondrocytes Identifies Putative OA Risk Genes

city: Chapel Hill

first: Douglas

last: Phanstiel

state: NC

address: 104 Manning Dr (Thurston Bowles Building), Rm 4019

institute: University of North Carolina at Chapel Hill

summary: Genome-wide association studies (GWAS) have identified over 100 loci associated with OA risk, but the majority of OA risk variants are non-coding, making it difficult to identify the impacted genes for further study and therapeutic development. To address this need, we used a multi-omic approach and genome editing to identify and functionally characterize putative OA risk genes. Computational analysis of GWAS and ChIP-seq data revealed that chondrocyte regulatory loci are enriched for OA risk variants. Mapping active enhancers in primary human chondrocytes and intersecting them with OA GWAS variants produced a refined list of putative causal variants. Identifying DNA loops in the chondrocyte cell line C28/I2 using in situ Hi-C allowed us to connect those putative causal variants to target genes and revealed SOCS2 as a putative mediator of OA risk. CRISPR-Cas9-mediated deletion of SOCS2 in primary human chondrocytes from three independent donors led to heightened expression of inflammatory markers in response to a cartilage matrix breakdown product of fibronectin. In total, we identified 56 putative OA risk genes—including 20 that are connected to OA risk SNPs via DNA looping—for further research and potential therapeutic development.

overall_design: In situ Hi-C was performed on C-28/I2 cells. C-28/I2 cells were cultured in DMEM/F12 media with 10% fetal bovine serum, 0.1% penicillin streptomycin solution, 0.1% amphotericin B, and 0.04% gentamicin. Cells were treated with DMEM/F12 media with 1% ITS-Plus for 48 hours prior to experiments to promote the chondrocyte phenotype. Cells were then washed with 1X PBS and treated with trypsin-EDTA (0.25%) for 3 minutes. Trypsin was quenched and cells were pelleted at 4°C for 5 minutes at 300g. Cells were resuspended in 1mL DMEM/F12 per million cells and crosslinked in 1% formaldehyde for 10 min with rotation before quenching in a final concentration of 0.2M glycine for 5 min with rotation. Cells were pelleted at 300g for 5 min at 4°C. Pellets were washed with cold PBS and aliquoted into ~3 million cell aliquots. Pellets were flash frozen in liquid nitrogen and stored at -80°C. In situ Hi-C was performed as described by Rao et al. 2014 (PMID: 25497547) for four technical replicates. Cut and run was performed on primary articular chondrocytes. Primary chondrocytes were isolated via enzymatic digestion from human femoral cartilage obtained from two tissue donors without a history of arthritis, as previously described (PMID: 12905472).

first: Eliza

last: Thulson

first: Eric

last: Davis

first: Susan

last: D’Costa

first: Philip

last: Coryell

first: Nicole

last: Kramer

first: Richard

last: Loeser

first: Brian

last: Diekman


title: CAG repeat-binding small molecule improves repeat-length-dependent dysregulation of gene expression profiles in a mouse model of Dentatorubral–pallidoluysian atrophy

city: Suita

first: Masayuki

last: Nakamori

state: Osaka

address: 2-2, D-4, Yamadaoka

institute: Osaka University Graduate School of Medicine

summary: Dentatorubral–pallidoluysian atrophy (DRPLA) is a devastating genetic disease presenting myoclonus, epilepsy, ataxia, and dementia. DRPLA is caused by the expansion of a CAG repeat in the ATN1 gene. The expanded CAG repeats are unstable, and ongoing repeat expansions contribute to disease onset, progression and severity. Previously, we characterized a small molecule, naphthyridine–azaquinolone (NA), which binds to CAG slip-out structures and induces repeat contraction in Huntington’s disease mice. Here, we demonstrate that long-term intracerebroventricular infusion of NA leads to repeat contraction in a murine model of DRPLA. To identify the effects of NA on transcriptional regulation, we conducted comprehensive gene expression analysis using RNA sequencing (RNA-Seq) in striatum from PBS-treated and NA-treated DRPLA mice.

overall_design: We analyzed of mRNA expression in striatum from DRPLA mice treated with PBS (n = 3) or naphthyridine-azaquinolone (NA) (n = 3).

first: Yuhei

last: Hasuike


title: Early life low-calorie sweetener consumption disrupts glucose regulation, sugar-motivated behavior, and memory function in rats

city: La Jolla

first: Francesca

last: Telese

state: CA

address: 9500 Gilman Drive

department: Psychiatry

institute: UCSD

summary: Low-calorie sweetener (LCS) consumption in children has increased dramatically due to widespread presence in the food environment and efforts to mitigate obesity through sugar replacement. However, mechanistic studies on the long-term impact of early-life LCS consumption on cognitive function and physiological processes are lacking. Here, we developed a rodent model to evaluate the effects of daily LCS consumption (acesulfame potassium, saccharin, or stevia) during adolescence on adult metabolic, behavioral, gut microbiome, and brain transcriptomic outcomes. Results reveal that habitual early-life LCS consumption impacts normal post-oral glucose handling and impairs hippocampal-dependent memory in the absence of weight gain. Furthermore, adolescent LCS consumption yielded long-term reductions in lingual sweet taste receptor expression and alterations in sugar-motivated appetitive and consummatory responses. While early life LCS consumption did not produce robust changes in the gut microbiome, brain region-specific RNA sequencing analyses reveal LCS-induced changes in collagen- and synaptic signaling-related gene pathways in the hippocampus and nucleus accumbens, respectively, in a sex-dependent manner. Collectively, these results reveal that habitual early-life LCS consumption has long lasting implications for glucoregulation, sugar-motivated behavior, and hippocampal-dependent memory in rats, which may be based in part on changes in nutrient transporter, sweet taste receptor, and central gene pathway expression.

overall_design: Male and female Sprague Dawley rats (Envigo, Indianapolis, IN, USA; postnatal day (PN) 25; 50-70g) were housed individually in a climate controlled (22–24 °C) environment with a 12:12 light/dark cycle (lights off at 6pm). Rats were maintained on standard chow (Lab Diet 5001; PMI Nutrition International, Brentwood, MO, USA; 29.8% kcal from protein, 13.4% kcal from fat, 56.7% kcal from carbohydrate) and water. All experiments were performed during the light cycle. At PN 26, rats were randomized into groups of comparable weights and provided with their experimental diets. Body weights were measured daily whereas water consumption and chow intake were measured 3 times per week. Female estrus phase was not manipulated nor tracked in any of the experiments.    Diet. Juvenile male and female rats (n=8 per sex) were provided with the maximum acceptable daily intake (ADI) in mg/kg body weight, as recommended by the U.S. FDA, for acesulfame potassium (ACE-K; catalog # A2815, Spectrum Chemical, Gardena, CA, USA; 0.1% weight/volume (w/v) in reverse osmosis (RO) water; ~15 mg/kg). The volume required for delivery of ACE-K was calculated based on body weight daily and injected into a rodent sipper tube with a vinyl cap, and placed on the wire rack of the home cage adjacent to the rat’s ad libitum standard chow and water bottle. Voluntary consumption of the entire sweetener ration was verified daily by inspecting the tube for all animals. Rats in the control group (CTL; n=8 per sex) were provided a sipper tube filled with RO water at an equivalent volume/body weight as the ACE-K and group. Sweetener access ceased at PN 80.

first: Linda

last: Tsan

first: Sandrine

last: Chometton

first: Anna

last: Hayes

first: Molly

last: Klug

first: Yanning

last: Zuo

first: Shan

last: Sun

first: Lana

last: Bridi

first: Rae

last: Lan

first: Anthony

last: Fodor

first: Emily

last: Noble

first: Xia

last: Yang

first: Scott

last: Kanoski

first: Lindsey

last: Schier


title: Multimerization of MYC shields stalled replication forks from RNA polymerase.

first: Martin

last: Eilers


title: Comparison of miRNA transcriptomes reveals differential regulation from ten tissues and four development stages of Sika Deer

city: Changchun

first: Boyin

last: Jia

state: Jilin

address: 2888 Xincheng Street

department: College of Animal Science and Technology

institute: Jilin Agricultural University

summary: To elucidate the complex physiological process of the growth, development and immunity response of Sika Deer, this study evaluated the changes of miRNA profiles in the four developmental stages (juvenile, adolescence, adult and aged) of ten tissue (adrenal, antler, brain, heart, kidney, lung, liver, skeletal muscle, spleen and testes). The results showed that a total of 306 known miRNAs and 143 novel miRNAs were obtained. Many miRNAs displayed organ-specificity and age-specificity. The largest number of miRNAs were enriched in the brain, some of which were shared only between the brain and adrenal. These miRNAs were involved in maintaining specific functions within the brain and adrenal. Additionally, the adolescence-adult transition of Sika Deer was a crucial stage in its life cycle. In conclusion, our study provided abundant data support for the current research Sika Deer. It also contributes to understand the role of miRNAs play in regulating the growth, development and immunity response of Sika Deer.

overall_design: The miRNA expression profiles in the four developmental stages of ten tissue in Sika Deer were generated by Illumina HiSeq2500 sequencing

first: Rui

last: Du

first: Fuhe


title: Multimerization of MYC shields stalled replication forks from RNA polymerase [BLISS]

first: Danie

last: Solvie

first: Apoorva

last: Baluapuri

first: Leonie

last: Uhl

first: Theresa

last: Endres

first: Elmar

last: Wolf


title: The highly conserved RNA-binding specificity of nucleocapsid protein facilitates the identification of drugs with broad anti-coronavirus activity.

city: Hong Kong

first: Jian

last: Yan

state: Hong Kong Special Administrative Region

address: 83 Tat Chee Avenue, Kowloon

department: Department of Biomedical Sciences

institute: City University of Hong Kong

summary: We performed the high-throughput RNA-SELEX (HTR-SELEX) to determine the RNA-binding specificity of the N proteins of various SARS-CoV-2 variants as well as other β-coronaviruses and showed that N proteins could bind two unrelated sequences, both of which were highly conserved across all variants and species.

overall_design: We purified nucleocapsid proteins of SARS-CoV-2 and other β-coronaviruses, by performed HTR-SELEX, we found it has strong and reproducible RNA sequence specificity.

first: Jilin

last: Zhang

first: Shaorong

last: Fan

first: Wenju

first: Ligang

last: Wu


title: Combined α- and β-adrenergic receptor activation triggers thermogenesis by the futile creatine cycle.

city: Montreal

first: Lawrence

last: Kazak

address: 3655 Prom Sir-William-Osler

institute: McGill University

summary: Noradrenaline regulates cold-stimulated adipocyte thermogenesis. Aside from cAMP signaling downstream of β-adrenergic receptor (βAR) activation, how noradrenaline promotes thermogenic output is still not fully understood. Here, we show that coordinated α1-adrenergic receptor (α1AR) and β3AR signaling induces the expression of thermogenic genes of the futile creatine cycle, and that EBFs, ERRs, and PGC1α are required for this response in vivo. Noradrenaline triggers physical and functional coupling between the α1AR subtype (ADRA1A) to Gαq to promote adipocyte thermogenesis in a manner that is dependent on the effector proteins of the futile creatine cycle, creatine kinase b (CKB) and tissue-nonspecific alkaline phosphatase (TNAP). Combined Gαq and Gαs signaling selectively in adipocytes promotes a continual rise in whole-body energy expenditure, and CKB is required for this effect. Thus, the ADRA1A-Gαq-futile creatine cycle axis is a key regulator of facultative and adaptive thermogenesis.

overall_design: Comparative ATACseq profiling analysis for brown adipose tissue (either 30°C or 6°C) with saline solution or PBZ injections.

first: Janane

last: Rahbani


title: Vitamin C Potentiates Plasma Cell Differentiation via TET-mediated DNA modification [Bisulfite-Seq]

city: Columbus

first: Chan-Wang

middle: Jerry

last: Lio

state: Ohio

address: 460 W 12th Ave

institute: Ohio State University

type: Methylation profiling by high throughput sequencing

summary: Ascorbate (vitamin C) is an essential micronutrient in humans. The chronic severe deficiency of ascorbate, termed scurvy, has long been associated with increased susceptibility to infections. How ascorbate affects the immune system at the cellular and molecular levels remained unclear. Here, from a micronutrient screen, we identified ascorbate as a potent enhancer for antibody response by facilitating the IL-21/STAT3-dependent plasma cell differentiation in mouse and human B cells. The effect of ascorbate is unique, as other antioxidants failed to promote plasma cell differentiation. Ascorbate is critical during early B cell activation by poising the cells to plasma cell lineage without affecting the proximal IL-21/STAT3 signaling and the overall transcriptome. Consistent with its role as a cofactor for epigenetic enzymes, ascorbate potentiates plasma cell differentiation by remodeling the epigenome via TET (Ten Eleven Translocation), the enzymes responsible for DNA demethylation by oxidizing 5-methylcytosines into 5-hydroxymethylcytosine (5hmC). Genomewide 5hmC profiling identified ascorbate responsive elements (EAR) at the Prdm1 locus, including a distal element with a STAT3 motif overlapped with a CpG that was methylated and modified by TET in the presence of ascorbate. The results suggest that an adequate level of VC is required for antibody response and highlight how micronutrients can cooperate with epigenetic enzymes to regulate gene expression. Our finding also implies that epigenetic enzymes can function as sensors to gauge the availability of metabolites and influence cell fate decisions.

overall_design: The characterize the effect of vitamin C on DNA modification in B cells.

first: Jerry

first: Heng-Yi

last: Chen

first: Michael

last: Hsu


title: ARID1A maintains transcriptionally repressive H3.3 through CHD4-ZMYND8 chromatin interactions [12Z_shARID1A_CHD4_H3.1_ChIP]

city: Grand Rapids

first: Ronald

middle: L.

last: Chandler

department: Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University

summary:
Background: SWI/SNF (BAF) chromatin remodeling complexes regulate lineage-specific enhancer activity by promoting accessibility for diverse DNA-binding factors and chromatin regulators. Additionally, they are known to modulate the function of the epigenome through regulation of histone post-translational modifications and nucleosome composition, although the way SWI/SNF complexes govern the epigenome remains poorly understood. Here, we investigate the function of ARID1A, a subunit of certain mammalian SWI/SNF chromatin remodeling complexes associated with malignancies and benign diseases originating from the uterine endometrium.
Results: Through genome-wide analysis of human endometriotic epithelial cells, we show that more than half of ARID1A binding sites are marked by the variant histone H3.3, including active regulatory elements such as super-enhancers. ARID1A knockdown leads to H3.3 depletion and gain of canonical H3.1/3.2 at ARID1A-bound active regulatory elements, and a concomitant redistribution of H3.3 towards genic elements. ARID1A interactions with the repressive chromatin remodeler CHD4 (NuRD) are associated with H3.3, and ARID1A is required for CHD4 recruitment to H3.3. ZMYND8 interacts with CHD4 to suppress a subset of ARID1A, CHD4, and ZMYND8 co-bound, H3.3+ H4K16ac+ super-enhancers near genes governing extracellular matrix, motility, adhesion, and epithelial-to-mesenchymal transition. Moreover, these gene expression alterations are observed in human endometriomas.
Conclusions: These studies demonstrate that ARID1A-containing BAF complexes are required for maintenance of the histone variant H3.3 at active regulatory elements, such as super-enhancers, and this function is required for the physiologically relevant activities of alternative chromatin remodelers.

overall_design: Human 12Z endometriotic epithelial cells were measured for genome-wide CHD4 binding and canonical H3.1/3.2 abundance, with or without ARID1A knockdown by shRNA (shARID1A), by chromatin immunoprecipitation followed by sequencing (ChIP-seq).

first: Jake

last: Reske

middle: L


title: Vitamin C Potentiates Plasma Cell Differentiation via TET-mediated DNA modification [ChIP-seq]

first: Ana

last: Almonte-Loya


title: Accumulation of Acetaldehyde in aldh2.1-/- Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: In conclusion, the data have identified acetaldehyde as the preferred substrate for Aldh2.1’s detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose-6-phosphatase. Moreover, Stress-activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1-/- zebrafish mutants.

overall_design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification, metabolomics, genomics and organ health - especially vascular health.

first: David

middle: P

last: Wohlfart

first: Jens

last: Kroll


title: RNA sequencing of blood-resident Eµ-myc lymphoma cells from TpoTg and wild-type mice after Eµ-myc tumour transplant.

city: Parkville

first: Connie

middle: S. N.

last: Li-Wai-Suen

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

summary: RNA sequencing of blood-resident Eµ-myc lymphoma cells from TpoTg mice post tumour transplant revealed upregulated hallmark gene sets associated with inflammatory response, when compared to Eµ-myc tumour transplanted wild-type mice.

overall_design: Murine mCherry+Eµ-myc lymphoma cells were transplanted into TpoTg and wild-type mice. Total RNA was prepared from FACS sorted tumour cells from blood of tumour bearing mice and RNA-seq was performed.

first: Emma

middle: C

last: Josefsson

first: Jason

last: Corbin

first: Amanda

last: Au

first: Alexandra

last: Garnham


title: Transcriptomic analysis reveals the multifaceted impairments of DC functions produced by a Morbillivirus infection

city: Madrid

first: Isabel

last: García-García

state: Madrid

address: Calle José Antonio Novais, 12

department: Genética, Fisiología y Microbiología

country: Spain

institute: Universidad Complutense de Madrid (UCM)

summary: Viruses have evolved numerous strategies to impair immunity so that they can replicate more efficiently, such as the immunosuppressive effects of Morbillivirus infection. In the present work we hypothesized that the highly contagious morbillivirus Peste des Petits Ruminants virus (PPRV) could target monocytes and dendritic cells (DC) to contribute to the immunosuppressive effects produced by the infection. Monocytes isolated from healthy sheep donor, a natural host of the disease, could be infected by PPRV and this impaired the differentiation and phagocytic ability of immature monocyte-derived DC (MoDC). Ovine MoDC could be productively infected by PPRV, and this drastically reduced MoDC capacity to activate allogeneic T cell responses. Transcriptomic analysis of infected MoDC indicated that several tolerogenic DC signature genes were upregulated upon PPRV infection.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for eight mMoDCs cultures (four PPRV-infected (48 hours post infection) and four mock-infected).

first: Daniel

last: Rodríguez-Martín

first: Verónica

last: Martín

first: José

last: Rojas

first: Noemí

last: Sevilla


title: ARID1A-dependent maintenance of H3.3 is required for repressive CHD4-ZMYND8 chromatin interactions at super-enhancers [12Z_ZMYND8_ChIP]

overall_design: Human 12Z endometriotic epithelial cells were measured for genome-wide ZMYND8 binding by chromatin immunoprecipitation followed by sequencing (ChIP-seq).


title: ARID1A-dependent maintenance of H3.3 is required for repressive CHD4-ZMYND8 chromatin interactions at super-enhancers [12Z_siH3F3B_siZMYND8_RNA]

overall_design: Human 12Z endometriotic epithelial cells were measured for transcriptome-wide gene expression by mRNA-seq following knockdown of H3.3 (siH3F3B) or ZMYND8 (siZMYND8) by siRNA.


title: ARID1A-dependent maintenance of H3.3 is required for repressive CHD4-ZMYND8 chromatin interactions at super-enhancers [12Z_siCHD4_siARID1A_RNA]

overall_design: Human 12Z endometriotic epithelial cells were measured for transcriptome-wide gene expression by mRNA-seq following knockdown of CHD4 (siCHD4), ARID1A (siARID1A), or both factors (siCHD4+siARID1A) by siRNA.


title: ARID1A-dependent maintenance of H3.3 is required for repressive CHD4-ZMYND8 chromatin interactions at super-enhancers [12Z_shARID1A_H4K16ac_ChIP]

overall_design: Human 12Z endometriotic epithelial cells were measured for genome-wide H4K16ac abundance, with or without ARID1A knockdown by shRNA (shARID1A), by chromatin immunoprecipitation followed by sequencing (ChIP-seq).


title: ARID1A-dependent maintenance of H3.3 is required for repressive CHD4-ZMYND8 chromatin interactions at super-enhancers [12Z_shCHD4_H3.3_ChIP]

overall_design: Human 12Z endometriotic epithelial cells were measured for genome-wide H3.3 abundance, with or without CHD4 knockdown by shRNA (shCHD4), by chromatin immunoprecipitation followed by sequencing (ChIP-seq).


title: ARID1A-dependent maintenance of H3.3 is required for repressive CHD4-ZMYND8 chromatin interactions at super-enhancers [12Z_shARID1A_H3.3_H2A.Zac_ChIP]

overall_design: Human 12Z endometriotic epithelial cells were measured for genome-wide H3.3 and H2A.Zac abundance, with or without ARID1A knockdown by shRNA (shARID1A), by chromatin immunoprecipitation followed by sequencing (ChIP-seq).


title: Single cell clonal analysis identifies an AID-dependent pathway of plasma cell differentiation

first: Carmen

middle: Gómez-Escolar

last: Arias

address: Calle Melchor Fernández Almagro 3

institute: CNIC

summary: Germinal centers (GC) are microstructures where B cells that have been activated by antigen can improve the affinity of their B cell receptors and differentiate into memory B cells (MBCs) or antibody secreting plasma cells. Here we have addressed the role of Activation Induced Deaminase (AID), which initiates somatic hypermutation and class switch recombination, in the terminal differentiation of GC B cells. By combining single cell transcriptome and immunoglobulin clonal analysis in a mouse model that traces AID-experienced cells, we have identified a novel subset of late prePB cells (L-prePB), which shares the strongest clonal relationships with PBs. Mice lacking AID have various alterations in the size and expression profiles of transcriptional clusters. We find that AID deficiency leads to a reduced proportion of L-prePB cells and severely impairs transitions between the L-prePB and the PB subsets. Thus, AID shapes the differentiation fate of GC B cells by enabling PB generation from a prePB state.

overall_design: Spleen tomato+ cells were isolated from 2 Aicda-Cre+/ki;Rosa26tdTomato+/ki and 2 Aicda-Cre-/ki;Rosa26tdTomato+/ki and multiplexed for single cell RNA sequencing. Libraries for gene expression (GEX), V(D)J and demultiplexing were generated.

last: Gómez-Escolar

first: Álvaro

last: Serrano-Navarro

first: Alberto

last: Benguria

first: Fátima

last: Sánchez-Cabo

first: Almudena

last: Ramiro


title: ARID1A-dependent maintenance of H3.3 is required for repressive CHD4-ZMYND8 chromatin interactions at super-enhancers [12Z_CHD4_ChIP]

first: Ronald

last: Chandler

overall_design: Human 12Z endometriotic epithelial cells were measured for genome-wide CHD4 binding by chromatin immunoprecipitation followed by sequencing (ChIP-seq).

first: Jake

last: Reske


title: ARID1A-dependent maintenance of H3.3 is required for repressive CHD4-ZMYND8 chromatin interactions at super-enhancers [12Z_shARID1A_H2A.Z_panH4ac_ChIP]

overall_design: Human 12Z endometriotic epithelial cells were measured for genome-wide H2A.Z and pan-H4ac abundance, with or without ARID1A knockdown by shRNA (shARID1A), by chromatin immunoprecipitation followed by sequencing (ChIP-seq).


title: Vitamin C Potentiates Plasma Cell Differentiation via TET-mediated DNA modification [RNA-seq]

first: Chan-Wang

last: Lio

overall_design: The characterize the effect of vitamin C on the transcritomes in B cells.

first: Jerry

first: Heng-Yi

last: Chen

first: Ana

last: Almonte-Loya


title: Vitamin C Potentiates Plasma Cell Differentiation via TET-mediated DNA modification [5hmC]

overall_design: The characterize the effect of vitamin C on 5hmC modification in B cells.


title: Roles of Runx2 in chromatin landscape in skeletal development

city: Bunkyo-ku

first: Hironori

last: Hojo

state: Tokyo

address: 7-3-1 Hongo

department: Center for Disease Biology and Integrative Medicine

institute: The University of Tokyo

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

overall_design: Refer to individual Series


title: Epigenetic Remodeling by Vitamin C Potentiates Plasma Cell Differentiation

relation:
SuperSeries of: GSE183679
SuperSeries of: GSE183680
SuperSeries of: GSE206452
SuperSeries of: GSE206453


title: Roles of Runx2 in chromatin landscape in skeletal development [RNA-Seq]

summary: The transcriptional regulator Runx2 has essential roles in chondrocytes and osteoblasts, central to the coordinated development of cartilage and bone. However, the regulatory mechanisms underlying Runx2’s roles in skeletal programming are not well understood. Here, we performed an integrative analysis of Runx2–DNA binding and chromatin accessibility in vivo and identified cell type-distinct chromatin accessibility underlying Runx2 roles in osteoblasts and chondrocytes.

overall_design: Examination of transcriptome in skeletal cells


title: Analysis on the transcriptomic changes by LINE-1 overexpression with CRISPRa in NIH3T3 cells

city: New Haven

first: Takehiro

last: Takahashi

state: Connecticut

address: 300 Cedar Street TAC S630

institute: Yale University

summary: We report the transcriptomic changes caused by activation of a class of endogenous retroelements long interspersed nuclear elements-1 (LINE-1) by CRISPR activation module. Using lentiviruses, we generated dCas9-CRISPR activator-stably expressing NIH3T3 cells and transfected the sgRNA plasmid targeting the promoter sequence of evolutionally young LINE-1 family (Tf family). RNA was extracted from those cells, sequenced, and analyzed for transcriptome of both cellular genes as well as retroelements expression. The results showed significant upregulation of anti-viral genes and interferon stimulated genes as well as many genes related to cellular homeostasis. This is the first detailed transcriptomic analysis of gene expression perturbation in the cells in which LINE-1 is directly targeted via its promoter and upregulated.

overall_design: Analysis on the RNA expression profile 48-hours after the transfection of scramble (Scr) or LINE1-targeting (L1) sgRNA plasmids to the dCas9-CRISPR activator stably expressing NIH3T3 cells.

first: Eric

last: Song

first: Yong

last: Kong


title: Transcriptomic profiling of THP-1 stable cell lines overexpressing genes associated with inflammatory bowel diseases (IBD)

city: Montréal

first: John

middle: D

last: Rioux

state: QC

address: 5000 Bélanger St.

department: Research Center

institute: Montreal Heart Institute

summary:
More than 200 genomic loci have been identified and validated by GWAS to be associated with IBD. However, for most of these loci, the causal gene remains unknown. The current study is aimed at uncovering the role of genes located within IBD-associated loci and endogenously expressed in the myeloid cell model THP-1 by over-expressing them in this cell lineage.
The open reading frames (ORF) for 42 genes from IBD-associated loci were expressed in the THP-1 model of human monocytes using lentivirus vector for plasmid transduction. An empty vector transduced into THP-1 as control. Three biological replicates have been done for each transduction.
The impact of each IBD ORFs on THP-1 transcriptome profile was analyzed using an whole RNA sequencing-based approach.
This functional genomics screen showed the affected genes (upregulated and downregulated) in response to the increased expression RNA of each IBD gene (ORF) in THP-1.
In order to find biological categories enriched of the affected genes, enrichment analyses  have been done using the g:GOSt functional profiling tool (using Ensembl database release 98) from the online g:Profiler service.

overall_design: mRNA profile of THP-1 overexpressing IBD genes

first: Sylvain

last: Foisy

first: Mohamad

last: Karaky

first: Gabrielle

last: Boucher

first: Melanie

last: Burnette

first: Guy

last: Charron


title: Analysis on the transcriptomic profile in NIH3T3 cells by LINE-1 overexpression with CRISPRa, and the cerebellar vermis of ataxia telangiectasia patients

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Genome-wide maps of chromatin state in human primary CAR-T cells [RNA-seq]

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

institute: Stanford University

summary: We report the transcriptomic and epigentic profile of human primary CD19-28z CAR-T cells.

overall_design: CRISPR gene editing was used to delete MED12 or the "safe harbor" control gene AAVS1. Gene-edited CAR-T cells were cultured in vitro for 15 days. Unstimulated cells were collected on day 15. Stimulated cells were collected after 3 hours of stimulation with plate-bound anti-idiotype antibodies specific for the CAR.

first: Katherine

last: Freitas


title: Effect of Notch inhibition on human iPSC-derived retinal organoids

status: Public on Sep 05 2022

city: San Francisco

first: Deepak

last: Lamba

address: 35 Medical Center Way, Rm1024

institute: University of California, San Francisco

summary:
To investigate the effects of Notch inhibition  at various stages of differentiation of human iPSC-derived retinal organoids. PF03084014 was added to media for 2 days and organoids analyzed 4 weeks later.
We then performed gene expression profiling analysis using data obtained from RNA-seq at three stages of differentiation D45, D60 and D90.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for organoids which are vehicle or notch inhibitor treated.


title: Genome-wide maps of chromatin state in human primary CAR-T cells [ChIPseq, ATAC-seq]

first: Bence

last: Daniel

first: Katalin

last: Sandor


title: Profiles of Pelvic organ prolapse [miRNA-seq]

city: chengdu

first: Xia

last: Yu

address: No.1617 Ri Yue Street, Chengdu, Sichuan

institute: Chengdu women and Children's hospital

summary: Pelvic organ prolapse (POP) affects a large proportion of adult women. With the increase in global population ageing, the prevalence of POP is expected to increase in upcoming decades, which will impose a substantial medical burden. Therefore, suitable therapeutical target is important. However, due to the pathogenesis of POP is still unclear, it leads to the failure of POP repair. Herein, we identified changes in ncRNA, and mRNAs in the anterior vaginal wall and uterosacral ligament in patients with POP, providing new insights into the pathogenesis of POP and new targets for treatment.

overall_design: Anterior vaginal wall and uterosacral ligaments were subjected to RNA sequencing


title: Profiles of Pelvic organ prolapse


title: KCNQOT1 ChIRP seq and perturbation epigentic profiles [ChIP-seq]

city: Beijing

first: Shiqiang

last: Zhang

state: Beijing

address: Peking University

institute: Peking University

summary: Transposon (de)repression and heterochromatin reorganization are dynamically regulated during cell fate determination and are hallmarks of cellular senescence. However, whether they are sequence specifically regulated remains unknown. Here, we uncover the KCNQ1OT1 lncRNA, by sequence-specific Hoogsteen base-pairing with double-stranded genomic DNA via its repeat-rich region and binding to heterochromatin protein HP1⍺, guides, induces and maintains epigenetic silencing at specific repetitive DNA elements. Repressing KCNQ1OT1 or deleting its repeat-rich region reduces DNA methylation and H3K9me3 on KCNQ1OT1 targeted transponsons. Engineering a fusion KCNQ1OT1 with an ectopically targeting guiding triplex sequence induces de novo DNA methylation at the target site. Phenotypically, repressing KCNQ1OT1 induces senescence associated heterochromatin foci, transposon activation and retrotransposition, and cellular senescence, demonstrating an essential role of KCNQ1OT1 to safeguard against genome instability and senescence.

overall_design: H3K9me3 modification status was analyzed by ChIP-seq in HEK293TWT, EV and KCNQ1OT1_K KD cells.

first: Xiaoli

first: Quanlong

last: Jiang

first: Jiyang

last: Li

first: Yaqiang

last: Cao

first: Jing-Dong

last: Han


title: KCNQOT1 ChIRP seq and perturbation epigentic profiles [Mouse eCLIP]

summary: To study the molecular function of lncRNA KCNQOT1, we performed ChIRP-seq HEK293T cells, and we knocked it down in NIH3T3 and HEK293T cells, and created knockout of the repeat-rich and non-repeat regions of KCNQOT1 separately in HEK293T cells, then performed H3K9me3 ChIP-seq, DNA methylation MeDIP-seq and RNA-seq in the perturbed and control wild type cells.

overall_design: HP1 alpha associated lncRNAs were analyzed by eCLIP-seq in NIH3T3 cells.


title: Lung neutrophil subsets transcriptomes in WT and CGD mouse in response to fungal PAMPs stimulation

city: St Louis

first: Mary

last: Dinauer

state: Missouri

address: 660 South Euclid Ave

department: Pathology & Immunology

institute: Washington University In St Louis

summary: The leukocyte NADPH oxidase 2 (NOX2) regulates inflammation independent of its anti-microbial activity. Inherited defects in NOX2 lead to chronic granulomatous disease (CGD), associated with recurrent bacterial and fungal infections, often with excessive neutrophilic inflammation that results in significant inflammatory burden and tissue damage. We previously showed that excessive leukotriene B4 production by NOX2-deficient mouse neutrophils was a key driver of elevated lung neutrophil infiltration in the initial response to pulmonary challenge with the fungal particle zymosan (Song et al Blood 135, 891-903).  We now identify IL-1β and downstream G-CSF as additional amplifying signals that augment and sustain neutrophil accrual in CGD mice.   Neutrophils, delivered into the lung via LTB4, were the primary source of IL-1β within the airways, and their increased numbers in CGD lungs led to significantly elevated local and plasma G-CSF.  Elevated G-CSF simultaneously promoted increased granulopoiesis and mobilized the release of higher numbers of an immature CD101neg  neutrophil subset from the marrow, which trafficked to the lung and acquired a significantly more pro-inflammatory transcriptome in CGD mice compared to WT mice.  Thus, neutrophil-produced IL-1β in the acute response to fungal cell walls acts sequentially but non-redundantly with LTB4 to deploy neutrophils and amplify inflammation in CGD mice.  This illustrates how NOX2 plays a critical role in dampening multiple components of a feed-forward pipeline for neutrophil recruitment, and highlights NOX2 as a key regulator of neutrophil number and function at inflamed sites.

overall_design: Mice were challenged with or without 20 µg sterile zymosan by intranasal (IN) instillation and euthanized at 24 hours for analysis of inflammation.Total lung was minced and then digested with 5 mg/ml type I collagenase (Worthington) and 1 mg/ml DNAseI (Worthington) in RPMI1640 (Corning) at 37 degree for 45 min and subsequently passed through a 70 μm cell strainer. ACK lysing buffer (Gibco) was used for red blood cell lysis. Lung single-cell suspensions were stained as Live (7-AAD-negative) CD45+CD11b+Ly6G+ along with CD101, and sorted as CD45+CD11b+Ly6G+CD101neg or CD45+CD11b+Ly6G+CD101pos cells on the FACSAria Fusion cell sorter (BD). 50,000-200,000 cells/sample were sorted into RPMI1640 + 20% heat-inactivated FBS, and each group had three replicate samples.

first: Zhimin

last: Song

first: Sourav

last: Battacharya

first: Guangming

last: Huang

first: Zev

last: Greenberg

first: Wei

last: Yang

first: Juhi

last: Bagaitkar

first: Laura

middle: G

last: Schuettpelz


title: Transcriptome analysis upon PHF14 and HMG20A knockdown in MDA-MB-231 cells

city: Sevilla

first: Jose

middle: C.

last: Reyes

address: Av. Américo Vespucio

department: Genome biology

institute: CABIMER

summary: High mobility group proteins are chromatin regulators with essential functions in development, cell differentiation and cell proliferation. We have shown that the high mobility group protein HMG20A copurifies with the histone reader PHF14. To understand the common functions of HMG20A and PHF14 proteins in regulating the transcriptome, we have performed RNA-Seq expression analysis following depletion of each protein in the triple-negative breast cancer cell line MDA-MB-231. Results indicate that genes regulated by PHF14 largely overlap with those regulated by HMG20A.

overall_design: mRNA profiles of the triple-negative breast cancer cell line MDA-MB-231 treated with siControl, siPHF14 or siHMG20A were generated by sequencing, in duplicates, using Illumina Nexseq.

first: Elena

last: Gómez-Marín

last: Basurto-Cayuela

last: Guerrero-Martínez


title: Profiles of Pelvic organ prolapse [mRNA-seq, lncRNA-seq, circRNA-seq]

first: Xia

last: Yu


title: Roles of Runx2 in chromatin landscape in skeletal development [ChIP-Seq, ATAC-Seq]

first: Hironori

last: Hojo

overall_design: Examination of chromatin accessiblity and associataions of transcriptional regulators with DNA in skeletal cells


title: KCNQOT1 ChIRP seq and perturbation epigentic profiles [MeDIP]

first: Shiqiang

last: Zhang

overall_design: DNA methylation status was analyzed by MeDIP-seq in HEK293T EV, KCNQ1OT1_K KD, WT, K non-rep KO, and K rep KO cells.

first: Xiaoli

last: Jiang

last: Li


title: KCNQOT1 ChIRP seq and perturbation epigentic profiles [ChIRP]

overall_design: KCNQ1OT1 binding sites on genomic DNA were analyzed by ChIRP-seq in HEK293T cells.

first: Quanlong

first: Jiyang

last: Cao

last: Han


title: KCNQOT1 ChIRP seq and perturbation epigentic profiles


title: Spinetoram sublethal exposure stimulates Dengue virus replication in Aedes aegypti by dysregulating oxidative phosphorylation

city: Guangzhou

first: Xiaoyun

last: Wang

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: Vector-borne diseases are closely linked to the environment by the ecology of the vectors and their hosts. Elucidating these causal relationships is one of the most pressing challenges faced by researchers and public health scientists as increasing anthropogenic alternations in the environment can drive shifts in vector-borne disease dynamics. However, as one of the major environmental stressors, the impact of sublethal exposure of insecticides on vector behavior remains poorly investigated. Here, we analyzed how sublethal exposure of the promising vector-control bioinsecticide spinetoram on Aedes aegypti larvae, the latest generation of the spinosyns that have been suggested as a promising new bioinsecticide for vector control, at the larval stage of Ae. aegypti alters adult performance and susceptibility to dengue virus (DENV) infection. While spinetoram sublethal exposure leads to extended immature development time, these survivors were significantly smaller and exhibited weaker blood-feeding capacity than normal females. More importantly, surviving females presented higher DENV susceptibility than the control group after spinetoram sublethal exposure on larvae. Mechanistically, the transcriptomic analysis showed that inhibition of oxidative phosphorylation (OXPHOS) may function in stimulating DENV production in adult Ae. aegypti. In vitro study revealed that spinetoram induces apoptosis via mitochondrial reactive oxygen species (mtROS)-regulated OXPHOS dysregulation in Aag2 cells, and thereby may stimulate DENV production through the metabolic switch between OXPHOS and glycolysis. Altogether, our data demonstrate that sublethal spinetoram exposure could act as a crucial factor on life traits and vector competence in Ae. aegypti. Given that other insecticides are known to induce mitochondrial dysfunction in mosquito vectors, this research may have wider implications.

overall_design: Spodoptera frugiperda were reared with the artificial diet with or without antibiotics, respectively from the newly hatched larvae to the 3-day-old sixth instar larvae. RNA-seq and 16S rDNA of midguts were performed to study the effects of gut microflora on host transcription.

first: Luoluo

first: Zhichang

last: Pang

first: Qi

last: Chen

first: Zhentao

last: Song

first: Meng

first: Jia


title: Analysis on the transcriptomic profile in the cerebellar vermis of ataxia telangiectasia patients

first: Takehiro

last: Takahashi

summary: Previous studies have demonstrated the possible roles of dysregulation of endogenous retroelements in the pathogenesis of neurodegenerative diseases. In our study, we demonstrated that the activation and upregulation of endogenous retroelement LINE-1 in the cerebellum can induce the cerebellar ataxia phenotype in vivo using mouse model. While there has been reports demonstrating that ATM gene, whose mutations are causative of Ataxia Telangiectasia (A-T) in humans, regulates LINE-1, and suggesting that the LINE-1 dysregulation caused by its mutation plays a role in the pathogenesis of ataxia phenotype in A-T, little is known about the transcriptome of the A-T patients’ cerebellum. This is the first detailed analysis of the cellular and retroelement transcriptome in A-T patient’s cerebellum, and the result of this analysis, together with the transcriptomic analysis in our LINE-1 activation mice, collectively suggests the profound roles of LINE-1 dysregulation in the development as well as the progression of ataxia in A-T patients.

overall_design: Transcriptomic profiles of the postmortem cerebellar vermis samples from ataxia telangiectasia patients and age/sex-matched controls (4 males + 2 females for both groups, age range 16-36-year-old) were analyzed.

first: Eric

first: Yong

last: Kong

first: Annsea

last: Park


title: Lats1/2 control TGF-beta directed EMT in the dorsal cranial neuroepithelium through YAP regulation

city: Cincinnati

first: Jeffrey

last: Steimle

email: jeffrey.steimle@cchmc.org, jeffrey.steimle@bcm.edu, jsteimle@uchicago.edu, jsteimle@alumni.nd.edu

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Medical Hospital Center

summary: Hippo signaling, an evolutionarily conserved pathway involved in organ size control, has been implicated to play key roles in developmental processes of various tissues, but its role in craniofacial development has not been largely explored. To examine the function of the Hippo signaling kinase cascade, we inactivated Hippo components Lats1 and Lats2 in the cranial neuroepithelium of mouse embryos using a Wnt1CreSOR driver. Double conditional knock out (DCKO) of Lats1/2 resulted in neural tube and craniofacial defects. Lats1/2 DCKO mutant embryos presented a minute head with delayed and defective neural tube closure. Furthermore, neuroepithelial cell polarity and cell integrity were disrupted within the cranial neural tube in Lats1/2 DCKO mutants. Embryonic neural tube RNA-seq revealed increased TGF-beta signaling in absence of Lats1/2. Moreover, markers of epithelial-to-mesenchymal transition (EMT) were upregulated in the cranial neural tube. Notably, modulation of Hippo signaling downstream effectors Yap and Taz prevented neuroepithelial defects, aberrant EMT, and TGF-beta dysregulation caused by Lats1/2 deficiency, indicating that Lats1/2 function via canonical Hippo-Yap pathway. Together, our findings revealed important roles for Hippo signaling kinases in pre-migratory neural crest EMT and migration.

overall_design: Poly-Adenylated RNA was extracted from E10.5 microdissected cranial neural tubes from two Lats1/2 double conditional knock out (Lats1 flox/flox; Lats2 flox/flox; E2f1 Tg(Wnt1-cre)2Sor/+, DCKO) and two control (no E2f1 Tg(Wnt1-cre)2Sor/+) embryos.

first: Idaliz

last: Martinez-Traverso

first: Paul

last: Swinton

first: James

middle: F

last: Martin


title: A comparative study of cellular diversity between the Xenopus pronephric and mouse metanephric nephron

status: Public on Sep 04 2022

city: New York

first: Mark

middle: E.

last: Corkins

state: NY

address: 1468 Madison Ave, Annenburg 25-86

department: CDRB

institute: Mount Sinai

summary: To characterize the cellular makeup of the Xenopus kidney, we dissected, dissociated, then processed X. laevis pronephric kidneys through the 10X Genomics single-cell pipline.

overall_design: scRNA-seq of 200 stage 40 X. laevis pronephric nephrons.

middle: E

first: Bridget

last: DeLay

first: Vanja

last: Krneta-Stankic

first: Rachel

middle: K

last: Miller


title: Intermittent hypoxia inhibits epinephrine-induced transcriptional changes   in human aortic endothelial cells

city: Chicago

first: Rengul

last: Cetin-Atalay

address: 5841 S. Maryland Avenue

department: Medicine

institute: The University of Chicago

summary: we investigated the effects of IH and epinephrine on gene expression in human aortic ECs using RNA-sequencing. We found a significant overlap between IH and epinephrine-induced differentially expressed genes (DEGs).

overall_design: Comparative gene expression profiling analysis of RNA-seq data from HAECs under intermittant hypoxia (20%-5% Oxygen) treated with Epinephrine.

first: Gokhan

last: Mutlu

first: Angelo

middle: Y

last: Meliton

first: Kaitlyn

middle: A

last: Sun


title: The small RNA landscape across age and loss of dFOXO in Drosophila

city: Waltham

first: Siobhan

last: Gartland

state: MA

address: 415 SOUTH STREET

department: Biology

institute: Brandeis University

overall_design: Refer to individual Series


title: Effect of aging and dFOXO knockout on small RNAs

summary: To examine the effect of loss of dFOXO on the small RNA landscape of aging animals, we sequenced total small RNA collected from whole wildtype (wDah) and dFOXO-null (dfoxoΔ94) flies at young (5-6 days) and old (31 days) age.

overall_design: Two biological replicates of total small RNA from whole control (wDah) and dFOXO-null flies at were collected at young and old ages

first: Michael

middle: T

last: Marr


title: Effect of aging and dFOXO knockout on small RNA in Ago1 and Ago2 RNA-induced silencing complexes

summary: To examine the effect of loss of dFOXO on Ago1 and Ago2 RISC loading in aging animals, we sequenced RNA immunoprecipitated from Ago1 and Ago2 RISC collected from whole wildtype (wDah) and dFOXO-null (dfoxoΔ94) flies at young (5 days) and old (35 days) age. dFOXO is a transcription factor that regulates Ago1 and Ago2 as well as lifespan.

overall_design: Two biological replicates of RNA immunoprecipitated from Ago1 and Ago2 from whole control (wDah) and dFOXO-null flies at were collected at young and old ages


title: Genomic signature of Fanconi anemia DNA repair pathway deficiency in cancer

first: Andrew

last: Webster

address: 1230 York Ave

institute: The Rockefeller University

summary: Fanconi anemia (FA), a model syndrome of genome instability, is caused by a deficiency in DNA interstrand crosslink (ICL) repair resulting in chromosome breakage. The FA repair pathway protects against carcinogenic endogenous and exogenous aldehydes. Individuals with FA are hundreds to thousands-fold more likely to develop head and neck (HNSCC), esophageal and anogenital squamous cell carcinomas (SCCs). Molecular studies of SCCs from individuals with FA (FA SCCs) are limited, and it is unclear how FA SCCs relate to sporadic HNSCCs primarily driven by tobacco and alcohol exposure or human papillomavirus (HPV) infection. Here, by sequencing FA SCCs, we demonstrate that the primary genomic signature of FA-deficiency is the presence of high numbers of structural variants (SVs). SVs are enriched for small deletions, unbalanced translocations, and fold-back inversions, and are often connected, thereby forming complex rearrangements. They arise in the context of TP53 loss, but not HPV infection, and lead to somatic copy number alterations of HNSCC driver genes. We further show that FA pathway deficiency may lead to epithelial-to-mesenchymal transition and enhanced keratinocyte intrinsic inflammatory signaling, which would contribute to the aggressive nature of FA SCCs. We propose that genomic instability in sporadic HPV-negative HNSCC may arise consequent to the FA repair pathway being overwhelmed by ICL damage caused by alcohol and tobacco-derived aldehydes, making FA SCC a powerful model to study tumorigenesis resulting from DNA crosslinking damage.

overall_design:
RNAseq of Fanca-/- vs Fanca+/+ transformed mouse keratinocytes serially, intradermally engrafted through immunodeficient NU/J mice. All cells are Trp53-/- , Ccnd1-overexpressing, and HRAS(G12V)-expressing.

GRANT title: Pershing Square Sohn Prize for Young Investigators in Cancer Research
GRANT Agency: Pershing Square Sohn Cancer Research Alliance
GRANT Grantee/Grant ID: Agata Smogorzewska

first: Agata

last: Smogorzewska

first: Mathijs

last: Sanders

first: Thomas

last: Carrol


title: RNA-sequencing analysis of ZsYellow-negative cells and ZsYellow-positive cardiopharyngeal progenitors and cardiomyocytes purified from the same 14-16 somites stage Tg(nkx2.5:ZsYellow) zebrafish embryos

city: Cambridge

first: Vincent

last: Butty

address: 77 Massachusetts Avenue Bldg 68-317A

department: Biology / Koch Institute / Bioengineering / CEHS

institute: Massachusetts Institute of Technology

summary: The identification of novel cardiomyocyte-intrinsic factors that support ventricular function will expand the number of candidate genes and therapeutic options for heart failure, a leading cause of death worldwide. Here, we demonstrate that a conserved RNA-binding protein RBPMS2 is required for ventricular function in zebrafish and for myofibril organization and the regulation of intracellular calcium dynamics in zebrafish and human cardiomyocytes. A differential expression screen uncovered co-expression of rbpms2a and rbpms2b in zebrafish cardiomyocytes. Double knockout embryos suffer from compromised ventricular filling during the relaxation phase of the cardiac cycle, which significantly reduces cardiac output. Evaluating rbpms2-null embryos with splicing-sensitive differential expression analysis, quantitative PCR, and in situ hybridization revealed differential alternative splicing of cardiomyopathy genes including myosin binding protein C3 (mybpc3) and phospholamban (pln). Cardiomyocytes in double mutant ventricles and those derived from RBPMS2-null human induced pluripotent stem cells exhibit myofibril disarray and calcium handling abnormalities. Taken together, our data suggest that RBPMS2 performs a conserved role in regulating alternative splicing in cardiomyocytes, which is required for sarcomere organization, optimal calcium handling, and cardiac function.

overall_design: Tg(nkx2.5:ZsYellow) zebrafish embryos at the 14-16 somites stage were dissociated to single cells and their ZsYellow-positive cardiopharyngeal progenitors and cardiomyocytes were purified by fluorescence activated cell sorting. ZsYellow-negative cells from the same embryos were collected in parallel. RNA-sequencing analysis was performed on both populations (two replicates each) and differentially expressed genes were identified.

first: Asya

last: Schwertner

first: C

last: Burns

first: Caroline


title: RNA-sequencing of rbpms2a; rbpms2b double-mutant and control-sibling zebrafish embryos at 33 hours post fertilization.

overall_design: rbpms2a-/-; rbpms2b-/- embryos at 33 hours post fertilization were identified visually, separated from control-sibling animals, and both groups were collected into multiple pools (n=10 per pool) prior to homogenization and RNA extraction. RNA-sequencing analysis was performed on both groups (five replicates each) and differentially expressed or spliced genes were identified.

first: Alexander

last: Akerberg


title: RNA sequencing of wild-type and RBPMS2-null human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs)

summary: The goal of this study was to identify differential alternative splicing events in RBPMS2-null hiPSC-CMs.

overall_design: Control parental hiPSCs (WTC-11 AAVS1cas9/+) and RBPMS2-null hiPSCs were differentiated into cardiomyocytes in a monolayer for 15 days using the two molecule CHIR/IWR system. Cardiomyocytes were purified using both positive and negative selection in series (Miltenyi) before being subjected to bulk RNA sequencing.


title: TLDA miRNA Screen for Candidate AD Biomarkers in CSF from Living Donors

status: Public on Sep 03 2022

city: Portland

first: Julie

last: Saugstad

state: Oregon

address: 3181 SW Sam Jackson Park Road

department: Anesthesiology & Perioperative Medicine

institute: Oregon Health & Science University

type:
Expression profiling by RT-PCR
Non-coding RNA profiling by array

summary: Identify candidate miRNA biomarkers for AD in CSF.

overall_design: 50 Alzheimers disease (AD), 49 age- and sex-matched neurologically normal subjects. No technical replicates.

first: Joseph

last: Quinn

first: Jodi

last: Lapidus

first: Theresa

last: Lusardi

first: Jay

last: Phillips

first: Betty

last: Lind

first: Jack

last: Wiedrick

first: Christina

last: Harrington


title: Validation Study for Candidate AD miRNA Biomarkers in Human CSF

summary: We used an independent cohort of patient CSF samples from living donors obtained from the Shiley-Marcos Alzheimer's Disease Research Center at the Univ of CA, San Diego to validate the expression of 36 candidate AD miRNA biomarkers. The miRNAs were quantified on custom Taqman Low Density miRNA Arrays from ThermoFisher Scientific; miRNA probes were consistent to those used in the UH2 discovery arrays.

overall_design: 47 Alzheimers disease (AD), 71 age- and sex-matched neurologically normal Controls. 1 reference standard (pooled from 2 donors) that was used to track variation across processing batches. Custom array comprised of 3 technical replicates per miRNA probe. One normal control (Sample EXR-JSAUG1UH3060-BS) was excluded due to complete lack of miRNA expression.

first: Trevor

last: McFarland

first: Douglas

last: Galasko


title: SECANT: a biology-guided semi-supervised method for clustering, classification, and annotation of single-cell multi-omics

city: Pittsburgh

first: Wei

last: Chen

address: 4401 Penn Ave, Rangos Research Building 9125

institute: UPMC Children's Hospital of Pittsburgh

summary: The recent advance of single cell sequencing (scRNA-seq) technology such as Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) allows researchers to quantify cell surface protein abundance and RNA expression simultaneously at single cell resolution. Although CITE-seq and other similar technologies have quickly gained enormous popularity, novel methods for analyzing this new type of single cell multi-omics data are still in urgent need. A limited number of available tools utilize data-driven approach, which may undermine the biological importance of surface protein data. In this study, we developed SECANT, a biology-guided SEmi-supervised method for Clustering, classification, and ANnoTation of single-cell multi-omics. SECANT can be used to analyze CITE-seq data, or jointly analyze CITE-seq and scRNA-seq data. The novelties of SECANT include 1) using confident cell type labels identified from surface protein data as guidance for cell clustering, 2) providing general annotation of confident cell types for each cell cluster, 3) fully utilizing cells with uncertain or missing cell type labels to increase performance, and 4) accurate prediction of confident cell types identified from surface protein data for scRNA-seq data. Besides, as a model-based approach, SECANT can quantify the uncertainty of the results, and our framework can be easily extended to handle other types of multi-omics data. We successfully demonstrated the validity and advantages of SECANT via simulation studies and analysis of public and in-house real datasets. We believe this new method will greatly help researchers characterize novel cell types and make new biological discoveries using single cell multi-omics data.

overall_design: Peripheral blood mononuclear cells were profiled by CITE-seq using a panel of 163 antibodies.

first: Zhongli

last: Xu

first: Xinjun

last: Wang