title: Dynamic chromatin architecture in ovarian follicle development in chickens

status: Public on Apr 19 2023

city: ChengDu

first: Diyan

last: Li

state: SiChuan

address: 2025 Shiling Street, Chengluo Avenue, Chengdu City, Sichuan Province, China

institute: Chengdu University

summary: Ovarian follicle development is a complex and well orchestrated biological process. Chromatin spatial organization has emerged as an important regulator of gene expression, but how these changes during follicle development are still unknown. Here, we integrated RNA-seq analyses of chicken follicular granulosa cells of 10 developmental stages. Our data revealed that SWF, F1, and POF had the greatest transcriptome differences from other stages. Our results provide a genome-wide atlas of chromatin interactions during chicken ovarian follicle development.

overall_design: We integrated RNA-seq (10 stages with 3 biological replicates in each stage) analyses of chicken follicular granulosa cells of 10 developmental stages.

first: Chunyou

last: Ning

first: Jiaman

last: Zhang

first: Mingzhou


title: Transcriptome analysis for LMP1 depletion in GM12878 Lymphoblastoid cell line (LCL)

status: Public on Apr 25 2023

city: Boston

first: Bidisha

last: Mitra

state: MA

address: 181 Longwood Avenue, 8th floor

department: Medicine

country: USA

institute: Brigham and Women's Hospital

type: Expression profiling by high throughput sequencing

summary: RNA-seq was used  to characterize the LMP1 mediated regulation of host target gene regulation. We knocked out LMP1 in GM12878  Lymphoblastoid cell line (LCL). The GM12878 LCL expressing control sgRNA was used as the control.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in GM12878 LCL upon LMP1 knock out through CRISPR-Cas9 approach.  The GM12878 LCL expressing control sgRNA was used as the control.

first: Rui

last: Guo

first: Eric

last: Burton

first: Laura

last: Murray-Nerger

first: Benjamin

middle: E

last: Gewurz


title: Thyroid hormone-regulated chromatin and transcriptional sensitivity of the pituitary gland

status: Public on Apr 17 2023

city: Bethesda

first: Hong

last: Liu

state: MD

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Thyroid hormone (3,5,3'-triiodothyronine, T3) sensitively influences the pituitary gland, a source of hormones that control tissues throughout the body. The underlying transcriptional response is believed to hinge crucially on interaction of T3 receptors with enhancers in the genome but it remains unknown how T3 regulates pituitary chromatin and how this regulation adjusts to hypothyroid and hyperthyroid conditions.

overall_design: The binding sites of the biotinlyated thyroid hormone receptor beta (Thrb) at mouse tissue under either euthyroid, hypothyroid or hyperthyroid conditions  by ChAP-seq. ChIP-Seq profiling of histone H3K27ac,H3K4me1 and H3K4me3 by ChIP-Seq  and ChAP-seq profiling of Thrb by ChAP-seq at mouse pituitary or brain under either hypothyroid or hyperthyroid conditions. The chromatin accessibility profiling  by ATAC-Seq at Thrb2 positive mouse pituitary cells  under either hypothyroid or hyperthyroid conditions. The gene expression profiling by RNA-Seq at mouse pituitary under either hypothyroid or hyperthyroid conditions.

first: Young-Wook

last: Cho

first: Yulong

last: Fu

first: Jeff

middle: C

last: Huang

first: Xuefeng

last: Wu

first: Douglas

last: Forrest


title: Time-dependent recruitment of GAF, ISGF3 and IRF1 complexes to GAS, ISRE and composite genes shapes IFNa and IFNg activated transcriptional responses and explains functional overlap

status: Public on May 04 2023

city: Poznan

first: Hans

last: Bluyssen

address: Uniwersytetu Poznańskiego 6

department: Laboratory of Human Molecular Genetics

country: Poland

institute: Adam Mickiewicz University

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

overall_design: Refer to individual Series


title: Potent and uniform fetal hemoglobin induction via base editing [Cut & Run]

status: Public on Apr 28 2023

city: Memphis

first: Jonanthan

last: Yen

state: TN

address: 262 Danny Thomas Pl

department: Hematology

institute: St. Jude Children's Research Hospital

summary: Genetic manipulations to increase fetal hemoglobin (HbF, α2γ2) in postnatal red blood cells (RBCs) can alleviate β-thalassemia and sickle cell disease. We compared five strategies in CD34+ hematopoietic stem and progenitor cells, using either Cas9 nuclease, which creates uncontrolled indel mixtures, or adenine base editors (ABE), which generate more precise nucleotide changes. The most potent modification was ABE generation of γ-globin (HBG1/HBG2) −175 A>G, which creates a promoter binding motif for the transcriptional activator TAL1. In erythroid colonies with >87.5% on-target edits, those with −175 A>G expressed 81 ± 7% HbF, versus 17 ± 11% in unedited controls. In comparison, HbF levels were lower and more variable in erythroid cells modified with either of two Cas9 nuclease strategies with similar editing efficiencies, being 32 ± 19% when a BCL11A repressor binding motif in the γ-globin promoter was targeted and 52 ± 13% when the +58 BCL11A erythroid enhancer was targeted. Contrary to currently accepted models of γ-globin regulation, HbF levels varied significantly with different Cas9 indels that disrupted the γ-globin promoter BCL11A binding motif. The −175 A>G base edit also induced HbF more potently than did the Cas9 nuclease approaches in RBCs generated after transplantation of modified normal or SCD patient CD34+ cells into mice. Our data suggest a strategy for potent, uniform induction of HbF and provide insights into γ-globin gene regulation. More generally, we demonstrate that diverse indels generated by Cas9 nuclease can cause unexpected variations in biological outcomes that can be circumvented by base editing, with important implications for therapeutic gene editing efforts.

overall_design: CUT&RUN experiments were performed in HUDEP-2 cells base editor edited HBG promoter region

first: Ruopeng

last: Feng

first: Jonathan


title: Unveiling the differential Senescence Phenotypes of MCF7 Cells Treated with Diverse Therapeutic Agents: A Comprehensive Transcriptome Analysis

status: Public on Apr 14 2023

city: Suwon

first: Dong Hyun

last: Lee

address: 206, World cup-ro

country: South Korea

institute: ajou university

summary: Therapeutic drugs are commonly used for treatment various cancers. However, despite to this purpose,  Cancer treated by drugs undergoes senescence phenotypes and is known to acquire more aggressive ability. Futhermore, senescence can be induced vairous type of drug via differential mechanisms. Therefore, we analyzed to validate differential charateristics of senescence phenotypes compare between drugs.

overall_design: control MCF7, Doxorubicin treated MCF7, Cisplatin treated MCF7 and Palbociclib treated MCF7 were compared

first: Dong-Hyun

first: Muhammad

last: Imran

first: Yong-Won

last: Choi

first: Tae-Jun

last: Park


title: Time-dependent recruitment of GAF, ISGF3 and IRF1 complexes to GAS, ISRE and composite genes shapes IFNa and IFNg activated transcriptional responses and explains functional overlap [CHIP-seq]

summary:
Although the core type I and type II IFN signaling pathways are distinct, their expression profiles show considerable overlap and are difficult to discern. Using a genome-wide RNAseq-ChIPseq integrative approach, our results identify a novel class of IFN-I and IFN-II responsive genes that use ISRE and GAS composite sites to recruit STAT1 and STAT2-containing ISGF3 and GAF-like complexes and IRF1 for optimal expression. Moreover, they support the existence of an analogous transcriptional regulatory mechanism of IFNα and IFNγ inducible genes, in which STAT1 and STAT2-containing ISGF3 and GAF-like complexes and IRF1 are recruited to individual or combined ISRE and GAS composite sites in an IFN- and time-dependent manner.
In addition, we present proof for the involvement of an ISRE and GAS composite-dependent regulatory system in IFN-activated positive feedback regulation of the STAT1, STAT2, IRF9 and IRF1 genes and long-term response to IFNs, which depends on phosphorylation and expression of ISGF3, IRF1 and GAF-like components. These findings provide further insight in the existence of a novel intracellular amplifier circuit that offer an explanation for the existing molecular and functional overlap between IFN-I and IFN-II activated ISG expression.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for pSTAT1, pSTAT2, IRF9 and IRF1 in Huh7.5 wild type cells treated with IFN alpha and IFN gamma

middle: A


title: CIRCLE-seq analyais for -175 site

summary: Adenosine base editing to recreate the HPFH mutations is a promising approach to induce HbF. We used CIRCLE-seq to identify 682 potential off-target sites in purified DNA treated with Cas9 nuclease complexed to sgRNA targeting -globin -175 .

overall_design: CIRCLE-seq was performed in HEK293T cells.

first: T

last: Mayuranathan


title: Wireless Electrical-Molecular Quantum Signalling for Cancer Cell Induced Death

status: Public on Jun 01 2023

city: Nottingham

first: Akhil

last: Jain

address: University Park

country: United Kingdom

institute: University of Nottingham

summary:
To investigate the effect of electric fileds on the electrical-molecular signalling, we performed transcriptomic analysis on a sample of glioblastoma cells and healthy cortical astrocytes.
Qiagen perform the RNA seq analysis of samples, to interrogate the effect of the of the bioelectronic communication tool on gene expression and regulation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for patient dervided glioblastoma cells (GIN and GCE) and normal cortical astrocytes upon treatment with nanoparticles and alternating current electric fields.

first: Frankie

last: Rawson


title: WT, ∆rhlB and ∆rppH mRNA half-life profiling.

status: Public on Apr 03 2023

city: Bloomington

first: Jared

middle: Michael

last: Schrader

state: IN

address: 212 S Hawthorne Dr

department: Biology

institute: Indiana University

summary: WT, ∆rhlB and ∆rppH strains were globally profiled for mRNA half-lives using rifampicin treatment followed by RNA-seq.  Wild type(WT) was compared to ∆rhlB (deleted RNA helicase RhlB gene) and ∆rppH (deleted RppH gene) strains

overall_design: WT and mutant strains ( ∆rhlB and ∆rppH) were globally profiled for mRNA half-lives using rifampicin treatment followed by RNA-seq.  Biological samples were taken before rifampicin treatment (0 minute), then at 1, 3, and 9 minutes after rifampicin treatment.  Two biologycal replicates were performed.

middle: M


title: Time series single-cell RNA sequencing of murine hematopoetic stem and progenitors (HSPCs) following in vivo IFNα treatment

status: Public on Apr 05 2023

city: Heidelberg

first: Yasmin

middle: Essam

last: Demerdash

state: Germany

address: Im Neunheimer Feld, 280

department: Inflammatory Stress in Stem Cells

country: Germany

institute: DKFZ

summary: The molecular and cellular dynamics of hematopoietic stem and progenitor cells (HSPCs) during the course of inflammation remain poorly studied. It has been challenging to characterize inflammation in HSPCs due to changes in cell type-specific surface markers. To address this challenge, we performed single-cell RNA sequencing of HSPCs at multiple time points (3, 24, and 72 hours) after treatment with the pro-inflammatory cytokine IFNα and developed a computational pipeline suitable for processing and analyzing single-cell time series dataset. Using a semi-supervised response-pseudotime inference approach, we discover a variety of different gene responses of the HSPCs to the treatment. Interestingly, we were able to associate the myeloid abundance changes with downregulated myeloid differentiation programs in HSCs and progenitors following IFNα treatment. Using single-cell time series we have been able to unbiasedly study the heterogeneous and dynamic impact of IFNα on the HSPCs

overall_design: We performed a time course single-cell RNA sequencing experiment. Bone marrow (BM) cells were collected from four different mice for each timepoint (including four control mice injected with PBS). Using oligo-tagged antibodies, or hashtags, we labeled the cells from each biological replicate and timepoint to address inter-animal heterogeneity of the inflammatory stress response. Following cell hashing, BM cells from mice of the same treatment were pooled together. BM cells were then sorted by using the broad lineage negative (Lin-) and c-kit positive (c-Kit+) (LK) gating strategy to capture a wide spectrum of the HSPC transcriptional landscape. To guarantee sufficient numbers of HSCs for analysis, we additionally enriched the sorted populations with LKSLAMCD34-, since they are much less frequent than the other populations in the LK gate. The cells from all four experimental time points (control, 3h, 24h, and 72h) were sequenced simultaneously using the 10x Genomics platform.

first: Brigitte

middle: J

last: Bouman

first: Laleh

last: Haghverdi

first: Marieke

last: Gertruda Essers


title: Prostate cancer androgen receptor activity dictates efficacy of bipolar androgen therapy through MYC [RNA-seq: patient biopsies]

status: Public on Apr 12 2023

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

summary: Testosterone is the canonical growth factor of prostate cancer but can paradoxically suppress its growth when present at supraphysiological levels. We have previously demonstrated that the cyclical administration of supraphysiological androgen (SPA), entitled Bipolar Androgen Therapy (BAT), can result in tumor regression and clinical benefit for patients with castration-resistant prostate cancer. However, predictors and mechanisms of response and resistance have been ill-defined. Here we show that growth inhibition of prostate cancer models by SPA requires high androgen receptor (AR) activity and is driven in part by downregulation of MYC. Using matched sequential patient biopsies, we show that high pre-treatment AR activity predicts downregulation of MYC, clinical response, and prolonged progression-free and overall survival for patients on BAT. BAT induced strong downregulation of AR in all patients, which is shown to be a primary mechanism of acquired resistance to SPA. Acquired resistance can be overcome by alternating SPA with the AR inhibitor enzalutamide, which induces adaptive upregulation of AR and re-sensitizes prostate cancer to SPA. This work identifies high AR activity score as a predictive biomarker of response to BAT and supports a new treatment paradigm for prostate cancer involving alternating between AR inhibition and activation

overall_design:
The COMbination of BAT and Nivolumab (COMBAT-CRPC; NCT03554317) clinical trial was a single-arm, multicenter, open-label phase II study of BAT in combination with the anti-PD1 agent nivolumab for patients with CRPC that had progressed on at least 1 novel AR-target therapy. Patients were required to have soft tissue metastases amenable to biopsy to participate. Patients were treated with 3 cycles of BAT — testosterone cypionate 400 mg intramuscular every 28 days — followed by concurrent BAT and 480 mg nivolumab intravenously every 28 days until progression. Paired core needle tumor biopsies were performed prior to treatment and after 3 cycles of BAT monotherapy. Response was assessed with PSA at each cycle, and chest, abdomen, and pelvis CT scans and technetium-99 bone scan every 3 cycles. 15 paired biopsies were analyzed via Bulk RNAseq (30 samples total).
>>> Submitter declares that the raw data will be deposited in dbGaP due to patient privacy concerns <<<

first: Laura

last: Sena

first: David

last: Sanin


title: Chromatin context-dependent regulation and epigenetic modulation of prime editing

city: Seattle

first: Xiaoyi

last: Li

state: WA

address: 3720 15th Ave NE

department: Department of Genome Sciences

institute: University of Washington


title: Chromatin context-dependent regulation and modulation of prime editing [RNA-seq]

summary: Prime editing is a powerful means of introducing precise changes to specific locations in mammalian genomes. However, the widely varying efficiency of prime editing across target sites of interest has limited its adoption in the context of both basic research and clinical settings. Here, we set out to exhaustively characterize the impact of the cis-chromatin environment on prime editing efficiency. Utilizing a newly developed and highly sensitive method for mapping the genomic locations of a randomly integrated “sensor”, we identify specific epigenetic features that strongly correlate with the highly variable efficiency of prime editing across different genomic locations. Next, to assess the interaction of trans-acting factors with the cis-chromatin environment, we develop and apply a pooled genetic screening approach with which the impact of knocking down various DNA repair factors on prime editing efficiency can be stratified by cis-chromatin context. Finally, we demonstrate that we can dramatically modulate the efficiency of prime editing through epigenome editing, i.e. enhancing (or restricting) local chromatin accessibility in order to increase (or decrease) the efficiency of prime editing at a target site. Looking forward, we envision that the insights and tools described here will broaden the range of both basic research and therapeutic contexts in which prime editing is useful.

overall_design: Bulk RNA sequencing of K562 cells (wild-type) and cells treated with CRISPRoff. For the CRISPRoff experiment, cells were transiently transfected with CRISPRoff-v2.1 and paired gRNA targeting gene promoters. After FACS sorting and expansion of the transfected cells, cells' total RNAs were extracted and used for bulk RNA sequencing. Differential gene expression analyses were performed between promoter-targeting gRNA (USP7, METTL2A, and LRRC8C) treated cells versus cells treated with non-targeting control gRNAs.

first: Wei

last: Chen

first: Beth

middle: K

last: Martin

first: Diego

last: Calderon

first: Choli

first: Junhong

first: Florence

last: Chardon

first: Troy

last: McDiarmid

first: Haedong

last: Kim

first: Jean-Benoît

last: Lalanne

first: Jenny

middle: F

last: Nathans

first: Jay

last: Shendure


title: NF-kB and Circadian Enhancers Link β-cell Function with Anti-IL1B Therapy [ChIP/HiChIP-seq]

city: Chicago

first: Benjamin

last: Weidemann

state: IL

address: 303 E. Superior St.

institute: NORTHWESTERN UNIVERSITY

summary: Crosstalk between lineage-determining and signal-dependent transcription factors controls chromatin plasticity within heterogeneous tissues, yet how alterations in these interactions within single cells contribute to disease remains unknown. Here, by profiling chromatin activity in single nuclei of human pancreatic islets, we identified 19 clusters of cells, including β-cell subpopulations defined by differences in accessibility at non-coding cis-regulatory elements (CREs) for the lineage-determining factor pancreatic duodenal homeobox factor 1 (PDX1). Single cells with a high density of PDX1 CREs were enriched in accessible enhancer landscapes driving gene networks controlling nutrient sensing, insulin exocytosis, and circadian rhythms. In contrast, cells with reduced opening at PDX1 CREs had increased accessibility at regulatory elements for pro-inflammatory genes controlled by NF-kB and IL-1β. Genetic deficiency of Pdx1 in mice led to increased chromatin occupancy by the classical NF-κB subunit p65 and glucose intolerance that was more pronounced at the time of day when mice were awake and feeding. Within murine and human islets, PDX1 formed long-range repressive contacts with canonical regions of p65-mediated transcription. Pharmacological inhibition of signaling through the IL-1β receptor, an abundant β-cell target of p65, enhanced glucose-dependent insulin secretion in Pdx1-deficient β cells. Together, our single-cell epigenomic analyses provide a rationale to antagonize NF-kB signaling as an insulinotropic therapy for β-cell failure and diabetes.

overall_design: Single-cell ATAC-sequencing, RNA-sequencing, ChIP-sequencing, HiChIP-sequencing, gene manipulation, metabolic studies


title: NF-kB and Circadian Enhancers Link β-cell Function with Anti-IL1B Therapy.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: The uterine secretory cycle: shifts to the recurring physiology of endometrial outputs in the presence of a preimplantation embryo

status: Public on Apr 26 2023

city: Ithaca

first: Vimal

last: Selvaraj

state: NY

address: 204 Morrison Hall

department: Animal Sciences

institute: Cornell University

summary: The bovine endometrium secretes proteins during early pregnancy that vary (in both protein identity and abundance) to be in synchrony with luminal reproductive events. To uncover the identity of these proteins, transcriptomics was performed to understand the secretory capability of the bovine endometrium through the distinct phases of early pregnancy in virgin heifers. This dataset should serve as a baseline for understanding the profile of luminal secretory outputs during early pregnancy, setting the stage for functional interpretation of how the uterus supports and directs biological events ranging from sperm transport to preimplantation embryo development.

overall_design: Bovine endometrial secretions across early pregnancy

first: Kasey

last: Schalich

first: Prasanthi

middle: P

last: Koganti


title: NF-kB and Circadian Enhancers Link β-cell Function with Anti-IL1B Therapy [Bulk ATAC-seq]


title: The role of AF10 (Mllt10) in maintaining cell identity (ChIP-Seq)

status: Public on Apr 01 2023

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Wisconsin Institute for Discovery

institute: University of Wisconsin

summary: AF10 is a cofactor of the H3K79 methyltransferase DOT1L. To uncover the role of H3K79me in reprogramming to induced pluripotent stem cells (iPSCs), we bred reprogrammable mice encoding doxycycline inducible Oct4-2A-Klf4-2A-IRES-Sox2-2A-c-Myc (OKSM) transgene with conditional flox (fl)-AF10 (Mllt10). We isolated mouse embryonic fibroblasts (MEFs), deleted AF10 with CRE-recombinase or treated cells with empty vector control, and initiated reprogramming in DOT1L chemical inhibitor SGC0946 or DMSO control. Gene expression was assessed using RNA-Seq and genome wide localization of H3K79me1, H3K79me2, and RNA Polymerase II (RNAPII) was determined by ChIP-Seq on day 4 of reprogramming.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K79me1, H3K79me2, and RNA Polymerase II (RNAPII) in cells on day 4 of reprogramming to iPSCs with wild-type (fl) or Cre-deleted AF10 (Mllt10)

first: Wille

last: Coral

first: Sridharan

last: Rupa


title: The role of AF10 (Mllt10) in maintaining cell identity (RNA-Seq)

summary: AF10 is a cofactor of the H3K79 methyltransferase DOT1L. To uncover the role of H3K79me in reprogramming to induced pluripotent stem cells (iPSCs), we bred reprogrammable mice encoding doxycycline inducible Oct4-2A-Klf4-2A-IRES-Sox2-2A-c-Myc (OKSM) transgene with conditional flox (fl)-AF10 (Mllt10). We isolated mouse embryonic fibroblasts (MEFs), deleted AF10 with CRE-recombinase or treated cells with empty vector control, and initiated reprogramming in DOT1L chemical inhibitor SGC0946 or DMSO control. Gene expression was assessed using RNA-Seq and genome wide localization of H3K79me1 and H3K79me2 was determined by ChIP-Seq on day 4 of reprogramming.

overall_design: Gene expression profiling analysis of RNA-seq data of MEFs and cells on day 4 of reprogramming to iPSCs with wild-type (fl) or Cre-deleted AF10 (Mllt10), in the presence and absence of DOT1L chemical inhibition (SGC0946).


title: single cell CRISPR analysis in human pluripotent stem cells

city: Kyoto

first: Mototsugu

last: Eiraku

address: 53 Kawahara-chi, Sakyo-ku

country: Japan

institute: Kyoto University

summary: Single-cell CRISPR experiment was performed that focused on the pluripotency network in human iPSCs. We selected 23 genes (TFs) that are thought to be involved in pluripotency in hiPSCs and constructed 2 gRNAs per gene. To capture the time-course expression changes, samples were taken from days 2, 3, 4, and 5 after transduction and scRNA-seq analysis was performed. Approximately 5,000 single cells should be captured in each sample to obtain approximately 100 cells per gRNA in the scRNA-seq.

overall_design: Human iPSCs (OILG-Cas9) were transduced with the pooled lentivirus for both gRNA and BFP expression at 8-9% transduction efficiency and maintained until harvesting without passaging. On days 2, 3, 4, and 5 after transduction, 8 × 104 BFP+ cells were collected using an MA900 cell sorter (Sony), then resuspended at 1 × 106 cells/mL in 0.05% BSA in PBS. These cells were then subjected to 5 ’single-cell RNA-seq library preparation using a Chromium Next GEM Single Cell 5’Library & Gel Bead Kit following the manufacturers’ protocol with minor modifications to simultaneously capture guide RNA molecules.

first: Kosuke

last: Yusa

first: Masato

last: Ishikawa


title: Chromatin state and chromatin architecture in mouse embryonic craniofacial tissue, neural crest cell culture model and human primary craniofacial tissue

status: Public on Mar 30 2023

city: Farmington

first: Justin

last: Cotney

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: UConn Health

summary: Examination of the chromatin state and chromatin architecture of a region on human chromosome 7 and the orthologous region on mouse chromosome 6.

overall_design:
ChIP-seq for multiple histone marks, RNA-seq, HiC and 4C-seq in a cell culture model of human cranial neural crest and mouse, both wild type and CRISPR/Cas9 edited with HiC of primary human tissue for comparison of chromatin architecture.
Human raw data is being submitted to dbGaP [CS17_HiC]

first: Andrea

last: Wilderman

first: Jennifer

last: vanOudenhove


title: NF-kB and Circadian Enhancers Link β-cell Function with Anti-IL1B Therapy [RNA-seq]


title: Effect of mechanical ventilation and mechanical ventilationon with positive end expiratory pressure(PEEP) application on diaphragmatic dysfunction in rabbits

city: Changchun

first: Tongjian

last: Zhao

address: 1266 Fujin Road

country: China

institute: School of Pharmaceutical Sciences, Jilin University

summary: To investigate the effect of mechanical ventilation and  mechanical ventilationon with PEEP application on diaphragmatic dysfunction, we established a model of mechanical ventilation on New Zealand rabbit, in which rabbits in the experimental group were ventilated  with/without PEEP application for 48 hours continuously

overall_design: Comparative gene expression profiling analysis of RNA-seq data on diaphragm between the control group and the mechanical ventilation group

first: Weimin

last: Shen

first: Huiqing

last: Ge


title: Effect of folate receptor depletion on gene expression in Caenorhabditis elegans

status: Public on Mar 20 2023

city: Helsinki

first: Olli

last: Matilainen

address: Viikinkaari 9C

department: Faculty of Biological and Environmental Sciences

country: Finland

institute: University of Helsinki

summary: Folate receptors transport folates into the cell via an endocytic mechanism. FOLR-1 is the sole ortholog of folate receptors in the nematode Caenorhabditis elegans. In this study, we examined how loss of FOLR-1 affects gene expression.

overall_design: We generated folr-1 mutant C. elegans, and compared its gene expression profile with wild-type (N2).

first: Bideep

last: Shrestha


title: The uterine secretory cycle: recurring physiology of endometrial outputs that setup the uterine luminal microenvironment

first: Vimal

last: Selvaraj

summary: The bovine endometrium secretes proteins across the estrous cycle that vary (in both protein identity and abundance) to be in synchrony with luminal reproductive events. To uncover the identity of these proteins, transcriptomics was performed to understand the secretory capability of the bovine endometrium through the distinct phases of the estrous cycle in cows. This dataset should serve as a baseline for understanding the profile of luminal secretory outputs across the estrous cycle, setting the stage for functional interpretation of how the uterus supports and directs biological events ranging from sperm transport to preimplantation embryo development.

overall_design: Bovine endometrial secretions across the estrous cycle


title: Association of NOTCH3 with Elastic Fiber Dispersion in the Infrarenal Abdominal Aorta of Cynomolgus Monkeys

status: Public on Mar 22 2023

city: Lexington

first: Hisashi

last: Sawada

state: KY

address: 741 South Limestone BBSRB B251

institute: University of Kentucky

summary:
OBJECTIVE: The regional heterogeneity of vascular components and transcriptomes is an important determinant of aortic biology. This notion has been explored in multiple mouse studies. In the present study, we examined the regional heterogeneity of aortas in non-human primates.

APPROACH AND RESULTS: Aortic samples were harvested from the ascending, descending, suprarenal, and infrarenal regions of young control monkeys and adult monkeys provided with high fructose for 3 years. The regional heterogeneity of aortic structure and transcriptomes was examined by histological and bulk RNA sequencing analyses. Immunostaining of CD31 and αSMA revealed that endothelial and smooth muscle cells were distributed homogeneously across the aortic regions. In contrast, elastic fibers were less abundant and dispersed in the infrarenal aorta compared to other regions and associated with collagen deposition. Bulk RNA sequencing identified a distinct transcriptome related to the Notch signaling pathway in the infrarenal aorta with significantly increased NOTCH3 mRNA compared to other regions. Immunostaining revealed that NOTCH3 protein was increased in the media of the infrarenal aorta. The abundance of medial NOTCH3 was positively correlated with the dispersion of elastic fibers. Adult cynomolgus monkeys provided with high fructose displayed vascular wall remodeling, such as smooth muscle cell loss and elastic fiber disruption, predominantly in the infrarenal region. The correlation between NOTCH3 and elastic fiber dispersion was enhanced in these monkeys.

CONCLUSION: Aortas of young cynomolgus monkeys display regional heterogeneity of their transcriptome and the structure of elastin and collagens. Elastic fibers in the infrarenal aorta are dispersed along with upregulation of medial NOTCH3.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ascending, descending, suprarenal, and infrarenal aortas from normal young cynomolgus monkeys.


title: The lncRNA Malat1 Inhibits miR-15/16 to Enhance Cytotoxic T Cell Activation and Memory Cell Formation

status: Public on Mar 17 2023

city: San Francisco

first: Karl

middle: Mark

last: Ansel

state: CA

address: 500 Parnassus Ave

department: Microbiology

institute: University of California, San Francisco

summary: Proper activation of cytotoxic T cells via the T cell receptor and the costimulatory receptor CD28 is essential for adaptive immunity against viruses, many intracellular bacteria and cancers. Through biochemical analysis of RNA:protein interactions, we uncovered a novel non-coding RNA circuit regulating activation and differentiation of cytotoxic T cells composed of the long non-coding RNA Malat1 (Metastasis Associated Lung Adenocarcinoma Transcript 1) and the microRNA family miR-15/16. miR-15/16 is a widely and highly expressed tumor suppressor miRNA family important for cell proliferation and survival. miR-15/16 also play important roles in T cell responses to viral infection, including the regulation of antigen-specific T cell expansion and T cell memory. Comparative Argonaute-2 high throughput sequencing of crosslinking immunoprecipitation (Ago2 HITS-CLIP, or AHC) combined with gene expression profiling in normal and miR-15/16-deficient T cells revealed a large network of several hundred direct miR-15/16 target mRNAs, many with functional relevance for T cell activation, survival and memory formation. Among these targets, the long non-coding RNA Malat1 contained the largest absolute magnitude miR-15/16-dependent AHC peak in T cells. This binding site was also among the strongest lncRNA:miRNA interactions detected in the T cell transcriptome. We used CRISPR targeting with homology directed repair to generate mice with a 5-nucleotide mutation in the miR-15/16 binding site in Malat1. This mutation interrupted Malat1:miR-15/16 interaction, and enhanced the repression of other miR-15/16 target genes, including CD28. Interrupting Malat1 interaction with miR-15/16 decreased cytotoxic T cell activation, including the expression of IL-2 and a broader CD28-responsive gene program. Accordingly, Malat1 mutation diminished memory cell persistence following LCMV Armstrong and Listeria monocytogenes infection. This study marks a significant advance in the study of long noncoding RNAs in the immune system by ascribing cell-intrinsic, sequence-specific in vivo function to Malat1. These findings have implications for T cell-mediated autoimmune diseases, antiviral and anti-tumor immunity, as well as lung adenocarcinoma and other malignancies where Malat1 is overexpressed.

overall_design: Comparative gene expression analysis was performed on RNA-seq data from primary mouse CD8+ T cells isolated from the spleens of naive mice. T cells were stimulated for 24 hours with anti-CD3 antibodies with and with out anti-CD28 stimulation. Cells from mice lacking the miR-15/16 binding site in Malat1, Malat1scr/scr; Bl6/J WT; miR-15/16 floxxed with out cre, miR-15/16fl/fl; and mir-15/16 deleted by CD4-cre, miR-15/16Δ/Δ were used in both stimulation conditions.

first: Benjamin

middle: D

last: Wheeler

first: John

last: Gagnon

first: Wandi

middle: S

last: Zhu

first: Priscila

last: Muñoz-Sandoval

first: Dimitre

last: Simeonov

first: Zhongmei

last: Li

first: Alex

last: Marson

first: Matthew

last: Spitzer

first: Simon

last: Wong

first: Rachel

last: Debarge


title: The Rfg1 and Bcr1 transcription factors regulate acidic pH-induced filamentous growth in Candida albicans

status: Public on Mar 24 2023

city: Beijing

first: Guobo

last: Guan

address: NO.1 Beichen West  Road, Chaoyang District, Beijing

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: To investigate the function of Rfg1 in sensing acidic pH and regulating filamentation in C. albicans, we performed the global gene expression profile analysis of WT and rfg1/rfg1 mutant.We reveal that Rfg1 is an essential acidic pH sensor in C. albicans. Rfg1 regulates filamentous growth in acidic pH condition via co-regulation of Rim101-Phr1 pathway, cAMP signaling pathway,and the transcription factors Bcr1, Efg1, Flo8, and Hgc1.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and rfg1/rfg1 mutant under acid pH condition

first: Jian

last: Bing

first: Guanghua

last: Huang

first: Li

last: Tao


title: The lncRNA Malat1 Inhibits miR-15/16 to Enhance Cytotoxic T Cell Activation and Memory Cell Formation [Ago2 HITS-CLIP]

overall_design: Comparative Ago2 HITS-CLIP (High Throughput Sequencing following Crosslinking Immuno-Precipitation) was performed on Ago2 HITS-CLIP data from primary mouse CD8+ T cells isolated from the spleens of naive mice. T cells were stimulated for 72 hours with anti-CD3 and anti-CD28 antibodies followed by 2 days resting in IL-2 supplemented media. Cells from mice lacking the miR-15/16 binding site in Malat1, Malat1scr/scr; Bl6/J WT; and mir-15/16 deleted by CD4-cre, miR-15/16Δ/Δ were used.


title: Single-cell and bulk RNA sequencing of mouse atherosclerosis disease stage course [aorta_bulkRNA-Seq]

city: Kuopio

first: Tiit

last: Örd

address: Neulaniementie 2

institute: A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland

summary: Atherosclerotic coronary artery disease (CAD) development encompasses endothelial dysfunction, vascular infiltration of immune cells and smooth muscle cell dedifferentiation. However, the specific disease-associated transcriptional changes occurring within each of the major lesional cell types remain incompletely characterized. Here, we identify disease-associated cell states within the major aortic cell types and investigate the similarities and differences in their gene signatures compared to each other and to healthy (non-diseased) cells. By integrating human genetic association data and generating polygenic risk scores, we further use the atherosclerosis-associated cell state gene signatures to interrogate how the perturbed states of different lesional cell types contribute to the genetic risk for CAD.

overall_design: A disease stage course of atherosclerosis in mouse was established by varying genotype (wild type and proatherogenic) and diet (0, 1 or 3 months of high-fat diet), followed by scRNA-Seq (all cell types) and bulk RNA-Seq of the thoracic aorta.

first: Tapio

last: Lönnberg

first: Henri

last: Niskanen

first: Senthil

last: Palani

first: Heidi

last: Liljenbäck

first: Jenni

last: Virta

first: Anne

last: Roivainen

first: Minna

middle: U

last: Kaikkonen


title: Single-cell and bulk RNA sequencing of mouse atherosclerosis disease stage course [aorta_scRNA-Seq]


title: Adverse effects of gestational Δ9-tetrahydrocannabinol exposure on the embryonic germline transcriptome and metabolome

status: Public on Mar 13 2023

city: Los Angeles

first: Roxane

last: Verdikt

address: Life Science Building 3360  621 Charles E. Young Drive S.

department: Institute for Society & Genetics

institute: UCLA

summary: An increasing number of women report cannabis use during their pregnancy, with little knowledge on the repercussions of such an exposure onto early embryonic processes. In particular, exposure to the most abundant phytocannabinoid, Δ9-tetrahydrocannabinol (Δ9-THC), could alter the development of embryonic germ cells, with potential consequences across generations. Here, we extensively characterized the impact of gestational exposure to Δ9-THC onto the developmental trajectory of an in vitro model for primordial germ cells. Our data reveals that Δ9-THC exposure increases glycolytic rates in embryonic stem cells, with consequences on their proliferation. We further show that, in the absence of continuous exposure, Δ9-THC has long-lasting adverse consequences on the metabolome and transcriptome of embryonic germ cells. These results constitute the first characterization of the impact of gestational Δ9-THC exposure onto the embryonic germline.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ESCs, EpiLCs, PGCLCs treated with 100nM of Δ9-THC or with the vehicle as a control

first: Abigail

last: Armstrong

first: Jenny

last: Cheng

first: Xia

last: Yang

first: Patrick

last: Allard


title: Chromatin context-dependent regulation and modulation of prime editing [amplicon]

first: Xiaoyi

last: Li

overall_design: We randomly integrated a complex library of the synHEK3 reporters into a monoclonal K562 cell line constitutively expressing the PE2 prime editor. We further bottlenecked the pool to ~500 clones, each containing a unique combination of randomly inserted reporters, and performed T7-assisted reporter mapping on this population (T7-500-1). We further performed amplicon sequencing of synHEK3 reporters to measure the outcomes of prime editing (K562-HEK3-insCTT) as well as Cas9 editing (K562-HEK3-Cas9) in this pool of synHEK3 reporters. A few monoclonal lines were also derived from the 500-clone population. Files named "K562-SC1-5-OFF*" contain prime editing efficiencies measured in synHEK3 reporters in one of the monoclonal lines (Clone 5) in the settings of targeted gene silencing by CRISPRoffv2.1. "K562-HEK3-SC*" experiments measured the effects of various shRNAs on prime editing efficiencies in synHEK3 reporters in two monoclonal lines. Finally, the rest files are amplicon sequencing results of endogenous prime editing targets in the presense and absense of CRISPRa.

first: Wei

last: Chen

first: Beth

last: Martin

first: Diego

last: Calderon

first: Choli

last: Lee

first: Junhong

last: Choi

first: Florence

last: Chardon

first: Troy

last: McDiarmid

first: Haedong

last: Kim

first: Jean-Benoît

last: Lalanne

last: Nathans

first: Jay

last: Shendure


title: NF-kB and Circadian Enhancers Link β-cell Function with Anti-IL1B Therapy [scATAC-seq]

first: Benjamin

last: Weidemann


title: Gene expression profile of MHCII+ cell subsets from bone marrow culture with FLT3L or GM-CSF

status: Public on Mar 05 2023

city: Seoul

first: Hyunju

last: In

state: Select One...

address: ABMRC #326, 50-1 Yonsei-ro, Seodaemun-gu

department: college of medicine

institute: Yonsei University

summary: BM culture comprises of various cell types including dendritic cells and macrophage-like cells. To understand the biology of BM-derived DCs, CD11c+MHCII+ cell subsets from BM cultures with FLT3L or GM-CSF were analyzed and are shown to have distinct transcriptional profiles.

overall_design:
This study includes data from various DC subsets and macrophages purified by flow cytometry sorting from BM culture with GM-CSF or FLT3L of WT C57BL/6 mice. At least two independent replicates were made for each cell type. Global mRNA expression profiles of the MHCII+ cell subsets from BM culture were done by Illumina Hi-seq 2500.
Submitter states that raw data for the cDC2 samples has been lost.

first: Chae

middle: G

last: Park


title: Human CXCR1+CD14+ monocytes are characterized by neutrophil-associated gene expression [RNA-seq human]

city: Hachioji

first: Kenichi

last: Asano

state: Tokyo

address: 1432-1 Horinouchi

department: Life Sciences

institute: Tokyo University of Pharmacy and Life Sciences

summary: This analysis was performed to identify markers discriminating human CXCR1+CD14+ monocytes from CXCR1-CD14+ classical monocytes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human neutrophils, CXCR1+CD14+ monocytes, CXCR1-CD14+ monocytes, CD14-CD16+ monocytes, and CD14+CD16+ monocytes.

first: Naoki

last: Ikeda

first: Akira

last: Nishiyama

first: Yoshihiro

last: Hayashi

first: Masato

last: Tanaka


title: mouse RNA-seq, human RNA-seq, ATAC-seq, and scRNA-seq analyses data

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

overall_design: Refer to individual Series


title: Copy number variation in tRNA isodecoder genes impairs mammalian development and balanced translation (RNA-seq)

city: Perth

first: Stefan

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

summary: The number of tRNA isodecoders has increased dramatically in mammals, but the specific molecular and physiological reasons for this expansion remain elusive. To address this fundamental question we used CRISPR editing to knockout the seven-membered phenylalanine tRNA gene family in mice, both individually and combinatorially. Using ATAC-Seq, RNA-seq and proteomics we observed distinct molecular consequences of individual tRNA deletions. We show that tRNA-Phe-1-1 is required for neuronal function and its loss is partially compensated by increased expression of other tRNAs but results in mistranslation. In contrast, the other tRNA-Phe isodecoder genes buffer the loss of each of the remaining six tRNA-Phe genes. In the tRNA-Phe gene family, the expression of at least six tRNA-Phe alleles is required for embryonic viability and tRNA-Phe-1-1 is most important for development and survival. Our results reveal that the multi-copy configuration of tRNA genes is required to buffer translation and viability in mammals.

overall_design: Differential gene expression analysis of wild type, tRNA-Phe-GAA-1-1-/-,  tRNA-Phe-GAA-2-1-/- and tRNA-Phe-GAA-3-1-/- mice, in brain and liver tissue

first: Laetitia

last: Hughes

first: Danielle

middle: L

last: Rudler

first: Tim

last: McCubbin

first: Jasmin

last: Brown

first: Judith

last: Ermer

first: Jeanette

last: Rientjes

first: Jennifer

last: Rodger

first: Esteban

last: Marcellin

first: Oliver

last: Rackham

first: Aleksandra

last: Filipovska


title: Viral and host RNA dynamics in tissues from lethal Ebola virus disease in rhesus monkeys

status: Public on Mar 03 2023

city: Cambridge

first: Siddharth

last: Raju

state: Massachusetts

address: 415 Main Street

institute: Broad Institute

summary: To assess the molecular basis of EVD infection across time, we performed host and viral RNA sequencing on 17 distinct tissue types from 21 infected rhesus monkeys. We then analyzed gene expression changes and viral mutation patterns.

overall_design: Rhesus monkeys were infected with Ebola virus, sacrificed at 0, 3, 4, 5, 6, 7, or 8 days post infection, and tissues were collected for data generation and analysis. Additionally, some blood samples were drawn from these monkeys 30, 28, and 14 days prior to infection (D-30, D-28, and D-14, respectively). Finally, there are organ-specific RNA samples which we received from the manufacturer Zyagen; these therefore do not have a "time".

first: Erica

last: Normandin

first: Sergio

middle: H

last: Sierra

first: Kim

last: Lagerborg

first: Tammy

last: Lan

first: Melissa

last: Rudy

first: Gordon

last: Adams

first: Katherine

last: DeRuff

first: James

last: Logue

first: David

last: Liu

first: Daniel

last: Strebinger

first: Arya

last: Rao

first: Molly

last: Sacks

first: Ricky

first: Krisztina

last: Janosko

first: Dylan

last: Kotliar

first: Rickey

last: Shah

first: Ian

last: Crozier

first: John

last: Rinn

first: Marta

last: Mele

first: Anna

middle: N

last: Honko

first: Feng

last: Zhang

first: Mehrtash

last: Babadi

first: Jeremy

last: Luban

first: Richard

last: Bennett

first: Alex

last: Shalek

first: Aaron

last: Lin

first: Nikolaos

last: Barkas

first: Lisa

last: Hensley

first: Pardis

last: Sabeti

last: Siddle

first: Katelyn

last: Messer


title: Impact of various high fat diets on intestinal gene expression in mouse

status: Public on Mar 01 2023

city: Riverside

first: Frances

last: Sladek

address: 900 University Avenue

institute: University of California

summary:
High fat diets (HFDs) are linked to several diseases including obesity, diabetes, insulin resistance, fatty liver, and susceptibility to inflammatory bowel disease (IBD) in both mouse and humans.
RNA-seq from male mice (C57BL/6N) fed Vivarium Chow (VIV) or any one of three high fat diets (40% kcal fat)  (SO+CO, PL+CO, CO) for 24 weeks was performed on four segments of the intestinal tract (Duodenum, Jejunum, Terminal Ileum and Proximal Colon).

overall_design: In this study, we analyzed the impact of three high fat diets (HFDs) on gene expression in four functionally distinct segments of the mouse intestinal tract using RNA-seq. The diets are described in Deol et al, 2017 (PMID: 28970503).

first: Jose

last: Martinez Lomeli

first: Poonamjot

last: Deol

first: Jonathan

middle: R

last: Deans

first: Tao

last: Jiang


title: Differentiation independent neuroprotective role of Vcan+ oligodendrocyte precursor cells in Post-stroke cognitive impairment recovery

status: Public on Apr 02 2023

city: Zhanjiang

last: Tao

state: Guangdong

address: 236 Yuanzhu Road, Guangdong

department: Department of Anesthesiology

institute: Central People’s Hospital of Zhanjiang

summary: We investigate the single cell transcriptome of hippocampus in both groups. A total of 27,069 cells were identified as 13 cell types, belong to neuronal, glial and vascular lineages. Then the cell-specific molecular changes and function in PSCI were analyzed.

overall_design: Examination of 2 sham and 2 two-vessel occlusion ischemia mouse model hippocampi samples

first: Shanghang

last: Shen

first: Yongjie

last: Wang

first: Ruixue

last: Xia


title: Dynamic changes in cellular atlases and communication patterns within yak ovaries across diverse reproductive states unveiled by single-cell analysis [scRNAseq_Yak_Ovary_Anestrus_2]

status: Public on Feb 24 2023

city: Lanzhou

first: Jie

last: Pei

state: Gansu

address: No. 335 Jiangouyan ST, Qilihe District

institute: Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences

summary: A cellular atlas of yak ovary was established successfully, containing oocytes, granulosa cells, stromal cells, endothelial cells, smooth muscle cells, natural killer cells, and macrophages. A cell-to-cell communication network was constructed in yak ovary.

overall_design: One sample from yak ovary in anestrus

first: Xian

last: Guo


title: Spatiotemporal analysis of SARS-CoV-2 infection in hamster lungs reveals an expansive wave of monocyte-derived macrophages associated with vascular damage and virus clearance

status: Public on Feb 20 2023

city: Bochum

first: Daniel

last: Todt

address: Universitätsstr. 150

department: Molecular & Medical Virology

institute: Ruhr University Bochum

summary: Characteristics of the innate immune response to SARS-CoV-2 in the lungs are pivotal for the ability of the organism to deal with infection. Excessive infiltration of macrophages is associated with poor disease outcome. Using 3D spatiotemporal analysis of optically clear hamster lung tissues in combination with virological, immunohistochemical and RNA sequence analyses we show the spread of SARS-CoV-2 through the lungs and rapid anti-viral response in infected lung epithelial cells, followed by a synchronized wave of CD68+ monocyte-derived macrophage (MDM) infiltration leading to virus elimination from the tissue. The SARS-CoV-2 induced innate immune processes are closely related with the onset of necrotic and lung remodelling responses in the lungs, which is manifested in extensive apoptosis, vascular damage, thrombosis, and an early initiation of cell proliferation. Here we show that MDM are directly linked to the virus clearance, and these cells appear in connection with tissue injury and blood vessel rupture. Rapid initiation of prothrombotic factor upregulation, tissue repair and alveolar cell proliferation results in tissue remodelling, which is followed by lung fibrosis development despite decrease in the inflammatory and anti-viral activities. Thus, although the animals are able to resolve the infection and repair lung tissue integrity, longer term structural changes in lungs indicate that the efficient balance between tissue damage and repair is critical for successful lung function restoration.

overall_design: 21 hamsters were infected orotracheally as described earlier (Blaurock et al., 2022) with 10^5 TCID50 of the ancestral SARS-CoV-2 (isolate 2019_nCoV Muc-IMB-1) per animal. Tissues from infected animals killed at day 1-7 and day 14 as well as mock-infected hamsters killed at day 7 were included in the study (n=3 per day). The left lung lobe was carefully removed, immersion-fixed in 10% neutral-buffered formalin, paraffin-embedded, and 2–3-μm sections were stained with hematoxylin and eosin (HE) for light microscopical examination. In parallel RNA extraction and Illumina RNAseq was performed.

first: Ola

last: Bagato

first: Angele

last: Breithaupt

first: Saskia

last: Weber

first: André

last: Gömer

first: Bingqian

last: Qu

first: Csaba

last: Miskey

first: Zoltan

last: Ivics

first: Kathrin

last: Müller

first: Sophienne

last: Touihri

first: Thomas

last: Mettenleiter

first: Stefan

last: Finke

first: Richard

last: Brown

first: Anne

last: Balkema-Buschmann

first: Dmitry

last: Ushakov


title: ccTaggedRP

status: Public on Feb 18 2023

city: Charlottesville

first: Jesse

last: Cochran

state: Virginia

address: 1221 Lee St

institute: University of Virginia

summary: Asynchronously cycling cells challenge the accurate characterization of phase-specific gene expression. Current strategies to characterize complex cell populations, including RNAseq, survey the steady state gene expression across the cell cycle and are inherently limited by the inability to resolve dynamic gene regulatory networks specific to subsets within the cell population. Single cell RNAseq (scRNAseq) provides an unbiased method to characterize the subpopulations and should identify different cell cycle transcriptomes if there are sufficient numbers of cycling cells present. Unfortunately, some cells are not amenable to scRNAseq. Therefore, we merged two powerful strategies, the incorporation of CDT1 and GMNN degrons used in FUCCI cell cycle sensors  and the epitope-tagging of ribosomal proteins used in RiboTrap/Tag technologies, to create a cell-cycle dependent, tagged ribosomes, named ccTaggedRP. ccTaggedRPs are differentially expressed during the cell cycle, have similar subcellular locations as endogenous ribosomal proteins, and facilitate the recovery of cell cycle phase-specific RNA for sequencing. ccTaggedRP has broad applications to investigate phase-specific gene expression in complex cell populations.

overall_design: Examine cell cycle phase-specifiic RNA expression profiles via RNA-seqeuncing of mRNAs associated with ribosomomal proteins immunoprecipitated by either their HA epitope tag or Flag epitope tag

first: Matthew

last: Wolf


title: Copy number variation in tRNA isodecoder genes impairs mammalian development and balanced translation [ATAC-seq]

last: Siira

overall_design: Examination of chromatin accessibility in wild type, tRNA-Phe-GAA-1-1-/-,  tRNA-Phe-GAA-2-1-/- and tRNA-Phe-GAA-3-1-/- mice, in brain and liver tissue

first: Laetitia

middle: A

last: Hughes

first: Danielle

last: Rudler

first: Tim

last: McCubbin

first: Jasmin

first: Judith

last: Ermer

first: Jeanette

last: Rientjes

first: Jennifer

last: Rodger

first: Esteban

last: Marcellin

first: Oliver

last: Rackham

first: Aleksandra

last: Filipovska


title: Long COVID manifests with T cell dysregulation, inflammation, and an uncoordinated adaptive immune response to SARS-CoV-2

status: Public on Feb 09 2023

first: Kailin

last: Yin

state: California

address: 1650 Owens street

institute: Gladstone Institutes

summary: Long COVID, a type of post-acute sequelae of SARS-CoV-2 infection (LC), occurs after at least 10% of SARS-CoV-2 infections, yet its etiology remains poorly understood. Here, we used multiple “omics” assays (CyTOF, RNAseq, Olink) and serology to deeply characterize both global and SARS-CoV-2-specific immunity from blood of unvaccinated individuals with clear LC and non-LC clinical trajectories, 8 months following infection. Our analysis focused on deep phenotyping of T cells, which play important roles in immunity against SARS-CoV-2 yet may also contribute to COVID-19 pathogenesis. Our findings demonstrate that LC individuals exhibit systemic inflammation and immune dysregulation. This is evidenced by global differences in T cell subset distribution in ways that imply ongoing immune responses, as well as by sex-specific perturbations in cytolytic subsets. LC individuals harbored increased frequencies of CD4+ T cells poised to home to inflamed tissues, and of exhausted SARS-CoV-2-specific CD8+ T cells. They also harbored significantly higher levels of SARS-CoV-2 antibodies, and they, but not non-LC individuals, exhibited a mis-coordination between their SARS-CoV-2-specific T and B cell responses. Collectively, our data suggest that proper crosstalk between the humoral and cellular arms of adaptive immunity has broken down in LC, and that this, perhaps in the context of a persistent reservoir of SARS-CoV-2, leads to the immune dysregulation, inflammation, and clinical symptoms associated with this debilitating disease.

overall_design: To study the phenotypes and effector functions of immune cells from individuals experiencing Long COVID-19 symptoms, we analyzed blood samples from 27 LC and 16 non-LC participants from the San Francisco-based Long-term Impact of Infection with Novel Coronavirus (LIINC) cohort. RNA-seq experiments were perfomed on the blood specimens fromour cohort of LC and non-LC participants.

first: Michael

last: Peluso

first: Timothy

last: Henrich

first: Nadia

last: Roan


title: Chlamydia trachomatis induces the transcriptional activity of host YAP in a Hippo-independent fashion

status: Public on Feb 13 2023

city: Omaha

first: Rey

last: Carabeo

state: Nebraska

address: 985900 Nebraska Medical Center

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

summary: The obligate intracellular pathogen Chlamydia trachomatis is the causative agent of the most common bacterial sexually transmitted disease worldwide. While the host response to infection by this pathogen has been well characterized, it remains unclear to what extent host gene expression during infection is the product of Chlamydia-directed modulation of host transcription factors. In this report, we show the transcriptome of Chlamydia-infected epithelial cells exhibits gene expression consistent with activity of YAP, a transcriptional coactivator implicated in cell proliferation, wound healing, and fibrosis. After confirming induction of YAP target genes during infection, we observed increased YAP nuclear translocation in Chlamydia-infected epithelial cells. We further show that increased YAP activation is a Chlamydia-directed process, requiring de novo protein synthesis during midcycle infection. Surprisingly, infection-mediated YAP activation bypasses YAP inhibition by the Hippo kinase cascade, with phosphorylation at S127 remaining unchanged. Instead, phosphorylation at Y357 was increased along with nuclear translocation, indicating that infection overrides phospho-inhibition at S127. Nuclear translocation of Y357F mutant YAP was not increased by infection, demonstrating that chlamydial YAP activation requires phosphorylation at this residue. Taken together, our results define a transcriptome-altering mechanism potentially linked to chlamydial fibrosis and other advanced disease sequelae.

overall_design: Gene expression data of immortalized endocervical epithelial cells infected with C. trachomatis serovar L2/434/Bu, B/Jali relative to mock-infected control samples. 3 biological replicates of each sample are provided.

first: Liam

last: Caven


overall_design: Gene expression data of immortalized endocervical epithelial cells infected with a ΔCTL0480-mutant strain of C. trachomatis serovar L2/434/Bu relative to a parent strain control group. 3 biological replicates of each sample are provided.


title: Activin pathway gene expression atlas in rainbow trout

status: Public on Feb 07 2023

city: Pullman

middle: Paul

last: Phelps

address: 100 Dairy Rd

institute: Washington State University

summary: The genome of many plant and animal species are heavily influenced by ancestral whole genome duplication (WGD) events.  These events transform the regulation and function of gene networks, yet the evolutionary forces at work on duplicated genomes are not fully understood.  Genes involved in cell surface signaling pathways are commonly retained following WGD.  To understand the mechanisms driving functional evolution of duplicated cell signaling pathways, we performed the activin receptor signaling pathway in rainbow trout (RBT).  Rainbow trout are a model salmonid species that exhibit a duplicated genome as a result of an ancestral WGD that occurred in all teleost fish, and a second more recent WGD found in salmonid fishes.  This makes RBT a powerful system for studying ohnolog evolution in a single species.  We observed that regulation of the duplicated activin receptor signaling pathway is commonly driven by tissue-specific expression of inhibitors and ligands along with the subfunctionalization of ligand ohnologs.  Evidence suggests that for inhibitors and R-Smad signaling molecules, there is ongoing pressure to establish a single copy state which may be driven, in part, by regulatory suppression of select ohnologs.  The core transmembrane receptors and Co-Smad signaling cascade members are high duplicated yet exhibit contrasting expression dynamics where receptors tend to share expression across tissues while dominance of a single ohnolog is common for the Smad4, Co-Smad gene family.  Our findings provide support for a generalized model where gene function and gene dosage have a complementary role in ohnolog evolution following WGD.

overall_design: Twenty-three adult rainbow trout tissues, five embryonic stages, and epaxial skeletal muscle from fry, parr, and juveniles were analyzed with a custom NanoString code set to profile the expression of 49 genes involved in the activin receptor signaling pathway.  Three-four biological replicates were used for every tissue.

first: Jasmine

last: Richman


title: Transcriptomic profiling by RNA-Seq of MCF-7 cells heterozygously depleted in the ARID4B locus by the CRISPR/Cas9 System

status: Public on Feb 04 2023

city: Monterrey

first: Fernando

last: Gonzalez-Salinas

state: Nuevo Leon

address: Morones Prieto avenue

department: Bioinformatica

country: Mexico

institute: Tecnologico de Monterrey

summary: The role of ARID4B in breast cancer development has not been completely elucidated. The aim of this study was to investigate the effect of loss of function mutations generated using the CRISPR/Cas9 system in human breast cancer cells. For this, we characterized the proliferation, viability, and migration rates of different clones with insertions and deletions compared to wild-type cells. We report the transcriptomic profile of mutated MCF-7 clones and negative control.

overall_design: Comparative gene expression profiling analysis of RNA-seq using three different clones with mutations in ARID4B and wild-type cells.

first: Jessica

last: Herrera-Gamboa

first: Rocio

last: Rojo

first: Victor

last: Trevino


title: Round or columnar and hypertrophic chondrocytes of Tric-b-KO mice

status: Public on Jan 31 2023

city: Kyoto city

first: Atsuhiko

last: Ichimura

state: Kyoto

address: 46-29, Yoshida Shimoadachi-cho, Sakyo-ku

department: Department of Biological Chemistry

institute: Kyoto University

summary:
To survey altered gene expreesion in round, colmnar and hypertrophic chondrocytes of Tric-b-KO mice, total RNA preparations from round chondrocytes and colmnar/hypertrophic chondrocytes were subjected to
gene microarray analysis. Results provide insight into the transcriptional profile of each Tric-b-KO chondrocyte and provide further insight into their functions.

overall_design: Total RNA preparations from three Tric-b-KO femoral cartilage plate portions enriched with round chondrocytes or columnar/hypertrophic chondrocytes were mixed and then subjected to Affymetrix Mus musculus microarrays. Round chondrocytes and columnar/hypertrophic chondrocytes were analyzed.

first: Hiroshi

last: Takeshima


title: mRNA therapy restores ureagenesis and corrects glutathione metabolism in argininosuccinic aciduria

city: London

first: Ana Luisa

last: Gil Martinez

address: 33 Queen Square

department: Clinical and Movement Neurosciences

institute: University College London

summary: Argininosuccinate lyase (ASL) is a key enzyme integral to the hepatic urea cycle which is required for ammonia detoxification, and the citrulline-nitric oxide (NO) cycle for NO production. ASL deficient patients present with argininosuccinic aciduria (ASA), an inherited metabolic disease with hyperammonaemia and a chronic systemic phenotype with neurocognitive impairment and chronic liver disease. ASL deficiency as an inherited model of systemic NO deficiency, shows enhanced nitrosative and oxidative stress. Here, we describe the dysregulation of glutathione biosynthesis and upstream cysteine utilization in ASL-deficient patients and mice using targeted metabolomics and in vivo positron emission tomography (PET) imaging using (S)-4-(3-18F-fluoropropyl)-L-glutamate ([18F]FSPG). Upregulation of cysteine metabolism contrasted with glutathione depletion and down-regulated antioxidant pathways. hASL mRNA encapsulated in lipid nanoparticles corrected and rescued the neonatal and adult Asl-deficient mouse phenotypes, respectively, enhancing ureagenesis and glutathione metabolism and ameliorating chronic liver disease. We further present [18F]FSPG PET as a novel non-invasive diagnostic tool to assess liver disease and therapeutic efficacy in ASA. These findings support clinical translation of mRNA therapy for ASA.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from liver samples from wild-type mice, Luc mRNA and hASL mRNA neonatal treated group of AslNeo/Neo mutant mice.

first: Sonam

last: Gurung

first: Oskar

middle: V

last: Timmermand

first: Dany

last: Perocheau

first: Ana

first: Magdalena

last: Minnion

first: Loukia

last: Touramanidou

first: Sherry

last: Fang

first: Martina

last: Messina

first: Youssef

last: Khalil

first: Justyna

last: Spiewak

first: Abigail

last: Barber

first: Richard

last: Edwards

first: Patricia

last: Pinto

first: Patrick

last: Finn

first: Alex

last: Cavedon

first: Summar

last: Siddique

first: Lisa

last: Rice

first: Paolo

last: Martini

first: Wendy

middle: E

last: Heywood

first: Ian

last: Hargreaves

first: Simon

last: Heales

first: Philippa

middle: B

last: Mills

last: Waddington

first: Paul

last: Gissen

last: Eaton

first: Mina

last: Ryten

first: Martin

last: Feelisch

first: Andrea

last: Frassetto

last: Witney

first: Julien

last: Baruteau


title: Single cell profiling of non-neuronal retinal cells reveals dynamic multicellular responses to central nervous system injury

status: Public on Feb 03 2023

first: Aviv

last: Regev

state: MA

department: Klarman Cell Observatory

summary: Non-neuronal cells play key roles in the complex cellular interplay that follows central nervous system (CNS) insult. To assess this interplay, we generated single-cell atlases of immune, glial and epithelial cells from adult mouse retina before and at multiple times after axonal transection (optic nerve crush; ONC), delineating changes in their composition, expression, and interactions. After injury, glial reactivation was coupled with chemokine upregulation and a unique retinal pigment epithelial (RPE) cell state. We resolved dynamic trajectories of mononuclear phagocytes, identified resident Ms4a7+MHC-IIhi and Ms4a7+MHC-IIlo subsets, and demonstrated that CCR2+ monocytes give rise to macrophages with overlapping signatures. We documented synchronized multicellular programs and interactions among neurons, glia, RPE and immune cells, highlighting coordinated gliosis, immune activation, and an interferon-response program. Finally, we mapped expression of human retinal disease-related genes by retinal and eyecup cells. Our atlas helps decipher the cellular circuitry, spatial relationships and molecular interactions following CNS injury.

overall_design: In these experiments, we FACS sorted for immune cells (CD45), Müller glia (GLAST), astrocytes (CD140a) and retinal pigment epithelial cells from dissociated retinas and eyecups of adult (6-8 wk old) mice, including uninjured controls, and at 6 time points following optic nerve crush (12h, 1d, 2d, 4d, 1w, 2w). Single cells were subjected to 10X Chromium library prep and RNA sequencing.

first: Benhar

last: Inbal

first: Jiarui

last: Ding

first: Wenjun

last: Yan

first: Irene

last: Whitney

first: Anne

last: Jacobi

first: Malika

last: Sud

first: Grace

last: Burgin

first: Karthik

last: Shekhar

first: Nicholas

middle: M

last: Tran

first: Chen

last: Wang

first: Zhigang

last: He

first: Joshua

last: Sanes


title: Whole transcriptome analysis after JEV infection in SH-SY5Y

status: Public on Feb 28 2023

city: Hyderabad

first: Shraddha

last: Tripathi

state: Telangana

address: Shamerpet, Kapra mandal

department: Biological sciences

country: India

institute: BITS Pilani Hyderabad

summary: Infection by neurotropic virus Japanese Encephalitis Virus (JEV) is characterized by profound neuronal cell death and neuroinflammation. Long non-coding RNAs (lncRNAs) are critical regulatory players in diverse biological processes, including viral pathogenesis. We use whole transcriptomic sequencing to identify a lncRNA JINR1 (JEV-induced non-coding RNA 1) induced upon JEV infection in neuronal cells. Transcription factor NF-κB triggers JINR-1 expression during JEV infection. Loss of JINR-1 impairs virus replication and reduces JEV-induced neuronal cell death and expression of genes involved in ER stress and neuroinflammation. Mechanistically, JINR1 inhibits the expression of mir-216-5p, which inhibits host factors GRP78 and c-JUN and the viral genome. In line with its role as a pro-viral host factor, JINR1 interacts with RBM10 and NF-κB to promote the expression of genes involved in ER stress and neuroinflammation.  Our results suggest a role for JINR-1 in promoting JEV-induced cell death and neuroinflammation.

overall_design: Cell line: SH-SY5Y; Sample names: control (C1, C2, C3) and JEV infected (I1, I2, I3); Total RNA was isolated from control (C1,C2,C3), or JEV (MOI 5) infected (I1, I2, I3) SH-SY5Y cells 48 h post-infection and RNA sequencing was performed.

first: Vivek

last: Sharma


title: Adult intracranial ependymoma - relevance of DNA methylation profiling for diagnosis, prognosis and treatment

status: Public on Feb 21 2023

city: Berlin

first: David

last: Kaul

address: Augustenburger Platz 1

department: Department of Radiation Oncology

institute: Charité - Universitätsmedizin Berlin

type: Methylation profiling by genome tiling array

summary: Background: A methylation-based classification of ependymoma has recently found broad application. However, the diagnostic advantage and implications for treatment decisions remain unclear. Here, we retrospectively evaluate the impact of surgery and radiotherapy on outcome after molecular reclassification of adult intracranial ependymomas.  Methods: Tumors diagnosed as intracranial ependymomas from 170 adult patients collected from eight diagnostic institutions were subjected to DNA methylation profiling. Molecular classes, patient characteristics, and treatment were retrospectively correlated with progression-free survival (PFS).  Results: The classifier indicated an ependymal tumor in 73.5%, a different tumor entity in 10.6% and non-classifiable tumors in 15.9% of cases, respectively. The most prevalent molecular classes were posterior fossa ependymoma group B (EPN-PFB, 32.9%), posterior fossa subependymoma (PF-SE, 25.9%), and supratentorial ZFTA fusion-positive ependymoma (EPN-ZFTA, 11.2%). With a median follow-up of 60.0 months, the 5- and 10-year-PFS rates were 64.5% and 41.8% for EPN-PFB, 67.4% and 45.2% for PF-SE and 60.3% and 60.3% for EPN-ZFTA. In EPN-PFB, but not in other molecular classes, gross total resection (p=0.009) and postoperative radiotherapy (p=0.007) were significantly associated with improved PFS in multivariable analysis. Histological tumor grading (WHO 2 vs. 3) was not a predictor of prognosis within molecularly defined ependymoma classes.   Conclusions: DNA methylation profiling improves diagnostic accuracy and risk stratification in adult intracranial ependymoma. The molecular class of PF-SE is unexpectedly prevalent among adult tumors with ependymoma histology and relapsed as frequently as EPN-PFB, despite the supposed benign nature. Gross total resection and radiotherapy may represent key factors in determining the outcome of EPN-PFB patients.

overall_design: Bisulphite converted tumor DNA of 170 patients were hybridised to the Illumina Infinium 450k or 850k Human Methylation Beadchip

first: Malte

last: Träger

last: Capper


title: Single-cell analysis reveals inflammatory interactions driving macular degeneration

status: Public on Jan 18 2023

city: New Haven

first: Marcello

last: DiStasio

address: 300 George St. Rm 353D

department: Pathology

institute: Yale School of Medicine

summary: Due to commonalities in pathophysiology, age-related macular degeneration represents a uniquely accessible model to investigate therapies for neurodegenerative diseases, leading us to examine whether pathways of disease progression are shared across neurodegenerative conditions. Here we use single-nucleus RNA sequencing to profile lesions from 17 retinas with age-related macular degeneration and controls. We create a machine learning pipeline based on recent advances in data geometry and topology and identify activated glial populations enriched in the early phase of disease. Examining single-cell data from Alzheimer’s disease and progressive multiple sclerosis with our pipeline, we find a similar glial activation profile enriched in the early phase of these neurodegenerative diseases. In late-stage age-related macular degeneration, we identify a microglia-to-astrocyte signaling axis mediated by interleukin-1beta which drives angiogenesis characteristic of disease pathogenesis. Thus, due to shared glial states, the retina provides a system for investigating therapeutic approaches in neurodegenerative diseases.

overall_design: Samples of retina were isolated from the macula in the central retina of post-mortem globes, located away from the optic disc and major arterioles. For each punch of tissue, the retina was mechanically separated from the underlying retinal pigment epithelium-choroid, nuclei were isolated and purified using the Nuclei EZ Prep Nuclei Isolation Kit (Sigma), following the manufacturer’s protocol. The nuclei suspensions were counted with trypan blue prior to loading on the microfluidics platform. Isolated nuclei from each macular sample were processed through microfluidics-based single nuclear RNA-seq. Single-cell libraries were prepared using the Chromium 3' v2 and v3 platforms (10X Genomics) following the manufacturer’s protocol.

first: Brian

last: Hafler

first: Le

last: Zheng


title: Region specific astrocyte response to mutant GFAP in Alexander disease model mice during postnatal development.

status: Public on Jan 17 2023

city: Madison

first: Tracy

last: Hagemann

state: WI

address: 1500 Highland Ave

department: Waisman Center

institute: University of Wisconsin-Madison

summary: Gene expression analysis was performed in Gfap+/+,  Gfap+/R236H, and mGFAPTg170-2 transgenic mice, using the Aldh1l1-eGFP-L10a transgenic line (JD130) to isolate translating ribosomes and purify astrocyte specific transcripts for RNAseq.

overall_design: Hippocampus and corpus callosum were collected from male mice at P14 in an FVBB6F1 background. Translating ribosomes were isolated using antibodies against EGFP to precipitate the EGFP-L10a fusion protein and the associated RNA purified for sequencing and gene expression analysis. N = 3 for each genotype with each sample consisting of tissues pooled from 5 mice (15 mice total).


title: Genetic modifiers of GFAP expression in mouse models of Alexander disease

summary: Gene expression analysis was performed in mouse models with Alexander disease associated GFAP mutations

overall_design: Hippocampus and corpus callosum were collected from male Gfap+/R236H and Gfap+/+ mice in FVB/N-Tac at 8 weeks of age, and total RNA isolated for RNA sequencing.

first: Albee

last: Messing


title: The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory (WGBS)

status: Public on Jan 11 2023

city: Napoli

first: Maria

middle: Rosaria

last: Matarazzo

address: Via Pietro Castellino 111

country: Italy

institute: Institute of Genetics and Biophysics "ABT"

type: Methylation profiling by high throughput sequencing

summary:
Bi-allelic hypomorphic mutations in DNMT3B disrupt DNA methyltransferase activity and lead to Immunodeficiency, Centromeric instability, Facial anomalies syndrome, type 1 (ICF1). While several ICF1 phenotypes have been linked to abnormally hypomethylated repetitive regions, the unique genomic regions responsible for the remaining disease phenotypes remain largely uncharacterized. Here we explored two ICF1 patient-induced pluripotent stem cells (iPSCs) and their CRISPR-Cas9 corrected clones to determine whether DNMT3B correction can globally overcome DNA methylation defects and related changes in the epigenome.
Hypomethylated regions throughout the genome were found highly comparable between ICF1 iPSCs carrying different DNMT3B variants, and significantly overlap with those in ICF1-peripheral blood and lymphoblastoid cell lines. These regions include large CpG island domains, as well as promoters and enhancers of several lineage-specific genes, in particular immune-related, suggesting that they are pre-marked during early development. CRISPR-corrected ICF1 iPSCs reveal that the majority of phenotype-related hypomethylated regions re-acquire normal DNA methylation levels following editing. However, at the most severely hypomethylated regions in ICF1 iPSCs, which also display the highest increased H3K4me3 levels and/or abnormal CTCF binding, the epigenetic memory persisted, and hypomethylation was uncorrected.
Overall, we demonstrate that restoring the catalytic activity of DNMT3B can reverse the majority of the ICF1 aberrant epigenome. However, a small fraction of the genome is resilient to this rescue, highlighting the challenge of reverting disease states that are due to genome-wide epigenetic perturbations. Uncovering the basis for the persistent epigenetic memory will promote the development of strategies to overcome this obstacle-

overall_design: In this study we examined the genome-wide DNA methylation level, gene expression, histone H3K4me3 and H3K36me3 marks enrichment, CTCF and DNMT3B binding in iPSCs derived from fibroblasts of healthy individuals, individuals affected by ICF syndrome type1 (ICF1 iPSCs) and ICF1 iPSCs corrected in the DNMT3B mutations following CRISPR/Cas9 editing.

first: Varsha

last: Poondi-Krishnan

first: Barbara

last: Morone

first: Claudia

last: Angelini

first: Sara

last: Selig


title: Apoptosis recognition receptors regulate skin tissue repair in mice

status: Public on Jan 29 2023

first: Miller-Jensen

last: Lab

address: 55 Prospect St

department: Biomedical Engineering

institute: Yale University

summary: Apoptosis and clearance of apoptotic cells via efferocytosis are evolutionarily conserved processes that drive tissue repair. However, the mechanisms by which recognition and clearance of apoptotic cells regulate repair are not fully understood. Here, we use single-cell RNA sequencing to provide a map of the cellular dynamics during early inflammation in mouse skin wounds. We find that apoptotic pathways and efferocytosis receptors are elevated in fibroblasts and immune cells, including resident Lyve1+ macrophages, during inflammation.

overall_design: 7-9 week-old male C57BL/6J mice were wounded during the telogen phase of hair cycling. To assess cellular and molecular heterogeneity of the wound bed during the inflammatory phase, we performed scRNA-seq on cells isolated from 4 mm full-thickness biopsy punches on mouse back skin at 24 and 48 hours (h) after injury. To ensure that we also captured the immediately adjacent tissue as well as cells that may have migrated into the wound site, we used a 6mm biopsy punch to collect the tissue before isolating cells using enzymatic digestion.

first: Olivia

last: Justynski

first: Kate

last: Bridges

first: Will

last: Krause

middle: F

last: Forni

first: Quan

last: Phan

first: Teresa

last: Sandoval-Schaefer

first: Ryan

last: Driskell

first: Kathryn

last: Miller-Jensen

first: Valerie

last: Horsley


title: Virome Data Explorer: A web resource to longitudinally explore respiratory viral infections, their interactions with other pathogens and host transcriptomic changes in over 100 people

status: Public on Jan 30 2023

city: New York

first: Angelica

last: Galianese

state: New York

address: 615 W 164th Street, Apt 21C

institute: Columbia University

summary: Viral respiratory infections are an important public health concern, due to their prevalence, transmissibility, and potential to cause serious disease. Disease severity is the product of several factors beyond the presence of the infectious agent, including specific host immune responses, host genetic makeup and bacterial co-infections. To understand these interactions within natural infections we designed a longitudinal cohort study actively surveilling 18 different respiratory viruses over the course of 19 months (2016-2018) in Manhattan, New York City. The cohort includes individuals related to daycare facilities, high school students and health care workers. We retrieved weekly epidemiological and clinical data and collected over 4,000 nasal swabs for molecular characterization from 214 participants. Transcriptomic data enabled the characterization of specific markers of immune response, the identification of signatures associated with symptom severity and bacterial co-infections. We created a computational resource to facilitate access to the data and visualization of analytical results.

overall_design: RNA-Seq, nasopharyngeal samples

first: Marta

last: Galanti

first: Juan

last: Patiño-Galindo

first: Ioan

last: Filip

first: Haruka

last: Morita

first: Sanjay

last: Natesan

first: Mariam

last: Youssef

first: Devon

last: Comito

first: Chanel

last: Ligon

first: Benjamin

last: Lane

first: Nelsa

last: Matienzo

first: Sadiat

last: Ibrahim

first: Eudosie

last: Tagne

first: Atinuke

last: Shittu

first: Oliver

last: Elliott

first: Tomin

last: Perea-Chamblee

first: Daniel

last: Scholes Rosenbloom

first: Jeffrey

last: Shaman

first: Raul

last: Rabadan


title: Structure primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference

first: Christopher

last: Jackson

state: NY

address: 101 Avenue of the Americas

department: Center for the Genomics of Neurodegenerative Disease

institute: New York Genome Center

summary: Regulation of gene expression in biological systems is a complex, nonlinear process composed of context specific interactions, from signaling and transcription to genome modification. Modeling gene regulatory networks (GRNs) can be limited due to a lack of direct measurements of regulatory features in genome-wide screens. Most GRN inference methods are consequently forced to model covariance between regulatory genes and their targets as a proxy for causal interactions.  This in turn complicates validation and reuse of predictive modeling frameworks. To disentangle covariance and casual influence require aggregation of independent and complementary sets of evidences, such as transcription factor (TF) binding and target gene expression. Common approaches include the overlap of evidence to infer causal relations. However the complete state of the system, e.g. TF activity (TFA) is unknown. Other methods tries to estimate these latent features.  These models often use linear frameworks that are unable to account for non-linearities, TF-TF interactions, and other higher order features. Deep learning frameworks can be used to model complex interactions between features and capture latent features of higher order. However deep learning methods often discard central concepts in biological systems modeling such as sparsity and latent feature interpretability in favour of increased complexity of the model.  In this work we demonstrate that gene regulatory network inference using latent features such as transcription factor activity can be built into a single framework. We present a novel deep learning approach (the Supirfactor framework) that incorporates multiple data-type orthogonal evidence of regulation and maintains interpretable parameter estimates.

overall_design: Single-cell RNA-sequencing of pooled saccharomyces cereivisae cells in rich media and minimal media

first: Andreas

last: Tjärnberg


title: Optimized CRISPR guide RNA library cloning reduces skew and enables more compact genetic screens

status: Public on Jan 10 2023

city: San Francisco

first: Scot

last: Federman

state: CA

address: 499 Illinois St

department: Biochemistry

institute: UCSF

summary: The development of CRISPR genetic screening tools has improved functional genomics, as these tools enable precise genomic editing, provide broad access to genomic regions beyond protein-coding genes, and have fewer off-target effects than other functional genomics modalities, allowing for novel applications with smaller library sizes compared to prior technologies. Pooled functional genomics screens require high cellular coverage per perturbation to accurately quantify phenotypes and average out phenotype-independent variability across the population. While more compact libraries have decreased the number of cells needed for a given screen, the cell coverage required for large-scale CRISPR screens still poses technical hurdles to screen in more challenging systems, such as iPSC-derived and primary cells. A major factor that influences cell coverage is screening library uniformity, as larger variation in individual guide RNA abundance requires higher cell coverage to reliably measure low-abundance guides. In this work, we have systematically optimized guide RNA cloning procedures to decrease bias. We implement these protocols to demonstrate that CRISPRi screens using 10-fold fewer cells than the current standard provides equivalent statistically significant hit-calling results to screens run at higher coverage, opening the possibility of conducting genome-wide and other large-scale CRISPR screens in technically challenging models.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: In this work, we have systematically optimized guide RNA cloning procedures to decrease bias : CRISPR guide RNA library cloning optimization, Genome-wide essential gene drop-out screens, Transduction titration experiments, 100-fold cell coverage dasatinib screen.

first: Seok-Jin

last: Heo

first: Lauren

last: Enriquez

first: Amy

middle: Y

last: Chang

first: Rachel

last: Mace

first: Kaivalya

last: Shevade

first: Phuong

last: Nguyen

first: Adam

middle: J

last: Litterman

first: Shawn

last: Shafer

first: Laralynne

last: Przybyla

first: Eric

last: Chow


title: Identification of Biomarkers and Outcomes of Endocrine Disruption in Human Ovarian Cortex using In Vitro Models

city: Solna

first: Tianyi

last: Li

address: Bioclinicum NKS J5:20, Solnavägen 30

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institute

summary: Endocrine disrupting chemicals (EDCs) are raising concerns about adverse effects on fertility in women. However, there is a lack of information regarding mechanisms of action and effects in humans. Our study aims to identify molecular mechanisms of endocrine disruption using two EDCs, diethylstilbestrol (DES) and ketoconazole (KTZ). Human ovarian cortical tissue obtained from Caesarean section patients were exposed to 10-9 M - 10-5 M KTZ and 10-10 M - 10-6 M DES in vitro for 6 days. Follicle survival and growth were studied via histology analysis and liquid-chromatography-mass spectrometry-based steroid quantification. RNA-sequencing was performed on primary ovarian cells and granulosa cancer cell lines COV434 and KGN that were exposed for 24 hours to the same concentrations of DES and KTZ as in the tissue culture. Significantly lower unilaminar follicle densities were observed in DES 10-10 M group, whereas low KTZ exposure reduced secondary follicle density. KTZ 10-5 M reduced levels of pregnenolone and progesterone. RNA-sequencing showed that 445 and 233 differentially expressed genes (FDR < 0.1) altogether in DES and KTZ exposed group. Gene set variation analysis showed that both chemicals modulated signalings that are important for folliculogenesis and steroidogenesis. We selected stearoyl-CoA desaturase (SCD) for validation because it was indicated in the affected gene sets by both chemicals. Up-regulation was confirmed in response to KTZ by qPCR in cell lines, and by in situ RNA hybridization and immunofluorescence in exposed ovarian tissue. Conclusively, SCD may serve as a potential novel human-relevant biomarker of EDC exposure and effects in ovaries.

overall_design: 45 samples from 3 passages of 3 cell lines (COV434, KGN, primary ovarian cells), 5 groups in total (DMSO, KTZ 10-5M, KTZ 10-9M, DES 10-6M, DES 10-10M)

first: Paraskevi

last: Vazakidou

first: Pim

last: E.G. Leonards

first: Anastasios

last: Damdimopoulos

first: Eleftheria

last: Panagiotou

first: Catarina

last: Arnelo

first: Kerstin

last: Jansson

first: Karin

last: Pettersson

first: Kiriaki

last: Papaikonomou

first: Majorie

last: van Duursen

first: Pauliina

last: Damdimopoulou


title: Epigenetic reprogramming shapes the cellular landscape of schwannoma, DNA Methylation

status: Public on Jan 02 2023

city: SAN FRANCISCO

first: John

last: Liu

address: 35 Medical Center Way

summary: Cell state evolution underlies tumor development and response to therapy, but mechanisms specifying cancer cell states and intratumor heterogeneity are incompletely understood. Schwannomas are the most common tumors of the peripheral nervous system and are treated with surgery and ionizing radiation. Schwannomas can oscillate in size for many years after radiotherapy, suggesting treatment may reprogram schwannoma cells or the tumor microenvironment. Here we show epigenetic reprogramming shapes the cellular landscape of schwannomas. We find schwannomas are comprised of 2 methylation based molecular groups distinguished by reactivation of neural crest development pathways or misactivation of nerve injury mechanisms that specify cancer cell states and the architecture of the tumor immune microenvironment. Schwannoma molecular groups can arise independently, but ionizing radiation is sufficient for epigenetic reprogramming of neural crest to immune-enriched schwannoma by remodeling chromatin accessibility, gene expression, and metabolism to drive schwannoma cell state evolution and immune cell infiltration. To define functional genomic mechanisms underlying epigenetic reprograming of schwannomas, we develop a technique for simultaneous interrogation of chromatin accessibility and gene expression coupled with genetic and therapeutic perturbations in single-nuclei. Our results elucidate a framework for understanding epigenetic drivers of cancer evolution and establish a paradigm of epigenetic reprograming of cancer in response to radiotherapy.

overall_design:
illumina EPIC methylation profiles of vestibular schwannomas.
Note: the 'classification'  samples (i.e. VS*, HEI193* samples) were only used as raw input data for a support vector machine classifier so only clinical tumor (S*) processed data are provided here.

first: S

first: David

last: Raleigh


title: Chlamydia trachomatis induces the transcriptional activity of host YAP in a Hippo-independent fashion

first: Rey

last: Carabeo

summary: The obligate intracellular pathogen Chlamydia trachomatis is the causative agent of the most common bacterial sexually transmitted disease worldwide. While the host response to infection by this pathogen has been well characterized, it remains unclear to what extent host gene expression during infection is the product of Chlamydia-directed modulation of host transcription factors. In this report, we show the transcriptome of Chlamydia-infected epithelial cells exhibits gene expression consistent with activity of YAP, a transcriptional coactivator implicated in cell proliferation, wound healing, and fibrosis. After confirming induction of YAP target genes during infection, we observed increased YAP nuclear translocation in Chlamydia-infected epithelial cells. We further show that increased YAP activation is a Chlamydia-directed process, requiring de novo protein synthesis during midcycle infection. Surprisingly, infection-mediated YAP activation bypasses YAP inhibition by the Hippo kinase cascade, with phosphorylation at S127 remaining unchanged. Instead, phosphorylation at Y357 was increased along with nuclear translocation, indicating that infection overrides phospho-inhibition at S127. Nuclear translocation of Y357F mutant YAP was not increased by infection, demonstrating that chlamydial YAP activation requires phosphorylation at this residue. Taken together, our results define a transcriptome-altering mechanism potentially linked to chlamydial fibrosis and other advanced disease sequelae.

overall_design: Gene expression data of immortalized endocervical epithelial cells infected with C. trachomatis serovar L2/434/Bu, B/Jali relative to mock-infected control samples. 3 biological replicates of each sample are provided.

first: Liam

last: Caven


title: Enteric nervous system: timecourse analysis of longitudinal muscle and myenteric plexus (LMMP) in mice

status: Public on Feb 06 2023

city: Baltimore

first: Loyal

last: Goff

state: MD

address: 733 N Broadway

institute: Johns Hopkins University

summary: Samples of dissociated mouse small intestinal longitudinal muscle-myenteric plexus were prepared from post natal day 10 (P10), P20, and P60, each with two biological replicates. Samples were run through the 10x Chromium 3' Single Cell Gene Expression platform v3.1

overall_design: Six Sample, two replicates three ages

first: Subhash

last: Kulkarni

first: Monalee

last: Saha

first: Laren

last: Becker

first: Alpana

last: Singh

first: Jared

last: Slosberg

first: Chengxiu

last: Zhang

first: Alicia

last: Bukowski

first: Zhuolun

last: Wang

first: Guosheng

first: Jenna

last: Leser

first: Mithra

last: Kumar

first: Shriva

last: Bakhshi

first: Matthew

last: Anderson

first: Mark

last: Lewandowski

first: Sushma

last: Nagaraj

first: Elizabeth

last: Vincent

first: Pankaj

last: Pasricha


title: Epigenetic profiles of chimeric antigen receptor T cells

status: Public on Jan 01 2023

city: Shinjuku-ku

first: Yusuke

last: Ito

state: Tokyo

address: 35 Shinanomachi

department: Division of Tumor Immunology

institute: Keio University

summary: In order to investigate chromatin accessibility of human T cells, we performed ATAC sequencing analysis usign human CAR-T cells.

overall_design: Human peripheral blood mononuclear cells derived from two different healthy donors were retrovirally transduced wih an anti-CD19 car gene (FMC63-28z). CD8+ CAR-T cells were isolated after 1 week, and chromatin accessibility was analyzed by ATAC sequencing.

first: Yuki

last: Kagoya


title: Antifibrogenic activities of CYP11A1-derived vitamin D3-hydroxyderivatives are modified by RORγ expression

status: Public on Jan 06 2023

city: Birmingham

first: Andrzej

middle: T

last: Slominski

state: AL

address: 1720 2nd Avenue South

department: Dermatology

institute: UAB

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

overall_design: Refer to individual Series


title: Effect of lactate on gene expression during myoblast differentiation of C3H C2C12 cells

city: Nanjing

first: Weilong

last: Dai

state: jiangsu

address: Xiaoling Wei Street

institute: Nanjingagricultureuniversity

summary:
To investigate the  function of lactate in the regulation of myoblast differentiation
We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for C3HC2C12 cells with lactate treatment or not.

first: Honglin

last: Liu


title: The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory

first: Maria

last: Matarazzo


title: Whole genome bisulfite sequencing comparing the DNA methylation level between monkey ICSI and SCNT blastocysts

status: Public on Dec 27 2022

city: Shanghai

first: Liao

last: Zhaodi

address: 500, Qiangye Road

department: Institute of Neuroscience

institute: Chinese Academy of Sciences

summary: Somatic cell nuclear transfer (SCNT) has been used to clone cynomolgus monkeys (Macaca fascicularis), but the cloning of other non-human primate species remains to be achieved. On the other hand, our histological examination indicated severe calcification of the placenta of SCNT fetuses. Additionally, we found that some of the maternal-biased imprinting genes were aberrantly lost in the cloned embryos by multi-omics analysis. We thus developed a trophoblast replacement (TR) method, providing an ICSI-derived placenta for the SCNT fetus, to support the full-term development of the cloned embryos after implantation. By combining this TR method with treatment with epigenetic modification factors, we obtained a healthy somatic cell cloned rhesus monkey. Thus, TR represents a useful approach for rhesus monkey cloning.

first: Zhaodi

last: Liao

first: Jixiang

last: Zhang