title: Effect of antivirals in NPCs derived from induced pluripotent stem cells

city: pittsburgh

first: Leonardo

last: D'aiuto

state: pa

address: 3811 O'Hare st

department: psychiatry

institute: UPMC

summary:
Neurotropic viral infections of the central nervous system (CNS) cause a broad spectrum of clinical manifestations, which include neuropathological changes and subsequent neurological conditions. Currently utilized antiviral drugs are targeted towards specific viruses or members of a specific family. However, the recent COVID-19 pandemic caused by the neurotropic virus SARS-CoV-2 has highlighted the importance of having broad spectrum agents available in our armamentarium that can limit replication of emerging and reemerging neurotropic viruses and future unidentified pathogens that can pose a risk for the next pandemic.
Neural progenitor cells (NPCs) were derived from hiPSC-neurons as previously described (D’Aiuto et al. Organogenesis. 2014;10(4):365-77).

overall_design:
Using a human induced pluripotent stem cells (hiPSCs)-based neuronal platform, we have identified a small molecule termed "R430", a lycorane-type alkaloid which is able to inhibit productive (lytic) HSV-1 infections in vitro and in a murine model of HSV-1 infection. Importantly, later experiments showed that R430 exhibits potency against other DNA viruses (HSV-1, HCMV, HBV, HCV), as well as RNA viruses (ZIKV strains FSS-13025 and PE-243). However, higher toxicity when compared to acyclovir (the gold standard drug for herpes infections) was observed in fibroblasts and hepatocytes.
Thus, we employed a structure-activity relationship (SAR) study to generate new R430 analogs which would possess a comparable antiviral activity but a reduced cell toxicity.

last: D'Aiuto

first: Vishwajit

last: Nimgaonkar


title: Targeting KAT6A/KAT6B dependencies in breast cancer with a novel selective, orally bioavailable KAT6 inhibitor, CTx-648/PF-9363 [ChIP-Seq - CUT&RUN]

status: Public on Jun 05 2023

city: San Diego

first: Chi-Yeh

last: Chung

state: CA

address: 10770 Science Center Drive

country: USA

institute: Pfizer Inc.

type: Genome binding/occupancy profiling by high throughput sequencing

summary: KAT6A, and its paralog KAT6B, are histone lysine acetyltransferases (HAT) that acetylate histone H3K23 and regulate diverse biological processes including transcription, cell-cycle progression, and stem cell development.  KAT6A exerts an oncogenic role in several tumor types including breast cancer where it is amplified in 10-15% of patients. However, pharmacologic targeting of KAT6A to achieve therapeutic benefit has been a challenge. Here we describe identification of a highly potent, selective and orally bioavailable KAT6A/KAT6B inhibitor CTx-648 (PF-9363), derived from a novel benzisoxazole series, which demonstrates anti-tumor activity in correlation with H3K23Ac inhibition in KAT6A over-expressing breast cancer. Transcriptional and epigenetic profiling studies show reduced RNA Pol II binding and downregulation of genes involved in estrogen signaling, cell cycle and stem cell pathways associated with CTx-648 anti-tumor activity in ER-positive (ER+) breast cancer. CTx-648 treatment leads to potent tumor growth inhibition in ER+ breast cancer in vivo models, including models refractory to endocrine therapy, highlighting the potential for targeting KAT6A in ER+ breast cancer.

overall_design: Human breast cancer cell lines were treated with DMSO or 30 nM PF9363 for24 hr in replicates, and subjected to ChIP-seq or CUT&RUN analysis

first: Shikhar

last: Sharma

first: Jelena

last: Petrovic

first: Thomas

middle: A

last: Paul


title: Protein-intrinsic properties and context-dependent effects regulate pioneer-factor binding and function [CUT&RUN]

status: Public on May 02 2023

city: Madison

first: Melissa

middle: M

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

summary: While chromatin presents a barrier to the binding of many transcription factors, pioneer factors access nucleosomal targets and promote chromatin opening. Despite binding to target motifs in closed chromatin, many pioneer factors display cell-type specific binding and activity. The mechanisms governing pioneer-factor occupancy and the relationship between chromatin occupancy and opening remain unclear. We studied three Drosophila transcription factors with distinct DNA-binding domains and biological functions: Zelda, Grainy head, and Twist. We demonstrated that the level of chromatin occupancy is a key determinant of activity. Multiple factors regulate occupancy, including motif content, local chromatin, and protein concentration. Regions outside the DNA-binding domain are required for binding and chromatin opening. Our results show that pioneering activity is not a binary feature intrinsic to a protein but occurs on a spectrum and is regulated by a variety of protein-intrinsic and cell-type-specific features.

overall_design: CUT&RUN on cells ectopically expressing Drosophila transcription factors.

first: Tyler

middle: J

last: Gibson


title: Context dependent function of transcriptional regulator Rap1 in gene silencing and activation

status: Public on May 09 2023

city: Berkeley

first: Eliana

middle: Rose

last: Bondra

state: California

address: 440 Barker Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

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

sample_organism:
Saccharomyces cerevisiae
Saccharomyces paradoxus

overall_design: Refer to individual Series


title: Transcriptome profiling in rumen, reticulum, omasum, and abomsum tissues of yak during the developmental transition of pre-ruminant to the ruminant

status: Public on Apr 30 2023

city: Chengdu

first: Li

middle: yi

last: Liu

state: None Selected

address: #16, South Section, 1st Ring Road, Chengdu, Sichuan, China, Post Code 610041

country: China

institute: Southwest Minzu University

type: Expression profiling by high throughput sequencing

summary: This study provides a clear and accurate dynamic transcriptome profile of mRNAs in rumen, reticulum, omasum and abomasum of yaks. The results include high-quality genomic data and help to elucidate the important roles of these mRNAs in regulation of growth, development and metabolism in yaks, and to further understand the molecular mechanisms underlying metabolic regulation of yak stomach tissues. At the same time, it provided a theoretical basis for age-appropriate weaning and supplementary feeding in yaks.

overall_design: we first compared mRNA expression levels of rumen, reticulum, omasum, and abomasum of yaks in five developmental stages (0 d, 20 d, 60 d, 15 m and adult after birth).

first: Yili

first: Mingfeng

last: Jiang

first: Qi

last: Min

first: Jiao

last: Tang


title: Context dependent function of transcriptional regulator Rap1 in gene silencing and activation [ChIP-seq timecourse]

summary: As part of a study on the function of Rap1 at HML and MAT in Saccharomyces cerevisiae, we performed an Anchor Away experiment on Rap1, inducibly depleting it from the nucleus upon addition of Rapamycin, followed by a ChIP-seq time-course. This was done in a strain that had SNPs introduced to HMLalpha to make it distinguishable from MATalpha. Samples were spiked with a constant amount (5% by OD) of a S.paradoxus strain that also expressed 2xV5-Rap1. Reads from the S.paradoxus sample served as the normalization factor. Peaks were then fit to a non-linear regression model to extract the k(off) and apparent residence time in vivo.

platform_organism:
Saccharomyces cerevisiae
Saccharomyces paradoxus

overall_design: 2xV5-FRB-Rap1 ChIP-seq timecourse (t = 0 (DMSO), 5min, 10min, 15min, 20min, 30min, 45min, 60min) following addition of Rapamycin in S. cerevisiae  + Spike-in of 5% cells (by OD) of 2xV5-tagged S.paradoxus strain. Replicates are included for each experiment.

first: Jasper

last: Rine


title: A Drosophila screen identifies a role for histone methylation in ER stress preconditioning

status: Public on Apr 25 2023

city: Salt Lake CIty

first: Katie

middle: G

last: Owings

state: UT

address: 15 North 2030 East EIHG 5200

department: Human Genetics

institute: University of Utah

summary: Stress preconditioning occurs when transient, sublethal stress events impact an organism's ability to counter future stresses. Although preconditioning effects are often noted in the literature, very little is known about the underlying mechanisms. To model preconditioning, we exposed a panel of genetically diverse Drosophila melanogaster to a sublethal heat shock and measured how well the flies survived exposure to endoplasmic reticulum (ER) stress. To identify genes with expression patterns predictive of preconditioning outcomes, we focused on the 10 DGRP strains at the extreme ends of our preconditioning screen. We compared the beneficial strains (RAL69, RAL93, RAL359, RAL387, RAL409) to the detrimental (RAL195, RAL304, RAL335, RAL737, RAL819) with and without heat shock (our preconditioning stress).

overall_design: To identify a standard mechanism for detrimental or beneficial preconditioning outcomes, we treated the five strains in each group as technical replicates instead of investigating each strain individually. We  performed gene expression profiling analysis using data obtained from RNA-seq of 10 DGRP lines with and without heat shock. We compared the benefical group to the detrimental group for each treatment. In the final processed data, RAL409 was omited as an outlier based on PCA.

first: Clement

middle: Y

last: Chow


title: Endothelial Identity of Porcine Double-sorted CD31+ Kidney Cells

city: Boston

first: Robert

last: Policastro

state: Massachusetts

address: 451 D St Unit #600

institute: Ensoma Inc.

summary: Endothelial cells of xenotransplanted gene-edited porcine kidneys are important due to the initial and prolonged exposure to host immune cells. To better study this cell population kidney endothelial cell lines (KECs) were generated by double CD31+ sorting. In order to ensure the endothelial identity of the cells RNA-seq was performed on KECs and the concomitant CD31- population from the initial sort. Analysis of gene expression in KECs showed a depletion of markers associated with tubular identity (SLC34A1, SLC2A2, SLC12A1), and enrichment for markers of endothelial (PECAM1, CDH5, VWF) and kidney endothelial (EHD3, HOX87, HOX89) identity.

overall_design: RNA-seq of double-sorted CD31+ and the concomitent CD31- cells of WT, 3KO, and payload 15S porcine kidneys to determine endothelial identity.

first: Sagar

last: Chhangawala


title: Changes in adenoviral chromatin organization precede early gene activation [ChIP-Seq]

status: Public on Apr 24 2023

city: Regensburg

first: Uwe

last: Schwartz

address: Universitätstraße 32

department: NGS Analysis Center

country: Germany

institute: University of Regensburg

summary: Within the virion, adenovirus DNA associates with the virus-encoded, protamine-like structural protein pVII. Whether this association is organized, and how genome packaging changes during infection and subsequent transcriptional activation is currently unknown. Here, we combined RNA-seq, MNase-seq, ChIP-seq and single genome imaging during early adenovirus infection to unveil the structure- and time-resolved dynamics of viral chromatin changes as well as their correlation with gene transcription. Our MNase mapping data indicates that the viral genome is arranged in precisely positioned nucleoprotein particles (Adenosomes), like nucleosomes. We identified 238 Adenosomes, being positioned by a DNA sequence code and protecting about 60 to 70bp of DNA. The incoming genome is more accessible at early gene loci that undergo additional chromatin de-condensation upon infection. Histone H3.3 containing nucleosomes specifically replaces pVII at distinct genomic sites and at the transcription start sites of early genes. Acetylation of H3.3 is predominant at the transcription start sites, preceding transcriptional activation. Based on our results we propose a central role for the viral pVII nucleoprotein-architecture, which is required for the dynamic structural changes during early infection, including the regulation of nucleosome assembly prior to transcription initiation. Our study thus may aid the rational development of recombinant adenoviral vectors exhibiting sustained expression in gene therapy.

overall_design: ChIP-seq of H3.1, H3.3 and H3K27ac , low and high MNase-seq of mono-nucleosomes and RNA-seq of polyA enriched RNA at 5 time points after Adenovirus infection; 2 biological replicates each

first: Tetsuro

last: Komatsu

first: Claudia

last: Huber

first: Michael

last: Rehli

first: Harald

last: Wodrich

first: Gernot

last: Laengst


title: Life-supporting function of genome edited porcine renal graft in cynomolgus macaques


title: Protein-intrinsic properties and context-dependent effects regulate pioneer-factor binding and function [ChIP-Seq]

first: Melissa

last: Harrison

overall_design: ChIP-seq on cells ectopically expressing Drosophila transcription factors.

first: Tyler

last: Gibson


title: OBOX regulates murine zygotic genome activation and early development

city: Beijing

first: Fengling

last: Chen

state: Beijing

address: 30 Shuangqing Rd.

institute: Tsinghua University

summary: Zygotic genome activation (ZGA) activates the quiescent genome to enable the maternal-to-zygotic transition. However, the identity of transcription factors (TFs) that underlie mammalian ZGA in vivo remains unresolved. Here, we showed that OBOX, a PRD-like homeobox domain TF family that includes 66 members (OBOX1-8), are key regulators of mouse ZGA. Knockout mice deficient for maternally transcribed Obox1/2/5/7 and zygotically expressed Obox3/4 led to 2-4 cell arrest accompanied by impaired ZGA. Maternal and zygotic expressed OBOX redundantly support embryonic development as Obox KO defects can be rescued by restoring either of them. Chromatin binding analysis revealed Obox knockout preferentially affected OBOX-binding targets. Mechanistically, OBOX facilitated RNA Pol II ?pre-configuration?, as Pol II relocates from the initial 1-cell binding targets to ZGA gene promoters and distal enhancers. The impaired Pol II pre-configuration in Obox mutants was accompanied by downregulation of ZGA genes, chromatin accessibility transition defects, as well as aberrant activation of one-cell Pol II targets. Finally, OBOX ectopically activated ZGA genes and MERVL in mESCs. Hence, these data demonstrate that OBOX regulates murine ZGA and early embryogenesis.

overall_design: By employing RNA-seq and Pol II Stacc-seq/ATAC-Seq in Obox mzKO embryos as well as RNA-seq in Obox OE mESCs, we revealed maternal OBOX is the key transcription factor regulating  murine zygotic genome activation.

first: Shuyan

last: Ji

first: Wei

last: Xie


title: Combinatorial immunotherapy with agonistic CD40 activates dendritic cells to express IL-12 and overcome PD-1 resistance

status: Public on Apr 19 2023

city: New Haven

first: Miller-Jensen

last: Lab

address: 55 Prospect St

department: Biomedical Engineering

institute: Yale University

summary: Checkpoint inhibitors have revolutionized cancer treatment, but resistance remains a significant clinical challenge. Myeloid cells within the tumor microenvironment can modulate checkpoint resistance by either supporting or suppressing adaptive immune responses. Using an anti-PD-1 resistant mouse melanoma model, we show that targeting the myeloid compartment via CD40 activation and CSF1R blockade in combination with anti-PD-1 results in complete tumor regression in a majority of mice. This triple therapy combination is primarily CD40 agonist-driven in the first 24 hours post-therapy and shows a similar systemic cytokine profile in human patients as in mice. Functional single-cell cytokine secretion profiling of dendritic cells (DCs) using a novel microwell assay identified a CCL22+CCL5+ IL-12-secreting DC subset as important early-stage effectors of triple therapy. CD4+ and CD8+ T cells are both critical effectors of treatment, and systems analysis of single-cell RNA-sequencing data supports a role for DC-secreted IL-12 in priming T cell activation and recruitment. Finally, we show that treatment with a novel IL-12 mRNA therapeutic alone is sufficient to overcome PD-1 resistance and cause tumor regression. Overall, we conclude that combining myeloid-based innate immune activation and enhancement of adaptive immunity is a viable strategy to overcome anti-PD-1 resistance.

overall_design: C57BL6/J mice were injected with 0.5x10^6 YUMMER1.7 cells on day 0, and then were either left untreated or treated with the combination of anti-PD-1, CSF1R blockade, and agonistic CD40 (i.e., TTx) by i.p. injection on day 7. To assess cellular and molecular heterogeneity in the tumor in response to treatment, we performed scRNA-seq on cells isolated from untreated and TTx-treated tumors 24 hours after treatment on day 8. One tumor was used per treatment condition.

first: Irina

last: Krkbaeva

first: Kate

last: Bridges

first: William

last: Damsky

first: Gabriela

last: Pizzurro

first: Amanda

middle: F

last: Alexander

first: Meaghan

middle: K

last: McGeary

first: Viswanathan

last: Muthusamy

first: James

last: Eyles

first: Nadia

last: Luheshi

first: Noel

last: Turner

first: Sarah

last: Weiss

first: Kelly

last: Olino

first: Susan

last: Kaech

first: Harriet

last: Kluger

first: Kathryn

last: Miller-Jensen

first: Marcus

last: Bosenberg


title: Longitudinal RNA-seq of Gene-edited Porcine Kidneys in Cynomolgus Macaques

status: Public on Apr 21 2023

first: Robert

last: Policastro

summary: Succesful xenotransplantation of porcine kidneys into humans requires durable expression of certain human transgenes. In order to ensure robust expression through the life of the transplanted kidney, RNA-seq was performed on gene-edited kidneys prior to and during transplantation into cynomolgus macaques. Analysis of this longitudinal transcriptomics data shows robust and stable transgene expression through the lifespan of numerous xenotransplanted organs.

overall_design: Illumina polyA RNA-seq was performed on gene-edited porcine kidney biopsies prior to and during transplant into cynomolgus macaques.

first: Sagar

last: Chhangawala


title: Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces

city: Baltimore

first: Elana

last: Fertig

state: MD

address: 550 N Broadway, Suite 1101

department: Oncology

institute: Johns Hopkins University Sidney Kimmel Comprehensive Cancer Center

summary: Recent advances in spatial transcriptomics (ST) enable gene expression measurements from a tissue sample while retaining its spatial context. This technology enables unprecedented in situ resolution of the regulatory pathways that underlie the heterogeneity in the tumor and its microenvironment (TME). The direct characterization of cellular co-localization with spatial technologies facilities quantification of the molecular changes resulting from direct cell-cell interaction, as occurs in tumor-immune interactions. We present SpaceMarkers, a novel bioinformatics algorithm to infer molecular changes from cell-cell interaction from latent space analysis of ST data. We apply this approach to infer molecular changes from tumor-immune interactions in Visium spatial transcriptomics data of metastasis, invasive and precursor lesions, and immunotherapy treatment. Further transfer learning in matched scRNA-seq data enabled further quantification of the specific cell types in which SpaceMarkers are enriched. Altogether, SpaceMarkers can identify the location and context-specific molecular interactions within the TME from ST data.

overall_design:
The HCC sample was obtained from a Phase I clinical trial that examined cabozantinib plus nivolumab as neoadjuvant therapy for advanced hepatocellular carcinoma. The PDAClymphnode was collected from a patient with pancreatic adenomarcinoma that received noeadjuvant therapy with a pancreatic cancer vaccine (GVAX). The PanIN was collected from a treatment naive pancreatic cancer patient. All three samples were analyzed using spatial transcriptomics. None of the samples had experimental replicates.
We performed latent space factorization of the 10x Visium spatial transcriptomics and used SpaceMarkers to identify genes associated with spatially overlapping latent features representing different cell types. For the HCCsinglecell sample, the tumor was enzymatically dissociated into single cells upon surgical resection. Tumor was minced and dissociated in digestion medium containing 0.1% (w/v) collagenase type IV (Invitrogen) in PBS at 37°C for 30 minutes on a shaking incubator set at 60 rpm. Cell collection was enriched with Percoll 40%−80% (GE Life Sciences) at 2000 × g for 25 minutes at RT without break, eliminating debris and erythrocytes.

*** Submitter declares that the raw data will be deposited in dbGaP due to patient privacy concerns ***

first: Atul

last: Deshpande

first: Luciane

middle: T

last: Kagohara


title: Changes in adenoviral chromatin organization precede early gene activation [MNase-seq]

first: Uwe

last: Schwartz

type: Methylation profiling by high throughput sequencing

overall_design: low and high MNase-seq of mono-nucleosomes and RNA-seq of polyA enriched RNA at 5 time points after Adenovirus infection; 2 biological replicates each

first: Tetsuro

last: Komatsu

first: Claudia

last: Huber

first: Harald

last: Wodrich

first: Gernot

last: Laengst


title: Changes in adenoviral chromatin organization precede early gene activation


title: scRNA-seq of Gene-edited Porcine Kidneys Prior to Xenotransplantation into Cynomolgus Macaques

summary: Succesful xenotransplantation of porcine kidneys into humans requires the ubiqutous expression of certain human transgenes. Modern transcriptomics now alllows gene expression to be measured at the per-cell level, which can provide important insights into the expression pattern of these life-sustaining transgenes in a complex organ such as the kidney. Analysis of this scRNA-seq data shows ubiquitous expression of transgenes in most major kidney cell populations which includes various subtypes of endothelial cells.

overall_design: 10X 3' scRNA-seq was performed on gene-edited porcine contralateral kidneys prior to xenotransplantation into cynomolgus macaques to measure transgene expression at cellular resolution.


title: RNA sequencing facilitates quantitative analysis of NPC cells, NPC-KRASG13D, and GSC cells (including U251-GSC, U118MG-GSC) transcriptomes

status: Public on Apr 14 2023

city: GuangZhou

first: Waiyip

last: Liang

address: Guangzhou Higher Education Mega Centre, Panyu District, Guangzhou

institute: South China of Technology

summary: To investigate the function of KRAS activation in the regulation of neoplastic features, we established NPC-KRASG13D cell lines in which KRAS has been overexpressed. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells (NPC cells, NPC-KRASG13D, U251-GSC, and U118MG-GSC).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NPC cells, NPC-KRASG13D, U251-GSC, and U118MG-GSC.

first: Zixi

last: Qin

first: Weiye

first: Lihui

last: Wang


title: Epimorphic Regeneration in the Mammalian Tympanic Membrane

status: Public on May 01 2023

city: San Francisco

first: Sonia

last: Scaria

address: 513 Parnassus Avenue, HSE 740

department: Otolaryngology-Head and Neck Surgery

institute: University of California, San Francisco

summary:
Purpose:  The goal of this study was to characterize the transcriptional response to injury of the murine tympanic membrane at multiple time points using single-cell RNA sequencing.
Methods: mRNA profiles of Unwounded (Pars Tensa and Pars Flaccida) and Wounded (Day 1, Day 3, Day 7 and Day 14) murine tympanic membranes from WT FVB mice. The sequence reads that passed quality filters were analyzed at the transcript isoform level from fastq to matrix files using standard 10x genomics pipeline via CellRanger
Results: Using the 10x Genomics Cell Ranger pipeline, we analyzed over 10,000 cells per timepoint from the UW and WO tympanic membranes, mapping the reads to the mouse genome (build mm10). The cells were then clustered primarily using the single-cell software package Seurat version 4.
Conclusions: Our study represents the first detailed analysis of the regeneration timeline of the injured murine tympanic membrane, generated by RNA-seq technology. Our results show the emergence of novel populations on the tympanic membrane as it regenerates and characterizes the changes in all layers of the organ.

overall_design: Injured murine tympanic membrane mRNA profiles of 14-, 7-, 3-, and 1-day post-inury  wild type (WT) and the unwounded state

first: Aaron

middle: D

last: Tward


title: Changes in adenoviral chromatin organization precede early gene activation [RNA-Seq]


title: WWOX-dependent gene expression profiling of glioblastoma

status: Public on Apr 11 2023

city: Lodz

first: Żaneta

last: Kałuzińska-Kołat

address: Zeligowskiego St. 7/9

department: Deparment of Molecular Carcinogenesis

country: Poland

institute: Medical University of Lodz

summary: In the current study we employed the CAGE-Seq method and investigated the four glioblastoma cell lines in which two variants through stable transduction were established, i.e., with overexpression of WWOX gene and control variant.

overall_design: The study was based on four glioblastoma cell lines, i.e., DBTRG-05MG, T98G, U87MG, and U251MG, for which overexpression of gene encoding WWOX was induced by lentiviral transduction. For each cell line, investigated variants included the Control variant (treated with Puro-Blank Lentivirus; abbreviated "vec") and WWOX overexpression variant (treated with GIPZ™ lentiviral system; abbreviated "WWOX"). Each variant was represented by three biological replicates per cell line.

first: Damian

last: Kołat

first: Katarzyna

last: Kośla

first: Elżbieta

last: Płuciennik

first: Andrzej

last: Bednarek


title: Transposable elements drive the evolution of metazoan zinc finger genes

status: Public on Apr 10 2023

city: Ithaca

first: Cédric

last: Feschotte

state: NY

address: 216 Biotechnology Building

institute: Cornell University

summary: Cys2-His2 Zinc finger genes (ZNFs) form the largest family of transcription factors in metazoans. Zebrafish posess a subfamily characterized by the presence of a domain dubbed Fish N-terminal Zinc finger associated (FiNZ). FiNZ-ZNFs are expressed at the onset of zygotic genome activation in zebrafishh, and blocking FiNZ-ZNF translation using morpholinos during early zebrafish embryogenesis results in a broad de-repression of young, transcriptionally active TEs.

overall_design: We designed a single translation-blocking morpholino targeting the translation start site of 400+ FiNZ-ZNF genes on zebrafish chromosome 4. Fertilized, single-celled zygotes were injected with either this morpholino or a scrambled 25N control, and embryos were collected 6h later at shield stage. Injections were repeated in triplicate. Embryos were sent for paired end RNA sequencing, and analysed using DESeq2.

first: Jonathan

middle: N

last: Wells


title: Protein-intrinsic properties and context-dependent effects regulate pioneer-factor binding and function [ATAC-Seq]

first: Melissa

last: Harrison

overall_design: ATAC-seq on cells ectopically expressing Drosophila transcription factors.

first: Tyler

last: Gibson


title: Symmetry breaking in gastruloid development

status: Public on Apr 29 2023

city: Basel

first: Nadim

last: Aizarani

address: Maulbeerstrasse 66

country: Switzerland

institute: FMI

summary: We use single cell RNA sequencing to describe the transcriptional changes during gastruloid development from 0 to 120h hours.

overall_design: Examination of transcriptional profiles of embryonic stem cells and gastruloids cultured in N2B27 at 0, 12, 24, 36, 48, 52, 56, 60, 72, 84,96, and 120 hours post-seeding. Examination of multiome profiles (single-cell ATAC-seq and sinlge-cell RNA-seq) in gastruloids at 48h and 52h.

first: Marietta

last: Zinner

first: Simon

last: Suppinger

first: Ilya

last: Lukonin

first: Michael

middle: B

last: Stadler

first: Prisca

last: Liberali


title: Gene expression profile at single cell level of decitabine induced HLAG+ regulatory T cells

status: Public on Apr 07 2023

city: Patras

first: Alexandros

last: Spyridonidis

state: Achaia

address: University Campus, Rio

department: Institute of Cell Therapy

country: Greece

institute: University of Patras

summary: Decitabine induced HLAG+ regulatory T cells present a novel approach for adoptive cellular immunotherapy for immune mediated diseases. We used single cell RNA sequencing (scRNA-seq) to further dissect their molecular identity.

overall_design: HLAG+ reulatory T cells were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Memnon

last: Lysandrou


title: Transcriptomic analysis of decitabine induced HLAG+ regulatory T cells

summary: To investigate the gene expression profile of decitabine induced HLAG+ regulatory T cells against their HLAG- counterparts

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 5 sorted paired samples of HLAG+ and HLAG- decitabine induced regulatory T cells


title: Effect of Smchd1 missense mutation on gene expression in embryonic frontonasal prominence tissue

status: Public on Apr 04 2023

city: Melbourne

first: Andres

last: Tapia del Fierro

state: Victoria

address: 1G Royal Parade

department: EDD

country: Australia

institute: WEHI

summary:
To investigate the reciprocal effect of the neomorphic MommeD43 mutation presented in this study, we examine here if Smchd1 loss shows converse effects on Wnt or other developmental pathways in frontonasal prominence (FNP) from E10.5 embryos
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 replicates for Smchd1MD1/MD1 and 7 replicates for Smchd1+/+. Each replicate was made by pooling 3 sex-matched and somite-matched embryos.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Smchd1MD1/MD1 and Smchd1+/+ in FNP tissue from embryos at the E10.5 stage of development.

first: Tamara

last: Beck

first: Marnie

middle: E

last: Blewitt


title: DEF cells infected with NDV II

city: Guangzhou

first: Lei

last: Fan

state: Guangdong

address: 483 Wushan Road,

institute: South China Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: To investigate the  role of gene expression during Newcastle disease virus (NDV) infection.The NDV GM strain was used to infect DEF cells with 1moi, while an uninfected group was set up as a control.

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of NDV infected DEF cells  and normal cells.
The control groups were DN-1, DN-2, and DN-3, while the experimental groups were DK-1, DK-2, and DK-3. NDV was used in the experimental group infected at 1 MOI, and samples were collected at 9 h post infection along with the control group for sequencing.

first: Bin

last: Xiang

first: Jinlian

last: Ren

first: Yiyi

last: Chen


title: Genome-wide DNA methylation and mRNA responses to a bout of higher versus lower load resistance training in previously trained men

city: Durham

first: Christopher

last: Vann

state: NC

address: 300 N Duke St

department: Molecular Physiology Institute

institute: Duke University School of Medicine

summary:
We sought to determine skeletal muscle genome-wide DNA methylation and transcriptome changes to one bout of lower-load (LL) versus higher-load (HL) resistance exercise. Previously trained college-aged males (n=11, age: 23±4 years old, training experience: 4 ± 3 years) performed LL or HL bouts to failure separated by one week. The HL bout (a.k.a., 80 Fail) consisted of four sets of back squats and four sets of leg extensions to failure using 80% of their estimated one-repetition maximum (i.e., est. 1-RM from 3-RM testing), whereas the LL bout (a.k.a., 30 Fail) consisted of this same paradigm using 30% of their est. 1-RM. Vastus lateralis muscle biopsies were collected before, 3 hours, and 6 hours after each exercise bout. DNA and RNA were batch-isolated from muscle and analyzed for genome-wide DNA methylation and mRNA expression using the 850k Illumina MethylationEPIC array and Clariom S mRNA microarray, respectively.
Although the total number of repetitions performed were significantly greater during the 30 Fail versus 80 Fail bout (p<0.001), total training volume (sets x reps x load) was not significantly different between conditions (p=0.571). Interestingly, 30 Fail led to decreased methylation across various promoter regions, albeit the transcriptome-wide responses between bouts were largely similar. According to bioinformatics, both bouts altered post-exercise mRNA profiles related to inflammatory signaling (e.g., Toll receptor, CCKR, chemokine and cytokine signaling), apoptosis, gonadotropin-releasing hormone, and integrin signaling. Also notable, more robust DNA methylation events occurred 3 hours versus 6 hours post-exercise regardless of bout (239,951 versus 12,419 CpG sites significantly hyper- or hypomethylated at these respective time points, p<0.01). Moreover, the percentage of significantly altered mRNAs that also demonstrated significantly inversed methylation patterns across one or more CpG sites was appreciably higher at 3 hours versus 6 hours following exercise (~75% versus ~15%, respectively). In conclusion, our transcriptomic data suggest that the molecular signaling events during the early post-exercise period are largely similar between LL and HL bouts, and this may explain why similar longer-term phenotypes (e.g., myofiber hypertrophy) result from these two training modalities. Additionally, our methylome data indicate that the majority of DNA methylation changes following an acute bout of resistance exercise occur rapidly (~3 hours) following exercise in previously trained men.

overall_design: Previously-trained college-aged males performed a LL (30% 1RM) or HL (80% 1RM) bout of resistance exercise to failure separated by a one week washout.  RNA was isolated from muscle biopsies collected prior to each exercsie bout (PRE), 3-hours following each bout (3H), and 6-hours following each bout (6H).  RNA was then subsequently processed on the Clariom S Human microarray for whole-transcriptome gene expression.

first: Casey

middle: L

last: Sexton

last: Roberts


title: Comparative study of the mechanism of natural compounds with similar structures using docking and transcriptome data

status: Public on Apr 03 2023

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

summary: This study aimed to compare the mechanisms of action (MOA) of similar natural compounds and observed the changes when they are mixed and used.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for albiflorin (10 uM), paeoniflorin (10 uM), combination of albiflorin and paeoniflorin (5 + 5 uM), and vehicle control (0.1% DMSO).


title: CTCF ChIP-seq in NSCs

summary:
Both Smchd1 deletion and its MommeD43 mutant version cause loss of long-range chromatin interactions in NSCs and a strengthening of more local interactions. We assayed CTCF binding in the relevant genotypes to see if this is related to altered CTCF binding.
ChIP-seq using an anti-CTCF antibody to check if chromatin binding of CTCF is altered in Smchd1MD43-GFP/MD43-GFP and Smchd1del/del neural stem cells (NSCs) compared to Smchd1GFP/GFP NSCs.

overall_design: 3 independent cell lines for each genotype (2 for Smchd1del/del) were derived from E14.5 embryos' cortices and cultured for less than 10 passages to be used as biological replicates. One cell line of Smchd1GFP/GFP was used for the whole cell extract library (input library).

last: del Fierro

first: Andrew

last: Keniry

first: Kelsey

last: Breslin


title: Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration [RNA-seq]

city: Vienna

first: Jingkui

last: Wang

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

summary:
The salamander limb regenerates only the missing portion. Each limb segment can only form segments equivalent to- or more distal to their own identity, relying on a property termed “positional information”. How positional information is encoded in limb cells has been unknown. By cell-type-specific chromatin profiling of upper arm, lower arm, and hand, we found segment-specific levels of histone H3K27me3 at limb homeoprotein gene loci but not their upstream regulators, constituting an intrinsic segment information code. During regeneration, regeneration-specific regulatory elements became active prior to the re-appearance of developmental regulatory elements. This means that, in the hand segment, the permissive chromatin state of the hand homeoprotein gene HoxA13 engages with regeneration regulatory elements, bypassing the upper limb program.
We performed Differential Gene expression analysis using data obtained from RNA-seq of two mature limb segments (mature arm vs hand). Therefore, we performed libraries from the mature arm and 5, 9, 13 dpa regenerating arm blastema.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mature UA vs Hand, and mature UA vs UA BLs in different time points.

first: Akane

last: Kawaguchi

first: Dunja

last: Knapp

first: Prayag

last: Murawala

first: Sergej

last: Nowoshilow

first: Wouter

last: Masselink

first: Yuka

last: Taniguchi-Sugiura

first: Jifeng

last: Fei

first: Elly

last: Tanaka


title: Repurposing disulfiram, an alcohol-abuse drug, in neuroblastoma causes KAT2A downregulation and in vivo activity with a water/oil emulsion

city: Montréal

first: Noel

last: Raynal

state: QC

address: 3175, Chemin de la Côte-Sainte-Catherine

department: Pharmacologie et physiologie

country: Canada

institute: Université de Montréal

summary: Neuroblastoma is the most common pediatric extracranial solid tumor accounting for 10% of cancer death in children. Despite intensive treatments involving surgery, chemotherapy, radiotherapy and stem cell transplantation, children with high-risk neuroblastoma still have a poor outcome. Thus, there is an urgent need to develop new therapeutic approaches that can be rapidly tested in clinical trials and with a safe long-term toxicity profile, particularly for children. A promising approach to meet those needs is drug repurposing. Here, we investigated disulfiram, an approved drug for chronic alcoholism treatment, with known anticancer and epigenetic effects. Disulfiram efficiently produced cell cycle arrest and decreased cell viability in five human neuroblastoma cell lines, with IC50 concentrations more than twenty times below its plasmatic level measured in patients treated for chronic alcoholism. We show that disulfiram induced a transcriptomic shift in neuroblastoma cells causing a decrease in cell replication and an increase in neuronal differentiation pathways. In line with these findings, disulfiram reduced significantly the protein level of the histone acetyltransferase KAT2A (GCN5), resulting in a drastic loss of histone acetylation in lysine residues (H3K9ac, H3K14ac, H3K27ac) targeted by KAT2A. To further investigate the anticancer effects of disulfiram in a high-risk neuroblastoma in vivo model, we developed a disulfiram-loaded emulsion suitable for the delivery of this highly liposoluble drug. Using this formulation, we showed that disulfiram significantly delayed the progression of neuroblastoma in mice. Overall, this study highlights a novel target of disulfiram, which directly impacts KAT2A expression and histone acetylation in neuroblastoma.

overall_design:
To investigate the transcriptional effects of disulfiram in neuroblastoma, we performed RNA-seq in untreated and treated (50 nM, 48 hours) N91 cells.
Comparative gene expression profiling analysis of RNA-seq data for N91 cells in untreated (n=3) and treated (n=3) conditions.

first: Jacques-Ricard

last: Simon

first: Caron

last: Maxime


title: TEAD4 delays cellular senescence by remodeling chromatin accessibility at H3K27ac-occupied enhancer regions [CUT&Tag]

status: Public on Apr 01 2023

city: Zhanjiang

first: Yiting

last: Guan

address: 236 Yuanzhu Road

department: Zhanjiang Institute of Clinical Medicine

institute: Guangdong Medical University

summary: Dramatic alterations in epigenetic landscapes are known to affect genome accessibility and their transcriptional program. Extensive evidences have emerged that senescent cells accumulate profound chromatin tremendous reordering upon senescence entry, yet, the underlying mechanisms between epigenetic parameters and gene expression profile have not been fully clarified. In this report, we delineate the genome-wide redistribution of accessible chromatin regions leading to broad transcriptome effects during UC-MSCs senescence. We report the distinct senescence-activated accessibility regions (SAAs) are always distributed in H3K27ac decorated enhancer regions, where the SAAs are responsible for elevated flanking SASP expression and aberrant cellular signaling relevant to SASP secretion. Mechanistically, a single transcription factor, TEAD4, shifting away from H3K27ac-labled SAAs and leading to prominent chromatin accessibility reconstruction during senescence. The enhanced signal of SAAs driven by TEAD4 suppression subsequently induce a robust decrease of adjacent SASP genes expression and downstream factors secretion, and finally, contributing to the progression of senescence. Our findings illustrate a dynamic landscape of chromatin accessibility following senescence entry and reveal an insightful function for TEAD4 in regulating the broad chromatin state that modulate the overall transcriptional program of the SASP genes.

overall_design: CUTTag analysis


title: TEAD4 delays cellular senescence by remodeling chromatin accessibility at H3K27ac-occupied enhancer regions [RNA-seq]

overall_design: gene expression profiling analysis of RNA-seq data


title: TEAD4 delays cellular senescence by remodeling chromatin accessibility at H3K27ac-occupied enhancer regions

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

overall_design: Refer to individual Series


title: TEAD4 delays cellular senescence by remodeling chromatin accessibility at H3K27ac-occupied enhancer regions [ATAC-seq]

overall_design: Chromatin accessibility analysis of ATAC-Seq data


title: Stem-like signatures in human meningioma cells are under the control of CXCL11/CXCL12 chemokine activity

city: Genoa

first: Paolo

last: Malatesta

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS Ospedale Policlinico San Martino

summary: Meningioma cells, isolated from human tumors, were selected in stem-cell-permissive or cell-differentiation media and analysed by single cell partitioning with 10X Chromium controller followed by sequencing.

overall_design: For each experimental sample (differentiated or stem), two different specimens, one from a male and one from a female patients were mixed before single cell partitioning. This allowed demultiplexing the samples by means of Y-linked genes.

first: Tullio

last: Florio

first: Davide

last: Ceresa


title: High througuput sequencing of skeletal muscle-specific Site-1 Protease knockout mouse gastrocnemius and soleus

city: Saint Louis

first: Rita

last: Brookheart

state: MO

address: 660 S. Euclid Ave

institute: Washington University School of Medicine

summary: The processes by which mitochondria respond to cellular energy demands brought on by physiologic and pathophysiologic stimuli are essential to cellular adaptation and organismal survival. Disrupted mitochondrial function is implicated in several human disease states, underscoring the need to elucidate the molecular mechanisms that control mitochondrial function and metabolism. We previously described a patient with a gain-of-function mutation in Site-1 Protease (S1P) who exhibited idiopathic hyperCKemia, myoedema, and altered muscle mitochondrial morphology. To date, S1P has been heavily characterized in liver and bone, with very little known about its potential function in skeletal muscle. In our current study, we generated a skeletal muscle-specific S1P knockout mouse line (S1PsmKO) to examine the role of S1P in skeletal muscle. S1PsmKO mice were overtly normal in their appearance and health. However, examination of 12-week-old S1PsmKO mice showed increased gastrocnemius muscle mass and aged S1PsmKO mice exhibited increased muscle mass in both gastrocnemius and soleus relative to age-matched controls. Moreover, isolated muscle from S1PsmKO exhibited increased maximal mitochondrial respiration relative to floxed littermates (controls). RNA-Seq analysis showed increased transcript numbers of the mitochondrial-resident gene, Mss51 in S1PsmKO gastrocnemius relative to control mice. Mss51 is a member of the TGF-β/MSTN pathway, which controls mitochondrial metabolism. Similar to S1PsmKO muscle, S1P-depleted C2C12 cells also had increased maximal respiration, which was reversed by exogenous MSS51 expression. These data identify S1P as a regulator of muscle mass and mitochondrial metabolism, and implicate S1P as a novel modulator of TGF-β signaling. Method: Male mice were maintained on standard chow diet until 12 weeks of age.

overall_design: Examination of gastrocnemius and soleus from Site-1 Protease floxed (control) and Site-1 Protease floxed HSACre+ (skeletal muscle-specific Site-1 Protease knockout) mice on standard chow diet, fasted for 4 h prior to organ harvesting. n=4/group

first: R


title: Identification of novel hyper- or hypo-methylated CpG sites and genes associated with anthracycline-induced cardiomyopathy

status: Public on Mar 31 2023

city: Birmingham

first: Smita

last: Bhatia

state: AL

address: 1600 7th Avenue South Lowder 500

department: Pediatrics

institute: University of Alabama at Birmingham

type: Methylation profiling by genome tiling array

summary:
Genome wide DNA methylation profiling of peripheral blood DNA from childhood cancer survivors with and without anthracycline induced cardiomyopathy. DNA methylation status of 850,000 CpG sites was analyzed using the Illumina HumanMethylation EPIC BeadChip arrays. Matched case-control study (COG-ALTE03N1); 52 non-Hispanic White, anthracycline-exposed childhood cancer survivors with cardiomyopathy were matched 1:1 with 52 survivors with no cardiomyopathy.
Anthracycline-induced cardiomyopathy is a leading cause of late morbidity in childhood cancers survivors. Aberrant DNA methylation plays a role in de novo cardiovascular disease. Epigenetic processes could play a role in anthracycline-induced cardiomyopathy, but remain unstudied.    We sought to examine if genome-wide differential methylation at ‘CpG’ sites in peripheral blood DNA is associated with anthracycline-induced cardiomyopathy. We observed significant differences in DNA methylation between anthracycline-exposed childhood cancer survivors with and without cardiomyopathy, implicating differential DNA methylation in anthracycline-induced cardiomyopathy.

overall_design: Genomic DNA (1 μg) was bisulfite-converted using EZ DNA Methylation kit (Zymo Research Corp, Orange, CA, cat. no. D5004), and a cyclic denaturation step during the conversion reaction. Four microliters of bisulfite-converted DNA was used for hybridization on Infinium HumanMethylation 850 BeadChip. According to the Illumina Infinium HD Methylation protocol, the following steps were performed: whole-genome amplification, end-point fragmentation, precipitation and resuspension. The resuspended samples were hybridized onto HumanMethylation 850 BeadChips at 48°C for 18 hours. Then unhybridized and nonspecifically hybridized DNA were washed away, followed by a single nucleotide extension and repeated rounds of staining. Finally, the BeadChip was washed, coated and scanned. After scanning, the intensities of images were extracted using GenomeStudio Methylation module software (Illumina, Inc.).

first: Purnima

last: Singh

first: David

last: Crossman


title: PR-DUB safeguards Polycomb repression through restricting H2AK119ub1

city: Tianjin

first: Rui

last: Li

state: Tianjin

address: Qixiangtai Road No.22

department: Department of Cell Biology, School of Basic Medical Sciences

institute: Tianjin Medical University


title: Capture-C in somite-matched pre-somitic mesoderm from Smchd1GFP/GFP, Smchd1MD43-GFP/MD43-GFP, Smchd1+/+ and Smchd1MD43/MD43 embryos.

first: Andres

last: Tapia del Fierro

summary: Capture-C from in situ HiC libraries in tailbud tissue containing pre-somitic mesoderm (PSM) dissected from  Smchd1GFP/GFP, Smchd1MD43-GFP/MD43-GFP, Smchd1+/+ and Smchd1MD43/MD43 embryos E8.5 embryos at the 7-9 somite stage of development. Somite stage is a good indicator of the precise stage of embryonic development.

overall_design: Embryonic somite-matched PSM tissue was dissected, dissociated and crosslinked to make DpnII-digested in situ HiC libraries, then captured using a custom protocol for low input. Each library was made from a pool of tissue 2 embryos of the same genotype. RNA capture oligos were designed and ordered from Agilent SureSelect, to enrich for reads representing contacts within the four Hox clusters, of central interest to this publication, and other known Smchd1 target loci (clustered protocadherins and various olfactory receptor gene clusters).

first: Natalia

last: Benetti

first: Timothy

last: Johanson

first: Marnie

last: Blewitt


title: PR-DUB safeguards Polycomb repression through restricting H2AK119ub1 [ChIP-seq]

summary: Polycomb group (PcG) proteins are critical chromatin regulators for cell fate control. The mono-ubiquitylation on histone H2AK119 (H2AK119ub1) is one of the well-recognized mechanisms for Polycomb Repressive Complex 1 (PRC1)-mediated transcription repression. However, the specific H2AK119 deubiquitylation complex composed by ASX-like proteins (ASXLs) and BAP1 has also been genetically characterized as a Polycomb Repressive complex (PR-DUB). Here we try to provide a rationale for these counterintuitive findings. Through re-examining the genomic distribution of H2AK119ub1, we find that H2AK119ub1 is non-negligibly distributed at non-promoter regions and associated with PRC1 sampling. Upon deletion of Asxl2 in mouse embryonic stem cells (ESCs), H2AK119ub1 is pervasively gained, especially at non-promoter regions, which is associated with increased RING1B occupancy. Meanwhile RING1B is significantly lost from a subset of the target promoters and thereby results in minor derepression in Asxl2-null ESCs. However notably, Asxl2 loss causes aberrant lineage differetiation, similar to PcG mutants. Therefore, our data reconcile seemingly paradoxical roles of PR-DUB on transcription repression and highlight the importance of a balanced H2AK119ub1 dynamics in developmental regulation.

overall_design: Examination of Polycomb proteins and H2AK119ub1 histone modification in both WT and Asxl2KO mESC.

first: Dandan

last: Huang


title: PR-DUB safeguards Polycomb repression through restricting H2AK119ub1 [RNA-seq]

overall_design: Examination of expression levels between WT and Asxl2KO during ESC to MES  differentiation.


title: Investigate the effect of gain of HAND2 on chromatin accessibility.

status: Public on Mar 29 2023

city: bethesda

first: Jack

last: Shern

address: 10 Center drive

institute: NCI

summary: The overexpression of HAND2 in IMR32 cells results in a increase of chromation accessibility at the HAND2 and MYCN common binding sites.

overall_design: In the HAND2 stably transfected IMR32 cells (IMR32tetHAND2), HAND2 expression is Doxcycline (Dox) inducible. The IMR32tetHAND2 cells were treated with or without Dox for 36 hr and ATAC seq was performed.

first: Man

last: Xu

first: Zhihui

last: Liu

first: Carol

last: Thiele


title: The cooperation between HAND2 and MYCN on DNA binding [HAND2-overexpression_ChIPseq]

summary: HAND2 assists MYCN bind to DNA.

overall_design: In the HAND2 stably transfected IMR32 cells (IMR32tetHAND2), HAND2 expression is Doxcycline (Dox) inducible. The IMR32tetHAND2 cells were treated with or without Dox for 6 hr or 36 hr, and ChIP seq was performed using anti-HAND2 antibody and anti-MYCN antibody.

first: Zhi

last: hui


title: Investigate the effect of loss of HAND2, MYCN, PHOX2B and GATA3 on chromatin accessibility.

summary: The knockdown of HAND2 in IMR32 cells results in a decrease of chromation accessibility at the HAND2 and MYCN common binding sites.

overall_design: IMR32 cells were transfected with control siRNA, HAND2 siRNA, MYCN siRNA, GATA3 siRNA and PHOX2B siRNA, and cultured in regular medium for 24 hr or 72 hr. Then the cells were harvested and ATAC seq experiment was performed.


title: Genome-wide screening reveals metabolic regulation of translational fidelity by cyclic AMP

status: Public on Mar 28 2023

city: College Park

first: Jiqiang

last: Ling

address: 2202 Microbiology Bldg., 4062 Campus Dr.

department: Cell Biology and Molecular Genetics

institute: The University of Maryland, College Park

summary: Translational quality control is critical for maintaining the accuracy of protein synthesis in all domains of life. Mutations in aminoacyl-tRNA synthetases and the ribosome are known to affect translational fidelity and alter fitness, viability, stress responses, neuron function, and life span. In this study, we used a high-throughput fluorescence-based assay to screen a knock-out library of Escherichia coli and identified 30 nonessential genes that are critical for maintaining the fidelity of stop-codon readthrough. Most of these identified genes have not been shown to affect translational fidelity previously. Intriguingly, we show that several genes controlling metabolism, including cyaA and guaA, unexpectedly enhance stop-codon readthrough. CyaA and GuaA catalyze the synthesis of cyclic adenosine monophosphate (cAMP) and guanosine monophosphate (GMP), respectively. Both CyaA and GuaA increase the expression of ribosomes and tRNAs, allowing aminoacyl-tRNAs to compete with release factors and suppress stop codons. In addition, the effect of guaA deletion on stop-codon readthrough is abolished by deleting prfC, which encodes release factor 3 (RF3). Our results suggest that nucleotide and carbon metabolism is tightly coupled with translational fidelity.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Escherichia coli BW25113 and its derivative cyaA knockout strain.

last: Lyu


title: Unresolved Immune Dysfunction is Lethal in Both COVID-19 and non-COVID-19 Sepsis

status: Public on Mar 24 2023

city: Vancouver

first: Robert

middle: E W

last: Hancock

state: British Columbia

address: Room 232 – 2259 Lower Mall Research Station

department: Microbiology and Immunology

institute: University of British Columbia

summary: In this prospective observational cohort study, we found transcriptional evidence that persistent immune dysfunction was associated with 28-day mortality in both COVID-19 and non-COVID-19 septic patients. COVID-19 patients had an early antiviral response but became indistinguishable on a gene expression level from non-COVID-19 sepsis patients a week later. Early treatment of COVID-19 and non-COVID-19 sepsis ICU patients should focus on pathogen control, but both patient groups also require novel immunomodulatory treatments, particularly later during ICU hospitalization, independent of admission diagnosis. Some T1 samples were uploaded in GSE185263 and were not re-uploaded in this series.

overall_design: Gene expression trajectories were compared between 20 severe COVID-19 patients and 22 contemporaneous non-COVID-19 sepsis patients in the intensive care unit (ICU). Whole blood was collected at two timepoints: ICU admission and ~1 week later.

first: Andy

last: An

first: Arjun

last: Baghela

first: Peter

last: Zhang

first: Reza

last: Falsafi

first: Amy

last: Lee

first: Uriel

last: Trahtemberg

first: Andrew

last: Baker

first: Claudia

middle: C

last: dos Santos

middle: W


title: HAND2 regulates regional chromation modification [HAND2-knockdown_histone_ChIPseq]

summary: The knockdown of HAND2 affects the regional chromation modification.

overall_design: IMR32 cells were transfected with control siRNA (siCtrl) or HAND2 siRNA (siHAND2) and cultured in regular medium for 72 hr, then ChIP experiments were performed using  ChIP-IT High Sensitivity Kit (Active Motif ).


title: RNA-sequencing analysis to investigate genes regulated by HAND2 and MYCN in IMR32 cells

summary: In this study we identified genes regulated by HAND2 or MYCN or both MYCN and HAND2 in IMR32 cells.

overall_design: RNA was isolated from IMR32 cells that transfected with siCtrl or siMYCN or siHAND2 or siMYCN+siHAND2 and cultured in regular medium for 72h.


title: RNA-sequencing analysis to investigate genes regulated by HAND2 and MYCN in LAN5 cells

summary: In this study we identified genes regulated by HAND2 or MYCN or both MYCN and HAND2 in LAN5 cells.

overall_design: RNA was isolated from LAN5 cells that transfected with siCtrl or siMYCN or siHAND2 and cultured in regular medium for 72h.


title: The cooperation among the core regulatory circuitry transcription factors and MYCN on DNA binding [HAND2-MYCN-CRC-knockdown_ChIPseq]

summary: MYCN and the core regulatory circuitry transcription factors HAND2, PHOX2B and GATA3 cooperate to bind to DNA.

overall_design: IMR32 cells were transfected with control siRNA (siCtrl), or HAND2 siRNA (siHAND2), or MYCN siRNA (siMYCN), or GATA3 siRNA (siGATA3), or PHOX2B siRNA (siPHOX2B), and cultured in regular medium for 24 hr or 72 hr, then ChIP experiments were performed using ChIP-IT High Sensitivity Kit (Active Motif ).


title: Effect of CDDO-2P-Im Treatment in Myeloma Cells

status: Public on Mar 19 2023

city: Cleveland

first: George

last: Luo

state: OH

address: 2103 Cornell Rd. Wolstein Research Bldg/Rm 3501

institute: Case Western Reserve University

summary: RPMI8226 Cells were treated with various concentrations of CDDO-2P-Im for 6 hours and then RNA was extracted for gene expression changes

overall_design: 5 x 10^5 cells were treated with Control (DMSO), 0.1 μM CDDO-2P-Im, or 0.4 μm CDDO-2P-Im for 6 hours. Groups were compared between each other.

first: John

last: Letterio


title: High-throughput transcriptomics of Celf1 conditional knockout lens identifies downstream networks linked to cataract pathology

status: Public on Mar 18 2023

city: Newark

first: Salil

middle: Anil

last: Lachke

state: Delaware

address: 351 Wolf Hall, University of Delaware

department: Biological Sciences

institute: University of Delaware

summary: Celf1 germline or conditional deletion mouse mutants exhibit fully penetrant lens defects including cataract. To gain insight into gene expression changes underlying these lens defects Differential Gene Expression analysis  was performed for lenses obtained from control and Celf1 conditional deletion mutant mice.

overall_design: Differential Gene Expression analysis of RNA-seq data from lens of  P0 mice Celf1 cko or Control, from mixed background (C57BL/6J ; FVB) control (Celf1lacZKI/+)and mutant (Celf1cKO) mice was performed

first: Archana

last: Siddam

middle: A


title: Analysis of HAND2 and MYCN

first: Jack

last: Shern

overall_design: Refer to individual Series


title: mRNA trans-splicing dual AAV vectors for (epi)genome editing and gene therapy

city: Munich

first: Elvir

last: Becirovic

state: Bavaria

address: Butenandtstrasse 7

department: Faculty for Chemistry and Pharmacy

institute: LMU Munich - Pharmacology for Natural Sciences

summary: Large genes including several CRISPR-Cas modules, such as gene activators (CRISPRa), require dual adeno-associated viral (AAV) vectors for efficient in vivo delivery and expression. Current dual AAV vector approaches have important limitations, e.g., low reconstitution efficiency, production of alien proteins, or low flexibility in split site selection. Here, we present a dual AAV vector technology based on reconstitution via mRNA trans-splicing (REVeRT). REVeRT is flexible in split site selection and can efficiently reconstitute different split genes in numerous in vitro models, in human organoids and in vivo. Furthermore, REVeRT can functionally reconstitute a CRISPRa module targeting genes in various mouse tissues and organs in single or multiplexed approaches upon different routes of administration. Finally, supplementation of ABCA4 (6.8 kb) via REVeRT improves retinal degeneration and function in a mouse model of inherited blindness. Due to its flexibility and efficiency REVeRT harbors great potential for basic research and clinical applications.

overall_design: sample 1: control sequence, sample 2: REVeRT (split) Prime Editor 2, sample 3: unsplit Prime Editor 2

first: Nina

last: Karguth


title: Understanding cancer drug resistance with Sleeping Beauty functional genomic screens: application to MAPK inhibition in cutaneous melanoma

status: Public on Mar 09 2023

city: Iowa City

first: Eliot

last: Zhu

state: IA

address: 376 Newton Road

department: Anatomy and Cell Biology

institute: The University of Iowa

summary: To determine how VAV1 drives drug resistance to BRAFi, we overexpressed VAV1 in A375 and compared these cells to A375 overexpressing RAC1P29S. We also determined the impact of SRCi on the transcriptional program elicited by VAV1.

overall_design: Overexpression of VAV1 or RAC1P29S in A375 melanoma cell line. Treatment of A375 overexpressing VAV1 with SRC inhibition. Biological triplicates were generated for each condition

first: Adam

last: Dupuy


title: The Hdc GC box is critical for Hdc gene transcription and histamine-mediated anaphylaxis [ATAC-Seq]

status: Public on Feb 23 2023

city: Denver

first: HUA

last: HUANG

state: Colorado

address: 1400 Jackson street, K511

department: Immunology and Genomic Medicine

institute: National Jewish Health

summary: Histamine is a critical mediator of anaphylaxis, a neurotransmitter, and a regulator of gastric acid secretion. Histidine decarboxylase is a rate-limiting enzyme for histamine synthesis. However, in vivo regulation of Hdc, the gene that encodes histidine decarboxylase is poorly understood. We sought to investigate how enhancers regulate Hdc gene transcription and histamine synthesis in resting conditions and in a mouse model of anaphylaxis. H3K27 acetylation histone modification and chromatin accessibility were used to identify candidate enhancers; The enhancer activity of candidate enhancers was measured in a reporter gene assay; and the function enhancers were validated using CRISPR deletion. Deletion of the GC box, which binds to zinc finger transcription factors, in the proximal Hdc enhancer, reduced Hdc gene transcription and histamine synthesis in the mouse and human mast cell lines. Mast cells, basophils, brain cells, and stomach cells from GC box-deficient mice transcribed the Hdc gene much less than similar cells from wild-type mice and Hdc GC box-deficient mice failed to develop anaphylaxis. Our results demonstrate that the HDC GC box within the proximal enhancer in the mouse and human HDC gene is essential for Hdc gene transcription, histamine synthesis, and histamine-mediated anaphylaxis in vitro and in vivo.

overall_design: Omni-ATAC-seq in WT and Hdc GC box KO BMMCs, in triplicate, using Illumina NovaSEQ6000 platform

first: Yapeng

last: Li

first: Junfeng

last: Gao

first: Dianzheng

last: Zhao

first: Hua

last: Huang


title: Allergen sensitization stratifies IL-31 production by memory T cells in atopic dermatitis patients.

status: Public on Mar 06 2023

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

summary: The role of allergen sensitization in IL-31 production by T cells and specifically in the clinical context of atopic dermatitis (AD) has not been characterized. The response to house dust mite (HDM) in purified memory T cells cocultured with epidermal cells from AD patients (n=58) and control subjects (n=11) was evaluated. AD-associated cytokines from culture supernatants, plasma proteins and mRNA expression from cutaneous lesions were assessed and related with the clinical features of the patients. HDM-induced IL-31 production by memory T cells defined two subsets of AD patients according to the presence or absence of IL-31 response. Patients in the IL-31 producing group showed a more inflammatory profile, and increased HDM-specific (sp) and total IgE levels compared to the IL-31 non-producing group. A correlation between IL-31 production and patient’s pruritus intensity, plasma CCL27 and periostin was detected. When the same patients were analyzed based on HDM-specific (sp) IgE and total IgE levels, an increased IL-31 in vitro response, as well as type 2 markers in plasma and cutaneous lesions, was found in patients with sp IgE levels > 100 kUA/L and total IgE levels > 1000 kU/L. The IL-31 response by memory T cells was restricted to the cutaneous lymphocyte-associated antigen (CLA)+ T-cell subset. IgE sensitization to HDM allows stratifying IL-31 production by memory T cells in AD patients and relating it to particular clinical phenotypes of the disease.

overall_design: 16 samples were analyzed

first: L

last: Sans-De San Nicolàs

first: I

last: Figueras-Nart

last: García-Jiménez

first: M

last: Bonfill-Ortí

first: A

last: Guilabert

last: Curto-Barredo

last: Bertolín-Colilla

last: Ferran

first: E

last: Serra-Baldrich

first: R

middle: M

last: Pujol

last: Santamaria-Babí


title: Gene expression profile at single cell level of mammary gland from Kindlin-2 genetically modified mouse model

status: Public on Mar 07 2023

city: beijing

first: lei

last: zhang

address: xueyuan road 38th

department: heath science center

institute: peking university

summary: During gestation, alveolar cells are derived from luminal progenitors in the mammary gland. However, the mechanism underlying luminal progenitor commitment to alveolar cells remains largely unknown. By using five genetically modified mouse lines and single cell RNA sequencing, we identified a Kindlin-2 - Stat3 - Dll1 signaling cascade in myoepithelial cells which controls the inactivation of Notch signaling in luminal cells that consequently drives luminal progenitor commitment to alveolar cells. We found that loss of Kindlin-2 in myoepithelial cells impairs mammary morphogenesis and alveologenesis, and lactation. Single-cell profiling reveals that Kindlin-2 loss significantly decreases the proportion of alveolar cells.

overall_design: mammary gland in late trimester of pregnancy  from myoepithelium/luminal epithelium specifically knock-out Kindlin-2 mouse model  were  isolated and analysis with single-cell RNA-seq

first: Zhenbin

last: Wang

first: Lei

last: Zhang

first: Jiagui

last: Song

first: Hongquan

first: Jun

last: Zhan


title: WGBS of parthenogenetic pig embryos

status: Public on Mar 04 2023

city: Columbus

first: Jinsoo

last: Ahn

address: 2029 Fyffe Rd

institute: The Ohio State University

summary: Porcine parthenogenetic embryos along with biparental control embryos were used to investigate imprinted genes in chromosome 11.

overall_design: Analyses of paternal or maternal methylation in porcine embryos

first: Seongsoo

last: Hwang

first: Kichoon

last: Lee


title: The Hdc GC box is critical for Hdc gene transcription and histamine-mediated anaphylaxis [CUT&Tag]

first: HUA

last: HUANG

overall_design: H3K27ac Histone modifications in WT and Hdc GC box KO BMMCs, in triplicate, using Illumina NovaSEQ6000 platform

first: Yapeng

last: Li

first: Junfeng

last: Gao

first: Dianzheng

last: Zhao

first: Hua

last: Huang


title: olfactory epithelium bulk RNAseq from 3 control male mice and 3 male mice with developmentally-induced degenerated olfactory bulb (sFlt1).

status: Public on Feb 20 2023

city: Jerusalem

first: Tamar

last: Licht

address: Hadassah ein karem

department: Medical Neurobiology

country: Israel

institute: Hebrew University

summary: To investigate the repertoire of olfactory receptors when the olfactory bulb is 30- 10% of normal size. Olfactory bulb was degenerated due conditional transgenic expression of the VEGF blocker sFlt1 in the brain at embryonic day 13.5

overall_design: Comparative gene expression profiling analysis of RNA-seq data from the olfactory epithelium

first: Dan

last: Rokni


title: RNA-seq of porcine parthenogenetic embryos

overall_design: Analyses of paternal or maternal allele-specific expression in porcine embryos.


title: A model of human asthma exacerbation identifies novel transcriptional programs and pathogenic cell circuits in the lower airway mucosa specific to allergic asthma

status: Public on Feb 24 2023

city: Charlestown

first: Neal

middle: Patrick

last: Smith

state: MA

address: 149 13th Street

institute: Massachusetts General Hospital

summary: Using a human model of asthma exacerbation, we compared the airway mucosa in allergic asthmatics and allergic non-asthmatic controls using single-cell RNA-sequencing frameworks. In response to allergen challenge, the airway epithelium in asthmatics was highly dynamic and upregulated genes involved in matrix degradation, mucus metaplasia, and glycolysis while failing to induce injury-repair and antioxidant pathways observed in controls. Asthmatics also had a unique mucosal immune profile, characterized by IL9-expressing pathogenic TH2 cells and enrichment of DC2 (CD1C) and CCR2-expressing monocyte-derived cells (MC) after allergen, with upregulation of genes that promote pathologic airway remodeling. In contrast, controls were enriched for macrophage-like MC that upregulated tissue repair programs after allergen challenge, suggesting these populations may protect against asthmatic airway remodeling. These findings reveal a novel TH2-mononuclear phagocyte-epithelial interactome unique to asthmatics, suggesting that pathogenic effector circuits and the absence of pro-resolution programs drive structural airway disease in response to type 2 inflammation.

overall_design: scRNAseq of lung cells captured by endobronchial brushes in allergic asthmatics (n = 4) and allergic controls (n = 4) under 3 conditions (baseline, diluent (saline), an allergen).

middle: P


title: MicroRNAs Associated with AGL6 and IAA9 function in tomato fruit set

status: Public on Feb 19 2023

city: Verona

first: Nicola

last: Vitulo

state: Select State

address: Strada le Grazie, 15

institute: University of Verona

summary: Fruit set is triggered after ovule fertilization, as a consequence of the downregulation of ovary growth repressors, such as the tomato transcription factors Auxin/indole-3-acetic acid 9 (IAA9) and Agamous-like 6 (AGL6). We produced small RNA libraries from IAA9- and AGL6-silenced ovaries to identify miRNAs differentially expressed in IAA9- and AGL6-silenced ovaries as compared with unpollinated control ovaries. The identified miRNAs represent a pool of regulatory sRNAs potentially involved in tomato fruit initiation.

overall_design: Gene expression profiling analysis of small RNA-seq data for tomato wild-type ovaries and AGL6- and IAA9-silenced ovaries. Each small RNA library was obtained from total RNA isolated from a pool of ovaries after treatment with exogenous dsRNA.

first: Barbara

last: Molesini

first: Federica

last: Pennisi

first: Tiziana

last: Pandolfini


title: The Hdc GC box is critical for Hdc gene transcription and histamine-mediated anaphylaxis

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


title: E2F1 mediates SOX17 Deficiency-Induced Pulmonary Hypertension

status: Public on Mar 15 2023

city: St. Louis

first: Zhiyu

last: Dai

address: 4960 Childrens Place

institute: Washington University in St. Louis

summary: SRY-Box Transcription Factor 17 (SOX17) enhancers variants and mutations are found in patients with pulmonary arterial hypertension (PAH). In human PAH pulmonary microvascular endothelial cells (HPMVEC), there is a significant downregulation of SOX17 expression. We hypothesized that SOX17 deficiency contributes to the pathogenesis of PAH and found that mice with endothelial specific disruption (ecKO Sox17) developed spontaneous pulmonary hypertension (PH) and exacerbated hypoxia-induced PH. Loss of SOX17 in lung ECs induces cell cycle programming, proliferative and anti-apoptotic phenotypes, a process mediated by the activation of E2F Transcription Factor 1 (E2F1) signaling. Pharmacological inhibition of E2F1 in ecKO Sox17 mice attenuated PH and cell cycle programming. Our study demonstrated that endothelial SOX17 deficiency induces PH and targeting E2F1 signaling represents a promising approach in PAH patients.

overall_design: Human lung microvascular endothelial cells were knocked down with siRNA against SOX17 or control for 48 hours. Equal amount of RNA from three replicates per condition was pooled together for RNA sequencing analysis.


title: Single cell RNA sequencing of paw skin from healthy and Col7a1 knockout (RDEB) mice

status: Public on Mar 02 2023

city: Valhalla

first: Morgan

middle: G

last: Anderson-Crannage

state: NY

address: 40 Sunshine Cottage Rd.

department: Cell Biology & Anatomy

institute: New York Medical College

summary: Recessive dystrophic epidermolysis bullosa (RDEB) is a genetic disorder caused by loss of function of the Col7a1 gene that encodes collagen VII, a critical structural protein that anchors the epidermis to the dermis. Manifestations of this disease include chronic wounding, blistering, immune dysfunction, and eventually squamous cell carcinoma. Symptoms are likely due to the disruption and dysregulation of the dermal microenvironment. Mice with RDEB symptoms, due to Col7a1 knockout, have been developed to study the disease's development and pathological manifestations in an in vivo model. Single cell RNA sequencing was performed on a single cell suspension of the paw skin of 2 week old RDEB mice, along with their wild-type littermates, to create a transcriptomic view of their dermal microenvironment. We analyzed the sequencing data at different resolutions. One focusing on the overall tissue level as well as closer analysis of specific cell types (fibroblasts, keratinocytes, immune cells, and vascular cells).

overall_design: Single cell supsensions were extracted from the paw skin of four, 2 week old mice. Two mice had Col7a1 knocked-out and displayed symptoms characteristic of RDEB, while the other two were normal.

first: Alex

last: Ascensión

first: Olga

last: Ibáñez-Solé

first: Ander

last: Izeta

first: Mitchell

last: Cairo

first: Yanling

last: Liao


title: RNA-seq and WGBS of parthenogenetic pig embryos

status: Public on Mar 03 2023

first: Jinsoo

last: Ahn


title: Transcriptional response across estrous in the mouse dorsal hippocampus is dysregulated by Cnih3 mutation

status: Public on Feb 17 2023

first: Joseph

last: Dougherty

address: Couch Biomedical Research Bldg 06316

department: Genetics

institute: Washington University of St. Louis

summary: The hippocampus is a critical brain region for coordinating learning, memory, and behavior. In adult females, the estrus cycle alters these functions through the activity of steroids hormones, with well-characterized effects on cellular physiology and behavior. However,the molecular genetic basis of these outcomes has not been systematically explored. In order to better understand the role of sex and the estrous cycle in the hippocampus, we profiled the transcriptome of hippocampi from female mice in each stage of the estrus cycle, along with those of males. We identify only subtle sex differences in gene expression between the sexes on average, yet comparing males to individual estrous stages reveals ~100 genes deviating from male expression patterns at one point in their cyclic fluctuations across estrous cycle. These estrus-responsive genes are especially enriched in oligodendrocytes and glycinergic neurons, and are potentially regulated downstream of estrogen receptor repressed pathways. To further understand our previous observations of female- and estrous-specific behavioral outcomes in knockout of Cnih3, we performed the same profiling in the knockout strain. Surprisingly, Cnih3 knockouts showed far broader transcriptomic differences between estrous cycle stages and males, despite very subtle within-group-across-genotype expression changes. We show that Cnih3 knockout drives expression changes in opposing directions between males and all points of the estrous cycle, extensively accentuating the magnitude of sex-differential hippocampal gene expression compared to wild-types. We thus provide a novel resource characterizing estrous-specific gene expression patterns in the adult hippocampus, which can provide insights into mechanisms of sex differential neuropsychiatric functions and dysfunctions, and identify a role for Cnih3 in buffering the female brain against the transcriptional effects of estrous.

overall_design: RNA-seq of dorsal hippocampus from wild-type C57/B6 and Cnih3 knockout (Frye 2021) adult male mice (n≥5 per genotype) and female mice at each estrous stage (n=4-7 females per stage)

first: Bernard

last: Mulvey

first: Stuart

last: Fass

first: Jose

last: Moron-Concepcion

first: Joe


title: Propionate reinforces epithelial identity and reduces aggressiveness of non-small cell lung carcinoma via chromatin remodelling [ChIP-seq]

status: Public on Feb 15 2023

city: Odense

first: Paolo

last: Ceppi

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: To investigate the effect of sodium propionate (SP) in enhancing the epithelial gene program via epigenetic remodelling in NSCLC, A549 cell line was treated with SP for 3 hours. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) was performed for the histone mark H3K27ac in A549 cell line treated with SP for 3 hours.

overall_design: Differential occupancy of H3K27ac mark at the promoter regions of epithelial genes were analyzed in SP treated A549 cells compared to the controls in replicates.

first: Vignesh

last: Ramesh

first: Simon

last: Toftholm Jakobsen

first: Rasmus

last: Siersaek


title: Propionate reinforces epithelial identity and reduces aggressiveness of non-small cell lung carcinoma via chromatin remodelling


title: Whole-genome genotyping of human islets using Illumina infinium chips

status: Public on Feb 07 2023

city: La Jolla

first: Maike

last: Sander

state: CA

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

type: Genome variation profiling by genome tiling array

summary: Genomic DNA was extracted from human islets using Dneasy Blood & Tissue Kit (QIAGEN) with RNase A treatment. 200-500ng DNA was genotyped using InfiniumOmni2-5-8v Genotyping BeadChips (Illumina).DNA was isolated from human islet cells from various donors. DNA was genotyped using Illumina Infinium whole-genome genotyping array. Genotypes were called with GenomeStudio (v.2.0.4) using default settings. Genotypes that passed quality filters (missing<0.05, minor allele frequency (MAF>0.01), non-ambiguous alleles defined by AT/GC variants with MAF>40%) were exported.

overall_design: Whole-genome genotyping of human islets from non-diabetic (n=12), pre-diabetic (n=9) and type 2 diabetes (n=15) individuals.


title: Integration of human genetics with single cell accessible chromatin profiles across phenotypes identifies islet cell type-specific regulatory programs of type 2 diabetes progression

overall_design: Refer to individual Series


title: Transcriptome profiling of liver samples from wild-type and Adamts12-/- mice in response to CCl4-induced liver injury.

status: Public on Feb 04 2023

city: Rennes

first: Vincent

last: Legagneux

address: 2 avenue du Professeur Léon Bernard, Bâtiment 5

country: France

institute: Inserm

summary:
We used Adamts12−/− and wild-type mice generated and genotyped by El Hour et al. 2010 (PMID: 20208563). eight-week-old females were treated by intraperitoneal injections of CCl4 (Sigma-Aldrich, St. Louis, MO, USA) diluted at 3% v/v in olive oil. A single dose of CCl4 0.3 ml/kg of mouse body weight was administered (acute treatment) and mice were sacrificed after 4h, 12h, 24h or 7 days. Control mice were treated with the vehicle (olive oil). Liver samples were collected, weighed and treated as previously described (Kesteloot et al. 2007, PMID: 17929299).
We performed gene expression profiling analysis using data obtained from liver samples of wild-type or Adamts12_KO mice at different time points after CCl4 (or vehicle) injection.

overall_design: Comparative gene expression profiling analysis using data obtained from liver samples of wild-type or Adamts12_KO mice at 4h, 12h, 24h or 7 days after CCl4 or vehicle injection.

first: Bassil

last: Dekky

first: Fida

last: Azar

first: Dominique

last: Bonnier

first: Christine

last: Monseur

first: Chiara

last: Kalebić

first: Alain

last: Colige

first: Nathalie

last: Théret


title: Transcriptome of ring-stage parasites responses to stress conditions upon knockdown of PfGCN5

status: Public on Feb 08 2023

city: Tampa

first: JUN

last: MIAO

state: Florida

address: 3720 Spectrum Boulevard, MDC84

department: Internal Medicine

institute: University of South Florida

summary:
Purpose: this study is to analyze the change of overal transcriptome after three stress conditions in ring-stage Plasmodium falciparum before and after knockdown of PfGCN5 by TetR-DOZI system.
Methods: In this study, the transcriptomes of a parasite line (TetR-PfGCN5::GFP) for knockdown (KD) of PfGCN5 by withdral of anhydrotetracycline (aTc) comparing to its control (TetR-PfGCN5::GFP with aTc) under three stress conditions [HS: heat shock, low-glucose starvation: L-Glu, and low dose of dihydroartemisinin (DHA) treatment] were analyzed at ring stage by RNAseq. Total RNA were harvested from the eary ring stages after 6 h of stress conditions using the Quick-RNA MiniPrep kit (Zymo Research). RNA sequencing libraries were prepared using the KAPA stranded RNA-seq library preparation kit (Roche) with 500 ng RNA from each sample. Illumina adapter sequence removal and quality trimming of reads were performed using Trimmomatic. Only reads that had a minimum length of 50 base pairs were retained. Reads were then mapped to the P. falciparum 3D7 strain reference genome with HISAT2.
Results: Using an optimized data analysis workflow, we mapped about 5 million sequence reads per sample to the malaria parasite genome (pf3D7_V3.0.) and identified over 5 thousands transcripts with high mapping rate at the range between 80% and 95. PfGCN5 KD profoundly changed the global transcription pattern upon stress conditions, indicating PfGCN5 is involved in stress responses.
Conclusions: Collectively, transcriptomic analysis of PfGCN5-dependent stress responses shows PfPfGCN5 plays important role in gene regulation of stress responses.

overall_design: mRNA profiles of TetR-PfGCN5::GFP with aTc, TetR-PfGCN5::GFP without aTc under three stress conditions (HS, L-Glu and DHA) were generated by deep sequencing, in two or three replicates

first: Jun

last: Miao

first: Liwang

last: Cui


title: Cross-species association of microRNA expression in mammary epithelial cells with stem/progenitor characteristics and cancer susceptibility

city: Ithica

first: Praveen

last: Sethupathy

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

summary: Comparison of mammosphere-derived epithelial cells across breast cancer susceptible and resistant species

sample_organism:
Homo sapiens
Canis lupus familiaris
Equus caballus
Sus scrofa
Bos taurus
Rattus norvegicus

overall_design: Identify differences in microRNA profiles by small RNA-sequencing of mammosphere-derived epithelial cells from three breast cancer susceptible and three breast cancer resistant species.

first: Gat

last: Rauner

first: Gerlinde

last: Van de Walle

first: Matt

last: Kanke


title: Extracellular Nicotinamide Phosphoribosyltransferase neutralisation harnesses T cell responses in breast cancer by repressing the PD-1/PD-L1 axis

status: Public on Jan 30 2023

city: Novara

first: Giorgia

last: Colombo

state: NO

address: Via Bovio 6, Presso Fondazione Novara Sviluppo

department: Department of Pharmaceutical Sciences

institute: UNIUPO

summary: Nicotinamide phosphoribosyltransferase (NAMPT) is a key intracellular enzyme that particulates in NAD homeostasis but is also a released cytokine (eNAMPT) that is found elevated in inflammatory conditions and in cancer. Given that in breast cancer patients, eNAMPT has been found elevated and its levels correlate with prognosis and staging, we set to investigate the effect of its neutralization with a specific monoclonal antibody. Neutralization of eNAMPT with C269 led to a decreased tumour size and reduced number of metastases. RNAseq and functional assays showed that eNAMPT controlled the PD-L1/PD-1 axis and its neutralization led to a restoration of antitumoural immune responses. These studies are highly consistent with eNAMPT as a novel immunotherapeutic target for triple negative breast cancer.

overall_design: We used 5 replicates of 6 samples (4T1 CTRL, 4T1 C269, CD4 CTRL, CD4 C269, CD8 CTRL, CD8 C269) using Illumina NextSeq 500

first: Armando

last: Genazzani


status: Public on Feb 06 2023

city: Berkeley

first: Yangnan

last: Gu

address: 371 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

summary:
Purpose: To understand MAC3BQ77A/D81A induced abnormal immunity, we performed the whole genome transcriptome analysis on 7-day-old seedlings of WT, 35S:MAC3BQ77A/D81A-GFP.
Conclusions: MAC3BQ77A/D81A positively regulates immune response.

overall_design: mRNA profiles of 7-day-old seedlings of wild type (Col-0) and MAC3BQ77A/D81A-GFP mutant were generated by deep sequencing, using Illumina Hiseq Xten platform.

first: Min

last: Jia

first: Xuanyi

last: Chen


title: Propionate reinforces epithelial identity and reduces aggressiveness of non-small cell lung carcinoma via chromatin remodelling [RNA-seq]

first: Paolo

last: Ceppi

summary: To investigate the effect of sodium propionate (SP) in enhancing the epithelial gene program in NSCLC, lung cancer cells were treated with SP at different time points. Gene expression profiling using RNA-Seq then performed with A549 cells treated with SP at different time points (3 hours, 24 hours, 3 days and 12 days).

overall_design: Differential gene expression analysis for A549 cells treated with SP and control cells at different time points in replicates.

first: Vignesh

last: Ramesh

first: Simon

last: Toftholm Jakobsen

first: Rasmus

last: Siersaek


title: Cellular Taxonomy of the Adult Human Spinal Cord

status: Public on Jan 31 2023

city: New York

first: Vilas

last: Menon

department: Neurology

institute: Columbia University Medical Center

summary: This study generates a census of cell signatures using single-nucleus RNA-sequencing data from dissociated lumbar human spinal cord. Nuclei were isolated using a triton-based dissociation protocol, processed using the 10x Genomic Chromium 3' platform (v3), and clustered into major cell classes as well as subtypes within each neuronal and glial class.

overall_design: Single-nucleus RNA-sequencing data on nuclei dissociated from frozen human spinal lumbar cord, from seven donors

first: Ariel

middle: J

last: Levine


title: Single-cell chromatin landscapes of human islets in normoglycemia, prediabetes and type 2 diabetes

first: Maike

last: Sander

summary: In this study, we used single cell nucleus ATAC-seq (snATAC-seq) to profile 218,973 islet cells from 34 individuals, including islets from non-diabetic, pre-diabetic and type 2 diectic (T2D) donors. We characterize changes in regulatory programs of islet cell types in T2D progression, describe the relationship of these programs to genetic risk for T2D, and use allelic imbalance mapping to define cell type-specific functions for candidate T2D causal variants.

overall_design: characterization of gene regulatory programs in individual islet cell types under both homeostatic and diabetic conditions.


title: Single-cell multiome (ATAC and RNA) landscapes of human islets in normoglycemia, prediabetes and type 2 diabetes

summary: We used single cell multiome (ATAC and RNA) sequencing to profile 85266 islet cells from 20 individuals, including islets from non-diabetic, pre-diabetic and type 2 diabetic (T2D) donors. We characterize changes in regulatory programs of islet cell types and subtypes in T2D progression, describe the relationship of these programs to genetic risk for T2D, and use allelic imbalance mapping to define cell type-specific functions for candidate T2D causal variants.


title: Guide-free Cas9 is detrimental to pig preimplantation embryo development

status: Public on Feb 05 2023

city: Guangzhou

first: Shixue

last: Gou

address: No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou

institute: GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH,CHINESE ACADEMY OF SCIENCES

summary:
Germline genome editing by the CRISPR/Cas9 system has potential for generation of genetically modified animals/the targeted correction of pathological mutations, understanding the mechanism of early embryonic development. Previous reports showed that Cas9 protein without sgRNAs could induce genomic damage in cell levels in vitro. However, whether the detrimental effects occurred in embryos after Cas9-treatment remains unknown. Here, by using pig embryos as the subjective, we found that Cas9 protein transcribed from injected Cas9 mRNA could persist to at least blastocyst stage. Cas9 protein alone could induce the genome damage of preimplantation embryos, represented by increased phosphorylated histone H2AX (pH2AX) foci on the chromatin fiber, leading to apoptosis and decreased cell number of blastocysts.
In addition, single-blastocyst RNA sequencing confirmed that Cas9 protein without sgRNAs could also cause the blastocyst transcriptome changes, depressing the embryo development signal pathway, such as cell cycle, metabolism, and cellular communication related signal pathways, while activating apoptosis and necroptosis signal pathway, both of which together resulted in impaired the preimplantation embryonic development.

overall_design: Comparative gene expression profiling analysis of single-blastocyst RNA-seq data for Cas9 injected embryos and tdTomato injected embryos.

first: Weikai

last: Ge

first: Xiaozhu

last: Zhao


title: Effect of depletion of ADAMTS12 on gene expression in the LX-2 cell line derived from activated human hepatic stellate cells (HSCs)

status: Public on Jan 29 2023

first: Vincent

last: Legagneux

summary:
Activated HSCs are liver stromal cells that play an important rôle in tissue repair and fibrosis.
We performed gene expression profiling analysis using data obtained from RNA-seq of LX-2 cells treated for 48h with control siRNAs (siCTL) or siRNAs specific for ADAMTS12 (siADAMTS12)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LX-2 cells treated for 48h with control siRNAs (siCTL) or ADAMTS12 siRNAs (siADAMTS12).

first: Bassil

last: Dekky

first: Fida

last: Azar

first: Dominique

last: Bonnier

first: Christine

last: Monseur

first: Chiara

last: Kalebić

first: Alain

last: Colige

first: Nathalie

last: Théret


status: Public on Feb 01 2023

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary: Human bronchial epithelial cell line Beas-2B were infected with Streptococcus pneumoniae at Multiplicity of Infection (MOI) of 0.5 and 1 or treated with lipoteichonic acid (LTA) for 9 and 16 h.  The mRNA profile changes upon infection shall be determined to investigate Streptococci pathogenesis.

overall_design: 8 groups, each with 3 biological replicates

first: André

last: Wesener

first: Evelyn

last: Vollmeister


title: Mechanically induced pyroptosis enhances cardiosphere oxidative stress resistance and metabolism for myocardial infarction therapy

status: Public on Jan 26 2023

first: Qi

last: Li

address: Jinan University, 601 Huangpu Avenue West, Tianhe District, Guangzhou City, Guangdong Province, China

department: Department of Developmental and Regenerative Biology

institute: Jinan University

summary: Cellular oxidative stress resistance and bioactivities showed great significance for long-term survival and cardiac regeneration. Cardiosphere-derived cells (CDCs) are favorable cell sources for myocardial infarction (MI) therapy, but effective culture systems for CDC spheroids, cardiospheres (CSps), cultivation and cell function enhancement are not well established. Here, a liquid crystal substrate, octyl hydroxypropyl cellulose ester (OPC), was developed for CSps production and preconditioning. With unique surface properties and mechanical responsiveness, significantly more size-controllable CSps were acquired using OPC substrate, and the OPC-CSps showed improved cell bioactivities and oxidative stress resistance under the stimulation of mechanical-induced pyroptosis. RNA sequencing and metabolism analysis demonstrated the increased metabolic level and improved mitochondrial function of OPC-CSps. In a rat MI model, OPC-CSps significantly improved long-term cardiac function, promoted angiogenesis, and reduced cardiac remodeling in the 3-month observation. Collectively, this study provides a promising and effective system for preparing massive functional CSps for myocardial infarction therapy.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for cardiosphere derived cells(CDCs) cultured on the polystyrene(PS) substrate, the ultralow attachment(ULA) substrate and the hydroxypropyl cellulose ester(OPC) substrate.

first: Yingwei

last: Wang

first: Jupeng

first: Jiamin

last: Chen

first: Dongxue

last: Wu

first: Youling

last: Zheng

first: Jiaxin

first: Jie

last: Liu

first: Jianlong

last: Lu

first: Jianhua

last: Zhang

first: Zheng


title: Lung transplantation-induced cold ischemia–reperfusion injury in the murine lung

status: Public on Jan 20 2023

city: Wuxi

first: Jin

last: Zhao

address: 299 Qingyang Road

institute: Wuxi People’s Hospital Affiliated to Nanjing Medical University

summary:
Cold ischemia-reperfusion induced injury contributes to poor lung transplant outcomes. We used transcriptome sequencing to study the biological response of mouse lungs to the cold ischemia-reperfusion process.
Mouse orthotopic left LTx was performed with standard cuff techniques. Briefly, the donor lungs were recovered after being flushed with 10ml low potassium dextran (LPD) solution and inflated with 50% oxygen. Cold ischemia was induced by storing donor lungs in 20ml LPD at 4°C for 24 hours. Then, the left donor lung was cuffed and implanted into recipients within 45 minutes. After the 4-hour reperfusion, the recipient mice were sacrificed and the transplanted lungs were collected.

overall_design: Transcriptional profiling were performed on three naive lung samples, and four lung allografts that experienced 24 hours of cold ischemia and 4 hours of reperfusion.

first: Jiawei

first: Dong

last: Wei

first: Fei

last: Gao

first: Xiucheng

last: Yang

first: BingQing

last: Yue

first: Dian

last: Xiong

first: Mingzhao

first: HongYang

last: Xu

first: ChunXiao

last: Hu

first: JingYu


title: Mapping the spatial transcriptomic signature of the hippocampus during memory consolidation

status: Public on Jan 18 2023

city: Iowa City

first: Yann

last: Vanrobaeys

address: 169 Newton Road

department: Neuroscience and Pharmacology

institute: University of Iowa

summary:
We report a bulk transcriptomic dataset of mouse dorsal hippocampus to identify gene expression changes of spatial object recognition training. We report a spatial transcriptomics dataset of mouse brain tissue generated with the 10x Genomics Visium platform to identify gene expression profiles of spatial object recognition training.

We report a single nuclei ATAC-seq and a Single nuclei RNA-sequencing using SPLiT-pool barcoding datasets of mouse dorsal hippocampus to identify chromatin and gene expression changes of spatial object recognition training.

overall_design:
We performed bulk sequencing gene expression analysis from dorsal hippocampus of 2 groups (trained spatial object recognition vs. home cage). We performed spatial gene expression profiling analysis using Visium data obtained from coronal mouse brain sections of 2 groups (trained spatial object recognition vs. home cage).

We performed single nuclei ATAC-seq and a Single nuclei RNA-sequencing using SPLiT-pool barcoding from dorsal hippocampus of 2 groups (trained spatial object recognition vs. home cage).

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