title: IFN𝛾-induced treatment of a Human Lung Adenocarcinoma Cell Line is Mediated by an Environmental Chemical Receptor (AhR) through PD-L1 and IDO Control (a549 bulk RNA)

status: Public on Jun 08 2024

city: Boston

first: David

last: Sherr

state: MA

address: 72 East Concord St

department: Environmental Health

institute: Boston University

summary: While immunotherapy has shown efficacy in non-small cell lung cancer (NSCLC) patients, many respond only partially or not at all. One limitation in improving outcomes is the lack of a complete understanding of factors regulating immune checkpoint targets. Here, we sought to address a possible link between an environmental chemical receptor implicated in NSCLC and immune regulation, the aryl hydrocarbon receptor (AhR), and a known but counterintuitive mediator of immunosuppression, IFN𝛾, in regulation of two immune checkpoints, PD-L1 and the IDO1, in lung adenocarcinoma (LUAD). To this end we used AhR, PD-L1, and IFN𝛾R gene-edited LUAD cell lines, a syngeneic LUAD mouse model, bulk- and single cell-RNA sequencing of LUADs and tumor-infiltrating leukocytes, and existing human transcriptomic databases. The data demonstrate that: 1) the AhR regulates both PD-L1 and IDO1 in murine and human LUAD cells, 2) AhR-driven IDO1 results in production of Kyn which likely mediates an AhR→IDO1→Kyn→AhR amplification loop, 3) the previously characterized induction by IFN𝛾of PD-L1 and IDO is mediated by the AhR, 4) transplantation of LUAD cells in which the AhR is deleted results in long-term tumor immunity in approximately half of the mice; slow growing tumors in the other half exhibit significantly higher densities of CD4+ and CD8+ T cells expressing immunocompetence markers, and 5) deletion of either IFN𝛾R1 or PD-L1 does not provide the same level of immune protection as AhR deletion. The data definitively link IFN𝛾- mediated immunosuppression to the AhR and support the targeting of the AhR in the context of LUAD.

overall_design: The experiment is comprised of 6 samples, profiling RNA extracted from human A549 lung adenocarcinoma cells. The cells were either unmodified (naive, or "wild-type"), subjected to CRISPR with a non-targeting control sgRNA, or subjected to CRISPR with an sgRNA designed to knock out the aryl hydrocarbon receptor (AHR) gene. Each experimental group was represented in triplicate.

first: Megan

last: Snyder

first: Zhongyan

last: Wang

first: Brian

last: Lara

first: Jocelyn

last: Fimbres

first: Muzamil

middle: K

last: Mohammed

first: Stefano

last: Monti


title: Morphogenesis and regeneration share a conserved core transition cell state program that control lung epithelial cell fate

status: Public on Jun 01 2024

city: New York

first: Xiangyi

last: Ke

state: New York

address: 650 West 168th Street

country: USA

institute: Columbia University

type: Expression profiling by high throughput sequencing

summary: We isolated and identified a population of Icam1/Nkx2-1 epithelial progenitors harboring a transitional state program remarkably conserved in humans and mice during lung morphogenesis and regeneration

overall_design: Epcam+ or Epcam+Icam1+ cells from E14.5 mouse embroynic lungs are isolated and proceeded to single cell sequencing

first: Benjamin

last: van Soldt


title: Effect of oxygen and carbon dioxide on gene expression in Bordetella bronchiseptica strain RB50

status: Public on Jun 07 2024

city: Chapel Hill

first: Peggy

middle: A.

last: Cotter

state: North Carolina

address: 125 Mason Farm Rd, 6101 Marsico Hall Cb7290

department: Microbiology & Immunology

institute: UNC Chapel Hill

summary: The classical bordetellae (Bordetella pertussis, B. parapertussis, and B. bronchiseptica) are obligate aerobes that use only oxygen as their terminal electron acceptor for electron transport-coupled oxidative phosphorylation. Therefore, access to oxygen is critical for these bacteria to survive. To better understand how B. bronchiseptica changes its gene regulation when faced with different levels of oxygen, we grew liquid cultures of B. bronchiseptica RB50 in ambient air, 5% oxygen, and 2% oxygen. We also measured how the presence of 5% carbon dioxide affected gene expression in these bacteria, since they are respiratory pathogens and therefore get exposed to higher carbon dioxide levels during infection than are found in ambient air.

overall_design: We grew wild-type RB50 in shaking liquid cultures in either ambient air, 5% O2, 2% O2, or 5% CO2. We then assessed gene expression of bacteria in these conditions. Differential gene expression was determined between bacteria grown in ambient air and bacteria grown under conditions (i.e. air vs. 5% O2, air vs 2% O2, and air vs 5% CO2).

first: Liliana

last: McKay


title: Immunologic drivers of immune checkpoint inhibitor therapy myocarditis, fatality and anti-tumor response in cancer patients

status: Public on Jun 22 2024

city: Charlestown

first: Neal

middle: Patrick

last: Smith

address: 149 13th Street

institute: Massachusetts General Hospital

summary: Immune checkpoint inhibitors (ICIs) can offer remarkable benefits to patients with cancer, but these agents can cause morbid and potentially fatal immune-related adverse events (irAEs), the most lethal of which is ICI-related myocarditis (irMyocarditis). The pathogenesis of irMyocarditis and its relationship to anti-tumor immunity remain poorly understood. We sought to define how immune cell trafficking between heart, tumor and blood contributes to irMyocarditis pathogenesis and fatality by leveraging single-cell (sc)RNA-seq coupled with T cell receptor (TCR) sequencing, microscopy, and proteomics analysis of 28 irMyocarditis patients and 23 controls. Our analysis of ~284,360 cells from the heart and blood specimens identified enrichment of cytotoxic T-cell subsets, inflammatory macrophage subsets, conventional dendritic cells (cDCs), and fibroblasts in the heart that accompany the upregulation of potentially targetable, pro-inflammatory transcriptional programs. Expanded TCR clones enriched in irMyocarditis are largely distinct from those in paired tumors, suggesting distinct mechanisms between anti-tumor immune response and irMyocarditis. We also identified circulating biomarkers of fatality, including decreased circulating CD4+ T cells, decreased cDCs, and the presence of cardiac-expanded TCRs in a circulating, cycling CD8+ T cell population. Collectively, these findings highlight critical biology driving disease pathogenesis and nominate putative biomarkers and tailored therapeutic interventions for patients with irMyocarditis.

overall_design:
Heart samples were taken through endomyocardial biopsies or autopsy from patients receiving an ICI for cancer.  Additionally, patients had PBMCs collected at multiple timepoints through their course of treatment.  Samples were then used for scRNA-seq.

>>>Submitter states: The raw data will be submitted via dbGaP as it needs to be under controlled access.<<<

middle: P

first: Isabela

middle: J

last: Kernin

first: Steven

middle: M

last: Blum

first: Daniel

middle: A

last: Zlotoff

first: Alexandra-Chloe

last: Villani


title: IL-21 induces antitumor response in NK cells via CEBPD

status: Public on Jul 09 2024

city: HOUSTON

first: Katayoun

last: Rezvani

state: TX

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: NK cells engineered to express IL-21 (IL-21 NK) acquire strong antitumor activity, with the ability to respond to glioblastoma (GBM) rechallenge in vitro and in vivo. IL-21 NK cells have a unique signature of chromatin accessibility, with CCAAT/Enhancer-Binding Protein (C/EBP), especially CEBPD, serving as key transcription factors regulating their memory response.

overall_design: The objective of this study was to investigate the epigenetic factors that contributing for memory formation in NK cells

first: Mayra

last: Shanley


title: Adaptation to an acid microenvironment promotes pancreatic cancer organoid growth and drug resistance

status: Public on Jun 04 2024

city: Copenhagen

first: Yifan

last: Dai

address: Ole Maaløes Vej 5

department: Department of Biology

country: Denmark

institute: Copenhagen University

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

overall_design: Refer to individual Series


title: A HDAC4-HDAC2 complex composes an epigenetic sensor that links the DNA damage response to the senescent program by erasing H2BK120 acetylation [I]

status: Public on Jun 18 2024

city: Udine

first: Emiliano

last: Dalla

state: UD

address: Piazzale Kolbe 4

department: Department of Medicine

country: Italy

institute: Università degli Studi di Udine

summary:
Purpose: Recognize the specific H2BK120ac profile around HDAC4 binding sites in proliferating, pre-senescent, senescent and senescence escaped cells during the accumulation of dsDNA damage, compared to undamaged regions.
Outcome:  We discovered a novel epigenetic complex formed by HDAC4 and HDAC2 that is involved in monitoring H2BK120 acetylation. The HDAC4/HDAC2 complex, through the dynamic deacetylation of H2BK120, modulates the efficiency of DNA repair by homologous recombination (HR) by controlling the recruitment of BRCA1 and CtIP to the site of lesions. Degradation of HDAC4 during senescence has a dual effect. First, it contributes to super-enhancers activation by limiting HDAC3 activity, and second, it causes the accumulation of DNA damage.

overall_design: Evaluation of H2BK120 and H4K16 acetylation, H2AX phosphorylation (gammaH2AX) and of HDAC4 binding in BJ-hTERT or hTERT/ HRAS-ER or hTERT/ HRAS-ER /HDAC4 cells at 2 or 8 days from 4-OHT treatment (to induce HRAS G12V).

first: C

last: Brancolini

first: E

last: Di Giorgio


title: IFN𝛾-induced Immunosuppression in Lung Carcinoma is Mediated by an Environmental Chemical Receptor (AhR) through PD-L1 and IDO Control

first: David

middle: H

last: Sherr

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: IFN𝛾-induced Immunosuppression in Lung Carcinoma is Mediated by an Environmental Chemical Receptor (AhR) through PD-L1 and IDO Control (cmt167 scRNA)

overall_design: To investigate the presence or absence of Ahr in malignant cells of the lung in regards to the functions related to tumorogenicity and immune signalling using an average of 5,792 viable cells from wildtype tumors from two mice and an average of 3,173 viable cells from AhR-KO tumors

first: Megan

last: Snyder

first: Zhongyan

last: Wang

first: Brian

last: Lara

first: Jocelyn

last: Fimbres

first: Muzamil

last: Mohammed

first: Stefano

last: Monti


title: Effect of epithelial depletion of Kdf1 on gene expression alteration during tooth crown development

status: Public on Jun 02 2024

city: Beijing

first: Jiayu

address: Haidian District,Beijing,China

country: China

institute: Peking university

summary: In our study, we observed that mice lacking epithelial Kdf1 exhibited rounded and blunt molar cusps, accompanied by abnormal folding of dental epithelium, suggesting that  epithelial Kdf1 played a regulatory role in molar crown morphogenesis. Nevertheless, the mechanism within dental epithelium regulating tooth crown morphogenesis remains unclear.

overall_design: To explore the downstream molecular alterations of Kdf1 deletion, we conducted RNA-Seq of inner enamel epithelium tissue from the mandibular first molar.

first: Miao

last: Yu


title: SMCHD1 activates the expression of genes required for the expansion of human myoblasts  (ChIP-seq)

status: Public on Jun 25 2024

city: Madison

first: Jeffrey

last: Dilworth

email: jdilworth@ohri.ca, fdilworth@wisc.edu

state: WI

address: 1111 Highland Ave - WIMR II 4518

department: Cell and Regenerative Biology

institute: University of Wisconsin - Madison

summary: In human muscle, SMCHD1 mutations are associated with the onset of FSHD2, but the mechanism driving the disease onset remains unclear. A commonly accepted explanation is the loss of SMCHD1 binding to the D4Z4 locus activates the expression of DUX4 in FSHD2 muscle. In this study, we used human myoblasts having DUX4 non-permissive 4qB alleles as a model to study DUX4-independent functions of SMCHD1 on myoblast cell growth. Surprisingly, depletion of SMCHD1 in these cells resulted in a cell proliferation defect. Despite the absence of DUX4 target genes’ activation, these cells showed a repression of PAX7 target genes (a hallmark of FSHD) and similar changes in expression profile compared to FSHD myoblasts. Interestingly, downregulation of cell proliferation-related genes and dysregulation of fibroblasts-specific genes were observed in SMCHD1 knockdown myoblasts and FSHD2 myoblasts but not FSHD1 myoblasts. Additionally, we identified LAP2 as direct targets of SMCHD1. Depletion of LAP2 leads to cell proliferation defect similar to the effect after SMCHD1 knockdown. These data imply that DUX4 is not the only driver for the onset of FSHD, and SMCHD1 has DUX4-independent functions in muscle growth and development.

overall_design: SMCHD1 ChIP-seq in proliferating human myoblast cell line WS234 (donor 15VBic)


title: SMCHD1 activates the expression of genes required for the expansion of human myoblasts


title: Adaptation to an acid microenvironment promotes pancreatic cancer organoid growth and drug resistance [acid]

summary: We investigated transcriptomic changes in pancreatic ductal organoids under adaptation to an acidic extracellular environment.

overall_design: Wild type ("mN10"), KrasG12D ("mP4"), p53 knockout ("mP4 p53KO"), and Trp53R273H ("mP4 p53R273H") organoids were gradually acid adapted from pH 7.4 to pH 6.7 ("AA") by decreasing pH of their culture medium by approximately Δ=0.125 pH every week for nine weeks. After reaching the desired pH of 6.7, the organoids were cultured for 2 weeks (week 8-9) at pH 6.7. Then, acid adapted organoids were split into two fractions: i) cultured at pH 6.7 until week 11, and ii) cultured at their physiological pH of 7.4 until week 11 ("AA->pH7.4").

first: Arnaud

last: Stigliani

first: Renata

last: Ialchina

first: Dominika

last: Czaplinska

first: Jiayi

last: Yao

first: Henriette

last: Berg Andersen

first: Stine

last: Falsig Pedersen

first: Albin

last: Sandelin


title: Regulation of stochastic gene bursting by chromatin-independent acetylation

status: Public on Jun 26 2024

city: Bethesda

first: Varun

last: Sood

state: Maryland

address: 41 Medlars Drive

department: Laboratory of receptor biology and gene expression

institute: National Institues of Health, National Cancer Institute, Center for Cancer Research

summary: Stochastic transcriptional bursting is now recognized as a universal property of gene expression.  While different genes exhibit distinct bursting patterns, the molecular basis for differences in bursting are largely unknown.  We have developed and applied a high-throughput-imaging based screening strategy to identify cellular factors and mechanisms that determine the bursting behavior of human genes.   Focusing on epigenetic regulators, we find that global acetylation is the strongest acute modulator of burst frequency, size and heterogeneity of bursting. Acetylation similarly affected the Off-time but On-time changes were gene-specific.  These effects were not strongly linked to promoter acetylation, which did not correlate with bursting properties and forced promoter acetylation altered bursting for only some genes. Instead, we identified acetylation of the Integrator complex as a key determinant of gene bursting with elevated Integrator acetylation leading to faster bursting. Taken together our results suggest a dominant role of non-histone proteins in determining gene bursting properties and they identify non-epigenetic acetylation of a transcription cofactor as an allosteric modulator of bursting via a pause-release related bursting checkpoint

overall_design:
Spike in calibrated ChIP-seq for H3K27ac in DMSO and Panobinostat treated HBEC cells
Spike-in and allele normalized PRO-seq in HBEC cells overexpressing ectopic INTS4 mutants at lysine 26 and 27 that are changed to either glutamine (acetylation-mimic) or alanine (acetylation-null)

first: Dan

last: Larson

first: Tom

last: Misteli


title: Col2a1-Cre;Idh1LSL/+ embryonic growth plate chondrocytes

status: Public on Jun 28 2024

first: Jianhong

last: Ou

state: Wisconsin

address: 330 N Orchard Street

institute: Morgridge Institute For Research


title: Identify H3K4Me3 occupancy on genome in Setd1a Knock out (KO) mouse undifferentiated pleomorphic sarcoma cells

status: Public on May 24 2024

summary:
As Setd1a is a methyltransferase targeting H3K4, we performed H3K4Me3 ChIP in control and Setd1a KO cell to observe the effects of Setd1a on H3K4Me3.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K4Me in control mouse UPS and Setd1a KO mouse UPS cells  .

overall_design: Ga I Ban

first: Benjamin

last: Alman


title: COMPASS complex inhibition targets the metastasis initiating cell in undifferentiated pleomorphic sarcoma

first: Aenjamin

first: Joy

last: Ban

first: Vijitha

last: Puviindran

first: Yuning

last: Tang


title: A multi-cancer CRISPR/Cas9 reveals distinct gene dysregulation by noncoding MSTRG transcripts

status: Public on Jun 17 2024

city: Guangzhou

first: wei

last: xiong

state: Guangdong

address: No.1023,South Shatai Road

department: Bioinformatics Section

institute: Southern Medical University

summary: Long noncoding RNAs (lncRNAs) regulate gene expression with their functional domains without being translated into proteins. Whether wrong noncoding transcripts have functions is of special interest and lacks systematic investigation.  Our study identified several MSTRG transcripts that may have regulatory functions through specific DNA-binding domains (DBDs). We selected three MSTRG noncoding transcripts and validated their roles in cancer through CRISPR/Cas9-mediated knockout experiments, using A549 and HCT116 cell lines as experimental models. Then, we conducted a comparative gene expression analysis using RNA-seq data to compare the knockout of three aberrant human non-coding transcripts to their respective wild-type controls.

overall_design: We selected three MSTRG transcripts for knockout of their DNA-binding domains (DBDs), including MSTRG.4401.1, MSTRG.2513.6, and MSTRG.34636.7. Specifically, MSTRG.4401.1 and MSTRG.2513.6 were knocked out in both A549 and HCT116 cell lines, while MSTRG.34636.7 was knocked out only in HCT116 cells. Both before and after the knockout, RNA sequencing (RNA-seq) was performed on the samples.

first: Hao

last: Zhu


title: Adaptation to an acid microenvironment promotes pancreatic cancer organoid growth and drug resistance [drug]

first: Yifan

last: Dai

summary: We investigated transcriptomic changes in PanIN ("mP4") mouse pancreatic ductal organoids under acute or long-term treatment of Gemcitabine and Erlotinib.

overall_design: The mP4 organoids were gradually adapted to growth in medium containing 10 nM of drugs (Erlotinib, Gemcitabine or combination), by increasing drug concentrations by 1 nM / week over a period of 12 weeks. As controls, we kept organoids at 0 nM drug concentrations for the same time. A subset of control organoids were acutely treated with 10 nM erlotinib, gemcitabine or the combination of the two at 12 weeks. Expression prolifing analysis was conducted based on RNAseq of 33 samples from 2 experiments: drug adaptation experiment (24 samples from week 1 and 12), and acute drug treatment experiment (9 samples).

first: Arnaud

last: Stigliani

first: Renata


title: Whole genome sequencing of mouse sarcoma clones

overall_design: Primary autochthonous mouse sarcoma driven by KrasG12D, p53-/- expressing R26-Confetti reporters are sorted for different reporter tumor clones by FACS.  Genomic DNA from the sorted clones are used for whole genome sequencing (WGS).


title: Dermal TRPV1 innervations engage a macrophage and fibroblast containing pathway to activate hair growth [dataset1]

status: Public on May 10 2024

city: SAN FRANCISCO

first: Konrad

last: Knopper

state: CA

address: 513 Parnassus Ave

institute: UCSF

summary: Pain, detected by nociceptors, is an integral part of injury, yet whether and how it can impact tissue physiology and recovery remain understudied. Here we applied chemogenetics in mice to locally activate dermal TRPV1 innervations in naïve skin and found it triggered new regenerative cycling by dormant hair follicles (HFs).This was preceded by rapid apoptosis of dermal macrophages, mediated by the neuropeptide calcitonin gene-related peptide (CGRP). TRPV1 activation also triggered a macrophage-dependent induction of Spp1-expressing dermal fibroblasts. The neuropeptide CGRP andSpp1were essential for the nociceptor-triggered hair growth. Finally, we show that epidermal abrasion injury induced Spp1-expressing dermal fibroblasts and hair growth via a TRPV1 neuron and CGRP dependent mechanism.Collectively, these data demonstrate a role for TRPV1 nociceptors in orchestrating a macrophage and fibroblast-supported mechanism to promote hair growth, and enabling the efficient restoration of this mechano- and thermo-protective barrier after wounding.

overall_design:
Back skin from TRPV1hM3Dq expressing and control mice (two mice per group) were collected 3.5 hours after a single intradermal CNO injection. The subcutis was removed mechanically and the dermal-epidermal fractions were then digested. Then, control and TRPV1 activated samples were stained using viability dyw and CD45 antibody and sorted. Treatment groups (two) were run on separate lanes of a 10X Chromium chip with 3′ v.2 chemistry (10X Genomics) as per the manufacturer’s instructions by the UCSF Institute for Human Genetics Sequencing Core. Transcripts captured in all the cells encapsulated with a bead were uniquely barcoded using a combination of a 16 bp 10x Barcode and a 10 bp unique molecular identifier (UMI). cDNA libraries were generated using the Chromium™ Single Cell 3’ Library & Gel Bead Kit v3 (10x Genomics) following the detailed protocol provided by the manufacturer. Libraries were sequenced with the NovaSeq 6000 platform (S1 Cartridge, Illumina) in 150 bp paired-end mode. The hashtag library was demultiplexed using CellRanger software (version 7.0.0), discriminating between spliced and unspliced transcripts. Aligned spliced reads were used to quantify the expression level of mouse genes and generation of gene-barcode matrix. Subsequent data analysis was performed using Seurat R package (4.0.4) and Scanpy (1.8.2). Quality control was performed, and viable cells were selected by excluding cells with features lower than 200 and above 4000, as well as cells having more than 5% of mitochondrial transcripts. Dermal and epidermal derived cells were demultiplexed with the HTODemux function integrated in Seurat with standard settings and dermal derived cells were included in the analysis all doublets were removed for the analysis. 2000 most variable genes used for the anchoring process were used for downstream analysis to calculate principal components, after log-normalization and scaling.
HTO; Barcode sequence; Hashtagged sample
Hashtag_1_(B0301);  ACCCACCAGTAAGAC; mouse1
Hashtag_2_(B0302);  GGTCGAGAGCATTCA; mouse2
Hashtag_3_(B0303);  CTTGCCGCATGTCAT; mouse3
Hashtag_3_(B0303);  CTTGCCGCATGTCAT; mouse4

first: Tamar

middle: L

last: Shaanan

first: Lihui

last: Duan

first: Jason

last: Cyster


title: Diet-induced obesity dysregulates rapid epigenetic response to hypoxia in macrophages (ChIP-Seq)

status: Public on May 05 2024

city: Syracuse

first: Norifumi

last: Urao

address: 750 E. Adams St.

department: Pharmacology

institute: SUNY Upstate Medical University

summary: Macrophages play important roles in tissue homeostasis and tissue healing process. The response to hypoxic environment is a trigger to induce key signaling pathways in macrophages. Functions of macrophages are dysregulated in metabolic diseases such as diabetes and obesity resulting in poor tissue healing. Epigenetic status including histone modification in macrophages is regulated by hypoxia. However, whether and how obesity influences histone modification under hypoxia is unknown. Using chromatin immunoprecipitation-sequencing (ChIP-seq), RNA-seq on mouse bone marrow-derived macrophages, we sought to determine whether hypoxia alters histone 3-lysine 4 trimethylation (H3K4me3) and gene expression profile in macrophages and how obesity influences H3K4me3 enrichment on the genome in hypoxia-dependent and -independent manner.

overall_design: Comparative H3K4me3 marked peak analysis of ChIP-seq data for bone marrow-derived macrophages (BMDMs) obtained from C57B6/J mice fed a high-fat diet or a normal-fat diet with or without 1% hypoxia treatment for 1 hour.

first: Kentaro

last: Takahashi


title: AP-1 regulates heterogeneous cellular dormancy in TNBC

status: Public on May 18 2024

city: Shanghai

first: Yang

last: Dong

state: 上海

address: Shanghai

institute: Tongji University

summary: Slow-cycling cells (SCCs) are a heterogeneous subpopulation of tumor cells. They pre-exist in tumor tissues and evade killing by chemotherapeutics that target mitosis due to their dormant nature. We here utilized varieties of fluorescent dyes or proteins (Claret, H2BeGFP, and Violet) retaining method to label and isolate SCCs, and RNA-seq was performed to understand the gene expression characteristics of subpopulations of SCCs.

overall_design: Here we reported that SCCs subgroups share similar gene expression profiles. Up-regulations of AP-1 subunits regulate triple negative breast cancer (TNBC) dormancy by up-regulating the expression of CDKN1A and GADD45 family as transcription factors.

first: Dean

middle: G


title: Reducing cholesteol in macrophages alters epigemone

status: Public on Apr 26 2024

first: Jeffrey

last: Dilworth

summary: Cholesterol reduction in macrophages by methyl-beta-cyclodextran (MCD) alters gene expression and genomic configuration in a cholesterol specific fashion.

overall_design: ATAC-seq was performed on RAW macrophages, treated with MCD (5 mM, 1 hour) or without. Two replicates were performed for untreated control (ctl); two replicastes for MCD treated cells MCD).

first: Zeina

last: Salloum

first: Kiran

last: Nakka

first: Xiaohui

last: Zha


title: IFN𝛾-induced Immunosuppression in Lung Carcinoma is Mediated by an Environmental Chemical Receptor (AhR) through PD-L1 and IDO Control (cm167 bulk RNA)

status: Public on Jun 08 2024

first: David

last: Sherr

summary: While immunotherapy has shown efficacy in non-small cell lung cancer (NSCLC) patients, many respond only partially or not at all. One limitation in improving outcomes is the lack of a complete understanding of factors regulating immune checkpoint targets. Here, we sought to address a possible link between an environmental chemical receptor implicated in NSCLC and immune regulation, the aryl hydrocarbon receptor (AhR), and a known but counterintuitive mediator of immunosuppression, IFN𝛾, in regulation of two immune checkpoints, PD-L1 and the IDO1, in lung adenocarcinoma (LUAD). To this end we used AhR, PD-L1, and IFN𝛾R gene-edited LUAD cell lines, a syngeneic LUAD mouse model, bulk- and single cell-RNA sequencing of LUADs and tumor-infiltrating leukocytes, and existing human transcriptomic databases. The data demonstrate that: 1) the AhR regulates both PD-L1 and IDO1 in murine and human LUAD cells, 2) AhR-driven IDO1 results in production of Kyn which likely mediates an AhR→IDO1→Kyn→AhR amplification loop, 3) the previously characterized induction by IFN𝛾of PD-L1 and IDO is mediated by the AhR, 4) transplantation of LUAD cells in which the AhR is deleted results in long-term tumor immunity in approximately half of the mice; slow growing tumors in the other half exhibit significantly higher densities of CD4+ and CD8+ T cells expressing immunocompetence markers, and 5) deletion of either IFN𝛾R1 or PD-L1 does not provide the same level of immune protection as AhR deletion. The data definitively link IFN𝛾- mediated immunosuppression to the AhR and support the targeting of the AhR in the context of LUAD.

overall_design: The experiment is comprised of 6 samples, profiling RNA extracted from mouse CMT 167 (C57 mouse tumor; referred to herein as CMT) cell lines. Each cell line was either unmodified (naive, or "wild-type"), subjected to CRISPR with a non-targeting control sgRNA, or subjected to CRISPR with an sgRNA designed to knock out the aryl hydrocarbon receptor (Ahr) gene. Each experimental group was represented in triplicate.

first: Megan

last: Snyder

first: Zhongyan

last: Wang

first: Brian

last: Lara

first: Jocelyn

last: Fimbres

first: Muzamil

last: Mohammed

first: Stefano

last: Monti


title: Dermal TRPV1 innervations engage a macrophage and fibroblast containing pathway to activate hair growth [dataset2]

first: Konrad

last: Knopper

overall_design:
Back skin from TRPV1hM3Dq and control mice (three mice per group) treated daily with a CNO intradermal injection for three consecutive days, were dissected, separated into the subcutis and dermal-epidermal fractions and then digested. The dermal-epidermal and subcutis fractions were stained separately with TotalSeq™ anti-mouse Hashtag antibodies (TotalSeq™ A0301 and A0302 from BioLegend) to mark the cells’ anatomical location. Thy1+ SCA1+ stromal cells (CD45−CD31− EpCAM−) were sorted and analysed. Treatment groups (two) were run on separate lanes of a 10X Chromium chip with 3′ v.2 chemistry (10X Genomics) as per the manufacturer’s instructions by the UCSF Institute for Human Genetics Sequencing Core. Transcripts captured in all the cells encapsulated with a bead were uniquely barcoded using a combination of a 16 bp 10x Barcode and a 10 bp unique molecular identifier (UMI). cDNA libraries were generated using the Chromium™ Single Cell 3’ Library & Gel Bead Kit v3 (10x Genomics) following the detailed protocol provided by the manufacturer. Libraries were sequenced with the NovaSeq 6000 platform (S1 Cartridge, Illumina) in 150 bp paired-end mode. The hashtag library was demultiplexed using CellRanger software (version 7.0.0), discriminating between spliced and unspliced transcripts. Aligned spliced reads were used to quantify the expression level of mouse genes and generation of gene-barcode matrix. Subsequent data analysis was performed using Seurat R package (4.0.4) and Scanpy (1.8.2). Quality control was performed, and viable cells were selected by excluding cells with features lower than 200 and above 4000, as well as cells having more than 5% of mitochondrial transcripts. Dermal and epidermal derived cells were demultiplexed with the HTODemux function integrated in Seurat with standard settings and dermal derived cells were included in the analysis all doublets were removed for the analysis. 2000 most variable genes used for the anchoring process were used for downstream analysis to calculate principal components, after log-normalization and scaling.
HTO; Barcode sequence; Hashtagged sample
Hashtag_1_(A0301);  ACCCACCAGTAAGAC; epidermis+dermis
Hashtag_2_(A0302);  GGTCGAGAGCATTCA; subcutis

first: Tamar

last: Shaanan

first: Lihui


title: RNA-seq analysis of lung tissues from Kiss1r+/+, Kiss1rflox/+, and Kiss1rflox/flox mice with KrasG12D mutation

status: Public on May 01 2024

city: seoul

first: seoyeon

last: lee

state: State...

address: space21, preventive medicine, room 861

country: South Korea

institute: KyungHee University

summary: Our aim is to investigate the transcriptional changes in Kiss1r+/+, Kiss1rflox/+, and Kiss1rflox/flox mice with Kras mutation during early stage of lung tumorigenesis using RNA-seq.

overall_design: Lungs of Kiss1r+/+, Kiss1rflox/+, and Kiss1rflox/flox mice at 5 weeks after induction of KrasG12D using Ad5-CMV-cre were isolated for RNA-seq.

first: SeoYeon

last: Lee

first: Sunggook

last: Cho


title: Cholesterol in macrophage regulate gene expersion with or without LPS [statin and LPS RNA-seq]

first: Jeffrey

summary: cholesterol reduction in macrophages by methyl-b-cyclodextran (MCD) or statin alters gene expression.  When activated by inflammatory stimilus LPS, macrophages responded in a cholesterol specific fashion.

overall_design: RNA-seq was performed on rest RAW macrophages, treated with MCD or statin.  Similar RNA-seq also performed on macropahges stimulated with LPS. Two replicates were performed for untreated control (ctl),; two replicates for MCD and statin treated cells (MCD and Statin), respectively.  Control cells were stimulated with LPS (ctl-LPS), two replicates, and also statin treated cells were stimulated LPS identically (statin-LPS).

first: Kristin

last: Dauner


title: Single nuclei RNA sequencing of PVN tissue across day and night

status: Public on Apr 16 2024

city: Houston

first: Yulin

last: Dai

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

summary: To examine the transcriptional landscape of the paraventricular nucleus of the hypothalmus across 24-hrs day and night we carried out snRANseq on PVN tissue harvested at two antiphase timepoints, ZT8 and ZT20

overall_design: Single nuclei isolation for the single nuclei RNA-seq analysis was performed on five pooled PVN tissues dissected from male C57Bl6 mice aged 10-12 weeks at two time points, ZT8 and ZT20.

first: Rachel

last: Van Drunen

last: Eckel-Mahan


title: Well-ST-seq: cost-effective and cellular level spatial transcriptomics with high RNA capture efficiency

city: Changchun

first: Zhengyang

last: Jin

state: Jilin

address: No. 1163 Xinmin Street

institute: Jilin University

summary: Spatial transcriptomic technologies are promising tools to reveal fine anatomical profiles of tissues. In the case of methodologies utilizing barcoded probe arrays, achieving a balance among probe barcoding complexity, cost, gene capture sensitivity, and spatial resolution is crucial for accelerating the spreading speed of spatial transcriptomic in basic science and clinical work. Here, we developed spatially cellular-level RNA-capture probe arrays using miniaturized microfluidic and microarray technologies. By leveraging the predetermined and cost-effective probe fixation characteristics of this methodology, we significantly reduced the consumable cost of the probe array to $0.31/mm2 and fabrication time to approximately 2 hours. Furthermore, the modification of the RNA-capture probe on sequencing slides by microfluidic chip does not rely on large imaging or printing instruments. Notably, the efficiency of the transcript captured by the probe array is even comparable to conventional single-cell RNA sequencing. Based on this technology, the stacked three-dimensional transcriptome atlas and the spatial cell heterogeneity of mouse brains were successfully visualized. Taken together, we present an experimental and analytical framework for the spatial investigation of mouse brain structures and cell phenotypes.

overall_design:
Applying new approach – Well-ST-seq for spatial transcriptomes sequencing to mouse tissues in different resolution (10 μm, 20 μm and 30μm).

Please note that the following files have been updated on April 27, 2026:
GSM7901412_10-matrix.mtx.gz
GSM7901412_10-spatial.zip
GSM7901413_20-matrix.mtx.gz
GSM7901413_20-spatial.zip

first: Nianzuo

last: Yu

first: Shoujun

last: Zhu

first: Zhiying

last: Hu

first: Xiaoduo

last: Tang

first: Jingwen

last: Fang

first: Chongyang

last: Liang

first: Junhu

last: Zhang

first: Bai

last: Yang


title: Conserved role of hnRNPL in alternative splicing of epigenetic modifiers enables B cell activation

status: Public on Apr 24 2024

city: Montrreal

first: Javier

last: Di Noia

state: Quebec

address: 110 Av des Pins Ouest

country: Canada

institute: Institut de Recherches Cliniques de Montreal

summary: The multifunctional RNA-binding protein hnRNPL has been implicated in antibody class switching but its broader function in B cells is unknown. Here, we show that hnRNPL is essential for B cell activation, and thereby germinal center and antibody responses. Upon activation, hnRNPL-deficient B cells show proliferation defects and increased apoptosis. The comparative analysis of RNA-seq data from B cells and another 8 hnRNPL-depleted cell types reveals a common function in the Myc and E2F transcriptional programs required for proliferation, likely borne out of a large alternative splicing change affecting multiple transcription regulators. Notably, while individual gene expression changes were cell type specific, several alternative splicing events affecting histone modifiers like SIRT1, KDM6A, and NSD2, were conserved across cell types, which could contribute to gene expression changes upon hnRNPL loss. SIRT1 reduction due to alternative splicing, and other transcriptional changes suggested mitochondrial defects in hnRNPL-deficient B cells. We confirmed dysfunctional mitochondria and ROS overproduction, which could explain the B cell activation defect. Thus, hnRNPL is essential for the resting to activated B cell transition by regulating transcriptional programs, most likely by splicing regulation affecting several histone modifiers.

overall_design:
To investigate gene expression and splicing changes upon hnRNPL depletion in activated B cells, CD21-cre mice were crossed with hnRNPL F/F mice.
We then perform paired-end RNA-seq of hnRNPL F/F CD21-cre and CD21-cre (control) splenic B cells, stimulated with LPS+IL4 for 24h.
Differential gene expression for WT vs hnRNPL-deficient activated B cells. Normalized counts, log2 fold changes and DESeq2 padj values are in the supplementary file "norm_counts.txt".

first: Poorani

last: Subramani

first: Jennifer

last: Fraszczak

first: Anne

last: Helness

last: Estall

first: Tarik

last: Möröy


title: Effect of depletion of Setd1a on gene expression in mouse Undifferentiated Pleomorphic Sarcoma (UPS)

first: Jianhong

last: Ou

summary:
To investigate the Setd1a function in the regulation of lung metastasis formation, we established mouse UPS cell lines in which each target gene has been knocked down by shRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse UPS cell and Setd1a KO derivatives

first: Ga

middle: I

last: Ban

first: Yu

last: Xiang

first: Benjamin

last: Alman


title: Foxp striatal compensation (ATAC-Seq)

status: Public on Apr 04 2024

city: Los Angeles

first: Genevieve

last: Konopka

address: 650 Charles Young Drive South, 73-214 CHS

department: Neurobiology

institute: UCLA David Geffen School of Medicine

summary: Spiny projection neurons (SPNs) of the striatum are critical in integrating neurochemical information to coordinate motor and reward-based behavior. Mutations in the regulatory transcription factors expressed in SPNs can result in neurodevelopmental disorders (NDDs). Paralogous transcription factorsFoxp1andFoxp2, which are both expressed in the dopamine receptor 1 (D1) expressing SPNs, are known to have variants implicated in NDDs. Utilizing mice with a D1-SPN specific loss ofFoxp1,Foxp2, or both and a combination of behavior, electrophysiology, and single-nuclei RNA (snRNA-seq) and single-nuclei Assay for Transposase-Accessible Chromatin sequencing (snATAC-seq), we find that loss of both genes results in impaired motor and social behavior as well as increased firing of the D1-SPNs. Differential gene expression analysis of snRNA-seq data implicates genes involved in autism risk, altered electrophysiological properties, and neuronal development and function. These data indicate complementary roles betweenFoxp1andFoxp2in the D1-SPNs.

overall_design: The transcription factors Foxp1 and Foxp2 are both expressed in the D1-SPNs of the striatum. We used single nuclei assay for transposase-accessible chromatin sequencing (snATAC-Seq) in both juvenile (P9) mouse striatum to investigate how loss of one or both of these genes from the D1-SPNs alters chromatin accessibility.

first: Newaz

last: Ahmed

first: Nitin

last: Khandelwal

first: Ashley

last: Anderson

first: Ashwinikumar

last: Kulkarni

first: Karthigayini

last: Sivaprakasam

first: Jay

last: Gibson


title: Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells

status: Public on Mar 27 2024

city: Pittsburgh

first: Jian

last: Ma

address: 5000 Forbes Ave

institute: Carnegie Mellon University

summary: The organization of mammalian genomes within the nucleus features a complex, multiscale three-dimensional (3D) architecture. The functional significance of these 3D genome features, however, remains largely elusive due to limited single-cell technologies that can concurrently profile genome organization and transcriptional activities. Here, we report GAGE-seq, a highly scalable, robust single-cell co-assay that simultaneously measures 3D genome structure and transcriptome within the same cell. Employing GAGE-seq on mouse brain cortex and human bone marrow CD34+ cells, we comprehensively characterized the intricate relationships between 3D genome and gene expression. We found that these multiscale 3D genome features collectively inform cell type-specific gene expressions, hence contributing to defining cell identity at the single-cell level. Integration of GAGE-seq data with spatial transcriptomic data revealed in situ variations of the 3D genome in mouse cortex. Moreover, our observations of lineage commitment in normal human hematopoiesis unveiled notable discordant changes between 3D genome organization and gene expression, underscoring a complex, temporal interplay at the single-cell level that is more nuanced than previously appreciated. Together, GAGE-seq provides a powerful, cost-effective approach for interrogating genome structure and gene expression relationships at the single-cell level across diverse biological contexts.

overall_design: GAGE-seq of cell lines (K562, GM12878, NIH3T3 and MDS-L) and  primary tissues (mouse brain cortex and human bone marrow CD34+ cells)

first: Zhijun

last: Duan

first: Tianming

last: Zhou


title: Gene expression profile at single cell level of FACS-sorted blood NK cells from kidney transplant recipients

status: Public on Mar 22 2024

first: Elodie

last: Bailly

state: PA

address: BST 200 lothrop street

department: Surgery

institute: Starzl Transplant Institute

summary: We explored NK cell differential gene expression profiles in patients with antibody-mediated rejection versus T-cell mediated rejection.

overall_design: From frozen PBMC, circulating NK cells from 8 patients (4 antibody-mediated rejection and 4 T-cell mediated rejection) were FACS-sorted. Samples were at the time of biopsy-proven rejection. Cells were processed for 3 prime V3 single cell RNA sequencing. Cell were hashed to process 4 samples together. Fastq files were demultiplexed by Cell Ranger v6 multi.

first: Tracy

last: Tabib

first: Diana

last: Metes

first: Robert

last: Lafyatis


title: Gene expression profile at single cell level of Wild type and Plagl1 knock out retina at P7

status: Public on Mar 24 2024

city: Toronto

first: yacine

last: touahri

address: 2075 Bayview Ave

institute: Sunnybrook Research Institute

summary: Plagl1 controls Muller glial cells proliferation in the retina.  We used single cell RNA sequencing (scRNA-seq) to analyze the prolirative state of Muller glial cells and identify the signals that might be involved in this process

overall_design: Retinal cells were isolated from P7 wild type and Plagl1 KO retinas at P7. Dead cells removed by magnetic cell sorting and cells were analyzed using csRNAseq

first: Yacine

last: Touahri

first: Chao

last: Wang

first: Carol

last: Schuurmans


title: Foxp striatal compensation (RNA-Seq)

first: Genevieve

last: Konopka

overall_design: The transcription factors Foxp1 and Foxp2 are both expressed in the D1-SPNs of the striatum. We used single nuclei RNA sequencing (snRNA-Seq) in both juvenile (P9) and adult (P56) mouse striatum to test the effects of loss of one or both of these genes from the D1-SPNs.

first: Newaz

last: Ahmed


title: On the way to elucidate the effects of cannabidiol (CBD) on living organisms - assessment of changes in the global transcription profile of liver in mouse model

status: Public on Mar 16 2024

city: Kraków

first: Artur

last: Gurgul

address: Rędzina 1C

department: Center for Experimental and Innovative Medicine

country: Poland

institute: University of Agriculture in Krakow

summary:
Cannabidiol (CBD) is a phytocannabinoid that has anti-inflammatory, immunomodulatory, antioxidant, anxiolytic, antipsychotic, and anticonvulsant effects. The metabolism of CBD occurs in the liver within a few hours after the dose is administered. This study aims to examine the effects of CBD on behavior, immune system activity, and stress levels, and to determine its impact on transcriptomic alterations in selected murine organs.

(Study funded by the National Science Centre, Poland; project no. 2020/39/O/NZ9/00821)

overall_design:
Male mice of the standard C57BL/6J strain were used. The animals were classified into two groups - (I) short-term CBD administration (2 days) and (II) long-term CBD administration (28 days). In each of the main groups, there were three subgroups receiving different doses of CBD - from low, commonly used in supplementation (0.2 mg/kg bw), through medium (10 mg/kg bw), to high, used in some clinical trials (20 mg/kg bw). Additionally, a control group (placebo/vehicle) was maintained in each of the main groups. Chemically pure Cannabidiol (CBD) was administered intraperitoneally (in the research group) to ensure that the substances reached the blood vessels of the digestive system. CBD was administered in a single daily dose. The mice were housed under standard conditions and with standard feeding and watering ad libitum. They were also tested daily (group I) or every third day (group II) to determine well-being and health. After the period of CBD administration, the mice were immediately euthanized and organs such as the brain, spleen and liver were collected. In this part of the experiment, liver samples were used to isolate total RNA. The recovered RNA was quality assessed and used to prepare directional libraries for high throughput transcriptome sequencing using CORALL mRNA-Seq V2 kit (Lexogen).  The libraries were sequenced commercially in a 2x150bp paired-end run. The obtained sequence data were used to analyze the differential expression between the different CBD dosages and the control group. Differentially expressed genes were classified into particular processes or functions and were subjected to statistical testing for overrepresentation. The synthesis of the obtained data will allow to propose potential mechanisms of CBD action and create an atlas of changes taking place in the transcriptome of the main target organs.

UPDATE: [11-04-2024] The Sample titles and treatments were corrected. The raw data and processed data associated with each GSMxxx accession number have not changed.

first: Jakub

last: Żurowski

first: Sebastian

last: Sawicki

first: Ewa

last: Ocłoń

first: Tomasz

last: Szmatoła

first: Igor

last: Jasielczuk

first: Karolina

last: Mizera-Szpilka


title: Epithelial relay of microbial signals coordinates intestinal macrophage supported barrier repair [E. coli strains]

status: Public on Mar 12 2024

city: New York

first: Ming-Ting

middle: Kessler

last: Tsai

state: NY

address: 408 E 69th Street Z1619

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

summary: The gastrointestinal tract is colonized by trillions of microorganisms collectively known as the gut microbiota. These microbes provide essential signals to support healthy gut function. The microbiota is separated from internal tissue by a single layer of intestinal epithelial cells that not only provides a physical barrier but also relays luminal signals to underlying gut immune cells. Altered microbiota composition including loss of anti-inflammatory microbes or outgrowth of mucosa-associated bacteria such as adherent-invasive E. coli (AIEC) are hallmarks of inflammatory disease including inflammatory bowel disease (IBD). In contrast to their hypothesized role in pathology, we recently identified select AIEC isolates that improve outcomes in mouse colitis models. These AIEC induce macrophage production of the anti-inflammatory cytokine IL-10 which limits gut inflammation and supports barrier repair. These benefits were lost if the AIEC was unable to attach to epithelial cells. However, the epithelial signaling underlying this protection remained unclear. To understand if intestinal epithelial cells signaled to immune cells after microbial attachment, we utilized human colonic organoid monolayers and found co-culture with a subset of AIEC isolates upregulated immune regulatory genes including CCL2, a macrophage recruiting chemokine. This effect was only observed in undifferenced epithelial cells, indicating epithelial stem cell recognition of microbes leads to macrophage recruitment. In vivo, antibody blockade of CCR2 abrogated the protective effect of AIEC colonization. Using bacterial transcriptome analysis, we identified high flagellin expression in AIEC isolates that activated epithelial signaling, with lost signaling in organoids deficient for TLR5, the receptor for flagellin. Together our findings suggest intestinal epithelial cells recognize microbial signals to coordinate macrophage recruitment that support intestinal repair, protecting from colitis.

overall_design: We screened a panel of E. coli strains, which were isolated from mucosal biopsy as part of the human microbiome projec, using Caco2 cells to indentify strains that induces epithelial responses. Of the strains tested, about half induced upregulation of the epithelial immune response genes as 541-15. We grouped them as "activators" while we classified the rest as "non-activators". To identify the signature genes that specifically expressed by the activators or non-activators, we performed bacterial transctiptome profiling.

first: Tsai

last: Ming-Ting

first: Diehl

last: Gretchen


title: Foxp striatal compensation

status: Public on Apr 03 2024

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

overall_design: Refer to individual Series


title: Reduced heart failure effects through novel integrin targeting approach

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

summary: Heart failure remains one of the largest clinical burdens globally, with little to no improvement in the development of disease-eradicating therapeutics. Integrin targeting has been used in the treatment of ocular disease and cancer, but little is known about its utility in the treatment of heart failure. Here we sought to determine whether the second generation orally available, αvβ3-specific RGD-mimetic, 29P, was cardioprotective. Male mice were subjected to transverse aortic constriction (TAC) and treated with 50μg/kg 29P or volume-matched saline as Vehicle control. At 3 weeks post-TAC, echocardiography showed that 29P treatment significantly restored cardiac function and structure indicating the protective effect of 29P treatment in this model of heart failure. Importantly, 29P treatment improved cardiac function giving improved fractional shortening, ejection fraction, heart weight and lung weight to tibia length fractions, together with partial restoration of Ace and Mme levels, as markers of the TAC insult. At a tissue level, 29P reduced cardiomyocyte hypertrophy and interstitial fibrosis, both of which are major clinical features of heart failure.  RNA sequencing identified that, mechanistically, this occurred with concomitant alterations to genes involved molecular pathways associated with these processes such as metabolism, hypertrophy and basement membrane formation. Overall, targeting αvβ3 with 29P provides a novel strategy to attenuate pressure-overload induced cardiac hypertrophy and fibrosis, providing a possible new approach to heart failure treatment.

overall_design: Left ventricle apex tissue from male C57Bl6/J mice following 3 weeks transverse aortic constriction treated with 50μg/kg of the RGD mimetic 29P or volume-matched saline as Vehicle control.

first: Alex

last: Njegic

first: Lina

last: Laid

first: Min

last: Zi

first: Laura

last: Wisniewski

first: Jenna

last: Hunter

first: Sukhpal

last: Prehar

first: Nicholas

last: Stafford

first: Chaim

last: Gilon

first: Amnon

last: Hoffman

first: Michael

last: Weinmüller

first: Horst

last: Kessler

first: Elizabeth

last: Cartwright

first: Jun

first: Kairbaan

last: Hodivala-Dilke


title: An integrated toolkit for human microglia functional genomics

status: Public on Apr 17 2024

first: Falak

last: Sher

address: 630 W 168th street

institute: Columbia University

summary:
Microglia, the brain’s resident immune cells, play vital roles in brain development, and disorders like Alzheimer’s disease (AD). Human iPSC-derived microglia (iMG) provide a promising model to study these processes. However, existing iMG generation protocols face challenges, such as prolonged differentiation time, lack of detailed characterization, and limited gene function investigation via CRISPR-Cas9.
In this study will generated iMG from human iPSCs using our newly developed protocol. We used single cell RNA-Seq to study the transcriptomic profiles of our newly formed iMG. The single cell RNA-Seq data under this accession is from wild type iMG (Hashtag 7) and SORL1 KO iMG (Hashtag 8)

overall_design: iPSC-derived microglia (iMG) were harvested from in vitro cultures, washed with PBS and hashtaged  with hash tagging antibodies as: WT: Hashtag 7, SORL1 KO Hashtag 8. scRNA-Seq was performed using 10X Genomics Chromium Next GEM single-cell 3' Reagent kit v3.1 leveraging its Feature Barcode technology.

first: Imdadul

last: Haq

first: Jason

middle: C

last: Ngo

first: Vilas

last: Menon


title: Cholesterol in macrophage regulate gene expersion with or without LPS [MCD and LPS RNA-seq]

first: Jeffrey

last: Dilworth

address: 1111 Highland Ave - WIMR II 4518

institute: University of Wisconsin - Madison

first: Kristin

last: Dauner

first: Xiaohui

last: Zha


title: Epithelial relay of microbial signals coordinates intestinal macrophage supported barrier repair

status: Public on Mar 11 2024

first: Ming-Ting

last: Tsai

overall_design: To understand epithelial responses to adherent microbes, we utilized human colonoid-derived monolayers as a model to study epithelial responses to different E. coli strains. Three human colonoid lines were used in this study: ASC103, MSK161N and MSK162N. Human colonoid monolayers cultured in transwell inserts were either maintained as undifferentiated (UD) monolayers or differentiated for 5 days as differentiated (DF) monolayers. Both UD and DF monolayers were left untreated (NT) or colonized with AIEC 541-15 or non-AIEC T75. Cells were harvested at 4 hours post colonization using Qiagen RNeasy kits. Each treatment (NT, T75, 541-15) were technically duplicated or triplicated.

first: Tsai

last: Ming-Ting

first: Diehl

middle: E

last: Gretchen


title: Mapping the tumor microenvironment response to bone mineral content

status: Public on Mar 04 2024

city: Ithaca

first: Iwijn

last: De Vlaminck

address: 237 Tower Rd

department: Meinig School of Biomedical Engineering

institute: Cornell University

summary: Decreased mineral density is a risk factor for skeletal pathologies including bone metastasis, the leading cause of mortality in patients with advanced breast cancer, but the underlying mechanisms are poorly understood. While reduced mineral density can drive pathological bone remodeling via direct effects on select cell types, indirect effects due to broad changes of the microenvironment may be similarly important. However, how bone mineral content affects microenvironmental heterogeneity remains to be elucidated. Here, we leverage decellularized bone matrices with varied mineral content in combination with single-cell RNA-sequencing to study how reduced bone mineral content affects microenvironmental complexity and tumor growth. We performed single-cell RNA sequencing on implanted decellularized bovine bone scaffolds in which the mineral was either maintained at physiological levels or removed to simulate scenarios of impaired bone mineralization as, for example, present during aging. Using this approach, we explored the heterogeneous stromal response to varied bone mineral content in both an immunocompromised and immunocompetent, syngeneic mouse model in the presence and absence of cancer cells.

overall_design: Single-cell RNA sequencing of metastatic breast cancer cell microenvironment on decellularized bovine bone scaffolds with varied mineral levels in immunocompromised and immunocompetent mouse models

first: Matthew

last: Whitman

first: Madhav

last: Mantri

first: Emmanuel

last: Spanos

first: Claudia

last: Fischbach


title: PABPC1L promotes tryptophan metabolism and immune suppression by stabilizing IDO1 in renal cell carcinoma [RIP-seq]

status: Public on Feb 14 2024

first: Jiaxing

last: Zhang

state: China

address: 58 Zhongshan 2nd Road

institute: First Affiliated Hospital of Sun Yat-sen University

summary: The tumor microenvironment (TME) in renal cell carcinomas (RCC) is marked by substantial immunosuppression and immune resistance though highly infiltrated by T cells. There is an urgent need to elucidate tumor immune evasion and to develop novel therapeutic target to boost the efficacy of immune checkpoint blockade (ICB) in RCC. Our study uncovers a mechanism wherein the polyadenylate-binding protein PABPC1L modulates indoleamine2, 3dioxygenase1 (IDO1), a prospective candidate for immunotherapy. PABPC1L, markedly upregulated in RCC, correlates with unfavorable prognosis and resistance to ICB. Overexpressed PABPC1L bolsters tryptophan metabolism and induces T-cell dysfunction by stabilizing IDO1. Conversely, silencing PABPC1L diminishes IDO1 expression, mitigates cytotoxic T-cell suppression, and enhances responsiveness to anti-PD-1 therapy. Our findings underscore PABPC1L's crucial role in facilitating immune evasion in RCC, making it a potential addition to ICB therapy.

overall_design: RIP-sequencing of total RNA of 769-P cells which was immunoprecipited by anti-PABPC1L RIP-INPUT vs RIP-PABPC1L

first: Junhang

last: Luo

first: Yihui

last: Pan

first: Guocang

last: Liu


title: Foxp1 regulates the development of glutamatergic synaptic input onto spiny projection neurons expressing Drd2 [snRNA-seq]

status: Public on Feb 20 2024

first: Genevieve

last: Konopka

summary: Long-range glutamatergic inputs from the cortex and thalamus provide important motor and cognitive information to the striatum where they are integrated for learning and action planning. Genetic programs and transcription factors that orchestrate the development of these inputs are relatively unknown. The transcription factor, FOXP1, is crucial for the development of spiny projection neurons (SPNs) in the striatum. We investigated the cell-specific role of Foxp1 in the formation of glutamatergic inputs – including corticostriatal inputs. Embryonic Foxp1 deletion in dopamine receptor 2-expressing SPNs (D2 Foxp1cKO) leads to reduced transmission of corticostriatal excitatory inputs and decreased synaptically driven excitability. Postnatal deletion of Foxp1 also resulted in decreased glutamatergic inputs onto D2 SPNs. Single nuclei RNA sequencing of D2 Foxp1cKO striatum identified downregulated postsynaptic genes, consistent with the synaptic phenotype. Reinstating Foxp1 postnatally rescued electrophysiological deficits and expression of a subset of genes that were altered by embryonic deletion in D2 SPNs. Postnatal Foxp1 reinstatement could also rescue behavioral phenotypes. In summary, we demonstrate that FOXP1 regulates the development of corticostriatal circuitry. Further, changes at multiple levels of brain function resulting from loss of Foxp1 are rescued with postnatal Foxp1 reinstatement, indicating a therapeutic approach for individuals with FOXP1 syndrome.

overall_design: We used single nuclei RNA sequencing (snRNA-Seq) in juvenile (P18) mouse striatum to test the effects of loss of Foxp1 in D2 SPNs and study gene expression changes with postnatal reinstatment of Foxp1 in striatum.

first: Nitin

last: Khandelwal

first: Ashwinikumar

last: Kulkarni

first: Newaz

last: Ahmed

last: Harper

first: Jay

last: Gibson


title: Sequential transcriptional waves and NFκB-driven chromatin remodeling direct drug-induced dedifferentiation in cancer

status: Public on Feb 13 2024

city: Seattle

first: Wei

last: Wei

address: 401 Terry Ave N

institute: INSTITUTE FOR SYSTEMS BIOLOGY


title: Ex vivo cultured mouse LT-HSCs RNA-seq

status: Public on Mar 10 2024

city: Hangzhou

first: lu

last: huan

address: 866 Yuhangtang Road

institute: Zhejiang University medical center

summary: Mouse LT-HSCs were co-cultured with polymer nanospheres for ex vivo expansion

overall_design: Mouse total bone marrow cells were isolated and  co-cultured with different polymer nanospheres for 3 days, LT-HSCs were sorted by FACS to perform bulk RNA-seq

first: Qiwei

last: Wang

first: Huan

last: Lu

first: Pengxu

last: Qian


title: The complex role of Naked cuticle in Drosophila wing development

status: Public on Jan 31 2024

city: Nanjing

first: Rui

state: Jiangsu

address: 2 Sipailou Road

department: School of Life Science and Technology

institute: Southeast University

summary: It is of tremendous interests to understand how Wnt signaling is regulated in a precise manner both temporally and spatially. Naked cuticle (Nkd) acts as a negative-feedback inhibitor for Wingless (Wg, a fly Wnt) signaling in Drosophila embryonic development. In the present study, we show that nkd is essential for wing pattern formation, such that both gain and loss of nkd result in the disruption of Wg target expression in larvae stage and abnormal adult wing morphologies. Our results of high-throughput sequencing suggest that nkd have profound effects on Drosophila wing development with several critical signaling pathways involved, we conclude that Nkd inhibits the canonical Wg pathway during Drosophila wing development beyond embryonic stage and may play a mediated role in cross-talk between development-related pathways.

overall_design: mRNA profiles of third instar larval wing discs expressing GFP or Nkd recombinant proteins under the control of MS1096-Gal4.

first: Hao

last: Xie

first: Lin

last: Yang

first: Ping


title: Il-17 p53 Developmental Series

status: Public on Jan 30 2024

city: Buffalo

first: Johnny

last: Cruz Corchado

address: Elm & Carlton Streets Buffalo,L3-L125

department: Cell Stress

institute: Roswell Park Comprehensive Cancer Institue

summary: Here, we show that the activity of the tumor suppressor p53 in the metazoan C. elegans switches organismal development between reproductive growth and dormancy by responding to nutrient availability signaled by the cytokine, ILC-17.1. ILC-17.1-dependent repression of the C. elegans p53 ortholog CEP-1 is required for larval growth and development; ILC-17.1 deficiency activates CEP-1/p53 in post-embryonically dividing progenitor blast cells, decreases glucose utilization and cytochrome C levels, upregulates cell cycle inhibitors, and causes larvae to arrest as stress-resistant, quiescent dauers.

overall_design: Comparative gene expression profiling analysis of RNA-seq data at two different developmental time points(15 hrs and 32 hrs) of C. elegans larvae in  the following gennotypes wild type (N2), ilc-17.1(syb5296) X,unc-119 (ed4); gtIs1 [CEP-1::GFP + unc-119 (+)],ilc-17.1 (syb5296)X; cep-1 (gk138) I

last: Cruz

first: Abhishiktha

last: Godthi

first: Venna

last: Prahlad


title: Neuronal IL-17 controls C. elegans developmental diapause through p53/CEP-1

summary: Metazoan growth and development requires the coordination of cell cycle progression and metabolism with nutrient availability1-3. Here, we show that in C. elegans, amphid neurons regulate the animals’ developmental decision to continue reproductive growth or arrest as quiescent dauer larvae in response to food, by controlling the activity of C. elegans p53-like ortholog, CEP-1. Specifically, upon food availability, larval neurons secrete a mammalian IL-17 ortholog, ILC-17.1, and ILC-17.1 signaling is needed for C. elegans to progress through development into reproductive adults. ILC-17.1 deficiency activates CEP-1/p53 in larval blast cells, and causes larvae to arrest as stress-resistant, quiescent dauers by activating DAF-16/FOXO, decreasing cytochrome C levels, decreasing glucose utilization and upregulating cell cycle inhibitors. Increasing ILC-17.1 levels represses CEP-1/p53 and promotes anabolic growth, but also inhibits apoptosis upon genotoxic stress. IL-17 also represses p53 in human epithelial cells. These studies describe a role for the tumor suppressor p53-like proteins in controlling developmental quiescence of a metazoan in response to neuronal activity and immunometabolic signals and are relevant to our understanding of neuroimmune mechanisms in cancer. This novel role for p53-like proteins in C. elegans supports the argument that their developmental function was a main driving force in their evolution4,5.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  C. elegans larvae of the following gennotypes wild type (N2), ilc-17.1(syb5296) X and praEx022 (unc-54p::ilc-17.1 cDNA::3XFLAG::tbb-2 3’UTR; pdat-1::GFP::unc-54 3’UTR).

first: Srijit

last: Das


title: RNA sequencing of BM myeloid cells treated with AAV-IL-27/ctrl in vivo

status: Public on Mar 09 2024

first: Jianmin

last: Zhu

state: Shanghai

address: Dongfang road 1678

institute: Shanghai Children's Medical Center

summary: Interleukin-27 (IL-27) is a pleiotropic cytokine that exhibits stimulatory/regulatory functions on multiple lineages of immune cells and has a potential to be used as a therapeutic for cancer. We have recently demonstrated that systemic delivery of IL-27 using adeno-associated virus (AAV-IL-27) exhibits potent inhibition of tumor growth in mouse models. In this work, we demonstrate that AAV-IL-27 treatment leads to significant expansion of CD11b+Gr1+ myeloid cells (MCs). AAV-IL-27-induced expansion of CD11b+Gr1+ cells is IL-27R-dependent, requires Stat3 signaling but is inhibited by Stat1 signaling. AAV-IL-27 treatment does not increase the self-renewal capacity of CD11b+Gr1+ cells but induces significant expansion of hematopoietic stem cells (HSCs) and granulocyte-monocyte progenitor (GMP) cells. IL-27-induced Ly6G+ MCs upregulate MHC class I/II molecules but are less immune suppressive in vitro, and their expansion does not promote, but rather inhibit tumor growth in vivo. In the tumor microenvironment, IL-27 gene therapy appears to promote Ly6G+ MCs to differentiate into MHC class I/IIhigh and F4/80high macrophages. Thus, IL-27 gene therapy induces expansion of CD11b+Gr1+ myeloid cells and promotes their differentiation into anti-tumor M1 macrophages in tumor microenvironment.Bone marrow myeloid cells of tumor-bearing C57BL/6 mice treated with AAV-IL-27/ctrl for 2 weeks were sepreated by MACS. Transcriptome profiling (RNA-seq) of these purified Ly6G+ cells (>95%) was completed by BGI. Changing in gene express profiling resulted by IL-27 was analyzed in this study.

overall_design: C57BL/6 mice were subcutaneously injected with B16.F10 1 week before AAV-ctrl/IL27 were intramuscularly injected. Ly6G+ myeloid cells were derived from 4 mice. 2 mice treated with AAV-ctrl and 1 mouse treated with AAV-IL-27.

first: Xue-Feng

last: Bai


title: ANXA1 promotes cell proliferation and drug-resistance in B cell acute lymphoblastic leukemia

status: Public on Feb 01 2024

city: Guiyang

first: Yunsheng

last: Ran

state: Guizhou

address: No. 9 Beijing Road, Guiyang City, Guizhou Province

department: Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D

institute: Guizhou Medical University

summary:
ANXA1 promoted cell proliferation, suppressed cell apoptosis induced cell cycle arrest in B-ALL cells by CCK8, Flow cytometry and RNA-seq Sequencing analysis. The in vivo results indicated that down-regulation of ANXA1 in B-ALL cells could significantly reduce leukemic cell burden.
We then performed gene expression profiling using data obtained from RNA-seq of B-ALL cells with the ANXA1 gene down-regulated in CCRF-SB.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CCRF-SB cells with its down-regulated ANXA1.

last: Liu

first: Dan

last: Ma


title: Glioma-Induced Alterations in Excitatory Neurons are reversed by mTOR Inhibition

first: Athanassios

last: Dovas

address: 1130St Nicholas Avenue

summary: Gliomas are highly aggressive brain tumors characterized by poor prognosis and composed of diffusely infiltrating tumor cells that intermingle with non-neoplastic cells in the tumor microenvironment, including neurons. Neurons are increasingly appreciated as important reactive components of the glioma microenvironment, due to their role in causing hallmark glioma symptoms, cognitive deficits, and seizures, as well as potentially driving glioma progression. Separately, mTOR signaling has been shown to have pleiotropic effects in the brain tumor microenvironment, including regulation of neuronal hyperexcitability. However, the local cellular level effects of mTOR inhibition on glioma-induced neuronal alterations are not well understood. Here we employed neuron-specific profiling of ribosome-bound mRNA via ‘Ribotag’, morphometric analysis, and intravital imaging, along with pharmacological mTOR inhibition to investigate the impact of glioma burden on excitatory neuronal pathophysiology as well as the impact of mTOR inhibition on these neuronal alterations. The Ribotag analysis of peritumoral excitatory neurons showed an upregulation in transcripts encoding for F-actin binding and other dendritic spine-enriched proteins. Light and electron microscopy analyses revealed marked decreases in dendritic spine density in peritumoral neurons. Intravital two-photon imaging in peritumoral excitatory neurons revealed progressive alterations in neuronal activity, both at the population and single neuron level, throughout tumor growth. Intravital two-photon imaging also revealed altered stimulus-evoked somatic calcium activity, both in rate and temporal alignment, which was most pronounced in neurons with high-tumor burden. A single acute dose of AZD8055, a mTORC1 and mTORC2 inhibitor reversed the translational effect of glioma on neurons, increased dendritic spine density, and functional neuronal alterations. These results point to mTOR-driven pathological plasticity in neurons at the infiltrative margin of glioma – manifested by alterations in ribosome-bound mRNA, dendritic spine morphology, and stimulus-evoked neuronal activity. Collectively, our work identifies the pathological changes that peritumoral neurons experience as both hyperlocal and reversible under the influence of mTOR inhibition, providing foundational knowledge for developing therapies targeting neuronal signaling in glioma.

overall_design:
In order to study the translational alterations in the neurons of glioma-bearing mice, we implanted glioma cells in the cortex of Camk2a-Cre-Rpl22HA mice.
We isolated total and immunoprecipitated (IP) polysomal RNA from three groups of mice: control (no tumor), tumor and tumor treated with the mTOR inhibitor AZD8055
We determined neuronally enriched genes in the tumor condition by perfoming DESeq2 between tumor input and IP fractions, then proceeded to compare the three conditions.

first: Daniela

last: Torres

first: Sohani

middle: D

last: Sharma

first: Peter

last: Canoll

last: Sims


title: Therapeutic application of human type 2 innate lymphoid cells via induction of granzyme B-mediated tumor cell death

status: Public on Jan 01 2024

city: Duarte

first: Zhenlong

last: Li

address: 1500 East Duarte Road

institute: City of hope

summary: The therapeutic potential for human type 2 innate lymphoid cells (ILC2s) has been underexplored.  While not observed in mouse ILC2s, we have found that human ILC2s secrete granzyme B (GZMB) and directly lyse tumor cells by inducing pyroptosis and/or apoptosis, which is governed by a DNAM-1-CD112/CD155 interaction that inactivates FOXO1. Over time, the high surface density expression of CD155 in AML impairs expression of DNAM-1 and GZMB, thus allowing for immune evasion. We describe a reliable platform capable of up to 2,000-fold expansion of human ILC2s within 4 weeks, whose molecular and cellular ILC2 profile has been validated by single-cell RNA sequencing. In both AML and solid tumor models, exogenously administered expanded human ILC2s show significant antitumor effects in vivo. Collectively, we demonstrate previously unreported properties of human ILC2s and identify this innate immune cell subset as a new member of the cytolytic immune effector cell family.

overall_design: Identification of the phenotypes of expanded ILC2s and freshly isolated ILC2s from PBMCs

first: Jianhua

last: Yu


title: Neoadjuvant immune checkpoint blockade in retroperitoneal dedifferentiated liposarcoma and extremity/trunk undifferentiated pleomorphic sarcoma (NCT03307616)

first: Jennifer

last: Wang

state: TX

address: 1515 Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

summary: Recent evidence suggests that immune checkpoint blockade (ICB) has some activity in metastatic dedifferentiated liposarcoma (DDLPS) and undifferentiated pleomorphic sarcoma (UPS). We conducted a randomized, non-comparative phase 2 trial (NCT03307616) of nivolumab or nivolumab/ipilimumab in patients with resectable retroperitoneal DDLPS (n=17) and extremity/truncal UPS (n=10), with UPS patients receiving concurrent radiation therapy. The primary endpoint of pathologic response as assessed by percent hyalinization was observed to be a median of 8.8% in DDLPS patients and 89% in UPS patients and similar in nivolumab and ipilimumab/nivolumab arms in both cohorts . Higher intratumoral densities of T-regulatory cells were associated with absence of pathologic response (hyalinization<30%). Tumor infiltration by B-cells was associated with higher densities of T-regulatory cells before treatment;  this association was lost upon ICB treatment. Our data demonstrate that neoadjuvant ICB with concurrent radiation may have significant efficacy in UPS and is associated complex immune changes in the tumor microenvironment in DDLPS and UPS.

overall_design: Tumor samples were collected at baseline, on treatment and at surgery for all patients, and analyzed using bulk RNA sequencing.

first: Christina

last: Roland

first: Chia

last: Wu

first: Elise

middle: F

last: Nassif

first: Emily

middle: Z

last: Keung


title: Unveiling the Role of EGFL7 in Cervical Cancer: Polymorphisms, Expression, and Biological Function

status: Public on Dec 31 2023

city: Kunming

first: Weipeng

state: Yunnan

address: Jiao ling road

department: Institute of Medical Biology

institute: Chinese Academy of Medical Sciences

summary: Prior investigations have delineated the multifarious roles of EGFL7 within various cancer contexts. Nevertheless, the precise involvement of EGFL7 in the realm of human cervical carcinoma remains unclear. In this study, we investigated the relationship between EGFL7 polymorphisms and cervical cancer susceptibility in the Han Chinese population. Concurrently, we have scrutinized the expression patterns of EGFL7 in both the neoplastic cervical tissues and the cell lines HeLa and C33A. Furthermore, we explored the potential biological functions that EGFL7 may assume in the tumorigenesis of cervical cancer. Our findings manifest that the single nucleotide polymorphism rs9411260, ensconced within the transcriptional regulatory domain of EGFL7, is associated with cervical cancer risk in a Han Chinese population. Additionally, the mRNA expression of EGFL7 within cervical carcinoma tissues and the HeLa and C33A cell lines exhibits a marked reduction when compared with their adjacent normal counterparts and ECT1/E6E7 cells. Manipulation of EGFL7 expression precipitates alterations in the adhesion and migratory ability of cervical cancer cells. This investigation endows us with novel insights into the pathogenesis of cervical cancer.

overall_design: Total RNA was extracted from 6 samples, including three negative control samples and three samples with EGFL7 overexpression. We then performed gene expression profiling analysis using data obtained from RNAseg of these samples.

first: Zhixin

last: Niu

first: Li

last: Shi

first: Yufeng

last: Yao


title: Meta-analysis of Genome-wide Associations and Polygenic Risk Prediction for Atrial Fibrillation in More Than 180,000 Cases

status: Public on Feb 08 2024

city: Cambridge

first: Matthew

last: Hill

state: MA

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

summary: Atrial fibrillation (AF) is the most common abnormality of heart rhythm and is a leading cause of heart failure and stroke. This large-scale meta-analysis of genome-wide association studies (GWAS) increased the power to detect single-nucleotide variant (SNV) associations, and we report more than 350 AF-associated genetic loci. At 139 loci we identified candidate genes related to muscle contractility, cardiac muscle development and cell-cell communication. We next assayed chromatin accessibility by ATAC-seq and histone H3 Lysine 4 trimethylation in stem cell derived atrial cardiomyocytes. We observed a marked increase in chromatin accessibility of our sentinel variants and prioritized genes in atrial cardiomyocytes. Finally, we found that a polygenic risk score (PRS) based on our updated effect estimates improved AF risk prediction compared to the CHARGE-AF clinical risk score and a previously reported PRS for AF. The doubling of known AF risk loci will facilitate a greater understanding of the pathways underlying this heart rhythm disorder.

overall_design: Human pluripotent stem (hPSCs) cells were differentiated to atrial-like cardiomyocytes and subjected to ATAC-seq and H3K4me3 CUT&RUN.

first: Carolina

last: Roselli

first: Patrick

middle: T

last: Ellinor


title: scRNA-seq of tailbud development in zebrafish

city: Irvine

first: Thomas

last: Schilling

address: 4462 Natural Sciences II

department: Developmental and Cell Biology

institute: University of California Irvine

summary: We have performed single-cell RNA-seq of whole tailbuds in WT zebrafish at 16 hours post fertilization (hpf).

overall_design: Single cells were captured via 10X Chromium platform at 16 hpf from whole tailbuds.

first: David

last: Tatarakis

first: Julia

last: Horsfield

first: Benjamin

last: Martin


title: Simultaneous single-cell three-dimensional genome and gene expression profiling Uncovers Dynamic Enhancer Connectivity Underlying Olfactory Receptor Choice [cell line, single-cell RNA-Seq & Hi-C]

status: Public on Jan 15 2024

city: Beijing

first: Xiaoliang

middle: Sunney

last: Xie

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

summary: The simultaneous measurement of three-dimensional (3D) genome structure and gene expression of individual cells is critical for understanding our genome’s structure–function relation, yet is extremely challenging for existing methods. Here we present Linking mRNA to Chromatin Architecture (LiMCA), which jointly profiles 3D genome and transcriptome with exceptional sensitivity and from low-input materials. Combining LiMCA and our high-resolution scATAC-seq assay, METATAC, we profiled the developing mouse olfactory epithelium and reported the first chromatin accessibility profiles and the first paired 3D genome structures and gene expression information of single neurons. We greatly expanded the repertoire of known OR enhancers, and discovered unexpected rules of their dynamics: ORs and their enhancers are most accessible during early differentiation, and the active OR typically does not associate with the largest enhancer hub. These findings offer valuable insights into how 3D connectivity of ORs and enhancers dynamically orchestrate the “one neuron–one receptor” selection process.

overall_design: 10X Genomics scRNA-seq and METATAC scATAC-seq for mouse olfactory epithelium

first: Honggui

first: Jiankun

last: Zhang

first: Fanchong

last: Jian


title: Simultaneous single-cell three-dimensional genome and gene expression profiling Uncovers Dynamic Enhancer Connectivity Underlying Olfactory Receptor Choice [olfactory, single-cell RNA & Hi-C]

overall_design:
simultaneous 3D genome and gene expression within the same single cell by LiMCA
Each cell was named according to the developmental stage/age and mouse strain information. For example, "p007" indicates that the developmental stage/age of the mouse from which this neuron was derived is postnatal day 7. "bc" and "bdf1" indicate the mouse strain. We labeled F1 hybrids of C57BL/6J (female) and DBA/2J (male) as bdf1 and F1 hybrids of C57BL/6J (female) and CAST/EiJ (male) as bc.


title: Neonatal microbes shape islet-immune interactions that determine life-long host metabolic capacity [scRNA-seq and bulk RNA-seq].

city: Salt Lake City

first: W. Zac

last: Stephens

state: UT

address: 15 N. Medical Drive, EEJMRB 4208, EEJMRB 4208

department: Pathology

institute: University of Utah

summary: The composition of the resident microbiota changes and diversifies as its host develops. Enrichment of specific taxa early in life is important for immune system development and maturation, but the impact of early life commensals on other host developmental processes is little studied. Here, we describe a critical window of postnatal life when specific microbes are necessary to establish an adequate supply of insulin-producing tissue for lifelong metabolic homeostasis of the host.

overall_design:
The main goal is to determine the effect of microbiota presence on developing neonatal pancreatic islets.
Samples are pancreatic islets purified away from acinar tissue by several rounds of hand picking.

scRNA-seq:
Each sample is representative of pooled islets from 20 animals at 15 days old (P15), either Germ-free (GF) or specific pathogen free (SPF).

bulk RNA-seq:
Islets from Germ-free (GF) and specific pathogen free (SPF) mice 10 days old (P10) or 20 days old (P20) are included.
Additionally, a subset of samples from P20 SPF mice were treated with Clodronate to diminish macrophages in order to investigate the effect of macrophages on neonatal islets.
Pacncreatic islets from male and female mice for each group are included.

first: Hill

last: Jennifer

first: Round

last: Lune

first: Stephens

last: W Zac


title: Identification of GLIS3 and HNF1b target genes in kidney

city: Research Triangle Park

first: Hong Soon

last: Kang

state: NC

address: 111 T.W. Alexander Dr.

department: IIDL

institute: NIH/NIEHS

summary: Comparison of cistromes from GLIS3 and HNF1b ChIP-Seq analysis using mouse kidney was performed to examine whether there was a significant overlap in target genes between GLIS3 and HNF1b.

overall_design: GLIS3 ChIP-Seq was performed with kidneys from Glis3-eGFP mice using GFP antibody, and HNF1b ChIP-Seq was performed with WT kidneys using HNF1b antibody (Invitrogen #720259).

first: Anton

last: Jetten

first: Hong

middle: S

first: Justin

last: Collier

first: Yun-Gil

last: Roh

first: Sara

last: Grimm


title: PABPC1L promotes tryptophan metabolism and immune suppression by stabilizing IDO1 in renal cell carcinoma

city: Guangzhou

first: Jiaxing

summary: The tumor microenvironment (TME) in renal cell carcinomas (RCC) is marked by substantial immunosuppression and immune resistance though highly infiltrated by T cells. There is an urgent need to elucidate tumor immune evasion and to develop novel therapeutic target to boost the efficacy of immune checkpoint blockade (ICB) in RCC. Our study uncovers a mechanism wherein the polyadenylate-binding protein PABPC1L modulates indoleamine2, 3dioxygenase1 (IDO1), a prospective candidate for immunotherapy. PABPC1L, markedly upregulated in RCC, correlates with unfavorable prognosis and resistance to ICB. Overexpressed PABPC1L bolsters tryptophan metabolism and induces T-cell dysfunction by stabilizing IDO1. Conversely, silencing PABPC1L diminishes IDO1 expression, mitigates cytotoxic T-cell suppression, and enhances responsiveness to anti-PD-1 therapy. Our findings underscore PABPC1L's crucial role in facilitating immune evasion in RCC, making it a potential addition to ICB therapy.

overall_design: RNA-sequencing (RNA-seq) of 769-P cells revealed substantial transcriptional alterations upon PABPC1L knockdown

first: Junhang

last: Luo

first: Jiefeng

last: Yang


title: Simultaneous single-cell three-dimensional genome and gene expression profiling uncovers dynamic enhancer connectivity underlying olfactory receptor choice

first: Xiaoliang

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

overall_design: Refer to individual Series


title: Regulation of gene expression by GLIS3 during neonatal kidney development

summary: Loss of transcription factor GLIS3 function in humans and mice leads to the development of neonatal polycystic kidney disease (PKD). To investigate how loss of GLIS3 function in kidney affects postnatal kidney development and PKD, we analyzed the gene expression profiles of kidneys from WT and Glis3-null mice at P7, P14, and P28 by RNA-Seq analysis using Glis3 global KO model Glis3-mCherry and kidney specific knockout model Glis3-PAX8Cre.

overall_design: Total kidney RNAs were isolated from WT and Glis3-null mice and gene expression profiles were analyzed by RNA-Seq.

first: Chitrangda

last: Srivastava


title: HiCAR analysis of zebrafish fin regeneration identifies cis-regulatory chromatin reorganization in response to injury

status: Public on Dec 22 2023

city: Madison

first: Jianhong

last: Ou

state: Wisconsin

address: 330 N Orchard Street

institute: Morgridge Institute For Research

summary: HiCAR (Hi-C on accessible regulatory DNA), which is a genome-wide profiling of chromatin accessibility and open chromatin anchored cis-regulatory element (cRE) interactions, identified 28690 calling loops from zebrafish caudal fins at three different time points (0, 1 and 4 day(s) post amputation (dpa)) including 5022 regeneration-responsive loops (17.5%).

overall_design: 10 caudal fins each of adult wild type zebrafish at 0, 1 and 4 dpa time points were pooled and three biological replicates were used for preparing HiCAR DNA libraries 10 caudal fins each of adult wild type zebrafish at 0, 1 and 4 dpa time points were pooled and three biological replicates were used for preparing HiCAR DNA libraries to find regeneration-responsive loops only in 1 and/or 4 dpa regenerating fins not in 0 dpa uninjured control fins..

first: Kenneth

last: Poss

first: Kazunori

last: Ando

first: Yarui

last: Diao

first: Xiaolin

last: Wei


title: Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome [Nanopore]

status: Public on Dec 21 2023

city: St. Louis

first: Jennifer

middle: E.

last: Phillips-Cremins

state: MO

address: 4515 McKinley Ave

department: Genetics

institute: Washington University in St. Louis

summary: Short tandem repeat (STR) instability causes transcriptional silencing in several repeat expansion disorders. In fragile X syndrome (FXS), mutation-length expansion of a CGG STR represses FMR1 via local DNA methylation. Here, we find Megabase-scale H3K9me3 domains on autosomes and encompassing FMR1 on the X-chromosome in induced pluripotent stem cell (iPSC)-derived neural progenitors, B-cells, and fibroblasts with mutation-length CGG expansion. H3K9me3 domains connect via inter-chromosomal interactions and demarcate severe misfolding of TADs and loops. They harbor long synaptic genes replicating at the end of S phase, replication stress-induced double strand breaks, and STRs prone to stepwise somatic instability. CRISPR engineering of the full-mutation CGG to premutation-length reverses H3K9me3 domains on the X-chromosome and multiple autosomes, refolds TADs, and restores expression. H3K9me3 domains also arise in a subset of normal-length iPSCs with increased STR instability burden. Our results reveal Mb-scale heterochromatinization and trans interactions among chromosomes susceptible to repeat genetic instability.

overall_design: Hi-C, H3K9me3 ChIP-seq, CTCF ChIP-seq, RNA-seq, H3K9me3 CUT&RUN, and short and long read genome sequencing were used in multiple cell types to interrogate epigenetic changes in cell lines with normal, premutation, and disease level repeat expansions in FMR1.

first: Thomas

last: Malachowski

first: Keerthivasan

middle: R

last: Chandradoss

first: Linda

last: Zhou

first: Ravi

last: Boya

first: Ashley

last: Cook


title: CUT&RUN profiling of Tfap2a binding genome-wide using zebrafish embryos at 24hpf

status: Public on Dec 18 2023

city: Iowa City

first: Colin

last: Kenny

state: Iowa

address: 51 Newton Road 100 Bowen Science Building Iowa

department: Anatomy and Cell Biology

institute: University of Iowa

summary: The purpose of this study was to identify Tfap2a binding genome-wide in zebrafish embryos at 24hpf. Tfap2 transcription factors are essential regulators of neural crest development, melanocyte differentiation, and melanoma progression. We aimed to identify Tfap2a-occupied genes to determine direct Tfap2a-regulated transcriptional networks.

overall_design: Zebrafish embryos at 24hpf were used to profile Tfap2a occupied genes genome-wide using CUT&RUN followed by sequencing

first: Coin

first: Robert

last: Cornell


title: Comparative Analysis of Paraspinal Muscle Imbalance Between Idiopathic Scoliosis and Congenital Scoliosis from the Transcriptome Aspect

first: Zhen

last: Wang

address: No.1 Shuaifuyuan

institute: Peking uinon medical college

summary: Comparison of paraspinal muscle imbalance between idiopathic scoliosis and congenital scoliosis  may shed some light on the causality of paraspinal muscle imbalance and idiopathic scoliosis. This study aims to compare the transcriptomic profiles of paraspinal muscle imbalance between idiopathic scoliosis and congenital scoliosis.

overall_design:
Bilateral paraspinal muscles of idiopathic scoliosis and congenital scoliosis patients were collected for transcriptome sequencing. Differentially expressed genes in paraspinal muscles of IS and CS between the convexity and the concavity were screened out.

Please note that 'A' samples indicate paraspinal muscles on the concavity from idiopathic or congenital scoliosis patients, whereas 'T' samples are muscles on the convexity in idiopathic or congenital scoliosis.

first: Junduo

last: Zhao

first: Haining

last: Tan

first: Yang

last: Jiao

first: Xin

last: Chen

first: Jianxiong

last: Shen


title: GLIS3

first: Hong Soon

last: Kang


title: gRNA-seq from Ishikawa after medroxyprogesterone treatment

status: Public on Feb 12 2024

city: Jinan

first: Yao

last: Liu

state: Shandong

address: Wenhuaxi Road 107#

institute: Qilu Hospital of Shandong University

summary: Hormone therapy serves as a primary choice for fertility preservation and is also considered for advanced and recurrent cases with endometrial cancer. While a number of patients fail to respond favorably to hormone treatments. In order to explore the mechanisms underpinning hormone resistance, Here we constructed a whole-genome library for EAC cell lines using the CRISPR-Cas9 system and performed high-throughput sequencing after medroxyprogesterone treatment in this study. For CRISPR screening, ishikawa cells were infected pooled GeCkov2 lentiviral library with functional MOI of 0.3. Genomic DNA from each group was isolated and amplified by PCR. The PCR products were purified and subjected to NGS by using the Novaseq 6000-PE150 platform. After 48h of puromycin selection, the cells were divided into three groups, the baseline group cells were collected and frozen at -80 degree centigrade, the control group cells were treated with DMSO for 10 days while the MPA group cells were treated with 15 μM MPA for 10 days.

overall_design: Genome-wild lentiviral Human_GeCKOv2_Library _B was purchased from AZENTA LIFE SCIENCES . For CRISPR screening, 1×10^8 ishikawa cells were infected with pooled GeCKOv2 lentiviral library with functional MOI of 0.3. After 48h of puromycin selection, the cells were divided into three groups, the "baseline" group cells were collected and frozen at -80C, the "control" group cells were treated with DMSO for 10 days while the "MPA" group cells were treated with 15 μM MPA for 10 days. Genomic DNA from each group was isolated using HMV DNA Kit and amplified by PCR. The PCR products were purified and subjected to NGS by using the Novaseq 6000-PE150 platform.

first: Shourong

first: Jie

last: Jiang


title: Whole blood transcriptome identifies interferon-regulated genes as key drivers in thrombotic primary antiphospholipid syndrome

status: Public on Dec 15 2023

city: Athens

first: Maria

middle: G.

last: Tektonidou

state: Please choose a State

address: Mikras Asias 75

country: Greece

institute: National and Kapodistrian University of Athens

summary:
Objective: Pathogenesis of antiphospholipid syndrome (APS) isn't fully elucidated. We aimed to identify gene signatures characterizing thrombotic primary APS (thrPAPS) and subgroups at high risk for worse outcomes.
Methods: We performed whole blood next-generation RNA-sequencing in 62 patients with thrPAPS and 29 age-/sex-matched healthy controls (HCs), followed by differential gene expression analysis (DGEA) and enrichment analysis. We trained models on transcriptomics data using machine learning.
Results: DGEA of 12.306 genes revealed 34 deregulated genes in thrPAPS versus HCs; 33 were upregulated by at least 2-fold, and 14/33 were type I and II interferon-regulated genes (IRGs) as determined by interferome database. Machine learning applied to deregulated genes returned 79% accuracy to discriminate thrPAPS from HCs, which increased to 82% when only the most informative IRGs were analyzed. Comparison of thrPAPS subgroups versus HCs showed an increased presence of IRGs among upregulated genes in venous thrombosis (21/23, 91%), triple-antiphospholipid antibody (aPL) positive (30/50, 60%), and recurrent thrombosis (19/42, 45%) subgroups. Enrichment analysis of upregulated genes in triple-aPL positive patients revealed terms related to 'type I interferon signaling pathway' and 'innate immune response'. DGEA among thrPAPS subgroups revealed upregulated genes, including IRGs, in patients with venous versus arterial thrombosis (n = 11, 9 IRGs), triple-aPL versus non-triple aPL (n = 10, 9 IRGs), and recurrent versus non-recurrent thrombosis (n = 10, 3 IRGs).
Conclusion: Upregulated IRGs may better discriminate thrPAPS from HCs than all deregulated genes in peripheral blood. Taken together with DGEA data, IRGs are highly expressed in thrPAPS and high-risk subgroups of triple-aPL and recurrent thrombosis, with potential treatment implications.

overall_design: Whole blood RNA sequencing of human whole blood. 29 Healthy controls and 62 Antiphospholipid Syndrome (APS) samples

first: Petros

middle: P

last: Sfikakis


title: Bulk RNA-seq analysis during fin regeneration of regeneration-associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes

first: Jianhong

last: Ou

summary: Bulk RNA-seq analysis during fin regeneration of regeneration-associated silencer (s1) knockout zebrafish identified several up-regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points (0, 1 and 4 day(s) post amputation (dpa)), indicating that s1 has repressive ability to control downregulation of the nearby genes.

overall_design: 10 caudal fins each of regeneration-associated silencer (s1) knockout zebrafish and their WT siblings at 0, 1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA-seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.

first: Kenneth

last: Poss

first: Kazunori

last: Ando

first: Yarui

last: Diao

first: Xiaolin

last: Wei


title: Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome

first: Jennifer

last: Phillips-Cremins