title: Tissue-specific interferon-gamma levels drive regulatory T cells to restrain DC1-mediated priming of cytotoxic T cells against lung cancer

city: CAMBRIDGE

first: Duncan

middle: Matthew

last: Morgan

address: 500 Main St

department: Koch Institute

institute: MIT

summary: Regulatory T cells (Tregs) are proposed to restrain anti-tumor T cell responses either directly or by suppression of antigen-presenting cells and can act in a tissue-specific manner. Treg abundance is typically reported as a measure of suppression, without consideration of Treg functional quality. Here, we find that Tregs suppress type 1 conventional dendritic cells (DC1) and thereby induce dysfunctional CD8+ T cell responses against lung cancer. This immunoregulatory effect is spatially coordinated within tissue-specific lymph node microniches and requires antigen-specific contact between DC1 and Tregs. Suppressive clonally expanded TH1-like effector Tregs were differentially induced in the lung lymph node in response to tissue-specific levels of interferon-gamma. In cancer patients, TH1-like Tregs but not CD8+/Treg ratios correlate with poor responses to checkpoint blockade immunotherapy. Thus, Tregs that adopt the interferon-gamma-dependent TH1-like effector state have increased potential to restrain tumor-reactive T cell responses and represent a critical barrier to productive anti-tumor immunity.

overall_design: For scRNA-seq of ex vivo-primed T cells, CD8+ OT-I T cells and ZsG+ DC1 sorted from tumor-draining mLN were cultured alone or in the presence of Tregs sorted from tumor-draining mLN (added at the 1:8 Treg:OT-I ratio) as described above. After the 3 day co-culture, cells were collected for sequencing. For scRNA-seq of Tregs, LN were mashed through a 70 μm filter into RPMI (GIBCO), then incubated with αCD16/CD32 (clone 93, BioLegend) in FACS buffer (PBS (GIBCO) with 1% FBS (Atlanta Biologicals) and 2 mM EDTA (Invitrogen)) for 15 min at 4°C, washed with FACS buffer and stained with a mix of αCD45-APC (1:200, clone 30-F11, Biolegend) and Total-seq A mouse hashtag antibody (1:100, clone 30-F11, Biolegend) in FACS buffer to label individual mice (hashtag labeling was only performed for tdLN, not naïve LN). Cells were then washed twice in FACS buffer and tdLN cells from multiple mice were pooled together for subsequent CD4+ T cell enrichment sing the mouse CD4+ T cell isolation kit (Miltenyi Biotec), following manufacturer’s instructions. Next, cells were stained for FACS and Tregs were sorted as previously described. Cells from ex vivo co-cultures and sorted Tregs were processed for scRNA-seq using the Seq-Well platform with second strand chemistry, as previously described (Gierahn et al., 2017; Hughes et al., 2020). Whole transcriptome libraries were barcoded and amplified using the Nextera XT kit (Illumina) and were sequenced on a Novaseq 6000 (Illumina). Hashtag oligo libraries were amplified as described previously and were sequenced on a Nextseq 550 (Stoeckius et al., 2018).

first: Maria

last: Zagorulya

first: Leon

last: Yim

first: Austin

last: Edwards

first: Elen

last: Torres-Mejia

first: Noor

last: Momin

first: Chloe

middle: V

last: McCreery

first: Izabella

last: Zamora

first: Brendan

last: Horton

first: James

last: Fox

first: K

middle: D

last: Wittrup

first: J

last: Love

first: Stefani

last: Spranger


title: Nail-associated mesenchymal cells contribute to and are essential for dorsal digit tip regeneration

status: Public on Nov 16 2022

city: Vancouver

first: Freda

last: Miller

address: 2125 East Mall

department: Medical Genetics

country: Canada

institute: The University of British Columbia

type: Expression profiling by high throughput sequencing

summary: Here, we have asked why the nail base is essential for mammalian digit tip regeneration, focusing on the inductive nail mesenchyme. We identify a transcriptional signature for these cells that includes Lmx1b, and show that the Lmx1b-expressing nail mesenchyme is essential for blastema formation. We use a combination of Lmx1bCreERT2-based lineage tracing and single cell transcriptional analyses to show that the nail mesenchyme contributes cells for two pro-regenerative mechanisms. One group of cells maintains their identity and regenerates the new nail mesenchyme. A second group contributes specifically to the dorsal blastema, loses their nail mesenchyme phenotype, acquires a blastema transcriptional state that is highly similar to blastema cells of other origins and ultimately contributes to regeneration of the dorsal but not ventral dermis and bone. Thus, the regenerative necessity for an intact nail base is explained, at least part by a requirement for the inductive nail mesenchyme.

overall_design: High-throughput single cell transcriptomic profiles of regenerating 14 days post amputation digit tips of transgenic PdgfraCreERT;TdTomato and transgenic Lmx1bCreERT2;TdTomato adult mice generated by single cell RNA sequencing, using the 10X Genomics platform. Processed data for the 2 datasets are included as indicated.

first: Neemat

last: Mahmud

first: Christine

last: Eisner

first: Sruthi

last: Purushothaman

first: Mekayla

middle: A

last: Storer

first: David

middle: R

last: Kaplan


title: Elevated CD47 is a hallmark of dysfunctional aged muscle stem cells that can be targeted to augment regeneration

city: Stanford

first: Helen

last: Blau

address: 3200 CCSR

country: USA

institute: Stanford University

summary: In aging, skeletal muscle strength and regenerative capacity declines due, in part, to functional impairment of muscle stem cells MuSCs, yet the underlying mechanisms remain elusive. Here we capitalize on mass-cytometry to identify high CD47 expression as a hallmark of dysfunctional MuSCs CD47hi  with impaired regenerative capacity that predominate with aging. The prevalent CD47 hi MuSC subset suppresses the residual functional CD47 lo MuSC subset through a paracrine signaling loop, leading to impaired proliferation. We uncover that elevated CD47 levels on aged MuSCs result from increased U1 snRNA expression, which disrupts alternative polyadenylation. The deficit in aged MuSC function in regeneration can be overcome either by morpholino-mediated blocking of CD47 alternative polyadenylation or antibody blockade of CD47 signaling, leading to improved regeneration in aged mice, with therapeutic implications. Our findings highlight a previously unrecognized age-dependent alteration in CD47 levels and function in MuSCs, which underlies reduced muscle repair in aging.

overall_design: Mouse myoblast from three 3mo, two 12mo, and three 24mo old mice. A 3 month old mouse and a 24 month old  mouse was used for single cell RNAseq

first: Thach

last: Mai

first: Ermelinda

last: Porpiglia


title: Polycomb Deficiency Drives a FOXP2-high Metastatic State Targetable by Epigenetic Inhibitors

city: Lexington

first: Fan

last: Chen

state: Kentucky

address: 1095 V.A. Drive, HSRB 461

department: Toxicology and Cancer Biology

institute: University of Kentucky

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The purpose of this research is to understand the role and expand the precision medicine of EZH2 inhibition in lung adenocarcinoma. Our data show that histone methyltransferase EZH2 acts in a context-dependent manner as an oncogene or tumor suppressor in KRAS+/Trp53-null murine lung adenocarcinoma. Moreover, EZH2 deprivation confers sensitivity to histone demethylase and BET inhibitors in 3D culture and in vivo models, representing precision medicine strategies for lung cancers with low canonical EZH2 activity. We found that the embryonic lung transcription factor FOXP2 is de-repressed when EZH2 is inactivated, and FOXP2 promotes stemness and migration, making it a promising therapeutic target. Finally, we identified that high EZH2 correlated with high FOXP2 and poorly differentiated lung cancers, a subgroup that may benefit from combined EZH2 and BET inhibition.

overall_design: Chromatin Immunoprecipitation-sequencing (ChIP-seq) profiles of EZH2 and H3K27me3 binding in KRAS+/Trp53-loss murine lung tumor 3D organoids with Ezh2 wild-type, heterozygous, null or wild-type with EPZ-6438 treatment.

first: Jinpeng

last: Liu

first: Chi

last: Wang

middle: F

last: Brainson


title: Cell Autonomous Lipid Handling Defects in Stargardt iPS Cell-Derived Retinal Pigment Epithelium Cells

city: Bethesda

last: McGaughey

state: MD

address: 10 Center Dr

department: NEI

institute: NIH

summary: Stargardt retinopathy is an inherited form of macular degeneration caused by mutations in gene ABCA4 and characterized by the accumulation of lipid-rich deposits in the retinal pigment epithelium (RPE), RPE atrophy, and photoreceptor cell death. Inadequate mechanistic insights into pathophysiological changes occurring in Stargardt RPE have contributed to its lacking treatments. Here we show that ABCA4 knockout or Stargardt patient’s induced pluripotent stem cells-derived RPE (STGD1-iRPE) differentiate normally but display intracellular lipid and ceramide deposits reminiscent of the disease phenotype. STGD1-iRPE also shows defective photoreceptor outer segment (POS) processing and reduced cathepsin B activity, indicating higher lysosomal pH. Lipid deposits in STGD1-iRPE are reduced by increasing the activity of ABCA1, a lipid transporter, and ABCA4 ortholog. Overall, our work suggests that ABCA4 is involved in POS and lipid handling in RPE cells and provides guidance for ongoing gene therapy approaches to target both RPE and photoreceptor cells for an effective treatment.

overall_design: RNA seq

first: Mitra

last: Farnoodian

middle: M

first: Kapil

last: Bharti


title: RNA-seq of Highly Metastatic and Lowly Metastatic 4T1 Single Clones Treated with Iron Chelator Deferasirox (DFX)

city: Okayama

first: Yuze

state: Okayama

address: Kitaku Shikada-cho 2 - 5 - 1

country: Japan

institute: Okayama University

summary: Using bulk RNA-seq, the transcriptional profile of two cell lines with high or low metastatic properties derived from single clones of the murine 4T1 cell line treated or untreated with iron chelator DFX was analyzed in order to determine the mechanism underlying the inhibition preference of DFX for highly metastatic 4T1 cells.

overall_design: 1) Single clonal lines were established using single limiting dilution from the 4T1 mammary cancer cell line.  2) Using in vitro and in vivo study to determine the metastatic property we selected 2 single clones to represent highly metastatic(HM) and lowly metastatic(LM) 4T1 cell lines.  3) 2 single clones were treated with 50 uM DFX or equivalent dose of DMSO as treatment and control groups for 48-hour.  4) Total RNA was extract and carried out using bulk RNA-seq.

first: Toshiaki

last: Ohara

first: Chunning

last: Li

first: Teizo

last: Yoshimura

first: Akihiro

last: Matsukawa


title: Polycomb Deficiency Drives a FOXP2-high Aggressive State Targetable by Epigenetic Inhibitors

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-sequencing profiles of KRAS+/Trp53-loss murine lung tumors with Ezh2 wild-type, heterozygous or null from in vitro 2D and 3D cultures and in vivo sorted tumors and fresh total tumors; RNA-sequencing profiles of 2D cells, 3D spheroids and in vivo allgrafts treated with JQ1 or DMSO (vehicle); RNA-sequencing profiles of human cell lines with or without FOXP2-overexpression.

first: Christine


title: Transcriptional reprogramming of infiltrating neutrophils drives lung disease in severe COVID-19 despite low viral load

city: Atlanta

first: Eliver

last: Ghosn

state: GA

address: 1760 Haygood Dr NE

department: School of medicine

institute: Emory University

summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the ensuing COVID-19 pandemic have caused ∼40 million cases and over 648,000 deaths in the United States alone. Troubling disparities in COVID-19-associated mortality emerged early, with nearly 70% of deaths confined to Black/African-American (AA) patients in some areas, yet targeted studies within this demographic are scant. Multi-omics single-cell analyses of immune profiles from airways and matching blood samples of Black/AA patients revealed low viral load, yet pronounced and persistent pulmonary neutrophilia with advanced features of cytokine release syndrome and acute respiratory distress syndrome (ARDS), including exacerbated production of IL-8, IL-1β, IL-6, and CCL3/4 along with elevated levels of neutrophil elastase and myeloperoxidase. Circulating S100A12+/IFITM2+ mature neutrophils are recruited via the IL-8/CXCR2 axis, which emerges as a potential therapeutic target to reduce pathogenic neutrophilia and constrain ARDS in severe COVID-19.

overall_design: Cells from blood and endotracheal aspirates (ETA) from 4 individual COVID-19 patients along with blood from 6 individual healthy participants for a total of 14 individual samples (10 blood, 4 ETA).

first: Devon

middle: J

last: Eddins

first: Junkai

last: Yang

first: Astrid

last: Kosters

first: Vincent

last: Giacalone

first: Ximo

last: Pechuan

first: Joshua

last: Chandler

first: Jinyoung

last: Eum

first: Benjamin

last: Babcock

first: Brian

middle: S

last: Dobosh

first: Mindy

last: Hernández

first: Fathma

last: Abdulkhader

first: Genoah

middle: L

last: Collins

first: Richard

middle: P

last: Ramonell

last: Moussion

first: Darya

middle: Y

last: Orlova

first: Ignacio

last: Sanz

first: F

middle: E

last: Lee

first: Rabindra

last: Tirouvanziam


title: HGFAC is a ChREBP Regulated Hepatokine that Enhances Glucose and Lipid Homeostasis

status: Public on Nov 15 2022

city: Houston

first: Mark

last: Herman

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

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

overall_design:
Refer to individual Series

Grant ID: 16CSA28590003
Grant title: Genomic and Genetic Investigation of Sugar-Induced Cardiometabolic Risk
Affiliation: American Heart Association
Name: Mark A Herman

Grant ID: 1-19-PDF-088
Grant title: The role of HGFAC in Lipid and Glucose Homeostasis
Affiliation: American Diabetes Association
Name: Ashot Sargsyan

Grant title: The Role of HGFAC in Metabolic Disease
Affiliation: Eli Lilly and Company
Name: Mark A Herman


title: Sentinel p16INK4a+ cells in the basement membrane form a reparative niche in the lung [scRNA-Seq]

city: San Francisco

first: Peng

last: Tien

state: CA

address: 513 Parnassus Ave, Health Sciences East 1350

department: Department of Pulmonary Medicine

institute: University of California San Francisco

summary: A single-cell transcriptional analysis was performed on p16INK4a+ cells from the adult murine lung. Whole adult murine lung tissue was dissociated to single cells and subjected to fluorescence activated cell sorting (FACS) to select all live p16INK4a + cells. The single cell RNA-sequencing library was then subsequently generated. Cells were sequenced at a depth of ~30,506 mean reads/cell. We captured approximately 8752 cells with a mean of 2457 genes detected per cell utilizing a droplet-based barcoding approach to capture single cells for RNA sequencing. The results demonstrate that the p16INK4a + population are predominantly in the immune CD45+ populations and PDGFRa+ mesenchyme.

overall_design: The INKBRITE animals we constructed by inserting a tandem cassette of H2B-GFP expressed in frame with the p16INK4A gene product in the murine Cdkn2a locus into a bacterial artificial chromosome (BAC). The expression of multiple copies of a stable fluorescent protein is driven by p16INK4A promoter. Whole adult murine lung tissue was dissociated to single cells stained with DAPI for live cells selection and subjected to FACS to select live GFP+ (p16INK4a+) cells. Doublets and dead cells were excluded based on forward scatter, side scatter and DAPI fluorescence. Live Gp16INK4a+ cells were prepared using the 10X single cell instrument and v1 10X single cell kits according to standard protocol. Single cell sequencing of adult murine lung GLI2+ population was performed by using the HiSeq2500.

first: Nabora

last: Reyes de Mochel

first: Tien

last: Peng


title: Transcriptomic study of G-1 treatment on GBM cells

status: Public on Nov 17 2022

city: Vandœuvre-lès-Nancy

first: Hélène

last: Dubois-Pot-Schneider

address: Site CRAN/Faculté de Médecine - Bâtiment D, 1er étage 9 avenue de la Forêt de Haye, BP 184

department: CRAN

country: France

institute: Université de Lorraine - UMR7039 CRAN

summary: Gene expression profile analysis allowed to clarify the G-1 mechanisms of action in GBM cells.

overall_design: Transcriptomic profile of U251 cells exposed to 1µM or the IC50 dose of G-1 for 24 or 72h. Four independent experiments were performed.

last: Dumond


title: HGFAC is a ChREBP Regulated Hepatokine that Enhances Glucose and Lipid Homeostasis [ChIP-Seq]

summary: Carbohydrate Responsive Element-Binding Protein (ChREBP) is a carbohydrate sensing transcription factor that regulates both adaptive and maladaptive genomic responses in coordination of systemic fuel homeostasis. Genetic variants in the ChREBP locus associate with diverse metabolic traits in humans, including circulating lipids. To identify novel ChREBP-regulated hepatokines that contribute to its systemic metabolic effects, we integrated ChREBP ChIP-seq analysis in mouse liver with human genetic and genomic data for lipid traits and identified Hepatocyte Growth Factor Activator (HGFAC) as a promising ChREBP-regulated candidate in mice and humans. HGFAC is a protease that activates the pleiotropic hormone Hepatocyte Growth Factor (HGF). We demonstrate that HGFAC KO mice have phenotypes concordant with putative loss-of-function variants in human HGFAC. Moreover, in gain- and loss-of-function genetic mouse models, we demonstrate that HGFAC enhances lipid and glucose homeostasis, which may be mediated in part through actions to activate hepatic PPARγ activity. Together, our studies show that ChREBP mediates an adaptive response to overnutrition via activation of HGFAC in the liver to preserve glucose and lipid homeostasis.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for ChREBP in liver from C57Bl/6J and C3H/HeJ mice 5 hours after gavage with water or fructose

first: Ashot

last: Sargsyan

first: Ludivine

last: Doridot

first: Harini

last: Srinivasan

first: Rachael

last: Ivison

first: Inna

last: Astapova

first: Linus

last: Tsai


title: Single-Cell RNA Sequencing reveals matrix stiffness induction of endothelial phenotypic modulation and its association with atherosclerosis

city: Baltimore

first: Patrick

last: Cahan

address: 733 N. Broadway

institute: Johns Hopkins University

summary: Here, we applied single-cell RNA seq to uncover the heterogeneity of endothelial cells (ECs) under different stiffness and TGF-β induction. We identified three distinct EC clusters that was consistenyl showed in all different conditions . Further subclustering analysis revealed finer heterogeneity which were differentially impacted by stiffness and TGF-β.

overall_design: We performed scRNA-seq on human coronary artery endothelial cells (ECs, passage 3-8, Lonza) cultured for 14 days on 4kPa hydrogel or TC, in the presence or absence of TGF-β stimulation. After quality control filtering based on mitochondrial transcript content and total transcript counts, we obtained 21,644 high-quality ECs.

first: Ngan

last: Huang


title: Immunoediting instructs tumor metabolic reprogramming to support immune evasion [TCR-seq]

city: Epalinges

first: Ping-Chih

last: Ho

address: Ch. des Boveresses 155

country: Switzerland

institute: Ludwig Cancer Institute, UNIL

summary: Immunoediting sculpts immunogenicity and thwarts host anti-tumor responses in tumor cells during tumorigenesis; however, it remains unknown whether metabolic programming of tumor cells can be guided by immunosurveillance. Here, we report that T cell-mediated immunosurveillance in early staged tumorigenesis instructs c-Myc upregulation and metabolic reprogramming in tumor cells. This previously unexplored tumor-immune interaction is controlled by a non-canonical IFNg-STAT3 signaling and supports tumor immune evasion. Our findings uncover that immunoediting instructs deregulated bioenergetic programs in tumor cells for empowering them to disarm the T cell-mediated immunosurveillance by imposing metabolic tug-of-war between tumor and infiltrating T cells and forming the suppressive tumor microenvironment.

overall_design: Examination of CD8 T cell receptor répertoire in tumor-infiltrating lymphocytes from tumor with or without early T cell depletion

first: Chin-Hsien


title: Immunoediting instructs tumor metabolic reprogramming to support immune evasion [CRISPR-screen]

overall_design: Identify metabolic vulnerability from tumor by CRISPR screening to improve host anti-tumor immunity


title: The influence of calcium and magnesium on the gene regulation of Gemmatimonas phototrophica

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

summary: Transcriptiomes of cells grown with 2mg/L CaCl2 and amended with 20 mg/L CaCl2 or MgCl2

overall_design: Three biological replicates for sorted subpopulations and RNAprotect- or formaldehyde-fixed and unsorted cells as controls.

first: Sahana

last: Shivaramu

first: Karel

last: Kopejtka

first: Michal

last: Koblížek


title: Hyphthalamic mRNA expression of leptin receptor-expressing cell-specific Slug knockout mice

city: Phoenix

first: Min-Hyun

last: Kim

state: Arizona

address: 850 N. 5th St, Wexford 360H

department: College of Health Solutions

institute: Arizona State University

summary:
Leptin resistance is a driving force for obesity and metabolic syndrome. Slug (Snai2 or Snail2) is an epignetic factor that may play a critical role in the development of leptin resistance in obesity.
We conducted a microarray to detect molecular targets of Slug in the hypothalamus.

overall_design: Hypothalamic RNAs were extracted from leptin receptor-expressing cell-specific Slug knockout (ΔLepR) or Slugfl/fl male mice at 8 weeks of age and subjected to Affymetrix microarray analysis.

first: Liangyou

last: Rui


title: Controlling therapeutic protein expression via inhalation of a butter flavor molecule

city: Basel

first: Adrian

last: Bertschi

address: Mattenstrasse 26

department: BSSE

institute: ETHZ

summary: Precise control of the delivery of therapeutic proteins is critical for gene- and cell-based therapies, and expression should only be switched on in the presence of a specific trigger signal of appropriate magnitude. Focusing on the advantages of delivering the trigger by inhalation, we have developed a mammalian synthetic gene switch that enables regulation of transgene expression by exposure to the semi-volatile small molecule acetoin, a widely used, FDA-approved food flavor additive. The gene switch capitalizes on the bacterial regulatory protein AcoR fused to a mammalian transactivator, which binds to promoter regions with specific DNA sequences in the presence of acetoin and dose-dependently activates expression of downstream transgenes. Wild-type mice implanted with alginate-encapsulated cells transgenic for the acetoin gene switch showed a dose-dependent increase in blood levels of reporter protein in response to either administration of acetoin solution via oral gavage or longer exposure to acetoin aerosol generated by a commercial portable inhaler. Intake of typical acetoin-containing foods, such as butter, lychees and cheese, did not activate transgene expression. As a proof of concept, we show that blood glucose levels were normalized by acetoin aerosol inhalation in type-I diabetic mice implanted with acetoin-responsive insulin-producing cells. Delivery of trigger molecules using portable inhalers may facilitate regular administration of therapeutic proteins via next-generation cell-based therapies to treat chronic diseases for which frequent dosing is required.

overall_design: This experiment was conducted to study the effect of the small molecule acetoin on HEK293T cells

first: Bozhidar-Adrian

last: Stefanov

first: Shuai

last: Xue

first: Ghislaine

last: Charpin-El Hamri

first: Ana

last: Palma Teixeira

first: Martin

last: Fussenegger


title: Immunoediting instructs tumor metabolic reprogramming to support immune evasion [smartseq]

overall_design: Examination of transcriptomes in tumor cell grew from control and T cell depletion treatment.


title: Effect of cisplatin + anti-PD1 + anti-CTLA-4 treatment on gene expression of mouse eosinophils in blood of mice with mammary-tumor derived metastasis

city: Amsterdam

first: Olga

middle: Sophia

last: Blomberg

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary: Immune checkpoint blockade (ICB) has opened a new era in cancer therapy. Here, we studied the potential role of eosinophils in the response to ICB treatment and chemotherapy combination in mouse models of primary and metastatic breast cancer. As a model of metastatic breast cancer, we used mice with metastasis originating from orthotopically transplanted mammary tumors, which in turn derived from spontaneous mammary tumors of K14cre;Cdh1F/F;Trp53F/F mice. In this study, the gene expression profile of circulating eosinophils sorted from mice with metastatic cancer treated with a combination of cisplatin and anti-PD1 plus anti-CTLA-4 antibodies was analyzed br RNA-sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse eosinophils sorted from blood of mice with metastatic cancer treated with cisplatin + anti-PD1 + anti-CTLA4 antibody (n=7 mice) or with control antibody alone (n=4 mice).

first: O

first: L

last: Spagnuolo

first: H

last: Garner

last: Voorwerk

middle: I

last: Isaeva

first: E

last: van Dyk

first: N

last: Bakker

first: M

last: Chalabi

first: C

last: Klaver

last: Duijst

first: K

last: Kersten

last: Bruggeman

first: D

last: Pastoors

last: Hau

last: Vrijland

last: Raeven

last: Kaldenbach

last: Kos

first: I

last: Afonina

first: R

last: Beyaert

first: P

last: Kaptein

last: Thommen

last: Hoes

first: W

last: Theelen

last: Baas

last: Voest

last: Wessels

last: de Visser

last: Kok


title: Immunoediting instructs tumor metabolic reprogramming to support immune evasion [RNA-seq]

first: Ping-Chih

last: Ho

overall_design: Examination of transcriptomes in tumor cell grown from immunocompetent and immunocompromised mice

first: Chin-Hsien

last: Tsai


title: Immunoediting instructs tumor metabolic reprogramming to support immune evasion [ExomeSeq]

type: Genome variation profiling by high throughput sequencing

overall_design: Examination of genetic mutation in tumor cell grown from immunocompetent and immunocompromised mice


title: Immunoediting instructs tumor metabolic reprogramming to support immune evasion [ATAC-seq]

overall_design: Examination of chromatin accessibility in tumor cells grown from immunocompetent and immunocompromised mice


title: Expanding the Scope of Bacterial CRISPR Activation with  PAM-flexible dCas9 Variants

city: New York

first: Neville

last: Sanjana

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: CRISPR-Cas transcriptional tools have been widely applied for programmable regulation  of complex biological networks. In comparison to eukaryotic systems, bacterial CRISPR  activation (CRISPRa) has stringent target site requirements for effective gene activation. While  genes may not always have an NGG protospacer adjacent motif (PAM) at the appropriate  position, PAM-flexible dCas9 variants can expand the range of targetable sites. Here we  systematically evaluate a panel of PAM-flexible dCas9 variants for their ability to activate  bacterial genes. We observe that dxCas9-NG provides a high dynamic range of gene activation  for sites with NGN PAMs while dSpRY permits modest activity across almost any PAM. Similar  trends were observed for heterologous and endogenous promoters. For all variants tested,  improved PAM-flexibility comes with the tradeoff that CRISPRi-mediated gene repression  becomes less effective. Weaker CRISPR interference (CRISPRi) gene repression can be  partially rescued by expressing multiple sgRNAs to target many sites in the gene of interest. Our  work provides a framework to choose the most effective dCas9 variant for a given set of gene  targets, which will further expand the utility of CRISPRa/i gene regulation in bacterial systems.

overall_design: K562 cells transduced with an Sp-Cas9 nuclease variant and sgRNA library targeting CD45 were pooled together prior to antibody staining and sorting based on the expression of the target gene. A475 cells transduced with an Sp-dCas9-VPR transcriptional activator variant and sgRNA library targeting CD45 were pooled together prior to antibody staining and sorting based on the expression of the target gene. sgRNA distribution in the cell pool prior to sorting was used as a reference.

first: Cholpisit

last: Kiattisewee

first: Ava

last: Karanjia

first: Mateusz

last: Legut

first: Zharko

last: Daniloski

first: Samantha

last: Koplik

first: Joely

last: Nelson

first: Benjamin

last: Kleinstiver

first: James

last: Carothers

first: Jesse

middle: G

last: Zalatan


title: Single cell RNAseq provides insight into altered immune cell populations in human fracture nonunions

city: Indianapolis

first: Keith

last: Avin

state: IN

address: 950 W. Walnut Street

department: Nephrology

institute: Indiana University

summary: Nonunion describes bone fractures that fail to heal, resulting in the fracture callus failing to fully ossify or, in atrophic cases, not forming altogether. Fracture healing is regulated, in part, by the balance of pro-inflammatory and anti-inflammatory processes occurring within the bone marrow and surface cell populations. We sought to further understand the role of osteoimmunology (i.e., study of the close relationship between the immune system and bone) by examining immune cell gene expression via single-cell RNA sequencing of intramedullary canal tissue obtained from human patients with femoral nonunions. Intramedullary canal tissue samples obtained by reaming were collected at the time of surgical repair for femur fracture nonunion (n=5) or from native bone controls when harvesting autologous bone graft (n=4). Cells within the samples were isolated and analyzed using the Chromium single cell system (10x Genomics, Inc) and Illumina sequencers. Twenty-three distinct cell clusters were identified, with higher cell proportions in the nonunion samples for monocytes and CD14+ dendritic cells (DC), and lower proportions of T cells, myelocytes, and promyelocytes in nonunion samples. Gene expression differences were identified in each of the cell clusters from cell types associated with osteoimmunology, including CD14+DC, monocytes, T cells, promyelocytes, and myelocytes. These results provide human derived gene profiles that can further our understanding of pathways that may be a cause or a consequence of nonunion, providing the clinical rationale to focus on specific components of osteoimmunology. Statement of Clinical Significance. The novel single-cell approach may lead to clinically relevant diagnostic biomarkers during earlier stages of nonunion development and/or investigation into therapeutic options.

overall_design: case-control study

first: Roman

last: Natoli

first: Sharon

last: Moe

first: Neal

last: Chen


title: MiaPaCa-2 xenografts SHP2i + ERKi

first: Sara

last: Mainardi

institute: The Netherlands Cancer Institute

summary: KRAS mutant pancreatic tumors have poor prognosis and few therapeutic options. Here, Frank et al. show that the combination of RMC4550 (SHP2 inhibitor) and LY3214996 (ERK inhibitor)  effectively impairs tumor growth and induces tumor regression in multiplein vivo models of PDAC .

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MiaPaCa-2 UT tumors or treated with Ly3214996 plus RMC-4550 at 3 weeks

first: Bram

last: Thijssen

first: Katrin

last: Frank

first: Antonio

last: Mulero-Sánchez


title: The combination of RMC4550 (SHP2 inhibitor) and LY3214996 (ERK inhibitor) effectively impairs tumor growth and induces tumor regression in multiplein vivo models of PDAC

overall_design: Refer to individual Series


title: KCP SHP2i + ERKi

overall_design: Comparative gene expression profiling analysis of RNA-seq data for KCP tumors treated with vehicle orwith  Ly3214996 plus RMC-4550 at 3 weeks


title: HGFAC is a ChREBP Regulated Hepatokine that Enhances Glucose and Lipid Homeostasis [RNA-Seq]

first: Mark

last: Herman

overall_design: 8-week old HGFAC KO male mice and their littermate controls were fed HF/HS diet or control chow diet.

first: Ashot

last: Sargsyan

first: Inna

last: Astapova


title: Application of a New Approach Methodology (NAM)-based Strategy for Genotoxicity Assessment of Data-poor Compounds

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

summary: The conventional battery for genotoxicity testing is not well suited to assessing the large number of chemicals needing evaluation. Traditional in vitro tests lack throughput, provide little mechanistic information, and have poor specificity in predicting in vivo genotoxicity. New Approach Methodologies (NAMs) aim to accelerate the pace of hazard assessment and reduce reliance on in vivo tests that are time-consuming and resource-intensive. As such, high-throughput transcriptomic and flow cytometry-based assays have been developed for modernized in vitro genotoxicity assessment. This includes: the TGx-DDI transcriptomic biomarker (i.e., 64-gene expression signature to identify DNA damage-inducing (DDI) substances), the MicroFlow® assay (i.e., a flow cytometry-based micronucleus (MN) test), and the MultiFlow® assay (i.e., a multiplexed flow cytometry-based reporter assay that yields mode-of-action (MoA) information). The objective of this study was to investigate the utility of the TGx-DDI transcriptomic biomarker, multiplexed with the MicroFlow® and MultiFlow® assays, as an integrated NAM-based testing strategy for screening data-poor compounds prioritized by Health Canada’s New Substances Assessment and Control Bureau. Human lymphoblastoid TK6 cells were exposed to 3 control and 10 data-poor substances, using a 6-point concentration range. Gene expression profiling was conducted using the targeted TempO-SeqTM assay, and the TGx-DDI classifier was applied to the dataset. Classifications were compared with those based on the MicroFlow® and MultiFlow® assays. Benchmark Concentration (BMC) modeling was used for potency ranking. The results of the integrated hazard calls indicate that five of the data-poor compounds were genotoxic in vitro, causing DNA damage via a clastogenic MoA, and one via a pan-genotoxic MoA. Two compounds were likely irrelevant positives in the MN test; two are considered possibly genotoxic causing DNA damage via an ambiguous MoA. BMC modeling revealed nearly identical potency rankings for each assay. This ranking was maintained when all endpoint BMCs were converted into a single score using the Toxicological Prioritization (ToxPi) approach. Overall, this study contributes to the establishment of a modernized approach for effective genotoxicity assessment and chemical prioritization for further regulatory scrutiny. We conclude that the integration of TGx-DDI, MicroFlow®, and MultiFlow® endpoints is an effective NAM-based strategy for genotoxicity assessment of data-poor compounds.

overall_design: A total of 276 samples were sequenced for this toxicogenomics study on 10 data-poor compounds, including technical controls (reference RNA; media only; cells with no treatment). The solvent controls were comprised of 0.1% DMSO. 6 concentrations of each data-poor chemical were tested in duplicate. Three reference chemicals, etoposide, 7,12-dimethylbenz[a]anthracene, and d-mannitol were also included in this study. Six chemicals (NSACB #1,12,13,14,18,D-mannitol) were tested both with and without metabolic activation.

first: Anne-Marie

last: Fortin

first: Alexandra

last: Long

first: Andrew

last: Williams

first: Julie

last: Cox

first: Claire

last: Pinsonnault

first: Paul

last: White

first: Carole

last: Yauk


title: RNA-seq of MV4;11 cells treated with Methyl Bestatin or Brefeldin A

first: Hsin-Che

last: Huang

state: NY

address: 417 E 68th St

department: Chemical Biology

institute: Memorial Sloan Kettering Cancer Center

summary: We report the application of RNA-seq for profiling gene transcription upon treatment of methyl bestatin (MeBs, aminopeptidase inhibitor) or brefeldin A (BFA, ER-to-Golgi transport inhibitor), compared to DMSO control. We found MeBs and BFA similarly upregulated genes pertinent to proteotoxic stress.

overall_design: Examination of gene transcription levels upon treatment of MeBs or BFA in Caspase-1 (CASP1) knockout MV4;11 cells over the course of 6 hours, compared to DMSO control. 4 replicates were analyzed per sample.

first: Elizabeth

last: Orth-He

first: Daniel

last: Bachovchin


title: Single cell transcriptomic analysis of human axioloids

city: Kyoto

first: Cantas

last: Alev

address: Medical Faculty Bldg. B, Yoshida-Konoe-cho, Sakyo-ku

department: Institute for the Advanced Study of Human Biology (ASHBi)

institute: Kyoto University

summary: We have established a pluripotent stem cell (PSC)-based 3D model of human axial development, which recapitulates in vitro key features of the somitogenesis process including axial elongation, segmentation and sequential formation of epithelial somites with proper rostrocaudal pattering, and traveling wave-like gene expression dynamics associated with the segmentation clock. Initial molecular and functional analysis of these axially-organized embryonic tail-like structures, which we termed axioloids, revealed the spatiotemporally controlled self-organization of somitogenesis associated human mesodermal cell populations. In order to gain a deeper understanding this model, we performed temporally resolved (10X-based) single cell RNA-seq (scRNA-seq) and analyzed axioloids at various timepoints (48h, 72h, 96h & 120h) and conditions (-MG vs. +MG alone or MG + Retinoic Acid (RA) or Retinal (RAL)).

overall_design: Time-resolved (10X) single cell transcriptomic analysis of human axioloids

first: Yoshihiro

last: Yamanaka

first: Sofiane

last: Hamidi

first: Kumiko

last: Yoshioka-Kobayashi

first: Yuzuru

last: Kurokawa

first: Takuya

last: Yamamoto

first: Taro

last: Tsujimura


title: Early growth response 1 transcription factor is essential for the pathogenic properties of human endometriotic epithelial cells

city: HOUSTON

first: Vineet

middle: Kumar

last: Maurya

state: TX

address: ONE BAYLOR PLAZA

department: Molecular & Cell Biology

institute: BAYLOR COLLEGE OF MEDICINE

summary:
The aim of this study is to compare transcriptome profiling of EGR1 siRNA treated immortalized human endometriotic epithelial cells expression luciferase (iHEECs/Luc) by RNA-sequencing
Methods: The mRNA profiles of non-targeting (NT) and EGR1 siRNA treated immortalized human endometriotic epithelial cells expression luciferase (iHEECs/Luc) were generated by deep sequencing, in triplicate using Illumina NovaSeq-6000 sequencers with 2×100 paired-end reads. Basecalls and demultiplexing were performed with Illumina’s RTA version 1.9 and bcl2fastq2 software with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the human genome (Genome Reference Consortium Human Build hg38) with STAR version 2.5.1a. qRT–PCR validation was performed using TaqMan assays.
Results: Using a 1.5-fold cutoff and Benjamini-Hochberg false discovery rate (FDR) of <0.05 threshold for inclusion, we identified 76 differentially expressed genes (DEGs) between (NT) and EGR1 siRNA treated immortalized human endometriotic epithelial cells.
Conclusions: Our study represents the first detailed analysis of EGR1 siRNA treated immortalized human endometriotic epithelial cells expression luciferase  (iHEECs/Luc) transcriptomes, with biologic replicates, generated by RNA-seq technology.

overall_design: Transcriptome profiling of NT and EGR1 siRNA treated immortalized human endometriotic epithelial cells expression luciferase (iHEECs/Luc)

middle: K

first: Maria

last: Szwarc

first: Rodrigo

last: Fernandez-Valdivia

first: David

last: Lonard

first: Yong

last: Song

first: Niraj

last: Joshi

first: Asgerally

middle: T

last: Fazleabas

first: John

last: Lydon


title: A clinical-grade HLA haplobank of human induced pluripotent stem cells derived from Japanese donors

first: Masayoshi

last: Tsukahara

state: Kyoto

address: Shogoin kawahara-cho, sakyo-ku,

department: Research and Develpoment center

institute: CiRA foundation

summary: We constructed a clinical-grade haplobank of 27 induced pluripotent stem cells (iPSCs) lines prepared in accordance with good manufacturing practice regulations from seven donors who were homozygous for one of the four most frequent human leukocyte antigen (HLA)-haplotypes in Japan. The haplobank could provide HLA-matched iPSCs lines to ~40% of the Japanese population. Since the first release in 2015, these iPSC lines have been used in more than 12 clinical studies. We performed rigorous quality control (QC) tests, including residual episomal vectors, genetic mutations in cancer-related genes, copy number alterations, karyotype, expression of markers of the undifferentiated state, morphology, identity (HLA typing and short tandem repeat analysis), sterility and endotoxin. Although the significance of most mutations in cancer-related genes is unknown, we excluded iPSC lines with such mutations to maximize the safety. The haplobank we have established here is an important step toward the clinical application of iPSCs in cell therapies.

overall_design: We obtained gene expression data from 309 HLA homozyogous iPSC lines generated by electroporation of episomal vectors (pCE) . The iPSC lines consist of 179 PBMC-derived iPSCs and 130 cord blood-derived iPSCs . The gene expression of 4 lines of embryonic stem cells (KthES) established in Kyoto university were also examined. As a control, total RNAs extracted from 201B7 and 409B2 iPSCs which were previousy generated by retrovirus infection and electroporation of other pisomal vectors (pCXLE), respectively at CiRA in Kyoto university were used. To confirm the pluripotency of iPSCs and ESCs, the cells were differentiated into three germ layers by using STEMdiff trilineage differentiation kits (STEMCELL technologies).

first: Tomoaki

last: Kato


title: Cell-specific Studies Through Novel Mouse Model Reveal the Transcriptomic Response of Retinal Müller Glia to Acute and Chronic Stress [INTACT]

city: Oklahoma City

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

summary: Epigenetic regulation of the genome through DNA modifications, mainly methylcytosine (mC) and hydroxymethylcytosine (hmC), alters DNA accessibility, genomic organization and gene expression and is thought to be altered during neurodegenerative diseases, such as  age-related macular degeneration (AMD). Analysis of retina epigenetic and transcriptomic signatures at the cell-type specific level is crucial to understanding the pathophysiology of retinal degeneration. We have discovered that Aldh1l1 is specifically expressed in the major macroglia of the retina, the Müller glia, and, unlike the brain, is not expressed in retinal astrocytes. This allows a novel model to study paired epigenetic and transcriptomic signatures in Müller glia using Nuclear Tagging and Translating Ribosome Affinity Purification (NuTRAP) for temporally controlled labeling and isolation of Müller glial DNA and RNA. As validated through a variety of approaches, the Aldh1l1cre/ERT2-NuTRAP model provides Müller glia specific translatome and epigenome profiles. Application of this approach to models of acute injury (optic nerve crush) and chronic stress (aging) uncovered common Müller glia-specific transcriptome changes in inflammatory pathways, as well as differential signatures for each stimulus. The expression of components of the IL1b signalling axis, complement system, and markers of gliosis was enhanced in Müller glia in response to optic nerve crush but not in response to aging. The expression of components of the purinergic receptor and focal adhesion signalling pathways changed uniquely in response to aging but not with optic nerve crush. The Aldh1l1cre/ERT2-NuTRAP model allows focusing molecular analyses to a single, minority cell type within the retina, providing more substantial effect sizes than whole tissue analyses. The NuTRAP model, nucleic acid isolation, and validation approaches presented here can be applied to any retina cell type for which a cell type-specific cre is available.

overall_design: Mouse retinal nuclear RNA from whole tissue (input) and Muller glia (positive) (n = 3)

first: Ana

last: Chucair-Elliott

first: Sarah

last: Ocanas

last: Van Der Veldt

first: Kevin

last: Pham

first: Ashley

last: Cheyney

last: Stanford

first: Jami

last: Gurley

middle: H

last: Elliott

first: Willard

last: Freeman


title: Cell-specific Studies Through Novel Mouse Model Reveal the Transcriptomic Response of Retinal Müller Glia to Acute and Chronic Stress [Basal]

overall_design: Mouse retinal RNA from total tissue (input) and Muller glia (positive) (n = 3).


title: Cell-specific Studies Through Novel Mouse Model Reveal the Transcriptomic Response of Retinal Müller Glia to Acute and Chronic Stress [oxBS]

type: Methylation profiling by high throughput sequencing

overall_design: Mouse retinal DNA from whole tissue (input) and Muller glia (positive) (n = 3)


title: Cell-specific Studies Through Novel Mouse Model Reveal the Transcriptomic Response of Retinal Müller Glia to Acute and Chronic Stress [ONC]

overall_design: Mouse retinal RNA from Muller glia in treated (ONC) and untreated (control) samples (n = 5)


title: Malignant progression of an ancestral bone marrow clone harboring a CIC-NUTM2A fusion in isolated myeloid sarcoma

status: Public on Nov 14 2022

city: Palo Alto

first: Tanja

middle: A

last: Gruber

address: 1000 Welch Road Suite 300

department: Pediatrics

institute: Stanford University

summary: Myeloid sarcoma is a rare condition consisting of extramedullary myeloid blasts found in association with acute myeloid leukemia (AML) or, in the absence of bone marrow involvement. We identified an infant with isolated myeloid sarcoma whose bone marrow was negative for involvement by flow cytometry. Sequencing revealed the fusion oncogene CIC-NUTM2A and identified the sarcoma to be clonally evolved from the bone marrow which carried the fusion despite the absence of pathology. Murine modeling confirmed the ability of the fusion to transform hematopoietic cells and identified receptor tyrosine kinase signaling activation when compared to other fusion driven murine AML models including AML1-ETO, CBFA2T3-GLIS2, NUP98-KDM5A, and MLL-AF6 consistent with disruption of the CIC transcriptional repressor. These findings extend the definition of CIC-rearranged malignancies to include hematologic disease, provide insight into the mechanism of oncogenesis, and demonstrate the importance of molecular analysis and tracking of bone marrow involvement over the course of treatment in myeloid sarcoma, including patients that lack flow cytometric evidence of leukemia at diagnosis.

overall_design: Mouse bone marrow was lineage depleted and transduced with CIC-NUTM2A, AML1-ETO9a, CBFA2T3-GLIS2 and JAK2 activating mutation, NUP98-KDM5A, or MLL-AF6 retroviral constructs. After 48 hours cells were transplanted into lethally irradiated syngeneic recipients. Bone marrow was collected from moribund mice for RNA sequencing.


title: Gluten-free diet affects faecal small non-coding RNA profiles and microbiome composition in celiac disease supporting a host-gut microbiota crosstalk

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

type: Non-coding RNA profiling by high throughput sequencing

summary: The current treatment for Celiac Disease (CD) is adhering to a gluten-free diet (GFD), although its long-term molecular effects are still undescribed. New molecular features detectable in faecal samples may improve and facilitate non-invasive clinical management of CD on GFD. For this purpose, faecal small non-coding RNAs (sncRNAs) and gut microbiome profiles were concomitantly explored in CD subjects in relation to strict (or not) GFD adherence over time. In the present observational study, we performed small RNA and shotgun metagenomic sequencing in stool from 63 treated CD (tCD) subjects and 66 sex- and age-matched healthy controls. tCD included 51 individuals on strict GFD and with negative transglutaminase (TG) serology (tCD-TG-) and 12 symptomatic with not strict/short-time of GFD adherence and positive TG serology (tCD-TG+). Samples from additional 40 adult healthy individuals and from a cohort of 19 untreated paediatric CD subjects and 19 sex/age matched controls were analyzed to further test the outcomes. Several miRNA, other sncRNA (piRNA and tRNA) and microbiota profiles were altered in tCD subjects(adj.p<0.05). Findings were validated in one external group of controls. In tCD-TG-, GFD duration correlated with five miRNA levels (p<0.05): for miR-4533-3p and miR-2681-3p, the longer the diet adherence, the less the expression differed from controls. tCD-TG+ and untreated paediatric CD patients showed a similar miRNA dysregulation. Immune-response, trans-membrane transport and cell death pathways were enriched in targets of identified miRNAs. Bifidobacterium longum, Ruminococcus bicirculans and Haemophilus parainfluenzae abundances shifted (adj. p<0.05) with a progressive reduction of denitrification pathways with GFD length. Integrative analysis highlighted 121 miRNA-bacterial relationships (adj.p<0.05). Specific faecal sncRNA and microbial patterns characterise CD subjects on GFD, reflecting either the long-term effects or the gut inflammatory status, in case of a not strict/short-time adherence. Our findings suggest novel host-microbial interplays and could help the discovery of biomarkers for the clinical monitoring of GFD over time.

overall_design: Hundred and thirty-two subjects were enrolled by the Italian Institute for Genomic Medicine (IIGM), the Gastroenterology Unit of Ospedale Mauriziano Umberto I and the Gastroenterology outpatient clinic of San Giovanni Antica Sede, all in Turin, Italy. The cohort included tCD (n=63), untreated CD (i.e., recruited before starting the GFD; n=3) and healthy volunteers with no dietary restrictions (n=66). Inclusion criteria for CD subjects were: disease diagnosis with histological confirmation; for all: no use of antibiotics and other drugs in the month before sampling, age >18 and no concomitant gastrointestinal disorders (e.g., allergies/intolerances, diabetes, inflammatory bowel diseases, or tumours). The TG IgA levels were measured in serum samples of all subjects who provided blood for the present study, unless not already clinically tested in concomitance with the recruitment.  All participants signed informed consent to participate in the study and received two questionnaires from the European Prospective Investigation into Cancer and Nutrition (EPIC) study (one on dietary habits and another, sex-specific, about lifestyle habits) and a disposable container for stool collection.  Small RNA sequencing and shotgun metagenomic sequencing was performed on all fecal samples collected.

first: Antonio

last: Francavilla

first: Ferrero

last: Giulio

first: Barbara

last: Pardini

first: Sonia

last: Tarallo

first: Laura

last: Zanatto

first: Gian

last: Caviglia

first: Sabina

last: Sieri

first: Sara

last: Grioni

first: Giulia

last: Francescato

first: Francesco

last: Stalla

first: Cristina

last: Guiotto

first: Lucia

last: Crocella

first: Marco

last: Astegiano

first: Mauro

last: Bruno

first: Pier

last: Calvo

first: Paolo

last: Vineis

first: Davide

last: Ribaldone

first: Alessio

last: Naccarati


title: Sex Chromosomes and Sex Phenotype Contribute to Biased DNA Methylation in Mouse Liver

city: Montreal

first: Anna

middle: K.

last: Naumova

state: Quebec

address: 2155 rue Guy

department: Departments of Obstetrics and Gynecology and Human Genetics

institute: McGill University

summary: Sex biases in the genome-wide distribution of DNA methylation and gene expression levels are some of the manifestations of sexual dimorphism in mammals. To advance our understanding of the mechanisms that contribute to sex biases in DNA methylation and gene expression, we conducted whole genome bisulfite sequencing (WGBS) as well as RNA-seq on liver samples from mice with different combinations of sex phenotype and sex-chromosome complement. We compared groups of animals with different sex phenotypes, but the same genetic sexes, and vice versa, same sex phenotypes, but different sex-chromosome complements. We also compared sex-biased DNA methylation in mouse and human livers. Our data show that sex phenotype, X-chromosome dosage, and the presence of Y chromosome shape the differences in DNA methylation between males and females. We also demonstrate that sex bias in autosomal methylation is associated with sex bias in gene expression, whereas X-chromosome dosage-dependent methylation differences are not, as expected for a dosage-compensation mechanism. Furthermore, we find partial conservation between the repertoires of mouse and human genes that are associated with sex-biased methylation, an indication that gene function is likely to be an important factor in this phenomenon.

overall_design: WGBS libraries prepared from genomic DNA extracted from the livers of 8 week old mice with different combinations of sex chromosomes and phenotypic sex

first: Qinwei

last: Zhuang

first: Jose

last: Galvez

first: Qian

last: Xiao

first: Najla

last: AlOgayil

first: Jeffrey

last: Hyacinthe

first: Teruko

last: Taketo

first: Guillaume

last: Bourque


title: RB1 expression and targeting by CDK4/6 inhibitors in small cell lung cancer

city: Cleveland

first: Ata

last: Abbas

state: OH

address: 10900 Euclid Ave

department: Division of Hematology & Oncology

institute: Case Western Reserve University

summary: The canonical model of small cell lung cancer (SCLC) depicts tumors arising from dual inactivation of TP53 and RB1. However, many genomic studies have persistently identified tumors with no RB1 mutations. Here, we examined RB1 protein expression and function in SCLC. RB1 expression was examined by immunohistochemical analysis of 62 human SCLC tumors. These studies showed that ~14% of SCLC tumors expressed abundant RB1 protein, which is associated with neuroendocrine (NE) gene expression and is enriched in YAP1 expression, but no other lineage proteins that stratify SCLC. SCLC cells and xenograft tumors with RB1 protein expression were sensitive to growth inhibition by the CDK4/6 inhibitor palbociclib, and this inhibition was shown to be dependent on RB1 expression by CRISPR knockout. Furthermore, a patient with biopsy-validated wt RB1 SCLC who received the CDK4/6 inhibitor abemaciclib demonstrated a dramatic decrease in mutant TP53 ctDNA allelic fraction from 62.1% to 0.4% and decreased tumor mass on CT scans. Importantly, immunohistochemistry of the diagnostic biopsy specimen showed RB1 positivity. Finally, we identified a transcriptomics-based RB1 loss-of-function signature that discriminates between SCLC cells with or without RB1 protein expression and validated it in the patient who was responsive to abemaciclib, suggesting its potential use to predict CDK4/6 inhibitor response in SCLC patients. Our study demonstrates that RB1 protein is an actionable target in a subgroup of SCLC, a cancer that exhibits no currently targetable mutations.

overall_design: We used RNA-seq data from RB1 wild-type SCLC biopsies, and compared RB1 loss-of-function signature scores between RB1 IHC positive (n=2) and RB1 IHC negative (n=3) SCLC tumors.

first: Afshin

last: Dowlati


title: The accessible genome regions in inducible melanoma tumor cells grown in the presence or absence of T cells

city: Vienna

first: Hana

last: Imrichova

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: CeMM, Vienna

summary: The goal of this ATAC sequencing design is to identify critical transcription factors in controlling melanoma tumor growth to evade T cell anti-tumor immunity. The melanoma was induced by tamoxifen followed by T cell depletion with anti-CD4/8. The tumor cells were sorted according to EGFP for following ATAC-seq library preparation.

overall_design: Examination of the different accessible genome regions in tumor cells grown in presence or absence T cells

first: Yu-Ming

last: Chuang

first: Chin-Hsien

last: Tsai

first: Yi-Ru

last: Yu

first: Ping-Chih

last: Ho


title: Immunoediting instructs tumor metabolic reprogramming to support immune evasion [Bisulfite-seq]

address: Ch. des Boveresses 155

institute: Ludwig Cancer Institute, UNIL

summary: Immunoediting sculpts immunogenicity and thwarts host anti-tumor responses in tumor cells during tumorigenesis; however, it remains unknown whether metabolic programming of tumor cells can be guided by immunosurveillance. Here, we report that T cell-mediated immunosurveillance in early staged tumorigenesis instructs c-Myc upregulation and metabolic reprogramming in tumor cells. This previously unexplored tumor-immune interaction is controlled by a non-canonical IFNg-STAT3 signaling and supports tumor immune evasion. Our findings uncover that immunoediting instructs deregulated bioenergetic programs in tumor cells for empowering them to disarm the T cell-mediated immunosurveillance by imposing metabolic tug-of-war between tumor and infiltrating T cells and forming the suppressive tumor microenvironment.

overall_design: Examination of DNA methylation in tumor cell grown from immunocompetent and immunocompromised mice


title: Circadian gene expression study of SMG6 and WT mouse livers

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

institute: UNIL

summary: Nonsense-mediated mRNA decay (NMD) has been intensively studied as a surveillance pathway that degrades erroneous transcripts arising from mutations or mis-splicing. Additional roles for NMD in determining mRNA stability in regular gene expression have emerged as well, yet it is poorly known which functions the pathway has in regular mammalian physiology in vivo. Here, we report a novel conditional Smg6 mouse allele that allows converting wild-type SMG6 to a nuclease-mutant version of the protein. We analyzed the consequences of an inactive NMD pathway on the function of the circadian clock whose mechanism is known to depend on high turnover rates of their oscillating mRNAs and proteins. Fibroblast and liver clocks show strong lengthening of free-running circadian periods under Smg6 mutant conditions. We identify a specific core clock component, Cry2, as directly NMD-regulated through its long 3' UTR. Our findings indicate that NMD has been co-opted as an mRNA decay pathway to limit the temporal availability of CRY2, one of the key transcriptional repressors in the rhythm-generating feedback loop, expanding the known scope of NMD regulation in vivo.

overall_design: Circadian comparative gene expression profiling analysis of RNA-seq data for WT and smg6 mutant livers.

first: Georgia

last: Katsioudi

first: René

first: Enes

last: Arpa

first: Sevasti

last: Gaspari

first: Angelica

last: Liechti

first: Miho

last: Sato

first: Steven

last: Brown

first: David

last: Gatfield


title: A novel Smg6 mouse model reveals circadian clock regulation through the nonsense-mediated mRNA decay pathway

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

overall_design: Refer to individual Series


title: Gene expression study of SMG6 and WT mouse fibroblast primary cell culture

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SMG6 mutant (flox/flox treated with 4-OHT), its control (flox/flox untreated), WT treated with 4-OHT and WT untreated.


title: COMPASS complexes redundantly regulate gene expression and DNA methylation in Arabidopsis [RNA-seq]

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences

summary: The evolutionally conserved COMPASS complexes are responsible for the catalyzation of H3K4 methylations. Recently, three types of COMPASS complexes which contains histone methyltransferases ATX1/2, ATX3, or ATX4/5 were identified in Arabidopsis. Here, we report the ATX proteins are essential for the survival of Arabidopsis. By RNA-seq and chromatin immunoprecipitation (ChIP-seq) analysis, we found ATX1/2-, ATX3-, and ATX4/5-containing COMPASS complex redundantly regulate gene expression and H3K4me3 modifications. In addition to the developmental-related genes, we found the expression of DNA methylation-related genes were also regulated by the COMPASS complexes. The transcript and H3K4me3 levels at the RdDM pathway genes (NRPE1, DCL3, IDN2, FDM2) and at the DNA demethylase encoding genes (ROS1, DML2, DML3) were down-regulated in atx1/2/4/5 mutants. Via bisulfate sequencing, we found the atx1/2/4/5 showed hypermethylation at CG and CHG contexts whereas the hypomethylation at CHH contexts. By comparing the differentially methylated regions (DMRs) in atx1/2/4/5 with that in ros1;dml2;dml3 (rdd) and in nrpe1, a large part of overlapping DMRs were identified. Based on these results and other findings, we propose that the hypermethylation in CG and CHG is partially caused by the down-regulation of ROS1/DML2/DML3, and the hypomethylation in CHH is mainly caused by the down-regulation of NRPE1. Furthermore, we revealed that the COMPASS complexes also play a redundant role in regulating the transcription of transposable elements (TEs). This study extends our knowledge about the function of COMPASS in plant development and illustrate the important roles for COMPASS complexes in the regulation of DNA methylation and TEs transcription.

overall_design: Examination of the mRNA expression of wild type and the COMPASS complex mutants grown under long day conditions.


title: Transcriptomic profiling of drug-treated human induced pluripotent stem cells (iPSCs) [DGE-GEO-Depot]

first: Ravi

last: Iyengar

address: 1425 Madison Avenue, Room 12-70C

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Kinase inhibitors (KIs) are a promising alternative to traditional chemotherapeutics in the treatment of multiple cancer types. Unfortunately, some KIs induce cardiotoxicity as a severe side effect. To identify gene expression signatures that might be indicative of KI-induced cardiotoxicity, we generated two cardiomyocyte cell lines from induced pluripotent stem cells that we obtained from six healthy volunteers. Treatment of these cell lines with 41 FDA-approved drugs, i.e. 22 kinase inhibitors, 4 monoclonal antibodies, 4 anthracyclines, 8 cardiac acting and 3 non-cardiac acting drugs, allowed generation of 81 lists of differentially expressed genes.

overall_design: Two different iPSC-derived cardiomyocyte cell lines were stimulated with one of 41 FDA-approved drugs or DMSO for 48 hours, followed by bulk transcriptomic analysis. Differentially expressed genes were identified between drug- and DMSO-treated cell lines.

first: Yuguang

last: Xiong

first: Priyanka

last: Dhanan

first: Bin

last: Hu

first: Gomathi

last: Jayaraman

first: Rosa

last: Tolentino

first: Yibang

last: Chen

first: Jens

last: Hansen

first: Kristin

last: Beaumont

first: Robert

last: Sebra

first: Dusica

last: Vidovic

first: Stephan

middle: C

last: Schürer

first: Joseph

last: Goldfarb

last: Gallo

first: Marc

middle: R

last: Birtwistle

first: Eric

last: Sobie

first: Evren

middle: U

last: Azeloglu

first: Seth

last: Berger

first: Angel

last: Chan

first: Christoph

last: Schanie

first: Nicole

last: Dubois


title: COMPASS complexes redundantly regulate gene expression and DNA methylation in Arabidopsis [Bisulfite-seq]

first: Xin-Jian

last: He

overall_design: Examination of the DNA methylation of wild type and atx1/2/4/5 grown under long day condition.


title: COMPASS complexes redundantly regulate gene expression and DNA methylation in Arabidopsis [ChIP-seq]

overall_design: Examination of H3K4me3 levels in wild type and the COMPASS complex mutants grown under long day conditions.


title: Expression data from the mouse brain after 90'-MCAO and sham-control surgery in: young male mice, young female mice, diabetic young male mice and aged male mice

city: Barcelona

first: Laura

last: Ramiro

state: Barcelona

address: Passeig De La Vall D'hebrón 119-129, Edificio Mediterránea, Laboratorio 120

country: Spain

institute: Vall d'Hebron Institute of Research

summary: Ischemic stroke is a major cause of death and disability worldwide. Translation into the clinical setting of neuroprotective agents showing promising results in pre-clinical studies has systematically failed. One of the reasons that could explain this failure is that the animal models used to test neuroprotectants do not represent properly the population affected by stroke, as the majority of pre-clinical studies are performed in healthy young male mice. In this regard, we aimed to determine if the response to cerebral ischemia differed depending on age, sex and the presence of comorbidities. Thus, we explored proteomic and transcriptomic changes triggered during the hyperacute phase of cerebral ischemia (by transient intraluminal middle cerebral artery occlusion) in the brain of: (1) young male mice, (2) young female mice, (3) aged male mice and (4) diabetic young male mice. Moreover, we compared the proteomic and transcriptomic changes of each group using an integrative enrichment pathways analysis to disclose key common and exclusive altered proteins, genes and pathways in the first stages of the disease. We found 61 differentially expressed genes (DEG) in male mice, 77 in females, 699 in diabetic and 24 in aged mice. Of these, only 14 were commonly dysregulated in all four groups. The enrichment pathways analysis revealed that the inflammatory response was the biological process with more DEG in all groups of animals, followed by hemopoiesis and lymphoid organ development. Our findings indicate that the response to cerebral ischemia regarding proteomic and transcriptomic changes differs depending on the sex, age and comorbidities, highlighting the importance of incorporating these groups of animals in future stroke research studies.

overall_design: Mice were submitted to 90'-middle cerebral artery occlusion (intraluminal model) or sham-control surgery. Thirty minutes later (2h from the induction of ischemia) animals were euthanized and transcardially perfused with cold-saline. Brains were collected and ipsilateral (IP) and contralateral (CL) brain hemispheres were separated.  mRNA fraction was obtained from each sample with the mirVana Paris kit and kept frozen (-80ºC) util the transcriptomic array was conducted.

first: Júlia

last: Faura

first: Alba

last: Simats

first: Joan

last: Montaner


title: COMPASS complexes redundantly regulate gene expression and DNA methylation in Arabidopsis


title: Study of bone marrow Nestin+ mesenchymal stromal cells in control and leukemic mice

city: Oslo

first: Lorena

last: Arranz

address: Forskningsveien 1

department: CRESCO - Centre for Embryology and Healthy Development

country: Norway

institute: University of Oslo

summary: NRAS-G12D+ mice show reduced numbers of mesenchymal stromal cells together with increased apoptotic rates as compared to healthy controls.

overall_design: Male Nes-gfp mice were lethally irradiated and transplanted with bone marrow cells from previously pI-pC induced control (Mx1-Cre-negative NRAS-G12D-positive) or leukemic (Mx1-Cre-positive NRAS-G12D-positive) mice, at the age of 28 weeks. Bone marrow Nes-gfp-positive mesenchymal stromal cells were FACS-sorted 4 weeks after the transplant, and total RNA was isolated and used for RNA sequencing.

first: Aurora

last: Bernal

first: Peter

last: Utnes

first: Ruth

last: Paulssen


title: Promoter sequence and architecture determine expression variability and confer robustness to genetic variants

city: Copenhagen

first: Robin

last: Andersson

address: Ole Maaloes Vej 5

department: Biology

country: Denmark

institute: University of Copenhagen


title: IL-1 receptor antagonist prevents bias to myelopoiesis in hematopoietic stem cells and protects from neoplasia

summary: Interleukin-1β (IL-1β) drives hematopoietic stem cell (HSC) differentiation into the myeloid lineage, and enhanced IL-1β signaling plays a key role in hematological malignancies. However, little is known on the role of its endogenous regulatory cytokine, IL-1 receptor antagonist (IL-1rn), on both healthy and malignant hematopoiesis. Here, we show that inflammation through unbalanced IL-1rn is present in the experimental model of acute myeloid leukemia (AML) driven by the NRAS-G12D oncogene.

overall_design: Total RNA was isolated from bone marrow (BM) HSC subsets of Mx1-Cre NRAS-G12D mice (IL-1rn-KO, n=3) and NRAS-G12D control (n=3) mic, 6 weeks after pI:pC injection. HSC were FACS sorted and immunophenotypically defined as follows: lin− c-kit+ Sca-1+ (LSK) CD34- Flt3- long term hematopoietic stem cells (LT-HSC), LSK CD34+ Flt3- short term HSC (ST-HSC) and LSK CD34+ Flt3+ multipotent progenitors (MPP). RNA was amplified and prepared for RNA-Seq using the SMART-Seq v4 Ultra Low Input RNA kit (Clontech).

first: Alicia

last: Villatoro


title: Promoter sequence and architecture determine expression variability and confer robustness to genetic variants [GM12878]

summary: Genetic and environmental exposures cause variability in gene expression. Although most genes are affected in a population, their effect sizes vary greatly, indicating the existence of regulatory mechanisms that could amplify or attenuate expression variability. Here, we investigate the relationship between the sequence and transcription start site architectures of promoters and their expression variability across human individuals. We find that expression variability can be largely explained by a promoter’s DNA sequence and its binding sites for specific transcription factors. We show that promoter expression variability reflects the biological process of a gene, demonstrating a selective trade-off between stability for metabolic genes and plasticity for responsive genes and those involved in signaling. Promoters with a rigid transcription start site architecture are more prone to have variable expression and to be associated with genetic variants with large effect sizes, while a flexible usage of transcription start sites within a promoter attenuates expression variability and limits genotypic effects. Our work provides insights into the variable nature of responsive genes and reveals a novel mechanism for supplying transcriptional and mutational robustness to essential genes through multiple transcription start site regions within a promoter.

overall_design: CAGE in untreated and 25ng/ml TNF-α for 6h GM12878 (4 replicates each)

first: Hjorleifur

last: Einarsson

first: Marco

last: Salvatore

first: Christian

last: Vaagenso

first: Nicolas

last: Alcaraz

first: Jette

last: Bornholdt

first: Sarah

last: Rennie


title: Neuronal ire-1 coordinates an organism-wide cold stress response by regulating fat metabolism -   Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and ire-1(ok799) Transcriptomes During Cold Stress.

city: Ramat-Gan

first: Ilana

last: Lebenthal-Loinger

address: Bar-Ilan University

department: The Mina & Everard Goodman Faculty of Life Sciences

country: Israel

institute: Bar-Ilan University

summary:
Cold affects many aspects of biology, medicine, agriculture and industry. Here, we identify a conserved endoplasmic reticulum (ER) stress response, distinct from the canonical unfolded protein response, which maintains lipid homeostasis during extreme cold stress. We establish that the ER stress sensor IRE-1 is critical for resistance to extreme cold and is activated by cold temperature. Specifically, neuronal IRE-1 signals via JNK-1 and neuropeptide-mediated signalling to regulate lipid composition throughout the animal. The requirement of this cold-response pathway can be bypassed by supplementation with unsaturated fatty acids or by altering the diet . Altogether, our findings define an ER-centric conserved organism-wide cold stress response pathway, consisting of sensors, effectors and signalling moieties, which control adaptation to cold throughout the organism. Better understanding of the molecular basis of cold adaptation is crucial for the design of safe and optimal use of cold conditions on live organisms and samples, and for the development of better treatments for hypothermia.
Conclusions: Our study represents a detailed analysis of C.elegans transcriptomes during cold stress, with biological replicates, generated by RNA-seq technology.

overall_design: Two-condition experiment (control and cold shock), Wild type (N2) C. elegans vs.ire-1(ok799) C. elegans. For control samples, worms were grown at 15 degrees from eggs until day 1 and harvested. For cold shock, worms were grown at 15 degrees from eggs until day 1 and then shifted to 2 degrees for 24 additional hours, and harvested thereafter. Data from 6 biological replicates were used for the N2 wild type strain.  Data from 3 biological replicates were used for the ire-1(ok799) strain.

first: Reut

last: Dudkevich

first: Sivan

last: Henis-Korenblit


title: Promoter sequence and architecture determine expression variability and confer robustness to genetic variants [immortalized lymphoblastoid cell lines]

overall_design: CAGE in 108 Eipstein-Barr virus immortalized lymphoblastoid cell lines


title: The efficacy of niclosamide on the intra-abdominal inflammatory environment in endometriosis

city: Pullman

first: Kanako

last: Hayashi

state: WA

address: BLS345, 1770 NE Stadium Way

department: School of Molecular Biosciences

institute: Washington State University

summary: Transcriptional states of peritoneal immune cells altered by induction of endometriosis-like lesions and niclosamide treatment

overall_design: Peritoneal lavage cells from the mice with the groups of Sham, Sham-niclosamide, ELL and ELL-niclosamide were analyzed by scRNA-seq

first: James

last: MacLean

first: Mingxin

last: Shi

first: Nikola

last: Sekulovski


title: Characterization of the innate immune response to Streptococcus pneumoniae infection in zebrafish

city: Tampere

first: Anni

last: Saralahti

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: we characterized the zebrafish innate immune response to pneumococcus through a whole-genome level transcriptome analysis. The analysis revealed the induction of genes coding for pro-inflammatory cytokines, chemokines, acute phase proteins, and antimicrobial peptides, indicating a well-conserved innate immune response to the human pathogen pneumococcus in zebrafish embryos. To gain understanding of the genetic factors associated with the increased risk for severe pneumococcal infection in humans, we carried out a medium-scale forward genetic screen in zebrafish. We identified a mutant fish line, which showed compromised defense against pneumococcus in septic larval infection model. Poor survival upon infection was associated with increased bacterial counts indicating defect in resistance. The transcriptome analysis of the mutant zebrafish embryos revealed otherwise normal innate immune response to pneumococcal infection but a deficient expression of a gene homologous for human C-reactive protein (CRP).

overall_design: identification of the up- and downregulated genes in Streptococcus pneumoniae infection in zebrafish embryos

first: Mika

last: Rämet


first: Lorena

last: Arranz

summary: Interleukin-1β (IL-1β) drives hematopoietic stem cell (HSC) differentiation into the myeloid lineage, and enhanced IL-1β signaling plays a key role in hematological malignancies. However, little is known on the role of its endogenous regulatory cytokine, IL-1 receptor antagonist (IL-1rn), on both healthy and malignant hematopoiesis. Here, we show that in vivo genetic deletion of IL-1rn induces HSC differentiation into the myeloid lineage and hampers B cell development. It also causes damage to the Stromal Compartment of the Bone Marrow.

overall_design: Total RNA was isolated from bone marrow HSC subsets of IL-1 receptor antagonist deficient mice (IL-1rn-KO, n=3) and control C57BL/6J (n=3) mice at the age of 20-25 weeks. HSC were FACS sorted and immunophenotypically defined as follows: lin− c-kit+ Sca-1+ (LSK) CD34- Flt3- long term hematopoietic stem cells (LT-HSC), LSK CD34+ Flt3- short term HSC (ST-HSC) and LSK CD34+ Flt3+ multipotent progenitors (MPP). Mesenchymal stromal cells (MSC) from the BM of the same groups of mice was also used for RNA-Seq. MSC were immunophenitypicall defined as CD45- Ter119- CD31- CD63+ (n=3 per group). RNA was amplified and prepared for RNA-Seq using the SMART-Seq v4 Ultra Low Input RNA kit (Clontech).


title: Cholinergic control of Th17 cell pathogenicity in experimental autoimmune encephalomyelitis [RNA-seq]

status: Public on Nov 13 2022

city: Toronto

first: Tak

last: Mak

state: ON

address: 610 University Ave

department: The Campbell Family Institute for Breast Cancer Research

institute: Princess Margaret Cancer Centre, University Health Network

summary: Elucidate a ChAT-associated gene expression program shared in ChAT-GFP-expressing splenic lymphocytes. (Seeking to answer the question, "Can we find a transcription factor that drives ChAT expression in lymphocytes?")

overall_design: Comparative RNA-seq analysis of splenic ChAT-GFP+ vs. ChAT-GFP- lymphocytes.  Cell types include Marginal zone B cells (MzB), Follicular B cells (FoB), and CD44+ Th cells.

first: Robert

last: Nechanitzky

first: Duygu

first: Parameswaran

last: Ramachandran

middle: W


title: Cholinergic control of Th17 cell pathogenicity in experimental autoimmune encephalomyelitis [ATAC-seq]

summary: Elucidate open chromatin regions associated with ChAT-GFP expression in in vitro polarized Th17 cells.

overall_design: Comparative analysis of open chromatin regions in ChAT-GFP-expressing versus ChAT-GFP-negative Th17 cell subsets.


title: Maize stalks infected with Fusarium graminearum PH-1 and Δcfem1

status: Public on Nov 12 2022

city: Shanghai

first: Weihua

last: Tang

address: 300 Fenglin Rd

institute: Shanghai Inst. Plant Phys. & Eco.

overall_design: Refer to individual Series


title: The transcriptomic analysis of maize stalks infected by Fusarium graminearum PH-1

summary: This experiment is to assess the transcript variants of genes ZmWAKFL, ZmWAKET and ZmLRR5 expression in F. graminearum-infected maize stalks

overall_design: The two-month-old maize stalks at 24 hours post F. graminearum PH-1 infection was named 1-PH-1. Total RNA extracted 1-PH-1 was used for library preparation. The RNA sequencing was performed at GENE DENOVO. The libraries for sequencing were prepared using Clontech SMARTer PCR cDNA Synthesis Kit. RNA sequencing was performed using an PacBio SequelII platform


title: The transcriptomic responses of maize stalks infected with Fusarium graminearum PH-1 and Δcfem1

summary: This experiment is to assess the changes of maize genes expression in response to Fusarium graminearum stains wild-type PH-1 and Δcfem1 mutant. F. graminearum  is the major casual fungal pathogen of Gibberella stalk rot on maize.

overall_design: Three biological replicates of two-month-old maize stalks at 24 hours post water treatment were named water-rep 1, 2, 3, used as control. Three biological replicates of two-month-old maize stalks at  24 hours post PH-1 infection were named PH-1-rep 1, 2, 3. Three biological replicates of two-month-old maize stalks at  24 hours post Δcfem1 infection were named Δcfem1-rep 1, 2, 3. Total RNA extracted from water-rep 1, 2, 3 and  PH-1-rep 1, 2, 3 and Δcfem1-rep 1, 2, 3 were used for library preparation. The RNA sequencing was performed at GENE DENOVO. The libraries for sequencing were prepared using NEBNext Ultra RNA Library Prep Kit. RNA sequencing was performed using an Illumina NovaSeq 6000 machine to obtain 150 nt paired-end reads.


title: Single-cell CRISPR immune screens reveal immunological roles of tumor intrinsic factors

city: Houston

first: Weiyi

last: Peng

state: Tx

address: 4800 Calhoun Rd

department: Department of Biology and Biochemistry

institute: University of Houston

summary: Genetic screens using CRISPR technology are widely exploited to explore novel targets and discover resistance mechanisms of cancer treatments, including cancer immunotherapy. As it is a time- and resource-intensive manner to individually validate potential candidates and clarify their working mechanisms, single-cell CRISPR screen platforms are designed and developed to parallelly characterize these factors and explore underlying mechanisms in a high-throughput manner. By leveraging the resources generated in our previous studies, Perturb-seq featured with capture sequences integrated into gRNA-expressing vectors and CROP-seq featured with poly(A)-tailed gRNA transcripts under the control of RNAPII promoters were selected among several independent single-cell CRISPR screen platforms to directly evaluate the performance of different scCRISPR screen platforms in determining underlying mechanisms of tumor intrinsic immune regulation and optimize experimental conditions and data analysis in immune-related scCRISPR screens. In the study, the influence of each perturbation on the gene expression profile and the response to in vitro T cell killing and in vivo anti-PD-1 treatment were comprehensively appraised at the single-cell level. It is clearly demonstrated that scCRISPR screen platforms could efficiently characterize gene expression profiles and perturbation effects present in individual cells during both in vitro and in vivo immune-related screen processes. Particularly, scCRISPR screen platforms presented more detail to determine heterogeneous change of gene expression in distinct knockout tumor cells in the presence of immune attack which cannot be easily assessed by canonical bulk RNA-seq. Collectively, scCRISPR screen technologies provide scalable and reliable platforms to validate identified tumor intrinsic immune factors identified from genome-wide CRISPR screens and elucidate their potential working mechanisms.

overall_design: We generated high-throughput scCRISPR datasets of MC38 mouse cells with various CRISPR perturbation, under in vitro and in vivo conditions, with and without T cell killing/anti-PD-1 treatment. Both mRNA and gRNA of cells were profiled by Perturb-seq and CROP-seq to determine the transcriptomic and purturbation status.

first: Jiakai

last: Hou

first: Shaoheng

last: Liang

first: Chunyu

last: Xu

first: Yanjun

last: Wei

first: Nidhi

last: Sahni

first: Daniel

last: McGrail

first: Yunfei

last: Wang

first: Chantale

last: Bernatchez

first: Michael

last: Davies

first: Stephen

last: Yi

first: Yiwen

last: Chen

first: Cassian

last: Yee

first: Ken


title: m6Am RNA methyltransferases PCIF1 regulate tumorigenesis of colorectal cancer and its immune responses to anti-PD-1 therapy

city: San Diego

first: Lingling

state: California

address: 9500 Gilman Dr

institute: University of California San Diego

summary: We applied RNA-seq on colon cancer tissues to profile the differentially expressed genes and compared the results with m6A-exo-seq

overall_design: To investigate the relationship between gene expression and m6Am modification on transcripts, differentially expressed genes (DEGs) are characterized by RNA-seq, m6Am modified transcripts are detected by m6A-exo-seq. Then DEGs and m6Am modified transcripts are intersected to obtain the genes whose expression are regulated by m6Am RNA modification

first: Tariq

last: Rana


title: The soluble guanylate cyclase stimulator praliciguat promotes ischemic leg reperfusion in leptin receptor-deficient mice

status: Public on Nov 11 2022

city: Pessac

first: Marie-Ange

last: Renault

address: 1 avenue de Magellan

institute: Inserm U1034

summary: Background: Lower-limb peripheral artery disease (PAD) is one of the major complications of diabetes mellitus. PAD is associated with poor limb and cardiovascular prognoses, along with a dramatic decrease in life expectancy. Despite major medical advances in the treatment of diabetes, a substantial therapeutic gap remains in the PAD population. Praliciguat is an orally available soluble guanylate cyclase (sGC) stimulator that has been reported both pre-clinically and in early-stage clinical trials to have favorable effects in metabolic and hemodynamic outcomes, suggesting that it may have a potential beneficial effect in PAD. Objective: We evaluated the effect of praliciguat on hind limb ischemia (HLI) recovery in a mouse model of type 2 diabetes. Methods: HLI was induced in leptin receptor-deficient (Leprdb/db) mice by ligation and excision of the left femoral artery. Praliciguat (10 mg/kg/day) was administered in the diet starting 3 days before surgery. Results: 28 days after surgery, ischemic foot perfusion and function parameters were better in praliciguat-treated mice than in vehicle controls. Improved ischemic foot perfusion was not associated with either improved traditional cardiovascular risk factors (i.e., weight, glycemia) or increased angiogenesis. However, treatment with praliciguat significantly increased arteriole diameter, decreased intercellular adhesion molecule 1 (ICAM1) expression, and prevented the accumulation of oxidative pro-angiogenic and pro-inflammatory muscle fibers. While investigating the mechanism underlying the beneficial effects of praliciguat therapy, we found that praliciguat significantly downregulated Myh2 and Cxcl12 mRNA expression in cultured myoblasts and that conditioned medium form praliciguat-treated myoblast decreased ICAM-1 mRNA expression in endothelial cells. These results suggest that praliciguat therapy may decrease ICAM-1 expression in endothelial cells by downregulating Cxcl12 in myocytes. Conclusion: Our results demonstrated that praliciguat promotes blood flow recovery in the ischemic muscle of mice with type 2 diabetes, at least in part by increasing arteriole diameter and by downregulating ICAM-1 expression.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ischemic tibialis anterior muscle of Leprdb/db treated or not with praliciguat

first: Ninon

last: Foussard


title: IL-17/CXCL5 signaling within the oligovascular niche mediates human and mouse white matter injury (OPC RiboTAG)

city: Los Angeles

first: Jason

middle: D

last: Hinman

state: CA

address: 635 Charles E. Young Dr. South, Rm 415

department: Neurology

institute: UCLA

summary: Cerebral small vessel disease and brain white matter injury are worsened by cardiovascular risk factors including obesity. Molecular pathways in cerebral endothelial cells activated by chronic cerebrovascular risk factors alter cell-cell signaling, blocking endogenous and post-ischemic white matter repair. Using cell-specific translating ribosome affinity purification(RiboTag) in white matter endothelia and oligodendrocyte progenitor cells (OPCs), we identify a coordinated interleukin-chemokine signaling cascade within the oligovascular niche of subcortical white matter that is triggered by diet-induced obesity (DIO).DIO induces IL-17B signaling that acts on the cerebral endothelia through IL-17Rb to increase both circulating and local endothelial expression of CXCL5. In white matter endothelia, CXCL5 promotes the association of OPCs with the vasculature and triggers OPC gene expression programs regulating cell migration through chemokine signaling. Targeted blockade of IL-17B reduced vessel-associated OPCs by reducing endothelial CXCL5 expression. In multiple human cohorts, blood levels of CXCL5 function as a diagnostic and prognostic biomarker of vascular cognitive impairment.

overall_design: Comparative gene expression profiling from the white matter of Tie2-Cre:RiboTAG mice on either control fat or high fat diet. RiboTAG gene expression analysis performed as IP vs. input

first: Guanxi

last: Xiao

first: Yutaro

last: Komuro

first: Riki

last: Kawaguchi


title: IL-17/CXCL5 signaling within the oligovascular niche mediates human and mouse white matter injury (Tie2-Cre RiboTAG)


title: Cholinergic control of Th17 cell pathogenicity in experimental autoimmune encephalomyelitis

first: Tak

last: Mak

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


title: Three classes of Arabidopsis SWI/SNF chromatin remodeling complexes differentially regulate development by affecting chromatin accessibility [ATAC-Seq]

first: xinjian

last: He

summary: We identify three classes of Arabidopsis SWI/SNF chromatin remodeling complexes and demonstrate that they regulate different developmental processes by affecting chromatin accessibility.

overall_design: Examination of the chromatin accessibility of the wild type and six mutants in Arabidopsis.

first: Xin-Jian


title: IL-17/CXCL5 signaling within the oligovascular niche mediates human and mouse white matter injury


title: Three classes of Arabidopsis SWI/SNF chromatin remodeling complexes differentially regulate development by affecting chromatin accessibility


title: Three classes of Arabidopsis SWI/SNF chromatin remodeling complexes differentially regulate development by affecting chromatin accessibility [ChIP-Seq]

overall_design: Examination of the enrichment of seven SWI/SNF subunits


title: Dissection of gastric homeostasis in vivo facilitates permenant capture of isthmus stem cells in vitro [Lgr5, Sox2]

status: Public on Nov 10 2022

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

institute: Juntendo University

summary: The glandular stomach is comprised of two regenerative compartments termed corpus and antrum, yet our understanding of the cell populations that maintain these epithelia is incomplete. Here, we show that cell types with equivalent functional roles in the corpus and antrum share similar transcriptional states including the immature isthmus population. To study isthmus cells, we developed a monolayer (2D) culture that is continually maintained via Lgr5-negative cells and produces diverse gastric cell types. Importantly, 2D cultures can be interconverted into conventional 3D organoids, recapitulating the plasticity of gastric epithelial cells in vivo. Finally, we utilized the 2D culture system to show that rare Sox2-expressing cells resemble enterochromaffin (EC) cells and Sox2 is both necessary and sufficient to generate EC cells. Together, our data provide important insights into the basis of gastric homeostasis, establish a tractable culture system to capture isthmus cells and uncover a role for Sox2 in EC cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for EpCAM high/low Lgr5 neg/pos and Sox2 neg/pos/high cells sorted from mouse corpus and antrum

first: Aaron

middle: J

last: Huebner


title: Three classes of Arabidopsis SWI/SNF chromatin remodeling complexes differentially regulate development by affecting chromatin accessibility [RNA-Seq]

overall_design: Examination of the mRNA expression of wild type and eleven mutants in Arabidopsis.


title: Dissection of gastric homeostasis in vivo facilitates permanent capture of isthmus stem cells in vitro [single-cell RNA-seq]

summary: The glandular stomach is comprised of two anatomically and functionally distinct epithelial tissues termed corpus and antrum. While these compartments continuously regenerate to ensure normal organ function, our understanding of the molecular and cellular determinants that maintain these tissues remains incomplete. Here, we established an unbiased account of all gastric epithelial cells of the mouse corpus and antrum using single cell RNA-sequencing, allowing us to compare these adjacent epithelia and their stem cell compartments. Our data reveals that epithelial cell types with equivalent functional roles in the corpus and antrum utilize similar transcriptional programs, and our results support the existence of two discernible stem cell populations within the gland base and isthmus regions of these tissues. To study isthmus stem cells, typically underrepresented in conventional, gland base-enriched organoid cultures, we developed a novel 2D monolayer culture system to propagate mouse and human gastric epithelia. These 2D cultures expand indefinitely via Lgr5- isthmus-like cells and maintain the ability to differentiate into diverse gastric cell types. While 2D corpus and antrum cultures were transcriptionally similar, they retained a molecular memory and differentiation bias that mirrored their tissue of origin. Furthermore, gastric 2D cultures could be readily and reversibly converted into conventional 3D organoids, highlighting the remarkable plasticity of undifferentiated stomach epithelial cells. Finally, we utilized the 2D culture system to show that rare primary epithelial cells with high levels of Sox2 expression, previously hypothesized to be gastric stem cells, most closely resembled enterochromaffin (EC) cells and Sox2 is both necessary and sufficient to generate EC cells in vivo. Together, our data (i) provide important insights into the basis of gastric epithelial regeneration and differentiation, (ii) establish a tractable 2D culture system to capture and manipulate primary gastric isthmus stem cells in vitro and (iii) uncover a role for the stem cell factor Sox2 during EC cell specification.

overall_design: Primary corpus and antrum samples of mouse glandular stomach; mouse and human 2D cultures for antrum and corpus; mouse antrum/corpus organoids.

first: Rebecca

last: Gorelov

first: Samuel

last: Demharter

first: Tobias

last: Kull

first: Ryan

middle: M

last: Walsh

first: Marty

middle: S

last: Taylor

first: Simon

last: Steiger

first: John

last: Mullen

first: Peter

middle: V

last: Kharchenko

first: Konrad

last: Hochedlinger


title: Dissection of gastric homeostasis in vivo facilitates permenant capture of isthmus stem cells in vitro


title: Dissection of gastric homeostasis in vivo facilitates permenant capture of isthmus stem cells in vitro [2D culture]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for cultured mouse forestomach, corpus and antrum


title: Dynamic partitioning of branched-chain amino acids- derived nitrogen supports renal cancer progression

city: Liverpool

first: Marco

last: Sciacovelli

state: Select State

address: Ashton Street, Sherrington Building

country: United Kingdom

institute: University of Liverpool

summary: Metabolic reprogramming is critical for tumor initiation and progression. However, the exact impact of specific metabolic changes on cancer progression is poorly understood. Here, we integrate multimodal analyses of primary and metastatic clonally-related clear cell renal cancer cells (ccRCC) grown in physiological media to identify key stage-specific metabolic vulnerabilities. We show that a VHL loss-dependent reprogramming of branched-chain amino acid catabolism sustains the de novo biosynthesis of aspartate and arginine enabling tumor cells with the flexibility of partitioning the nitrogen of the amino acids depending on their needs. Importantly, we identify the epigenetic reactivation of argininosuccinate synthase (ASS1), a urea cycle enzyme suppressed in primary ccRCC, as a crucial event for metastatic renal cancer cells to acquire the capability to generate arginine, invade in vitro and metastasize in vivo. Overall, our study uncovers a mechanism of metabolic flexibility occurring during ccRCC progression, paving the way for the development of novel stage-specific therapies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HK2, 786-O and its metastatic derivatives 786-M1A

first: Aurelien

last: Dugourd


title: Dbf4 Zn-finger motif is specifically required for stimulation of Ctf19-activated origins  in S. cerevisiae

first: Meghan

last: Petrie

address: 1050 Childs Way

department: Molecular Biology

institute: University of Southern California

summary: Eukaryotic genomes are replicated in spatiotemporal patterns that are stereotypical for individual genomes and developmental profiles.  In the model system S. cerevisiae, two primary mechanisms determine the preferential activation of replication origins during early S phase, thereby largely defining the consequent replication profiles of these cells.  Both mechanisms are thought to act through specific recruitment of a rate-limiting initiation factor, Dbf4-dependent kinase (DDK), to a subset of licensed replication origins.  Fkh1/2 is responsible for stimulation of most early-firing origins, except for centromere (CEN)-proximal origins that recruit DDK via the kinetochore protein Ctf19, which is required for their early-firing.  The C-terminus of Dbf4 has been implicated in its recruitment to origins via both the Fkh1/2 and Ctf19 mechanisms.  Here, we show that the Zn-finger motif within the C-terminus is specifically required for Dbf4 recruitment to CENs to stimulate CEN-proximal/Ctf19-dependent origins, whereas stimulation of origins via the Fkh1/2 pathway remains largely intact.  These findings re-open the question of exactly how Fkh1/2 and DDK act together to stimulate replication origin initiation.

overall_design:
Quantitative BrdU-IP-seq (QBU) Divided into 'IP' and the corresponding 'Total'.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for WT and mutant Dbf4 in S. cerevisiae

first: Haiyang

last: Zhang

first: Emily

last: Arnold

first: Yan

last: Gan

first: Oscar

last: Aparicio