title: Spatial transcriptomics of human plastic and non-plastic breast cancer subtypes

status: Public on Oct 16 2023

city: Lyon cedex 08

first: Pierre

last: Martinez

address: 28 rue Laennec

country: France

institute: Cancer Research Centre of Lyon

summary:
Cellular plasticity is a hallmark of rare Claudin-low (CL) and metaplastic (MBC) breast cancer subtypes, with a documented overlap whose exact extent is yet unknown, and which are associated to resistance and poor survival. We used spatial transcriptomics to further characterise these plastic subtypes, respectively defined molecularly and histopathologically. We identified 3 putative CL tumours (CL-like) and 4 genomically unstable TNBC samples via molecular analyses, combined with 4 MBCs identified by a breast pathologist.
High resolution images are available on Zenodo https://zenodo.org/records/20727406

overall_design: Fresh frozen tissue slides analysed using the 10X Genomics Visium spatial transcriptomics technology

first: Maria

last: Ouzounova

first: Cyril

last: Degletagne

first: Lauriane

last: Muller

first: Angele

last: Coutant


title: SOX9-positive pituitary stem cells differ according to their position in the gland and maintenance of their progeny depends on context.

status: Public on Oct 12 2023

city: London

first: Probir

last: Chakravarty

address: 1Midland Road

country: United Kingdom

institute: Francis Crick

type: Expression profiling by high throughput sequencing

summary: Pituitary stem cells are heterogeneous and differentiate more than formerly thought but maintenance of their progeny is selective.

overall_design: Single cell RNAseq analyses of FACSorted Sox9iresGFP pituitary cells.

first: Karine

last: Rizzoti

first: Robin

last: Lovell-Badge


title: Somatic mouse models of gastric cancer reveal genotype-specific features of metastatic disease

status: Public on Sep 03 2023

city: New York

first: Yu-Jui

last: Ho

address: 1275 York Avenue

country: USA

institute: Memorial Sloan Kettering Cancer Center

summary: Metastatic gastric carcinoma is a highly lethal cancer that responds poorly to conventional and molecularly targeted therapies. Despite its clinical relevance, the mechanisms underlying the behavior and therapeutic response of this disease are poorly understood owing, in part, to a paucity of tractable models that faithfully recapitulate different subtypes of the human disease. To close this gap, we developed methods to somatically introduce different oncogenic lesions directly into the stomach epithelium and show that genotypic configurations observed in patients produce metastatic gastric cancers that recapitulate the histological, molecular, and clinical features of all non-viral molecular subtypes of the human disease. Applying this platform to both wild-type and immune-deficient mice revealed previously unappreciated links between the genotype, organotropism and immune surveillance of metastatic cells that produced distinct patterns of metastasis that were mirrored in patients. Our results establish and credential a highly portable platform for producing autochthonous cancer models with flexible genotypes and host backgrounds, which can unravel mechanisms of gastric tumorigenesis or test new therapeutic concepts aimed at improving outcomes in gastric cancer patients.

overall_design: For RNA-seq analysis of the transcriptional profiles of MYC-p53, MYC-Apc and MYC-p53-Msh2 EPO-GEMM gastric tumors, as well as normal stomach of wild-type (WT) C57BL/6 mice, total RNA was extracted from bulk tissue using the RNeasy Mini Kit (Qiagen). Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.

first: Josef

last: Leibold

first: Corina

last: Amor

first: Kaloyan

middle: M

last: Tsanov

first: Francisco

middle: J

last: Sánchez-Rivera

first: Judith

last: Feucht

first: Hsuan-An

last: Chen

first: Timour

last: Baslan

first: Sha

last: Tian

first: Janelle

last: Simon

first: Alexandra

last: Wuest

first: John

middle: E

last: Wilkinson

first: Scott

middle: W

last: Lowe


title: A laboratory-based model ecosystem reveals genetic determinants of methanotroph phenotypic heterogeneity in a methane-oxygen counter gradient

status: Public on Oct 05 2023

city: Salt Lake City

first: Aaron

last: Puri

state: UT

address: 1390 Presidents Circle

institute: University of Utah

summary: Connecting genes to phenotypic traits in bacteria is often challenging because of a lack of environmental cues in laboratory settings. However, laboratory-based model ecosystems offer a means to better account for natural conditions compared to standard planktonic cultures, aiding in the linking of genotypes and phenotypes. Here, we present a simple, cost-effective, laboratory-based model ecosystem to study aerobic methane-oxidizing bacteria (methanotrophs). This system, referred to as the gradient syringe, is made by inoculating bacteria into semi-solid agarose held within a disposable syringe. Empty space at one end of the syringe is flushed with methane gas, while the other end is open to the atmosphere through a sterile filter. We show this system replicates the methane-oxygen counter gradient typically found in the natural soil environment of methanotrophs. Culturing the methanotroph Methylomonas sp. strain LW13 in this system produced a distinct horizontal band at the intersection of the counter gradient, which we discovered was due not to increased cell growth at this location but instead to an increased amount of extracellular polymeric substances (EPS). We also discovered that different methanotrophic taxa formed EPS bands with distinct locations and morphologies when grown in the methane-oxygen counter gradient. By comparing transcriptomic data from LW13 growing within and surrounding this EPS band, we identified genes implicated in cell growth and EPS formation within the gradient syringe, and validated the involvement of these genes with knockout strains. This work highlights the use of a laboratory-based model ecosystem that more closely mimics the natural environment to uncover methanotroph phenotypes missing from standard planktonic cultures, and link these phenotypes their genetic determinants.

overall_design: To investigate the cellular functions underlying the extracellular polymeric substance (EPS) phenotype observed at the midpoint of the methane-oxygen counter gradient within a semi-solid agarose matrix, we compared transcriptomes of the aerobic methanotroph Methylomonas sp. LW13 isolated from increasing depths. Late exponential/early stationary phase gradient syringes inoculated with LW13 were divided into three 2 mL segments, with the middle segment centered around the EPS band. These segments were designated “above”, “band”,  and “below”, representing oxygen-exposed, band-centered, and methane-flushed regions. For each of three independent replicates, RNA from eight LW13-inoculated syringes were pooled.

first: Delaney

middle: G

last: Beals


title: Single nucleus ATAC-seq datasets for "Temporally Specific Gene Expression and Chromatin Remodeling Programs Regulate a Conserved Pdyn Enhancer"

status: Public on Aug 07 2023

city: Birmingham

first: Jeremy

last: Day

state: Alabama

address: 1825 University Blvd SHEL 910

department: Neurobiology

institute: University of Alabama at Birmingham

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This dataset contains single nucleus Assay for Transposase-Accessible Chromatin (ATAC) sequencing results from rat nucleus accumbens tissue. Rats received repeated cocaine injections (20mg/kg, intraperitoneal injection), or saline injections as a control. Single-nucleus ATAC-seq was carried out with FACS-sorted nuclei using the 10X Genomics Chromium single cell sequencing platform using the Chromium Next GEM Single Cell ATAC Kit v2.

overall_design: This experiment contains 4 biological samples. Samples were adult rat nucelus accumbens brain tissue isolated from rats 1hr after the final (7th) daily treatment with either saline or cocaine. Tissue was lysed to allow for nuclei collection via centrifugation. FACS-sorted nuclei were subject to 10X Genomics GEM generation and barcoding followed by preparation of snATAC-seq libraries using the Chromium Next GEM Single Cell ATAC Kit v2. Libraries underwent paired-end sequencing on an Illumina Next-seq 500. Each sample has multiple raw fastq files, corresponding to different sequencing lanes (e.g., L001, L002, etc) and different reads (e.g., R1, R2, R3). Additional index files are also provided for each sample and each lane (I1).

first: Robert

middle: A

last: Phillips

first: Lara

last: Ianov


title: RNA-seq datasets for "Temporally Specific Gene Expression and Chromatin Remodeling Programs Regulate a Conserved Pdyn Enhancer" [RNA-seq]

summary: This dataset contains RNA-seq results from rat embryonic striatal neuronal cultures treated with either vehicle (complete Neurobasal media) or potassium chloride (10mM) for 4 h.

overall_design: This experiment contains 8 biological samples, each of which underwent RNA-seq on an Illumina NextSeq500 instrument. Samples were treated with neurobasal media (vehicle; samples V1, V2, V3, V4), or 10mM KCl (samples K1, K2, K3, K4) . The first letter of sample names denotes acute treatement (V = vehicle, K = KCl). The second digit denotes the unique replicate ID. Forward and reverse paired-end reads are denoted as "R1" or "R2" in raw file names.


title: IL-33–ST2 signaling promotes stemness in subtypes of myeloid leukemia cells through the Wnt and Notch pathways

status: Public on Aug 28 2023

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Medical Oncology

country: Switzerland

institute: Bern University Hospital

summary:
Purpose: The goal was to compare transcriptome profile of FACS-purified bone marrow AML1/ETO positive LSPCs from AML patients treated with rhIL-33 or controls (untreated).
Methods: The transcriptomic analysis of AML1/ETO positive LSPCs were assessed in biological replicates upon treatment treated rhIL-33 or controls using Illumina NextSeq 500.
Results: We mapped around 30 million sequence reads per sample to the human genome (GRCh38 - hg38) and identified differentially expressed transcripts in FACS-purified bone marrow AML1/ETO positive LSPCs from AML patients treated with rhIL-33 or controls (untreated). Differentially expressed genes between LSPCs treated with rhIL-33 or controls, were identified with a fold change ≥1.5 and FDR p-value <0.05.
Conclusions: Our study represents the first detailed RNA-seq analysis of FACS-purified bone marrow AML1/ETO positive LSPCs from AML patients treated with rhIL-33 or controls. Our results show that IL-33 treatment induces the regulation of metabolic process, cell cycle, regulation of NF-κΒ, MAPK and canonical Wnt signaling pathways, as well as the regulation of stem cell division and maintenance.

overall_design: mRNA of FACS-purified bone marrow derived AML1/ETO positive LSPCs from AML patients treated w/o rhIL-33 and profiled using Illumina NextSeq 500.

first: Pascal

last: Naef

first: Carsten

last: Riether

first: Adrian

middle: F

last: Ochsenbein


title: RNA-seq datasets for "Temporally Specific Gene Expression and Chromatin Remodeling Programs Regulate a Conserved Pdyn Enhancer"

summary: This dataset contains Assay for Transposase-Accessible Chromatin (ATAC) sequencing results from rat embryonic striatal neuronal cultures treated with either vehicle (complete Neurobasal media) or potassium chloride (10mM) for 4 h.

overall_design: This experiment contains 18 biological samples, each of which underwent ATAC-seq on an Illumina NextSeq500 instrument. Data are from two experiments. In the first experiment, samples were treated with neurobasal media (vehicle; samples V1, V3, V4), or 10mM KCl (samples K2, K3, K4) . The first letter of sample names denotes acute treatement (V = vehicle, K = KCl). The second digit denotes the unique replicate ID. In the second experiment, samples were treated with anisomycin (40µM) or DMSO control 30 minutes prior to depolarization with 10mM KCl. "DV" samples received DMSO followed by vehicle. "DK" sample received DMSO followed by 10mM KCl. "AK" samples received 40µM anisomycin followed by 10mM KCl.  Forward and reverse paired-end reads are denoted as "R1" or "R2" in raw file names.


title: Lysosomal cystine governs ferroptosis sensitivity in cancer via nuclear cysteine response

status: Public on Aug 30 2023

city: Ithaca

first: Saori

last: Uematsu

address: 526 Campus Road, Cornell University

department: Division of Nutritional Sciences

institute: Cornell University

summary: The amino acid cysteine and its oxidized dimeric form cystine are commonly believed to be synonymous in metabolic functions. Cyst(e)ine depletion not only induces amino acid response, but also triggers ferroptosis, a non-apoptotic cell death. Here we report that, unlike general amino acid starvation, cyst(e)ine deprivation triggers ATF4 induction at the transcriptional level. Unexpectedly, it is the shortage of lysosomal cystine, but not the cytosolic cysteine, that elicits the adaptative ATF4 response. The lysosome-nucleus signaling pathway involves the aryl hydrocarbon receptor (AhR) that senses lysosomal cystine via the kynurenine pathway. A blockade of lysosomal cystine efflux attenuates ATF4 induction and sensitizes ferroptosis. To potentiate ferroptosis in cancer, we develop a synthetic mRNA reagent CysRx that converts cytosolic cysteine to lysosomal cystine. CysRx maximizes cancer cell ferroptosis and effectively suppresses tumor growth in vivo. Thus, intracellular nutrient reprogramming has the potential to induce selective ferroptosis in cancer without systematic perturbation.

overall_design: RNA-seq of MEF cells with no treatment, cyteine starvation, full amino acid starvation, cyteamine treatment, transfected with sh-CTNS, transfected with sh-CTNS and CTNS plasmid.

middle: V

last: Swanda

first: Quanquan

last: Ji

first: Xincheng

last: Wu

first: Jingyue

last: Yan

first: Leiming

last: Dong

first: Yuanhui

last: Mao

first: Yizhou

first: Shu-Bing

last: Qian


title: An intersectional genetic cell depletion unravels the unique role of Th1-Treg cells in tumor immunity

status: Public on Jul 13 2023

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: The immune system comprises various cell types including regulatory T (Treg) cells, and their subsets. Since most of inducible depletion of immune cells for the functional analysis rely on a single protein or gene, it is no longer optimal for the analysis of cell subsets defined by multiple genes. Here we create the Cre- and Flp-double recombinase-dependent intersectional genetic VeDTR mouse system that can selectively label and inducibly deplete a subpopulation of Treg cells called T helper 1 (Th1)-Treg cells. Characterization of Th1-Treg cells using the VeDTR mice revealed the high resistance under oxidative stress, which was required for Th1-Treg cells to accumulate in tumor tissues. Moreover, short-term depletion of Th1-Treg cells only led to anti-tumor immunity but not autoimmunity, whereas that of whole Treg cells did both. Collectively, we have established a novel intersectional genetic immune cell depletion system to reveal unique features of Th1-Treg cells in tumor immunity.

overall_design: To characterize the difference between Th1-Treg cells and non-Th1-Treg cells, we analyzed gene expression pattern of YFP+ CD4+ CD25+ T cells (YFP+ Treg cells) and YFP- CD4+ CD25+ T cells (YFP- Treg cells) in the spleens of Foxp3-Cre/Tbx21-Flp/VeDTR(LF) mice.

first: Masaaki

last: Okamoto

last: Okuzaki

first: Masahiro

last: Yamamoto


title: Mouse microglia express unique miRNA-mRNA networks to facilitate age-specific functions in the developing central nervous system

status: Public on May 25 2023

city: Brisbane

first: Alexander

last: Walsh

state: Queensland

address: QBI Building 79, University of Queensland, St Lucia

country: Australia

institute: University of Queensland

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Mouse microglia express unique miRNA-mRNA networks to facilitate age-specific functions in the developing central nervous system [smRNA-seq]

summary: To investigate the expression of miRNA/mRNA regulatory networks in a developmental cohort of C57Bl/6 mice. This submission is the miRNA sequencing dataset.

overall_design: Sequenced the miRNAome and mRNAome of primary mouse microglia during brain development and adult homeostasis (three age groups; P6, P15 and 8 weeks). Sequenced and compared small RNA expression in both CD45+ microglial cells and CD45- bulk CNS cells in each sample. mRNA expression was sequenced in CD45+ microglial cells.

middle: D

first: Michele

last: Binder

first: Brendan

middle: R

last: E Ansell

first: Sarrabeth

last: Stone

first: Saskia

last: Freytag

first: Trevor

last: Kilpatrick


title: RNA-Seq Transcriptomic Analysis of Human Trabecular Meshwork Explants Exposed to TGF-β2: A Novel Approach Beyond Traditional Cell Culture Models

status: Public on Jul 03 2023

city: Paris

first: Frederic

last: Blond

address: 17 rue Moreau

institute: Institut de la Vision

summary: Glaucoma is a progressive optic neuropathy that can lead to irreversible blindness. Its main risk factor is elevated intraocular pressure (IOP). The trabecular meshwork (TM) acts as a filter between the anterior chamber of the eye and the aqueous humor collecting ducts, and dysfunction of this meshwork is responsible for the increased IOP in primary open-angle glaucoma (POAG). Considering that the culture conditions of human TM cells (HTMC) influence gene expression, we used human TM explants (HTMEx), which most closely mimic physiological conditions, to study the transcriptome of HTMC. The transforming growth factor-beta 2 (TGF-β2) signaling pathway has been implicated in the pathophysiology of POAG. To better characterize the role of TGF-β2 in this pathophysiology, we used bulk RNA sequencing and immunohistological analyses to establish gene signatures of TGF-β2-exposed HTMEx and correlate them with morphological alterations.  We identified differentially upregulated genes primarily involved in ECM regulation, as well as profibrotic TGF-β signaling pathways, confirmed using confocal microscopy to highlight changes in trabecular architecture, TGFβ2-induced F-actin rearrangements, and extracellular matrix (ECM) deposition. Enrichment analysis also revealed modulations of gene expression related to cytoskeletal organization, as well as activation of the bone morphogenic protein (BMP) and Wnt signaling pathways in response to TGF-β2.

overall_design: To gain a better understanding of the role of TGF-β2 in the molecular pathology of glaucoma, we used bulk RNA-Seq to analyze changes in the transcriptome of HTMEx exposed to TGF-β2.

first: Juliette

last: Buffault

first: Élodie

last: Reboussin

first: Karima

last: Kessal

first: Murat

last: Akkurt Arslan

first: Frédéric

first: Xavier

last: Guillonneau

first: Stéphane

last: Melik Parsadaniantz

first: Annabelle

last: Reaux Le Goazigo

first: Antoine

last: Labbé

first: Françoise

last: Brignole-Baudouin

first: Christophe

last: Baubouin


title: Single cell immune landscape of human atherosclerosis reveals the transcriptional signature of PLIN2hi/TREM1hi inflammatory lipid-associated macrophages and its association with cerebrovascular complications.

status: Public on May 22 2023

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

institute: Kennedy Institute of Rheumatology

summary: Atherosclerosis is a lipid-driven inflammatory disease.However, evidence emerging so far from single cell atlases suggests a dichotomy between lipid associated and inflammatory macrophage states. Here, we present the most inclusive reference atlas of human intraplaque immune cell communities to date.

overall_design:
Carotid plaques were collected from patients undergoing carotid endarterectomy. Tissues were enzymatically digested, and single cells were sorted for CD45+ cells.
CD45+ single cell suspensions were processed using the 10x Genomics platform with the aim to capture 5,000 cells/sample.
Update 10/6/26: Patients P1, P2, P6 and P7 were symptomatic (GSM6422822, GSM6422823, GSM6422826, GSM6422827). Patients P3 and P5 were asymptomatic (GSM6422824, GSM6422825).

first: Lea

last: Dib

first: Lada

last: Koneva

middle: N

first: Claudia

last: Monaco


title: Human SAMD9 is a Virus-Activatable Anticodon Nuclease Inhibiting Codon-Specific Protein Synthesis

status: Public on Jun 07 2023

first: Saori

last: Uematsu

summary: Transfer RNAs (tRNAs) are one of the most conserved components of protein synthesis machinery. An effective strategy for microbes to defend against viruses or competitors is to employ anticodon nucleases (ACNases) to deplete essential tRNAs and thereby shut off global protein synthesis, but this strategy has not been observed in multicellular eukaryotes. Here, we report that human SAMD9 is a virus-activatable ACNase that specifically depletes phenylalanine tRNA (tRNAPhe), causing codon-specific ribosomal pausing and inducing stress signaling. SAMD9 ACNase can be activated by poxvirus infection or by SAMD9 mutations associated with a spectrum of developmental or immunological disorders, implicating tRNAPhe deficiency as a major toxic effect in these human diseases and suggesting a new therapeutic strategy. The specificity of the ACNase, located to an N-terminal effector domain of SAMD9, is largely determined by a eukaryotic tRNAPhe specific 2’-O-methylation at the wobble position, making eukaryotic tRNAPhe a universal but specific target for SAMD9. The SAMD9 ACNase differs from the microbial ACNases in structure and substrate specificity, suggesting convergent evolution resulted in a universal immune defense strategy targeting tRNAs.

overall_design: tRNA-seq, Ribo-seq and RNA-seq. For tRNA-seq, HeLa cells were uninfected or infected with either WT or vK1-C7- VACV for 8 hours. tRNAs were isolated from total RNAs resolved on a denaturing gel, untreated or treated with a tRNA demethylase and subjected to tRNA-seq. For Ribo-seq and RNA-seq,  BT20 cells transduced with SAMD9-R1293W were uninduced or induced for SAMD9-R1293W expression.

first: Yan

last: Xiang

first: Yuanhui

last: Mao


title: Next-generation sequencing reveals IL11 drives preeclampsia by disrupting trophoblast differentiation and activating the placental inflammasome

status: Public on May 09 2023

city: Parkville

first: Guannan

last: Yang

address: Grattan Street

institute: University of Melbourne

summary: Preeclampsia is a life-threatening disorder of pregnancy unique to humans. Interleukin (IL)11 is elevated in serum from pregnancies that subsequently develop early-onset preeclampsia and pharmacological elevation of IL11 in pregnant mice causes the development of preeclampsia-like features (hypertension and proteinuria), however, the mechanism by which IL11 drives preeclampsia-like features is unknown. Using Next-generation sequencing we demonstrate that treatment with PEGylated IL11 (PEGIL11) inhibited placental expression of markers of spongiotrophoblast and syncytiotrophoblast linages and increased placental cathepsin production in wild-type and Asc-/- mice. Function studies showed that IL11 acts via Asc inflammasomes to induce tissue fibrosis and preeclampsia in mice. This study has far-reaching implications on our understanding of the underlying etiology of preeclampsia and the mechanism by which IL11 causes inflammation and fibrosis in many tissues and disease states.

overall_design: mRNA profiles of embryonic day 13 placenta following PEGylated (PEG) interleukin (IL)11 treatment in wild-type and Asc-/- (Pycard-/-) mice.

first: Ellen

last: Menkhorst

first: Leilanie

middle: L

last: Santos

first: Wei

last: Zhou

first: Kim-Anh

last: Lê Cao

first: Evdokia

last: Dimitriadis


title: A versatile nuclei extraction protocol for single nucleus sequencing in non-model species - optimization in various Atlantic salmon tissues

status: Public on May 08 2023

city: Roslin

first: rose

middle: ruiz

last: daniels

address: The University Of Edinburgh

institute: The University of Edinburgh

summary: The use of single cell sequencing technologies has exploded in non-model organisms, including fish and invertebrates in an aquaculture setting. One of the most expanding areas is the use sequencing nucleus from frozen tissues allowing being able to sample and sequence at different sites. Here we present a tested nucleus isolation protocol that outperforms the most reliable methods to extract nuclei (chopping in salt tween buffer) and improves its performance in non-model organisms.

overall_design: A versatile nuclei extraction protocol for single nucleus sequencing in fish species – optimization in various Atlantic salmon tissues. dx.doi.org/10.17504/protocols.io.261genwm7g47/v2

first: Rose

last: Ruiz Daniels

first: Richard

last: Taylor

first: Ross

last: Dobie

first: Sarah

last: Salisbury

first: Emily

last: Clark

first: Dan

last: Macqueen

first: Diego

last: Robledo


title: Reversible epigenetic alterations mediate PSMA expression heterogeneity in advanced metastatic prostate cancer.

status: Public on May 03 2023

city: Seattle

first: Brian

last: Hanratty

state: WA

address: 1100 Fairview Avenue

department: Division of Human Biology

institute: Fred Hutchinson Cancer Cancer

type: Methylation profiling by high throughput sequencing

summary: Purpose: Prostate-specific membrane antigen (PSMA) is a cell surface protein expressed in prostate cancer. PSMA targeted imaging and therapeutic approaches have shown clinical benefit, but there are limited data on the heterogeneity of PSMA tissue expression in metastatic castration-resistant prostate cancer (mCRPC) and the mechanisms involved in regulating PSMA expression are not well understood. Results: PSMA expression differed across molecular subtypes of CRPC. In a rapid autopsy cohort in which multiple metastatic sites per patient were sampled, we found that 13/52 (25%) of cases had no PSMA detected and 24/52 (46%) showed heterogeneous PSMA expression between individual metastases. Of these 52 cases, 35 (67%) cases harbored at least one PSMA negative metastatic site. Transcriptomic analyses of PSMA negative tumors revealed distinct differences relative to PSMA-positive tumors including expression of several drug targets. DNA methylation studies showed a tight correlation between CpG methylation and PSMA expression. Treatment with histone deacetylase (HDAC) and DNA methyl transferase (DNMT) inhibitors restored of PSMA expression in vitro and in vivo. Conclusions: Here, we document the extent of PSMA expression diversity in CRPC, highlight novel targeting approaches for PSMA-negative tumors and propose strategies to overcome resistance to PSMA-directed therapies. Collectively, these data can help to guide the clinical development of PSMA targeting agents for diagnosis and therapy.

overall_design: Experimental Design: Genome wide methylation changes were determined by whole genome bisulfite sequencing in prostate cancer patient derived xenografts (LuCaP 77,78, 93).

first: Erolcan

last: Sayar

first: Radhika

last: Patel

first: Ilsa

last: Coleman

first: Martine

middle: P

last: Roudier

first: Ailin

last: Zhang

first: Jin-Yih

last: Low

first: Lisa

last: Ang

first: Vipul

last: Bhatia

first: Mohamed

last: Adil

first: Hasim

last: Bakbak

first: David

last: Quigley

first: Michael

middle: T

last: Schweizer

first: Jessica

last: Hawley

first: Lori

last: Kollath

first: Lawrence

last: True

first: Felix

middle: Y

last: Feng

first: Neil

middle: H

last: Bander

first: Eva

last: Corey

first: John

middle: K

last: Lee

first: Colm

last: Morrissey

first: Roman

last: Gulati

first: Peter

middle: S

last: Nelson

middle: C

last: Haffner


title: Single cell-resolved study of advanced murine MASH reveals a homeostatic pericyte signaling module

status: Public on Feb 01 2023

city: Odense M

first: Kim

last: Ravnskjaer

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Non-alcoholic steatohepatitis (NASH) is associated with hepatic steatosis, intralobular inflammation, and fibrosis. The degree of hepatic fibrosis, mainly caused by excessive production of extracellular matrix proteins, is the sole predictor of liver-related and overall mortality in NASH patients. The hepatic stellate cells (HSCs) are causally implicated in fibrogenesis during NASH development but as sinusoidal pericytes also vital for vascular homeostasis of the healthy liver. Using single-cell RNA-sequencing we have analyzed whole liver plasticity and interrogated the transition of HSCs from pericytes in the healthy liver to collagen-producing cells in a diet-induced murine model of advanced NASH. We show how postprandial cues are sensed and integrated by HSCs promoting their phenotypic stabilization and, through paracrine mediators, sinusoidal health. While dominant under healthy conditions the basis for this multimodal signaling through stellate cell-specific Gs protein-coupled receptors and the bile-acid receptor NR1H4/FXR deteriorates in activated HSCs of the NASH liver. Expression of key signaling components were validated in situ in human and murine liver tissue supporting the translatability of our findings and pharmacological relevance in treatment of chronic liver diseases as NASH.

overall_design: Comparative bulk RNA-seq analysis of eight 52 weeks western diet-treated mice and nine 52 weeks chow diet-treated mice

first: Sofie

middle: M

last: Bendixen

last: Sørensen

first: Mike

last: Terkelsen

first: Daniel

last: Hansen

first: Kamilla

last: Hejn

first: Frederik

last: Bjerre

first: Annemette

last: Thulesen

first: Niels

last: Eriksen

first: Phillip

last: Hallenborg

first: Trine

last: Dam

last: Larsen

first: Charlotte

middle: W

last: Wernberg

first: Janusa

last: Vijayathurai

first: Emma

last: Scott

first: Ann-Britt

last: Marcher

first: Sönke

last: Detlefsen

first: Lars

last: Groentved

first: Henrik

last: Dimke

first: Mette

last: Lauridsen

first: Aleksander

last: Krag

first: Blagoy

last: Blagoev


title: EZH2 inhibition remodels the inflammatory senescence-associated secretory phenotype to potentiate pancreatic cancer immune surveillance

status: Public on Mar 13 2023

first: Yu-Jui

last: Ho

summary: Immunotherapies that produce durable responses in some malignancies have failed in pancreatic ductal adenocarcinoma (PDAC) due to rampant immune suppression and poor tumor immunogenicity. We and others have demonstrated that induction of the senescence-associated secretory phenotype (SASP) can be an effective approach to activate anti-tumor Natural Killer (NK) and T cell immunity. Here we found the pancreas tumor microenvironment (TME) suppresses NK and T cell surveillance following therapy-induced senescence through EZH2-mediated epigenetic repression of pro-inflammatory SASP genes. EZH2 blockade stimulated production of SASP chemokines CCL2 and CXCL9/10, leading to enhanced NK and T cell infiltration and PDAC eradication in mouse models. EZH2 activity was also associated with suppression of chemokine signaling and cytotoxic lymphocytes and reduced survival in PDAC patients. These results demonstrate that EZH2 represses of the pro-inflammatory SASP, and that EZH2 inhibition combined with senescence-inducing therapy could be a powerful means to achieve immune-mediated tumor control in PDAC.

overall_design: For RNA-seq analysis of PIP, PIL, LIL, and LIP tumor samples, GFP+ tumor cells were FACS sorted on a FACSAria (BD Biosciences) from the lungs or pancreas of tumor-bearing mice following 2-week treatment with vehicle or combined trametinib (1 mg/kg body weight) and palbociclib (100 mg/kg). Total RNA was extracted from tumor cells using the RNeasy Mini Kit (Qiagen). Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation. For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition. RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic, version 0.36, aligning sequencing data to GRCm38 (Ensembl, version 101) with STAR, version 2.5.3a, and genome wide transcript counting using featureCounts, version 1.6.3 to generate a RPKM matrix of transcript counts. Genes were identified as differentially expressed using R package DESeq2, version 1.28.1 with a cutoff of absolute log2FoldChange ≥ 1 and adjusted p-value <0.05 between experimental conditions. Heatmaps were generated using pheatmap, version 1.0.12. Over-representation analysis of differentially expressed genes (DEGs) against KEGG Pathways was performed using clusterProfiler, version 4.0.5.

first: Loretah

last: Chibaya

first: Katherine

last: Murphy

first: Kelly

last: DeMarco

first: Sneha

last: Gopalan

first: Haibo

last: Liu

first: Chaitanya

last: Parikh

first: Yvette

last: Lopez-Diaz

first: Melissa

last: Faulkner

first: Junhui

last: Li

first: John

last: Morris IV

first: Sachliv

last: Chana

first: Janelle

last: Simon

first: Wei

last: Luan

first: Amanda

last: Kulick

first: Elisa

middle: J

last: de Stanchina

first: Karl

middle: G

last: Simin

first: Lihua

last: Zhu

first: Thomas

last: Fazzio

first: Scott

last: Lowe

first: Marcus

last: Ruscetti


title: Pancreatic stellate and cancer cell transcriptomes from heterocellular, 3D invasive, cultures

status: Public on Mar 22 2023

city: Bath

first: Ed

last: Carter

address: Claverton Down

institute: University of Bath

summary: When combined into spheres and embedded in extracellular matrix, hetero-cellular cultures of pancreatic cancer and stellate cells produce invasive, stellate-led, projections. In order to establish what cancer and stellate cells are expressing in this context we generated chimeric spheres of mouse and human cells. Invasive spheroids could then be processed for RNA sequencing, with reads mapped back to parent species and thus cell type.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Two sets of human (Miapaca2 and Panc1) and mouse (DT6066, R254) pancreatic cancer cells were combined with mouse and human pancreatic stellate cells, respectively, and formed into hetero-cellular spheres.  Spheres were then embedded in collagen : matrigel hydrogels and cultured for 72 hours at which point invasive projections are evident. Total RNA was obtained through Trizol extraction and processed for sequencing. Cell type specific information was then extracted my matching reads to host species and therefore cell type.

first: Edward

first: Richard

last: Grose


title: Adult nucleus accumbens single-nucleus RNA-seq dataset for "Distinct subpopulations of D1 medium spiny neurons exhibit unique transcriptional responsiveness to cocaine"

status: Public on Jan 15 2023

first: Jeremy

last: Day

summary: This dataset contains single-nucleus RNA sequencing results from adult rat brain (nucleus accumbens) and serves as the basis for characterization of transcriptional response to repeated cocaine injections (20mg/kg, intraperitoneal injection). The goal of this experiment was to define the transcriptional response to repeated cocaine across distinct cell types in the nucleus accumbens. Single-cell sequencing was carried out with FACS-sorted nuclei isolated from these experiments using the 10X Genomics Chromium single cell sequencing platform.

overall_design: This experiment contains 4 biological samples. Samples were adult rat nucelus accumbens brain tissue isolated from rats 1hr after the final (7th) daily treatment with either saline or cocaine. Tissue was lysed to allow for nuclei collection via centrifugation. FACS-sorted nuclei were subject to 10X Genomics GEM generation and barcoding, GEM-RT cleanup and cDNA amplication, and library construction using a Chromium Single Cell 3ʹ Reagent Kit (v3 chemistry). Libraries underwent directional, paired-end PolyA+ RNA-seq on an Illumina Next-seq 500. Each sample has multiple raw fastq files, corresponding to different sequencing lanes (e.g., L001, L002, etc) and different reads (e.g., R1, R2). Additional index files are also provided for each sample and each lane (I1).

first: Robert

middle: A

last: Phillps

first: Corey

last: Duke

first: Jennifer

last: Tuscher

first: Morgan

middle: E

last: Zipperly

first: Lara

last: Ianov


title: Senescence rewires microenvironment sensing to facilitate anti-tumor immunity (bulk RNA-Seq)

status: Public on Jan 17 2023

first: Yu-Jui

last: Ho

summary: Cellular senescence involves a stable cell cycle arrest coupled to a secretory program that, in some instances, stimulates the immune clearance of senescent cells. Using an immune competent tumor model in which senescence triggers CD8 T cell-mediated tumor rejection, we show that senescence also remodels cell surface proteome to alter how they sense environmental factors, as exemplified by Type II interferon gamma (IFN-γ). Compared to proliferating cells, senescent cells upregulate IFN-γ receptor, become hypersensitized to microenvironmental IFN-γ, and more robustly induce antigen presenting machinery -effects also recapitulated in human tumor cells treated with senescence-inducing drugs. Disruption of the IFN-γ sensing by senescent cells blunts their immune-mediated clearance without disabling their characteristic secretory program or immune cell recruitment. Our results demonstrate that senescent cells have an enhanced ability to both send and receive environmental signals, and imply that each process is required for their effective immune surveillance.

sample_organism:
Mus
Mus musculus

platform_organism:
Mus
Mus musculus

overall_design: Transcriptomic characterization of in vitro proliferating (p53 suppressed) and senescent Nras mutant-p53 retorable (NSP) liver tumor cells:1) comparison between proliferating and senescent cells induced by different  triggers (p53 restoration, trametinib+palbociclib); 2) identification of BRD4-dependent transcriptional programs by JQ1 treatment upon proliferating and senescent (p53-restored) cells; 3) characterization of the effect of IFNg on proliferating or senescent (p53-restored) cells. For in vivo bulk tumor RNA-seq, proliferating tumor (p53 suppressed) was harvested 7-10 day after randomization point and senescent-induced tumor (p53 restored) was harvested 12 days after p53 restoration, allowing similar size of tumor at harvest.

first: Hsuan-An

last: Chen

first: Riccardo

last: Mezzadra

first: Jose

last: Adrover

first: Ryan

last: Smolkin

first: Changyu

first: Wei

first: Alexandra

last: Wuest

first: Sha

last: Tian

first: Xiang

last: Li

first: Ronald

last: Hendrickson

first: Mikala

last: Egeblad

first: Direna

last: Alonso-Curbelo


title: Comparative Computational RNA Analysis of Cardiac-Derived Progenitor Cells and Their Extracellular Vesicles [RNA-Seq]

status: Public on Dec 31 2022

city: Atlanta

first: Michael

last: Davis

state: GA

address: 2015 Uppergate Dr

institute: Emory University

summary: We aimed to examine differences between c-kit+ progenitor cells (CPCs) and CPC-derived extracellular vesicles (EV) RNA content. We isolated CPCs from cardiac biopsies of patients with congenital heart disease using magnetic bead sorting. We expanded CPCs, reduced serum for 24hrs, and collected secreted EVs from conditioned media with sequential ultracentrifugation. We isolate RNA from CPCs and CPC-EVs and sequence total RNA and miRNA. Sequencing was performed in at two different facilities: "E" and "N".

overall_design: Examination of CPC and CPC-derived EV RNA content

first: Jessica

middle: R

last: Hoffman

first: Hyun-Ji

last: Park


title: Impact of bacterial mono-colonization on intestinal and splenic CD4 T cells responses

status: Public on Sep 27 2022

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Intestinal T cells responses are strongly influenced by microbes. In this study we aimed to adress how different microbes and what microbial factors  influce intestinal T cells  differentiation and subsequent clonal expansion. Paticularly we choose Clostridium ramosum (Cr) as a strong induced of a subest of intestinal Tregs (Rorc+),  a medium inducer or Rorc+ Tregs an T1h7  Escherichia coli Nissle (EcN) and a strain that did not impact either o those cell (Pm). In addition,  to study the impact of  Escherichia coli Nissle (EcN) ploysaccharide K5 capsule on intestinal  T cells  activation, we used a EcN strain lacking the K5 capsule (kfiCD). At day 21 post-monocolonization we isolated CD4 T cells from monocolonized mice in both intestinal Lamina Propria and spleen and performed single cells RNA and TCR seq.

overall_design: Germ-free mice were monocolonized by oral gavage for 2 weeks with the indicated microbes: C. ramosum (CR), P.magnus (PM), E.coli Nissle (EcN) and EcN mutant kifCD (kif).  To assess the transcriptional inductions in colonic and splenic CD4 T cells, we flow-cytometrically sorted CD4 T cells (DAPI- CD19- CD4+ TCRβ+) or for somesamples CD4 (DAPI- CD19- CD4+ TCRβ+ CD44+)  from Germ-free mice (GF), CR, PM, EcN wild-type (EcN) and EcN kfiCD (kif) mutant at day 14 post-monocolonization and single cell RNA and TCR seq.

first: Martina

last: Sassone-Corsi

first: Deepshika

last: Ramanan

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Chromosome 9p21.3 Coordinates Cell Intrinsic and Extrinsic Tumor Suppression [scRNA-seq]

status: Public on Sep 08 2022

first: Yu-Jui

last: Ho

summary: Somatic chromosomal deletions are prevalent in cancer, yet their effects are poorly understood. The most prominent homozygous deletions affect chromosome 9p21.3 and eliminate the CDKN2A/B tumor suppressor genes, thus disabling a cell intrinsic barrier to tumorigenesis. However, half of 9p21.3 deletions encompass a cluster of 16 type I interferons (IFNs) whose co-deletion remains unexplored. To functionally dissect 9p21.3 and other genomic deletions, we developed MACHETE (Molecular Alteration of Chromosomes with Engineered Tandem Elements), a genome engineering strategy that enables flexible modeling of megabase-sized deletions. Applying MACHETE to a syngeneic mouse model of pancreatic cancer, we show that concomitant loss of the IFN cluster with Cdkn2a/b enhanced immune evasion, metastasis, and immunotherapy resistance compared to Cdkn2a/b deletions alone. Mechanistically, IFN co-deletion disrupted type I IFN signaling in the tumor microenvironment, leading to marked changes in infiltrating immune cells and escape from CD8+ T cell surveillance, effects largely driven by the poorly understood interferon epsilon (Ifne). These results reveal how IFN-encompassing 9p21.3 deletions disable cell intrinsic and extrinsic tumor suppression, thereby providing a pervasive route for immune evasion, metastasis, and immunotherapy resistance. Our study provides a framework for interrogating large deletion events in cancer and beyond.

overall_design: sc RNA-seq analysis was performed on CD45+ cells sorted from from KrasG12D; sgP53; dS or KrasG12D; sgP53; dL tumors, which were harvested from immune-competent mice treated with control IgG or anti-IFNAR1 blocking antibody.

first: Francisco

last: Barriga

first: Kaloyan

last: Tsanov

first: Yu

last: Jo

first: Noor

last: Sohail

first: Amy

last: Zhang

first: Timour

last: Baslan

first: Isabella

last: Del Priore

first: Brigita

last: Meskauskaite

first: Geulah

last: Livshits

first: Janelle

last: Simon

first: Almudena

last: Chaves-Perez

first: Dafna

last: Bar-Sagi

first: Christine

last: Iacobuzio-Donahue

first: Faiyaz

last: Notta

first: Ronan

last: Chaligne

first: Roshan

last: Sharma

first: Dana

last: Pe'er

first: Scott

last: Lowe


title: Chromosome 9p21.3 Coordinates Cell Intrinsic and Extrinsic Tumor Suppression

first: Yu-Jui

last: Ho

overall_design: RNA-seq analysis was performed from KrasG12D; sgP53; dS or KrasG12D; sgP53; dL tumors, which were harvested from immune-competent mice treated with control IgG or anti-IFNAR1 blocking antibody. Bulk tumor pieces were flash frozen on dry ice and stored at -80C. Tissues were then mechanically disrupted in Trizol and RNA was extracted following manufacturer’s instructions. RNA integrity was analyzed with an Agilent 2100 Bioanalyzer. Samples that passed QC were then used for library preparation and sequencing. Samples were barcoded and run on a HiSeq (Ilumina) in 76 bp SE run, with an average of 50 million reads per sample. RNA-Seq data was then trimmed by removing adapter sequences and reads were aligned to the mouse genome (GRCm38.91; mm10), and transcript counts were used to generate an expression matrix.

first: Francisco

last: Barriga

first: Kaloyan

last: Tsanov

first: Alexandra

last: Wuest

first: Direna

last: Alonso-Curbelo


title: LncRNA CHROME regulates the interferon response to viral challenge  [COVID]

status: Public on Aug 23 2022

first: Coen

last: van Solingen

state: NY

address: 435 E30th street SB 704

department: Medicine/Cardiology

institute: NYU Grossman School of Medicine

summary: Long non-coding RNAs (lncRNAs) are important regulators of the immune response. Here we identify a novel function for the primate-specific lncRNA, CHROME. We established that CHROME is most highly transcribed in human macrophages treated with influenza virus and/or polyIC.

overall_design: Whole blood RNAseq performed on subjects with COVID and controls.

first: Tessa

last: Barrett

first: Jeffrey

last: Berger

first: Kathryn

last: Moore


title: LncRNA CHROMR regulates antiviral immunity in humans [ChIRP-Seq]

summary: Long non-coding RNAs (lncRNAs) are important regulators of the immune response. Here we identify a novel function for the primate-specific lncRNA, CHROMR. We established that CHROME is most highly transcribed in human macrophages treated with influenza virus and/or polyIC.

overall_design: We used three replicate samples of THP1 macrophages and performed ChIRP-Seq


title: LncRNA CHROME regulates the interferon response to viral challenge [ChIP-Seq]

summary: Long non-coding RNAs (lncRNAs) are important regulators of the immune response. Here we identify a novel function for the primate-specific lncRNA, CHROME. We established that CHROME is most highly transcribed in human macrophages treated with bacterial lipopolysaccharide and RNA viruses.

overall_design: We used three replicate samples of THP cells that were treated with gapmer targeting CHROME compared to two replicate control samples. In these cells we performed H3k27ac ChIP-Seq

first: Michael

last: Gildea


title: LncRNA CHROME regulates the interferon response to viral challenge [RNA-Seq]

overall_design: We used three replicate samples of THP cells that were treated with gapmer targeting CHROME and subsequently treated these cells with polyIC.


title: LncRNA CHROME regulates the interferon response to viral and bacterial challenge [RNA-Seq]

overall_design: We used three replicate samples of THP cells that were treated with gapmer targeting CHROME compated to three replicate control samples. We repeated this experiment in which we treated the cells with LPS.


title: Effect of hypertonicity on Gene expression and contribution of Nfat5

status: Public on Aug 17 2022

city: Halle

first: Bayram

last: Edemir

address: Ernst-Grube-Str. 20

country: Germany

institute: University Hospital Halle (Saale)

summary: We analyzed the  gene expression in WT and Nfat5 deficient kidneys

overall_design: Renal cortex and renal inner medulla from WT and NFAT5-KO mice were used for gene expression analysis.


title: A method to investigate muscle target-specific transcriptional signatures of single motor neurons

status: Public on Jul 29 2022

city: Basel

first: Patrick

last: Tschopp

address: Vesalgasse 1

department: Department of Environmental Sciences

institute: University of Basel

summary: To investigate target-specific transcriptional signatures of single motor neurons, here we combine ex-ovo retrograde axonal labelling in mid-gestation chicken embryos with manual isolation of individual fluorescent cells and Smart-seq2 single-cell RNA-sequencing. We validate our method by injecting the EMR and FDQ wing muscles and harvest a total of 50 fluorescently labeled cells, in which we detect upto 10000 transcribed genes. Additionally, we present visual cues and cDNA metrics predictive of sequencing success.

overall_design: SMART-seq2 single neuron RNA-seq of manually picked motor neurons identified by axonal backfill from EMR and FDQ muscles of Day 9  chicken embryos.

first: Bianka

last: Berki

first: Fabio

last: Sacher

first: Antoine

last: Fages

first: Maëva

last: Luxey


title: LncRNA CHROME regulates the interferon response to viral challenge

status: Public on Aug 22 2022

city: New York

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

overall_design: Refer to individual Series


title: Combination treatment with BMI1 and MAPK/ERK inhibitors is effective in medulloblastoma

status: Public on Feb 28 2022

city: London

first: Silvia

last: Marino

address: 4, Newark St

institute: Queen Mary University of London

summary: Epigenetic changes play a key role in the pathogenesis of medulloblastoma (MB), the most common malignant pediatric brain tumor. Here we identify a synergic vulnerability of BMI1High;CHD7Low MB cells to a combination treatment with BMI1 and MAPK/ERK inhibitors and we elucidate the molecular mechanisms underpinning the CHD7-BMI1-MAPK regulatory axis which mediates the anti-tumor effect of these inhibitors in vitro and in vivo, in a pre-clinical mouse model. Enhanced ERK1 and ERK2 phosphorylation activity is found in BMI1High;CHD7Low G4 MB patients, raising the possibility that they could be amenable to a similar therapy.

overall_design:
RNA-Seq of MB cells treated with BMI1 and MAPK/ERK inhibitors.

UPDATE: [Jun-03-2026] "28h" was corrected to "24h" in the Sample titles and treatments.

first: Sara

last: Badodi

first: Nicola

last: Pomella


title: A preclinical platform for assessing anti-tumor effects and systemic toxicities of cancer drug targets

status: Public on Mar 30 2022

first: Yu-Jui

last: Ho

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

summary: Anti-cancer drug development campaigns often fail due to an incomplete understanding of the therapeutic index differentiating the efficacy of the agent against the cancer and its on-target toxicities to the host. To address this issue, we established a versatile preclinical platform in which genetically defined cancers are produced using somatic tissue engineering in transgenic mice harboring a Doxycycline-inducible short hairpin RNA against the target of interest. In this system, target inhibition is achieved by addition of doxycycline, enabling simultaneous assessment of efficacy and toxicity in the same animal. As proof-of-concept, we focused on CDK9 — a cancer target whose clinical development has been hampered by compounds with poorly understood target specificity and unacceptable toxicities. We systematically compared phenotypes produced by genetic Cdk9 inhibition to those achieved using a recently developed highly specific small molecule CDK9 inhibitor and found that both perturbations led to robust anti-tumor responses. Remarkably, non-toxic levels of CDK9 inhibition could achieve significant treatment efficacy, and dose-dependent toxicities produced by prolonged CDK9 suppression were largely reversible upon Cdk9 restoration or drug withdrawal. Overall, these results validate a versatile in vivo target validation platform that can be employed for rapid triaging of therapeutic targets and lend support to efforts aimed at advancing CDK9 inhibitors for cancer therapy.

overall_design: For RNA-seq analysis of the transcriptional profiles of Myc;p53-/- liver tumors expressing shCdk9 or shRenilla (control) induced by doxycycline, as well as normal liver tissues with doxycycline-induced shRenilla expression, total RNA was extracted from bulk tissue using the RNeasy Mini Kit (Qiagen). Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.

first: Xiang

last: Li

first: Chun-Hao

last: Huang

first: Francisco

last: Sánchez-Rivera

first: Margaret

last: Kennedy

first: Darjus

middle: F

last: Tschaharganeh

first: John

last: Morris IV

first: Antonella

last: Montinaro

first: Kevin

last: O'Rourke

first: Ana

last: Banito

last: Wilkinson

first: Chi-Chao

last: Chen

first: Lukas

last: Dow

first: Sha

last: Tian

first: Wei

last: Luan

first: Elisa

last: de Stanchina

first: Tinghu

last: Zhang

first: Nathanael

last: Gray

first: Henning

last: Walczak

first: Scott

last: Lowe


title: Increased expression of p53 with APR-246 (eprenetapopt) reprograms tumor-associated macrophages to promote the efficacy of immune checkpoint blockade

status: Public on Feb 11 2022

first: Yu-Jui

last: Ho

summary: Expression of genes in sorted CD4, CD8 and non-T CD45 cells isolated from TME of B16 tumors in wildtype B6, APR-246 treated wildtype B6 and Super p53 mice.

overall_design: mice bearing B16 tumors were implanted in super p53 or WT mice. WT mice were treated with vehicle or APR-246 starting day 7 for 6 days and single cell suspensions of the tumors were obtained and antibody stained for CD45, CD8. CD4 and live/dead. CD45+ CD8+, CD45+CD8+ and CD45+CD4-CD8- sorted and RNA was extracted with the PAXgene RNA kit and purified in accordance with the manufacturer’s protocols. RNA was assessed with the Agilent BioAnalyzer for quantity and quality.

first: Arnab

last: Ghosh

first: Taha

last: Mergoub


title: Multimodal profiling of the transcriptional regulatory landscape of the developing mouse cortex identifies Neurog2 as a key epigenome remodeler

status: Public on Jan 27 2022

city: Neuherberg

first: Boyan

last: Bonev

state: Deutschland

address: Ingolstädter Landstr. 1

institute: Helmholtz Zentrum München

summary: How multiple epigenetic layers and transcription factors (TFs) interact to facilitate brain development is largely unknown. Here, we combined single-cell RNA-seq and single-cell ATAC-seq with cell-type-specific measurements of enhancer activity, DNA methylation and three-dimensional genome architecture to systematically map the regulatory landscape of neural differentiation in the mouse neocortex in vivo. This allowed us to identify thousands of new enhancers, their predicted target genes and the temporal relationships between enhancer activation, epigenome remodeling and gene expression. We characterize specific neuronal transcription factors associated with extensive and frequently coordinated changes across multiple epigenetic modalities. In addition, we functionally demonstrate a new role for Neurog2 in directly mediating enhancer activity, DNA demethylation, increasing chromatin accessibility and facilitating chromatin looping in vivo. Our work provides a global view of the gene regulatory logic of lineage specification in the cerebral cortex.

sample_organism:
Escherichia coli
Mus musculus

platform_organism:
Escherichia coli
Mus musculus

overall_design: scRNA-seq and scATAC-seq of the somsatosensory area of the E14.5 mouse cortex. Additionally, massively parallel reporter assay (MPRA) and MethylHiC from isolated cell populations, namely neuronal stem cells (NSC), intermediate progenitors (IPC),  projection neurons (PN), obtained from the somatosensory area of the E14.5 mouse cortex. Functional validation of Neurog2 using Hi-C, RNA-seq and NOME-seq in GFP and Neurog2 in vivo overexpression via in utero electroporation.

first: Florian

last: Noack

first: Silvia

last: Vangelisti

first: Gerald

last: Raffl

first: Madalena

last: Carido

first: Jeisimhan

last: Diwakar

first: Faye

last: Chong


title: TNFRSF4-expressing regulatory T cells promote immune escape of chronic myeloid leukemia stem cells

status: Public on Nov 03 2021

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

institute: Bern University Hospital

summary:
Purpose: The goal of this study was to compare transcriptome profile of FACS-purified bone marrow (BM) Tregs isolated from CML or naive mice.
Methods: Transcriptomic profiles of BM Tregs from CML or naïve mice were assessed in biological replicates using Illumina NextSeq 500.
Results: We mapped around 30 million sequence reads per sample to the mouse genome (GRCm38 - mm10) and identified expressed transcripts in FACS-purified BM Tregs isolated from CML or naive mice. RNA-seq data confirmed stable expression of known housekeeping genes. Differentially expressed genes between Tregs derived from the BM of CML and naïve mice were identified.
Conclusions: Our study represents the first detailed RNA-seq analysis of FACS-purified BM Tregs isolated from CML or naive mice. Our results show that Tregs derived from the BM of CML mice have an increased metabolic activity, cell cycle activity and immunosuppressive capacity.

overall_design: BM Tregs from CML or naive mice were then isolated for RNA extraction and profiled using Illumina NextSeq 500.

first: Magdalena

last: Hinterbrandner

first: Carsten

last: Riether


title: Comprehensive molecular and clinical characterization of NUP98 fusions in pediatric acute myeloid leukemia

status: Public on Dec 15 2021

first: Soheil

last: Meshinchi

state: Washington

address: 1100 Fairview Ave N.

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

summary: Genome wide DNA methylation profiling of pediatric acute myeloid leukemia (AML) from diagnostic and relapsed specimens.

overall_design: Bisulphite converted DNA from primary pediatric AML  samples were hybridised to the Illumina Infinium HumanMethylationEPIC BeadChip.

first: Rhonda

last: Ries

first: Jason

last: Farrar

first: Tim

last: Triche Jr.


title: Senescence induction dictates response and resistance to chemo- and immunotherapy in preclinical models of ovarian cancer

status: Public on Dec 31 2021

first: Yu-Jui

last: Ho

summary: High-grade serous ovarian carcinoma (HGSOC) is associated with a dismal prognosis. While most patients initially respond to platinum-based chemotherapy, they almost always acquire resistance, and only a small subset of HGSOC patients benefit from immune checkpoint blockade (ICB). To elucidate the disease mechanisms and factors underlying sensitivity and resistance to conventional and immune-based therapies, we developed a fast and flexible pre-clinical mouse model based on somatic introduction of HGSOC-associated genetic alterations into the ovary of immune competent mice using tissue electroporation. Tumors in these mice recapitulate both the proclivity of HGSOC to metastasize to the peritoneum and omentum and display histological, molecular, and treatment response features reminiscent of the human disease. Using this model, we show that the clinically observed increase in sensitivity of homologous recombination (HR) deficient ovarian tumors to platinum-based chemotherapy is driven by the preferential induction of senescence in the tumor cells. Intriguingly, HR-deficient (but not HR-proficient) tumors are uniquely sensitive to the combination of cisplatin and ICB owing to senescence-mediated activation of the cytosolic DNA sensing. This output becomes deactivated in a therapy-resistant model. Thus, genetically defined electroporation-based mouse models can be leveraged to elucidate the biology and therapy responses of HGSOG with the goal of improving treatment options for this deadly disease.

overall_design: For RNA-seq analysis of the transcriptional profiles of MP EPO-GEMM ovarian tumors, as well as normal ovaries of wild-type (WT) C57BL/6, total RNA was extracted from bulk tissue using the RNeasy Mini Kit (Qiagen). Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.

first: Stella

middle: V

last: Paffenholz

first: Camilla

last: Salvagno

first: Yu-jui

first: Matthew

last: Limjoco

first: Timour

last: Baslan

first: Sha

last: Tian

first: Amanda

last: Kulick

first: Elisa

last: de Stanchina

first: John

last: Wilkson

first: Francisco

last: Barriga

first: Dmitriy

last: Zamarin

first: Juan

last: Cubillos-Ruiz

first: Josef

last: Leibold

first: Scott

last: Lowe


title: NMNAT2 Is Downregulated in Glaucomatous RGCs and RGC-Specific Gene Therapy with NMNAT2 Overexpression Rescues Glaucomatous Neurodegeneration and Visual Function

status: Public on Aug 22 2021

city: Palo Alto

first: Xue

last: Feng

state: CA

address: 1651 Page Mill road

institute: Stanford

summary: The lack of neuroprotective treatments for retinal ganglion cells (RGCs) and optic nerve (ON) is a central challenge for glaucoma management. Emerging evidence suggests that redox factor NAD+ decline is a hallmark of aging and neurodegenerative diseases including glaucoma. Supplementation with NAD+ precursors and overexpression of the nicotinamide mononucleotide adenylyltransferase (NMNAT), the key enzyme involved in the NAD+ biosynthetic process, have significant neuroprotection effect on glaucoma. Among the three NMNAT isoforms, only NMNAT2 is enriched in neurons, especially in axons, however, its role in glaucoma is not well studied. Here we present the expression levels of the enzymes that involved in NAD+ metabolism in both naïve and glaucomatous mouse RGCs. Intriguingly, NMNAT2 is the dominant form of NMNATs in RGCs and only its mRNA level, but not NMNAT1 or NMNAT3, is significant decreased in glaucomatous RGCs. We then demonstrated proof-of-principal gene therapy strategy of restoring RGC-specific NMNAT2 and NAD+ levels by AAV2-mediated RGC-specific promoter mSncg-driven long half-life NMNAT2 mutant. This gene therapy strategy is further tested in two optic neuropathy models, traumatic ON crush model and ocular hypertension glaucoma model. RGC-specific NMNAT2 overexpression significantly promotes RGC somata and axons survival and preserves visual function in both models. Our studies suggest that the weaking of NMNAT2 expression in glaucomatous RGCs contributes to detrimental NAD+ decline and that modulating RGC intrinsic NMNAT2 level by AAV2-mSncg vector is a potent gene therapy for glaucomatous neuroprotection.

overall_design: RGC mRNA profiles of  naive and SOHU mice

first: Pei

last: Zhuang


title: Single-cell RNA-seq to decipher the subpopulations of human decidual leukocytes in normal and RSA pregnancies

status: Public on Jul 20 2021

city: Beijing

first: Yan-Ling

last: Wang

state: Beijing

address: Beichen West Rd., Chaoyang, Beijing

department: State Key Laboratory of Stem Cell and Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Maternal fetal immune tolerance is a biological event that plays a key role in pregnancy. In particular, the mechanism by which the maternal immune system does not exclude the semi-identical antigen of the fetus has not been fully answered so far. The most serious result of the maternal fetal immune tolerance balance is the recurrent spontaneous abortion (RSA). The fetus is rejected by the mother in the early pregnancy and cannot continue to develop in the uterus. Based on these scientific questions, we used single-cell sequencing technology to analyze nearly 30,000 leukocytes in the decidua of normal and RSA. A total of 13 immune cell subsets were found, of which dNK cells were more prominent, The lineage differentiation pathway of dNK cells was excavated, and the pathological role of dNK differentiation abnormality in the occurrence of RSA was analyzed. Our results deepen our understanding of the differentiation and function of human decidual leukocytes, especially dNK cells. We clearly recognize that the immune system has dynamic changes compared with normal pregnancy under pathological conditions, which is likely to occur in RSA. The important factors, we expect our results to provide a new basis for RSA's immune diagnosis and treatment strategy.

overall_design: Single cell sequencing on decidual immune cellss was performed from normmal pregnancy women and recurrent spontaneous abortion (RSA) patients. CD45+  leukocytes were sorted from decidua at early pregnancy period  through MoFLo XDP.

first: Feiyang


title: An epigenetic program established by gene – environment interactions initiates pancreatic carcinogenesis [ATACSeq_shBrd4]

status: Public on Jul 13 2021

first: Yu-Jui

last: Ho

summary: Damaged tissues have increased risk of cancer development through poorly understood mechanisms. In the pancreas, tissue damage collaborates with activating mutations in the Kras oncogene to dramatically accelerate the formation of early neoplastic lesions and ultimately pancreatic cancer. By integrating genomics, single-cell chromatin assays and spatiotemporally-controlled functional perturbations in autochthonous mouse models, we show that the combination of Kras mutation and tissue damage promotes a unique chromatin state in the pancreatic epithelium that distinguishes neoplastic transformation from normal regeneration and is selected for throughout malignant evolution. This cancer-associated epigenetic state emerges within 48 hours of pancreatic injury, and involves large-scale chromatin accessibility changes that contribute to the early dysregulation of genes defining human pancreatic cancer. Among the genes most rapidly activated by tissue damage in the pre-malignant pancreatic epithelium is the alarmin cytokine IL33, which cooperates with mutant Kras in unleashing the epigenetic remodeling program of early neoplasia and neoplastic transformation in the absence of injury. Collectively, our study demonstrates how gene-environment interactions can rapidly produce gene regulatory programs that dictate early neoplastic commitment and provides a molecular framework for understanding the interplay between genetics and environmental cues in cancer initiation.

overall_design: Characterization of the chromatin accessibility (ATAC-seq) profiles of bulk lineage-traced Kras-mutant pancreatic epithelial cells expressing shRen.713 or shBrd4.552, isolated by FACS-sorting from pancreata of on dox KCsh mice subjected to caerulein treatment (Kras*+Injury condition).

first: Direna

last: Curbelo

first: Richard

last: Koche


title: An epigenetic program established by gene – environment interactions initiates pancreatic carcinogenesis [ATACSeq_rIL33]

overall_design: Characterization of the chromatin accessibility profiles (ATAC-seq) of bulk lineage-traced Kras-mutant pancreatic epithelial cells isolated by FACS-sorting from pancreata of KC (p48-Cre;RIK;LSLKrasG12D) mice treated with murine recombinant IL-33 (rIL-33) or PBS.


title: RNA sequence of embryonic dorsal skin and AGM (Aorta-gonad-mesonephros) tissues

status: Public on Jun 01 2021

summary:
Purpose: The goals of this study are to identify the different gene expresion level in dorsal skin cells or AGM region at different embryonic stages
Methods: Dorsal skin cells were collected from different-staged embryo: E9.5, E10.5 E12.5 and E14.5. AGM were collected from different-staged embryo: E9.5, E10.5 and E11.5.  In duplicate. RNA were extrated and analyzed using RNA sequencing. For dorsal skine tissues, we screened the genes were highly expressed at early embryonic stage E9.5, but not later stages (E10.5, E12.5, and E14.5). For embryonic AGM tissues, we selected the genes were highly expressed at early embryonic stage E9.5, but not later stages (E10.5 and E11.5). The gene list were filtered based on secreted potein candidates. These gene candidates might function as novel embryonic anti-tumor factors
Results: Using an optimized data analysis workflow, we mapped the gene list for potential secretory anti-tumor factors.
Conclusions: One of the top gene from the gene lists is NEPN which we hypotherze it has unique anti-tumor function in the early embryonic microenvirnemt and might be used as a novel cancer therapeutic drug

overall_design: RNA seq analysis of embryonic doral skin cells , in duplicate

first: Tzu-Pei

last: Chang


title: High throughput screening identifies microRNAs regulating PCSK9 and LDL receptor expression

status: Public on Jul 07 2021

first: Coen

last: van Solingen

summary: Using a high throughput human microRNA library screen, we identified microRNAs targeting the 3’untranslated region of human PCSK9

overall_design: The high throughput human miRNA screen was conducted with the NYU RNAi Core using a human microRNA library from Ambion mirVana, Life Technologies. HEK293T cells were seeded in a 384-well, white solid bottom polystyrene TC-treated microplates and co-transfected with 1.5 pmol of miRNA mimic, and 10 ng of total DNA plasmids composed of a 2:1 ratio of PCSK9 3’-UTR firefly luciferase reporter plasmid (Switchgear Genomics) to renilla luciferase control plasmid using Lipofectamine 2000 (Invitrogen). The cells and transfection mix and were dispensed into the 384-well plates using a Wellmate/BioTek Dispenser (ThermoScientific) outfitted with small-bore tubing. The plates were centrifuged at 1,000x g for 1 min to settle the contents and then incubated in a humidified incubator at 37°C and 5% CO2 for 48 hours. To measure PCSK9 3’UTR-luciferase activity, media was aspirated and the wells were washed with 1xPBS using a EL406 Microplate Washer (BioTek). Luciferase activity was assayed with the Dual-Glo Luciferase Assay® (Promega) according to the manufacturer’s instructions and read on a spectrophotometer (Envision). Positive (miR-224) and negative control miRNAs were included on each screen plate, and the miRNA library was assayed in quadruplicate. PCSK9 3’UTR firefly luciferase values were normalized to those of control renilla luciferase values for each replicate.

first: Kathryn

last: Moore


title: Normalization of cholesterol metabolism in spinal microglia alleviates neuropathic pain

status: Public on Apr 16 2021

city: Saint Louis

first: Juliana

last: Navia Pelaez

state: MISSOURI

address: 1500 S Grand Blvd, apt 201

institute: SLU

summary: Neuroinflammation is a major component in the transition to and perpetuation of neuropathic pain states. Spinal neuroinflammation involves activation of TLR4, localized to enlarged, cholesterol-enriched lipid rafts, designated here as inflammarafts. Conditional deletion of cholesterol transporters ABCA1 and ABCG1 in microglia, leading to inflammaraft formation, induced tactile allodynia in naïve mice. The apoA-I binding protein (AIBP) facilitated cholesterol depletion from inflammarafts and reversed neuropathic pain in a model of chemotherapy-induced peripheral neuropathy (CIPN) in wild-type mice, but AIBP failed to reverse allodynia in mice with ABCA1/ABCG1-deficient microglia, suggesting a cholesterol-dependent mechanism. An AIBP mutant lacking the TLR4-binding domain did not bind microglia nor reversed CIPN allodynia. The long-lasting therapeutic effect of a single AIBP dose in CIPN was associated with anti-inflammatory and cholesterol metabolism reprogramming and reduced accumulation of lipid droplets in microglia. These results suggest a cholesterol-driven mechanism of regulation of neuropathic pain by controlling TLR4 inflammarafts and gene expression program in microglia and blocking the perpetuation of neuroinflammation.

overall_design: RNA-seq of lumbar spinal microglia from wild type or inducible  Abca1 and Abcg1 microglial conditional Knockout mice. Microglia were sorted from naïve and CIPN (chemotherapy-induced peripheral neuropathy) mice treated with Saline or AIBP.

last: Navia-Pelaez

first: Christopher

last: Durant

first: Holger

last: Winkels

first: Yanal

last: Ghosheh

first: Klaus

last: Ley

first: Yury

middle: I

last: Miller


title: Experimental and clinical assessment of angiogenesis-related parameters inpatients with juvenile idiopathic arthritis-associated uveitis

status: Public on Apr 09 2021

city: Muenster

first: Karoline

last: Walscheid

address: Hohenzollernring 74

institute: Department of Ophthalmology and Ophtha-Lab at St. Franziskus-Hospital

summary: Introduction: In chronic and treatment-resistant cases of juvenile idiopathic arthritis-associated uveitis (JIAU), alterations of the iris vasculature may be observed clinically. We sought to investigate this phenomenon by combining clinical and laboratory analyses.  Methods: Iris tissue (IT), aqueous humor (AH) and serum samples from patients with clinically inactive JIAU (n=30) or acute anterior uveitis (AAU; n=18), and primary open angle glaucoma (POAG; n=20) were obtained during ocular surgery. Samples were analyzed by RNA-sequencing (RNA-Seq), qRT-PCR, liquid chromatography, high–definition mass spectrometry technique (LC-MS), Western-Blot (WB), and LEGENDplex analysis. Pattern of iris vasculature in JIAU patients was assessed qualitatively via fluorescein and indocyanine green angiography (FLA/ICGA).  Results: RNA-Seq of IT showed significantly differential expression (DE) of 136 genes between JIAU and POAG, of which 15 were associated with angiogenesis. qRT-PCR, performed to validate RNA-Seq results, showed significant upregulation of the angiogenesis-related genes Kdr, Angpt-1, Tie-1, Tie-2 and Mmrn2 in IT (JIAU vs POAG). LC-MS of IT revealed a total number of 56 DE proteins (JIAU vs POAG), of which asporin, lumican and decorin were associated with angiogenesis and showed increased (p>0.05) expression on WB analysis. LEGENDplex analysis showed upregulation of ANGPT-2 in AH from JIAU compared to AAU and POAG, whereas VEGF was upregulated in AAU. Iris vascular leakage, hypoperfusion and neovascularization were observed by FLA/ICGA in JIAU patients with treatment-refractory complicated course of uveitis.  Conclusion: Angiogenesis-related genes and proteins are upregulated in the iris tissue of JIAU patients, correlating with increased vascular permeability, hypoperfusion, and neovascularization of the anterior uveal tissue in chronic and complicated JIAU.

overall_design: JIAU (study group): 4 samples; POAG (control group): 4 samples

first: Lena

last: Wildschütz

first: Doreen

last: Ackermann

first: Maren

last: Kasper

first: Martin

last: Busch

first: Solon

last: Thanos

first: Dirk

last: Bauer

first: Monika

last: Stoll

first: Simone

last: König

first: Arnd

last: Heiligenhaus


title: Adult rat ventral tegmental area single-nucleus RNA-seq dataset for "An atlas of transcriptionally defined cell populations in the rat ventral tegmental area"

status: Public on Mar 31 2021

city: Birmingham

first: Jeremy

last: Day

address: 1825 University Blvd SHEL 910

institute: University of Alabama at Birmingham

summary: This dataset contains single-nucleus RNA sequencing results from adult rat brain (ventral tegmenal area, or VTA). The goal of this experiment was to define the transcriptional landscapes of distinct cell types in the VTA. Single-cell sequencing was carried out with nuclei suspensions (sorted using flow cytometry) using the 10X Genomics Chromium single cell sequencing platform.

overall_design: This experiment contains 4 biological samples, each of which combined tissue collected from 3 animals of the same sex. Samples were adult rat VTA microdissections isolated from male and female rats. Tissue was lysed to allow for nuclei collection via centrifugation. FACS-sorted nuclei were subject to 10X Genomics GEM generation and barcoding, GEM-RT cleanup and cDNA amplication, and library construction using a Chromium Single Cell 3ʹ Reagent Kit (v3 chemistry). Libraries underwent directional, paired-end PolyA+ RNA-seq on an Illumina Next-seq 500. Each sample has multiple raw fastq files, corresponding to different sequencing lanes (e.g., L001, L002, etc) and different reads (e.g., R1, R2). Additional index files are also provided for each sample and each lane (I1).

first: Robert

last: Phillps

first: Jennifer

last: Tuscher

first: Samantha

middle: L

last: Black

first: Lara

last: Ianov


title: RNA-seq analysis of HeLa cell lines

status: Public on Mar 25 2021

city: Frederick

first: Zhi-Ming

last: Zheng

state: Maryland

department: Center for Cancer Research

institute: National Cancer Institute

summary: We perfomed RNA-seq analysis using HPV18-postive HeLa cells for HPV integration and expression analyses

overall_design: Examination of HPV integration and expression in HeLa cell lines

first: Lulu

last: Yu

first: Alexei

last: Lobanov

first: Vladimir

last: Majerciak


title: The expression profiling of the anterior cingulate cortex and hippocampus in chronic inflammatory pain mice

status: Public on Apr 01 2021

city: Hirosaki

first: Shuji

last: Shimoyama

state: Aomori

address: 5 Zaifu-cho

department: Department of Neurophysiology

institute: Hirosaki University Graduate School of Medicine

summary:
Chronic pain is a persistent unpleasant sensation that produces pathological synaptic plasticity in the central nervous system. Some of the studies demonstrate that the anterior cingulate cortex (ACC) is a critical area for nociceptive and chronic pain processing. Our previous study revealed that animal models of chronic pain alter excitatory and inhibitory synaptic transmission in the ACC. However, it is not clear what molecules are involved in the alterations of synaptic plasticity in the ACC of chronic pain models.
To identify genes with altered expression in the ACC of a chronic pain model, whole transcriptome analysis were performed. In addition to the ACC, whole transcriptome analysis was also performed in the hippocampus, a brain region that has not been reported to be associated with chronic pain. Complete freund's adjuvant (CFA, Sigma-Aldrich, #F5881) into the left hind paw was used for induce chronic inflammatory pain in this study.

overall_design: Control or 50% of CFA were injected into the dorsal surface of the left hindpaw of mice (n=3, respectively). Two days after the injection, the mice were deeply anesthetized and transcardially perfused, then brains were quickly removed and punched out the ACC and hippocampus. The samples were subjected to whole transcriptome analysis or qRT-PCR.

first: Kohei

last: Koga


title: Metoclopramide treatment blocks CD93-signaling mediated self-renewal of chronic myeloid leukemia stem cells

status: Public on Feb 07 2021

first: Ramin

last: Radpour

summary:
Purpose: The goal of this study was to compare the transcriptome of FACS-purified bone marrow BL/6 (WT) or CD93-/- (KO) LSKs and BL/6 (WT) or CD93-/- (KO) LSCs. We also compared the transcriptome of FACS-purified bone marrow LSCs isolated from BL/6 mice previously treated with MCP or Veh in vivo.
Methods: Transcriptomic analysis of CD93-proficient and deficient bone marrow LSKs and CML LSCs or CML LSCs upon treatment with MCP or Veh, were assessed in biological replicates using Illumina. qRT–PCR validation was performed using SYBR Green assays.
Results: We mapped around 30 million sequence reads per sample to the mouse genome (GRCm38 - mm10) and identified expressed transcripts in studied samples. RNA-seq data confirmed stable expression of known housekeeping genes. Differentially expressed genes among conditions were identified with a fold change ≥1.5 and FDR p-value <0.05.
Conclusions: Our study represents the first detailed transcriptome analysis of CD93-proficient and deficient bone marrow LSKs and LSCs isolated from BM of naïve and CML mice generated by RNA-seq. technology. Our results show that CD93-signaling triggers stem cell maintenance- and cell proliferation-promoting signaling pathways in CML LSCs. In addition, we showed transcriptome analysis of FACS-purified bone marrow LSCs isolated from BL/6 (WT) mice which were previously treated with MCP or Veh in vivo. Our results show that MCP treatment suppresses the stem cell maintenance- and cell proliferation-promoting signaling pathways in CML LSCs.

overall_design: mRNA of CD93-proficient and deficient LSKs and LSCs was isolated from BM of naïve and CML mice and profiled using Illumina. mRNA of FACS-purified bone marrow LSCs isolated from BL/6 (WT) mice treated with MCP or Veh in vivo and profiled using Illumina.

first: Carsten

last: Riether

first: Adrian

last: Ochsenbein


title: Mechanisms of Triggering Malaria Gametocytogenesis by AP2-G [DIP-seq]

status: Public on Feb 01 2021

city: Tsu

first: Tsubasa

last: Nishi

state: Mie

address: Edobashi

institute: Mie university

summary: AP2-G is a transcription factor (TF) that is essential for gametocytogenesis of malaria parasites; however, the mechanisms for its inducing the cell linage for sexual reproduction remain unclear. In this paper, this problem is addressed by investigating its expression profile and by determining target genes genome-wide in Plasmodium berghei.

overall_design: Mice were infected with P. berghei expressing GFP-fused AP2-G. Sulfadiazine was added to their drinking water in order to deplete asexual blood-stage parasites. Chromatins associated with GFP-tagged AP2-G was IPed with anti-GFP antibody, and.target genes of this transcription factor were predicted.

first: Masao

last: Yuda

first: Izumi

last: Kaneko

first: Shiroh

last: Iwanaga

first: Yuho

last: Murata


title: Mechanisms of Triggering Malaria Gametocytogenesis by AP2-G

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

overall_design: Refer to individual Series


title: Single-cell Transcriptomics Reveal Signatures of Altered B cell Response and T cell Senescence in Geriatric Non-responders to COVID-19 mRNA Vaccination

status: Public on Mar 20 2026

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

summary: The immune response to COVID-19 vaccines is diminished in older individuals. To understand the underlying immunobiology, we analyzed single-cell RNA-seq data from PBMCs of SARS-CoV-2 naïve nursing home residents with varying humoral responses following BNT162b2 vaccination and validated via flow cytometry. Responders (>4500 AU/mL anti-spike titers) showed enrichment for naïve B cell (IGHD, BACH2, CD22) and naïve CD4 T cell and early Tfh-related genes (CCR7, TCF7, LEF1, IL6ST, TGFBR2). Non-responders (<20 AU/mL) displayed elevated markers of T cell senescence (KLRG1, CCL4, CCL5, IL32), immune exhaustion (PD-1), and inflammation (TNF-α, IFN-γ). Flow cytometry revealed reduced CD4 T and B cell frequencies but higher CD8 T and NK cells in non-responders. Despite reduced B cell frequency, non-responders upregulated plasma B cell genes (PRDM1, XPB1, IRF4), suggesting dysregulated B cell differentiation. Our findings point to impaired lymphocyte responses and increased immunosenescence in non-responders, emphasizing the need for enhanced vaccine strategies in aging populations.

overall_design: Peripheral blood mononuclear cells (PBMCs) were isolated from human donors two weeks after receiving the BNT162b2 mRNA COVID-19 vaccine. PBMCs were obtained from buffy coats using Ficoll-Hypaque gradient centrifugation, cryopreserved, and later thawed for analysis. Approximately 10,000 PBMCs per sample were processed using the 10x Genomics Chromium Single Cell 3’ v3.1 platform to generate single-cell transcriptomes. Libraries were sequenced on an Illumina NovaSeq 6000 using an S2 flow cell, targeting ~40,000 reads per cell.

first: Jeeda

last: Ismail

first: Banumathi

last: Tamilselvan

first: Michael

last: Rubsamen

first: Jilian

last: Petrosky

first: Brian

last: Richardson

first: Leah

last: Zagore

first: Oladayo

last: Oyebanji

first: Debbie

last: Keresztesy

last: Payne

first: Dennis

last: Wilk

first: Lenore

last: Carias

first: Htin

last: Aung

first: Kerri

last: St. Denis

first: Maeghanm

last: Sheehan

first: Brigid

last: Wilson

first: Alejandro

middle: B

last: Balazs

first: Stefan

last: Gravenstein

first: Christopher

last: King

first: David

last: Canaday

first: Cheryl


title: Sprayable Nanozyme Hydrogel Epigenetically Reprograms Inflammation for Diabetic Wound Regeneration [ATAC-seq]

status: Public on Mar 22 2026

city: Cheonan-si

first: Amal

middle: George

last: Kurian

state: Chungcheongnam-do

address: Pharmacy Bldg, Dankook University

department: Department of Nanobiomedical Science and Tissue regeneration Engineering

country: South Korea

institute: Institute of Tissue Regeneration Engineering

summary: Chronic diabetic wounds present a critical clinical challenge due to persistent inflammation and compromised healing. Here we report a novel sprayable nanozyme hydrogel that epigenetically reprograms macrophages to suppress inflammation and coordinate regeneration. Ultrasmall copper-based nanozymes (CuNZ, ~4 nm) synthesized via an eco-friendly one-pot method demonstrated potent multi-radical scavenging activity. When integrated into gelatin methacryloyl (Gel), CuNZ@Gel exhibited excellent sprayability, conformal skin coverage, and long-term storage stability, offering substantial translatable potential. Notably, the nanozyme hydrogel induced distinct epigenetic modifications in macrophages by remodeling chromatin accessibility, effectively shifting gene expression from pro-inflammatory to anti-inflammatory profiles. This epigenetic modulation persisted under oxidative stress, actively suppressing inflammatory while facilitating regenerative responses. In diabetic wound models, CuNZ@Gel significantly accelerated healing through its coordinated antioxidant, anti-inflammatory, and pro-regenerative actions. Unlike conventional passive dressings, our sprayable nanozyme hydrogel proactively reprograms the wound microenvironment via epigenetic antioxidant mechanisms, offering novel insights and strategy for managing chronic diabetic wounds and inflammatory skin complications.

overall_design: ATAC seq profiling of RAW 264.7 macrophage cells treated with hydrogels for 48 hours

first: Amal George

first: Jeong-Hui

last: Park

first: Shanika

last: Karunasagara

first: Archita

last: Gupta

first: Shreyas Kumar

last: Jain

first: Tanza

last: Baby

first: Ueon Sang

last: Shin

first: Sak

last: Lee

first: Rajendra

last: Singh

first: Jung-Hwan

first: Kam

last: Leong

first: Hae-Won

last: Kim


title: An epigenetic program established by gene – environment interactions initiates pancreatic carcinogenesis  [Set1]

status: Public on Nov 25 2020

first: Yu-Jui

last: Ho

overall_design: Characterization of the transcriptional profiles of bulk lineage-traced pancreatic epithelial cells isolated directly by FACS-sorting (mKate2+ or GFP+) from normal, regenerating, early neoplastic and malignant murine pancreatic tissues: To compare the effects of tissue injury in mutant Kras-expressing or Kras wild-type pancreatic epithelial cells, cells were sorted from KC;RIK (p48-Cre;RIK;LSLKrasG12D) or C;RIK (p48-Cre;RIK) male mice treated with caerulein or PBS (vehicle control) at 5 weeks of age, using littermates when possibe. To characterize invasive disease, pancreatic ductal adenocarcinoma (PDAC) cells were isolated from cancer lesions arising in autochthonous transgenic models (KPflC;RIK (p48Cre;RIK;LSL-KrasG12D;p53fl/+). 3-6 biological replicates (independent mice) were used per experimental condition.

first: Direna

last: Curbelo

first: Scott

last: Lowe


title: An epigenetic program established by gene – environment interactions initiates pancreatic carcinogenesis [Set2]

overall_design: Identification of the transcriptional changes induced upon doxycycline (dox)-inducible Brd4 knockdown in either wild-type or mutant Kras bulk pancreatic epithelial cells triggered to undergo regenerative (Injury condition) or proneoplastic (Kras*+Injury condition) transitions, respectively: Brd4-suppressed vs Brd4-expressing pancreatic epithelial cells were FACS-sorted (mKate2+;GFP+) from pancreata from p48Cre;RIK;TRE-GFP-shRNA (Kras wild-type) or p48Cre;RIK;TRE-GFP-shRNA;LSL-KrasG12D (Kras mutant) mice (harbouring Brd4 shRNA -1448, 552- or control Renilla shRNA -713-) at day 2 after treatment with caerulein. Brd4-expressing (shRen) pancreatic epithelial cells FACS-sorted from p48Cre;RIK;TRE-GFP-shRNA (Kras wild-type) mice which were placed on dox diet but not subjected to caerulein treatment served as additional control to pinpoint caerulein- and mutant Kras-specific effects. 3 biological replicates (independent mice) were used per experimental condition.


title: An epigenetic program established by gene – environment interactions initiates pancreatic carcinogenesis [Set3]

overall_design: Characterization of the transcriptional profiles (RNA-seq) of bulk lineage-traced Kras-mutant pancreatic epithelial cells isolated by FACS-sorting from pancreata of Kras-mutant KC (p48-Cre;RIK;LSLKrasG12D) or Kras wild-type C (p48-Cre;RIK) mice treated with murine recombinant IL-33 (rIL-33) or PBS.


title: LIGHT/LTβR signaling regulates self-renewal and differentiation of hematopoietic and leukemia stem cells

status: Public on Oct 23 2020

first: Ramin

last: Radpour

summary:
Purpose: The goal of this study is to compare NGS-derived transcriptome profiling (RNA-seq) of Ltbr-deficient and -proficient LT/ST-HSCs isolated from chimeric mice.
Methods: Transcriptomic profiles of Ltbr-/- and Ly5.1 LT/ST-HSCs isolated from chimeric mice 6 weeks after reconstitution were assessed in triplicate by deep sequencing, using Illumina NextSeq 500. qRT–PCR validation was performed using TaqMan and SYBR Green assays.
Results: We mapped about 60 million sequence reads per sample to the mouse genome (GRCm38 - mm10) and identified expressed transcripts in Ltbr-/- and Ly5.1 LT/ST-HSCs isolated from chimeric mice. RNA-seq. data confirmed stable expression of known housekeeping genes. Differentially expressed genes between the Ltbr-/- and Ly5.1 LT/ST-HSCs were identified with a fold change ≥1.5 and FDR p-value <0.05.
Conclusions: Our study represents the first detailed transcriptome analysis of Ltbr-deficient and -proficient LT/ST-HSCs, with biologic replicates, generated by RNA-seq. technology. Our results show that Ltbr signaling regulates HSC proliferation and differentiation. Evaluation of mRNA content in Ltbr-/- LT/ST-HSCs revealed that Ltbr-deficiency enhances HSC proliferation, differentiation, cell cycle and reduces the activity of canonical NFkB signaling.

overall_design: mRNA of Ltbr-/- and Ly5.1 LT/ST-HSCs isolated from bone marrow of chimeric mice using Illumina NextSeq 500.

first: Sabine

last: Höpner

first: Ana

last: Raykova

first: Adrian

last: Ochsenbein


title: Bronchoalveolar lavage of healthy human adults

status: Public on Oct 21 2020

city: Denver

first: Camille

last: Moore

state: CO

address: 1400 Jackson St.

institute: National Jewish Health

summary: Rationale: Airspace macrophages are the most abundant cell in airspaces and are viewed as a homogeneous population during health. Single cell RNA sequencing allows for examination of transcriptional heterogeneity between cells and between individuals. Understanding the conserved repertoire of airspace leukocytes during health is essential to understanding cellular programing during disease.  Objective: We sought to determine the transcriptional heterogeneity of human bronchoalveolar lavage cells in healthy adults. Methods: Ten healthy subjects underwent bronchoscopy. Cells obtained from lavage fluid were subjected to single cell RNA sequencing. Unique cell populations and putative functions were identified. Transcriptional profiles were compared across individuals. Measurements and Main Results:  Based on transcriptional profiling we identify highly conserved macrophage, monocyte-like, lymphocyte, dendritic cell, and cycling cell populations. We define two unique subgroups of resident airspace macrophages - one defined by a pro-inflammatory profile and one by metallothionein gene expression. We identify distinct subsets of monocyte-like cells and directly compared them to peripheral blood mononuclear cells. Finally, we compare global macrophage and monocyte programing between male and female subjects. Conclusions: Healthy human airspaces contain multiple populations of leukocytes that are highly conserved between individuals and between the sexes. Resident macrophages comprise the largest population and include novel subsets defined by inflammatory and metal-binding gene signatures. Monocyte-like cells within the airspaces are transcriptionally distinct from circulating blood cells and include a rare population defined by expression of cell-matrix interaction genes. This study is the first to define airspace immune cell heterogeneity and identifies three previously unrecognized myeloid cell subsets.

overall_design: Fifteen  bronchoalveolar lavage samples from ten healthy adults were included.

first: Kara

last: Mould

first: Shannon

last: Hott

first: Alexandra

last: McCubbrey

first: Christine

last: Griesmer

first: Peter

last: Henson

first: William

last: Janssen


title: Notch activity determines a common hepatocellular carcinoma subtype with unique molecular and clinicopathologic features

status: Public on Sep 28 2020


title: Notch activity determines a common hepatocellular carcinoma subtype with unique molecular and clinicopathologic features [L-NICD]

summary: Hepatocellular carcinoma (HCC) is the predominant primary liver cancer and an increasing cause of cancer-related deaths worldwide, due in part through increased obesity-associated nonalcoholic steatohepatitis (NASH) and associated fibrosis. The Notch signaling pathway is inappropriately “reactivated” in hepatocytes in obesity and plays an active role in the pathogenesis of NASH-associated fibrosis. We aimed to understand the involvement of Notch in the pathogenesis of mouse and human HCC.

overall_design: 6 samples of mouse liver tissues (surrounding non-tumor livers and tumors) from 3 different NASH diet-fed Notch-overexrepssed mice (L-NICD) were analyzed.

first: Changyu

last: Zhu

first: Utpal

last: Pajvani


title: An epigenetic program established by gene - environment interactions initiates pancreatic carcinogenesis

status: Public on Nov 24 2020


title: Epigenetic and Expression Profiling of Tissue Selective Estrogen Compounds in Breast Epithelial Cell Lines

status: Public on Aug 01 2020

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont


title: ATAC-seq datasets for chromatin accessibility quantification in "Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems"

status: Public on Jul 28 2020

first: Jeremy

last: Day

state: Alabama

summary: This dataset contains Assay for Transposase-Accessible Chromatin (ATAC) sequencing results from rat embryonic cortical, hippocampal, and striatal neuronal cultures treated with either vehicle (complete Neurobasal media) or potassium chloride (10mM) for 1hr.

overall_design: This experiment contains 18 biological samples, each of which underwent ATAC-seq on an Illumina NextSeq500 instrument. Samples were treated with neurobasal media (vehicle; samples V1C, V2C, V3C, V1H, V2H, V4H, V1S, V2S, V4S), or 10mM KCl (samples K2C, K3C, K4C, K1H, K2H, K4H, K1S, K2S, K3S) . The first letter of sample names denotes acute treatement (V = vehicle, K = KCl). The second digit denotes the unique replicate ID for a given brain region and treatment. The third digit denotes the region of cultured neuron (C = cortex, H = hippocampus, S = striatum). Forward and reverse paired-end reads are denoted as "R1" or "R2" in raw file names.

first: Nancy

middle: N

last: Carullo

first: Robert

last: Phillips

first: Lara

last: Ianov