title: Gene expression data from ileal intestine of chickens

city: Nagoya

first: Atsushi

last: Murai

address: Furo-cho, Chikusa-ku

department: Department of Animal Sciences

institute: Nagoya University

summary:
Paddy rice with husk can be availbale for chicken dietary resource instead of yellow corn. Ingestion of paddy rice potentially affects on gastrointestinal physiology and function including digestion/absorption of nutrients and gut barrier function such as mucosal immunity, but the details of changes is unknown.
To obtain insight into the physiological modifications in the small intestine of chickens fed paddy rice, we conducted a comprehensive analysis of gene expression in small intestine by DNA microarray. In the paddy rice group, a total of 120 genes were elevated >1.5-fold in the paddy rice group, whereas a total of 159 genes were diminished < 1.5-fold. Remarkably, the gene expression levels of IGHA (immunoglobulin heavy chain α), IGJ (immunoglobulin J chain), and IGLL1 (immunoglobulin light chain λ chain region), which constitute immunoglobulin A, decreased 3 to 10 times in the paddy rice group.

overall_design: GeneChip® Chicken Genome Array was used for high-throughput screening of upregulated and downregulated genes in ileal intestine of chickens fed corn-based diet or paddy rice-based diet. The ileal tissues of three birds were pooled, and their total RNA was used for microarray analysis.

first: Mizuki

last: Yamamoto

first: Ayako

last: Ueno

first: Hayato

last: Watanabe

first: Mayuko

last: Okamoto

first: Kyohei

last: Furukawa


title: Senescence induction in ID8 P53 KO ovarian cancer model, injected intraperitouneusly (IP) in C57BL/6 mice.

status: Public on Sep 19 2024

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

type: Expression profiling by high throughput sequencing

summary: We report the analysis of RNA sequencing aimed at understanding senescence induction in this tumor model and the composition of the tumor microenvironment.

overall_design: 5*10^6 ID8 cells were injected IP in 24 mice. After 1 month, 6 mice receive vehicle (PBS), 6 mice receive cisplatin (4mg/kg) for one week, 4 mice receive vehicle (PBS), 6 mice receive cisplatin (4mg/kg) for two weeks.

first: Mariantonietta

last: D'Ambrosio

first: Virinder

last: Reen

first: Jesus

last: Gil

first: Sanjay

last: Khadayate


title: Transcript profiling of global PKM2 knockout mouse hearts to evaluate the cardiac role of PKM2 after myocardial infarction

status: Public on Sep 18 2024

city: Honolulu

first: Katie

middle: CY

last: Lee

state: HI

address: 651 Ilalo St., BSB 311

department: Center for Cardiovascular Research

country: USA

institute: University of Hawaii at Manoa

summary: During myocardial infarction (MI), energy production decreases as hypoxia inhibits oxidative metabolism. Our lab has identified an ischemia-regulated alternative splicing event of the glycolytic enzyme pyruvate kinase (muscle, PKM), reducing PKM1 expression and increasing PKM2 expression. We hypothesized the upregulation of PKM2 aids in energy production to maintain heart function after MI. We utilized high-throughput sequencing to evaluate altered gene expression and identify pathways that may be regulated by PKM2.

overall_design: To investigate the role of PKM2 during MI, we generated global PKM2 knockout mice. We then performed gene expression profiling analysis using RNA-seq of knockout and control left ventricle tissue at baseline, or 3 days after sham surgery or ligation of the left anterior descending artery (LAD). At the time of harvest, tissue was flash frozen, and then pulverized before RNA extraction. Sham mice were used as controls for MI samples. Two biological replicates were used for baseline samples and three biological replicates for sham and MI samples per genotype.

middle: C

first: Allison

middle: L

last: Williams

first: Ralph

middle: V

last: Shohet


title: Chromatin remodeler CHD4 establishes chromatin states required for ovarian reserve formation, maintenance, and germ cell survival [ATAC-seq]

status: Public on Sep 27 2024

city: Davis

first: Satoshi

middle: H

last: Namekawa

state: CA

address: One Shields Avenue

department: Department of Molecular and Cellular Biology

institute: University of California, Davis

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To understand the functional role of CHD4, a member of the Nucleosome Remodeling and Deacetylase (NuRD) complex, in establishing chromatin states in the formation and maintenance of ovarian reserve and the maintenance of female and male germ cells, we eliminated CHD4 function in germ cells using Ddx4-Cre and Gdf9-iCre to generate CHD4 conditional knockout (Chd4 DcKO and GcKO) mice. We discover that CHD4 defines the chromatin state that ensures germ cell survival, thereby enabling the long-term maintenance of female and male germ cells. We then performed ATAC-seq in Chd4 Dctrl and Chd4 DcKO non-growing oocytes and undifferentiated spermatogonia.

overall_design: Comparative chromatin profiling analysis of ATAC-seq data for (1) Chd4 Dctrl and DcKO P1  non-growing oocytes; (2) Chd4 Dctrl and DcKO P3 undifferentiated spermatogonia.

first: Yasuhisa

last: Munakata


title: Patient-Derived Tumor Organoid and Fibroblast Assembloid Models for interrogation of the tumor microenvironment in Esophageal Adenocarcinoma

status: Public on Sep 20 2024

city: Southampton

first: Ian

last: Reddin

address: Tremona Road

department: School of Cancer Sciences

institute: University of Southampton

summary: The tumor microenvironment (TME) comprises all non-tumor elements of cancer and strongly influences disease progression and phenotype. To understand tumor biology and accurately test new therapeutic strategies, representative models should contain both tumor cells and normal cells of the TME. Here we describe and characterize co-culture tumor-derived organoids and cancer-associated fibroblasts (CAFs), a major component of the TME, in matrix-embedded assembloid models of esophageal adenocarcinoma (EAC). We demonstrate that the assembloid models faithfully recapitulate the differentiation status of EAC and different CAF phenotypes found in the EAC patient TME. We evaluate cell phenotypes by combining tissue clearing techniques with wholemount immunofluorescence and histology, providing a practical framework for characterization of cancer assembloids.

overall_design: To characterize our assembloids and the respective components, we performed bulk RNA-sequencing on two CAFs, three patient-derived esophageal adenocarcinoma organoid lines and corresponding assembloid co-cultures for one CAF (CAF669) with all three organoids

first: Benjamin

middle: P

last: Sharpe

first: Liliya

middle: A

last: Nazlamova

first: Carmen

last: Tse

first: David

last: Johnston

first: Jaya

last: Thomas

first: Rhianna

last: Blyth

first: Oliver

middle: J

last: Pickering

first: Ben

last: Grace

first: Jack

last: Harrington

first: Rushda

last: Rajak

first: Matthew

last: Rose-Zerilli

first: Zoe

middle: S

last: Walters

first: Tim

last: Underwood


title: Integrator complex subunit 12 knockout overcomes a transcriptional block to HIV latency reversal [CRISPR]

status: Public on Sep 17 2024

city: Seattle

first: Michael

last: Emerman

state: Washington

address: 1110 Fairview Ave N

institute: Fred Hutch Cancer Research Center

summary: The latent HIV reservoir is a major barrier to HIV cure. Combining latency reversal agents (LRAs) with differing mechanisms of action such as AZD5582, a non-canonical NF-kB activator, and I-BET151, a bromodomain inhibitor is appealing towards inducing HIV-1 reactivation. However, even this LRA combination needs improvement as it is inefficient at activating proviruses in cells from people living with HIV (PLWH). We performed a CRISPR screen in conjunction with AZD5582 & I-BET151 and identified a member of the Integrator complex as a target to improve this LRA combination, specifically Integrator complex subunit 12 (INTS12). Integrator functions as a genome-wide attenuator of transcription that acts on elongation through its RNA cleavage and phosphatase modules. Knockout of INTS12 improved latency reactivation at the transcriptional level and is more specific to the HIV-1 provirus than AZD5582 & I-BET151 treatment alone. We found that INTS12 is present on chromatin at the promoter of HIV and therefore its effect on HIV may be direct. Additionally, we observed more RNAPII in the gene body of HIV only with the combination of INTS12 knockout with AZD5582 & I-BET151, indicating that INTS12 induces a transcriptional elongation block to viral reactivation. Moreover, knockout of INTS12 increased HIV-1 reactivation in CD4 T cells from virally suppressed PLWH ex vivo. We also detected viral RNA in the supernatant from CD4 T cells of all three virally suppressed PLWH tested upon INTS12 knockout suggesting that INTS12 prevents full-length HIV RNA production in primary T cells.

overall_design: Latency HIV-CRISPR is performed by generating a pool of ZAP-knockout J-Lat 10.6 and 5A8 cells that are each knocked out for human epigenome genes using the HuEpi guide RNA library or a NFkB-related gene library (NFkB) with all Integrator complex members added in. The dosage and timing of drugs varied by screen: all HuEpi screens were performed with 10 nM AZD5582 & 100 nM I-BET151 for 48 hrs whereas all NFkB screens were performed with 1 nM AZD5582 & 2.5uM I-BET151 for 24hrs. Each screen is performed in two biological replicates. Afterwards, for each condition, the cell pellets were harvested, genomic DNA (gDNA) was extracted, and sequencing was performed to evaluate the single guide RNA (sgRNA) representation of the library. Simultaneously, the viral supernatant was harvested, viral RNA (vRNA) was extracted, and sequencing was performed. By comparing the sgRNA representation of the viral RNA to the library representation of the genomic DNA, the sgRNAs that are enriched and depleted in the viral population are associated with potential HIV-1 latency factors. The plasmid library of the HIV-CRISPR HuEpi or NFkB guide RNA library was also sequenced.

first: Gray

last: Carley

first: Emerman

last: Michael


title: A PWWP domain-containing protein Crf4-3 specifically modulates fungal azole susceptibility by regulating sterol C-14 demethylase ERG11

status: Public on Sep 15 2024

city: Beijing

first: pengju

last: YU

address: No.1 Beichen West Road

country: China

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: The widespread use of azole antifungal drugs in agriculture and clinical settings has led to serious drug resistance issues. Under azole treatment, resistant strains can upregulate the expression of the azole drug target 14α-demethylase ERG11 through transcription factors to alleviate the stress induced by sterol synthesis inhibition, which is a common resistance mechanism. Additionally, the currently reported regulatory factors related to resistance are not sufficient to explain all resistance issues. In this study, we constructed a GFP gene reporter system based on the erg11 promoter in the model filamentous fungus, Neurospora crassa, and identified a key region of the promoter that governs the erg11 response to azole drug by stepwise deletion. Using specific probes for DNA pulldown and combined with phenotype analysis, we identified a protein, Crf4-3, containing a PWWP domain that has a positive regulatory effect. Specific deletion of Crf4-3 leads to hypersensitivity to azole drugs and loss of transcriptional response of erg11 and erg6 to ketoconazole. Furthermore, the basal expression of erg1, erg11, erg25, and erg3A is affected by the deletion of crf4-3. Crf4-3 homologs are widely present in the Pezizomycotina fungi. Deletion of the homologous protein of Crf4-3 in Aspergillus fumigatus also significantly reduced sensitivity to azole drugs like voriconazole by reducing the transcriptional response of erg11. In summary, our study revealed a new regulatory factor Crf4-3 involved in the azole stress response in filamentous fungi and its mechanism, providing new insights into understanding the mechanisms of azole drug resistance.

overall_design: To thoroughly investigate mechanism of Crf4-3, we sequenced the transcriptome of crf4-3 mutant treated with or without Ketoconazole.

first: Pengju

last: Yu


title: WT and N88S seipin-expressing cells upon bathophenanthrolinedisulfonate (BPS) treatment

status: Public on Sep 12 2024

city: Porto

first: Vitor

last: Teixeira

state: Porto

address: Rua Alfredo Allen 208

department: YSN

country: Portugal

summary: WT and N88S seipin-expressing cells were grown in SC-glucose medium to exponential phase and then iron chelator bathophenanthrolinedisulfonate (BPS) was added to a final concentration of 100 micromolar. Cells were incubated in the presence of BPS for an additional 4 hour period. We intend to evaluate differentially expressed genes (DEGs) between the two strains. Four biological replicates (classified as 1-4 for the corresponding strain) were used per strain.

overall_design:
Cells were treated with BPS to induce iron starvation conditions and evaluate differentially expressed genes (DEGs): WT (G1, 4 biological replicates) vs N88S (G2, 4 biological replicates).
2024 BGI Genomics Co.,Ltd.

first: Mariana

last: Ribeiro


title: Gene expression signature of castrate resistant prostate cancer

status: Public on Sep 11 2024

city: Bengaluru

first: Prathibha

last: Ranganathan

state: Karnataka

address: Electronic City Phase I

country: India

institute: Centre for Human Genetics

summary: Prostate gland is a highly androgen dependent gland.  The first line of treatment for metastatic prostate cancer therefore, is androgen ablation. This can be achieved by multiple non-surgical methods. However, most of these cancers although respond well initially, become resistant to androgen ablation sooner or later. These cancers then become extremely aggressive and difficult to treat, thereby drastically affect the patient prognosis.  A gene expression signature for castrate resistant prostate cancer would be useful in identification of mechanisms responsible for castrate resistance, as well as to predict the progression of the cancer into castrate resistance. For this, our group has done a RNA-seq analysis of  a. Control group (C); b. Castrate Sensitive group (B) and c. Castrate Resistant group (A). Gene expression profiling was performed on these samples using RNA-seq. Differentially expressed genes between control and castrate sensitive as well as control and castrate resistant groups were identified.

overall_design: In order to find a gene expression signature of castrate resistant prostate cancer, biopsy samples from a. Control (Benign Prostatic Hyperplasia), b. Castrate Sensitive and c. Castrate Resistant prostate cancer were collected. Total RNA was isolated then subjected to RNA-seq on HiSeq platform. Genes differentially expressd between the groups were identified and grouped as CaS and CaR genes.

first: Dixcy

last: Sheeba JM

first: Shraddha

last: Hegde

first: Ninad

last: Tamboli

first: Namratha

last: Nadig

first: Ramaiah

last: Keshavamurthy


title: Unravelling the transcriptomic dynamics of Hyphopichia pseudoburtonii in co-culture with Botrytis cinerea

city: Stellenbosch

first: Evelyn

last: Maluleke

state: Western cape

address: Victoria street

department: Viticulture and Oenology

country: South Africa

institute: Stellenbosch University

summary: Hyphopichia pseudoburtonii,  is considered as promising biological control agents due to its large spectrum of antifungal activity. H.pseudoburtonii strain Y963 isolated from grape must in Stellenbosch, possesses significant antifungal activity against B.  cinerea, the causal agent of grey mould, a significant disease affecting grapes world-wide. Several modes of action, like competition for nutrients and space, production of extracellular lytic enzymes and volatile organic compounds, have been demonstrated for the biological control activity exhibited by H. pseudoburtonii through which it inhibits B. cinerea. To reveal the underlying antifungal genetic mechanisms, this study examined the changes in gene expression of H. pseudoburtonii when exposed to B. cinerea over 24, 48, and 120 h using RNA sequencing.  The results show that H. pseudoburtonii undergoes a responsive reaction upon encountering B. cinerea, leading to increased production of nucleotides and proteins. Subsequently, a period followed during which various forms of stress were induced. This led to increased signaling and cell communication, as well as the activation of genes responsible for pseudohyphal growth. In later stages, vigorous growth and competition for nutrients became apparent. Up-regulation of genes associated with transmembrane functions, iron homeostasis, zinc homeostasis, hydrolases, and glycosyl hydrolases was observed at 120 h. This research offers new insights into H.pseudoburtonii transcriptomic response to B.cinerea and illuminates the adaptive strategies and molecular mechanisms behind its antifungal activity.

sample_organism:
Botrytis cinerea
Hyphopichia pseudoburtonii

overall_design: H. pseudoburtonii was co-cultured with B. cinerea, and RNA was extracted to evaluate the molecular mechanisms by which this yeast inhibits B. cinerea.

first: Neil

last: Jolly

first: Hugh-George

last: Patterton

first: Mathabatha

middle: E

last: Setati


title: Effect of OLIG2 inhibition on medulloblastoma stem cells

city: Toronto

first: Kinjal

last: Desai

state: ON

address: 686 Bay Street, PGCRL 16-14

department: Developmental and Stem Cell

country: Canada

institute: The Hospital for Sick Children

summary: To investigate the role2 in brain tissue and medulloblastoma stem cells, we inhibited OLIG2 using an inhibitor, CT-179.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of vehicle vs. CT-179-treated cells at three different time points.

first: Peter

last: Dirks


title: Gene expression profile at single cell level of sonic hedgehog subgroup (SHH) medulloblastoma (MB) tumors from Ptch1+/- mice irradiated at birth (Ptc)

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the transcriptomic diversity of the functionally distinct cell sub-populations of primary MB tumor cells obtained from a transgenic mouse model (Ptc).

overall_design: Live cells from 4 end-point tumors were analyzed using single-cell mRNA-seq using the 10x Genomics platform, as per the manufacturer’s guidelines.


title: Simultaneous Profiling of Chromatin-Associated RNA at Targeted DNA Loci and RNA-RNA Interactions through TaDRIM-Seq II

city: Wuhan

first: guoting

last: chen

address: 1 Shizishan Street, Hongshan District

institute: National Key Laboratory of Crop Genetic Improvement

summary: The enormous variety of different RNAs are transcribed from eukaryotic genome. Some RNAs, particular long non-coding RNAs (lncRNAs),  enrich on chromatin via transcribed RNAs to retain at their transcription site (Cis-acting RNAs) and recruited to different genomic regions (Trans-acting RNAs), which play significant roles in regulating gene transcription, epigenomic modifications and mediating chromatin states. Here, we developed TaDRIM-Seq (Targeted DNA-associated RNA and RNA-RNA Interactions Mapping by Sequencing) method to capture RNA-DNA  on specific protein region and RNA-RNA spatial interactions in nuclei. We performed TaDRIM-Seq of antibodies H3, H3K9ac and H3K27me3 in rice and H3K4me3 and CTCF in human K562 cells, to identify chromatin-interacting RNAs and RNA-RNA interactions.

sample_organism:
Arabidopsis thaliana
Homo sapiens
Oryza sativa Indica Group

overall_design: We report TaDRIM-Seq technique PG-Tn5-mediated targeted DNA element and proximity ligation to simultaneously detect chromatin-associated RNAs in diverse regions of the genome and RNA-RNA spatial interactions in nuclei.

first: Cheng

last: Ding

first: Guoting

last: Chen


title: Identification of rejection-associated indirect CD4 T cell epitopes provides a target for donor-specific transplant tolerance

city: Atlanta

first: Christian

last: Larsen

state: Georgia

address: 101 Woodruff Circle

department: Department of Surgery

institute: Emory University

summary: Antibody-mediated rejection, caused by antibodies against the donor human leukocyte antigen (HLA) molecules plays a fundamental role in graft rejection in transplantation. Most significant is transplant patients who generate antibodies against the donor HLA-DQ have the highest risk of rejection. In this study, we investigated the role of indirect CD4 T cell epitopes in the formation of donor-specific antibodies (DSA). Using antigen mapping techniques in kidney and heart transplant recipients with HLA-DQ DSA, we identified two polymorphic hotspots in the HLA-DQ gene that generated alloreactive CD4 T cell responses. To study the functional significance of indirect CD4 T cells, we first mapped epitopes recognised by H2-Kb C57Bl6 mice against a skin graft from H2-Kd Balb/c mice. We identified a CD4 T cell epitope, specific for amino acids 287-301 derived from the H2-Kd protein, that generated tetramer-binding Kd287+ CD4 T cells during rejection. Importantly, the transfer of Kd287+ CD4 T cells into T cell-deficient mice was sufficient to drive an antibody response against the donor H2-Kd molecule.  Lastly, we found that administration of systemic high-dose donor H2-Kd peptides combined with CTLA4-Ig reduced the formation of Kd287+ CD4 T cells and diminished DSA formation. Together, these findings demonstrate that the identification of donor antigens indicates the potential for inducing donor-specific immune tolerance in transplantation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To investigate the TCR composition and diversity of alloreactive indirect CD4 T cells, we performed TCR sequencing on flow-sorted Kd287+ CD4 T cells isolated on day 14 after transplantation in mice that exhibited donor allograft rejection and underwent peptide treatment.

first: Haydn

middle: T

last: Kissick

first: Zhuldyz

last: Zhanzak


title: Sex differences in Non-Alcoholic Steatohepatitis (NASH) in mice evoked by a fructose-palmitate-cholesterol (FPC)-enriched diet [single_nucleus]

status: Public on Sep 24 2024

city: New York

first: Sofie

last: Delbare

state: NY

address: 435 East 30th Street

institute: NYU Langone

summary: To study sex differences in the response to NASH in mice, single nucleus RNA sequencing of livers was performed. Single nucleus RNAseq demonstrated enrichment of differentially-expressed genes particularly in hepatocytes and stellate cells in females versus males fed FPC-NASH. Multiple regulons (transcription factors and target genes) implicated in lipid and other metabolic processes and hormone signaling (hepatocytes) and cell-cell communication and cell adhesion (stellate cells) were noted, which were enriched in female versus male FPC-NASH diet. Bulk liver RNAseq and RNAseq of isolated hepatocytes and hepatic stellate cells were analyzed as validation experiments.

overall_design: Male and female C57BL/6J mice were fed fructose-palmitate-cholesterol (FPC-NASH) diet or standard chow (SC) for 16 weeks. Single-nucleus RNAseq was performed on the top left lobe of livers from control and FPC diet fed male and female mice (N = 2 independent mice/group, resulting in 8 samples total). Samples from each of the 2 replicate groups were hashtagged and sequenced as one pool.

first: Lakshmi

last: Arivazhagan

first: Robin

last: Wilson

first: Boyan

last: Zhou

first: Henry

last: Ruiz

first: Kaamashri

last: Mangar

first: Ryoko

last: Higa

first: Emily

last: Brown

first: Huilin

last: Li

first: Michael

last: Garabedian

first: Ravichandran

last: Ramasamy

first: Kathryn

last: Moore

first: Edward

last: Fisher

middle: D

last: Theise

first: Ann

middle: M

last: Schmidt


title: Determining the chromatin accessibility profiles of functionally distinct SHH-medulloblastoma sub-populations

first: Kinjal

last: Desai

summary: Using FACS sorting on SOX2-eGFP and MKi67-RFP mice on a Ptch1+/- background, we identified cycling& non-cycling stem cells and tumor bulk subpopulations in endpoint mouse SHH-subgroup medulloblastoma tumors, and determined their chromatin accessibility progiles to identify unique regulators of cell state.

overall_design: We sorted SHH-subgroup medulloblastoma cells from endpoint mouse tumors into SOX2+ and SOX2- based on presence of eGFP signal to distinguish the stem-like and bulk tumor compartments. We also sorted the SOX2+ stem cells into cycling (MKI67+) and non-cycling (MKI67-) sub-compartments based on presence of RFP. We then performed sequencing on ATAC libraries generated from these cells.

first: Peter

last: Dirks


title: Sex differences in Non-Alcoholic Steatohepatitis (NASH) in mice evoked by a fructose-palmitate-cholesterol (FPC)-enriched diet

last: Delbare

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

overall_design: Refer to individual Series


title: STAT1 regulates immune-mediated intestinal stem cell proliferation and epithelial regeneration

status: Public on Sep 09 2024

first: Alan

last: Hanash

state: New York

address: 417 E 68th St

institute: MSKCC

summary: The role of the immune system in regulating tissue stem cells remains poorly understood, as does the relationship between immune-mediated tissue damage and regeneration. Graft vs. host disease (GVHD) occurring after allogeneic bone marrow transplantation (allo-BMT) involves immune-mediated damage to the intestinal epithelium and its stem cell compartment. To assess impacts of T-cell-driven injury on distinct epithelial constituents, we performed single cell RNA sequencing on intestinal crypts following experimental BMT. Intestinal stem cells (ISCs) from GVHD mice exhibited global transcriptomic changes associated with a substantial Interferon-γ response and upregulation of STAT1. To determine its role in crypt function, STAT1 was deleted within murine intestinal epithelium. Following allo-BMT, STAT1 deficiency resulted in reduced epithelial proliferation and impaired ISC recovery. Similarly, epithelial Interferon-γ receptor deletion also attenuated proliferation and ISC recovery post-transplant. Investigating the mechanistic basis underlying this epithelial response, ISC STAT1 expression in GVHD was found to correlate with upregulation of ISC c-Myc. Furthermore, activated T cells stimulated Interferon-γ- dependent epithelial regeneration in co-cultured organoids, and Interferon-γ directly induced STAT1-dependent c-Myc expression and ISC proliferation. These findings illustrate immunologic regulation of a core tissue stem cell program after damage and support a role for Interferon-γ as a direct contributor to epithelial regeneration.

overall_design: Cells from mice small intestine were isolated and processed using scRNA-seq.


title: Comprehensive analysis of Poly(A) tails in Mouse Testes and Ovaries using Nanopore direct RNA Sequencing.

status: Public on Sep 10 2024

city: Warsaw

first: Andrzej

last: Dziembowski

address: 4 Ks. Trojdena Street

country: Poland

institute: International Institute Of Molecular And Cell Biology In Warsaw

summary: Germ cell development, gametogenesis, is a complex process in which dysfunction leads to infertility, a growing health and sociological problem worldwide. In both spermatogenesis and oogenesis, post-transcriptional gene expression regulation is crucial. Essentially, all mRNAs possess non-templated poly(A) tails, which composition and dynamics (elongation, shortening, and modifications) determine the fate of mRNA. In this context, we present a comprehensive transcriptomic dataset that focuses on mRNA poly(A) tails metabolism in murine testes. Analyzed RNA samples are isolated from wild-type and transgenic mice lacking TENT5C polymerase, which can extend poly(A) tails in the cytoplasm. Both whole testes material, as well as male gametes at different developmental stages (round or long spermatids) were analyzed.

overall_design: To investigate the role of Tent5c in spermatogenesis we generated RNAseq libraries from (1) whole testes (2) and round or (3) elongated spermatids isolated from either WT or Tent5c -/- mice, followed by differential expression analysis.

first: Agnieszka

last: Czarnocka-Cieciura

first: Michał

last: Brouze

first: Monika

last: Kusio-Kobiałka

first: Olga

last: Gewartowska


title: A neoadjuvant, phase II trial demonstrates efficacy and tolerability of Talimogene laherparepvec in cutaneous basal cell carcinoma (NeoBCC trial)

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

summary: Cutaneous basal cell carcinoma (BCC) is the most common cancer worldwide. We present a single arm, phase II neoadjuvant trial with the oncolytic virus Talimogene laherparepvec (T-VEC) in 18 patients with difficult-to-resect basal cell carcinomas. Six cycles of T-VEC were applied intralesionally. The primary endpoint of the study, defined as the proportion of patients, who after six cycles of T-VEC (13 weeks) at the time point of surgery, become resectable with primary wound closure without the need for plastic reconstructive surgery like skin flaps or skin grafts, was already achieved after stage I (9/18 patients; 50.0%), thus the study was discontinued for early success. The objective response rate was 55.6% and the complete pathological response rate was 33.3%. Only mild adverse events occurred. The 6-months RFS and OS rates were 100%. T-VEC led to a significant increase of cytotoxic T cells, B cells and myeloid cells, and a decrease of Tregs within the tumor microenvironment. We observed a potent induction of T cell receptor clones of antitumoral and antiviral origin, as well as a strong humoral immune response. Together, neoadjuvant T-VEC represents a viable treatment option for patients with difficult-to-resect BCCs (EudraCT Number 2018-002165-19).

overall_design:
Single-cell RNA-sequencing (10x Genomics 5’ V1.1 protocol, Single Cell 5' PE chemistry): 12 Basal Cell Carcinoma biopsies after 6 cycles of intralesionally applied T-VEC

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Submitter states that missing raw data are being made available for controlled access in EGAD50000000371.
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first: Julia

last: Ressler

first: Maud

last: Plaschka

first: Rita

last: Silmbrod

first: Victoria

last: Bachmayr

first: Lisa

last: Shaw

first: Thomas

last: Silly

first: Nina

last: Zila

first: Andreas

last: Stepan

first: Anna

last: Kusienicka

first: Philipp

last: Tschandl

last: Tittes

last: Roka

first: Werner

last: Haslik

last: Petzelbauer

first: Franz

last: Koenig

first: Rainer

last: Kunstfeld

first: Matthias

last: Farlik

first: Wolfgang

last: Weninger

first: Christoph

last: Hoeller


title: cSTAR analysis identifies endothelial cell cycle as a key regulator of flow-dependent artery remodeling

status: Public on Sep 05 2024

city: Dublin

first: Oleksii

last: Rukhlenko

address: Systems Biology Ireland, University College Dublin

department: Systems Biology Ireland

country: Ireland

institute: University College Dublin

summary: Fluid shear stress (FSS) from blood flow sensed by vascular endothelial cells (ECs) determines vessel behavior but regulatory mechanisms are only partially understood. We used cell State Transition Assessment and Regulation (cSTAR), a powerful new computational method, to elucidate EC transcriptomic states under low shear stress (LSS), physiological shear stress (PSS), high shear stress (HSS), and oscillatory shear stress (OSS) that induce vessel inward remodeling, stabilization, outward remodeling or disease susceptibility, respectively. Combined with publicly available EC transcriptomic responses to drug treatments from the LINCS database, this approach inferred a regulatory network controlling EC states and made several novel predictions. Particularly, inhibiting cell cycle dependent kinase (CDK) 2 was predicted to initiate inward vessel remodeling and promote atherogenesis. In vitro, PSS activated CDK2 and induced late G1 cell cycle arrest. In mice, EC deletion of CDK2 triggered inward artery remodeling, pulmonary and systemic hypertension and accelerated atherosclerosis. These results validate use of cSTAR and identify key determinants of normal and pathological artery remodeling.

overall_design: Human umbilical vein ECs (HUVECs) were seeded on tissue culture plastic slides coated with 20 μg/mL fibronectin for two hours at 37°C and grown to confluence. Shear stress (FSS) was applied in parallel flow chambers. HUVECs were subjected to oscillatory FSS (OSS, 0.5±4 dynes/cm^2), low FSS (LSS, 3 dynes/cm^2), physiological FSS (PSS, 16 dynes/cm^2) and high FSS (HSS, 40 dynes/cm^2) for 24 hours, in each case in comparison to STAT as an internal control. Total RNA was extracted and prepared for RNA sequencing (RNA-seq). To evaluate how CDK2 affects cell cycle state, we performed CDK2 knockdown in HUVECs in static and PSS conditions.

first: Hanqiang

last: Deng

first: Divyesh

last: Joshi

first: Xiaoyue

last: Hu

last: Junk

last: Tuliakova

first: Boris

middle: N

last: Kholodenko

first: Martin

last: Schwartz


title: Comparative analyses of genome methylation in monocytes trained by cholesterol and LPS

city: Blacksburg

first: Blake

middle: Alexander

last: Caldwell

state: VA

address: 149 Life Sciences I Building, 970 Washington Street SW

department: Biological Sciences

institute: Virginia Tech

type: Methylation profiling by genome tiling array

summary: We performed comparative studies of monocytes trained by either PBS, cholesterol or varying dosages of LPS, in order to examine the differential innate responses to stress signals.  Differentially trained monocytes were subjected to whole genome methylation array analyses. Our data reveal that monocytes trained by either cholesterol or very low dose LPS preferentially clustered together in terms of their genome methylation profiles, separate from the naïve PBS treated monocytes or monocytes trained by high dose LPS.  Our findings suggest that monocytes may similarly respond to the generic membrane stress signals caused by either very low dose LPS or cholesterol, in contrast to the exhausted state induced by high dose LPS.

overall_design: Genome-wide DNA methylation profiling was performed using Infinium Mouse Methylation BeadChip arrays. Based on variability observed in previous studies, a minimum of 4 biological replicates was determined to be sufficient for most BMMC culture experiments, which is sufficiently powered to detect differences in 5mC as low as 5%. All experiments were performed on at least two separate days and with mice from at least 3 separate litters.

first: Shuo

last: Geng

first: Liwu

last: Li


title: Spatial tumor immune heterogeneity facilitates subtype co-existence and therapy response via AP1 dichotomy in pancreatic cancer

city: Göttingen

first: Shiv

middle: K.

last: Singh

address: Robert-Koch-Straße 40

department: Gastroenterology, GI-Oncology and Endocrinology

country: Germany

institute: University Medical Center Göttingen


title: Mediator kinase inhibition suppresses hyperactive interferon signaling in Down syndrome II

status: Public on Sep 01 2024

city: Boulder

first: Meaghan

last: Courvan

state: CO

address: 596 UCB

department: Biofrontiers

institute: University of Colorado, Boulder

summary: Individuals with Down syndrome have a increased likelihood of suffering from inflammatory and autoimmune conditions, due to the presence of four interferon receptors on chromosome 21. Transcription of genes plays a key role in the interferon response, and the Mediator kinases, CDK8 and CDK19, are essential in potentiating this transcription. Given the role CDK8/19 play in the interferon response, and the fact that selective inhibitors of these kinases exist (such as Cortistatin A), it is possible that targetting Mediator kinase activity may alleviate symptoms of chronic inflammation in Down syndrome.

overall_design: Immortalized lymphoblastoid cells from an individual with Down syndrome were pre-treated for 30 minutes with either vehicle (10% DMSO) or 100 nM Cortistatin A. After pre-treatment, they were subsequently exposed to  vehicle (40 mM Tris pH 7.4) . After 45 minutes of exposure to vehicle, nuclei were isolated from cells and nuclear run-on reactions containing biotinylated CTP were performed. Nascent RNA was captured using strepdavidin, and RNA from each condition was reverse-transcribed into cDNA and labeled with unique indices for sequencing.

first: Kira

last: Cozzolino


title: Gene expression profiling for circPETH overexpression and knockout

status: Public on Aug 29 2024

city: Chengdu

first: Tian

last: Lan

state: Sichuan

address: No. 37 of Guoxue Lane

department: Department of Liver Surgery & Liver Transplantation

institute: West China Hospital

summary: Metabolic reprogramming fuels cancer cell metastasis and remodels immunosuppressive tumor microenvironment (TME). We report here that a circRNA packaged by extracellular vesicles (EVs) from tumor-associated macrophages (TAMs) to hepatocellular carcinoma (HCC) cells, circPETH, facilitates glycolysis and metastasis of HCC cells. Mechanistically, circPETH-147aa, encoded by circPETH in m6A-driven manner, promotes the PKM2-catalyzed ALDOA-S36 phosphorylation via MEG pocket. Furthermore, circPETH-147aa impairs anti-HCC immunity by elevating the HuR-dependent SLC43A2-mRNA stability and stimulating the deficiency of methionine and leucine in cytotoxic CD8+ T cells. Importantly, we successfully identified a novel small molecule, Norathyriol, by virtual and experimental screening as an effective inhibitor targeting MEG pocket on circPETH-147aa surface. Norathyriol reverses circPETH-147aa-facilitated metabolic and metastatic phenotypes of HCC cells, improves anti-PD1 efficacy and boosts cytotoxic CD8+ T cells function. Our findings determine Norathyriol as a promising anti-HCC agent, and contribute to overcoming the resistance of advanced HCC to immune checkpoint blockades (ICBs) therapies.

overall_design: To gain insights into the regulatory mechanism of circPETH in terms of comprehensive gene expression, RNA-sequencing (RNA-seq) was conducted to compare the following two expression profiles: OE-circPETH versus Vector; and circPETH KO versus NTC.

first: T

first: F

last: Gao

first: Y

last: Cai


title: ICI-SJS/TEN mediated by macrophage-derived CXCL10 and abated by TNF blockade

status: Public on Aug 26 2024

city: Taoyuan

first: Chuang-Wei

last: Wang

address: No. 5, Fusing St

country: Taiwan

institute: cgmh

summary: Immune checkpoint inhibitors (ICI) represent new anticancer agents and have been used worldwide. However, ICI can potentially induce life-threatening severe cutaneous adverse reaction (SCAR), such as Stevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN), hindering continuous ICI therapy. We examined 6 cohorts within 25 ICI-induced SJS/TEN patients and conducted single-cell RNA sequencing (scRNA-seq) analysis, which revealed overexpression of macrophage-derived CXCL10 that recruited CXCR3+ cytotoxic T lymphocytes (CTL) in blister cells from ICI-SJS/TEN skin lesions. ScRNA expression profiles and ex vivo blocking studies further identified TNF signaling as the key pathway responsible for macrophage-derived CXCL10 and CTL activation. Based on the trajectory analysis, ICI-activated T cells from whole blood are proposed to serve as the initial cells involved in inflammation, that lead to monocytes differentiating into macrophages and increasing their susceptibility to migrate to the lesion sites. Compared with systemic corticosteroids treatment, ICI-induced SJS/TEN patients treated with biologic TNF blockade showed a significantly rapid recovery and no recurrence of SCAR with continuous ICI therapy. Our findings identified that macrophage-eliciting CTL contribute the pathogenesis of ICI-induced epidermal necrolysis and provide the therapeutic targets for the management and prevention of SCAR induced by ICI therapy.

overall_design: Single-cell RNA Sequencing


title: Spatial transcriptomics reveals tanscriptional perturbations leading to uterine squamous metaplasia, atrophy, and infertility in a mouse model of RTHa

city: Jefferson

first: Elijah

middle: F

last: Edmondson

state: MD

address: 4310 Mountville Rd

institute: Frederick National Laboratory for Cancer Research

summary: This study identifies an unknown role for KLF9 signaling in normal uterine development, which is decreased in a mouse model of resistance to thyroid hormone (RTHa), resulting in infertility through ectopic IL-33 expression produced by abnormally differentiated, KLF9-deficient endometrial cells. Utilizing a combination of genetically engineered mouse models, histopathology, spatial transcriptomics, and pharmacological inhibitors, we revealed that infertility in RTHa results from abnormal endometrial differentiation mediated by KLF9 suppression. These abnormally differentiated endometrial cells were the source of ectopic IL-33 overexpression. Increased endometrial IL-33 led to T-cell infiltration, destruction of glands, and endometrial fibrosis, which culminated in infertility. This study uncovers a link between TRa1 and KLF9 signaling for normal endometrial differentiation, reveals a mechanism for ectopic uterine IL-33 in female fertility, and provides new insights on the impact of hypothyroidism in female reproduction.

sample_organism:
Mus musculus
blank sample

platform_organism:
Mus musculus
blank sample

overall_design: A total of 190 regions of interest (ROI) were taken from 13 mouse uterus sections (6 Thra1 PV/+ and 7 wild-type mice), which included endometrial mucosa, glands, and stroma; a minimum of 5 ROIs were taken per category per mouse.

first: Sheue-yann

last: Cheng


title: Mapping naturally presented T-cell antigens in medulloblastoma based on integrative multi-omics [Methylation array]

status: Public on Aug 24 2024

city: Tuebingen

first: Jonas

last: Scheid

state: Baden-Wuerttemberg

address: Auf der Morgenstelle 15

department: Peptide-based Immunotherapy

institute: University and Universityhospital Tuebingen

summary: Medulloblastoma is the most frequent malignant primary brain tumor in children. Despite recent advances in integrated genomics, the prognosis in children with high-risk medulloblastoma remains devastating, and new tumor-specific therapeutic approaches are needed. Here, we present an atlas of naturally presented T-cell antigens in medulloblastoma. We mapped the human leukocyte antigen (HLA)-presented peptidomes of 28 tumors and performed comparative immunopeptidome profiling against an in-house benign database. Medulloblastoma proved to be a rich source of novel tumor-associated antigens, naturally presented on HLA class I and II molecules. Remarkably, most tumor-associated peptides and proteins were subgroup-specific, whereas shared presentation among all subgroups of medulloblastoma (WNT, SHH, Group 3 and Group 4) was rare. Functional testing of top-ranking novel candidate antigens demonstrated the induction of peptide-specific T-cell responses, supporting their potential for T-cell immunotherapy. This study is an in-depth mapping of naturally presented T-cell antigens in medulloblastoma. Integration of immunopeptidomics, transcriptomics, and epigenetic data led to the identification of a large set of actionable targets that can be further used for the translation into the clinical setting by facilitating the informed design of immunotherapeutic approaches to children with medulloblastoma.

overall_design: DNA-methylation profiles were obtained from 28 tumor samples. Based on molecular classification using the Heidelberg Brain Tumor Methylation Classifier the patient samples were classified into the subgroups WNT, SHH, Group3 and Group4

first: Julia

last: Velz

first: Lena

middle: K

last: Freudenmann

first: Gioele

last: Medici

first: Marissa

last: Dubbelaar

first: Malte

last: Mohme

first: David

middle: R

last: Ghasemi

first: Daniel

last: Kowalewski

first: Angelica

middle: B

last: Patterson

first: Anna

last: Zeitlberger

first: Katrin

last: Lamszus

first: Manfred

last: Westphal

first: Matthias

last: Eyrich

first: Martina

last: Messing-Jünger

first: Andreas

last: Röhrig

first: Harald

last: Reinhard

first: Kévin

last: Beccaria

first: Rogeiro

last: Craveiro

first: Beat

last: Frey

last: Sill

first: Sven

last: Nahnsen

first: Marie

last: Gauder

first: Konstantina

last: Kapolou

first: Manuela

last: Silginer

first: Tobias

last: Weiss

first: Hans-Georg

last: Wirsching

first: Patrick

last: Roth

first: Michael

last: Grotzer

first: Niklaus

last: Krayenbühl

first: Oliver

last: Bozinov

first: Luca

last: Regli

last: Rammensee

first: Elisabeth

last: Rushing

first: Felix

last: Sahm

first: Juliane

last: Walz

last: Weller

first: Marian

last: Neidert


title: Mapping naturally presented T-cell antigens in medulloblastoma based on integrative multi-omics [RNA-seq]

first: Jonas

last: Scheid

overall_design: RNA-seq was used to profile subgroup-specific differential expression of target antigens and to characterize the immune microenvironment of medulloblastoma patients

first: Julia

last: Velz

first: Lena

last: Freudenmann

first: Gioele

last: Medici

first: Marissa

last: Dubbelaar

first: Malte

last: Mohme

first: David

last: Ghasemi

first: Daniel

last: Kowalewski

first: Angelica

last: Patterson

first: Anna

last: Zeitlberger

first: Katrin

last: Lamszus

first: Manfred

last: Westphal

first: Matthias

last: Eyrich

first: Martina

last: Messing-Jünger

first: Andreas

last: Röhrig

first: Harald

last: Reinhard

first: Kévin

last: Beccaria

first: Rogeiro

last: Craveiro

last: Frey

first: Martin

last: Sill

last: Nahnsen

middle: C


title: iFlpMosaic enable the multispectral barcoding and high-throughput comparative analysis of mutant and wildtype cells.

status: Public on Sep 03 2024

city: Madrid

first: Rui

last: Benedito

state: Madrid

address: C. de Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: In order to understand gene function, cells mutated for a gene need to be compared with normal cells. In most biomedical studies this comparative analysis is carried out with cells present in different animals and therefore not experiencing the same microenvironment or epigenetic changes. Here we present a large set of new genetic tools and mouse lines, that enable the Flp recombinase-dependent ratiometric induction and single cell clonal tracking of multiple fluorescently labelled normal and Cre-mutant cells, from distinct or the same progenitor cells. The labelled cells can be profiled in situ by multispectral imaging, or by FACS and scRNA-seq. With these new tools, normal and mutant cells can be ratiometrically induced and multispectrally barcoded within the same temporal window and tissue microenvironment. This enables a better understanding of how induced genetic mutations affect the biology of single cells with higher accuracy and reliability during tissue development, homeostasis, or disease.

overall_design: For RNA-seq analysis, embryos were dissociated and Tomato-KO or YFP-WT cells were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of Tomato signal and YFP signal.  Then both cell populations were analyzed using scRNAseq.

first: Irene

last: García-González

first: Álvaro

last: Regano

first: Susana

last: Rocha


title: Comparative analysis between single-cell RNA-seq and single-molecule RNA FISH indicates that the pyrimidine nucleobase idoxuridine (IdU) globally amplifies transcriptional noise

status: Public on Aug 28 2024

city: San Francisco

first: Binyamin

last: Zuckerman

state: California

institute: UCSF

summary: Stochastic fluctuations (noise) in transcription generate substantial cell-to-cell variability, but the physiological roles of noise have remained difficult to determine in the absence of generalized noise-modulation approaches.  Previous single-cell RNA-sequencing (scRNA-seq) suggested that the pyrimidine-base analog (5′-iodo-2′-deoxyuridine, IdU) could generally amplify noise without substantially altering mean-expression levels but scRNA-seq technical drawbacks potentially obscured the penetrance of IdU-induced transcriptional noise amplification.  Here we quantify global-vs.-partial penetrance of IdU-induced noise amplification by assessing scRNA-seq data using numerous normalization algorithms and complement our previous results with data from Human Jurkat T Lymphocytes, including two biological replicates to allow rigorous statistical analysis.  Collectively, this analysis indicates which scRNA-seq algorithms are appropriate for quantifying noise and argues that IdU is a globally penetrant noise-enhancer molecule that could enable investigations of the physiological impacts of transcriptional noise in various cell types and organisms.

overall_design: Jurkat cells were treated with either DMSO or 20 uM IdU for 48h. Two biological replicates were performed, resulting in total four samples of scRNA-seq.

first: Leor

last: Weinberger


title: Gene expression profiling of CD8+ T cells in the Norathyriol versus PBS-treated co-culture system

first: Tian

last: Lan

summary: Metabolic reprogramming fuels cancer cell metastasis and remodels the immunosuppressive tumor microenvironment (TME). We report here that a circRNA, circPETH, packaged by extracellular vesicles (EVs) from tumor-associated macrophages (TAMs) to hepatocellular carcinoma (HCC) cells, facilitates glycolysis and metastasis of recipient HCC cells. Mechanistically, circPETH-147aa, encoded by circPETH in a m6A-driven manner, promotes PKM2-catalyzed ALDOA-S36 phosphorylation via MEG pocket. Furthermore, circPETH-147aa impairs anti-HCC immunity by elevating HuR-dependent SLC43A2 mRNA stability and driving methionine and leucine deficiency in cytotoxic CD8+ T cells. Importantly, by virtual and experimental screening, we found that the novel small-molecule Norathyriol was an effective inhibitor that targets the MEG pocket on circPETH-147aa surface. Norathyriol reverses circPETH-147aa-facilitated acquisition of metabolic and metastatic phenotypes for HCC cells, increases anti-PD1 efficacy and boosts cytotoxic CD8+ T-cell function. Our findings determine Norathyriol as a promising anti-HCC agent that contributes to the attenuation of advanced HCC resistance to immune checkpoint blocker (ICB) therapies.

overall_design: To understand the mechanistic association of Norathyriol with CD8+ T cells, RNA-seq was performed to compare the expression profiles of CD8+ T cells in the Norathyriol versus PBS-treated co-culture system.

first: T

first: F

last: Gao

first: Y

last: Cai


title: Integrative gene regulatory analysis reveals transcriptional mechanisms required in mature human hepatocytes and during in vitro hepatocyte differentiation (scRNA-Seq)

status: Public on Aug 22 2024

city: Nijmegen

first: Haoyu

last: Wu

address: Mr. van Houtenstraat, 24

country: Netherlands

institute: Radboud University

summary: Advances in 3D cell culture systems, including the hepatic organoids, has shown the potential to model the liver development in vitro. However, hepatocyte-like cells obtained by these means are still immature compared to the primary human hepatocytes. Here we applied single-cell RNA-seq and ATAC-seq to identify gene regulatory mechanisms distinct to mature human hepatocytes (in vivo) and organoid derived hepatocyte like cells (in vitro). Using a modified two-step perfusion protocol, primary hepatocytes from all lobular zones were obtained with high purity. Integrative analysis revealed a key role of transcription factors of the AP-1 family in cooperation with hepatocyte-specific transcription factors, such as HNF4A, in establishing cellular identity of mature hepatocytes. Furthermore, it revealed distinct transcription factor sets required/active in human hepatocytes and liver organoids. Function analysis of an organoid-enriched transcription factor ELF3, showed that decreased expression of ELF3 in liver organoids promotes increased expression of genes typical to mature hepatocytes. This study indicates that ELF3 functions as a barrier of hepatocyte differentiation from liver organoids. Collectively, our integrative analysis provides critical insights into the transcriptional regulatory networks of human hepatocytes and liver organoids, which will further efficient differentiation of functional hepatocytes in vitro.

overall_design: scRNA-seq

first: Hendrik

last: Marks

first: Richárd

last: Bártfai


title: Protein arginine methyltransferase 5 mediates the increase in interferon stimulated genes during replication stress

status: Public on Aug 30 2024

city: Singapore

first: Phuong

last: Hoang

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

summary: Replication stress (RS) is a hallmark of cancer and is defined as the perturbation of DNA replication that results in stalled or collapsed DNA replication forks. Chemotherapeutic drugs exploit this phenomenon by enhancing the RS, resulting in cell death. Protein arginine methyltransferase 5 (PRMT5) is responsible for post-translational symmetric dimethylarginine (SDMA) modification. This modification is important for regulating RS. PRMT5 is upregulated in several malignancies and therefore inhibitors have been developed. To understand the consequences of PRMT5 inhibition, we investigated its role in replication stress response. Employing the RS inducer hydroxyurea (HU) and the PRMT5 inhibitor GSK591, we discovered a PRMT5-mediated increase in SDMA during RS. Furthermore, we observed that RS resulted in a PRMT5-dependent transcriptional increase in interferon-stimulated genes (ISGs). Therefore, we demonstrated a previously unreported role for PRMT5-mediated SDMA in the context of RS.

overall_design: This dataset contains RNA-seq data from breast epithelial cell lines - MCF10A - treated withDMSO or hydroxyurea (HU) or PRMT5 inhibitor GSK591 or combination HU and GSK591.

first: Hoang

last: Phuong

first: TohChinMin

last: Clarissa

first: Patrick

last: Jaynes

first: Ernesto

last: Guccione

first: Anand

last: Jeyasekharan


title: Transmission of extracellular vesicles (EVs)-packaged circRNA from tumor-associated macrophages (TAMs) to hepatocellular carcinoma (HCC) cells

summary: We compared the circRNA expression profiles of TAMs versus MDMs, EVs from TAMs versus those from MDMs and Hep3B cells co-cultured with TAMs versus those cultured alone.

overall_design: Microarrays were employed to identify circRNAs packaged by EVs and transmitted from TAMs to HCC cells. The following three circRNAs profiles were subjected to intersection analysis: TAMs versus MDMs; EVs from TAMs versus those from MDMs; and Hep3B cells co-cultured with TAMs versus those cultured alone


title: Integrative gene regulatory analysis reveals transcriptional mechanisms required in mature human hepatocytes and during in vitro hepatocyte differentiation (RNA-Seq)

overall_design: RNA-seq


title: Integrative gene regulatory analysis reveals transcriptional mechanisms required in mature human hepatocytes and during in vitro hepatocyte differentiation

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

overall_design: Refer to individual Series


title: Zongertinib (BI01810631), an irreversible HER2 TKI, spares EGFR signaling and improves therapeutic response in preclinical models and patients with HER2-driven cancers

first: Malgorzata

middle: Emilia

last: Kamuda

address: Dr.Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

institute: Boehringer-Ingelheim

summary: To investigate the effects of Zongertinib, a HER2 inhibitor on different cell lines and under various conditions, we used expression data from dedicated biomarker in vivo and in vitro studies.

overall_design: CDX models were generated using engineered PC-9 cells (HER2 exon 20 insertion YVMA clone 5) and  NCI-N87 cell line. Models were treated with Zongertinib (BI01810631) , while control samples were treated with Natrosol or DMSO.

first: Sylvia

last: Tilandyova

first: Donat

last: Aplar

first: Daniel

last: Gerlach

first: Malgorzta


title: LXRα genomic binding in murine macrophages

status: Public on Aug 27 2024

first: ANTONIO

last: CASTRILLO

address: Arturo Duperier 4

department: metabolism and cellular signaling

institute: Instituto Investigaciones Biomedicas Alberto Sols CSIC

summary: Liver X receptors (LXRα and LXRβ) are nuclear receptor transcription factors that play crucial roles in regulating metabolic and immune functions in macrophages. Both receptors are present in macrophages and exhibit significant sequence similarity, yet their specific roles in various macrophage models, especially in inflammatory contexts, remain underexplored. Prior research has demonstrated that ligand-activated LXRs can suppress the expression of pro-inflammatory cytokines in macrophages. Here, we explored the genomic landscape of LXRa under inflammatory conditions using BMDM lacking LXRb as previously described (de la Rosa et al 2024); we treated BMDM with synthetic LXR ligand GW3965 alone or in combination with lipopolysaccharide for 24h.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for nuclear receptor LXR-alpha in bmdm cells.

first: Antonio

last: Castrillo

first: Juan

middle: V

last: de la Rosa Medina


title: Poly-A transcriptome changes in mouse embryonic fibroblasts (MEFs) after spontaneous immortalization

city: St. John's

first: Michael

last: Leitges

state: NL

address: 300 Prince Philip Drive

department: Division of BioMedical Sciences, Faculty of Medicine

institute: Memorial University of Newfoundland

summary: In our study, we characterized the changes in poly-A gene expression atributed to the process of spontaneous immortalization using a mouse embryonic fibroblasts (MEF) model. Primary MEFs were established, serially passaged and spontaneously immortalized using a modified 3T3 NIH protocol. We then performed gene expression profiling analysis using RNA-seq data of 3 different clones at two time points (primary and immortalized).

overall_design: Gene expression profiling of RNA-seq data for MEF spontaneous immortalization.

first: Jocshan

last: Loaiza-Moss

first: Ursula

last: Braun


title: Spatiotemporal profile of an optimal host response to virus infection in the primate central nervous system

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Viral infections of the central nervous system (CNS) are a major cause of morbidity largely due to lack of prevention and inadequate treatments. While mortality from viral CNS infections is significant, nearly two thirds of the patients survive. Thus, it is important to understand how the human CNS can successfully control virus infection and recover. Since it is not possible to study the human CNS throughout the course of viral infection at the cellular level, here we analyzed a non-lethal viral infection in the CNS of nonhuman primates (NHPs). We inoculated NHPs intracerebrally with a high dose of La Crosse virus (LACV), a bunyavirus that can infect neurons and cause encephalitis primarily in children, but with a very low (? 1%) mortality rate. To profile the CNS response to LACV infection, we used an integrative approach that was based on comprehensive analyses of (i) spatiotemporal dynamics of virus replication, (ii) identification of types of infected neurons, (iii) spatiotemporal transcriptomics, and (iv) morphological and functional changes in CNS intrinsic and extrinsic cells. We identified the location, timing, and functional repertoire of optimal transcriptional and translational regulation of the primate CNS in response to virus infection of neurons. These CNS responses involved a well-coordinated spatiotemporal interplay between astrocytes, lymphocytes, microglia, and CNS-border macrophages. Our findings suggest a multifaceted program governing an optimal CNS response to virus infection with specific events coordinated in space and time. This allowed the CNS to successfully control the infection by rapidly clearing the virus from infected neurons, mitigate damage to neurophysiology, activate and terminate immune responses in a timely manner, resolve inflammation, restore homeostasis, and initiate tissue repair. An increased understanding of these processes may provide new therapeutic opportunities to improve outcomes of viral CNS diseases in humans.

overall_design: To profile the CNS response to La Crosse virus (LACV) infection, we used an integrative approach that was based on comprehensive analyses of (i) spatiotemporal dynamics of virus replication, (ii) identification of types of infected neurons, (iii) spatiotemporal transcriptomics, and (iv) morphological and functional changes in CNS intrinsic and extrinsic cells.

first: Olga

middle: A

last: Maximova

first: Sarah

last: Anzick

first: Richard

last: Bennett

first: Lawrence

last: Faucette

first: Marina

last: Rahman

first: Marisa

last: St Claire

first: Stephen

last: Whitehead

first: Brian

last: Murphy

first: Anthony

last: Gresko

first: Kishore

last: Kanakabandi

first: Zong-mei

last: Sheng

first: Yongli

last: Xiao

first: John

last: Kash

first: Jeff

last: Taubenberger

first: Jerrold

last: Ward

first: Craig

last: Martens

first: Jeffrey

middle: I

last: Cohen


title: Analysis of NS2-dependent effects on influenza PB1 segment extends replication requirements beyond the canonical promoter

city: San Diego

first: Alistair

middle: Brian

last: Russell

state: CA

address: 9500 Gilman Dr,

institute: University of California, San Diego

summary: Influenza A virus encodes promoters in both the sense and antisense orientations. These support the generation of new genomes, antigenomes, and mRNA transcripts. Characterization of the influenza promoters using minimal replication assays—transfections with viral polymerase, nucleoprotein, and a genomic template—defined their sequence as 13nt at the 5’ end of the viral genomic RNA (U13) and 12nt at the 3’ end (U12).Other than a single position the U12 and U13 sequences are identical between all eight RNA molecules that comprise the segmented influenza genome.Nevertheless, each segment can exhibit different transcriptional dynamics despite possessing identical promoters.Minimal replication assays lack  the influenza protein NS2, which can modulate transcription and replication differentially between influenza segments.This suggests that NS2 expression may redefine the influenza A virus promoter.In this work we assess how internal regions of sequence in two genomic segments, HA and PB1, may contribute to NS2-dependent replication as well as map such interactions down to individual nucleotides in PB1. We find that the expression of NS2 significantly alters sequence requirements for efficient replication beyond the identical U12 and U13 sequence, providing a mechanism for the divergent replication and transcription dynamics across the influenza A virus genome.

overall_design: To understand the contribution of individual positions to NS2-dependent replication, a combination of barcoded, length-variant libraries, and single-nucleotide variant libraries were generated, sequenced, and used in minimal replication assays with and without the additional expression of NS2.

last: Mendes


title: Unraveling autophagic imbalances and therapeutic insights in Mecp2-deficient models

city: Milano

first: Stefano

last: de Pretis

address: Via Olgettina, 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Institute

summary: Loss of function mutations in MECP2are associated to Rett syndrome (RTT), a severe neurodevelopmental disease. Mainly working as a transcriptional regulator, MECP2 absence leads to gene expression perturbations resulting in deficits of synaptic function and neuronal activity. In addition, RTT patients and mouse models suffer from a complex metabolic syndrome, suggesting that related cellular pathways might contribute to neuropathogenesis. Along this line, autophagy is critical in sustaining developing neuron homeostasis by breaking down dysfunctional proteins, lipids, and organelles. Here, we investigated the autophagic pathway in RTT and found reduced content of autophagic vacuoles in Mecp2 knock-out neurons. This correlates with defective lipidation of LC3B-II probably caused by a deficiency of the autophagic membrane lipid phosphatidylethanolamine. The administration of the autophagy inducer trehalose recovers LC3B lipidation, autophagosomes content in knock-out neurons, and ameliorates their morphology, neuronal activity and synaptic ultrastructure. Moreover, we provide evidence for attenuation of motor and exploratory impairment in Mecp2 knock-out mice upon trehalose administration. Overall, our findings open new perspectives for neurodevelopmental disorders therapies based on the concept of autophagy modulation.

overall_design: To investigate threalose effect on Mecp2-KO primary neurons, we performed gene expression profiling analysys on 4 different groups of samples: WT primary neurons, threalose treated WT primary neurons, Mecp2-KO primary neurons, and  threalose treated Mecp2-KO primary neurons

first: Michela

last: Palmieri


title: Specific pre-plasma cell states and local proliferation at the dark zone – medulla interface characterize germinal center-derived plasma cell differentiation in lymph node (Figure2) 1

city: Marseille

first: chuang

last: dong

address: 163 Av. de Luminy

country: France

institute: CIML

summary: High affinity antibody-producing plasma cell (PC) production in germinal centers (GC) is crucial for antibody-mediated immune protection after vaccination or infection. The selection of high affinity B cells in the GC light zone instructs PC differentiation in a subset of cells, but the phenotype, differentiation trajectory and spatial localization of those prePC intermediates remain to be characterized. Here, we have used a mouse model to track GC-derived B cells with integrative single-cell and spatial analyses in draining lymph node after immunization. We first identified putative prePC in scRNA-seq datasets, then enriched those cells through their specific surface phenotype for further analysis of their gene expression trajectories and BCR repertoire. We found a continuum of actively proliferating transitional states bridging selected LZ GC B cells and recently exported PCs, with gradually increasing levels of endoplasmic reticulum stress-associated genes and immunoglobulin transcripts. Spatial analyses revealed that recently differentiated PC continued their maturation and proliferation at the interface between the DZ and extensions of the lymph node medulla. Our results provide insights into the intermediate stages and microenvironmental factors involved in the differentiation of GC B cells into PC, with implications for vaccine development and understanding antibody responses.

overall_design: Mice were primed with OVA in Alum, for some of them also boosted with OVA in Alum, and we investigated cells 4 days after tamoxifen gavage, at day 10 and day 20 of either the primary response (D10P, D20P), or the secondary response after boosting (D10S, D20S), using the FACS-based 5-prime-end sequencing (FB5P-seq) method for integrative scRNA-seq analysis described by Attaf et al. (DOI : 10.3389/fimmu.2020.00216). Individual cells were sorted into a 96-well PCR plate, with each well containing 2 µL of lysis buffer. Index sort mode was activated to record the fluorescence intensities of all markers for each individual cell. Flow cytometry standard (FCS) files from the index sort were analyzed using FlowJo software, and compensation parameters were exported as CSV tables for subsequent bioinformatic analysis. Immediately after sorting, plates containing individual cells were stored at -80°C until further processing. Following thawing, reverse transcription was performed, and the resulting cDNA was preamplified for 22 cycles. Libraries were then prepared according to the FB5P-seq protocol. The FB5P-seq data were processed to generate both a single-cell gene count matrix and single-cell B cell receptor (BCR) repertoire sequences for B cell analysis. Two separate bioinformatic pipelines were employed for gene expression and repertoire analysis, as detailed in Attaf et al. (DOI : 10.3389/fimmu.2020.00216).

first: Pierre

last: Milpied

first: Laurine

last: Binet

first: Chuang

last: Dong


title: Mapping naturally presented T-cell antigens in medulloblastoma based on integrative multi-omics

first: Jonas

last: Scheid


title: Integrative gene regulatory analysis reveals transcriptional mechanisms required in mature human hepatocytes and during in vitro hepatocyte differentiation (ATAC-Seq)

first: Haoyu

last: Wu

overall_design: ATAC-seq

first: Hendrik

last: Marks

first: Richárd

last: Bártfai


title: The mechanism of cardiotoxicity induced by evodiamine and matrine was revealed by epitranscriptomics

status: Public on Aug 20 2024

city: Fuzhou

first: Dongshan

last: Liao

address: 福建省福州市鼓楼区新权路29号

institute: 福建医科大学附属协和医院

summary: By using epitranscriptomics, the mechanism of cardiotoxicity induced by evodiamine and matrine was discovered. Experimental findings indicated that evodiamine and matrine altered m6A levels within the cells.

overall_design: To investigate whether m6A modification is involved in cardiotoxicity following evodiamine and matrine treatment, we performed MeRIP-seq on control cells and cells treated with evodiamine and matrine.

first: Guanhua

last: Fang

first: Yanming

last: Shen


title: RNF20-mediated transcriptional pausing and alternative splicing of pro-angiogenic genes orchestrate vessel growth [04Po2t_OE_ERG_ChIP_HUV]

status: Public on Aug 18 2024

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

institute: Medical Faculty Mannheim/University of Heidelberg

summary: Signal-responsive gene expression is essential for vascular growth and patterning, yet the mechanisms allowing the integration of signaling inputs and transcriptional activities are largely unknown. Here we show that RNF20, the major E3 ubiquitin ligase of histone H2B, plays a key role during sprouting angiogenesis by mediating Pol II promoter-proximal pausing at pro-angiogenic genes. Furthermore, it orchestrates large-scale mRNA processing events, which change the bioavailability and function of critical pro-angiogenic factors, such as VEGFA. Mechanistically, we show that RNF20 restricts ERG-dependent gene activation through the VEGF-ERK1/2 axis while enabling Notch1 to bind to chromatin, thereby modulating the VEGF-Notch signaling circuits. Since perturbations of RNF20 are associated with cardiovascular malformations in human patients, our work may provide novel therapeutic avenues for diseases caused by vascular dysfunction.

overall_design: HUVEC cells were transfected with lentivirus either with Ctr or ERG Over expression or STAT3 Over Expression. Chromatin was harvested to perform ChIP-seq.

first: Julio

last: Cordero

first: Nalan

last: Tetik


title: Analysis of lncRNA expression in myasthenia gravis (MG) and normal subjects

status: Public on Aug 15 2024

city: Harbin

first: Jianjian

last: Wang

address: No. 246 Xuefu Road, Nangang District, Harbin, China

institute: The Second Affiliated Hospital of Harbin Medical University

summary: To further development of MG-related lncRNA expression differences, we have employed whole lncRNA microarray expression profiling as a discovery platform to identify MG-related lncRNA with the potential to distinguish MG.

overall_design: Our study used the Arraystar Human LncRNA Microarray V5.0, a microarray designed for global profiling of human lncRNA and protein-coding transcripts. Eight myasthenia gravis patients and eight normal patients were analyzed.

first: Lifang

last: Li


title: Expression analysis of C2C12 cells treated with scramble siRNA or siRNA directed against Fndc1

status: Public on Aug 17 2024

city: Yangling, Shaanxi

first: xin

middle: rui

last: zhang

address: Yangling, Shaanxi

institute: Northwest A&F University

overall_design:
We transfected C2C12 cells with 100nM of scrambled siRNA scramble and an siRNA directed against Fndc1. Cells were harvested at 48h post-transfection and RNAseq was performed with polyA selection
For RNA-Seq library preparation we followed the Illumina TruSeq RNA Sample Preparation Kit v2 manual. At least 40 million, 75bp long paired end reads were mapped to the mm9 version of the mouse genome per replicate using STAR 2.4.2a (doi: 10.1093/bioinformatics/bts635) using the default parameters.

first: ruixin


title: Context-aware single-cell multiomics approach identifies cell-type specific lung cancer susceptibility genes

status: Public on Aug 14 2024

city: Rockville

first: Jiyeon

last: Choi

state: Maryland

address: 9615 Medical Center Drive, Rm 3116

institute: NCI

summary: Genome-wide association studies (GWAS) identified over fifty genomic loci associated with lung cancer risk. However, the genetic mechanisms and target genes underlying these loci are largely unknown, as most risk-associated-variants might regulate gene expression in a context-specific manner. Here, we generated a barcode-shared multiome (transcriptome and chromatin accessibility map) of 117,911 human lung cells from ever- and never-smokers to profile context-specific gene regulation. We observed that most of differentially expressed genes based on smoking status (smoking-responsive genes) were cell-type specific, and inter-cellular communication strength for Major Histocompatibility Complex-I and -II pathways were inverted between ever- and never-smokers. Accessible chromatin peak detection identified candidate cis-regulatory elements (cCREs) from each lung cell type, and 37% of them were cell-type specific. Colocalization of lung cancer candidate causal variants (CCVs) with these cCREs prioritized the variants for 68% of the GWAS loci, a subset of which was also supported by transcription factor footprinting. cCRE colocalization and single-cell based trait relevance score nominated epithelial and immune cells as the main cell groups contributing to lung cancer susceptibility. Notably, cCREs of rare epithelial cell types, including AT2-proliferating (0.13%) and basal cells (1.8%), overlapped with CCVs from multiple GWAS loci. A multi-level cCRE-gene linking system identified candidate susceptibility genes from 57% of lung cancer loci, including smoking-responsive genes. Our multiome dataset identified lung cancer susceptibility genes that were not detected in previous tissue- or cell-line-based approaches and further revealed the cell types and contexts where the susceptibility genes are functional, including the interplay of epithelial and immune cell types even in a single locus.

overall_design:
Tumor-distant normal lung tissues from smokers and never-smokers were dissociated into single-cell suspension and analyzed using 10X Genomics multiome kit to perform single-nuclear RNAseq and single-nuclear ATACseq from the same single cell. A total of 16 samples (8 from smokers and 8 from never-smokers) were analyzed. The main goal of the study was to perform peak-gene linkage in normal lung tissues to identify cell-type-specific cis-regulatory elements and their target gene. Smoking effect on differential gene expression of lung cells were also assessed.
Please note that each processed data h5 file was generated from both GEX and ATAC samples, and is linked to the corresponding GEX sample records.

UPDATES
[Jan-24-2025] The GSE241468_sc-multiome-SeuratObj.rds file was removed because it had errors.
[Feb-21-2025] The errors in the GSE241468_sc-multiome-SeuratObj.rds were corrected. The revised file is GSE241468_share_seur.rds.

first: Erping

last: Long

first: Jinhu

last: Yin

first: Eun

middle: Y

last: Kim

first: Bolun


title: Monoclonal Antibody Blockade of CD226 Decreases Spontaneous Diabetes in the NDO Mouse by Augmenting Treg and Diminishing Effector Functionality

status: Public on Aug 16 2024

city: Gainesville

first: Rhonda

last: Bacher

address: 2004 Mowry Rd.

institute: University of Florida

summary: Immunotherapeutics that modulate T cell activation represent a crucial component for inhibiting the autoimmune pathogenesis of type 1 diabetes (T1D) and improving the efficacy of β-cell replacement therapy. Here, we present a novel strategy for reducing diabetes incidence in the NOD mouse using monoclonal antibodies (mAbs) to block the T cell costimulatory receptor, CD226. Notably, female NOD mice treated with 600 µg of ⍺-CD226 mAbs between 7-8 weeks of age showed decreased disease incidence at 30 weeks and reduced insulitis severity compared to mice treated with an isotype control. Ex vivo analysis performed five weeks post-treatment revealed ⍺-CD226 mAbs persist in vivo, reducing the availability of CD226 on CD8+ T cells and Tregs. Flow cytometric analysis demonstrates that ⍺-CD226 mAbs inhibit the proliferation of both CD4+ and CD8+ T cells in vitro. Similarly, ex vivo samples had reduced CD4+ and CD8+  effector memory T cell proliferation following ⍺-CD226 mAb treatment. Splenocytes treated with ⍺-CD226 mAbs exhibited a more immunoregulatory cytokine profile with decreased IFN-γ and increased IL-10 production. This phenotype was further corroborated by 51Cr-release assays demonstrating reduced cell-mediated lympholysis (CML) of murine β-cells by ⍺-CD226 mAb-treated autoreactive cytotoxic lymphocytes. Ex vivo phenotyping of FOXP3+Helios+ Tregs revealed increased CD25 expression following ⍺-CD226 mAb treatment, with Tregs displaying augmented suppressive capacity of CD4+ responders during in vitro suppression assays. These data suggest that ⍺-CD226 mAbs both reduce T cell cytotoxicity and improve Treg function, with important therapeutic implications for the prevention or suspension of T1D.

overall_design:
NOD mice received three doses of either ⍺-CD226 mAb or Isotype Control between 7-8 weeks of age. At 12 weeks of age, CD3+ T cells enriched from pancreatic-draining lymph nodes (pLN) and collagenase-digested pancreas were stained with ADT antibodies before generating gene expression, V(D)J and surface protein libraries.
ADT: Barcode Sequence
TotalSeq-C0001 anti-mouse CD4: AACAAGACCCTTGAG
TotalSeq-C0002 anti-mouse CD8⍺: TACCCGTAATAGCGT
TotalSeq-C0073 anti-mouse CD44: TGGCTTCAGGTCCTA
TotalSeq-C0112 anti-mouse CD62L: TGGGCCTAAGTCATC
TotalSeq-C0848 anti-mouse TIGIT: GAAAGTCGCCAACAG

first: Matthew

middle: E

last: Brown

first: Puchong

last: Thirawatananond

first: Leeana

middle: D

last: Peters

first: Elizabeth

middle: J

last: Kern

first: Sonali

last: Vijay

first: Lindsey

last: Sachs

first: Amanda

middle: L

last: Posgai

first: Maigan

last: Brusko

first: Melanie

last: Shapiro

first: Clayton

last: Mathews

first: Todd


title: TET2 Mutant Clonal Hematopoiesis Enhances Severity of COVID-19 Related Cytokine Release Syndrome and is Associated with Increased Mortality

city: Rochester

first: Alexandre

last: Gaspar-Maia

state: MN

address: 200 First street SW

institute: Mayo Clinic

summary: In this study we performed single-cell DNAseq + proteogenomics of PBMCs from COVID19 patients and patients with clonal hematopoiesis to identify the cell types that carry the mutations of interest.

overall_design: Single-cell DNAseq + proteogenomics was performed using the Mission Bio Tapestri platform

first: Minsuk

first: Terra

last: Lasho

first: Wazim

middle: M

last: Ismail

first: Mrinal

last: Patnaik

middle: G

last: Maia


title: TET2 Mutant Clonal Hematopoiesis Enhances Severity of COVID-19 Related Cytokine Release Syndrome and is Associated with Increased Mortality [scRNA-seq]

summary: Coronavirus disease 2019 (COVID-19) is associated with significant morbidity and mortality, albeit with considerable heterogeneity among affected individuals.  Emerging evidence points towards an important role of preexisting host factors, such as a deregulated inflammatory response at the time of infection. Here, we demonstrate the negative impact of clonal hematopoiesis, a prevalent clonal disorder of ageing individuals, on COVID-19-related cytokine release severity and mortality. In this study we perform single cell RNA sequencing of PBMCs from COVID19 patients and patients with clonal hematopoiesis.

overall_design: Live PBMCs were isolated and processed for single cell RNA sequencing following 10x Genomics protocol.

first: Amelia

last: Mazzone

first: Kwan

middle: H

last: Kim

first: Vernadette

last: Simon

first: Fariborz

last: Rakhshan

first: Amik

last: Munankarmy

first: Jeong-Heon

last: Lee


title: Effects of mirror-image nucleosides on DNA replication and transcription in human cells

status: Public on Aug 13 2024

city: Beijing

first: ZHAOYANG

last: JIN

institute: Chinese Academy of Sciences

summary: Mirror-image nucleosides, as potential antiviral drugs, can inhibit virus DNA polymerase to prevent virus replication. Conversely, they may be inserted into the DNA strands during DNA replication or transcription processes, leading to mutations that affect genome stability. Accumulation of significant mutation damage in cells may result in cell aging, apoptosis, and even uncontrolled cell division. We have previously explored replicative repair of mirror-image nucleosides within Escherichia coli, and this study focuses on human cells. We constructed several plasmid substrates, each carrying a specific mirror-image nucleoside, to investigate their impact on intracellular DNA replication and transcription processes. The results showed that in HepG2 cells, L-adenosine (L-dA) was the most potent substrate in inhibiting cell replication and transcription. L-cytidine (L-dC) exhibited the highest bypass efficiency in both template and non-template strands and had the most diverse mutation types. We also observed that L-dC induced immunoregulation of the JAK-STAT signaling pathway. Therefore, our results provide a theoretical basis for the disruptions caused by mirror-image nucleosides in replication and transcription and give us some understanding that mirror-image nucleoside drugs can cause cytotoxicity.

overall_design: Cells were transfected with recombinant plasmids containing L-dC (A207P, S206A), with cells transfected with normal plasmids serving as the control group. Total cellular RNA was isolated using TRIZOL reagent (Invitrogen, Karlsruhe, Germany) following the manufacturer's instructions. The isolated RNA was then shipped to BGI for transcriptome sequencing and basic data analysis, preserved on dry ice. After quality control of the samples, the clean data were aligned with the reference genome, generating 1.15-1.19Gb of data per sample. Gene expression quantification was conducted based on the alignment results. Differential analysis of cell gene expression was performed using DESeq to identify differentially expressed genes. Functional annotation databases such as GO and KEGG were utilized to obtain significant enrichment of functional information and related pathway information based on the genes differentially expressed between samples or groups.


title: TET2 Mutant Clonal Hematopoiesis Enhances Severity of COVID-19 Related Cytokine Release Syndrome and is Associated with Increased Mortality [DNA-seq]

summary: In this study we performed  DNA Sequencing of PBMCs to identify mutations associated with clonal hematopoiesis in patients with COVID19 and non-COVID19 patients.

overall_design: Target Capture Chip Assay for Bulk DNA Sequencing of PBMCs

first: Christy

last: Finke


title: Primary Aldosteronism: Spatial Multiomics Mapping of Genotype-Dependent Heterogeneity and Tumor Expansion of Aldosterone-Producing Adenomas

city: Munich

first: Tracy

middle: Ann

last: Williams

address: Ziemssenstraße

institute: LMU Munich

summary: Primary aldosteronism is frequently caused by an adrenocortical aldosterone-producing adenoma (APA) carrying a somatic mutation that drives aldosterone overproduction. APAs with a mutation in KCNJ5 (APA-KCNJ5MUT) are characterized by heterogeneous CYP11B2 (aldosterone synthase) expression, a particular cellular composition and larger tumor diameter than those with wild-type KCNJ5 (APA-KCNJ5WT). Here, we used spatial transcriptomics profiling of adrenal tissue cryosections to define the role of transcriptomic reprogramming in APA pathophysiology. Our findings advance the understanding of the transcriptional context of inter- and intra-tumoral APA heterogeneity and provide novel insight into the genotype-dependent tumor expansion capabilities of APAs.

overall_design: Consecutive adrenal cryosections (7 APAs and 7 paired adjacent adrenal cortex) were analyzed by spatial transcriptomics (10x Genomics platform) with CYP11B2 immunohistochemistry. To delineate and compare APA intra-tumoral transcriptional heterogeneity stratified by genotype, we conducted spatial transcriptomics of adrenal cryosections from APA-KCNJ5MUT(n= 4) and APA-KCNJ5WT(n= 3)

first: Siyuan

last: Gong

last: Sun

first: Lucie

middle: S

last: Meyer

first: Martina

last: Tetti

first: Christina

last: Koupourtidou

first: Stefan

last: Krebs

first: Giacomo

last: Masserdotti

first: Helmut

last: Blum

first: William

last: Rainey

first: Martin

last: Reincke

first: Axel

last: Walch


title: Methylation analysis of patients with COVID-19 and Clonal Hematopoiesis

first: Alexandre

last: Gaspar-Maia

summary: Coronavirus disease 2019 (COVID-19) is associated with significant morbidity and mortality, albeit with considerable heterogeneity among affected individuals.  Emerging evidence points towards an important role of preexisting host factors, such as a deregulated inflammatory response at the time of infection. Here, we demonstrate the negative impact of clonal hematopoiesis, a prevalent clonal disorder of ageing individuals, on COVID-19-related cytokine release severity and mortality. In this study we perform use the Illumina MethylationEPIC array to quantify methylation levels in PBMCs from COVID19 patients and patients with clonal hematopoiesis.

overall_design: DNA was isolated from purified PBMCs from 18 patients. There are three sample groups: 5 individuals with clonal hematopoiesis, 4 individuals with COVID-19, and 9 individuals with both clonal hematopoiesis and COVID-19.  Samples were processed for DNA methylation using Tecan TrueMethyl oxBS module.

first: Jenna

last: Fernandez

first: Terra

last: Lasho

first: Wazim

last: Ismail

first: Mrinal

last: Patnaik

last: Maia


title: TET2 Mutant Clonal Hematopoiesis Enhances Severity of COVID-19 Related Cytokine Release Syndrome and is Associated with Increased Mortality [scMULT]

summary: Coronavirus disease 2019 (COVID-19) is associated with significant morbidity and mortality, albeit with considerable heterogeneity among affected individuals.  Emerging evidence points towards an important role of preexisting host factors, such as a deregulated inflammatory response at the time of infection. Here, we demonstrate the negative impact of clonal hematopoiesis, a prevalent clonal disorder of ageing individuals, on COVID-19-related cytokine release severity and mortality. In this study we perform Multiome single cell sequencing of PBMCs from COVID19 patients and patients with clonal hematopoiesis.

overall_design:
Nuclei from PBMCs were isolated and processed for single cell Multiome sequencing following 10x Genomics protocol.
Please note that the processed data for the ATAC part of the 10x Genomics Multiome assay is included in the same files as the GEX part of the Multiome.

first: Amelia

last: Mazzone

first: Kwan

last: Kim

first: Vernadette

last: Simon

first: Fariborz

last: Rakhshan

first: Amik

last: Munankarmy

first: Jeong-Heon

last: Lee


title: Transcriptional profiling of antigen-responding CD4 T cells from PLWH to antigenic stimulation or global T cell activation

status: Public on Aug 07 2024

city: Baltimore

first: Milica

last: Moskovljevic

address: 733 N Baltimore St, Miller Research Building

department: School of Medicine

institute: Johns Hopkins University

summary: Despite antiretroviral therapy (ART), HIV-1 persists in latently-infected CD4+ T cells, preventing cure. Antigen (Ag) drives proliferation of infected cells, preventing latent reservoir decay. However, the relationship between antigen recognition and HIV-1 gene expression is poorly understood since most studies of latency reversal use agents that induce non-specific global T cell activation. Here, we isolated rare CD4+ T cells responding to cytomegalovirus (CMV) or HIV-1 Gag antigens from participants on long-term ART and assessed T cell activation and HIV-1 RNA expression upon co-culture with autologous dendritic cells (DCs) presenting cognate antigens. Physiological presentation of cognate antigens induced broad T cell activation (median 42-fold increase in CD154+CD69+ cells) and significantly increased HIV-1 transcription (median 4-fold), mostly through the induction of rare cells with higher viral expression. Thus, despite low proviral inducibility, physiologic antigen recognition can promote HIV-1 expression, potentially contributing to spontaneous reservoir activity on ART and viral rebound upon ART interruption. Additionally, we observed striking differences in the transcriptome profiles of Ag-responding CD4+ T cells after stimulations with Ag or global T cell activators. This analysis revealed quantitative differences between NFAT and NFkB target genes and may guide future approaches to Ag-mediated HIV-1 latency reversal.

overall_design: Gene expression profiling analysis was performed by using RNA-seq data from 6 study participants with each study participant having antigenic stimlation and global T cell activating treatment.

first: Francesco

middle: R

last: Simonetti

first: Robert

middle: F

last: Siliciano

first: James

last: White


title: RD2-mediated regulation of gene expression following GAS exposure to human plasma

status: Public on Aug 12 2024

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

summary: We used RNA-Seq to assess how the presence/absence of the RD2 pathogenicity island influences global gene expression in a serotype M28 GAS isolate following exposure to human plasma for 15 mins and for 60 mins

overall_design: A parental M28 isolate (MGAS6180) and mutant derivative that lacks the RD2 pathogenicity island (M28ΔRD2) were compared.  Each strain was grown in triplicate in THY broth to the exponential phase of growth, pelleted by centrifugation, and resuspended in human plasma.  Samples were taken and processed for RNA isolation after 15 and 60 minutes of incubation (37 degrees centrigrade) in human plasma.

first: Ira

last: Jain


title: Centrophilic retrotransposon integration via targeting CENH3 chromatin in Arabidopsis [ChIP-Seq]

status: Public on Aug 08 2024

city: Bunkyo-ku

first: Sayuri

last: Tsukahara

state: Tokyo

address: Hongo 7-3-1

country: Japan

institute: The University of Tokyo

type: Methylation profiling by high throughput sequencing

summary: In organisms ranging from vertebrates to plants, major components of centromeres are rapidly-evolving repeat sequences, such as tandem repeats (TRs) and transposable elements (TEs). These repeats harbor centromere-specific histone H3 (CENH3), which also evolves rapidly. Complete centromere structures recently determined in human and Arabidopsis suggest frequent integration and purging of retrotransposons within the TR regions of centromeres. Despite the high impact of “centrophilic” retrotransposons on the paradox of rapid centromere evolution, the mechanisms involved in centromere targeting remain poorly understood in any organism. Here we show that both Ty3 and Ty1/Copia LTR elements rapidly turnover within the centromeric TRs of Arabidopsis species. We demonstrate that the Ty1/Copia element Tal1 (Transposon of Arabidopsis lyrata 1) integrates de novo into regions occupied by CENH3 in A. thaliana, and that ectopic expansion of the CENH3 region results in spread of Tal1 integration regions. The integration spectra of chimeric TEs revealed the key structural variations responsible for the contrasting chromatin targeting specificities to centromeres versus gene-rich regions, which have recurrently converted during the evolution of these TEs. Our findings reveal the impact of centromeric chromatin on TE-mediated rapid centromere evolution, with relevance across eukaryotic genomes.

overall_design:
2-week-old Arabidopsis seedlings grown on plates of MS medium were used for ChIP-seq.
CENH3 localization was examined by ChIP-seq, and DNA methylation was examined by ONT sequencing in the CENH3 overexpression lines.

first: Sota

last: Yamaguchi

first: Aimi

last: Nakano

first: Juli

last: arni

first: Matthew

last: Naish


title: Prtg+ve Rhombic Lip Ventricular Zone Stem Cells Initiate and Maintain Group 3 Medulloblastoma [prtg_sort_scRNAseq]

status: Public on Aug 06 2024

city: Toronto

first: Liam

last: Hendrikse

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

institute: University Health Network

summary: We sorted Group 3 MB xenografts tumors by PRTG surface expression and performed single-cell RNA sequencing on the PRTG-pos and PRTG-neg fractions.

overall_design: Cells from three different Gr3 PDX lines (Med411FH, Med211FH, and Med114FH) were orthotopically injected into the cerebellums of NSG mice. At humane endpoint, tumours were resected and dissociated for sorting by Flow Cytometry using Anti-PRTG antibody.

first: Michael

last: Taylor


title: Low Vaccine Responder, Infection- and Asthma-prone Children Demonstrate Distinct Mononuclear Cell DNA methylation Pathways

status: Public on Aug 05 2024

city: Boston

first: Ofer

last: Levy

state: MA

address: 300 Longwood Avenue

department: Infectious Disease

country: USA

institute: Boston Children's Hospital

summary: In this proof-of-concept study, we piloted a precision endotyping approach focused on DNA methylation biomarkers (CpG methylation) which are regulatory base modifications to DNA that influence cellular immune responses across the life course. The aims of this study were to (a) pilot a precision endotyping approach in a selected group of children from the Rochester prospective cohort who exhibited characteristics of high respiratory infection allergy/asthma prone (IAP) and low vaccine responsiveness (LVR) in early childhood, compared to non-respiratory infection allergy/asthma prone (NIAP) children and (b) assess whether stimulation of PBMCs with stimuli a vaccine adjuvant that activating activates a pattern recognition receptors (PRRs) could re-shape the epigenome.

overall_design: proof-of-concept study, piloted a precision endotyping approach focused on DNA methylation biomarkers (CpG methylation)

first: David

last: Martino

first: Simon

last: Van Haren

first: Joann

last: Arce

first: Kaur

last: Ravinder


title: Prtg+ve Rhombic Lip Ventricular Zone Stem Cells Initiate and Maintain Group 3 Medulloblastoma [mouse_tumours_bulk]

summary: We identified a putative marker of cell of origin in Gr3 medulloblastomas using single cell studies on patient samples

overall_design: We transformed the Prtg+ve hind brain cells at e9.5 with following oncogenic aberrations -Myc and Tp53 inhibition or Myc and dominant negative form of Tp53 (Tp53DN). These cells were injected into the cerebellum of NSG mice, and the tumors were dissected out after they reach humane end point.


title: TET2 Mutant Clonal Hematopoiesis Enhances Severity of COVID-19 Related Cytokine Release Syndrome and is Associated with Increased Mortality.

first: Alexandre

last: Gaspar-Maia

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

overall_design: Refer to individual Series


title: Prtg+ve Rhombic Lip Ventricular Zone Stem Cells Initiate and Maintain Group 3 Medulloblastoma.

sample_organism:
Homo sapiens
Mus

platform_organism:
Homo sapiens
Mus


title: Prtg+ve Rhombic Lip Ventricular Zone Stem Cells Initiate and Maintain Group 3 Medulloblastoma [shPRTG_bulk

summary: PRTG+ve cells show high self renewability in Group 3 medulloblastoma tumors and depletion of these cells reduce tumor burden in vivo. To study the functions, we silenced PRTG expression in Gr3 lines

overall_design:
Group 3 cells from three different lines (Med411FH, D425, MB002) were infected with lentiviral vectors containing shNT or shPRTG. Infected cells were harvested post 72 hours of transduction. Each experiment was performed in 2 replicates.
Please note that each processed data file contains processed data for both replicates and is linked to the corresponding *R1 sample records.