title: DNA methylome sequencing of aged vs young AT2 cells

city: New York

first: Yingqian

middle: Ada

last: Zhan

state: New York

address: 430 East 67th Street

department: EPIGENETICS RESEARCH CENTER

institute: MSKCC

type: Methylation profiling by high throughput sequencing

summary: EM-Seq of DNA derived from freshly sorted AT2 cells from aged (24-30 months old) and young (3-4 months old) C57BL6/J mice

overall_design: Alveolar type 2 epithelial cells from aged (24-30 months old) and young (3-4 months old) wildtype C57BL6/J mice were isolated by FACS and DNA from those cells were prepped by NEB EM-Seq kit for sequencing.

first: Tuomas

last: Tammela

first: Xueqian

last: Zhuang

first: Richard

last: Koche


title: GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity of many human transcription factors

status: Public on Nov 11 2024

city: Toronto

first: Arttu

last: Jolma

state: Ontario

address: 160 College Street, Room 1350

department: Donnelly Centre

country: Canada

institute: University of Toronto

summary: A long-standing challenge in human regulatory genomics is that transcription factor (TF) DNA-binding motifs are short and degenerate, while the genome is large. Motif scans therefore produce many false-positive binding site predictions. By surveying TFs across 25 families using >1,500 cyclic in vitro selection experiments with fragmented, naked, and unmodified genomic DNA – a method we term GHT-SELEX (Genomic HT-SELEX) – we find that many human TFs possess much higher sequence specificity than anticipated. Moreover, genomic binding regions from GHT-SELEX are often surprisingly similar to those obtained in vivo (i.e. ChIP-seq peaks). We find that comparable specificity can also be obtained from motif scans, but performance is highly dependent on derivation and use of the motifs, including accounting for multiple local matches in the scans. We also observe alternative engagement of multiple DNA-binding domains within the same protein: long C2H2 zinc finger proteins often utilize modular DNA recognition, engaging different subsets of their DNA binding domain (DBD) arrays to recognize multiple types of distinct target sites, frequently evolving via internal duplication and divergence of one or more DBDs. Thus, contrary to conventional wisdom, it is common for TFs to possess sufficient intrinsic specificity to independently delineate cellular targets.

overall_design:
We used fragmented genomic DNA based in vitro selection method to analyze target locations of putative transcription factors in order to understand how well TFs can define their target sitesd independently of other chromatin proteins. This project was carried out as part of Codebook consortium and the dataset contributes to several other studies in it.

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The table below lists ENA accessions for raw data already submitted to ENA under PRJEB76622.
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first: Aldo

last: Hernandez-Corchado

first: Ally

middle: W

last: Yang

first: Ali

last: Fathi

first: Kaitlin

middle: U

last: Laverty

first: Alexander

last: Brechalov

first: Rozita

last: Razavi

first: Codebook

last: Consortium

first: Ivan

last: Kulakovskiy

first: Hamed

middle: S

last: Najafabadi

first: Timothy

middle: R

last: Hughes


title: miR-193b-5p and miR-374b-5p are aberrantly expressed in endometriosis and suppress endometrial cell migration in vitro

status: Public on Nov 08 2024

city: Solna

first: Nageswara Rao

last: Boggavarapu

state: stockholm

address: Visionsgatan 4

department: Women and Children health

country: Sweden

institute: Karolinska Institutet

type: Expression profiling by high throughput sequencing

summary: Endometriosis is a highly prevalent gynecological disease affecting 10% of women of reproductive age worldwide. miRNAs may play a role in endometriosis, though their exact function remains unclear. Here, we identified differentially expressed miRNAs in endometriosis and studied their functional role in the disease. (2) Methods: Endometrial tissue was collected from women with endometriosis (n=15) and non-endometriosis controls (n=17). Dysregulated miRNAs were identified through small RNA-sequencing, and their biological significance was explored by target gene prediction and pathway analysis. Selected miRNAs were examined in paired ectopic endometriomas and eutopic endometrium (n=10) using qRT-PCR. Their roles in cell migration and proliferation were further examined in vitro using functional assays. To identify potential target genes, we performed mRNA sequencing on transfected cells and the endometrioma cohort. (3) Results: We identified 14 dysregulated miRNAs in the eutopic endometrium of women with endometriosis compared to endometrial tissue from women without endometriosis. Pathway analysis indicated enrichment in cell migration and proliferation associated pathways. Further ex-vivo studies of miR-193b-5p and miR-374b-5p showed that both miRNAs were up-regulated in endometriomas. Overexpression of these two miRNAs in vitro inhibited cell migration and mRNA sequencing revealed several migration-related genes that are targeted by these miRNAs. (4) Conclusions: Our study identified two key endometrial miRNAs that may be involved in the pathogenesis of endometriosis by regulating cell migration.

overall_design: Endometrial tissue was collected from women with endometriosis (n=15) and non-endometriosis controls (n=17). Dysregulated miRNAs were identified through small RNA-sequencing, and their biological significance was explored by target gene prediction and pathway analysis. Selected miRNAs were examined in paired ectopic endometriomas and eutopic endometrium (n=10) using qRT-PCR. Their roles in cell migration and proliferation were further examined in vitro using functional assays. To identify potential target genes, we performed mRNA sequencing on transfected cells （n=3 for each cell transfection condition）and the endometrioma cohort (n=10).


title: Elucidating human female genital tract resident DC response to HIV-1 exposure.

city: Detroit

first: Marta

last: Rodriguez-Garcia

state: MI

address: 275 E Hancock St

country: USA

institute: Wayne State University

summary: The female genital tract (FGT) represents a complex and dynamic environment with specialized immune mechanisms uniquely designed to maintain a delicate balance between protection against invading pathogens and accommodating the unique physiological changes associated with reproductive function. Dendritic cells (DCs) are critical in shaping mucosal immunity against pathogens and maintaining tissue homeostasis. The unique ability of DCs to recognize invading pathogens through pattern recognition receptors (PRRs), and prime naive T cell function, make DCs ideal targets for vaccination and therapeutic strategies against cancers and infections. However, in HIV pathogenesis, DCs are considered a double-edged sword due to their ability to secrete anti-viral proteins and resist viral replication but capture and transfer active viral particles to target CD4+ T cells. Understanding the heterogeneity of DC populations in the FGT, along with their unique contribution to HIV pathogenesis is key for targeted interventions.

overall_design: Hysterectomy samples of endometrium, endocervix and ectocervix of female donor, determined to be healthy according to study criteria, (no cancer or active infections) were enzymatically digested to generate single-cell suspensions. To enrich for myeloid immune cells, the single cell suspensions were filtered to remove cells larger than 30mm, followed by depletion of CD3+ T cells, CD19+ B cells, CD235a+ red blood cells and fibroblasts through magnetic bead selection. Purified cells were incubated with HIV-BaL (R5) isolates (MOI=0.5) or media alone for 30 minutes at 37C, after which the cells were washed to remove excess unbound virus. The cells were subsequently stained with CITE-seq antibodies (AbSeq) and sample multiplexing antibodies (hs_SampleTag). Single-cell suspensions were processed on the BD Rhapsody system according to manufacturer’s protocols. cDNA libraires were constructed using BD Rhapsody Whole Transcriptome (WTA) Amplification KIT (BD Biosciences, Catalog# 633801).

first: Ragav Siddharth

last: Parthasarathy


title: Extensive binding of uncharacterized human transcription factors to genomic dark matter

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Extensive binding of uncharacterized human transcription factors to genomic dark matter [NewChIP_ERP163147]

summary: Most of the human genome is thought to be non-functional, and includes large segments often referred to as “dark matter” DNA. The genome also encodes hundreds of putative and poorly characterized transcription factors (TFs). We determined genomic binding locations of 166 uncharacterized human TFs in living cells. Nearly half of them associated strongly with known regulatory regions such as promoters and enhancers, often at conserved motif matches and co-localizing with each other. Surprisingly, the other half often associated with genomic dark matter, at largely unique sites, via intrinsic sequence recognition. Dozens of these, which we term “Dark TFs” mainly bind within regions of closed chromatin. Dark TF binding sites are rarely under purifying selection, and are enriched for transposable elements. Many Dark TFs are KZNFs, which contain the repressive KRAB domain, but many are not, and may represent potential pioneer TFs: based on compiled literature information, the Dark TFs exert diverse functions ranging from early development to tumor suppression. Thus, a large fraction of previously uncharacterized human TFs may have unappreciated activities within the dark matter genome.

overall_design: Stable cell lines for each TF was established via Flp recombination of EGFP-tagged TF plasmid in HEK293 Flp-In-TRex. Cells were treated with doxycyclin and after 24 hours, ChIP is performed using anti-GFP antibody.

first: Isaac

last: Yellan

first: Hong

last: Zheng

first: Marjan

last: Barazandeh

first: Chun

last: Hu

first: Ilya

last: Vorontsov

first: Zain

last: Patel

first: Philipp

last: Bucher

first: Quaid

last: Morris


title: Functional Genomics of Human Skeletal Development and the Patterning of Height Heritability [RNA-Seq]

status: Public on Nov 15 2024

city: Stanford

first: Daniel

last: Richard

state: CA

address: 290 Jane Stanford Way

department: Genetics

institute: Stanford University

summary: High-resolution profiling of epigenetic/transcriptomic behaviours of chondrocytes during skeletal development suggest the importance of generalized growth to adult height patterning

overall_design: Epigenetic and transcriptomic profiling of in-vivo chondrocyte populations

first: Pushpanathan

last: Muthuirulan

first: Mariel

last: Young

first: Terence

middle: D

last: Capellini


title: Histone lactylation mediated by Fam172a in POMC neurons regulates energy balance [RNA-seq]

status: Public on Nov 06 2024

city: Shanghai

last: Zhang

address: 600 Yishan Road

department: Shanghai Diabetes Institute

country: China

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Glycolysis-derived lactate was identified as substrate for histone lactylation, which has been regarded as a significant role in transcriptional regulation in many tissues. However, the role of histone lactylation in the metabolic center, the hypothalamus, is still unknown. Here, we show that hypothalamic pro-opiomelanocortin (POMC) neuron-specific deletion of family with sequence similarity 172, member A (Fam172a) can increase histone lactylation and protect mice against diet-induced obesity (DIO) and related metabolic disorders. Conversely, overexpression of Fam172a in POMC neurons led to an obesity-like phenotype. Using RNA-seq and CUT&Tag chromatin profiling analyses, we find that knockdown of Fam172a activates the glycolytic process and increases peptidylglycine α-amidating monooxygenase (PAM), which affects the synthesis of α-MSH, via H4K12la (histone lactylation). In addition, pharmacological inhibition of lactate production clearly abrogates the anti-obesity effect of PFKO (POMC-Cre, Fam172aloxP/loxP, POMC neurons Fam172a knockout). These findings highlight the importance of Fam172a and lactate in the development of obesity.

overall_design: To illustrate the mechanism how Fam172a regulate diet induced obesity, we did gene-expression profiles of neuro2a cells treated with ADV-shCtrl or ADV-sh Fam172a were analyzed.

first: Zhuo

last: Chen

first: Cheng


title: Multi-omic analysis of dendritic cell populations in the female genital tract.

summary: The female genital tract (FGT) represents a complex and dynamic environment with specialized immune mechanisms uniquely designed to maintain a delicate balance between protection against invading pathogens and accommodating the unique physiological changes associated with reproductive function. Dendritic cells (DCs) are critical in shaping mucosal immunity against pathogens and maintaining tissue homeostasis. The unique ability of DCs to recognize invading pathogens through pattern recognition receptors (PRRs), and prime naive T cell function, make DCs ideal targets for vaccination and therapeutic strategies against cancers and infections. DC subsets and mononuclear phagocyte populations at human mucosal surfaces remain poorly defined. Local characterization of these populations is important, since DCs and mononuclear phagocyte populations are highly specialized depending on the tissue of residence.

overall_design: Hysterectomy samples of endometrium and endocervix of female donor, determined to be healthy according to study criteria, (no cancer or active infections) were enzymatically digested to generate single-cell suspensions. To enrich for myeloid immune cells, the single cell suspensions were filtered to remove cells larger than 30mm, followed by depletion of CD3+ T cells, CD19+ B cells, CD235a+ red blood cells and fibroblasts through magnetic bead selection. The cells were subsequently stained with CITE-seq antibodies (AbSeq) and sample multiplexing antibodies (hs_SampleTag). Single-cell suspensions were processed on the BD Rhapsody system according to manufacturer’s protocols. cDNA libraires were constructed using BD Rhapsody Whole Transcriptome (WTA) Amplification KIT (BD Biosciences, Catalog# 633801).


title: Fosl2 facilitates chromatin accessibility to determine developmental events during follicular maturation [scRNA-Seq]

status: Public on Nov 10 2024

city: Zhanjiang

first: Yiting

last: Guan

address: 236 Yuanzhu Road

department: Zhanjiang Institute of Clinical Medicine

institute: Guangdong Medical University

summary: Granulosa cells (GCs) are the most dynamically responsive cell lineage to encourage continuous folliculogenesis; however, developmental dynamics and interplay with downstream transcription circuitry remain unclear. Here, we unravel the redistribution of genome-wide chromatin areas that drive broad developmental-related transcriptomic alterations during follicular maturation in murine and porcine GCs. Distinct GC-activated accessibility regions (GAAs) at the ovulatory phase are responsible for augmenting flanking GC-involved developmental gene (GDG) expression, which are essential for transcriptional responses to developmental cues. Mechanistically, the transcription factor (TF) Fosl2 is strongly recruited to GAAs, facilitating chromatin accessibility state transition. Elevated GAA signals driven by Fosl2 loading induce a significant upregulation of adjacent GDG expression. Additionally, GC-specific Fosl2 deletion in mice perturbs GC cellularity, leading to subfertility related to reproductive aging. Together, we highlight a dynamic chromatin accessibility landscape during follicular maturation, revealing the indispensable Fosl2 function not only controls transcriptional activation via a reconfigured chromatin state, but also orchestrates intricate signaling pathways that are fundamental for ovulation and reproduction.

overall_design: scRNA-seq of ovaries from 8-week-old Fosl2flox/flox and Cyp19a1-Cre; Fosl2flox/flox female mice to sought the changes of cell trajectories after knockout Folsl2 conditionally within GCs


title: ESRP2-miR122 axis regulates postnatal onset of polyploidization

status: Public on Nov 05 2024

city: Urbana

first: Sushant

last: Bangru

state: Illinois

address: 600 S Mathews Avenue

department: Biochemistry

institute: University of Illinois, Urbana-Champaign

summary: Postnatal period of development is critical for mammalian tissues and is coordinated through precise activation of genetic programs that govern differentiation, growth and maturation. Here, we describe a cell type- and developmental stage-specific program of alternative splicing that drives sequential replacement of fetal-to-adult protein isoforms in the mouse liver. Using deep transcriptome analysis of loss- & gain-of-function models we identified Epithelial Splicing regulatory protein 2 (ESRP2) as the major regulator for these developmental splicing decisions. Targeted deletion of ESRP2 in mice resulted in the failure of fetal-to-adult switch in splicing for hundreds of RNA transcripts that encode proteins involved in functional competence of hepatocytes. To delineate its role in activation of adult splicing program, we generated transgenic mice with tetracycline-inducible and hepatocyte-specific expression of ESRP2. Remarkably, premature expression of ESRP2 in the livers of newborn pups forced an earlier-than-normal onset of adult splicing program. To determine the in vivo ESRP2 RNA binding landscape within hepatocytes, we used CRISPR-Cas9 technology to FLAG-tag the endogenous locus of ESRP2 in mice and performed FLAG-eCLIP to identify genomewide binding sites. We identified ESRP2 as a regulator of miR-122 levels in hepatocytes, wherein this axis balances the polyploidization and proliferation states in postnatal hepatocytes.

overall_design: gene expression and alternative splicing analysis between WT and ESRP2 KO hepatocytes

first: Auinash

last: Kalsotra


title: Transcriptome signatures of the medial prefrontal cortex underlying GABAergic control of resilience to chronic stress exposure

city: University Park

first: Meiyu

last: Shao

state: PA

address: 301 Life Sciences Building

department: Department of Biology

institute: Penn State University

summary: To understand the mechanisms underlying resilience to chronic stress exposure observed in mice with disinhibited SST neurons (SSTCre:γ2f/f mice), we analyzed and compared the transcriptome profiles of the medial prefrontal cortex (mPFC) from male and female control (SSTCre) and mutant (SSTCre:γ2f/f) mice, with and without exposure to 21 days of chronic variable stress (CVS). We found that SSTCre:g2f/f male, but not female, mice are resilient to CVS-induced changes in the mPFC transcriptome. The CVS-induced transcriptome of stress-resilient male mice was characterized by fewer and distinct CVS-induced gene expression changes compared to the CVS-induced transcriptome of stress-vulnerable SSTCre controls. The transcriptome of non-stressed stress-resilient male mice showed stress-like transcriptome changes along with defects in signal transduction similar to stress exposed SSTCre stress-vulnerable controls. These features of non-stressed stress-resilient mice were normalized by chronic stress exposure, along with enhancement of mRNA translation. Stress-induced differentially expressed genes of stress-vulnerable, but not stress-resilient mice were prominently associated with risk genes of human stress-related psychiatric disorders.

overall_design: RNA sequencing data from mPFC of 3-6 male mice (SSTCre or SSTCre:γ2f/f) and 5 female mice (SSTCre or SSTCre:γ2f/f ), with and without 21 days of CVS

first: Julia

last: Botvinov

first: Deepro

last: Banerjee

first: Santhosh

last: Girirajan

first: Bernhard

last: Lüscher


title: Prenatal dexamethasone exposure  modificates H3K9me2 at the Mkp-1 locus in bone marrow osteoprogenitors

city: Shenzhen

first: Yongheng

last: Xie

address: 1017 Dongmen North Road, Luohu District, Shenzhen

institute: Shenzhen People’s Hospital

summary: Prenatal dexamethasone exposure (PDE) has long-term consequences in bone development. we investigated how PDE exerts persistent effect on bone metabolism in mouse offspring. Our results showed that PDE offspring exhibited reduced bone mass, fewer osteoblasts and diminished osteoprogenitors proliferation.And PDE increased MKP-1 expression, while decreasing H3 lysine 9 dimethylation (H3K9me2)  at Mkp-1 gene locus. Mechanistically, dexamethasone suppressed osteoprogenitors proliferation by upregulating MKP-1 expression, notably through the inhibition of H3K9me2 modifications, which promoted demethylation and transcriptional activation of the Mkp-1 gene. Importantly, restoring histone methylation balance with PFI-90 treatment blocked the inhibitory effects of PDE on MAPK signaling in osteoprogenitors, and mitigated the detrimental impact of PDE on osteoprogenitor proliferation and bone development in the offspring. Therefore,we performed ChIP-seq for H3K9me2 to identify its role in related epigenetic changes.

overall_design: Bone mesenchymal progenitors were isolated from the long bones of PDE and control mice offspring , cultured for 2 weeks, and  colleted for ChIP-sequencing.

first: Jianwen

last: Su

first: Mankai

last: Yang

first: Xianrong


title: A gene network of uterine luminal epithelium organizes mouse blastocyst implantation

status: Public on Nov 04 2024

city: Bunkyo-ku

first: Shizu

last: Aikawa

state: Tokyo

address: 7-3-1 Hongo

country: Japan

institute: The University of Tokyo

summary: RNA-seq analyses using embryos and uterine luminal layers collected from female mice on day 3 am, day 4 am, day 4 pm and day 5 am of pregnancy.

overall_design: Wildtype C57BL/6N females were used. lThe day when the vaginal plug was detected was considered day 1 of pregnancy. Pregnant mice were euthanized by cervical dislocation on designated days of pregnancy for the evaluation of pregnancy phenotypes and sample collection. On day 3, oviducts were flushed to confirm presense of 8 cells. On day 4, one uterine horn was flushed with saline to confirm the presence of blastocysts and the other side of the uterine horn was snap-frozen for cryosectioning. On day 5, mice were treated with 1% Chicago blue in saline i.v. to visualize implantation sites. Laser microdissection was performed to collect luminal layers.

first: Yasushi

last: Hirota


title: Identification of LRP1 and CD13 expressing human periosteal cells for stem cell-mediated bone repair [human scRNA-seq]

city: Houston

first: Dongsu

last: Park

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Human periosteal skeletal stem cells (P-SSCs) are critical for cortical bone maintenance and repair. However, their in vivo identity, molecular characteristics, and specific markers remain unknown. Here, single-cell sequencing revealed human periosteum contains SSC clusters  expressing known SSC markers, PDPN and PDGFRA. Notably, human P-SSCs, but not bone marrow SSCs (BM-SSCs), selectively expressed newly identified markers, LRP1 and CD13. Single-cell analysis of mouse periosteum further supported the preferential expression of LRP1 and CD13 in Prx1 P-SSCs. These LRP1CD13 human P-SSCs were perivascular cells with high osteochondrogenic but minimal adipogenic potential. In addition, LRP1CD13 human P-SSCs are maintained in vitro and self-renew in vivo upon transplantation into bone injuries in mice. When Lrp1 was conditionally deleted in Prx1-lineage cells, it led to severe bone deformity, short statue, and periosteal defects. By contrast, local treatment with a LRP1 agonist at the injury sites induced early P-SSC proliferation and bone healing. Thus, human periosteum contains unique osteochondrogenic stem cell subsets, and these P-SSCs express specific markers, LRP1 and CD13, with regulatory mechanism through LRP1 that enhances P-SSC function and bone repair.

overall_design: Non-hematopoietic and non-endothelial cells from human periosteum were isolated by Fluorescence-activated cell sorting and analyzed by 10x scRNA-seq

first: Youngjae

last: Jeong


title: Multi-omics analysis of molecular changes during early progression of precancerous lesion to lung adenocarcinoma in never-smokers

status: Public on Nov 01 2024

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: The prevalence of lung adenocarcinoma (LUAD) has increased sharply in East Asia. Early diagnosis leads to better survival rates, but this requires an improved understanding of the molecular changes during early tumorigenesis, particularly in non-smokers. We performed whole exome-sequencing and RNA-sequencing of samples from 94 East Asian patients with precancerous lesions (25 with atypical adenomatous hyperplasia [AAH]; 69 with adenocarcinoma in situ [AIS]) and 73 patients with early invasive lesions (minimally invasive adenocarcinoma [MIA]). Cellular analysis revealed that the activities of endothelial and stromal cells could be used to categorize tumors into molecular subtypes within pathology-defined types of lesions. These subtypes were linked with the advanced radiology-defined type of lesions and corresponded to immune cell infiltration throughout the early progression of LUAD. Characterization of these lesion types identified positively selected mutation patterns and suggested that angiogenesis of the late-stage AIS type potentially contributes to tissue invasion of the MIA type. Our findings offer a novel resource that may help to improve early diagnosis and patient prognosis, and also suggest possible approaches for early disease interception.

overall_design: Spatial transcriptomics data were generated using the 10x Visium CytAssist Spatial Gene Expression for the FFPE platform (11 × 11 mm, Human, PN-1000522)


title: Histone lactylation mediated by Fam172a in POMC neurons regulates energy balance [CUT&TAG]

first: Hong

last: Zhang

overall_design: To illustrate the mechanism whether H4K12la regulated the transcription of genes, we did gene-expression profiles of neuro2a cells treated with Ctrl or Lactate were analyzed.

first: Zhuo

last: Chen

first: Cheng

last: Hu


title: Fetal programming by the maternal microbiome of offspring behavior, and DNA methylation and gene expression within the hippocampus

city: Columbia

first: Rene

middle: Gabriel

last: Cortese

state: MO

address: 1 Hospital Dr. MA104E

department: Child health Research Institute

institute: University of Missouri

summary: The microorganisms colonizing the gastrointestinal tract of animals, collectively referred to as the gut microbiome, affect numerous host behaviors dependent on the central nervous system (CNS). Studies comparing germ-free mice to normally colonized mice have demonstrated influences of the microbiome on anxiety-related behaviors, voluntary activity, and gene expression in the CNS. Additionally, there is epidemiologic evidence supporting an intergenerational influence of the maternal microbiome on neurodevelopment of offspring and behavior later in life. There is limited experimental evidence however directly linking the maternal microbiome to long-term neurodevelopmental outcomes, or knowledge regarding mechanisms responsible for such effects.  Here we show that that the maternal microbiome has a dominant influence on several offspring phenotypes including anxiety-related behavior, voluntary activity, and body weight. Adverse outcomes in offspring were associated with features of the maternal microbiome including bile salt hydrolase (Bsh) expression, abundance of certain bile acids, and hepatic expression of S1pr2. In cross-foster experiments, offspring resembled their birth dam phenotypically, despite faithful colonization in the postnatal period with the surrogate dam microbiome. Genome-wide methylation analysis of hippocampal DNA identified microbiome-associated differences in methylation of 196 loci in total, 176 of which were imprinted by the maternal microbiome. Further, single-cell transcriptional analysis revealed accompanying differences in expression of several differentially methylated genes within certain hippocampal cell clusters, and vascular expression of genes associated with bile acid transport. Inferred cell-to-cell communication in the hippocampus based on coordinated ligand-receptor expression revealed differences in expression of neuropeptides associated with satiety. Collectively, these data provide proof-of-principle that the maternal gut microbiome has a dominant influence on the neurodevelopment underlying certain offspring behaviors and activities, and selectively affects genome methylation and gene expression in the offspring CNS in conjunction with that neurodevelopment.

overall_design: This study consists of n=48 microarrays divided in six experimental groups: i) DamGM1: GM1 dams, ii) DamGM4: GM4 dams, iii) GM1 offspring, iv) GM4 offspring, v) GM1CF: GM1 ofsspring crossfostered in GM4 dams, and iv) GM4CF: GM4 offspring crossforstered in GM1 dams. Microarray data was analyzed using Illumina Genome Studio v2011.1.  Data was processed with background normalization.

first: Aaron

last: Ericsson

first: Kevin

last: Gustafson


title: Single cell RNA sequencing of ID8 mouse ovarian tumor samples with genetic pertrubation of cytokine signaling

status: Public on Oct 30 2024

first: Gurkan

last: Mollaoglu

address: Hess Center for Science and Medicine 5th Floor 302

department: Immunology and Immunotherapy

institute: Icahn School of Medicine at Mount Sinai

summary: We profiled the the tumor immune microenvironment by single cell transcriptomics in ID8 mouse model for ovarian cancer upon perturbation of select cytokine signaling. Ccl7 and Il4 KO in cancer cells were compared to a control KO in cancer cells. Additionally, cancer cells grown in Ms4a3-Cre;Il4rafl/fl mice (where IL4RA is specifically knocked-out in macrophages) were compared to those grown in littermate control WT mice.

overall_design: ID8 tumors were collected and digested with enzymatic and physical tissue dissociation followed by enrichment of CD45+ cells with magnetic bead-based selection. Freshly isolated and enriched cells were then quality-controlled for cell numbers and viability and immediately processed for sequencing.

first: Hunter

last: Potak

first: Alessia

last: Baccarini

first: Chiara

last: Falcomata


title: The nitrone compound OKN-007 delays motor neuron loss and disease progression in the G93A mouse model of Amyotrophic Lateral Sclerosis

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

summary: Our study investigated the therapeutic potential of OKN-007 in the SOD1 G93A mouse model of amyotrophic lateral sclerosis (ALS). The impact of OKN-007, known for its antioxidant, anti-inflammatory, and neuroprotective properties, was tested at two doses (150 mg/kg and 300 mg/kg) at onset and late-stage disease. Results demonstrated a significant delay in disease progression at both doses, with treated mice showing a slower advance to severe disease stages compared to untreated controls. Transcriptomic analysis using bulk RNA sequencing identified dysregulated genes in G93A mice that were restored by OKN-007 treatment and pathways that showed altered expression in response to OKN-007. Overall, our findings suggest that OKN-007 holds potential as a disease-modifying treatment for ALS, although further research is needed to optimize dosing regimens and understand its long-term effects.

overall_design: mRNA profiling of wildtype control mice and a transgenic model of ALS ( G93A mice), treated or not with drug OKN007 for a period of 90 days or 155 days (4 replicates for each setting)

first: Shylesh

last: Bhaskaran

first: Holly

last: Van Remmen


title: CEACAM6 orchestrates gallbladder cancer aggressiveness through molecular interplay with Integrin and PRKCD [SNU308]

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: Gallbladder cancer (GBC) comprises the most common biliary tract cancer (BTC). However, GBC is a rare disease often manifesting as aggressive malignancy due to its late diagnosis and resistance to chemotherapy. The identification of molecular drivers of GBC and identification of targeted therapies is still urgently needed. This study combined proteomic analysis of GBC patient samples, functional and molecular characterization of potential oncogenes, and identification of potential therapy strategy for GBC. We identified Carcinoembryonic Antigen-related Cell Adhesion Molecule 6 (CEACAM6) as one of the strongest and most significant upregulated proteins in GBC samples. Functional analysis and in vivo mouse models revealed that CEACAM6 supported the initial steps of cancer metastasis by decreasing cell adhesion while promoting migration and invasion of GBC cells. BirA-BioID followed by mass-spectrometry revealed Integrin Beta-1 (ITGB1) and Protein Kinase C Delta (PRKCD) as direct molecular and functional partners of CEACAM6 in supporting GBC cell migration through regulation of ERK and AKT downstream target genes MMP13, MMP14, and OCLN. Conversely, CEACAM6 knockdown abolished GBC aggressiveness, and treatment using AKT inhibitor Capivasertib and ERK inhibitor Ulixertinib counter-acted the CEACAM6-induced migration.These findings demonstrate that CEACAM6 is crucial for gallbladder oncogenesis through ERK and AKT signaling, providing insights into the design of therapeutic strategies for GBC.

overall_design: We used SNU308 cells transiently tranfected with two siRNAs targeting CEACAM6 (siCEACAM6#2 and siCEACAM6#3) and siRNA Non-Targeting Control (NTC).  We then performed gene expression analysis obtained from RNA-Seq. Four individual experiments were performed.

first: Raisatun

middle: N

last: Sugiyanto

first: Stephanie

last: Roessler


title: CEACAM6 orchestrates gallbladder cancer aggressiveness through molecular interplay with Integrin and PRKCD [GB-d1]

overall_design: We used GB-d1 cells stably tranfected with pTRIPZ-CEACAM6. CEACAM6 protein expression was induced with doxycycline (Dox). We then performed gene expression analysis obtained from RNA-Seq of four biological replicates of GB-d1-CEACAM6-Dox and GB-d1-CEACAM6+Dox.


title: miR-193b-5p and miR-374b-5p Are Aberrantly Expressed in Endometriosis and Suppress Endometrial Cell Migration In Vitro

status: Public on Oct 29 2024

city: Münster

first: Eberhard

last: Korsching

state: NRW

address: Niels-Stensen-Str. 14

department: Inst. of Bioinformatics

institute: University of Muenster

type: Non-coding RNA profiling by high throughput sequencing

summary: (1) Background: Endometriosis is a prevalent gynecological disease affecting 1 out of 10 women of reproductive age. MicroRNAs (miRNAs) may play a role in endometriosis, though their exact function is unclear. In this study we aimed to identify differentially expressed miRNAs in endometriosis and study their functional role in the disease. (2) Methods: Endometrial tissue was collected from patients with endometriosis (n=15) and healthy controls (n=17). Dysregulated miR-NAs were identified through small RNA-sequencing, and their function were explored by target gene prediction and pathway analysis. Selected miRNAs were validated in a cohort of paired ec-topic endometriomas and eutopic endometrium (n=10) using RT-qPCR. Their role in cell migration and proliferation were further examined in vitro using functional assays. To identify potential target genes, we performed mRNA sequencing of the miRNA-transfected cells and endometrioma cohort. (3) Results: We identified 14 dysregulated miRNAs in eutopic endometrium from women with en-dometriosis. Pathway analysis indicated enrichment in cell migration and proliferation pathways. miR-193b-5p and miR-374b-5p, selected for validation, were up-regulated in endometrioma. Over-expression of these two miRNAs in-vitro inhibited cell migration and mRNA sequencing further revealed that several genes related to cell migration are targeted by these miRNAs. (4) Conclusions: Our study identified two key endometrial miRNAs that may be involved in the pathogenesis of endometriosis by regulating cell migration.

sample_organism:
Homo sapiens
blank sample

platform_organism:
Homo sapiens
blank sample

first: Caroline

last: Frisendahl


title: Transcriptomic profile of macrophages activation state in healthy controls and MS patients

city: Paris

first: violetta

last: zujovic

address: 47 boulevard de l'hôpital

country: France

institute: Paris brain institute

summary: CD14+CD16- monocytes from MS patients and  healthy controls (HC) were activated in vitro to obtain homeostatic-like, pro-inflammatory and pro-regenerative macrophages. Macrophage activation profiles were assessed through RNA sequencing

overall_design: Blood was sampled from all participants in acid citrate dextrose (ACD) tubes. From blood samples, peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll Paque Plus (GE Healthcare Life Sciences) and centrifugation (2200 rpm, 20 min). Cells were washed in PBS (2x10 min at 1500 rpm) and RPMI 1640 + 10% fetal bovine serum (FBS) (5 min at 1500 rpm) (all products from ThermoFisher). Monocytes were isolated with anti-CD14 microbeads (Miltenyi) and plated in 12-well plates (500 000 cells/well) or in 24-well plates (200 000 cells/well) in RPMI 1640 + 10% FBS and granulocyte macrophage colony-stimulating factor (GM-CSF) (500 U/ml, ImmunoTools). After 72h, media was replaced with fresh media and one of the following: GM-CSF (500 U/ml); IL4 (1000 U/ml, ImmunoTools); or combined IFNγ (200 U/ml, ImmunoTools) and ultra-pure LPS (10 ng/ml, InvivoGen). Macrophage samples were processed 24h post-activation for RNA extraction using Nucleospin RNA extraction kit. Transcriptome sequencing was performed on 28 patients and 11 HC using Truseq stranded mRNA kit on a NextSeq 500 sequencer. Raw data quality was assessed with FastQC and trimmed with Fastp. Reads were aligned to hg38 genome using Star v2.5.3a, and gene abundances were quantified with RSEM 1.2.28.

first: Violetta

last: Zujovic

first: Jennifer

last: Fransson


title: Uncovering human DCP1 is essential for mRNA decapping process and paralog-specific functions in gene regulation

status: Public on Oct 26 2024

city: Hsinchu

first: Tingwen

last: Chen

address: No. 75, Boat Street, East District

institute: National Yang Ming Chiao Tung University

summary: The decapping complex is crucial in regulating gene expression by removing the mRNA cap structure. While DCP2 serves as the catalytic subunit in this complex, DCP1 is recognized as its major activator. In humans, there exist two distinct paralogs of DCP1, DCP1a and DCP1b, which each form separate decapping complexes. However, the endogenous mRNA targets of these DCP1 paralogs are largely unknown. To address the role of human DCP1 paralogs, we generated multiple DCP1-knockout cell lines and evaluated the importance of human DCP1 in mRNA decapping. Surprisingly, our results revealed that human DCP1 is essential for decapping process. We also discovered that the EVH1 domain of DCP1 is indispensable for the decapping activity of DCP2, as it enhances the mRNA-binding affinity of DCP2.  Additionally, the knock-out of DCP1 paralogs led to the significant activation of several pathways associated with cancer and mRNA processing, as well as the downregulation of DCP1a in various cancer types. Moreover, the knock-out cell lines of the two paralogs also exhibited distinct metabolome profiles. Overall, our findings highlight the crucial role of human DCP1 in mRNA decapping and shed light on the distinct functions of its two paralogs.

overall_design: HEK-293T wild-type, DCP1a, DCP1b, or DCP1a/b-null cells were plated on 15 cm dishes 24 hrs before harvesting as previously described (46). Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and a library prepared using the TruSeq RNA Sample Prep Kit (Illumina). Three biological replicates were analyzed. RNA-Seq libraries were sequenced using the HiSeq 3000 sequencing system (Illumina).

first: Ting-Wen

first: Chung-Te

last: Chang


title: m6ATM: a deep learning framework for demystifying m6A epitranscriptome via Nanopore long read RNA-seq data

status: Public on Oct 28 2024

city: Tokyo

first: Boyi

last: Yu

address: 4-6-1 Komaba, Meguro-ku

institute: RCAST

summary: N6-methyladenosine (m6A) has been one of the most abundant and well-known modifications in mRNA since its discovery in 1970s. Recent studies have demonstrated that m6A gets involved in various biological processes such as alternative splicing and RNA degradation, playing an important role in all kinds of diseases. To better understand the role of m6A, transcriptome-wide m6A profiling data is indispensable. In these years, the Oxford Nanopore Technology Direct RNA Sequencing (DRS) platform has shown promise in RNA modification detection based on current disruptions measured in transcripts. However, decoding current intensity data into modification profiles remains a challenging task. Here, we introduce m6A Transcriptome-wide Mapper (m6ATM), a novel Python-based computational pipeline that applies deep neural networks to predict m6A sites at single-base resolution using DRS data. The m6ATM model architecture incorporates a WaveNet encoder and a dual-stream multiple instance learning model to extract features from specific target sites and characterize the m6A epitranscriptome. For validation, m6ATM achieved an accuracy of 80 to 98% across in-vitro transcription datasets containing varying m6A modification ratios and outperformed other tools in benchmarking with human cell-line data. Moreover, we demonstrated the versatility of m6ATM in providing reliable stoichiometric information and used it to pinpoint PEG10 as a potential m6A target transcript in liver cancer cells. In conclusion, we showed that m6ATM is a high-performance m6A detection tool and our results paved the way for epitranscriptomic precision medicine.

overall_design: To evalutate the performance of our m6A detection software, we generated in-vitro transcription RNA datasets containing sparsely m6A-modified sequences using Oxford Nanopore Technologies Direct RNA sequencing.

first: Genta

last: Nagae

first: Yutaka

last: Midorikawa

first: Kenji

last: Tatsuno

first: Bhaskar

last: Dasgupta

first: Satoshi

last: Ota

first: Hiroyuki

last: Aburatani

first: Hiroki

last: Ueda


title: Extensive binding of uncharacterized human transcription factors to genomic dark matter [GSE76494 Reanalysis]

city: Toronto

first: Arttu

last: Jolma

address: 160 College Street, Room 1350

institute: University of Toronto

summary: Most of the human genome is thought to be non-functional, and includes large segments often referred to as “dark matter” DNA. The genome also encodes hundreds of putative and poorly characterized transcription factors (TFs). We determined genomic binding locations of 166 uncharacterized human TFs in living cells. Nearly half of them associated strongly with known regulatory regions such as promoters and enhancers, often at conserved motif matches and co-localizing with each other. Surprisingly, the other half often associated with genomic dark matter, at largely unique sites, via intrinsic sequence recognition. Dozens of these, which we term “Dark TFs” mainly bind within regions of closed chromatin. Dark TF binding sites are rarely under purifying selection, and are enriched for transposable elements. Many Dark TFs are KZNFs, which contain the repressive KRAB domain, but many are not, and may represent potential pioneer TFs: based on compiled literature information, the Dark TFs exert diverse functions ranging from early development to tumor suppression. Thus, a large fraction of previously uncharacterized human TFs may have unappreciated activities within the dark matter genome.

relation:
SubSeries of: GSE280248
Reanalysis of: GSM2026744
Reanalysis of: GSM2026856
Reanalysis of: GSM2026857
Reanalysis of: GSM2026765
Reanalysis of: GSM2026858
Reanalysis of: GSM2026750
Reanalysis of: GSM2026751
Reanalysis of: GSM2026831
Reanalysis of: GSM2026768
Reanalysis of: GSM2026815
Reanalysis of: GSM2026836
Reanalysis of: GSM2026793
Reanalysis of: GSM2026761
Reanalysis of: GSM2026851
Reanalysis of: GSM2026771
Reanalysis of: GSM2026772
Reanalysis of: GSM2026794
Reanalysis of: GSM2026888
Reanalysis of: GSM2026819
Reanalysis of: GSM2026762
Reanalysis of: GSM2026852
Reanalysis of: GSM2026854
Reanalysis of: GSM2026790
Reanalysis of: GSM2026837
Reanalysis of: GSM2026758
Reanalysis of: GSM2026805
Reanalysis of: GSM2026763
Reanalysis of: GSM2026791
Reanalysis of: GSM2026865
Reanalysis of: GSM2026841
Reanalysis of: GSM2026774
Reanalysis of: GSM2026843
Reanalysis of: GSM2026853
Reanalysis of: GSM2026812
Reanalysis of: GSM2026764
Reanalysis of: GSM2026860
Reanalysis of: GSM2026795
Reanalysis of: GSM2026769
Reanalysis of: GSM2026855
Reanalysis of: GSM2026773

overall_design:
This entry describes re-analysis of previously existing datasets in located in SRA entry SRP068022. These datasets have been analyzed previously (in GSE76494), but they were re-analyzed here to be consistent with the newly generated ChIP-seq datasets. Previous datasets were mapped into hg19 assembly and analyzed with different computational approaches

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

first: Rozita

last: Razavi

first: Ali

last: Fathi

first: Isaac

last: Yellan

first: Alexander

last: Brechalov

first: Kaitlin

last: Laverty

first: Hong

last: Zheng

first: Ally

last: Yang

first: Marjan

last: Barazandeh

first: Chun

last: Hu

first: Ilya

last: Vorontsov

first: Zain

last: Patel

first: Ivan

last: Kulakovskiy

first: Philipp

last: Bucher

first: Hamed

last: Najafabadi

first: Quaid

last: Morris

first: Timothy

last: Hughes


title: Maternal SARS-CoV-2 impacts fetal placental macrophage programs and placenta-derived microglial models of neurodevelopment

city: Medford

first: rebecca

last: batorsky

state: MA

address: 177 College Ave

department: Tufts Institute of Artificial Intelligence

institute: Tufts University

summary: Using single-cell RNA-sequencing, we demonstrated that HBC subpopulations exhibit distinct cellular programs, with specific subpopulations differentially impacted by SARS-CoV-2.  Assessment of differentially expressed genes implied impaired phagocytosis, a key function of both HBCs and microglia, in some subclusters.  Leveraging previously validated models of microglial synaptic pruning, we showed that HBCs isolated from placentas of SARS-CoV-2 positive pregnancies can be transdifferentiated into microglia-like cells (HBC-iMGs), with impaired synaptic pruning behavior compared to HBC models from negative controls.

overall_design: We assessed the impact of maternal SARS-CoV-2 on HBCs isolated from 24 term placentas (N=10 SARS-CoV-2 positive cases, 14 negative controls).

first: Andrea

middle: G

last: Edlow

first: Rebecca

last: Batorsky


title: The Dlk1-Dio3 noncoding RNA cluster coordinately regulates mitochondrial respiration and chromatin structure to establish proper cell state for muscle differentiation

status: Public on Oct 31 2024

city: Boston

first: Frank

last: Naya

address: 24 Cummington Mall

institute: Boston University

summary: To investigate the collective role of the Dlk1-Dio3 ncRNA cluster in myogenesis, we developed two stable CRISPR-Cas9 gene-edited C2C12 skeletal muscle cell lines, Meg3-proximal cis-acting sequence (Meg3-CAS or 2-4) to over-express and Meg3-transcription start site (Meg3-TSS or 2-7) to under-express the entire mega-cluster of Dlk1-Dio3 ncRNAs. Mutations affecting the dosage of all ncRNAs expressed from the Dlk1-Dio3 locus cause profound changes in myoblast fusion and differentiation. To evaluate genome-wide perturbations in chromatin accessibility we evaluated specific histone lysine modifications, inducing the repressive histone mark, H3K27me3, and the activating mark, H3K4me3

overall_design: CUT&RUN for H3K27me3 and H3K4me3 in gene-edited (Dlk1-Dio3 ncRNA locus) C2C12 cells compared to C2C12 control cells

first: Amanda

last: Pinheiro

first: Eric

last: Palanques-Tost

first: Kevin

last: Cabrera

first: Francisco


title: Pathogenic mtDNA mutations inhibit melanoma metastasis

status: Public on Oct 25 2024

city: Dallas

first: Prashant

last: Mishra

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: We report the transcriptome profiles of A375 melanoma tumors containing distinct mtDNA mutations. This study was performed using subcutaneous tumors implanted into NSG mice, and identifies transcriptomice changes in response to pathogenic mtDNA mutations.

overall_design: A375 cells containing various mtDNA mutations were implanted into NSG mice to create subcutaneous tumors. Subcutaneous tumors were harvested at 20-25mm in diameter for RNAseq analysis.

first: Alpaslan

last: Tasdogan

first: Spencer

last: Shelton


title: Mitochondrial calcium uniporter complex controls T-cell-mediated immune responses

status: Public on Oct 23 2024

city: Göttingen

last: Bogeski

address: Humboldallee 23

department: Institute of Cardiovascular Physiology

institute: University Medical Center

summary: T-cell receptor-induced Ca2+ signals are essential for proper T-cell activation and function. In this context, mitochondria play an important role and take up Ca2+ to support elevated bioenergetic demands. The protein machinery that regulates mitochondrial Ca2+ (mCa2+) uptake; the mitochondrial calcium uniporter (MCU) complex, could be thus implicated in T-cell immunity. However, the exact role of MCU in T-cells is not understood. Here, we show that upon activation of naïve T-cells, the MCU complex undergoes a compositional rearrangement that causes elevated mCa2+ uptake and increased bioenergetic output. Transcriptome and proteome analyses reveal molecular determinants involved in mitochondrial functional reprograming and identify signaling pathways controlled by MCU. MCUa knockdown diminishes mCa2+ uptake, mitochondrial respiration and ATP production as well as T-cell invasion and cytokine secretion. In vivo, downregulation of MCUa in rat CD4+ T-cells suppresses autoimmune responses in a multiple sclerosis model of inflammatory experimental autoimmune encephalomyelitis. In summary, Ca2+ uptake through MCU is essential for proper T-cell function and is involved in autoimmunity. T-cell specific MCU inhibition is a potential tool for treating autoimmune disorders.

overall_design:
To examine the role of MCU in T-cell mediated immune response, two RNA-seq dataset were equired. The first dataset was created to determine differences between effector and naive, human CD4 T-cells using two donors.
The second  dataset was used to evaluate the function of MCU in T-cells. Therefore, a MCUa knockdown was achived using siRNA in effector CD4 T-cells. RNA-seq expression levels from two siMCU donors and two siControl donors were obtained.

first: Magdalena

last: Shumanska

first: Dmitry

last: Lodygin

first: Christine

last: Gibhardt

first: Christian

last: Ickes

first: Ioana

last: Stejerean-Todoran

first: Lena

last: Krause

first: Kira

last: Pahl

first: Lianne

last: Jacobs

last: Paluschkiwitz

first: Shuya

last: Liu

first: Angela

last: Boshnakovska

first: Niels

last: Voigt

first: Tobias

last: Legler

first: Martin

last: Haubrock

first: Miso

last: Mitkovski

first: Gereon

last: Poschmann

first: Peter

last: Rehling

first: Sven

last: Dennerlein

first: Jan

last: Riemer

first: Alexander

last: Flügel


title: Effect of TNFα and RELA inhibition on gene expression in human PDAC cells

city: London

first: Chris

last: Bakal

address: 237 Fulham Road

department: Cancer Biology

country: United Kingdom

institute: The Institute of Cancer Research

summary: The canonical NF-κB transcription factor RELA is a master regulator of immune and stress responses and is upregulated in PDAC tumours. Here, we characterised previously unknown endogenous RELA-GFP dynamics in PDAC cell lines by live single cell imaging, which revealed rapid, sustained and non-oscillatory nuclear RELA following TNFα stimulation. Using Bayesian analysis of single cell datasets with variation in nuclear RELA, we predicted that RELA heterogeneity in PDAC cell lines is dependent on F-actin dynamics. Using RNA-seq, we identified the actin regulators NUAK2 and ARHGAP31 as transcriptionally regulated by RELA. In turn, NUAK2 or ARHGAP31 siRNA depletion downregulates TNFα-stimulated RELA nuclear localisation in PDAC cells, establishing a novel negative feedback loop regulating RELA activation by TNFα. We identify an additional actin-independent feedback loop involving RELB, which suppresses TNFα-mediated RELA nuclear localisation following RELA mediated upregulation of RELB. Taken together, we provide computational and experimental support for interdependence between the F-actin network and RELA translocation dynamics in PDAC.

overall_design: To study the role of TNFα-activated RELA on gene expression in PDAC cells, we introduced doxycycline-inducible lentiviral IκB-SR (RELA inhibitor) into the human PDAC cell lines MIA PaCa2 and PANC1. We performed RNA-seq analysis on cells treated with TNFα at 0, 0.01, 0.1 or 10 ng/ml in the presence or absence of IκB-SR induction.

first: Francesca

last: Butera

first: Lucas

last: Dent


title: Gene expression data from THP-1 cells infected with different Mycobacterium tuberculosis strains

status: Public on Oct 24 2024

city: Davis

first: Loubna

last: Tazi

address: 451 Health Science Drive

department: Medical Microbiology & Immunology

institute: UC Davis School of Medicine

summary:
Host-pathogen interactions in Mycobacterium tuberculosis infection still remain poorly understood. We investigated the host immune response to different reference Mycobacterium tuberculosis strains in THP-1 cells. Major differences in the gene expression profiles were identified in response to infection with these strains. These findings shed new insights into the dynamic variation in tuberculosis immune response and pathogenesis.
We used Affymetrix GeneChip Human Exon 1.0 ST microarrays to investigate host differential gene expression in response to different Mycobacterium tuberculosis strains.

overall_design: Gene expression profiling from THP-1 cells infected with different reference Mycobacterium tuberculosis strains (drug-sensitive H37Ra, drug-sensitive H37Rv, isoniazid-resistant H37Rv, rifampin-resistant H37Rv).


title: m6ATM: a deep learning framework for demystifying m6A epitranscriptome via Nanopore long read RNA-seq data [HepG2 ]

first: Boyi

last: Yu

overall_design: The m6A epitranscriptome in wild-type HepG2 cell-line was sequenced and analyzed using Oxford Nanopore Technologies Direct RNA sequencing.

first: Genta

last: Nagae

first: Yutaka

last: Midorikawa

first: Kenji

last: Tatsuno

first: Bhaskar

last: Dasgupta

first: Satoshi

last: Ota

first: Hiroyuki

last: Aburatani

first: Hiroki

last: Ueda


title: Auranofin as a novel anticancer drug for anaplastic thyroid cancer

city: Seongnam

first: Hyun-Ju

last: An

state: --- Select One ---

address: Seongnam-si, 13496

country: South Korea

institute: CHA university

summary: To explore the functional roles of deregulated genes in thyroid cancer, Gene Ontology Biological Process (GOBP) and KEGG enrichment analyses were conducted on the overlapping upregulated and downregulated mRNAs. The results of the GOBP analysis suggested significant enrichment in extracellular matrix organization, positive regulation of gene expression, and multicellular organism development. The biological pathways in KEGG were mainly enriched in ECM-receptor interactions, amoebiasis, steroid biosynthesis, and focal adhesions

overall_design: Quantification of changes in mRNA expression by treating two ATC cell lines(FRO, 8505c) with drug auranofin


title: Characterization of SMA Type II Skeletal Muscle from Treated Patients shows Mitochondrial Deficiency and Denervation

status: Public on Oct 22 2024

first: Fiorella

last: Grandi

address: 105 Bld d'Hopital

department: Centre de Recherche de Myologie

institute: Sorbonne Universite

summary: Spinal muscular atrophy (SMA) is a recessive, developmental disorder caused by the genetic loss or mutation of the gene SMN1 (Survival of Motor Neuron 1). SMA is characterized by neuromuscular symptoms and muscle weakness. Several years ago, SMA treatment underwent a radical transformation, with the approval of three different SMN-dependent disease modifying therapies. This includes two SMN2 splicing therapies - Risdiplam and Nusinersen. One main challenge for Type II SMA patients treated with these drugs is ongoing muscle fatigue, limited mobility, and other skeletal problems. To date, few molecular studies have been conducted on SMA-patient derived tissues after treatment, limiting our understanding of what targets remain after the principal spinal cord targeted therapies are applied. Therefore, we collected paravertebral muscle from eight Type II patients undergoing spinal surgery for scoliosis and seven controls. We used RNA-sequencing to characterize their transcriptional profiles and correlate these with muscle histology. Despite the limited cohort size and heterogeneity, we observed a consistent loss of oxidative phosphorylation machinery of the mitochondria, a decrease in mitochondrial DNA copy number, and a correlation between signals of cellular stress, denervation and increased fibrosis. This work provides new putative targets for combination therapies for Type II SMA.

overall_design: RNA was extracted from paravetebral muscle tissue from consented patients undergoing spinal surgery, and libraries were generated with the Takara SMART-seq v4 kit for low-input samples. All RNA used for this study had a RIN value of >6.

first: Piera

last: Smeriglio

first: Stephanie

last: Astord


title: The histone acetylation module and histone chaperone in the Arabidopsis NuB4 complex have synergistic effect on chromatin accessibility

city: Beijing

first: xinjian

last: He

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

institute: National Institute of Biological Sciences

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

overall_design: Refer to individual Series


title: The Therapeutic Potential of Adipose-Derived Mesenchymal Stem Cell Secretome in Osteoarthritis: A Comprehensive Study

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

summary: Osteoarthritis (OA) is a degenerative joint disease characterized by cartilage degradation and inflammation. This study investigates the therapeutic potential of secretome derived from adipose tissue mesenchymal stem cells (ASCs) in mitigating inflammation and promoting cartilage repair in an in vitro model of OA. Our in vitro model comprised chondrocytes inflamed with TNF. To assess the therapeutic potential of secretome, inflamed chondrocytes were treated with it and concentrations of pro-inflammatory cytokines, metalloproteinases (MMPs) and extracellular matrix markers were measured. In addition, secretome-treated chondrocytes were subject to a microarray analysis to determine which genes were upregulated and which were downregulated. Treating TNF-inflamed chondrocytes with secretome in vitro inhibits the NF-κB pathway, thereby mediating anti-inflammatory and anti-catabolic effects. Additional protective effects of secretome on cartilage are revealed in the inhibition of hypertrophy markers such as RUNX2 and COL10A1, increased production of COL2A1 and ACAN and upregulation of SOX9. These findings suggest that ASC-derived secretome can effectively reduce inflammation, promote cartilage repair, and maintain chondrocyte phenotype. This study highlights the potential of ASC-derived secretome as a novel, non-cell-based therapeutic approach for OA, offering a promising alternative to current treatments by targeting inflammation and cartilage repair mechanisms.

overall_design: Four different conditons were analysed: 1. Condrocytes 2. AT-MSCs 3. Inflamed chondrocytes 4. Inflamed chondrocytes treated with CM. All experiments were completed in triplicate.

first: Elsa

last: González-Cubero

first: Maria

middle: L

last: González-Fernández

first: Marta

last: Esteban-Blanco

first: Saúl

last: Pérez-Castrillo

first: Esther

last: Pérez-Fernández

first: Juan

last: Anguita

first: Nicolás

last: Navasa

middle: M

first: Vega

last: Villar-Suárez


title: Circulating proteins linked to apoptosis processes and  fast development of end stage kidney disease in diabetes.

status: Public on Oct 21 2024

city: Salt Lake City

first: Marcus

last: Pezzolesi

state: Utah

address: HELIX Building, 30 N Mario Capecchi Dr, 3rd floor South

department: Internal Medicine

institute: University of Utah

summary:
Background: Many circulating proteins are associated with risk of ESKD but their source and the biological pathways/disease processes they represent are unclear.
Methods: Using OLINK proteomics platform, concentrations of 455 proteins were measured in plasma specimens obtained at baseline from 399 individuals with diabetes.
Results: Elevated concentrations of 46 circulating proteins were associated (p <10-5) with development of ESKD (n=149) during 7-15 years of follow-up. Twenty of these proteins enriched apoptosis/TNF receptors signaling pathways. A subset (5-7), summarized as an apoptosis score, together with clinical variables accurately predicted risk of ESKD. Expression of genes encoding the 46 proteins in peripheral white blood cells showed no difference between cells from individuals who did or did not develop ESKD. In contrast, plasma concentration of many of the 46 proteins differed by this outcome. In snRNA-seq analysis of kidney biopsies, the majority of genes encoding for the 20 apoptosis/TNF receptors proteins were overexpressed in injured versus healthy proximal tubule cells. Expression of these 20 genes also correlated with the overall index of apoptosis in these cells.
Conclusion: Elevated levels of circulating proteins flagging apoptotic processes/TNF receptors signaling pathways, and likely originating from injured/apoptotic proximal tubular cells, preceded the development of ESKD.

overall_design:
RNAseq was performed in mRNA from peripheral blood (collected in PAXgene tubes) from 72 individuals with diabetes (23 T1D, 49 T2D) to examine the expression of 46 genes encoding end-stage kidney disease risk associated proteins.  71 individuals were included in the analysis (18992X7 was excluded from the analysis), including who 16 developed end-stage kidney disease during 7-15 years of follow-up.
Please note that differential expression analysis was performed among individuals with ESKD versus those non-ESKD (not by diabetes type). Therefore diabetes type information is not provided.

first: Katsuhito

last: Ihara

first: Eiichiro

last: Satake

first: Parker

middle: C

last: Wilson

first: Bozena

last: Krolewski

last: Kobayashi

first: Zaipul

middle: I

last: Md Dom

first: Joseph

last: Ricca

first: Jonathan

last: Dreyfuss

first: Monika

middle: A

last: Niewczas

first: Alessandro

last: Doria

first: Robert

last: Nelson

first: Benjamin

last: Humphreys

first: Kevin

last: Duffin

first: Andrzej


title: Glioblastoma scRNA-seq shows treatment-induced, immune-dependent increase in mesenchymal cancer cells and structural variants in distal neural stem cells

city: Montreal

last: Petrecca

state: Quebec

address: 3801 Rue University

department: Neuro

institute: McGill

summary: Glioblastoma is a treatment-resistant brain cancer. Its hierarchical cellular nature and its tumor microenvironment (TME) before, during, and after treatments remain unresolved. Here, we used single-cell RNA sequencing to analyze new and recurrent glioblastoma and the nearby subventricular zone (SVZ). We found 4 glioblastoma neural lineages are present in new and recurrent glioblastoma with an enrichment of the cancer mesenchymal lineage, immune cells, and reactive astrocytes in early recurrences. Cancer lineages were hierarchically organized around cycling oligodendrocytic and astrocytic progenitors that are transcriptomically similar but distinct to SVZ neural stem cells (NSCs). Furthermore, NSCs from the SVZ of patients with glioblastoma harbored glioblastoma chromosomal anomalies. Lastly, mesenchymal cancer cells and TME reactive astrocytes shared similar gene signatures which were induced by radiotherapy in a myeloid-dependent fashion in vivo. These data reveal the dynamic, immune-dependent nature of glioblastoma’s response to treatments and identify distant NSCs as likely cells of origin.

overall_design:
Single-Cell RNA sequencing and analysis Brain metastasis samples were harvested under a protocol approved by the Montreal Neurological Hospital’s research ethics board (protocol NEU-10-066). All patients gave consent. Surgeries were performed at the Montreal Neurological Hospital. Samples were obtained from within the contrast-enhancing area of the tumor and just outside of the contrast-enhancing region. To extract brain tumour cancer stem (BTCS) cells, fresh tumour specimens were washed 3 times in sterile PBS containing 1% penicillin and streptomycin (PBS+PS). Using scalpels, specimens are minced into fragments of less than 1mm in size and digested in 4ml collagenase solution (1mg/ml; final; Sigma) containing DNAse (50U/ml final; Biorad) and MgCl2 (1mM final) for 1h at 37°C. The digested specimens were washed once with sterile PBS+PS, and large undigested samples were removed with a 70μm strainer and cells were centrifuged for 10 min at 1300 rpm to remove collagenase solution. Cell pellets were then resuspended in 21ml PBS+PS and 9ml of percoll and a centrifugation step at 15000 rpm for 30min at 4C was done to separate cells from blood and debris. Cells were then transferred to a 50ml tube and counted (using trypan blue) before being centrifuged at 1400 rpm for 10 min, then cell pellets were resuspended in PBS +0.04%BSA to a final concentration of 1000 cells/ul, and 100ul of the sample was sent for single-cell capture.

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Raw data files not provided as there are privacy concerns regarding sequencing file (BAM, FASTQ)
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first: Charles

middle: P

last: Couturier

first: Javad

last: Nadaf

first: Zhaorong

last: Li

first: Salma

last: Baig

first: Gabriele

last: Riva

first: Phuong

last: Le

first: Daan

middle: J

last: Kloosterman

first: Jean

last: Monlong

first: Andriniaina

last: Nkili-Meyong

first: Redouane

last: Allache

first: Theresa

last: Degenhard

first: Mariam

last: Al-Rashid

first: Marie-Christine

last: Guiot

first: Guillaume

last: Bourque

first: Jiannis

last: Ragoussis

first: Leila

last: Akkari

first: Francisco

last: Quintana


title: Transcriptomic analysis of human gastric cancer cell lines following T-DXd treatment

status: Public on Oct 20 2024

city: Seoul

first: Kyoung-Seok

last: Oh

address: 101 Daehak-ro, Jongno-gu

institute: Seoul National University Cancer Research Institute

summary: Despite the clinical success of trastuzumab deruxtecan (T-DXd) in treating HER2-positive gastric cancers (GCs), its precise immunomodulatory mechanisms remain elusive. This study investigates T-DXd's immune-related actions in GC cells through RNA sequencing.

overall_design: NCI-N87, and SNU-484 cell lines were treated with 1 ug/ml of trastuzumab or T-Dxd for 72 h followed by RNA isolation for subsequent RNA sequencing.

first: Ah-Rong

last: Nam

first: Ju-Hee

last: Bang

first: Yoojin

last: Jeong

first: SeaYoung

last: Choo

first: HyoJung

last: Kim

first: SuIn

last: Lee

first: Jae-Min

first: Jeesun

last: Yoon

first: Tae-Yong

first: Do-Youn


title: Transcriptome analysis of coding and ncRNA isoforms in monocytes and macrophages purified from bone marrow of xenotransplanted mice during leukemia progression.

city: Houston

first: Maria Teresa

middle: Sabrina

last: Bertilaccio

state: Texas

address: 1901 East Road

department: Leukemia

institute: The University of Texas MD Anderson Cancer Center

summary:
Immune cells of the myeloid lineage and CLL cells support each other during leukemia progression and dissemination. We have investigated the molecular interactions supporting this cell-cell interdependence with a special focus on ncRNAs and microRNAs, whose role in nonmalignant monocytes and macrophages is largely unknown.
In the CLL xenograft model based on the engraftment of MEC1 human CLL cell line into Rag2-/-γc-/-, we analyzed the transcriptome of monocytes/macrophages isolated from the bone marrow during leukemia progression.
We found a significant enrichment of both upregulated and downregulated ncRNAs including miRNAs and long ncRNAs.
These findings corroborate the hypothesis that ncRNA have a role in the protumor function of nonmalignant immune cells during leukemia progression.

overall_design: Rag2-/-γc-/- were injected intravenously with MEC1 cells and sacrificed at early and late stage of leukemia with age-matched wt Rag2-/-γc-/- mice (n=3/group). RNA was isolated from bone marrow murine monocytes/macrophages purified by magnetic separation and processed for mouse GeneChip Clariom D (Mouse Transcriptome 1.0) hybridization assay.

first: Maria

first: Cristina

last: Ivan

first: Marisela

last: Mendoza

first: Erika

last: Thompson


title: A dual role for PSIP1/LEDGF in T-cell acute lymphoblastic leukemia

city: Gent

first: Igor

last: Fijalkowski

address: Sint-Pietersnieuwstraat 33

country: Belgium

institute: Ugent

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: A dual role for PSIP1/LEDGF in T-cell acute lymphoblastic leukemia [CUT&RUN]

summary: T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy. Although intensified therapeutic protocols have improved the outcome of T-ALL patients, they coincide with severe short- and long-term side effects. In addition, no salvage therapeutic strategies are available for primary therapy-resistant or relapsed T-ALL, resulting in a dismal outcome for these patients. It highlights the need to identify new targets in T-ALL biology that allow the development of less toxic targeted therapies. PSIP1, a histone mark reader, is a dependency factor in KMT2A-rearranged myeloid leukemia, but is dispensable for normal hematopoiesis, making it an attractive therapeutic target. Nonetheless, rare recurrent inactivating mutations and deletions of PSIP1, suggest that PSIP1 could act as a tumor suppressor in T-ALL. Here, we demonstrate that the loss of Psip1 accelerates T-ALL initiation in mice and we identified a correlation with reduced H3K27me3 binding. Contrastingly, loss of PSIP1 impaired cell proliferation in several human and murine T-ALL cell lines. In these cell lines, PSIP1 loss leads to a significant downregulation of COX20, an assembly factor of the cytochrome c oxidase in the mitochondria, and is associated with a reduction in mitochondrial respiration. Similarly to what was observed for PSIP1, loss of COX20 expression also leads to an impairment of proliferation in these T-ALL cell lines. These data corroborate that PSIP1 can exert a dual role in the context of T-ALL, either as a tumor suppressor gene during tumor initiation or as a dependency factor in tumor maintenance.

overall_design:
For this study, quantitave spike-in controlled CUT&RUN was performed to evaluate alterations in H3K27me3 levels in thymi of healthy mice (42 days old) with and without Psip1 expression.
Aditionally to investigate where in the genome PSIP1 binds, CUT&RUN was performed to onthe human T-ALL cell line Jurkat for PSIP1 and H3K36me3.

first: Lisa

last: Demoen

first: Filip

last: Matthijssens

first: Lindy

last: Reunes

first: Bruno

last: Palhais

first: Béatrice

last: Lintermans

first: Sara

last: T’Sas

first: Muluembet

middle: Z

last: Akele

first: Siska

last: Van Belle

first: Dieter

last: Deforce

last: Van Nieuwerburgh

first: Panagiotis

last: Ntziachristos

first: Zeger

last: Debyser

first: Kaat

last: Durinck

first: Tim

last: Pieters

first: Steven

last: Goossens

first: Pieter

last: Van Vlierberghe


title: Effector Memory CD4+ T cells from the spleens of Interleukin1-receptor antagonist knockout mice

status: Public on Oct 17 2024

city: sinjuku-ku

first: Sho

last: Ishigaki

address: 35 shinanomachi

department: Division of Rheumatology

institute: Keio University

summary: Interleukin-1, a pro-inflammatory cytokine, plays a crucial role in inflammatory disease pathogenesis. Interleukin-1 receptor antagonist knockout (IL-1Ra KO) mice spontaneously develop aortitis, arthritis, and dermatitis, and are employed as a model for human inflammatory diseases. Previous studies have shown that transferring total T cells from IL-1Ra KO mice into nude mice induces aortitis and arthritis; however, the roles of specific T cell subsets in these inflammatory responses remain unclear. In this study, we aimed to investigate the T cell subsets in IL-1Ra KO mice. We found that the proportion of PD-1+CD44+CD62L˗CD4+ T cells in the spleen and lymph nodes of IL-1Ra KO mice was significantly higher than that of wild type mice. RNA sequencing revealed elevated expression of basic helix-loop-helix family member e40 and granulocyte macrophage colony stimulating factor (GM-CSF) in splenic CD44+CD62L˗CD4+ T cells from IL-1Ra KO mice. In addition, GM-CSF production from splenic CD4+ T cells of IL-1Ra KO mice was significantly higher than that of wild type mice when stimulated with PMA and ionomycin in vitro. Notably, immunohistochemical staining showed infiltration of GM-CSF+CD4+ T cells at inflammatory sites in IL-1Ra KO mice. Our results suggest that a subset of GM-CSF+CD4+T cells emerges under IL-1 signal-enhanced inflammatory conditions.

overall_design: Total RNA was isolated from sorted live effector memory CD4+ T cells with the FACSAria III (BD Biosciences) cell sorter, using a miRNeasy micro kit (QIAGEN, Venio, The Netherlands). The integrity and quantity of the total RNA was measured with an Agilent 2100 Bioanalyzer RNA 6000 Pico kit (Agilent Technologies, Santa Clara, CA, USA). A 10-ng aliquot of the total RNA obtained from each sample was used to construct a sequencing library with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, MA, USA) with the NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturer’s protocols. The quality of the libraries was assessed using the Agilent 2200 TapeStation High Sensitivity D1000 (Agilent Technologies).  The pooled libraries of the samples were sequenced using the NovaSeq 6000 (Illumina, Inc., San Diego, CA, USA) in 150-base pair (bp) paired-end reads.


title: The fork protection complex generates DNA topological stress-induced DNA damage while ensuring full and faithful genome duplication [ChIP-seq]

city: Brighton

first: Andrea

last: Keszthelyi

address: University of Sussex, Sussex House, Falmer

department: Genome Damage and Stability Centre

institute: University of Sussex

summary: The fork protection complex (FPC), composed of Mrc1, Tof1, and Csm3, supports rapid and stable DNA replication. Here, we show that FPC activity also introduces DNA damage by increasing DNA topological stress during replication. Mrc1 action increases DNA topological stress during plasmid replication, while Mrc1 or Tof1 activity causes replication stress and DNA damage within topologically constrained regions. We show that the recruitment of Top1 to the fork by Tof1 suppresses the DNA damage generated in these loci. While FPC activity introduces some DNA damage due to increased topological stress, the FPC is also necessary to prevent DNA damage in long replicons across the genome, indicating that the FPC is required for complete and faithful genome duplication. We conclude that FPC regulation must balance ensuring full genome duplication through rapid replication with minimizing the consequential DNA topological stress-induced DNA damage caused by rapid replication through constrained regions.

overall_design: Chromatin immunoprecipitation of H2AS129P or Rfa1, followed by next generation sequencing (ChIP-SEQ) in Saccharomyces cerevisiae (W303), in wt and tof1∆, mrc1∆, tof1997, tof1627, ars501∆ and tof1∆ars501∆ cells, in exponential or M phase.  Transferase-Activated End Ligation sequencing (TrAEL-seq) in Saccharomyces cerevisiae (W303) in exponential phase wt∆, and tof1∆ cells.

first: Sahar

last: Mansoubi

first: Alex

last: Whale

first: Jonathan

last: Houseley

last: Baxter


title: Porphyromonas gingivalis triggers microglia activation and neurodegenerative processes through NOX4

status: Public on Oct 18 2024

city: örebro

first: isak

last: demirel

address: campus usö

institute: örebro University

summary: Periodontitis and infections with periodontal bacteria have been highlighted as  risk factors for dementia. In recent years attention has been drawn to the role of microglia cells in neurodegenerative diseases. However, there is limited knowledge of the influence of periodontal bacteria on microglia cells. The aim of the present study was to investigate the interactions between the periodontal bacteria P. gingivalis and microglia cells, and to unravel if these interactions could contribute to Alzheimer’s pathology. Periodontitis and infections with periodontal bacteria have been highlighted as  risk factors for dementia. In recent years attention has been drawn to the role of microglia cells in neurodegenerative diseases. However, there is limited knowledge of the influence of periodontal bacteria on microglia cells. The aim of the present study was to investigate the interactions between the periodontal bacteria P. gingivalis and microglia cells, and to unravel if these interactions could contribute to Alzheimer’s pathology.  We found, through microarray analysis, that stimulation of microglia cells with P. gingivalis resulted in upregulation of several Alzheimer´s disease associated genes, including NOX4. We also showed that P. gingivalis LPS mediated ROS production and IL-6 and IL-8 induction via NOX4 in microglia. The viability of neurons was shown to be reduced by conditioned media from microglia cells stimulated with P. gingivalis LPS, and that the reduction was NOX4 dependent. The levels of total and phosphorylated Tau in neurons were increased by conditioned media from microglia cells stimulated with P. gingivalis or LPS. This increase was NOX4 dependent. In summary our findings give us a potential mechanistic explanation of how the periodontal pathogen P. gingivalis could trigger or exacerbate AD pathogenesis.

overall_design: HMC3 cells were stimulated with P. gingivalis strains W50, E8 and K1A (MOI 10) for 24 hours and the gene expression was evaluated.

first: Anna

last: Magnusson

first: Rongrong

last: Wu

first: Isak

last: Demirel


title: Investigating genes regulated by Nrg1 nuclear back signaling.

city: Bethesda

first: David

last: Talmage

state: MD

address: 35 Convent Dr, Room 3B-101

department: NINDS

institute: National Institutes of Health

summary: Nrg1 proteins can be cleaved by gamma secretase in the synaptic membrane. Following cleavage the c-terminal domain of Nrg1 translocates to the nucleus. Which genes are regulated by this signaling is unclear. Here we investigated which genes are regulated.

overall_design: We cultured hippocampal neurons from postnatal day 4 pups. Neurons were cultured for 8 days after which they were either treated with vehicle or the gamma secretase inhibitor DAPT (20uM) overnight. The following day, neurons were either treated with vehicle, soluble ectodomain of ErbB4 (20nM), DAPT (20uM), or DAPT+sErbB4.

first: Prithviraj

last: Rajebhosale

first: Kory

last: Johnson


title: NLRP10 Maintains Epidermal Homeostasis by Promoting Keratinocyte Survival and P63-Dependent Differentiation and Barrier Function

city: South San Francisco

first: Xin

last: Luo

address: 750 Gateway Blvd

department: Research and Development

institute: Amgen Inc

summary: Atopic dermatitis (AD) is a common chronic inflammatory skin disorder characterized by disrupted epidermal barrier function and aberrant immune responses. Despite recent developments in new treatments for AD, there are still unmet needs for the disease management due to its complex and multifactorial nature. Recent genome-wide association studies (GWAS) have identified NLRP10 as an AD susceptible gene. However, the physiological role of NLRP10 in skin homeostasis and its relevance to AD are unknown. Here we show that NLRP10 promotes keratinocyte survival and facilitates epidermal differentiation and barrier function. Mechanistically, NLRP10 limits cell death by preventing the recruitment of caspase-8 onto the death inducing signaling complex and inhibiting its subsequent activation. NLRP10 also stabilizes p63, the master regulator of keratinocyte differentiation, to drive proper keratinocyte differentiation and to reinforce the barrier function. Importantly, NLRP10 is downregulated in AD skin samples. Our findings underscore NLRP10 as a key player in atopic dermatitis pathogenesis, highlighting NLRP10 as a potential target for therapeutic intervention to restore skin barrier function and homeostasis in AD.

overall_design: mRNA sequencing of  human skin equivalent cultures of NLRP-10 knockout (KO) and control wildtype (WT) primary normal human epidermis keratinocytes NHEKs.

first: Yeonhee

last: Cho

first: Zhongzheng

last: Cao

first: Yi

last: Zhou


title: PRMT1-mediated methylation regulates MLL2 stability and gene expression

city: Daejeon

first: Kim

last: Hyoungmin

address: 291, Daehak-ro, Yuseong-gu, Daejeon, 34141, Rep. of KOREA

department: Department of Biological Sciences

institute: Korea Advanced Institute of Science and Technology

summary: The interplay between multiple transcription factors precisely regulates eukaryotic transcription. Here, we report that the protein methyltransferases, MLL2 and PRMT1, interact directly and act collectively to regulate gene expression. PRMT1 binds to the N-terminal region of MLL2, considered an intrinsically disordered region, and methylates multiple arginine residues within its RGG/RG motifs. Notably, overexpression of PRMT1 decreased poly-ubiquitylation of MLL2, whereas mutations on methylation sites in MLL2 increased MLL2 poly-ubiquitylation, suggesting that PRMT1-mediated methylation stabilizes MLL2. MLL2 and PRMT1 cooperatively stimulated the expression of a chromosomal reporter gene in a PRMT1-mediated, MLL2-methylation–dependent manner. RNA-seq analysis found that MLL2 and PRMT1 jointly regulate the expression of genes involved in cell membrane and extracellular matrix functions, and depletion of either resulted in impaired cell migration and invasion. Our study provides evidence that PRMT1-mediated MLL2 methylation regulates MLL2 protein stability and the expression of their target genes.

overall_design: To identify differentially expressed genes when MLL2 and PRMT1 are depleted, we performed RNA sequencing analyses on control, MLL2 knockout (generated by the CRISPR/Cas9 gene-editing system), and PRMT1 knockdown (mediated by shRNA targeting PRMT1) 293T cells. Two biological replicates were analyzed.

first: Hyoungmin

last: Kim

first: Dongju

last: An

first: Jaehoon


title: Transcriptional profiling of Arabidopsis responses to phytosulfokine (PSK)

city: Chicago

first: Dian

last: Liu

state: IL

address: 929 East 57th Street GCIS W519P

department: Department of Molecular Genetics and Cell Biology

institute: The University of Chicago

summary: Our study reveals that phytosulfokine (PSK) promotes plant growth by suppressing defense mechanisms, highlighting a key link between growth regulation and immune response. By demonstrating how PSK downregulates WRKY TFs and associated kinase activity, this research provides valuable insights into plant biology, offering potential strategies for improving crop yield and pathogen resistance. This SuperSeries is composed of the SubSeries listed below.

first: Jean

last: Greenberg


title: The fork protection complex generates DNA topological stress-induced DNA damage while ensuring full and faithful genome duplication [TrAEL-seq]

first: Andrea

last: Keszthelyi

overall_design: Transferase-Activated End Ligation sequencing (TrAEL-seq) in Saccharomyces cerevisiae (W303) in exponential phase wt∆, and tof1∆ cells.

first: Sahar

last: Mansoubi

first: Alex

last: Whale

first: Jonathan

last: Houseley

last: Baxter


title: Genetic and phenotypic changes to Venezuelan equine encephalitis virus following treatment with β-D-N4-hydroxycytidine, an RNA mutagen

city: Louisville

first: Jae Yeon

last: Hwang

state: Kentucky

address: 505 S. Hancock Street

department: Division of Medical Oncology & Hematology

institute: University of Louisville

summary: The high mutation rate of RNA viruses provides viral populations with the ability to adapt to new environments but also makes them vulnerable to extinction due to the deleterious effects of mutations, which is the conceptual basis for the antiviral activity of RNA mutagens. However, there are still gaps in the quantitative understanding of the dynamics between the mutations induced by an RNA mutagen and its effects on viral fitness. To address this, we used Venezuelan Equine Encephalitis Virus (VEEV) and the potent RNA mutagen β-d-N4-hydroxycytidine (NHC) as a model to analyze virus replication competency and mutation frequency following treatment in the total and replication-competent viral populations separately. We found that NHC induced transition mutations in a concentration dependent manner in the total population, while the replication-competent population maintained itself within an increased, yet narrow, mutation spectrum. The incorporation of NHC mainly happened during the positive sense RNA synthesis of VEEV. A growth kinetic analysis of VEEV population treated with NHC pointed to a lower but more diverse distribution in mutational fitness, demonstrating that NHC-induced mutations negatively and broadly affect the fitness of the virus. Together, our study provides mechanistic insight into how RNA mutagens affect viral population landscape and the potential of RNA mutagens as an antiviral strategy for alphaviruses.

sample_organism: Venezuelan equine encephalitis virus (strain TC-83)

overall_design: Each sample is a PCR-amplified region of TC-83 genome encoding the non-structural proteins 2, 3, and 4. The samples were derived from viruses that were either (1) untreated, (2) treated with an RNA mutatgen, or (3) treated both with a direct antiviral and RNA mutatgen. The majority of the samples were from individually isolated virus clones (Nanopore sequencing), while the samples sequenced by PacBio were from TC-83 virus stock (heterogeneous population).

first: Brian

last: Alejandro

first: Eun

first: Jae

middle: Y

first: Juw

middle: W

last: Park

first: Melissa

last: Smith

first: Donghoon

last: Chung


title: Transcriptional profiling of Arabidopsis seedlings responses to phytosulfokine (PSK)

summary: Phytosulfokine (PSK) is a plant peptide hormone that contributes to plant signaling and induced various of effects, including growth, senescence, stress tolerant and defense responses. PSK is a pentapeptide with two tyrosine sulfated by tyrosylprotein sulfotransferase (TPST) enzyme. The sulfated PSK can bind to its cell surface receptors, but the transcriptional readouts remain largely unknown. Here, we treated tpst mutant that are unable to produce native sulfated PSK with synthetic active PSK to capture concentration-sensitive readouts of PSK signaling.

overall_design: To further explore transcriptional readouts of PSK, we did RNA-seq of tpst mutant treated with PSK peptide. We grew tpst mutant for 7 days in liquid MS medium and treated with 100 nM or 1 uM PSK for 5 hours; we also included non-treated wild type Col-0 and tpst mutant as control. Whole seedlings were profiled to gain dose-affected response to PSK at seedling level. Gene expression data obatined from RNA-seq at different concentrations were compared to non-treated control.


title: Transcriptional profiling of Arabidopsis shoots and roots responses to phytosulfokine (PSK)

summary: Phytosulfokine (PSK) is a plant peptide hormone that contributes to plant signaling and induced various of effects, including growth, senescence, stress tolerant and defense responses. PSK is a pentapeptide with two tyrosine sulfated by tyrosylprotein sulfotransferase (TPST) enzyme. The sulfated PSK can bind to its cell surface receptors, but the transcriptional readouts remain largely unknown. Here, we treated tpst mutant that are unable to produce native sulfated PSK with synthetic active PSK to capture time-series and tissue-specific readouts of PSK signaling.

overall_design: To capture transcriptional readouts of PSK, we did RNA-seq of tpst mutant treated with PSK peptide. We grew tpst mutant for 11 days in liquid MS medium and treated with 10 nM PSK for 30 minutes, 2 hours, 5 hours to gain early response to PSK and for 11 days to gain late response to PSK; we also included non-treated wild type Col-0 and tpst mutant as control. The shoot and roots were profiled separately to explore tissue-specific response to PSK at different time points. Gene expression data obtained from RNA-seq at different time points and from different tissues were compared to non-treated control accordingly.


title: A dual role for PSIP1/LEDGF in T-cell acute lymphoblastic leukemia [RNA-seq]

first: Igor

last: Fijalkowski

overall_design:
To investigate the role of PSIP1 in both tumor initiation and maintenance, we conducted both in vivo and in vitro experiments in which we modulate PSIP1 expression.
We crossed the conditional Psip1 fl/fl model with the spontaneous T-ALL Lck-Cre Pten mouse model and performed survival analysis on these mice. We performed gene expression profiling analysis using data obtained from RNA-seq of tumors derived from the thymus of these mice with or without Psip1 expression.
Similarly, we crossed the conditional Psip1 fl/fl model with another spontaneous T-ALL CD2-iCre CD2-Lmo2 mouse model and performed survival analysis on these mice. We performed gene expression profiling analysis using data obtained from RNA-seq of tumors derived from the thymus of these mice with or without Psip1 expression.
On the other hand, we performed a knockdown of PSIP1 in a human T-ALL cell line Jurkat by shRNAs. We performed gene expression profiling analysis of RNA-seq data on Jurkat cells for a control hairpin (shCtrl) and 2 different hairpins targetting PSIP1 (shPSIP1 1, shPSIP1 2) 72h after transduction.

first: Lisa

last: Demoen

first: Filip

last: Matthijssens

first: Lindy

last: Reunes

first: Bruno

last: Palhais

first: Béatrice

last: Lintermans

first: Sara

last: T’Sas

first: Muluembet

last: Akele

first: Siska

last: Van Belle

first: Dieter

last: Deforce

last: Van Nieuwerburgh

first: Panagiotis

last: Ntziachristos

first: Zeger

last: Debyser

first: Kaat

last: Durinck

first: Tim

last: Pieters

first: Steven

last: Goossens

first: Pieter

last: Van Vlierberghe


title: Assessing the transcriptional landscape of Pseudomonas chlororaphis phage 201f2-1: uncovering the small regulatory details of a giant phage

city: Heverlee

first: Rob

last: Lavigne

address: Kasteelpark Arenberg 21

department: Biosystems

institute: KU Leuven

summary: The global transcriptional profile of Pseudomonas chlororaphis infecting phage 201f2-1 was obtained using the long-read RNA sequencing technique ONT-cappable-seq. this resulted in a comprehensive genome-wide map of viral transcription start and termination sites. In addition, we were able to identify different transcription units and gained new insights in the molecular mechanisms of of transcriptional regulation of members of the Phikzvirus.

overall_design: Full-length transcriptional profiling of P. chlororaphis 200B-1 infected with phage 201f2-1 using ONT-cappable-seq

first: Jorien

last: Poppeliers

first: Mathijs

last: Focquet

first: Maarten

last: Boon


title: The Capicua C1 Domain is Required for Full Activity of the CIC::DUX4 Fusion Oncoprotein.

status: Public on Oct 16 2024

city: San Francisco

first: Ross

last: Okimoto

address: 513 Parnassus Ave

institute: University of California, San Francisco

summary: Rearrangements between genes can yield neomorphic fusions that drive oncogenesis. Fusion oncogenes are made up of fractional segments of the partner genes that comprise them, with each partner potentially contributing some of its own function to the nascent fusion oncoprotein. Clinically, fusion oncoproteins driving one diagnostic entity are typically clustered into a single molecular subset and are often treated a similar fashion. However, knowledge of where specific fusion breakpoints occur in partner genes, and the resulting retention of functional domains in the fusion, is an important determinant of fusion oncoprotein activity and may differ between patients. This study investigates this phenomena through the example of CIC::DUX4, a fusion between the transcriptional repressor capicua (CIC) and the double homeobox 4 gene (DUX4), which drives an aggressive subset of undifferentiated round cell sarcoma. Using a harmonized dataset of over 100 patient fusion breakpoints from the literature, we show that most bona fide CIC::DUX4 fusions retain the C1 domain, which is known to contribute to DNA binding by wild type CIC. Mechanistically, deletion or mutation of the C1 domain reduces, but does not eliminate, activation of CIC target genes by CIC::DUX4. We also find that expression of C1-deleted CIC::DUX4 is capable of exerting intermediate transformation-related phenotypes compared with those imparted by full-length CIC::DUX4, but was not sufficient for tumorigenesis in a subcutaneous mouse model. In summary, our results suggest a supercharging role for the C1 domain in the activity of CIC::DUX4.

overall_design: To investigate the impact of deleting the C1 domain from the CIC::DUX4 oncoprotein on target gene induction, clonal C2C12 cells expressing empty vector (EV), full-length CIC::DUX4 (CD4), or C1-deleted CIC-DUX4 (dC1) were generated by retroviral transduction and FACS. Two clones per group were used for polyA-selected bulk RNA sequencing, with each clone acting as a "biological replicate" within each group. Differential gene expression analyses were performed between EV and both of the full-length and C1-deleted CIC::DUX4 expressing clones.

first: Cuyler

last: Luck

first: Kyle

last: Jacobs


title: PdgfrB signaling impairs skeletal muscle regeneration

status: Public on Oct 15 2024

city: Ithaca

first: Abigail

last: Benvie

address: 526 Campus Rd

institute: Cornell University

summary: Genetically deleting PdgfrB in mature myocytes enhances skeletal muscle regeneration and fusion capability whereas activating PdgfrB inhibits it.

overall_design: Comparative gene expression profile analysis of RNA-Seq data between 2 month old control, moygenin specific PdgfrB knock out, and myogenin specific PdgfrB constitutively active male mice

first: Daniel

last: Berry

first: Siwen

last: Xue

first: Nikolai

last: Kolba