title: RNA sequencing of 15 patient derived cSCC cell lines

first: Max

last: Bone

address: Switchback Road

institute: CRUK Scotland institute

summary: 15 patient derived cscc cell lines were subjected to RNA sequencing to determine the RNA landscape of cutaneous squamous cell carcinoma (cSCC) tumour cells only.

overall_design: Generating RNA read counts for cSCC cell lines for comparison with existing datasets of cSCC patient derived RNAseq data

first: Gareth

last: Inman

first: Peter

last: Bailey

first: Irene

last: Leigh


title: Preclinical efficacy of targeting epigenetic mechanisms in AML with 3q26 lesions and EVI1 overexpression

status: Public on May 06 2024

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

country: USA

institute: MD Anderson Cancer Center

type: Expression profiling by high throughput sequencing

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: Sex-specific regulation of the cardiac transcriptome by the protein phosphatase 2A regulatory subunit B55α

status: Public on May 05 2024

city: Parkville

first: Adam

middle: James

last: Trewin

state: Victoria

address: Royal Pde

department: Anatomy and Physiology

country: Australia

institute: University of Melbourne

summary: Protein phosphatase 2A (PP2A) enzymes containing the regulatory subunit isoform B55α (PP2A-B55α) suppress HDAC5/MEF2 signalling in cardiac myocytes, implicating B55α in the transcriptional regulation of cardiac growth and fibrosis. The role of B55α in the heart has not been investigated. In this study, we generated and characterised two loss-of-function mouse models, with global or cardiomyocyte-specific disruption of the gene encoding B55α (Ppp2r2a). Mice with global homozygous knockout of B55α died in utero, but cardiac morphology was unremarkable compared with wildtype littermates. Mice with global heterozygous knockout of B55α had thinner left ventricular walls compared with wildtype mice at 12 months of age, an effect that was more pronounced in males. Mice with cardiomyocyte-specific deletion of B55α displayed normal cardiac morphology at 10-12 weeks of age, demonstrating that cardiomyocyte B55α is not required for postnatal heart growth. Despite no obvious morphological differences, gene expression analyses revealed extensive remodelling of the cardiac transcriptome in male, but not female, mice. In males, B55α knockout increased the expression of genes associated with extracellular matrix composition, and downregulated genes associated with mitochondrial energy production. This study reveals a sexually dimorphic role for B55α in postnatal cardiac transcriptional regulation and provides a foundation for future work investigating the role of B55α in cardiac stress settings.

overall_design: Samples are left ventricle tissue from cardiomyocyte-specific Ppp2r2a knockout (cKO) mice (genotype: aMHC-CreTg/0-Ppp2r2aL/L) or floxed control (Ctrl) mice (genotype: aMHC-Cre0/0-Ppp2r2aL/L), on a mixed background (floxed Ppp2r2a mice: C57BL6/N, aMHC-Cre mice: FVB).

middle: J

first: Kate

middle: L

last: Weeks


title: Preclinical efficacy of targeting epigenetic mechanisms in AML with 3q26 lesions and EVI1 overexpression [RNA-Seq]

summary: AML with chromosomal alterations involving 3q26 overexpress the transcription factor (TF) EVI1, associated with therapy refractoriness and inferior overall survival in AML. Consistent with a CRISPR screen highlighting BRD4 dependency, treatment with BET inhibitor (BETi) repressed EVI1, LEF1, c-Myc, c-Myb, CDK4/6, and MCL1, and induced apoptosis of AML cells with 3q26 lesions. Tegavivint (TV, BC-2059), known to disrupt binding of nuclear β-catenin and TCF7L2/LEF1 with TBL1, also inhibited co-localization of EVI1 with TBL1 and dose-dependently induced apoptosis in AML cell lines and patient-derived (PD) AML cells with 3q26.2 lesions. TV treatment repressed EVI1, attenuated enhancer activity at ERG, TCF7L2, GATA2 and MECOM loci, abolished interactions between MYC enhancers, repressing AML stemness while upregulating mRNA gene-sets of interferon/inflammatory response, TGF-β signaling and apoptosis-regulation. Co-treatment with TV and BETi or venetoclax induced synergistic in vitro lethality and reduced AML burden, improving survival of NSG mice harboring xenografts of AML with 3q26.2 lesions.

overall_design: Paired end RNA Seq of MECOM (EVI1) expressing AML treated with tegavivint for 16 hours.

first: Warren

last: Fiskus

first: Kapil

middle: N

last: Bhalla


title: Effect of Trp53 knockout on fallopian tube epithelial organoids

status: Public on May 07 2024

city: Shinjuku

first: Tomohiro

last: Tamura

state: Tokyo

address: Shinanomachi 35

department: Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory

country: Japan

institute: Keio University School of Medicine

summary: We established murine fallopian tube epithelial organoids from a B6J.129(B6N)-Gt(ROSA)26Sortm1(CAG-cas9*,-EGFP)Fezh/J mouse. Subsequently, we knocked out Trp53 by introducing sgRNA into the organoids, nutlin-3 selection, and single-organoid cloning. The Trp53-knocked organoids grew faster than the normal organoids. We also analyzed the transcriptomic differences caused by Trp53-knockout by RNA-sequencing and gene set enrichment analysis (GSEA), which indicated that Trp53-knockout reduced cilium-related gene expression. In human HGSC precancerous lesions, such as serous tubal intraepithelial carcinoma (STIC), differentiation to ciliated cells has been reported to be down-regulated; therefore, the genetic manipulation was supposed to mimic the process of carcinogenesis of HGSC.

overall_design: To investigate the biological changes caused by TRP53 dysfunction in fallopian tube epithelium, we established murine fallopian tube epithelial organoids and knocked out Trp53. A control sample was normal fallopian tube epithelial organoids established from a B6J.129(B6N)-Gt(ROSA)26Sortm1(CAG-cas9*,-EGFP)Fezh/J mouse.

first: Shimpei

last: Nagai

first: Kenta

last: Masuda

first: Keiyo

last: Imaeda


title: PI3Kα inhibition blocks osteochondroprogenitor specification and the hyper-inflammatory response to prevent heterotopic ossification

city: Oviedo

first: Gonzalo

last: Sánchez-Duffhues

state: Asturias

address: Avda. de Roma, s/n

country: Spain

institute: Nanomaterials and Nanotechnology Research Center (CINN-CSIC)

summary: Heterotopic ossification (HO) occurs following mechanical trauma, burns, or congenitally in patients suffering from fibrodysplasia ossificans progressiva (FOP). Recently, we demonstrated that inhibitors of phosphatidyl-inositol 3-kinase alpha (PI3Kα), including the already marketed BYL719/Alpelisib/Piqray, may become a useful therapy for patients undergoing HO. In this study, we have confirmed these results and optimized the timing of administration of BYL719. We found that BYL719 effectively prevents HO when administered even up to three to seven days after injury. We demonstrate in cell cultures and in a mouse model of HO, that the major actions of BYL719 are on-target effects through inhibition of PI3Kα, without directly affecting ACVR1/ALK2 kinase activity. In vivo, we found that lack of PI3Kα in progenitors at injury sites is sufficient to prevent HO. Moreover, time course assays in HO lesions demonstrate that BYL719 not only blocks osteochondroprogenitor specification, but also reduces the inflammatory response. BYL719 inhibits the migration, the proliferation, and the expression of pro-inflammatory cytokines in monocytes and mast cells, suggesting that BYL719 hampers the hyper-inflammatory status of HO lesions. As part of this study, we have conducted bulk RNA sequencing using human mesenchymal stem cells (hMSCs) expressing ACVR1/ALK2-R206H to assess molecular effectors driving the therapeutic potential of BYL719 in FOP. Altogether, these results highlight the potential of PI3Kα inhibition as a safe and effective therapeutic strategy for HO.

overall_design: We performed bulk RNA-sequencing using human fetal bone-marrow derived mesenchymal stem cells (hMSCs) transduced with lentiviral particles containing ACVR1-R206H or ACVR1-WT. These cells were serum starved for 16 hours before pre-stimulation with BYL719 (1uM) and subsequent Activin A (50ng/ml) or BMP6 (50ng/ml) stimulation for 1 hour. The control cells were not treated with BYL719 or ligand, but with DMSO and ligand vehicle, respectively, instead (all groups n=4).

first: Marius

last: Wits

first: Marie-José

last: Goumans

first: Francesc

last: Ventura


title: Expression profiles of ncRNA and mRNA in C57 and AD model mice(APP/PS1 and P301S) at the age of 3, 6 and 12 months respectively

status: Public on May 01 2024

city: Nan Chong

first: Zhuoze

last: Wu

address: Dongshun Road, Gaoping District

country: China

institute: North Sichuan Medical College

summary: Alzheimer's disease(AD) is a neurodegenerative disease with a long incubation period.Most of the constructed lncRNA-associated ceRNA regulatory networks are  only based on the differences between clinical AD and control people or mice at a single time piont, the dynamic changes of these transcripts expression profiles with age from non-set to onset of AD need to be further elucidated.

overall_design: LncRNAs and mRNAs profiles of the hippocampus of 3, 6, 12 months old C57 mice and AD mice(APP/PS1 and P301S) were measured ( n=3 per group)

first: Chuan

last: Yao


title: Histone Lactylation Antagonizes Senescence and Skeletal Muscle Aging by Modulating Aging-Related Pathways [snRNA-seq]

city: Beijing

first: Wei

last: Tao

address: No.5 Yiheyuan Road

department: School of Life Sciences

institute: Peking University

summary: Epigenetic alterations are among the prominent drivers of cellular senescence and/or aging. In this study, we show that histone lactylation plays a pivotal role in counteracting senescence and mitigating dysfunctions of skeletal muscle in aged mice. Mechanistically, histone lactylation and lactyl-CoA levels markedly decrease during cellular senescence but are restored under hypoxic conditions primarily due to elevated glycolytic activity. The enrichment of histone lactylation at promoters is essential for sustaining the expression of genes involved in the cell cycle and DNA repair pathways, thereby inhibiting cellular senescence. Furthermore, the modulation of enzymes crucial for histone lactylation, including p300 and HDAC1, leads to reduced histone lactylation and accelerated cellular senescence. Consistently, the suppression of glycolysis and the depletion of histone lactylation are also observed during skeletal muscle aging. Modulating the enzymes also leads to the loss of histone lactylation in skeletal muscle, downregulating DNA repair and proteostasis pathways and accelerating muscle aging. Running exercise increases the levels of glycolysis and histone lactylation, thereby helping to preserve the proper function of skeletal muscle. Our study highlights the significant roles of histone lactylation in modulating cellular senescence and muscle aging, suggesting that this modification may serve as an innovative biomarker for senescence.

overall_design: snRNA-seq data for old and young, sedentary and running mouse skeletal muscle.

first: Fanju

last: Meng

first: Jianuo

last: He

first: Xuebin

last: Zhang


title: Histone Lactylation Antagonizes Senescence and Skeletal Muscle Aging by Modulating Aging-Related Pathways [RNA-seq]

overall_design: RNA-seq data for IMR90 cells during replicative senescence, upon hypoxia and 2-DG treatment.


title: Evaluating the effects of polyoma small T antigen on gene expression

city: Boston

first: Cherubin

last: Manokaran

state: Massachusetts

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana Farber Cancer Institute

summary: We developed an inducible degradation system for murine polyoma small T antigen (PyST) to study the effects of PyST on gene expression. We examined changes in expression following ectopic expression of tagged antigen and following their degradation in the MCF10A human mammary epithelial cell line.

overall_design: Examination of the effects of murine polyoma small T expression and degradation in mammary epithelial cells

first: Yubao

last: Wang

first: Thomas

middle: M

last: Roberts


title: Histone Lactylation Antagonizes Senescence and Skeletal Muscle Aging by Modulating Aging-Related Pathways [RNA-Seq II]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq data for IMR90 cells during replicative senescence, upon hypoxia, 2-DG, A485, MS-275, and pyruvate treatment; RNA-seq data for mouse skeletal muscle upon MS-275 and NALA treatment.


title: Histone Lactylation Antagonizes Senescence and Skeletal Muscle Aging by Modulating Aging-Related Pathways [CUT&Tag]

overall_design: CUT&Tag data for IMR90 cells during replicative senescence, upon hypoxia, 2-DG, and pyruvate treatment. CUT&Tag data for mouse skeletal muscle upon MS-275 treatment; CUT&Tag data for old and young, sedentary and running mouse skeletal muscle.


title: PD1 blockade improves survival and CD8+ cytotoxic capacity, without increasing inflammation, during normal microbial experience in old mice

status: Public on Apr 25 2024

city: Minneapolis

first: Christina

middle: D

last: Camell

state: MN

address: 312 Church St; NHH 4-108

department: Biochemisty, Biophysics and Molecular Biology

institute: University of Minnesota

summary: The elderly and those with chronic diseases have a 2 to 10-fold increased risk of hospitalization and mortality following infection as compared with healthy adults. A significant contributor to disease severity is the aging of the immune system, including an expansion of exhausted T cells. These cells simultaneously promote excessive levels of inflammation and display impaired T cell activation and function. How exhausted T cells from aged individuals respond to infection and whether acute restoration of T cell activation further exacerbates the inflammatory environment or generates functional T cells is unclear. Previously, we used a mouse model of normal microbial experience (NME), where old specific pathogen-free (SPF) mice show 100% mortality following exposure to multiple microbes ordinarily found in pet store mice. In the present study, we show that when exposed to NME, old SPF mice have increased expression of multiple inflammatory pathways and exhibit elevated frequencies of a heterogenous exhausted CD8+ T cell pool that expresses differing combinations of the inhibitory receptor programmed cell death protein 1 (PD1), TOX, and CXCR5. Pre-treatment or intervention with an anti-PD1 monoclonal blocking antibody during the exposure of old SPF mice to NME significantly improves both antibody production and survival, without altering the acute inflammatory response. Anti-PD1 checkpoint blockade-mediated survival is dependent on CD8+, but not CD4+ T cells. Correspondingly, CD8+ PD1+ T cells from old mice given anti-PD1 monoclonal antibody have increased granzyme B production. These data reveal a new approach for reducing vulnerability to infections in the elderly by targeting CD8+ T cell exhaustion through checkpoint blockade immunotherapy.

overall_design: We performed gene expression analysis obtained from RNA-seq of livers from young SPF, young NME, old SPF, and old NME mice.

first: Soto-Palma

last: Carolina

first: Camell

last: Christina

first: Dahlquist

last: Korbyn


title: Histone Lactylation Antagonizes Senescence and Skeletal Muscle Aging by Modulating Aging-Related Pathways


title: High-Dimensional Single-Cell Multimodal Landscape of Human Carotid Atherosclerosis

status: Public on Apr 12 2024

city: New York

first: Chenyi

last: Xue

state: NY

institute: Columbia University


title: Single-cell gene expression profiles of cells from colorectal cancer and chemically induced PDOs [scRNA-Seq]

status: Public on Apr 17 2024

first: Ying

last: Xu

address: No.5 Yiheyuan Road Haidian District

summary: Phenotypic plasticity is a hallmark feature driving cancer progression, metastasis, and therapy resistance. Fetal-like transcriptional programs have been increasingly implicated in promoting plastic cell states, yet their roles remain difficult to study due to limitations of existing culture models. Here, we establish a chemically defined patient-derived organoid (PDO) system that enables long-term expansion of colorectal cancer (CRC) cells while preserving fetal-like features associated with phenotypic plasticity. Using this model, we identify an oncofetal-like state (OnFS) that is enriched in advanced tumors and linked to key features of plasticity, including epithelial-mesenchymal plasticity, as well as increased metastasis and treatment resistance. Mechanistically, we show that FGF2–AP-1 signaling maintains the OnFS program and associated phenotypic plasticity in CRC. This model offers a powerful platform for studying the fetal-like features underlying cancer cell plasticity and their role in tumor progression and treatment resistance in CRC.

overall_design: Cells in primary tumor, conventional PDO and CiPDO of the same patient P18 were used for scRNA-seq analysis.

first: Molong

last: Qu

first: Liang

last: Xiong


title: Gene expression profiles of cells from PDOs of normal colon and colorectal cancers [RNA-Seq]

overall_design: We performed gene expression profiling analysis using CiPDOs from 5 normal colons and 8 CRC tumors. Conventional organoids from 2 normal colons and 3 tumors are used as controls. To compare 3C condition with 4C condition, 4 3C-tumoroids are also included. Additionally, to explore the function of FOS and JUND, we compare 3 shFOS replicates and 3 shJUND replicates with one shControl.


title: Transcriptional atlas of Daphnia magna

status: Public on Apr 19 2024

city: Johnson City

first: Lev

middle: Y

last: Yampolsky

state: Tennessee

address: 811 Lazywood Dr

department: Biological sciences

institute: East Tennessee State University

summary: Transcriptomics studies are more likely to achieve predictive results when they rely on tissue- and cell-specific transcriptional data. Identification of cell types in novel model organisms by their transcriptional profiles is difficult without data on transcriptional differences among major tissues and anatomical features. Here we report the first dataset on tissue- and organ-specific transcriptomics in freshwater plankton crustacean Daphnia magna, reporting markers of eggs, hemocytes, gut, carapace, antennae and head (as well as the remaining carcass).

overall_design: RNAseq of RNA tissue extracts from Daphnia eggs, hemocytes, guts, antennae, heads, carapace and carcass.

first: Ishaan

last: Dua


title: Deubiquitinase USP29 Ameliorates Pathological Cardiac Hypertrophy Through Inhibiting TAK1

status: Public on Apr 20 2024

city: Shenyang

first: Xi

last: Jiang

address: Shengjing Hospital of China Medical University, No.39 Huaxiang Road

institute: Shengjing Hospital of China Medical University department   Department of Cardiology

summary: The identification of key factors involved in pathological cardiac hypertrophy is crucial to exploring novel treatments for heart failure. In this study, we elucidated the role of Ubiquitin-specific protease 29 (USP29), a deubiquitinase, in pressure overload-induced cardiac hypertrophy.  Genetic knockout of USP29 in mice significantly exacerbated TAC-induced heart hypertrophy, dysfunction, and fibrosis; whereas overexpression of USP29 in cardiomyocytes  attenuated the hypertrophic response. Similarly, USP29 markedly alleviated PE-induced hypertrophy of primary neonatal rat cardiomyocytes. Mechanistically, the cardio-protective effects mediated by USP29 were attributed to its suppression of transforming growth factor β-activated kinase 1 (TAK1)-JNK/P38 signaling pathway activation.  Collectively, our study suggests that targeting either USP29 or its interaction with TAK1 could represent an innovative therapeutic strategy for treating heart failure and cardiac hypertrophy.

overall_design: To investigate the impact of USP29 on pathological cardiac hypertrophy, we generated a global mouse strain with Usp29 knockout (USP29-KO, C57BL/6 background mice).Subsequently, both USP29-KO and control mice (littermate WT mice) were subjected to transverse aortic constriction ( TAC ) for 4 weeks.We then performed gene expression analysis using data obtained from RNA-seq of 6 different left ventricular myocardial tissues. Comparative gene expression analysis of RNA-seq data for left ventricular myocardial tissues from USP29-KO mice or littermate WT mice treated with TAC for 4 weeks.

first: Tiesheng

last: Niu


title: High-Dimensional Single-Cell Multimodal Landscape of Human Carotid Atherosclerosis [CITE-seq]

summary:
Atherosclerotic plaques are complex tissues composed of a heterogeneous mixture of cells. However, our understanding of the comprehensive transcriptional and phenotypical landscape of the cells within these lesions is limited.
To characterize the landscape of human carotid atherosclerosis in greater detail, we combined cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) and single-cell RNA sequencing (scRNA-seq) to classify all cell types within lesions (n=21; 13 symptomatic) to achieve a comprehensive multimodal understanding of the cellular identities of atherosclerosis and their association with clinical pathophysiology.
We identified 25 cell populations, each with a unique multi-omic signature, including macrophages, T cells, NK cells, mast cells, B cells, plasma cells, neutrophils, dendritic cells, endothelial cells, fibroblasts, and smooth muscle cells (SMCs). Among the macrophages, we identified 2 proinflammatory subsets enriched in IL1B or C1Q expression, 2 TREM2 positive foam cells (one expressing inflammatory genes), and subpopulations with a proliferative gene signature and SMC-specific gene signature with fibrotic pathways upregulated. Further characterization revealed various subsets of SMCs and fibroblasts, including SMC-derived foam cells. These foamy SMCs were localized in the deep intima of coronary atherosclerotic lesions. Utilizing CITE-seq data, we developed a flow cytometry panel, using cell surface proteins CD29, CD142, and CD90, to isolate SMC-derived cells from lesions. Lastly, we observed reduced proportions of efferocytotic macrophages, classically activated endothelial cells, and contractile and modulated SMC-derived cells, while inflammatory SMCs were enriched in plaques of clinically symptomatic vs asymptomatic patients.
Our multimodal atlas of cell populations within atherosclerosis provides novel insights into the diversity, phenotype, location, isolation, and clinical relevance of the unique cellular composition of human carotid atherosclerosis. These findings facilitate both the mapping of cardiovascular disease susceptibility loci to specific cell types as well as the identification of novel molecular and cellular therapeutic targets for the treatment of the disease.

overall_design: CITE-seq was performed on carotid atherosclerotic plaques from 6 subjects (5 symptomatic)

first: Alexander

last: Bashore


title: Early Host Immune Responses in Human Gallbladder to Salmonella Typhi Strains from Patients with Acute and Chronic Infections

status: Public on Apr 05 2024

city: Baltimore

first: Adonis

last: D'Mello

state: Maryland

address: Health Science Facility III, 670 W Baltimore St 3rd floor

institute: IGS- University of Maryland Baltimore

summary: Salmonella enterica serovar Typhi (S. Typhi), a human-restricted pathogen, enters the host through the gut to cause typhoid fever. Recent calculations of the typhoid fever burden estimated that more than 20 million new typhoid fever cases occur in low and middle-income countries, resulting in 129,000-223,000 deaths yearly. Interestingly, upon the resolution of acute disease, 1%-5% of patients become asymptomatic chronic carriers of S. Typhi. Chronically infected hosts are not only critical reservoirs of infection that transmit the disease to naive individuals but are also predisposed to developing gallbladder carcinoma (GBC). Nevertheless, the molecular mechanisms involved in the early interactions between gallbladder epithelial cells and S. Typhi remain largely unknown. Based on our previous studies showing that very closely related S. Typhi strains elicit distinct innate immune responses, we hypothesized that host molecular pathways activated by S. Typhi strains derived from acutely and chronically infected patients will differ. To test this hypothesis, we used a novel human organoid-derived polarized gallbladder monolayer (HODGM) model, and 13 S. Typhi strains derived from acutely (n=6) and chronically (n=7) infected patients. We found that S. Typhi strains derived from acutely and chronically infected patients differentially regulate mitogen-activated protein kinase (MAPK) and S6 transcription factors. This differential regulation impacts, at least in part, the cytokine signaling pathway involved in the production of TNF- and IL-6 and is likely to play a critical role in inducing chronic S. Typhi infection in the gallbladder.

overall_design: A human organoid-derived gallbladder monolayer (HODGM) model infected with 13 S. Typhi strains derived from acutely (n=6) and chronically (n=7) infected patients.

first: Rosângela

last: Salerno-Goncalves

first: Haiyan

last: Chen

first: Andrea

middle: C

last: Bafford

first: Mariana

last: Izquierdo

first: Juan

last: Carlos Hormazábal

first: Hervé

last: Tettelin

first: Jayaum

middle: S

last: Booth

first: Alessio

last: Fasano

first: Myron

last: Levine

first: Marcelo

middle: B

last: Sztein


title: Targeting lipid metabolism in pancreatic cancer [CRISPR]

status: Public on Apr 10 2024

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

summary: Pancreatic ductal adenocarcinoma (PDAC) thrives in a nutrient-deprived microenvironment, making it particularly susceptible to treatments that interfere with cancer metabolism. For example, PDAC utilizes and is dependent on high levels of autophagy and other lysosomal processes. Although targeting these pathways has shown potential in pre-clinical studies, progress has been hampered by the challenge of identifying and characterizing favorable targets for drug development. Here, we characterize PIKfyve, a lipid kinase integral to lysosomal functioning as a novel and targetable vulnerability in PDAC. Through comprehensive metabolic analyses we find that PIKfyve inhibition obligates PDAC to upregulate de novo lipid synthesis, a relationship previously undescribed. PIKfyve inhibition triggers a distinct lipogenic gene expression and metabolic program, creating a dependency on de novo lipid metabolism pathways, including genes such as FASN and ACACA. These results suggest that targeting PIKfyve disrupts lysosome-dependent lipid metabolism in PDAC and may be a favorable metabolic target for therapeutic development. Further, this data suggests that one could take advantage of this synthetic dependency by co-targeting PIKfyve and FASN or ACACA as a therapeutic strategy.

overall_design: Human PDAC cells (MIA PaCa-2) were transduced with a pooled gRNA library (Addgene #110066).  After selection, untreated cells (initial population), or cells treated with DMSO (control) or apilimod for 14 days were harvested for a CRISPR screen.

first: Caleb

last: Cheng

first: Qiao

last: Yuanyuan

first: Zhang

last: Yuping

first: Arul

last: Chinnaiyan

first: Costas

middle: A

last: Lyssiotis


title: High-Dimensional Single-Cell Multimodal Landscape of Human Carotid Atherosclerosis [scRNA-seq]

first: Chenyi

last: Xue

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed on carotid athersclerotic plaques from 12 subjects (6 symptomatic).

first: Alexander

last: Bashore


title: Targeting lipid metabolism in pancreatic cancer

overall_design: Refer to individual Series


title: Single Nuclei RNA-Seq to map progression of non-alcoholic fatty liver disease (NAFLD) in patients II

status: Public on Apr 04 2024

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

summary: Non-alcoholic fatty liver disease (NAFLD) is of increasing prevalence and concern. NAFLD can progress to non-alcoholic steatohepatitis (NASH), to cirrhosis and finally to end-stage liver disease where liver transplantation is required. We aimed to characterise this progression by performing single nuclei transcriptomic analysis of liver biopsies taken from patients across the disease spectrum. We have observed that hepatocytes are the cell type affected mostly by the disease and describe plasticity between cell types which may represent a regenerative process.

overall_design:
Single nuclei RNA-seq was performed on biopsies taken from patients diagnosed with NAFLD (3 samples), NASH (5 samples), NASH with cirrhosis (4 samples) . Additionally, samples were analysed with from patients with end-stage disease due to NAFLD progression (6 samples) requiring transplantation. Healthy liver material was analysed from healthy donors (4 samples) as a control. Samples were cryopreserved by snap freezing in liquid nitrogen and nuclei isolation achieved by using tissue lysis and FACS sorting to purify nuclei prior to loading on the 10x.

UPDATE: [June 06, 2025] The metadata for Samples GSM6112262 and GSM6112263 were swapped. The raw and processed data associated with each accession number were not changed.

first: Christopher

last: Gribben

first: Vasileios

last: Galanakis

first: Alex

last: Calderwood

first: Ruben

last: Chazarra Gil

first: Ludovic

last: Vallier


title: Effect of gut microbiome transplant from neonates of particle-exposed mothers on the epigenome of dendritic cells

status: Public on Apr 01 2024

city: Providence

first: Alexey

middle: V

last: Fedulov

state: Rhode Island

address: 593 Eddy St.

department: RIH / Surgical Research

institute: Alpert Medical School of Brown University

summary: In our model the newborns of asthmatic mother mice or of mothers exposed to air pollutant particles are born with a predisposition to asthma. Gut microbiome of these pups is altered, and the transplant of the pups’ microbiome (GMT) has conferred the asthma predisposition to naïve recipients. We hypothesized that bacteria alter metabolomic profile in the gut, which polarizes the dendritic cells (DC) in the recipient by affecting epigenetic regulation in these key decision-maker cells. Here we examined DNA methylation profiles in the recipient host’s DCs to test the prediction that GMT confers alterations in DNA methylation (not seen with sterilized GMT).

overall_design: Pregnant dams are exposed to concentrated urban air particles (CAP). A fraction of their offspring is tested for asthma predisposition seen as airway inflammation after an intentionally low dose of allergen that remains innocuous in control neonates. Another fraction becomes donors of gut microbiome; after a transplant the recipients are similarly tested. A subset of microbiome transplants is gamma-sterilized prior to instillation into recipients. Hence the 4 groups are: offspring of PBS control mother, offspring of CAP mother, GMT recipients of the material from the offspring of CAP mother, and recipients of sterilized GMT material from the offspring of CAP mother.

first: Mohankumar

last: Ramar

first: Naohiro

last: Yano


title: Targeting lipid metabolism in pancreatic cancer [RNA-seq]

first: Brian

last: Magnuson

overall_design: Murine PDAC cells (7940B) were treated with DMSO (control), apilimod (25nM), or ESK981 (250nM) for 8 hours in duplicate for a total of 6 samples.


title: A multiplexed chemical screen identifies a novel, species-specific Pseudomonas aeruginosa inhibitor that targets LPS interaction with the outer membrane protein, OprH [1401_dataset2]

status: Public on Mar 15 2024

first: Thulasi

last: Warrier

state: MA

address: 415 Main Street

department: IDMP

institute: Broad Institute

summary: The surge of antimicrobial resistance in recent decades threatens efficacy of current antibiotics, particularly against Pseudomonas aeruginosa, a highly resistant gram-negative pathogen. The asymmetric outer membrane of P. aeruginosa combined with its array of efflux pumps provide a barrier to xenobiotic intracellular accumulation, thus making the discovery of novel drugs with whole cell antibacterial activity very challenging. We adapted PROSPECT, a genome-wide, target-based, whole cell screening strategy, to take a focused approach to discover small molecule probes with specific activity against engineered P. aeruginosa mutants depleted for essential proteins localized at the outer membrane. We identified BRD1401, a small molecule that has specific activity against a P. aeruginosa mutant depleted for the essential lipoprotein, OprL. Genetic studies identified a novel link between OprL and the non-essential, outer membrane β barrel protein, OprH, to modulate BRD1401 activity. BRD1401 directly bound to OprH to disrupt the known interaction between OprH and lipopolysaccharide (LPS) in vitro and in whole bacteria. OprH also biochemically interacted with OprL, thus providing a link between outer membrane and peptidoglycan in P. aeruginosa. Thus, a whole cell, multiplexed screen against P. aeruginosa identified a species-specific inhibitor and probe molecule that revealed novel pathogen biology.

overall_design: P. aeruginosa strains, either wildtype PA14 strains, or engineered oprL-hypomorph or ΔoprL or  ΔPA14_50630 strains, were exposed to either 0.5% DMSO vehicle control or 256 µM BRD1401 in standard LB medium for 120 minutes.

first: Deborah

middle: T

last: Hung

first: Bradley

middle: E

last: Poulsen

first: Keith

middle: P

last: Romano

first: Josephine

last: Bagnall


title: The impact of PCR duplication on RNAseq data generated using NovaSeq 6000, NovaSeq X, AVITI and G4 sequencers

status: Public on Mar 13 2024

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: Gene expression profiles generated with RNA sequencing can be biased by RNA amount and methods utilised for cDNA library generation. Polymerase chain reaction (PCR) amplification can generate high PCR duplicate proportions and introduce bias in transcript counts. In this study, we investigate the impact of input amount and PCR cycle number on the PCR duplication rate and on the RNA-seq data quality. We used a range of inputs (1 ng - 1,000 ng) and assessed the PCR duplication rate using unique molecular identifiers (UMIs). For broader applicability, we sequenced the data on four different short-read sequencing platforms: Illumina NovaSeq 6000, Illumina NovaSeq X, Element Biosciences AVITI, and Singular Genomics G4. We highlight the limitations of using input amounts below 125 ng and the advantages for using UMIs for deduplication. We contrast the data obtained from different sequencers and discuss the benefits and drawbacks of using Illumina library conversion kits.

overall_design: bulk RNA-seq of human liver, serial dilution of 1 ng to 1000 ng, sequencing performed on 4 sequencers (NovaSeq 6000, NovaSeq X, AVITI and G4)

first: Natalia

last: Zajac

first: Ioannis

last: Vlachos

first: Sija

last: Sajibu

first: Lennart

last: Opitz

first: Shuoshuo

last: Wang

first: Sridar

last: Chittur

last: Mason

first: Kevin

last: Knudtson

first: John

last: Ashton

first: Catharine

last: Aquino


title: A multiplexed chemical screen identifies a novel, species-specific Pseudomonas aeruginosa inhibitor that targets LPS interaction with the outer membrane protein, OprH

overall_design: P. aeruginosa strains, either wildtype PA14 or PAO1 strains, or engineered oprL-hypomorph or oprL-KD strains, or BRD1401-resistant strains, were exposed to either varying salt in the growth medium in the presence of either 0.5% DMSO vehicle control or 125 or 250 µM BRD1401 or to varying doses of arabinose in the presence of either 0.5% DMSO vehicle control or 125 µM BRD1401.

first: Phuong

middle: H

last: Nguyen


title: Loss of UBE3A impacts both neuronal and non-neuronal cells in human cerebral organoids.

city: Raleigh

first: Albert

last: Keung

state: NC

address: 840 Main Campus Drive

department: Chemical and Biomolecular

institute: North Carolina State University

summary: Angelman syndrome is a neurodevelopmental disorder caused by (epi)genetic lesions of maternal UBE3A. Research has focused largely on the role of UBE3A in neurons due to its imprinting in that cell type. Yet, evidence suggests there may be broader neurodevelopmental impacts of UBE3A dysregulation. Human cerebral organoids can investigate these understudied aspects of UBE3A as they recapitulate diverse cell types of the developing human brain. We performed single-cell RNA-sequencing on organoids to reveal the effects of UBE3A disruption on cell type-specific transcriptomic alterations and compositions. In the absence of UBE3A, progenitor proliferation and structures were disrupted while organoid composition shifted away from proliferative cell types. We observed impacts on non-neuronal cells including choroid plexus enrichment. Furthermore, EMX1+ cortical progenitors were negatively impacted, disrupting corticogenesis, and potentially delaying neuron maturation. This work reveals novel impacts of UBE3A on understudied cell types and related neurodevelopmental processes and elucidates potential new therapeutic targets.

overall_design: We dissociated 3-D cerebral organoid cultures using the Worthington papain dissociation system and carried out scRNA-seq and library prep using Parse Biosciences Evercode kit.

first: R

last: Estridge

first: Z

last: Yagci

first: Dilara

last: Sen

first: Travis

last: Ptacek

first: Jeremy

last: Simon


title: Oocyte mitochondria link maternal environment to offspring phenotype in C. elegans

status: Public on Mar 09 2024

city: Grand Rapids

first: Robert

last: Fillinger

state: Michigan

address: 333 Bostwick Ave NE

institute: Van Andel Institute

summary: Oocytes undergo a recently discovered mitochondrial proteome remodeling event in flies1, frogs1, and humans2. This oocyte mitochondrial remodeling event, which includes substantial changes in electron transport chain (ETC) subunit abundance1,2, is regulated by maternal insulin signaling1. However, why oocytes undergo mitochondrial remodeling is unknown, with some speculating that it might be a conserved mechanism to protect oocytes from genotoxic damage by reactive oxygen species (ROS)2. In Caenorhabditis elegans, we previously found that maternal exposure to osmotic stress drives a 50-fold increase in offspring survival in response to future osmotic stress, and that this intergenerational adaptation is regulated by insulin signaling to oocytes3. Here, we used proteomics and genetic manipulations to show that insulin signaling to oocytes regulates offspring’s ability to adapt to future stress via a mechanism that depends on ETC composition in maternal germ cells/oocytes. Specifically, we found that maternally expressed mutant alleles of nduf-7 (complex I subunit) or isp-1 (complex III subunit) altered offspring’s response to osmotic stress at hatching independently of offspring genotype. Furthermore, we found that expressing wild-type isp-1 in maternal germ cells (oocytes) was sufficient to restore offspring’s normal response to osmotic stress. Chemical mutagenesis screens revealed that oocyte ETC composition regulates offspring’s response to osmotic stress by altering AMP kinase function in offspring which in turn regulates both ATP and glycerol metabolism in offspring in response to continued osmotic stress. To our knowledge, these data are the first to show that changes in oocyte mitochondrial ETC composition can affect an animal phenotype that manifests after embryonic development is complete. The data also suggest that the reason diverse animals exhibit insulin regulated remodeling of oocyte mitochondria might be to tailor offspring metabolism to best match the environment of their mother.

overall_design: C. elegans mothers were cultured from the adolescent L4 stage until the first day of adulthood on control NGM culture or on osmotic stress 300mM NaCl culture. The mature oocytes were then dissected and collected in SMART seq buffer.

first: Jason

last: Cooper

first: Nick

last: Burton

first: Kim

last: Nygen


title: Single-cell multimodal profiling of atherosclerosis identifies CD200 as a cell surface lineage marker of vascular smooth muscle cells and their derived cells

first: Chenyi

last: Xue

summary: Vascular smooth muscle cells (VSMCs) play a central role in the development of atherosclerosis due in part to their capability to phenotypically transition into either a protective or harmful state. However, the ability to identify and trace VSMCs and their progeny in vivo is limited due to the lack of well-defined VSMC cell surface markers. Therefore, investigations into VSMC fate must utilize lineage-tracing mouse models, which are time-consuming and challenging to generate and not feasible in humans. Here, we employed CITE-seq to characterize the phenotypic expression of 119 cell surface proteins in mouse atherosclerosis. We found that CD200 is a highly expressed and specific marker of VSMCs, which persists even with phenotypic modulation. We validated our findings using a combination of flow cytometry, qPCR, and immunohistochemistry, all confirming that CD200 can identify and mark VSMCs and their derived cells in early to advanced mouse atherosclerotic lesions. Additionally, we describe a similar expression pattern of CD200 in human coronary and carotid atherosclerosis. Thus, our data support the use of CD200 as a lineage marker for VSMCs and VSMC-derived cells in mouse and human atherosclerosis.

overall_design: Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) was used to perform in-depth cell surface phenotyping of all cells within mouse atherosclerotic lesions. Aortas from ROSA26LSL-ZsGreen1/+Myh11-CreERT2 vascular smooth muscle cell lineage traced mice at various times of western diet feeding (0, 8, 16, and 26 weeks) were digested in an enzyme cocktail containing 4U/mL Liberase, 60U/mL Hyaluronidase and 60U/mL DNase in RPMI for 1 hour. Cell suspension was then labeled with the TotalSeq-A Mouse Universal Cocktail (BioLegend: 199901) oligo-conjugated antibodies and subsequently fluorescently activated cell sorted and viable cells were identified as being DRAQ5+ and DAPI-. Cells were then submitted for single cell profiling using the 10x Genomics 3’ v3 protocol. Single cell analysis identified CD200 as a potential cell surface lineage marker for VSMCs and their derived cells. To validate this, we used flow cytometry to isolate CD200+ and CD200- cells and performed qPCR on isolated cells.

first: Alexander

last: Bashore


title: Effects of depletion of EPAS1 and knocking down TNFSF10 in 786-O cell lines.

status: Public on Mar 08 2024

city: South Bend

first: XUECHUN

last: WANG

state: Indiana

address: university of notre dame

institute: University of Notre Dame

summary: VHL loss leads to the stabilization of hypoxia-inducible factor α (HIFα), which may drive various tumor-promoting pathways. Here, we depletion expression of HIF2α in 786-O and performed transcriptome profiling to assess the molecular impact.  TRAIL represents a promising avenue for cancer therapy due to its ability to selectively target and kill tumor cells. However, its effectiveness is variable across different cancer types, even with some tumors exhibiting high levels of TRAIL expression. To investigate this situation, we used shRNA to target TNFSF10, aiming to understand its impact on tumor development.

overall_design: To analyze the differntial gene expression  of 786-O kidney cancer cell lines under four different conditions to understand the effect of  HIF2α knocking out via CRISPR-Cas9 and TNFSF10 knocking down using inducible shRNA (with and without doxycycline induction for 48 hours). Each condition will have its set of biological replicates to ensure statistical significance.

first: Xuechun

last: Wang


title: Deciphering the role of RNA in regulating CTCF’s DNA binding affinity in leukemia cells [CTCF-HA-ChIP]

city: Memphis

first: Beisi

last: Xu

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

summary: CTCF is the most studied transcription factor, which is essential for chromatin interaction maintenance. Although several independent studies reported that CTCF protein could pull down RNAs in vitro and in cells, there are continuous debates about authenticity of the RNA-binding affinity of CTCF and its biological role, mainly due to the concerns of limited research techniques such as CLIP-seq. To systematically investigate the RNA-interaction with CTCF and the impact on gene regulation, we conducted in vivo CTCF ChIP-seq under three conditions, including RNase A treatment, Triptolide-mediated transcription inhibition and auxin-inducible degron mediated RNA-binding domain mutant swap. Our results consistently suggest that when RNA-interaction with CTCF protein was impaired in vivo, the DNA occupancy of CTCF remains the same at the genome-wide scale. Our data provide a complementary approach and in silico evidence to re-considerate the role of RNA-binding affinity of CTCF.

overall_design: HA-tag-ChIP-Seq samples were collected from DMSO, Triptolide and RNase A treatment to CTCFAID2+HA-CTCF-WT cells. Data from CTCFAID2+HA-CTCF-dRBR cells could be found at GSE205408

first: Judith

last: Hyle

first: Mohamed

last: Nadhir Djekidel

first: Wojciech

last: Rosikiewicz

first: Chunliang

last: Li


title: Deciphering the role of RNA in regulating CTCF’s DNA binding affinity in leukemia cells

summary:
RNA-seq could be found under GSE205311(sample names with DeltaRBR).
HA-tagged CTCF-ChIP-seq for dRBR could be found under GSE205408(sample names with Delta_RBR).
This SuperSeries is composed of the SubSeries listed below.


title: Transcriptomic analysis indicates a role for oxidative phosphorylation in postnatal development of rat carotid body hypoxic sensitivity

status: Public on Mar 05 2024

city: Chicago

first: Jayasri

last: Nanduri

state: IL

address: 5841 S. Maryland Avenue

institute: University of Chicago

summary: The carotid body (CB), located bilaterally at the carotid artery bifurcations,  is the primary sensory organ for monitoring arterial blood O2 levels. Carotid bodies are immature at birth, exhibiting low sensitivity to hypoxia and become more sensitive with maturation during the first few weeks of neonatal life. To understand the molecular basis for the postnatal developmental hypoxic responses of CB, we isolated CBs from 5-day and 21-day-old Sprague Dawley rats, and performed RNA-sequencing, which allows comprehensive analysis of gene expression. Differentially expressed genes (DEGs) were generated using Edge R, while functional enrichment analysis was performed using GSEA. Analysis of RNA seq data showed 1769 DEGs of the total 12,696 genes shared between neonates and adults. Of the 1769 DEGs, 924 genes were upregulated, and 1680 genes were downregulated. Further analysis showed that genes related to oxidative phosphorylation (Ox/phos) and hypoxia-signaling pathways were significantly upregulated in neonatal compared to adult CBs, suggesting a possible link to differential developmental hypoxic responses seen in CB. Genes related to cytokine signaling (INF and TNFα) and transcription factors (CREB and NFB) mediated pathways were enriched in adult CBs suggesting expression of these pathways may be linked to developmental regulation. The RNA-seq results were verified by analyzing mRNA changes in selected genes by qRT-PCR. Our results of enrichment analysis of biological pathways offer a valuable insight into CB hypoxic sensing responses and development process.

overall_design: Sprague Dawley pregnant rats purchased from Charles River Laboratories were used for the experiments. Mother was housed on a 12h light dark cycle and fed ad libitum a standard pelleted rodent diet with free access to the water. Pups aged 5 days were sacrificed by IP urethane injection and bifurcations were harvested. One third of the litter was allowed to grow to 21 days after which they were sacrificed, and CB bifurcations were harvested.  CBs were isolated from the bifurcations and immediately transferred to RNA Later at 40C. Total RNAs were extracted using the Direct-ZOL RNA micro prep kit (Zymo Research; #R2060) according to the manufacturer’s instructions. For each experiment, CBs from 6 pups (post-natal day 5) or 3 adult rats (post-natal day 21) were pooled per sample. We then performed gene expression profiling analysis using data obtained from RNA seq of CBs at two time points (5day and 21 day old) run in duplicates


title: Effect of Dis3 depletion on gene expression in hematopoietic stem cells of C57BL/6 mice

status: Public on Feb 28 2024

city: Kumamoto

first: Hiroto

last: Ohguchi

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: IRDA

institute: Kumamoto University

summary: Multiple myeloma (MM) is a plasma cell neoplasm that remains incurable regardless of the introduction of novel agents. Therefore, it is of necessity to decode the molecular mechanisms of myelomagenesis to identify novel therapeutic strategies. Recent advances in next-generation sequencing technologies have not only reconfirmed the significance of known driver events in MM but also have identified novel genetic alterations in MM. Importantly, mutations of DIS3 genes have been identified in ~10% of MM patients, and loss of heterozygosity at chromosome 13q that leads to deletion of one allele of DIS3 has been observed in ~ 40% of MM patients. However, the roles of DIS3 in hematopoiesis and myelomagenesis remain incompletely understood. Here we show that Dis3 prevents accumulation of DNA damage in hematopoietic cells, thereby supporting hematopoiesis. We also show that loss of Dis3 alone and in combination with c-MAF transgene in GC B cells do not exhibit plasma cell neoplasm in mice.

overall_design: Hematopoietic stem cells of wild type and hematopoietic cell-specific Dis3-/- mice were isolated and subjected to RNA-seq (n = 2 mice).

first: Shingo

last: Usuki

first: Goro

last: Sashida


title: The differential gene screening for invasive pituitary adenoma and non-invasive pituitary adenoma

status: Public on Mar 04 2024

city: Beijing

first: Yu

last: Zhang

address: 119 South Fourth Ring Road West

institute: Beijing Tiantan Hospital, Capital Medical University

summary: Pituitary adenomas are benign tumors originating from the endocrine cells of the pituitary gland, but some pathological subtypes are highly invasive, known as invasive pituitary adenomas. Invasive pituitary adenomas are relatively rare, progress rapidly, easily invade surrounding tissues, have a high risk of recurrence, and have poor response to standard treatments. This study collected tumor specimens from 17 patients with non-invasive pituitary adenomas (FSH type) and 15 patients with invasive pituitary adenomas (ACTH-silent type), and performed transcriptome sequencing, aiming to explore the genetic differences between invasive and non-invasive pituitary adenomas.

overall_design: This study collected 17 samples of non-invasive pituitary adenomas (FSH type) and 15 samples of invasive pituitary adenomas (silent expression ACTH type), established mRNA libraries using RNA-Seq sequencing technology.

first: Zhijun

last: Yang

first: Xing

last: Ma

first: Hongyu

last: Wu


title: Global transcriptome of the fungal pathogen Sclerotinia sclerotiorum (strain 1980) during the colonization of 23 Accessions of Arabidopsis thaliana

status: Public on Feb 27 2024

city: Castanet-Tolosan

first: Florent

last: Delplace

address: 24 chemin de Borde Rouge

country: France

institute: INRAe

summary: Quantitative disease resistance (QDR) is an almost universal and often broad-spectrum process in plants, serving to limit the damage caused by pathogen infections. It represents the primary form of plant immunity that reduces disease symptoms induced by numerous pathogens actively killing host cells during infection, including the necrotrophic pathogen Sclerotinia sclerotiorum. Investigating the evolutionary origins of QDR against necrotrophic fungi is crucial for comprehending how plant resistance evolves. To explore the diversity of local responses to S. sclerotiorum within a plant species level, we conducted a comprehensive analysis of the entire transcriptomes from 23 accessions of Arabidopsis thaliana, mainly distributed across Europe. More than half on the pan-transcriptome displayed local responses toS. sclerotiorum, including similar transcriptome patterns. Notably, core S. sclerotiorum-responsive genes exhibited a clear gene age pattern, dominated by older genes forming protein-protein networks that continuously acquiring new hubs. Comparative transcriptome analyses revealed QDR is associated with quantitative expression variations specific to accession subsets. By comparison of promoter sequences, we have shown evidence that accession subsets independently evolved and acquired specific cis-regulatory elements, confering Sclerotinia resistance. This scenario suggests multiple exaptation trajectories of novel QDR genes through species-level cis-regulation. This study sheds light on the regulation of QDR-associated genes within a species, contributing to our understanding of the molecular mechanisms of plant fungal resistance.

overall_design: Periphery of S. sclerotiorum disease lesions (Ss) and uninfected plants grown together (control), Ss and control samples collected simultaneously in three independent replicates

first: Delplace

last: Florent

first: Khafif

last: Mehdi

first: Raffaele

last: Sylvain


title: Differential mRNA expression analysis of H358 and AsPC-1 cell xenograft mouse model after MCB-294 treatment

status: Public on Feb 22 2024

city: Shang Hai

first: zhengke

last: lian

address: 500 Dongchuan Rd

institute: East China Normal University

summary: The mechanism of action of a pan-Kras inhibitor MCB-294 remains unknown. We determined gene expression profiling in H358 and AsPC-1 cell line xenograft mouse models after MCB-294 treatment using RNA-seq analysis.

overall_design:
To investigate the action of a pan-Kras inhibitor MCB-294 in vivo, we established H358 and AsPC-1 cell line xenograft mouse models in which each mouse model was then treated with vehicle or MCB-294 (Bid, 30 mg/kg), followed by harvest and RNA extraction at 1 hours and 6 hours after the last dose.
We then performed transcription profiling analysis using data obtained from RNA-seq of H358 and AsPC-1 cell line xenograft mouse models treated as mentioned above.

first: Juanjuan

last: Feng

first: Xinting

last: Xia


title: DMT1 silencing effects in 2D versus 3D cel culture conditions in MDA-MB-231 triple negative breast cancer cells

status: Public on Feb 26 2024

city: New York

first: Jonathan

last: Barra

state: New York

address: 1468 Madison Avenue

institute: Mount Sinai

summary:
To investigate the differential transcriptomics upon DMT1 in 2D vs 3D cell culture in breast cancer cells
Gene expression  analysis from MDA-MB-231 RNA-seq data of WT and DMT1 KO cells both in 2D and 3D cell culture conditions

overall_design:
Gene expression profiling analysis using data obtained from MDA-MB-231 RNA-seq of 3 replicates of WT and DMT1 KO cells both in 2D and 3D cell culture conditions
Raw files from MdaWT and Mda KO (2D cell culture) were truncated and complete raw data are not available.

first: Margarida

last: Barroso


title: A Unified Framework for Systematic Identification of Post-Transcriptional Regulatory Modules [Ribosomal profiling]

status: Public on Feb 21 2024

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Department of Biochemistry and Biophysics

institute: UCSF

summary: RNA-binding proteins (RBPs) are multifunctional regulators of gene expression with complex and context-dependent mechanisms of action, yet the regulatory grammar that underlies RBP-mediated functions remains underexplored. Here, we performed a multi-omic data integration to systematically decipher the context-specific functions of RBPs. First, we report a compendium of in vivo proximity-dependent biotinylation (BioID) datasets of 50 human RBPs, which we used to generate a large-scale map of RBP protein neighborhoods. In parallel, we took advantage of CRISPR-interference with single-cell RNA-seq read-out (Perturb-seq) to capture rich transcriptomic phenotypes downstream of each RBP knockdown. By combining these physical and functional interaction readouts, along with the ENCODE transcriptome-wide atlas of RBP binding sites from eCLIP assays, we generated an integrated map of functional RBP interactions. This map not only captures well-studied post-transcriptional processes, but also reveals numerous previously unknown RBP-mediated regulatory functions. For a number of these cases, we have validated their predicted context-specific RBP functions using biochemical and genetic approaches. By deciphering these complex modes of functional interactions between RBPs, we have taken the first step towards a more comprehensive understanding of post-transcriptional regulatory processes and their underlying molecular grammar.

overall_design: Ribosomal profiling of K562 TAF15 KD cells

first: Matvei

last: Khoroshkin

first: Andrey

last: Buyan

first: Martin

last: Dodel

first: Albertas

last: Navickas

first: Johnny

last: Yu

first: Fathima

last: Trejo

first: Anthony

last: Doty

first: Rithvik

last: Baratam

first: Shaopu

last: Zhou

first: Tanvi

last: Joshi

first: Kristle

last: Garcia

first: Benedict

last: Choi

first: Sohit

last: Miglani

first: Vishvak

last: Subramanyam

first: Hailey

last: Modi

first: Daniel

last: Markett

first: Ivan

last: Kulakovskiy

first: M

middle: R

last: Corces

first: Faraz

last: Mardakheh


title: A Unified Framework for Systematic Identification of Post-Transcriptional Regulatory Modules [perturb_seq]

first: Hani

last: Goodarzi

overall_design: We obtained transcriptome-wide gene expression measurements for 68 RBPs (representing a variety of regulatory processes) knockdowns using single-cell RNA sequencing and used the resulting high-dimensional data to systematically delineate genetic interactions between RBPs.  Perturb-seq experiment was performed as previously described (Datlinger et al. 2017).

first: Matvei

last: Khoroshkin

first: Andrey

last: Buyan

first: Martin

last: Dodel


title: Screening the crucial RNA among the 0, 1, 7, and 14 days during the proceeding of the C3H10 T1/2 osteogenesis differentiation.

status: Public on Feb 19 2024

city: Nanjing

first: Wang

last: Bin

state: Jiangsu

address: No.305Zhongshan East Rd

institute: Jinling hospital, Medical School of Nanjing University

summary: Cultivate C3H10T1/2 cell lines using an osteogenic induction medium, extract RNA on the day of induction, the first day after induction, the seventh day after induction, and the 14th day after induction, and screen for key molecules in the osteogenic induction process through RNA seq.

overall_design: 1. C3H10T1/2 cells were cultured using DMEM (10% FBS), and when the cell density reached 80, the cells were seeded onto a 6-well plate at a density of 1 * 10^6; 2. Cultivate cells using an osteogenic induction medium; 3. RNA sequencing was extracted at 0, 1, 7, and 14 days after osteogenic induction.

first: Bin

last: Wang

last: Xu


title: Screening the crucial exosome miRNA in the human serum

status: Public on Feb 18 2024

summary: With the increasing aging population, the incidence of osteoporosis is increasing year by year. Fractures caused by osteoporosis are one of the main causes of disability and death in elderly people. Therefore, the purpose of this study is to recruit postmenopausal osteoporosis and healthy patients, collect their blood and isolate serum, screen for miRNAs related to osteoporosis through exosomal miRNA sequencing and bioinformatics analysis, validate these molecules through experiments, and finally screen for key miRNAs.

overall_design: 1. Recruit 10 postmenopausal female patients, including 5 healthy controls and the other 5 patients with osteoporosis; 2. Collect whole blood, let it stand at 4 ℃ for 2-3 hours, and then isolate the serum; 3. Extract serum exosomes using the reagent kit method; 4. Extract extracellular RNA and perform sequencing; 5. Bioinformatics screening of key miRNAs in sequencing data; 6. Verify miRNA through in vitro and in vivo experiments


title: A Unified Framework for Systematic Identification of Post-Transcriptional Regulatory Modules [ATAC-Seq]

first: Albertas

last: Navickas

first: Johnny

last: Yu

first: Fathima

last: Trejo

first: Anthony

last: Doty

first: Rithvik

last: Baratam

first: Shaopu

last: Zhou

last: Joshi


title: Targeting the SWI/SNF complexes in POU2F transcription factor driven malignancies [RNA-seq]

status: Public on Feb 15 2024

first: Arul

last: Chinnaiyan

address: 1500 East Medical Center Dr

department: MCTP

institute: University of Michigan

summary: The SWI/SNF chromatin-remodeling complex, pivotal in transcriptional regulation, has emerged as a significant player in tumorigenesis, unveiling therapeutic targeting prospects in specific malignancies. This investigation accentuates the potential of targeting the SWI/SNF complex in POU2F3-driven Small Cell Lung Cancer (SCLC) and POU2AF1-dependent multiple myelomas. Employing functional CRISPR screening and pharmacological validation, we identified a distinct and biased dependency of POU2F3-driven SCLC cells on the SWI/SNF complex. In vivo studies exhibited significant tumor growth inhibition in POU2F3-driven SCLC xenografts with an orally administered SMARCA2/4 PROTAC degrader. Furthermore, the exploration extended to POU2AF1 complex-dependent B-cell malignancies, revealing similar sensitivity to the SWI/SNF ATPase PROTAC degrader, suggesting a shared therapeutic potential in POU2F complex-driven malignancies. These collective findings highlight the SWI/SNF complex as a promising therapeutic target, catalyzing the advancement of innovative and efficacious treatment approaches to address these transcription factor-driven malignancies, addressing a critical medical challenge.

overall_design: Distinct small cell lung cancer cells were treated in vitro with the 1uM SMARCA2/4 degrader (AU-15330, abbreviated as AU) for indicated durations (ranging from 4 to 12h), and processed for multi-omic characterization.

first: Tongchen

last: He

first: Lanbo

last: Xiao

first: Eleanor

last: Young


title: Targeting the SWI/SNF complexes in POU2F transcription factor driven malignancies [ChIP-seq]


title: WNK1 enforces macrophage lineage fidelity

status: Public on Feb 06 2024

first: Justin

middle: Shaun Arnold

last: Perry

address: 408 East 69th Street, 408-15

department: Immunology Program

institute: Sloan Kettering Institute for Cancer Research

summary: The appropriate development of myeloid progenitors into macrophages, the body’s professional phagocyte, is essential for organismal development, especially in mammals1. This dependence is exemplified by the observation that loss-of-function mutation in colony stimulating factor 1 receptor (CSF1R) results in multiple tissue abnormalities including osteopetrosis2. Despite this importance, little is known about the molecular and cell biological regulation of macrophage development. Here, we report the surprising finding that the chloride-sensing kinase With-no-lysine 1 (WNK1) is required for embryonic development of tissue-resident macrophages (TRMs). Myeloid-specific deletion of Wnk1 caused a dramatic loss of TRMs and subsequently disrupted organ development, induced systemic neutrophilia, and resulted in mortality between 3 and 4 weeks of age. Specifically, we observed that WNK1 absence stalled macrophage differentiation at the myeloid multipotent progenitor (MPP) stage, instead skewing MPP differentiation towards granulopoiesis. Mechanistically, the cognate CSF1R cytokine, macrophage-colony stimulating factor (M-CSF), triggers macropinocytosis in myeloid progenitors, which in turn induces phosphorylation of WNK1. Importantly, macropinocytosis by myeloid progenitors increases cytosolic chloride, which is directly sensed by WNK1. Perturbing chloride flux during macropinocytosis, inhibiting WNK1 chloride-sensing, and blocking macropinocytosis each skew progenitor differentiation from macrophage lineage to granulocyte lineage. Thus, we have uncovered a novel mechanism that links a cell biological process to a molecular circuit whereby WNK1 chloride-sensing and chloride flux act downstream of M-CSF-induced macropinocytosis by multipotent progenitors to ensure macrophage lineage fidelity.

overall_design: Single cell RNA sequencing (scRNAseq) of MPP3s from CSF1R-Cre x WNK1 flox mice or littermate controls. MPP3s (Lin- cKit+ Sca-1+ Flt3- CD48+ CD150-) were sorted using multi-color flow cytometry (FACS Aria, BD) into fresh tubes containing PBS with 0.04% BSA (Sigma-Aldrich, A8806). Cells were washed 1x and resuspended in PBS containing 0.04% BSA at a final concentration of 700–1,300 cells per μl. Cell viability was confirmed to be above 80% via staining with 0.2% (w/v) Trypan Blue (Countess II). Each mouse (n=3 Cre-, n=4 Cre+) was labeled separately by staining with MHC Class I- barcoded antibodies bearing hashtags 1-7 (BioLegend, A0301-A0307). Library prep and sequencing were performed by the Single Cell Research Initiative (SCRI) at MSKCC as follows: scRNAseq was performed on a Chromium instrument (10X Genomics) following the user guide manual for 3′ v3.1. Cells were captured in droplets, then subjected to reverse transcription and cell barcoding. Following this step, emulsions were broken, and cDNA purified using Dynabead MyOne SILANE, followed by PCR amplification per manual instruction. Approximately 30,000 cells were targeted for each sample. Samples were multiplexed together on one lane of a 10X Chromium following a published cell hashing protocol69. Final libraries were sequenced on the Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles).

first: Alissa

last: Trzeciak

first: Waleska

last: Rojas

first: Adam

last: Krebs

first: Giulia

last: Zago

first: Ya-Ting

first: Zhaoquan

first: Pedro

last: Saavedra

first: Jian

last: Xie

first: Chou-Long

last: Huang

first: Michael

last: Overholtzer

last: Glickman

first: Christopher

last: Parkhurst

first: Thomas

last: Vierbuchen

last: Lucas


title: Targeting the SWI/SNF complexes in POU2F transcription factor driven malignancies

first: Arul

last: Chinnaiyan

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

overall_design: Refer to individual Series


title: Generation of human induced pluripotent stem cell-derived 3D human diencephalic organoids, and comparison to a human primary tissue

status: Public on Feb 05 2024

city: STANFORD

first: Yuki

last: Miura

state: California

address: 318 Campus Drive, W200

department: Department of Psychiatry and Behavioral Sciences

institute: Stanford University

summary: Single cell RNA-seq characterization of stem cell derived organoids resembling the human diencephalon and comparison to a human primary diencephalon

overall_design:
Single-cell RNA sequencing of human induced pluripotent stem (hiPS) cell-derived diencephalic organoids from three hiPS cell lines, and a human primary diencephalon sample
--------------------------------
Authors state "This upload include human samples, so we cannot upload identifiable raw data. We are able to upload only de-identified processsed data."

first: Ji-il

last: Kim

first: Sergiu

last: Pașca


title: Targeting the SWI/SNF complexes in POU2F transcription factor driven malignancies [ATAC-seq]

city: Ann Arbor

first: Tongchen

last: He

first: Lanbo

last: Xiao

first: Eleanor

last: Young


title: Enhancer formation during cell reprogramming is edited by the chromatin remodeling factor CHD4

status: Public on Jan 29 2024

city: Grand Forks

first: Motoki

last: Takaku

state: ND

address: W221 Biomedical Sciences 1301 N. Columbia Road

institute: University of North Dakota

type: Methylation profiling by high throughput sequencing


title: Enhancer formation during cell reprogramming is edited by the chromatin remodeling factor CHD4 [RNA-Seq]

summary: Transcription factors induce dynamic chromatin reorganization during cell fate transition. Pioneer transcription factors are defined as their capability to engage chromatin by binding to nucleosomal DNA in closed chromatin and inducing chromatin opening. However, it has been also shown that these activities are context dependent. Only a subset of pioneer factors’ binding sites become open and the rest of binding sites remain closed. The molecular mechanisms of this context dependent action are still largely unknown. Here, we explore dynamic chromatin rearrangement during GATA3 dependent mesenchymal-to-epithelial transition (MET) in breast cancer cells. We found site-specific kinetic differences in chromatin binding, nucleosome remodeling and chromatin opening by the pioneer factor GATA3. We also identified that a chromatin remodeling enzyme, CHD4, negatively regulates the GATA3-mediated chromatin opening. The silencing of CHD4 induces abnormal chromatin opening leading to unnecessary gene expression for MET. Our study suggests the active regulation of chromatin potential by the chromatin remodeling enzyme for successful cellular reprogramming.

overall_design: Chromatin profiling using doxycycline-inducible GATA3 expression system in MDA-MB-231 cells. We conducted time-course experiments to analyze dynamic chromatin transitions during mesenchymal-to-epithelial transition.

first: Sara

last: Grimm

first: Deepak

last: Poduval

first: Mika

last: Saotome

first: Paul

last: Wade


title: Enhancer formation during cell reprogramming is edited by the chromatin remodeling factor CHD4 [ChIP-Seq]


title: Enhancer formation during cell reprogramming is edited by the chromatin remodeling factor CHD4 [MNase-Seq]


title: Enhancer formation during cell reprogramming is edited by the chromatin remodeling factor CHD4 [ATAC-Seq]


title: Targeting Iron - Respiratory Reciprocity Promotes Bacterial Death

status: Public on Jan 16 2024

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

summary: Discovering new bacterial signaling pathways offers unique antibiotic strategies.  Here, through an unbiased resistance screen of 3,884 gene knockout strains, we uncovered a previously unknown non-lytic bactericidal mechanism that sequentially couples three transporters and downstream transcription to lethally suppress respiration of the highly virulent P. aeruginosa strain PA14 - one of three species on the WHO's 'Priority 1: Critical' list.  By targeting outer membrane YaiW, cationic lacritin peptide 'N-104' translocates into the periplasm where it ligates outer loops 4 and 2 respectively of the inner membrane transporters FeoB and PotH to respectively suppress both ferrous iron and polyamine uptake.  This broadly shuts down transcription of many biofilm-associated genes, including ferrous iron-dependent TauD and ExB1.  The mechanism is innate to the surface of the eye enhanced by synergistic coupling with thrombin peptide GKY20.  This is the first example of an inhibitor of multiple bacterial transporters.

overall_design: Mid-log P. aeruginosa PA14 cells were incubated without treatment or with 5 or 20 uM lacritin N-104 (or 20 uM N-80/C-25 as negative control peptide) for 45 min at 35oC. RNA isolation from the cells was carried out using the RNeasy mini kit (74104, Qiagen). The quality of the RNA samples was examined prior to sequencing by using gel electrophoresis, which revealed two sharp peaks with very low background. An RNA Integrity Number equivalent (RINe) of 8.4-9.2 and a concentration of approximately 40-60 ng/ul were obtained. Three independent RNA samples were sequenced for each experimental condition. Library construction and sequencing were executed at the Genome Analysis and Technology Core of the University of Virginia. Specifically, mRNA enrichment was conducted using the NEBNext® rRNA Depletion Kit (Bacteria) (E7850L, New England BioLabs). Transcriptome sequencing was then performed on a Next Seq 500 Mid Output platform, with 150-bp pair-end reads produced. The range of raw reads for each sample varied from 8-10 million, thus ensuring an optimal depth of sequencing. The analysis of RNA-seq data was conducted at the Bioinformatics Core facility of the University of Virginia.

first: Mohammad

last: Sharifian Gh

first: Fatemeh

last: Norouzi

first: Mirco

last: Sorci

first: Gerald

last: Pier

first: Alecia

last: Achimovich

first: George

last: Ongwae

first: Binyong

last: Liang

first: Margaret

last: Ryan

last: Lemke

first: Georges

last: Belfort

first: Mihaela

last: Gadjeva

first: Andreas

last: Gahlmann

first: Marcos

last: Pires

first: Henrietta

last: Venter

first: Thurl

last: Harris

first: Gordon

middle: W

last: Laurie


title: A mucus production programme promotes classical pancreatic ductal adenocarcinoma

status: Public on Jan 24 2024

city: Cold Spring Harbor

first: Olaf

last: Klingbeil

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary:
CUT&RUN for IgG, H3K4me3 and HA-SPDEF in human PDA HPAF-II cells and CUT&RUN HA-Spdef in murine KPC 2D FC1245 cells

We performed CUT&RUN assay in human and murine PDA cells to profile the direct binding of SPDEF to target genes.

overall_design: Mapping of SPDEF binding sites in human and murine PDA cells.

first: David

last: Tuveson

first: Claudia

last: Tonelli


title: Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations

status: Public on Jan 18 2024

city: Worcester

first: Summer

last: Thyme

address: 364 Plantation St

institute: UMass Chan Medical School

summary: Hundreds of human mutations are linked to autism and related disorders, yet the functions of many of these mutated genes during vertebrate neurodevelopment are unclear. We generated 27 zebrafish mutants with presumptive protein-truncating mutations or specific missense variants corresponding to autism-risk alleles in 17 human genes. We observed baseline and stimulus-driven behavioral changes at larval stages, as well as social behavior differences in lines tested as juveniles. Imaging whole-brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa, defined by increased activity mainly in the thalamus and mesencephalon. Mutating 7 of the 17 risk genes resulted in substantial brain size differences, localized to the diencephalon in three cases and more widespread in others. Using RNA sequencing, we further defined molecular drivers of the observed phenotypes for three mutants, identifying targetable disruptions in neuropeptide signaling, neuronal maturation, and cell proliferation. This multimodal screen nominated brain regions, cell types, and molecular pathways that may contribute to autism susceptibility.

overall_design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism, which were generated using CRISPR/Cas9 mutagenesis.

first: Thyme

last: Summer


title: Effect of over-expression of lncRNA HEGBC on gene expression of GBC-SD cell

city: shanghai

first: Liang

last: Yang

address: No.2699,West Gaoke Road, Pudong New Area, Shanghai

institute: Shanghai First Maternity and Infant Hospital

summary: LncRNAs play an important role in regulating cancer progression. We have report lncRNA HEGBC as a key regulator of tumorigenesis and metastasis of gall bladder cancer. To further illustrate the biological function of lncRNA HEGBC, we overexpressed it in GBC-SD cells. Through enrichment analysis, pathways like chemical carcinogenesis - DNA adducts, IL-17 signaling pathway, metabolism of xenobiotics by cytochrome P450, lipid and atherosclerosis and ECM-receptor interaction were enriched. Taken together, our project revealed the function of lncRNA HEGBC in gallbladder cancer progression, especially in the response to chemical carcinogens.

overall_design: To reveal the biological function of lncRNA HEGBC in gallbladder cancer, we overexpressed lncRNA HEGBC in GBC-SD cells by overexpression plasmid.

first: Zhiyuan

last: Fan


title: Activin A marks a novel progenitor cell population during fracture healing and reveals a therapeutic strategy

status: Public on Jan 11 2024

city: Shenyang

first: Lutian

last: Yao

address: 155 Nanjing st

department: Department of Orthopedic

institute: the First Affiliated Hospital of China Medical University

summary: Bone fraction healing is effective in most individuals, but can be subpar and not easily treatable in patients such as the elderly, requiring new remedies. Here we tested whether activin A promotes fracture repair, inspired by recent studies showing that the protein stimulates ectopic bone formation in other systems. Using a standard mouse tibia fracture model, we found that activin A became very abundant in the developing callus soon after fracture. Single cell RNA-seq and immunostaining showed that initially, expression of the activin A-encoding gene Inhba characterized inflammatory cells and periosteal mesenchymal lineage cells. Over time, Inhba expression became prominent in a unique, highly-proliferative progenitor cell (PPC) population that displayed a myofibroblast character and was at the center of a developmental trajectory bifurcation toward cartilage and bone cells in callus. Systemic administration of a neutralizing activin A monoclonal antibody delayed fracture healing, whereas local implantation of recombinant activin A enhanced it. Cells engaged in healing produced phosphorylated SMAD2 through which activin A normally signals intracellularly, and were also positive for aSMA, a recognized marker of myofibroblasts. In vitro gain- and loss-of-function assays showed that activin A directly stimulated chondrogenesis, osteogenesis and myofibroblast differentiation in periosteal progenitors. Our study reveals that activin A is a positive regulator of fracture repair and may represent a new therapeutic tool to enhance it. Its action involves a prominent and transient PPC population with a myofibroblastic character that would rapidly gear up to bring about repair in a timely and effective manner.

overall_design: mesenchymal cell atlas during fracture healing process

first: Ling

last: Qin

first: Maurizio

last: Pacifici


title: KDM3A and KDM3B maintain naïve pluripotency through regulation of alternative splicing

status: Public on Jan 14 2024

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Wisconsin Institute for Discovery

institute: University of Wisconsin

summary: Histone modifying enzymes play a central role in maintaining cell identity by establishing a conducive chromatin environment for lineage specific transcription factor activity. Pluripotent embryonic stem cells (ESCs) identity is characterized by lower abundance of gene repression associated histone modifications that enables rapid response to differentiation cues. The KDM3 histone demethylase family remove the repressive histone H3 lysine 9 dimethylation (H3K9me2). Here we uncover a surprising role for the KDM3 proteins in the maintenance of the pluripotent state through post-transcriptional regulation. We find through immunoaffinity purification of the KDM3A or KDM3B interactome and proximity ligation assays that KDM3A and KDM3B interact with the RNA processing factors such as EFTUD2 and PRMT5. By generating double “degron” ESCs to degrade KDM3A and KDM3B in the rapid timescale of splicing, we find altered splicing independent of H3K9me2 status. These splicing changes partially resemble the splicing pattern of the more blastocyst like ground state of pluripotency and occurred in important chromatin and transcription factors such as Dnmt3b, Tbx3 and Tcf12. Our findings reveal non-canonical roles of histone modifying enzymes in splicing to regulate cell identity. Cells were plated, allowed to adhere overnight, then treated for four hours with dTAG-13.

overall_design: Gene expression analysis of mouse ESCs (WT or KDM3A/KDM3B degron ESCs +/- dTAG-13 at four hours of degradation. Three biological replicates per condition.

first: Caleb

last: Dillingham

first: Harshini

last: Cormaty

first: Ellen

last: Morgan

first: Andrew

last: Tak

first: Dakarai

last: Esgdaille

first: Paul

last: Boutz


title: Activation of XBP1s attenuates disease severity in models of proteotoxic Charcot-Marie-Tooth type 1B

status: Public on Jan 15 2024

first: John

last: Svaren

address: 1500 Highland Ave.

department: Comparative Biosciences

summary: Mutations in myelin protein zero (MPZ) are generally associated with Charcot-Marie-Tooth type 1B (CMT1B) disease, one of the most common forms of demyelinating neuropathy. Pathogenesis of some MPZ mutants, such as S63del and R98C, involves protein misfolding and retention in the endoplasmic reticulum (ER) of myelinating Schwann cells. To cope with proteotoxic ER-stress, Schwann cells mount an unfolded protein response (UPR) characterized by activation of the PERK, ATF6 and IRE1/XBP1 pathways. Previous studies have reported that targeting PERK pathway can mitigate the neuropathy in CMT1B mice. To unravel the role of the XBP1 pathway in normal myelination and in CMT1B, we generated mouse models of in which XBP1 is deleted specifically in Schwann cells.  We observed that whereas XBP1 is dispensable for normal developmental myelination, myelin maintenance and remyelination after injury, the absence of XBP1 dramatically worsens the hypomyelination and the electrophysiological and locomotor parameters in young and adult CMT1B neuropathic animals. RNAseq analysis suggested that XBP1 exerts its adaptive function in large part via the induction of genes involved in misfolded protein degradation. Accordingly, the exacerbation of the neuropathy was accompanied by upregulation of ER-stress pathways and of IRE1-mediated RIDD signaling, suggesting that the activation of XBP1 plays a critical role in limiting mutant proteins toxicity, which cannot be compensated by other stress responses. Schwann cell specific overexpression of spliced XBP1 partially re-established Schwann cell proteostasis and attenuated CMT1B severity in vivo in both the S63del and R98C mouse models. In addition, the pharmacologic selective activation of XBP1 signaling ameliorated myelination in S63del dorsal root ganglia explants.

overall_design: RNA-seq of mouse sciatic nerve samples, with 4 biological replicates per genotype.

first: Touvier

last: Thierry

first: Claessens

last: Anke

first: Duong

last: Phu

first: Svaren

last: John

first: D'Antonio

last: Maurizio


title: Single-cell analysis of murine pancreatic ductal adenocarcinoma cells reveals the transcriptional dynamics of pancreatic cancer progression..

first: David

middle: A.

last: Tuveson

state: NY

address: 1 Bungtown Rd.

department: Cancer Center

summary: This study used 10X Genomics, single-cell RNA-sequencing to examine the differentiation states of cancer cells present in tumors derived from the KrasLSL-G12D; Trp53LSL-R172H; Pdx1-Cre (KPC) mouse model of pancreatic ductal adenocarcinoma. The study analyzed tumors from 8 different mice.

overall_design: Single-cell RNA-sequencing analysis (10X Genomics and Illumina sequencing) of cancer cells isolated from 8 KPC tumors.

first: Claudia

last: Tonelli

first: Yuan

last: Hao

first: Jonathan

last: Preall


title: Histone deacetylase inhibition sensitizes TP53-mutated B-cell precursor acute lymphoblastic leukemia to chemotherapy

status: Public on Jan 10 2024

city: Utrecht

first: Frank

middle: van

last: Leeuwen

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

summary: To determine how histone deacetylation inhibition synergizes with cytarabine, we performed RNA sequencing investigating which genes are affected in response to romidepsin, cytarabine or the combination

overall_design: Nalm6 and RCH-ACV cells were either left untreated or treated for 16 h 2 nM romidepsin, 200 nM Cytarabine or a combination of both drugs, after which mRNA is isolated and transcriptome analyzed

first: Willem

last: Cox

first: Laurens

last: van der Meer

middle: N

last: van Leeuwen


title: Identificatinon of differentially expressed genes in Docetaxel-resistant cell lines PC3 and DU145 after combination treatment with RU486 and docetaxel

status: Public on Dec 31 2023

city: Mainz

first: Maximilian

middle: Peter

last: Brandt

state: Rheinland Palatine

address: Langenbeckstrasse 1

department: Urology and Pediatric Urology

country: Germany

institute: University Medical Center Mainz

summary: Upregulation of the glucocorticoid receptor (GR) has been identified as a possible bypass mechanism in CRPC. Recently, it has been demonstrated that the combination of docetaxel with mifepristone (D+M), an inhibitor of the GR, reinduces sensitivity to docetaxel in docetaxel resistant cell models. This study was designed to uncover and characterize molecular mechanisms responsible for this observation.

overall_design: We performed RNA-Seq with 2 docetaxel resistant (DR) cell lines PC3-DR and DU145-DR and treatment with DSMO, RU486 a glucocorticoid receptor inhibitor, docetaxel and the combination of RU486 plus docetaxel.

first: Holger

last: Erb

first: Hubert

last: Hackl

first: Tamas

last: Daher

first: Katrin

last: Tagscherer

first: Wilfried

last: Roth

first: Christian

last: Thomas

first: Axel

last: Haferkamp

first: Eva

last: Jüngel

first: Martin

last: Puhr


title: Pioneer transcription factors coordinate active and repressive gene expression states to regulate cell fate [RNA-seq]

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: Pioneer transcription factors (TFs) regulate cell fate by establishing transcriptionally primed and active states. However, cell fate control requires the coordination of both lineage-specific gene activation and repression of alternative lineage programs, a process that is poorly understood. Here, we demonstrate that the pioneer TF Forkhead box A (FOXA), required for endoderm lineage commitment, coordinates with the PR domain zinc finger 1 (PRDM1) TF to recruit Polycomb repressive complexes, which establish bivalent enhancers and repress alternative lineage programs. Similarly, the pioneer TF OCT4 coordinates with PRDM14 to repress cell differentiation programs in pluripotent stem cells, suggesting this is a common feature of pioneer TFs. We propose that pioneer and PRDM TFs coordinate recruitment of Polycomb complexes to safeguard cell fate.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human PSCs, endoderm, mesoderm, and neuroectoderm and their KD derivatives (FOXA-TKD, PRDM1-KD, and OCT4-KD)

first: Satoshi

last: Matsui

first: Marissa

last: Granitto

first: Morgan

last: Buckley

first: Joseph

last: Shiley

first: William

last: Zacharias

first: Christopher

last: Mayhew

first: Makiko

last: Iwafuchi


title: Pioneer transcription factors coordinate active and repressive gene expression states to regulate cell fate [CUT&Run and ChIP-seq]

overall_design: ChIP-seq or CUT&RUN for transcription factors, PRC components, and histone modifications in human PSCs, definitive endoderm, foregut cells, and their KD derivatives (FOXA-TKD and OCT4-KD) .


title: Genome scale analysis of DNA methylation patterns in prostate cancer patient derived xenograft models

city: Seattle

first: Brian

last: Hanratty

state: WA

address: 1100 Fairview Avenue

department: Division of Human Biology

institute: Fred Hutchinson Cancer Cancer


title: Genome scale analysis of DNA methylation patterns in prostate cancer patient derived xenograft models [EPIC Set 1]

summary:
DNA methylation alterations are a universal feature of cancer. In prostate cancer, site specific DNA methylation changes have been suggested as driver in disease initial and progression. Here we provide a comprehensive assessment of DNA methylation changes in prostate cancer patient derived xenograft (PDX) models. We delineate patterns of both site specific and global methylation changes and nominate novel candidates for biomarker development.
Genome wide DNA methylation profiling of prostate cancer patient derived xenograft and cell line models using Infinium EPIC arrays

overall_design: Bisulphite converted DNA from 62 samples were hybridised to the Illumina EPIC methylation arrays

first: Mohamed

last: Adil

first: Michael

last: Haffner


title: Genome scale analysis of DNA methylation patterns in prostate cancer patient derived xenograft models [EPIC Set 2]


title: DNA methylation alterations in prostate cancer patient derived xenograft models revealed by whole genome bisulfite sequencing

summary: DNA methylation alterations are a universal feature of cancer. In prostate cancer, site specific DNA methylation changes have been suggested as driver in disease initial and progression. Here we provide a comprehensive assessment of DNA methylation changes in prostate cancer patient derived xenograft (PDX) models. We delineate patterns of both site specific and global methylation changes and nominate novel candidates for biomarker development.

overall_design: Whole genome bisulfite sequencing of PDX samples

first: Hanratty

last: Brian

first: Adil

last: Mohamed

first: Haffner

last: Michael C


title: AP-2β activates enhancers that define mammary hormone sensing cell identity

city: ADELAIDE UNIVERSITY

first: Geraldine

last: Laven-Law

state: South Australia

address: Adelaide Health & Med Sci Bldg, Corner George St & North Terrace

institute: The University of Adelaide

overall_design:
Refer to individual Series

The data included in this SuperSeries are duplicated in SuperSeries GSE176010.


title: cis-RSV and trans-RSV have differential effects on gene transcription in human embryonic stem cells derived neurons

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

summary: To investigate the differential effects of cis-RSV and trans-RSV on gene transcription in neurons, human embryonic stem cells (hESC) - derived neurons were examined after 24 hour treatment using 50μM of each.

overall_design: We performed RNA-sequencing analysis using data obtained from DIV 49

first: Megha

last: Jhanji

first: Janay

last: Vacharasin

first: Ji

last: Hao


title: Transcriptomic responses to SEL1L-HRD1 ERAD deficiency in HEK293T cells and mouse brown adipose tissue

status: Public on Dec 17 2023

first: You

last: Lu

state: MI

address: 210 Washtenaw Avenue

department: Life Sciences Institute

summary: The mamallian SEL1L-HRD1 endoplasmic reticulum-associated degradation (ERAD) complex is essential for retrotranslocation and degradatin of misfolded proteins in the ER. HRD1 is an E3-ligase with multiple transmembrane domains that consititute the retrotranslocation channel, while its cofactor SEL1L is responsible for the stability of the complex and for substrate recruitment. This study aims to identify transcriptionally-regulated genes responding to SEL1L-HRD1 ERAD deficiency in two different mammalian cell types.

overall_design: Transcript abundance in wildtype, SEL1L and HRD1 (SYVN1) knockout HEK293T cells generated using CRISPR-Cas9 technology and in brown adipose tissue (BAT) from 12-week-old wildtype, Sel1l flox/flox;Ucp1-Cre and Syvn1 flox/flox;Ucp1-Cre C57BL/6J mice measured by RNA-seq.

first: Xiaoqiong

last: Wei

first: Siwen

last: Wang

first: Xinxin

last: Chen

first: Ling

last: Qi


title: Mutant NLRP3 causing Cryopyrin-Associated Periodic Syndromes forms a constitutively active inflammasome and results in alteration in monocyte immunometabolism to limit IL-1β production

status: Public on Dec 13 2023

city: Murcia

first: Pablo

middle: Pelegrin

last: Vivancos

state: Murcia

address: Av. Buenavista, 32

institute: IMIB-Arrixaca Pascual Parrilla

summary: Cryopyrin-associated periodic syndrome (CAPS) is an autoinflammatory condition resulting from monoallelic NLRP3 variants that exacerbate IL-1 production. Although these are gain-of-function variants, the exact regulatory mechanism of the NLRP3-inflammasome in CAPS is not yet well understood. Despite being considered a hypersensitive inflammasome triggered by cell priming, patients with CAPS and animal models of the disease may present inflammatory flares even in the absence of identifiable external triggers. Herein, we found that CAPS-associated variants result in constitutively active NLRP3-inflammasome, which induce an increased basal cleavage of gasdermin D, IL-18 release and pyroptosis, with a concurrent basal pro-inflammatory gene expression signature, including the induction of nuclear receptors 4A. The constitutively active NLRP3-inflammasome was blocked by MCC950 and was dependent on NLRP3 expression level, further regulated by deubiquitination. Additionally, we determined that the activation of the NF-B pathway with lipopolysaccharide or other endogenous molecules (palmitate, S100A9, IL-6) further modulated the activation of the NLRP3-inflammasome in CAPS, thus expanding the repertoire of molecules secreted from patients’ macrophages involved in disease pathogenesis. NLRP3-inflammasomes with CAPS-associated variants mainly affected the immunometabolism of the myeloid compartment, leading to disruptions in lipids and amino acid pathways and impaired glycolysis, limiting IL-1β production. These findings demonstrate that NLRP3 variants causing CAPS form a constitutively active inflammasome that induces basal pyroptosis and IL-18 release without cell priming, favouring the host's innate defense against pathogens while also tempering the onset of IL-1β–dependent inflammatory episodes through immunometabolism modulation.

overall_design: Nlrp3−/− immortalized macrophages (iMos) with a doxycyclyne inducible system were used.  iMos were treated for 16 h with or without doxycycline (1 µg/ml) to induce the expression of the human NLRP3 wild-type or  p.D303N variant, in the absence or presence of MCC950 (10 µM). Total RNA was extracted from Nlrp3−/− immortalized mouse macrophages expressing NLRP3 wild type or NLRP3 p.D303N using the RNeasy kit (74104, Qiagen) following manufacturer instructions. Upon extraction, total RNA was quantified with Qubit RNA BR Assay (Invitrogen), and RNA integrity was analysed with TapeStation 4200 (Agilent Technologies). All samples showed RIN >8. cDNA synthesis and library generation were performed using Stranded mRNA Prep Kit (Illumina) following the manufacturer’s instructions.RNA-seq libraries were sequenced using Paired-End 200 bases (PE200) sequencing chemistry on NextSeq 2000 Sequencing Systems (Illumina).

first: Cristina

last: Molina-López

first: Laura

last: Hurtado-Navarro

first: Carlos

middle: J

last: García

first: Diego

last: Angosto-Bazarra

first: Fernando

last: Vallejo

first: Ana

last: Tapia-Abellán

first: Marques-Soares

last: Joana

first: Carmen

last: Vargas

first: Segundo

last: Bujan-Rivas

first: Francisco

last: Tomás-Barberán

first: Juan

middle: I

last: Arostegui

last: Pelegrín


title: Single-cell gene expression profiles of mouse macrophages stimulated with immune ligands.

status: Public on Dec 12 2023

city: Los Angeles

first: Katherine

middle: M

last: Sheu

address: 611 Charles E Young Dr E

institute: UCLA

summary: Immune sentinel macrophages initiate responses to pathogens via hundreds of immune response genes. Each immune threat demands a tailored response, suggesting that the capacity for stimulus-specific gene expression is a key functional hallmark of healthy macrophages. To quantify this property, termed Response Specificity, we developed a single-cell experimental workflow and analytical approaches based on information theory and machine learning. We found that Response Specificity of macrophages is driven by combinations of specific immune genes that show low cell-to-cell heterogeneity and are targets of separate signaling pathways. The Response Specificity Profile, a systematic comparison of multiple stimulus response distributions, was distinctly altered by polarizing cytokines and enabled an assessment of the functional state of macrophages. Indeed, the Response Specificity Profile of peritoneal macrophages from old and obese mice showed characteristic differences, suggesting that Response Specificity may be a basis for measuring the functional state of innate immune cells.

overall_design: Macrophages were collected from the mouse peritoneum or differentiated from myeloid progenitors, and stimulated with a panel of immune ligands for 3hrs. Cells were collected into suspension and scRNAseq was performed using the BD Rhapsody platform.

first: Alexander

last: Hoffmann