title: The role of 7-dehydrocholesterol in inducing ER stress and apoptosis of head and neck squamous cell carcinoma

city: Suwon-si

first: Ji-Hye

last: Choi

state: Gyeonggi-do

address: World cup-ro

institute: Ajou university

summary: Alterations of metabolic pathways that sustain cancer cell survival often offer promising therapeutic avenues. Here, we show that enhanced de novo cholesterol biosynthesis is crucial for the survival of head and neck squamous cell carcinoma (HNSCC). Transcriptomic analysis of HNSCC tissues identified profound dysregulation in steroid and cholesterol metabolism compared to normal tissues. Inhibition of two key enzymes, DHCR7 and DHCR24, which mediate cholesterol biosynthesis, induced apoptosis in HNSCC cells, even when cholesterol levels were restored. Metabolomic profiling revealed the accumulation of 7-dehydrocholesterol (7-DHC) upon DHCR7 or DHCR24 inhibition, triggering endoplasmic reticulum (ER) stress and promoting further cell death. These findings suggest that HNSCC cells adapt to ER stress by modulating 7-DHC levels through enhancing DHCR7 and DHCR24 levels, highlighting a metabolic vulnerability in HNSCC and demonstrating a direct link between cholesterol metabolism and ER stress in cancer cell viability.

overall_design: Transcriptome profiling of tumor and non-tumor pairs from 16 HNSCC patients

first: Bok-Soon

last: Lee

first: Chul-Ho

last: Kim

first: Jiyoung


title: Proteogenomic characterization reveals that lipid droplet formation promotes esophageal squamous cell cancer progression

status: Public on Apr 02 2025

city: Shanghai

first: Zihan

last: Yu

address: 130 Dongan road, Xuhui district, shanghai

country: China

institute: Fudan University

type: Expression profiling by high throughput sequencing

summary: This study aims to uncover the transcriptomic variations in ESCC. Our study provides a resource to explore the relationships between genetic variation and transcriptional or translational regulations.

overall_design: mRNA profiles of 50 ESCC patient's tumors and 52 normal tissues


title: Comprehensive Gene Expression and Epigenetic Profiling of Human Mast Cells: Effects of Butyrate Treatment

status: Public on Apr 01 2025

city: Palo Alto

first: Jelle

last: Folkerts

state: CA

address: 1291 Welch Road

department: Center for Clinical Sciences Research

country: USA

institute: Stanford University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This study delves into gene expression and epigenetic modifications in human peripheral blood mononuclear cell-derived mast cells (PBCMCs) with a focus on the effects of butyrate treatment. PBCMCs were generated from CD34+ precursor cells isolated from healthy donors, cultured under serum-free conditions, and tested for maturity. RNA-Seq analysis was conducted to assess differentially expressed genes post-butyrate treatment, revealing significant transcriptional changes. Chromatin Immunoprecipitation Sequencing (ChIP-Seq) was used to explore histone modifications, focusing on H3K27Ac and H3K4Me2 marks.

overall_design: Mature human mast cells were treated with 5 mM butyrate or vehicle for 1, 3, 12 or 24 hours. RNA-Seq was performed to assess differentially expressed genes via Illumina HiSeq 4000, with reads aligned using HISAT, quantified and normalized through HOMER, and differential expression analyzed using DESeq2, followed by pathway enrichment analysis with Metascape. Chromatin Immunoprecipitation Sequencing (ChIP-Seq) was conducted on crosslinked and sonicated chromatin using H3K27Ac and H3K4Me2 antibodies, with sequencing on Illumina HiSeq2500. Data processing involved alignment with HISAT2, peak identification using HOMER, and differential enrichment analysis using DESeq2.

first: Ralph

last: Stadhouders

first: Rudi W

last: Hendriks


title: Therapeutic Potential of NRF2 activating drug RTA-408 in suppressing T-cell effector responses and inflammatory bowel disease

city: Kansas City

first: Kalyani

last: Pyaram

state: KS

address: 2060 W 39th Ave

institute: University of Kansas Medical Center

summary: Targeting T-cells has emerged as a promising therapeutic strategy for treating inflammatory diseases. Triterpenoids, classified as antioxidant inflammatory modulator (AIM) compounds, are known to influence immune cell functions. RTA-408 is an AIM drug that was approved last year for the treatment of neurological disorders. In this study, we demonstrate the anti-inflammatory effects of RTA-408, on both mouse and human T-cells. At picomolar concentrations, RTA-408 robustly induces NRF2 activation in T-cells and reduces T-cell activation, proliferation, and cytokine functions. In in vitro activated CD4 and CD8 T-cells isolated from mice and human blood, we observed a significant decrease in proliferation, and expression of inflammatory cytokine IFN-γ, and cytotoxic granules (perforin and granzyme B). Mechanistically, treatment with RTA-408 significantly suppressed glycolysis and mitochondrial respiration in human T-cells, while increasing the expression of pentose phosphate pathway genes, such as transketolase (TKT) and transaldolase (TALDO). These findings suggest that RTA-408 modulates T-cell metabolism. Furthermore, treatment of circulating T-cells from inflammatory bowel disease (IBD) patients with RTA-408 caused a reduction in expansion and the expression of the inflammatory cytokine IL-17. Our results highlight the therapeutic potential of RTA-408 in treating chronic inflammatory conditions like IBD by modulating T-cell activity.

overall_design: Human T-cells were activated in vitro in presence of anti-CD3 and anti-CD28 to mimic T-cell activation with 0 and 100pM of RTA-408 (MedChemExpress). After 72 hours, total RNA was extracted using RNeasy Plus Micro kit (Qiagen) and processed at the Genomics Core Facility at the University of Kansas Medical Center. 100ng of the RNA was used to perform Agilent TapeStation QC analysis to verify RNA integrity and generate RNA Integrity number (RIN). Using Nova-Seq 6000 S1 200 cycle reagent kit, 25 million pair-ended reads were recorded for construction of mRNA libraries. For bioinformatic analysis, following quality check through fastQC data were aligned to human reference genome using RSEM (RNA-Seq by Expectation Maximization) resulting in the generation of gene count matrix. Further differential expression analysis was performed between untreated human T-cells and 100pM RTA-408 treated human T-cells for gene ontology (GO) enrichment using ClusterProfiler R-package, to identify significant biological processes, molecular pathways and metabolic pathways associated with the samples. The enrichment results were prioritized based on significance and the top GO terms were visualized using dotplots. Box-plots for genes were also generated using ggplot2 to illustrate the variability of the genes between the 2 groups with mean P-values annotated on each plot, respectively.

first: Debolina

last: Dasgupta

first: Aprajita

last: Tripathi

first: Rachel

last: Griffard-Smith

first: Nandakumar

last: Yellapu


title: MicroRNA mechanisms instructing Purkinje cell specification

city: San Diego

first: Norjin

last: Zolboot

address: 10550 North Torrey Pines Rd, DNC-222

department: Neuroscience

institute: The Scripps Research Institute

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

overall_design: Refer to individual Series


title: Gene expression profile of healthy control organoids, a Parkinson disease patient specific midbrain organoid carrying a triplication in the SNCA gene and two healthy control organoids co-cultured with either healthy or PD hindbrain organoids

city: Belval

first: Gemma

last: Gomez Giro

address: 6, Avenue du Swing

country: Luxembourg

institute: Luxembourg Centre for Systems Biomedicine

summary: Single nuclei RNAseq was used to characterize the cell diversity in healthy control hindbrain organoids, as well as in PD  midbrain organoids. Sequencing of healthy midbrain organoids after co-culture with either healthy or PD hinbrain organoids was used to compare the influence of the healthy versus the disease hindbrain context to the healthy midbrain model.

overall_design: Individual organoids were cultured for 2-months. Assembloids were established at age of 1-month and co-cultured for 1 additional month, reaching 2-months of age. After which midbrain orgaonids were separated again. All samples were snap-frozen. Nuclei were extracted, FACS sorted and processed for sequencing.

last: Gomez-Giro

first: Jens

last: Schwamborn


title: Profiling the RNA m6A changes after Gamma ray radiation exposure with MeRIP-seq

city: Beijing

first: Yiming

last: Lu

address: Taiping Road

institute: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine

overall_design: MeRIP-seq using RNA m6A antibody in HeLa cells with or without Gamma ray radiation

first: Hongxia

last: Chen

first: Gangqiao

last: Zhou


title: Neurodevelopmental hijacking of oligodendrocyte lineage programs drives glioblastoma infiltration [snRNAseq]

city: Toronto

first: Federico

last: Gaiti

state: Ontario

address: 101 college street

country: Canada

institute: Princess Margaret Cancer Centre

summary: Glioblastoma cells infiltrate and incorporate into the normal brain parenchyma. We conduct unbiased multimodal single-cell and spatial sequencing to capture GBM cells and the surrounding tumor microenvironment using a regional sampling strategy. For each patient, we profile the peritumoral region, tumor edge, and tumor core, providing a comprehensive characterization of the transcriptional and epigenetic landscape of GBM spatial heterogeneity, with a specific focus on infiltrative cells.

overall_design:
Regionally sampled GBM patient tissue was dissociated and nuclei were processed unsorted or by sorting with 7AAD to remove debris and dead cells.

***************************************************************
fastq files submitted to EGA due to patient privacy
***************************************************************

first: Yiyan

last: Wu


title: Lichenoid chronic graft-versus-host skin displays high interferon score with promising effect of IFNAR1 inhibitor on local inflammation

city: Paris

first: Thomas

last: Poisot

address: 1 Avenue Claude Vellefaux

country: France

institute: INSERM

summary: Chronic cutaneous graft-versus-host disease (ccGVHD) is a debilitating complication of allogeneic haematopoietic stem cell transplantation, presenting as sclerotic or lichenoid (lGVHD) lesions. Although frequent, the pathogenesis of lGVHD remains mainly unknown.   This study aimed to decipher the immunological mechanisms mediating the lichenoid reaction in lGVHD skin. To this end, we performed single-cell RNA-sequencing (scRNA-seq) on lGVHD (n=3) compared with healthy control (HC, n=4) skins and analyzed the distribution and inflammatory signatures of immune cells.

overall_design: Single-cell RNA-sequencing on lichenoid GVHD and healthy control skins

first: Chloé

last: Grolleau

first: Andreea

last: Calugareanu

first: Regis

last: Peffault De Latour

first: Marie

last: Robin

first: David

last: Michonneau

first: Thibault

last: Mahevas

first: Adèle

last: De Masson

first: Maxime

last: Battistella

first: Gerard

last: Socié

first: Hélène

last: Le Buanec

first: Jean-David

last: Bouaziz


title: Cellular and Molecular Characteristics of Drug Resistance in AML cells Unveiled by Multi-Omics Analysis

city: Guangzhou

first: Xinghua

last: Pan

state: Guangdong

address: Shatai South Road

department: Department of Biochemistry and Molecular Biology

institute: Southern Medical University

type: Methylation profiling by genome tiling array

summary: Acute myeloid leukemia (AML) exhibits a spectrum of responses to chemotherapy, with drug resistance being a significant clinical challenge. This study employs a multi-omics approach, particularly multiplexed single-cell RNA sequencing (scRNA-seq), to characterize the molecular mechanisms underlying drug resistance in AML cells. We identified significant cellular heterogeneity and a dynamic transcriptomic trajectory in AML cells with specific drug treatment, and discovered a reprogramming towards a more stem-like state. Interestingly, Ara-C-resistant KG-1a cells predominantly originated from G2/M subpopulations, indicating a cell cycle-specific resistance mechanism. Our analysis also revealed that epigenetic changes of DNA methylation and chromatin architechture, and altered transcription factor activities were implicated in rapid Ara-C resistance, whereas exomic mutations did not significantly contribute to it. We suggest both intrinsic and acquired resistance mechanisms act together and build a resultant force that aids AML cells in evading therapeutic interventions. The multidimensional changes observed post-treatment showed a complex interplay in the development of drug resistance. This study provides a cellular and molecular portrait of drug response and resistance in AML, offering potential therapeutic targets and a foundation for future research aimed at overcoming chemoresistance.

overall_design: The Illumina Infinium Human Methylation EPIC (850 K) BeadChip array (Illumina, San Diego, CA, USA) was performed by Novogene Co., Ltd (Beijing, China), following the manufacturer’s instructions. The assay determines DNA methylation levels at >850,000 CpG sites and provides coverage of CpG islands, RefSeq genes, ENCODE open chromatin, ENCODE transcription factor-binding sites, and FANTOM5 enhancers. To increase credibility, two samples (naive and Ara-C resistant KG-1a) were arrayed in each group.

first: Yulong

last: Zhang


title: VEXAS syndrome, myelodysplasia cutis and sweet syndrome skin lesions share a common transcriptomic profile led by interferon signaling

address: 1 avenue Claude Vellefaux

department: Hopital saint Louis

institute: INSERM U1342, eq 16

summary: VEXAS syndrome (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) is a recently described monogenic disease of adult men cause by somatic mutations in UBA1 in hematopoietic progenitor cells. It associates inflammatory-related symptoms, frequently involving the skin, and hematologic disorders. Myelodysplasia cutis, also recently described, is a cutaneous manifestation of myelodysplasia in which clonal myeloid cells infiltrate the skin. In both cases, skin lesions are due to the infiltration of clonal mutated myeloid cells and may clinically and histologically resemble sweet syndrome, a non-clonal neutrophilic skin disease. The aim of this study was to decipher the underlying mechanisms driving these three myeloid-related skin diseases using RNA-sequencing compared with healthy control skins and leukemia cutis, a neoplastic myeloid-related skin condition.

overall_design: Bulk RNA-sequencing was performed on formaldehyde-fixed paraffine-embeded skins biopsies of VEXAS syndrome, myelodysplasia cutis, idiopathic sweet syndrome and leukemia cutis lesions compared with healthy control skins.

first: François

last: Chasset


title: Therapeutic targeting of the NOTCH1 and neddylation pathways in T cell acute lymphoblastic leukemia

city: New York

first: Teresa

last: Palomero

state: New York

address: 1130 St Nicholas Ave Rm 607

institute: Institute for Cancer Genetics -Columbia University

summary:
Gamma Secretase Inhibitors (GSIs) effectively block the activation of oncogenic protein Notch homolog-1 (NOTCH1), a frequent event in T-cell Acute Lymphoblastic Leukemia (T-ALL). However, their clinical application is hampered by severe gastrointestinal toxicity due to the inhibition of NOTCH1 signaling and subsequent increase in goblet cell differentiation in the gut. Genome-wide CRISPR loss-of-function (LOF) screen in the colon cancer cell line LS174T identified the neddylation pathway as a main regulator of goblet cell differentiation upon NOTCH1 inhibition. Consistently, genetic deletion or pharmacologic inhibition of the neddylation pathway with the small molecule inhibitor MLN4924 rescued GSI-induced differentiation and cell death in LS174T cells. Mechanistically, neddylation inhibition by MLN4924 increases the protein stability of Hairy and enhancer of split-1 (HES1), a known NOTCH1 target and a regulator of absorptive and secretory cell fate decisions. Combined treatment with GSI and MLN4924 in murine Notch1-induced model of T-ALL showed leukemia regression and improved overall survival without any associated gut toxicity. Overall, these results substantiate the potential of targeting NOTCH1 and neddylation pathway in the treatment of NOTCH1-induced T-ALL.
To elucidate the mechanisms mediating LS174T (adenocarcinoma cell line) differentiation upon NOTCH inhibition, we performed gene expression profiling in LS174T cells treated with vehicle (DMSO) or GSI (CompE) (250 nm) for 48 hours

overall_design: We extracted RNA from triplicate cultures of LS174T cells treated for 48 h with vehicle (DMSO) or CompE (250 nM) using RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s protocol. RNA of each sample was amplified and labeled using the 3’ IVT Express Kit (Affymetrix) and hybridized on Affymetrix Human U133 Plus 2.0 arrays according to the manufacturer’s protocol as previously described (Real PJ et al., 2009). We normalized inter array intensity differences using the Dchip 36 package and selected for analysis the 10,896 probes with the least variation among experimental replicas.

first: Kalay

last: Bertulfo

first: Pablo

last: Perez Duran

first: Hannah

middle: I

last: Miller

first: Cindy

last: Ma

first: Alberto

last: Ambesi-Impiombato

first: Jeremy

last: Samon

first: Adam

middle: L

last: Mackey

first: Adolfo

middle: A

last: Ferrando


title: Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons

city: St. Louis

first: Lite

last: Yang

state: MO

address: 4922 Parkview Place

institute: Washington University in St. Louis

summary: Single-cell multiomic techniques have sparked immense interest in developing a comprehensive multi-modal map of diverse neuronal cell types and their brain-wide projections. However, investigating the complex wiring diagram, spatial organization, transcriptional, and epigenetic landscapes of brain-wide projection neurons is hampered by the lack of efficient and easily adoptable tools. Here we introduce Projection-TAGs, a retrograde AAV platform that allows multiplex tagging of projection neurons using RNA barcodes. By using Projection-TAGs, we performed multiplex projection tracing of the mouse cortex and high-throughput single-cell profiling of the transcriptional and epigenetic landscapes of the cortical projection neurons. Projection-TAGs can be leveraged to obtain a snapshot of activity-dependent recruitment of distinct projection neurons and their molecular features in the context of a specific stimulus. Given its flexibility, usability, and compatibility, we envision that Projection-TAGs can be readily applied to build a comprehensive multi-modal map of brain neuronal cell types and their projections.

overall_design: Projection neurons in the mouse cortex are labeled with Projection-TAGs. Nuclei are extracted and isolated using FACS based on 7-AAD (all nuclei) or 7-AAD and GFP (Projection-TAG+ nuclei). Sorted nuclei are then sequenced using 10X Genomics Chromium Single Cell Gene Expression 3’ V3.1 Assay or 10X Genomics Chromium Single Cell Multiome Assay.

first: Fang

last: Liu

last: Hahm

first: Takao

last: Okuda

first: Xiaoyue

last: Li

first: Yufen

first: Vani

last: Kalyanaraman

first: Monique

middle: R

last: Heitmeier

first: Vijay

middle: K

last: Samineni


first: Teresa

last: Palomero

summary:
Gamma Secretase Inhibitors (GSIs) effectively block the activation of oncogenic protein Notch homolog-1 (NOTCH1), a frequent event in T-cell Acute Lymphoblastic Leukemia (T-ALL). However, their clinical application is hampered by severe gastrointestinal toxicity due to the inhibition of NOTCH1 signaling and subsequent increase in goblet cell differentiation in the gut. Genome-wide CRISPR loss-of-function (LOF) screen in the colon cancer cell line LS174T identified the neddylation pathway as a main regulator of goblet cell differentiation upon NOTCH1 inhibition. Consistently, genetic deletion or pharmacologic inhibition of the neddylation pathway with the small molecule inhibitor MLN4924 rescued GSI-induced differentiation and cell death in LS174T cells. Mechanistically, neddylation inhibition by MLN4924 increases the protein stability of Hairy and enhancer of split-1 (HES1), a known NOTCH1 target and a regulator of absorptive and secretory cell fate decisions. Combined treatment with GSI and MLN4924 in murine Notch1-induced model of T-ALL showed leukemia regression and improved overall survival without any associated gut toxicity. Overall, these results substantiate the potential of targeting NOTCH1 and neddylation pathway in the treatment of NOTCH1-induced T-ALL.
We used microarray to profile the gene expression in mouse intestinal stem cells upon NOTCH1 inhibition through GSI (DBZ treatment). This will allow us to explore the mechanisms of NOTCH1 inhibition in intestinal cell fate in vivo.

overall_design: We collected mouse intestinal stem cells by sorting GFPhigh cells from Lgr5-EGFP-IRES-creERT2 mice treated with vehicle (DMSO) or DBZ (30 mol kg-1) for 24 hours for RNA extraction and hybridization to Affymetrix arrays (n=3 per treatment). Gene expression profiling was analyzed to identify gene expression signatures inhibition of NOTCH1 by gamma secretase inhibitor (DBZ) in mouse intestine.


title: Neurodevelopmental hijacking of oligodendrocyte lineage programs drives glioblastoma infiltration [scMultiome]

first: Federico

last: Gaiti

overall_design:
Regionally sampled GBM patient tissue were dissociated and nuclei were processed unsorted or by sorting with 7AAD to remove debris and dead cells.

***************************************************************
fastq files submitted to EGA due to patient privacy
***************************************************************

first: Yiyan

last: Wu


title: Comparing DNA binding specificities between orthologous Pho4 transcription factors using extended length probes that include flanking genomic sequences.

city: Iowa City

first: Bin

last: He

email: emptyhb@gmail.com, bin-he@uiowa.edu

state: IA

address: 129 East Jefferson St., Biology Building 450

department: Biology

institute: the University of Iowa

summary: Combinatorial control by multiple transcription factors (TFs) is a hallmark of eukaryotic gene regulation. Despite its prevalence and crucial roles in enhancing specificity and integrating information, the mechanisms behind why eukaryotic TFs depend on one another, and whether such interdependence evolves, are not well understood. We exploit natural variation in co-TF dependence in the yeast phosphate starvation (PHO) response to address this question. In the model yeast Saccharomyces cerevisiae, the main TF, Pho4, relies on the co-TF Pho2 to regulate ~28 genes. In a related yeast pathogen, Candida glabrata, its Pho4 exhibits significantly reduced Pho2 dependence and has an expanded target set of ~70 genes. Chomatin IP based motifs for the two orthologous Pho4s are highly similar, with no detectable difference in their core E-box motif. However, past studies found that preference for sequences flanking the core motif can provide additional specificities to TFs in the same family. To determine if ScPho4 and CgPho4 differ in their flanking nucleotide preference, we conducted the genomic context Protein Binding Microarray (gcPBM) using 36 bp oligos centered on E-box motifs from ChIP-identified Pho4 binding locations in both S. cerevisiae and C. glabrata genomes. The results confirmed that the two Pho4 orthologs do not show divergence in their sequence preference even after including the genomic context.

sample_organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

overall_design: Four protein binding microarray (PBM) experiments were performed for recombinant, full-length Pho4 transcription factors from S. cerevisiae and C. glabrata. Briefly, the PBMs  measured the binding of GST-tagged Pho4 from either species to double-stranded 60k Agilent microarrays at two different concentrations, for putative DNA binding sites in native genomic context. Each genomic DNA sequence represented on the array is present in 6 replicate spots. We report the PBM signal intensity of both Pho4 orthologs for each spot.

first: Zhang

last: Yuning

first: Snyder

last: Lindsey

first: Gordan

last: Raluca

first: He

last: Bin


title: Retrospective and multifactorial single-cell profiling reveals sequential chromatin reorganization during X inactivation

city: Utrecht

first: Jop

last: Kind

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: The regulation of gene expression is governed at multiple levels  of chromatin organization. How coordination between these levels is achieved remains relatively unexplored. Here we present Dam&ChIC, a method that experimentally combines scDamID and sortChIC to enable time-resolved and single-cell chromatin profiling at high resolution. Analysis of genome lamina associated domains (LADs) in haploid cells, reveals highly dynamic spatial repositioning of small LADs during interphase and partial inheritance over mitosis. When applied to study random X-inactivation Dam&ChIC reveals that spreading of H3K27me3 on the inactive X chromosome (Xi) overlaps with a remarkable detachment of the same domains from the nuclear lamina. We find that detachment precedes H3K27me3 accumulation on the Xi and occurs after the exit from mitosis. Domains that retain strong genome-lamina interactions are marked by high pre-existing H3K9me3 levels. These findings imply an important role for LADs in regulating H3K27me3 accumulation on the Xi. We anticipate that Dam&ChIC will be instrumental in unravelling interconnectivity and the order of chromatin events that underlie cell-state changes in single cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single cell Dam&ChIC was performed for combination of different Dam fusion proteins for DamID (Dam, Dam-LMNB1, Dam-ER, Dam-scFv-K27me3-ER) and antibodies for ChIC (IgG, Lamin B1, H3, H3K4me1, H3K4me3, H3K9me3, H3K27me3, H3K36me3) in haploid Kbm7 cells as well hybrid mESCs undergoing Vitamin C induced differentiation.


title: Topoisomerase 3b Facilitates piRNA Biogenesis to Promote Transposon Silencing and Germ Cell Development

city: Baltimore

first: Weidong

last: Wang

state: Maryland

address: 251 Bayview Blvd

institute: National Institute on Aging/NIH

type: Non-coding RNA profiling by high throughput sequencing

summary: Topoisomerases typically function in nucleus to relieve topological stress in DNA. Here we show that a dual-activity topoisomerase Top3b and its partner TDRD3 largely localize in cytoplasm, and interact biochemically and genetically with piRNA processing enzymes to promote piRNA biogenesis, post-transcriptional gene silencing (PTGS) of transposons, and Drosophila germ cell development. Top3b requires its topoisomerase activity to promote PTGS of a transposon reporter, and preferentially silences long and highly-expressed transposons, suggesting that RNAs with these features may produce more topological stress for topoisomerases to solve. The double mutants between Top3b and piRNA processing enzymes exhibit stronger disruption of the signatures and levels of germline piRNAs, more de-silenced transposons, and larger defects in germ cells, than either single mutant. Our data suggest that Top3b can act in an RNA-based process—piRNA biogenesis and PTGS of transposons; and this function is required for Top3b to promote normal germ cell function.

overall_design: Test if Top3b mutant exhibits de-silencing of transposons by genetic interaction with piRNA pathway mutants - aub, ago3, vas, armi, zuc. We performed RNA-seq and small RNA-seq to profile transposon level as compared to control.

first: Seung Kyu

last: Lee

first: Weiping

last: Shen

first: William

last: Wen

first: Yuyoung

last: Joo

first: Yutong

last: Xue

first: Aaron

last: Park

first: Amy

last: Qiang

first: Shuaikun

last: Su

first: Tianyi

last: Zhang

first: Megan

first: Jinshui

last: Fan

first: Yongqing

first: Supriyo

last: De

first: Ildar

last: Gainetdinov

first: Alexei

last: Sharov

first: Manolis

last: Maragkakis


title: Multimodal integration of transcriptomics, proteomics and radiomics improves prediction of recurrence in patients with IDH-mutant Glioma

city: Pessac

first: Andreas

last: Bikfalvi

address: Allée Geoffroy St-Hilaire

institute: University of Bordeaux

summary:
Isocitrate dehydrogenase mutant gliomas remain lethal brain cancers which impair quality of life in young adults. These tumors are molecularly and cellularly heterogeneous and have a wide range of survival prognoses. Consequently, the identification of pa
Here, we analyzed imaging, transcriptomic, and proteomic profiles using machine learning to 1) describe the biological characterization of subtypes of IDH-mutant gliomas categorized by PET and histology, 2) reinforce the integration of PET metrics in the

overall_design: Patient samples were collected during tumor resection and snap-frozen. RNAs were isolated from 59 patients with IDH-mutant gliomas and subjected to RNA sequencing.

first: Tiffanie

last: Chouleur

first: Christèle

last: Etchegaray

first: Laura

last: Villain

first: Antoine

last: Lesur

first: Thomas

last: Ferté

first: Marco

last: Rossi

first: Laetitia

last: Andrique

first: Costanza

last: Simoncini

first: Anne-Sophie

last: Giacobbi

first: Matteo

last: Gambaretti

first: Egesta

last: Lopci

first: Bethania

last: Fernades

first: Gunnar

last: Dittmar Olivier

first: Rolf

last: Bjerkvig

first: Boris

last: Hejblum

first: Rodolphe

last: Thiébaut

first: Olivier

last: Saut

first: Lorenzo

last: Bello


title: Expression profiling of circular RNAs in cells from human carotid plaque biopsies by single-cell RNA sequencing

city: Munich

first: Bernd

middle: Henrik

last: Northoff

address: Marchioninistr. 15

department: Institute of Laboratory Medicine

country: Germany

institute: Ludwig-Maximilians-University Munich

summary: To identify the origin of circular RNAs (circRNAs) in human atherosclerotic plaques, we analyzed the expression levels of circRNAs identified during the differentiation of human pluripotent stem cells (hiPSCs) into vascular endothelial cells (ECs) and smooth muscle cells (SMCs) in carotid biopsies by single-cell RNA sequencing.

relation:
Reanalysis of: GSM8121894
Reanalysis of: GSM8121895
Reanalysis of: GSM8121896
Reanalysis of: GSM8121897
Reanalysis of: GSM8121898
Reanalysis of: GSM8121899
Reanalysis of: GSM8121900
Reanalysis of: GSM8121901
Reanalysis of: GSM8121902
Reanalysis of: GSM8121903
Reanalysis of: GSM8121904
Reanalysis of: GSM8121905
Reanalysis of: GSM8121906
Reanalysis of: GSM8121907
Reanalysis of: GSM8121908

overall_design:
Dissociated cells from human carotid atherosclerotic plaques (n = 15 subjects) were enriched for SMCs, ECs and immune cells and sorted by FACS. Single-cell cDNA libraries were prepared according to the Smart-Seq2 protocol using oligo(dT) primers and sequenced (PubMed ID: 38639096, GEO: GSE260657).

For circRNA analyzes, raw reads were mapped to a sequence assembly consisting of GRCh37 and previously defined circRNAs (GEO: GSE210361) using segemehl, with circRNA contigs consisting of 100 nt at each site of each backsplicing event. Reads located on the backsplicing event were counted with featureCounts if the sequenced reads covered at least 8 nt of a 10 nt window located on the backsplicing event. Processed data are given as tab-delimited text files with raw counts for each circRNA and cell.

For this third-party reanalysis, the reanalyzed samples were submitted to GEO previously in GSE260657. The table below lists the GEO accessions reused/reanalyzed for this study.

middle: H


title: Bulk RNA-Seq from kidneys of uninephrectomized db/db mice as a model of severe diabetic kidney disease

city: Takatsuki

first: Mariko

last: MAEKAWA

state: Osaka

address: Murasaki-cho

country: Japan

institute: Japan Tobacco Inc.

summary: This dataset utilized uninephrectomized db/db mice and db/m mice as a control for comparison. We performed bulk RNA-seq studies at two time points (26 and 35 weeks of age) to identify the mechanism of severity of diabetic kidney disease.

overall_design: We performed bulk RNA-seq from the kidneys of 26- and 35-week-old uninephrectomized db/db mice as a model of severe diabetic kidney disease

first: Tatsuya

first: Tomohiko

last: SASASE


title: Reannotation of cancer mutations based on expressed RNA transcripts reveals novel functional non-coding mutations in melanoma.

status: Public on Mar 31 2025

city: Leuven

first: Kim

last: De Keersmaecker

address: ON4 Herestraat 49 - bus 810

department: Oncology

country: Belgium

institute: KUL

summary: The role of synonymous mutations in cancer pathogenesis is currently underexplored. We developed a method to detect significant clusters of synonymous and missense mutations in public cancer genomics data. In melanoma, we show that 22% (11/50) of these mutation clusters are misannotated as coding mutations because the reference transcripts used for their annotation are not expressed. Instead, these mutations are actually non-coding. This, for instance, applies to the mutation clusters targeting known cancer genes kinetochore localized astrin (SPAG5) binding protein (KNSTRN) and BCL2 like 12 (BCL2L12), each affecting 4-5% of melanoma patients. For the latter, we show that these mutations are functional non-coding mutations that target the shared promoter region of the interferon regulatory factor 3 (IRF3) and BCL2L12 genes. This results in downregulation of IRF3, BCL2L12 and tumor protein p53 (TP53) expression in a CRISPR-Cas9 primary melanocyte model and in melanoma patients, in which these mutations are also associated to a worse response to immunotherapy. Finally, we propose a simple automated method to more accurately annotate cancer mutations based on expressed transcripts. This work shows the importance of integrating DNA- and RNA-sequencing data to properly annotate mutations, and identifies a number of previously overlooked and wrongly annotated functional non-coding mutations in melanoma.

overall_design: Long read Nanopore RNA sequencing

first: Daniele

last: Pepe

first: Xander

last: Janssens

first: Kalina

last: Timcheva

first: Grecia

middle: M

last: Marrón-Liñares

first: Benno

last: Verbelen

first: Vasileios

last: Konstantakos

first: Dylan

last: De Groote

first: Jolien

last: De Bie

first: Amber

last: Verhasselt

first: Barbara

last: Dewaele

first: Arne

last: Godderis

first: Charlotte

last: Cools

first: Mireia

last: Franco-Tolsau

first: Jonathan

last: Royaert

first: Jelle

last: Verbeeck

last: Kampen

first: Karthik

last: Subramanian

first: David

last: Cabrerizo Granados

first: Gerben

last: Menschaert


title: Effect of exosomal miRNA of cancer-associated adipocyte (CAA) on the malignant transformation of pancreatic ductal adenocarcinoma

city: Tokushima

first: Toshihito

last: Tanahashi

address: Kuramotocho 3-18-5

institute: Tokushima University

summary:
CAAs were generated by co-culturing human adipocytes with a human pancreatic cancer cell line (Panc-1), and exosomes were isolated from the CAA-conditioned medium (CAA-CM).
We then performed gene expression profiling analysis using small RNA-seq of three differernt CAA-CMs and normal A-CMs.

overall_design: Comparative gene expression profiling analysis of small RNA-seq data for three CAA-CMs and A-CMs

first: Kazuyoshi

last: Noda


title: Expression profiling of circular RNAs during differentiation of human pluripotent stem cells into vascular endothelial and smooth muscle cells

first: Bernd

last: Northoff

summary:
To identify novel circular RNAs (circRNAs) and to investigate their expression levels during human pluripotent stem cells (hiPSC) differentation, we have converted these cells to vascular endothelial cells (ECs) and smooth muscle cells (SMCs).
Circular RNAs were de novo identified using RNase R treated samples and quantified in total RNA samples at 13 timepoints per differentiation.

overall_design: Comparative gene expression profiling of genes, transcripts and circular RNAs in RNA-seq data of hiPSC differentiations into ECs and SMCs.


title: Metabolic reprogramming of the neovascular niche promotes regenerative angiogenesis in proliferative retinopathy

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

institute: CHU Sainte Justine

summary: Healthy blood vessels supply neurons to preserve metabolic function. In blinding proliferative retinopathies (PRs), pathological neovascular tufts often emerge in lieu of needed physiological revascularization. Here we show that metabolic shifts in the neovascular niche define angiogenic fate. Fatty acid oxidation (FAO) metabolites accumulated in human and murine retinopathy samples. Neovascular tufts with a distinct single-cell transcriptional signature highly expressed FAO enzymes. The deletion of Sirt3, an FAO regulator, shifted the neovascular niche metabolism from FAO to glycolysis and suppressed tuft formation. This metabolic transition increased Vegf expression in astrocytes and reprogrammed pathological neovessels to a physiological phenotype, hastening vascular regeneration of the ischemic retina and improving vision. Hence, strategies to change the metabolic environment of vessels could promote a regenerative phenotype in vascular diseases.

overall_design: WT and Sirt3 KO mice pups and their adoptive lactating S129 mother were exposed to 75% oxygen from P7 to P12. Mice were returned to room air at P12 until used for experimentation. At the endpoints (P14 and P17), retina were dissociated, and CD31-enriched single-cell suspensions were used for scRNA-Seq analysis (Drop-Seq).

first: Sheetal

last: Pundir

first: Przemyslaw

last: Sapieha

first: Jean-Sebastien

last: Joyal


title: Reduced Notch signaling in BBB vascular endothelial cells mediates high fat diet-induced alterations in brain glucose uptake and insulin signaling

city: Cologne

first: Jens

last: Brüning

address: Gleueler Str. 50

institute: Max Planck Institute for Metabolism Research

summary: Short term transition to high-fat diet (HFD) feeding causes rapid changes in the molecular architecture of the blood-brain-barrier (BBB), BBB permeability and brain glucose uptake. However, the precise mechanisms responsible for these changes remain elusive. Here we detected a rapid downregulation of Notch signaling after short-term HFD feeding. Conversely, Notch activation restores HFD-fed mouse serum induced reduction of Glut1 expression and glycolysis in cultured brain microvascular endothelial cells (BMECs). Selective, inducible expression of Notch-intracellular domain (IC) in BMECs prevents HFD-induced reduction of Glut1 expression and hypothalamic glucose uptake. Caveolin (Cav)-1 expression in BMECs is increased upon short term HFD feeding. However, NotchICBMECs mice display reduced caveola formation and BBB permeability. This ultimately translates into reduced hypothalamic insulin transport, action and systemic insulin sensitivity. Collectively, we highlight a critical role of Notch-signaling in the pleiotropic effects of short-term dietary transitions on BBB functionality.

overall_design:
We aimed at comparing a transcriptional signature of BBB VECs of animals exposed to control diet (CD) or high-fat diet (HFD) feeding for 3 days. To achieve that, we employed a genetically modified mouse model: Slco1c1-CreERT2, which expresses a tamoxifen-inducible variant of the Cre-recombinase under the control of Slco1c1 promoter specifically in BBB VECs. These animals were crossed with mice allowing for Cre-dependent expression of the ribosomal protein L10a with GFP. Mice expressing L10aGFP in BBB VECs were either fed a control or high fat diet for 3 days, hypothalami were dissected, GFP-tagged ribosomes precipitated and ribosome-associated RNA subjected to RNA sequencing.

For cEND cells treated with WZB117: we aimed to investigate, whether the observed downregulation in Notch signaling could potentially represent acompensatory response to downregulated glucose transport and glycolysis in VECs of HFD-fed mice. To this end, we incubated cultured cEND cells with either vehicle or the Glut1 inhibitor WZB117 and subjected these cells to mRNA sequencing.

first: Yiyi

last: Zhu

first: Paul

last: Klemm


title: RNA-seq from atirmociclib resistant versus sensitive and vehicle treated HR+ HER2- ZR751  breast cancer xenografts .

city: San Diego

first: Lars

last: Anders

address: 10555 Science Center Dr

institute: Pfizer

summary: We investigated the mechanisms of acquired resistance to the CDK4 selective inhibitor atirmociclib in HR+ HER2- breast cancer in vivo, using the ZR751 xenograft model. Atirmociclib resistant tumors appeared after long-term (>50 day) treatment with atirmociclib. Tumor material was isolated from resistant (85-day treatment) as well as sensitive/vehicle treated (3-day) tumor bearing mice and subjected to RNA-seq analysis.

overall_design: To establish ZR751 tumors, (5-10) x106 ZR751 cells were subcutaneously implanted in the dorsal region of female NSG mice. When average tumor volume reached 150 mm3, tumor bearing mice were randomly assigned to treatment groups. Atirmociclib was then administered, PO, 60 mg/kg BID (7 hr apart). Following 3-day treatment (3 h after last dosing) of ZR751 xenograft bearing mice with vehicle and atirmociclib, tumors from 3–5 mice per treatment group were excised, segmented, and immediately flash frozen in liquid nitrogen. In a separate study, mice were treated for 84 to 91 days with atirmociclib, and tumors processed as above. Frozen tumor samples from all three treatment groups were then split for analysis by WB and mRNA sequencing (RNA-seq). For RNA processing and sequencing, tumor powder samples were provided directly to Genewiz (Azenta).

first: Whijae

last: Roh


title: Chromosomal instability in human trophoblast stem cells and placenta

city: SEATTLE

first: Min

last: Yang

state: WA

address: 850 Republican ST

institute: University of Washington

summary: The human placenta, a unique tumor-like organ, is typically thought to exhibit rare aneuploidy associated with adverse pregnancy outcomes. Discrepancies in reported aneuploidy prevalence in placenta likely stem from limitations in modeling and the resolution of detection methods. Here, we used isogenic trophoblast stem cells (TSCs) derived from both naïve and primed human pluripotent stem cells (hPSCs) to reveal the spontaneous occurrence of aneuploidy, suggesting chromosomal instability (CIN) as an inherent feature of the trophoblast lineage. We identified potential pathways contributing to the occurrence and tolerance of CIN. These findings were further validated using single-cell multiome data from healthy human placentas, where we observed a high prevalence of heterogeneous aneuploidy across trophoblast cells. Despite extensive chromosomal abnormalities, TSCs maintained their proliferative and differentiation capacities, suggesting that CIN is a typical aspect of placental development. Our study challenges the traditional view of aneuploidy in the placenta and provides new insights into the role of CIN in normal placental function.

overall_design:
We derived four types of isogenic TSCs from both naïve and primed hPSCs using previously published protocols. RUES2: primed pluripotent stem cell; nRUES2: naïve pluripotent stem cell, derived from primed pluripotent stem cell; nTSC: trophoblast stem cells derived from naïve pluripotent stem cell; nbTSC: trophoblast stem cells derived from blastoid, which was derived from naïve pluripotent stem cell; ccTSC: trophoblast stem cells derived from primed pluripotent stem cell through chemical conversion; pdTSC: trophoblast stem cells derived from primed pluripotent stem cell through trophectoderm-like cells; BAP cell: trophoblast cells derived from primed pluripotent stem cell through BAP method.
Gene expression profiling and karyotype analyses were conducted on all cells. Additionally, we analyzed published single-cell multiome data from in vivo placentas.

first: Danyang

last: Wang

first: Andrew

last: Cearlock

first: Katherine

last: Lane

first: Ian

last: Jan

first: Rajiv

last: McCoy


title: Effects of Srsf3 deletion on gene expression and 3' UTR profiles in macrophages and atherosclerotic plaques [RNA-seq]

city: Shanghai

first: Yuanyuan

last: Wei

address: No. 130, Dong'an Road

institute: Fudan University

summary: Serine and arginine rich splicing factor 3 (Srsf3) is the smallest member of the serine/arginine rich protein family and directly modulates 3' UTR length, which may impact the stability, localization, and translation efficiency of the mRNAs. Here, we report that genetic ablation of Srsf3 disturbs macrophage maturation from circulating monocytes, thus limiting phagocytosis of low-density lipoproteins and dead cells in plaques, which aggravates atherosclerosis in Apoe-/- mice fed a high-cholesterol diet for 12 weeks. Deficiency in Srsf3 suppresses mitochondrial translation by shortening 3' UTRs of mitochondrial aminoacyl-tRNA synthetase, consequently leading to mitochondrial dysfunction in macrophages. Our study reveals that Srsf3-mediated distal polyadenylation site usage is required for mitochondrial translation during macrophage maturation, which may have broad pathophysiological implications for atherosclerosis.

overall_design: To characterize the effects of Srsf3 on gene expression and 3' UTR profiles in lesional macrophages, we performed 3' end sequencing and scRNA-seq of plaque cells in Apoe-/- mice with or without myeloid Srsf3 deletion after high-cholesterol diet feeding, as well as 3' end sequencing of murine bone marrow-derived macrophages treated with oxLDL.

first: Xian

first: Xin

last: Zhang

first: Dejian

last: Zhao


title: Effect of CCS1477 treatment on gene expression in NRF2-activated lung cancer cells

city: Sendai

first: KE

last: WANG

state: Miyagi

address: 仙台市青葉区星陵町2-1

institute: Tohoku University, Tohoku Medical Megabank Organization,

summary: Constitutive activation of NRF2 provides a selective advantage to malignant tumour clones through the hijacking of the NRF2-dependent cytoprotective transcriptional program, which allows the cancer cells to survive and thrive in the chemically stressful tumour niche, whilst also providing resistance to anti-cancer drugs due to the upregulation of xenobiotic metabolizing enzymes and drug efflux pumps. Through a small-molecule epigenetic screen carried out in KEAP1 mutant lung cancer cells, in this study, we identified CCS1477 (Inobrodib) to be an inhibitor of the global NRF2-dependent transcription program. Mechanistically, CCS1477 is able to repress NRF2’s cytoprotective response through the inhibition of its obligate transcriptional activator partner CBP/ p300. Importantly, in addition to repressing NRF2-dependent anti-oxidative stress and xenobiotic metabolizing enzyme gene expression, CCS1477 treatment is also able to reverse the chemoresistance phenotype and re-sensitize NRF2-activated tumour cells to anti-cancer drugs. Furthermore, in co-culture experiments of KEAP1 mutant cancer cells with primary human T cells, CCS1477 treatment suppressed the acquisition of the T cell exhaustion transcriptional state, which should function to augment the anti-cancer immune response. Thus, CCS1477-mediated inhibition of CBP/ p300 represents a novel therapeutic strategy with which to target the currently untreatable tumours with aberrant NRF2 activation.

overall_design: RNA-Seq profiling of NRF2-activated lung cancer cells H460, H2023 and wildtype lung cancer cell ABC-1 at 24 hours treatment by 5 mM CCS1477

first: Ke

first: Liam

last: Baird

first: Masayuki

last: Yamamoto


title: Effects of Srsf3 deletion on gene expression and 3' UTR profiles in macrophages and atherosclerotic plaques [scRNA-seq]

summary: Serine and arginine rich splicing factor 3 (Srsf3) is the smallest member of the serine/arginine rich protein family and directly modulates 3' UTR length, which may impact the stability, localization, and translation efficiency of the mRNAs. Here, we report that genetic ablation of Srsf3 disturbs macrophage maturation from circulating monocytes, thus limiting phagocytosis of low-density lipoproteins and dead cells in plaques, which aggravates atherosclerosis in Apoe-/- mice fed on high-cholesterol diet for 12 weeks. Deficiency in Srsf3 suppresses mitochondrial translation by shortening 3' UTRs of mitochondrial aminoacyl-tRNA synthetase, consequently leading to mitochondrial dysfunction in macrophages. Our study reveals that Srsf3-mediated distal polyadenylation site usage is required for mitochondrial translation during macrophage maturation, which may have broad pathophysiological implications for atherosclerosis.


title: Transcriptomic analysis of FLCNLiKO, a study performed on males and females at 12- and 90-weeks of age

status: Public on Mar 28 2025

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

summary: Mutations in the Folliculin (FLCN) gene are responsible for the Birt-Hogg-Dube’ (BHD) syndrome, a rare inherited condition that predisposes affected individuals to develop pulmonary cysts, skin and kidney tumors. However, its involvement in liver carcinogenesis has never been investigated so far. Here we demonstrated that FLCN depletion in mice results in sporadic liver cancer associated with inflammation and fibrosis with features of cholangiocarcinoma (CCA). Total RNA was extracted from n=4 for each experimantal group: Transcriptomic analysis was performed on males and females at 12- and 90-weeks of age.

first: R

first: N

last: Pastore


title: Endothelial response to type I interferon contributes to vasculopathy and fibrosis and predicts disease progression of systemic sclerosis

first: Hanlin

last: Yin

state: Please Select

address: 145 Middle Shandong Road

institute: Renji Hospital Affiliated to Shanghai Jiao Tong Univeristy School of Medicine

summary: Type I interferon (IFN-1) signatures are a hallmark of patients with systemic sclerosis (SSc). However, its significance in clinical stratification and contribution to deterioration still need to be better understood. For hypothesis generation, we performed single-cell RNA sequencing (scRNAseq) on skin biopsies (SSc=4, control =2) using the BD Rhapsody platform. The IFN-1 signature was mapped, functionally investigated in a bleomycin plus IFNα2-adeno-associated virus (IFNA2-AAV) induced model, and verified in an SSc cohort (n=61). Endothelial cells (EC) had the most prominent IFN-1 signature among dermal non-immune cells. The EC IFN-1 signature was increased both in SSc vs. controls and in dcSSc vs. lcSSc.  IFNA2-AAV deteriorated bleomycin-induced dermal fibrosis, EndoMT, and perivascular fibrosis and caused blood vessel loss with EC apoptosis. Vascular MX1, an IFN-1 response protein, was significantly increased both in total SSc skin vs. healthy controls and in dcSSc vs. lcSSc. Baseline vascular MX1 performed similarly to skin score in predicting disease progression over 6-34 months in total SSc and was superior in the dcSSc subpopulation. To sum up, the EC IFN-1 signature distinguished SSc skin subtypes and disease progression and may contribute to vasculopathy and fibrosis.

overall_design: Distal forearm skin from 2 healthy volunteers, 1 patient with diffuse cutaneous systemic sclerosis (dcSSc) and 3 patients with limited cutaneous systemic sclerosis (lcSSc)

first: Qingran

last: Yan

first: Liangjing

last: Lu


title: Postnatal epigenetic differences in calves following transient fetal infection with bovine viral diarrhea virus

city: Fort Collins

first: Thomas

middle: R.

last: Hansen

state: Colorado

address: 3107 Rampart Road

department: Biomedical Sciences

institute: Colorado State University

type: Methylation profiling by high throughput sequencing

summary: Bovine Viral Diarrhea Virus (BVDV) is the most detrimental flavivirus within the cattle industry. Infection with vertically transmissible BVDV prior to 125 days of gestation results in the generation of a persistently infected (PI) calf. These PI calves are unable to clear the virus in utero, due to an incomplete immune response. However, when infection with BVDV occurs after 150 days of gestation, the fetus clears the transient infection (TI) in utero and is born with BVDV specific antibodies. Variations in DNA methylation have been identified in white blood cells (WBC) of TI heifers at birth. It was hypothesized that epigenomic alterations persist into the postnatal period and lead to previously undocumented pathologies. To study these possible effects, DNA was isolated from the WBCs of 5 TI heifers and 5 control heifers at 4 months of age and subjected to reduced representation bisulfite sequencing (RRBS). Differential analysis of the methylome revealed a total of 3,047 differentially methylated CpG sites (DMSs), 1,349 of which were hypermethylated and 1,698 were hypomethylated. Genes containing differential methylation were associated with inflammation, reactive oxygen species (ROS) production, and metabolism. Complete blood count (CBC) data identified a higher lymphocyte percentage in TI heifers. When compared in the context of the CD45+ parent population, spectral flow cytometry revealed increased intermediate monocytes, B cells, and CD25+/CD127- T cells, and decreased CD4+/CD8b+ T cells. Comparative analysis revealed differential methylation of CpG sites contained in 205 genes, 5 promoters, and 10 CpG islands at birth that were also present at 4 months of age. Comparison of differential methylation in TI heifers and PI heifers at 4 months of age showed 465 genes, 18 promoters, and 34 CpG islands in common. Differential methylation of WBC DNA persists to 4 months of age in TI heifers and is associated with dysregulation of inflammation, metabolism, and growth. Analysis of differential methylation in TI heifers contributes to the understanding of how fetal infection with BVDV induces postnatal detriments related to profit loss.

overall_design: Reduced-representation bisulfite sequencing (RRBS-Seq ) for five randomly selected 4 month old calves known to be seronegative for BVDV and five experimentally generated fetal TI calves. Jugular vein was collected, and PMBC were collected for DNA analysis.

first: Jessica

middle: N

last: Kincade

first: Terry

middle: E

last: Engle

first: Marcela

last: Henao-Tamayo

first: Jordan

last: Eder

first: Erin

last: McDonald

first: Darcy

last: Deines

first: Brie

last: Wright

first: Dilyara

last: Murtazina

first: Jeanette

middle: V

last: Bishop

first: Hana

last: Van Campen


title: Iron supplementation alleviates pathologies in a mouse model of facioscapulohumeral muscular dystrophy

city: Chuo-ku, Kumamoto-shi

first: Kodai

last: Nakamura

state: Kumamoto-ken

address: 2-2-1 Honjo

department: Institute of molecular embryology and genetics

institute: Kumamoto university

summary: Facioscapulohumeral muscular dystrophy (FSHD) is a genetic muscle disease caused by ectopic expression of the toxic protein DUX4, resulting in muscle weakness. However, the mechanism by which DUX4 exerts its toxicity remains unclear. In this study, we observed abnormal iron accumulation in muscles of patients with FSHD and in muscle-specific DUX4-expressing (DUX4-Tg) mice. Treatment with iron chelators, an iron-deficient diet, and genetic modifications inhibiting intracellular uptake of iron did not improve but rather exacerbated FSHD pathology in DUX4-Tg mice. Unexpectedly, however, iron supplementation, either from a high-iron diet or intravenous iron administration, resulted in remarkable improvement in grip strength and running performance in DUX4-Tg mice. Iron supplementation suppressed abnormal iron accumulation and the ferroptosis-related pathway involving increased lipid peroxidation in DUX4-Tg muscle. Muscle-specific DUX4 expression led to retinal vasculopathy, a part of FSHD pathology, which was prevented by iron administration. Furthermore, high-throughput compound screening of the ferroptosis pathway identified drug candidates including Ferrostatin-1 (Fer-1), a potent inhibitor of lipid peroxidation. Treatment with Fer-1 dramatically improved physical function in DUX4-Tg mice. Our findings demonstrate that DUX4-provoked toxicity is involved in the activation of the ferroptosis-related pathway and that supplementary iron could be a promising and readily available therapeutic option for FSHD.

overall_design: To investigate the effect of HID on phenotypic amelioration, skeletal muscle of FSHD mouse model was used.

first: Yusuke

last: Ono


title: The topoisomerase inhibitor amonafide enhances defense responses to promote longevity in C. elegans.

status: Public on Mar 30 2025

city: Amsterdam

first: Man

middle: Iman

last: Hu

address: Meibergdreef 9

department: Laboratory Genetic Metabolic Diseases

institute: Amsterdam UMC Location University of Amsterdam

summary: Aging is a major risk factor for disease, and developing effective pharmaceutical interventions to improve healthspan and promote longevity has become a high priority for society. One of the molecular pathways that has emerged from research in various model organisms revolves around lowering AKT1 levels. This prompted our in silico drug screen for small molecules capable of mimicking the transcriptional effects of AKT1 knockdown. We found topoisomerase inhibitors as a top candidate longevity-drug class. Evaluating multiple compounds from this class in C. elegans revealed that the topoisomerase inhibitor amonafide has the greatest benefit on healthspan and lifespan. Intriguingly, the longevity effect of amonafide was not solely dependent on DAF-16/FOXO, the canonical pathway for lifespan extension via AKT1 inhibition. We performed RNA-seq on amonafide-treated worms and revealed a more youthful transcriptional signature, along with the activation of diverse molecular and cellular defense pathways. We found the mitochondrial unfolded protein response (UPRmt) regulator afts-1 to be crucial for both improved healthspan and extended lifespan upon amonafide treatment. Moreover, healthspan was partially dependent on the immune response transcription factor zip-2 and the integrated stress response transcription factor atf-4. We further examined the potential of amonafide in age-related disease. Treating a C. elegans model for Parkinson's disease with amonafide improved mobility. In conclusion, we identified amonafide as a novel geroprotector, activating mitochondrial- pathogenic- and xenobiotic-associated defense responses and may serve as a candidate for Parkinson's disease therapy.

overall_design: N2 worms were synchronized and treated with DMSO or 50 µm amonafide from the L1 stage. L4 animals were harvested by washing three times with M9 buffer and two times with water before being snap-frozen in liquid nitrogen. ~2000 worms for each sample. 4-5 replicates per condition.

first: Iman

first: Ana

last: Serna

first: Stacia

last: Everts

first: Lale

last: Güngördü

first: Bauke

last: Schomakers

first: Ellen

last: Nollen

first: Arwen

middle: W

last: Gao

first: Riekelt

last: Houtkooper

first: Georges

last: Janssens


title: Aberrant EZHIP Expression Drives Tumorigenesis in Osteosarcoma [CUT&RUN]

first: Claudia

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

institute: Lady Davis Institute for Medical Research

summary: Osteosarcomas (OS) are aggressive bone tumors characterized by extensive structural variation, and rare recurrent oncogenic driver mutations. Here, we identify ectopic expression of the oncohistone-mimic EZHIP in more than 20% of patients, in two independent OS cohorts. Through gain- and loss-of-function experiments, we provide evidence that EZHIP expression is oncogenic, increasing the aggressive features of OS in vitro and in vivo. EZHIP-mediated epigenetic rewiring promotes reactivation of developmental transcriptional programs and stalled differentiation of mesenchymal progenitors, which are skewed towards smooth muscle commitment at the expense of other lineages. Our findings of EZHIP expression as a prevalent driver in OS provide new insights into pathogenic pathways and therapeutic alternatives for this debilitating cancer.

overall_design: To investigate the effect of EZHIP expression on H3.3K27me3, we used an osteosarcoma cell line with ectopic EZHIP expression (U2OS), to knock out EZHIP and perform CUT&RUN. 16 samples are provided, 4 samples using the KHOS cell line, 5 samples using the MG63 cell line and 7 samples using the U2OS cell line.

first: Wajih

last: Jawhar

first: Geoffroy

last: Danieau

first: Alva

last: Annett

first: Nada

last: Jabado

first: Livia

last: Garzia


title: CxxC-finger protein 1 regulates Treg fragility associated with H3K4me3 breadth

status: Public on Mar 29 2025

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

summary: Foxp3-expressing regulatory T cells (Treg cells) play a central role in maintaining immune homeostasis and tolerance. Activation of Treg cells prevents various types of inflammatory responses. However, it remains unclear how the epigenetic program in Treg cells is maintained during the dynamic activation process. Here we show that Cxxc1 is associated with Foxp3 and positively regulates the expression of target genes at H3K4me3-enriched sites. Treg cell-specific ablation of Cxxc1 in mice resulted in a lethal inflammatory disease characterized by spontaneous T-cell activation. Cxxc1-deficient Treg cells showed reduced immunosuppressive capacity in vivo but also induced aberrant expression of genes associated with Treg fragility. Mechanistically, Cxxc1 promotes the accumulation of H3K4me3 in the broad domain of Ikzf4, suppressing the expression of fragile genes including IFN-γ, and Ikzf4 expression partially restores Treg function.

overall_design:
Wild type and Cxxc1 knock out Treg cells were collected for CUT&Tag and WGBS analysis.
Wild type and Cxxc1 knock out Treg cells were collected for CUT&Tag and RNA-seq analysis.

first: Xiaoyu

last: Meng

first: Yezhang

last: Zhu

first: Lie

last: Wang


title: Oxaliplatin-induced cardiotoxicity in mice is connected to the changes in energy metabolism in the heart tissue

city: St Louis

first: Mikhail

last: Berezin

state: Missouri

address: 4515 McKinley  Ave

institute: Washington University in St. Louis

summary: Oxaliplatin is a platinum-based alkylating chemotherapeutic agent used for cancer treatment. At high cumulative dosage, the negative effect of oxaliplatin on the heart becomes evident and is linked to a growing number of clinical reports. The aim of this study was to determine how chronic oxaliplatin treatment causes the changes in energy-related metabolic activity in the heart that leads to cardiotoxicity and heart damage in mice. C57BL/6 male mice were treated with intraperitoneal oxaliplatin (0 and 10 mg/kg) once a week for eight weeks with the human equivalent dosage. During the treatment, mice were followed for physiological parameters, ECG, histology and RNA sequencing of the heart. We identified, that oxaliplatin induces strong changes in the heart and affects the heart's energy-related metabolic profile. Histological post-mortem evaluation identified focal myocardial necrosis infiltrated with a small number of associated neutrophils. Accumulated doses of oxaliplatin led to significant changes in gene expression related to energy related metabolic pathways including fatty acid (FA) oxidation, amino acid metabolism, glycolysis, electron transport chain, and NAD synthesis pathway. At high accumulative doses of oxaliplatin, the heart shifts its metabolism from FAs to glycolysis and increases lactate production. It also leads to strong overexpression of genes in NAD synthesis pathways such as Nmrk2. Changes in gene expression associated with energy metabolic pathways can be used to develop diagnostic methods to detect oxaliplatin-induced cardiotoxicity early on as well as therapy to compensate for the energy deficit in the heart to prevent heart damage.

overall_design: After 8 weeks of oxaliplatin treatment, mice heart were collected and total RNA was extracted. There were 9 RNA samples, 4 from control and 5 from oxaliplatin group passed the integrity threshold (larger than 8) and were used for RNA sequencing. Differentially expressed genes between control and oxaliplatin-treated mice were identified with Partek software to study the effects of oxaliplatin on gene expression profile in mice heart.

first: Junwei

last: Du

first: Leland

middle: C

last: Sudlow

first: Kiana

last: Shahverdi

first: Haiyin

last: Zhou

first: Megan

last: Michie

first: Madhulika

last: Kastury

first: Monique

last: Latif

first: Thomas

last: Schindler

first: Joshua

last: Mitchell

first: Shamim

last: Mollah

middle: Y


title: Oncogenic fusions converge on shared mechanisms in initiating astroblastoma [RNA-Seq of TREx293]

status: Public on Mar 27 2025

city: Beijing

first: wei

last: Shi

address: Chinese Institute for Brain Research, Beijing(CIBR), Jianzan Building, No.26, Science Park Road, Zhongguancun Life Science Park, Changping District, Beijing, China

institute: Chinese institute for brain research

summary: Chromosomal rearrangements and gene fusions are the initial events in the development of many cancers. Astroblastoma (ABM), a challenging brain cancer of unknown cellular origin, is associated with diverse in-frame gene fusions, including MN1:BEND2 and MN1:CXXC5. However, it remains unclear if these gene fusions contribute to tumorigenesis. Here, we show that the two ABM-associated fusions converge on similar molecular activities and initiate malignancy specifically in ventral telencephalon neural progenitors. BEND2 and CXXC5 recognized similar DNA motifs, suggesting a convergence on downstream gene regulation. Expressing MN1:BEND2 in ventral telencephalon neural progenitors results in aberrant cell proliferation, impaired differentiation, a perivascular occupancy pattern of cells reminiscent of ABM, and acquisition of an ABM-associated transcriptional signature. In stark contrast, MN1:BEND2 expression in dorsal telencephalon neural progenitors leads to extensive cell death. This cell-type specific malignancy is dependent on Olig2 expression. Mechanistically, both ABM-associated fusion proteins (MN1:BEND2 and MN1:CXXC5) induce overlapping transcriptional responses, including the activation of a therapeutically targetable PDGFRα pathway. Collectively, our data suggests that distinct ABM-associated fusions upregulate shared transcriptional networks, thereby disrupting the normal development of ventral telencephalon neural progenitors and culminating in oncogenic transformation. These findings uncover new avenues for targeted ABM treatment.

overall_design: To investigate the transcriptional activation function of MN1:BEND2 at the genomic level using TREx293.

first: Yang

last: Yu

first: Qianqian

last: Sun

first: Fuchuan

last: Jia

first: Wei


title: Oncogenic fusions converge on shared mechanisms in initiating astroblastoma [RNA-seq of Pdgfra lineage cells]

overall_design: Analysis of Bulk RNA-seq from P4 PdgfraCreER;MB;AI14 mice and PdgfraCreER;AI14 mice.

first: Yixing

first: Xiangyu


title: Aberrant EZHIP Expression Drives Tumorigenesis in Osteosarcoma [RNA-Seq]

first: Claudia

last: Kleinman

overall_design: To investigate the effect of EZHIP expression we established human mesenchymal stem cells (hMSC) and osteosarcoma cell lines (MG63, KHOS) with overexpression of EZHIP. We also used an osteosarcoma cell line with ectopic EZHIP expression (U2OS) to knock out EZHIP. The two osteosarcoma cell lines with EZHIP overexpression were used to create xenograft models. For each cell line and xenograft model the expression profiles were compared between EZHIP expressing and WT/EZHIP knock out.35 samples are provided, including 6 hMSC cell lines, 18 osteosarcoma cell lines and 11 xenograft tumours. 3 replicates per condition

first: Wajih

last: Jawhar

first: Geoffroy

last: Danieau

first: Alva

last: Annett

first: Nada

last: Jabado

first: Livia

last: Garzia


title: Stem and progenitor cell proliferation are independently regulated by cell type-specific cyclinD genes

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

department: Computational Biology

institute: Stowers Institute for Medical Research

summary: Regeneration and homeostatic turnover of solid tissues depend on the proliferation of symmetrically dividing adult stem cells, which either remain stem cells or differentiate based on their niche position. Here we demonstrate that in zebrafish lateral line sensory organs, stem and progenitor cell proliferation are independently regulated by two cyclinD genes. Loss of ccnd2a impairs stem cell proliferation during development, while loss of ccndx disrupts hair cell progenitor proliferation but allows normal differentiation. Notably, ccnd2a can functionally replace ccndx, indicating that the respective effects of these Cyclins on proliferation are due to cell type-specific expression. However, even though hair cell progenitors differentiate normally in ccndx mutants, they are mispolarized due to hes2 and Emx2 downregulation. Thus, regulated proliferation ensures that equal numbers of hair cells are polarized in opposite directions. Our study reveals cell type-specific roles for cyclinD genes in regulating the different populations of symmetrically dividing cells governing organ development and regeneration, with implications for regenerative medicine and disease.

overall_design: Two replicates per sibling or ccndx mutant were used

first: Tatjana

last: Piotrowski

first: Mark

last: Lush


title: Oncogenic fusions converge on shared mechanisms in initiating astroblastoma [scRNA-seq of Olig2 lineage cells]

overall_design: Olig2 lineage cells from brain of Olig2Cre;AI14 mouse and Olig2Cre;MN1:BEND2;AI14 mouse collected at postnatal day 3 (P3) were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNA-seq.

last: Zhou

first: Li

last: Zhang


title: Oncogenic fusions converge on shared mechanisms in initiating astroblastoma [ATAC-Seq]

first: wei

overall_design: To investigate the impact of MN1:BEND2 expression on chromatin accessibility profiles using cells sorted from Olig2Cre;MN1:BEND2;Ai14 mouse forebrains.


title: EMP1 preserves hematopoietic stem cell potential under homeostasis and radiation-induced injury by alleviating ER stress

city: Chongqing

first: Zhe

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing Medical University

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

overall_design: Refer to individual Series


title: Altered gene expression related to fuel use and sensory capacity in tanycytes throughout the hibernation season in the golden hamster

city: Tromsoe

first: Shona

last: Wood

address: Hansine Hansens veg 18

country: Norway

institute: UiT

summary: Hibernation is a physiological and behavioural adaptation that permits survival during periods of reduced food availability and extreme environmental temperatures. This is achieved through cycles of metabolic depression which results in reduced body temperature (torpor) and rewarming (arousal). This cannot be achieved without extensive preparative physiological changes prior to the hibernation season. Dramatic changes in body temperature set-point observed over the hibernation season, pointing towards the hypothalamus, and several lines of evidence implicate a specialised glial cell type, the tanycyte, in hypothalamic control mechanisms linked to metabolic regulation. To investigate changes in tanycytic cell phenotype over the course of the hibernation season, we exposed golden hamsters (Mesocricetus auratus) to short photoperiod (SP) and reduced ambient temperature (8C) and then LASER capture microdissected the tanycytic region from animals at physiologically defined points across the season. RNAseq followed by combined hierarchical clustering and pathway analysis defined major changes in the tanycytic transcriptome linked to physiological status. Our analysis revealed a marked reduction in the expression of genes linked to ciliary assembly and GPCR-signalling during the hibernation season, as well as evidence for a shift towards increased glycolytic metabolism. These aspects all spontaneously reversed in refractory animals which have ceased to express torpor despite continued exposure to SP 8C. Tanycytes sampled mid-torpor show increased expression of immediate-early genes compared to the interbout euthermic state, while genes linked to RNA processing and translation show the reverse. The putative involvement of tanycytes in hibernation control are discussed.

overall_design: Three months old male golden hamsters (Mesocricetus auratus) were housed under long photoperiod (LP, 14 hr of light/24 hrs) and an ambient temperature of 22°C. At the start of the experiment, one group were kept on LP at 22°C and were sampled immediately prior to the photoperiodic switch and at the end of the experiment (LP). The remaining animals were transferred to short photoperiod (SP, 10 hr of light/24 hrs) and an ambient temperature of 8°C to initiate hibernation. Animals were sampled 4 weeks after transfer to SP (pre-hibernation), after 8-12 weeks of SP prior to intiating T-A cycling (late pre-hibernation), or after three T-A cycles either when interbout euthermic (IBE) or torpid. The average IBE duration in this experiment was approximately 24 hours, animals were sampled late in their interbout euthermia phase (23 hours). Torpid animals were sampled at their mid-point of torpor, which in this experiment was 13 hours. After approximately 20 weeks of SP exposure, animals spontaneously stopped hibernating and were sampled at least 2 weeks after the last torpor bout (refractory).   Brain were collected and laser capture microdissection of the ependymal region of the hypothalamus, to enrich for tancytes was undertaken. RNAseq analysis was performed.

first: Vebjørn

last: Melum

first: David

last: Hazlerigg

first: Valerie

last: Simonneaux


title: Oncogenic fusions converge on shared mechanisms in initiating astroblastoma [differentiated iNPC]

last: Shi

overall_design: Analysis of RNA-seq in human iNPCs and the neurons induced from iNPCs.

first: Yang

last: Yu

first: Qianqian

last: Sun

first: Fuchuan


title: PROTein Evolution Using Selection (PROTEUS) [Illumina]

status: Public on Apr 03 2025

city: Camperdown

first: Graham

middle: Gregory

last: Neely

state: NSW

address: John Hopkins Drive

country: Australia

institute: Charles Perkins Centre, The University of Sydney

summary: Directed evolution (DE) is a process of mutation and iterative artificial selection to breed biomolecules with new or improved activity. DE platforms are primarily prokaryotic or yeast-based, and stable highly mutagenic mammalian systems have been challenging to establish and apply. To this end, we developed PROTein Evolution Using Selection (PROTEUS), a new platform that uses chimeric virus-like vesicles (VLVs) to enable extended mammalian DE campaigns without loss of system integrity. This platform, consisting of a minimal modified Semliki Forest virus genome controlling expression of the Indiana vesiculovirus G coat protein, is stable and can generate sufficient diversity for DE in mammalian systems. Using PROTEUS, we altered the doxycycline responsiveness of tetracycline-controlled transactivators, generating a more sensitive TetON-4G tool for gene regulation. PROTEUS is also compatible with intracellular nanobody evolution, and we use it to design a novel DNA damage-responsive anti-p53 nanobody. Overall, PROTEUS is a robust, efficient, and stable platform to direct evolution of biomolecules within mammalian cells.

sample_organism:
Homo sapiens
Semliki Forest virus
synthetic construct

overall_design: Long-read nanopore sequencing and short-read Illumina sequencing of VLV transgenes to determine transgene sequence proportions and mutations. Long-read sequencing samples arise from pooled (N=6) VLV samples at each sampling timepoint. Short-read sequencing samples arise from single VLV samples at each sampling timepoint.

first: Alexander

middle: J

last: Cole

first: Christopher

last: Denes

first: Daniel

last: Hesselson

middle: G


title: Oncogenic fusions converge on shared mechanisms in initiating astroblastoma [CUT&Tag]

overall_design: CUT&Tag against HA-MN1:BEND2 was generated using mutant cells sorted from Olig2Cre;MN1:BEND2;Ai14 mouse forebrains to explore the molecular mechanisms underlying MN1:BEND2’s oncogenic function. the molecular mechanisms underlying MN1:BEND2’s oncogenic function.

last: Jia

first: Xiangyu


title: Aberrant EZHIP Expression Drives Tumorigenesis in Osteosarcoma

city: Montréal

first: Claudia

middle: L

last: Kleinman


title: EMP1 preserves hematopoietic stem cell potential under homeostasis and radiation-induced injury by alleviating ER stress [ER-stress ATAC-seq]

last: Chen

summary: Hematopoietic stem cells (HSCs) play a crucial role in lifelong hematopoiesis by generating all blood lineages. The long-term maintenance of HSCs relies on the regulation of endoplasmic reticulum (ER) stress at a low level. However, the precise control of ER stress in HSCs remains largely unknown. In this study, we demonstrate that suppression of ER stress enhances the in vitro maintenance and in vivo repopulation capacity of HSCs, while also protecting HSCs against radiation-induced injury. Integrated multi-omics analysis has revealed that epithelial membrane protein 1 (Emp1) functions as an ER stress sensor in HSCs. Loss of Emp1 leads to increased protein aggregates and elevated ER stress, ultimately resulting in impaired HSC maintenance and self-renewal. Mechanistically, EMP1 is located within the ER and interacts with ceramide synthase 2 (CERS2) to limit the production of dihydroceramides (dhCers), which are a class of sphingolipids. DhCers accumulate in Emp1-deficient HSCs and directly induce protein aggregation. Inhibition of CERS2 significantly restores the maintenance of Emp1-deficient HSCs. Furthermore, Emp1 deficiency renders HSCs more susceptible to radiation, while overexpression of Emp1 or inhibition of CERS2 protects HSCs against radiation-induced injury. These findings highlight the critical role played by the EMP1-CERS2-dhCers axis in constraining ER stress and preserving HSC potential, uncovering a new link between sphingolipid metabolism and HSC homeostasis, and have clinical implications.

overall_design: HSCs (CD48-CD150+LSK) were sorted from wild-type C57BL/6J mice injected intraperitoneally with DMSO or Tunicamycin (2 mg/kg) and then subjected to ATAC-seq.


title: Opposing Regulation of TNF Responses and IL-1b+ Macrophages by PGE2-cAMP Signaling and IFN-g [ATAC-seq]

city: New York

first: HSS Genomics

last: Research Center

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

summary: IL-1b-expressing macrophages elicited by cooperation between PGE2 and TNF signaling have been identified and proposed to be pathogenic in rheumatoid arthritis (RA) and pancreatic cancer, but mechanisms that induce these cells and the extent to which they contribute to arthritic phenotypes are not known. In this study we used an integrated transcriptomic and epigenomic analysis in primary human monocytes to study PGE2-TNF crosstalk, and how it is regulated by IFN-g, as occurs in RA synovial macrophages. We identified a (TNF + PGE2)-induced gene expression signature that is enriched in RA and post-immune checkpoint blockade arthritis macrophage subsets and includes genes in pathogenic IL-1, Notch and neutrophil chemokine pathways. This gene expression signature, which is distinct from canonical inflammatory NF-kB target genes such as TNF, IL6 and IL12B, was driven by cooperation of PGE2-induced AP-1, CEBP and NR4A family transcription factors with TNF-induced NF-kB activity. Unexpectedly, IFN-g suppressed induction AP-1, CEBP and NR4A activity to ablate induction of IL-1, Notch and neutrophil chemokine genes, while promoting expression of distinct inflammatory genes such as TNF and T cell chemokines like CXCL10. These results reveal the basis for synergistic induction of inflammatory genes by PGE2 and TNF, and a novel regulatory axis whereby IFN-g and PGE2 oppose each other to determine the balance between two distinct TNF-induced inflammatory gene expression programs.

overall_design: We wished to understand the full spectrum of pathogenic inflammatory genes induced by cooperation between PGE2 and TNF signaling, to gain insight into mechanisms underlying signaling crosstalk, and address the important question of how PGE2-TNF crosstalk is modulated by IFN-g, as occurs in RA synovial macrophages. We performed an integrated transcriptomic and epigenomic analysis of gene expression and chromatin accessibility using primary human monocytes, which correspond directly to cells that migrate into inflamed synovium and provide an opportunity to model in vivo activation.

first: Upneet

last: Sokhi

first: Bikash

last: Mishra

first: Ruoxi

last: Yuan

first: Lionel

middle: B

last: Ivashkiv


title: EMP1 preserves hematopoietic stem cell potential under homeostasis and radiation-induced injury by alleviating ER stress [ER-stress RNA-seq]

first: Zhe

overall_design: HSCs (CD48-CD150+LSK) were sorted from wild-type C57BL/6J mice injected intraperitoneally with DMSO or Tunicamycin (2 mg/kg) and then subjected to RNA-seq.


title: Opposing Regulation of TNF Responses and IL-1b+ Macrophages by PGE2-cAMP Signaling and IFN-g [RNA-seq]


title: Oncogenic fusions converge on shared mechanisms in initiating astroblastoma [RNA-seq of iNPC]

first: wei

overall_design: To investigate how MN1:BEND2 impacts target gene expression, we overexpressed MN1:BEND2 in human induced neural progenitor cells (iNPCs).


title: Semaglutide and bariatric surgery induce distinct changes in the composition of mouse white adipose tissue

status: Public on Mar 26 2025

city: Boston

first: NORC

last: Boston

state: MA

address: 3 Blackfan Circle, CLS0733

institute: Beth Israel Deaconess Medical Center

summary: Adipose tissue is a central player in energy balance and glucose homeostasis, expanding in the face of caloric overload in order to store energy safely. If caloric overload continues unabated, however, adipose tissue becomes dysfunctional, leading to systemic metabolic compromise in the form of insulin resistance and type 2 diabetes. Changes in adipose tissue during the development of metabolic disease are varied and complex, made all the more so by the heterogeneity of cell types within the tissue. Here we present detailed atlases of murine WAT in the setting of diet-induced obesity, as well as after weight loss induced by either vertical sleeve gastrectomy (VSG) or treatment with the GLP-1 receptor agonist semaglutide. We focus on identifying populations of cells that return to a lean-like phenotype versus those that persist from the obese state, and examine pathways regulated in these cell types across conditions. These data provide a resource for the study of the cell type changes in WAT during weight loss, and paint a clearer picture of the differences between adipose tissue from lean individuals who have never been obese, versus those who have.

overall_design: C57BL/6J DIO male mice, 12-13 weeks of age, were purchased from Jackson Labs and maintained on 60% HFD for an additional 2-4 weeks prior to surgery. Mice were fasted overnight prior to surgery. Animals were anesthetized using isoflurane, and a small laparotomy incision was made in the abdominal wall. The lateral 80% of the stomach along the greater curvature was excised in VSG animals by using an ETS 35-mm staple gun. Sham surgery was performed by the application of gentle pressure on the stomach with blunt forceps for 15 seconds. All mice received one dose of Buprinex (0.1 mg/kg) and Carprofen (5 mg/kg) immediately after surgery. All mice received Carprofen (5 mg/kg) for 3 days after surgery. Animals were placed on DietGel Boost for 3 days after surgery. They were placed back on the pre-operative solid diet (60% HFD) on day 4 post-surgery. Body weight and food intake as well as overall health were monitored daily for the first 7 days after surgery and once weekly until the end of the studies. Semaglutide (0.04 mg/kg) was administered to some sham-operated mice subcutaneously once daily starting at day 1 post-surgery. Animals were sacrificed at two timepoints post-surgery, at 10 days for all groups (timepoint 1), and at 25 days for semaglutide treated animals and at 35 days for sham and VSG animals (timepoint 2). All mice were fasted for 4 hours prior to tissue collection.

first: Margo

middle: P

last: Emont

first: Evan

middle: D

last: Rosen


title: Molecular landscape of respiratory infection: A large-scale, multi-centre blood transcriptome dataset

city: Darlington

first: Tracy

last: Chew

address: Merewether Building (H04) City Rd & Butlin Ave

department: Sydney Informatics Hub

institute: University of Sydney

summary: Respiratory infections pose significant challenges to global health, impacting millions of individuals annually. Understanding the molecular mechanisms underlying the pathogenicity of these infections is crucial for developing effective interventions. RNA sequencing provides insights into a patient’s global transcriptome changes, facilitating the identification of host gene signatures in response to infection and potential therapeutic targets. Here we present an extensive whole blood transcriptome dataset from a demographically diverse cohort of 502 patients with infections including COVID-19, seasonal coronavirus, influenza A or influenza B, sepsis, septic shock, and co-infections (Viral/Viral, Bacterial/Viral, Bacterial/Viral/Fungal, Viral/Fungal, Viral/ Viral/Fungal).

overall_design: Comparative gene expression profiling analysis of patients wiith respiritory infections.

first: Benjamin

last: Tang

first: Maryam

last: Shojaei


title: EMP1 preserves hematopoietic stem cell potential under homeostasis and radiation-induced injury by alleviating ER stress [EMP1 RNA-seq]

overall_design: HSCs (CD48-CD150+LSK) from Emp1fl/fl and Emp1fl/fl,Tie2-Cre mice were sorted and then subjected to RNA-seq


title: Lineage-resolved analysis of embryonic gene expression evolution in C. elegans and C. briggsae

city: Seattle

first: Robert

middle: H

last: Waterston

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington School of Medicine

summary: We measured the spatiotemporal divergence of gene expression across embryogenesis by collecting, annotating and comparing the transcriptomes of homologous embryonic cell types, using a dataset comprising >200,000 C. elegans cells and >175,000 C. briggsae cells.  What constraints govern the evolution of gene expression patterns across development remains a fundamental question. Single-cell RNA-sequencing can learn these constraints by systematically profiling homologous cells. The conserved invariant embryonic lineage of C. elegans and C. briggsae makes them ideal for comparing cell type gene expression across evolution. Measuring the spatiotemporal divergence of gene expression across embryogenesis, we find a high level of similarity in gene expression programs between species despite tens of millions of years of evolutionary divergence. Nonetheless, thousands of genes show divergence in their cell-type specific expression patterns, with enrichment for functions in environmental response and behavior. Neuronal cell types show higher divergence than others such as the intestine and germline. This work identifies likely constraints on the evolution of developmental gene expression.

relation:
Reanalysis of: GSM3618670
Reanalysis of: GSM3618671
Reanalysis of: GSM3618672
Reanalysis of: GSM3618673
Reanalysis of: GSM3618674
Reanalysis of: GSM3618675
Reanalysis of: GSM3618676

sample_organism:
Caenorhabditis briggsae
Caenorhabditis elegans

overall_design:
Highly synchronized L1 larvae were obtained by repeated cycles of bleaching young adults to obtain eggs, which were then hatched in the absence of food to arrest development in the L1 stage. 50,000 of such highly synchronized L1 stage worms were placed on a large peptone rich plate seeded with OP50 bacteria. The L1 worms were allowed to grow at 20 degrees C for around 48 hours to reach the young adult stage, with most adults holding just 1-4 eggs. To obtain a broader range of developmental stages, in some experiments the adults were incubated for additional time before harvesting. The worms were washed off the plate with M9, gently centrifuged and washed again with M9 to remove bacteria. Embryos were released from adult worms with a 1.2 percent bleach solution in 0.5 N KOH. The bleach/adult worm suspension was gently agitated in the tube and checked under the microscope to closely monitor the worm disintegration. Once most of the worms had disintegrated (approximately 5-6 minutes), the tube containing dissociated embryos was vortexed for about 15 seconds and immediately centrifuged. The supernatant was discarded, and the embryos were washed three times with M9 buffer. After the final wash, the embryos were resuspended in M9 and filtered through a 40-micron nylon mesh cell strainer to eliminate remaining worm carcasses. To obtain embryos of different ages, the eggs were incubated on a petri dish with shaking at 20 for the desired time before single cell dissociation.
For samples the C. elegans samples wt_600, ceh9_300, ceh9_600, mec3_300, mec3_600, M03D4.4_300 and M03D4.4_500, the adults were harvested as soon as they showed eggs, and the eggs were allowed to develop for the time (minutes) indicated. Similarly, for the C. briggsae samples, Cb_EMB_300, Cb_EMB_400 and Cb_EMB_500, the adults were harvested as soon as they showed eggs and the eggs were allowed to develop for the time indicated before the cells were dispersed. For two samples, Cb_EMB_120 and Cb_ EMB_240, the adults were allowed to develop for 410 minutes after the eggs appeared and the eggs were allowed to develop 120 or 240 minutes. For two samples, Cb_EMB_180 and Cb_EMB_360, the adults were allowed to develop 180 minutes after the first eggs appeared and the eggs dispersed either immediately after capture or after an additional 180 minutes.
Embryos were concentrated by centrifugation for single-cell dissociation. To dissociate embryos into single cells, 1U/ml chitinase was added to the embryos at a ratio of 1 ml chitinase to 0.5 ml embryo suspension. The embryo chitinase suspension was transferred to a 30mm petri dish. Degradation of eggshell was continuously monitored for approximately 20-30 min. When the eggshell was degraded, egg buffer was added to the petri dishes. Then 100 microliters of 15 mg/ml pronase solution was added to the sample.
The dissociation of embryos into single cells was carried out by passing embryos repeatedly through a 21gauge needle (approx 20 times) into a 1.5ml Eppendorf tube. The single-cell suspension was confirmed under a microscope. Single-cell concentration was determined using a cell counter and subjected to the 10X Chromium GEM version 3.0 single-cell capture procedure immediately.
RNA library preparation followed the 10X Chromium procedure. Samples were sequenced with Illumina NextSeq 550 instruments using NextSeq Hi 75 cycles.
These sequence files as well as the seven sequence files from the seven samples from GEO Series GSE126954 were processed as described in the data processing step descriptions.

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

first: Christopher

middle: R

last: Large

first: Rupa

last: Khanal

first: LaDeana

last: Hillier

first: Chau

last: Huynh

first: Connor

last: Kubo

first: Junhyong

last: Kim

first: John

middle: I

last: Murray


title: Hepatic lipid remodeling in cold exposure uncovers direct regulation of bis(monoacylglycero)phosphate lipids by Pla2g15

status: Public on Mar 25 2025

city: Madison

first: Thomas

last: Kizzar

state: Wisconsin

address: 711 S Dickinson St Apt 2

department: Biochemistry

institute: University of Wisconsin-Madison

summary: Cold exposure is a selective environmental stress that elicits a rapid metabolic shift to maintain energy homeostasis. In response to cold exposure, the liver rewires the metabolic state shifting from glucose to lipid catabolism. By probing the liver lipids in cold exposure, we observed that the lysosomal bis(monoacylglycero)phosphate (BMP) lipids were rapidly increased during cold exposure. BMP lipid changes occurred independently of lysosomal abundance but were dependent on the lysosomal transcriptional regulator transcription factor EB (TFEB). Knockdown of TFEB in hepatocytes decreased BMP lipid levels and led to cold intolerance in mice. We assessed TFEB binding sites of lysosomal genes and determined that the phospholipase Pla2g15 regulates BMP lipid catabolism. Knockdown of Pla2g15 in mice increased BMP lipid levels, ablated the cold-induced rise, and improved cold tolerance. Knockout of Pla2g15 in mice and hepatocytes led to increased BMP lipid levels, that were decreased with re-expression of Pla2g15. Mutation of the catalytic site of Pla2g15 ablated the BMP lipid breakdown. Together, our studies uncover TFEB regulation of BMP lipids through Pla2g15 catabolism.

overall_design: Chromatin immunoprecipitation was performed on livers from individually housed male C57BL/6J mice (11 weeks old) that were placed at 4°C without food for 6 hours or kept at RT with ad libitum access to food (n=2 per group). All mice had ad libitum access to water. SimpleChIP Plus Enzymatic Chromatin IP Kit was used according to manufacturer’s instructions. Briefly, 100mg of tissue was used per mouse and two immunoprecipitations were performed with rabbit anti-TFEB antibody, and two immunoprecipitations were performed with normal rabbit IgG control. ChIP DNA was purified using Zymo ChIP DNA Clean and Concentrator Kit. Purified immunoprecipitated and input DNA was quantified and assessed for sheering using the Qubit dsDNA HS Assay Kit and Agilent DNA HS chip, respectively. Samples were prepared according the TruSeq ChIP Sample Preparation kit. Libraries were size selected for an average insert size of 350 bp using SPRI-based bead selection. Quality and quantity of the finished libraries were assessed using an Agilent Tapestation and Qubit dsDNA HS Assay Kit, respectively. Paired end 150bp sequencing was performed on the NovaSeq 6000 by the UW-Madison Biotechnology Center. Sequenced reads were checked for: sequencing quality, insert length, read concordance, duplications, and adapters via FastP and then aligned to the mouse genome (UCSC build mm10) via bowtie2 v2.2.5 using the sensitive end-to-end read alignment mode. Aligned reads are sorted and indexed with SAMtools 1.9 and peaks are called at p<0.05 and q<0.05 (separately) using the input/IgG as the background control with the MACS2.  Primary and differential peaks were annotated for their positioning relative to genomic elements with Homer v4.11. De novo and known motif analysis were carried out with Homer. Pathway ontology information was generated by inputting genes differentially bound in cold or RT into geneontology.org for ‘Reactome’ pathway results

first: Jessica

last: Davidson

first: Raghav

last: Jain

first: Gisela

last: Geoghegan

first: Daniel

last: Nesbitt

first: Amy

last: Cavanagh

first: Akira

last: Abe

first: Kwamina

last: Nyame

first: Andrea

last: Hunger

first: Xiaojuan

last: Chao

first: Isabella

last: James

first: Helaina

last: Von Bank

first: Dominique

middle: A

last: Baldwin

first: Gina

last: Wade

first: Sylwia

last: Michorowska

first: Rakesh

last: Verma

first: Kathryn

last: Scheuler

first: Vania

last: Hinkovska-Galcheva

first: Evgenia

last: Shishkova

first: Wen-Xing

last: Ding

first: Joshua

last: Coon

first: James

last: Shayman

first: Monther

last: Abu-Remaileh

first: Judith

last: Simcox


title: Specific origin selection and excess functional MCM2-7 loading in ORC-deficient cells

city: Charlottesville

first: Anindya

last: Dutta

state: VA

address: 1300 Jefferson Park Ave

department: Biochemistry & Molecular Genetics

institute: University Of Virginia

summary: Origin Recognition Complex (ORC) is composed of six subunits, ORC1-6, and the entire complex loads excess MCM2-7 on chromosomes to promote initiation of DNA replication in organisms ranging from S. cerevisiae to humans.  ORC is also believed to be important for origin specification. Mapping of origins in the cancer cell lines engineered to delete three of the subunits, ORC1, ORC2 or ORC5 shows that origin specification continues at mostly the same sites in the absence of ORC.  The few hundred origins that were up-regulated in the absence of ORC suggest that GC/TA skewness and simple repeat sequences facilitate origin selection in the absence of the six-subunit ORC. In the absence of ORC, MCM2-7 association with chromatin continues to be sufficiently in excess to license reserve origins, used under replication stress, and to permit re-replication, which requires repeated loading of MCM2-7 at origins in the same cell-cycle.  Thus, origin specification and excess MCM2-7 loading on origins can be executed in mammalian cancer cells in the absence of the six-subunit ORC.

overall_design: SNS-seq for HCT116 WT and ORC1, ORC2 and ORC5 knockout cells

first: Yoshiyuki

last: Shibata

first: Mihaela

last: Peycheva

first: Etsuko

first: Daniel

last: Malzl

first: Rushad

last: Pavri