title: Gene expression radiation response in female mice after protracted external irradiation simulating internal 137Cs.

city: New York

first: Shanaz

middle: Adi

last: Ghandhi

address: 630, W 168th street

department: Center for Radiological Research

institute: Columbia University Medical Center

summary: We then performed gene expression profiling analysis using data obtained from RNA-seq of different time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for blood cell response to radiation profilte simulating internal 137Cs

first: Sally

last: Amundson


title: Single-cell transcriptomic landscape of epithelial heterogeneity in metastatic hormone-naïve prostate cancer

status: Public on Feb 05 2026

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

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

type: Expression profiling by high throughput sequencing

summary: Single-cell transcriptomic profiling was performed on diagnostic prostate biopsy specimens from patients with metastatic hormone-naïve prostate cancer to characterize epithelial tumor heterogeneity at diagnosis. Integrated and case-specific analyses revealed that tumors are composed of heterogeneous epithelial cell populations, including basal-associated and epithelial–mesenchymal transition–related transcriptional states, in addition to conventional luminal epithelial cells. No discrete epithelial cluster with high expression of canonical neuroendocrine markers was detected at baseline. These data provide a single-cell–level resource describing epithelial transcriptional states in treatment-naïve metastatic prostate cancer.

overall_design: Diagnostic prostate biopsy specimens from five patients with metastatic hormone-naïve prostate cancer were subjected to single-cell RNA sequencing using the 10x Genomics Fixed RNA Profiling (Flex) platform. The study was designed to characterize epithelial tumor heterogeneity at diagnosis using integrated and case-specific single-cell transcriptomic analyses.

first: Ryuta

last: Watanabe

first: Noriyoshi

last: Miura

first: Tadahiko

last: Kikugawa

first: Takashi

last: Saika


title: Common pathogenic mechanisms in the hippocampus across neurodegenerative dementias: Alzheimer's disease, Down syndrome, and Parkinson's disease

city: Barcelona

first: René

middle: Albert Johan

last: Crans

state: Catalonia

address: Carrer del Dr. Aiguader, 88

department: Systems and Synthetic Biology

country: Spain

institute: Centre for Genomic Regulation

summary: Extensive evidence suggests overlapping pathological mechanisms in the brain of individuals with Parkinson´s disease dementia, Down syndrome dementia, and Alzheimer´s disease. For these neurodegenerative dementias, we observed that the chronological age did not align with their biological age, which was determined based on hippocampal transcript levels (i.e., transcriptional age). Subsequently, we performed a transcriptomic analysis that corrected for the transcriptional age in the hippocampus of affected individuals, highlighting common underlying pathogenic mechanisms. There were 45 common differentially expressed genes (DEGs), whereas enriched functional terms were related to lysine N-methyltransferase activity and intermediate filament. Co-expression network analysis displayed a module that was significantly downregulated in the non-demented control group only. This module identified EHMT2 and LMNB2 as hub genes, which were also common DEGs. Overall, these findings uncover shared functional insights in the hippocampus, while specifically highlighting EHMT2 and LMNB2 as potential universal biomarkers or disease-altered targets across neurodegenerative dementias.

overall_design: Total RNA-seq profiling of hippocampal tissue originating from non-demented, Parkinson's disease dementia, Down syndrome dementia, and Alzheimer's disease individuals.

first: André

last: Strydom

first: Debby

last: Van Dam

first: Peter

last: De Deyn

first: Marie-Claude

last: Potier

first: Mara

last: Dierssen


title: TGF-β controls epigenetic re-programing of IFN-antiviral trained immunity and impairs virologic control in SIV-infected rhesus macaques [scMultiome]

status: Public on Feb 06 2026

city: Atlanta

first: Felipe

last: ten Caten

state: Georgia

address: 1750 Haygood Road

department: Department of Pathology and Laboratory Medicine

country: USA

institute: Emory University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Current immunotherapeutic approaches to eliminate latently HIV-infected cells have focused on targeting the adaptive arm of the immune system using vaccines and passive transfer of broadly neutralizing antibodies (bNAbs). Epigenetic reprogramming of innate myeloid cells triggered by adjuvants was recently shown to promote a state of interferon (IFN)-induced antiviral immunity and resistance to heterologous viral infections. Herein, flow cytometry, bulk and single-cell RNA-Seq/ATAC-Seq were performed on samples from a cohort of SIV-infected, virologically suppressed rhesus macaques (RMs) treated with anti-IL-10 and anti-PD-1 monoclonal antibodies (combo treatment) prior to analytical treatment interruption (ATI). These experiments revealed that combo treatment led to selective changes in chromatin accessibility, expression of IRF7/3 and STAT1, and expression of IFN-stimulated antiviral genes in myeloid cells and CD4+ T cells. These RMs showed a stringent and prolonged control of SIV viral rebound following ATI and a decay in levels of cell-associated viral DNA (CA-vDNA) in lymph nodes. These RMs showed reduced chromatin accessibility for the SMAD2/SMAD3, AP-1, and NFKB1 loci and lower expression of TGF-b and SMADs target genes. This signature is consistent with that observed in HIV elite controllers, who maintain undetectable levels of virus in the absence of ART and whose HIV reservoir size is small. These results highlight the critical role of the interplay between TGF-b and IFN in epigenetically regulated innate antiviral immune responses that can impact the viral reservoir.

overall_design: Twenty-eight rhesus macaques were infected intravenously with SIVmac239. After 14 months on antiretroviral therapy (ART), RMs were randomized into 3 groups: 8 RMs received vehicle and served as controls; 10 RMs received deimmunized aIL-10, and 10 RMs received deimmunized aIL-10 and deimmunized aPD-1 (combo group). Combo-treated animals were dichotomized as CA-vDNAlo (n = 4) and CA-vDNAhi (n = 6) based on the size of the SIV reservoir 24 weeks post-ATI (<2 log10 and >2 log10 CA-vDNA copies per 106 CD4+ T cells, respectively)

last: ten-Caten

first: Khader

last: Ghneim

first: Mirko

last: Paiardini

first: Susan

middle: P

last: Ribeiro

first: Rafick

last: Sekaly


title: Ago2 protects against diabetic cardiomyopathy via activating mitochondrial gene translation

city: Wuhan

first: zhan

last: jiabing

address: Jiefang Avenue

country: China

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

type: Non-coding RNA profiling by high throughput sequencing

summary: Diabetes is associated with cardiovascular complications. microRNAs translocate into subcellular organelles to modify genes involved in diabetic cardiomyopathy. However, functional properties of subcellular Ago2, a core microRNA, remain elusive. We elucidated the function and mechanism of subcellular localized Ago2 on mouse models for diabetes mellitus and diabetic cardiomyopathy. Ago2 decreased in cardiomyocyte mitochondria in both models. Overexpression of mitochondrial Ago2 attenuated diabetes-induced cardiac dysfunction. Ago2 recruited TUFM, a mitochondria translation elongation factor, to activate translation of electron transport chain (ETC) subunits and decrease reactive oxygen species. Malonylation, a post-translational modification of Ago2, reduced the importing of Ago2 into mitochondria in diabetic cardiomyopathy. Ago2 malonylation was regulated by a cytoplasmic-localized short isoform of SIRT3 through a previously unknown demalonylase function. Our results reveal that the SIRT3–Ago2–CYTB axis links glucotoxicity to cardiac ETC imbalance, providing new mechanistic insights and the basis to develop mitochondria targeting therapies for diabetic cardiomyopathy.

overall_design: Comparative microRNA profiling analysis of RNA-seq data for mitochondria extracted from STZ-treated mouse heart and its control.

first: Jiabing

last: Zhan

first: Kunying

last: Jin

first: Jiahui

last: Fan

first: Chen

last: Chen

first: Huaping

last: Li

first: Dao

middle: W

last: Wang


title: Gene expression profile at single cell level of Merkel cells from embryonic, neonatal and postnatal mouse skin

city: Bethesda

first: Lingling

last: Miao

state: MD

address: 9000 Rockville Pike

department: NIAMS

institute: National Institutes of Health

summary: Merkel cells (MCs) are neuroendocrine touch sensors in the epidermis. We used single cell RNA sequencing (scRNA-seq) to analyze the differentiation of MCs in mouse skin.

overall_design: GFP-expressing cells including MCs were isolated from the skin of Sox2-GFP and Gfi1-GFP reporter mice by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Isaac

last: Brownell


title: TRalpha Deficiency Drives Sarcopenia by Disrupting Perimitochondrial Targeting of Pink1 mRNA and Mitophagy

city: nanjing

first: Yusheng

last: Zhang

address: Nanjing Medical university

institute: Division of Geriatrics

summary: Skeletal muscle-specific ablation of thyroid hormone receptor alpha (TRalpha) in young mice is sufficient to recapitulate key phenotypic hallmarks of age-related sarcopenia—including myofiber atrophy, exercise intolerance, and mitochondrial quality control failure—establishing receptor decline as a cell-autonomous driver of sarcopenia pathogenesis rather than a passive biomarker. The underlying mechanism reveals how systemic endocrine signals culminate in organelle-specific quality control defects: TRalpha transcriptionally drives the RNA-binding protein CLUH, which facilitates the perimitochondrial enrichment of Pink1 mRNA for localized synthesis of the mitophagy-initiating kinase. Consequently, TRalpha loss disrupts perimitochondrial Pink1 mRNA localization, impairing local PINK1 abundance and mitophagic priming, leading to accumulation of damaged mitochondria. Restoring CLUH expression rescues Pink1 mRNA spatial localization, mitophagy flux, and cellular senescence markers in both TRalpha-deficient myofibers and naturally aged muscle cells. These findings identify spatial transcriptome organization as an underappreciated regulatory layer in muscle wasting and provide a genetically defined framework linking endocrine decline to organelle-level post-transcriptional regulation.

overall_design: Transcriptomic analysis of gastrocnemius muscle from 8-week-old male TRalpha-mKO mice (Myf5-Cre; Thrafl/fl) versus wild-type littermates (n=3 per genotype)

first: Runqing

last: Shi

first: Yu

last: Duan


title: Alterations to the bronchial gene-expression effects of tobacco smoking in people living with HIV

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

summary: Background: Although acquired immunodeficiency syndrome-related mortality has decreased since the introduction of antiretroviral therapy, the incidence of lung cancer in patients living with HIV (PLWH) remains high. Understanding the effects of tobacco smoke on airway gene expression in PLWH may provide insight into the elevated lung cancer risk associated with HIV. Methods: Airway epithelial brushings were collected from 12 PLWH who smoke and 19 PLWH who have never smoked and profiled using RNA-seq. Linear models were used to identify genes differentially expressed between people who smoke and have never smoked and between people who previously smoked and have never smoked. Gene set enrichment analysis was used to validate smoking-related gene signatures across datasets. Data was integrated with gene expression data from a cohort of patients without HIV to identify genes differentially modulated by both smoking and HIV status. Results: We found that previous smoking-related gene signatures are similarly associated with smoking in PLWH, including the persistent differential expression of a subset of "irreversibly altered" genes in people who previously smoked compared to people who have never smoked. We also identified and validated two gene signatures specifically modulated in people who smoke without HIV. Conclusions: Many of the effects of smoking on bronchial gene expression are shared between PLWH and non-HIV individuals. Of the subset of genes that differ between PLWH and non-HIV individuals, it appears that the effect of smoking on gene expression is more attenuated in PLWH.  This includes genes related to oxidative stress and epithelial integrity, and suggests potential mechanisms that may contribute to smoking-related outcomes that are more prevalent in PLWH, such as lung cancer.

overall_design:
Airway epithelial brushings were collected from 12 PLWH who smoke and 19 PLWH who have never smoked and profiled using RNA-seq.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Minyi

last: Lee

first: Marc

middle: E

last: Lenburg


title: Next Generation Sequencing to evaluate effects of AhR on mouse livers

city: Maastricht

first: Han

address: P. Debyelaan 25

country: Netherlands

institute: Maastricht University

summary: In this study, Apoe-/- control mice and Apoe-/-AhR-/- mice were placed on a HFD for 12 weeks. Livers from these mice were used to perform NGS analysis.

overall_design: Mouse livers isolated from Apoe-/- control mice and Apoe-/-AhR-/- mice after 12 weeks HFD.

first: Emiel

last: Van der Vorst


title: Coordination of nuclear RNA processing by speckle-localized kinase TAOK2

city: Philadelphia

first: Kristen

last: Lynch

state: Pennsylvania

address: 906 Stellar Chance Labs 422 Curie Blvd

department: Biochemistry and Molecular Biophysics

institute: University of Pennsylvania

summary: Nuclear speckles are membraneless organelles that act as active splicing hubs especially at sites of high transcription. Emerging views of this dynamic subnuclear structure place it as a hub of RNA processing, impacting steps from transcription to export. To manage this complex microcosm of RNA metabolism, nuclear speckles also require kinases and phosphorylation to execute their functions. The nuclear speckle-localized kinase, TAOK2, mediates the splicing and export of viral transcripts at the nuclear speckle, but its role in the processing of cellular transcripts was unknown. We used siRNA knockdown of TAOK2 and assessed RNA transcripts in both whole cell and nucleocytoplasmic fractions to characterize the complete endogenous effects of TAOK2. We found that TAOK2 knockdown impacts over 10% of the transcriptome, through changes in alternative splicing, export and transcript abundance. Cellular and biochemical phosphoproteomics further revealed nuclear speckle scaffolding proteins SRRM1 and SRRM2 as potential direct phosphorylation targets of TAOK2, mediating its large effects on speckle integrity and speckle-localized splicing. Indeed, knockdown of TAOK2 perturbs almost all speckle-resident serine/arginine (SR)-rich proteins while leaving heterogeneous ribonucleoproteins unperturbed. Altogether, we propose that phosphorylation of SRRM1/2 by TAOK2 plays a structural maintenance role that impacts SR protein-driven exon inclusion at the nuclear speckle.

overall_design: siRNA knockdown of TAOK2 and RNA-seq with controls (3 replicates each condition[siTAOK2, siCON]); siRNA knockdown RNA-seq and nucleocytoplasmic fractionation and controls (2 replicates each condition[siTAOK2: nuc, cyt, total, siCON: nuc, cyt, total])

first: Bridget

last: Begg

first: Shengyan

last: Gao

first: Beatriz

last: Fountoura


title: Small molecule-directed differentiation of submerged-cultured human nasal airway epithelia for respiratory disease modelling [scRNA-seq]

city: Utrecht

first: Gimano

last: Amatngalim

address: Heidelberglaan 100

department: Pediatrics

institute: University Medical Center Utrecht

summary: Submerged cultures of undifferentiated or transformed epithelial cells are widely used in respiratory research due to their ease of use and scalability. However, these systems fail to capture the cellular diversity of the human airway epithelium. Here, we describe a submerged differentiation model using cryopreserved human nasal epithelial cells obtained via minimally invasive brushings. By targeting Notch and BMP signaling with small-molecule inhibitors, we differentiate these cells into complex epithelial cultures containing basal, secretory, and ciliated cell types on standard plastic cultureware. This method supports scalable culturing of both 2D epithelial monolayers and 3D organoids, and is applied to disease modeling in primary ciliary dyskinesia, cystic fibrosis, and respiratory syncytial virus infection. The resulting system enables scalable assessment of disease-relevant epithelial functions in respiratory research

overall_design:
HNEC were submerged differentiated in 6-well plastic plates (n=3 independent healthy donors), dissociated using TrypLE express enzyme and resuspended to a single cell suspension. Samples were pelleted, washed with PBS, resuspended in FACS buffer (PBS0, 1% FBS, 0.5 mM EDTA and DAPI) and strained (35 µm). 376 cells per donor were immediately sorted into 384-well cell-capture plates containing ERCC spike-ins (Agilent), RT primers and dNTP (Promega) using a BD FACSJazz. ScRNA-seq was performed according to the SORT-seq protocol Muraro, M. J. et al. A Single-Cell Transcriptome Atlas of the Human Pancreas. Cell Syst. 3, 385-394.e3 (2016).

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Hetty

middle: M

last: Dreyer

first: Jeffrey

last: Beekman

middle: D


title: Pathway-Specific Canalization and Plasticity of Gene Expression during C. elegans Dauer Development

city: Buffalo

first: Johnny

last: Cruz Corchado

state: NY

address: Elm & Carlton Streets Buffalo,L3-L125

department: Cell Stress

institute: Roswell Park Comprehensive Cancer Institue

summary: Caenorhabditis elegans development, where different environmental or genetic stimuli can each induce larvae to switch from continuous growth to a seemingly identical dauer (dormancy) state, provides a tractable model to explore this question. To identify dauer features that differ or are invariant, we compared gene expression of dauers induced by different dauer-inducing conditions, globally and within >100 sets of curated covarying genes or “modules” enriched for functional features such as ‘protein expression’, mitochondria’, ‘germline’, etc., through gene co-expression network analyses.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  C. elegans dauer following treatment with Pheromone and Starvation

last: Cruz

first: Kavinila

last: Selvarasu

first: Veena

last: Prahlad


title: Multi-omics analysis of human placentas from first year of the COVID-19 pandemic reveals sex-dependant effects

city: Laval

first: Cathy

last: Vaillancourt

state: QC

address: 531 boulevard des Prairies

department: Centre Armand Frappier Santé Biotechnologie

country: Canada

institute: INRS

summary: The COVID-19 pandemic affected millions of pregnant persons, yet the consequences of maternal SARS-CoV-2 infection on the placental function and the fetal health remain poorly characterized. While inflammatory and structural alterations have been described in placentas from exposed pregnancies, the underlying molecular mechanisms are still unclear. The aim of this study was to evaluate transcriptomic alterations in placentas exposed to maternal SARS-CoV-2 infection (COVID+) compared to unexposed placentas (COVID-). We analyzed 67 placentas collected between March 2020 and June 2021 from singleton pregnancies with (n = 41) or without (n = 26) a history of maternal SARS-CoV-2 infection during pregnancy. Demographic, obstetric, placental, and fetal data were extracted from the medical records. SARS-CoV-2 RNA was not detected in any placental sample. Bulk RNA-sequencing was performed on villous biopsies preserved either frozen or in RNALater. Global transcriptomic analysis comparing COVID+ and COVID- placentas revealed an upregulation of genes involved in cytoskeleton organization. Stratified analysis by fetal sex identified a marked sex-specific response, with 43 differentially expressed genes (DEGs) in placenta from female fetuses (XX) in the COVID+ group compared to COVID-, whereas only one DEG was identified in placenta from male fetuses (XY). In XX COVID+ placentas, pathways related to cytoskeleton organization, pregnancy specific processes, and muscle development were altered. These results highlight a sex-specific dysregulation of placental gene expression following maternal SAR-CoV-2 infection, predominantly affecting placentas from female fetuses.

overall_design: Bulk rRNA-depleted RNA sequencing was performed on placental villous biopsies from human pregnancies with or without a history of maternal SARS-CoV-2 infection. Transcriptomic analyses were conducted globally and stratified by fetal sex.

first: Hélène

last: Pinatel

first: Marie-Pier

last: Scott-Boyer

first: Marie-Ève

last: Brien

first: Sylvie

last: Girard

first: Arnaud

last: Droit

first: Géraldine

last: Delbès

first: Laurent

last: Chatel-Chaix


title: Genome-wide EGR1 chromatin occupancy in wild-type C57BL/6J bone-marrow–derived macrophages measured by CUT-taq

city: Shanghai

first: Qiancheng

last: Xiao

address: Building 25, No. 1188, LIANHANG Road, Pujiang Town, Minhang District, Shanghai

institute: Shanghai OE Biotech Co., Ltd

summary: This study generated CUT-taq (tagmentation-based in situ ChIP; CUT&Tag-like) sequencing data to profile genome-wide EGR1 chromatin binding in mouse bone-marrow–derived macrophages (BMDMs). BMDMs were differentiated from wild-type C57BL/6J bone marrow in GM-CSF for 7 days, harvested at 4.0 × 10^5 cells per sample, and processed using the Hyperactive™ In-Situ ChIP Library Prep Kit for Illumina (Vazyme TD901–TD902). Cells were immobilized on concanavalin A beads, permeabilized with digitonin, incubated with anti-EGR1 primary and secondary antibodies (Thermo), and tagmented with Hyperactive pA-Tn5 (Vazyme). Libraries were PCR-amplified with P5/P7 primers, quality-checked on an Agilent 2100 Bioanalyzer, and sequenced on an Illumina NovaSeq 6000 (paired-end 150 bp). Raw sequencing files (FASTQ) and processed data files are provided to enable reuse and reanalysis of EGR1 binding profiles in GM-CSF–differentiated macrophages.

overall_design: Genome-wide EGR1 binding was profiled by CUT-taq in GM-CSF–differentiated wild-type C57BL/6J BMDMs. Biological replicate samples were prepared from independent macrophage preparations, and each replicate was processed through the complete CUT-taq workflow (concanavalin A bead binding, digitonin permeabilization, anti-EGR1 antibody binding, pA-Tn5 tagmentation, PCR amplification, and Illumina sequencing). Sequencing was performed on Illumina NovaSeq 6000 with paired-end 150 bp reads. The submission includes raw FASTQ files (and associated metadata) and, where applicable, processed outputs (e.g., aligned files and peak calls) to support reproducible downstream analyses of EGR1 chromatin occupancy.

first: Yifan

last: Tu

first: Ke

last: Sui

first: Zheng

last: Wang

first: Jiawei

last: Zhang

first: Ying

last: Gu


title: An integrin α3β1-CSTF3 signaling axis regulates alternative polyadenylation of Mmp9 mRNA

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

summary: The laminin-binding integrin α3β1 is highly expressed in epidermal keratinocytes, where it coordinates diverse cellular functions and gene expression during skin remodeling. Here, we show that α3β1-MEK/ERK signaling operates in vivo to promote proximal polyadenylation site (PAS) usage in the Mmp9 gene, generating a short, more stable mRNA transcript. Using mice with inducible, epidermis-specific α3 deletion, RNA in situ hybridization revealed that loss of α3β1 increased the long Mmp9 transcript in healing wounds and epidermal tumors. α3β1-MEK/ERK signaling in keratinocytes induced the expression of the cleavage stimulation factor CSTF3, a known regulator of alternative polyadenylation (APA), while CSTF3 knockdown shifted Mmp9 toward distal PAS usage. Moreover, α3 deletion reduced Cstf3 gene expression and altered APA in vivo. Genome-wide DaPars2 analysis identified α3β1-dependent APA across numerous genes, including some encoding components of the keratinocyte secretome. Together, these findings define a novel α3β1-MEK/ERK-CSTF3 axis that orchestrates post-transcriptional gene regulation through APA, revealing α3β1 as a potential target for wound and cancer therapies.

overall_design: Immortalized mouse keratinocytes (MK cells) that lack α3 integrin (MK-/-), and  MK-/- cells reconstituted with human α3 integrin (MK-/-:hα3), were cultured on collagen-coated tissue culture dishes in supplemented low calcium Minimum Essential Medium (MEM; Thermo Fisher Scientific; cat. # 11380037) and incubated at 33oC with 8% CO2. RNA isolation and sequencing was performed by Azenta Life Sciences. All downstream analyses were conducted by the Albany Medical College Bioinformatics Core, including quality control (FastQC, MultiQC), read alignment, gene quantification, and integrative analyses.

first: Giesse

last: Albeche Duarte

first: Michael

last: DiPersion


title: Small molecule-directed differentiation of submerged-cultured human nasal airway epithelia for respiratory disease modelling [bulkRNA-seq]

first: Gimano

last: Amatngalim

overall_design:
RNAseq profiling of nasal-brushing derived basal cells (BCs), submerged-differentiated human nasal epithelial cells (S-diff HNEC) and air-liquid interface differentiated HNEC (ALI-HNEC), both differentiated for 21 days.

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Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Hetty

last: Dreyer

first: Jeffrey

last: Beekman


title: Self-clustering of three CBX2 molecules drives PRC2 to promote facultative heterochromatinization of Polycomb target genes [RNA-Seq]

city: Aurora

first: Srinivas

last: Ramachandran

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

summary: Phase separation is increasingly recognized in facultative heterochromatinization of Polycomb target genes; however, the underlying mechanisms remain obscure. Using single-molecule imaging and tracking, we show that individual condensates in mESCs contain approximately 3 CBX2 molecules and numerous PRC1 and PRC2 subunits and indicate that the composition and dynamics of condensates are developmentally regulated. We reveal that CBX2 clusters PRC2 and controls the spatial distribution of both PRC2 and H3K27me3. Using genomic approaches, we demonstrate that CBX2 binds condensate initiation sites enriched for PRC2 nucleation sites. CBX2 deletion causes PRC2 and H3K27me3 to redistribute from their regular targets. By developing a separate-of-function variant, we determine that CBX2 relies on its self-clustering ability to function. These findings collectively support a novel phase-separation model driven by nucleation and bridging, in which low-abundance proteins self-cluster to initiate condensate assembly, a process tightly coupled to function.

overall_design: CUT&RUN of tagged CBX2 and EZH2 in CBX2fl/fl-HaloTag EZH2-Venus-dTag, CUT&RUN of tagged CBX2-PSM-HT  in CBX2fl/fl-HaloTag & Parental Cells,  CUT&Tag of H3K27me3 in mESCs (CBX2 WT, CBX2 KO, CBX2 PSM, and PGK12.1) in two biological replicates.

first: Steven

last: Ingersoll

first: Abby

last: Trouth

first: J. Carlos

last: Angel

first: Xinlong

last: Luo

first: Axel

last: Espinoza

first: Joey

last: Wen

first: Chengjie

last: Zhu

first: Joseph

last: Tucker

first: Kalkidan

last: Astatike

first: Christopher

middle: J

last: Phiel

first: Hatim

last: Sabaawy

first: Tatiana

middle: G

last: Kutateladze

first: Tao

last: P. Wu

first: Tingting

last: Yao

first: Chao

last: Lu

first: Xiaojun

last: Ren


title: HIF regulatory network reflects kidney disease progression in diabetes and reversal with SGLT2 inhibition

city: Ann Arbor

first: Jennifer

middle: A.

last: Schaub

state: MI

address: 1500 Medical Center Dr

department: Internal Medicine

institute: University of Michigan

summary: Hypoxia drives diabetic kidney disease (DKD) progression through Hypoxia Inducible Factor (HIF) signaling. The kidney’s cellular heterogeneity and complex architecture pose challenges for directly assessing the pharmacologic effects on kidney oxygenation and hypoxia responsive pathways in vivo, such as treatment with SGLT2 inhibitors (SGLT2i), presumed to impact kidney oxygenation. Using single-cell transcriptional profiling of kidney tissue from youth with type 2 diabetes (T2D) who showed minimal clinical evidence of DKD, we identified cell type enrichment of HIF regulated genes, findings that replicated in people with later stage DKD in the Kidney Precision Medicine Project (KPMP). Using conserved transcription factor (TF) binding motifs, higher-order promoter regulatory structures identified potential cooperating TFs that explained the cell type enrichment pattern. From these promoter elements, 7 interconnected regulatory pathways were identified, comprising a network of 237 genes.  Analysis of multiome data from reference tissue in KPMP demonstrated that 80% of the network genes resided in accessible chromatin. Expression of network genes increased significantly in late compared to early stage DKD and were validated in a hypoxic human organoid model system. Kidney tissue from individuals with T2D treated with SGLT2i demonstrated reversal of the accumulated changes in the HIF network compared to those not treated with SGLT2i. Most high confidence genes showed concordant differential expression in spatial transcriptomics from individuals with T2D.  Hypoxic kidney organoids treated with SGLT2i confirmed these protective effects. Our promoter-anchored HIF regulatory network provides a multi-component read-out that captures disease progression and quantifies therapeutic response to SGLT2i.

overall_design:
Formalin fixed paraffin embedded (FFPE) biopsy cores from four individuals with type 2 diabetes (T2D) not treated with SGLT2i were sectioned, placed on a slide, and run through the VisiumHD platform (v1; 10x). Each slide is comprised of a grid of 8 um by 8 um squares and each square or spot is covered in a lawn of one unique barcode identifier that anneals to any RNA within that grid space.

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Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Viji

last: Nair

first: Cathy

last: Smith

first: Celine

last: Berthier

first: Matthias

last: Kretzler

middle: A


title: Self-clustering of three CBX2 molecules drives PRC2 to promote facultative heterochromatinization of Polycomb target genes [Hi-C]

first: Srinivas

last: Ramachandran

first: Steven

last: Ingersoll

first: Abby

last: Trouth

first: J. Carlos

last: Angel

first: Xinlong

last: Luo

first: Axel

last: Espinoza


title: Sodium Alginate Activates Subcutaneous Fat Differentiation via the PPAR Pathway

city: Nabjing

first: Yufan

last: Gan

address: Longmian Avenue

institute: Nanjing Medical University

summary: To investigate the effect of sodium alginate on adipocyte differentiation, we isolated the stromal vascular fraction (SVF) from wild-type C57BL/6J mice and subjected it to whitening treatment. During the induction of differentiation, sodium alginate reagent at concentrations of 0 μM, 50 μM, and 100 μM was added to the experimental groups, respectively. On the sixth day of culture, cells from both the experimental and control groups were collected for transcriptome analysis.

overall_design: SVF cells were isolated from wild-type C57BL/6J mice and cultured in vitro until they reached contact inhibition.For white adipogenesis induction, a medium containing insulin (1μg/ml), dexamethasone (1μM), and isobutylmethylxanthine (0.5mM) was used. After 48 hours, the medium was replaced with one containing only insulin to maintain adipocyte differentiation. Throughout the 6-day induction period, sodium alginate was continuously supplemented at concentrations of 0,50,or100μM. Following differentiation, samples were collected for RNA extraction and transcriptome sequencing.

first: Kai

last: Li


title: SAGA/ATAC complexes sustain aberrant chromatin regulation and promote tumorigenesis in diffuse midline glioma [CUT&Run]

city: Houston

first: Jamie

middle: N.

last: Anastas

state: TX

address: 1 Baylor Plaza

department: Neurosurgery

institute: Baylor College of Medicine

summary: Diffuse midline gliomas (DMG) are aggressive pediatric brain tumors characterized by chromatin and transcriptional dysregulation induced by H3K27M mutations. Strategies for overcoming epigenetic dysfunction to reduce DMG tumorigenesis remain limited. We identified multiple components of the SAGA and ATAC chromatin regulatory complexes as DMG genetic dependencies and found that genetic or pharmacological inhibition of the SAGA/ATAC-associated chromatin reader, SGF29, reduces DMG proliferation. Small molecules targeting SAGA/ATAC-associated histone acetylation, ubiquitination, and methylation similarly suppressed DMG growth. Further chromatin profiling and RNAseq analyses reveal that SGF29 controls H3K9ac and H3K4me3 dynamics at both H3K27M-bound and H3K27M-independent target genes linked to proliferation, differentiation, and metabolism. Finally, we find that SAGA/ATAC inhibition may reduce DMG viability by repressing cholesterol metabolism gene expression and show that combinations of cholesterol- and SAGA/ATAC-targeting drugs synergistically reduce DMG growth. These findings reveal a functional link between SAGA/ATAC-dependent chromatin regulation and both transcriptional and metabolic dysregulation underlying DMG malignancy.

overall_design: For CUT&RUN, a single cell suspension of 5x105 of control of SGF29KO SU-DIPGXIII+Cas9 cells were immobilized on ConA beads, permeabilized with 0.01% Digitonin, incubated with primary antibodies, and then cut with pAG-MNase to release DNA fragments as previously described. The following antibodies were used in CUT&RUN analyses: rabbit IgG (cat# C15410206, Diagenode), H3K4me3 (cat# C15410003, Diagenode), H3K9ac (cat# 9649, Cell Signaling Technology), and H3K27M (cat# ABE419, Millipore Sigma). Yeast spike-in DNA (S. cerevisiae; Cell Signaling Technology) was added at 0.5% to each reaction following chromatin digestion.

first: Richard

last: Rosemary

first: Akdes

last: Serin-Harmanci

middle: N


title: Acsl1 mediated FA Synthesis Impairs Osseointegration in type I diabetes [ATAC-Seq]

city: Chongqing

first: Tao

last: Chen

address: No.426, Songshi North Road, Yubei District

institute: Stomatological Hospital of Chongqing Medical University

summary: Diabetes mellitus is considered a relative contraindication for oral implant therapy, as hyperglycemia frequently precipitates vascular and osseous pathologies. Although clinicians routinely prioritize glycemic control before initiating implant-related treatment plans, diabetic patients often exhibit impaired osseointegration. However, the specific mechanisms remain to be elucidated. Emerging evidence suggests that this refractory bone loss is mediated by trained immunity, a process in which innate immune cells retain an epigenetic memory of prior inflammatory stimuli and mount an exaggerated response upon secondary challenge such as the invasive implantation process or inflammatory insult. Here, integrating RNA-seq, metabolomics, and ATAC-seq analyses, we demonstrate that stringent glycemic control in type I diabetes fails to normalize fatty-acid biosynthetic process, which remain persistently activated and potentiate macrophage-mediated inflammation and osteoclastogenesis when experiencing the secondary challenge. Mechanistically, prior hyperglycemic exposure enhances chromatin accessibility and sustaining Acsl1 transcription by H3K4me1 epigenetic modification at the Acsl1 locus in macrophages. This epigenetic imprint augments fatty-acid anabolism, amplifies pro-inflammatory cytokine production, and accelerates osteoclastic differentiation, ultimately compromising osseous repair. Collectively, our findings reveal that diabetes-induced H3K4me1 modification at Acsl1 drives metabolic reprogramming underpinning trained immunity and consequent bone damage. Targeting H3K4me1 or Acsl1 therefore represents a promising therapeutic strategy to improve implant osseointegration and skeletal regeneration in diabetic patients.

overall_design: This in vitro model was adapted from Edgar et al.(Edgar et al. 2021) to mimic diabetic-trained and untrained BMDM states. Male C57BL/6J mice (8 weeks old) from the Laboratory Animal Center of National Bioindustry (Chongqing, China) were randomly allocated to control or diabetic groups. For diabetes induction, mice received low-dose streptozotocin (42-45 mg/kg/d; Solarbio, China) via intraperitoneal injection after a 12h fast, repeated daily for 5 days. One week post-final injection, mice with nonfasted blood glucose >16.9 mmol/L were deemed type 1 diabetic. After 6 weeks of hyperglycemia, bone marrow progenitors from both groups were isolated and cultured in 5 mmol/L glucose DMEM with recombinant murine M-CSF for 7 days (rest phase). Cells were then stimulated with 10 ng/mL IFN-γ and 100 ng/mL LPS for 16 hours (2nd phase). The trained BMDMs were analyzed for their epigenetic modifications and metabolic profiles. Additionally, osteoclast differentiation assays were performed to assess the impact of diabetic memory on osteoclastogenesis.

first: Xinghui

last: Zheng

first: Xingyu

last: Zhu

first: Xu

first: Qingqing

last: He

first: Qingming

last: Zhai


title: Self-clustering of three CBX2 molecules drives PRC2 to promote facultative heterochromatinization of Polycomb target genes

first: Srinivas

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

overall_design: Refer to individual Series


title: Environmental Amino Acid Sensing Regulates the Rate of ASC Translation and NLRP3 Inflammasome Assembly

first: Montana

last: Knight

state: PA

address: 3615 Civic Center Blvd

department: Department of Biomedical and Health Informatics

institute: Children's Hospital of Philadelphia

summary: The NOD-, LRR-, and pyrin domain-containing protein 3 (NLRP3) inflammasome is a multiprotein signaling complex that triggers pyroptotic cell death and interleukin (IL)-1 family cytokine release during infection and cell injury. Its assembly is driven by the adaptor protein, apoptosis-associated speck-like protein containing a CARD (ASC), whose filamentation forms a supramolecular speck upon NLRP3 activation to amplify inflammasome signaling. While the NLRP3 inflammasome is well appreciated as a sensor of environmental danger and damage, little is known about how homeostatic environmental factors like dietary metabolites regulate its activity. Here, we find that environmental availability of the branched-chain amino acids (BCAAs), leucine, isoleucine, and valine, controls NLRP3 inflammasome assembly. While ASC is typically viewed as a constitutively expressed, unregulated inflammasome component, we find that Toll-like receptor 4 (TLR4) activation triggers localization of ASC mRNA to the perinuclear space. Moreover, our data demonstrate that ASC undergoes TLR4-driven translational bursting from polyribosomes during inflammasome priming. This translational engagement is dependent on BCAA availability and mechanistic target of rapamycin (mTOR) activity, which regulate the kinetics of inflammasome assembly. In contrast, the translation of NLRP3 and caspase-1 is largely insensitive to these inputs. Furthermore, we find that BCAAs regulate NLRP3 inflammasome activation in both mouse and human macrophages, in the context of bacterial infection, and during lipopolysaccharide (LPS)-induced sepsis in vivo. Altogether, this work unveils a novel inflammasome priming event governed by the amino acid environment. These findings further highlight how the activity of proteins maintained in equilibrium like ASC can be dynamically regulated through rapid changes in mRNA translation.

overall_design: Mus musculus macrophage samples stimulated with LPS in either normal control media or undergoing a torin treatment. RNAsequencing data collected examining both total and polysomal RNA in the samples. Three samples per group.

first: Mikel

last: Haggadone

first: Brian

last: Goldspiel

first: Aoife

last: O’Farrell

first: Nora

middle: T

last: Kiledjian

first: Talia

middle: R

last: Smith

first: Elena

last: Anderson

first: Víctor

last: Vázquez Marrero

first: Mark

last: Boyer

first: Peining Jimmy

last: Xu

first: Michael

last: Scaglione

first: Zachary

last: Powers

first: Clemence

last: Queriault

first: Aaron

last: Wu

first: Qihua

last: Yang

first: Mary

middle: X

last: O’Riordan

first: Arjun

last: Raj

first: Clementina

last: Mesaros

first: Crystal

middle: S

last: Conn

first: Sunny

last: Shin

first: Will

last: Bailis


title: RNA localization to nuclear speckles follows splicing logic

city: New York

first: Oded

last: Regev

address: 215 Mercer St

institute: New York University

summary: Nuclear speckles are membraneless organelles implicated in multiple RNA processing steps. In this work, we systematically characterize the sequence logic determining RNA localization to nuclear speckles. We find extensive similarities between the speckle localization code and the RNA splicing code, even for transcripts that do not undergo splicing. Specifically, speckle localization is enhanced by the presence of unspliced exon-like or intron-like sequence features. We demonstrate that interactions required for early spliceosomal complex assembly contribute to speckle localization. We also show that speckle localization of isolated endogenous exons is reduced by disease-associated single nucleotide variants. Finally, we find that speckle localization strongly correlates with splicing kinetics of splicing-competent constructs and is linked to the decision between exon inclusion and skipping. Together, these results suggest a model in which RNA speckle localization is associated with the formation of the early spliceosomal complex and enhances the efficiency of splicing reactions.

overall_design: To ensure that RNA transcribed from our synthetic constructs does not deviate from the intended sequence, we performed Nanopore full-length RNA sequencing after plasmid transfection. We applied unbiased transcriptome-wide sequencing without using any gene-specific primers, ensuring that even transcripts significantly deviating from the intended sequence (e.g., cryptic transcription start site, or cryptic splicing) will be captured.

first: Li

last: Wen

first: Mauricio

last: Arias

first: Xinqi

last: Fan

first: Joyce

last: Xie

first: Sneha

last: Paul

first: Susan

last: Liao

first: Marek

last: Sobczyk

first: Jingyi

last: Fei


title: Endotrophin and CD44-Mediated Heterotypic Signaling Mediates Tumor-Stroma Crosstalk and Facilitates Malignant Progression in Hepatocellular Carcinoma

city: Ulsan

first: Jiyoung

last: Park

state: Ulsan

address: Building No. 110, Room 501-7

department: Department of Biological Sciences

country: South Korea

institute: Ulsan National Institute of Science and Technology (UNIST)

summary: This study profiles gene expression changes in the human SK-Hep1 cell line, a mesenchymal-like liver-derived cell model, under conditions of differential sorafenib responsiveness. Bulk RNA sequencing was performed on sorafenib-sensitive (SS) and sorafenib-resistant (SR) cells treated with control siRNA (siCtrl), COL6A3 siRNA (siCOL6A3), or siCOL6A3 combined with recombinent endotrophin (rhETP). The data were generated to characterize transcriptional patterns associated with altered proliferation-and  survival-related phenotypes across defined experimental conditions.

overall_design: Bulk RNA sequencing was performed on human SK-Hep1 cell line, categorized as  sorafenib-sensitive (SS) or sorafenib-resistant (SR). SR cells were further treated with control (siCtrl) or COL6A3-targeting siRNA (siCOL6A3), with or without supplementation of recombinant endotrophin (rhETP). Comparative transcriptomic analyses were performed across the defined experimental groups to assess treatment-dependent transcriptional changes.

first: Woobeen

last: Jo

first: Chanho

first: Min

last: Kim

first: Chu-Sook

first: Jungsun

last: Yoo

first: Sahee

first: Jiseon

first: Hyun-Woo

last: Rhee


title: The Cd4+ T cell population Partners with Tpex CD8 T cells to mediate Antitumor Immunity in the Tumor Microenvironment.[renal cancer]

city: Hidaka-City, Saitama

first: Satoshi

last: Yamasaki

department: Department of Respiratory Medicine

institute: Saitama Medical University

summary: The priming, expansion, and function of CD8⁺ T cells are helped by CD4⁺ T cells via dendritic cells. Precursor exhausted T cells (Tpex) maintain self-renewal and supply cytotoxic CD8⁺ T cells in the tumor microenvironment (TME), but the identity of their CD4⁺ T-cell partners remains unclear. Here, we perform scRNA-seq, scTCR-seq, and mass cytometry analysis on peripheral blood, tumor, and lymph nodes derived from lung cancer patients and identify a population of IL-7Rhigh CCR6⁺ Th1-like CD4⁺ T cells, namedTh7R, that is numerically and spatially partnered with Tpex cells. Th7R cells express lymphotoxin-β and CXCL13, correlate with high endothelial venules, and co-localize with Tpex in tertiary lymphoid structures. Furthermore, Th7R cell abundance correlates with Tpex numbers in the TME and lymph nodes, and adoptive transfer of Th7R increases Tpex in a preclinical mouse model of skin cancer. In lung cancer patients, Th7R and Tpex in TME are associated with better response to neoadjuvant PD-1 blockade therapy. Thus, these results suggest that Th7R cells act as partners of Tpex CD8 T cells to sustain antitumor T-cell immunity.

overall_design: The scRNA-seq analysis of PBMC samples from pre-clinical renal cancer patients. Single-cell RNA sequencing, TCR repertoire profiling, and surface protein expression analysis were performed using the 10x Genomics Chromium Next GEM Single Cell 5' Reagent Kits. Gene expression (GEX), TCR (V(D)J), and antibody-derived tag (ADT) libraries were generated from the same cells, enabling integrated analysis of transcriptomes, clonotypes, and surface markers to compare T cell phenotypes and clonal structures across compartments.

first: Shota

last: Takei

first: Ou

last: Yamaguchi

first: Atsuto

last: Mouri

first: Ayako

last: Shiono

first: Yu

last: Miura

first: Kosuke

last: Hashimoto

first: Hisao

last: Imai

first: Kyoichi

last: Kaira

first: Hiroyuki

last: Nitanda

first: Hirozo

last: Sakaguchi

first: Tomoyuki

last: Hishida

first: Katsuhisa

last: Horimoto

first: Hiroshi

last: Kagamu


title: Comparative RNA seq analysis of Salmonella enterica serovar Typhimurium and a pan methionine sulfoxide reductase gene deletion (Δ5msr mutant) strain

city: Bareilly

first: Manish

last: Mahawar

state: Uttar Pradesh

address: Izzatnagar

department: Division of Biochemistry

country: India

institute: Indian Veterinary Research Institute

summary: Salmonella enterica serovar Typhimurium (S. Typhimurium) is a major foodborne pathogen which suffers but survives oxidative stress. Methionine sulfoxide reductases (Msrs) are important antioxidant enzymes that protect cells from oxidative damage by reducing oxidized methionine residues (free) or bound in proteins, back to methionine. To examine the global transcriptional consequences of deleting all five known msr genes, RNA sequencing was performed on S. Typhimurium and Δ5msr mutant strains. This dataset provides a comprehensive transcriptomic resource for investigating the impact of msrs deletion on oxidative stress–associated regulatory pathways and cellular processes in S. Typhimurium.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: S. Typhimurium and Δ5msr mutant strains were grown to mid-logarithmic phase (OD₆₀₀ ≈ 1.0). Total RNA was extracted, ribosomal RNA was depleted, and strand-specific RNA-seq libraries were prepared and sequenced on an Illumina platform. Sequencing reads were quality filtered, rRNA reads were removed, and the remaining reads were aligned to the Salmonella Typhimurium LT2 reference genome (GCF_000006945.2). Gene-level read counts were generated and normalized for comparative analysis of gene expression between the two strains.

first: Lalhmangaihzuali

last: Lalhmangaihzuali

first: Raj

last: Sahoo

first: Tapan Kumar

last: Singh Chauhan

first: Suchitra

last: Upreti

first: Shikha

last: Bishnoi


title: Phage homing endonuclease amplifies anti-defense genes to evade bacterial immunity [SITE-seq]

city: Tokyo

first: Kotaro

last: Chihara

address: 1-23-1 Toyama

department: Research Center for Drug and Vaccine Development

institute: National institute of infectious diseases

summary: Bacteriophages must overcome diverse bacterial immune systems, yet the molecular principles enabling such escape remain poorly understood. Here, we show that the phage homing endonuclease SegB facilitates immune evasion by promoting the segmental amplification of anti-defense loci. The antiphage defense Septu inhibits phage T6 replication by cleaving the variable loop of tRNATyr. We show that SegB enables immune evasion by amplifying a genomic segment that contains the full-length tRNATyr gene. This repeat expansion increases tRNATyr expression, allowing the phage to overcome Septu immunity. Remarkably, SegB also mediates in trans amplification of distinct anti-defense genes that counteract OLD and toxin-antitoxin ToxIN defense systems. Collectively, our findings demonstrate that SegB-mediated segmental amplification represents a versatile mechanism by which phages rapidly adapt to and circumvent diverse bacterial antiphage defenses.

overall_design: Identification of genomic positions cleaved by SegB homing endonuclease in high-molecular-weight T6 phage genomic DNA using the selective enrichment and identification of tagged genomic DNA ends by sequencing (SegB treatment vs. Mock treatment)

first: AaHaeruman

last: Azam

first: Egor

last: A. Syroegin

first: Ilya

last: Terenin

first: Masanori

last: Hashino

first: Koichi

last: Watashi

first: Kazuhiro

last: Horiba

first: Vasili

last: Hauryliuk

last: Kiga


title: Focal white matter lesions drive grey matter inflammation, neuronal dysfunction and synapse loss

city: Cambridge

first: Ragnhildur

middle: Thora

last: Karadottir

address: Puddicombe Way

country: United Kingdom

institute: Cambridge Stem Cell Institute

summary: Focal white matter lesions occur in most neurodegenerative disorders. Despite occurring early in disease, white matter lesions are considered either independent of, or secondary to, grey matter neuroinflammation, synapse loss and altered neuronal activity. Notably their functional impact on neuronal circuits has been understudied. To address this, we generated a focal white matter lesion in an anatomically well-defined circuit, in which white matter lesions occur in many neurodegenerative disorders. Here we show that focal white matter lesions evoke transient neuronal activity changes and microgliosis, with subsequent synapse loss and increased microglia engulfment in the grey matter, which is reversed if myelin regeneration completes. Grey matter microgliosis is often considered detrimental but we show that it is an integral part of the myelin regenerative process. When we prevent these transient changes in the grey matter, myelin regeneration is blocked in the white matter. Conversely, inducing myelin regeneration failure leads to chronic neuroinflammation in the grey matter, suggesting that myelin regeneration failure drives sustained grey matter microglial activation. This recapitulates the low-grade inflammation considered to be a dominant mechanism underlying neurodegeneration. Our findings reveal a form of regenerative plasticity coupling white matter integrity to grey matter function - a novel mechanism of neuroplasticity that may underlie multiple neurodegenerative conditions - and highlights the potential of targeting myelin regeneration to prevent chronic inflammation.

overall_design: The caudal cerebellar peduncle (CCP) of 9–12-week-old Sprague Dawley rats was bilaterally injected stereotaxically using a 10 μl Hamilton syringe. 4 μl of saline (controls) or ethidium bromide (0.01% in saline) were injected at a rate of 1 μl min−1 to induce a focal white matter demyelination.  CCP coordinates were -7.3 mm (dorsal-ventral, DV); -2.3 mm (anterior-posterior, AP); ±2.6 mm (medium-lateral, ML) from lambda. Rats were culled at 7 and 14 dpl.

first: Omar

last: de Faria Jr

first: Stavros

last: Vagionitis

first: Joseph

last: Wong

first: Leslie

last: Rubio Rodriguez-Kirby

first: Eneritz

last: Agirre

first: Andrea

last: Lopez-Lopez

first: Bastien

last: Hervé

first: Goncalo

last: Castelo-Branco


title: Zeb2os Hinders Cardiac Healing by Suppressing ZEB2 Reactivation and Cardiomyocyte Dedifferentiation [2]

city: Amsterdam

first: Monika

middle: M.

last: Gladka

address: Meibergdreef 9

institute: Amsterdam University Medical Centers

summary: Background: Long noncoding RNAs (lncRNAs) have emerged as critical regulators in cardiovascular biology, influencing cardiac development, remodeling, and regeneration. Zeb2os, a natural antisense transcript (NATs) of the Zeb2 gene, has been linked to these processes in various organs. While ZEB2 promotes cardiac repair, the role of Zeb2os in these processes remains unclear. This study investigates the role of Zeb2os in modulating ZEB2 expression and cardiac remodelling after ischemic injury. Methods: We used adeno-associated virus (AAV9) vectors to overexpress Zeb2os in mouse models of cardiac IR injury. RNA sequencing, immunofluorescence, and high-resolution respirometry were employed to evaluate the effects of Zeb2os delivery on gene expression, ZEB2 reactivation, cardiomyocyte phenotype, scar composition and mitochondrial function. Experiments in cultured cardiomyocytes under hypoxia further explored the regulatory dynamics between Zeb2os and Zeb2. Results: We identified Zeb2os as a hypoxia-responsive lncRNA that displays an inverse and oscillatory expression pattern with Zeb2 in both in vitro and in vivo models of cardiac injury. Functional experiments revealed that Zeb2os negatively regulates ZEB2 expression, impairing the cardiomyocyte dedifferentiation and metabolic remodelling necessary for effective repair. AAV9-mediated delivery of Zeb2os resulted in preserved sarcomere structure, altered scar composition, reduced expression of regenerative genes, and diminished cardiac function following injury. In contrast, silencing of Zeb2os increased ZEB2 protein expression, suggesting a potential therapeutic strategy to enhance repair. Mechanistically, modulation of Zeb2os levels inversely regulated ZEB2 protein expression, whereas ZEB2 modulation had no effect on Zeb2os levels, indicating a unidirectional regulatory axis between the two transcripts. Conclusions: Our findings identify Zeb2os as a stress-responsive inhibitor of ZEB2 reactivation that limits cardiomyocyte plasticity and hinders repair following ischemic injury. Given its specific activity under ischemic conditions, targeting  os may represent a novel therapeutic strategy to enhance endogenous cardiac regeneration

overall_design: Bulk RNA-seq of SHAM or I/R-operated mice intracardially injected with AAV9-carriers

first: Rocco

last: Caliandro

first: Merel

middle: L

last: Ligtermoet

first: Alexandra

last: Giovou

first: Azra

last: Husetic


title: Developing a multimodal therapy for glioblastoma using oncolytic virus delivering CD19 and EGFRvIII antigens and bi-specific CARs

city: Duarte

first: Guihua

last: Sun

state: CA

address: 1500 East Duarte Rd.

department: Department of Neurodegenerative Diseases

institute: City of hope

summary: Glioblastoma (GBM) is the most malignant primary brain tumor with no cure. While chimeric antigen receptor (CAR)-T cell therapy has exhibited considerable success for hematopoietic malignancies, CAR-T therapy for GBM is limited by heterogeneous tumor antigen expression, antigen loss after treatment with CAR-T targeting single antigens, and an immunosuppressive tumor microenvironment (TME). To address these challenges, we developed a multimodal immunotherapy platform for effective GBM treatment by combining bispecific CAR-T (BiCAR-T) cells with oncolytic virus carrying dual antigens and membrane-bound cytokines. Specifically, we developed a dual-antigen-encoding oncolytic virus (OVDual) that delivers truncated CD19 (CD19t) and EGFRvIII (EGFRvIIIt) antigens to GBM cells and BiCAR-T cells that are equipped with both CD19 CAR and EGFRvIII CAR. We demonstrated that OVDual effectively delivers CD19t and EGFRvIIIt to GBM cells and that BiCAR-T cells exhibited superior tumor-killing efficacy when combined with OVDual. To improve immune cell expansion/persistence and cytotoxicity, we engineered an OV expressing membrane-bound IL-15 and IL-21 (OVmIL15/21) and showed that OVmIL15/21 enhanced the expansion and killing activity of BiCAR-T and BiCAR-NK cells against GBM cells in vitro and boosted the anti-tumor effect in vivo. The combination of OVDual with BiCAR-T or BiCAR-NK cells allowed us to address the main challenges associated with inefficient CAR-T therapy for GBM, including heterogeneous antigen expression, antigen escape, and the immunologically ‘cold’ TME, and cytokine-armed OV further boosted the expansion/persistence and cytotoxicity of CAR immune cells. The multimodal platform developed in this study offers promising potential for effective GBM therapeutic development.

overall_design: GBM cells were infected with an oncolytic virus encoding truncated CD19 and EGFRvIII antigens at a multiplicity of infection (MOI) of 1 for 4 hours, together with an oncolytic virus encoding membrane-bound IL-15 and membrane-bound IL-21 (mIL15/mIL21) or a control virus encoding GFP. After infection,Bi-specific CAR-T cells were added at a 1:1 effector-to-target (E:T) ratio. Following 48 hours of co-culture, cells were collected for RNA extraction using TRIzol reagent. The purified RNA samples were subsequently submitted to the vendor for bulk RNA sequencing (RNA-seq) analysis.

first: Jia

last: Li

first: Yanhong

last: Shi


title: The role and mechanism of hypoxia-induced lncRNA in regulating ferroptosis in hepatocellular carcinoma

city: Hefei

first: Kejia

last: Liu

address: No. 96 Jinzhai Road

institute: University of Science and Technology of China

summary: One of the key alterations within solid tumors involves hypoxia, defined as oxygen tension below non-physiological levels. In liver cancer, hypoxia promotes disease progression through effects on cancer and non-cancer cells alike, impacting diverse processes including cell metabolism, proliferation, programmed cell death pathways, angiogenesis, metastasis, resistance to radiotherapy and systemic therapies.Consequently, defining how tumor cells benefit from reprogramming to survive challenging environmental conditions such as hypoxia has clear importance for identifying novel therapeutic targets and advancing treatments.In this study, we focus on the role of the hypoxia-responsive long noncoding RNA SHIELD in regulating ferroptosis in hepatocellular carcinoma.

overall_design: RNA-seq profiling of Huh7 human hepatocellular carcinoma cells cultured under normoxic (21% O2) or hypoxic (1% O2) conditions for 24 h.

first: Ying

first: Lianxin


title: Deciphering sepsis molecular subtypes using large-scale data to identify subtype-specific drug repurposing

city: Gainesville

middle: Anne

last: Smith

state: Fl

address: 1889 Museum Rd

department: Computer Information Science and Engineering

institute: University of Florida

summary:
Rationale: Sepsis is a life-threatening syndrome that can quickly cause organ failure and death if untreated. Patient variability complicates therapy development, and its molecular mechanisms remain poorly understood. Advancing knowledge of these mechanisms is essential for effective treatments and clearer phenotype definitions.
Objectives: To address this issue, we created a large-scale transcriptomic atlas of publicly available adult sepsis patient data with which we performed molecular phenotyping to evaluate patterns of gene expression and identified potential phenotype-specific drug therapies.
Methods: We identified studies of bacterial sepsis in three genomic databases (SRA, GEO, and refine.bio) and reviewed metadata from each study to ensure samples met our predetermined inclusion criteria. We combined this data into one large comprehensive data atlas and harmonized gene expression and associated metadata from each sample. Molecular phenotypes of sepsis were identified via clustering analysis of this sepsis transcriptomic data atlas. We then examined clinical correlates of each phenotype and identified gene signatures associated with each. We performed gene set enrichment analysis on those signatures and identified phenotype-specific potential drug repurposing candidates. We also evaluated the associations between computed phenotypes and mortality.
Measurements and Main Results: We harmonized data from 3,713 samples across 28 data sets, of which 2,251 were sepsis patients. Clustering analysis identified four phenotypes within the data. We identified statistically significant phenotype associations with survival, disease, and age. Pathway analysis revealed that MHC class II functions, DNA damage, homeostatic pathways and coagulation may characterize underlying response phenotypes, and may have the potential to guide drug development of sepsis therapeutics.
Conclusions: We created the largest transcriptomic sepsis atlas to date, from which we identified four molecular sepsis phenotypes. We described underlying dysregulated molecular mechanisms of these phenotypes, associated clinical covariates, and several potential candidate therapies specific to each phenotype. Future studies should seek to validate such drug-phenotype links to advance sepsis precision medicine.

overall_design:
Meta-analysis of sepsis transcriptomic studies for adult sepsis patients with bulk transcriptomic data. The datasets used for analysis in this study consists of 1 new dataset of RNA-Seq sepsis samples as well as samples from 27 reanalyzed studies from one of three data repositories: GEO, SRA, or refine.bio. The pipeline for preprocessing of reanalyzed samples differs slightly depending on the source repository. Processing information for each study is described below. All samples were adult patients who met sepsis/septic shock criteria and had bulk RNA-Seq expression data from whole blood with blood being drawn within 48 hours.
Processing of reanalyzed studies:
Reanalyzed studies (10 total) from GEO:
GSE100159 - All samples available in the expression matrix for GSE100159 on GEO were reanalyzed. The expression matrix and associated platform mapping probe IDs were downloaded from GEO. Probe IDs were mapped to associated value in expression matrix in R. Duplicate gene HUGO symbol IDs were merged by taking the mean of expression as is done in refine.bio processing. Samples were then quantile normalized in R using preprocess Core (v1.62.1) with the reference distribution provided by refine.bio (downloaded from https://api.refine.bio/v1/qn_targets/ on June 28th 2022). This expression matrix was combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE13015 - All samples available in the expression matrix for GSE13015 on GEO were reanalyzed. The expression matrix and associated platform mapping probe IDs were downloaded from GEO. Probe IDs were mapped to associated value in expression matrix in R. Duplicate gene HUGO symbol IDs were merged by taking the mean of expression as is done in refine.bio processing. Samples were then quantile normalized in R using preprocess Core (v1.62.1) with the reference distribution provided by refine.bio (downloaded from https://api.refine.bio/v1/qn_targets/ on June 28th 2022). This expression matrix was combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE131761 - All samples available in the expression matrix for GSE131761 on GEO were reanalyzed. The expression matrix and associated platform mapping probe IDs were downloaded from GEO. Probe IDs were mapped to associated value in expression matrix in R. Duplicate gene HUGO symbol IDs were merged by taking the mean of expression as is done in refine.bio processing. Samples were then quantile normalized in R using preprocess Core (v1.62.1) with the reference distribution provided by refine.bio (downloaded from https://api.refine.bio/v1/qn_targets/ on June 28th 2022). This expression matrix was combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE137340 - All samples available in the expression matrix for GSE137340 on GEO were reanalyzed. The expression matrix and associated platform mapping probe IDs were downloaded from GEO. Probe IDs were mapped to associated value in expression matrix in R. Duplicate gene HUGO symbol IDs were merged by taking the mean of expression as is done in refine.bio processing. Samples were then quantile normalized in R using preprocess Core (v1.62.1) with the reference distribution provided by refine.bio (downloaded from https://api.refine.bio/v1/qn_targets/ on June 28th 2022). This expression matrix was combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE236713 - All samples available in the expression matrix for GSE236713 on GEO were reanalyzed. The expression matrix and associated platform mapping probe IDs were downloaded from GEO. Probe IDs were mapped to associated value in expression matrix in R. Duplicate gene HUGO symbol IDs were merged by taking the mean of expression as is done in refine.bio processing. Samples were then quantile normalized in R using preprocess Core (v1.62.1) with the reference distribution provided by refine.bio (downloaded from https://api.refine.bio/v1/qn_targets/ on June 28th 2022). This expression matrix was combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE236892 - All samples available in the expression matrix for GSE236892 on GEO were reanalyzed. The expression matrix was downloaded from GEO. Ensembl gene IDs were mapped to HUGO symbols in R using biomaRt (v2.56.1) with ensembl gene annotations. Duplicate gene HUGO symbol IDs were merged by taking the mean of expression as is done in refine.bio processing. Samples were then quantile normalized in R using preprocess Core (v1.62.1) with the reference distribution provided by refine.bio (downloaded from https://api.refine.bio/v1/qn_targets/ on June 28th 2022). This expression matrix was combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE32707 - All samples available in the expression matrix for GSE32707 on GEO were reanalyzed. The expression matrix and associated platform mapping probe IDs were downloaded from GEO. Probe IDs were mapped to associated value in expression matrix in R. Duplicate gene HUGO symbol IDs were merged by taking the mean of expression as is done in refine.bio processing. Samples were then quantile normalized in R using preprocess Core (v1.62.1) with the reference distribution provided by refine.bio (downloaded from https://api.refine.bio/v1/qn_targets/ on June 28th 2022). This expression matrix was combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE69063 -  All samples available in the expression matrix for GSE69063 on GEO were reanalyzed. The expression matrix and associated platform mapping probe IDs were downloaded from GEO. Probe IDs were mapped to associated value in expression matrix in R. Duplicate gene HUGO symbol IDs were merged by taking the mean of expression as is done in refine.bio processing. Samples were then quantile normalized in R using preprocess Core (v1.62.1) with the reference distribution provided by refine.bio (downloaded from https://api.refine.bio/v1/qn_targets/ on June 28th 2022). This expression matrix was combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE134347 - All samples available in the expression matrix for GSE134347 on GEO were reanalyzed. The expression matrix and associated platform mapping probe IDs were downloaded from GEO. Probe IDs were mapped to associated value in expression matrix in R. Duplicate gene HUGO symbol IDs were merged by taking the mean of expression as is done in refine.bio processing. Samples were then quantile normalized in R using preprocess Core (v1.62.1) with the reference distribution provided by refine.bio (downloaded from https://api.refine.bio/v1/qn_targets/ on June 28th 2022). This expression matrix was combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE189400 - All samples available in the expression matrix for GSE189400 on GEO were reanalyzed. The expression matrix was downloaded from GEO. Ensembl gene IDs were mapped to HUGO symbols in R using biomaRt (v2.56.1) with ensembl gene annotations. Duplicate gene HUGO symbol IDs were merged by taking the mean of expression as is done in refine.bio processing. Samples were then quantile normalized in R using preprocess Core (v1.62.1) with the reference distribution provided by refine.bio (downloaded from https://api.refine.bio/v1/qn_targets/ on June 28th 2022). This expression matrix was combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
Reanalyzed studies (11 total) from SRA:
SRP198776 - All RNA-Seq reads available on SRA for SRP198776 were reanalyzed. The following processing pipeline used for available reads followed the pipeline defined by refine.bio. Reads for each available sample in the dataset were initially downloaded from SRA using prefetch and fasterq-dump. Fastp was used for read trimming and quality control. Transcript quantification was performed using Salmon. The transcript level estimates for the expression matrix were done using tximport in R. Gene ananotation was done with Ensembl gene annotations. Duplicate gene HUGO symbol IDs were merged by taking the mean of expression as is done in refine.bio processing. Samples were then quantile normalized in R using preprocess Core (v1.62.1) with the reference distribution provided by refine.bio (downloaded from https://api.refine.bio/v1/qn_targets/ on June 28th 2022). This expression matrix was combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE154918 - All RNA-Seq reads available on SRA for GSE154918 were reanalyzed. The following processing pipeline used for available reads followed the pipeline defined by refine.bio. Reads for each available sample in the dataset were initially downloaded from SRA using prefetch and fasterq-dump. Fastp was used for read trimming and quality control. Transcript quantification was performed using Salmon. The transcript level estimates for the expression matrix were done using tximport in R. Gene ananotation was done with Ensembl gene annotations. Duplicate gene HUGO symbol IDs were merged by taking the mean of expression as is done in refine.bio processing. Samples were then quantile normalized in R using preprocess Core (v1.62.1) with the reference distribution provided by refine.bio (downloaded from https://api.refine.bio/v1/qn_targets/ on June 28th 2022). This expression matrix was combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE185263 - All RNA-Seq reads available on SRA for GSE185263 were reanalyzed. The following processing pipeline used for available reads followed the pipeline defined by refine.bio. Reads for each available sample in the dataset were initially downloaded from SRA using prefetch and fasterq-dump. Fastp was used for read trimming and quality control. Transcript quantification was performed using Salmon. The transcript level estimates for the expression matrix were done using tximport in R. Gene ananotation was done with Ensembl gene annotations. Duplicate gene HUGO symbol IDs were merged by taking the mean of expression as is done in refine.bio processing. Samples were then quantile normalized in R using preprocess Core (v1.62.1) with the reference distribution provided by refine.bio (downloaded from https://api.refine.bio/v1/qn_targets/ on June 28th 2022). This expression matrix was combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE196117 - All RNA-Seq reads available on SRA for GSE196117 were reanalyzed. The following processing pipeline used for available reads followed the pipeline defined by refine.bio. Reads for each available sample in the dataset were initially downloaded from SRA using prefetch and fasterq-dump. Fastp was used for read trimming and quality control. Transcript quantification was performed using Salmon. The transcript level estimates for the expression matrix were done using tximport in R. Gene ananotation was done with Ensembl gene annotations. Duplicate gene HUGO symbol IDs were merged by taking the mean of expression as is done in refine.bio processing. Samples were then quantile normalized in R using preprocess Core (v1.62.1) with the reference distribution provided by refine.bio (downloaded from https://api.refine.bio/v1/qn_targets/ on June 28th 2022). This expression matrix was combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE199816 - All RNA-Seq reads available on SRA for GSE199816 were reanalyzed. The following processing pipeline used for available reads followed the pipeline defined by refine.bio. Reads for each available sample in the dataset were initially downloaded from SRA using prefetch and fasterq-dump. Fastp was used for read trimming and quality control. Transcript quantification was performed using Salmon. The transcript level estimates for the expression matrix were done using tximport in R. Gene ananotation was done with Ensembl gene annotations. Duplicate gene HUGO symbol IDs were merged by taking the mean of expression as is done in refine.bio processing. Samples were then quantile normalized in R using preprocess Core (v1.62.1) with the reference distribution provided by refine.bio (downloaded from https://api.refine.bio/v1/qn_targets/ on June 28th 2022). This expression matrix was combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE211210 - All RNA-Seq reads available on SRA for GSE211210 were reanalyzed. The following processing pipeline used for available reads followed the pipeline defined by refine.bio. Reads for each available sample in the dataset were initially downloaded from SRA using prefetch and fasterq-dump. Fastp was used for read trimming and quality control. Transcript quantification was performed using Salmon. The transcript level estimates for the expression matrix were done using tximport in R. Gene ananotation was done with Ensembl gene annotations. Duplicate gene HUGO symbol IDs were merged by taking the mean of expression as is done in refine.bio processing. Samples were then quantile normalized in R using preprocess Core (v1.62.1) with the reference distribution provided by refine.bio (downloaded from https://api.refine.bio/v1/qn_targets/ on June 28th 2022). This expression matrix was combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE216902 - All RNA-Seq reads available on SRA for GSE216902 were reanalyzed. The following processing pipeline used for available reads followed the pipeline defined by refine.bio. Reads for each available sample in the dataset were initially downloaded from SRA using prefetch and fasterq-dump. Fastp was used for read trimming and quality control. Transcript quantification was performed using Salmon. The transcript level estimates for the expression matrix were done using tximport in R. Gene ananotation was done with Ensembl gene annotations. Duplicate gene HUGO symbol IDs were merged by taking the mean of expression as is done in refine.bio processing. Samples were then quantile normalized in R using preprocess Core (v1.62.1) with the reference distribution provided by refine.bio (downloaded from https://api.refine.bio/v1/qn_targets/ on June 28th 2022). This expression matrix was combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE222393 - All RNA-Seq reads available on SRA for GSE222393 were reanalyzed. The following processing pipeline used for available reads followed the pipeline defined by refine.bio. Reads for each available sample in the dataset were initially downloaded from SRA using prefetch and fasterq-dump. Fastp was used for read trimming and quality control. Transcript quantification was performed using Salmon. The transcript level estimates for the expression matrix were done using tximport in R. Gene ananotation was done with Ensembl gene annotations. Duplicate gene HUGO symbol IDs were merged by taking the mean of expression as is done in refine.bio processing. Samples were then quantile normalized in R using preprocess Core (v1.62.1) with the reference distribution provided by refine.bio (downloaded from https://api.refine.bio/v1/qn_targets/ on June 28th 2022). This expression matrix was combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE232404 - All RNA-Seq reads available on SRA for GSE232404 were reanalyzed. The following processing pipeline used for available reads followed the pipeline defined by refine.bio. Reads for each available sample in the dataset were initially downloaded from SRA using prefetch and fasterq-dump. Fastp was used for read trimming and quality control. Transcript quantification was performed using Salmon. The transcript level estimates for the expression matrix were done using tximport in R. Gene ananotation was done with Ensembl gene annotations. Duplicate gene HUGO symbol IDs were merged by taking the mean of expression as is done in refine.bio processing. Samples were then quantile normalized in R using preprocess Core (v1.62.1) with the reference distribution provided by refine.bio (downloaded from https://api.refine.bio/v1/qn_targets/ on June 28th 2022). This expression matrix was combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE232753 - All RNA-Seq reads available on SRA for GSE232753 were reanalyzed. The following processing pipeline used for available reads followed the pipeline defined by refine.bio. Reads for each available sample in the dataset were initially downloaded from SRA using prefetch and fasterq-dump. Fastp was used for read trimming and quality control. Transcript quantification was performed using Salmon. The transcript level estimates for the expression matrix were done using tximport in R. Gene ananotation was done with Ensembl gene annotations. Duplicate gene HUGO symbol IDs were merged by taking the mean of expression as is done in refine.bio processing. Samples were then quantile normalized in R using preprocess Core (v1.62.1) with the reference distribution provided by refine.bio (downloaded from https://api.refine.bio/v1/qn_targets/ on June 28th 2022). This expression matrix was combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE63311 - All RNA-Seq reads available on SRA for GSE63311 were reanalyzed. The following processing pipeline used for available reads followed the pipeline defined by refine.bio. Reads for each available sample in the dataset were initially downloaded from SRA using prefetch and fasterq-dump. Fastp was used for read trimming and quality control. Transcript quantification was performed using Salmon. The transcript level estimates for the expression matrix were done using tximport in R. Gene ananotation was done with Ensembl gene annotations. Duplicate gene HUGO symbol IDs were merged by taking the mean of expression as is done in refine.bio processing. Samples were then quantile normalized in R using preprocess Core (v1.62.1) with the reference distribution provided by refine.bio (downloaded from https://api.refine.bio/v1/qn_targets/ on June 28th 2022). This expression matrix was combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
Reanalyzed studies (6 total) from refine.bio:
GSE33118 - All samples available in the expression matrix for GSE33118 on refine.bio were reanalyzed. The expression matrix was downloaded from refine.bio, no transformations were selected/performed at the time of download. Quantile normalization is performed as part of the refine.bio download process. The dataset was downloaded from refine.bio independently (not as part of a larger downloaded dataset) in order to ensure quantile normalization is performed independently on the dataset. After download Ensembl gene names were mapped to HUGO Symbols using biomaRt (v2.56.1) with ensembl gene annotations. This expression matrix was then combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE57065 - All samples available in the expression matrix for GSE57065 on refine.bio were reanalyzed. The expression matrix was downloaded from refine.bio, no transformations were selected/performed at the time of download. Quantile normalization is performed as part of the refine.bio download process. The dataset was downloaded from refine.bio independently (not as part of a larger downloaded dataset) in order to ensure quantile normalization is performed independently on the dataset. After download Ensembl gene names were mapped to HUGO Symbols using biomaRt (v2.56.1) with ensembl gene annotations.  This expression matrix was then combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE65682 - All samples available in the expression matrix for GSE65682 on refine.bio were reanalyzed. The expression matrix was downloaded from refine.bio, no transformations were selected/performed at the time of download. Quantile normalization is performed as part of the refine.bio download process. The dataset was downloaded from refine.bio independently (not as part of a larger downloaded dataset) in order to ensure quantile normalization is performed independently on the dataset. After download Ensembl gene names were mapped to HUGO Symbols using biomaRt (v2.56.1) with ensembl gene annotations.  This expression matrix was then combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE66890 - All samples available in the expression matrix for GSE66890 on refine.bio were reanalyzed. The expression matrix was downloaded from refine.bio, no transformations were selected/performed at the time of download. Quantile normalization is performed as part of the refine.bio download process. The dataset was downloaded from refine.bio independently (not as part of a larger downloaded dataset) in order to ensure quantile normalization is performed independently on the dataset. After download Ensembl gene names were mapped to HUGO Symbols using biomaRt (v2.56.1) with ensembl gene annotations.  This expression matrix was then combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE74224 - All samples available in the expression matrix for GSE74224 on refine.bio were reanalyzed. The expression matrix was downloaded from refine.bio, no transformations were selected/performed at the time of download. Quantile normalization is performed as part of the refine.bio download process. The dataset was downloaded from refine.bio independently (not as part of a larger downloaded dataset) in order to ensure quantile normalization is performed independently on the dataset. After download Ensembl gene names were mapped to HUGO Symbols using biomaRt (v2.56.1) with ensembl gene annotations.  This expression matrix was then combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.
GSE95233 - All samples available in the expression matrix for GSE95233 on refine.bio were reanalyzed. The expression matrix was downloaded from refine.bio, no transformations were selected/performed at the time of download. Quantile normalization is performed as part of the refine.bio download process. The dataset was downloaded from refine.bio independently (not as part of a larger downloaded dataset) in order to ensure quantile normalization is performed independently on the dataset. After download Ensembl gene names were mapped to HUGO Symbols using biomaRt (v2.56.1) with ensembl gene annotations.  This expression matrix was then combined with all other datasets included in the study and batch corrected using ComBat from the sva (v3.48) package for final use in analysis.

first: Kiley

last: Graim

first: Faheem

last: Guirgis

first: Beulah

last: Augustin

first: Vinitha

last: Jacob

first: Lauren

middle: P

last: Black

first: Andrew

last: Bertrand

first: Emilio

last: Cagmat

first: Susmita

last: Datta

first: Srinivasa

last: Reddy

first: Charlotte

last: Hopson


title: Acsl1 mediated FA Synthesis Impairs Osseointegration in type I diabetes

first: Tao

last: Chen

overall_design: This in vitro model was adapted from Edgar et al.(Edgar et al. 2021) to mimic diabetic-trained and untrained BMDM states. Male C57BL/6J mice (8 weeks old) from the Laboratory Animal Center of National Bioindustry (Chongqing, China) were randomly allocated to control or diabetic groups. For diabetes induction, mice received low-dose streptozotocin (42-45 mg/kg/d; Solarbio, China) via intraperitoneal injection after a 12h fast, repeated daily for 5 days. One week post-final injection, mice with nonfasted blood glucose >16.9 mmol/L were deemed type 1 diabetic. After 6 weeks of hyperglycemia, bone marrow progenitors from both groups were isolated and cultured in 5 mmol/L glucose DMEM with recombinant murine M-CSF for 7 days (rest phase). RNA samples were thermally denatured and mRNA enriched using oligo (dT) beads. The mRNA was fragmented, followed by synthesis of first- and second-strand cDNA. The cDNA ends were repaired, adenine bases added, and adapters ligated. PCR amplification was then performed. The sequencing library was quality checked, and the PCR product was denatured and circularized, with linear DNA digested. Finally, rolling circle replication generated DNA nanoballs (DNBs) for sequencing using combinatorial probe-anchor synthesis (cPAS) technology on a high-density nanochip. The raw data were processed with SOAPnuke (version 1.5.6) to filter out sequences. This step eliminated reads that included adapter sequences, indicating contamination, as well as those with more than 5% unknown base 'N' content or that were low-quality quality (defined as reads with more than 20% of their total bases having quality values below 15). The result of this filtering process was clean data. The clean data were aligned to the reference genome (https://hgdownload.soe.ucsc.edu/goldenPath/mm10/) using HISTA2 software (v2.1.0). Subsequently, gene fusion detection was performed using Ericscript (v0.5.5), and alternative splicing and differential alternative splicing analysis were conducted using rMATS (V3.2.5). Differential gene expression analysis was conducted using limma (v3.66.0) with the criteria of P value < 0.05. KEGG and GO enrichment analysis were performed using DAVID functional annotation clustering tool (https://david.ncifcrf.gov/summary.jsp).

first: Xinghui

last: Zheng

first: Xingyu

last: Zhu

first: Xu

first: Qingqing

last: He

first: Qingming

last: Zhai


title: Self-clustering of three CBX2 molecules drives PRC2 to promote facultative heterochromatinization of Polycomb target genes [Cut & Run, Cut & Tag]

first: Srinivas

last: Ramachandran

summary: Phase separation is increasingly recognized in facultative heterochromatinization of Polycomb target genes; however, the underlying mechanisms remain obscure. Using single-molecule imaging and tracking, we show that individual condensates in mESCs contain approximately 3 CBX2 molecules and numerous PRC1 and PRC2 subunits and indicate that the composition and dynamics of condensates are developmentally regulated. We reveal that CBX2 clusters PRC2 and controls the spatial distribution of both PRC2 and H3K27me3. Using genomic approaches, we demonstrate that CBX2 binds condensate initiation sites enriched for PRC2 nucleation sites. CBX2 deletion causes PRC2 and H3K27me3 to redistribute from their regular targets. By developing a separate-of-function variant, we determine that CBX2 relies on its self-clustering ability to function. These findings collectively support a novel phase-separation model driven by nucleation and bridging, in which low-abundance proteins self-cluster to initiate condensate assembly, a process tightly coupled to function.

overall_design: CUT&RUN of tagged CBX2 and EZH2 in CBX2fl/fl-HaloTag EZH2-Venus-dTag, CUT&RUN of tagged CBX2-PSM-HT  in CBX2fl/fl-HaloTag & Parental Cells,  CUT&Tag of H3K27me3 in mESCs (CBX2 WT, CBX2 KO, CBX2 PSM, and PGK12.1) in two biological replicates.

first: Steven

last: Ingersoll

first: Abby

last: Trouth

first: J. Carlos

last: Angel

first: Xinlong

last: Luo

first: Axel

last: Espinoza

first: Joey

last: Wen

first: Chengjie

first: Joseph

last: Tucker

first: Kalkidan

last: Astatike

first: Christopher

last: Phiel

first: Hatim

last: Sabaawy

first: Tatiana

last: Kutateladze

last: P. Wu

first: Tingting

last: Yao

first: Chao

last: Lu

first: Xiaojun

last: Ren


title: The Cd4+ T cell population Partners with Tpex CD8 T cells to mediate Antitumor Immunity in the Tumor Microenvironment.[PB cohort2]

first: Satoshi

last: Yamasaki

overall_design: The scRNA-seq analysis of PBMC samples from pre-clinical lung cancer patients. Single-cell RNA sequencing, TCR repertoire profiling, and surface protein expression analysis were performed using the 10x Genomics Chromium Next GEM Single Cell 5' Reagent Kits. Gene expression (GEX), TCR (V(D)J), and antibody-derived tag (ADT) libraries were generated from the same cells, enabling integrated analysis of transcriptomes, clonotypes, and surface markers to compare T cell phenotypes and clonal structures across compartments.

first: Shota

last: Takei

first: Ou

last: Yamaguchi

first: Atsuto

last: Mouri

first: Ayako

last: Shiono

first: Yu

last: Miura

first: Kosuke

last: Hashimoto

first: Hisao

last: Imai

first: Kyoichi

last: Kaira

first: Hiroyuki

last: Nitanda

first: Hirozo

last: Sakaguchi

first: Tomoyuki

last: Hishida

first: Katsuhisa

last: Horimoto

first: Hiroshi

last: Kagamu


title: Zeb2os Hinders Cardiac Healing by Suppressing ZEB2 Reactivation and Cardiomyocyte Dedifferentiation

first: Monika

last: Gladka

overall_design: Bulk RNA-seq of uninjured mice retro-orbitally (RO) injected with AAV9-carriers

middle: M

first: Rocco

last: Caliandro

first: Merel

last: Ligtermoet

first: Alexandra

middle: E

last: Giovou

first: Azra

last: Husetic


title: Spatial gene expression profiling of aortitis samples.

first: Dogukan

last: Mizrak

address: NCRC Building 26, 263S

department: Cardiac Surgery

summary: 10X Xenium profiling of ascending aorta samples isolated from subjects with aortitis.

overall_design: We performed spatial profiling (10X Xenium in-situ spatial platform) on ascending aorta samples resected from three subjects with giant cell aortitis  (denoted as GCA1, GCA2 and GCA3), one subject with IgG4-related aortitis and three subjects with aortic stenosis (denoted as AS1, AS2 and AS3). Two tissue sections (denoted as R1 and R2)  were processed from each giant cell aortitis subject.

first: Bo

last: Yang


title: The Oxysterol Receptor GPR183 Senses Metabolic Niche Signals that Promote Differentiation of Monocytes into Tissue-Resident Lung Macrophages

city: Liège

first: Thomas

last: Marichal

address: Avenue de l'Hopital 11

department: GIGA Institute

country: Belgium

institute: University of Liege

summary: Monocytes populate tissues when local niches are depleted of tissue-resident macrophages, yet the tissue-derived signals controlling monocyte-to-macrophage differentiation are largely undefined. Here, we discovered that the oxysterol receptor GPR183 enables monocytes to sense metabolic niche signals that induce lung macrophage differentiation. We found that interstitial macrophages that continuously turn over express the oxysterol receptor GPR183, whereas alveolar macrophages that derive from embryonic progenitors and slowly turn over did not. Models of conditional tissue-resident macrophage depletion showed that newcomer monocyte-derived macrophages expressed GPR183 along their differentiation trajectory. Recruited GPR183+ monocytes interacted with fibroblasts and lack of GPR183 caused defective lung macrophage differentiation. Single-cell RNA analysis over time identified lung fibroblasts as the source of the GPR183 ligand 7a,25-dihydroxycholesterol in the empty niche. Our findings identify oxysterols as key instructive signals for tissue-resident macrophage development from monocytes.

overall_design: To define the cellular source of the GPR183 ligand, single-cell RNAseq was performed in lung fibroblasts, endothelial cells, and epithelial cells before and after DT-mediated alveolar macrophage depletion.

first: Domien

last: Vanneste

first: Qiang

last: Bai

first: Joan

last: Abinet


title: Elevated levels of Ube2g1 in hematopoietic stem cells lead to segmental aging of the hematopoietic system

city: Ulm

first: Julian

last: Niemann

address: Meyerhofstrasse

department: Institute of Molecular Medicine

country: Germany

institute: University Ulm

summary: Aged hematopoietic stem cells (HSC) show diminished capacity of self-renewal, skewed lineage output and compromised proteostasis. Ubiquitin proteasomal systems are critical for maintaining protein homeostasis. We show that the levels of Ube2g1, a E2 ubiquitin-conjugating enzyme likely involved in clonal selection of HSC, was elevated in aged murine and human HSC. We hypothesized that elevated levels of Ube2g1 causally contribute to hematopoietic system aging. Elevated levels of Ube2g1 in young murine HSCs resulted in increased myeloid-to-lymphoid ratio and reduced naïve T-cells, both known hematopoietic aging hallmarks. Interestingly, the ubiquitination function of Ube2g1 didn’t primarily account for the observed phenotypes. Elevated levels of Ube2g1 affected global tyrosine phosphorylation, mediated through a Ube2g1-Shp2 axis, which correlated with impaired Tcell development and reduced HSC function. Our work identifies a novel connection between proteins involved in the regulation of ubiquitination and phosphorylation in HSC that affect phenotypes linked to aging of HSC.

overall_design: RNA-Sequencing profiling of young and aged HSC transduced with Control or Ube2g1-OE.

first: Medhanie

last: Mulaw

first: Hartmut

last: Geiger