title: microRNA-497-5p-based Screening Identifies a Novel Synthetic Lethal-type Interaction via PKMYT1 and WEE1 in Pleural Mesothelioma

city: Tempe

first: Christopher

last: Plaisier

state: Arizona

department: SBHSE

institute: Arizona State University

summary: We discovered direct targets of miR-497-5p through biotinylated miRNA pull-down of target mRNA molecules from a epithelial subtype derived diffuse pleural mesothelioma (DPM) cell line (H2052). The pulldowns were done side by side with RNA-seq to capture the effects of miRNA on the transcriptomes of the DPM cells.

overall_design: DPM cells (H2052) were seeded in 6-well plates at a density of 2.0 x 105 cells/well. Cells were transfected with custom-made 3’-biotinylated miR-497-5p mimic (experimental) or 3’-biotinylated scrambled, non-targeting miRNA mimic (control) for 12 hours and 72 hours (20 nM, Dharmacon). All steps involved in the biotin-miRNA streptavidin pulldown affinity purification were performed per established protocol 24. At both timepoints, purified miRNA-bound products were obtained from the experimental and control cells. In parallel, at both timepoints, transcripts altered (up- and down-regulated) by miRNA mimics were isolated (i.e. input). Cytoplasmic extract and Streptavidin-Dynabeads (M-280, Invitrogen) were prepared, then incubated for 4 hours. Biotin-miR-mRNA complexes were collected in a magnetic stand. Specificity and quality of pulldown method was validated by measuring transcript levels of known miR-497-5p targets (CDK4, CCND1 , VEGFA)18 and housekeeping gene (GAPDH) in miR-497- and control miR-treated cells. For high-throughput RNA-sequencing (RNA-seq), libraries were constructed with Poly(A) selection by GeneWiz© for both the 12h (pulldown and input) and 72h (pulldown and input) products. In the manuscript pulldown is referred to as bound targets, and input is treated as RNA-seq to find differentially expressed genes. The libraries were paired-end sequenced (2 x 150bp) using an Illumina HiSeq. Reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome using the STAR aligner v.2.5.2b. The number of mapped reads per transcript were calculated using featureCounts from the Subread package v.1.5.2, and only unique reads that fell within the exon regions were counted.

first: Nathanael

last: Pruett

first: Sierra

last: Wilferd

first: Anand

last: Singh

first: Agnes

middle: Y

last: Choi

first: Shivani

last: Dixit

first: Charlize

last: Nguyen

first: Olivia

last: Lin

first: David

last: Schrump

first: Chuong

middle: D

last: Hoang


title: TAMs-derived exosomal Meg8 promotes the EMT and metastasis of SACC by regulating EGFR through sponge absorption of miR-148a-3p

status: Public on Jun 27 2026

city: Xi'an

first: Yang

last: Xinjie

address: No.127 Changle West Road, Xincheng District

department: Department of Head and Neck Oncology

country: China

institute: ir Force Medical University Institution: The Third Affiliated Hospital

summary: Tumor-associated macrophages (TAMs) infiltrate extensively in salivary adenoid cystic carcinoma (SACC) tissues. Our previous study found that TAMs were significantly associated with the tumor metastasis and poor patients’ prognosis. However, the role and molecular mechanism of TAMs in SACC metastasis are still to be elucidated. Present study found that TAMs-derived exosomes can be internalized by SACC cells, initiating the epithelial-mesenchymal transition (EMT) process of SACC cells. TAMs-derived exosomal RNA microarray and metastasis-related SACC tissues RNA sequencing suggested that Lnc-Meg8 was involved in TAMs-SACC interaction. RNA. In vitro assays revealed that TAMs-derived exosomes transferred Lnc-Meg8 to SACC cells, which promoted EGFR expression via sponge absorption of miR-148a-3p, thus promoting the EMT process of SACC cells. In vivo assays confirmed that inhibition of TAMs-derived exosomal Meg8 significantly improved the therapeutic efficacy of EGFR inhibitor cetuximab on the EMT and metastasis of SACC cells. In summary, our results demonstrated that the TAMs-derived exosomes promoted the EMT process of SACC cells via the Lnc-Meg8/miR-148a-3p/EGFR molecular axis. Blocking exosomal Lnc-Meg8 of TAMs may be a potential therapeutic strategy for SACC.

overall_design: Overall design: Expression profiling by Agilent mRNA-lncRNA microarray. A total of 6 samples were analyzed, including 3 control groups and 3 TAMs-derived exosome-treated SACC cell groups. The aim was to identify differentially expressed lncRNAs and mRNAs between control and exosome-treated SACC cells, and to explore the ceRNA regulatory network involving lncRNA Meg8, miR-148a-3p, and EGFR in SACC EMT and metastasis. All samples were processed and hybridized on the same Agilent platform to minimize batch effects.

first: Xinjie

last: Yang

first: Wanpeng

last: Gao


title: Dual profiling of DNA modifications with enhancer features during the exit of naive pluripotency [RNA-Seq]

city: Paris

first: Marlet

last: Morales Franco

state: Île-de-France

address: 15 rue Hélène Brion

country: France

institute: Institut Jacques Monod, CNRS, Université Paris Cité

type: Expression profiling by high throughput sequencing

summary: Cis-regulatory elements, such as enhancers, play an essential role in coordinating gene expression programs during cellular transitions. As such, substantial efforts have been made to characterize enhancer elements, e.g., chromatin accessibility, transcription factor (TF) binding sites, histone post-translational modifications (PTMs), and 5-cytosine DNA methylation and hydroxymethylation (5mC and 5hmC). Elevated 5mC levels are typically correlated with the inactive enhancer state. However, whether 5mC precludes TF binding or is simply a downstream consequence of enhancer decommissioning is difficult to determine. Bulk genomics assays from cell populations fail to fully capture cellular heterogeneity, and single-cell assays often suffer from limited read counts per cell. Here, we leveraged tagmentation-based technologies to assess chromatin features with 5mC simultaneously: Methyl-ATAC and Methyl-CUT&Tag. In addition, we modified the technique to interrogate 5hmC dynamics (hM-ATAC). We employed these techniques during the exit of naive pluripotency in mouse embryonic stem cells (mESCs), which recapitulates the embryonic DNA methylation establishment program. This system withstands the complete absence of DNA methylation and demethylation machinery, allowing us to further dissect the temporal contributions of 5mC and 5hmC. Given the affordability of these techniques, we were able to obtain robust, dynamic single-molecule 5mC/5hmC information during this cellular transition for chromatin accessibility and histone marks in wild-type and mutant conditions. The sum of these data allowed for unprecedented insight into the role that 5mC turnover plays at enhancers during a key window of mammalian embryonic development.

overall_design: RNA-seq of Tet KO cells at Days 0, 2, 4, and 7 of mESC-to-EpiLC differentiation.

last: Morales-Franco

first: Baptiste

last: Demaret

first: Pol Arnau

last: Romero

first: Hortense

last: Bouvier

first: Julien

last: Richard Albert

first: Angélique

last: David

first: Pierre-Antoine

last: Defossez

first: Anaïs Flore

last: Bardet

first: Priscillia

last: Lhoumaud

first: Maxim

last: Greenberg


title: Dual profiling of DNA modifications with enhancer features during the exit of naive pluripotency [5hmC-seq]

type: Methylation profiling by high throughput sequencing

overall_design: Whole genome 5hmC sequencing (5hmC-seq) of WT cells at Day 0 (mESCs), Day 2 (EpiLCs), and Day 4 (Extended EpiLCs) of mESC-to-EpiLC differentiation.


title: Dual profiling of DNA modifications with enhancer features during the exit of naive pluripotency [hMethyl-ATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: hMethyl-ATAC-seq of WT cells at Day 0 (mESCs), Day 2 (EpiLCs), and Day 4 (Extended EpiLCs) of mESC-to-EpiLC differentiation. hMethyl-ATAC-seq of Dnmt KO and Tet KO at Day 4.


title: scRNA-seq analysis of peritoneal immune cells from NCD- and HFD-fed mice

status: Public on Jun 28 2026

city: Beijing

first: Weixuan

last: Wang

address: No. 38 Xueyuan Road, Haidian District

institute: Peking University

summary: To determine how a high-fat diet (HFD) alters peritoneal immune cells, we performed single-cell RNA sequencing (scRNA-seq) to characterize the peritoneal immune microenvironment in mice fed a chow diet (CD) or HFD.

overall_design: To assess diet-induced changes in the peritoneal immune microenvironment, mice were fed either a chow diet (CD) or a high-fat diet (HFD) beginning at 4 weeks of age and maintained for three months. Peritoneal immune cells were collected by intraperitoneal lavage with serum-free RPMI 1640 medium. CD45⁺ immune cells were then isolated by flow cytometry and subjected to single-cell RNA sequencing.

first: Linjiang

last: Han

first: Dan

last: Lv


title: Rb-driven transcription limits its tumour suppressive effects in breast cancer

city: Melbourne

first: Shom

last: Goel

state: Victoria

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

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

overall_design: Refer to individual Series


title: Dual profiling of DNA modifications with enhancer features during the exit of naive pluripotency [Methyl-CUT&Tag-seq]

overall_design: Methyl-CUT&Tag-seq of WT, Dnmt KO, and Tet KO cells at Day 0 (mESCs), Day 2 (EpiLCs), and Day 4 (Extended EpiLCs) of mESC-to-EpiLC differentiation. Methyl-CUT&Tag-seq of H3K4me1 and H3K27ac.


title: Multiple mechanisms lead to differential loss-of-function effects of pathogenic SARS2 variants: implications for genotype-phenotype analyses

status: Public on Jun 29 2026

city: Ann Arbor

first: Christina

last: Del Greco

state: MI

address: 1241 Catherine Street

country: USA

institute: University of Michigan

summary: Seryl-tRNA synthetase 2 (SARS2) encodes the enzyme responsible for charging tRNA with serine in the mitochondria. SARS2 has been associated with a spectrum of recessive diseases including HUPRA syndrome and progressive spastic paresis (PSP). Previous studies showed that pathogenic SARS2 variants cause decreased tRNA charging; however, the mechanism by which specific variants lead to distinct recessive phenotypes has not been defined. To address this lack of knowledge, we studied an allelic series of pathogenic SARS2 variants for differential effects on mitochondrial function. We generated a SARS2 knockout Hap1 cell line with a second, doxycycline-inducible wild-type copy of SARS2 to support cell growth. We first assessed the effects of ablated SARS2 expression on the transcriptome and on mitochondrial function. We found that, in the absence of SARS2 expression, transcriptional changes indicate activation of cellular stress responses including the integrated stress response. Furthermore, loss of SARS2 resulted in severely depleted oxygen consumption in Seahorse assays. We next individually transduced an allelic series of 11 pathogenic SARS2 variants into this cell model to assess the effects of each variant on mitochondrial function. These efforts revealed compelling variant-dependent effects on oxygen consumption that will be useful for phenotype-genotype correlations. Interestingly, the most commonly detected pathogenic SARS2 variant (R402H) had no effect on mitochondrial function in our model system. We performed computational and functional studies, which showed that this missense variant has a partial effect on exon inclusion, which predicts a hypomorphic allele consistent with certain patients being reported as homozygous for this variant. Overall, this study expands our understanding of SARS2 biology, reveals the differential effects that pathogenic variants have on SARS2 function, and provides the foundation for defining the clinical heterogeneity of patient phenotypes.

overall_design: Differential gene expression of Hap1 cells expressing SARS2 compared to Hap1 cells after SARS2 expression is depleted for 3, 6, or 9 days.

first: Anthony

last: Antonellis


title: Targeting palmitoylation enhances neutrophil-mediated cancer cell killing in liver metastases

city: Leuven

first: Juan

last: Fernández-García

address: Campus Gasthuisberg, O&N4, Herestraat 49, box 912

department: VIB-KU Leuven Center for Cancer Biology

country: Belgium

institute: VIB/KU Leuven


title: Dual Deficiency of IL4I1 and LAO1 Promotes Inflammatory Diarrhea via Disruption of L-Amino Acid Metabolism and the IDO1-Kynurenine Pathway

city: shijiazhuang

first: Hong

last: LIU

address: East side of South Taihang Street

institute: Hebei Public Security Police Vocational College

summary:
The oxidoreductases interleukin 4-induced gene 1 (IL4I1) and L-Amino acid oxidase 1 (LAO) are known to catalyze L-amino acid metabolism, yet their physiological roles in intestinal homeostasis remain largely unexplored. In this study, we investigated the impact of IL4I1 and LAO1 deficiency on colonic inflammation by generating wild-type, single knockout (IL4I1 KO and LAO1 KO), and double knockout (DKO) mice. Notably, DKO mice exhibited spontaneous diarrhea and histologically confirmed colitis, which were absent or rare in the other genotypes. Transcriptomic profiling and qRT-PCR analyses revealed upregulated expression of pro-inflammatory cytokines (IL-6, IL-17, IFN-γ) and Th1/Th17 transcription factors, along with overexpression of indoleamine 2,3-dioxygenase 1 (IDO1) in the colon of DKO mice. Metabolomic analysis indicated elevated colonic kynurenine levels and impaired metabolism of L-phenylalanine, L-tyrosine, and L-tryptophan. These changes were associated with a significant reduction in hydrogen peroxide (H₂O₂) production. Furthermore, 16S rRNA gene sequencing revealed altered beta diversity and reduced abundance of Short-chain fatty acid-producing bacteria in DKO mice. Among short-chain fatty acids, pentanoate was significantly decreased in DKO cecal contents. Collectively, these findings suggest that IL4I1 and LAO1 are essential for maintaining intestinal immune and metabolic balance. Their combined deficiency disrupts L-amino acid metabolism and H₂O₂-mediated regulation of the IDO1–kynurenine pathway, ultimately promoting gut dysbiosis and inflammatory diarrhea. This study provides novel insights into the metabolic and microbial mechanisms underlying colonic inflammation and highlights IL4I1 and LAO1 as potential targets for therapeutic intervention in inflammatory bowel diseases.
This study provides novel insights into the metabolic and microbial mechanisms underlying colonic inflammation and highlights IL4I1 and LAO1 as potential targets for therapeutic intervention in inflammatory bowel diseases.

overall_design: Male healthy colonic tissues at 12-16 weeks of age were selected for RNA extraction and hybridization on Affymetrix microarrays. To explore the underlying mechanisms of IL4I1 and LAO1 double knockout-induced colonic inflammation in mice, wild-type, single knockout (IL4I1 KO and LAO1 KO), and double knockout (DKO) mice were used.

first: Kentaro

last: Nagaoka

last: Liu


title: Rb CUT&RUN profiling in MCF7 parent and RB1 knockout cells following abemaciclib treatment

summary: The retinoblastoma protein (Rb) is a tumour suppressor best known for repressing E2F transcription factors and halting cell cycle progression. In hormone receptor-positive (HR+) breast cancer, CDK4/6 inhibitors activate Rb by preventing its phosphorylation, forming a key component of current endocrine therapy regimens. How pharmacologically activated Rb remodels chromatin and influences transcription beyond cell cycle arrest remains poorly understood. Here we show that CDK4/6 inhibition induces redistribution of hypo-phosphorylated Rb to promoters and enhancers. While Rb predictably binds to cell cycle gene promoters to repress transcription, at other sites it unexpectedly promotes expression of oestrogen-responsive genes by integrating into oestrogen receptor (ER)-rich transcriptional hubs. CDK4/6 inhibition enhances ER target gene expression in breast cancer cells, patient-derived xenografts, and clinical HR+ breast cancer samples in an Rb-dependent manner. This reprogramming is mediated in part by KDM5A, whose interaction with Rb contributes to gene regulation at these loci. Critically, components of this Rb-driven ER transcriptional program are pro-proliferative. In endocrine-sensitive tumours, this can be neutralised with anti-oestrogen therapy, explaining therapeutic synergy. In endocrine-resistant settings such as ESR1-mutant breast cancer, the program persists, limiting therapeutic efficacy. These findings reframe Rb as a dual-function transcriptional regulator that, while enforcing cell cycle arrest, can also activate programs that counteract its tumour suppressor function.

overall_design: CUT&RUN for Rb in estrogen receptor-positive cell line MCF7, parental cells and isogenic RB1 knockout cells, treated with DMSO control or abemaciclib 500 nM for 2 days. Two biological replicates per group.


title: Influence of temporal interference electrical stimulation on mRNA expression in primary rat progenitor cells in vitro.

city: London

first: Sofia

last: Peressotti

address: Exhibition Rd, South Kensington, London

country: United Kingdom

institute: Imperial College London

summary: Electrical stimulation has been shown to modulate the proliferation and differentiation of neural progenitor cells (NPCs). Although stimulation therapies, such as deep brain stimulation (DBS) have been widely used in the clinic, the mechanisms underlying clinical efficacy remain unknown. DBS via temporally interfering (TI) electric fields has emerged as a promising strategy for non-invasive stimulation (Grossman et al., 2017). However, its effect on neural development remains unexplored. Here, the influence of TI stimulation on gene expression of primary embryonic rat NPCs was investigated in vitro. We previously demonstrated that TI stimulation at the theta frequency induces increases cellular metabolism and neural differentiation at the protein level. Transcriptome analysis using mRNA-seq is carried out to investigate changes in gene expression following stimulation, identifying the activation of the MAPK/ERK pathway and changes in the extracellular matrix in the stimulated condition from GO enrichment analyses.

overall_design: Cells were dissected from the ventral-mesencephalic region of rats at embryonic day 14. Upon tissue dissociation, the cells were grown in a monolayer in vitro for 7 days and subsequently stimulated with with a temporal interference protocol (theta band amplitude modulation, 1 kHz frequency, 2 s on-2 s off, 2 mA peak-to peak, 300-500 mV/mm) for 3 days, 6 h per day. The mRNA was extracted at day in vitro 10.

first: Roberto

last: Portillo Lara

first: Rylie

last: Green


title: A mycovirus from entomogenous fungi Beauveria acts as a mobile effector of phytopathogen antagonism through cross-taxonomic transmission

city: Changchun

first: Xiaohui

last: Dong

address: No. 1363, Shengtai Street, Jingyue High-tech Industrial Development Zone

department: Institute of Plant Protection

institute: Jilin Academy of Agricultural Sciences

summary: Fungal antagonism shapes microbial community structure and provides an ecological basis for biological control. Although mycoviruses have been implicated in fungal antagonism, their effects are generally attributed to indirect modulation of resident host physiology.

overall_design: Here, we show that a mycovirus can function as a mobile effector of antagonism through cross-taxonomic transmission. We characterized Beauveria brongniartii victorivirus 1 (BbrVV1), a totivirus infecting the plant-colonizing entomopathogenic fungus Beauveria brongniartii. BbrVV1 enhanced the in planta suppression of Sclerotinia sclerotiorum by B. brongniartii, an effect associated with transmission of BbrVV1 from B. brongniartii to the invading pathogen within colonized plants. In its native host, BbrVV1 caused only moderate fitness effects, whereas host shift to S. sclerotiorum induced pronounced hypovirulence, including restricted vegetative growth, impaired sclerotial development and attenuated pathogenicity. The virus also spread horizontally within S. sclerotiorum populations, but was not transmitted through mono-sclerotial progeny. These findings expand the ecological significance of mycoviruses as mobile agents of fungal interaction and provide a conceptual foundation for plant-associated viral delivery in biological control. Keywords:  mycovirus; cross-taxonomic transmission; hypovirulence; biological control; Beauveria brongniartii


title: Fos regulates age-dependent neuroinflammation in VAPBALS

city: Pune

first: Girish

last: Ratnaparkhi

state: Maharashtra

address: NCL Colony, Dr. Homi Bhabha Road

department: Biology

country: India

institute: IISER-Pune

summary: Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disorder characterized by progressive loss of motor function. We have developed a Drosophila model of ALS8 (VAPBP58S) using CRISPR/Cas9 genome editing. VAPB is an ER-based adapter protein associated with and regulating intracellular membrane:membrane contact sites. VAPBP58S flies show progressive age-dependent motor deficits and a shortened lifespan, paralleling features of the human disease. VAPBP58S brains exhibit age-dependent neuroinflammation, as measured by whole-transcriptome quantitative mRNA sequencing, suggesting a broad, low-grade enhancement in signalling in multiple (Toll, IMD, Jak-STAT and Jun-kinase) immune pathways. We implicate glial cells in the brain as the site of brain inflammation and identify Drosophila Fos (Kayak) as a key modulator of age-dependent inflammation. In accordance, we find that overexpression of wild-type kayak or its dominant-active variant kayakK357R in glia reduces inflammation and, concomitantly, improves motor function. In contrast, knockdown of glial kayak accelerates age-dependent deterioration of motor function and enhances neuroinflammation. Our study underscores the roles of glial-modulated brain inflammation in dictating ALS8 progression and identifies kayak as a central negative regulator of neuroinflammation in disease.

overall_design: RNA Seq profiling of VAPBP58S vs Wildtype for males (Day 5, 15 and 20) and female (Day 5 and 20) for heads and female (Day 5 and 20) for guts. A second RNA seq profiling for the male heads of VAPBP58S; RepoGal4 and in this backgroun Kayak knockdown, Kayak wildtype overexpression and KayakSCR overexpression at days 5 and 15.


title: Spatio-temporal mapping of immune cell dynamics during human sequential lymph node metastasis

city: jinan

first: pengfei

last: qiu

address: 440 Jiyan Rd, Jinan, P.R. China

institute: Shandong First Medical University and Shandong Academy of Medical Sciences

summary: Regional lymph node metastasis critically influences distant metastatic progression, anti-tumour immunity, and patient prognosis. This study systematically characterised immune cell dynamics across paired primary tumours, sentinel tumour-draining lymph nodes (S-TDLNs), and secondary axillary lymph nodes (ALNs) from treatment-naïve triple-negative breast cancer (TNBC) patients using integrated multi-omics approaches, including imaging mass cytometry, single-cell RNA sequencing, Visium and Xenium spatial transcriptomics, and multiplex immunofluorescence. Xenium profiling was performed on FFPE lymph node sections spanning different metastatic stages to resolve high-resolution spatial organisation, neighbourhood complexity, and immune cell co-localisation during sequential lymph node metastasis.

overall_design: Treatment-naïve TNBC specimens were collected at upfront surgery. FFPE lymph node sections representing uninvolved, intermediate-metastatic, and metastatic stages were analysed using Xenium Prime 5K in situ spatial transcriptomics. Cells were classified into major immune and stromal populations and used to assess spatial organisation, neighbourhood complexity, and ligand-receptor interactions during lymph node metastasis. Xenium data were integrated with scRNA-seq, imaging mass cytometry, and clinical validation analyses.

first: Qiuchen

last: Zhao

first: Yongjin

last: Lu

first: Bidesh

last: Mahata

first: Pengfei

last: Qiu


title: Single-cell RNA sequencing of CD45+ immune cells across primary tumor, sentinel tumor-draining lymph node, and axillary lymph node in treatment-naive triple-negative breast cancer

summary: Regional lymph node metastasis critically influences distant metastatic progression, anti-tumor immunity, and patient prognosis in triple-negative breast cancer (TNBC). In this study, fresh surgically resected specimens from treatment-naive TNBC patients were collected and CD45+ immune cells were isolated for single-cell RNA sequencing to characterize immune remodeling across matched primary tumors, sentinel tumor-draining lymph nodes (S-TDLNs), and secondary axillary lymph nodes (ALNs). The overall project integrated scRNA-seq with imaging mass cytometry, Visium and Xenium spatial transcriptomics, and multiplex immunofluorescence. This GEO submission contains processed scRNA-seq expression matrices and associated metadata only. Raw sequencing data have been deposited previously in in the Genome Sequence Archive (GSA) for human data, and the GSA ID is HRA010347.

overall_design:
CD45+ immune cells were isolated from fresh treatment-naive TNBC primary tumors, sentinel tumor-draining lymph nodes, and axillary lymph nodes collected at surgery. Single-cell suspensions were prepared by mechanical dissociation, red blood cell lysis, filtration, and fluorescence-activated cell sorting. Libraries were generated using the 10x Genomics Chromium Single Cell 3' v3 platform, targeting about 8,000 cells per sample, and sequenced on an Illumina NovaSeq 6000 using 150 bp paired-end reads. Cell Ranger v7.0.0 was used for alignment to GRCh38 and generation of feature-barcode matrices. This submission includes processed matrices for the scRNA-seq libraries; raw FASTQ data are available through in the Genome Sequence Archive (GSA) under HRA010347.

***************************************************************
The raw data has been uploaded to the Genome Sequence Archive (GSA) for human data, and the GSA ID is HRA010347, link:https://ngdc.cncb.ac.cn/gsa-human/s/63zB6hyK
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title: Coordinated immune activation following KRAS inhibition reveals molecular pathways that potentiate and limit anti-tumor immunity

city: Newton

first: Matt

last: Kanke

state: MA - Massachusetts

address: 112 Harding Street

institute: Amgen

summary: While mutant-specific KRAS inhibitors are approved to treat cancer, a deeper understanding of intratumoral changes driven specifically by KRAS inhibition is needed to maximize therapeutic responses. Here we apply single-cell RNA-seq, flow cytometry, and spatial transcriptomics to distinguish mechanisms of tumor control after KRASG12C inhibition (KRAS(G12C)i), MEK inhibition (MEKi) and following combination therapy with KRAS(G12C)i and PD-1 blockade. Despite inhibiting overlapping pathways, KRAS(G12C)i drives the adaptation of distinct neoplastic cell fates affecting metabolism and cell cycle regulation, leading to synergistic tumor suppression after co-administration with MEKi. In turn, this modulates intercellular communication patterns and induces robust dendritic cell maturation and PD-1+ macrophage activation mediated through non-immune mediators. Both KRAS(G12C)i and MEKi elicit a similar magnitude of cytotoxic T-cell infiltration despite a reduced capacity for T-cell proliferation after MEKi, implicating distinct adaptive immune activation mechanisms. Combination treatment of KRAS(G12C)i with anti-PD-1 overcomes immune activation barriers by prolonging the activation window and clonal persistence for T cells and by promoting the re-wiring of pro-inflammatory macrophages associated with higher survival, Furthermore, combination treatment amplifies intercellular communication among non-PD-1+ expressing cells to perpetuate dendritic cell activation. Our findings connect neoplastic KRAS inhibition with the coordination of distinct levers for immune activation and reveal pro- and anti-tumor mechanisms that can be modulated following specific treatment types to contain malignant growth.

overall_design: C57BL/6 mice were challenged with KPC-KRAS-G12C tumors and treated with KRAS(G12C) inhibitor Sotorasib, MEK inhibitor Mirdametinib, or Vehicle. Immune signatures were analyzed by dissociating tumors and sorting CD45+ or dendritic cells and performing low-input RNA-seq.

first: Daniel

first: Tao

last: Osgood

first: Chi-Ming

last: Li


title: Histone Variant H1.0 Regulates Terminal Erythroid Differentiation via Phase Separation-Mediated Chromatin Organization

city: zhengzhou

first: Hengchao

last: Zhang

state: Henan

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

institute: zzu

summary: Mammalian erythroblasts require enucleation to form mature red blood cells during terminal stage of erythroid differentiation, in which chromatin and nuclear condensation are considered prerequisites for enucleation. Linker histone H1 is a key player in heterochromatin condensation and silencing, but it is unclear how H1 compresses chromatin and regulates erythroid differentiation. Here, we demonstrated that H1.0 was significantly overexpressed in terminal erythropoiesis among all histone H1 variants, whose deletion resulted in abnormal chromatin and nuclear condensation, impaired enucleation and increased apoptosis in terminal erythropoiesis. In addition, we established that H1.0 deficiency decompressed chromatin by increasing chromatin long-range and proximal interactions and remodeling topologically associating domain (TAD) boundaries of the genome. We demonstrated that H1.0 compressed chromatin via binding to nucleosomal DNA to form a phase separation, which required the C/N-terminal intrinsically disordered region (C-IDR) and G domain (GD). A truncated H1.0 lacking the C-IDR failed to compress chromatin in H1.0-deleted erythroid cells, whereas a truncated H1.0 lacking the N-IDR partially rescues this defect. In conclusion, our findings suggest that H1.0 remodels chromatin high-order structure and regulates erythropoiesis through a phase separation mechanism, providing novel insights into the regulation of chromatin condensation and enucleation in terminal erythropoiesis.

overall_design: Cells (1×106) were collected and washed twice with PBS. RNA was extracted and used as the cDNA input, the cDNA library was prepared using a Truseq DNA library kit (FC-121-2001, Illumina, U.S.A.), and the library was sequenced on a sequencing platform (Illumina NovaSeq 6000). Reads with quality less than 30 and length less than 20 bp were trimmed using Trim Galore version 0.6.6. Trimmed reads were then mapped to the GRCh38.87 genome (http://www.ensembl.org/index.html,human genome build GRCh38.87) using HISAT2 version 2.2.1 (http://daehwankimlab.github.io/hisat2/) . Gene expression was analyzed using the StringTie version 2.1.7 (https://ccb.jhu.edu/software/stringtie/) . TPM (Transcripts Per Kilobase of exon model per Million mapped reads) method was used for normalization. Principal component analysis (PCA) and correlation analysis were performed on expressed genes using the R software version 3.6.3 (https://www.r-project.org/) package. Differentially expressed genes (DEGs) were defined by TPM > 1, q < 0.05, and fold change > 2 using DESeq2 version 1.38.3 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html) . Gene Ontology (GO) enrichment analysis and visualization of DEGs was performed using the Meta scape (www.metascape.org/) online tool with q < 0.05.

first: Qianqian

last: Yang

first: Lixiang

last: Chen


title: SF3A3 regulates the proliferation and migration capabilities of hepatocellular carcinoma cells via the Notch signaling pathway

city: Fuzhou

first: Kunqi

address: Fujian Medical University

institute: Fujian Medical University

summary: This study aims to investigate the expression, biological function, and molecular mechanism of the splicing factor SF3A3 in hepatocellular carcinoma (HCC). Analysis of the TCGA-LIHC cohort revealed that SF3A3 is significantly upregulated in HCC tissues and its high expression correlates with poor overall survival. We established SF3A3 knockdown and overexpression models in HepG2 and Huh7 cells. Functional assays (CCK-8, colony formation, EdU, wound healing, flow cytometry for cell cycle and apoptosis) demonstrated that SF3A3 overexpression promotes HCC cell proliferation and migration, whereas knockdown exerts opposite effects. To explore the underlying mechanism, we performed transcriptome sequencing (RNA-seq) on SF3A3-depleted HCC cells. Combined with bioinformatic analysis and validation using the GEO dataset GSE287381, we identified the Notch signaling pathway as a key target of SF3A3. Western blotting confirmed that SF3A3 knockdown reduces Notch1 and HES1 protein levels, while overexpression increases them. Collectively, our findings indicate that SF3A3 promotes HCC cell proliferation and migration by activating the Notch signaling pathway, providing a rationale for targeting the SF3A3-Notch axis in HCC therapy.

overall_design: HepG2 and Huh7 cells were subjected to SF3A3 knockdown (siRNA) and overexpression (plasmid). Phenotypes (proliferation, migration, apoptosis, cell cycle) were assessed by CCK-8, EdU, colony formation, wound healing, and flow cytometry. RNA-seq followed by bioinformatic analysis and validation via Western blot and GEO dataset GSE287381 revealed the Notch pathway as a downstream effector.

first: LiYing


title: Single-cell sequencing and spatial transcriptomics revealed that the coacervate–cell–drug system effectively protects articular cartilage in osteoarthritic rats from wear and degenerative deterioration.

city: Guangzhou

first: Tianshen

last: Jiang

state: Guangdong

address: Tianhe, South China University of Technology

institute: South China Univerisity of Technology

summary: We employed DNBSEQ technology to perform single-cell RNA sequencing of rat macrophages, as well as single-cell and spatial transcriptomic analyses of rat knee joint tissues. Single-cell profiling of macrophages demonstrated that the coacervate–cell–drug system effectively reversed the pro-inflammatory phenotype by driving the transition of M1 macrophages toward a reparative M2c phenotype. Single-cell analysis of joint tissues further revealed strong interactions between exogenous GFP-labeled stem cells delivered by the coacervate–cell–drug system and endogenous joint-resident cells. Spatial transcriptomic analysis demonstrated that the coacervate–cell–drug system effectively promotes extracellular matrix repair in osteoarthritic cartilage.

overall_design:
In the macrophage single-cell RNA sequencing experiments, anti-inflammatory IL-4 and the coacervate–cell–drug system were separately co-cultured with IFN-γ and lipopolysaccharide (LPS)–induced pro-inflammatory (M1) macrophages, followed by analysis using single-cell RNA sequencing.
For tissue-level single-cell RNA sequencing, osteoarthritic rats were treated by intra-articular injection with either HA & GFP-cells & drug or coacervate & GFP-cells & drug. GFP-positive cells were subsequently isolated by fluorescence-activated cell sorting (FACS) and subjected to single-cell RNA sequencing analysis.
For spatial transcriptomic analysis, knee joint tissues from osteoarthritic rats treated with coacervate & GFP-cells & drug were cryosectioned and analyzed using spatial transcriptomics.

first: Sirong

first: Pengchao

first: Liming

last: Bian


title: Transcriptomic analyses of PDX tumors (QQX-17) to gain insight into the mechanisms underlying FOLFOXIRI-induced DTP state.

city: Jinan

first: Shuohui

address: Qilu Hospital, Shandong University, No.107, Wen Hua Xi Road, Jinan, Shandong, 250012, P.R. China

institute: Qilu Hospital of Shandong University

summary: Chemotherapy resistance remains a significant challenge, often leading to tumor relapse and poor prognosis. While past efforts to overcome treatment resistance have focused primarily on genetic alterations—such as somatic mutations, chromosomal aberrations, and dysregulated signaling pathways—these insights have yet to translate into effective clinical interventions. The recent discovery of drug-tolerant persister (DTP) cells, which survive therapy through reversible, non-genetic adaptations akin to embryonic diapause, has unveiled a novel mechanism of chemotherapy resistance. To investigate this further, we employed treatment-naïve colorectal cancer (CRC) patient-derived xenograft (PDX) models. Upon reaching a tumor volume of 100 mm³, the PDX models were treated with a single maximum-tolerated dose of the FOLFOXIRI regimen. Post-treatment responses varied, including initial tumor shrinkage followed by regrowth, mirroring the "sensitivity-DTP-regrowth" pattern observed in CRC patients. Transcriptomic analyses of these PDX tumors were then conducted to elucidate the mechanisms underlying the FOLFOXIRI-induced DTP state.

overall_design: RNA-seq profiling of QQX-17 models across control (baseline), DTP (residual), and regrowth status.


title: Gene expression profile changes in brown adipose tissue after 20 hours of fasting following BMP4 specific knockdown in brown adipose tissue

city: Shanghai

first: Zhenyu

last: Xu

state: 枫林校区

address: Dongan Road

institute: Shanghai Medical College, Fudan University

summary: This transcriptome analysis compares gene expression profiles in brown adipose tissue (BAT) from BAT-specific BMP4 knockout mice and their wild-type littermates under a prolonged fasting 20 hours condition. The goal of this study was to investigate the mechanistic role of BMP4 signaling in regulating lipid metabolic pathways and mitochondrial function in BAT during an energy-deficient state.

overall_design: BMP4 specific-knockout in brown adipose tissue mice were constructed and fed normally until 12 weeks. The BMP4 knockout mice and their littermate controls were fasted for 20 hours, and RNA was extracted from brown adipose tissue for sequencing analysis


title: bulk ATACseq of Ccd18-Co cell line treated with cytokines

city: Cambridge

first: Simon

last: Koplev

address: Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Puddicombe Way

department: Cambridge Stem Cell Institute

institute: University of Cambridge

overall_design: Ccd18-Co cell line unstimualted or stimulated with cytokines, followed by vehicle or epigenetic modulators. N=4 replicates per treatment group.

first: Matthias

last: Friedrich


title: Effects of ER stress and inflammation on chromatin accessibility in macrophages

city: Suita

first: Tomohiko

last: Murakami

state: OSAKA

address: 1-8 Yamada-Oka

country: Japan

institute: Osaka University

summary: To understand the effects of ER stress and inflammation on chromatin accessibility, primary bone marrow derived macrophages (BMDMs) were stimulated with tunicamycin (Tm)  and/or LPS. Chromatin accessibility was analyzed by ATAC-seq.

overall_design: ATAC-Seq of primary bone marrow derived macrophages (BMDMs) stimulated with tunicamycin (Tm) and/or LPS


title: Elevated IGFBP1 triggers musculoskeletal defects in mice

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

summary: Here we showed that IGFBP1, a liver-derived hormone belonging to the insulin-like growth factor family of binding proteins (IGFBPs), plays a causative role in driving musculoskeletal complications. In our initial studies, IGFBP1 was found elevated in colorectal cancer (CRC) cachectic patients and in CRC hosts, along with muscle and bone loss. In vitro, IGFBP1 induced myotube atrophy and osteoclast differentiation. Therefore, the objective of this study was to define the mechanisms by which IGFBP1 contributes to muscle and bone depletion. Our central hypothesis is that elevated circulating (hepatic) IGFBP1 initiates events consistent with musculoskeletal wasting. We infected normal mice (without tumors) with adeno-associated viruses carrying the full-length IGFBP1 gene, injected via the tail vein. At time of sacrifice (after 54 days) the animals presented drastically elevated IGFBP1 circulating levels, along with severe loss of muscle and bone mass. In order to shed light on the IGFBP1-related effects in skeletal muscle only, we generated an RNAseq dataset in quadriceps muscles from animals infected with AAV-IGFBP1. Our study revealed modulation of several signaling pathways, in line with the cachectic phenotype. Therefore, our findings contribute to define the mechanistic effects of IGFBP1 in cachexia and identify IGFBP1 as a new therapeutic target for the treatment of the musculoskeletal complications of cancer.

overall_design: To study the effects resulting from in vivo overexpression of IGFBP1, 8-week-old C57BL/6J male mice (The Jackson Laboratory, Bar Harbor, ME, USA) were group housed (up to 5 per cage) and infected with 200ul of 10^12 vg/ml serotype 8 recombinant replication-deficient adeno-associated virus (AAV8) vectors, characterized by tropism for the liver, by injecting via the tail vein either AAV8-Alb-IGFBP1 (AAV-IGFBP1) or AAV8-Alb-Null (AAV-Null) using a 30-gauge syringes (Becton-Dickinson, Franklin Lakes, NJ, USA). The AAV8 constructs were purchased from Vector Builder (Chicago, IL, USA). After 54 days from virus injection, the animals were sacrificed. Skeletal muscles (e.g., quadriceps) were excissed and snap frozen in liquid nitrogen.

first: Livingston

last: Patrick D

first: Goodspeed

last: Andrew

first: Lee

last: Schuyler

first: Gao

last: Bifeng

first: Bonetto

last: Andrea


title: The gene expression of osteoarthritic knee cartilage from rats treated with different methods

summary: Comparison between the gene expression of osteoarthritic cartilage treated with HA and coacervate demonstrates that coacervate delays osteoarthritis progression by primarily suppressing osteoclast differentiation and inflammatory responses.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the healthy cartilage, osteoarthritic cartilage, osteoarthritic cartilage treated with HA&cells&drug, and osteoarthritic cartilage treated with coacervate&cells&drug (Age: 10 weeks)

last: Zhao


title: The dynamic N1-methyladenosine methylome of RNA provides insights intotheregulation oftomato fruit ripening

city: Beijing

first: Lili

last: Ma

address: 50 Changhua Road, Haidian District

institute: Beijing Academy of Agriculture and Forestry Science

summary: N1-methyladenosine (m1A) methylation is crucial for the biogenesis of diverse RNAs, thereby influencing distinct biological functions. Previous studies have established extensive m1A modifications in petunia mRNAs. However, the specifics of the abundance, distribution, and functional role of mRNA m1A modification during tomato fruit ripening remain unclear. Our study shows that m1A modifications are prevalent in tomato mRNA and are also detected in lncRNA and circRNA. The distribution of m1A peaks in mRNA segments indicates that m1A is mainly enriched at the start codon and CDS regions. By comparing wild-type (AC) tomatoes and ethylene receptor-mutant (Nr) tomatoes from the mature green (MG) stage to six days after the breaker (Br+6) stage, we observed a decrease in the overall methylation level with fruit ripening, with the Nr mutant fruits showing significantly lower methylation levels than AC fruits. Additionally, we identified differences in m1A methylation and expression levels of numerous key genes related to fruit ripening. The integrated analysis of RNA-seq and MeRIP-seq data uncovered the possible positive impact of m1A modifications on gene expression regulation. This research offers novel insights into the specific m1A methylation modifications occurring during the ripening of both wild-type AC and Nr mutant tomato fruits for the first time. Collectively, our study contributes to the growing evidence highlighting the potential significance of m1A methylation modifications in plant development and maturation.

overall_design: The wild type (WT) tomato “Ailsa Craig” (AC) and the homozygous ethylene receptor mutant tomato “Never-ripe” (Nr), both in the AC background. Fruits were harvested at two stages: the mature green (MG) stage, approximately 39 days post-anthesis, and the red ripening stage, 6 days after the breaker stage (Br+6). At the Br+6 stage, the Nr mutant displayed an orange phenotype. For each group, fruits from both maturity stages were sampled, with three biological replicates taken at each stage.

first: Jinhua

last: Zuo

first: Chunmei

last: Bai

first: Anzhen

last: Fu

first: Qing

last: Wang

first: Zhongjing

last: Zhou

first: Zhiping

last: Deng

first: Jinjuan

last: Tan

first: Mondher

last: Bouzayen

first: Yanyan

last: Zheng


title: Role of mitochondrial RNase P complex in the processing of primary RNA in human mitochondria

city: Warsaw

first: Damian

last: Graczyk

address: ul. Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

summary: The human mitochondrial genome is transcribed into long polycistronic RNA that undergoes subsequent endonucleolytic processing. The role of the mitochondrial RNase P, a protein complex composed of RNA methyltransferase, ribonuclease and dehydrogenase, has been revealed in the processing of the primary mitochondrial RNA. Still, the contribution of catalytic activities of RNase P subunits in the processing of individual processing sites has not been fully described. This study aims to define the role of RNase P subunits in regulating the efficiency of the processing of the primary mitochondrial RNA.

overall_design: Expression of TRMT10C, HSD17B10 and PRORP genes encoding subunits of the mitochondrial RNase P complex was silenced in HeLa Flp-In T-Rex cells using RNAi, total cellular RNA was isolated, rRNA-depleted and subjected to NGS analysis. RNA isolated from untreated HeLa Flp-In T-Rex cells was analysed as a control. In addition, transcriptomes of HeLa Flp-In T-Rex cells transfected with siRNAs targeting TRMT10C, HSD17B10 and PRORP genes and co-expressing exogenous siRNA-insensitive either active or catalytically inert versions of the studied genes were analysed (rescue experiment).

first: Joanna

last: Grochowska

first: Roman

middle: J

last: Szczesny


title: CASC15 dictates vascular smooth muscle cell growth fate and pathological vascular remodeling through post-transcription regulation of mitotic fidelity

status: Public on Jun 26 2026

city: Pittsburgh

first: Delphine

last: Gomez

state: Pennsylvania

address: 203 Lothrop Street

department: Vascular Medicine Institute

institute: University of Pittsburgh

summary: Vascular smooth muscle cell (SMC) growth, whether hyperplastic or hypertrophic, is a central determinant of vascular remodeling in cardiovascular disease, yet the molecular regulators that direct SMC toward a specific growth fate remain poorly understood. Here, we identify the long non-coding RNA CASC15 as a critical regulator of SMC growth and vascular remodeling. CASC15 is enriched in the vasculature and SMC-rich tissues in humans and mice, and its locus harbors SNPs significantly associated with coronary artery disease and blood pressure. We identify a novel SMC-selective CASC15 isoform (S-CASC15) whose expression level determines SMC growth fate: elevated S-CASC15 promotes proliferation, while its loss drives hypertrophy, polyploidization, and binucleation. In vivo depletion of CASC15 limited vascular injury-induced neointima formation and atherosclerotic lesion expansion. Conversely, CASC15 overexpression exacerbates injury-induced neointimal hyperplasia. However, CASC15 KO mice exhibited spontaneous medial hypertrophy and vascular hypercontractility. Mechanistically, loss of S-CASC15 expression causes mitotic defects, followed by arrest in the G1 phase of hypertrophic and polyploid cells. We found that S-CASC15 interacts with RNA-binding proteins, including Nucleolin, to control RNA processing, splicing, and stability. Specifically, CASC15 regulates the stability of cell cycle checkpoint gene transcripts, thereby ensuring mitotic fidelity. Together, these findings establish CASC15 as a pivotal molecular switch governing the balance between hyperplastic and hypertrophic vascular remodeling and a potential therapeutic target in cardiovascular disease.

overall_design: RNA-seq profiling of wild type mouse aortic smooth muscle cells and knockdown and overexpression of CASC-15 with no treatment, PDGF-BB treatment, and Angiotensin II treatment.

first: Ibrahim

middle: A

last: Ahmed

first: Lakshanya

last: Rajaganapathi

first: Santiago

last: Rivero

first: Jianxin

last: Wei

first: Sebastian

last: Morales-Bermudez Espinel

first: Ariane

last: Bruder

first: Angelina

last: Kendi

first: Thiago

last: Bruder do Nascimento

first: Cristina

last: Espinosa-Diez


title: γ-Tocopherol attenuates COPD-associated macrophage inflammation through the PSEN1–SYT7–PI3K/Akt axis

first: Yue

last: Dong

address: No.801 Heqing Rd. Minhang District

institute: Fudan University

summary: Rationale: Chronic obstructive pulmonary disease (COPD) features persistent airway inflammation, oxidative/nitrative stress, and macrophage activation. γ-tocopherol has antioxidant and anti-inflammatory activity, but its disease relevance and molecular targets are unclear. Objectives: To test whether γ-tocopherol attenuates disease-associated inflammation and define the macrophage mechanism. Methods: Multi-omics integrated analysis combined with γ-tocopherol-treated COPD-like mouse models was performed to evaluate the anti-inflammatory effects of γ-tocopherol and identify its target cell populations. Furthermore, target prediction, cellular thermal shift assay, co-immunoprecipitation, and other experimental approaches were used to identify the molecular target of γ-tocopherol and elucidate the downstream mechanisms underlying its anti-inflammatory and antioxidant effects. Measurements and Main Results: COPD was associated with altered γ-tocopherol metabolism and vitamin E-related transcriptional programs. γ-tocopherol reduced inflammatory cell accumulation, nitric oxide metabolites, macrophage activation, and lung inflammation in COPD-like mouse models. Alveolar macrophages were identified as the primary target cell population of γ-tocopherol in lung tissue. γ-tocopherol treatment suppressed nitric oxide synthesis and inflammatory cytokine release in macrophages, and this effect depended on the engagement of γ-tocopherol with PSEN1. Further mechanistic analysis identified SYT7 as a downstream effector of PSEN1, linking γ-tocopherol treatment to reduced PI3K/AKT signaling activity and attenuated inflammatory readouts. Conclusions: γ-tocopherol attenuates macrophage-centered inflammation in COPD-like models through a PSEN1–SYT7–PI3K/AKT signaling axis.

overall_design: RAW264.7 cells were divided into three groups: control, vehicle, and γ-tocopherol-treated groups, with three biological replicates per group, for a total of nine RNA-seq samples. The control group consisted of untreated RAW264.7 cells. The vehicle group consisted of RAW264.7 cells stimulated with LPS at 100 ng/mL for 24 h and treated with solvent control. The γ-tocopherol group consisted of RAW264.7 cells stimulated with LPS at 100 ng/mL for 24 h and treated with 500 μM γ-tocopherol. Bulk RNA-seq was performed to investigate transcriptomic changes associated with LPS-induced inflammatory activation and the effect of γ-tocopherol treatment.

first: Jindong

last: Shi

first: Chengyue

last: Zhu

first: Changjiang

last: Guo

first: Thea

last: Golden

first: Haoran

first: Bixi

last: Tang

first: Ying

first: Tingting

last: Ge

first: Junqing

last: Li

first: Andrew

last: Gow

first: Chung S

last: Yang

first: Yi

last: Zang

first: Zhijun

last: Jie

first: Junhong

last: Jiang


title: Whole genome bisulfite sequencing of human prostate cell lines

city: Houston

last: Lu

state: TX

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: We performed whole genome bisulfite sequencing (WGBS) of five human prostate cell lines in order to establish their 5mC profile, with the goals of generating a dataset for comparison to multiple epigenetic and transcriptome analyses done for the same lines.

overall_design: Three prostate cancer (DU 145, LNCaP, and PC-3) and two normal-derived (PWR-1E and RWPE-1) were purchased from ATCC and cultured under standard conditions according to the vendor's handling information.

first: Marcos

middle: R

last: Estecio

first: Kimie

last: Kondo


title: Genome-wide CRISPR screening on cytotoxic T lymphocytes mediated cell killing independent of Casp3

city: Lørenskog

first: Shixiong

last: Wang

address: Sykehusveien 25

country: Norway

institute: Akershus University Hospital

summary: To gain insight into cytotoxic lymphocyte–mediated, Casp3-independent cancer cell death, we leveraged the a CTL–αCD3–P815 killing system and performed a genome-wide CRISPR screen. Cas9 expressing and Casp3-/- mouse mastocytoma P815 cells were first transduced with Brie gRNA library and subjected to cytotoxic T lymphocytes-mediated selection. Surviving cells were collected and sequenced to identify genes/gRNAs enriched following selection.

overall_design: Genome-wide CRISPR screen on Casp3⁻/⁻ P815 cells with cytotoxic T lymphocyte (CTL) mediated cell killing. sgRNA transduced Casp3-/- P815 cells were collected before (control) and after 3 rounds of CTL killing (CTL_treated). There are 3 replicates with control and 4 replicates with CTL_treated.

first: Youxian


title: Genome-wide CRISPR screening on cytotoxic T lymphocytes mediated cell killing independent of Casp3, Mlkl, and Bid

summary: To gain insight into cytotoxic lymphocyte–mediated, Casp3, necroptosis, and Mitochondrial outer membrane permeabilization (MOMP) independent cancer cell death, we leveraged the a CTL–αCD3–P815 killing system and performed a genome-wide CRISPR screen. Cas9 expressing and Casp3-/-Mlkl-/-Bid-/- mouse mastocytoma P815 cells were first transduced with Brie gRNA library and subjected to cytotoxic T lymphocytes-mediated selection. Surviving cells were collected and sequenced to identify genes/gRNAs enriched following selection.

overall_design: Genome-wide CRISPR screen on Casp3-/-Mlkl-/-Bid-/- P815 cells with cytotoxic T lymphocyte (CTL) mediated cell killing. sgRNA transduced Casp3-/-Mlkl-/-Bid-/- P815 cells were collected before (control) and after 2 rounds of CTL killing (CTL_treated). There are 3 replicates with both control and CTL_treated conditions.


title: CAR-T-drug conjugate against solid tumor [Spatial Transcriptomics]

city: New Haven

first: Chuanpeng

last: Dong

state: CT

address: 850 West Campus Dr

department: Genetics

institute: Yale University School of Medicine

summary: Chimeric antigen receptor (CAR)-T cell therapy has been clinically successful in hematologic malignancies but faces challenges in solid tumors, including limited infiltration, immunosuppressive microenvironments and antigen heterogeneity. While combining CAR-T cell therapy with chemotherapy can enhance antitumor activity, this often leads to substantial systemic toxicity. Here we show that CAR-T-drug conjugate (CAR-T-D-C), generated through click chemistry-mediated conjugation of cytotoxic payloads to antigen-specific CAR-T cells, enable localized drug delivery while preserving CAR-T cell function. CAR-T-D-Cs incorporating different CAR-T cell binders exhibit robust antitumor activity across multiple human xenografts and syngeneic tumor models. Spatial transcriptomic analyses reveal enhanced intratumoral CAR-T infiltration and activation following CAR-T-D-C treatment . Compared with conventional CAR-T therapy, CAR-T-D-C enhances immune cell infiltration, augments effector functions, promotes antigen spreading and amplifies systemic anti-tumor immunity. CAR-T-D-C represents a versatile therapeutic platform that combines the specificity of cellular immunotherapy with the potency of small-molecule therapeutics for treatment of solid tumors.

overall_design: One million HT29-GL cells were intravenously injected into NSG mice, and tumor progression was monitored using IVIS imaging. On day 21 post-injection, the mice were treated with 5 million CAR-T or CAR-T-D-C cells. The lungs were harvested 24 hours post-treatment for spatial transcriptomics. To collect the lung samples, the harvested lungs bearing HT29 tumors were preserved with Optimal Cutting Temperature (OCT) compound and stored at -80°C for future use. The samples were sectioned at a thickness of 7-10 μm and centrally mounted on Poly-L-Lysine coated 1 x 3" glass slides. Serial tissue sections were collected simultaneously for Digital Barcoding in Tissue (DBiT) and Hematoxylin and Eosin (HE) staining.

first: Shan

last: Xin

first: Yanzhi

last: Feng

first: Feifei

last: Zhang

first: Sidi

last: Chen


title: Human Cellular Clock of the Aging Lung Parenchyma spatial transcriptomics data

first: Alexander

last: Tsankov

state: MA

address: 7 Divinity Drive

institute: Harvard University

summary: This Xenium spatial transcriptomics data from normal lung samples of different ages used in the study Human Cellular Clock of the Aging Lung Parenchyma.

overall_design: High throughput RNA in-situ hybridization with Xenium with the segmentation kit together with the 10x hLung 289-gene panel and a custom 100-gene senescence panel to capture gene expression profiles at single-cell resolution within intact lung parenchyma.

first: Patty

last: Lee

first: So-Jin

last: Kim

first: Alter

last: Klausner

middle: M

first: Ke

last: Xu

first: Atharva

last: Bhagwat

first: Vignesh

middle: V

last: Venkat


title: CAR-T-drug conjugate against solid tumor

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Regulatory T cells Restrain CD4 T Cell Control of MHC-I-Deficient Metastatic Pancreatic Cancer Emerging After PD-L1 Blockade

city: Minneapolis

first: Ingunn

last: Stromnes

state: Minnesota

address: 2-186 Wallin Medical Biosciences Building, 2101 6th St SE

department: Medical School

institute: University of Minnesota


title: CAR-T-drug conjugate against solid tumor [RNA-seq/BCR-seq]

overall_design:
CAR-T cells were seeded at 3×10^5 cells per well in 96-well plates and treated with DMSO, Ac4ManNAz, or MMAE. Cells were harvested at 0h, 6h and 24h post-treatment for RNA preparation.
CA9-mRNA were synthesized with the Hiscribe™ T7 ARCA mRNA Kit (with tailing) (NEB, Cat. E2060S) and formulated using the NanoAssemblr® Ignite™ instrument (Precision Nanosystems) according to manufacturers’ guidelines. The particle size of LNP-mRNA was determined using dynamic light scattering (DLS) device (DynaPro NanoStar, Wyatt, WDPN-06). The encapsulation efficiency and mRNA concentration were quantified by Quant-iT™ RiboGreen™ RNA Assay (Thermo Fisher, Cat. R11490). Humanized ATX-GK mice (Alloy Therapeutics), engineered with with human IgG and IgK transgene knock-ins, were immunized with 10μg of CA9 LNP-mRNA per dose for both prime and booster injections on day 0 and day 14, respectively.  Blood samples were collected retro-orbitally on days 14 and 21 post-immunization to evaluate the immune response using ELISA. Spleen and lymph nodes from immunized mice were harvested on day 23 for memory B cells isolation using a magnetic positive selection kit (Miltenyi Biotec, Cat. 130-095-838).


title: Platelet-derived S100A9 contributes to Endotheliopathy in Alcohol-Associated Hepatitis

first: Matthew

last: McConnell

state: Connecticut

address: PO Box 208019, 300 Cedar St

institute: Yale University

summary: Alcohol-associated liver disease (ALD) is a growing global health concern, with alcohol-associated hepatitis (AH) leading to the highest morbidity and mortality. Available therapies are limited and often inadequate. Platelets contribute in a variety of ways to the pathogenesis of liver diseases, but their role in AH remains largely unexplored. In this study we address the hypothesis that platelets contribute to pathological inflammation in AH. Using patient samples and a multi-omics approach, we found that platelets undergo proinflammatory transcriptomic and proteomic changes in AH, with two alarmins, S100A8 and S100A9, being among the top upregulated genes/proteins.  Additionally, the abundance of platelet-derived microparticles containing S100A8 and S100A9 in AH patient plasma was increased (p=0.032) and correlated with disease severity (MELD-Na, r=0.51, p=0.03) and endotheliopathy (ICAM1, r=0.70, p=0.001) (CXCL8, r=0.48, p=0.04) (vWF, r=0.59, p=0.01). We mechanistically linked S100A9 with endotheliopathy via crosstalk between primary human liver sinusoidal endothelial cells and primary human monocytes. We also demonstrate that Interleukin-6 (IL6) upregulates S100A9 in megakaryocytic cells in a JAK/STAT-dependent manner, modeling changes occurring in the bone marrow in patients with AH. Our studies establish proinflammatory platelets as important contributors to AH disease pathology. Moreover,  anti-platelet agents, or more specifically S100A9 targeted drugs, are potential therapeutic strategies in AH.

overall_design: RNAseq of platelets from healthy donors and alcohol-associated hepatitis patients

first: Kirlin

last: Fallyn

first: McConnell

last: Matthew


title: Single-Cell Multimodal Atlas Reveals Regulatory Programs in the Human Brain

city: New York

first: Yang

last: Xie

state: NY

address: 101 6th Ave

institute: New York Genome Center

summary: Directly measuring chromatin states alongside transcription is essential for understanding how cell-type-specific regulatory programs are established and maintained in the adult human brain. We present a large-scale single-cell multimodal atlas generated by jointly profiling transcriptome with active (H3K27ac) and repressive (H3K27me3) histone modifications across 18 brain regions. We profile >750,000 nuclei spanning 160 cell types and integrate these data with chromatin accessibility, DNA methylation, 3D genome architecture, and spatial transcriptome. This framework annotates >500,000 regulatory elements and resolves cell-type-specific chromatin states. We link enhancers to target genes, infer gene regulatory networks, and classify chromatin interactions, revealing neuron-enriched long-range Polycomb repression of developmental genes. Integrating these maps with GWAS data and sequence-based model prioritizes noncoding variants, effector genes, and vulnerable cell types for neuropsychiatric disorders. Finally, cross-species comparisons show conserved activation but more divergent repression. Together, this study provides a functional reference for interpreting noncoding variants, epigenetic memory, and brain organization.

overall_design: Droplet Paired-Tag (DPT) and multiplexed DPT in 18 human brain regions from three neurotypical male donors.

first: Xie

last: Yang

first: Chang

last: Lei


title: Stage-related transcriptional changes in HR-positive/HER2-negative breast cancer

first: William

middle: Fraser

last: Symmans

address: 2130 W Holcombe Blvd #11.4000

institute: University of Texas MD Anderson Cancer Center

summary: It is important to understand how the biology of breast cancer might differ with the burden of disease. Analyzing the expression of cancer-relevant genes with increasing diagnostic stage can provide insight into the changing biology of breast cancer and is therefore clinically useful. Here, we evaluated the transcriptional activity according to stage of breast cancer (American Joint Commission on Cancer, AJCC Stage I to IV) from 1,152 patients with hormone receptor-positive HER2-negative breast cancer. Samples were prospectively collected fresh for clinical/translational research with transcriptional profiling. Most transcriptional signatures remained consistent across stage categories, while most of the significant changes associated with increasing stage were attributed to endocrine escape, decreasing differentiation, increased complexity of signal transduction, and some metabolic changes. The clinical relevance and implications of these findings are discussed, and the public availability of these expression data from high-quality samples is a resource for researchers.


title: Curcumin and Sulforaphane Preserve Mobility in Aging Caenorhabditis  elegans via Distinct yet Complementary Transcriptional Signatures

city: Novato

first: Nathan

last: Price

state: California

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

summary: Aging involves a progressive decline in bodily functions, underscoring the need for interventions that enhance healthspan. In this study, we screened nine natural products in Caenorhabditis elegans using whole-organism phenotyping to assess mobility endpoints, and subsequently focused on curcumin, sulforaphane, and their combination. In replicated follow-up experiments, all three interventions improved late-adult mobility after Day 2 of adulthood. Sulforaphane and the combination provided the strongest gains, whereas curcumin showed a distinct benefit profile, with more pronounced effects on time active measures than on speed-based metrics. To examine associated molecular changes, we performed transcriptomic profiling on Day 3 adults. Curcumin was associated with lipid and sphingolipid remodeling together with reduced expression of several innate immune effectors, whereas sulforaphane induced glutathione-linked detoxification signatures involving multiple gst genes. The combination retained major features of both single-compound responses while adding combination-specific changes that broadened detoxification-associated signatures and extended repression of lectin- and lysozyme-associated genes. Transcription factor activity inference further supported SKN-1-linked detoxification responses under sulforaphane and the combination. Overall, these results suggest that curcumin and sulforaphane engage distinct yet partially convergent maintenance-related programs, and that their combination broadens the underlying molecular response without producing additive mobility gains. These findings motivate further testing of natural product combinations in healthspan-related contexts.

overall_design: Transcriptomic profiling (RNA-Seq) of Caenorhabditis elegans strain SS104 glp-4(bn2) at Day 3 of adulthood. The experiment includes four conditions to investigate the effects of natural products on healthspan: Control, Curcumin treatment (5 mg/mL), Sulforaphane treatment (0.625 mg/mL), and a combination treatment (Curcumin + Sulforaphane) at the same concentrations. Each of the four conditions consists of four independent biological replicates, for a total of 16 samples.

first: R

middle: P

last: Vivek-Ananth

first: Durai

last: Sellegounder

first: Karthik

last: Mohanraj

first: Sushmita

last: Maitra

first: Chris

last: Saunter

first: David

last: Weinkove

first: Eric

last: Verdin

first: Stephen

last: Phipps


title: Integrating fine needle aspiration and single-cell RNA sequencing for studying metabolic dysfunction-associated steatotic liver disease

city: Los Angeles

first: Ana

middle: C

last: Maretti-Mira

state: CA

address: 1450 Biggy Street, NRT 3514

department: Medicine

institute: USC

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) is currently the leading cause of chronic liver disease and hepatocellular carcinoma. The immune response plays a central role in disease onset and progression and is the focus of many experimental studies. However, traditional models typically rely on terminal sampling procedures that require large tissue quantities, substantial numbers of animals per experimental condition, and cross-sectional study designs. Here, we propose the integration of two powerful techniques to longitudinally study a MASLD animal model: image-guided fine-needle aspiration (FNA) and single-cell RNA sequencing (scRNA-seq).

overall_design: Two groups of mice (n = 3 each) were fed the Fructose, Palmitate, Cholesterol, and Trans-Fat (FPC) diet with varying cholesterol content for a total of 32 weeks. During the first 24 weeks (Progression phase), one group received low dietary cholesterol (0.05%), and the other received high cholesterol (1.25%). At week 24, mice underwent the FNA sampling and continued into the second phase of the study, in which they transitioned to an FPC diet with 0.05% cholesterol for an additional 8 weeks (Intervention phase). At the end of this phase (week 32), all animals underwent a second FNA procedure. During each FNA procedure, we collected one biopsy per major liver lobe, totaling 4 biopsies per animal. Biopsies were pooled at the subgroup level for downstream cell dissociation, and viable cells were profilled using scRNA-seq.

last: Salomon

first: Lucy

last: Golden-Mason


title: The effects of expression of the EWS-FLI1 oncoprotein on alternative splicing

city: Boston

first: Huy

last: Nguyen

address: 450 Brookline Ave

department: Radiation Oncology

institute: Dana-Farber Cancer Institute

summary: Ewing sarcoma (EwS) is a group of bone and soft tissue cancers in children and young adults. Since expression of the EWS-FLI1 oncoprotein perturbs the function of a splicing factor, EWSR1, EWS-FLI1 may induce alternative splicing events in Ewing saocoma cells.

overall_design: To investigate the genome-wide effects of EWS-FLI1 expression, we generated EWS-FLI1 knockout cells in an Ewing sarcoma cell line, A673 cell, and performed RNA sequencing with A673 EWS-FLI1 wildtype and EWS-FLI1-depleted cells.

first: Shuhei

last: Asada

first: Guangli

last: Zhu

first: Alan

last: D’Andrea


title: Effect of NFAP2 treatment on early-stage filamentous Candida albicans and pseudohyphal Candida auris cultures

city: Szeged

first: Krisztián

last: Laczi

address: 52. Közép Fasor

department: Biotechnology and Microbiology

country: Hungary

institute: University of Szeged

summary: The Neosartorya (Aspergillus) fischeri antifungal protein 2 (NFAP2) represents a particularly promising candidate in the fight against fungal infections. To facilitate the progression of NFAP2 toward clinical application, a comprehensive understanding of its antifungal mode of action against filamentous Candida forms is essential. In the present study, we analyzed the transcriptomic responses of filamentous Candida albicans and pseudohyphal Candidozyma (Candida) auris cells following exposure to NFAP2.

sample_organism:
Candida albicans
Candidozyma auris

platform_organism:
Candida albicans
Candidozyma auris

overall_design: Early-stage filamentous C. albicans cells were treated with 1.56 µg mL −1 NFAP2 in liquid complete medium (LCM) for 60 min at 37 °C with continuous shaking at 400 rpm in four independent experiments (CaT1–4). Transcriptomic profiles were compared with those of untreated controls incubated under identical conditions (CaU1–4). Pseudohyphal C. auris cells were exposed to 3.12 µg mL −1 NFAP2 for 45 min under the same conditions in three independent experiments (CaurT5–7), and transcriptomes were compared with corresponding untreated controls (CaurU5–7). This treatment was additionally performed at a higher concentration of 25 µg mL −1 NFAP2 in four independent experiments (CaurT1–4; CaurU1–4).

first: László

last: Galgóczy

first: Richárd

last: Merber

first: Gábor

last: Bende

first: Erika

last: Kazinczi


title: Can caffeine improve the survival of the ant Formica fusca under pathogenic infection of the fungus Beauveria bassiana?

city: Graz

first: Danae

last: Nyckees

address: Universitätsplatz 2

country: Austria

institute: University of Graz

summary: Caffeine, a widely occurring plant alkaloid, has been shown to exhibit antimicrobial properties and influence insect behaviour. This study investigates the potential of caffeine to mitigate the effects of the fungal pathogen Beauveria bassiana in colonies of the ant Formica fusca. Using field-collected colonies, we examined the impact of a naturally relevant caffeine concentration (100 ppm) on ant survival, foraging behaviour, and gene expression under fungal exposure. Caffeine consumption delayed peak mortality and altered foraging dynamics in exposed ants, although it did not prevent fungal spore germination at the tested concentration. Transcriptomic analysis revealed significant upregulation of immune- and metabolism-related genes in exposed ants, alongside changes in genes linked to feeding behaviour and symbiotic interactions. While caffeine was a deterrent to sham-treated ants, exposed ants did not exhibit avoidance/preference. Additionally, caffeine demonstrated antifungal activity at higher concentrations, suggesting potential disruption of fungal development. These findings highlight the complex interplay between dietary compounds, pathogen defence, and ant behaviour, emphasizing the role of plant secondary metabolites in shaping insect-pathogen interactions.

overall_design: Ant samples (Formica fusca) either exposed to the fungal pathogen Beauveria bassiana or sham treated, then either fed with ant food or spiked ant food with 100 ppm of caffeine. Ants were collected 4 days post-infection treatment.

first: Christoph

last: Hahn

first: Heikki

last: Healnaterä

first: Dalial

last: Freitak


title: ALKBH5 in Cancer-associated Fibroblasts Facilitates Pancreatic Cancer Metastasis via HSF1–LIF Axis [ATAC-seq]

first: Xianglin

last: Yin

state: Other (Non U.S.)

address: No.1 Shuaifu garden, Dongcheng District

institute: Peking Union Medical College Hospital

summary: Cancer-associated fibroblasts (CAFs) are principal determinants of pancreatic ductal adenocarcinoma (PDAC) progression, yet the epitranscriptomic mechanisms governing tumor–stroma crosstalk remain poorly understood. Here, we identify N6-methyladenosine (m6A) remodeling as a hallmark of CAF activation and define a critical role for the m6A demethylase AlkB homolog 5 (ALKBH5) in PDAC metastasis. Activated CAFs exhibit a global reduction in m6A abundance, with ALKBH5 emerging as a key regulator of the CAF epitranscriptome. Functionally, CAF-derived ALKBH5 enhances pancreatic cancer cell migration and invasion in vitro and promotes epithelial–mesenchymal transition–associated gene expression in tumor cells in an m6A-dependent manner. In vivo, orthotopic co-implantation models and host genetic ablation models demonstrate that ALKBH5 plays a critical role in metastatic dissemination, with minimal impact on primary tumor growth. Mechanistically, ALKBH5 enhances the m6A-dependent translation of heat shock factor 1 (HSF1) in CAFs, at least in part by relieving insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3)-associated translational constraints. Elevated HSF1 subsequently activates leukemia inhibitory factor (LIF) transcription through distal enhancer elements, establishing an ALKBH5–HSF1–LIF signaling axis that mediates pro-metastatic CAF–tumor cell communication. Clinically, enrichment of ALKBH5⁺/HSF1⁺ CAFs independently predicts poor prognosis and is preferentially observed in metastatic PDAC. Collectively, these findings uncover a CAF-intrinsic epitranscriptomic program that drives PDAC metastasis and highlight stromal m6A regulation as a potential therapeutic vulnerability.

overall_design: ATAC-seq was performed on CAF#1 and imCAF#1 following transfection with either scrambled control RNA or HSF1-specific siRNA. Two CAF lines were derived from distinct pancreatic cancer patients.

first: Yujie

last: Fu

first: Lin

last: Yang

first: Yamei

last: Niu


title: Integrated epigenomic and transcriptomic profiling of super-enhancer networks in mouse small intestine [RNA-seq]

city: Nanjing

first: Lei

last: Chen

address: No.2 Sipailou

institute: Southeast University

summary: Super-enhancers (SEs) are crucial regulators of small intestinal architecture and epithelial function. Compartment-specific SEs maintain crypt-villus zonation by controlling spatially defined gene expression programs. This study also demonstrates the roles of the core transcription factors HNF4 and SMAD4 as gatekeepers of these SEs.

relation:
Reanalysis of: GSM3091823
Reanalysis of: GSM3091824
Reanalysis of: GSM3091825
Reanalysis of: GSM3091832
Reanalysis of: GSM3091833
Reanalysis of: GSM3091834

overall_design:
We employed an integrated epigenomic and transcriptomic approach to delineate SE networks in the mouse small intestine. Crypt and villus compartments were isolated, followed by H3K27ac ChIP-seq to map SEs and establish compartment-specific gene regulatory programs. To dissect transcription factor-specific SE regulation of intestinal epithelium, we analyzed of HNF4A and HNF4G double knockout mice, SMAD4 knockout mice with their littermate controls using ChIP-seq and RNA-seq.

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

first: Wenxin

last: Fang

first: Michael

last: Verzi


title: Spatial profiling of hypoxic injury in human kidney organoids

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

institute: Monash University

summary: This dataset relates to a spatial transcriptomic experiment investigating potential reparative and inflammatory roles for macrophages in human iPSC-derived kidney organoids exposed to hypoxic injury, linked to a broader study of ischaemic kidney injury and repair in this model (https://doi.org/10.1101/2023.10.04.558359). Acute kidney injury (AKI) is a common clinical disorder linked to high rates of illness and death. Ischaemia is a leading cause of AKI, where reduced blood flow to the kidney triggers hypoxia and cell death in the nephron epithelium, impairing essential fluid handling and waste removal functions. While injured tubules have some capacity to recover, severe injury can result in chronic kidney disease (CKD) through a maladaptive repair process characterised by failed epithelial regeneration, inflammation, and metabolic dysregulation. Immune cells critically influence kidney injury responses in vivo, with tissue-resident macrophages driving either repair or harmful inflammation, fibrosis, and progression to CKD. To complement prior bulk RNAseq analysis and investigate the role of macrophages in AKI and maladaptive repair within the tissue microenvironment, we integrated iPSC-derived macrophages into kidney organoids and investigated their response to hypoxic injury and effect on the surrounding tissue with spatial transcriptomics.

overall_design: Kidney organoids and macrophages were independently differentiated from induced pluripotent stem cells (iPSCs). iPSC-derived macrophages (iMacs) were integrated into the kidney differentiation at the point of aggregate formation (day 7, 5% iMacs, 95% kidney diff) alongside controls without iMacs. Kidney organoids were differentiated to day 18, then cultured in hypoxic (1% O2) or ‘normoxic’ (19% O2) conditions for 48h. Organoids were collected immediately (day 20) to asses injury, or after a 5-day recovery in normoxic conditions to assess repair (day 25). The experimental groups are: day 20 hypoxia (d20h), day 20 normoxic control (d20n), day 25 hypoxic injury/normoxic recovery (d25h), day 25 normoxic control (d25n), day 25 hypoxic injury/normoxic control with iMacs (d25h 5pct_imacs) and a d25 normoxic control with iMacs (d25n 5pct_imacs). Whole organoids from each group were embedded in paraffin and sectioned  together. Sections from each organoid group were placed directly onto the Xenium slide. The kidney organoids in this experiment were ~100 microns thick and 1.5mm wide before injury, or in the normoxic control group. Some of the samples buckled during tissue processing, leading to a stripe-like or disconnected tissue morphology in some sections. Constraints on tissue size and capacity to control the plane of sectioning led to sub-optimal representation of some samples. Hypoxic injury severely disrupts the tissue morphology, leading to smaller organoids with less epithelial structures. 25 kidney organoids from 6 experimental groups were profiled with the 10X Genomics Xenium Human Immuno-Oncology panel containing probes to 380 genes. Sample names indicate the experimental group, days of differentiation, and biological replicate.

first: Ana

middle: N

last: Nescolarde

first: Yang

last: Liao

first: Julie

last: Moreau

first: Casey

last: Anttila

first: Ruvimbo

last: Mishi

first: Ling

last: Ling

first: Daniela

last: Zalcenstein

first: Alex

last: Combes


title: Mapping the Dialogue: Decoding Alveolar Stem-Niche Interactions

city: South San Francisco

first: Anne

last: Biton

address: 1 DNA way

institute: Genentech


title: Integrated epigenomic and transcriptomic profiling of super-enhancer networks in mouse small intestine [ChIP-Seq]


title: ALKBH5 in Cancer-associated Fibroblasts Facilitates Pancreatic Cancer Metastasis via HSF1–LIF Axis [MeRIP-seq]

first: Xianglin

last: Yin

summary: The role of N6-methyladenosine (m6A) in pancreatic ductal adenocarcinoma (PDAC) progression has garnered significant attention, yet its specific function within cancer-associated fibroblasts (CAFs)—key players in the tumor microenvironment—remains poorly understood. Here, using both primary and immortalized CAFs that we established from patient-derived samples, we identified m6A demethylase AlkB homolog 5 (ALKBH5) as a critical regulator of CAF-driven PDAC metastasis. We show that CAF activation induces a global reduction in m6A levels, with ALKBH5 emerging as a core modulator of the m6A epitranscriptome. Mechanistically, ALKBH5 enhances the m6A-dependent translational efficiency of heat shock factor 1 (HSF1), which in turn activates leukemia inhibitory factor (LIF) transcription by binding to its enhancer elements. Paracrine LIF signaling promotes epithelial–mesenchymal transition in pancreatic cancer cells, thereby facilitating tumor metastasis to the liver and lungs. Clinically, enrichment of ALKBH5+HSF1+ CAFs is strongly associated with poor prognosis and is predominantly observed in primary PDAC with metastasis. Together, this work demonstrates a CAF–intrinsic ALKBH5–HSF1–LIF axis as a critical driver of PDAC metastasis, suggesting a promising therapeutic strategy targeting the tumor stroma.

overall_design: This datasets includes MeRIP-seq profiling of CAFs under two experimental conditions: (1) DMSO (control) vs ATRA (all-trans retinoic acid) treatment; and (2) SC (scramble control) vs ALKBH5 KD (A5 knockdown). All CAF lines were derived from distinct pancreatic cancer patients.


title: ALKBH5 in Cancer-associated Fibroblasts Facilitates Pancreatic Cancer Metastasis via HSF1–LIF Axis [RIP-seq]

overall_design: RIP-seq profiling of imCAF#1 and imCAF#2 using ALKBH5 antibody (Sigma). Two immortalized CAF lines were derived from a pancreatic cancer patient and a chronic pancreatitis patient, respectively.

first: Yujie

last: Fu


title: ALKBH5 in Cancer-associated Fibroblasts Facilitates Pancreatic Cancer Metastasis via HSF1–LIF Axis [CUT&Tag]

overall_design: CUT&Tag-seq using an HSF1 antibody was performed on CAF#1 and imCAF#1 with HSF1 overexpression. Two independent CAF lines were derived from distinct pancreatic cancer patients.

first: Lin

last: Yang


title: Dual profiling of DNA modifications with enhancer features during the exit of naive pluripotency [Methyl-ATAC--Seq]

city: Paris

first: Marlet

last: Morales Franco

state: Île-de-France

address: 15 rue Hélène Brion

institute: Institut Jacques Monod, CNRS, Université Paris Cité

summary: Cis-regulatory elements, such as enhancers, play an essential role in coordinating gene expression programs during cellular transitions. As such, substantial efforts have been made to characterize enhancer elements, e.g., chromatin accessibility, transcription factor (TF) binding sites, histone post-translational modifications (PTMs), and 5-cytosine DNA methylation and hydroxymethylation (5mC and 5hmC). Elevated 5mC levels are typically correlated with the inactive enhancer state. However, whether 5mC precludes TF binding or is simply a downstream consequence of enhancer decommissioning is difficult to determine. Bulk genomics assays from cell populations fail to fully capture cellular heterogeneity, and single-cell assays often suffer from limited read counts per cell. Here, we leveraged tagmentation-based technologies to assess chromatin features with 5mC simultaneously: Methyl-ATAC and Methyl-CUT&Tag. In addition, we modified the technique to interrogate 5hmC dynamics (hM-ATAC). We employed these techniques during the exit of naive pluripotency in mouse embryonic stem cells (mESCs), which recapitulates the embryonic DNA methylation establishment program. This system withstands the complete absence of DNA methylation and demethylation machinery, allowing us to further dissect the temporal contributions of 5mC and 5hmC. Given the affordability of these techniques, we were able to obtain robust, dynamic single-molecule 5mC/5hmC information during this cellular transition for chromatin accessibility and histone marks in wild-type and mutant conditions. The sum of these data allowed for unprecedented insight into the role that 5mC turnover plays at enhancers during a key window of mammalian embryonic development.

overall_design: Methyl-ATAC-seq of WT, Dnmt KO, and Tet KO cells at Day 0 (mESCs), Day 2 (EpiLCs), and Day 4 (Extended EpiLCs) of mESC-to-EpiLC differentiation.

last: Morales-Franco

first: Baptiste

last: Demaret

first: Pol Arnau

last: Romero

first: Hortense

last: Bouvier

first: Julien

last: Richard Albert

first: Angélique

last: David

first: Pierre-Antoine

last: Defossez

first: Anaïs Flore

last: Bardet

first: Priscillia

last: Lhoumaud

first: Maxim

last: Greenberg


title: Dual profiling of DNA modifications with enhancer features during the exit of naive pluripotency [Bisulfite-Seq]

overall_design: Whole genome bisulfite sequencing (WGBS) of Tet KO cells at Day 0 (mESCs), Day 2 (EpiLCs), and Day 4 (Extended EpiLCs) of mESC-to-EpiLC differentiation. Whole genome bisulfite sequencing (WGBS) of WT cells at Day 2.


title: DNAmBERT: A Transformer-Based Model for Robust, Non-Invasive Cancer Diagnosis Using DNA Sequence and Methylation Data

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

summary: We generatedcell-free Reduced Representation Bisulfite Sequencing (cfRRBS) data for 55 samples (7 early-stage lung cancer, 41 late-stage lung cancer, and 7 non-malignant controls) to identify markers for early lung cancer detection.

overall_design: cfDNA methylation profiling by high-throughput sequencing.

first: Euan

last: J. Rodger

first: Mark

last: Ezegbogu

first: Maryam

last: Yassi

first: Matthew

last: Parry


title: United we stand: Plants that physically touch each other are more resilient to stress.

city: Columbia

first: Sameep

last: Dhakal

state: MO

address: 1201 Rollins St.

department: Institute for data science and Informatics

institute: University of Missouri

summary: Plants use sophisticated signaling networks to communicate with each other. These are thought to support the overall health and resilience of plant communities, but could also reflect eavesdropping between plants, used for competition. Here we reveal that plants that physically touch each other aboveground are more resilient to stress, and that this phenomenon is dependent on the ability of plants to exchange systemic electric, calcium, and reactive oxygen species (ROS) signals between them. We further separate electric- from calcium/ROS plant-to-plant systemic signals and show that the function of certain calcium/ROS-dependent transcripts is required for stress acclimation. Our study reveals that plants living in a community can support each other, enhancing the overall resilience of the community to stress.

overall_design: Individual plants were positioned so that they did not touch any other plant. Two different three-plant configurations were tested for plant communities: (1) a chain of three wild-type (WT) plants, and (2) a chain consisting of WT–hpca1–WT. In both setups, plants were subjected to control or elevated light conditions (2000 µmol photons m⁻² s⁻¹ for 30 minutes), with the light applied to a local leaf of a wild-type plant.

first: María

last: Peláez-Vico

first: Yosef

last: Fichman

first: Abdul

last: Ghani

first: Stanislaw

last: Karpiński

first: Trupti

last: Joshi

first: Ron

last: Mittler


title: Chronic Electronic Cigarette Exposure Promotes Atherosclerosis and Chondrogenic Modulation of Smooth Muscle Cells

city: Stanford

first: Chad

middle: S

last: Weldy

address: 870 Quarry Road, CVRC Falk

department: Medicine, Cardiovascular Medicine

institute: Stanford University

summary: Electronic cigarettes (E-cigs) represent a rapidly growing public health concern, particularly due to their widespread adoption among adolescents. Recent epidemiological and experimental evidence has linked E-cig use to accelerated atherosclerosis, though the underlying mechanisms remain incompletely understood. Here, we investigated how E-cig exposure promotes atherosclerotic lesion formation and vascular remodeling through phenotypic modulation of vascular smooth muscle cells (SMCs). We utilized SMC lineage-tracing mice crossed onto an ApoE-null hyperlipidemic background and exposed them to pod-based E-cigs (Juul) three times weekly over a 12-week period (n=16 per group), comparing results to control mice exposed to Ambient air. Single-cell RNA sequencing (scRNA-seq) and assay for transposase-accessible chromatin sequencing (scATAC-seq) were conducted on cells isolated from the aortic sinus, complemented by histological assessment of osteogenic markers. Our analyses revealed a significant shift in SMC phenotype toward a chondrogenic lineage (CMC) in e-cigarette-exposed mice, evidenced by markedly increased expression of chondrogenic markers Col2a1 and Tnfrsf11b. Correspondingly, histological evaluations demonstrated increased osteogenic activity in E-cig-exposed animals. Chromatin accessibility profiling further identified a unique cellular cluster enriched for glutamatergic signaling pathways, particularly showing enhanced accessibility at Grin2a, a gene encoding the NMDA receptor subunit GluN2A. Notably, GRIN2A expression was upregulated in HCASMCs upon e-cigarette exposure, and the observed E-cig-induced phenotypic modulation was found to be GRIN2A-dependent, suggesting a robust gene-environment interaction. Collectively, these findings elucidate critical mechanistic pathways through which e-cigarette exposure promotes atherosclerosis, underscoring GRIN2A as a potential therapeutic target to address cardiovascular risks associated with electronic nicotine delivery systems.

overall_design: Tissues were collected and dissociated for single cell capture as previously described. Briefly, vascular tissue was washed three times in PBS, tissues were then placed into an enzymatic dissociation cocktail (2 U ml−1 Liberase (5401127001; Sigma–Aldrich) and 2 U ml−1 elastase (LS002279; Worthington) in Hank’s Balanced Salt Solution (HBSS)), and minced. After incubation at 37 °C for 1 h, the cell suspension was strained and then pelleted by centrifugation at 500g for 5 min. The enzyme solution was then discarded, and cells were resuspended in fresh HBSS. Cells were FACS sorted and live cells were identified as previously described. Briefly, cells were sorted on a BD Aria II instrument, where cells were gated on forward/side scatter parameters to exclude small debris and then gated on forward scatter height versus forward scatter area to exclude obvious doublet events. A portion of cells were taken directly to scRNAseq capture. For single cell ATAC, cells were collected in BSA-coated tubes, and nuclei isolated per 10X recommended protocol, and captured on the 10X scATAC platform in a 1:1 ratio of tdT positive and tdT negative cells.  Cells were loaded into a 10x Genomics microfluidics chip and encapsulated with barcoded oligo-dT-containing gel beads using the 10x Genomics Chromium controller according to the manufacturer’s instructions. Single-cell libraries were then constructed according to the manufacturer’s instructions (Illumina). Libraries from individual samples were multiplexed into one lane before sequencing on an Illumina platform with targeted depth of 50,000 reads per cell for RNA and 75,000 reads/cell for ATAC. Post filtering for non-cells, mean number of reads within peaks per cell in scATAC data was 18,000-20,000 as was seen in our prior report.


title: CD4+ T cells in the developing human brain shape angiogenesis and neurogenesis

city: San Francisco

first: Loukas

last: Diafos

address: 35 Medical Center Way

institute: UCSF

summary: Although entry is limited, immune cells reside within and influence neural tissue function in health and disease. Unique T cell populations throughout the body may shape organogenesis, but these cells are absent during mouse embryogenesis. To investigate human prenatal T cell roles, we captured T cells from four midgestation organs: spleen, mesenteric lymph node, small intestine, and brain. Single-cell RNA sequencing identified dominant CD4 populations and smaller subsets of cytotoxic CD8 and innate T cells. In the brain, distinct expression profiles were revealed, including a unique Trav1-2+ MAIT-like population. Spatial mapping showed T cells are predominantly localized within the ventricular angiogenic-neurogenic niche, adjacent to microglia. Functionally, co-culture of CD4 T cells and endothelial cells enhanced vascular network maturity, while transplanted CD4 T cells in brain organoids localized to the VZ niche and reduced cell death. Rag2 knock-out mice also show changes in brain vasculature and neuronal structure in the absence of B and T cells. These findings suggest T cells support tissue health and growth in the developing human brain and have implications for neurodevelopment in a growing population of surviving patients with immunodeficiency syndromes.

overall_design: We isolated T cells from paired brain, mesenteric lymph node (MLN), spleen and small intestine from 2 donors. We sort-purified CD3+ T cells from CD45+ single cell suspensions and performed scRNA-seq using a 5' v2 kit from 10x

first: Joanna

last: Halkias

first: Elizabeth

last: Crouch

first: Madeline

last: Andrews


title: Endothelial PIEZO1 activation impairs osteogenesis via GREM1-mediated inhibition of BMP signaling

city: Harbin

first: Haoran

last: Zhang

state: Heilongjiang

address: 246 Xuefu Road

institute: Harbin Medical University

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

overall_design: Refer to individual Series


title: Endothelial PIEZO1 activation impairs osteogenesis via GREM1-mediated inhibition of BMP signaling [hBMEC_RNA-seq]

summary: The mechanosensitive ion channel PIEZO1 has emerged as a key regulator of vascular and skeletal biology. Here, we show that systemic activation of PIEZO1 using the chemical agonist Yoda1 in 3-week-old mice disrupts bone homeostasis by impairing type H endothelial cells and inhibiting osteogenic differentiation. In vivo, Yoda1 treatment significantly reduced the abundance of CD31hiEMCNhi type H vessels and altered trabecular bone microarchitecture without affecting total bone mass. In vitro, Yoda1 inhibited osteogenic gene expression and alkaline phosphatase activity in MC3T3-E1 preosteoblasts. Transcriptomic analysis of Yoda1-treated human bone microvascular endothelial cells (hBMECs) revealed a shift from an angiogenic H-type to a quiescent L-type, accompanied by upregulation of BMP signaling antagonists, particularly GREM1. Functional assays confirmed that GREM1 secreted from Yoda1-stimulated endothelial cells suppresses BMP4-induced osteoblast differentiation via paracrine signaling. Together, these findings uncover a novel endothelial-to-osteoblast regulatory axis mediated by PIEZO1-GREM1-BMP4 signaling, and underscore the context-dependent effects of PIEZO1 activation on bone regeneration.

overall_design: Human bone microvascular endothelial cells (hBMECs) were obtained from Sunncell (Cat#SNP-H101) and maintained in the corresponding growth medium (Sunncell, Cat#SNPM-H101). After treated with 10μM Yoda1 (MedChemExpress, Cat#18723) or DMSO as a vehicle control for 24 hours, total RNA was extracted from four biological replicates per condition and subjected to bulk RNA sequencing.

first: Bowen

last: Wang

first: Jing

last: He

first: Shengyi

last: Zhou

first: Juan

last: Song

first: Ziwen

last: Liu

first: Xiangyu

last: Zeng

first: Ying

last: Xing

first: Feng

last: Guo

first: Jianyu


title: TET3 Promotes Tumor Immune Evasion Through Negative Regulation of Type I Interferon Signaling [ChIP-Seq]

city: Shanghai

first: Lu

address: 131 Dongan Road

institute: Fudan University

summary: The Ten-eleven translocation (TET) family genes, which encode 5-methylcytosine (5mC) dioxygenases, have been described as tumor suppressors or oncogenes in various cancers. However, the functional role of TET3 in cancer immunity and the underlying molecular mechanisms remain incompletely understood. Here, we reported that TET3 restrains the innate immune response in MCF7 and B16F10 cells. Mechanistically, TET3 does not influence the generation of endogenous dsRNA but represses the expression of major dsRNA sensor genes (i.e., MDA5 and RIG-I) as well as the activation of JAK-STAT1 pathway. Importantly, depletion of Tet3 in B16F10 melanoma cells significantly curbed the synergistic tumor growth, accompanied with increased proportion of tumor-infiltrating CD4+ T cells, CD8+ T cells and dendritic cells. Analysis of the TCGA data also revealed elevated expression of TET3 in most types of cancer. Notably, elevated TET3 expression levels were inversely associated with overall survival rate and exhibited a negative correlation with tumor-infiltrating cytotoxic CD8+ T cells. Taken together, our findings identify TET3 as a negative regulator of type I interferon signaling, suggesting that TET3 may be a new target of anti-tumor immunity and immunotherapy.

overall_design: Examination of TET3 binding in Parental and TET3 KO MCF7 cells using ChIP-seq.

first: Li

last: Tan

first: Yujiang

last: Shi


title: TET3 Promotes Tumor Immune Evasion Through Negative Regulation of Type I Interferon Signaling