title: The catalytically inactive KDM5B-NTT isoform associates with chromatin and increases H3K4 trimethylation in breast cancer cells

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

summary: Background. Histone lysine demethylases are key regulators of cancer-related processes. Beyond their enzymatic activity, catalytically independent functions are increasingly recognized. We previously identified a N-terminal truncated and catalytically inactive isoform of KDM5B, called NTT, stably expressed in several human cell lines. Overex-pression of NTT-FLAG in MCF7 breast cancer cells was shown to increase global H3K4me3 levels and modulate transcription of several genes. Methods. In this study, we used the CUT&RUN assay to investigate the genomic lo-calization and the local effects on histone methylation of ectopically expressed NTT-FLAG. Moreover, phenotypic assays were performed to assess the effects of NTT-FLAG over-expression on cell migration and invasion. Results. NTT-FLAG preferentially associates with actively transcribed genes enriched in H3K4me3 at promoter regions, contributing to increased H3K4me3 levels at target sites. Functionally, NTT overexpression enhances MCF7 cell migration and invasiveness. Conclusions. Our findings support a model in which NTT and PLU-1 scan chromatin via PHD1 in a transient, low-affinity manner, while H3K4me3 stabilizes their binding by interacting with PHD3. However, catalytic activity likely depends on corepressor en-gagement, whose availability is influenced by endogenous KDM5B levels. Functionally, NTT appears to enhance cell migration and invasiveness by regulating genes such as PLAUR and CSF1, supporting its role in driving tumour-associated phenotypes inde-pendently of catalytic activity.

overall_design: CUT&RUN for in transfected MCF7 cell line overexpressing the vector for PLU-1-FLAG or NTT-FLAG or empty FLAG.

first: Valeria

last: Manzini

first: Elena

last: Di Nisio

first: Alessandro

last: Piana

last: Perticaroli

first: Rodolfo

last: Negri


title: Skeletal muscle reprogramming of metabolic, ribosomal and developmental pathways contributes to Roux-en-Y gastric bypass-induced adaptation in women [2]

status: Public on Jul 31 2026

city: Ottawa

first: Mary-Ellen

last: Harper

state: ON

address: 451 Smyth Rd

country: Canada

institute: University of Ottawa

type: Expression profiling by high throughput sequencing

summary: Background: Understanding how skeletal muscle responds to weight loss is crucial for developing targeted strategies to manage obesity and promote sustained improvement in metabolic health. Here, we investigated the molecular mechanisms underlying skeletal muscle reprogramming of gene expression and metabolic activity following Roux-en-Y gastric bypass (RYGB). Methods: Forty-one women were studied before and one year after RYGB surgery. We leveraged multi-omics (DNA methylomics and transcriptomics) and machine learning approaches to complement muscle metabolic analyses and clinical data to identify mechanisms underlying RYGB-induced muscle metabolic reprogramming. Findings: RYGB markedly decreased body weight and fat mass and improved metabolic health. Integrative analysis of vastus lateralis muscle identified 8233 genes with differentially methylated regions and 2173 differentially expressed genes post-RYGB surgery, of which 1197 genes were both differentially methylated and differentially expressed. Promoter hypomethylation was associated with the enhanced expression of transcription factors involved in skeletal muscle development and ribosomal subunits. In contrast, expression of genes encoding mitochondrial proteins decreased despite increases in mitochondrial content and enhanced mitochondrial function in skeletal muscle post-RYGB. Pre-operative muscle OXPHOS capacity, and expression of skeletal muscle hypertrophy and differentiation genes MYOC and EHMT2 were associated with weight loss success. Interpretation: RYGB improves systemic metabolic health and induces sustained skeletal muscle bioenergetic reprogramming characterised by enhanced expression of genes involved in myogenesis and protein translation, but decreased expression of genes involved in mitochondrial metabolism, which may reflect improved mitochondrial quality and function. These findings advance our understanding of skeletal muscle metabolic responses to weight loss and of individual variability in metabolic phenotypes.

overall_design: Skeletal muscle biospsies (m. vastus lateralis) were collected from 35 individuals before Roux-en-Y-Gastric Bypass (RYGB) bariatric surgery and one-year after RYGB surgery. Genomic DNA from 70 samples were bisulfite-converted and subsequently hybridised to the Illumina Infinium EPIC-8v2.0 Human Methylation Beadchips.

first: Chantal

middle: A

last: Pileggi

first: Dhanuddara

last: Mohottalage

first: Luke

middle: S

last: Kennedy

first: Majid

last: Nikpay

first: Lauren

last: Hamilton

first: Martín

last: Roffe

first: Michel

middle: N

last: Kanaan

first: Amer

last: Jarrar

first: Nicole

last: Kolozsvari

first: Dongdong

last: Wang

first: Miroslava

last: Cuperlovic-Culf

first: Tommy

last: Alain

first: Gregory

middle: R

last: Steinberg

first: Robert

last: Dent

first: Ruth

last: McPherson


title: OxyR regulates the oxidative stress response in Zymomonas mobilis during oxic growth and anoxic biofuel fermentation

city: Madison

first: Kevin

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

country: USA

institute: University of Wisconsin - Madison

summary: The bacterium Zymomonas mobilis is widely studied for its potential as an industrial biofuel producer. Anoxic fermentation by Z. mobilis in lignocellulosic hydrolysate can generate bioethanol from renewable plant biomass. In this study, we deleted a gene from the Z. mobilis genome encoding a homolog of OxyR, a transcription factor that activates an oxidative stress response in bacteria to reduce reactive oxygen species (ROS). Deletion of this transcription factor inhibited growth of Z. mobilis in oxic, but not anoxic, conditions in laboratory media. RNA-Sequencing was perfromed on wild-type Z. mobilis (ZM4) and ∆oxyR in both oxic and anoxic conditions in rich media (ZRMG). This study reveals the indirect regulon of OxyR in Z. mobilis, which is important for both oxic growth and anoxic biofuel fermentation.

overall_design: RNA-seq of both WT Zymomonas mobilis and Z. mobilis with the homolog of oxyR deleted. Samples were grown under both oxic and anoxic conditions.

first: Emma

middle: C

last: Boismier

first: Magdalena

middle: M

last: Felczak

first: Michaela

last: TerAvest


title: Skeletal muscle reprogramming of metabolic, ribosomal and developmental pathways contributes to Roux-en-Y gastric bypass-induced adaptation in women [1]

first: Mary-Ellen

last: Harper

type: Methylation profiling by genome tiling array

first: Chantal

last: Pileggi

first: Dhanuddara

last: Mohottalage

first: Luke

last: Kennedy


title: Transcriptomic profiling of zebrafish znf804a mutant heads under light cycling and dark only conditions

city: Worcester

first: Summer

last: Thyme

state: MA

address: 364 Plantation St

institute: UMass Chan Medical School

summary: Sleep disturbances are a common symptom in individuals with schizophrenia and can exacerbate disruptions in cognitive processes like learning and memory. Elucidating pharmacologically targetable molecular pathways perturbed by high-risk schizophrenia genes may improve treatment outcomes. Here, we investigate the relationship between the schizophrenia gene znf804a and sleep and circadian behaviors/pathways. Using multi-day tracking of behavior, we show znf804a mutants display changes in circadian behaviors when external light cues are removed. Using bulk RNA sequencing of fish raised in normal light/dark and dark/dark conditions, we identified altered expression of genes in the core and auxiliary pathways controlling circadian rhythms. Further analysis revealed a znf804a-gene-dosage-dependent reduction in fbxl3a RNA expression. Transcriptomic analysis also revealed shifts in the relative abundance of specific transcripts without changing overall gene expression in genes linked to sleep and circadian pathways, including idh1, suggesting znf804a could influence transcript processing or stability. Together, these findings are the first to link ZNF804A orthologs to sleep and circadian phenotypes in model organisms and identify the regulation of fbxl3a and transcript processing as candidate mechanisms through which this schizophrenia risk gene may influence circadian biology.

overall_design: RNA-sequencing of dissected heads of larval zebrafish of znf804a gene. Two heterozygous parents were crossed together, and larvae from one clutch were dissected at 6 days post-fertilization. Homozygous, heterozygous, and wild-type control sibling embryos were identified by genotyping after dissection, and four heads were pooled for each biological replicate. Four biological replicates were collected per genotype and condition. One condition was samples in constant darkness from 2 dpf until 6 dpf, and the other was collected under normal light cycling conditions. The 2 dpf data was collected from a homozygous female crossed to heterozygous male and three heads were pooled for each biological replicate.

first: Thyme

last: Summer


title: Two waves of activation drive systemic innate immune responses to alphavirus infection

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

state: PA

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

summary: Venezuelan equine encephalitis virus (VEEV), like many mosquito-borne RNA viruses, causes severe prodromal illness characterized by robust systemic cytokine responses including type I interferon (IFN-I), yet the mechanisms initiating these systemic responses remain undefined. Using mutant viruses with altered lymph node (LN) tropism, we show that the extent of VEEV LN infection is positively associated with systemic induction of IFN-I and other proinflammatory cytokines. Further, robust IFN-I induction requires coordinated activation of multiple IRF-7-dependent pathways, with Toll-like receptor (TLR) and RIG-I-like receptor (RLR) pathways playing distinct, nonredundant roles. Combining targeted cell depletion and Visium HD spatial transcriptomics, we uncover a two-wave innate immune response to infection in vivo, with early cytokine induction driven by VEEV-infected myeloid cells at 8 hours post-infection (hpi), and a second wave dominated by uninfected bystander cells once active infection in the LN subsides by 16hpi. Together, these findings highlight the importance of early virus-host interactions in lymphoid tissues, revealing an opportunity for development of therapeutics against disseminated virus infection and immune-driven viral pathologies.

overall_design: To compare the spatial transcriptomic profiles of VEEV-infected mice and their mock counterparts and the differences between timepoints, we had 4 total samples. The samples are lymph nodes of a VEEV-infected mouse 8 hpi, lymph nodes of a VEEV-infected mouse 16 hpi, lymph nodes of a mock-infected mouse 8 hpi, and lymph nodes of a mock-infected mouse 16 hpi.

first: Melaina

middle: L

last: Jacoby

first: Chengqun

last: Sun

first: Jessica

last: Farren

first: Michelle

last: Marti

first: Thomas

last: Donovan

first: Alyssa

last: Lee

first: William

middle: B

last: Klimstra


title: Human body single-cell atlas of three-dimensional genome organization and DNA methylation

city: La Jolla

first: Joseph

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Higher-order chromatin structure and DNA methylation are critical for gene regulation, but how these vary across the human body remains unclear. We performed multiomic profiling of three-dimensional (3D) genome structure and DNA methylation for 86,689 single nuclei across 16 tissues, identifying 35 major and 206 cell subtypes. We revealed extensive changes in CG and non-CG methylation across cell types and characterized 3D chromatin structure at an unprecedented cellular resolution. Extensive discrepancies exist between cell types delineated by DNA methylation and genome structure, which indicates that the role of distinct epigenomic features in maintaining cell identity may vary by lineage. This study expands our understanding of the diversity of DNA methylation and chromatin structure and offers a reference for exploring gene regulation in human health and disease.

overall_design: Apply snm3C-seq to 16 adult human organs with 2 donors per organ. Variability of DNA methylation and 3D genome structure across 206 cell types was investigated.

first: Jingtian

last: Zhou

first: May

last: Wu

first: Rosa

middle: G

last: Castanon

first: Anna

last: Bartlett

first: Ben

last: Clock

first: Samantha

last: Marcotte

last: Nery

last: Liem

first: Naomi

last: Claffey

first: Lara

last: Boggeman

first: Cesar

last: Barragan

first: Rafael

last: Arrojo e Drigo

first: Annika

last: Weimer

first: Johnathan

last: Cooper-Knock

first: Sai

last: Zhang

first: Michael

middle: P

last: Snyder

first: Carolyn

last: O’Connor

first: Chongyuan

last: Luo

first: Jesse

last: Dixon


title: Prior targeted therapy treatment and cellular composition modulate the effects of Axl inhibition on myeloid cells in the human in vitro melanoma tumor microenvrionment

city: Cambridge

first: Douglas

last: Lauffenburger

address: 77 Massachusetts Avenue

institute: Massachusetts Institute of Technology

summary: Axl has gained momentum as a promising target in cancer therapy due to its contribution to both cancer progression and immunosuppression. While pre-clinical studies in mice have demonstrated its potential as a dual target - to be both tumoricidal and immunostimulatory - clinical trials have reported mixed results. We built a human in vitro model system to understand how prior standard-of-care treatment in the context of melanoma impacts the effects of the small molecule Axl inhibitor bemcentinib on myeloid cells in the tumor microenirnoment. In our previous work we reported differences in macrophage state and activity primarily resulted from whether the melanoma cells they were co-cultured with had prior trametinib + dabrafenib treatment, and that this then impacted the macrophage resposne to Axl inhibition. We also showed that the addition of donor-matched dendritic cells to the in vitro system resulted in a dampened macrophage response. In this current work, we generated single-cell RNA-sequencing data to understand the changes in cell signaling that underlie our previously reported observations.

overall_design: Primary human monocyte-derived macrophages (HMDMs) were co-cultured with either untreated A375s (DMSO) or injured A375s (trametinib + dabrafenib). These co-cultures were treated with either DMSO or bemcentinib. Following 24 hours of co-culture, the cells were either harvested for scRNAseq processing or donor-matched human monocyte-derived dendritic cells (HMDDCs) were added to generate tri-culture samples. Following 24 hours of tri-culture, the cells were harvested for scRNAseq processing.

first: Anisha

last: Datta

first: Kate

last: Bridges

first: Laura

last: Bahlmann

first: Diana

last: Gong

first: Erin

last: Tevonian

first: Alexei

last: Stortchevoi

first: Noelani

last: Kamelamela

first: Stuart

last: Levine


title: DUSP2 Suppresses the Chromatin Remodeling BAF Complex to Orchestrate CD8+ T Cell Effector Programming [ATAC-seq]

city: Rochester

first: Emilia

last: Dellacecca

state: MN

address: 200 First Street SW, Kellen Building 02-102

department: Immunology

institute: Mayo Clinic

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Effector gene expression in CD8⁺ T cells is tightly controlled at epigenetic and transcriptional levels; however, crucial regulatory signals remain incompletely understood. In this study, we identify Dual Specificity Phosphatase 2 (DUSP2) as a key epigenetic modulator of effector CD8⁺ T cell state, by elucidating inhibition of BAF-mediated chromatin opening by DUSP2. Induced downregulation of DUSP2 in human CD8+ T cells enhanced cytotoxicity and effector phenotypes by increasing chromatin accessibility through upregulation of BAF subunits, such as SMARCA4, and permitting binding of ETS1 to BAF subunit gene loci and those essential for effector programs. Conversely, during chronic activation, DUSP2 knockout in murine CD8+ T cells predisposed terminally differentiated effector cells to exhaustion. These findings uncover a previously unrecognized role of DUSP2 in the management of the chromatin landscape in CD8+ T cells and the epigenetic fine-tuning of their functionality, highlighting DUSP2 as a promising therapeutic target for T cell-based immunotherapy.

overall_design: Bulk ATAC-sequencing of CD8+ T cells from the peripheral blood of healthy human donors with transfection of DUSP2-targeting silencing RNA (siRNA) or negative control siRNA at rest or after anti-CD3/CD28 soluble antibody-based ex-vivo activation for 48-hours.

first: Jacob

last: Hirdler

first: Whitney

last: Barham

first: Ying

last: Li

first: Joanina

middle: K

last: Gicobi

first: Yiyi

last: Yan

first: Haidong

last: Dong


title: An ASCL1 C-Terminal Phospho-Degron Control ASCL1 Protein Stability in Small Cell Lung Cancer

city: Boston

first: Yixiang

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: ASCL1 is a lineage transcription factor dependency in small cell lung cancer (SCLC) and other high-grade neuroendocrine cancers, but remains undruggable. To uncover mechanisms that control ASCL1 abundance, we combined genome-wide CRISPR knockout and base-editor tiling screens with an endogenous ASCL1 reporter, quantitative proteomics, and structural modeling. We identify HUWE1 as the dominant E3 ligase for ASCL1 in SCLC and define a conserved C-terminal phospho-degron centered on Ser207 and terminal Trp/Phe residues that is necessary for HUWE1 binding and ASCL1 protein degradation. Disrupting this degron prevents HUWE1 binding and hyperstabilizes ASCL1, locks it on chromatin, and paradoxically impairs SCLC proliferation. These findings reveal a more generalizable phospho-degron recognition module in HUWE1 as a targetable regulatory switch for ASCL1 protein degradation.

overall_design: To explore the mechanism by which hyperstabilization of ASCL1 blocks SCLC　proliferation, we performed ChIP-seq in human ASCL1⁺ SCLC CORL47 cells expressing doxycycline-inducible (DOX-ON) ASCL1 constructs (wild-type or ASCL1del217–236, both C-terminally FLAG-tagged). Following 72 hours of doxycycline treatment, ChIP-seq with a FLAG antibody was performed, alongside endogenous ASCL1 ChIP-seq in DOX-ON empty vector cells as a comparator.

first: Keita

last: Masuzawa

first: Tianchu

last: Wang

first: Oser

last: Matthew


title: DUSP2 Suppresses the Chromatin Remodeling BAF Complex to Orchestrate CD8+ T Cell Effector Programming [ChIP-Seq]

overall_design: TAF-ChIP-sequencing of CD8+ T cells from the peripheral blood of healthy human donors with transfection of DUSP2-targeting silencing RNA (siRNA) or negative control siRNA with ETS1 pulldown at rest or after anti-CD3/CD28 soluble antibody-based ex-vivo activation for 48-hours.


title: Immunometabolic Endotypes Define Distinct Clinical Trajectories in Type 2 Diabetes [scRNA-seq II]

city: Paris

first: Nicolas

last: Venteclef

address: 156 rue de Vaugirard

country: France

institute: Institut Necker Enfants Malades, INSERM U1151

summary: Type 2 diabetes (T2D) exhibits substantial heterogeneity, yet current classifications do not fully capture its immune complexity. Here, we provide transcriptomic datasets from circulating CD14⁺ monocytes (bulk RNA-seq) and peripheral blood mononuclear cells (PBMCs, single-cell RNA-seq) derived from newly diagnosed T2D patients. Using neutrophil, lymphocyte, and monocyte counts, patients were stratified into four immune endotypes via unsupervised clustering: Severe Inflammatory Diabetes (SIND), Mild Inflammatory Diabetes (MIND), Lymphocyte Rich Diabetes (LYRD), and Lymphocyte Deficient Diabetes (LYDD). Bulk and single-cell transcriptomic analyses reveal endotype-specific immune signatures, including selective expansion of CCR2hi and CD39hi classical monocytes in SIND, enrichment of monocyte states associated with chemotaxis and myeloid activation, and altered adaptive immune programs. These profiles were modulated by IL-1β antagonism and bariatric surgery–induced remission. This dataset provides a resource for exploring the immune heterogeneity of T2D.

overall_design:
Single-cell RNA-seq (PBMCs)

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

first: Bao Tran

last: Vuong

first: Chloé

last: Delepine

first: Magali

last: Chiral

first: Marc

last: Diedisheim

first: Aymeric

last: Silvin


title: Immunometabolic Endotypes Define Distinct Clinical Trajectories in Type 2 Diabetes

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

overall_design: Refer to individual Series


title: Immunometabolic Endotypes Define Distinct Clinical Trajectories in Type 2 Diabetes [scRNA-seq I]


title: Spatial transcriptomics reveals injury-responsive compartments and coordinated immune–fibrotic signaling  in ANCA-associated renal vasculitis

city: Nanjing

first: Yucheng

last: Tang

state: Jiangsu

address: No. 639, Longmian Avenue

country: China

institute: China Pharmaceutical University

summary: Immune dysregulation is a hallmark of anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV), particularly in the kidney; however, the spatial organization of renal microenvironments remains poorly understood. Here, we applied spatial transcriptomics to renal biopsies from pediatric patients with AAV representing distinct histological classes defined by the Berden classification (4 control, 2 focal, and 3 non-focal cases), generating an in situ map of localized disease programs. Four disease-associated compartments—immune/interstitial fibroblasts (IM/Fib), glomeruli, myofibroblasts, and vascular compartments—showed distinct compartment-specific signatures that correlated with patient-level histopathology. We further identified coordinated immune–fibrotic signaling associated with different histopathological classes. Within IM/Fib, the CXCR4–CD74 receptor complex co-localized with IgM⁺ cells, and lumican (LUM) co-localized with collagen I/III; both were validated by immunofluorescence and associated with fibrotic injury.  These tissue-anchored signatures represent potential disease-associated molecular features with possible diagnostic relevance, and highlight the value of this foundational spatial transcriptomics map for generating testable hypotheses to be further evaluated in larger, stratified, treatment-annotated cohorts.

overall_design:
For spatial transcriptomics, cryopreserved kidney tissue sections from patients with ANCA-associated vasculities (biopsies) and control patients with hematuria (biopsies containing non-diseased regions) were mounted on Visium (10X Genomics) slides and processed according to the manufacturer's instructions.

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

first: Chunhua

last: Zhu

first: Aihua

last: Zhang

first: Enrico

last: Petretto


title: Mecp2 acts as a key stabilizer of glucocorticoid-induced genes in active chromatin regions [scATAC-Seq]

city: Hangzhou

first: Xiaoping

last: Han

state: Zhejiang

address: Yuhangtang Road 866

department: Center for Stem Cell and Regenerative Medicine

institute: Zhejiang University School of Medicine

summary: Mutations in methyl-CpG-binding protein 2 (MECP2) constitute the primary cause of Rett syndrome (RTT). Although Mecp2 is ubiquitously expressed throughout the body, its functional profiling at the pan-tissue and multi-omics levels remains lacking. Here, we obtained transcriptomic and epigenomic profiles of various tissues from wild-type and RTT mice; revealed global hyperactivation of the glucocorticoid (GC)-induced genes (GIGs) following Mecp2 KO. Further analysis of the nervous system revealed that non-neuronal cells were more susceptible to abnormalities of the GC system, playing a crucial role in the neurological disturbances of RTT mice. Mechanistically, we found that MECP2 binds to the regulatory elements of active GIGs to suppress their hyperactivation; and competitively inhibits the binding between NR3C1 and NCOA1 to maintain GC system homeostasis. Our study dissects the critical functions of Mecp2 at the epigenomic, transcriptomic, and protein levels, providing new insights into the pathomechanisms of RTT.

overall_design: For pan-tissue analysis, we collected single-cell chromatin accessibility data of 28 tissues from a Mecp2 KO male mouse and six tissues from a WT male mouse. For neural analysis, we obtained scATAC-seq data of six regions (brain stem, cerebellum, diencephalon, pituitary, spinal cord, and telencephalon) from WT and Mecp2 KO mice, with each condition containing three biological replicates.

first: Daiyuan

last: Liu

first: Jianhui

last: Chen

first: Xueyi

first: Guoji

last: Guo


title: snRNASeq of Metastatic Urothelial carcinoma samples

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

summary: Histological variation is a common feature of metastatic cancer but its clonal origins and impact on disease history remains poorly defined. In this study, we developed a first-in-kind metastatic bladder cancer (BLCA) rapid autopsy cohort enriched in rare histological subtypes to extensively profile individuals with terminal disease. By reconstructing the evolutionary history of patient tumors, we determined that metastasis-to-metastasis seeding was the dominant driver of cancer spread and that increased polyclonal migration contributed to poor prognosis. The burden, heterogeneity, and timing of acquired genomic alterations were markedly different between histological subtypes. Plasmacytoid and neuroendocrine variants developed early genomic driver alterations that associated with shorter survival. Mutational signature analysis further revealed that plasmacytoid, but not other subtypes, utilized the Fanconi Anemia pathway to shield from chemotherapy-induced genomic scarring. Using experimental models, we demonstrated that Fanconi Anemia pathway activity positively correlated with resistance to cisplatin chemotherapy, demonstrating a molecular basis for therapy resistance in plasmacytoid patients. We report the first single-nucleus profiling of mBLCA histological subtypes, revealing mixed cell states in plasmacytoid tumors and that increased overall transcriptional heterogeneity was associated with longer patient survival. Characterization of the tumor microenvironment uncovered distinct patterns of immune activation across histological subtypes, with plasmacytoid tumors exhibiting an immune-inflamed profile, while squamous subtype was dominated by immunosuppressive interactions. Lastly, we demonstrated that post-mortem cell-free DNA captured both genomic heterogeneity and transcriptional activity of the subtypes, providing a potential strategy to non-invasively assess tumor identity and aggressiveness in patients with mBLCA. Our results provide new principles into how tumor heterogeneity shapes the evolutionary history of cancer progression within subtypes of human bladder cancer

first: Hung-Ming

last: Lam

first: Gavin

last: Ha

first: Michael

last: Haffner

first: Andrew

last: Hsieh

first: Rubin

last: Raychaudhuri


title: MeCP2 stabilizes the glucocorticoid system in active chromatin regions [CUT&Tag]

summary: Methyl-CpG-binding protein 2 (MeCP2), a key epigenetic factor regulating gene expression via DNA/chromatin interactions, causes Rett syndrome when dysfunctional. However, its regulatory mechanisms at the pan-tissue and multi-omics levels remain poorly understood. Here, we constructed comprehensive pan-tissue transcriptional profiles and chromatin accessibility profiles from wild-type and Mecp2-knockout mice. Integrative analyses revealed that glucocorticoid (GC)-induced genes (GIGs) exhibited global hyperactivation following Mecp2 knockout, highlighting a crucial role for MeCP2 in maintaining GC signaling homeostasis. Through innovative single-cell multi-omics profiling of the nervous system, we found that GIG dysregulation primarily disrupts neural homeostasis via non-neuronal cells. Mechanistically, we uncovered a dual regulatory mode of MeCP2: (1) competitively limiting NR3C1 occupancy at GIG cis-regulatory elements in active chromatin regions, and (2) specifically disrupting NR3C1-NCOA1 coactivator interactions. Importantly, pharmacologically suppressing aberrant GC system activation ameliorated pathological phenotypes and significantly prolonged survival in Mecp2-knockout mice. Our study demonstrates the critical pathological role of hyperactivated GC signaling in the multisystem disturbances of Mecp2-knockout mice and suggests potential therapeutic targets for Rett syndrome.

overall_design: We obtained MECP2-binding sites in 31 tissues using cleavage under targets and tagmentation (CUT&Tag) to characterize DNA binding properties of MECP2. We also examined H3K27ac modification and NR3C1-binding sites in six neural regions (brain stem, cerebellum, diencephalon, pituitary, spinal cord, and telencephalon) from WT and Mecp2 KO mice. Additionally, NR3C1-binding sites were profiled in the telencephalon and pituitary from WT and MECP2 OE mice.

last: Wang


title: MeCP2 stabilizes the glucocorticoid system in active chromatin regions [RNA-seq]

overall_design: To systematically investigate the global transcriptomic alterations following Mecp2 knockout (KO; C57BL/6J background), we collected RNA-seq data from 31 tissues of wild-type (WT) and Mecp2 KO mice, totaling 368 samples: 110 male WT (y/+), 77 female WT (+/+), 75 female heterozygotes (+/−), and 106 male hemizygotes (y/−). Among these, 25 tissues were derived from both sexes, 3 were male-specific (epididymis, prostate, and testis), and 3 were female-specific (mammary gland, ovary, and uterus). Four specific tissues (bone, muscle, thymus, and white fat) were dedicated to calculating the correlations between key glucocorticoid-induced gene (GIG) expression and pathological indicators. To analyze differentially expressed genes under human MECP2 overexpression (MECP2 OE; FVB/NJ background), four tissues (thymus, thyroid, adrenal gland, and telencephalon) were selected for RNA-seq from WT and MECP2 OE mice. To validate the crucial pathogenic role of the glucocorticoid (GC) system in MeCP2 deficiency-mediated multisystem manifestations, transcriptomic profiling was conducted across four in vivo experiments involving dexamethasone (Dex) and RU486 administration in WT and Mecp2 KO mice.


title: RNA-seq of TGF-β-Induced A549 cells for comparison with H3K4me3 ChIP-seq data

city: Kumamoto

first: Minoru

last: Terashima

state: Kumamoto

address: 2-2-1 Honjo

country: Japan

institute: Kumamoto University

summary: RNA-seq was performed to compare changes in broad H3K4me3 occupancy with gene expression levels during TGF-β-induced epithelial-to-mesenchymal transition (EMT) in A549 lung adenocarcinoma cells, allowing for the identification of transcriptional changes associated with EMT.

overall_design: RNA-seq in TGF-β-induced A549 cells. A549 cells were treated with 1ng/ml TGF-β for 24h.

first: Shoichiro

last: Tange


title: Type I IFN Drives ILC2 to ILC1 Plasticity in Radiation-Induced Lung Injury

city: Duarte

first: Jaeho

last: Kim

address: 1500 E Duarte Rd

department: RadiationOncology

institute: City of Hope

summary: Radiation-induced lung injury (RILI) is a common dose-limiting toxicity after radiotherapy for lung cancer, especially after ablative radiotherapy such as Stereotactic Body Radiation Therapy (SBRT). However, the immunological mechanisms driving its pathogenesis remain poorly understood. Here we show that innate lymphoid cells (ILCs) orchestrate early immune remodeling after ablative irradiation. Flow cytometry and cytokine profiling revealed a radiation-induced shift from lung-resident ILC2s toward pro-inflammatory ILC1s. Single cell RNA sequencing analysis of lung ILC populations after radiation suggested that type I interferon (IFN) promoted radiation-induced ILC2 to ILC1 plasticity. In addition, IFN-β stimulation of ILC2s in vitro led to increased expression of T-bet and IFN-γ. Inhibition of type I IFN signaling attenuated lung damage in irradiated mice, suggesting a potential therapeutic strategy for mitigating RILI. Our findings highlight a previously unrecognized role of type I IFN in radiation-induced ILC plasticity that contributes to RILI pathogenesis. Importantly, this work provides a framework for developing immune-targeted interventions to reduce normal tissue toxicity during radiotherapy.

overall_design: To investigate transcriptional changes in immune cell subsets following irradiation, cells were enriched using the EasySep™ Mouse Pan-ILC Enrichment Kit (STEMCELL Technologies). Enriched cells were stained with anti-CD45.2 and Zombie Aqua dye. live CD45⁺ cells and CD45⁻ cells were sorted using a FACS Aria II (BD Biosciences). We prepared the samples by mixing the sorted CD45.2⁺ and CD45.2⁻ cells at a 1:1 ratio and the samples were processed using the Chromium Single Cell 3′ Reagent Kit v3 (10X Genomics) according to the manufacturer’s protocol.

first: Haiqing

last: Li

first: Rifat

last: Mannan

first: Taylor

last: Doherty

first: Heather

last: McGee


title: Mecp2 stabilizes the glucocorticoid system in active chromatin regions

first: Xiaoping

last: Han


title: H3K4me3 ChIP-seq Identifies EMT-TFs in TGF-β-Induced A549 cells

summary: H3K4me3 marks active gene regions and broad H3K4me3 occupancy is associated with genes critical for cell identity and function. To identify novel EMT-inducing transcription factors (EMT-TFs), we analyzed changes in broad H3K4me3 occupancy during TGF-β-induced epithelial-to-mesenchymal transition (EMT) in A549 lung adenocarcinoma cells using H3K4me3 ChIP-seq.

overall_design: ChIP-seq of H3K4me3 in TGF-β-induced A549 cells. A549 cells were treated with 1ng/ml TGF-β for 24h.

first: Katsuhiko

last: Shirahige

first: Ryuichiro

last: Nakato


title: Genome wide transcriptional changes underlie gradual and recurrent adaptation to protein malnutrition in zebrafish

status: Public on Jul 30 2026

city: Chapel Hill

first: Jieun

last: Park

state: North Carolina

address: 116 Manning Drive, CB 7250, Unive7008B Mary Ellen Jones Building

institute: University of North Carolina at Chapel Hill

summary: Lysosome-rich enterocytes (LREs) are a specialized population of intestinal cells that mediate the uptake and absorption of dietary proteins in zebrafish and neonatal mammals. Loss of LRE function causes severe stunting and poor survival due to protein malnutrition. Previously, we reported that loss of Plasmolipin (pllp), an endosomal membrane protein highly expressed in LREs, impairs LRE differentiation and dietary protein absorption, resulting in marked reduction in survival rates. Raising pllp homozygous mutants surviving to adulthood and in-crossing them for multiple generations resulted in their adaptation to malnutrition, with pllp mutants showing robust suppression of survival deficits. To uncover mechanisms underlying this adaptive response, we conducted transcriptome profiling and protein absorption assays to compare the older adapted pllp allele with genetically related wild type (WT) fish and a newly generated pllp mutant allele. We found that adapted pllp mutants exhibit upregulation of LRE endocytic components and have a capacity for protein absorption that exceeds that of WT. This hyperactivation of LRE endocytic and absorptive activity, appears also to be aided by the intricate transcriptional regulations of immune genes that may contribute to the enhanced survival of pllp mutants in the face of increased exposure to environmental antigens. Overall, our study illustrates a genetic adaptation mechanism for enhancing organ function and organismal survival in response to severe protein malnutrition.

overall_design:
RNAseq profiling of EK, and adapted pllp pd1245 20 dpf zebrafish larvae to investigate transcriptomic changes caused by adapted pllp pd1245 mutation.
RNAseq profiling of EK, pllp pd1116, and pllp pd1245 20 dpf zebrafish larvae to investigate transcriptomic changes caused by new pllp mutation (pd1245; survival defect under nutritional restriction) and old pllp mutation (pd1116; survival defect adapted under nutritional restriction).

first: Siyao

first: Laura

last: Childers

first: Fernando

last: Martinez III

first: Michel

last: Bagnat


title: Time-Dependent Nucleosome Remodeling During Galactose-Induced Ty1 Expression in Saccharomyces cerevisiae

status: Public on Jul 29 2026

city: Vancouver

first: Marjan

last: Barazandeh

state: BC

address: 6622-2405 Wesbrook Mall

department: Pharmaceutical Sciences

institute: University of British Columbia

summary: The relationship between chromatin structure and transposable element (TE) integration is a fundamental question as nucleosomes can either mediate or inhibit TE insertion. The Ty1 element in Saccharomyces cerevisiae preferentially inserts upstream of RNA Polymerase III-transcribed genes, in a manner coincident with nucleosome positioning. Ty1 insertion positions have largely been inferred from nucleosome occupancy maps, but this approach is imperfect. Nucleosome occupancy maps are typically generated from wild-type Saccharomyces cerevisiae cells grown in standard conditions. Many Ty1 studies rely on a galactose-inducible expression system and it is not yet known if Ty1 overexpression from the GAL1 promoter itself alters nucleosome organization under inducing conditions. Here, we used a galactose-inducible Ty1 expression system and genome-wide MNase-seq to determine whether Ty1 donor plasmid transformation and overexpression alter nucleosome occupancy. We find that changes in carbon source do not substantially alter genome-wide nucleosome organization. In contrast, galactose induction of Ty1 expression revealed time-dependent changes in nucleosome occupancy. Nucleosome organization is unchanged across pre-induction, 6-hour galactose exposure, and post-induction repressing conditions, but nucleosome occupancy shifted at 12 and 24 hours, with changes evident at both Pol II and tRNA genes. We also found that Ty1 integration events are rare at early time points, emerge by 12 hours, and accumulate substantially by 24 hours. Ty1 preferentially targets nucleosomal DNA, but prolonged induction shifts insertion positions relative to nucleosomes. We also find that Ty1 preferentially targets nucleosomal DNA that lies in close proximity to histones, with this preference showing time-dependent shifts during induction.

overall_design: Genome-wide MNase-seq and Ty1 insertion profiling across Ty1 induction time points in S. cerevisiae.

first: Rutuja

last: Pattanshetti

first: Stephanie

last: Cheung

first: Hamid

last: Gaikani

first: Vivien

last: Measday

first: Corey

last: Nislow


title: IL7R depletion mitigates neuroinflammation and ischemic stroke via AKT dephosphorylation dependent LCP1 suppression in mice

city: BEIJING

first: Qianqian

last: Yin

address: 49 North Garden Road, Haidian District

department: Center of Basic Medical Research

institute: Peking University Third Hospital

summary: Stroke remains a leading cause of death and long-term disability worldwide. After reperfusion following ischemic stroke, peripheral immune cells infiltrate the injured brain hemisphere and exacerbate secondary damage. Among these cells, monocytes are among the predominant population. In this study, we performed single-cell RNA sequencing of immune cells isolated from the brain 72 h after infarction and characterized the heterogeneity of brain infiltrating monocyte-derived macrophages. We identified an IL7R+ macrophage subset with high fatty-acid metabolism scores 3 days after ischemic stroke in mice. In vitro oxygen glucose deprivation cell model, Il7r expression was significantly increased, accompanied by upregulation of the PI3K-AKT pathway. IL7R knockdown decreased phosphorylated Akt and LCP1 levels, and LCP1 knockdown further reduced arachidonic acid, a key mediator of proinflammatory protein translation, as revealed by bulk RNA-seq and metabolomics analyses. Consistent with these in vitro results, IL7R depleted mice exhibited smaller infarct volumes and improved neurological function. Collectively, our findings provide mechanistic insight into how IL7R–pAKT-LCP1 signaling shapes immune-cell metabolism during stroke-induced neuroinflammation and suggest potential therapeutic opportunities targeting immunometabolic pathways in ischemic stroke.

overall_design: we performed RNA sequencing (RNA-seq) on RAW264.7 cells in the LCP1 knockdown group (siLCP1 cells) and scramble siRNA control group

first: Yan

last: Wang


title: Locus-Scale Massively Parallel Reporter Assays

status: Public on Jul 28 2026

first: Abby

middle: V

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: Interactions among cis-regulatory elements (CREs) are central to mammalian gene regulation. Long @$$ massively parallel reporter assays (LAMPRAs) integrate combinatorial cloning, molecular barcoding and long- and short-read sequencing, to scalably measure how CRE identities, numbers, spacings, orders, orientations, and interactions shape regulatory output at multi-kilobase length scales. As a proof-of-concept, we assay 36,000 x 5-kb synthetic cis-regulatory loci (sCRLs), each a 5 x 1-kb random combination of enhancers, insulators and spacers, to model how locus composition drives gene expression.

overall_design: To link barcodes to their corresponding sCRLs, we performed sCRL-BC mapping using PacBio sequencing to create a lookup dictionary prior to MPRA experiments. Using paired-end Illumina sequencing, each BC was captured from both DNA and RNA for MPRA experiments.

first: Carina

last: Biar

first: Beth

last: Martin

first: Tony

last: Li

first: Jean-Benoit

last: Lalanne

first: Haedong

last: Kim

first: Jay

last: Shendure


title: Development and Preclinical Evaluation of Tetraspecific Antibodies  in Combination with Ex Vivo Expanded NK Cells Infusion for Improved Control of Esophageal Cancer

city: Zhengzhou

first: Yafei

last: Liu

address: East Jianshe Road NO.1

institute: The first affiliated hospital of zhengzhou university

summary: Background: Esophageal squamous cell carcinoma (ESCC) is highly heterogeneous, leading to limited drug effectiveness and resistance. Antibody therapies offer limited benefits due to low response rates. multispecific antibodies, targeting multiple tumor antigens and NK cell receptors, may overcome these challenges, but their effectiveness and mechanisms in ESCC therapy are not yet understood. Methods: Whole transcriptome sequencing was performed on tumor tissues from 32 ESCC patients to identify tumor antigens. Tetraspecific antibodies, referred as NK cell engagers (NKCEs), were designed and constructed to target two ESCC antigens and two surface markers of NK cells. AlphaFold was used to predict the spatial structure of tetraspecific NKCEs and its binding properties with antigens. Fast protein liquid chromatography and surface plasmon resonance were applied for quality control of NKCEs. Using multiple human ESCC cell lines, chemoresistant ESCC cell lines and NK cells from different donors, we carried out flow cytometry to assess NK cell cytotoxicity and activation. Immunofluorescence assays were used to confirm NKCEs binding and colocalization. Transcriptome sequencing, flow cytometry and western blot were performed to explore molecular mechanisms. Subcutaneous and metastatic xenograft tumor models were established in nude mice to evaluate the in vivo anti-tumor efficacy of NKCEs combined with adoptive transfer of NK cells. Results: We found that EGFR was consistently highly expressed in all ESCC samples while MET was specifically upregulated in recurrent ESCC. Tetraspcific NKCEs were successfully engineered and could specifically bind to EGFR, MET, CD16, NKp30 or NKp46. The tetraspecific NKCEs significantly enhanced the cytotoxicity of NK cells against ESCC cell lines as well as paclitaxel-resistant ESCC cell lines in vitro, compared with the commercial antibody Amivantamab. Transcriptomic analysis followed by functional validation revealed that tetraspecific NKCEs triggered immune activation pathways and increased the expression of TNF-α, IFN-γ, and granzyme B in NK cells, but also induced NK cell exhaustion. In vivo studies demonstrated that tetraspecific NKCEs combined with NK cell infusions exerted better antitumor efficacy against esophageal tumors in different stages. The combination therapy was well tolerated, with enhanced NK cell infiltration in tumor tissues. Conclusions: We developed tetraspecific NKCEs targeting two tumor antigens (EGFR, MET) and two NK-cell activating receptors (CD16, NKp30 or NKp46) to effectively bridge ESCC cells and NK cells. The tetraspecific NKCEs exert the potential to enhance antitumor activity of NK cells against ESCC. This study supports the clinical translation of multispecific NKCEs for NK cell-based immunotherapy for ESCC.

overall_design: In this study, an in vitro co‑culture system was established to explore the transcriptomic profiles of natural killer (NK) cells under different treatment conditions, providing original sequencing data for investigating the mechanistic basis of antibody‑mediated tumor immunotherapy. NK cells were subjected to five experimental conditions: NK cells co‑cultured with tumor cells, NK cells + tumor cells + Amivantamab, NK cells + tumor cells + Tri‑Ab, NK cells + tumor cells + Tetra‑Ab (46.3), and NK cells + tumor cells + Tetra‑Ab (30.1). Following co‑incubation, CD3CD56 NK cells were purified by flow cytometry cell sorting to eliminate tumor cells and impurities and ensure sample purity. Total RNA was subsequently extracted from sorted NK cells using the Trizol reagent, and high‑quality RNA samples were used for subsequent transcriptome sequencing.

first: Xueyuan

last: Fan

first: Xueyang

last: Zuo

first: Jiaqi

last: Zhao

first: Lan

last: Huang

first: Feng

first: Yu

last: Qi


overall_design: Focal ischemia was induced using a middle cerebral artery occlusion (MCAO) method, a procedure that was maintained for 45 min, with sham group as control. we performed scRNA-seq analysis on all CD45+ cells collected from brains on day 3 after MCAO treatment.


title: Concentration-dependent MNase-seq with yeast spike-in normalization resolves nucleosome occupancy and accessibility in human induced pluripotent stem cells (nucMACC)

city: Darlinghurst

first: David

middle: Thomas

last: Humphreys

address: 405 Liverpool Street

department: Genome core

country: Australia

institute: Victor Chang Cardiac Research Institute

summary: Micrococcal nuclease sequencing (MNase-seq) maps nucleosome occupancy and positioning genome-wide but is sensitive to digestion conditions and lacks standardized, quantitative normalization. We developed a refined, scalable MNase-seq workflow and applied it to human induced pluripotent stem cells (hiPSCs; FUCCI-reporter line PB010.5) across a five-point MNase digestion titration (0.5, 1, 3, 6, and 10 U), with an in-house Saccharomyces cerevisiae mononucleosomal spike-in (~5% of input DNA) added for cross-sample normalization. Libraries were sequenced on two platforms (Illumina NovaSeq X, 150 bp paired-end; Illumina NextSeq 2000, 50 bp paired-end) and analyzed with the nucMACC pipeline to quantify concentration-dependent shifts between mononucleosomal and subnucleosomal fragments and to resolve the nucleosome-depleted region and +1/-1 nucleosome positioning at transcription start sites. nucMACC accessibility scores stratified nucleosomes into hyper- and hypo-accessible classes corresponding to active and repressive chromatin states.

overall_design: Undifferentiated hiPSCs (FUCCI-reporter line PB010.5) were digested with micrococcal nuclease across a graded enzyme titration (0.5, 1, 3, 6, and 10 U) under otherwise identical conditions. Purified MNase-digested DNA from each condition was spiked with in-house Saccharomyces cerevisiae (BY4742) mononucleosomal DNA at ~5% of total DNA prior to library preparation. Each library was sequenced on two platforms — Illumina NovaSeq X (150 bp paired-end, high depth) and Illumina NextSeq 2000 (50 bp paired-end, low input) — constituting technical sequencing replicates of the same libraries. Differential MNase digestion across the titration was exploited by the nucMACC pipeline to derive genome-wide nucleosome occupancy, accessibility (nucMACC scores), and positioning.

first: Chris

last: Thekkedam

middle: T

first: Marina

last: Naval-Sanchez

first: Osvaldo

last: Contreras


title: GABPA recruits the Integrator endonuclease complex to promote transcription elongation

status: Public on Jul 26 2026

city: Beijing

first: Hang

last: Yang

state: Beijing

address: No.1 West Beichen Road,Chaoyang District

institute: CAS

summary: Transcription factors (TFs) coordinate gene regulatory programs essential for cell identity, yet how individual TFs modulate distinct transcriptional stages remain incompletely understood. GABPA, an ETS family TF, is crutial for naïve pluripotency in mouse preimplantation development, but its molecular functions have remained elusive. Using an acute protein degradation system, we dissect GABPA activity with high temporal resolution, identifying immediate transcriptional targets and mechanisms while avoiding secondary effects associated with conventional gene knockouts. We find that GABPA is essential for mESC viability through a previously unrecognized mechanism that is independent of its canonical heterotetrameric partner, GABPB. Mechanistically, GABPA physically engages the INTS4/9/11 endonuclease module of the Integrator complex to facilitate productive elongation of RNA polymerase II (Pol II) at ribosome biogenesis genes. Acute GABPA loss causes promoter-proximal Pol II accumulation and reduces gene body Ser2-phosphorylated Pol II, indicative of elongation defects, while prolonged depletion diminishes chromatin accessibility and enhancer activity at pluripotency-associated loci. Together, these findings reveal dual temporally distinct roles for GABPA, an immediate function in transcriptional elongation and a later function in chromatin regulation. Our study redefines GABPA as a multifaceted transcriptional regulator acting independently of GABPB, and provides a framework for temporally resolved dissection of TF function in stem cell biology.

overall_design: By generating dTAG mESCs and employing RNA-seq, SLAM-seq, ATAC-seq and CUT&Tag, we systematically investigated the role of the ETS family transcription factor GABPA in regulating gene expression. In this study, samples for each condition were collected in biological duplicates. Cells were treated with dTAG13 for 1, 2, 4 and 12 hours, and the corresponding control cells were treated with DMSO. Our acute and prolonged GABPA depletion results revealed that GABPA is a multifaceted transcriptional regulator acting independently of GABPB, which has an immediate function in transcriptional elongation and a later function in chromatin regulation.

first: Jinjing

last: Geng

first: Danyi

last: Lu

first: Wusa

last: Baqie

first: Fei Xavier

last: Chen

first: Chunxia

last: Zhang


title: Therapy Induced Senescence Promotes Immunogenicity in Acute Myeloid Leukemia through Reduced EZH2 Activity (RNA-seq TAZ)

status: Public on Jul 24 2026

city: Milan

first: Raffaella

last: Di Micco

address: Via Olgettina, 60

institute: San Raffaele Telethon Institute for Gene Therapy

summary: Chemotherapy resistance and disease relapse are major determinants of treatment failure in acute myeloid leukemia (AML). Therapy-induced senescence (TIS) is one outcome of chemotherapy, but its immunological consequences in AML remain unclear. Here we show that ex vivo chemotherapy induces senescence in a subset of therapy-naïve AML samples. TIS is marked by elevated interferon signaling, upregulation of human leukocyte antigen (HLA) class I and II molecules, and increased presentation of leukemia- and senescence-associated peptides, conferring AML cells antigen-presenting cell-like features. These changes enhance autologous CD4+ and CD8+ T cell responses against AML, both ex vivo and in patient-derived xenograft models. TIS also restores AML sensitivity to immune checkpoint blockade therapy. Mechanistically, we identify reduced Polycomb Repressive Complex 2 (PRC2) activity as central to TIS induction and its immunogenicity. PRC2 inhibition reactivates senescence-related genes and HLA expression in non-senescent AML cells, enabling T cell activation. These findings uncover a senescence-driven immune mechanism with potential to improve therapy outcomes in AML.

overall_design: RNA-seq analysis of patient derived AML blasts from Sen Low cohort untreated or upon tazemetostat (TAZ) treatment

first: Simona

last: Fusco

first: Diego

last: Gilioli

first: Nicolò

last: Gualandi

first: Ivan

last: Merelli


title: Transcriptional Profiles of Select Histone Deacetylase Inhibitors in Human HepaRG Cells

status: Public on Jul 27 2026

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

summary: New approach methods (NAMs), such as human-derived in vitro models integrated with transcriptomic biomarkers, offer an efficient, animal-free means to predict toxic responses. Biomarkers including GENOMARK and TGx-DDI enable high-throughput transcriptomic analysis and accurate genotoxicant classification. Histone deacetylase inhibitors (HDACi), a class of epigenotoxicants, disrupt chromatin structure and gene expression, which may lead to impaired DNA repair, apoptosis, and cell cycle perturbation. A transcriptomic biomarker (TGx-HDACi) was previously developed in human TK6 cells to classify HDACi; however, its performance in other cell types is suboptimal. Herein, we conducted a biomarker discovery study to identify a transcriptomic signature capable of discriminating HDACi from non-HDACi compounds in human HepaRG cells, a metabolically competent hepatic cell line increasingly used in genotoxicity testing. HepaRG cells were exposed to 22 reference chemicals (8 HDACi, 14 non-HDACi) at five increasing concentrations in a 72-hour repeated exposure design, and whole transcriptome profiling was performed using TempO-Seq with maximum concentrations selected based on cytotoxicity and solubility thresholds. One concentration per compound was used for biomarker development. A nearest shrunken centroid (NSC) approach identified a 102-gene panel (TGx-HDACi-HepaRG) that achieved 100% predictive accuracy by cross-validation and correctly classified compounds across multiple independent analytical approaches. Concentration-response evaluation further demonstrated the biomarker’s ability to identify exposure levels associated with HDAC inhibition. These findings establish TGx-HDACi-HepaRG as a promising transcriptomic biomarker for epigenotoxicity screening in a metabolically competent human liver model. As this study represents the biomarker discovery phase, future work will focus on external validation using independent chemical sets and case studies to support its application in mechanism-informed chemical risk assessment.

overall_design: Whole transcriptome TempO-Seq concentration-response analysis was conducted in human HepaRG cells following exposure to eight histone deacetylase inhibitors (HDACi) in order to identify a transcriptomic biomarker to classify HDACi in this cell line. A total of 144 samples were sequenced, including technical controls (reference RNA and cells with no treatment). The solvent controls were comprised of 0.5% DMSO in medium. Five concentrations of each chemical were tested in triplicate (three different batches of HepaRG cells).

first: Julie

last: Buick

first: Eunnara

last: Cho

first: Anouck

last: Thienpont

first: Andrew

last: Williams

first: Birgit

last: Mertens

first: Vera

last: Rogiers

first: Tamara

last: Vanhaecke

first: Carole

last: Yauk

middle: J


title: The Sox2 Regulatory Region 42 (SRR42) Produces eRNAs that Influence Neuronal Migration during Cortical Development

status: Public on Jul 23 2026

city: Tokorozawa-si

first: Noriko

last: Mizota

state: Saitama

address: 2-579-15 Mikajima

department: Faculty of Human Sciences

institute: Waseda University

summary: During mammalian neural development, precise regulation of gene expression in neural progenitor cells (NPCs) is critical for proper formation of the cortex. Although the regulatory mechanism of the transcription factor Sox2 has been extensively examined, the role of its distal regulatory elements remains poorly understood. Here, we identified a Sox2 regulatory region located 42 kb downstream of the Sox2 TSS (SRR42) that exhibits hallmark features of an active regulatory element, including open chromatin, histone modifications, and bidirectional transcription of enhancer RNAs (eRNAs).  Using transgenic reporter mice, we found that SRR42 is specifically active in NPCs in the developing mouse brain. CRISPR-Cas9-mediated deletion of SRR42 in mice together with single-cell multiome analysis further revealed the involvement of SRR42 regions in the regulation of neuronal migration and cortical lamination. Knockdown of SRR42 eRNAs in vivo impaired neuronal migration, indicating that these eRNAs regulate neuronal development. Our study demonstrated that SRR42 functions through an eRNA-mediated mechanism to precisely control neuronal positioning during mammalian cortical development, which is not associated with Sox2 transactivation. These findings provide new insights into the epigenetic regulation of cortical formation and may help understand neurodevelopmental disorders.

overall_design: Neurospheres were generated from the human iPS cell line YZWJs513 (Umekage et al., Inflamm. Regen. 2019, 39:17) by passaging eight times using the previously reported differentiation method (Iida et al., Stem Cells 2017, 35:1316-1327). Total RNA was then purified from the neurospheres and processed via CAGE sequencing.

first: Satoe

last: Banno

first: Tukasa

last: Sanosaka

first: Ryo

last: Tomooka

first: Akinori

last: Tokunaga

first: Hideyuki

last: Okano

first: Jun

last: Kohyama


overall_design: Total RNA was extracted separately from the cerebral cortex of E14.5 mice. The RNA from three wild-type (WT) mice was pooled and subsequently analyzed using CAGE sequencing.


title: Single nucleus RNA-sequencing for mice posterior substantia innominata (house mouse)

city: hangzhou

first: kaiyuan

last: li

state: zhejiang

address: Zhejiang University School of Medicine, Hangzhou, 310058, China

department: Zhejiang University School of Medicine

institute: School of Brain Science and Brain Medicine

summary: To characterize the cell types in the substantia innominata of male and female mice using single-nucleus RNA-seq.

overall_design: The microdissected posterior substantia innominata (pSI) from male and age-matched control female mice (8 weeks) was dissociated into a single-nucleus suspension for snRNA-seq. Quantitative assessment of sex differences in pSI neurons in mice.

first: Kaiyuan

last: Li

first: Quan

last: Wang


overall_design: This study consists of multiple sequencing datasets. Nuclei were isolated from the brains of WT and deletion mutant (chr3: 34692107-34692549) mice for single-nucleus multiome (ATAC and RNA-seq) analysis.

first: Tsukasa


title: Conditional deletion of Wnt5a in myeloid osteoclast precursors results in low bone mass via disruption of osteoblast migration and focal adhesion dynamics

status: Public on Jul 22 2026

city: Atlanta

first: Valentina

last: Daponte

state: Georgia

address: 21 Ortho Ln

institute: Emory University

summary: Bone remodeling relies on the coordinated signaling between bone-resorbing osteoclasts and bone-forming osteoblasts through locally secreted coupling factors, including WNT5A. Although osteoblast-derived WNT5A is known to promote osteoclastogenesis, the contribution of osteoclast-derived WNT5A to bone homeostasis remains poorly defined. We previously showed that conditional deletion of Wnt5a in mature osteoclasts using the Ctsk-Cre driver results in low bone mass, suggesting an anabolic role for osteoclast-derived WNT5A.  However, Ctsk expression in other cell types, including periosteal cells, precluded definitive attribution. Here, we used the more specific LysM-Cre line to validate the osteoclast-specific function of Wnt5a in vivo. LysM-Cre; Wnt5aF/F mice displayed significantly reduced trabecular bone driven by decreased osteoblast number and activity, while osteoclast number and resorptive function were preserved. Transcriptomic profiling of osteoblast-enriched cells revealed dysregulation of genes involved in cell adhesion, integrin binding, and cell communication, alongside upregulation of stress-related genes. Histological analyses and functional assays showed that loss of osteoclast-derived Wnt5a led to impaired extracellular matrix maturation together with defective osteoblast focal adhesion assembly and migration, respectively. Collectively, these data provide a mechanistic link between Wnt5a and osteoblast function. In summary, our study establishes osteoclast-derived Wnt5a as a clastokine supporting bone formation through regulation of osteoblast migration and adhesion dynamics, highlighting the context-dependent and cell-specific roles of WNT5A in skeletal homeostasis.

overall_design: RNA-seq profiling of endosteal cells isolated from long bones of 10-week-old control and LysM-Cre;Wnt5aF/F mice.

first: Katrin

last: Henke

first: Hicham

last: Drissi


title: Pharmacological inhibition of PRKDC-mediated DNA damage response by 3-hydroxyflavone selectively alleviates MLL-rearranged acute myeloid leukemia

status: Public on Jul 21 2026

city: Guangzhou

first: Yage

last: Nie

address: No.74 Zhongshan Rd.2, Guangzhou

institute: Sun Yat-sen University

summary: Genetic rearrangements involving mixed lineage leukemia (MLL-r) in acute myeloid leukemia (AML) have been associated with resistance to chemotherapy, and there is currently a clinical unmet need for effective targeted therapies. In this study, we performed high-throughput drug screening and identified 3-Hydroxyflavone (3-HF) as a selective inhibitor of the survival and growth of MLL-r AML cells, while having minimal effects on leukemia cells with wildtype MLL. Mechanistically, 3-HF suppresses the transcription of MLL-targeted genes and exerts antileukemic activity by disrupting PRKDC-mediated DNA damage repair. Additionally, 3-HF enhances chemosensitivity in MLL-r AML cells and demonstrates synergistic antileukemic effects when combined with cytarabine, a standard chemotherapy agent, both in vitro and in vivo using two distinct mouse models of murine MLL-AF9 and human MLL-AF4 leukemia. Our findings provide a novel strategy and targeted therapeutic drug disrupting PRKDC-mediated DNA damage repair pathways for MLL-r leukemia.

overall_design: RNA-seq profiling of MOLM13, MV411, and U937 cells were treated with either DMSO (vehicle control) or 3‑HF for 12, 24, and 24 hours, respectively.

first: Jing

last: Liu

last: Cao


title: Therapy Induced Senescence Promotes Immunogenicity in Acute Myeloid Leukemia through Reduced EZH2 Activity

first: Raffaella

last: Di Micco

summary:
Chemotherapy resistance and disease relapse are major determinants of treatment failure in acute myeloid leukemia (AML). Therapy-induced senescence (TIS) is one outcome of chemotherapy, but its immunological consequences in AML remain unclear. Here we show that ex vivo chemotherapy induces senescence in a subset of therapy-naïve AML samples. TIS is marked by elevated interferon signaling, upregulation of human leukocyte antigen (HLA) class I and II molecules, and increased presentation of leukemia- and senescence-associated peptides, conferring AML cells antigen-presenting cell-like features. These changes enhance autologous CD4+ and CD8+ T cell responses against AML, both ex vivo and in patient-derived xenograft models. TIS also restores AML sensitivity to immune checkpoint blockade therapy. Mechanistically, we identify reduced Polycomb Repressive Complex 2 (PRC2) activity as central to TIS induction and its immunogenicity. PRC2 inhibition reactivates senescence-related genes and HLA expression in non-senescent AML cells, enabling T cell activation. These findings uncover a senescence-driven immune mechanism with potential to improve therapy outcomes in AML.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Time-resolved transcriptomics and gene networks identify the primary targets for abscisic acid signalling in Populus nigra roots

city: CHAMPENOUX

first: David

last: Cohen

address: rue d'Amance

department: UMR1434 SILVA

institute: INRAE

summary: The phytohormone abscisic acid (ABA) regulates major aspects of plant growth and development. ABA is involved in diverse key processes, such as germination, root growth, bud bursts or stomata opening. ABA acts as a key signalling molecule that mediates plant response to environmental cues. Changes in endogenous ABA level triggered rapidly transcriptional and post-transcriptional events. The core ABA signalling cascade consisted in a three-step regulatory processes in which ABA receptor complex activated protein kinases which in turn mediated ABA signal towards specific targets such transcription factors or channels. While the core ABA signalling cascade has been established mainly using mutagenesis on the model plant Arabidopsis, it appeared highly conserved across plant genomes.  In the present study, time-resolved transcriptomics and gene co-expression networking were used to decipher the primary ABA targets in the roots of a perennial model. We documented the ABA-triggered transcriptional events in the growing roots of the Populus nigra. Transcriptome was studied throughout two time-series experiments where hydroponically rooted cuttings were exposed to 2 µM ABA treatments. Controls were treated with ABA-free solution. Hormone profiling not only confirmed that ABA uptake occurred but also highlighted the gradual accumulation of abscissate forms and a rapid rewiring of other hormones. For all time points, transcript abundance was quantified using RNA-Seq technology (Illumina). Two computational approaches were employed, based either on pairwise differential expression (DESeq2 R package and IDREM) or on co-expression relationships (WGCNA and DGCA R-packages). The ABA targets involved in the poplar root response to osmotic stress were investigated further (DGCA, WGCNA R-packages), as the rapid growth of poplar species required a large water amount to sustain their field productivity. Our study revealed the molecular components of ABA interference and the time-dependant structuration of ABA-responsive-gene expression.

overall_design: 48 RNA samples were analysed (two to four replicates) through 2 experiments (exp1: 34 samples and exp2:14 samples)

first: Irène

last: Hummel


title: Leaf Gene Expression Profiles in CMV-Resistant and Non-Resistant Cassava

status: Public on Jul 20 2026

city: Bangkok

first: Apidet

last: Rakpenthai

state: Chatuchak

address: 50 Ngamwongwan Rd

country: Thailand

institute: Kasetsart University

summary: To elucidate the molecular mechanisms underlying Cassava Mosaic Virus (CMV) resistance in cassava (Manihot esculenta), we performed high-throughput RNA-sequencing (RNA-seq) on 6-month-old leaf tissues from contrasting cultivars. Transcriptomic profiling was conducted on the susceptible, non-CMV resistant line 'Huay Bong 100' (HB100) alongside two elite CMV-resistant lines, 'MKUC64-36-160' and 'TMS-IBA 980581'. This dataset provides a comprehensive comparative gene expression profile during a critical physiological growth stage, enabling the identification of differentially expressed genes, defense-related pathways, and potential molecular markers associated with durable virus resistance. The datasets serve as a valuable resource for cassava breeding programs aimed at enhancing crop resilience against viral pathogens.

overall_design: RNA-seq profiling was performed on six-month-old leaf tissues from distinct genotypes, including the CMV-susceptible line Huay Bong 100 (HB100) and two CMV-resistant lines, MKUC64-36-160 and TMS-IBA 980581.

first: Chalermpol

last: Phumichai

first: Piya

last: Kittipadakul


title: Intrinsic Reprogramming of Dermal ILC2s in RAG1-Deficient Mice Shapes Cutaneous Inflammation

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: Group 2 innate lymphoid cells (ILC2s) are key regulators of skin immunity and barrier homeostasis. RAG1-deficient (Rag1⁻/⁻) mice are widely used to study ILC2 biology owing to their elevated ILC2 frequencies and absence of adaptive lymphocytes. However, RAG1 is transiently expressed during ILC2 development, raising the question of whether its loss intrinsically alters dermal ILC2 (dILC2) identity and function. We performed transcriptomic and functional analyses of dILC2s from Rag1⁻/⁻ and wild-type mice. RNA sequencing revealed 2,503 differentially expressed genes in Rag1⁻/⁻ dILC2s, including upregulation of Il7r, Thy1, Il5 and Il13, and enrichment of JAK/STAT, PI3K/Akt, IL-23 and apoptosis pathways. Functionally, Rag1⁻/⁻ dILC2s displayed increased basal proliferation and apoptosis. In a DNFB-induced contact hypersensitivity model, Rag1⁻/⁻ mice exhibited attenuated ear swelling and a failure to expand dILC2s upon challenge, in contrast to wild-type mice. Adoptive transfer of lymphocytes partially restored these dynamics, indicating contributions of both intrinsic RAG1-dependent programming and extrinsic adaptive–innate interactions. Our findings demonstrate that RAG1 deficiency fundamentally reprograms dILC2 homeostasis and responsiveness to cutaneous stress. These results highlight the need for careful interpretation of ILC2 biology in Rag1⁻/⁻ models and reveal a previously underappreciated role of RAG1-dependent developmental cues in shaping skin immune responses.

overall_design: For transcriptome analysis we sorted and purified dILC2s of 30 WT and 16 RAG1-/- mice, respectively. RNA quality was assessed by measuring the RIN (RNA integrity number) using a Fragment Analyzer (Advanced Bioanalytical). Library preparation for RNA sequencing was performed using the TruSeq RNA Sample Prep Kit v2 (Illumina) starting from 200 ng of total RNA. Accurate quantification of cDNA libraries was performed by using the QuantiFluor dsDNA System (Promega). The size range of final cDNA libraries was determined by applying the DNA 1000 chip on the Fragment Analyzer (average 290–320 bp). Libraries were sequenced on the HiSeq 4000 from Illumina (SR; 1 × 50 bp; ∼30 million reads per sample). Raw read & Quality check: Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.17.1.14. The quality check was done using FastQC (Andrews, Simon."FastQC a quality-control tool for high-throughput sequence data http://www." Bioinformaticsbabraham. ac. uk/projects/fastqc (2014) (version 0.11.5, Babraham Bioinformatics). Mapping & Normalization: Sequences were aligned to the genome reference sequence of Mus Musculus (ENSEMBL version GRCm38) using the STAR alignment software (version 2.5) allowing for 2 mismatches within 50 bases. Subsequently, reads were counted for each gene in Mus musculus GTF file Mus_musculus.GRCm38.103.gtf (ftp://ftp.ensembl.org/pub /release 103/gtf/mus_musculus/Mus_musculus.GRCm38.103.gtf.gz) using featureCounts (version 1.5.0-p1). Read counts were analyzed in the R/Bioconductor environment (version 3.2.0, www.bioconductor.org) using the DESeq2 package version 1.8.2. Candidate genes were filtered using an absolute log2 fold-change >1 and FDR-corrected p-value <0.05. Gene annotation was performed using the Mus musculus dataset in biomaRt R package version 2.24.1

first: Mohamed

last: Saleh

first: Kexin

last: Liao

first: Andrea

last: Braun

first: Michael

last: Schön

first: Prasad

last: Dasari

first: Timo

last: Buhl


title: Identification of progenitor cells that drive Interleukin 11-dependent tumor-stroma coevolution in advanced melanoma [TGFB_scRNAseq]

status: Public on Jul 18 2026

city: Boston

first: Ian

last: Dryg

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: Tumor mesenchymal stem cells (TMSCs) orchestrate tumor microenvironment (TME) transformation via their ability to transdifferentiate. Metastatic solid tumors often feature neural crest-like/mesenchymal phenotypes characterized by high expression levels of TGFβ-dependent epithelial-to-mesenchymal transition (EMT) and EMT-like programs. Specifically, EMT-like endothelial-to-mesenchymal (EndMT) programs are responsible for the differentiation of TMSCs towards cancer-associated fibroblasts (CAFs). CAFs dictate tumor progression, invasiveness, and immune evasion.  Exploring the molecular determinants of CAFs generation and pathobiology is thus of paramount importance to improve therapy response. The in vitro responses of patient-derived TMSCs were investigated upon recapitulating TGFβ-driven EMT-like TME traits. The resulting myofibroblastic CAFs (myCAFs) originated from TMSCs via EndMT were characterized by enhanced Interleukin-11 (IL11) expression and secretion. We propose IL11+ myCAFs as a driver of the tumor-stromal crosstalk responsible for the pro-tumorigenic, mesenchymal, angiogenic, and immunosuppressive TME transformation in metastatic melanoma.

overall_design:
Cells were grown in 10cm plates to 90% confluency prior o/n starvation and 1) 24hrs [10ng/mL] TGFB1 treatment (+TGFB1) or 2) no treatment (Untr.).

***************************************************************
Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) for controlled access to the personally identifiable sequence data.
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first: Giorgia

last: Pisoni

first: Shoko

last: Kure

first: Saba

last: Tabasum

last: Manos

middle: D

first: Robert

last: Gentleman

first: Joanna

last: Baginska

first: Julia

last: Huezo

first: Scott

last: Ficarro

first: Farzaneh

last: Kordbacheh

first: Geoffrey

last: Fell

first: Srinika

last: Ranasinghe

first: Jason

last: Weirather

first: Anita

last: Giobbie-Hurder

first: F

last: Hodi


title: Identification of progenitor cells that drive Interleukin 11-dependent tumor-stroma coevolution in advanced melanoma [TGFB_bulkRNAseq]

overall_design:
Cells were serum-starved for 16hrs prior to 24hrs TGFB1 stimulation (T groups) or no stimulation control (C groups). Groups were comprised of three commercially available control MSCs: Adipose-Derived MSCs "ADMSCs", Bone Marrow-Derived MSCs "BMMSCs", and Normal Healthy Donor-Derived MSCs "NMSCs"; and three patient-derived TMSCs: patient C823-derived "C8TMSCs", patient C913-derived "C9TMSCs", and patient P4-derived "P4TMSCs".

***************************************************************
Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) for controlled access to the personally identifiable sequence data.
***************************************************************

first: Michael


title: Diseaase context dictates the cellular targets of IL-17 in inflammatory skin disease [1]

status: Public on Jul 17 2026

city: San Diego

first: Kellen

last: Cavagnero

state: California

address: 9500 Gilman Dr

institute: Univeristy of California, San Diego

summary: Therapeutic blockade of IL-17 and TNF can effectively treat inflammatory skin diseases such as hidradenitis suppurativa and psoriasis, yet the relative importance of the different cell types that respond to IL-17 and TNF remains unresolved. Keratinocytes are viewed as the dominant effector cells, whereas fibroblasts have recently emerged as important contributors. In mice, topical imiquimod induces IL-17- and TNF-dependent skin inflammation and is frequently used to model psoriasis. Here, we demonstrate that intradermal injection of recombinant IL-17 and TNF elicits skin inflammation with features of hidradenitis suppurativa, including a gene expression program that is distinct from psoriasis and imiquimod-induced inflammation. Single-cell transcriptomic network analysis identified dermal fibroblasts as the dominant cell communication hub in hidradenitis suppurativa and in mice injected with IL-17 and TNF. In contrast, fibroblasts and keratinocytes both show strong network involvement in psoriasis and in mice challenged with imiquimod. Cell-type-specific deletion of IL-17 receptor A in mice revealed that imiquimod-induced inflammation depends equally on IL-17 signaling in fibroblasts and keratinocytes, whereas inflammation induced by intradermal IL-17 and TNF only requires fibroblasts to recognize IL-17 and is independent of keratinocyte IL-17 sensing. Single-cell transcriptomic analysis of these conditional knockout mice further demonstrated that keratinocytes and fibroblasts activate divergent and disease-dependent transcriptional programs following activation by IL-17. Together, these findings introduce a new conceptual framework wherein IL-17 signaling is routed through distinct cellular and molecular pathways depending on disease context and establish complementary experimental systems for interrogating type 17 skin inflammation.

overall_design: Bulk RNA-seq of fibroblasts stimulated in vitro


title: Identification of progenitor cells that drive Interleukin 11-dependent tumor-stroma coevolution in advanced melanoma [Full_Low_Serum]

overall_design:
Cells were grown with either full serum (10% FBS) or low serum (2% FBS).

***************************************************************
Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) for controlled access to the personally identifiable sequence data.
***************************************************************


title: RNA-Seq of CD3+ T cells flow sorted from MLR assays with TNF/TNFR inhibitory compound combination treatments

city: Cambridge, MA

first: Praveen Krishna

last: Veerasubramanian

address: 1 Portland Street

institute: Pfizer Inc.

summary: This experiment aims to study the transcriptomic changes in T cells from mixed lymphocyte reactions (MLR) upon treatment with mono- or combo- TNF/TNFR inhibitory agents.

overall_design: CD3+ T cells from 4 biological replicates (donors) isolated from PBMCs were stimulated by coculture with X-ray irradiated non-T PBMC cells from a different (HLA-mismatched) donor. MLR reactions were treated with TNF/TNFR inhibitory molecules, and T cells were flow-sorted after 5 days of MLR. CTLA4-Fc, IgG, and anti-CD3/CD28 treatment, and non-stimulation conditions served as controls.

first: Wenlan

last: Zang

first: Vijaya

last: Amancha

first: Thomas

last: Wynn

first: Jie

last: Quan

first: Fridrik

last: Karlsson


title: Multimodal single cell profiling identifies nclTECs and links chromatin remodeling to TEC differentiation and self-antigen expression modes [scATAC-seq]

city: Oslo

first: Hanne

middle: Sagsveen

last: Hjorthaug

address: Kirkeveien 166

country: Norway

institute: Oslo University Hospital

summary: Using single-cell profiling of the paediatric human thymus, we characterise the chromatin landscape and cell type heterogeneity of TECs and identify regulatory programs underlying thymic epithelial differentiation and tissue-restricted antigen expression. Based on differences in chromatin accessibility, we resolve three subpopulations within the previously reported mcTEC progenitor population, and show that differentiation towards mTEC(III) involves chromatin remodelling reminiscent of epidermal differentiation. Substantial differences in chromatin accessibility are observed across TEC populations at distal regulatory elements, which we hypothesise contribute to stochastic expression of tissue-restricted antigens. Our findings provide insight into mechanisms underlying immunodeficiencies, autoimmune diseases, and certain cancer types, and may inform therapies using engineered or transplanted thymic tissue to induce or enhance T-cell function.

overall_design:
Human thymic tissue samples (N = 5) were collected from paediatric donors undergoing corrective cardiac surgery. Following tissue dissociation, a sample enriched for stromal cells was obtained for each donor by gradient centrifugation and CD45 depletion. For each donor, scATAC-seq was performed on nuclei isolated from a cryopreserved aliquot of the stromal enriched sample.

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

first: Marte

last: Heimli

first: Siri

last: Flåm

first: Benedicte

last: Lie


title: Multimodal single cell profiling identifies nclTECs and links chromatin remodeling to TEC differentiation and self-antigen expression modes [scMultiome-seq]

overall_design:
Human thymic tissue samples (N = 5) were collected from paediatric donors undergoing corrective cardiac surgery. Following tissue dissociation, a sample enriched for stromal cells was obtained for each donor by gradient centrifugation and CD45 depletion. scMultiome-seq was performed on a pool of nuclei from all donors, isolated from cryopreserved aliquots of the stromal enriched samples.

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

middle: A


title: RNA-Seq of T cells stimulated with anti-CD3/CD28 for 4 h

status: Public on Jul 16 2026

summary: This experiment aims to study the transcriptomic changes that occur in human T cells upto costimulatory activation using anti-CD3/CD28.

overall_design: CD3+ T cells from 3 biological replicates (donors) isolated from PBMCs were stimulated with anti-CD3/CD28 antibody cocktail (ImmunoCult T cell activator - Stemcell Technologies, Cat. 10991) and 30 IU/ml of recombinant human IL-2 (R&D Systems, Cat. 202-IL-010) to activate them for 4 h and study the transcriptomic profile of cells.


title: Recognition of ubiquitinated histone H2A constitutes a treatment target for RSF1-driven ovarian cancer

city: RICHMOND

first: Hengbin

last: Wang

state: VA

address: 401 college st

institute: Virginia Commonwealth University

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


title: FOXA2 potently represses NF-κB–dependent transcription from viral promoters in liver cells

city: Rehovot

first: Amir

last: Szitenberg

address: 234 Herzl St

department: INCPM

country: Israel

institute: Weizmann Institute

summary:
The transcription factor Forkhead box A2 (FOXA2) is a key regulator of endoderm development and mature endoderm-derived organs, including the liver, and tight control of its expression and activity is paramount for proper execution of developmental and homeostatic gene programs.
Despite its established role as a pioneer transcription factor and transcriptional activator, FOXA2 exhibited robust repressive activity in differentiated liver cells. FOXA2 over-expression led to widespread repression of endogenous genes, including autorepression of the FOXA2 locus, and to dramatic suppression of viral regulatory elements. Among these, the SV40 virus early promoter—an essential driver of viral replication and cellular transformation—was strongly repressed by FOXA2.
Repression was most pronounced on regulatory elements whose activity is dependent on nuclear factor κB (NF-κB). For the SV40 early promoter, NF-κB binding sites were necessary and sufficient for FOXA2–dependent repression. Consistent with this, the DNA binding domain of FOXA2 was sufficient to mediate repression of NF-κB–driven promoters. EMSA and immunoblot analyses indicated that FOXA2 does not repress these promoters through direct competition with NF-κB for DNA binding. Instead, FOXA2 expression was associated with reduced NF-κB protein abundance, at least in part through proteasome-dependent degradation, revealing a novel indirect mechanism by which FOXA2 constrains NF-κB–dependent transcription. Since many viruses, including SV40 and HIV-1, rely heavily on NF-κB activity to drive early gene expression and the transition from latency to productive infection, our findings suggest that FOXA2 may function as a host-derived, context-dependent restriction factor that limits viral gene expression in differentiated tissues.

overall_design: Comparing the effects on global gene expression following the over-expression of FOXA2 isoforms P1 and P2.


title: Multiome analysis of PDxOs (HCI-003, HCI-005, HCI-011) treated with a CDK4/6 inhibitor for 3 weeks

status: Public on Jul 13 2026

city: Salt Lake City

first: Katherine

middle: E

last: Varley

state: UT

address: 2000 Circle of Hope, Room 3719

department: Department of Oncological Sciences

institute: Huntsman Cancer Institute University of Utah

summary: This study uses single-nucleus multiome profiling, as well as bulk methylation profiling, to characterize the transcriptional, chromatin accessibility, and DNA methylation changes after 3 weeks of CDK4/6 inhibitor treatment in organoids grown from patient-derived xenograft tumors (PDxOs) generated from 3 patients: HCI-003, HCI-005, and HCI-011.

overall_design: Two replicates each of PDxOs from HCI-003, HCI-005, and HCI-011 were cultured and treated with either a CDK4/6 inhibitor or DMSO vehicle control for 3 weeks. Nuclei isolated from each condition and replicate underwent 10x Genomics Multiome single-nucleus sequencing to measure gene expression (snRNA-seq) and chromatin accessibility (snATAC-seq) in the same single cells. Leftover nuclei from each condition and replicate were subjected to bulk reduced representation enzymatic methylation sequencing (RREMS) to measure DNA methylation.


title: Transcriptional Regulation by NFATc1 and NFATc2 in chronically activated CD8+ T cells

status: Public on Jul 14 2026

city: Würzburg

first: Stefan

last: Klein-Hessling

address: Josef-Schneider-Str. 2

department: Institute of Pathology

institute: University of Würzburg

summary: Both chronic viral infections and progressing tumors result in dysfunctional CD8+T cells in a process called exhaustion. Such TEX cells exhibit a reduced proliferative capacity, reduced cytokine expression and target cell killing. They are characterized by increased expression of co-inhibitory receptors as PD-1, Tim-3, Lag-3 and TIGIT, and resistance against immune checkpoint therapies (ICT). These cells develop from so called precursors of exhaustion (TPEX) that express high levels of TCF1 and Ly108 and still respond to ICT. The NFAT factors NFATc1 and NFATc2 play a crucial role in exhaustion of CD8+ T cells and, thereby, in suppression of tumor formation by immune cells. NFATc1 is the most prominent NFAT factor in nuclei of activated T cells and the inducible isoform NFATc1/aA, is strongly expressed in chronically induced CD8+ T cells. The inducible expression of NFATc1/aA is controlled by the distal enhancer E2 and conditional ablation of E2 abolish this induction. We compared here the transcriptome of in vitro chronically stimulated CD8+ T cells with different NFAT deficiencies. While the ablation of NFATc2 resulted in reduced expression of exhaustion markers Tim3 and Tigit and increased expression of Tcf7 and Slamf6, only minor effects on exhaustion markers were detected upon ablation of inducible NFAT1/aA or entire NFATc1.

overall_design: To investigate the impact of different NFAT proteins on the exhaustion of CD8+ T cells we used an in vitro model of chronic antiCD3 stimulation for 6 days. Under these conditions we compared purified splenic CD8+ T cells from different mouse lines to wildtypes (WT, n=5). While Nfatc1flox.Cd4cre (Nc1ko, n=3) CD8+ T cells do not express any functional NFATc1 protein the deletion of the distal enhancer E2 in Nfatc1-E2flox.Cd4cre (E2ko, n=3) CD8+ T cells abolishes only the expression of the inducible NFAT1/aA. Nfatc2ko (Nc2ko, n=3) CD8+ cells are deficient for NFATc2 and the Nfatc2ko.Nfatc1flox.Cd4cre (Nc1Nc2ko, n=2) CD8+ cells for both NFATc1 and NFATc2.

first: Salvador

last: Sampere Birlanga

first: Edgar

last: Serfling

first: Thorsten

last: Bischler


title: Expression landscape and circadian regulation of lncRNAs in the kidney

status: Public on Jul 08 2026

city: Lausanne

first: Leonore

last: Wigger

address: Amphipôle Building

country: Switzerland

institute: Swiss Institute of Bioinformatics


title: Diurnal regulation of Acyl-CoA synthetase 3 (ACSF3) governs rhythmic mitochondrial lysine-malonylation and daily hepatic metabolism

status: Public on Jul 07 2026

city: Nantes

first: Daniel

last: Mauvoisin

address: 8 quai Moncousu

institute: Inserm

summary: Hepatic daily rhythms are coordinated by feeding and the molecular circadian clock, ensuring metabolic homeostasis. Disrupted feeding schedules promote circadian misalignment and metabolic diseases but the underlying mechanisms remain scarce. Post-translational modifications have emerged as key regulators of circadian metabolic outputs. Here, we show that the mitochondrial enzyme Acyl-CoA synthetase family member 3 (ACSF3) oscillates in phase with different feeding schedules to drive rhythmic lysine-malonylation and coordinate daily hepatic metabolism. Hepatic Acsf3 knockdown drastically affected lysine-malonylation rhythms, decreased fasting glycemia, insulin sensitivity and AKT phosphorylation indicative of perturbed glucose homeostasis. Concomitantly, Acsf3 knockdown shifted lipid oxidation from mitochondria to peroxisomes, enhanced lipogenesis and triglyceride synthesis, while increasing diurnal autophagy. Multi-omics profiling uncovered specific lysine-malonylation targets in glycolysis, the TCA cycle, fatty-acid oxidation and autophagy. Our findings uncover hepatic ACSF3 as a pivotal molecular nexus that integrates feeding time with dynamic protein lysine-malonylation and orchestrates the diurnal rhythm of liver metabolism.

overall_design: RNA-seq was performed on liver mRNA collected across the course of a day from two groups of male C57BL/6J mice. The time-series dataset includes hepatic mRNA profiles from mice fed ad libitum with a liver-specific knockdown of Acsf3 achieved by AAV8-shRNA injection (sh-Acsf3) and their respective controls (sh-Ctl). Liver tissues were collected 4 weeks after AAV8 injection.

first: Enora

last: Le Questel


title: Type 1 interferon perturbates clonal competition by reshaping human blood development

city: New York

first: Anna

middle: S.

last: Nam

state: New York

address: Weiss Research Building, Floor 11

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medicine

summary: Inflammation perturbs evolutionary dynamics of hematopoietic stem cell (HSC) clones in clonal hematopoiesis and myeloid neoplasms. We studied HSCs, progenitors and immune cells from patients with myeloproliferative neoplasm (MPN) at baseline and following interferon-⍺ (IFN⍺) treatment, the only MPN therapy to deplete clonal stem cells. We focused on essential thrombocythemia, an informative model of early-phase neoplastic hematopoiesis. We integrated somatic genotyping, transcriptomes, immunophenotyping, and chromatin accessibility across single cells. IFN⍺ simultaneously activated HSCs into two polarized states, a lymphoid progenitor expansion associated with an anti-inflammatory state and an IFN⍺-specific inflammatory granulocytic progenitor (IGP) state derived directly from HSCs. The augmented lymphoid differentiation balanced the typical MPN-induced myeloid bias, associated with normalized blood counts. Clonal fitness upon IFN⍺ exposure was due to resistance of clonal stem cells to differentiate into IGPs. These results support a paradigm wherein inflammation perturbs clonal dynamics by HSC induction into the precipitous IGP differentiation program.

overall_design: Single-cell GoT-IM (built upon genotyping and whole transcriptomics from GoT and CITE-seq). Single-nucleus GoT-ATAC (GoT and snATAC-seq). CUT&RUN

first: Chhiring

last: Lama

first: Danielle

last: Isakov

first: Shira

last: Rosenberg

first: Miguel

last: Quijada-Álamo

first: Mirca

middle: S

last: Saurty-Seerunghen

first: Sara

last: Moein

first: Tsega-Ab

last: Abera

first: Olivia

last: Sakaguchi

first: Mansi

last: Totwani

first: Grace

last: Freed

first: Chi-Lam

last: Poon

first: Neelang

last: Parghi

first: Andrea

last: Kubas-Meyer

first: Amy

middle: X

last: Xie

first: Mohamed

last: Omar

last: Choi

first: Franco

last: Castillo-Tokumori

first: Ghaith

last: Abu-Zeinah

first: Alicia

last: Dillard

first: Nathaniel

last: Omans

first: Neville

last: Dusaj

first: Paulina

last: Chamely

first: Eleni

last: Mimitou

first: Peter

last: Smibert

first: Heidi

last: Kosiorek

first: Amylou

last: Dueck

first: Rona

last: Weinberg

first: Ronan

last: Chaligne

first: Bridget

last: Marcellino

first: Luigi

last: Marchionni

first: Sanjay

last: Patel

first: Paul

last: Simonson

first: Dan

last: Landau

first: Elvin

last: Wagenblast

first: Ronald

last: Hoffman


title: SpxA1 and SpxA2 Function as a Stoichiometry-Dependent Regulatory Rheostat Governing Virulence Gene Expression in Group A Streptococcus — CovR ChIP-exo dataset

city: Nashville

first: Anthony

last: Flores

state: TN

address: 1161 21st Avenue S, MCN D7219

institute: Vanderbilt University Medical Center

summary: Group A Streptococcus (GAS) encodes two paralogs of the Spx transcriptional regulator, SpxA1 and SpxA2, which interact with RNA polymerase to modulate virulence gene expression. SpxA2 is directly regulated by the LiaFSR three-component system in response to antimicrobial peptide stress. To define how SpxA2 influences CovR DNA occupancy genome-wide, we performed chromatin immunoprecipitation with exonuclease treatment (ChIP-exo) targeting CovR in wild-type MGAS10870 (emm3), an isogenic spxA2 deletion mutant (deltaSpxA2), and a LiaSQ146A constitutively active LiaS mutant used as a SpxA2 overexpression surrogate (SpxA2-OE). Differential binding analysis identified 439 sites with significantly altered CovR occupancy between wild-type and deltaSpxA2 (FDR < 0.05), with class-specific enrichment of CovR dimer and monomer binding motifs consistent with the two-class CovR binding model (Horstmann et al. 2023). These data contribute to a multi-omic analysis including RNA-seq, DIA proteomics, and NanoString nCounter that defines the regulatory roles of SpxA1 and SpxA2 in GAS pathogenesis.

overall_design: Wild-type MGAS10870 (emm3), isogenic deltaSpxA2, and LiaSQ146A (SpxA2-OE surrogate) strains were grown in THY medium to mid-exponential phase (OD600 ~0.45) in biological triplicate. Cells were cross-linked with 1% formaldehyde for CovR ChIP-exo using a polyclonal anti-CovR antibody (N-terminal domain). ChIP-exo performed by Cornell ChIP-exo core facility. Reads aligned to NZ_CP067090.1. Peaks called using MACS3. Differential CovR binding assessed using DiffBind v3.20 with DESeq2 (FDR < 0.05). Motif analysis performed using FIMO v5.5.9 (MEME Suite).

middle: R

first: Misu

last: Sanson

first: Luis

last: Vega


title: SpxA1 and SpxA2 Function as a Stoichiometry-Dependent Regulatory Rheostat Governing Virulence Gene Expression in Group A Streptococcus — NanoString nCounter dataset

summary: Group A Streptococcus (GAS) encodes two paralogs of the Spx transcriptional regulator, SpxA1 and SpxA2, which interact with RNA polymerase to modulate virulence gene expression. SpxA2 is directly regulated by the LiaFSR three-component system in response to antimicrobial peptide (AMP) stress. To define how SpxA1 and SpxA2 influence virulence gene expression under cell envelope stress, we performed NanoString nCounter analysis using a custom 119-probe codeset (116 endogenous targets plus 3 housekeeping probes: tufA, gyrA, guaB) in wild-type MGAS10870 (emm3) and isogenic deletion mutants (deltaSpxA1 and deltaSpxA2) under three conditions: uninduced (UI), sub-MIC bacitracin (BAC), and sub-MIC human neutrophil peptide-1 (hNP-1). Differential expression analysis identified condition- and paralog-specific changes in CovR-regulated virulence factor-encoding genes consistent with a stoichiometry-dependent regulatory model.

overall_design: NanoString nCounter data set using Custom Codeset.