title: Pax4 R192H variant impairs β cell function by disrupting β cell identity and compensatory capacity in response to metabolic stress

status: Public on May 11 2026

city: Daegu

first: Kyun Hoo

last: Kim

address: 680, Gukchaebosang-ro, Jung-gu

country: South Korea

institute: Kyungpook National University School of Medicine

summary: Type 2 diabetes is characterized by progressive β cell dysfunction, yet the mechanisms by which genetic susceptibility contributes to β cell area and function remain poorly understood. Pax4 is a transcription factor critical for β cell development, and a nonsynonymous variant resulting in an arginine-to-histidine substitution at position 192 (R192H) has been associated with increased type 2 diabetes risk and identified only in individuals of East Asian ancestry. Here, we generated Pax4 R192H knock-in (Pax4R192H/R192H) mouse and integrated metabolic phenotyping, bulk and single cell transcriptomics, and human cohort analyses to investigate how Pax4 R192H mutation increases the risk of type 2 diabetes. Homozygote knock-in mice (Pax4 R192H) exhibited normal pancreatic endocrine development but developed glucose intolerance and impaired insulin secretion when fed a high-fat diet. Bulk and single-cell RNA-seq of islets from Pax4 R192H mice fed high-fat diet revealed impaired β cell adaptation to metabolic stress characterized by enhanced endoplasmic reticulum stress and impaired β cell maturity, with upregulation of dedifferentiation and α cell markers and downregulation of β cell identity genes. Pax4 deletion in β cells resulted in similar phenotypic and transcriptomic profiles to Pax4 R192H mice. In humans, the trajectories of β cell function were evaluated over a 14-year period using biennial oral glucose tolerance tests from 4,242 participants, where Pax4 R192H carriers showed 1.4-fold accelerated decline in disposition index, with increasing body mass index further exacerbating their type 2 diabetes risk. Overall, Pax4 is essential for maintaining β cell identity and compensatory function under metabolic stress, and the R192H variant predisposes to type 2 diabetes by impairing this adaptive capacity.

overall_design: We generated a mutant mouse carrying an R200H substitution in the endogenous Pax4 allele, corresponding to the human Pax4 R192H variant. Mice homozygous for this variant are referred to as the Pax4 HH mice. We performed bulk RNA sequencing on pancreatic islets isolated from Pax4 WT and Pax4 HH mice fed an SCD (12-week-old) and 4 weeks of an HFD (16-week-old). To further validate the role of Pax4 in adult β cell, we generated inducible β cell specific Pax4 KO (Pax4-BiKO) mice by crossing Pax4(floxed/floxed) mice with Pdx1-CreERT2 mice. Tamoxifen was administered to both control and Pax4-BiKO mice at 7 to 9 weeks of age, and an HFD was introduced starting at 12 weeks of age. We performed bulk RNA sequencing on islets isolated from Pax4-BiKO and control mice following 8 weeks of HFD.

first: Jungsun

last: Park

first: Hyunsuk

last: Lee

first: Joon Ho

last: Moon

first: Jong Il

first: Hail

first: Kyong Soo


title: Pax4 R192H variant impairs β cell function by disrupting β cell identity and compensatory capacity in response to metabolic stress [scRNA-Seq]

type: Expression profiling by high throughput sequencing

overall_design: We generated a mutant mouse carrying an R200H substitution in the endogenous Pax4 allele, corresponding to the human Pax4 R192H variant. Mice homozygous for this variant are referred to as the Pax4 HH mice. we performed single-cell RNA-seq (scRNA-seq) on pancreatic islets isolated from Pax4 WT and Pax4 HH mice fed an SCD (12-week-old) and 4 weeks of an HFD (16-week-old).


title: Targeting the αvβ5 Integrin Modifies the TGF-β-Rich Tumor Microenvironment of Pancreatic Cancer

city: New York

first: Kazuki

middle: N.

last: Sugahara

state: NY

address: 1130 St. Nicholas Ave

country: USA

institute: Columbia University Vagelos College of Physicians and Surgeons

summary: Pancreatic ductal adenocarcinoma (PDAC) is notorious for its aggressive, therapy-resistant nature that is in part driven by the desmoplastic, hypo-perfused, and immunosuppressive tumor microenvironment (TME). Here, we demonstrated that the αv integrin- and neuropilin-1 (NRP-1)-dual targeting iRGD peptide reverses some of these TME features by inhibiting transforming growth factor-β (TGF-β) activation in the tumor, a process mediated by the αvβ5 integrin. In addition to PDAC epithelial cells and fibroblasts, regulatory T cells (Tregs) in PDAC tumors also expressed the αvβ5 integrin and NRP-1. The αvβ5+ Tregs potently inhibited T cell proliferation, and systemic iRGD therapy not only depleted αvβ5+ Tregs from PDAC tumors but also reduced their αvβ5- counterparts. Mechanistically, iRGD inhibited the activation of TGF-β mediated by the αvβ5-rich TME, thereby depriving Tregs of the cytokine essential for their development and maintenance. NRP-1-dependent tumor penetration was required for this effect because a traditional RGD peptide without an NRP-1-binding motif failed to inhibit TGF-β signaling or deplete Tregs in vivo. Treatment with iRGD induced a series of additional TME changes, such as improved vascular patency and perfusion, reduced stromal fibers, and increased CD8+ T cell entry into the core of the tumors. Combining iRGD with immune checkpoint blockade led to an enhanced anti-tumor effect. Together, these findings support targeting the αvβ5 integrin with affinity ligands such as iRGD as a potential approach to enhance immunotherapy efficacy against PDAC and other desmoplastic tumors with high TGF-β and αvβ5 expression.

overall_design: RNA-seq analysis was conducted on KPC78 pancreatic ductal adenocarcinoma cells (n = 3 biological replicates) to assess integrin subunit gene expression.


title: IL-16 production is a mechanism of resistance to BTK inhibitors and R-CHOP in lymphomas

city: Bellinzona

first: Alberto

middle: J

last: Arribas

address: Via Francesco Chiesa 5

country: Switzerland

institute: Institue of Oncology Research

summary: Resistance to Bruton tyrosine kinase (BTK) inhibitors remains a major clinical challenge in B-cell lymphomas and often occurs without BTK or PLCG2 mutations. Here, we investigated non-genetic mechanisms of ibrutinib resistance in marginal zone lymphoma (MZL) and their broader therapeutic implications. Chronic ibrutinib exposure generated a resistant MZL model that showed cross-resistance to BTK inhibitors and degraders, without evidence of multidrug resistance or genetic alterations. Integrated transcriptomic, epigenetic, and proteomic analyses revealed extensive reprogramming, including activation of PI3K/AKT, MAPK, and MYC pathways, repression of apoptosis and oxidative phosphorylation, and a prominent cytokine-secretory phenotype. Interleukin-16 (IL-16) emerged as a central mediator of resistance. IL-16 was transcriptionally upregulated, actively secreted, and sufficient to induce ibrutinib resistance across multiple CD9-positive models of MZL, mantle cell lymphoma, chronic lymphocytic leukemia (CLL), and activated B-cell-like diffuse large B-cell lymphoma. Serum IL-16 levels were elevated in ibrutinib-refractory CLL patients without BTK/PLCG2 mutations. Mechanistically, IL-16 engaged CD9-enriched membrane microdomains to activate PI3Kδ, thereby sustaining AKT and ERK signaling, stabilizing MYC, inducing NF-κB–dependent programs, and upregulating antiapoptotic effectors, including BFL1 (BCL2A1). Pharmacological or genetic disruption of the IL-16/CD9/PI3K axis restored sensitivity to BTK inhibitors and R-CHOP and abrogated IL-16-induced signaling in primary CLL samples. In conclusion, an IL-16/CD9-driven, epigenetically regulated survival pathway represents one possible mechanism of resistance to BTK inhibitors and chemoimmunotherapy, supporting therapeutic targeting of this axis in refractory B-cell lymphomas.

overall_design: RNA-seq profiling of VL51 parental and ibrutinib-resistant cells. Gene expression profiles of VL51 cells were studied upon stimukation with IL-16, a CD9-binding peptide (CD9-BP), the combination of both, or PBS (as control) for 24 hr.

first: Cascione

last: Luciano

first: Bertoni

last: Francesco


title: Divergent signaling profiles in mTOR gain-of-function Smith-Kingsmore syndrome and TSC2 deficiency

city: GAINESVILLE

first: Andrew

middle: C

last: Liu

state: FL

address: 1345 CENTER DR M548

department: Department of Physiology and Aging

institute: University of Florida

summary: Smith-Kingsmore syndrome (SKS) is a rare neurodevelopmental disorder caused by gain-of-function mutations in MTOR, yet whether these mutations phenocopy TSC2 loss or establish a distinct signaling state remains unclear. Using quantitative proteomics, phosphoproteomics, and transcriptomics in isogenic cell models of SKS (MTORΔ4aa), TSC2 loss (TSC2–/–), and wild-type controls under glucose depletion and refeeding, we find that MTORΔ4aa and TSC2–/– cells occupy fundamentally distinct regulatory states. TSC2–/– cells exhibit broad anabolic remodeling and a transcriptional program dominated by NF-κB- and STAT-driven inflammatory responses. MTORΔ4aa cells instead display enrichment of nuclear and RNA processing programs, E2F/MYC-driven transcription, and a constrained proteomic dynamic range across nutrient states. Phosphoproteomic analysis of MTORΔ4aa reveals rerouting of nutrient-responsive signaling toward MAPK/ERK- and Ca2+/CaMK-dependent pathways with limited canonical mTORC1/S6K1 engagement. These findings establish SKS as a signaling rewiring disorder distinct from classical mTORC1 hyperactivation, with implications for therapeutic targeting.

overall_design: RNA-seq profiling of wild-type, MTOR(ΔR1480-C1483/ΔR1480-C1483), and TSC2 deficiency U2OS cells after 2 hours of glucose depletion.

first: Curtis

middle: R

last: Carlson

first: Yang

last: Shen

first: Hongzhi

last: He

first: Erwin

middle: K

last: Gudenschwager

first: Chunya

last: Hou

first: Junfeng

last: Ma

first: Joanna

last: Chiu


title: Fibroblast-derived CCL2 function in skin infection

city: San Diego

first: Tatsuya

last: Dokoshi

state: California

address: 9500 Gilman

department: Department of Dermatology

institute: Univeristy of California, San Diego

summary: This dataset includes bulk RNA-seq, single-cell RNA-seq, and spatial transcriptomic analyses performed to investigate the role of fibroblast-derived CCL2 in cutaneous host defense against Staphylococcus aureus infection. Samples include control and infected mouse skin, as well as fibroblast-specific Ccl2-deficient skin, and were used to define transcriptional, cellular, and spatial changes associated with impaired CCL2 signaling during skin infection.

overall_design: Bulk RNA-seq of MHS macrophagecellline treated with fibroblast supernatant, and single-cell RNA-seq, and spatial transcriptomic analyses of mouse back skin were performed to investigate the role of fibroblast-derived CCL2 during Staphylococcus aureus skin infection. Samples included uninfected and infected control mice, as well as fibroblast-specific Ccl2-deficient mice.

first: Richard

middle: L

last: Gallo


title: The effects of adiponectin knockout on hepatic gene expression in male and female C57BL/6NCrl mice fed ad libitum or undergoing caloric restriction

city: Edinburgh

first: William

middle: P

last: Cawthorn

address: 47 Little France Crescent

department: University/BHF Centre for Cardiovascular Science

country: United Kingdom

institute: The University of Edinburgh

summary: To understand the role of adiponectin under caloric restriction (CR) in the liver, we collected liver samples from male and female adiponectin KO mice and wild-type (WT) mice, on a C57BL/6NCrl background, that were fed ad libitum (AL) or underwent 30% caloric restriction (CR; receiving 70% of daily AL intake) from 9-13 weeks of age. Livers were then analysed by bulk RNA-seq.

overall_design:
The experiment included five AL-fed WT/females, six AL-fed KO/females, six CR WT/females, six CR KO/females, six AL WT/males, five AL KO/males, five CR WT/males, and five CR KO/males.
Mice were fed AL or 30% CR from 9-13 weeks of age. To minimise effects resulting from differences in fasting duration, mice in both the AL and CR groups were fasted for ~8 hours prior to necropsy and liver sampling. The raw data from WT mice has been deposited in GSE230402; therefore, this GEO Series includes KO raw data only but shows the normalized count data for both KO and WT.

first: Yoshiko

middle: M

last: Ikushima

first: Hiroshi

last: Kobayashi

first: Kuan-Chan

last: Chen


title: Single-nucleus profiling reveals age-associated remodeling opposed by parity in the postmenopausal human ovary

city: Novato

first: Simon

last: Melov

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

summary: The postmenopausal ovary is commonly viewed as a passive organ, and its biology and cell composition remain incompletely characterized. Here, we generated a single-nucleus atlas of the aging postmenopausal human ovary comprising 439,011 nuclei across 64 ovarian samples from 28 donors. We resolved 37 fine cell states, revealing extensive stromal, vascular, and immune heterogeneity in the postmenopausal ovary. Aging was associated with stromal stress-state expansion, vascular and immune depletion, and enrichment of steroidogenic programs consistent with ovarian androgenization. Several major age-associated compositional shifts were supported in an independent GTEx ovary bulk RNA-seq cohort. Notably, the number of live births broadly opposed age-associated transcriptional and compositional remodeling. Together, our findings show that the postmenopausal ovary remains an actively remodeled aging tissue and that reproductive history leaves durable molecular and cellular imprints on ovarian aging.

overall_design: De-identified human ovarian tissue was obtained from donors through the Northwestern University Reproductive Tissue Library (NU-RTL) under Institutional Review Board-approved protocols (STU00215770 and STU00215938). Ovarian tissue was collected from women aged 50–84 years undergoing bilateral salpingo-oophorectomy and/or total laparoscopic hysterectomy for benign gynecologic conditions, endometrial malignancy or premalignancy, or cervical premalignancy. Only cases without ovarian neoplasia were included, and donors with endometriosis were excluded. Upon collection, ovaries were sectioned into 3–5 mm thick cross-sections perpendicular to the long axis of the ovary. In the absence of significant gross pathology, as assessed by a certified gynecologic pathologist, up to two cross-sections were designated for research and transported on ice in ORIGIO Handling IVF medium (CooperSurgical, Trumbull, CT, USA). One half of each cross-section was subdivided in a 60 mm glass Petri dish into 20–30 mg tissue pieces containing both cortex and medulla. Tissue pieces were washed in PBS, flash-frozen in 1.5 mL tubes, shipped overnight to the Buck Institute for Research on Aging on dry ice, and stored at −80°C upon arrival. Cryopreserved ovarian tissue pieces containing both cortex and medulla were thawed and analyzed using snucRNA-seq with the 10x Genomics Fixed RNA Profiling kit.

first: Josef

last: Byrne

first: Nicolas

last: Martin


title: Kava and DHM inhibit chronic hexavalent chromium exposure-induced cell malignant transformation through down-regulating RNA splicing factor SNRPA1 expression

city: Stony Brook

first: Chengfeng

last: Yang

address: 101 Nicolls Road

department: Pathology

institute: Stony Brook University

summary: Hexavalent chromium [Cr(VI)] is a common occupational and environmental toxicant and an established carcinogen causing lung cancer in humans. The mechanism through which Cr(VI) exposure causes lung cancer remains to be clearly defined. No effective strategies are currently available to prevent lung cancer resulting from chronic Cr(VI) exposure. Kava is traditionally consumed by south Pacific islanders to reduce anxiety. Epidemiology and experimental studies suggest that Kava has anticancer potential and may be used as a preventive agent to reduce the risk of various cancers including lung cancer. The purpose of this study is to determine the effect of Kava and its active component dihydromethysticin (DHM) on chronic Cr(VI) exposure-induced cell malignant transformation and the underlying mechanism. The study was performed by pre-treating immortalized but non-tumorigenic human bronchial epithelial cells (BEAS-2B) with Kava (25 µg/ml) or DHM (10 µM) followed by exposing cells to 0.25 µM of Cr(VI) (K2Cr2O7) for 20 weeks to determine the impact of Kava or DHM on chronic Cr(VI) exposure-induced cell transformation, cancer stem cell (CSC)-like property and tumorigenesis. The extent of cell transformation was evaluated by soft agar colony formation assay, Western blot analysis of cancer stemness marker expression levels and nude mouse xenograft tumorigenesis assay. It was found that Kava or DHM pre-treatment significantly reduces Cr(VI)-induced cell transformation, CSC-like property and tumorigenesis. Mechanistically, it was determined that Kava or DHM impairs Cr(VI)-induced cell transformation by down-regulating RNA splicing factor small nuclear ribonucleoprotein polypeptide A' (SNRPA1) expression to reduce the protooncogene, cancer stemness marker and driver c-MYC expression. It was further determined that DHM/SNRPA1 regulate c-MYC expression through affecting c-MYC protein stability. It was concluded that Kava or DHM inhibits Cr(VI)-induced cell transformation, CSC-like property and tumorigenesis by down-regulating RNA splicing factor SNRPA1 expression to increase the protooncogene c-MYC protein degradation.

overall_design: RNA-seq profiling of BEAS-2B cells that were continuously exposed to vehicle control plus Cr(VI) [BEAS-2B-Control-Cr(VI)] or Kava plus Cr(VI) [BEAS-2B-Kava-Cr(VI)]; and BEAS-2B cells that  were continuously exposed to vehicle control plus Cr(VI) and trasnfected with control siRNA [BEAS-2B-Cpntrol-Cr(VI)-Control siRNA] or SNRPA1 targeting siRNA [BEAS-2B-Control-Cr(VI)-SNRPA1 siRNA]

first: Zhishan

last: Wang


title: D-SPIN constructs regulatory network models from scRNA-seq that reveal organizing principles of perturbation response

first: Jialong

last: Jiang

address: 1230 York Avenue, Center for Studies in Physics and Biology, The Rockefeller University

institute: The Rockefeller University

summary: Gene regulatory networks modulate the expression of the genome in response to signals and environmental conditions. Reconstructions of such networks can reveal the control principles cells use to maintain homeostasis and execute cell-state transitions. Here, we introduce a computational framework, D-SPIN, that infers mechanistically interpretable and generative models of gene regulatory networks from single-cell mRNA-seq datasets collected across thousands of perturbation conditions. The models explain how perturbations modulate cell state proportions by reconfiguring underlying regulatory interactions. Using large Perturb-seq and drug-response datasets, D-SPIN models reveal key regulators of cell-fate decisions and the coordination of distant cellular pathways in response to gene knockdowns and drug treatments, elucidate how combinations of immunomodulatory drugs induce combinatorial cell states through additive recruitment of gene expression programs, and simulate shifts in immune cell population structures across unobserved drug dosage combinations. D-SPIN provides a computational framework for revealing principles of cellular information processing and physiological control.

overall_design: High-throughput small molecule drug profiling of human PBMCs during T-cell-mediated immune activation, profiled by multiplexed single-cell RNA sequencing.

first: Sisi

first: Tiffany

last: Tsou

first: Christopher

middle: S

last: McGinnis

first: Jong

middle: H

last: Park

first: Jost

last: Vielmetter

first: Eric

middle: D

last: Chow

first: Zev

last: Gartner

first: Matt

last: Thomson


title: Transcription factor TFEB antagonizes cardiac hypertrophy and failure by enhancing lysosomal capacity and mitochondrial function

city: Dallas

first: Joseph

middle: A.

last: Hill

state: TX

address: 6000 Harry Hines Blvd

department: Cardiology

institute: UT Southwestern Medical Center

summary: Pathological cardiac remodeling and increased afterload-driven demand contribute to heart failure. TFEB is a key regulator of lysosomal genes and mitochondrial function and is activated in response to external stress. To elucidate TFEB-dependent transcriptional programs under hypertrophic stress, we profiled left ventricular transcriptomes from a cardiomyocyte-specific TFEB knockout mouse model subjected to transverse aortic constriction (TAC) or sham surgery, with wild-type littermate controls, followed by downstream multi-omics integration.

overall_design: Bulk RNA-seq was performed on mouse left ventricular tissue from cardiomyocyte-specific TFEB knockout mice and control mice subjected to sham surgery or transverse aortic constriction (TAC), with four biological replicates per condition.

first: Daou

last: Daniel

first: Urquiza-Zurich

last: Sebastián

first: Hill

middle: A

last: Joseph

first: Gillette

middle: G

last: Thomas


title: Particle Reprogramming of the TLR–Ferroptosis Axis and Immunometabolic Pathways Inhibits Myeloid Suppression to Improve Checkpoint Blockade in Prostate Cancer [RNA-Seq Hi-Myc mice]

first: Genomics-core-facility

last: WCM

address: 1300 York Ave.

institute: Weill Cornell Medicine

summary: The limited efficacy of immunotherapies (IT) in advanced prostate cancer (PCa) stems from a tumor microenvironment where myeloid-driven immune suppression, stromal remodeling, and metabolic barriers converge to limit antitumor immunity. We highlight the immuno-metabolic properties of an ultrasmall PSMA-targeting silica particle therapy as a first-in-class strategy to reprogram the Toll-like receptor (TLR)–ferroptosis axis in Myc-driven PCa. As single agents, these particles suppress lipid and steroid biosynthesis, disrupt lipid peroxidation control, and impair nutrient flux, sensitizing tumors to ferroptosis. Coordinated redox remodeling, stromal reprogramming, and innate immune activation reverse myeloid suppression and promote CD8⁺ T cell infiltration. When combined with CSF-1R inhibition and/or immune checkpoint blockade, particles suppress tumor growth, extend survival beyond 100 days, and achieve up to 50% complete remissions in Myc-overexpressing models. These findings position TLR–ferroptosis axis remodeling as a mechanistic blueprint for rational, particle-driven ITs with broad translational potential in PCa and other immunologically refractory malignancies.

overall_design: RNA-seq profiling of tumors from Hi-Myc mice treated with saline, C' dots, ICB or Dual Tx

first: Nabil

last: Siddiqui

first: Michelle

last: Bradbury


title: Particle Reprogramming of the TLR–Ferroptosis Axis and Immunometabolic Pathways Inhibits Myeloid Suppression to Improve Checkpoint Blockade in Prostate Cancer

overall_design: RNA-seq profiling of Myc-tumors from FVB/N mice treated with saline, Dual Tx or Triple Tx.


title: RegVelo: gene-regulatory-informed dynamics of single cells

city: Wuhan City

first: Zhiyuan

last: Hu

address: No. 115 East Lake Road (Donghu Road), Wuchang District

department: Medical Research Institute

country: China

institute: Wuhan University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: RNA velocity has emerged as a popular approach for modeling cellular change along the phenotypic landscape but routinely omits regulatory interactions between genes. Conversely, methods that infer gene regulatory networks (GRNs) do not consider the dynamically changing nature of biological systems. To integrate these two currently disconnected fields, we present RegVelo, an end-to-end dynamic, interpretable, and actionable deep learning model that learns a joint model of splicing kinetics and gene regulatory relationships and allows us to perform in silico perturbation predictions. When applied to datasets of the cell cycle, human hematopoiesis, and murine pancreatic endocrinogenesis, RegVelo demonstrates superior predictive power for interactions and perturbation simulations, for example, compared to methods that focus solely on dynamics or GRN inference. To leverage RegVelo’s full potential, we studied the dynamics of zebrafish neural crest development and underlying regulatory mechanisms using our Smart-seq3 dataset and shared gene expression and chromatin accessibility measurements. Using RegVelo's in silico perturbation predictions, validated by CRISPR/Cas9-mediated knockout and single-cell Perturb-seq, we establish transcription factor tfec as an early driver and elf1 as a novel regulator of pigment cell fate and propose a gene-regulatory circuit involving tfec and elf1 interactions via the toggle-switch model.

overall_design: Biotin‑ChIP‑seq for Sox10 was performed in Danio rerio embryos at the ~10, 15, 21‑somite stage using an Avi‑tagged Sox10 line with BirA mRNA injection, with two ChIP biological replicates and two sample-matching input controls. Cut&RUN for Elf1 was performed in Danio rerio embryos at the 16 somite stage with two technical replicates and two IgG controls.

first: Weixu

last: Wang

first: Philipp

last: Weiler

first: Sarah

last: Mayes

first: Marius

last: Lange

first: Daniel

last: Fountain

first: Julianna

middle: O

last: Haug

first: Jingye

first: Zhengyuan

last: Xue

first: Tatjana

last: Sauka-Spengler

first: Fabian

last: Theis


title: The transcriptome and miRNA expression profiles of SOX10-knockdown uveal melanoma

city: Tampere

first: Xin

last: Lai

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere University

type: Non-coding RNA profiling by high throughput sequencing

summary: SOX10 is essential for melanocyte development and maintenance and plays a critical role in uveal melanoma (UM) initiation and progression. While SOX10’s transcriptional regulation of protein-coding genes is well characterized, its role on microRNA (miRNA) regulatory landscape in UM remains unexplored. Here, we employed network-based modeling to systematically characterize miRNA regulatory functions following SOX10 depletion in UM. First, we profiled mRNA and miRNA expression levels in SOX10 wild-type and knockdown UM cells. Then, we integrated the transcriptomic data, a UM network, and a Bayesian model to quantify miRNAs’ regulatory activities and identify key miRNAs. Subsequently, we employed pathway enrichment analysis combined with literature mining to elucidate the functional roles of identified miRNAs through their target genes and associated signaling pathways in UM. We identified 17 miRNAs that show significant changes in regulatory activities following SOX10 knockdown in UM cells. These miRNAs regulate the expression of genes involved in cancer hallmark pathways, including cell cycle progression, mTORC1 signaling, and fatty acid metabolism. Notably, miR-34a, miR-25, miR-186, and miR-211 have tumor-suppressive potential by targeting genes involved in UM progression and metastasis. Our computational analysis suggests that SOX10 depletion in UM reshapes the miRNA regulatory landscape in a manner potentially consistent with tumor-suppressive activity, requiring experimental validation.

overall_design: We used two UM cell lines (92.1 and Mel270) to investigate gene expression profiles (including mRNA and miRNA) under two experimental conditions: SOX10 knockdown (SOX10-KD) and control. The experimental design included four biological replicates for each cell line under each condition, resulting in a total of 16 samples.


title: 6 week old KPPC mice treated with vehicle or C-E-G for 14 days

city: St Louis

first: Kian-Huat

last: Lim

state: MO

address: 4566 Scott Avenue

department: Oncology

institute: Washington University Medical school

summary: We pooled three KPPC mice tumors into one sample for vehicle (n=3) or C-E-G  (n=3), prepared single cell suspension and performed  10X genomics scRNASeq to assess transcriptomic changes all cell populations

overall_design: scRNAseq analysis of KPPC tumors treated with vehicle and C-E-G

first: Vikas

last: Somani


title: 5-hydroxymethylcytosine deposition mediates Polycomb Repressive Complex 2 function in MYCN-amplified neuroblastoma [nano-seal, 5hmC]

status: Public on May 12 2026

city: Chicago

first: Mark

last: Applebaum

state: IL

address: 900 E 57th St

department: Pediatrics, Section of Hematology/Oncology

institute: University of Chicago

summary: MYCN-amplification is a strong predictor of poor prognosis in neuroblastoma, an embryonal malignancy that accounts for 15% of pediatric cancer deaths. Here, we found that MYCN-amplified neuroblastoma tumors have increased 5-hydroxymethylcytosine (5-hmC) deposition on Polycomb Repressive Complex 2 (PRC2) target genes. 5-hmC and H3K27me3, a catalytic product of PRC2, directly co-localize at the nucleosomal level in MYCN-amplified neuroblastoma. Genes with co-localization of 5-hmC/H3K27me3 are involved in development related pathways and are transcriptionally repressed in MYCN-amplified neuroblastoma. Chemical and genetic inhibition of 5-hmC deposition results in a loss of H3K27me3 deposition on protein-coding genes. Furthermore, 5-hmC deposition predisposes H3K27me3 marked genes to transcriptional activation upon PRC2 inhibition with tazemetostat. Low expression of genes marked by 5-hmC/H3K27me3 is associated with poor clinical outcome. Our results suggest that 5-hmC/H3K27me3 co-operate to repress mediators of development highlighting a novel link between DNA modifications and chromatin modifications with potential therapeutic implications in MYCN-amplified neuroblastoma.

overall_design: CUT&RUN, nano-HMC-seal, and RNA-Seq performed under various conditions in neuroblastoma cell lines

first: Mohansrinivas

last: Chennakesavalu

first: Gabriel L.

last: Lopez

first: Varsha

last: Gupta

first: Kelley

last: Moore

first: Yuxing

first: Josie

last: Majowka

first: Sahil

last: Veeravalli

first: Ryan

last: Borchert

first: Monica

last: Pomaville

first: Alexandre

last: Chlenski

first: Chuan

last: He

first: Andrea

last: Piunti

first: Mark A.


title: Targeting PRMT9 Overcomes Venetoclax Resistance In AML By Modulation Splicing And Inhibiting Translation

city: Monrovia

first: Ling

last: Li

address: 1218 S 5TH AVE, MONROVIA

department: Hem Malignancies Trans Sci

institute: City of Hope National Medical Center

summary: Arginine methylation catalyzed by protein arginine methyltransferases (PRMTs) is critical for promoting acute myeloid leukemia (AML) growth. But its role in BCL2 inhibitor venetoclax resistance (VEN-R) remains elusive. Here, through a loss-of-function screen in VEN-R primary AML patient-derived xenograft (PDX) cells and cell lines, we identified PRMT9 as a critical regulator to promote VEN resistance. Among PRMTs, PRMT9 is preferentially overexpressed in VEN-R AML cell lines and samples, and its inhibition re-sensitized the cells to VEN treatment. We further report synergy of a PRMT9 inhibitor LD2 with VEN in eradicating resistant AML in preclinical models. Mechanistically, PRMT9 ablation in VEN-R cells disrupted RNA splicing by inducing exon skipping of key regulators such as ALG13, eventually leading to downregulation of ATP-binding transporter encoded by ABCC1 responsible for VEN efflux. Concurrently, PRMT9 inhibition suppressed protein translation, resulting in the degradation of short-lived oncoproteins, including MCL1. These findings establish a critical role for PRMT9-mediated arginine methylation in promoting VEN-R and highlight the potency of combining PRMT9 inhibition with VEN as a novel therapeutic strategy against AML.

overall_design: Molm13 VEN-R cells with Ctrl or Prmt9-KD administered by Dox induction were collected for analysis.

first: Li

last: Yang

first: He

last: Xin

first: Dong

last: Haojie

first: Zhang

last: Lei

first: Che

last: Yuan

first: Wang

first: Yadav

last: Umesh Yadav

first: Liu

last: Meng

last: Lianjun

first: Ge

last: Shuaishuai

first: Wu

last: Guohua

first: Fu

last: Yu-Hsuan

first: Chen

last: Wei

first: Kuo

last: Ya-huei

last: Liang

first: Marcucci

last: Guido

last: Shaoyuan

last: Ling


title: Putative SET Domain-Containing Proteins Play Significant Roles in Regulating Sporulation, and Pathogenicity in Phytophthora capsici

city: Dandzhou

first: Justice

last: Norvienyeku

state: Hainan

address: Dandzou-Campus

department: School of Tropical Agriculture and Forestry

institute: Hainan University

summary: RNA-sequencing based comparative assessment of the expression profile of genes coding for SET domain-containing proteins during P. capsici's interactions with different host plants

overall_design: Total RNA was extracted from selected tissues using a universal RNA extraction kit, ensuring minimal degradation and contamination. We then performed quality assessment of the isolated RNA using gel electrophorensis and bioanalyzer to confirm integrity and purity.

first: Bingting

last: Lai

first: Hengyuan

last: Guo


title: Essential Role of Apoptosis in Immature B Cells for Preventing Autoimmune Disease in Mice

first: Chengsong

last: Zhu

address: 5323 Harry Hines Blvd

department: Immunology

summary: Autoreactive B cells are generated through V(D)J recombination during development and somatic hypermutation during immune responses. Clonal deletion via programmed cell death  is a key mechanism to eliminate these cells, as evidenced by autoimmune disease development in mice with defective B cell apoptosis. However, the specific stages of B cell development or activation where autoreactive B cells are deleted to prevent autoimmune diseases remain unclear. Here, we directed anti-apoptotic Bcl-2 expression to early B cell progenitors in the bone marrow and to activated B cells.Our findings revealed that Bcl-2 expression during B cell development expanded peripheral transitional, anergic and follicular, but not bone marrow immature B cells. Follicular and anergic B cell accumulation were partly due to increased production.Notably, Bcl-2 expression during development, but not during activation, caused an antibody-dependent autoimmune disease with a specific autoantibody profile. Thus, peripheral transitional B cells are particularly sensitive to apoptosis and disrupting immature B cell apoptosis allows autoreactive clones derived from V(D)J recombination to enter mature and activated B cell repertoires to promote autoimmune disease.

sample_organism:
Mus musculus
blank sample

overall_design: Serum from 40-weeks-old female mice of different genotypes (Aicda-Cre x Rosa26-LSL-Bcl2, n=4 replicates; Mb1-Cre x Rosa26-LSL-Bcl2, n=4 replicates) or age and sex-matched control mice (n=3 replicates) was analyzed by an autoantigen array to determine the IgG and IgM autoantibody profiles. PBS was included as additional negative control.

first: Christian

middle: T

last: Mayer


title: Regulation of endothelial cell chromatin availability and transcription factor activity in arterial-venous specification - Murine Retinal EC scATACseq

city: Charlottesville

first: Nicholas

middle: W

last: Chavkin

address: 415 Lane Road

institute: University of Virginia

summary: Arterial-venous specification of endothelial cells during vascular development requires coordination between intracellular signaling, cell cycle state, and transcription factor activity. However, the intrinsic regulatory mechanisms that govern these processes are poorly understood. To investigate this, we assessed endothelial chromatin accessibility during vascular development. Murine postnatal day (P)6 and P15 retinal endothelial cells were analyzed by single cell Assay for Transposase Accessible Chromatin (ATAC) sequencing, revealing heterogeneous accessibility of chromatin across an arterial-venous continuum. Enhancer regulatory network analysis predicted transcription factors with high activity, including Sox17. Transcription factors with differential arterial-venous activity showed dual activator and repressor functions, with many regulated by cell cycle-dependent chromatin accessibility. We validated SOX17 function in human endothelial cells, identifying that SOX17 inhibits proliferation and promotes arterial gene expression. Our findings suggest that dual roles of key endothelial transcription factors are regulated by chromatin accessibility in a cell cycle- and subtype-specific manner to control arterial-venous specification.

overall_design: Mice at ages P6 and P15 were euthanized according to approved protocols, and retinal tissue was immediately harvested from isolated eyes by microdissection removal of cornea, adventitial, and vitreous body tissue. Retinal tissue was then enzymatically digested in a digestion solution containing 1.0 mg/mL Collagenase Type II and 10% FBS in DMEM for 20 min at 37°C. Digested cells were washed and resuspended in staining buffer containing 10% FBS, 20 mM HEPES, and 1.0 mg/mL D-Glucose in HBSS with fluorescently-conjugated anti-CD31 and anti-CD45 antibodies. Immuno-stained cells were washed, resuspended in FACS buffer containing 1% FBS in PBS, stained with Propidium Iodide (PI), and sorted by FACS using a FACSMelody sorter (BD Biosciences) to isolate the PI-CD31+CD45- population as endothelial cells. Isolated endothelial cells from P6 and P15 murine retinal tissue were pelleted at 300 rcf for 5 min and resuspended in 50 µL Cell Buffer containing 0.04% BSA in PBS. Cells were re-pelleted and resuspended in 50 µL Lysis Buffer containing 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40 Substitute, 0.01% Digitonin, and 1% BSA in Nuclease-free water, then mixed by pipetting and incubated on ice for 5 min. Then, 50 µL chilled Wash Buffer containing 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, and 1% BSA in Nuclease-free water was added, and extracted nuclei were pelleted by centrifugation at 500 rcf for 5 min. Supernatant was removed and 45 µL chilled Diluted Nuclei Buffer containing a 1x dilution of Nuclei Buffer 20x (from 10x Chromium Next GEM Single Cell ATAC Library and Gel Bead Kit) in Nuclease-free Water was added. Nuclei were pelleted, supernatant was removed, and 7 µL chilled Diluted Nuclei Buffer was added. Nuclei were immediate used in the Chromium Next GEM Single Cell ATAC Kit v1.1 protocol with subsequent quality control and sequencing according to validated standard operating procedures established by the University of Virginia Genome Analysis and Technology Core, RRID:SCR_018883, using a 10x Chromium Controller and Illumina NextSeq 2000.

first: Chavkin

last: Nicholas

first: Hirschi

last: Karen


title: Cancer stem cells are hyper-responsive sensors of tumor microenvironment in orchestrating metastasis dynamics

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

summary: Cancer stem cells (CSCs) are key drivers of metastasis and therapy resistance but have been challenging to visualize and study in situ. Using a fluorescent CSC reporter, we observed very different population  dynamics for CSCs and nonCSCs during metastatic lung colonization in breast cancer models. CSC  expansive self-renewal drives early lesion formation before switching to a maintenance mode of balanced self-renewal and differentiation, whereupon nonCSC proliferation takes over as the main  driver of metastatic expansion. Mechanistic analyses showed that CSCs are hyper-responsive to  microenvironmental cues such as cell crowding and nutrient availability, suggesting a novel role for CSCs  as sensors and early responders to fluctuating local conditions in the tumor. Most inputs converge on YAP/TAZ/TEAD, with heightened CSC sensitivity and response supported by elevated receptor  expression and increased chromatin accessibility around enhancers with TEAD binding sites. Targeting inputs to the YAP/TAZ/TEAD node reversed chemotherapy-induced enrichment of CSCs in lung metastases.

overall_design: Three MDAMB231 human breast cancer sublines were transduced with a fluorescent cancer stem cell reporter (SORE6>dsmCherry). The cells were cultured to approximately 70% confluency and sorted via FACS into SORE6+ (CSCs) and SORE6- (non-CSCs) subpopulations for RNA preparation.

first: Binwu

last: Tang

first: Maxwell

last: Lee

first: Lalage

last: Wakefield


overall_design: RNA-seq profiling of  cancer stem cell (CSC) and more differentiated tumor cells (nonCSCs) recovered from pooled (n=6-8) metastasis-bearing lungs of nude mice 4-5 weeks after injection of MDAMB231-LM2 human breast cancer cells via the tail vein.   MDAMB231-LM2 cells had been transduced with a fluorescent CSC reporter (SORE6>dsmCherry) to allow FACS sorting of recovered cells into CSC and nonCSC subpopulations.


title: Estrogen deprivation alters gingival and dentoalveolar complex transcriptomes during ligature-induced periodontitis in mice

status: Public on May 20 2026

city: Somerville

last: Yakar

state: Massachusetts

address: 100 Chestnut St

institute: ADA Forsyth

summary: Bulk RNA sequencing was performed to investigate estrogen-responsive transcriptomic changes during ligature-induced periodontitis in female C57BL/6J mice. Gingiva and dentoalveolar complex tissues were collected from sham-operated, ovariectomized, and estrogen-replaced ovariectomized mice following ligature-induced periodontitis. Differential expression and pathway analyses were used to identify estrogen-responsive changes in repair-, stromal-, and immune-related gene programs

overall_design: Female C57BL/6J mice underwent sham surgery, ovariectomy, or ovariectomy followed by estradiol replacement. All animals underwent ligature-induced periodontitis. Gingiva and dentoalveolar complex tissues were collected for bulk RNA sequencing. The study included two tissue types (gingiva and dentoalveolar complex), three experimental groups (Sham, OVX, OVX+E2), and four biological replicates per group for each tissue.

first: Hatice

last: Hasturk

first: Alpdogan

last: Kantarci


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

overall_design: Refer to individual Series


title: A stable subgenomic reporter coronavirus enables transcriptional profiling of bystander cells.

status: Public on May 19 2026

city: London

first: James

last: Boot

address: 1 Midland Road

department: Bioinformatics and Biostatistics

institute: Francis Crick Institute

summary: Insertion of fluorescent reporter genes into viral genomes is a powerful tool for monitoring infection. In coronaviruses, this is commonly achieved by replacing accessory open reading frames, thereby deleting endogenous gene functions. An alternative strategy is to manipulate viral transcription by inserting copies of the viral transcription regulatory sequence (TRS) which drive viral subgenomic RNA transcription. However, coronavirus transcription is tightly regulated, and these modifications frequently disrupt native subgenomic RNA synthesis and attenuate viral growth. Here, we report a reporter coronavirus that overcomes these limitations. Using human coronavirus (HCoV)-OC43 as a model system, we inserted an mNeonGreen reporter between the Spike and ORF5 coding regions, engineering the TRS and surrounding sequence to minimise off-target effects to transcription. This virus is genetically stable, with wildtype growth kinetics and unaltered subgenomic RNA transcriptional ratios. We developed a flexible reverse genetics system, which allows rapid cloning and virus recover, supported by optimised HCoV-OC43 culture conditions, which support high titre stock growth, and validated analytical reagents. Our reporter virus enabled sensitive detection and isolation of infected cells, facilitating transcriptomic analyses that distinguish host responses in infected and bystander populations. Together, these tools expand the experimental utility of HCoV-OC43, an important seasonal respiratory pathogen and low containment model for betacoronavirus biology.

overall_design: A549 cells were infected with HCoV-OC43-dNS2-mNG, HCoV-OC43-ORF4.5-mNG, or WT virus. A549 cells are a human lung carcinoma cell line which can sense and respond to viral infection, and support productive HCoV-OC43 replication. HCoV-OC43-dNS2-mNG and HCoV-OC43-ORF4.5-mNG each contain a fluorescent GFP reporter. After 24 hours, RNA was extracted from the whole cell population (bulk) for all 3 virus', for the virus' containing a fluorescent GFP reporter, cells underwent live-cell fluorescence-activated cell sorting, to isolate infected and bystander cells. Bulk RNAseq of these samples allows for the assessment of host transcriptomic responses as well as quantification of viral RNA species such as genomic and sub-genomic RNAs.

first: Ciaran

last: Gilbride

first: Joe

last: Hemsley-Taylor

first: Catarina

last: Nunes

first: Rebecca

last: Penn

first: Nima

last: Pieris

first: Rupa

last: Tripathy

first: Ziyi

first: Matthew

last: Hutchinson

first: Rachel

last: Ulferts

first: Richard

last: Mitter

first: Molly

last: Strom

first: Nuno

middle: B

last: Santos

first: David

last: Bauer

first: Harriet

middle: V

last: Mears


title: Quantitative RNA pseudouridine landscape reveals dynamic modification patterns and evolutionary conservation across bacterial species

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

summary: Pseudouridine (Ψ) modifications play crucial roles in RNA regulation, yet their distribution and functional significance in bacteria remain largely unexplored compared to eukaryotic systems. Here, we present the first comprehensive transcriptome-wide mapping of Ψ modifications across five diverse bacterial species (Klebsiella pneumoniae, Escherichia coli, Bacillus cereus, Pseudomonas aeruginosa, Pseudomonas syringae) using bisulfte-induced deletion sequencing at single-base resolution. Ψ modifications exhibit enriched distribution in coding sequences and notable conservation across orthologous genes involved in central metabolism. Comparative analysis revealed evolutionarily conserved modification patterns in operons, such as the atp operon, and growth phase-dependent dynamics, particularly elevated modification levels in transfer RNA T-arms and transfer-messenger RNAs under stress conditions. We uncovered that Ψ modifications modulate mRNA translation in Pseudomonas syringae under nutrition-limited condition and enhance interactions with the RNA chaperone Hfq in Pseudomonas aeruginosa under stationary growth phase. We found local RNA architecture significantly influences modification levels, with highly modified sites sharing distinct structural features reminiscent of different type of RNA. To facilitate broader studies, we developed an integrated deep learning framework combining convolutional neural networks with transformer architecture to effectively capture both sequence patterns and RNA secondary structural features, enabling accurate prediction of Ψ modification sites across bacterial transcriptomes. Overall, our study provides fundamental insights into bacterial RNA Ψ modification landscapes and establishes a foundation for future mechanistic studies.

sample_organism: Pseudomonas savastanoi pv. phaseolicola 1448A

overall_design: Bisulfte-induced deletion sequencing at single-base resolution

last: Deng

first: Letong

last: XU


title: The effect of human TCIM expression on spinal cord regeneration in zebrafish.

city: St. Louis

first: Mayssa

last: Mokalled

email: mmokalled@wustl.edu, vishnu@wustl.edu, saini@wustl.edu, mmokalledlab@gmail.com

address: 4523 Clayton Ave, CB 8103

department: Developmental Biology

institute: Washington University in St. Louis

summary: Immune cells elicit a continuum of transcriptional and functional states after spinal cord injury (SCI). In mammals, inefficient debris clearance and chronic inflammation impede recovery and overshadow pro-regenerative immune functions. We found that, unlike mammals, zebrafish SCI elicits transient immune activation and efficient debris clearance, without causing chronic inflammation. Single-cell transcriptomics and inducible genetic ablation showed zebrafish macrophages are highly phagocytic and required for regeneration. Cross-species comparisons between zebrafish and mammalian macrophages identified transcription and immune response regulator (tcim) as a macrophage-enriched zebrafish gene. Genetic deletion of zebrafish tcim impairs phagocytosis and regeneration, causes aberrant and chronic immune activation, and can be rescued by transplanting wild-type immune precursors into tcim mutants. Conversely, genetic overexpression of human TCIM accelerates debris clearance and regeneration by reprogramming myeloid precursors into activated phagocytes. This study establishes a central requirement for elevated phagocytic capacity to achieve innate spinal cord repair.

overall_design:
To establish the effect of overexpression of human TCIM on spinal cord regeneration, we performed single nuclear RNA-sequencing of the spinal cord in control and TCIM-overexpressing siblings.
We generated Tg(hsp70:TCIM-2A-EGFP) transgenic zebrafish.
At 4 months post-fertilization, adult zebrafish underwent full spinal cord transection.
Fish were treated with one hour of heatshock (at 37 degrees C) daily at 2, 3, and 4 days post-injury.
Spinal cord tissue was collected at 5 days post-injury.
Sequencing results were compared between Transgene-positive and Transgene-negative siblings.

first: Dana

last: Klatt Shaw

first: Vishnu

last: Muraleedharan Saraswathy

first: Lili

last: Zhou


title: The effect of tcima/b loss after spinal cord injury in zebrafish.

overall_design:
To establish the effect of tcima and tcimb loss, we generated tcima and tcimb complete loss-of-function alleles.
We next bred both alleles into the same background to generate double mutants and control siblings.
At 4 months post-fertilization, adult zebrafish underwent full spinal cord transection.
Spinal cord tissue was collected at 5 days post-injury.
Sequencing results were compared between tcima/b mutants and control siblings.

first: Ryan

last: McAdow


title: Single-cell multiomic study of zebrafish cranial neural crest [Smart-seq3]

first: Zhiyuan

last: Hu

overall_design: Smart-seq3 scRNA-sequencing of zebrafish neural crest cells from both wild-type and foxd3-mutant embryos from seven developmental stages. The samples came from eight batches (384-well plates).

first: Sarah

last: Mayes

first: Tatjana

last: Sauka-Spengler


title: TMEM63B Regulates Nucleocytoplasmic Transport and Placental Development

city: Shenzhen

first: Mengya

last: Cai

address: Gaoke Innovation Center, Guangqiao Road, Guangming District, Shenzhen

institute: Shenzhen Bay Laboratory

summary: The placenta is critical for embryonic development, orchestrating nutrient exchange, hormone production, and immune protection. Trophoblast proliferation and differentiation, governed by precise cell cycle regulation, are fundamental to placental development. Here, we identify TMEM63B, an osmo/mechano-sensitive ion channel, as a key regulator of trophoblast cell cycle progression and placental development. Our findings show that TMEM63B modulates nucleocytoplasmic transport (NCT), particularly through its impact on the Ran-XPO1-RanGAP1 complex, which governs the nuclear shuttling of key cell cycle regulators in response to mechanical cues. Loss of TMEM63B results in a reduction of Ran protein levels, destabilizing the export machinery and impairing the nuclear export of CDKN1A (p21), a critical cell cycle inhibitor. This disruption leads to defective trophoblast proliferation, placental dysfunction, and ultimately embryonic lethality. Our findings establish TMEM63B as a pivotal mechanosensitive molecule that regulates nucleocytoplasmic shuttling, providing new insights into how mechanical cues are integrated into nuclear mechanoresponses and placental development.

overall_design: RNA-seq profiling of wildtype BeWo cells and TMEM63B knockout BeWo cells.

first: Yang

last: Zhang


title: Single-cell multiomic study of zebrafish cranial neural crest [scRNA-seq (Direct Capture Perturb-seq)]

overall_design: Perturb-seq of zebrafish F0 crispants. To investigate TFs with potentially significant knockout effects, we employed zebrafish F0 crispant technique alongside direct-capture Perturb-seq using chemically modified sgRNAs. Our knockout panels included pigment regulons as a proof of concept and newly identified regulons for functional validation.


title: Postnatal conversion of methylcytosine to hydroxymethylcytosine reconfigures the human neuronal epigenome

status: Public on May 10 2026

city: La Jolla

first: Eran

last: Mukamel

address: 9500 Gilman Dr

institute: University of California San Diego

type: Methylation profiling by high throughput sequencing

summary: Healthy brain development requires a coordinated process of postnatal cellular maturation throughout the first two decades of life that transforms neuronal morphology, connectivity, physiology, and gene expression. The maturation and stable maintenance of neuron identity is driven, in part, by large-scale reconfiguration of the neuronal DNA methylome. Neurons have uniquely high levels of 5-hydroxy-methyl-cytosine (hmC) compared to other cell types, yet the relative contributions of 5hmC and 5-methyl-cytosine (mC) remain unknown because most experimental assays do not distinguish these marks. We measured mC and hmC using bisulfite- and oxidative-bisulfite sequencing in excitatory and inhibitory neurons, along with mRNA and histone modifications, from the prefrontal cortex of 103 human donors, ranging from 38 days to 77 years of age. Up to half of all CG dinucleotides convert from mC to hmC in a gradual process extending throughout the first decade of life, dramatically reshaping the neuronal methylome. Asymmetric enrichment of hmC on the sense strand of actively transcribed genes increases in a linear, clock-like fashion throughout the lifespan, indicating a mechanistic link between transcription and hmC. We found that sex differences in X-linked DNA methylation in the human brain are primarily driven by hmCG rather than mCG, suggesting an important role for hmC in X-chromosome inactivation (XCI) and escape gene expression. We found key changes in 5hmC at dynamic cis-regulatory elements marked by changing cell type-specific levels of active and repressive histone modifications. Collectively, our findings reveal the dynamic trajectory of hmC in human neurons across the lifespan and highlight the association of DNA hydroxymethylation with transcription, chromatin state, and sex-specific gene regulation.

overall_design:
Whole-genome bisulfite-and oxidative-bisulfite sequencing for 103 human donors in sorted Glu and MGE-GABA neurons.

***************************************************************
FASTQ files are deposited in NDA (collection #5862) under controlled access and are not included in this GEO submission due to patient privacy concerns.
***************************************************************

first: Xu

last: Heng

first: Chien

last: Jo-Fan

first: Kozlenkov

last: Alexey

first: Vadukapuram

last: Ramu

first: Li

last: Junhao

first: Wei

last: Yu

first: Dwork

last: Andrew J.

first: Liu

last: Chunyu

first: Dracheva

last: Stella

first: Mukamek

last: Eran A.


title: PARP inhibition induces cytotoxicity in mESCs by activating endogenous retroviruses [ATAC-seq]

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

summary: PARP inhibitors (PARPi) have been approved to treat patients with BRCA-deficient cancers via synthetic lethality. How PARPi kill BRCA-proficient cells remains an important unanswered question. Here we provide evidence that naïve murine embryonic stem cells, although being homologous-recombination potent, are very sensitive to PARPi such as Talazoparib (Tal). Tal acts on ARTD1 and activates p53 by blocking TOP2A dissociation from chromatin. Genome-wide CRISPR screening showed that the loss of TET1 reduces Tal induced cytotoxicity, which is recapitulated by the depletion of TDG. TET and TDG mediated DNA demethylation turnover renders the local chromatin accessible and facilitates p53 dependent transcription. Consequently, Tal treatment strongly activates the expression of endogenous retroviruses in a p53- and TET/TDG-dependent manner. The uncovered contribution of TET/TDG into Tal induced cytotoxicity sheds further light on future personalized medicine and suggests that TET/TDG mediated active DNA demethylation may represent a biomarker for the predication of sensitivity to PARPi.

overall_design: ATAC-seq of 2i-cultivated murine embryonic stem cells (+/- TDG), treated with PARP-inhibitor Talazoparib

first: Jianming

last: Xu

first: Simon

last: Schwarz

first: Primo

last: Schär


title: Stable maintenance of MERVL-positive embryonic stem cells reveals sustained transcriptional programs and enhancer remodeling

city: Detroit

first: Benjamin

last: Kidder

state: MI

address: 4100 John R St

institute: Wayne State University

summary: Mouse embryonic stem cells (ESCs) occasionally transit into a rare two-cell-like (2C) state characterized by transient activation of endogenous retroviruses such as MERVL and expression of 2C-specific genes including the Zscan4 cluster. These 2C-like cells (2CLCs) resemble early blastomeres and display expanded developmental potential, but their unstable and sporadic nature has hindered mechanistic studies. Here, we demonstrate the transiently stable maintenance of MERVL-positive ESCs that exhibit persistent MERVL expression and activation of 2C-associated genes. Live-cell imaging revealed uniform and sustained MERVL activity in these MERVL-positive ESCs, contrasting with the heterogeneous and transient expression observed in conventional ESCs. Transcriptome profiling demonstrated robust induction of 2C-specific regulatory networks, and embryoid body differentiation combined with machine learning uncovered increased lineage variability and altered developmental trajectories. Single-cell RNA sequencing revealed clear separation of control ESCs from MERVL-positive populations and redistribution across distinct transcriptional states, with Red and Mosaic lines showing graded shifts within a shared transcriptional manifold. Epigenomic profiling further revealed distinct chromatin states, specialized super-enhancer landscapes, and active enhancer marking at MERVL loci. Together, these findings demonstrate that stable maintenance of MERVL-positive ESCs is achievable in vitro, providing a powerful model to dissect ERV-driven transcriptional regulation, epigenomic remodeling, and 2C-like transcriptional and epigenetic programs.

overall_design: RNA-Seq of ESCs. The 2C::tdTomato reporter plasmid (Addgene #40281) was modified to include the HisD cassette from pENTR-R2L3-cGR-ID plasmid (Addgene #139541). ZBHTc4 ES cells were transfected with this modified plasmid and stably selected. 1-5 red, 1-19 red, 2-10 red, 2-1 mosaic, 3-1 mosaic, and 3-2 mosaic are 2C::tdTomato reporter positive. ZHBTc4 ESCs were cultured in the presence or absence of dox and LIF.


title: In the Drosophila germline H2Av and Arp6 suppress germline transposons indirectly by driving piRNA pathway expression [small RNA-seq]

status: Public on May 18 2026

city: Ithaca

first: Katalin

last: Fejes-Tóth

address: Biotechnology Building Room 358, 526 Campus Rd

department: MBG

institute: Cornell University

summary: The spatiotemporal control of transcription and the maintenance of germline genome integrity depend on dynamic chromatin architecture. In Drosophila, the actin-related protein Arp6—a core subunit of the SWR1-like Domino chromatin remodeling complex—mediates the deposition of the histone variant H2Av. Previous studies have established H2Av as a key transcriptional regulator that modulates the +1 nucleosome barrier to promote RNA Polymerase II (Pol II) pause release and productive elongation. Conversely, H2Av is also integral to heterochromatin assembly and gene silencing. Here we demonstrate that Arp6 and H2Av are essential for female fertility and the global repression of transposable elements (TEs) in the Drosophila ovary. Rather than repressing TEs directly, we show that Arp6 and H2Av maintain genomic stability indirectly by driving the transcription of core PIWI-interacting RNA (piRNA) pathway genes. Depletion of either chromatin factor leads to a significant loss of piRNAs and reduced non-canonical transcription of dual-strand piRNA clusters. This defect stems from a failure to express the Rhino-Deadlock-Cutoff (RDC) complex, alongside the downregulation of multiple other piRNA biogenesis factors. Genomic profiling confirms that H2Av acts predominantly as an activating signal at host gene promoters. Upon H2Av or Arp6 depletion, genes that rely on H2Av for their expression exhibit a distinct upstream shift and more precise spatial localization of the Pol II peak at the TSS, indicating an impaired transition from transcription initiation into productive elongation. Together, our findings build upon the known transcriptional activation functions of the Arp6-H2Av axis, revealing that this established chromatin mechanism is critical for licensing piRNA-mediated genome defense and ensuring germline maintenance.

overall_design: Small RNA sequencing to profile piRNA in Drosophila melanogaster ovaries upon knockdown of H2Av and Arp6.

first: Andrasi

last: Norbert

first: Ryon

last: Hannah

first: Luo

last: Yicheng

first: Fejes-Tóth

last: Katalin


title: Spatiotemporal Role of GLI2 in Driving SHH-Medulloblastoma Tumorigenesis

city: Washington

first: Najiba

last: Murad

state: DC

address: 7144 13th Pl NW

department: CCIR/BTI

institute: Children's National Hospital

summary: Medulloblastoma (MB) is a malignant cerebellar tumor primarily affecting children. SHH MB with GLI2 amplification is associated with a particularly poor prognosis. Although GLI2 amplification is clinically recognized, its role in driving SHH-MB remains unclear.  We generated novel mouse models of GLI2-amplified MB to investigate the role of GLI2 in driving tumorigenesis and assessed their similarity to human tumors using immunohistological and scRNA-seq analyses. Additionally, we examined the spatiotemporal window of tumor development using our mouse models and explored the mechanisms underlying the susceptibility of embryonic cerebellar granule cell progenitors (GCPs) to GLI2-induced tumorigenesis through scRNA-seq analysis. We further investigated the involvement of MAPK pathway in GLI2-driven tumorigenesis and progression by genetically disrupting the pathway. We demonstrate that GLI2 is a primary oncogenic driver in SHH-MB, with its overexpression driving embryonic Math1+ progenitor cells to form SHH-MB. The resulting GLI2-driven tumors closely resemble human GLI2-amplified SHH-MB cellularly and molecularly. Additionally, we determined that embryonic Math1+ GCPs at E13.5–E15.5 are the most susceptible to tumor initiation with GLI2 overexpression alone.  In postnatal Math1+ GCPs, additional Trp53 inactivation is required for GLI2-induced tumor formation. scRNA-seq analysis reveals MAPK pathway enrichment in embryonic GCPs and GLI2-driven tumors. Functional studies show that knocking down MEK1/2 in Math1+ progenitor cells or GLI2-driven MB cells prevents tumorigenesis and tumor progression, respectively. Our studies uncover the developmental origins and molecular mechanisms underlying GLI2-amplified SHH-MB. We also reveal that the MAPK pathway plays a critical role in GLI2-driven SHH-MB tumorigenesis and progression.

overall_design: RNA-seq profiling of cerebellar tumor cells derived from Math1-Cre;GLI2A mice.

first: Samuel

last: Rivero-Hinojosa


title: Diversity and evolution of chromatin regulatory states across eukaryotes

city: Barcelona

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

summary: Histone post-translational modifications (hPTMs) are key regulators of chromatin states, influencing gene expression, epigenetic memory, and transposable element repression across eukaryotic genomes. While many hPTMs are evolutionarily conserved, the extent to which the chromatin states they define are similarly preserved remains unclear. Here, we developed a combinatorial indexing ChIP-seq method to simultaneously profile specific hPTMs across diverse eukaryotic lineages, including amoebozoans, rhizarians, discobans, and cryptomonads. Our analyses revealed highly conserved euchromatin states at active gene promoters and gene bodies. In contrast, we observed diverse configurations of repressive heterochromatin states associated with silenced genes and transposable elements, characterized by various combinations of hPTMs such as H3K9me3, H3K27me3 and/or different H3K79 methylations. These findings suggest that while core hPTMs are ancient and broadly conserved, their functional readout has diversified throughout eukaryotic evolution, shaping lineage-specific chromatin landscapes.

sample_organism:
Physcomitrium patens
Arabidopsis thaliana
Saccharomyces cerevisiae
Acanthamoeba castellanii
Naegleria gruberi
Tetrahymena thermophila
Dictyostelium discoideum
Nematostella vectensis
Guillardia theta
Spizellomyces punctatus
Bigelowiella natans
Creolimax fragrantissima

overall_design: Strand-specific 3' RNA-seq data (using MARS-seq protocol) was generated for teh same stages/sample types for all species.

first: Cristina

last: Navarrete

first: Sean

last: Montgomery


title: polr3a mutant vs wild-type

status: Public on May 16 2026

city: Aurora

first: Kristin

last: Watt

state: CO

department: Craniofacial Biology

institute: University of Colorado Anschutz - School of Dental Medicine

summary: We examined zebrafish with a mutation in polr3a, encoding the largest subunit of RNA Polymerase III. We then compared transcriptional responses of different cell types in the head of polr3a mutant zebrafish versus wild-type using a single cell RNA-seq approach.

overall_design: Following genotyping, groups of 10 mutant and 10 wild-type zebrafish were pooled at 3 dpf. Heads were cut just anterior to the pectoral fin. The groups of 10 heads were dissociated and analyzed by scRNA-seq. scRNA-seq pipeline and downstream analysis were performed using Pluto Bio software (https://pluto.bio).


title: In Vitro Single-Cell Transcriptomic Profiling of Cultured SCAP and DPSCs: Unveiling Cellular Heterogeneity

city: Dubai

first: Yousef

middle: Ahmed

last: Elkenawi

address: Al Razi

country: United Arab Emirates

institute: Mohammed Bin Rashid University of Medicine and Health Sciences

summary: Abstract: Introduction: Dental-derived mesenchymal stem cells show considerable variability in their differentiation potential, due to use of non-specific surface markers and technical limitations in isolation protocols. This study aimed to employ single-cell RNA sequencing to compare the cellular composition of cultured stem cells from apical papilla (SCAPs) and dental pulp (DPSCs), with the goal of detecting subpopulations underlying their divergent regenerative behavior and identify markers that can facilitate future isolation and functional targeting. Methodology: SCAP and DPSC tissues were obtained from three human donors and cultured to passage 2. Single-cell suspensions were sequenced to generate gene expression profiles. Dimensionality reduction and clustering were performed using the Seurat package and visualized via UMAP. Cluster-specific differential gene expression was computed as log2fold change, followed by gene set enrichment analysis. Pseudotime trajectory analysis was used to map lineage progression based on transcriptional gene expression. Results: Transcriptomic analysis identified 12 distinct clusters shared across DPSC and SCAP cultures. While both cell types contributed comparably to overall biological processes, key differences emerged within specific clusters. Clusters 3, 4, 5, 6, and 9 expressed high levels of proliferative markers (MKI67, TOP2A, TYMS), suggesting active proliferating populations. Cluster 9 was notable for the co-expression of pericyte-associated markers (NOTCH3, PDGFRB) alongside canonical MSC markers (MCAM, THY1, DCN), identifying a previously uncharacterized progenitor-like subset. NOTCH3 and PDGFRB were also present in a more mature fibroblast-enriched population in cluster 7, dominated by collagen-related genes. IGFBP3 and IGFBP5 were selectively enriched in SCAP-derived clusters 7 and 9, whereas IGFBP4, 6, and 7 were expressed across both DPSC and SCAP populations. Clusters 10 and 11, primarily derived from DPSCs, were enriched in stress-response, heat shock, and apoptotic genes, which may reflect culture-induced adaptations. Pseudotime trajectory inference positioned cluster 9 at a putative progenitor-like node; however, this represents a hypothesis-generating model based on transcriptional similarity in cultured cells rather than validated lineage relationships. Conclusion: This study provides a high-resolution single-cell transcriptomic comparison of cultured SCAPs and DPSCs, revealing distinct transcriptional profiles and cellular heterogeneity. SCAPs may harbor a broader spectrum of proliferative progenitors under these culture conditions, particularly in clusters 7 and 9, enriched in IGF-, PDGFRB-, and NOTCH-associated genes. These findings generate testable hypotheses regarding subpopulation-specific regenerative roles. Future studies using prospective isolation based on NOTCH3/PDGFRB and functional in vitro and in vivo validation are needed to establish their regenerative potential and translational relevance.

overall_design: scRNAseq experiment of cultured cells (early passage 2) harvested from human dental pulp and apical papilla tissue from non carious healthy premolars

first: Maanas

last: Shah

first: Mohamed

last: Al Sayegh

first: Mennatullah

last: Khalil

first: Mano

last: Sundarabupathi

first: Omer

last: AlKhnbashi

first: Costerwell

last: Khyriem

first: Lakshman

last: Samaranayake

first: Mehar

last: Sultana

first: Hiroshi

last: Egusa

last: Jamal


title: Diversity and evolution of chromatin regulatory states across eukaryotes [ChIP-Seq]

platform_organism:
Physcomitrium patens
Arabidopsis thaliana
Saccharomyces cerevisiae
Acanthamoeba castellanii
Naegleria gruberi
Tetrahymena thermophila
Dictyostelium discoideum
Nematostella vectensis
Guillardia theta
Spizellomyces punctatus
Bigelowiella natans
Creolimax fragrantissima

overall_design: Biological samples from various species were fixed prior to chromatin extraction and processing and library generation using iChIP2. Libraries were sequenced on the indicated machines.


title: Murine host response to Borrelia burgdoferi OppA2tn mutant

status: Public on May 15 2026

city: Hamilton

first: Ashley

last: Groshong

address: 903 S 4th St

institute: NIAID

summary: Mice were infected with wild-type and OppA2tn mutant strains and skin and lymph node samples were analyses with Nanostring nCounter mouse host response panel to evaluate the immunological impact of a non-hematogenous dissemination route

overall_design: Infected and mock-infected mouse tissues were evlauated at 9d, 2w, 4w, and 8wpi, samples included skin inoculation site, primary axillary lymph node, accessory axillary lymph node, subiliac lymph node

first: Samantha

last: Crane


title: Recurrent ZC3H18 mutations stabilize oncogenic endogenous retroviral RNA [A375_polyA]

city: Boston

first: Tanzina

last: Tanu

state: MA

address: 450 Brookline

department: Medical Oncology

institute: DFCI

summary: Endogenous retroviral (ERV) RNA is highly expressed in cancer, although the molecular causes and consequences remain unknown. In multiple cancer types, we identified recurrent truncating mutations in ZC3H18 (Z18), a nuclear RNA surveillance component. We show that Z18 truncating (Z18trunc) mutations are oncogenic and that Z18 plays an evolutionarily conserved role in nuclear RNA surveillance of oncogenic ERV RNA. In zebrafish, Z18trunc accelerated melanoma onset and selectively increased ERV RNA. Z18 mutant human cell lines from the Cancer Cell Line Encyclopedia, TCGA melanoma, and TCGA uterine cancer patient samples also expressed higher levels of ERV RNA. In engineered human melanoma cells, Z18trunc enhanced ERV RNA accumulation more than loss of one Z18 allele, indicating dominant negative activity. In human melanoma cells, Z18trunc directly bound to and stabilized ERV RNA in the cytoplasm. Expression of zebrafish and human Z18-regulated ERV RNA was sufficient to accelerate melanoma in zebrafish. Z18-regulated ERV RNA was required for Z18trunc melanocyte development in zebrafish and for human melanoma cell growth. Our work suggests that ERV RNA, the most highly expressed transposable element RNA in cancer, promotes melanoma and potentially other cancers. This work illuminates a mechanism for elevated ERV transcripts in cancer and supports that aberrant RNA accumulation is broadly oncogenic.

overall_design:
pLENTI CMV Clover (fluorescent control) and pLENTI CMV Z18trunc-expressing human melanoma A375 cell lines were generated via lentiviral transduction. polyA-selected RNA-sequencing was done.
Lentivirus transduction and antibiotic selection was used to generate Clover-expressing (n=3) and ZC3H18 trunc-expressing (n=3) cell lines.

first: Anna

last: Cox

first: Jennifer

last: Karlow

first: Priyanka

last: Sharma

first: Kaiwen

last: Sun

first: Xueyang

last: He

first: Swathy

last: Babu

first: Madeline

last: Roelofs

first: Ethan

last: Jeon

first: Jiajia

last: Chen

first: Constance

last: Wu

first: Jared

last: Brown

first: Nelson

last: Barrientos

first: Andrew

last: McCallion

first: Kevin

first: Stephen

middle: J

last: Chanock

first: David

last: Liu

first: Tongwu

last: Zhang

first: Kathleen

last: Burns

first: Paul

last: Boutz

first: Megan

last: Insco


title: Transcriptomics of THP-1-derived macrophages infected with mycobacteria

city: NanJing

first: Tian

last: Gan

address: Jiang-wang-miao street 12

institute: Chinese Acdemy of Medical Science

summary: Transcriptomic profiling was performed on PMA-differentiated THP-1-derived human macrophages to investigate host transcriptional responses to infection with novel mycobacterial species (Mycobacterium camsae, Mycobacterium pumcae) in comparison with known reference strains (Mycobacterium gordonae, Mycobacterium abscessus, Mycobacterium marinum). This dataset provides insights into host-pathogen interactions and identifies key differentially expressed genes and pathways involved in macrophage responses to mycobacterial infection.

overall_design: Transcriptomic profiling was performed on PMA-differentiated THP-1-derived human macrophages to investigate host responses during infection with two novel mycobacterial species, Mycobacterium camsae and Mycobacterium pumcae. Infections with reference strains (Mycobacterium gordonae, Mycobacterium abscessus, Mycobacterium marinum) were included for comparison.

first: Youming

last: Mei

first: Haiqin

last: Jiang

first: Wenyue

first: Yin

last: Shi

first: Hongsheng

last: Wang


title: Time-course transcriptome of skeletal muscle after contusion in Bama pigs

city: Jinzhong

first: Jun-hong

last: Sun

state: Shanxi Province

address: 98 University Street, Yuci District, Jinzhong

department: School of Forensic Medicine

institute: Shanxi Medical University

summary: Accurately estimating the time since injury remains a critical challenge in forensic science and clinical medicine. To address the significant gap in cross‑species applicability, we first established a high‑resolution transcriptomic atlas of skeletal muscle contusion in Bama miniature pigs. Based on this model, we systematically characterized the early transcriptional dynamics following skeletal muscle injury (SMI) in the same species. Skeletal muscle tissues were collected at 4, 8, 12, 16, 20, 24, and 48 hours post‑injury for RNA sequencing. Our analysis delineates the time‑dependent transcriptional kinetics and reveals key molecular transitions underlying the injury response and early repair processes.

overall_design: A skeletal muscle contusion model was established using eight Bama minipigs. Muscle tissues were collected at seven post-injury time points (4, 8, 12, 16, 20, 24, and 48 hours), with four biological replicates obtained per time point for transcriptomic profiling by RNA sequencing.

first: Junhong

first: Liangliang

first: Kang

last: Ren

first: Zhenning

last: Xu

first: Zichen

last: Wen

first: Qiuxiang

last: Du

first: Jie

last: Cao


title: Effect of knockdown of FLI1 on gene expression  in the human glioblastoma cell lines

city: Changchun

first: Xue

address: Xinmin Street

institute: Cancer Center, First Hospital of Jilin University

summary: To examined the role of FLI1 in glioblastoma cells and identify FLI1-associated target molecules, FLI1 knockdown cells were used for RNA-seq.

overall_design: Two short hairpin RNAs (shRNA) against FLI1 mRNA were inserted into the lentiviral vector (pGreen plasmid).      The human glioblastoma (U87MG, U251MG) cell lines were infected with lentiviruses using polybrene (8 mg/mL).   After puromycin selection, mixed stable cells were collected for each group. RNA-seq profiling of the empty vector control cells（pGreen）and their knockdown derivatives cells(shFLI1).

first: Jiuwei

last: Cui

first: Ji-Fan

last: Hu


title: An ancient retrotransposon provides species-specific tuning of IL18 inflammatory signaling [EL4_RNAseq]

status: Public on May 09 2026

city: Boulder

first: Edward

last: Chuong

state: Colorado

address: 3415 East Colorado Ave, JSC biotech building

department: MCDB

institute: University of Colorado Boulder

summary: Species differ markedly in how they regulate immune responses, yet the molecular basis of this variation remains incompletely understood. Here, we show that an ancient LINE2 retrotransposon introduced an intronic polyadenylation signal into the IL18R1 locus, generating a truncated isoform, IL18R1-Short, that lacks the intracellular signaling domain. Using bulk RNA-seq across nine mammals, we find that although this cis-regulatory element is broadly conserved, robust IL18R1-Short expression is species- and tissue-restricted: bats and mice express it at high levels, particularly in barrier tissues (lung, skin, intestine), whereas most other species, including humans, show absent or limited expression. Single-cell lung profiling further shows that this truncated isoform is enriched in mouse epithelial cells. Known IL18 negative regulators, SIGIRR and IL18BP, also show distinct expression patterns across mouse and human lung cell populations, suggesting that these brakes on IL18 signaling are deployed in context-dependent and non-redundant manner. Functionally, IL18R1-Short dampens IL18-induced NFkB signaling in both human and mouse systems, and knockdown of the mouse ortholog amplifies IL18-driven immune and inflammatory gene expression in mouse T cells. Together, these results identify IL18R1-Short as a TE-derived decoy receptor that attenuates IL18 signaling and show that conservation of a TE-derived cis element does not predict conserved regulatory output. More broadly, these findings establish IL18R1-Short as an example of how TEs can generate alternative immune transcripts with species-specific regulatory consequences, highlighting TE-mediated alternative transcription as an underappreciated source of mammalian immune variation.

overall_design: RNA-seq profiling of mouse EL4 T-lymphoblast cells treated with 10 ng/mL IL-18 for 4 hours following transfection with non-targeting control siRNA or I18r1-short-targeting siRNA.

first: Andrea

last: Ordonez

first: Holly

last: Allen

first: Lynn

last: Sanford

first: Atma

last: Ivancevic

first: Ashley

last: Agyepong

first: Mia

last: Chaw

first: James

last: Bridges

first: Tony

last: Schountz


title: An ancient retrotransposon provides species-specific tuning of IL18 inflammatory signaling [RNAseq_LongRead]

overall_design: ONT Long-read RNA-sequencing of Jamaican fruit bat (Artibeus jamaicensis) primary tissues for transcriptome assembly and isoform studies.


title: Uncovering Critical Lysines in Mammalian Histone H3 with High-Throughput CRISPR Prime Editing [CUT&Run]

city: London

first: Aliaksandra

last: Radzisheuskaya

address: 237 Fulham road

department: Cancer Biology

institute: The Institute of Cancer Research

summary: Histone proteins are central to regulating eukaryotic genomes, and their post-translational modifications play key roles in controlling gene expression, DNA repair and chromatin structure. Understanding the functions of individual histone modifications is a significant challenge in mammalian chromatin biology, primarily due to the multiple copies of histone genes found in mammalian genomes. In this study, we present a high-throughput CRISPR prime editing platform that allows for base-precise, combinatorial, and reversible mutagenesis of all canonical and non-canonical histone H3 genes within their native genomic context. Using this system, we systematically substituted each lysine residue in histone H3 with arginine and compared each mutation against synonymous lysine-to-lysine controls. This unbiased functional screen revealed a core set of lysines, including H3K4, H3K9, H3K14, H3K18, and H3K79, whose mutations impair cellular fitness in mouse embryonic stem cells, highlighting the critical roles of their post-translational modifications in chromatin function. In addition, our approach demonstrated that H3K56 acetylation, previously linked to genome stability in yeast and Drosophila, plays a conserved role in safeguarding the genome in mammalian cells. Extending this approach, we generated double histone H3 mutants to probe functional redundancy between several lysine residues. While individual substitutions caused minimal defects, specific combinations, most notably H3K27R+H3K36R, revealed impairments in stem cell self-renewal and distinct transcriptional consequences, uncovering regulatory crosstalk not evident from single-site perturbations. This study presents the first comprehensive functional map of histone H3 lysines in a mammalian system, establishing a broadly applicable platform for dissecting histone modifications with advanced precision.

overall_design: CUT&RUN profiling to assess genomic localisation of H3K23ac in mouse embryonic stem cells carrying H3K23K or H3K23R mutations.


title: Inhibition of Acetyl-CoA-carboxylase induces endoplasmic reticulum stress and has synergistic effects with anti-cancer therapies

city: New Haven

first: Lajos

last: Pusztai

state: Connecticut

address: 333 Cedar Street

institute: Yale Cancer center

summary: Background: Acetyle-CoA-carboxylase-1 (ACC1) is overexpressed in many cancer types relative to normal tissues and catalyzes the rate limiting step of de novo fatty acid synthesis. In this study, we identified a new downstream effect of ACC inhibition and demonstrate synergy between a small molecule inhibitor of ACC, PF0517515, and clinically used anti-cancer agents.  Methods: High throughput cell line (N=300 10 cell lines) and combinatorial drug screens (n=166 FDA-approved drugs) were performed along with in vivo mice xenograft experiments. We analyzed bulk and single cell RNA sequencing, and lipid profiling results of PF0517515 treated cells, and performed western blot analysis of endoplasmic reticulum stress proteins to elucidate cellular effects of ACC inhibition.  Results: Single agent PF-05175157 inhibited the growth of several different cancer types, myeloma, ovarian, lung and breast cancer cells resistant to various targeted therapies. PF-05175157 augmented the anti-cancer efficacy of a range of drugs including tyrosine kinase inhibitors and chemotherapy agents. Synergy with doxorubicin and vinorelbine were also demonstrated in mice xenografts. In breast cancer cells, ACC inhibition increased the protein (and mRNA) expression levels of genes involved in endoplasmic reticulum stress and unfolded protein response including a rapid increase in phospho-IRE1 by 6h, and more gradual increase in phospho-EIF2, ATF4, and ATF6 expressions by 24h and 72h. Lipid profiling after 48h exposure to drug showed decrease in many membrane components including c14:0/c16:0 and c16:0/c18:1 that facilitate membrane protein integration. There was an increase in unsaturated long-chain fatty acids and an increase in 4-Hydroxynonenal and 4-Hydroxyhexenal indicating increased lipid peroxidation. Single cell RNA sequencing showed large scale metabolic slowdown with decreased oxidative phosphorylation, amino acid and steroid biosynthesis, glutathione-, carbon-, pyruvate-, and purine-metabolism. Pathways of ferroptosis, reactive oxygen, sphingolipid, steroid hormone and folate biosynthesis were upregulated suggesting response to oxidative stress and compensatory lipid synthesis. Seven-day post-recovery cells compared to pretreatment, continued to show downregulation of proteasome, spliceosome, amino acid synthesis, DNA replication/DNA repair, cell cycle, oxidative phosphorylation, and glycolysis /gluconeogenesis indicating less than full metabolic recovery.  Conclusion: PF-05175157 alters cellular lipid composition, induces endoplasmic reticulum stress, and shows broad synergy with various anti-cancer therapies in vitro and in vivo.

overall_design: High throughput cell line (10 cell lines) and combinatorial drug screens, along with in vivo mice xenograft experiments, were conducted. We analyzed bulk and single cell RNA sequencing, and lipid profiling results of PF0517515 treated cells, and performed western blot analysis of endoplasmic reticulum stress proteins to elucidate cellular effects of ACC inhibition.

first: Shan

last: Naing Lin

first: Dai

last: Jiawei

first: Wang

last: Yueyue

first: Pusztai

last: Lajos


title: An ancient retrotransposon provides species-specific tuning of IL18 inflammatory signaling [RNAseq_ShortRead]

overall_design: Short-read Illumina RNA-sequencing of Jamaican fruit bat (Artibeus jamaicensis) primary tissues for  isoform studies.


title: PAR3-mediated coordination of hepatocyte proliferation, maturation, and architecture in liver development and regeneration

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

institute: Peking University

summary: The coordination of cell proliferation, polarization, and maturation with architectural assembly is crucial for liver development and regeneration, yet the mechanisms underlying this coordination remain unclear. Using both murine and human models, we demonstrate that hepatic cell polarity and bile canaliculi (BC) formation initiate at sites of cell division during the hepatoblast stage, while BC elongation occurs following hepatocyte differentiation. This elongation requires suppression of ERK/MAPK activity mediated by PAR3 and YAP. PAR3 interacts with a complex network of proteins, including IQGAP1, at tight junctions, thereby sequestering IQGAP1 from basolateral membranes where it typically promotes growth factor-induced ERK/MAPK activation. This PAR3-ERK/MAPK pathway further regulates actin organization and oriented cell division, both essential for BC elongation and hepatocyte maturation throughout liver development and regeneration. These findings provide new insights into a fundamental mechanism integrating cell proliferation, maturation, and architectural assembly, with implications for regenerative medicine and liver disease therapies.

overall_design: scRNA-seq was performed on mouse embryo hepatoblasts/hepatocytes (E11.5-E19.5) and on E15.5 liver tissue cultured for two days with PD, TPPB, or U0126, as well as on adult mouse hepatocytes following a 70% hepatectomy.

first: Li

last: Yang

first: Yu-Heng

last: Zhou

first: Junya

last: Hayase

first: Lei

last: Wang

first: Weiguang

last: Zhang

first: Erfei

last: Bi

first: Cheng-Ran


title: Uncovering Critical Lysines in Mammalian Histone H3 with High-Throughput CRISPR Prime Editing [CUT&Tag]

overall_design: CUT&Tag profiling of multiple histone modifications or histone variants in mouse ES cells engineered with CRISPR Prime Editing.


title: Regulation of endothelial cell chromatin availability and transcription factor activity in arterial-venous specification

city: Charlottesville

first: Nicholas

last: Chavkin

address: 415 Lane Road

institute: University of Virginia

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: RNA-seq of PRDM15 overexpression in HCAEC

first: Fangzhou

last: Li

address: 167 Beilishi Rd, Xicheng District,

department: Fuwai hospital

institute: Peking Union Medical College

summary: The internal and external mechanism that drive endothelial transition are still largely unknown. Here, we reported the critical role of PRDM15 in regulating endothelial cell function

overall_design: We conducted RNA-seq of PRDM15-overexpression in HCAEC.

first: Zhe

last: Zheng

first: Fang

last: Yao


title: scRNA-seq of human coronary artery

summary: The internal and external mechanism that drive endothelial transition are still largely unknown. Besides, we conducted scRNA-seq of human coronary artery to explore the cellular composition of plauqe and the different function of multiple endothelial subtypes.

overall_design:
We conducted scRNA-seq of human coronary artery across different atherosclerotic stages.
**Submitter declares that "scRNA-seq of human Coronary artery samples" raw data was uploaded to the "Genome Sequence Archive for human" according to the local institution law requested**


title: Hepatocyte Hedgehog Signaling Controls Ferroptosis to Alleviate Aging-related Organ Dysfunction

status: Public on May 08 2026

city: Durham

first: Rajesh Kumar

last: Dutta

state: NC

address: 1049 Umstead Grove Way

department: Medicine

institute: Duke University

summary: Aging drives systemic metabolic dysfunction (SMD) and increases the risk of chronic illnesses such as metabolic dysfunction–associated steatotic liver disease (MASLD) and chronic kidney disease (CKD). However, mechanisms that connect aging to multi-organ deterioration are poorly understood. In this study, we identify hepatocyte Hedgehog signaling as a central regulator of ferroptosis.  Using  mice with hepatocyte-specific deletion of Smoothened (Smo), a key Hedgehog pathway component, we show that loss of hepatocyte Hedgehog signaling induces ferroptotic stress, lipid peroxidation, and cellular senescence. These changes were sufficient to cause spontaneous MASLD and to trigger secondary kidney injury. Smo deletion also disrupted systemic iron balance, increased hepatocyte production of the angiotensinogen, and reduced liver perfusion. Similar responses (iron dysregulation, vascular dysfunction, and reduced Hedgehog signaling) were observed in patients with MASLD and advanced fibrosis. Inhibition of ferroptosis with ferrostatin-1 reversed hepatocyte senescence, restored hepatic blood flow, and improved both liver and kidney injury in Smo-deficient mice. Overall, these findings show that hepatocyte Hedgehog signaling preserves liver homeostasis by restraining ferroptotic stress and coordinating iron-dependent vasoactive pathways. The results reveal an unrecognized aging-related communication axis between liver and kidney and identify the Hedgehog–ferroptosis pathway as a promising therapeutic target for age-associated metabolic diseases.

overall_design: Fresh-frozen human liver samples from control individuals and patients with MASLD were profiled using the 10x Genomics platform to generate single-nucleus RNA-seq (snRNA-seq) datasets.

first: RajeshKumar

first: AnnaMae

last: Diehl


title: Impact of Reduced Maternal Tryptophan on the Placenta-Brain Axis

city: Columbia

first: Trupti

last: Joshi

state: Missouri

address: 103 Math Science Building

department: Department of Biomedical Informatics, Biostatistics and Medical Epidemiology (BBME)

institute: University of Missouri-Columbia

summary: Tryptophan is critical to mothers and their conceptuses, and this amino acid is the precursor to serotonin. Serotonin modulates placenta function and fetal neurodevelopment. It is not clear if the placenta directly synthesizes serotonin or uses the serotonin transporter (SERT/Sl6a4) to accrue this catecholamine from the dam. The hypothesis tested herein is that reduction in maternal tryptophan would lead to reductions in maternal tryptophan, serotonin, and 5-HIAA (a metabolite of serotonin) and corresponding reductions of these metabolites in placenta and fetal brain of female and male conceptuses. Female mice were placed on either a low tryptophan diet (1%) or control diet (2%).These diets were administered for two weeks prior to breeding (periconception period) until conceptuses were collected at approximately12.5 days post-coitus (dpc). While no reductions in maternal tryptophan and serotonin were observed, both metabolites were significantly reduced in in the placenta and fetal brain of male and female conceptuses (p < 0.05). Female conceptuses were particularly sensitive to reductions in maternal tryptophan with 652 and 29 transcripts being altered in the female placenta and fetal brain of low maternal tryptophan dams compared to control dams. Transcriptome changes, such as Sl6ca4 and Slc6a19 (transporter for tryptophan), in these organs were linked to reductions in tryptophan and serotonin amounts. Findings might have clinical relevance to pregnant women as they show even subtle reductions in one amino acid might profoundly influence offspring development and potential later risk for neurobehavioral disorders and the female conceptuses might be more vulnerable to in utero nutrient changes.

overall_design: RNA-seq and metabolite profiling of mouse dam serum, uterine tissue, and male and female placentas and fetal brains from 6 dams given a 1% tryptophan diet (low-tryptophan group) and a 2% tryptophan diet (control group).

first: Rosalind

last: Herrington

first: Zhen

last: Lyu

first: Sarah

middle: E

last: Seda

first: Emmett

last: Boling

first: Andrea

middle: K

last: Goldstein

first: Nathan

last: Bivens

first: Zhentian

last: Lei

first: Tanhaul

last: Islam

first: Lloyd

last: Sumner

first: Cheryl

last: Rosenfeld


title: Immune niche analysis in breast tumour derived lung metastasis

first: Luigi

last: Ombrato

address: Charterhouse Square

institute: Queen Mary University of London

summary: We used our Cherry-niche labelling system to specifically isolate immune cells from the metastatic niche of established 4T1 lung metastases and compared their profile with immune cells isolated from the distal lung away from the tumour growth.

overall_design: Labelling-4T1 cells were intravenuosly injected into female Balb/c mice and metastatic lungs collected after 7 days. From the dissociated lung tissue, cells were collected via fluorescence-activated cell sorting (FACS) and 10x Genomics single cell RNA seqeuncing (scRNA-seq) was performed.

first: Christos

last: Ermogenous


title: miR-205-5p drives endothelial dysfunction and senescence in pulmonary fibrosis

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Idiopathic Pulmonary Fibrosis (IPF) is a fatal, aging-related disease characterized by persistent lung fibroblast activation, progressive lung scarring and several vascular abnormalities. We have previously demonstrated that aging-associated vascular dysfunction drives maladaptive endothelial responses to injury and exacerbates lung fibrosis via secretion of pro-fibrotic endothelial-derived factors. However, regulatory mechanisms governing endothelial dysfunction during progressive lung fibrosis remain poorly understood. Here, using preclinical mouse models of progressive lung fibrosis as well as human IPF lungs, we demonstrate that miR-205-5p is overexpressed in lung ECs from fibrotic lungs, and coordinates gene expression programs implicated in endothelial dysfunction and progressive fibrosis. Transcriptomic profiling revealed that miR-205-5p downregulates genes involved in cell cycle progression while upregulating multiple genes encoding secreted mediators of fibrosis and components of the senescence-associated secretory phenotype, that recapitulating the aberrations observed in lung ECs isolated from human IPF lungs. In addition, miR-205-5p induces the expression of the senescence marker β-galactosidase in lung ECs, mirroring the phenotype of IPF lung ECs, which are also β-galactosidase positive. Consistently, conditioned medium derived from lung ECs overexpressing miR-205-5p promotes lung fibroblast activation. Importantly, miR-205-5p inhibition in IPF lung ECs reduced the transcription of genes encoding soluble mediators of fibroblast activation, confirming the role of miR-205-5p in driving pathogenic endothelial phenotypes during IPF. Collectively, our findings support a novel connection between lung endothelial miR-205-5p and pro-fibrotic alteration of the endothelial secretome, highlighting miR-205-5p as potential therapeutic target in pulmonary fibrosis.

overall_design:
RNA-seq profiling of cultured normal human lung endothelial cells following transfection with a control mimimic or miR-205-5p mimic.

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

last: Muscato

first: Nunzia

last: Caporarello