title: The shelterin subunit TRF-1 mediates PRC2 function at ectopic telomere repeats in Neurospora crassa [HiC]

city: Sapporo

first: Hideki

last: Tanizawa

address: Kita 15, Nishi 7, Kita-ku

institute: Hokkaido University

summary: Telomeres are crucial for maintaining chromosomal integrity and are characterized by repetitive sequences, which may be stabilized by the shelterin protein complex and/or by formation of secondary structures, such as G-quadruplexes (G4 DNA). Frequently, subtelomeric regions are decorated with di- and tri-methylated lysine 27 on histone H3 (H3K27me), repressive marks associated with facultative heterochromatin in many eukaryotes.  Our previous work with the filamentous fungus Neurospora crassa demonstrated that native telomere repeats induce H3K27me at ectopic loci.  Here we report investigations into the mechanism of this and demonstrate that nonnative telomere repeats can also induce H3K27me.  Chromatin immunoprecipitation (ChIP) experiments with an anti-G4-DNA antibody showed that establishment of H3K27me does not depend on the formation of G4 DNA.  Other ChIP experiments demonstrated binding of the shelterin member TRF-1 to interstitial telomere repeats that induce H3K27me but not to similar sequences that do not.  Tethering experiments revealed that TRF-1, but not other proteins tested, is sufficient to induce H3K27me.  Hi-C analyses demonstrated that ectopic telomeric repeats can interact with native telomeres.  Together these results suggest that the shelterin complex plays a crucial role in establishment of H3K27me and repression at telomere sequences.

overall_design: Hi-C experiments were performed to investigate genome-wide chromatin interactions and to assess whether ectopically inserted telomere repeats at the csr-1 locus physically associate with native telomeres in Neurospora crassa.

first: Colleen

last: Mumford

first: Peregrine

last: Painter

first: Kevin

middle: J

last: McNaught

first: Nolan

last: Smith

first: Shinji

last: Honda

first: Osamu

last: Iwasaki

first: Sanki

last: Tashiro

first: Ken-ichi

last: Noma

first: Eric

last: Selker


title: Xenoestrogen-induced elimination of asymmetric gene expression in the Müllerian ducts of female Japanese quail embryos

status: Public on Mar 30 2026

city: Saitama

last: Tsukahara

address: 255 Shimo-Okubo, Sakura-ku

department: Graduate School of Science and Engineering

country: Japan

institute: Saitama University

type: Expression profiling by high throughput sequencing

summary: An RNA-seq analysis was performed to determine the differentially expressed genes between the left and right Müllerian ducts of female Japanese quail embryos with or without in ovo xenoestrogen exposure.

overall_design: The gene expression in the Müllerian ducts of femele embryos with or without exposure to ethynylestradiol (EE) during embryonic days 3–12 were compared between the left and right sides.

first: Suzuki

last: Takehiro


title: multiplexed RNA imaging of human forebrain organoids from typical and autism subjects [MERFISH]

city: Singapore

first: Jinyue

last: Liu

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

summary: the goal of this experiment is to define cellular phenotypes in human brain organoid models of autism.

overall_design:
human forebrain organoids were cultured with minor modifications using a published protocol (Qian et al. 2016), harvested at 8-weeks, cryosectioned and imaged using multiplexed error-robust fluorescence in situ hybridization.

***Submitters declare that the raw image data will be made available through a generalist archive -or- upon request.

first: Li

last: Lin

first: Wan

middle: K

last: Chock


title: R-loops shape the H2A.Z landscape and promote balanced lineage allocation during differentiation [CUT&Tag]

city: Worcester

first: Chun-Hao

last: Chao

address: 364 Plantation St. LRB560D

department: MCCB

country: USA

institute: UMass Chan Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: R-loops—RNA:DNA hybrids that often form co-transcriptionally—are emerging as key regulators of genome function, yet their roles in shaping chromatin architecture and developmental potential remain incompletely defined. Here, we use inducible Rnaseh1 expression in mouse embryonic stem cells (mESCs) to achieve acute, global R-loop depletion and systematically interrogate their impact on chromatin structure and lineage specification. We find that R-loop loss has minimal effect on steady-state gene expression or self-renewal. Instead, it leads to a striking reduction in H2A.Z occupancy at both active and bivalent promoters, accompanied by increased nucleosome density—revealing a previously unrecognized role for R-loops in maintaining promoter architecture. During gastruloid differentiation, R-loop-depleted mESCs exhibit accelerated ectodermal differentiation, along with dysregulation of lineage-specific transcription factors and impaired cell-cell signaling. Consistent with these alterations, R-loop-depleted cells show widespread perturbations in gene regulatory networks across several early cell types. These findings uncover a critical role for R-loops in shaping the H2A.Z chromatin landscape and preserving balanced lineage trajectories during early development, offering new insights into the epigenomic regulation of stem cell fate.

overall_design: Rnaseh1-inducible cells or ZX-1 with or without Dox treatment were subjected to CUT&Tag with antibodies/proteins including H2A.Z, H3K4me3, H3K9me3, H3K27me3, H3K27ac, H3K36me3, RNAPIISer2P, H3.3, H4ac, IgG

first: Thomas

last: Fazzio


title: Foliar iron application delays flavonoid degradation during the later grain-filling stage and regulates sugar metabolism in colored rice

status: Public on Mar 29 2026

city: Yibin

first: Xia

last: Zhao

state: Sichuan

address: Daxue road 5

country: China

institute: Yibin University

summary: Introduction Colored rice is recognized for nutritious function due to its flavonoid compounds. Flavonoid aglycones are conjugated with various sugar moieties. Iron (Fe) is an essential mineral nutrient for plants; however, the regulatory mechanisms by which Fe influences flavonoid accumulation dynamics and sugar metabolism remain unclear. Methods FeSO4 was foliar-applied to black rice cultivar Nanheinuo and red rice cultivar Yuhongdao 5815 to study regulatory mechanisms by which Fe influences flavonoid accumulation dynamics and sugar metabolism Results and discussion The content of anthocyanins, proanthocyanidins, and total flavonoids in the grains decreased throughout the later filling stages. Fe application delayed their degradation during this phase. The differential expression of numerous genes associated with flavonoid transformation may be the primary reason. Genes annotated as key enzymes involved in phenylpropanoid and flavonoid biosynthesis were significantly upregulated in Nanheinuo. Additionally, foliar Fe application significantly impacted sugar and sugar alcohol content by regulating the expression of genes involved in polysaccharide decomposition, phosphorylation and dephosphorylation processes, and sugar interconversion. A close relationship was observed between sugar content and flavonoid-related compound content in the grains of colored rice. Multiple hub genes annotated as glycoside hydrolases in KEGG occupied central nodes within the co-expression network, suggesting that glycoside hydrolases may mediate the crosstalk between sugar and flavonoid metabolism in colored rice grains under Fe treatment, although glycosyltransferases primarily function in flavonoid glycosylation. Foliar Fe application delays flavonoid degradation during the later filling stage and regulates sugar metabolism in colored rice, thereby influencing flavonoid enrichment and eating quality.

overall_design: The experimental field was located at the experimental farm of Yibin University in Yibin City, Sichuan Province, China. All field experiments were conducted in 2023 and 2024. Paddy soil was used for this study, with a pH of 5.92, 30.28 mg kg-1 available iron, 96.41 mg kg-1 available nitrogen, 70.35 mg kg-1 exchangeable potassium, and 27.63 mg kg-1 available phosphorus. The black rice variety Nanheinuo (BR) and the red rice variety Yuhongdao 5815 (RR) were used in this research. The seeds were sown in seedling trays and cultivated for approximately 27 days. The seedlings were transplanted into 20 L pails and cultivated under natural environmental conditions. The average temperature at the experimental site ranged from approximately 23 °C to 28 °C, characteristic of a subtropical humid monsoon climate. A completely randomized design with three biological replicates was implemented (Liu and Ming, 2020). And a biological replicate contained six pails. A compound fertilizer (2 g) was applied to each pail as a base fertilizer before transplantation. Additionally, 2 g of urea was applied at both the tillering and jointing stages. Based on the results of the preliminary experiment for screening Fe concentration, the foliar Fe treatments were applied as follows: (1) Control, using deionized water as the foliar spray; (2) 1Fe, with 0.1% FeSO4·7H2O (w/v) as the foliar fertilizer; and (3) 2Fe, with 0.2% FeSO4·7H2O (w/v) as the foliar fertilizer. All foliar solutions contained Fe absorption enhancer nicotinamide (0.5% w/v) and surfactant Tween 80 (0.005% v/v). Approximately 40 mL of solution was applied to the leaves of the plants in each bucket. Foliar spraying was conducted after sunset at the end of the booting stage and repeated 7 d later. Panicles of BR and RR were sampled at 10, 15, 20, 25, 30, 35, and 40 days after flowering (DAF). Samples were rapidly frozen in liquid nitrogen and then stored at −80 °C for following analyses. The rest of rice panicles were harvested at maturity.


title: R-loops shape the H2A.Z landscape and promote balanced lineage allocation during differentiation [scRNA-Seq]

overall_design: Rnaseh1-inducible cells were differentiated into gastruloids with and without Dox treatment. Samples were collected at Days 0 (0 hr), 3 (72 hrs), and 5 (120 hrs) for scRNA-seq


title: In situ fate mapping identifies the neonatal origin of platelet-biased hematopoietic stem cells [Tppp3Naive]

city: BARCELONA

first: Elvira

last: Gonzalez-Saiz

state: BARCELONA

address: CARRER BALDIRI REIXAC 10

country: Spain

institute: IRB BARCELONA

summary: Hematopoietic stem cells (HSCs) display heritable and deterministic gene regulatory states associated with functional heterogeneity. However how these biased fate programs change through development remains poorly understood. Here, using single-cell lineage tracing, we map the function and state of thousands of individual mouse HSCs spanning from the earliest mature fetal stages until young adults. We identify a burst of platelet- and myeloid-biased HSCs during the first postnatal week. Fetal HSCs retain a fetal-like program even after 4 months in the recipient bone marrow, suggesting that the adult HSC program is epigenetically configured early after birth. Creating a single-cell atlas of mouse perinatal HSCs, we identify a transient HSC state with hallmarks of Epithelial-Mesenchymal Transition (EMT), mTOR complex 1 activity, and cholesterol synthesis (SREBP targets). Tracing the rare cells that traverse this transient state, we reveal the neonatal origin of long-term platelet/myeloid-biased HSCs in both native and transplantation hematopoiesis. Transient treatment with mTORC1 inhibitor rapamycin during the first postnatal week suffices to reduce the platelet-biased adult HSC programming, without affecting total HSC numbers. In sum, we reveal a late developmental origin for platelet-biased HSCs, with important implications for hematopoietic aging.

overall_design: HSCs were isolated from 2 Tppp3CreER LSLTdTomato mice that were labelled at P0 and P3 with Tamoxifen. When they have 3 month of age HSCs were isolated to get this scRNAseq dataset to study the possible mechanism under Tppp3 program. From each mice TdTomato pos was sorted in one tube and TdTomato negative sorted in other. A total of 4 tubes were stained with Totalseq. Loaded half of this tube in the GEM-X and the other half by classical sequencing v3.1 as in this experiment we also wanted to compare both technologies as GEM-X just started.

first: Marta

last: López-Osias

last: González-Saiz

first: Daniel

last: Fernández-Pérez

first: Pedro

last: Sánchez

first: Indranil

last: Singh

first: Anna

last: Adrover

first: Alejo

middle: E

last: Rodríguez-Fraticelli


title: In situ fate mapping identifies the neonatal origin of platelet-biased hematopoietic stem cells [TamRapaTreatments]

overall_design: HSCs were isolated from 6 Tppp3CreER LSLTdTomato mice that were labelled at P0 and P3 with Tamoxifen only, Tamoxifen+ rapamycin and just rapamycin (this at day 30). After 2 weeks HSCs were isolated to get this scRNAseq dataset to study the possible mechanism under Tppp3 program. We had 6 mice, processed 3 per day to run 10x and then libraries sequenced together, so we have two day-batches in the fastq files.


title: Immune-remodeling mRNAs expressing IRF8 or NIK generate durable anti-tumor immunity in multiple cancer models

city: Cambridge

first: Akash

last: Gupta

state: MA

address: 500 Main Street, Building 76

institute: Massachusetts Institute of Technology

summary: Although immunotherapy has a subset of cancer patients, its broader efficacy remains limited, primarily due to an immunosuppressive tumor microenvironment characterized by insufficient numbers of functional tumor-specific T cells, antigen-presenting cells (APCs) and tumor-infiltrating lymphocytes. Here we engineer immune cells in the tumor microenvironment using lipid nanoparticles (LNPs) to deliver immune remodeling mRNAs (IR-mRNAs) encoding NF-κB inducing kinase (NIK) or interferon regulatory factor 8 (IRF8). These IR-mRNAs activate APCs in tumors, significantly increasing activated type 1 conventional dendritic cells, immunostimulatory cytokines, and priming anti-tumor CD8+ T cells. IR-mRNAs encapsulated in LNPs elicited durable antitumor responses in multiple syngeneic mouse tumor models via both intratumoral and intravenous delivery. Co-administration of IR- and OVA-mRNA elicited ~10-fold increase of antigen-specific CD8⁺ T cell responses, sustained long-term memory, and effectively prevented tumor growth in vaccinated mice. Additionally, adjuvanting influenza vaccines with IR-mRNAs enhanced the humoral response by 5-fold and the cellular response by ~15-fold, underscoring their potential as adjuvants for boosting adaptive immunity.

overall_design: We investigated how immune remodeling mRNAs modulate immature dendritic cells to acquire mature phenotypes capable of efficient T-cell priming, using flow cytometry and single-cell RNA sequencing (scRNA-seq)

first: Riddha

last: Das

first: Kaelan

last: Reed

first: Taewon

last: Jeon

first: Quang Trung Chinh

last: Nguyen

first: Arnab

last: Rudra

first: Xinying

last: Ge

first: Suthathip

last: Trongjit

first: Yann

middle: S

last: Vanrobaeys

first: Robert

last: Langer

first: Ralph

last: Weissleder

first: Christopher

last: Garris

middle: G

last: Anderson


title: Photoactivatable CRISPR/Cas13d via upconversion nanoparticles for deep tissue RNA engineering and orthopedic therapy

city: tianjin

first: miaomiao

last: gao

address: tianjin

country: Algeria

institute: tianjin university

summary: To overcome the limited tissue penetration of blue light, we engineer polyethylenimine-functionalized upconversion nanoparticles (UCNPs-PEI) that serve dual roles as gene carriers and photon transducers, converting tissue-penetrating near-infrared (980 nm) to blue light (470 nm). The UCNPs-PEI@paCas13d system achieves precise spatiotemporal control of RNA targeting within bone tissue in vivo. In a murine steroid-associated osteonecrosis model, NIR-activated paCas13d achieves robust TET3 knockdown, disrupting the TET3-5hmC-PTEN axis that drives glucocorticoid-induced osteocyte apoptosis. This targeted intervention prevents bone deterioration, with treated mice showing preserved trabecular architecture, enhanced bone volume, and favorable shifts in bone turnover markers, while maintaining systemic glucocorticoid efficacy. Our platform combines the programmability of CRISPR/Cas13d with non-invasive optical control, offering a versatile approach for treating diseases requiring localized RNA modulation while minimizing systemic effects.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HEK293T cells transfected with non-targeting control or ANXA4-targeting paCas13d

first: Jie

last: Zhao

first: Jun

last: Jiao

first: Miaomiao

last: Gao

first: Jingyu

last: Zhang

first: Jinbin

last: Pan

first: Xinlong

last: Ma


title: R-loops shape the H2A.Z landscape and promote balanced lineage allocation during differentiation [CUT&Run]

first: Chun-Hao

last: Chao

overall_design: Rnaseh1-inducible cells or ZX-1 with or without Dox treatment were subjected to CUT&RUN or MapR with antibodies/proteins including  CTCF, RHD-MNase, IgG

first: Thomas

last: Fazzio


title: R-loops shape the H2A.Z landscape and promote balanced lineage allocation during differentiation [ATAC-Seq]

overall_design: Rnaseh1-inducible cells with or without Dox treatment were subjected to ATAC-seq


title: In situ fate mapping identifies the neonatal origin of platelet-biased hematopoietic stem cells [TransplantTracing_Tppp3]

first: Elvira

last: Gonzalez-Saiz

overall_design: HSCs were isolated from 4 Tppp3CreER LSLTdTomato mice labelled at P0 and P3 with Tamoxifen only, they were infected with the LARRY barcoding system and Larry+ HSCs were transplanted into 4 irradiated mice with a 1:1 proportion of TdTomato+:TdTomato-. At 8th month after transplant, donor hematopoietic cells (stem, progenitor and differentiated cells) were isolated and sorted into TdTomato+ or TdTomato- subpopulations to label them with Totalseq antibodies in order to distinguish the recipient mice. Finally, we got this scRNAseq and barcoding dataset (one library for TdTomato+ and the other for TdTomato-) to track clonal HSC behaviours.

first: Marta

last: López-Osias

last: González-Saiz

first: Daniel

last: Fernández-Pérez

first: Pedro

last: Sánchez

first: Indranil

last: Singh

first: Anna

last: Adrover

first: Alejo

last: Rodríguez-Fraticelli


title: Inhibition of BCL2 family proteins overcomes acquired resistance to standard of care BRAF and MEK inhibitors in a subset of BRAFV600E-mutant melanomas

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

type: Genome variation profiling by high throughput sequencing

summary: Despite recent advances, a significant number of melanoma patients treated with BRAF and MEK targeted therapies (BRAFi/MEKi) or immunotherapies develop progressive disease. Anti-apoptotic BCL family proteins have been shown to promote de novo resistance to a number of therapies, including single-agent BRAF inhibitors in BRAF-mutant melanomas. In this study, in vivo testing of a collection of BRAFi- or BRAFi/MEKi treatment-refractory melanoma patient-derived xenograft (PDX) models showed that combining BCL2 inhibitors (BCL2i, navitoclax or venetoclax) with BRAFi and MEKi surprisingly induced potent regressions of a significant subset of these treatment-refractory PDXs. High basal BCL2 expression correlated with improved sensitivity, while high basal MCL1 predicted resistance to BCL2i combination with BRAFi/MEKi. Studies with MCL1 overexpression functionally validated its role in resistance. Further, combination of BRAFi/MEKi with a MCL1 inhibitor (MCL1i) counteracted the resistance and also decreased MCL1i-associated cardiotoxicity markers.

overall_design:
RNA-seq and WES for PDX samples in response to BCL2 inhibitors

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

first: Vashisht

middle: N

last: Gopal

first: Michael

middle: A

last: Davies


title: Investigating the role of muscle fibers in the early stage of nerve regeneration within a Muscle-in-Vein graft

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

summary: Background: Every year, many people experience a reduced quality of life due to peripheral nerve damage, resulting in significant healthcare costs, with painful neuroma formation as a common drawback following improper nerve regeneration. The Muscle-in-Vein (MIV) technique, consisting of a vein enriched with skeletal muscle fibres, offers a promising approach to nerve repair, in which the vein serves as a conduit, while muscle fibres avoid vein collapse and provide essential growth factors. The MIV-technique advantages include natural axon guidance through muscle fibre basal laminae, enhanced Schwann cell migration, reduced scar formation and a lower incidence of neuroma formation compared to synthetic conduits. This research aims to explore the role of muscle fibres in the early stages of nerve regeneration - an essential yet understudied phase - within the MIV graft in a rat median nerve injury and repair model. Methods: The study was performed in vivo inducing an 8 mm gap in the rat median nerve, subsequently repaired through the Muscle-in-vein technique. Regenerating nerves were harvested at 3-, 7-, 14-, and 21-days post-injury for comprehensive molecular and morphological analyses, with particular emphasis on the vascularization process, identified as an emerging key factor in nerve regeneration. Results: Immunofluorescence data reveal complete macrophage colonization and a well-structured vascularization throughout the entire graft 7 days post-injury. RNA sequencing analysis on early time points further confirms the pathways involved in vasculature development among the most enriched ones and provides insights into the behaviour of specific angiogenesis- associated genes. A deep evaluation of differentially expressed genes suggests that endothelial cell differentiation occurs in the early stages, as confirmed by the expression profiles of subtype-specific endothelial cell markers. Conclusions: Our data supports the hypothesis of a partial anastomosis between the vessels of the nerve stumps and those of the muscle guided by macrophages. This insight enhances our understanding of the MIV technique and provides valuable guidance for improving tissue engineering approaches for developing more effective treatments for peripheral nerve injuries.

overall_design: The median nerves of adult female Rattus norvegicus were transected to create an 8 mm gap and repaired using 10 mm muscle-in-vein graft. Regenerating nerves were collected at 3 and 7 days for RNA extraction, which was sent to Novogene SRL for Illumina Next-Generation sequencing.

first: Federica

last: Zen

first: Alessandro

last: Crosio

first: Debora

last: Molinaro

first: Giulia

last: Ronchi

first: Stefano

last: Geuna

first: Giovanna

last: Gambarotta

first: Stefania

last: Raimondo


title: Inducible XIST-mediated trisomy 21 correction uncovers a USP16-p16 senescence axis driving epileptogenesis in Down syndrome [scRNA-Seq]

city: Chongqing

first: Kai

last: Guo

address: 1 Youyi Road, Yuzhong District

institute: Chongqing Medical University

summary: Down syndrome (DS), caused by human chromosome 21 (HSA21) trisomy, carries elevated epilepsy risk with unknown mechanisms. We integrated clinical epidemiology, fetal brain single-nucleus RNA sequencing, patient-derived induced pluripotent stem cell (iPSC) models, cerebral organoids, and in vivo chimeric mice to dissect this link. Clinical analysis of 1,365 DS individuals exhibited an age-stratified epilepsy prevalence pattern, with higher rates in older children. Fetal brain transcriptomes revealed neurogenesis defects, aging-related signatures, synaptic/metabolic dysregulation. We engineered an inducible XIST-mediated extra HSA21 silencing system in female DS iPSCs, showing HSA21 dosage correction reduced neural progenitor cell (NPC) senescence markers and neuronal hyperexcitability. Transcriptomic screening pinpointed USP16 as a key pro-aging candidate. Moreover, USP16 suppression and the senolytic combination dasatinib/quercetin reduced senescence-linked and hyperexcitability-associated readouts, supporting a USP16-p16-NPC aging axis as a therapeutic target for DS-associated epilepsy, with broader implications for aging-linked neurological disorders.

overall_design: Cell-type-resolved transcriptomic profiling of human fetal forebrain tissue and iPSC-derived cerebral organoids to identify trisomy 21-dependent molecular alterations associated with epilepsy.

first: Jianhe

first: Yating

last: Wang

first: Yifan

last: zhang

first: Shuo

last: Zhang

first: Tongfei

last: Liu


title: Distinct phases of immune system programming during ART-suppressed immunodeficiency virus infection

city: Beaverton

first: Benjamin

last: Bimber

state: OR

address: 505 NW 185th Ave

summary: This project contains rhesus macaque immune cell single-cell RNA-seq data, from SIV/ART studies.

overall_design: These data are bulk immune cells from the indicated tissue, processed using the 10x genomics scRNA-seq platform. Cells were isolated from tissue biopsies or at necropsy at the indicated timepoints.


title: Single-cell RNA sequencing of leukocytes at the maternal-fetal interface in psyhiological and pathological Nodal-deficient pregnancies

city: Montreal

first: Alain

last: Pacis

state: QC

address: 1010 Sherbrooke #1800

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

summary: Leukocytes at the maternal-fetal interface have critical functions during pregnancy to prevent maternal reactivity towards fetal alloantigens, suppress excess inflammation and promote placental angiogenesis. Failed maternal immune adaptations to pregnancy can lead to placental insufficiency and the development of severe reproductive complications. Recent evidence from mouse models has suggested that Nodal, a secreted morphogen of the TGFB superfamily, is an immunoregulator of pregnancy. The absence of Nodal expression in the female reproductive tract resulted in the loss of preimplantation regulatory T cells and a 50% implantation failure rate. By mid-gestation, Nodal Δ/Δ pregnancies showed placental dysfunction, fetal loss and intrauterine growth restriction. Therefore, the Nodal Δ/Δ model represents a unique system to study immune-mediated reproductive failure. In this study, single-cell RNA-sequencing was used to characterize leukocytes within the mid-gestational decidua and placenta during physiological and pathological Nodal Δ/Δ pregnancies. Eleven distinct immune cell clusters were identified, with an emphasis on myeloid populations (macrophages and neutrophils). In particular, the characterization of placenta-associated maternal macrophages revealed novel functions in the regulation of angiogenesis, immune suppression and endocytosis. In Nodal Δ/Δ females, the differential abundance and expression profile of these leukocytes reflected the immune dysfunction observed in human reproductive pathologies. Taken together, elucidating roles of leukocytes in placental development provides a basis in the understanding of mechanisms associated with physiological pregnancy and reproductive failure.

overall_design: Cells from the Nodal loxP/loxP and Nodal Δ/Δ myometrium, decidua and placenta were isolated on day 10.5 of pregnancy by enzymatic digestion. CD45+ immune cells were enriched by magnetic-activated cell sorting (MACS) for scRNA-seq analysis.

first: Sarah

last: Yull

first: Laura

last: Girardet

first: Daniel

last: Dufort


title: Effect of HNF1A-MODY on stem cell islets [scRNA-seq]

city: Bergen

first: Lucas

last: Unger

address: Haukelansbakken 15

country: Norway

institute: University of bergen

summary: This project investigates the impact of the hotspot mutation P291fsinsC in HNF1A-MODY (Maturity-Onset Diabetes of the Young) on stem cell-derived islets. RNA sequencing (RNA-seq) was performed on islets differentiated from mutant and control HNF1A-MODY stem cells to study the mutation's effect on gene expression. By comparing the transcriptomic profiles of these islets, the study aims to uncover molecular mechanisms underlying the dysfunction caused by the P291fsinsC mutation during islet development and maturation.

overall_design: HNF1A-MODY stem cells with the P291fsinsC hotspot mutation and wild-type controls were differentiated into pancreatic islets. RNA sequencing was performed on these islets to compare gene expression profiles and assess the impact of the mutation on islet development and function.

first: Simona

last: Chera


title: Single-cell multi-omic analysis of post-transplant mesenchymal cells reveals molecular signatures and regulators of lung fibrosis (scRNA-seq)

city: Ann Arbor

first: Lu

last: Lu

state: MI

address: 100 Washtenaw Ave.

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan, Ann Arbor

summary: Chronic lung allograft dysfunction (CLAD) is a critical challenge in lung transplantation. Dysregulated gene expression and epigenomic states in lung mesenchymal cells (MCs) play a key role in these conditions. We performed single-cell multi-omic profiling on MCs isolated from human bronchoalveolar lavage samples of lung transplant recipients with CLAD, compared with time-matched controls. Our results provide deeper insights into the transcriptomic and epigenomic changes in post-transplant MCs, nominating biomarkers and disease-associated factors with implications for future therapeutic efforts.

overall_design: We collected and performed scRNA-seq on cells from human lung autopsy samples, including one from a CLAD patient and two from healthy controls. Due to the low number of MCs detected in these initial samples, we sequenced two additional samples (one from the same CLAD patient and one from the same healthy control) after CD45+ depletion.

first: Aidan

middle: P

last: McLinden

first: Natalie

middle: M

last: Walker

first: Ragini

last: Vittal

first: Michael

last: Combs

first: Joshua

middle: D

last: Welch

first: Vibha

last: Lama


title: Role of CARM1 in Glioblastoma

city: Bronx

first: Ronald

last: Cutler

state: NY

address: 1300 Morris Park Ave

department: Genetics & Biochemistry

institute: Albert Einstein College of Medicine

summary: One driving factor of Glioblastoma (GBM) heterogeneity and therapy resistance is the capacity of glioma stem-like cells (GSCs) to hijack developmental signaling programs. However, it remains unclear how glioma stem-like cells regulate many of their developmental signaling pathways and how these pathways might be therapeutically exploited. The arginine methyltransferase, CARM1, has been shown to play critical roles in maintaining stem cell pluripotency, preventing differentiation, and recently has been found to be upregulated in Glioblastoma. To date, there is little to no understanding of what role CARM1 plays in regulating developmental processes in Glioblastoma. To address this gap in knowledge, we use a multi-omics approach to characterize which developmental processes are specifically regulated by CARM1 in GSCs. We find that loss of CARM1 results in dysregulation of several developmental markers: ARX, GFAP, NGFR, PDGFRA and results in both a proteomic and transcriptomic shift towards the radial glia cell lineage. Moreover, CARM1 KO cells develop an increased survival dependency on NGFR/NTRK signaling and are hypersensitive to the FDA approved brain penetrant NTRK inhibitor, Entrectinib. Mechanistically, we find that NFIA is a CARM1 substrate and can repress NGFR signaling just as CARM1 does, and thus the CARM1/NFIA relationship is likely a key regulator of NGFR/NTRK signaling in GSCs. Altogether, we demonstrate that CARM1 regulates the cell lineage of GSCs at the transcriptomic/proteomic level, likely driven by CARM1 dependent NFIA methylation, and creates a therapeutic vulnerability to NTRK inhibition.

overall_design: RNA-Sequencing of glioblastoma cell line with and without CARM1 knockdown

first: Dejauwne

last: Young

first: Simone

last: Sidoli


title: Single-cell multi-omic analysis of post-transplant mesenchymal cells reveals molecular signatures and regulators of lung fibrosis (RNA-seq)

overall_design: We used cells from the same CLAD MCs samples as our single-cell multiome profiling, along with an additional line not included in the multiome profiling. These cells were treated with either a C/EBPD-targeting siRNA (treated group) or a scrambled siRNA (control group) for 16 hours. To measure the gene expression changes induced by C/EBPD silencing, we performed bulk RNA-seq on both the treated and control groups across the four CLAD samples.


title: Andrographolide Ameliorates Aortic Lesion via Inhibition of NF-κB Signaling Pathway in Angiotensin-II Treated Murine Model of Abdominal Aortic Aneurysm

city: Guangzhou

first: Xing

last: Fu

address: jinsui road NO.9

institute: Guangzhou Medical University

summary: Abstract Introduction: Abdominal aortic aneurysm (AAA) is a severe aortic disease with a high mortality rate in the event of rupture. There is an urgent need for pharmacological treatment to address the progression and development of AAA. Andrographolide, a natural anti-inflammatory compound derived from Chinese medicine, has proven effective in clinical trials for treating inflammatory diseases by selectively suppressing NFκB1 nuclear translocation. However, the role of Andrographolide in the development and progression of AAA remains elusive. Methods: Genome-wide RNA sequencing analysis was performed on the aorta isolated from saline-treated mice and those treated with Ang II for 14 or 28 days. Vascular smooth muscle cells (VSMCs) differentiation markers and plasma Elisa were used to evaluate vascular phenotypic switching and inflammation. We used Andrographolide (an NFκB1 inhibitor) for the pre-treatment of vascular lesions before AAA formation and explored the underlying mechanisms through transcriptomic and functional studies. Results: We demonstrated that the NFκB signaling pathway contributes to the phenotypic switch and inflammation of vascular smooth muscle cells (VSMCs), with NFκB1 identified as a potential key gene for AAA development, particularly in the early stages of the aneurysm. Andrographolide significantly attenuated vascular lesions at the early stage and reduced aneurysm formation at the later stages of the disease in Ang II-treated AAA mice. Our ChIP results further demonstrated that NFκB1 regulates its direct target KLF4 to induce VSMC dedifferentiation. Meanwhile, TNF-alpha was identified as a target of NFκB1, indicating that NFκB1 exacerbates inflammation via the TNF-alpha signaling pathway. Discussion: Our results demonstrate a previously unrecognized role of vascular lesions in AAA development and progression, and the pre-treatment with Andrographolide may serve as a novel therapeutic approach for AAA.

overall_design: Abdominal Aortic Aneurysm (AAA) Animal Models:Angiotensin II (Ang II) (1,000 ng/kg/min, HY-13948, MedChemExpress, NJ, USA) was dissolved in normal saline and was infused using osmotic pumps (Alzet 2004, Durect Corporation, USA) for 4 weeks. Mice were anesthetized via intraperitoneal injection of 50 mg/kg pentobarbital sodium, and the suprarenal abdominal aortas, located between the last pair of intercostal arteries and the right renal branch, were harvested 28 days post-implantation surgery. An aneurysm was diagnosed when the abdominal aorta diameter increased by 50% or more. Any mouse that died before the study endpoint underwent autopsy, with aneurysm rupture identified by blood clots outside the adventitia of the dilated aortic wall. Samples:Genome-wide RNA sequencing (RNAseq) analysis was performed on the aorta isolated from saline or Ang II-induced AAA mice for 14 days or 28 days.

first: Ying

last: Wen

first: Zheng

last: Chen

first: Jianxiang

last: Wang

first: Yingying

last: Liu

last: Yang

first: Yixian

last: Ren

first: Zefeng

last: Lin

first: Luhao

first: WaiHo

last: Tang


title: Adaptive cellular evolution in the intestinal tracts of hyperdiverse African cichlid fishes [RNA-Seq]

city: Basel

first: Antoine

last: Fages

address: Vesalgasse 1

country: Switzerland

institute: University of Basel

summary: Adaptations relating to how nutrients are acquired and processed play a central role in the colonization of novel ecological niches and, therefore, in organismal diversification. While the evolution of feeding structures has been studied extensively in this context, the nature of dietary adaptations in the digestive tract remains largely unexplored. Here, we investigate the cellular and molecular basis of dietary adaptations in the massive radiation of cichlid fishes in Lake Tanganyika using comprehensive single-cell transcriptomic data derived from the intestines of 25 African cichlid species with distinct habitats and diets. We show that, at the cellular level, dietary adaptations are primarily driven by anterior enterocytes, and that both the abundance and gene expression profiles of these cells have evolved in response to dietary specializations. These dietary adaptations in enterocytes are driven by rapidly evolving cell population-specific genes, suggesting that alterations in gene regulatory programmes and cell-state specification promote ecological diversification.

sample_organism:
Haplochromis burtoni
Eretmodus cyanostictus
Lepidiolamprologus attenuatus

overall_design: bulk RNAseq data from intestinal tracts of African cichlid fishes


title: RNA sequencing of Panc-1 cells co-cultured with CAF overexpressing PAI-1

city: Tianjin

first: Yu

state: Tianjin

address: No22.Qixiangtai Rd.,Heping Dist

institute: Tianjin Medical University

summary: To investigate the effect of CAF overexpressing PAI-1 on tumor cells, CAF overexpressing PAI-1 was used to co-culture with Panc-1 cells, and then gene expression profiling of Panc-1 cells was performed using RNA-seq.

overall_design: Co-culture of CAF overexpressing PAI-1 with Panc-1 cells

first: Xuan

last: Zhou

first: Jihui

last: Hao


title: Antiviral Tfh response by “tolerant” congenitally infected virus carriers drives antibody-mediated viral load control

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

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

overall_design: Refer to individual Series


title: High Resolution Spatial Mapping of Microbiome-Host Interactions via in situ Polyadenylation and Spatial RNA Sequencing [STOmics]

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: 237 Tower Road

department: Biomedical Engineering

institute: Cornell University

summary: Inter-microbial and host–microbial interactions are thought to be critical for the functioning of the gut microbiome, but few substantive tools are available to measure these interactions. Here, we report a method for unbiased spatial sampling of microbiome-host interactions in the gut at high spatial resolution. This method combines enzymatic in situ polyadenylation of both bacterial and host transcripts with spatial RNA-sequencing. Application of this method revealed the biogeography of the mouse gut microbiome as function of location in the intestine, short-range intermicrobial interaction, local shaping of the microbiome by the host, and tumor-associated changes in the architecture of the host-microbiome interface. This method is compatible with broadly available commercial platforms for spatial RNA-sequencing, and can therefore be readily adopted to broadly study the role of short-range, bidirectional host-microbe interactions in microbiome health and disease.

overall_design:
Spatial transcriptomics
Intestial tissue profiled with the STOmics  platform with in situ polyadenylation

first: Ioannis

last: Ntekas

first: David

middle: W

last: McKellar

first: Lena

last: Takayasu


title: Real-time quantitative PCR analysis of Triticum aestivum leaves under heat stress

status: Public on Mar 28 2026

city: Giza

first: Marwa

last: Sanad

address: 33 El Bohouth St, Dokki

department: Genetics and Cytology

country: Egypt

institute: National Research Centre

summary: Triticum aestivum leaves were collected under heat stress compared to non stressed plants during anthesis stage to assay peroxiosme biogenesis genes (pex11.3, pex11.4, Fis1A, DRP5B), antioxdant gens (CAT and SOD), and heat shock proteins (HSP90, and HSP101)

overall_design: Comparative Ct experiments, 3-5 leaves on the each biological replicate were bullked to extract the RNA, 3 random biological plants were sampled per treatment and RNA isolated, notmalized, and cDNA synthesized, and equal amount of synthesied cDNA for each sample has used to assay the qPCR

first: Joseph

last: Shenoda


title: Antiviral Tfh response by “tolerant” congenitally infected virus carriers drives antibody-mediated viral load control [scTCR-Seq]

summary:
Congenital infection can result in viral persistence as commonly observed for hepatitis B virus in humans. The accompanying “neonatal tolerance” state remains immunologically ill-defined and treatment options are unsatisfactory.
Studying congenital lymphocytic choriomeningitis virus infection, the prototypic mouse model of neonatal antiviral tolerance, we observe antibody-mediated suppression of viral replication. These responses are driven by canonical antiviral CD4 Tfh responses, whereas CD8 T cells are irrelevant for viral load control. Viral epitope-specific CD4 T cells of congenitally infected animals are less abundant than in adult infection. They exhibit reduced clonal diversity and distinct differences in gene expression patterns. Importantly, exogenous supplementation of T help augments antiviral germinal center B responses of congenitally infected mice.
These findings reveal that humoral immune defense is partially exempt from neonatal tolerance and remains effective against congenital infection. Imperfect virus control by limited CD4 Tfh responses may offer opportunities for a functional cure by immunotherapy.

overall_design: 1. Experimental group, "neonat.": Neonatal, intercranial infection (i.c.) (within first 24h after birth) with artLCMV (Kallert et al., Nat.Comm., 2017) leading to life long virus carriage, harvest of splenocytes 8 weeks post infection. 8 biological replicates 2. Experimental group, "chronic": Intra venous (i.v.) infection of adult animals at 7 weeks age with LCMV(Cl13/WE-GP) leading to chronic infection, harvest of splenocytes 24 days post infection. 6 biological replicates In both groups, LCMV GP66-77 tetramer+, CD44hi, CD4+T cells were subjected to scRNA-and scTCR-sequencing.

first: Katrin

last: Martin

first: Peter

last: Reuther

first: Florian

last: Geier

first: Anna-Friederike

last: Marx

first: Tiago

last: Abreu-Mota

first: Jonas

last: Fixemer

first: Anna

middle: L

last: Kastner

first: Karen

last: Tintignac

first: Karsten

last: Stauffer

first: Ingrid

last: Wagner

first: Doron

last: Merkler

first: Daniel

last: Pinschewer


title: Antiviral Tfh response by “tolerant” congenitally infected virus carriers drives antibody-mediated viral load control [scRNA-Seq]

first: DBM Bioinformatics

last: Core Facility

overall_design: 1. Experimental group, "neonat.": Neonatal, intercranial infection (i.c.) (within first 24h after birth) with artLCMV (Kallert et al., Nat.Comm., 2017) leading to life long virus carriage, harvest of splenocytes 8 weeks post infection. 8 biological replicates 2. Experimental group, "chronic": Intra venous (i.v.) infection of adult animals at 7 weeks age with LCMV(Cl13/WE-GP) leading to chronic infection, harvest of splenocytes 24 days post infection. 6 biological replicates In both groups, LCMV GP66-77 tetramer+, CD44hi, CD4+T cells were subjected to scRNA- and scTCR-sequencing.


title: The role of Akh in the systemic gene expression changes induced by Drosophila C Virus infection

city: Wuhan

first: chen

last: cheng

address: No. 169 Donghu Road, Wuchang District, Wuhan City, Hubei Province

institute: Wuhan University

summary: Drosophila C Virus (DCV) is a natural pathogen that induces profound systemic wasting and metabolic dysfunction in Drosophila melanogaster. In this study, we identify Adipokinetic Hormone (Akh), a functional analog of mammalian glucagon, as a central endocrine mediator of this process. Our results show that DCV infection robustly increases Akh production and signaling, which correlates closely with the progression of host wasting phenotypes, including lipid loss, hyperglycemia, muscle dysfunction, and ovary atrophy. To elucidate the transcriptomic basis of Akh-mediated wasting, we performed RNA-sequencing (RNA-seq) on whole-body samples from four groups: wild-type (WT) and Akh-null mutant flies, each challenged with either PBS (control) or DCV. Differential expression analysis reveals that a significant subset of genes (183 up-regulated and 308 down-regulated) are modulated by DCV in an Akh-dependent manner. These genes are primarily enriched in pathways associated with carbohydrate, lipid, and protein metabolism. Notably, while DCV infection also affects the systemic insulin pathway and various stress-related signaling axes (e.g., Jak/Stat, TNF/JNK), these alterations occur largely independently of Akh. Our findings suggest that Akh drives infection-induced energy wasting through a distinct regulatory axis. This dataset provides a comprehensive resource for understanding the endocrine mechanisms governing host-pathogen interactions and metabolic homeostasis.

overall_design: Flies of the indicated genotypes (w1118 and Akh mutant:AkhA) were subjected to PBS or Drosophila C Virus (DCV) infection. Whole fly bodies were collected at 5.5 day post-infection(dpi) for w1118 and 3.5 dpi for AkhA

first: Wei

last: Song

first: Chen

last: Cheng

first: Zehua

last: Wu


title: Hamp deletion disrupts hemoglobin synthesis by ferropotosis during zebrafish embryogenesis

city: Shanghai

first: mingjian

last: peng

address: No. 999 Hucheng Ring Road

institute: Shanghai Ocean University

summary: Iron is a nutrient element necessary for cell proliferation and growth, and it can participate in various processes such as DNA synthesis and energy metabolism. Especially, it is essential for hematopoietic . Hepcidin (hamp) is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here, we have generated a stable hamp mutant zebrafish model by  using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish, and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed, and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development, accompanied by ferroptosis.

overall_design: To investigate the effect of the hamp gene on the early development of zebrafish embryos,we used CRISPR/Cas9 to knock out hamp in zebrafish and performed scRNA-seq.

first: Wenyi

last: Yang

first: Mingjian

last: Peng


title: Intratumoral CD40 agonist sotigalimab in combination with pembrolizumab induces rapid activation of antigen presenting cells and drives anti-tumor responses in non-injected tumors in metastatic melanoma: Results of a phase 1/2 study

city: Houston

first: Salah-Eddine

last: Bentebibel

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

summary: Checkpoint inhibitors (CPIs) benefit metastatic melanoma (MM) patients, but resistance remains a challenge. This phase 1/2 (NCT02706353) study evaluated intratumoral sotigalimab (an anti-CD40 agonistic antibody) with pembrolizumab in 32 CPI-naïve MM patients. Primary endpoints included determining safety and tolerability, the recommended phase 2 dose (RP2D) of  sotigalimab, and the objective response rate (ORR). The most common adverse events (AEs)  related to sotigalimab were injection-site reactions, pruritus, and fatigue. The ORR was 47% and the disease control rate (DCR) was 91% for all patients, and 50% and 92% at the RP2D, respectively. Multiomic biomarker analyses of tumor and blood samples collected before and during treatment demonstrated that sotigalimab effectively engaged the CD40 pathway, boosting the infiltration and activation of myeloid cells, including CD11c+DC-LAMP+ dendritic cells (DCs) and macrophages. The combination therapy activated both innate and adaptive immunity, in both  injected and non-injected tumors. TCR sequencing analysis showed increased T-cell clonality  with expanded new clones shared between injected and non-injected tumors. Clinical responses correlated with these immunologic changes, but not with baseline immunological features  associated with response to anti-PD1 monotherapy. In the B16 melanoma mouse model, single- cell RNA sequencing analysis showed that the combination therapy enhanced antitumor immunity and reduced the immunosuppressive tumor environment. These findings suggest that intratumoral sotigalimab may enhance anti-PD1 therapy, supporting the need for further randomized phase 2 trials to better evaluate its therapeutic potential in the 'in situ' immunization  approach.

overall_design: Preclinical study: single cell RNA-seq was performed on 4 samples of CD45+ live immune cells sorted from tumors. Each sample contained intratumoral immune cells collected from 6 mice per each experimental group. Experimental groups: control (IgG-treated), CD40 Ab-treated, PD1 Ab-treated, and Combo (CD40 Ab & PD1 Ab-treated)

first: Jingjing

last: Liu

first: Jianhua

last: Zhang

first: Barbara

last: Pazdrak

first: Heather

last: Sonnemann

first: Adi

last: Diab

first: Gregory

last: Lizee


title: bulk RNA sequencing of human forebrain organoids from typical and autism subjects

city: Singapore

first: Jinyue

address: 60 Biopolis Street

institute: Genome Institute of Singapore

summary: The goal of this experiment is to define cellular phenotypes in human brain organoid models of autism.

overall_design: Human forebrain organoids were cultured with minor modifications using a published protocol (Qian et al. 2016), harvested at 33 days, and processed for bulk RNAseq.

first: Li

last: Lin

first: Wan

last: Chock


title: Single-cell RNA sequencing of human forebrain organoids from typical and autism subjects

overall_design: Human forebrain organoids were cultured with minor modifications using a published protocol (Qian et al. 2016), harvested at 8-weeks, dissociated and processed for single-cell RNA sequencing as per manufacturer's recommendations (10x genomics).


title: Machine-learning prediction of affinity and epistasis in the bovine pancreatic trypsin inhibitor–chymotrypsin complex

city: Be'er Sheva

first: Noam

last: Tzuri

address: David Ben Gurion Blvd 1

country: Israel

institute: Ben Gurion University

summary: Protein–protein interactions (PPIs) are shaped by evolutionary pressures that fine-tune binding affinities and drive the epistatic relationships that support functional outcomes. Here, we used the complex of bovine pancreatic trypsin inhibitor (BPTI) and chymotrypsin as a model system to study how mutations at one or two positions affect binding affinity and epistasis. To predict the binding affinity landscape of the BPTI–chymotrypsin complex, we combined deep sequencing data, obtained from a saturation scanning mutagenesis BPTI library, with a machine-learning (ML) model. Using this ML model, which was trained on a subset of experimental binding data, we predicted the binding affinities and epistatic interactions across thousands of single and double BPTI mutants, including those not observed in the library. Our predictive approach completed missing data points and enabled us to reveal global trends in affinity changes and mutation couplings within specific binding interface positions. Our analysis revealed that different mutations in the same position may have different effects on affinity, with most double mutations leading to increased epistasis, particularly at hotspot positions, thereby indicating a cooperative binding effect. In most cases, affinity and epistasis were inversely correlated, with affinity enhancement of double-mutant variants being associated with negative epistasis. Our approach can be readily generalized to predict mutation effects in larger combinatorial libraries and in proteins for which structural information is lacking.

overall_design: This study investigates the binding affinity of BPTI variants toward chymotrypsin. A yeast surface display (YSD) library containing single- and double-mutant BPTI variants at selected positions was generated. The variants were sorted by fluorescence-activated cell sorting (FACS) into four affinity gates (HI, WT, SL, and LO) using labeled chymotrypsin. The sorted populations were analyzed by next-generation sequencing (NGS) on the Illumina platform to determine variant frequencies in each gate

first: Itamar

last: Kass

first: Yaron

last: Orenstein

first: Niv

last: Papo


title: Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome

city: Piscataway

first: Joshua

last: Thackray

state: NEW JERSEY

address: 145 Bevier Road

department: Human Genetics Institute of New Jersey

institute: Rutgers University

summary:
Sirtuins are deacetylases implicated in stress responses and longevity in mammals. Although their differential impact on disease for the two sexes have been noted, underlying reasons are not known. Here, using Sirtuin 7 (SIRT7) as a model in mice, we probe mechanisms leading to sex differences and find that Sirt7-/- females have decreased fitness throughout the lifespan. Intriguingly, SIRT7 preferentially localizes to the sex chromosomes. In females, SIRT7 loss affects “X-chromosome inactivation” (XCI), the 1st arm of dosage compensation that equalizes X-linked gene expression between males and females. Xist is overexpressed and gene silencing becomes more efficient. Surprisingly, however, SIRT7 loss has greatest impact on the active X (Xa). The Xa becomes hyperacetylated on H3K36ac, structurally disorganized, prone to DNA damage, and overexpressed. Increased Xa expression leads to genome imbalance and augmented “X-chromosome upregulation” (XCU) — the 2nd arm of dosage compensation that balances X-chromosome versus autosomal gene expression. These data reveal an essential crosstalk between sirtuins and the sex chromosomes, with SIRT7 safeguarding X-chromosome integrity and dosage balance with autosomes. We propose that the sex bias in Sirtuin 7 biology can be explained in part by unequal effects on the sex chromosomes.

This SuperSeries is composed of the SubSeries listed below.

first: Nicolas

last: Simonet

first: Barry

last: Kesner

first: Anna

last: Guitart-Solanes

first: François

last: Serra

first: Maria

last: Espinosa-Alcantud

last: Lappala

first: Laia

last: Marín-Gual

first: Cristina

last: Marín-García

first: Uri

last: Weissbein

first: Josema

last: Castelló-García

first: Moritz

last: Bauer

first: Danni

last: Wang

first: Llorenç

last: Rovirosa

first: Jay

last: Tischfield

first: Lourdes

last: Serrano

first: Bernhard

last: Payer

first: Aurora

last: Ruiz-Herrera

first: Berta

last: Vazquez

first: Biola

last: Javierre

first: Alejandro

last: Vaquero

first: Jeannie

middle: T

last: Lee


title: Mouse heart RNA-seq in isoproterenol (ISO) injury model with or without polystyrene nanoplastics co-exposure

city: Beijing

first: Yilin

last: Pan

address: Anzhen Road #2, Chaoyang District

institute: Beijing Anzhen Hospital

summary: Male C57BL/6 mice were assigned to three groups (n=6 per group): ISO, ISO+100 nm polystyrene nanoplastics (PS), and ISO+1 µm PS. Hearts were collected at the study endpoint and profiled by bulk mRNA-seq to identify transcriptional signatures associated with PS size in the setting of ISO-induced myocardial injury. Libraries were prepared and sequenced in two batches (Batch 1 by Novogene; Batch 2 by Majorbio Bio-Pharm Technology).

overall_design: Bulk RNA-seq was performed on mouse heart tissue (n=18). Differential expression analyses compared ISO+PS groups versus ISO, accounting for sequencing batch. Raw sequencing reads (FASTQ) and processed gene-level count are provided.

first: Linqi

last: Liu

first: Jiyuan

last: Luo

first: Xiaozheng

last: Zhou

first: Kun

last: Hua

first: Hanqing

last: Chen

first: Xiubin

last: Yang


title: Bulk RNA-seq of SIT1 knockout and control T cells from human healthy donors

city: Oslo

first: Pu

address: Gaustadalléen 21

department: Norwegian Center for Molecular Biosciences and Medicine

institute: University of Oslo

summary: The transmembrane adaptor protein SIT1 is a negative regulator of T cell receptor (TCR) signaling, but its role in human immunity remains poorly characterized. We performed bulk RNA sequencing (RNA-seq) on T cells derived from human healthy donors. SIT1 knockout (KO) was generated in primary T cells, and transcriptomic profiles were compared between SIT1 KO and control cells. This dataset enables the characterization of gene expression changes associated following SIT1 loss. Due to applicable data privacy regulations, identifiable information, including raw sequencing data from the participants, cannot be deposited in public repositories. Qualified researchers may request access to the data by submitting a formal application demonstrating compliance with the participants’ consent conditions. The consent signed by the study participants enables the use of data for study of rare immunological and hematological diseases. Requests should be directed to j.s.saarela@ncmbm.uio.no Processed gene expression data (read counts) and associated metadata are provided in this submission, providing a resource for studying SIT1-dependent transcriptional regulation in human T cells

overall_design:
CRISPR-Cas9 KOs of SIT1 were generated from PBMCs of three healthy donors using two guide RNA (sgRNA), separately. Control samples were electroporated with AAVS1 sgRNA complexes. Assays were performed seven days post-electroporation. Cells were stimulated with 200 ng/ml anti-CD3 (Hit3a, Thermofisher) or left unstimulated for 2 hours before proceeding to RNA extraction using a total RNA purification kit (Norgen Biotek Corp).

***************************************************************
Due to privacy regulations and participant consent,raw sequencing data cannot be deposited in public repositories. Data access is restricted to ensure compliance with consent for studying rare immunological/hematological diseases. Qualified researchers may request the raw data by submitting a formal application demonstrating compliance with these conditions. Direct requests to: j.s.saarela@ncmbm.uio.no.
***************************************************************

first: Janna

last: Saarela


title: Butyrylcholinesterase alleviates hepatic stellate cell activation via paracrine muscarinic signaling.

first: Tao

last: Le

address: LANXI ROAD 164

institute: Shanghai University of traditional Chinese Medicine

summary:
Background & Aims: Butyrylcholinesterase (BuChE) is an enzyme involved in Alzheimer’s disease (AD), detoxification and depression. While BuChE expression is reduced in liver cirrhosis, its physiological substrate, acetylcholine (ACh), promotes fibrogenic responses in hepatic stellate cells (HSCs). However, the function of BuChE in liver fibrosis and mechanistic link between these two observations is not known.
Methods: BuChE expression and HSC activation were assessed in liver biopsies from patients with liver fibrosis using qPCR and immunostaining. To investigate the functional role of BuChE in fibrogenesis, we employed BucheΔHep, knock-in (BucheKI/KI-Hep) mice, as well as pharmacological inhibition. The inhibitory effect of BuChE on HSC activation was further confirmed using conditioned medium from cells expressing mutant BuChE, in hepatocyte-HSC co-culture experiments, and analyses of recombinant BuChE protein. The release of ACh was measured with patch-clamp and the expression and functionality of its receptor were detected via intracellular Ca2+ influx measurements. The role of the muscarinic acetylcholine receptor 3 (ChRM3) in HSCs was investigated through gain- and loss-of-function experiments, utilizing Chrm3ΔHSC mice and AAV-mediated Chrm3 overexpression driven by the alpha-smooth muscle actin (Acta2) promoter.
Results: Buche mRNA expression in livers and enzymatic activity in serum are downregulated in patients and mouse models with liver fibrosis, and show a negative correlation with F stage and ACTA2 expression. Pharmacological inhibition or depletion of BuChE in hepatocytes results in increased HSC activation and aggravates liver fibrosis in various mouse models, whereas its overexpression exerts the opposite effect, indicating a causative role of BuChE downregulation in liver diseases. BuChE is predominantly expressed in hepatocytes in the liver, which can be reduced by TGFβ treatment. Notably, BuChE enzymatic activity is required to prevent HSC activation and fibrogenesis in homeostatic liver. As consequence of the lost BuChE metabolic activity, levels of released unmetabolized ACh are increased, which acts as DAMP to activate HSCs via ChRM3 signaling. This finding was confirmed using Chrm3ΔHSC mice, which exhibit diminished HSC activation and liver fibrosis. Conversely, ChRM3 overexpression in HSCs is promoting the fibrogenic process.
Conclusion: Hepatocyte injury disrupts BuChE activity, causing local ACh accumulation and subsequent HSC activation via ChRM3 signaling. This novel cholinergic circuit drives fibrosis and represents a promising new target for therapeutic intervention.

overall_design: Overexpression of BUCHE in hepatocytes and modeling with  BDL

first: Le

last: Tao

first: Nuoya

first: Wei

last: Zhang

first: Zongguo

first: Jianrong

last: Xu

first: Guang

last: Ji

first: Cheng


title: The role of Voclosporin administration and Inmt TG in renal proximal tubules.

city: Tokushima

first: Kazuhiro

last: Hasegawa

address: 3-18-15 Kuramoto-cho

department: Department of Nephrology

institute: Tokushima University Graduate School of Biomedical Sciences

summary: Indolethylamine N-methyltransferase (Inmt), an enzyme responsible for detoxifying local uremic toxins, including indole. We next investigated a strategy for preventing the significant decrease in Inmt expression in proximal tubules induced by high‑dose Voc administration and I/R. Accordingly, we used transgenic (Tg) mice with proximal tubule-specific Inmt overexpression and comparatively analyzed the changes with WT mice. Both WT and Tg mice were treated with high‑dose Voc, followed by I/R or sham operation for controls. Two experimental groups were campared using RNA-seq as follows: 1. I/R+WT+Voc (WT mice subjected to I/R and treated with high‑dose Voc)=WT+AKI, 2. I/R+Tg+Voc (Tg mice subjected to I/R and treated with high‑dose voclosporin)=TG+AKI.  Results: Inmt-overexpressing mice treated with high-dose voclosporin exhibited absence of peroxisomal abnormalities and resistance to I/R injury.

overall_design: Bulk RNAseq using the whole kidneys of Inmt TG mice and WT mice with voclosporin administration.


title: Loss of Gαq reshapes fibroblast traits and drives tumor-stroma remodeling in oral cancer progression

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

institute: CIEMAT

summary: Head and neck squamous cell carcinoma (HNSCC) is an aggressive malignancy with limited therapeutic options and poor outcomes due to metastasis.  A major driver of tumor progression is the tumor microenvironment, particularly cancer-associated fibroblasts (CAFs), which remodel the extracellular matrix and secrete pro-tumorigenic signals. Emerging evidence suggests that autophagy and vesicle trafficking pathways regulate these secretory functions, though their role in HNSCC remains unclear. Building on our discovery of Gαq as a central autophagy regulator, we investigated how its absence reshapes fibroblast behavior and modulates crosstalk with oral HNSCC cells. Our findings demonstrate that loss of Gαq reprograms murine fibroblasts into a CAF-like phenotype, in part through deregulated intracellular trafficking and increased ceramide accumulation. Gαq-deficient fibroblasts display increased collagen I deposition, ECM remodeling, and a shift toward secretory activity. Their exosomes, enriched in tumor-promoting growth factor receptors, suppress Caveolin 1 expression in tumor cells and induce an EMT-like phenotype that fuels aberrant HNSCC growth. In co-culture and in vivo, Gαq-silenced fibroblasts assemble into “railroad-track” structures that guide cancer cell migration and invasion. Reduced Gαq expression in human fibroblasts recapitulate these features underscoring a conserved mechanism of stromal activation. Overall, Gαq emerges as a key regulator of fibroblast plasticity and tumor-stroma interactions in HNSCC progression.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data obtained from WT and GαqKO mouse embrionary fibroblasts (3 biological replicates each genotype)

first: Inmaculada

last: Navarro-Lérida

first: Raquel

last: Huertas-Lárez

first: Ramón

last: García-Escudero

first: Federico

last: Mayor Jr

first: Catalina

last: Ribas


title: Human left atrial appendage RNA-seq in cardiac surgery patients with high versus low micro(nano)plastic burden

first: Yilin

last: Pan

summary: Micro(nano)plastics (MNPs) were quantified in left atrial appendage tissue collected intraoperatively from adult cardiac surgery patients at Beijing Anzhen Hospital. Samples were stratified into high (H1–H9) versus low (L1–L9) NP burden groups and profiled by bulk mRNA-seq to identify transcriptional signatures and pathways associated with tissue NP burden.

overall_design: Bulk RNA-seq was performed on human left atrial appendage tissue (n=18). Differential expression and pathway analyses compared high versus low NP burden groups. Raw sequencing reads (FASTQ) and processed gene-level count matrices are provided.

first: Linqi

last: Liu

first: Jiyuan

last: Luo

first: Xiaozheng

last: Zhou

first: Kun

first: Hanqing

first: Xiubin


title: Rbm24 promotes outer hair cell survival through Insm1 repression while independently regulating hair bundle morphogenesis

first: Zhiyong

address: Kexueyuan Road

institute: National Institute of Biological Sciences, Beijing

summary: The inactivation of Rbm24, an RNA-binding protein, leads to cell death and hair bundle defects in cochlear outer hair cells (OHCs). However, the underlying molecular mechanisms remain unclear. To address this, we have performed comprehensive transcriptomic profiling of purified wild type and Rbm24-/- OHCs at postnatal day 7 (P7). Loss of Rbm24 perturbs numerous genes associated with hair bundle morphogenesis and delays the overall OHC differentiation program. Insm1, a key transcription factor normally downregulated by P2, remains aberrantly and persistently expressed in Rbm24-/- OHCs. Overexpression of Insm1 alone induces OHC death, whereas simultaneous inactivation of Rbm24 and Insm1 largely rescues OHC survival but only partially restores hair bundle morphology. It demonstrates that Rbm24 promotes OHC survival independently of its role in regulating hair bundle morphogenesis. Collectively, our findings establish Rbm24 as a dual function regulator that ensures OHC survival by acting as a critical repressor of Insm1 expression, while independently orchestrating hair bundle assembly. These results highlight the central role of Rbm24 in coordinating OHC differentiation and structural maturation and provide insights into potential molecular targets for hair cell regeneration.

overall_design: The Ctrl HCs at P7 were manually picked via Atoh1P2A-Tdtomato/+ mice in which Atoh1 gene expression is intact and both IHCs and OHCs are Tdtomato+. Similarly, Rbm24-/- HCs at P7 were obtained by using the Atoh1P2A-Cre/P2A-Tdtomato; Rbm24flox/flox mice. Briefly, both Ctrl and Rbm24-/- HCs were Tdtomato+ and they were picked and immediately subjected to smart-seq based single cell full length RNA-seq. Finally, 81 Ctrl HCs and 82 Rbm24-/- HCs passed our quality check and used for subsequent analysis.

first: Chao

last: Li

first: Yishu

last: Zhao

first: Luyue

last: Wang

first: Shuting

first: Jie

first: Yunpeng

last: Gu

first: Shunji

last: He

first: Guangqin

first: Fang

last: Lei

first: Ying

last: Lu

first: Liqin

first: Shengjin

first: Wei

last: Xiong

first: Bin


title: Ketogenesis promotes leukemia development by inhibiting ferroptosis in leukemic stem cells [RNA-Seq]

city: guangzhou

first: Songqi

last: Zhu

state: guangdong

address: No. 74, Zhongshan 2nd Road, Yuexiu District

institute: Sun Yat-sen University

summary: Hepatic ketogenesis generates ketone bodies as an alternative energy source during carbohydrate restriction or ketogenic diets, yet its role in non-hepatic cell types remains poorly defined. Here, we show that leukemic stem cells (LSCs) in acute myeloid leukemia (AML) engage elevated ketogenesis, driven by fatty acid oxidation (FAO), to produce D-β-hydroxybutyrate (BHB). LSCs express high levels of 3-hydroxymethylglutaryl-CoA synthase 2 (HMGCS2), the rate-limiting enzyme in ketogenesis than blast cells and normal hematopoietic stem cells (HSCs). Deletion of Hmgcs2 in AML cells markedly decreases BHB levels, disrupts LSC function, and impairs leukemia progression in both mouse and human AML models, while largely sparing normal hematopoiesis. Mechanistically, BHB suppresses ferroptosis by limiting pro-ferroptotic phospholipid remodeling through epigenetic regulation of fatty acid desaturase 2 (FADS2). Together, these findings identify autonomous ketogenesis as a critical metabolic program that protects LSCs from ferroptotic cell death and sustains leukemia progression.

overall_design: RNA-seq profiling of LICs derived from three groups of C57BL/6J mice: AML, AML with Hmgcs2 knockout (HMGCS2 KO), and AML HMGCS2 KO supplemented with BHB. This study aims to elucidate autonomous ketogenesis as a critical metabolic mechanism that protects LICs from ferroptotic cell death and supports leukemia progression.

first: Xue

last: Han

first: Kexin

first: Weiwei

last: Ma

first: Jingjing

last: Guan

first: Xiaobin

last: Tian

first: Zhuangzhhuang

first: Linjia

last: Jiang


title: Inducible XIST-mediated trisomy 21 correction uncovers a USP16-p16 senescence axis driving epileptogenesis in Down syndrome

city: Chongqing

first: Kai

last: Guo

address: 1 Youyi Road, Yuzhong District

institute: Chongqing Medical University

summary: Down syndrome (DS), caused by human chromosome 21 (HSA21) trisomy, carries elevated epilepsy risk with unknown mechanisms. We integrated clinical epidemiology, fetal brain single-nucleus RNA sequencing, patient-derived induced pluripotent stem cell (iPSC) models, cerebral organoids, and in vivo chimeric mice to dissect this link. Clinical analysis of 1,365 DS individuals exhibited an age-stratified epilepsy prevalence pattern, with higher rates in older children. Fetal brain transcriptomes revealed neurogenesis defects, aging-related signatures, synaptic/metabolic dysregulation. We engineered an inducible XIST-mediated extra HSA21 silencing system in female DS iPSCs, showing HSA21 dosage correction reduced neural progenitor cell (NPC) senescence markers and neuronal hyperexcitability. Transcriptomic screening pinpointed USP16 as a key pro-aging candidate. Moreover, USP16 suppression and the senolytic combination dasatinib/quercetin reduced senescence-linked and hyperexcitability-associated readouts, supporting a USP16-p16-NPC aging axis as a therapeutic target for DS-associated epilepsy, with broader implications for aging-linked neurological disorders.

overall_design: Transcriptome profiling of human NPCs under distinct genetic/experimental conditions to identify trisomy 21 (HSA21) dosage-dependent gene expression changes.

first: Jianhe

first: Yating

first: Yifan

last: zhang

first: Shuo

last: Zhang

first: Tongfei

last: Liu


title: Ketogenesis promotes leukemia development by inhibiting ferroptosis in leukemic stem cells [ATAC-Seq]

overall_design: ATAC-seq profiling of LICs derived from two groups of C57BL/6J mice: AML and AML with Hmgcs2 knockout (HMGCS2 KO). This study aims to elucidate autonomous ketogenesis as a critical metabolic mechanism that protects LICs from ferroptotic cell death and supports leukemia progression.

last: Zhao


title: Sex-Dependent Effects of Glutamatergic Disruption on Dopaminergic Neuron Subtype Vulnerable in Parkinson’s Disease

city: Bethesda

first: Mark

middle: R

last: Cookson

state: MD

address: NIHBC 35 - PNRC I BG RM 1A-116

institute: National Institutue on Aging, NIH

summary: Aldehyde dehydrogenase 1A1-positive (ALDH1A1+) dopaminergic neurons are selectively vulnerable in Parkinson’s disease (PD), yet how their activity is shaped by presynaptic inputs is unclear. We investigated the role of glutamatergic input by conditionally deleting Grin1, encoding a critical NMDA receptor subunit, in ALDH1A1+ neurons. Grin1 conditional knockout mice showed normal locomotion and motor learning, but females exhibited increased operant reward acquisition along with excessive feeding and weight gain after food restriction. To determine regional contributions in female mice, we selectively knocked down Grin1 in ALDH1A1+ neurons of the ventral tegmental area (VTA) or substantia nigra pars compacta. VTA-specific knockdown in females reproduced the post-restriction feeding and weight gain phenotype. Bulk whole-brain mRNA sequencing revealed significant gene expression changes based on sex primarily in Grin1 conditional knockout mice following food restriction. Many of the differentially expressed genes were associated with energy production, metabolic responses, and glial function. These findings reveal a sex-specific role for NMDA receptor–mediated glutamatergic input to ALDH1A1+ VTA neurons in regulating feeding behavior, providing mechanistic insight into how dysfunction of this vulnerable subpopulation may contribute to PD-related non-motor symptoms.

overall_design: mRNA-seq was used to characterize the sex- and feeding state-dependent transcriptomic effects of impaired glutamatergic input to ALDH1A1+ midbrain dopaminergic neurons following conditonal knockout of the Grin1 gene. The brains of female and male Grin1 conditional knockout and control mice were collected either: 1) prior to any food restriction, 2) immediately after two consecutive nights of food restriction, or 3) after two consecutive nights of food restriction followed by three consecutive days of free access to food via an automatic feeding device.

first: Kathleen

middle: F

last: Carmichael

first: Gavin

last: Riccobono

first: Victor

last: Martinez Smith

first: Jinhui

last: Ding

first: Lisa

last: Chang

first: Lixin

last: Sun

first: Lupeng

last: Wang

first: Huaibin

last: Cai


title: Modular Scalable Synthetic Gene Circuits for Complex Functions Within Minimal Computational Layers in Human Cells

city: Rehovot

first: Fabian

last: Stamp

address: Herzl St 234

department: department of brain science

institute: The Weziamnn institiute of science

summary: Engineering mammalian cells to execute complex genetic programs remains a significant challenge in synthetic biology. Synthetic gene circuits typically implement sophisticated programs through cascaded computational layers, but these architectures require numerous orthogonal parts, increase genetic payload, and deplete cellular resources, which limits functionality and scalability. We developed a modular design framework to engineer scalable gene circuits that execute complex functions within fewer computational layers. The platform integrates a toolkit to generate orthogonal trans-splicing-based AND gates, native-synthetic hybrid promoters for tunable regulation, and synthetic microRNAs that implement inhibitory logic. Using this approach, we engineered a three-input combinatorial logic gate, a half adder, a full adder, and a dynamic 3-to-1 multiplexer with a dedicated Selector Overload Status output, activated only when both selector inputs are activated. By minimizing computational layers while maintaining function, this strategy addresses scalability barriers in gene circuit engineering and expands opportunities for clinically relevant programmable therapies, biotechnology, and fundamental biology.

overall_design: RNA-seq profiling of HEK293T cells transfected with different pairs of trans-splicing constructs BD5-BD10, and a positive control(mKate2) and a negative control, non-treated cells ( NT).

first: Keren

last: Roas

first: Ilanit

last: Kovalski

first: Odelia

last: Mouhadeb

first: Tamar

last: Aminov

first: Hadas

last: Weinstein-Marom

first: Lior

last: Nissim


title: Study on the analgesic and anti-inflammatory mechanisms of Jingu Zhitong Gel in the treatment of knee osteoarthritis through the IL-17, NGF-TrkA, and COX-2/PGE2 pathways

city: Nan jing

first: 璐

last: 李

state: jiangsu

address: 龙眠大道578号

institute: 江苏康缘药业股份有限公司

summary: To investigate the therapeutic effects of JGZTG on KOA and elucidate the potential mechanism.Initially, we established a KOA rat model and treated it with JGZTG for 21 days. This study integrated systems pharmacology, transcriptomics, and experimental validation to decipher its mechanisms.After 21days’ treatment, JGZTG significantly increased the pain threshold and the weight bearing on the right foot in KOA rats, reduced inflammatory factor levels of TNFα, IL-6, IL-1β, and PGE2 in the serum and joint lavage fluid of KOA rats with dose dependency. In addition, JGZTG could significantly decrease joint morphology score, improve pathological synovial damage, ameliorate pathological cartilage injury, and alleviate loss of cartilage collagen in KOA models. The results of transcriptomic analysis showed that the anti-inflammatory effect of JGZTG treating KOA might be related to the IL-17 signaling pathway. Further validation via RT-qPCR,WB,and IF of synovial and DRG tissue revealed that JGZTG exhibits pain-relieving and anti-inflammatory effects in KOA, which were potentially achieved by modulating IL-17, NGF-TrkA, and COX-2/PGE2 pathways. These findings provided theoretical support for the mechanisms underlying the therapeutic effects of JGZTG in KOA.

overall_design: RNA extraction, library construction, and transcriptome sequencing were conducted by Hangzhou Lianchuan Biotechnology Co., Ltd. The total RNA of three synovial tissue samples from each group was extracted using TRIzol reagent (Thermo Fisher). The concentration and purity of total RNA were assessed using the 6000 Nano LabChip Kit (Agilent, CA, USA), while the total RNA integrity number (RIN) was analyzed using Bioanalyzer 2100. The synovial tissue RNA samples with RIN > 7.0 were used to construct the sequencing library. Transcriptome sequencing was performed using the Illumina HiSeq NovaSeq 6000 platform (Illumina, USA).

first: Lu

last: Li

first: Yiyao

last: Liang

first: Jing

last: Dong

first: Zhenzhen

last: Su

first: Xinyu

last: Xu

first: Ziying

last: Wu

first: Xinzhuang

last: Zhang

first: Liang

last: Cao

first: Zhenzhong

first: Wenjun

last: Liu**

first: Wei

last: Xiao*


title: Abemaciclib enhances Antitumor Activity of Dasatinib in Papillary Renal Cell Carcinoma

city: BETHESDA

first: Ramaprasad

last: Srinivasan

address: 1-W-5888, 10 center drive

department: Urologic Oncology Branch

institute: National Cancer Institute – NIH

summary: We aimed to utilize next-generation sequencing to gain deeper insights into the molecular pathways underlying the anti-tumor activity of the SRC inhibitor Dasatinib in papillary renal cancer. Our findings revealed a distinct set of target genes and pathways of relevance to this cancer subtype, offering promising avenues for the development of clinically effective therapeutic strategies.

overall_design: To investigate the molecular effects of Dasatinib in papillary renal cell carcinoma (PRCC), we performed mRNA sequencing on PRCC cell lines (UOK345 and UOK342) treated with 25 nM Dasatinib for 48 hours. Untreated and treated samples were subjected to transcriptomic analysis to identify differentially expressed genes and pathways.

first: Roma

last: Pahwa

first: Alexei

last: Lobanov


title: Integrative single cell RNA-sequencing and spatial transcriptomics uncovers distinct macrophage-fibroblast cross-talk in human hip synovium between patients with femoroacetabular impingement and osteoarthritis

city: Rochester

first: Gulzada

last: Kulzhanova

address: 310 University Park

institute: University of Rochester

summary: Femoroacetabular impingement (FAI) and synovitis have been recognized as essential factors for developing osteoarthritis (OA) in the hip joints. However, little is known about altered synovial cellular compositions, their associated transcriptomic profiles, and cell-cell interactions between patients with FAI and hip OA. In the current study, by using integrative single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (Spatial-seq), we identified the molecular mechanisms by which synovial cells promote hip OA pathogenesis from FAI. Compared to FAI synovium, epiregulin (EREG)-enriched lining fibroblast-like synoviocytes (FLS) were significantly increased in the hip OA synovium. These EREG+ FLS are pro-inflammatory due to their high expression of CXCL1, IL8 (CXCL8), and MMPs. Furthermore, pseudotime analysis predicts that EREG+ FLS are potentially derived from DPP4+PI16+ sublining FLS. Importantly, analysis of cell-cell interactions indicates that fibroblast growth factor 2 (FGF2) secreted from COL1A1+IGFBP5+ fibrotic macrophages may signal through syndecan 4 (SDC4) expressed by EREG+ lining FLS, inducing the expression of IL6, IL8, MMP1, and PTGS2. The GO term analysis of activated genes downstream of FGF2-SDC4 signaling revealed that biological processes associated with inflammation and angiogenesis were upregulated in hip OA, while mechanical stimulus and skeletal muscle differentiation were dominant in FAI. Moreover, we also found that EREG+CCL20+MMP3hi lining FLS as well as most macrophage and monocyte populations are unique to hip OA patients when compared to knee OA and RA patients. The findings of this study offer a groundwork in tailoring novel targets and therapies for FAI and hip OA patients.

overall_design: Single cell RNA-sequnecing and Spatial transcriptomics of the human hip synovium samples from patients with femoroacetabular impingement and osteoarthritis

first: Chia-Lung


title: Compare the loci-specific histone acetylation on the chromatin of FK228 and Class I HDACs YF mutants overexpression

city: Suzhou

first: Hang

last: Ruan

state: Jiangsu

address: 199 Ren'ai Road

department: IBMS

institute: Soochow University

summary: To compare the H3K27ac effects of FK228 and Class I HDACs YF mutants overexpression and to characterize their inter-dependency, we performed ChIP-seq in AML12 cells in the above-mentioned 4 groups: control, FK228, YF overexpression, and FK228 + YF overexpression.

first: Zheng

last: Sun

first: Chaitra

last: Rai

first: Leng

last: Han

first: Wenbo


title: Single-Cell Transcriptomics Reveal Distinct Biological and Immunometabolic Landscapes in Renal Medullary Carcinoma Compared to Clear Cell Renal Cell Carcinoma

first: Pavlos

last: Msaouel

state: Texas

address: 1155 Pressler Street, Unit 1374

department: Genitourinary Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

summary: Renal medullary carcinoma (RMC) is a rare, highly aggressive kidney malignancy primarily affecting young individuals of African descent with sickle cell trait. The currently available targeted therapies and immunotherapies approved for clear cell renal cell carcinoma (ccRCC) are ineffective against RMC, highlighting the urgent need for novel treatment approaches specifically tailored to the distinct biological and immune hallmarks of RMC. Here, we performed single-cell RNA-sequencing (scRNA-seq) of tumor samples from five patients with RMC and five patients with ccRCC to define their immunometabolic and transcriptomic landscapes. Differential expression analysis identified ENPP3 and CA9 as distinct cell surface markers upregulated in ccRCC, whereas MUC16, TROP2, and EPCAM were upregulated in RMC tumors cells. RMC displayed a more immunosuppressive tumor microenvironment (TME), with lower infiltration of T and NK cells but an enrichment of immunosuppressive SPP1+ macrophages, contrasting with the more immune-rich TME in ccRCC. Ligand-receptor interaction analyses revealed stronger VEGF-VEGFR signaling in ccRCC and enhanced APP-CD74 signaling in RMC. Nephron anatomy mapping indicated that RMC originates in the loop of Henle, whereas ccRCC arises from proximal tubule cells. We uncovered distinct metabolic reprogramming, with RMC demonstrating higher oxidative phosphorylation (OXPHOS) and lower glycolysis compared to ccRCC. These findings were validated in vitro with RMC cell lines showing elevated oxygen consumption and diminished extracellular acidification compared with ccRCC cell lines. Overall, this study underscores the distinct origins, gene expression patterns, and immunometabolic features of RMC versus ccRCC, offering insights for future tailored therapeutic strategies against RMC.

overall_design:
we performed single-cell RNA-sequencing (scRNA-seq) of tumor samples from five patients with RMC and five patients with ccRCC to define their immunometabolic and transcriptomic landscapes.

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

first: Xinmiao

last: Yan

first: Jianfeng

last: Chen

first: Jianjun

last: Gao

first: Linghua

last: Wang


title: Compare the transcriptomic effects of FK228 and Class I HDACs YF mutants overexpression

summary: To compare the transcriptomic effects of FK228 and Class I HDACs YF mutants overexpression and to characterize their inter-dependency, we performed RNA-seq in AML12 cells in the above-mentioned 4 groups: control, FK228, YF overexpression, and FK228 + YF overexpression.

last: Li


title: ASCL1 chromatin binding in neuroblastoma cell lines [ChIP-seq]

city: Cambridge

first: Lidiya

last: Mykhaylechko

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

country: United Kingdom

institute: University of cambridge

summary: To compare the ASCL1 protein binding to chromatin in two MYCN-amplified neuroblastoma cell contexts, we have used a doxycycline-inducible lentivirus system to induce ASCL1 overexpression in SK-N-BE(2)C and IMR-32 cell lines, and assessed ASCL1 binding using ChIP-seq.

overall_design: ASCL1 ChIP-seq in ASCL1-induced lines

first: Laura

last: Woods

first: Anna

last: Philpott


title: Regulatory Effects of Smoking Cessation on the Cellular Microenvironment and Differentially Expressed Genes in Precancerous Lesions of Pulmonary Nodules in Mice based on Single-Cell RNA-Sequencing and Immune Repertoire-Sequencing

city: Harbin

first: Xintong

address: No. 37, Yiyuan Street, Nangang District, Harbin 150001, China

institute: Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital of Harbin Medical University

summary: Smoking cessation is known to reduce lung cancer progression, but its impact on precancerous lesions remains largely unexplored. In this study, a smoking-induced mouse model of pulmonary precancerous lesions was established using 6-week benzo[a]pyrene (B[a]P) exposure. Lung nodules were identified through micro-MRI imaging and histopathological evaluation by H&E staining and fluorescence microscopy. Smoking cessation interventions were applied for 4 and 8 weeks following lesion confirmation. Nodule size was quantified with Generic Medical Imaging software. Single-cell RNA sequencing (scRNA-seq) and immune repertoire sequencing (IR-seq) were performed to analyze immune cell composition, intercellular communication pathways, and receptor diversity. These approaches provide a comprehensive framework for investigating the cellular and molecular changes associated with smoking cessation in early lung lesion development.

overall_design: A benzo[a]pyrene (B[a]P)-induced mouse model of pulmonary precancerous lesions was established by oral gavage in 5-week-old female Kunming mice. Mice were divided into four groups (n=32 each) based on planned interventions: Group A (continuous B[a]P for 6 weeks), Group B (6-week B[a]P followed by 4-week cessation), Group C (6-week B[a]P followed by 8-week cessation), and Group D (untreated control). However, only Groups A, B, and C were included in the actual sequencing experiments due to resource and experimental constraints. Lung nodule formation was assessed by 9.4T MRI. Tissues from Groups A–C were collected for H&E staining, single-cell RNA sequencing (scRNA-seq), and immune repertoire sequencing (IR-seq) to analyze immune cell composition, gene expression profiles, and BCR/TCR clonal dynamics under different smoking cessation conditions.

first: Fang

last: Tang

first: Chunli

last: Che

first: Jiayu

last: Qin

first: Tiquan

last: Xiao

first: Liwei

last: Shi

first: Shujun

last: Zhang


title: Heterologous expression of interferon-stimulated genes reveals conserved anti-Toxoplasma properties between human and porcine cells

city: Edinburgh

first: Marzuq

last: Ungogo

state: Midlothian

address: Easter Bush Campus, Easter Bush Campus

department: Roslin Institute

institute: University of Edinburgh

summary: Toxoplasma is a zoonotic parasite that can cause life-threatening illness in humans and animals. The similarities in Toxoplasma pathogenesis between pigs and humans make pigs an attractive model for studying human toxoplasmosis. However, the mechanisms underpinning these similarities remain poorly understood. Since interferon-gamma (IFNg) is crucial for immunity to Toxoplasma, we hypothesized that IFNg signaling pathways conserved between humans and pigs contribute to comparable Toxoplasma pathogenesis. Using a genetic gain-of-function strategy, we observed that human or porcine interferon regulatory factor 1 (IRF1) and indoleamine 2,3-dioxygenase 1 (IDO1) inhibited Toxoplasma replication in both homologous and heterologous human and porcine cells. IRF1-depleted porcine cells that failed to control Toxoplasma growth could be rescued by ectopic expression of human IRF1, which induces genes similar to those regulated by porcine IRF1. Additionally, the expression of either human or pig IRF1 dampened Toxoplasma-induced transcriptional remodeling of porcine genes. These findings highlight conserved IFN-induced anti-Toxoplasma mechanisms between pigs and humans and enhance the potential of pigs as large animal models for human toxoplasmosis.

overall_design: IRF1-depleted cells were transduced with lentivirus expressing human IRF1, pig IRF1 or empty vector. At 72 h post-transduction, cells were left uninfected or infected with Toxoplasma PruA7 and incubated for further 48 h. Cells were harvested, and RNA was isolated from each group, sequenced and analysed. Gene expression was compared between empty vector and IRF1-expressing groups, and between infected and uninfected cells in each group.

first: Praveena R

last: Chandrasegaran

first: Hamza

last: Khalid

first: Jessica

last: Powell

first: Hamna

last: Jamil

first: Finn

last: Grey

first: Musa

last: Hassan


title: Transcriptome analysis of BJ cells after treatment with siRNA knockdown of Agrin.

city: Singapore

first: Pierre-alexis

last: Goy

state: Singapore

address: 60 Biopolis Street

institute: Genome Institute of Singapore (GIS-ASTAR)

summary: This work describes the alteration in the expression of genes in response to siRNA knockdown of Agrin.

overall_design: This dataset contains RNA-seq analysis of siRNA control and siRNA Agrin knockdown cells, taken as triplicates.

first: Sayan

last: Chakraborty

first: Pierre-Alexis

first: Divyaleka

last: Sampath


title: KMT2C and KMT2D amplify GRHL2-driven enhancer activation [CUT&Tag]

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 35 Medical Center Way

institute: UCSF

summary: The activation of cis-regulatory enhancers is essential for cell fate specification by driving cell type-specific gene expression. Differentiation models are widely used to study enhancer biology but the asynchronous and interdependent nature of gene regulatory changes during cell state transitions can complicate mechanistic studies. To overcome these limitations, here we develop a tamoxifen-gated system for acute enhancer activation in embryonic stem cells (ESCs) based on GRHL2, a pioneer transcription factor which naturally becomes expressed as naive ESCs differentiate into the formative ESC state. Using this system, we investigate the functional relationship between GRHL2 and the histone mono-methyltransferases KMT2C and KMT2D (KMT2C/D). GRHL2 readily binds its target sites independent of KMT2C/D. However, in the absence of KMT2C/D, there are dramatic reductions in H3K4me1/2, P300 recruitment, and H3K27ac deposition at these sites as well as diminished transcriptional activation. Still, strikingly, a basal level of active enhancer mark acquisition and transcriptional activation occurs. Consistent with these findings, during the naive to formative ESC differentiation, GRHL2 enhancer remodeling and target expression is also strongly but incompletely dependent on KMT2C/D. Together, these results define a functional co-activator relationship in which KMT2C/D act as important amplifiers of GRHL2-driven enhancer activation in ESCs and establish a rapid inducible system for dissecting the kinetics and enzymatic dependencies of pioneer transcription factor mediated enhancer remodeling.

overall_design:
In general, Kmt2CKO (CKO)  or Kmt2c/d double KO (dKO) cells were transposed with the GRHL2-ERT system and clones were selected with comparable levels of GRHL2 expression. Cell lines were then treated with EtOH or Tamoxifen for 8 before harvesting cells for CUT&Tag and CUT&Run experiments. Some CUT&tag samples were generated using the naive to formative differentiation on CKO and dKO cells which did not harbor the GRHL2-ERT system.
For each rep1 & rep2 pair, the bw processed data file is linked to the Sample record for rep1.

first: Ryan

last: Boileau

first: Kevin

middle: X

last: Chen

middle: H


title: KMT2C and KMT2D amplify GRHL2-driven enhancer activation [Cut&Run]

overall_design: Kmt2CKO (CKO)  or Kmt2c/d double KO (dKO) cells were transposed with the GRHL2-ERT system and clones were selected with comparable levels of GRHL2 expression. Cell lines were then treated with EtOH or Tamoxifen for 8 or 16hours before harvesting RNA and performing 3' end capture RNA-seq. Included are cell controls treated with EtOH/Tam but without GRHL2-ERT.


title: Spatial predictors of response to chemo-immunotherapy in microsatellite stable metastatic colorectal cancer

status: Public on Mar 27 2026

first: Solomonraj

last: Wilson

address: 8A Biomedical Grove

institute: SIgN

summary: Microsatellite-stable (MSS) colorectal cancers (CRC) are largely unresponsive to immune checkpoint inhibition (ICI). The MAYA trial used temozolomide (TMZ) in MGMT-silenced MSS mCRC, hypothesizing that TMZ-induced hypermutation could sensitize tumors to ICI; the primary endpoint was met, showing durable responses with TMZ plus ipilimumab and nivolumab. We perform integrated spatial, transcriptomic, and immune profiling of longitudinal tumor and blood samples from patients treated on the MAYA trial. Post-TMZ increases in tumor mutational burden associate with improved progression-free survival. Spatial profiling demonstrates that clinical benefit is greatest in permissive tumor microenvironments. Responders exhibit enrichment of cytotoxic T cells across tumor and stromal compartments, whereas non-responders display heterogeneous cellular neighborhoods, with fibroblasts in close spatial proximity to T cells, consistent with barriers to immune mediated clearance. Longitudinal peripheral immune profiling shows that early upregulation of TIGIT and PD-1 following TMZ exposure predicts resistance. Together, these findings indicate that both mutational evolution and spatial immune architecture contribute to immune sensitization in MGMT-silenced MSS CRC.

overall_design: We profiled formalin-fixed and paraffin embedded (FFPE) tumor samples from patients with MSS colorectal cancer who received Nivolumab + Ipilimumab + Temozolomide on the MAYA study to generate histologic and  spatial transcriptomics profiling using Visium  (10x Genomics, Inc.).

first: Joan

last: Choo

first: Joseph J

last: Zhao

first: Mai Chan

last: Lau

first: Raghav

last: Sundar

first: Filippo

last: Pietrantonio


title: KMT2C and KMT2D amplify GRHL2-driven enhancer activation [RNA-Seq]