title: ABHD11-mediated mtDNA transcription restored mitochondrial function to attenuate cardiomyocyte ferroptosis after myocardial infarction

city: Guangzhou

first: Yu

last: Liu

address: No. 1838, Guangzhou Avenue North

institute: NANFANG HOSPITAL SOUTHERN MEDICAL UNIVERSITY

summary:
BACKGROUND: Cardiomyocytes (CMs) exhibit marked susceptibility to ferroptosis following myocardial infarction (MI), rendering ferroptosis inhibition as a promising therapeutic strategy to mitigate ischemic myocardial injury. Although mitochondrial dysfunction is well-established as a central driver of ferroptosis via redox imbalance and lipid metabolism disruption, the regulatory role of mtDNA transcription in CM ferroptosis remains unexplored.
METHODS: To clarify the temporal role of the various modes of cell death in MI progression, we performed time-course echocardiography in MI models treated with various cell death inhibitors. To characterize the crucial process and molecular regulator in CM ferroptosis, we integrated RNA-seq and snRNA-seq data from murine post-MI hearts and performed functional rescue experiments using mitochondrial protective agents. To determine the role of ABHD11 in CM ferroptosis and cardiac repair post-MI, we employed loss- and gain-of-function approaches. To elucidate the underlying mechanisms, we conducted transcriptomics, non-targeted lipidomics, site-specific mutagenesis, molecular docking, Co-IP, native gel electrophoresis, and proximity ligation assay.
RESULTS: We found that cardiac ferroptosis peaked at day 7 post-MI and was enriched in peri-infarct CMs. Mitochondrial dysfunction was a key driver of CM ferroptosis post-MI and the lipid enzyme ABHD11 (αβ-hydrolase domain-containing protein 11) was identified as a potential regulator of both processes. ABHD11 expression was consistently reduced in mouse and human MI hearts. Functionally, cardiac-specific overexpression of ABHD11 markedly alleviated CM ferroptosis and improved cardiac function after MI. Conversely, loss of ABHD11 in adult mice exacerbated pathological cardiac remodeling and heart failure. Independent of its canonical enzymatic activities, ABHD11 enhanced the TEFM-POLRMT interaction, thereby promoting mtDNA transcription, restoring mitochondrial function, and thus inhibiting ROS/PUFA-PLs-driven lipid peroxidation and 4-HNE generation. The reduction in 4-HNE stabilized the transcription factor YY1, which subsequently downregulated key ferroptosis drivers and upregulated the nuclear-encoded ETC and FAO genes, thereby establishing a mitochondrial-nuclear crosstalk.
CONCLUSIONS: This study revealed that ABHD11-mediated mtDNA transcription attenuated CM ferroptosis post-MI by orchestrating a mitochondrial-nuclear crosstalk, offering a novel therapeutic strategy for ischemic myocardial injury.

overall_design: RNA‑seq data of primary cardiomyocytes overexpressing ABHD11 via Adv‑ABHD11 and their control group, followed by 24‑hour hypoxia treatment

first: Yijin

last: Chen

first: Hao

last: Zheng

first: Jianping

last: Bing

first: Yanmei


title: Spatial biology reveals macrophage dysfunction in immunosuppressed non-melanoma skin cancer

status: Public on Aug 07 2026

city: Houston

first: Veena

last: Kochat

state: TX

address: 1901 East Road

department: Genomic Medicine

country: USA

institute: The University of Texas MD Anderson Cancer Center

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary: The rising incidence of non-melanoma skin cancer (NMSC), including basal cell carcinoma (BCC) and cutaneous squamous cell carcinoma (cSCC), particularly among immunosuppressed individuals, underscores the need for a deeper understanding of the tumor microenvironment (TME) to develop effective and safe immunotherapies. This study employed single-cell multi-omic analyses to investigate the spatial distribution and transcriptional profiles of immune cells in NMSC from both immunocompetent and immunosuppressed patients. Our results challenge the prevailing notion that immunosuppression is primarily driven by reduced immune cell abundance or lymphocytic dysfunction. Instead, we identified a critical deficiency in antigen presentation by macrophages, leading to impaired T-cell diversity and clonal expansion. Additionally, a spatial epigenomic atlas of the NMSC TME revealed distinct spatial niches and epigenetic programs associated with immunosuppression. These findings highlight the central role of innate immunity in shaping anti-tumor responses and offer potential therapeutic targets to enhance immunotherapy in this vulnerable patient population.

overall_design:
Single cell multiome was performed in 8 samples of tumor tissue obtained from 8 untreated patients (4 immunosuppressed, 4 immunocompetent) with basal cell carcinoma or cutaneous squamous cell carcinoma.
Submitters state that the raw data generated in this study will not be uploaded or made publicly available, as it contains information that could potentially compromise patient privacy. In order to comply with institutional and regulatory requirements for protecting human subject confidentiality, only processed and de-identified data have been shared.

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

first: Kochat

last: Veena

first: Satpati

last: Suresh

first: Rai

last: Kunal

first: Moran

last: Amit


address: 1515 Holcombe Blvd

department: Head & Neck Surgery

institute: University of Texas - MD Anderson Cancer Center

summary: The rising incidence of non-melanoma skin cancer (NMSC), including basal cell carcinoma (BCC) and cutaneous squamous cell carcinoma (cSCC), particularly among immunosuppressed individuals, underscores the need for a deeper understanding of the tumor microenvironment (TME) to develop effective and safe immunotherapies. This study employed single-cell multi-omic analyses to investigate the spatial distribution and transcriptional profiles of immune cells in NMSC from both immunocompetent (IC) and immunosuppressed (IS) patients. Our results challenge the prevailing notion that immunosuppression is primarily driven by reduced immune cell abundance or lymphocytic dysfunction. We found that IS tumors retain all requisite immune cell populations but display functional suppression and disrupted spatial organization. Our data revealed a limited number of distinct programs, particularly in macrophages and their spatially organized niches, that are linked to restricted T-cell repertoire diversity and impaired clonal expansion, providing a mechanistic bridge between innate dysfunction and adaptive immune failure. These perturbations were further confirmed by a novel spatial epigenomic atlas of the NMSC TME that revealed immune status–specific regulatory programs, including MAF- and ATF3-driven macrophages and CUX1- enriched fibroblast niches, that shape the epigenetic landscape of immunosuppressed tumors. These findings highlight the central role of innate immunity in shaping anti-tumor responses and offer potential therapeutic targets to enhance immunotherapy in this vulnerable patient population.

overall_design: 36 samples of tumor tissue (23 immunosuppressed and 13 immunocompetent) obtained from 30 untreated patients with basal cell carcinom or cutaneous squamous cell carcinoma. FACS was used to enrich for CD45+ cells and then single cell RNA sequencing was performed.

first: Shorook

last: Naara

first: Xiayu

last: Rao

first: Emre

last: Arslan

first: Robert

last: Saddawi-Konefka

first: Suresh

last: Satpai

first: Jennifer

last: Garbarino

middle: L

last: Anderson

first: Frederico

middle: O

last: Gleber-Netto

first: Priyadharsini

last: Nagarajan

first: Travis

middle: D

last: Kerr

first: Shamima

last: Akhter

first: Sophie

last: Li

first: Ray

last: Fodor

first: Shlomo

middle: A

last: Koyfman

first: Dan

last: Yaniv

first: Tongxin

last: Xie

first: Mica

last: Glaun

first: Michael

last: Bobian

first: William

middle: I

last: Pardon

first: Colin

last: Ng

first: Preethi

last: Gunaratne

first: Shiyanth

last: Thevasagayampillai

middle: R

last: Migden

first: Hussein

last: Abbas

first: Patrick

middle: K

last: Reville

first: Keneth

middle: Y

last: Tsai

first: Daniel

last: McGrail

first: Jing

last: Wang

first: Jeffrey

middle: N

last: Myers

first: Neil

last: Gross

first: Kunal

last: Rai


title: Profiling the RNA-Binding Proteome of KSHV-Infected Cells Uncovers a Viral Strategy for Hijacking Host Signaling via RNA-Dependent Interactions.

city: Nashville

first: John

last: Karijolich

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

summary: Viruses encode RNA-binding proteins (RBPs) to manipulate host processes and promote infection. However, due to limited genomic space, many viral proteins are multifunctional and may engage RNA through non-canonical domains, making their identification difficult using traditional sequence-based approaches. Kaposi’s sarcoma-associated herpesvirus (KSHV) is the etiological agent of many AIDS-associated cancers. Here, leveraging an unbiased proteomic approach we identified all RBPs in KSHV-infected primary effusion lymphoma (PEL) cells, uncovering 7 previously unrecognized KSHV-encoded RBPs. Among these is viral Interferon Regulatory Factor 1 (vIRF1), which we found is both necessary and sufficient to activate oncogenic RAS/MAPK signaling through an RNA-dependent interaction with host G3BP proteins. Importantly, a KSHV vIRF1 mutant lacking the ability to bind RNA exhibits a B cell-specific replication defect, highlighting the essential role of RNA interactions in viral gene regulation and pathogenesis. These findings reveal a novel strategy by which KSHV hijacks RNA-mediated signaling to support its lifecycle.

overall_design: Yang, Zhao

first: Xiang

last: Ye

first: Ruilin

last: Zhang

first: Hayes

last: McDonald


title: Spatial biology reveals macrophage dysfunction in immunosuppressed non-melanoma skin cancer [Xenium Spatial Transcriptomics]

first: Veena

last: Kochat

overall_design: Xenium was performed on 12 tissue samples and 2 tissue microarrays containing 91 cores of tumor tissues collected from patients with basal cell carcinoma or cutaneous squamous cell carcinoma

first: Emre

last: Arslan

first: Suresh

last: Satpati

first: Moran

last: Amit


title: Integrating proteomics and metabolomics to reveal MAT2A for metabolic reprogramming and relative combination strategies in non-small cell lung cancer

city: Shanghai

first: Yimin

last: Chen

state: Shanghai

address: No. 555, Zuchongzhi Road, Zhangjiang, Pudong, Shanghai

country: China

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

summary: MAT2A, a key enzyme in the methionine cycle, generates S-adenosylmethionine (SAM), a critical metabolite involved in multiple metabolic pathways and epigenetic regulation. Although MAT2A is frequently overexpressed in tumors, its role in metabolic reprogramming within non-small cell lung cancer (NSCLC) remains poorly understood. Current MAT2A inhibitors, such as AG270, exhibit limited efficacy and are primarily used in MTAP-deleted tumors, highlighting the need to explore additional therapeutic strategies. Here, we employed proteomics and untargeted metabolomics in NSCLC cell lines, complemented by targeted metabolomics, RT-qPCR and ATAC-seq, to systematically characterize MAT2A-rewired metabolic reprogramming and identify potential combination treatment strategies. Totally, MAT2A knockdown or inhibition significantly disrupted fatty acid biosynthesis, cholesterol homeostasis, glycolysis and the transsulfuration pathways. In lipid metabolism, MAT2A inhibition impaired cell proliferation by suppressing fatty acid biosynthesis, and induced cholesterol biosynthesis and efflux impairment. Combining MAT2A inhibitors with the liver X receptor agonist LXR-623, which facilitated cholesterol efflux, effectively depleted intracellular cholesterol and augmented anti-tumor efficacy. In energy metabolism, MAT2A mainly inhibited glycolysis through HIF1A regulation and GLUT1 inhibitor BAY-876 demonstrated a synergetic effect when combined with AG270. In the transsulfuration pathway, MAT2A transcriptionally regulated a key enzyme CBS, and combination treatments using AG270 with either the SLC7A11 inhibitor HG106 or the PHGDH inhibitor NCT-503 exhibited enhanced anti-tumor activity. Overall, our findings identified MAT2A as a critical regulator of metabolic networks in NSCLC and propose several rational combination therapies to enhance MAT2A inhibitor efficacy.

overall_design: ATAC-seq in H1299 cells with siRNA-induced silencing of S-adenosylmethionine synthase isoform type-2 (MAT2A).

first: Cheng

first: Xiongjun

first: Hu

last: Zhou


title: HIV-1 reprograms CD4 T cell responses by impairing antigen-specific communication with dendritic cells

city: Heidelberg

first: Oliver

middle: Till

last: Fackler

address: Im Neuenheimer Feld 344

department: CIID

country: Germany

institute: Universityhospital Heidelberg

summary: HIV-1 infection causes general dysfunction of adaptive immune cells that persists even under therapy but the underlaying mechanisms remain elusive. Antigen-specific interactions of the main target cells of HIV, CD4 T cells, with dendritic cells (DCs) orchestrate global T cell responses and convey help to CD8 T cells. Here we report that HIV-1, by virtue of its pathogenesis factor Nef, impairs activation and transcriptionally reprograms CD4 T cells to dampen Th1 differentiation in response to antigen-specific stimulation by DCs. These alterations also disrupt functional communication to DCs to reduce DC activation and limit Th1 helper cytokine production. Mechanistically, Nef achieves this modulation of antigen-specific CD4 T cell function by reducing T cell surface levels of CD4. These results define modulation of CD4 T cell-DC communication as pathogenic principle by which HIV-1 disrupts adaptive immunity and emphasize the direct role of CD4 in immune cell communication.

overall_design: transduced CD4 T cells from OT-II.2 mice expressing a control reporter or HIV-1 SF2 Nef were co-cultured with immature or matured BMDCs pulsed with OVA323-339 or unpulsed and harvested 4 or 24h later for single cell analysis

first: Katharina

last: Morath


title: Spatial biology reveals macrophage dysfunction in immunosuppressed non-melanoma skin cancer [spatial_ATAC]

overall_design:
Spatial ATAC was performed in 16 samples of tumor tissue obtained from 14 untreated patients (7 immunosuppressed, 9 immunocompetent) with basal cell carcinoma or cutaneous squamous cell carcinoma.

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

first: Kochat

last: Veena

first: Garbarino

last: Jennifer

first: Chafi

last: Nouroddin Sotoudeh

first: Abigail

last: Tyree

first: Rai

last: Kunal


title: Effects of trans, trans-2,4-decadienal on gene expression in ARPE-19 cells

city: Hangzhou

first: Chengpeng

last: Wu

state: Zhejiang

address: Huajiachi, RM C-329, Zhejiang University, Hangzhou, China

institute: Zhejiang University

summary: trans, trans-2,4-decadienal (tt-DDE) is a toxic compound generated during frying processes. Emerging evidence suggests its potential role in inducing age-related macular degeneration (AMD), a leading cause of vision loss in older adults. To investigate the underlying mechanisms, we performed transcriptome sequencing on ARPE-19 cells following a 24-hour treatment with tt-2,4-DDE. The results revealed significant alterations in the expression of genes involved in pathways regulating endomembrane system homeostasis, including those associated with the endoplasmic reticulum, Golgi apparatus, and lysosomes. These findings indicate that tt-2,4-DDE may disrupt endomembrane system function in retinal pigment epithelial cells, providing novel insights into the molecular basis by which environmental toxicants like tt-2,4-DDE could contribute to AMD pathogenesis.

overall_design: RNA-seq profiling of ARPE-19 cells treated with trans, trans-2,4-decadienal or DMSO for 24 hours.


title: Semaglutide  and exercise synergy in obesity: preserving muscle mass and uncovering organ crosstalk

city: Leiden

first: Eveline

last: Gart

state: Zuid Holland

address: Sylviusweg 71

department: MHR

country: Netherlands

institute: TNO

summary: Background and aims: The glucagon-like peptide-1 receptor agonist semaglutide is an antidiabetic medication that has recently been approved for treatment of obesity as well. While its efficacy on weight management is well established, associated concomitant loss of muscle mass can be a potential drawback. In this study, we investigated whether combining semaglutide with exercise could enhance its metabolic effects while mitigating muscle loss. Method: Ldlr−/−.Leiden mice were fed a high fat diet (HFD) for 20 weeks to induce obesity, insulin resistance, metabolic dysfunction-associated steatohepatitis (MASH) and atherosclerosis. Mice were subsequently left untreated (control) or treated for 14 weeks with semaglutide, exercise (running wheel) or the combination thereof. Histological examination and comprehensive transcriptome analyses were conducted on white adipose tissue, muscle, liver and heart to explore underlying mechanisms. Results: Semaglutide significantly reduced fat mass (-31%) but also lean mass (-11%). Combining semaglutide with exercise further reduced fat mass (-45%) and lean mass as well but to a lesser extent (-8%). Semaglutide alone or combined with exercise significantly improved insulin sensitivity, plasma cholesterol and triglycerides. The combination of semaglutide with exercise improved , adipose tissue inflammation, liver steatosis, liver inflammation and atherosclerotic lesion area. With regard to muscle parameters, combination treatment significantly improved grip strength and diameter of gastrocnemius myocytes, while these parameters were not affected by either treatment alone. Pathway analysis revealed complementary effects of semaglutide and exercise on metabolic, inflammatory and a variety of other pathways, thereby substantiating the added value of combining semaglutide with exercise. Conclusion: Semaglutide has broad beneficial effects on circulating risk factors of metabolic syndrome, liver, vascular and adipose parameters but decreases lean mass and muscle strength. By combining semaglutide intervention with exercise, these parameters are further improved with a partial preservation of lean mass and muscle function.

first: José

last: Inia

first: Simone

last: Droog

first: Jessica

last: Snabel

first: Aswin

last: Menke

first: Martien

middle: P

last: Caspers

first: Jelle

middle: C

last: de Jong

first: J

middle: W

last: Jukema

first: Hans

middle: M

last: Princen

first: Anita

last: van den Hoek


title: Global identification of ER stress-regulated RNA binding Proteins in clonal pancreatic beta-cells, reveals an important role for DEAD-box helicase 3 X-linked (DDX3X) in the execution of the Unfolded Protein Response and the determination of cell fate.

city: Lincoln

first: Terence

middle: Patrick

last: Herbert

address: Green Lane

department: Pharmacy

country: United Kingdom

institute: University of Lincoln

summary: Endoplasmic reticulum (ER) stress plays an important role in pancreatic β-cell dysfunction and death, contributing to both type 1 and type 2 diabetes. The Unfolded Protein Response (UPR) is a key adaptive mechanism that helps cells cope with ER stress by altering gene expression. RNA-binding proteins (RBPs), which regulate gene expression at multiple levels, are likely to influence the UPR, yet their role in the UPR remain largely unexplored. To investigate this, we examined global changes in RBP-RNA interactions in the mouse β-cell line MIN6 under ER stress. This analysis identified 339 RBPs, with 13 showing significant changes in RNA binding. Among these, DEAD-box helicase 3 X-linked (DDX3X) emerged as a candidate for further study. Functional experiments revealed that inhibiting or knocking down DDX3X in MIN6 cells suppressed the ER stress-induced expression of the pro-apoptotic protein CHOP and its upstream regulator ATF4. Transcriptomic profiling of DDX3X-deficient MIN6 cells showed that DDX3X is essential not only for the upregulation of CHOP but also 24 other ER stress-responsive genes, including apoptosis-related genes such as Bcl2 and Bid. Notably, DDX3X knockdown conferred partial protection against ER stress-induced cytotoxicity and improved cell viability. In summary, these findings reveal widespread changes in the RBP landscape during ER stress in β-cells and highlight DDX3X as a key regulator of the UPR. DDX3X promotes the expression of stress-responsive genes and contributes to β-cell death under chronic ER stress, suggesting it may be a potential therapeutic target in diabetes.

overall_design: Mouse Insulinoma 6 (MIN6) cells either stably carrying the parental control vector (Wild type (WT)) (designated as PLKO1 in data files), or DDX3X knock-down MIN6 cells (DDX3X-KD), stably expressing an shRNA directed towards Ddx3x (designated as DDX3X1 in data files), were incubated in DMEM high glucose in the presence or absence of 200 µM of cyclopiazonic acid (CPA) for 24 h (n=3, 12 samples in total) to induce endoplasmic reticulum (ER) stress. After treatments total RNA was extracted from cells using Monarch® Total RNA Miniprep kit (New England BioLabs, USA) and sent to Novogene for subsequent RNA sample quality control, mRNA library preparation (poly A enrichment) and RNA transcriptomic sequencing and analysis (NovaSeq X Plus Series (PE150)) (https://www.novogene.com/eu-en/services/research-services/transcriptome-sequencing/mrna-sequencing/).

first: Wei

last: See

first: Chutima

last: Charoensuk

first: Razan

last: Al-Momani


title: Transcriptional profiles of UVB-induced BRAFV600E mouse melanoma tumors with or without p38α (whole tumor, CD45⁺ and CD45⁻ populations)

city: Barcelona

first: Paula

last: Granado Martínez

state: Barcelona

address: Passeig de la Vall d'Hebron 129

department: eCore Cancer

country: Spain

institute: Vall d'Hebron Research Institute (VHIR)

summary:
The role of tumor-intrinsic signaling pathways in shaping the anti-tumor immune response remains poorly defined. Using a conditional UVB-induced melanoma mouse model (Tyr::CreERT2;BrafCA/CA and Tyr::CreERT2;BrafCA/CA;p38αlox/lox), we investigated how the loss of the stress kinase p38α in melanocytes affects tumor development and immune evasion. We performed transcriptional profiling on whole tumors, as well as on separated CD45⁺ (immune) and CD45⁻ (tumor/stroma) populations. Comparative transcriptomic analysis revealed that p38α deficiency reprograms both tumor and immune compartments, promoting immune-stimulatory gene expression and reducing immunosuppressive and pro-tumorigenic signals. Many of the genes modulated by p38α loss are associated with an improved response to immune checkpoint blockade in melanoma patients. These findings underscore the role of p38α in shaping an immunosuppressive and pro-tumorigenic microenvironment, suggesting p38α as a potential target to enhance the efficacy of immunotherapy.
We used microarrays to profile the global gene expression landscape of UVB-induced melanoma tumors and uncovered transcriptional changes driven by the loss of p38α specifically in tumor cells, which extended to reshape gene expression in both the immune (CD45⁺) and tumor/stroma (CD45⁻) compartments.

overall_design: There are a total of 20 samples. These were obtained from UVB-induced mouse melanoma tumors generated in two genotypes: B (Tyr::CreERT2;BrafCA/CA) and B;p38α (Tyr::CreERT2;BrafCA/CA;p38αlox/lox), where BrafV600E is expressed and p38α is conditionally deleted in melanocytes. Samples include three different tissue compartments, each with biological replicates: complete tumors (5 samples from B mice and 3 from B;p38α mice), CD45⁺ immune populations (3 replicates from B and 3 from B;p38α tumors), and CD45⁻ tumor/stroma populations (3 replicates from B and 3 from B;p38α tumors), which were separated using the MagniSort Mouse CD45 Positive Selection Kit (Invitrogen). All samples were collected at endpoint. Differential expression analysis was performed between the two genotypes (B vs. B;p38α) within each tissue compartment (whole tumor, CD45⁺, and CD45⁻), allowing the identification of genotype-specific transcriptional changes in distinct cellular contexts.

first: Juan

last: Recio

last: Granado-Martínez


title: Preliminary Screening and Application of Quorum Quenching Genes Targeting the Phc System in Ralstonia solanacearum

first: Huagui

last: Gao

state: Guangdong

address: No. 483 Wushan Road, Tianhe District

institute: South China Agricultural University

summary: The signal 3-OH-PAME produced by the phc QS system in Ralstonia solanacearum is a conserved and important quorum sensing signal molecule in this genus. This signal participates in the activation of signal transduction by the PhcA regulatory factor, regulating the transcriptional control of 30% of the genes in Ralstonia solanacearum. Quorum quenching technology is a biocontrol strategy that mediates quorum sensing regulatory networks, and has achieved very significant results in the study of quenching AHL and DSF signals. Previous studies identified HS-18 as a biocontrol bacterium with quorum sensing-inhibiting effects on multiple quorum sensing signals. This study aimed to identify quorum quenching enzymes capable of degrading 3-OH PAME using HS-18, identifying six enzymes encoded by genes that exhibit degradation activity toward 3-OH PAME. Among these, gene 12725 demonstrated the most significant quorum quenching effect, while genes 24610 and 03720 also exhibited strong quorum quenching activity. Additionally, these quench enzymes can reduce the pathogenicity of Ralstonia solanacearum on tomatoes, demonstrating promising application prospects.

overall_design: The experimental treatment group was conducted in MM medium (without carbon source), with 10 mM glucose as the control group for transcriptomic analysis.

first: Xiangtao

last: Chen


title: Changes in ovarian granulosa cell chromatin interactions in response to LH surge

city: Adelaide

first: Thao

last: Dinh

state: South Australia

address: North Terrace

country: Australia

institute: University of Adelaide

summary: Luteinising hormone (LH) surge leads to widespread genomic changes in ovarian granulosa cells, leading to global regulation of genes that are important for ovulation and female reproduction. While LH-dependent changes in chromatin accessibility, histone modification and transcription factor activation have been previously described, the influence of the LH-surge on three-dimensional chromatin organisation as well as the activation of enhancer regulatory elements remain unknown. This study aims to characterise the chromatin 3D structure in granulosa cells, from which to determine changes in chromatin-chromatin interactions and enhancer activation in response to the LH-surge.

overall_design: Micro-C of pre- and post-LH mouse granulosa cells

first: Darryl

last: Russell


title: The single-cell transcriptome defines an effector Vd1 gd T cell-dependent anti-tumor immunity in human gastrointestinal stromal tumor (GIST) [10X]

city: Philadelphia

first: Ronald

last: DeMatteo

state: PA

address: 3400 Spruce St

department: Department of Surgery

institute: University of Pennsylvania

summary: Gamma-delta (gd) T cells bridge innate and adaptive immunity and have the ability to recognize diverse tumor-associated antigens. However, the function of gd T cells in human gastrointestinal stromal tumor (GIST), the most common type of human sarcoma, is unknown. Here, we combined single-cell RNA-seq (scRNA-seq), immunophenotyping, and next-generation T-cell receptor (TCR) sequencing of sorted human circulating and intratumoral gd T cells to query their impact on tumor immunity in GIST. We identified major subtypes of Vd1 and Vd2 cells, which were more differentiated in tumors. The effector Vd1 subset exhibited higher expression of cytotoxicity-related transcription and exhaustion molecules, and highly expressed the key transcription factors TBX21 and EOMES. Tyrosine kinase inhibitor (TKI) treatment induced the tumor-enriched Vd1 cells to undergo profound phenotype differentiation, alternative clonal expansion, and TCR diversity. Upon antigen exposure, the Vd1 subset maintained enhanced cytotoxicity properties through an innate-effector phenotype and adaptive-like activation. In a genetically engineered murine GIST model, combination therapy of imatinib with a checkpoint inhibitor increased the adaptive immune response of gd T cell subsets in GIST. Collectively, our findings highlight the importance of Vd1-dependent anti-tumor immunity and open the possibility of specific targeting of gd T subsets based on V gene usage for immunotherapy of GIST.

overall_design: Fresh frozen tumor and PBMC single cell suspensions were FACS sorted for gamma-delta CD45+CD3+TCRgd and sequenced using the 10X Genomics NextGEM 3' V3.1

first: Shan

last: Zeng

first: Jonathan

middle: H

last: Sussman

first: Yuntian

last: Fu

first: Juan Esteban

last: Perez

first: Jiazhen

last: Rong

first: Katherine

last: Tardy

first: Hyunjee

last: Kwak

first: Taylor

last: Hartlein

first: Kevin

last: Do

first: Ferdinando

last: Rossi

first: Jennifer

middle: Q

last: Zhang


title: The single-cell transcriptome defines an effector Vd1 gd T cell-dependent anti-tumor immunity in human gastrointestinal stromal tumor (GIST)

overall_design: Bulk RNA-seq was performed on flow sorted regulatory T-cells (Treg) obtained from treatment naïve and imatinib treated KitV558Δ/+ mice tumor and tumor draining lymph node.


title: Temporal changes in metabolism guide oligodendrocyte precursor cell dynamics in aging and multiple sclerosis

city: Palo Alto

first: Erin

last: Gibson

state: California

address: 3165 Porter Drive

department: Psychiatry and Behavioral Sciences

institute: Stanford University

summary: Impaired oligodendrocyte precursor cell (OPC) differentiation limits myelin renewal in aging and contributes to multiple sclerosis (MS) progression. How aging drives OPC deficits remains incompletely understood. We find dysregulation of genes associated with the circadian clock, including Bmal1, and metabolism in aged compared with young OPCs. Targeted loss of Bmal1 in OPCs drives metabolic dysfunction, leading to cellular senescence and impaired dynamics. OPC proliferation and differentiation occur at different rates throughout the day in young adult mice and become disrupted with aging. Chronotherapeutic targeting of BMAL1-controlled sirtuin signaling restores Bmal1-disrupted OPC dynamics after demyelination via sirtuin 2 (Sirt2)-dependent mechanisms. Induced pluripotent stem cell (iPSC)-derived OPCs from MS patients and MS lesion oligodendroglia recapitulate BMAL1 and SIRT2 disruptions. These findings establish BMAL1 as a key regulator of OPC energy metabolism, sirtuin homeostasis, and senescence. We anticipate that this work will provide a foundation for future studies investigating the interconnected roles of aging, circadian disruption, and myelin biology.

overall_design: To better understand the interplay between aging and circadian dysfunction in OPCs, single-nucleus RNA sequencing was performed on brains from young (5-6 months) and aged (20-22 months) adult OPC-Bmal1-WT or OPC-Bmal1-KO mice, collected at two timepoints of the day (ZT0 or ‘lights-on’ and ZT12 or ‘lights-off’).

first: Tess

last: Dierckx

first: Sarah

middle: E

last: Wilson

first: Maria

last: Sacconi Nunez

first: Dena

last: Kumsa

first: Daniela

last: Rojo;

first: Yohan

last: Auguste

first: Sam

last: Vanherle

first: Sander

last: Bouwman

first: Louisa

last: Dal Cengio

first: Kelly

last: Strickland

first: Celia

last: Lerma-Martin

first: Lucas

last: Schirmer

first: Jeroen

last: Bogie

first: Bart

last: Eggen

first: Yassene

last: Mohammed

first: Yuhsiang

last: Cheng

first: Themistoklis

last: Tsarouchas

first: Rebecca

last: Buchanan


title: Dissecting cellular state alterations critical for the synergistic response and therapy resistance of the combined Abemaciclib, Temozolomide, and Radiation in DIPG PDOX models

city: Chicago

first: Xiao-Nan

last: Li

state: Illinois

address: 303 E Superior st

institute: Northwestern University

summary: Diffuse intrinsic pontine glioma (DIPG) is a lethal pediatric brain cancer. Here, we demonstrated that combining the CDK4/6 inhibitor abemaciclib with temozolomide and radiation (the triple therapy) yields synergistic anti-tumor effects in DIPG organoids and significantly extends survival times in patient-derived orthotopic (intra-brain stem) xenograft (PDOX) models. Mechanistically, we performed scRNA-seq and identified dynamic reprogramming of tumor cell states, including the expansion of NPC-like, depletion of OPC- and AC-like subpopulations, and persistence of MES-like and mitotic-like cells, that contributed to therapeutic resistance. Pseudotime trajectory analysis further revealed therapy-induced cell fate transitions within NPC- and OPC-like compartments, including the enrichment of stem-like cells. More importantly, we discovered that an alternative trajectory—exit from stemness toward more differentiated states—may also contribute to therapeutic failure. Additionally, we identified a novel radiation-resistant subpopulation and found a new set of transcriptional targets indicative of therapeutic vulnerability. This study demonstrated the triple therapy as a promising DIPG regimen that can be rapidly translated into clinical trials and nominated new cellular and molecular targets to overcome residual disease.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Samples were collected from two diffuse intrinsic pontine glioma (DIPG) patient-derived orthotopic xenograft (PDOX) models, IBs-A0317DIPG and IBs-9119DIPG. Each model was subjected to one of six treatment conditions: vehicle control, abemaciclib (a CDK4/6 inhibitor), radiation (XRT), temozolomide (TMZ) combined with radiation, abemaciclib combined with radiation, or abemaciclib combined with both temozolomide and radiation (triple therapy). An additional primary biopsy sample was obtained directly from a DIPG patient (9119DIPG). All tumor tissues were dissociated into single-cell suspensions and filtered to retain only human-origin cells. Libraries were prepared using single-cell RNA sequencing protocols and analyzed through standard pipelines. Downstream analysis included clustering, cell-type annotation based on canonical markers, pseudotime trajectory inference, and evaluation of differentiation potential using CytoTRACE.


title: Sexual dimorphism in epidermal stem cell dynamics [scRNA-Seq]

city: Bruxelles

first: Yura

last: Song

address: 808, route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

summary: The epidermis is a stratified epithelium comprising proliferative basal cells and differentiated suprabasal cells that are continuously renewed throughout life. Conflicting theories have been proposed regarding the heterogeneity of basal cell layer, with some studies proposing that all proliferative cells have self-renewal potential during homeostasis while others posit a model in which stem cell differentiation occurs through an intermediate progenitor state with strictly limited proliferative potential. To elucidate the heterogeneity and pattern of cell fate, we performed intravital timelapse imaging to track the fate of individual lineage-labeled cells over the long term in the ear skin interfollicular epidermis. Quantitative analysis of clonal dynamics supports a two-compartment model of epidermal homeostasis, with basal cells organized in a stem-progenitor cell hierarchy. Critical to these conclusions was the discovery of a sexual dimorphism in epidermal fate, with female mice showing a highly synchronized pattern of differentiation and delamination. Single-cell RNA sequencing, transcriptional profiling, and clonal analysis following castration revealed that male sex hormones promote SC differentiation and delamination. As well as providing insight into the functional identity of the SC population during homeostasis, our  study highlights sex-specific differences in the regulation of epidermal stem and progenitor cell fate.

overall_design: FACS isolated keratinocyte CD34- Itga6+ cells from male, female and castrated male CD1 mouse (Epidermis)

first: Dan

last: Engelman

first: Qiuyu

last: Lian

first: Cédric

last: Blanpain


title: Sexual dimorphism in epidermal stem cell dynamics


title: Decaying and expanding Erk gradients process memory of skeletal size during zebrafish fin regeneration [Fin tip]

city: Madison

first: Jianhong

last: Ou

state: Wisconsin

address: 330 N Orchard Street

institute: Morgridge Institute For Research

summary: Regeneration of amputated salamander limbs or fish fins restores pre-injury size, illustrating positional memory. Although appreciated for centuries, the identity of position-dependent cues and how they control tissue growth are not resolved. Here, we quantify Erk signaling events in populations of osteoblasts during zebrafish fin regeneration. We find osteoblast Erk activity depends on Fgf receptor signaling and organizes into millimeter-long gradients spanning the distal tip to the amputation site. Erk activity scales with amount of tissue amputated, predicts likelihood of osteoblast cycling, and predicts size of regenerated skeletal structures. Mathematical modeling suggests gradients are established by transient deposition of long-lived ligands that are transported by tissue growth. This is supported by the observed scaling of expression of the essential epidermal ligand fgf20a with extents of amputation. Our work provides evidence that localized, scaled expression of pro-regenerative ligands instructs long-range signaling and cycling to control size in regenerating appendages.

overall_design: To isolate RNA from the distal tip of regenerating rays, a region spanning the distal ~250 µm of each ray was collected from fish at 0, 3.5, 7, 10, and 14 dpa. For each time point, tissue samples from 10 animals were pooled for each of 3 biological replicates and collected in Tri-Reagent (Sigma). Only 2 biological replicates of the 14 dpa time point were of high enough quality for bulk RNAseq. Bulk RNAseq libraries were prepared to identify gene expression profiles at the distal tip of regenerates.

first: Ashley

last: Rich

first: Ziqi

last: Lu

first: Alessandro

last: De Simone

last: Garcia

first: Jacqueline

last: Janssen

first: Kazunori

last: Ando

first: Massimo

last: Vergassola

first: Kenneth D

last: Poss

first: Stefano

last: Di Talia


title: Chilling Accumulation Shapes Transcriptomic Responses to Warming Exposure During Grapevine Deacclimation

city: Geneva

first: Hongrui

last: Wang

state: NY

address: 630 W. North Street

department: School of Integrative Plant Science, Horticulture section

institute: Cornell University

summary: Dormancy transitions in grapevine (Vitis vinifera) buds during winter are regulated by chilling accumulation and temperature cues, but the underlying molecular mechanisms remain unclear. We conducted time-series RNA-seq on ‘Cabernet Sauvignon’ buds collected across a chilling gradient and exposed to warm temperatures. Using weighted gene co-expression network analysis, empirical modeling, and a novel approach to estimate molecular temperature, we identified distinct gene expression patterns responsive to temperature alone, chilling alone, and their interaction.

overall_design: We collected buds from field-grown Vitis vinifera ‘Cabernet Sauvignon’ vines at five time points across the 2021–2022 winter season, representing a gradient of natural chilling accumulation (341 to 1298 chill units, NC model). At each time point (Collection 1–5), buds were excised and subjected to a warm forcing assay under controlled growth chamber conditions (22 °C, 16 h light/8 h dark) for 0 h,2h, 4 h, 1 d, 3 d and 7 d. Bud samples were flash-frozen at each time point for RNA-seq data collection.

first: Jason P.

last: Londo


title: Bioengineered 3D human heart valve tissues with enhanced maturational properties for disease modelling and therapeutic applications

city: Parkville

first: Michael

last: See

state: VIC

address: Royal Children's Hospital, 50 Flemington Rd

institute: MCRI

summary: Therapeutic management of heart valve disease is currently hampered by a lack of mechanistic understanding of human valve development and pathobiology. Here, we develop a protocol to generate 3-dimensional human heart valve tissues from pluripotent stem cells with enhanced maturational properties closely mirroring the valve interstitial cell, resident myeloid cells and protein expression profile of native heart valves. Importantly, bioengineered heart valves transplanted subcutaneously in rats did not calcify, highlighting potential clinical utility as a cellular therapy. In parallel, using a high-throughput 96-well platform, we demonstrate that bioengineered human heart valves can be used for modelling valve disease. Treatment with inflammatory cytokines augmented tissue passive tension and upregulated molecular markers associated with valve calcification and fibrosis. Thus, bioengineered human heart valve tissues provide a platform to understand human heart valve development, disease pathogenesis and offer a potential regenerative therapy for heart valve disease.

overall_design: Following 30 days in culture, macroVETs were dissociated and analysed using scRNA sequencing

first: Holly

last: Voges

first: Jessica

last: Durrant-Whyte

first: Serene

last: Yeow

first: Benjamin

middle: L

last: Parker

first: Kaitlyn

last: Bibby

first: Ellen

last: Keen

first: Ingrid

last: King

first: Adam

middle: T

last: Piers

first: Anita

last: Thomas

first: Daniel

middle: G

last: Donner

first: Akriti

last: Varshney

first: Natalie

last: Charitakis

first: Lina

last: Le

first: James

last: Burgess

first: Sean

last: Humphrey

first: Salvatore

last: Pepe

first: Hazem

last: Alkazemi

last: Heath

first: Fernando

middle: J

last: Rossello

first: Mirana

last: Ramialison

first: David

last: Elliott

first: Christian

last: Brizard

first: Alejandro

last: Hidalgo

first: Enzo

last: Porrello


title: Quantitative Analysis of RNA Modifications and Processing Dynamics in the Course of Large Ribosomal Subunit Assembly

city: El Paso

first: Eda

last: Kocui

address: 500 W. University Avenue

department: Chemistry and Biochemistry

institute: University of Texas at El Paso

summary: Ribosome assembly, which requires the temporal and spatial coordination of multiple interconnected processes, is essential for life in every known organism. The large ribosomal subunit (LSU) of Escherichia coli (E. coli) contains two RNA molecules, 23S and 5S, which serve as a platform for assembly. Ribosomal RNA (rRNA) modifications and processing are key steps in this process. We simultaneously detect and quantify eight classes of 23S rRNA modifications in the mature 50S LSU from E. coli cells expressing wild-type DbpA, the 50S LSU from cells expressing the helicase-inactive R331A DbpA construct, and two LSU intermediates, 35S and 45S, which accumulate in distinct ribosome maturation pathways in R331A DbpA-expressing cells. Additionally, we analyze the 3′-end processing of 23S and 5S rRNA in all these particles. Most 23S rRNA modifications are incorporated into the 35S and 45S intermediates at levels comparable to those in the 50S LSU from both wild-type and R331A DbpA-expressing cells, indicating that modification enzymes complete their functions before 35S and 45S accumulation. However, three enzymes exhibit differential modification patterns. RlmN incorporates N²-methyladenosine (m²A) at position 2507 more extensively in the 50S LSU from wild-type DbpA-expressing cells than in the 35S, 45S, and 50S LSU from R331A DbpA-expressing cells. Conversely, RluC incorporates pseudouridine (Ψ) at position 2508 at lower levels in the 50S LSU from wild-type DbpA-expressing cells than in the 35S, 45S, and 50S LSU from R331A DbpA-expressing cells. The RluF enzyme incorporates Ψ at position 2508 at a lower level in the 50S LSU from R331A DbpA-expressing cells than in the 35S and 45S intermediates and the 50S LSU from wild-type DbpA-expressing cells. Since the pathways leading to 35S and 45S account for only ~50% of total ribosome assembly in R331A DbpA-expressing cells, these findings reveal that RluF activity is reduced in a subset of maturation pathways. The 3′ end of 23S rRNA is less mature in the early-stage LSU intermediate, 35S, and more mature in the late-stage LSU intermediate, 45S. Interestingly, the 3′ end of 5S rRNA is less processed in the 45S than in the 35S, suggesting that 5S rRNA in the 45S intermediate matures during the final steps of large subunit ribosome assembly. A complete understanding of ribosome assembly demands a precise characterization of ribosome assembly pathways and processes across diverse cellular conditions. This study reveals critical insights into rRNA modifications and processing dynamics in bacterial ribosomes under stress.

overall_design: The ribosomal particles were isolated using sucrose gradients from cells  expressing the wild type DbpA or the R331A DbpA construct.

last: Koculi


title: The C3-C3aR axis modulates trained immunity in alveolar macrophages

city: Los Angeles

first: Hrishikesh

last: Kulkarni

address: 10833 Le Conte Ave 52-257 CHS

department: Pulmonary, Critical Care, Sleep Medicine

institute: University of California Los Angeles

summary: Complement protein C3 is crucial for immune responses in mucosal sites like the respiratory system, where it aids in microbe elimination and enhances inflammation. While trained immunity – enhanced secondary responses of innate immune cells after prior exposure – is well-studied, the role of the complement system in trained immune responses remains unclear. We investigated the role of C3 in trained immunity and found that in vivo, trained wild-type mice showed significantly elevated pro-inflammatory cytokines and increased C3a levels upon a second stimulus, whereas C3-deficient mice exhibited a blunted cytokine response and heightened evidence of lung injury. Ex vivo, C3-deficient alveolar macrophages (AMs) displayed reduced chemokine and cytokine output after training, which was restored by exogenous C3 but not by C3a. Inhibiting C3aR, both pharmacologically and with a genetic C3aR knockout, prevented this restoration, indicating the necessity of C3aR engagement. Mechanistically, trained WT AMs demonstrated enhanced glycolytic activity compared to C3-deficient AMs – a defect corrected by exogenous C3 in a C3aR-dependent manner. These findings reveal that C3 modulates trained immunity in AMs through C3aR signaling, affecting cytokine production and metabolic reprogramming, and highlight a novel role for C3 in trained immunity.

overall_design: To investigate the role of C3 in pulmonary immune cell trained immunity, we first inoculated C57BL/6J wild-type (WT) and B6.129S4-C3tm1Crr/J C3 knockout (C3KO) mice intranasally with heat-killed Pseudomonas aeruginosa (HKPA) for training or vehicle control-untrained (PBS). After 14 days, lipopolysaccharide (LPS) from Escherichia coli was also administered intranasally to both mouse strains to induce secondary stimulation for 24 h, followed by sacrifice and bronchoalveolar lavage (BAL) as previously described.

first: Alexander

last: Earhart

first: Alberto

last: Lopez

first: Josue

middle: I

last: Hernandez

first: Aasritha

last: Nallapu

middle: S


title: PNMC exposure disturbs the global gene expression in mice 2-cell embryos

city: Wuhan

first: fan

last: chen

state: Hubei

address: Nanhu Av. 4

institute: Hubei Academy of Agricultural Sciences

summary: To investigate the molecular mechanism about how PNMC affects early embryo development,  control and PNMC-exposed 2-cell embryos were collected for transcriptome sequencing

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and 25 nM PNMC exposure 2-cell embryos.

first: Fan

last: Chen

first: Yan

last: Zhen Bi


title: Single cell multiomic profiling of heterogenous PROCR+ cells in mouse mammary gland

city: Memphis

first: Jiyang

last: Yu

address: 262 Danny Thomas Pl

department: Department of Computational Biology

institute: St Jude Children's Research Hospital

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

overall_design: Refer to individual Series


title: Rejuvenating endogenous antitumor immunity via a chimeric receptor-engineered oncolytic virus targeting tumor-associated macrophages

city: Xiamen

first: Chaolong

last: Lin

address: 4221-117 Xiang Annan Road, Xiang 'an District, Xiamen City, Fujian Province

institute: Xiamen University

summary: Immunosuppressive tumor-associated macrophages (TAMs) create a barrier to effective antitumor immunity and promote therapeutic resistance. Reeducating TAMs to enhance their antitumor capabilities through phenotypic remodeling remains challenging. Here, we report a modular oncolytic herpesvirus platform, engineered with a PD-L1–specific chimeric receptor integrated into the viral envelope protein (CAR-oHSV). This design endows the virus with dual tropism, enabling it to target both tumor cells and TAMs within the tumor microenvironment. In virus-resistant tumor models, CAR-oHSV preferentially targets PD-L1⁺ TAMs and triggers a STING-dependent reprogramming into a CXCL9⁺ phenotype, enhancing their tumor antigen cross-presentation capability and inducing an endogenous antitumor T cell response. Furthermore, this platform can synergize with adoptive T cell therapy and immune checkpoint blockade therapy to overcome immunotherapy resistance. Collectively, our findings define a precision-oncolytic platform that dismantles TAM-mediated immunosuppression while amplifying adaptive immunity, offering a promising translational avenue for cancer immunotherapy.

overall_design: The B16-F10 tumors were excised and homogenized using a gentleMACS tissue dissociator with a Tumor Dissociation Kit for mice.  Fluorescence-activated cell sorting (FACS) was employed to isolate CD45+ cells, ensuring a cell viability exceeded 90%. These sorted cells were then prepared for single-cell RNA sequencing (scRNA-seq)

first: Shaopeng

last: Li

first: Rui

last: Lou

first: Wenzhong

last: Teng

first: Yang

last: Tian

first: Naizhen

last: Wang

first: Chenxi

last: Feng

first: Lu

first: Xiaoxuan

last: Huang

first: Yisen

first: Yipeng

last: Rao

first: Jun

last: Zhang

first: Chenghao

first: Ningshao

last: Xia


title: Androgen receptor action in mouse granulosa cells in response to LH surge

first: Thao

last: Dinh

summary: Androgen receptor (AR) plays a prominent role  in folliculogenesis and steroidogenesis, as well as ensuring the responsiveness to luteinising hormone (LH) surge in granulosa cells. The irregular elevation of canonical ligands for AR can induce polycystic ovary syndrome (PCOS) in animal models and is a clinical diagnostic indicator of PCOS in women. To determine the interrelationship between different steroid receptors in the ovarian context, we generated comprehensive AR  cistrome datasets from granulosa cells of mice  that were wildtype of knockout for progesterone receptor (PGRO) in response to in vivo LH stimulus.

overall_design: Chromatin immunoprecipitation (ChIP-seq) of AR in post-LH PGRKO mouse granulosa cells

first: Darryl

last: Russell


title: CUT&TAG analysis of R-loops in Mcm8 knockout MEFs and CUT&TAG analysis of R-loops and MCM8-binding site in HEK293 cells

city: Jinan

first: Can

middle: xin

last: Wen

address: 44 West Wenhua Rd

department: Center for Reproductive Medicine

institute: Shandong University

summary: To reveal the role of MCM8 in suppressing R-loop accumulation, we performed the CUT&TAG assay using the S9.6 antibody to map genome-wide R-loops in MEFs derived from Mcm8 knockout and wildtype embryos. To investigate the underlying molecular mechanism of MCM8 suppressing R-loops, we conducted the DNA sequencing of libraries from CUT&TAG assay using the antibody against FLAG in HEK293 cells  transfected with FLAG-MCM8 plasmid and using the S9.6 antibody in HEK293 cells.

overall_design: CUT&TAG-seq for R-loops using the S9.6 antibody in Mcm8 wildtype and knockout MEFs. CUT&TAG-seq for R-loops using the S9.6 antibody in HEK293 cells and for MCM8 using the anti-FLAG antibody in HEK293 cells expressing FLAG-MCM8.

first: Canxin

first: Shidou

last: Zhao

first: Yajuan

last: Yang


title: Glucocorticoid receptor action in mouse granulosa cells in response to LH surge

summary: Cortisol is important for folicle survival and oocyte quality. Its ligand, glucocorticoid receptor (GR), is induced in granulosa cells in response to the LH surge, and emerging data suggests that GR plays a role in ovulation. To determine the interrelationship between different steroid receptors in the ovarian context, we generated comprehensive GR cistrome datasets from granulosa cells in response to in vivo LH stimulus.

overall_design: Chromatin immunoprecipitation (ChIP-seq) of GR in post-LH mouse granulosa cells


title: Melanocyte-specific regulation of PD-L1 by MITF confers immune tolerance to UV mutagenesis

city: Urbana

last: Song

email: songj@illinois.edu, jssong137@gmail.com

state: IL

address: 1110 West Green Street, MC 704

institute: University of Illinois, Urbana-Champaign

summary: Genomic sequencing of human cancers has revealed that melanoma exhibits a strikingly high mutational density, the vast majority being recognizably derived from UV irradiation. This high mutational burden is associated with greater numbers of tumor-specific neoantigens that contribute to effective immunotherapy responses. However, the same high mutational density raises the question of how precursor melanocytes could accrue UV-induced mutations without undergoing immune recognition and destruction. In fact, immunoediting has been observed for numerous human malignancies, but surprisingly there is no evidence for such pruning in melanomas, which harbor among the highest density of mutations across cancers. Here we identify MITF, the master transcriptional regulator of melanocyte development and survival, as a lineage-specific constitutive inducer of PD-L1 expression in melanocytes. MITF directly promotes transcription of PD-L1 in melanocytes upon binding a conserved E-box-containing upstream enhancer. In addition to determining baseline cutaneous PD-L1 expression, MITF helps drive PD-L1 upregulation in response to UV radiation. This PD-L1 regulatory pathway is independent of interferon (IFN) signaling, in contrast to PD-L1 on melanoma cells, which is regulated primarily by IFN signaling and is associated with inflammation in the tumor microenvironment. We further observed that UV irradiation of PD-L1–/– mice produced an exaggerated inflammatory response together with vitiligo-like epidermal melanocyte destruction.  These results suggest that within normal skin, melanocytes harbor a distinct MITF-mediated mechanism driving PD-L1 production. This PD-L1 in turn may confer local immune privilege, permitting survival of UV-mutated (neoantigen-containing) melanocytes and protecting against immune destruction of melanocytes. These findings raise the possibility that similar lineage- specific mechanisms may induce immune tolerance towards other cell types subjected to mutagenic exposures and eventual carcinogenic risk.

overall_design: Examination of PD-L1 transcriptional regulation and function in melanocytes

first: Jennifer

middle: A

last: Lo

last: Allouche

first: Akinori

last: Kawakami

first: Miroslav

last: Hejna

first: Lajos

middle: V

last: Kemeny

first: Anita

last: van der Sande

first: Jeffrey

middle: B

last: Cheng

first: Torrey

middle: R

last: Utne

first: Yao

last: Zhan

first: Nisma

last: Mujahid

first: Elisabeth

last: Roider

first: Elizabeth

last: Byrne

first: Gordon

last: Freeman

first: Nir

last: Hacohen

first: Keith

last: Flaherty

first: Genevieve

last: Boland

first: Arlene

last: Sharpe

first: Shadmehr

last: Demehri

first: David

last: Fisher


title: CSMD3 loss drives aggressive behavior and tumor consolidation in oral squamous premalignant cells

status: Public on Aug 06 2026

city: Houston

first: Xiao

last: Zhao

state: Texas

address: 6550 Bertner Avenue

department: Head and Neck Surgery

institute: MD Anderson Cancer Center

summary: Oral squamous cell carcinoma (OSCC) remains a significant global health burden. Genomic data identify Csmd3 as the third most frequently mutated gene in HNSCC (29% of cases) correlating with poor clinical outcome and prognosis. Despite this, the functional role of CSMD3 in oral premalignancy and malignant transformation remains largely unexplored. In this study, we utilized CRISPR-Cas9 system to inactivate CSMD3 in an oral premalignant cell line and characterize knockout in in vitro oral premalignant cell line and in vivo orthotopic model. Functional assays demonstrate that CSMD3 loss significantly enhances cell survival (P < 0.001), while decreasing migration (P = 0.005). Transcriptomic profiling and Gene Set Enrichment Analysis (GSEA) revealed multi-faceted reprogramming characterized by enriched expression of oncogenic survival and stress signaling genes, metabolic rewiring, inflammatory mediators, and structural remodeling driven by altered expression of contraction, actin cross-linking proteins, and polymerization genes. Orthotopic modeling further revealed that CSMD3 loss resulted in significantly increased tumor area fraction (P < 0.0001) and intratumoral cellular density (P < 0.0001). Our study emphasizes the role of CSMD3 loss in promoting aggressive behavior of oral premalignancy, which has a potential for risk stratification, a novel prognostic or diagnostic biomarker, and a target for therapeutic intervention.

overall_design: RNA-seq profiling of CSMD3 knockout (clone 1 and clone 2) murine oral squamous cell cancer cell line using non-knockout control as the reference. There were 3 replicates per group.

first: Jeremy

last: Ceriales

first: Jianghua

last: Wang

first: Roberto

last: Rangel

first: Sophie

last: Li

first: Leslie

last: Dalmacio

middle: N

last: Myers


title: Claudin 5 regulates blood-brain barrier permeability by modifying brain microvascular endothelial cell proliferation, migration, and adhesion to prevent lung cancer metastasis

city: Beijing

first: Shunchang

last: Ma

address: No. 119, South Fourth Ring West Road, Fengtai District

department: Beijing Tiantan Hospital

institute: Capital Medical University

summary: To investigate the roles of Claudin- 5 (CLDN5) in regulating the permeability of  the blood- brain barrier (BBB) during lung cancer brain metastasis.

overall_design: By silencing and overexpressing the CLDN5 gene in human brain vascular endothelial (hCMEC/D3) cells, we demonstrated the attenuation of cell migration ability and CLDN5’s significant positive role in cell proliferation in CLDN5- overexpressing hCMEC/D3 cells and observed the opposite result in the CLDN5 knockdown group. The reinforced CLDN5 expression reduced the paracellular permeability of hCMEC/ D3 cells and decreased the invasion of lung adenocarcinoma A549 cells. Overall, 1685 genes were found to be differentially expressed between the CLDN5- overexpressing cells and the control cells using the Affymetrix Human Transcriptome Array 2.0 (HTA 2.0), and the function of these genes was determined by Gene Ontology and pathway  analyses. The possible biological functions of the 1685 genes include cell proliferation, adhesion molecules, and the Jak- STAT, PI3K- Akt, Wnt, and Notch signaling pathways. The identified sets of mRNAs that were specific to CLDN5- overexpressing hCMEC/ D3 cells were verified by a qRT- PCR experiment.


title: Spatial transcriptomic profiling of vascular compartments of chronic antibody-mediated rejection in kidney allografts identified compartment-specific signatures: a pilot study

city: Goyang-si

first: Sung-Eun

last: Choi

state: --- Select One ---

address: 100 Ilsan-ro, Ilsan-donggu

country: South Korea

institute: NHIS Ilsan hospital

summary: Chronic antibody-mediated rejection (CAMR) is a leading cause of late kidney allograft loss, and its vascular compartments are the principal site of injury. To resolve compartment-specific transcriptomic programs, we applied GeoMx Digital Spatial Profiling with the Human NGS Whole Transcriptome Atlas (18,677 targets) to formalin-fixed paraffin-embedded kidney allograft biopsies. Forty-eight regions of interest (ROIs) were profiled across three vascular compartments (glomerulus, peritubular capillary, and vessel) in patients with CAMR or no evidence of rejection (NER), stratified by donor-specific antibody (DSA) status, together with normal (non-transplant) kidney as a control. As a pilot study with one patient per group, this dataset is intended to be descriptive and hypothesis-generating rather than definitive.

overall_design: GeoMx DSP whole transcriptome profiling of 48 ROIs sampled from five kidney specimens (one patient per group: DSA-positive CAMR, DSA-negative CAMR, DSA-positive NER, DSA-negative NER, and normal kidney control). Within each specimen, ROIs were selected from three vascular compartments: glomerulus, peritubular capillary, and vessel. Each ROI was collected as a single Full ROI segment and sequenced as one library.

first: Minsun

last: Jung


title: Sodium oxybate, a narcolepsy therapeutic, remodels the gut microbiota and alleviates metabolic dysfunction in developing and established obesity

city: Leiden

first: Sen

last: Zhang

address: Albinusdreef 2, Einthoven Laboratory, D4-29

institute: Leiden Univesity Medical Center

summary: Using diet-induced pre-obese and obese mouse models, we found that SXB reduced hepatic steatosis and inflammation in both conditions, together with increased expression of genes linked to mitochondrial respiratory function. In obese mice, SXB further improved insulin resistance and attenuated body weight gain by limiting fat mass expansion. These metabolic improvements were accompanied by enhanced adipose tissue function, reflected by reduced adipocyte hypertrophy and inflammation in white adipose tissue and by reduced lipid content and increased uncoupling protein 1 (UCP-1) abundance in brown adipose tissue. Mechanistically, SXB reshaped the gut microbiota in a manner that contributed toassociates with improved liver metabolic function. Consistent with a causal role for microbiota, fecal microbiota transplantation (FMT) from SXB-treated obese donors recapitulated these benefits in untreated obese recipients, rescuing diet-induced weight gain, hyperglycemia, and hepatic steatosis. These findings identify suggest the gut microbiota as a key potential mediator of the metabolic effects of SXB, support further investigation of gut microbiota alterations in narcolepsy, and underscore the broader translational relevance of drug-microbiota interactions in metabolic dysfunction.

overall_design: To elucidate how SXB induces weight loss and to identify potential therapeutic targets for obesity and related metabolic disorders, we set out to explore the role of SXB in body weight control in both established and developing obesity in mice.


title: Transcriptomic and H3K27ac chromatin responses of human microglia to acute PFOS exposure and recovery

first: Yi-Lan

last: Weng

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

summary: Per- and polyfluoroalkyl substances (PFAS) are persistent environmental contaminants associated with adverse neurological effects, but their impact on microglial gene regulation remains unclear. In this study, human HMC3 microglial cells were exposed to vehicle control or perfluorooctane sulfonate (PFOS) at 25 or 50 µM for 24 hours. RNA sequencing was used to characterize transcriptomic changes, and H3K27ac CUT&Tag was used to profile active chromatin. Additional samples were collected after PFOS withdrawal and a 24-hour recovery period to assess persistent molecular alterations. These datasets support integrated analysis of acute and persistent PFOS-induced transcriptomic and epigenetic changes in human microglia.

overall_design: HMC3 human microglial cells were treated with vehicle control or PFOS at 25 or 50 µM for 24 hours. For recovery samples, PFOS was withdrawn after the 24-hour exposure and cells were cultured for an additional 24 hours in PFOS-free medium. Three biological replicates were included for each treatment and time condition. RNA-seq and H3K27ac CUT&Tag libraries were sequenced using paired-end sequencing.

first: Cheng

last: Yating

first: Weng

last: Yi-Lan


title: Bacterial effector modifies host messenger RNA to promote virulence

status: Public on Aug 13 2026

city: Clayton

first: Kathleen

last: McCaffrey

address: 25-31 Wright Street

institute: Hudson Institute of Medical Research

summary:
Bacterial pathogens harbor specialized secretion systems that inject effector proteins into the host cell to
establish infection and disease. While many bacterial effectors post-translationally modify proteins to influence
host responses, the extent to which effectors modify host RNA is currently unknown. Here we performed
RNA-interactome capture (RIC) to isolate effectors bound to host cellular messenger RNA (mRNA)
during Legionella pneumophila infection. RIC identified an uncharacterized effector, FadA (Lpw16921), which
localized to the host-cell nucleus and interacted with host mRNAs at uracil (U)-rich RNA motifs. FadA exhibited
NADPH-oxidase activity that mediated 8-oxo-guanine (oxo8G) modifications of mRNA substrates, resulting
in oxidative damage and inhibition of translation. Infection with L. pneumophila harboring wild-type
FadA, but not a catalytically inactive mutant, increased oxo8G modifications, suppressed cytokine responses,
and promoted bacterial persistence in vivo. Our findings demonstrate the potential for a secreted
Q2 effector to post-transcriptionally modify host mRNA as a mechanism to promote bacterial virulence.

overall_design: iCLIP2 sequencing analysis of RNAs bound to Legionella pneumophila T4SS-effector FadA during infection. 4HA-FadA was expressed in a fadA-gene knockout strain of Legionella pneumophila and used to infect human monocyte derived THP-1 macrophages for 6 h. Legionella pneumophila fadA-gene knockout strain carrying the HA-vector was used as a control for non-specific interactions.

first: Elizabeth

last: Hartland


title: Tumor-targeted IL-10 combined with IL-2 amplifies anti-tumor immunity

city: Dallas

first: Qiao

last: Jian

state: TX

address: 6000 Harry Hines Blvd

department: department of pathology

institute: University of Texas southwestern medical center

summary: Tumor-targeting cytokines have emerged as a promising strategy for cancer immunotherapy, although their mechanisms of action often remain complex. In this study, we developed a novel approach by combining tumor-targeted IL-10 (CmAb-(IL10)2) with IL-2 (CmAb-IL2) to enhance antitumor immunity while minimizing Immune-Related Adverse Events (irAEs). We demonstrated that endogenous IL-10 plays a critical role in IL-2-mediated antitumor effects, and importantly, the combination of CmAb-(IL10)2 and CmAb-IL2 preferentially expands less-exhausted CD8+ T cells within tumors. Mechanistically, we identified that the IL-10/IL-10 receptor (IL-10R) axis in dendritic cells (DCs) is critical for mediating the efficacy of this combination therapy by promoting intratumoral DC function. Our findings reveal that tumor-targeted IL-10 synergizes with IL-2 to enhance antitumor immunity through the IL-10/IL-10R/DC axis within tumors, while mitigating IL-2-associated irAEs through the IL-10/IL-10R/macrophage axis.  This approach offers a promising IL-10 based strategy to improve the efficacy of immunotherapy while reducing irAEs.

overall_design: Following CmAb-(IL10)2 and CmAb-IL2 combination treatment, CD3+ and CD3- live CD45+ cells from B16-cEGFR tumors were isolated by using CD45 (TIL) selection kit (STEMCELL) and Fluorescence-activated cell sorting (FACS) and analyzed using scRNA-seq.

first: Zhichen

last: Sun

first: Yifei

last: Hu

first: Tao

first: Jian

last: Qiao


title: A configurable AP-1 network governs cell-state heterogeneity and adaptive plasticity in melanoma cells

city: Charlottesville

first: Mohammad

last: Fallahi-Sichani

state: Virginia

address: Box 800759, Health System

department: Biomedical Engineering

institute: University of Virginia

summary: AP-1 transcription factors have been implicated in cellular plasticity, differentiation-state heterogeneity, and phenotype switching in response to cancer therapies. To understand the transcriptional consequences of AP-1 perturbations at a single-cell level, we depleted JUND and JUNB expression in COLO858 cells using shRNA-mediated knockdown (JUNDKD and JUNBKD, respectively). We then performed single-cell multiome (RNA + ATAC) sequencing in these cells and compared with COLO858 cells expressing non-targeting shRNA control.

overall_design: A human melanoma cell line (COLO858) was transduced with shRNAs targeting JUND or JUNB (JUNDKD and JUNBKD, respectively) in one biological replicate, or with a nontargeting control shRNA (NTC) in 2 biological replicates. Cells were then subjected to single-nucleus multiome (ATAC + Gene Expression) analysis. Library preparation was performed by the University of Virginia Genome Analysis and Technology Core using the 10x Chromium Next GEM platform, and libraries were sequenced on a NextSeq 2000 platform.

first: Magda

last: Bujnowska

first: Yonatan

last: Degefu


title: Developmental Synchrony of Retinal Waves, Apoptosis, and Angiogenesis in Postnatal Retina

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

institute: Newcastle University

summary: Postnatal mouse retinal development is a multi-faceted process involving the coordinated interaction of spontaneous neural activity as retinal waves, vascular plexus growth, and programmed cell death. While these processes are known to interact at a coarse scale, the specific mechanisms integrating them have remained elusive. Using large-scale, widefield calcium imaging, high-density multielectrode array recordings, single cell RNA-seq, and immunohistochemistry, we characterise a tightly aligned centrifugal expansion pattern during retinal development. This pattern is common to stage II retinal wave onsets, vascular development, Heme oxygenase-1 (Hmox1) expressing microglia, apoptotic cell markers, and a novel set of auto-fluorescent cluster complexes (ACCs) identified in this study. Apoptotic cells are known to upregulate functional Pannexin1 (PANX-1) hemichannels. These voltage-gated channels release purinergic molecules which act as “eat me” signals to neighbouring microglia. PANX-1 hemichannel blockade with the drug probenecid results in a profound decrease in spontaneous wave frequency and strength, suggesting that retinal waves are indeed triggered by these apoptotic cells. Taken together, our observations suggest that spontaneous waves are initially triggered in hotspots by hyperactive apoptotic RGCs in unvascularised retinal areas. These apoptotic cells release purinergic molecules via PANX-1 hemichannels, leading to wave generation. This hyperactivity leads to local hypoxic conditions, which, coupled with high extracellular ATP concentrations, promotes angiogenesis. Once blood vessels reach a particular hotspot, ATP release activates Hmox1 positive microglia, which engulf the dying RGCs, creating the auto-fluorescent clusters. Herein, we present a unified mechanism linking causally linking early neural activity, programmed cell death and angiogenesis in the mammalian retina.

overall_design: ACCs from P5 dissociated retinas were enriched using flow activated cells sorting (FACS) and subjected to scRNA-Seq

first: Michael

last: Savage

first: Cori

last: Bertram

first: Jean

last: de Montigny

first: Courtney

last: Thorne

first: Rachel

last: Queen

first: Gerrit

last: Hilgen

first: Evelyne

last: Sernagor


title: Chromatin accessibility profiling of high endothelial cells (HECs) from mouse peripheral lymph node and Peyer's patch by ATAC-seq

city: Palo Alto

first: Yuhan

last: Bi

state: CA

address: 3801 Miranda Ave

department: Pathology

institute: Stanford University

summary: High endothelial venules (HEVs) are specialized blood vessels that mediate lymphocyte entry into secondary lymphoid organs. We performed ATAC-seq on high endothelial cells (HECs) isolated by flow cytometry from mouse peripheral lymph nodes (PLNs, identified by PNAd expression using the MECA-79 antibody) and Peyer's patches (PPs, identified by MAdCAM-1 expression using the MECA-367 antibody) to characterize genome-wide chromatin accessibility and identify HEC-specific cis-regulatory elements.

overall_design: ATAC-seq libraries were prepared from flow-sorted HECs isolated from mouse PLN and PP (one sample per tissue, no biological replicates), following the tagmentation-based method of Buenrostro et al. (2013, Nat Methods).

first: Junliang

last: Pan

first: Eugene

last: Butcher

first: Kevin

last: Brulois

first: Menglan

last: Xiang


title: APE1-Mediated Transcriptional Reprogramming in Esophageal Adenocarcinoma Cells under Acidic Bile Reflux Stress

city: Miami

first: Wael

last: El-Rifai

state: FL

address: Griffin Cancer Research Building,1425 NW 10th Ave

department: Department of Surgery and Sylvester Comprehensive Cancer Center

institute: University of Miami Miller School of Medicine

summary: Esophageal adenocarcinoma (EAC) arises in the setting of Barrett's esophagus, an intestinal metaplastic precursor lesion that can develop in patients with chronic Gastroesophageal reflux disease (GERD). This study investigates the genome-wide transcriptional adaptations and molecular stress responses mediated by Apurinic/apyrimidinic endonuclease 1 (APE1) in EAC cells under reflux-induced stress. By utilizing APE1 genetic silencing alongside exposure to an acidic bile salt (ABS), this dataset defines the global differential gene expression profiles, altered signaling pathways, and transcriptional networks that depend on APE1 for survival during reflux stress.

overall_design: To evaluate the role of APE1 in mediating transcriptional adaptation and genomic stability under simulated reflux conditions, two human EAC cell lines (OE33 and FLO-1) were stably transduced with either a non-targeting control shRNA (shCtrl) or two distinct APE1-targeted shRNAs (shAPE1#1 and shAPE1#3). To model GERD pathophysiology, shCtrl cells and two shAPE1 cells (shAPE1#1 and shAPE1#3) were exposed to an acidic bile salt cocktail (200 µM, pH 4.0) for 20 minutes and allowed to recover in complete medium for 6 h. Total RNA was isolated from three independent biological replicates for each experimental group.

first: Heng

last: Lu

first: Lei

last: Chen

first: Dunfa

last: Peng


title: SIRT2 deacylase modulators control B cell metabolic reprogramming in EBV infection and mitogenic activation

city: Durham

first: Ashley

last: Barry

state: NC

address: 213 Research Drive Room 0045 CARL, DUMC box 3054, General Delivery

department: MGM

institute: Duke University

summary: Sirtuin-2 (SIRT2) is a cellular deacylase, regulating cell cycle progression and metabolic homeostasis. Recently, SIRT2 has emerged as a target with both anticancer and antiviral potential. However, the role and targetability of SIRT2 in viral-driven cancers remains unexplored. Epstein-Barr virus (EBV) is a ubiquitous herpesvirus with oncogenic potential that establishes latency in B lymphocytes and is typically controlled by a robust T cell immune response. In settings that compromise this response, such as immune suppression following transplant, EBV can cause B cell lymphomas. With broad immunosuppression and varying response rates limiting the effectiveness of existing lymphoma therapeutics, new strategies are necessary. SIRT2 modulation significantly alters gene expression and metabolism of EBV-infected B cells. Treatment with SIRT2 modulators drives hyperacetylation of targets involved in lipid metabolism, central carbon metabolism, and oxidative phosphorylation. EBV-positive and EBV-negative B cell lymphomas rely on glycolysis to avoid cell death after SIRT2 modulation, revealing a metabolic vulnerability that can be harnessed to kill lymphoma cells. Overall, we have identified how SIRT2 could be implicated as a novel target of therapeutic potential for B cell lymphomas, while also defining fundamental roles for extranuclear lysine acetylation in regulating B cell proliferation and metabolism.

overall_design:
Bulk RNAseq of 2 lymphoblastoid cell lines treated with 10µM of sirtuin 2 modulator FLS-359 or equivalent DMSO concentration at 24 and 48 hours

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Submitter states that missing raw files are due to file loss.
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middle: P

first: Kaeden

middle: K

last: Hill

first: Micah

last: Luftig


title: Transcriptomic profiling of small intestine from irinotecan-treated wild-type and Gsdme-deficient mice

city: Shimotsuke

first: Tadayoshi

last: Karasawa

address: 3311-1, Yakushiji

country: Japan

institute: Jichi Medical University

summary: Irinotecan (CPT-11) is a topoisomerase I inhibitor that is widely used for solid tumors, including colorectal and pancreatic cancers. Although irinotecan exerts potent antitumor effects, it also causes intestinal mucositis. In the present study, the effect of irinotecan on intestinal mucositis was investigated in wild-type and Gsdme-deficient mice.

overall_design: Ileum tissue was collected from irinotecan-treated wild-type and Gsdme-deficient mice (n=[4] per group). Total RNA was extracted from ileum samples and subjected to bulk RNA sequencing to compare the transcriptomic profiles between the two genotypes.

first: Hidetoshi

last: Aizawa

first: Masafumi

last: Takahashi


title: Bulk long-read RNA-sequencing of four brain regions from SNCA-GR humanized-knock-in mice for SNCA isoform characterization

city: Seattle

first: Benjamin

last: Logsdon

state: WA

address: 1150 Eastlake Ave E Ste 600/700

institute: Cajal Therapeutics

summary: Parkinson's disease is a progressive neurodegenerative disorder often characterized by the accumulation of misfolded alpha-synuclein protein (aSyn) in the brain. While rare genetic variants in SNCA can cause neuronal aSyn accumulation and neurodegeneration in some cases of familial disease, the molecular mechanisms driving SNCA associated risk in idiopathic Parkinson's disease remain elusive. The canonical SNCA mRNA transcript contains a 5'UTR iron response element (IRE) that regulates translation based on cellular iron content. In this study we investigate an alternative transcript isoform lacking this element (dIRE) by evaluating SNCA transcript profiles across neuronal cell lines and post-mortem brain datasets. We show evidence that elevated dIRE expression correlates with increased disease risk in genome-wide association studies and is preferentially expressed in dopaminergic cells. Further, we show that dIRE expression may depend on transcription start site selection controlled by CpG methylation overlapping a known transcription factor binding site, where a PD associated risk haplotype exhibits lower methylation of this CpG site. To probe isoform function, we design and test isoform-specific antisense oligonucleotides (ASOs). With these ASO tools we demonstrate that the protective IRE isoform uniquely suppresses ATF4, an integrated stress response marker elevated in the substantia nigra of post-mortem Parkinson's disease brains. These analyses suggest that uncoupling aSyn translation from intracellular iron concentration may drive neurodegeneration in idiopathic Parkinson's disease. Importantly, non-isoform-selective SNCA-lowering strategies may trigger stress pathways and worsen disease progression, establishing isoform-specific ASOs as key stepping stones toward design of precision therapeutics for Parkinson's disease.

overall_design: Bulk Oxford Nanopore long-read RNA-sequencing of four brain regions (right olfactory bulb, right midbrain, right hippocampus, anterior brain) from six SNCA-GR homozygous mice (JAX #39166; humanized SNCA). Twenty-four samples were prepared as barcoded cDNA libraries with ONT cDNA-PCR Barcoding Kit V14 (SQK-PCB114.24; 13 PCR cycles) and pooled on a single R10.4.1 PromethION P2 Solo flow cell (ONT run LL3-250218-01). 23/24 barcodes produced usable data (barcode 01 / sample M8274 R-OB is not deposited). Reads were basecalled with MinKNOW and aligned with minimap2 (splice-aware). Per-sample SNCA transcript-isoform counts (dIRE1..7, IRE, total SNCA locus, and housekeeping genes) are provided as the Series-level processed data file bulk_ONT_SNCA_isoform_counts.tsv (see companion README).

first: Arvis

last: Sulovari

first: Kayla

middle: M

last: Hardwick

first: Madison

last: Baird

first: Jake

last: Gockley

first: Jennifer

last: Luyapan

first: Thuc

last: Nguyen

first: Nicole

last: Sanford

first: Anna

last: Minkina

first: Ya-Lin

first: Angelique

last: Nelson

first: Molly

last: Lindbo

first: Kat

last: Korvas

first: Karla

last: Hirokawa

first: Jeremy

last: Capalungan

first: Luke

last: Funk

first: Pilar

last: Alvarez Jerez

first: Kensuke

last: Daida

first: Kimberley

last: Billingsley

first: James

last: Evans

first: Emil

last: Gustavsson

first: John

last: Hardy

first: Sonia

last: Gandhi

first: Mina

last: Ryten

first: Andrew

last: Dervan

first: Valerie

last: Huang

first: Rob

last: Hershberg

last: Singleton

first: Cornelis

last: Blauwendraat

first: Ian

last: Peikon


title: Matched short-read and long-read single-nucleus RNA-sequencing of substantia nigra / VTA and olfactory bulb from SNCA-GR humanized-knock-in mice

first: Benjamin

last: Logsdon

overall_design: Single-nucleus RNA-sequencing of two brain regions (SNc-VTA, olfactory bulb) from three SNCA-GR homozygous male mice (JAX #39166; 55 days old, sacrificed 2025-04-28), n=6 nuclei suspensions. From each suspension, one 10x Genomics Chromium Next GEM Single Cell 5' v2 library was prepared and sequenced across three Illumina NextSeq 2000 P3 flow-cell runs (26 bp cell-barcode + UMI on Read 1, 90 bp cDNA on Read 2, dual 10 bp indices). In parallel, a matched Oxford Nanopore long-read library was prepared from 10 ng of the same amplified 10x cDNA using Ligation Sequencing Kit V14 (SQK-LSK114) with custom 5' cDNA priming oligos and sequenced on a PromethION P2 Solo (R10.4.1 chemistry, FLO-PRO114M). Short-read data processed with Cell Ranger v6.1.1; long-read data basecalled with MinKNOW and aligned with minimap2 (splice-aware).

first: Arvis

last: Sulovari

first: Kayla

last: Hardwick

first: Madison

last: Baird

first: Jake

last: Gockley

first: Jennifer

last: Luyapan

first: Thuc

last: Nguyen

first: Nicole

last: Sanford

first: Anna

last: Minkina

first: Ya-Lin

last: Lu

first: Angelique

last: Nelson

first: Molly

last: Lindbo

first: Kat

last: Korvas

last: Hirokawa


title: Transcriptional Remodeling of Esophageal Adenocarcinoma Cells Under Reflux Conditions

first: Wael

last: El-Rifai

summary: Gastroesophageal reflux disease (GERD) is the leading risk factor for esophageal adenocarcinoma (EAC), a malignancy that exhibits marked resistance to chemotherapy and results in poor clinical outcomes. This study investigates the genome-wide transcriptional adaptations and downstream molecular stress responses of EAC cells following exposure to acidic bile salts (ABS) to mimic the reflux conditions of GERD. The primary objective of this dataset is to define the differential gene expression profiles, altered signaling pathways, and transcriptional networks activated by acute ABS exposure in an EAC model.

overall_design: Human EAC cells (OE33) were exposed to acidified bile salts (ABS) cocktail (200 µM in pH4.0 null medium) for 20 minutes to model acute reflux injury. Untreated cells work as control (Ctrl). Following exposure, cells were washed and allowed to recover in complete maintenance medium for 6 hours prior to harvesting. Total RNA was isolated from three independent biological replicates per experimental condition (Total n = 6 samples).

first: Dunfa

last: Peng


title: Isoform-selective antisense oligonucleotide knockdown of SNCA-dIRE and SNCA-IRE transcripts in SK-MEL-28 cells (dose-response)

overall_design: Bulk poly(A) short-read RNA-seq (Illumina 2x150 bp paired-end, Azenta project 30-1251841615) of SK-MEL-28 human melanoma cells transfected with four antisense oligonucleotides (ASO2 non-targeting control, ASO43 dIRE-selective, ASO550 dIRE-selective, ASO387 IRE-selective) at three doses (0.2 uM, 2 uM, 10 uM) in three biological replicates per condition (n=36 libraries). Cells were plated on 2025-09-29, transfected on 2025-09-30 with ASO/Lipofectamine RNAiMAX complexes in 24-well format, and collected as cell pellets on 2025-10-03 (3 days post-transfection). RNA was extracted with Trizol/chloroform + Qiagen RNeasy MinElute. Gene-level quantification was performed with Salmon (v1.10.0) and normalized with DESeq2 v1.38.3 (TMM).

first: Karla

first: Jeremy

last: Capalungan

first: Luke

last: Funk

first: Pilar

last: Alvarez Jerez

first: Kensuke

last: Daida

first: Kimberley

last: Billingsley

first: James

last: Evans

first: Emil

last: Gustavsson

first: John

last: Hardy

first: Sonia

last: Gandhi

first: Mina

last: Ryten

first: Andrew

last: Dervan

first: Valerie

last: Huang

first: Rob

last: Hershberg

last: Singleton

first: Cornelis

last: Blauwendraat

last: Peikon


title: REMODEL: A modular framework for longitudinal ctDNA methylation profiling reveals treatment response and relapse-associated epigenetic remodeling

city: Bergamo

first: Nicola

last: Bianchi

address: Piazza OMS 1

department: Department of Pathology

country: Italy

institute: ASST Papa Giovanni XXIII Hospital

type: Methylation profiling by high throughput sequencing

summary: Circulating tumour DNA (ctDNA) methylation profiling is a promising non-invasive tool for disease monitoring, but longitudinal interpretation is limited by variable sequencing coverage and the loss of clinically relevant signals. We developed REMODEL (Recovery-based Epigenetic Monitoring of Dynamic methylation for Longitudinal analysis), an integrated framework combining coverage-aware binning, count-based longitudinal statistics, and a novel Epigenetic Recovery Score (ERS) to quantify post-treatment methylation recovery. Applied to 17 serial plasma samples from two T-cell lymphoma patients (2,025 genomic bins), REMODEL distinguished durable remission, characterized by coordinated demethylation (86.4% of bins) and sustained positive ERS, from relapse, marked by widespread hypermethylation (64.9% of bins) and persistently negative ERS despite clinical remission. By integrating dynamic methylation detection with recovery modelling, REMODEL provides an interpretable framework for longitudinal ctDNA methylation analysis and minimal residual disease monitoring.

overall_design:
Longitudinal plasma samples from two patients with peripheral T-cell lymphoma (PTCL) were collected at multiple clinically relevant timepoints spanning diagnosis, treatment, autologous stem-cell transplantation (ASCT), and follow-up. One patient also contributed samples collected at relapse and after salvage therapy. Circulating tumor DNA (ctDNA) methylation was profiled using the Avida Methyl 3400 DMR Cancer Panel to characterize treatment-associated epigenetic remodeling and longitudinal disease evolution.

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Raw files for human/patient samples are being made available in EGA (https://www.ebi.ac.uk/ega/) for controlled access to the personally identifiable sequence data.
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first: Mohamed

last: Hegazi

first: Alessandro

last: Putelli

first: Giulia

last: Ghirardi

first: Marta

last: Cardisperi

first: Sara

last: Licini

first: Federica

last: Paleni

last: Berbenni

last: Melis

first: Andrea

last: Gianatti

first: Giuseppe

last: Gritti

first: Fabio

last: Grizzi

first: Denise

last: Morotti


title: PGK1 moonlights as an NF-kB/p65 kinase to orchestrate M2-like macrophage-mediated immunosuppression in triple-negative breast cancer

city: Wuhan

first: Tinglin

last: Yang

address: 1277 Jie Fang Avenue, Jianghan District

department: Department of Breast and Thyroid Surgery

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

summary: Triple-negative breast cancer (TNBC) is the most aggressive molecular subtype with limited therapeutic options. Metabolic reprogramming is a hallmark of cancer, and emerging evidence indicates metabolic enzymes possess non-canonical moonlighting functions. We identified phosphoglycerate kinase 1 (PGK1) as a key link between glycolysis and immunosuppression in TNBC. To investigate the role of PGK1 in shaping the tumor immune microenvironment, we performed single-cell RNA sequencing (scRNA-seq) on TNBC cells (4T1) with PGK1 knockdown (shPgk1) and negative control (shNC), each with three biological replicates. Single-cell libraries were prepared on the TaiM4 scRNA platform and sequenced on the BGI DNBSEQ platform using paired-end sequencing. A total of 33,138 high-quality cells were retained after quality filtering. Our analysis revealed that PGK1 knockdown significantly altered the transcriptional landscape and immune signaling pathways in TNBC cells.

overall_design: Two-group comparison: shNC (negative control shRNA, 3 biological replicates) vs shPgk1 (PGK1 knockdown shRNA, 3 biological replicates) in 4T1 TNBC cells. Single-cell RNA-seq was performed.

first: Wenhui

last: Li

first: Chaocong

last: Xu

first: Anwen

last: Ren

first: Yiyang

last: Shen

first: Pengfei

last: Yi

first: Tao

last: Huang


title: Genome-Wide Transcriptomic Analysis Reveals Jasmonate-Mediated Defense Reprogramming and Glucosinolate Accumulation in Brassica rapa var. trilocularis

city: An-seong si

first: Hyunjoon

last: Kim

address: 4726, Seodong-daero, Daedeok-myeon, Anseong-si, Gyeonggi-do, Republic of Korea

institute: Chung-ang University

summary: Jasmonates (JAs) are key phytohormones that orchestrate plant defense and developmental responses. To characterize transcriptome-wide JA responses in Brassica rapa var. trilocularis, we performed time-course RNA sequencing of mock- and methyl jasmonate (MeJA)-treated R-o-18 seedlings. Leaf tissues were collected at 10 min, 24 h, and 72 h after treatment. MeJA induced rapid and extensive transcriptional reprogramming, including activation of defense-related metabolic pathways and suppression of auxin-responsive, cell-cycle, and stomatal-development genes. MeJA also induced ethylene biosynthesis and signaling genes and coordinately activated transcription factors and biosynthetic genes associated with aliphatic and indolic glucosinolate accumulation. These data provide a transcriptomic resource for understanding jasmonate-mediated growth-defense tradeoffs and chemical defense metabolism in B. rapa.

overall_design: Ten-day-old Brassica rapa var. trilocularis inbred line R-o-18 seedlings were treated with 50 μM methyl jasmonate (MeJA) or mock solution. Leaf tissues were harvested at 10 min, 24 h, and 72 h after treatment. Three independent biological replicates were collected for each treatment and time point, yielding 18 RNA-seq libraries. Strand-specific mRNA libraries were sequenced using paired-end sequencing on an Illumina NovaSeq 6000 platform. MeJA-treated samples were compared with the corresponding mock-treated controls at each time point.

first: Dasom

last: Choi

first: Dong-Hwan


title: Pan-SNCA vs. isoform-selective antisense oligonucleotide knockdown of SNCA-dIRE in SK-MEL-28 cells (ATF4 follow-up)

first: Benjamin

last: Logsdon

overall_design: Bulk poly(A) short-read RNA-seq (Illumina 2x150 bp paired-end, ~30 M reads/sample; Azenta project 30-1296162709) of SK-MEL-28 human melanoma cells transfected at a single 2 uM dose with four antisense oligonucleotides (ASO2 non-targeting control, ASO3 pan-SNCA, ASO43 dIRE-selective, ASO550 dIRE-selective). Follow-up to the earlier SK-MEL-28 dose-response study to test whether VMP1 reduction observed after dIRE-selective knockdown is recapitulated by pan-SNCA knockdown. Cells plated on 2026-02-09 (100,000 cells/well, 24-well), transfected on 2026-02-10 with 60 uL of ASO/Lipofectamine RNAiMAX complex per well (final 2 uM ASO), harvested as cell pellets on 2026-02-13. Sixteen RNA samples prepared (4 biol reps per ASO); 12 samples passing NanoDrop QC selected for sequencing (3 reps per ASO). RNA extraction: Trizol + Qiagen RNeasy MinElute Micro. Quantification: Salmon; normalization: DESeq2 (TMM).

first: Arvis

last: Sulovari

first: Kayla

last: Hardwick

first: Madison

last: Baird

first: Jake

last: Gockley

first: Jennifer

last: Luyapan

first: Thuc

last: Nguyen

first: Nicole

last: Sanford

first: Anna

last: Minkina

first: Ya-Lin

last: Lu

first: Angelique

last: Nelson

first: Molly

last: Lindbo

first: Kat

last: Korvas

first: Karla

last: Hirokawa

first: Jeremy

last: Capalungan

first: Luke

last: Funk

first: Pilar

last: Alvarez Jerez

first: Kensuke

last: Daida

first: Kimberley

last: Billingsley

first: James

last: Evans

first: Emil

last: Gustavsson

first: John

last: Hardy

first: Sonia

last: Gandhi

first: Mina

last: Ryten

first: Andrew

last: Dervan

first: Valerie

first: Rob

last: Hershberg

last: Singleton

first: Cornelis

last: Blauwendraat

first: Ian

last: Peikon


title: Whole-Transcriptome Profiling Reveals RNA Expression Dynamics and ceRNA Network Remodeling across Health, Sepsis, and Sepsis-Associated Acute Respiratory Distress Syndrome [miRNA-Seq]

city: Nanning City

first: Qicheng

last: Long

state: Guangxi Zhuang Autonomous Region

address: No.6 Shuangyong Road

department: Department of Intensive Care Unit

institute: The First Affiliated Hospital of Guangxi Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Background: Sepsis-associated acute respiratory distress syndrome (ARDS) is a severe manifestation of infection-related organ dysfunction characterized by dysregulated immune-inflammatory responses and disruption of tissue barriers. However, the whole-transcriptome alterations underlying the progression from sepsis to sepsis-associated ARDS remain insufficiently characterized. Therefore, this study aimed to systematically characterize the expression patterns of mRNAs, long non-coding RNAs (lncRNAs), circular RNAs (circRNAs) and microRNAs (miRNAs) in peripheral blood from healthy controls, sepsis without ARDS, and sepsis-associated ARDS patients.Methods: 12 participants were enrolled, comprising four healthy controls (HC group), 4 patients with sepsis without ARDS (SWA group), and 4 patients with sepsis-associated ARDS (SA group). Peripheral blood samples were obtained and subjected to whole-transcriptome sequencing. Trend analysis was performed to identify transcripts exhibiting monotonic increases or decreases across the HC–SWA–SA sequence. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were subsequently performed. Target-gene prediction and expression-correlation analyses were also performed to construct a competing endogenous RNA (ceRNA) regulatory network.Results: All sequencing datasets passed the quality control and were suitable for the following analyses. A total of 773 trend genes were identified, of which 350 were progressively upregulated and 423 were progressively downregulated. These genes were predominantly enriched in immune responses, cell adhesion, cytokine production, extracellular matrix-related processes, MAPK and PI3K–Akt signaling pathways, integrin signaling, focal adhesion, ECM–receptor interaction, and antigen processing and presentation. A total of 189 trend lncRNAs, 252 trend circRNAs, and six trend miRNAs were identified. Their predicted functions were associated with RNA metabolism, translational regulation, chromatin-associated regulation, cytoskeletal organization, epithelial barrier integrity, cell polarity, and intracellular trafficking. The resulting ceRNA network contained several miRNA-centered modules involving hsa-miR-193b-3p, hsa-let-7b-3p, hsa-miR-223-3p, hsa-miR-223-5p, novel_mir_76, and novel_mir_177. These modules were functionally associated mainly with ion transport, calcium signaling, membrane-channel activity, tight-junction regulation, and vesicular trafficking. Conclusion: This study delineates an integrated whole-transcriptome landscape of progressive RNA expression alterations across the transition from health to sepsis without ARDS and, ultimately, to sepsis-associated ARDS. The findings suggest that coordinated dysregulation of coding and non-coding RNAs may contribute to immune-inflammatory activation, extracellular matrix remodeling, barrier dysfunction, and altered post-transcriptional regulation. Collectively, these findings highlight candidate molecular signatures and regulatory axes that warrant further investigation in mechanistic and biomarker-oriented studies of sepsis-associated ARDS.

first: Yongkang

last: Ye

first: Aifang

last: Huang

first: Shuqing

last: Liang

first: Wei

last: Wang


title: Whole-Transcriptome Profiling Reveals RNA Expression Dynamics and ceRNA Network Remodeling across Health, Sepsis, and Sepsis-Associated Acute Respiratory Distress Syndrome

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

overall_design: Refer to individual Series