title: Conserved sleep disturbances in FOXP1 syndrome originate from developmental dysregulation of peptidergic signaling

city: Nijmegen

first: Nicholas

last: Raun

address: Geert Grooteplein 10

country: Netherlands

institute: Radboudumc

summary: We have profiled gene expression from whole dissected brains of FoxP mutant Drosophila melanogaster.

overall_design: Gene expression profiles in adult Drosophila brains were compared between FoxP mutants and their genetic background controls. 4 replicates per condition were used, each replicate was comprised of genetic material from 12 dissected fly brains.

first: Mireia

last: Coll-Tané

first: Anna

last: Castells-Nobau

first: Annette

last: Schenck


title: EBF1 regulates sensory establishment in the cochlea by positioning the medial boundary of the prosensory domain and restricting proliferation of the sensory progenitor population

status: Public on Jan 23 2026

city: Seattle

first: Joshua

middle: William

last: Hahn

state: WA

address: 3747 W Stevens Wy NE

department: Department of Neurobiology & Biophysics

country: USA

institute: University of Washington

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary: In our previous study, we reported that Ebf1 excision throughout the inner ear epithelium and before the onset of cochlear development leads to dramatic sensory expansion in the cochlea by neonatal stages. Ebf1 conditional knockout cochleae possess over twice as many sensory cells as littermate controls and develop ectopic sensory patches in their Kölliker’s organs. To better understand the mechanism behind EBF1’s role in restricting sensory establishment, we performed multiome sequencing in our current study. EBF1 is a traniption factor best known for its importance in B cell lineage specification, during which it acts as both an activator and a repressor. Our results indicate that EBF1 prevents the Kölliker’s organ cells from being recruited to the prosensory domain by promoting expression of Prdm16 and repressing expression of Jag1 and Sox2. We also found that EBF1 may promote cell cycle exit by repressing Ccnjl expression. In summary, medial expansion of the prosensory domain, together with delayed cell cycle exit in the developing cochlear epithelium, underlies the robust increase in sensory cells seen in Ebf1 conditional knockouts.

overall_design: To enable investigation of EBF1-dependent changes in cochlear development at the single cell level, we performed multiome sequencing, combining single nucleus RNA sequencing (snRNA-seq) and single nucleus ATAC sequencing (snATAC-seq), on mouse cochlea at E14.5 and E16.5 in control mice and in a Ebf1 conditional knockout model.

first: Kathryn

middle: G

last: Powers

first: Juliette

last: Wohlschlegel

first: Olivia

last: Bermingham-McDonogh


title: G549 EP300_KO RNA-seq

city: Toronto

first: Fatemeh

last: Molaei

state: Ontario

address: 160 College St. Room 830, Terrence Donnelly Centre for Cellular & Biomolecular Research

country: Canada

institute: University of Toronto

summary: EP300 was identified as potential regulator of Injury-response/Mesenchymal state in Glioblastoma stem cells. Our objective was to identify the effect of EP300 KO on transcriptomic signature of Injury-response/Mesenchymal GSC.

overall_design: RNA was harvested from G549-EP300_KO cells (N=4) and  G549-AAVS1_KO cells (control). Gene expression profiling and differential expression analysis were conducted.

first: Graham

last: MacLeod

first: Stephane

last: Angers


title: ELK1 is a novel prognostic and therapeutic target for AML which controls the maturation of neutrophils

city: chengdu

first: Yong

last: Dong

state: sichuan

address: Xindu road 783, Xindu district

department: Immunology

country: China

institute: Chengdu medical college

summary: It is encouraging to identify new target genes that can promote the differentiation and maturation of undifferentiated leukemia cells for the treatment of acute myeloid leukemia (AML). In this study, we discovered that ELK1 is highly expressed in AML, and its expression negatively correlates with the survival of AML patients. Subsequently, we utilized Elk1 and KrasG12D conditional expression mouse models to investigate how upregulating Elk1 contributes to the progression of myeloid leukemia induced by the KrasG12D mutation through various mechanisms. To further understand the role of Elk1 in regulating hematopoiesis, we conducted both single-cell RNA sequencing and bulk-cell RNA sequencing.

overall_design: To dissect the mechanism of Elk1 regulating hematopoiesis, CD3/CD19/NK1.1/Ter119－ CD11b+ and CD3/CD19/NK1.1/Ter119－C-kit+ cells derived from Mx1-Elk1 and littermate control mice are sorted and  mixed together at the ratio 1:2 for single cell RNA sequencing. The populations of Lin-Kit+Sca1+( LSK), common myeloid progenitors (CMP), granulocyte-monocyte progenitors (GMP), megakarocyte-erythrocyte progenitors ( MEP), Immature neutrophils and mature neutrophils derived from Mx1-Elk1 and littermate control mice are sorted for bulk-cell RNA sequencing.


title: Total RNA transcriptomic profiling of mouse thoracic and abdominal perivascular adipose tissue of mice with an adipocyte-specific deletion of PRDM16 and flox control mice.

city: New York

first: Wei

last: Wang

state: New York

address: 1230 York Ave.

department: Bioinformatics Resource Center

institute: The Rockefeller University

summary: Thoracic and abdominal perivascular adipose tissue (tPVAt and aPVAT) is in direct contact with the outer layer of the aorta. While tPVAT exhibits a thermogenic phenotype, aPVAT is mostly comprised of white adipocytes with a few scattered thermogenic adipocytes. To investigate the relevance of this change in adipocyte identity along the aorta, we used mice with an adipocyte-specific deletion of Prdm16 resulting in loss of thermogenic and gain of white adipocyte-like features and compare gene expression signature in these mice.

overall_design: Total mRNA RNAseq was performed on total RNA extracted  from PRDM16flox (controls) and PRDM16flox, AdipoQCre+ mice.

first: Mascha

last: Koenen

first: Thomas

last: Carroll

first: Paul

last: Cohen


title: Functional dissection of ovarian aging-associated genes NDUFS5 and UBE2L3 through integrated genomic analyses and validation

city: Hangzhou

first: Yifei

last: Lv

address: 1 Xueshi Rd, Hangzhou, People’s Republic of China

institute: Women’s Hospital, Zhejiang University School of Medicine

summary: Ovarian aging, culminating in menopause, involves a gradual decline in ovarian function. Genetic factors influencing age at natural menopause (ANM) especially premature ovarian insufficiency (POI) warrant further research. We employed a Bayesian framework to integrate a genome-wide association study (GWAS) on ANM (N=69,360) with an expression quantitative trait loci (eQTL) dataset (N=1,490), identifying 28 significant risk genes. Peripheral blood analysis from patients with POI and healthy controls, combined with RNA sequencing, differential gene (DEGs) expression analysis, and RT-qPCR verification, pinpointed MSH5, GAB2, NDUFS5, LST1, and UBE2L3 as top DEGs. NDUFS5 and UBE2L3 were aberrantly expressed in hydrogen peroxide or cyclophosphamide-treated human granulosa cells. Immunohistochemisty revealed decreased NDUFS5 and increased UBE2L3 expression in human ovarian samples of varying ages. NDUFS5 knockdown reduced granulosa cell proliferation and increased apoptosis in cell culture; UBE2L3 knockdown exhibited the opposite effect. Together, our findings indicate NDUFS5 and UBE2L3 as key risk genes involved in ovarian aging.

overall_design: Peripheral blood samples were obtained from women diagnosed with POI and from women without ovarian disorders identified through physical examinations. Total RNA was isolated from PBMCs.

first: Yunlong

last: Ma

first: Yizhou

last: Huang

first: Linjuan

first: Jianhong

last: Zhou


title: LDHA induces β cell dedifferentiation in diabetes through metabolic epigenetic reprogramming [RNA-Seq]

city: Nanjing

first: Xirui

last: Li

address: #101 Longmian Avenue, Jiangning District

institute: Nanjing Medical University

summary: Aims/hypothesis Pancreatic β cell dedifferentiation underlies the reversible reduction in β cell mass and function in diabetes. Interventional targets and adjuvant therapies to prevent/reverse β cell dedifferentiation and transdifferentiation may provide evidence to support the effective treatment of diabetes, while the underlying molecular mechanism remains elusive. Methods LDHA expression and activity were analysed in islets obtained from humans with type 2 diabetes, hyperglycaemic db/db mice, and a high-fat diet (HFD)-induced mouse model of diabetes. The impact of LDHA inhibition on β cell function and identity was investigated in high-fat diet (HFD) feeding mice and db/db mice. ChIP-seq and RNA-seq were used to investigate the specific molecular mechanism underlying the effect of LDHA on the H3K9la enhancement and beta cell function under glucotoxic conditions. Results We demonstrated that inhibition of LDHA effectively preserved β cell identity, which not only delay disease progression in prediabetic stage, but also improve insulin output and glucose homeostasis in diabetic models. Mechanistically, the activation of LDHA led to a marked increase in histone H3 lysine 9 lactylation (H3K9la) in the promoter region of the β cells dedifferentiation markers Sox9, Hes1 and Aldh1a3, and facilitated their transcription, thereby triggering β cell dedifferentiation as well as impaired glucose homeostasis and β cell function in mice. Conclusions/interpretation We unraveled the role of lactate dehydrogenase A (LDHA)-mediated metabolic and epigenetic reprogramming in β cell dedifferentiation during diabetes development. This study suggests that LDHA inhibition could be a novel therapeutic strategy for diabetes treatment.

first: Haoqiang

last: Gong

first: Can

last: Xiong

first: Xinyue

first: Mei

last: He

first: Liangjun

last: Sun

first: Wenyue

last: Yin

first: Suyun

last: Zou

first: Min

last: Sha

first: Wanhua

last: Guo

first: Tijun

last: Wu

first: Qingguo

first: Yaqin

last: Zhang

first: Fang

last: Chen


title: Commonalities in gene expression and methylation changes across two rat models of acquired epilepsy [RRBS]

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

type: Methylation profiling by high throughput sequencing

summary: Epileptogenesis, the process by which a normal brain develops epilepsy, is characterized by complex changes in DNA methylation and gene expression. In this study, RNA sequencing and reduced-representation bisulfite sequencing were utilized to investigate these molecular alterations in two distinct and widely used rat models of temporal lobe epilepsy: intrahippocampal electrical kindling and systemic kainic acid. These models, involving rats, differ significantly in their underlying mechanisms and histopathological outcomes, providing a unique opportunity to identify both shared and model-specific changes during epileptogenesis. By comparing these models, we uncovered common pathways that may reflect generalizable, model-independent mechanisms of epileptogenesis, alongside distinct changes that highlight the diverse molecular landscapes of each model. This integrative, multi-omics approach not only enhances our understanding of the molecular drivers of epileptogenesis but also underscores the importance of cross-model comparisons for uncovering robust and potentially therapeutic targets in epilepsy research. This dataset serves as a valuable resource for exploring the epigenomic and transcriptomic underpinnings of epilepsy.

overall_design: Adult male Sprague–Dawley rats (~170–280 g) were used to investigate molecular alterations during epileptogenesis in two distinct models of temporal lobe epilepsy: systemic kainic acid and intrahippocampal electrical kindling. Animals were housed under a 12:12 light/dark cycle with ad libitum access to food and water. In the systemic kainic acid model, rats underwent electrode implantation surgery, followed by incremental kainic acid injections to induce status epilepticus. In the intrahippocampal kindling model, rats were instrumented with hippocampal electrodes and subjected to twice-daily stimulations until fully kindled. Whole hippocampi were surgically dissected 24 hours after the last seizure, flash-frozen in liquid N2, and stored at -80°C. Total RNA and DNA were extracted from left hippocampal samples using Qiagen’s AllPrep DNA/RNA Mini Kit. RNA sequencing libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit and sequenced with a single-end read length of 110 bases on an Illumina NovaSeq platform. Reduced representation bisulfite sequencing (RRBS) libraries were prepared following Msp1 digestion, bisulfite conversion, and PCR amplification, and sequenced with the same platform. The resulting RNA-seq and RRBS datasets provide comprehensive insights into gene expression and DNA methylation changes associated with epileptogenesis across these models.

first: Benton

last: Purnel

first: Detlev

last: Boison


title: Targeting ADAR1-mediated RNA editing inhibits hepatic stellate cell activation and liver fibrosis by enhancing HSC-intrinsic IFN signaling

city: Wuhan

first: Yue

last: Xi

state: Hubei

address: 81 St

department: College of life sciences

institute: Wuhan University

summary: This study aims to characterize the RNA editome during fibrogenesis and to elucidate the role of ADAR1 in hepatic stellate cell (HSC) activation and liver fibrosis. We showed that ADAR1 ablation in primary mouse HSCs ameliorated HSC activation. Mechanistically, ADAR1 ablation led to dsRNA accumulation and activated HSC-intrinsic IFN signaling in an MDA5-dependent manner. RNA editome analysis revealed that the 3’ UTR of the pro-fibrogenic gene Col3a1 was highly edited by ADAR1, leading to mRNA stabilization and increased protein expression. Targeting ADAR1-mediated RNA editing in HSCs holds promise to prevent and treat liver fibrosis.

overall_design: Primary HSCs isolated from Adar1f/f/Cre-ER mice were treated with vehicle or 100 nM of 4-OHT to induce Adar1 ablation and culture-activated for 4 days.

first: Pengfei

last: Xu

first: Wen

last: Xie


title: Inflammasome activation and oxidative stress in SARS-CoV-2 breakthrough infection and symptomatic rebound

city: BETHESDA

first: Cihan

last: Oguz

state: MD

address: NIHBC 29B BG RM 1NN20, 9000 ROCKVILLE PIKE

institute: NIH

summary: Despite the efficacy of therapeutics and vaccines in reducing risk of severe COVID-19, breakthrough infections and rebound symptoms after initial improvement have been reported. We evaluated critical inflammatory responses in vaccinated individuals presenting with early acute (EA), late acute (LA) and clinical rebound (REBOUND) symptoms using single cell RNA sequencing.

overall_design: We performed single cell RNA sequencing (scRNA-Seq) of peripheral blood mononuclear cells (PBMCs) samples from vaccinated patients presenting with early acute (EA), late acute (LA) and clinical rebound (REBOUND) symptoms of COVID-19. The experimental design for sequencing involved a total of 15 PBMC samples (13 patients) distributed across the three conditions: EA, LA, and REBOUND.

first: Silvia

middle: L

last: Lage

first: Joseph

middle: M

last: Rocco

first: Francisco

last: Otaizo-Cassaquero

first: Adam

last: Rupert

first: Kristin

last: Boswell

first: Brian

middle: P

last: Epling

first: Logan

last: Cook

first: Eduardo

last: Amaral

first: Elizabeth

last: Laidlaw

first: Frances

last: Galindo

first: Richard

middle: A

last: Koup

first: Princy

last: Kumar

first: Rita

last: Poon

first: Glenn

middle: W

last: Wortmann

first: Andrea

last: Lisco

first: Maura

last: Manion

first: Irini

last: Sereti


title: Chronic variable mild stress alters the transcriptome and signaling properties of the anterodorsal bed nuceleus of the stria terminalis in a sex-dependent manner

city: New Brunswick

first: Thomas

middle: J

last: Degroat

state: NJ

address: 10 Suydam Street, Apt 12

department: Animal Sciences

institute: Rutgers University

summary: Chronic stress is a physiological state marked by dysregulation of the hypo-pituitary-adrenal axis and high circulating levels of stress hormones, such as corticosterone in mice or cortisol in humans. This dysregulated state may result in the development of mood disorders but the process by which this occurs is still unknown. The bed nucleus of the stria terminalis (BNST) serves as an integration center for stress signaling and is therefore likely an important area for the development of mood disorders. This project utilized a chronic variable mild stress (CVMS) paradigm to persistently stress mice for 6 weeks followed by RNA-Sequencing of the anterodorsal (ad) BNST and electrophysiology of corticotropin releasing hormone-expressing cells in the adBNST. Our results show significant sex-biases in the transcriptome of the adBNST as well as effects of CVMS on the transcriptome of the adBNST specifically in males. Female biased genes are related to synaptic transmission while male biased genes are related to RNA processing. Stress sensitive genes in males are related to synaptic transmission and synapse formation. Additionally, electrophysiology data showed that CVMS suppressed the M-current in males but not females. However, CVMS increased the strength of excitatory post-synaptic currents in females but not males. This suggests significant differences in how males and females process chronic stress. It also suggests that the BNST is more sensitive to chronic stress in males than in females.

overall_design: At 7-9 weeks of age, male and female mice were selected for either control conditions or chronic variable mild stress (CVMS). This resulted in 4 experimental groups with 15 mice each. After CVMS or control conditions, mice were anesthetized with ketamine, then the brain was dissections, sliced, and microdissected to isolate the anterodorsal bed nucleus of the stria terminalis. This occured 1 hour after the last stressor in CVMS mice, which was wet bedding. Tissue samples from 3 biological replicates were then pooled prior to RNA extraction. RNA-Sequencing had a sample size of n=5 for each group with no outliers.

first: Sarah

last: Paladino

first: Benjamin

last: Samuels

first: Troy

last: Roepke


title: Commonalities in gene expression and methylation changes across two rat models of acquired epilepsy [RNA-seq]

first: Junguk

last: Hur

first: Benton

last: Purnel

first: Detlev

last: Boison


title: NR2F6 deletion revives CAR‑T cell function and induces antigen‑agnostic immune memory in solid tumors

city: Innsbruck

first: Dietmar

last: Rieder

address: Innrain 80

department: Biocenter

country: Austria

institute: Medical University of Innsbruck

summary: CAR‑T cell therapy is effective in hematologic malignancies but remains challenging in solid tumors owing to antigen heterogeneity and tumor microenvironment‑induced exhaustion. Here, gene editing of the nuclear receptor NR2F6 restores CAR‑T cell functionality, sustaining a TCF1⁺ progenitor‑exhausted T cell phenotype, enhancing metabolic fitness, and preserving cytotoxic potency under chronic antigen exposure. In immunocompetent models, Nr2f6‑deficient CAR‑T cells suppress solid tumor growth and induce robust, polyclonal host antitumor responses, as shown by protection in tumor re‑challenge experiments. Although infused CAR‑T cells disappear within 2 weeks, durable tumor control coincides with epitope spreading and secondary immune responses, likely via dendritic and other antigen‑presenting cell reactivation. Protection against antigen‑negative tumors and transferable immunity reveal a dual mode of direct cytotoxicity followed by durable immune reprogramming. This broadened host immunity may offset immune escape driven by antigen loss and tumor heterogeneity, establishing NR2F6 inhibition as a promising CAR‑T engineering strategy for durable, antigen‑agnostic solid‑tumor immunotherapy.

overall_design:
Bulk RNA sequencing: Transcriptional profiling of wildtype and Nr2f6 knockout CAR-T cells in co-culture with Panc02-EpCAM tumor cells at day 0, day 4 and day 8.
Single cell RNA sequencing: single cell transcriptomic profiling and V(D)J analysis of either naive or Nr2f6 knock-out CAR-T treated survivor mice challenged with Panc02-EpCAM negative tumors.

first: Dominik

last: Humer

first: Victoria

last: Klepsch

first: Gottfried

last: Baier


title: Identification of β-catenin dependent and independent genes in an orthotopic model of pancreatic cancer

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

country: United Kingdom

institute: Cardiff University

summary: Wnt signaling regulates metazoan development and homeostasis, in part by β-catenin dependent activation and repression of a large number of genes. However, Wnt signaling also regulates genes independent of β-catenin, genes that are less well characterized. In this study, using a pan-Wnt inhibitor we performed a comprehensive transcriptome analysis in a Wnt-addicted orthotopic cancer model to delineate the β-catenin-dependent and independent arms of Wnt signaling. We find that while a large percentage of Wnt-regulated genes are regulated by β-catenin, ten percent of these genes are regulated independent of β-catenin. Interestingly, a large proportion of these β-catenin independent genes are Wnt-repressed.

overall_design: Timecourse RNA-seq in HPAF-II cells treated with ETC-159 with or without mutation in β-catenin

first: Nathan

last: Harmston

first: David

last: Virshup

first: Babita

last: Madan


title: The potential impact of VHL on chromatin accessibility using the assay for ATAC-seq in Caki-1 cells.

city: Zhengzhou

first: Kenan

last: Zhang

address: Jianshe Street

institute: The First Affiliated Hospital of Zhengzhou University

summary: To investigate the potential impact of VHL on chromatin accessibility,  the assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq)  was performed in renal cell carcinoma cells.The VHL wild-type Caki-1 cells were used to generate control or VHL knockout cells by CRISPR/Cas9-mediated genome editing (sgCTR and sgVHL Caki-1 cells).Following ATAC-seq,  DNAs were amplified using non-biased conditions, labeled, and sequenced with Illumina NovaSeq 6000.

overall_design: The VHL wild-type Caki-1 cells were used to generate control or VHL knockout cells by CRISPR/Cas9-mediated genome editing (sgCTR and sgVHL Caki-1 cells). In sgCTR and sgVHL Caki-1 cells, nuclei were removed from samples and resuspended in the Tn5 transposase reaction mix. For 30 min, the transposition process was incubated at 37°C. After transposition, equimolar Adapter 1 and Adapter 2 were introduced, and the library was amplified using PCR. Libraries were purified using DNA clean beads after the PCR process, and library quality was evaluated with Qubit. The library preparations were sequenced on an Illumina NovaSeq 6000 platform after cluster creation, yielding 150 bp paired-end reads.

first: Lin

last: He


title: Ageing promotes metastasis via activation of the integrated stress response [RNA-Seq OE]

city: Gothenburg

first: Volkan

last: Sayin

address: Medicinaregatan 1F

department: Department of Surgery

country: Sweden

institute: University of Gothenburg

summary: Lung cancer predominantly affects older individuals, yet how physiological aging influences tumor evolution remains poorly understood. Here, we show that aging reprograms the evolutionary trajectory of KRAS-driven lung adenocarcinoma, limiting primary tumor growth while promoting metastatic dissemination through epigenetic activation of the integrated stress response (ISR). The ISR effector ATF4 drives epithelial and metabolic plasticity, conferring metastatic competence. Mechanistically, aged tumor cells exhibit increased sensitivity to the PERK–eIF2α arm of the unfolded protein response, sustaining persistent ATF4 signaling. Targeting the ISR-ATF4 genetically or pharmacologically abolishes these adaptations and limits dissemination, whereas ATF4 overexpression alone is sufficient to induce metastasis. The aging–ATF4 axis imposes a dependency on glutamine metabolism, revealing a therapeutically actionable vulnerability. Clinical analyses confirm that ATF4 is enriched in aged tumors and correlates with poor survival and advanced-stage disease. Collectively, these results define epigenetic ISR–ATF4 activation as a causal driver of lineage plasticity and metastasis in aged tumors, revealing a therapeutic opportunity in older patients with lung adenocarcinoma, the most common yet understudied subset of lung cancer

overall_design: To investigate transcriptomic differences between Old and Young primary cultures from KP-Young and KP-Old mice with and without Atf4 over-expression.

first: Angana

last: Patel

first: Clotilde

last: Wiel

middle: I


title: The transcription factor Traffic jam orchestrates the somatic piRNA pathway in Drosophila ovaries [RNA-seq]

city: CLERMONT FERRAND

first: Stephanie

last: MAUPETIT MEHOUAS

address: Faculté de Médecine, 28 place Henri DUNANT

country: France

institute: CNRS UMR6293, INSERM U1103 - l’Université Clermont Auvergne (UCA)

summary: The PIWI-interacting RNA (piRNA) pathway is essential for transposable element (TE) silencing in animal gonads. While the transcriptional regulation of piRNA pathway components in germ cells has been documented in mice and flies, their control in somatic cells of Drosophila ovaries remains unresolved. Here, we demonstrate that Traffic jam (Tj), the Drosophila orthologue of large Maf transcription factors in mammals, is a master regulator of the somatic piRNA pathway. Tj binds to regulatory regions of somatic piRNA factors and the major piRNA cluster flamenco, which carries a Tj-bound enhancer downstream of its promoter. Depletion of Tj in somatic follicle cells causes downregulation of piRNA factors, loss of flam expression and de-repression of gypsy-family TEs. We propose that the arms race between the host and TEs led to the co-evolution of promoters in piRNA pathway genes as well as TE regulatory regions that both rely on a shared transcription factor.

overall_design: mRNA Seq data from ovaries of somatic TJ knockdown drosophila compared to ovaries of somatic white knockdown flies ; mRNA seq data from ovaries of flamenco mutant drosophila

first: Azad

last: Alizada

first: Aline

last: Martins

first: Nolwenn

last: Mouniée

first: Julia V

last: Rodriguez Suarez

first: Benjamin

last: Bertin

first: Nathalie

last: Gueguen

first: Vincent

last: Mirouse

first: Anna-Maria

last: Papameletiou

first: Austin J

last: Rivera

first: Nelson C

last: Lau

first: Abdou

last: Akkouche

first: Stéphanie

last: Maupetit-Mehouas

first: Gregory J

last: Hannon

last: Czech Nicholson

first: Emilie

last: Brasset


title: Effect of IVNS1ABP mutation, knockout on gene expression during iPSCs differentiation to Neural Progenitors

city: La Jolla

first: FANG

last: YUAN

address: 10901 N Torrey Pines Rd

institute: Sanford Burnham Prebys

summary: We identified a new disease characterized by severe neurological deficits in addition to progeria symptoms. It is caused by IVNSABP gene mutation. The association between IVNS1ABP and aging has never been reported before. By generating isogenic iPSCs from the patients’ fibroblasts and differentiating the iPSCs into neural progenitor cells (NPCs), we found that mutant IVNS1ABP fibroblasts, iPSCs, and NPCs exhibited disrupted cytokinesis, DNA damage, and cellular senescence. Transcription analysis of isogenic iPSCs and iPSCs derived neural progenitors (NPCs) also showed impaired cytokinesis and senescence alteration.  Correspondingly, cerebral organoids displayed premature differentiation of NPCs to neurons. Molecular profiling as well as biochemical and cellular analysis revealed altered binding of mutant IVNS1ABP to actin and actin-associated proteins and dysregulated actin dynamics during cytokinesis. Taken together, we propose that IVNS1ABP mutation dysregulates actin polymerization and organization which is at least partly responsible for the cellular senescence phenotypes in this undiagnosed disease.

overall_design: To get insight into the gene’s affection in CNS (central nerve system), we corrected one patient iPSC line, and generated the mutation corrected isogenic iPSC line and KO iPSC line by CRISPR/Cas9. These iPSCs lines were further differentiated to NPCs. We then performed gene expression profiling analysis using data obtained from RNA-seq of the isogenic cell lines (CON, MT and KO), at two tome points (iPSCs and NPCs)

first: Fang

last: Yuan

first: Haofei

last: Wang

first: Su-Chun

last: Zhang


title: Ageing promotes metastasis via activation of the integrated stress response (ATAC-Seq)

first: Volkan

last: Sayin

overall_design: To investigate epigenetic differences between Old and Young primary cultures from KP-Young and KP-Old mice.

first: Angana

middle: H

last: Patel

first: Clotilde

last: Wiel


title: LDHA induces β cell dedifferentiation in diabetes through metabolic epigenetic reprogramming

first: Xirui

last: Li

overall_design: ChIP-seq and RNA-seq were used to investigate the specific molecular mechanism underlying the effect of LDHA on the H3K9la enhancement and beta cell function under glucotoxic conditions.

first: Haoqiang

last: Gong

first: Can

last: Xiong

first: Xinyue

last: Huang

first: Mei

last: He

first: Liangjun

last: Sun

first: Wenyue

last: Yin

first: Suyun

last: Zou

first: Min

last: Sha

first: Wanhua

last: Guo

first: Tijun

last: Wu

first: Qingguo

first: Yaqin

last: Chen


title: Pde10a gates light responses in the SCN to regulate circadian photoentrainment

city: Bethesda

first: Samer

last: Hattar

address: 9000 Rockville Pike

department: National Institute of Mental Health

institute: National Institutes of Health

summary: Earth's rotation around its axis provides the principal cue for synchronizing the circadian clock with environmental light. A common feature of the clock is the lack of responsiveness to light during the daytime hours. To investigate the interaction between the circadian clock and light, we analyzed the transcriptomic profiles of the suprachiasmatic nucleus (SCN) in mice across different circadian times under constant darkness (DD) and in response to light exposure. We classified SCN neurons into 10 molecularly defined subtypes and described an elaborate transcriptional program both in DD and in response to light. Notably, we uncovered that the SCN exhibits significant transcriptomic responsiveness to light during daytime, the so-called behavioral “dead zone”. We further identified Pde10a, involved in cAMP signaling, as the first critical component for gating SCN responsiveness to light across the day and for maintaining robust daily oscillations under regular light-dark conditions.

overall_design: Single nucleus RNA-sequencing of the mouse anterior hypothalamus following light exposure at three key time points: Circadian Time 6 (CT6, mid-day), CT14 (early night), and CT22 (late night). At each time point, animals housed in constant darkness were either exposed to 15 minutes of bright white light (L) or kept in darkness (D), and hypothalamus tissue containing the SCN was collected 45 minutes after exposure.

first: Michael

middle: B

last: Thomsen

first: Ruchi

last: Komal

first: Hui

last: Wang

first: Haiqing

last: Zhao


title: RoCK and ROI: a single-cell RNA-sequencing method with enhanced transcriptome information via targeted enrichment of transcripts and preselected, region-specific sequencing IV

city: Zürich

first: Giulia

middle: Arianna

last: Moro

address: Winterthurerstrasse 190

department: DMLS

country: Switzerland

institute: University of Zurich

summary: Many scRNAseq-based methods suffer from a high number of non-detects and a bias towards the 3' or 5' end of transcripts. We developed a method termed RoCK and ROI to address these two biases. RoCK and ROI leads to the enrichment of the transcriptome profile of cells with information on transcripts of interest

overall_design:
RoCK and ROI is based on barcoded beads of the BD Rhapsody platform. For RoCKseq specific capture, TSO oligos on BD Rhapsody beads are modified with a/ multiple capture sequence(s) specific to transcripts of interest. ROIseq, on the other hand, is based on specific primers which are spiked in during library generation, directing reads to regions of interest (ROIs). For this set of experiments, RoCK and ROI was performed to enhance the detection of BCR::ABL1 fusion transcripts in a mix of patient-derived leukemic cell lines (K562, SUP-B15, Loucy) and a  B-cell precursor acute lymphoblastic leukemia (BCP-ALL) patient at first diagnosis.

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

last: Mallona

first: Malwine

last: Barz

first: Lorenz

last: Bastian

first: Claudia

middle: D

last: Baldus

first: Mark

last: Robinson

first: Erich

last: Brunner

first: Konrad

last: Basler


title: Ageing promotes metastasis via activation of the integrated stress response

first: Volkan

last: Sayin

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

overall_design: Refer to individual Series


overall_design: To investigate differences in transcriptomics between Old and Young primary cultures from KP-Young and KP-Old mice.

first: Angana

last: Patel

first: Clotilde

last: Wiel


title: Energy-sensing molecule RORγ regulates Cholesterol Metabolism and Immune Signaling in Diabetic Kidney Disease and Aging

status: Public on Jan 22 2026

city: Shenzhen

first: Shu

last: Yang

address: 1017 Dongmen North Road, Luohu District, Shenzhen

institute: shenzhen people's hospital

summary: Aging is a major risk factor for diabetic kidney disease (DKD), with both conditions exhibiting similar renal pathology. We identify the energy-sensing molecule Retinoic acid-related orphan receptor γ (RORγ) as significantly downregulated in diabetic and aged kidneys. Tubule-specific RORγ deficiency exacerbates kidney injury, whereas its overexpression protects. Mechanistically, RORγ stabilizes insulin-induced gene 1 (INSIG1) by upregulating the deubiquitinase YOD1 and enhancing AMPK activity via CAB39, which together promote INSIG1 phosphorylation and subsequent stabilization. Stabilized INSIG1 potently blocks the ER-to-Golgi transport and activation of SREBP2 (cholesterol synthesis) and STING (inflammatory signaling). In diabetes, RORγ itself is suppressed transcriptionally by CTCF and functionally by impaired AMPK/SIRT1 signaling, which hinders its activation. Importantly, administration of a RORγ agonist or RORγ-enriched exosomes effectively alleviates diabetic kidney injury. Thus, RORγ emerges as a key regulatory node that mitigates DKD and renal aging by co-regulating AMPK-mediated metabolic and STING-driven innate immune pathways through INSIG1 stabilization.

overall_design: We induced RORγ overexpression in human TECs and conducted RNA sequencing (RNA-seq) analysis.


title: Quantitative Analysis of sham and cerebral ischemia Transcriptomes in mouse hippocampus

city: Changsha

first: Wei

last: Jiang

state: Hunan

address: Lushan Road (S), Yuelu District,Changsha, Hunan Province

department: College of Biology

institute: Hunan University

summary: The goals of this study are to compare hippocampus transcriptome profiling (RNA-seq) after cerebral ischemia for 2 h in mouse stroke model

overall_design: Hippocampus mRNA profiles of 56-day old wild type mice for cerebral ischema of 2 h and sham operation.

first: Haijun

last: Tu


title: Gene expression induced by DREADD activation in cultured astrocytes

city: Sendai

first: Momono

last: Segawa

state: Miyagi

address: Katahira 2-1-1, Aoba-ku

department: Graduate School of Life Sciences

country: Japan

institute: Tohoku University

summary: Astrocytes are essential regulators of neuronal function and brain homeostasis. While chemogenetic strategies, such as DREADD (Designer Receptors Exclusively Activated by Designer Drugs), are frequently employed to specifically modulate astrocyte activity, the molecular mechanisms accompanying their activation remain incompletely understood. Here, we characterized the transcriptional responses of cultured cortical astrocytes to DREADD stimulation. These findings provide a molecular framework for interpreting astrocytic DREADD manipulations.

overall_design: RNA-seq profiling was performed on cultured cortical astrocytes expressing hM4Di, hM3Dq, or rM3Ds following DCZ stimulation for 90 min. For astrocytes expressing hM3Dq, an additional RNA-seq analysis was conducted three days after stimulation, following replacement with the ligand-free medium at 90min post-stimulation.

first: Hajime

last: Yanmamoto

first: Kentaro

last: Abe


title: Mithramycin Alters EWS::FLI1 DNA Binding and RNA Polymerase II Processivity to Inhibit Nascent Transcription [RNA-seq]

city: Ann Arbor

first: Patrick

last: Grohar

state: MI

address: 1600 Huron Pkwy

institute: University of Michigan Medical School

summary: Although many DNA binding natural products exert their effects through non-specific mechanisms, a therapeutic opportunity exists for a subset of these compounds that alter the expression or activity of specific driver oncogenes in specific cell contexts. In this study, we integrate CUT&Tag with Global Run-On Sequencing (CUT, Tag, and GRO) to show that the minor groove binding compound, mithramycin (MMA), inhibits the Ewing sarcoma oncogenic driver, the EWS::FLI1 transcription factor. MMA causes either an increase or decrease in EWS::FLI1 binding to chromatin at downstream target response elements to poison nascent transcription. The reversal of EWS::FLI1 activity is limited by non-specific effects of the drug on RNAPII processivity but can be optimized by continuous administration at low concentration to cause more precise reversal of the oncogenic transcriptome and striking Ewing sarcoma xenograft regressions. The activity in vivo is further improved with a less-toxic second-generation analog, AIT-102.

overall_design: Bulk RNAseq data of TC32 with or without knockdown of EWS::FLI1 achieved with a 30-hr incubation with siEF or non-specific siNEG

first: Rebecca

last: Kaufman


title: Rational design of immune gene therapy combinations via in vivo CRISPR activation screening of tumor microenvironment modulators

city: New Haven

first: Chuanpeng

last: Dong

state: CT

address: 850 West Campus Dr

department: Genetics

institute: Yale University School of Medicine

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Impaired removal of dying brain cells by microglia in GPR34 deficient mice

city: Cambridge

first: Joshua

last: Levin

state: MA

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

summary: GPR34, a G protein coupled receptor present selectively in microglia and other myeloid cells, is highly expressed in homeostatic microglia but is downregulated in disease associated microglia such as are found in Alzheimer’s disease brain. However, little is known about GPR34’s role in microglia function or brain development. Here, we studied Gpr34 knockout (KO) mice at postnatal 18-day (18 d) and 3 months (3 mo) age. In the brains of 18 d GPR34 KO mice, there were elevated numbers of neurons, oligodendrocytes and microglia, many of which were IHC-positive for cell death markers cleaved-caspase 3, phospho-RIP3, or annexin V. There was no increase in cell death markers or in steady state numbers of neurons, oligos and microglia at 3 months, indicating that GPR34-independent mechanisms are able to compensate during brain maturation. Based on RNA sequencing analysis and phagocytosis functional assays, as well as computational modeling, we provide evidence  that Gpr34 KO microglia have deficiencies in chemotaxis, but not phagocytic efficiency, which leads to a slower clearance of dead cells from the developing brain. Collectively, these results indicate that Gpr34 is required for microglia to clear dead or dying cells.

overall_design: GPR34 KO and WT mice were generated, and for each numerous brain regions were sequenced with RNA-seq. For more details see our publication.

first: Diana

last: Bohannon

first: Ana

last: Geller

first: Sean

middle: K

last: Simmons

first: John

last: Cintron

first: William

middle: E

last: Martenis

first: Katherine

last: Stalnacker

first: Autumn

last: Masse

first: Min Jee

last: Kwon

first: Yan-Ling

last: Zhang

middle: Z

first: Prabhat

last: Kunwar

first: Morgan

last: Sheng


title: GDF15 reprograms the microenvironment to drive the development of uveal melanoma liver metastases [bulk RNA-seq]

city: Tampa

first: Keiran

last: Smalley

state: FL

address: 12902 Magnolia Dr

institute: Moffitt Cancer Center

summary: Uveal melanoma (UM) results in fatal liver metastasis, yet little is known about the interactions between UM and host cells in the tumor microenvironment that promote this distinctive proclivity. We used single cell (sc)-RNA-Seq analysis of UM-hepatic stellate cell (HSC) co-cultures to demonstrate that HSCs enriched for UM cell states that expressed genes implicated in cell survival, metabolic reprogramming and angiogenesis. A lead candidate driver of HSC reprogramming was the TGF-b family member GDF15, which was associated with a metastatic UM phenotype. Silencing of BAP1 in UM cells led to increased GDF15 expression and accumulation of H3K27ac marks at the GDF15 promoter. Treatment of HSCs with GDF15 led to increased expression extracellular matrix proteins, inflammatory cytokines and angiogenic factors, including IL-8. Both exogenous GDF15, IL-8 and conditioned media from UM-HSC co-cultures increased endothelial cell network formation in vitro, an effect that was blocked by anti-GDF15 antibodies. In multiple models of metastatic UM, silencing of GDF15 inhibited the outgrowth of metastatic lesions, associated with reduced deposition of extracellular matrix and recruitment of endothelial cells. UM liver metastasis development is dependent upon GDF15-mediated remodeling of the liver microenvironment leading to an angiogenic response and matrix deposition that supports tumor growth.

overall_design: Conducted bulk RNA-seq analysis on normal hepatic stellate cells in presence or absence of GDF15 treatment. Performed differential gene expression to study the effect of GDF15 on hepatic stellate cells post 24hrs treatment

first: Sathya

middle: N

last: Sriramareddy

first: Navya

last: Siddarajappa

first: Jun Sung

last: Park

first: Thanh

last: Nguyen

first: Jeffim

last: Kuznetsoff

first: Stefan

last: Kurtenbach

first: James

last: Dollar

first: David

last: Adams

first: Jonathan

last: Licht

first: Zelia

last: Correa

first: Ann

middle: Y

last: Chen

last: Harbour

middle: S


title: E4BP4 Safeguards Brown Fat Mitochondria from Obesity-Induced Fragmentation via Ceramide Repression

city: Ribeirão Preto

first: Carlos

last: Sponton

state: São Paulo

address: Av. Bandeirantes, 3900

department: Department of Physiology, Ribeirão Preto Medical School, Universidade de São Paulo (FMRP-USP)

country: Brazil

institute: USP

summary: Brown adipose tissue (BAT) counteracts obesity-related metabolic dysfunction through both thermogenic and non-thermogenic means. However, substantial evidence indicates that obesity negatively affects BAT mitochondrial morphology and oxidative capacity, impairing systemic energy homeostasis. Motivated by this apparent contradiction, we investigated the relationship between obesity and mitochondrial dynamics, as the underlying mechanisms remain incompletely understood. Here, we identified E4BP4 as a transcriptional repressor that prevents obesity-induced mitochondrial fragmentation and oxidative dysfunction by inhibiting ceramide synthesis in brown fat. Specifically, E4BP4 interacts with PRDM16 to repress Cers6 mRNA expression and consequently reduces C16:0 ceramide levels by binding to a 65 kb upstream enhancer region of the Cers6 gene. Notably, the preservation of mitochondrial integrity in BAT by E4BP4 gain-of-function improves systemic glucose homeostasis, independent of weight loss. Collectively, our findings establish E4BP4 as a molecular safeguard against obesity-induced mitochondrial fragmentation and oxidative dysfunction, primarily by suppressing ceramide synthesis in brown fat.

overall_design: RNA-seq profilling of brown adipose tissue of E4BP4-OE and Control after 10 weeks of HFD

first: Fernando

last: Valdivieso-Rivera

first: Vanessa

last: O. Furino

last: E. Leher

first: Ariane

last: M. Zanesco

first: Monara

last: Kaélle Cruz

first: Flavia

last: C. Gan

first: Adriana

last: Leandra Santoro

first: Lara

last: Regina-Ferreira

first: Giovanna

last: Leite Santos

first: Tiago

last: Gonçalves

first: Luiz

last: Osório Leiria

first: Pedro

last: M. Moraes-Vieira

first: Roger

last: Frigério Castilho

first: Shingo

last: Kajimura

first: Marcelo

last: A. Mori

first: Licio

last: A. Velloso

last: H. Sponton


title: GDF15 reprograms the microenvironment to drive the development of uveal melanoma liver metastases [scRNA-seq]

first: Keiran

last: Smalley

overall_design: Conducted a comparative scRNA-seq analysis of normal hepatic stellate cells and uveal melanoma cell line. Performed cell-cell communication analysis to infer the signaling pathways between hepatic stellate cells and tumor cells. By utilizing an unbiased transcriptomic approach, we aimed to identify specific intercellular crosstalk that promotes tumor survival.

first: Sathya

last: Sriramareddy

first: Navya

last: Siddarajappa

first: Jun Sung

last: Park

first: Thanh

last: Nguyen

first: Jeffim

last: Kuznetsoff

first: Stefan

last: Kurtenbach

first: James

last: Dollar

first: David

last: Adams

first: Jonathan

last: Licht

first: Zelia

last: Correa

first: Ann

last: Chen

first: William

last: Harbour


title: Mithramycin Alters EWS::FLI1 DNA Binding and RNA Polymerase II Processivity to Inhibit Nascent Transcription [CUT&Tag]

first: Patrick

last: Grohar

overall_design: CUT&Tag data using FLI1 antibody, H3K27ac antibody or IgG control following incubation with PBS solvent control or mithramycin at either 20 nmol/L for 72 hours or 100 nmol/L for 18 hours.

first: Rebecca

last: Kaufman


title: Gene expression analysis of TGFβ1-stimulated fibroblasts to assess anti-fibrotic effects of the bisubstrate-like NNMT inhibitor II559

first: Bioinformatics

last: Core

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: Fibroblast activation drives tissue fibrosis and is often mediated by TGFβ1 signaling. Human fibroblasts were pre-treated with the NNMT inhibitor II559 for 12 hours, followed by TGFβ1 stimulation for 72 hours. Transcriptomic profiling revealed that II559 prevented pro-fibrotic gene expression, providing a resource for understanding how NNMT inhibition modulates fibroblast activation and fibrotic remodeling.

overall_design: Human dermal fibroblasts(n=3) were treated with TGF-ß1 (10 ng/mL) in the presence or absence of II559 (30 µM). Following 72 h incubation, RNA was harvested and subjected to RNA-seq.

first: Kamal

last: Saba

first: Priyanka

last: Verma

first: M. Asif

last: Amin

first: John

last: Varga


title: Multi-omics profiling reveals microenvironmental remodeling as a key driver of house dust mite-induced lung cancer progression

first: Shams

last: Al-Azzam

state: CA

address: 9500 Gilman Dr

institute: University of California San Diego

type: Methylation profiling by genome tiling array

summary: Chronic exposure to the common aeroallergen house dust mite (HDM) induces lung inflammation and DNA damage, but its impact on lung cancer development remains largely unexplored. Using whole-genome sequencing, RNA-seq, and DNA methylation profiling, we assessed HDM effects in lung epithelial cell lines and a mouse orthotopic lung cancer model. HDM accelerated tumor growth without altering mutational burden. Transcriptomic and epigenetic analyses revealed tissue-specific effects: in normal lung, HDM enhanced pro-inflammatory and immune activation programs, whereas in tumors it suppressed T cell responses, antigen presentation, and chemokine signaling. Immune deconvolution showed a shift toward myeloid enrichment and lymphoid suppression, with reduced cytotoxic T and NK signatures. Notably, HDM-driven tumor promotion was abolished in Il17a−/− but not Il1b−/− mice, identifying IL-17A as a critical mediator. These findings demonstrate that chronic aeroallergen exposure reshapes the lung microenvironment to promote immune suppression and accelerate lung cancer progression.

overall_design: Methylation  profiling of mouse lung tumors and matched adjacent normal tissues following chronic HDM exposure

first: Al-Azzam

last: Shams

first: Bertin

last: Samuel


title: Gene expression changes in right atrial tissue were identified through RNA-seq analysis using a monocrotaline (MCT)-induced pulmonary hypertension (PH) rat model

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary: Manganese(III) tetrakis(4-benzoic acid) porphyrin chloride (MnTBAP) exhibits well-documented anti-inflammatory, antioxidant, and anticancer properties. While its therapeutic potential in ameliorating pulmonary hypertension (PH) has been well established, its role in PH-induced atrial fibrillation (AF) remains poorly understood.

overall_design: Rats were randomly assigned to four experimental groups: Saline + Vehicle, Monocrotaline (MCT) + Vehicle, and MCT + MnTBAP. The pulmonary arterial hypertension (PAH) model was established on day 0 via intraperitoneal injection of MCT at a dose of 60 mg/kg. Starting two days prior to MCT administration and continuing until day 28 post-injection, MnTBAP (10 mg/kg) was administered intraperitoneally every other day.Total RNA was isolated with TRIzol (Invitrogen) from heart organs (n=4 per group) at each time point according to manufacturer’s instructions.

first: Zhang

last: Yun-Long

first: He

last: Jia-Kang

first: Han

last: Xiao


title: Seq-Scope-eXpanded (Seq-Scope-X): Spatial Omics Beyond Optical Resolution

first: Jun Hee

last: Lee

address: 109 Zina Pitcher Pl

summary: Sequencing-based spatial transcriptomics (sST) enables transcriptome-wide gene expression mapping but falls short of reaching the optical resolution (200–300 nm) of imaging-based methods. Here, we present Seq-Scope-X (Seq-Scope-eXpanded), which empowers submicrometer-resolution Seq-Scope with tissue expansion to surpass this limitation. By physically enlarging tissues, Seq-Scope-X minimizes transcript diffusion effects and increases spatial feature density by an additional order of magnitude. In liver tissue, this approach resolves nuclear and cytoplasmic compartments in nearly every single cell, uncovering widespread differences between nuclear and cytoplasmic transcriptome patterns. Independently confirmed by imaging-based methods, these results suggest that individual hepatocytes can dynamically switch their metabolic roles. Seq-Scope-X also works in brain and colon, and can be adapted for spatial proteomics, profiling hundreds of barcode-tagged antibody stains at microscopic resolutions in mouse spleens and human tonsils. Together, these findings establish Seq-Scope-X as a transformative platform for ultra-high-resolution whole-transcriptome and proteome profiling, providing unparalleled precision and biological insights.

overall_design:
Tissue Samples
Mouse liver, colon, and spleen tissues were collected from 8-week-old male C57BL/6 wild-type mice, and brain tissue was obtained from a 6-month-old male mouse. All animal procedures were approved by the Institutional Animal Care and Use Committee at the University of Michigan (protocol PRO00011369).
Human tonsil tissue was obtained from the UCLA Pathology Biobank as a discarded surgical specimen from an adult patient with chronic tonsillitis. The sample was fully de-identified prior to acquisition and classified as IRB-exempt under institutional and federal guidelines, with no access to identifiable patient information.
Seq-Scope-X Transcriptome Workflow
Fresh frozen tissues were cryosectioned, mounted on charged slides, fixed with formaldehyde, and permeabilized with methanol. Anchor probes were hybridized in a formamide-containing buffer under humidified conditions. Tissues were then embedded in a polyacrylate-based monomer solution, polymerized, and cleared using digestion buffer with Proteinase K.
Tissue expansion was performed by incubation in diluted SSC, and DAPI staining was used to assess tissue integrity. Expanded gels were trimmed for imaging and alignment, then placed onto Seq-Scope Chips. Probe release and transcript transfer were achieved by heat incubation, followed by standard Seq-Scope library preparation, omitting tissue digestion as tissues were not directly attached to the chip.
Seq-Scope-X Proteome Workflow
For spatial proteomic analysis, tissues were permeabilized with methanol, blocked with a BSA-containing solution, and incubated overnight with TotalSeq™-A oligonucleotide-tagged antibody cocktails. After washing and post-fixation, tissues were processed using the same embedding, clearing, and expansion steps as in the transcriptome workflow.
Library preparation was modified to capture antibody-bound DNA oligonucleotides. Following reverse transcription, antibody tag libraries were eluted, purified, amplified by AT-PCR and indexing PCR, size-selected to isolate ~250 bp fragments, and sequenced on an Illumina NovaSeq-X platform.
Data Processing and Analysis
Seq-Scope-X transcriptome data were processed using the Seq-Scope pipeline with adjustments for experimentally determined expansion factors, following the NovaScope and NEDA workflows. Processing included generation of spatial barcode maps, alignment to reference genomes, construction of spatial gene expression matrices, and clustering using Seurat v5.
Spatial factor discovery was performed using Latent Dirichlet Allocation, and FICTURE was used to project cell-type factors into raw pixel space. Microscopy images, which lacked fiducial markers, were aligned to transcriptomic data using QGIS and further processed with CellProfiler and Photoshop. Differential expression, clustering, and integration analyses were conducted on hexagonally binned data to enable spatial and functional interpretation.

first: Angelo

last: Anacleto

first: Weiqiu

last: Cheng

first: Hee Sun

last: Han

first: Hyun Min

last: Kang


title: Genetic Recording of Pancreatic Beta Cell Proliferation

city: Shanghai

first: Zhixin

address: 320 Yue Yang Road, Shanghai

institute: Shanghai Institute of Biochemistry and Cell Biology

summary: Pancreatic beta cell generation and proliferation primarily rely on self-renewal of pre-existing beta cells, making precise quantification of beta cell proliferation essential for understanding pancreatic homeostasis and pathogenesis. However, technical limitations have previously restricted the ability to trace beta cell proliferation in vivo over extended periods. Here, we developed beta cell-ProTracer, a genetic system utilizes dual recombinase technology to enable continuous and cell type-specific recording of beta cell proliferation in mice. The beta cell-ProTracer system allows for the quantification of the proliferation rate of adult pancreatic beta cells during homeostasis and in response to injury or drug treatment. Clonal analysis of the proliferated beta cell population reveals a uniform proliferative capacity among these cells. Our findings enhance the understanding of beta cell proliferation dynamics in pancreatic homeostasis, repair, and regeneration.

overall_design: Pancreatic live cell of beta cell-ProTracer system were isolated and performed scRNA-seq.

first: Huan

last: Zhao

first: Hui

last: Chen


title: Canonical BAF complex orchestrates mesenchymal stem cell niche composition and fate via cofactor-guided chromatin remodeling

city: Los Angeles

first: Mingyi

last: Zhang

address: 2250 Alcazar Street, CSA103, HSC

department: Center for Craniofacial Molecular Biology

institute: University of Southern California


title: Spatial transcriptomic profiling of bronchioles using GeoMx DSP

city: Houston

first: Akira

last: Yamamoto

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Bronchiolitis obliterans (BO) is a severe, fibrotic manifestation of chronic graft-versus-host disease (GVHD) after hematopoietic stem cell transplantation (HSCT). Macrophage-derived TGF-β is linked to GVHD-related fibrosis; however, its role in BO remains unclear. Given emerging evidence of macrophage-to-myofibroblast transition (MMT) in fibrosis, this study aimed to investigate whether MMT contributes to BO development. We analyzed lung samples from three HSCT recipients with BO who underwent lung transplantation, with tissues from two patients with lung cancer as controls. Spatial transcriptomics was performed to profile gene expression in foamy macrophages across anatomical regions and histological stages, compared to control peribronchiolar regions.

first: Nobuharu

last: Fujii


title: Lymphotoxin Beta Receptor Activity in Fibroblasts Regulates Collagen Synthesis and is Crucial for Lung Fibrosis

first: Michael

last: Croft

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

summary: Fibroblast-specific deletion of LTβR in mice exposed to allergen significantly reduces lung collagen deposition and inflammation, despite unchanged fibroblast numbers. LIGHT-LTβR signaling in human pulmonary fibroblasts increases the expression of multiple collagen isoforms, molecules involved in structural rigidity, and molecules controlling cell migration and adhesion, explaining the importance of LTβR in promoting lung fibrosis.

overall_design: Bulk RNA seq. analysis from human pulmonary fibroblasts stimulated with 50 ng/ml LIGHT, 5 ng/ml TGFβ, 25 ng/ml IL-13, and 100 ng/ml IL-17A and in combination of IL13 or IL17A with LIGHT

first: Nandita

last: Ghosh

first: Rinkesh

last: Gupta

first: Gurupreet

last: Sethi

first: Kai

last: Fung

first: Jeamin

last: Jung

first: Ann

last: Balancio


title: Analysis of LARP6 impact on RNA localisation to cell protrusions of Glioblastoma cells

city: Oxford

first: Faraz

middle: K.

last: Mardakheh

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

summary: LARP6 is a conserved RNA-binding domain that regulates the localisation of Ribosomal Protein mRNAs to the protrusions of mesenchymal-like cells. Our results had revealed that in addition to its folded La-module RNA binding domain, LARP6 makes direct contacts with its RNA targets via its disordered N-terminal region, which precedes the La-module. To assess the contribution of this region to the regulation of RNA localisation by LARP6, we carried out a spatial transcriptomics analysis of U-87 MG Glioblastoma cells, treated with scrambled control vs LARP6 3'UTR targeting siRNAs, with or without rescuing the LARP6 expression using a doxycycline-inducible full-legth or delta N-terminal mutant of LARP6. The cells were subjected to siRNA knockdown for 72hrs, before being seeded on 3um transwell filters and allowed to protrude through the pores for 90 mins. The protrusions and cell-bodies on opposite sides of the filter were isolateed, with total RNA extracted and subjected to RNA-sequencing using Lexogen QUANTSEQ 3' mRNA sequencing library preparation. Three independent biological replicates of each experiment were performed.

overall_design: A total of three independent experiments were performed, each with the following conditions: 1- U87-MG control cells + scrambled (scr) siRNA; 2- U87-MG control cells + LARP6 3'UTR targeting (si3UTR) siRNA; 3- U87-MG cells + Full-length (FL) myc-LARP6 + scr siRNA; 4- U87-MG cells + FL myc-LARP6 + si3UTR; 5- U87-MG cells + delta-NTR myc-LARP6 + scr siRNA; 6- U87-MG cells + delata-NTR myc-LARP6 + si3UTR;  Each sample was then fractionated into protrusion and cell-body fractions using transwell filters, before RNA extraction and sequencing using Lexogen's Quantseq 3' mRNA sequencing. For more details, please see the associated preprint: https://doi.org/10.1101/2024.09.20.614075.

first: Federica

last: Capraro

first: Maria

middle: R

last: Conte


title: Cytoplasmic mRNA decay by the anti-viral nuclease RNase L promotes transcriptional repression [S2P Pol II CUT&RUN]

city: Berkeley

first: Britt

middle: Aspen

last: Glaunsinger

address: 565 Li Ka Shing Center

department: Department of Plant and Microbial Biology

institute: University of California, Berkeley

summary: Ribonuclease (RNase) L is an antiviral factor that promiscuously degrades viral and cellular RNA in the cytoplasm. This results in extensive translational reprogramming, altering mRNA processing and export. Here, we reveal that another major consequence of cytoplasmic RNase L activity is the repression of nascent RNA synthesis in the nucleus. This is not associated with altered nuclear RNA stability but instead results from transcriptional repression. For RNA polymerase II, repression is primarily associated with reduced occupancy of serine 2-phosphorylated polymerase in gene bodies, indicating an elongation defect. Prominent among the transcriptionally downregulated loci are immune-related genes, supporting a role for RNase L in tempering innate immune and inflammatory responses. RNase L activation also caused disruption of nucleoli and reduced RNA polymerase I and III transcription. Crosstalk between RNA decay and transcription thereby contributes to the large-scale modulation of gene expression in RNase L-activated cells.

overall_design: Pol II occupancy measurement by CUT&RUN of A549 WT or RNase L-KO cells either transfected with Lipofactamine RNAiMAX alone or with poly(I:C) for 4 hours (3 biological replicates per condition). For each replicate, an additional RNAiMAX-transfected WT sample was included for IgG control.

first: Xiaowen

last: Mao

first: Sherzod

last: Tokamov

first: Felix

last: Pahmeier

first: Azra

last: Lari

first: Jinyi

last: Xu

first: Eva

last: Harris


title: A Nanopore-Based HIV-1 Reference Epitranscriptome

city: Winston-Salem

first: Keith

last: Gagnon

state: NC

address: 575 Patterson Ave

department: Biochemistry

institute: Wake Forest Baptist Medical Center

summary: Post-transcriptional modifications to RNA, which comprise the epitranscriptome, play important roles in RNA metabolism, gene regulation, and disease pathogenesis. However, mapping modifications and characterizing their function is often challenged by a lack of consensus on their presence and significance. The availability of reference epitranscriptomes to benchmark data would significantly advance epitranscriptomic studies. Toward this goal, we established a reference epitranscriptome for human immunodeficiency virus 1 (HIV-1), an important human pathogen. We sequenced a model HIV-1 genome from infected T cells using the latest nanopore technology. A sense and novel preliminary antisense HIV-1 epitranscriptome were generated where N6-methyladenosine, 5-methylcytosine, pseudouridine, inosine, and 2'-O-methyl modifications were mapped by multiplexed base calling at nucleotide resolution. Modification miscalling due to sequence and modification context was corrected with synthetic RNA fragments and m6A was validated with an inhibitor. Modifications were stable under combination antiretroviral therapy (cART) treatment, in primary CD4+ T cells, and in HIV-1 virions. In contrast, spliced transcript-dependent modification levels were observed. Sequencing samples from people living with HIV (PLWH) revealed substantial conservation of m6A in circulating strains. Our approach offers a benchmark reference to advance HIV-1 epitranscriptomics and provides a roadmap for the creation of reference epitranscriptomes for other viruses or pathogens.

overall_design:
Nanopore direct RNA-seq of Jurkat and CD4+ T cells, infected with HIV-1 and treated with or without cART, in order to detect changes in HIV-1 RNA modification patterns. Synthesized fragments with known RNA modifications were used as modification-calling controls.
POD5 files for these samples are available at https://zenodo.org/records/18223642 .

first: Michael

last: Bosmeny

first: Adrian

middle: A

last: Pater

first: Li

last: Zhang

first: Lydia

middle: L

last: Larkai

first: Beverly

last: Sha

first: Zidi

last: Lyu

first: Masad

last: Damha

first: João

last: Mamede

middle: T


title: Polycyclic-fused cytochalasins with anti-liver fibrosis activity from the endophytic fungus Trichoderma harzianum [TGF-β1+ DMSO or TGF-β1 + 20 μM 8]

city: Guangzhou

first: 雷名

last: 吴

address: sun-yat san university

institute: 中山大学药学院

summary: A molecular networking-guided investigation of the endophytic fungus Trichoderma harzianum MLJ-4 resulted in the isolation of eight new polycyclic-fused cytochalasins, triharziachalasins A–H (1–8), along with six known analogues (9–14). Their structures including absolute configurations, were elucidated by comprehensive spectroscopic analysis, NMR calculations with DP4+ analysis, and theoretical ECD simulations. Compounds 1–3 feature a rare 5/6/5/8-fused tetracyclic system, while 4–8 possess a novel 5/6/6/7/5-fused pentacyclic scaffold. Notably, compound 1 is the first cytochalasin analogue containing a cis-fused 5/8 ring within the 5/6/5/8 framework. All CYTs were evaluated for anti-liver fibrosis activity in TGF-β1-stimulated LX-2 cells using high content screening assays. The most promising compound, triharziachalasin H (8), dose-dependently suppressed the expression of key fivrotic markers, including fibronectin (FN), collagen I, and α-smooth muscle actin (α-SMA). Mechanism studies revealed that its anti-liver fibrosis effectis mediated via inhibition of the NF-κB signaling pathway. This work expands the structural diversity of bioactive cytochalasins and reveals the anti-liver fibrosis activity of this novel polycyclic-fused architecture, highlighting its potential as a lead compound for anti-liver fibrosis drug development.

overall_design: LX-2 cells mRNA profiles of treatment with TGF-β1+ DMSO or TGF-β1 + 20 μM 8 for 48 h.

first: Guihua

last: Tang

first: Yanjiang

first: Yiling

last: liao

first: Lu

last: Gan


title: Canonical BAF complex orchestrates mesenchymal stem cell niche composition and fate via cofactor-guided chromatin remodeling [CUT&Run DKO]

first: Mingyi

summary: The canonical BAF (BRG1/BRM-associated factor) chromatin remodeling complex plays a pivotal role in governing stem cell behavior, yet how it regulates adult stem cell niche remains unclear. Here, we show that ARID1-containing cBAF complex orchestrates the spatial organization of the mesenchymal stem cell niche and fate in the adult mouse incisor. Dual loss of ARID1A and ARID1B in Gli1+ mesenchymal stem cells using conditional knockout mouse models disturbs chromatin accessibility in a cell-type-specific manner and alters cofactor recruitment, leading to niche cell disorganization, disrupting progenitor cells (transit-amplifying cells, TACs) fate commitment during tissue homeostasis. Single-cell multi-omics profiling and in vivo functional validations reveal that the cBAF complex partners with DLX2 to coordinate niche cell composition and recruits FOXO1 and DLX2 to balance TAC proliferation and differentiation. Our findings establish cBAF as a master regulator of chromatin state and microenvironment architecture, essential for maintaining adult mesenchymal stem cell function and tissue homeostasis.

overall_design: DKO mouse incisor proximal end tissue were collected and digested into cells, then underwent the process following the CUT&RUN protocol.


title: Step-wise signal integration governs adaptive programming of lymphocytes

city: New York

first: Hyunu

last: Kim

state: NY

address: 417 E 68th St

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

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

overall_design: Refer to individual Series


title: Step-wise epigenetic signal integration governs adaptive programming of cytotoxic lymphocytes [ATAC-seq AP1inhibitor]

summary: Lymphocyte differentiation depends on activation via antigen and cytokines during the immune response to infection. How the timing and integration of these signals program the epigenetic and functional fate of these cells is not completely understood. In this study, we find that inflammatory cytokine signals received by innate and adaptive lymphocytes have a context-dependent role for immune memory formation. Without preceding and sufficient antigen receptor signaling, inflammatory cytokines drive terminal differentiation into short-lived effector cells. In contrast, sufficient antigen-receptor signaling redirects inflammatory cytokine signals to promote memory differentiation via cooperation of STAT and AP-1 transcription factors. By this crucial epigenetic mechanism, optimally equipped lymphocytes are selected for memory formation rather than a terminal effector cell fate. Whereas T cells are hardwired to be shielded from premature inflammatory signals, NK cells rely on coincidental early antigen receptor signaling for adaptive responses. Together, step-wise integration of antigen and cytokine signaling optimizes both effector and memory differentiation, allowing for promiscuous recruitment into the acute immune response while promoting avidity maturation in memory populations of both innate and adaptive lymphocytes.

overall_design: ATAC-seq of stimulated NK cells

first: Simon

last: Grassmann

first: Joseph

last: Sun


title: RORγ drives non-small cell lung cancer progression by upregulating the NGF signalling

first: Guodi

last: Cai

state: Guangdong Province

address: 132, Waihuandonglu, Daxue Cheng

department: School Of Pharmaceutical Sciences

institute: Sun Yat-Sen university

summary: Lung cancer remains one of the most prevalent and lethal malignancies worldwide, with non-small cell lung cancer (NSCLC) representing the most common subtype—highlighting the critical need for novel therapeutic approaches. Here, we identify the retinoic acid receptor-related orphan receptor gamma (RORγ) as a key driver of NSCLC progression. Integrative bioinformatics and immunohistochemical analysis revealed that RORγ is highly expressed in NSCLC tissues and that its expression correlates with poor patient prognosis. Functionally, elevated RORγ significantly enhanced the proliferation, migration, and invasion capabilities of NSCLC cells. Conversely, treatment with the RORγ antagonist or genetic silencing of RORγ potently suppressed these malignant phenotypes both in vitro and in vivo. Mechanistically, RORγ directly binds to the promoter region of NGF, stimulates NGF gene transcription, and thereby promotes NSCLC progression. RORγ antagonists suppress NGF expression and inhibit its downstream signalling pathways, whereas exogenous NGF supplementation or overexpression of NGF notably reverses the inhibitory effects of RORγ antagonists on NSCLC cells. Taken together, these results establish RORγ as a critical regulator of NSCLC and a promising therapeutic target for NSCLC treatment.

overall_design: H157 cells were treated with vehicle (DMSO) or W6134 (2.5 μM) for 48 hours before total RNA extraction. The extraction steps of total RNA were according to the manufacturer's protocol of the Vazyme Super FastPure Cell RNA Isolation Kit (Vazyme Biotech, Nanjing, China). Transcriptomic sequencing of RNA-seq libraries were validated through MGISEQ2000 machine (BGI Tech, China). Enrichment analysis of co-downregulated genes (expression changes of ≥ 1.5-fold) in both cell lines following W6134 treatment was performed using R (v4.2.1), with the most significantly enriched pathways visualized via volcano plots (considering p adjust (FDR) < 0.05 as statistically significant).

first: Yechun

last: Zeng

first: Junjian

last: Wang


title: SGLT2 inhibition decreases complement C1q, maintaining renal antibacterial response

city: Bonn

first: Georg

last: Sendtner

address: Venusberg Campus 1a

department: Medical Clinic 1, Nephrology Section

country: Germany

institute: University Hospital Bonn

summary: SGLT2 inhibitors, which inhibit glucose reabsorption in the proximal tubule, are well established in the treatment of diabetes mellitus, chronic kidney disease, and heart failure. Although these agents induce glucosuria, clinical trials have consistently shown no increase in renal bacterial infection rates. To investigate the mechanisms that compensate for the increased risk of bacterial growth associated with glucosuria, we employed a pyelonephritis mouse model. In this model, approximately 40-day-old C57BL/6J mice were treated with or without empagliflozin and subsequently infected with the uropathogenic Escherichia coli strain 536. RNA-seq data were obtained from kidneys 16 hours post-infection.

overall_design: Female C57BL/6J mice were treated with 20 mg/L empagliflozin or control for three days prior to urethral infection with uropathogenic E. coli strain 536, which was instilled into the bladder twice at a 3-hour interval. Kidneys were harvested 16 hours after the second infection.

first: Sibylle

last: von Vietinghoff

middle: W

first: Julia

last: Miranda

first: Pia

last: Neumann

first: Maximilian

last: Weiss

first: Pelin

last: Güls

first: Ernst

last: Molitor

first: Uta

last: Scheidt

first: Axel

last: Schmidt

first: Kerstin U

last: Ludwig

first: Annika

last: Hilger

first: Ulrich

last: Dobrindt

first: Christian

last: Kurts

first: Florian

last: Wagenlehner

first: Olga

last: Shevshuk

first: Thomas

last: Mayrhofer


title: Step-wise epigenetic signal integration governs adaptive programming of cytotoxic lymphocytes [CUT&RUN STAT1 STAT5 cJun]

first: Hyunu

last: Kim

overall_design: CUT&RUN of stimulated NK and CD8+ T cells

first: Simon

last: Grassmann

first: Joseph

last: Sun


title: Recombinant Spider Silk Membranes Promote Human Renal Epithelial Differentiation and Function

city: Stuttgart

last: Büttner

address: Auerbachstraße 112

institute: Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology

summary: Porous membranes are frequently used as supports of cell monolayers in functional studies of epithelial and endothelial barriers. However, conventional polymer-based membranes such as those made of polycarbonate do not mimic the structural and biochemical properties of native basement membranes, which may limit cellular differentiation and function. Here, we use a nanofibrillar membrane made of recombinant spider silk functionalized with the integrin-binding RGD motif of fibronectin and coated with human kidney-specific laminin-521 (LN/FN-silk) as a novel substrate for renal epithelial monolayer cultures. Cellular morphology, mRNA expression, barrier properties and transporter activity were assessed using scanning and transmission electron microscopy, RNA-sequencing, lucifer yellow permeability assays, immunofluorescence staining and fluorescent probe transport assays. Immortalized renal proximal tubular epithelial cell (RPTEC/TERT1) monolayers cultured on LN/FN-silk membranes and in co-culture with human fibroblasts (fHDF/TERT166) exhibited cuboidal morphology, reduced cell death and maintained barrier integrity with tight junction expression compared to conventional polymer-based transwell membranes. In contrast to the LN/FN-silk membranes, the polycarbonate membranes released the endocrine disrupting toxicant bisphenol A, triggering estrogen-mediated signalling. Furthermore, cells on LN/FN-silk membranes showed enhanced directional anion and cation transport, compared to cells cultured on conventional membranes. In summary, the results indicate that LN/FN-silk membranes improve differentiation and functional maintenance of renal epithelial cell cultures, thereby allowing preservation of renal epithelial transport functions.

overall_design: RNA-Seq of RPTEC/TERT1 monocultures on LN/FN-silk (SR), RPTEC/TERT1 / fHDF/TERT166  co-cultures on LN/FN-silk (SRF), RPTEC/TERT1 monocultures on LN/PC (PR), RPTEC/TERT1 / fHDF/TERT166 co-cultures on LN/PC (PRF) and fHDF/TERT166 monocultures (F).

first: Alina

last: Meyer

first: Lea-Maria

last: Mayer

first: Linnea

last: Gustafsson

first: Jens

last: Eriksson

first: Kathrin

last: Klein

first: Son

last: Vo

first: Volker

middle: M

last: Lauschke

first: Mikael

last: Sellin

first: My

last: Hedhammar

first: Per

last: Artursson


title: The deacetylase Sir2 is the primary sensor driving transcriptional changes in response to low NAD+ in the yeast Kluyveromyces lactis

city: Buffalo

first: Charikleia

last: Karageorgiou

address: 109 Cooke Hall, Mary Talbert Way

department: Department of Biological Sciences

institute: University at Buffalo

summary: The coenzyme NAD+ (nicotinamide adenine dinucleotide) is a critical electron carrier in central metabolism and is required for cellular health. It is proposed that cells sense intracellular NAD+ levels using sirtuin deacetylases, which require NAD+ for their enzymatic activity.  We tested this hypothesis by examining how intracellular NAD+ levels affect expression of Sir2-repressed genes in the yeast Kluyveromyces lactis. Because K. lactis cannot synthesize NAD+, we could create a gradient of intracellular NAD+ levels by growing cells in varying concentrations of the precursor nicotinic acid. We found that as NAD+ levels decreased, acetylation of histones at target promoters increased, as did expression of these genes. RNA-Seq analysis revealed that genes induced in low nicotinic acid include some that would restore NAD+ levels, such as the high-affinity nicotinic acid transporter TNA1, and some that would enable long term survival, such as genes promoting sporulation. Most genes induced in low nicotinic acid (100 of 114 or 88%) were also induced in the absence of Sir2. Moreover, in sir2Δ cells, few transcriptional changes occurred in response to low nicotinic acid. Thus, Sir2 is the primary sensor responsible for the transcriptional response to low NAD+ in K. lactis. In addition, the degree of induction varied across NAD+ levels, suggesting that Sir2 behaves as a rheostat, tuning gene expression to NAD+ availability.

overall_design: Kluyveromyces lactis wild-type (WT; CBS2359) and sir2Δ strains were grown in yeast nitrogen base supplemented with nicotinic acid (NA) at four concentrations, 15 to 400 μg/L, to create a gradient of intracellular NAD⁺. Cultures were harvested at mid-log phase (OD₆₀₀ ≈ 1.0). For each strain × condition combination, two independent biological replicates were collected (17 total RNA-seq libraries).

first: Mahasweta

last: Acharjee

first: Kristen

last: Humphrey

first: Vincent

last: Lactaoen

first: Omer

last: Gokcumen

first: Laura

last: Rusche


title: Diploid Hepatocytes Resist Acetaminophen-Induced Liver Injury Through Suppressed JNK Signaling

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: Background & Aims: The liver contains both diploid and polyploid hepatocytes, but their functional differences remain poorly understood. Emerging evidence suggests that each ploidy state contributes to regeneration in an injury-specific manner. We hypothesized that diploid hepatocytes promote healing after acetaminophen (APAP)-induced liver injury. Approach & Results: To study ploidy populations in vivo, we utilized mice with a lifelong liver-specific knockout of E2f7/E2f8 (LKO), which are enriched in diploid hepatocytes (>70%) but otherwise normal. Control and LKO mice were treated with APAP (300 or 600 mg/kg), and injury was assessed over 0-96 hours. Although both groups sustained injury, LKO mice showed improved survival, lower serum liver enzyme levels, and reduced necrosis and DNA fragmentation, indicating resistance to APAP-induced injury. To determine if resistance was due to E2f7/E2f8 loss or increased diploidy, we deleted E2f7/E2f8 in adult hepatocytes (HKO), a model that does not alter ploidy. Injury was similar between controls and HKO, ruling out gene deletion as the protective factor. Transcriptomic and protein analyses revealed minimal baseline differences; however, following APAP treatment, LKO livers exhibited reduced JNK activation and less mitochondrial injury. Finally, APAP-treated wild-type hepatocytes exhibited a shift toward lower ploidy, supporting the idea that diploid cells are more resistant to injury. Conclusions: Diploid hepatocytes resist APAP-induced liver injury through reduced JNK activation and mitochondrial damage. These findings highlight hepatocyte ploidy as a key determinant of injury response and suggest a protective role for diploid hepatocytes in promoting liver resilience and regeneration.

overall_design: Wild-type (WT) and Alb-Cre–driven liver-specific E2f7/E2f8 knockout mice (LKO; indicated as “KO” in the sample list) were used. Hepatocyte-specific knockouts (HKO; indicated as “CRE” in the sample list) were generated by intravenous injection of AAV8-TBG-Cre viral particles into 2-month-old floxed mice; control mice (indicated as “NULL” in the sample list) received AAV8-TBG-Null. Male, 2.5-month old mice were fasted overnight (~16 hours) and administered 300 mg/kg acetaminophen (APAP) via intraperitoneal injection. Livers were harvested at 0, 12, 24, 48, 72, and 96 hours post-injection and snap-frozen. Total RNA was extracted from frozen liver tissue using TRIzol reagent. For baseline (0 hour) samples, RNA was isolated from individual mice (n = 4 per genotype). For time points from 12 to 96 hours, RNA from three biological replicates per genotype per time point was pooled prior to sequencing (n = 3 mice pooled per group).

first: Sierra

last: Wilson

first: Evan

last: Delgado

first: Frances

last: Alencastro

first: Rosa

last: Loewenstein

first: Madeleine

middle: P

last: Leek

first: Leah

last: Peters

first: Kerollos

last: Kamel

first: Patrick

last: Wilkinson

first: Siddhi

last: Jain

first: Joseph

last: Locker

first: Silvia

first: Bharat

last: Bhushan

first: Andrew

last: Duncan


title: pTα enhances mRNA translation and potentiates CAR T cells for solid tumor eradication [eCLIP-seq]

first: Yuzhe

last: Shi

address: 1250 First Avenue

department: Immunolgy

summary: Current chimeric antigen receptor (CAR) therapies are effective against a range of hematological malignancies and autoimmune disorders but have shown limited activity against solid tumors. In searching for effective means to enhance the functional persistence and potency of CAR T cells, we explored the potential of integrating pre-T cell features into canonical CD28-based CARs. Thymocytes undergo a proliferation burst during the β-selection developmental stage, which is driven by the pre-T cell receptor and its unique pTα chain. CARs harboring the pTα 1A domain imparted greater expansion, cytokine production, and in vivo persistence to T cells, accompanied by lowered exhaustion and greater long-term tumor control in multiple liquid and solid tumor models. CARs incorporating the 1A domain showed sustained phosphorylation of the mRNA translation master regulator YBX1, which was required for enhanced tumor eradication. The programing of mRNA translation in T cells opens another avenue for regulating and potentiating immunotherapy.

overall_design: 19-28z and 19-28z-1A CAR T cells 48hour post NALM6 stimulation


title: pTα enhances mRNA translation and potentiates CAR T cells for solid tumor eradication [Ribo-seq]


title: Non-invasive epidermis sampling for DNA methylation-based prediction of skin cancer phenotypes

city: Heidelberg

first: Oliver

last: Gilliam

address: Im Neuenheimer Feld

institute: German Cancer Research Center

summary: The epidermis is uniquely exposed to the effects of environmental factors such as ultraviolet radiation, which induce progressive genetic and epigenetic modifications contributing to aging and the onset of keratinocyte carcinomas. DNA methylation is the best-characterized epigenetic modification and a valuable biomarker for assessing epidermal health. However, broad screening approaches have been hindered by the limited quantity and quality of the genomic DNA obtained from the epidermis and the resulting need for invasive sampling methods. Here we describe an integrated method that enables the non-invasive sampling of epidermal DNA for subsequent analysis by DNA methylation microarrays. This procedure combines a gel-based adhesive tape for keratinocyte collection, a robust gDNA extraction protocol and a curated selection of microarray probes optimized for low-input DNA conditions. Analysis of >100 corresponding methylomes demonstrates that our approach can be used for both the training of epigenetic clocks capable of predicting epidermal age with high accuracy, as well as the investigation of various DNA methylation-based biomarkers relevant to keratinocyte cancer development. These findings underscore the potential of our method for broad and non-invasive skin health assessment and cancer prevention strategies.

overall_design: We aimed to profile skin epidermis using the TapeLift, a non-invasive sampling method of epidermal DNA. DNA methylation analysis was performed with the EPIC V2 methylation bead chip.

first: Manuel

last: Rodríguez-Paredes

first: Yan

last: Feng

first: Katrin

last: Wegner

first: Günter

last: Raddatz

first: Elke

last: Grönniger

first: Frank

last: Lyko


title: Induction of antigen-presenting monocyte-derived dendritic cells by nanoparticles inhibits metastasis and relieves immunosuppression in the metastatic niche

city: Ann Arbor

first: Lonnie

last: Shea

address: 1600 Huron Pkwy

institute: University of Michigan- Ann Arbor

summary: Myeloid immune cells play a major role in establishing a suitable microenvironment for metastatic tumor cells. Dysregulated myeloid cells suppress antigen-presentation pathways and effector T cell responses at distal organs, and reprogramming these cells may enhance anti-tumor cytotoxicity. Targeting myeloid cells with poly(lactide-co-glycolide) nanoparticles, which possess intrinsic immunomodulatory properties, can promote monocyte maturation to inhibit metastasis. Intravenously delivered nanoparticles made with polyvinyl alcohol, but not other surfactants, reduce the accumulation of neutrophils at the metastatic niche and induce the differentiation of monocytes into antigen-presenting monocyte-derived dendritic cells. The internalization of nanoparticles was linked to the upregulation of gene expression programs in monocyte-derived dendritic cells associated with antigen presentation and T cell stimulation, and ligand-receptor network modeling supports increased activation of Th1 cells by these monocyte-derived dendritic cells. Nanoparticle administration increased the proportion of CD4 cells with Th1 and Th17 phenotypes and did not inhibit metastasis in mice where monocytes or T cells were depleted, indicating that interactions between monocyte-derived dendritic cells and T cells are essential to the mechanism of action. Collectively, our findings demonstrate that nanoparticles can reprogram circulating monocytes into monocyte-derived dendritic cells to modulate the metastatic niche and enhance antigen presentation to stimulate intrinsic T cell responses.

overall_design: Lungs were isolated from female BALB/c 4T1-tumor bearing mice at D14 post-inoculation (inoculated with 50 uL of 2e6 4T1 cells/mL). Mice were treated with saline (control) or 1mg of NPs every three days starting at D1 post-inocluation (D1, 4, 7, 10, 13 NP treatments). Cells were then prepared for flow-assisted cell sorting by staining with AF488-CD45 and sorted into CD45+NP+, CD45+NP-, and CD45- populations on the Bigfoot Cell Sorter. Sorted samples were fixed with the 10x Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit following manufacturer instructions. Fixed samples were submitted to the University of Michigan Advanced Genomics Core for library preparation with the 10x Single Cell Fixed RNA Hybridization & Library Kit and Single Cell Fixed RNA Mouse Transcriptome Probe Kit following manufacturer guidelines for the 10x Single Cell Gene Expression Flex platform. Samples were sequenced on the NovaSeq X 10B flow cells (300 cycle) at a depth of approximately 25,000 reads per cell.

first: Jeffrey

last: Ma

first: Kate

middle: V

last: Griffin

first: Kathryn

last: Kang

first: Agustina

last: Diener

first: Ian

last: Schrack

first: Elizabeth

middle: J

last: Bealer

first: Laila

last: Rad

first: Rebecca

last: Pereles

first: Jacqueline

last: Jeruss


title: Canonical BAF complex orchestrates mesenchymal stem cell niche composition and fate via cofactor-guided chromatin remodeling [scATAC-seq]

first: Mingyi

last: Zhang

overall_design: Single-cell transposase-accessible chromatin were obtained from the digested proximal region of mouse incisor of at 4 days post-tamoxifen induction for DKO mice at the age of 1 month.


title: nuclear basekt mutants

city: WeiFang

first: Xiangyun

last: Yang

state: ShanDong

address: 699 Binhu Road, 699 Binhu Road, Xiashan District

institute: Institute of Advance Agricultural Sciences, Peking University

summary: Purpose: To understand the molecular mechanism and phenotype caused by the mutation of nup50c, nup82, nup136, nup50c nup82, nup50c nup136, nup82 nup136, nup50c nup82 nup136, we performed the whole genome transcriptome analysis on 9-day-old seedlings of WT, nup50c, nup82, nup136, nup50c nup82, nup50c nup136, nup82 nup136 and nup50c nup82 nup136. Conclusions: Nuclear basekt regulates stress- and growth- related gene expression.

overall_design: mRNA profiles of 9-day-old seedlings of wild type (Col-0), nup50c, nup82, nup136, nup50c nup82, nup50c nup136, nup82 nup136 and nup50c nup82 nup136 mutants were generated by deep sequencing, in duplicate, using Illumina HiSeq PE-150.

first: Yu

last: Tang


title: Cytoplasmic mRNA decay by the anti-viral nuclease RNase L promotes transcriptional repression [S5P Pol II CUT&Run]

first: Britt

last: Glaunsinger

overall_design: Pol II occupancy measurement by CUT&RUN of A549 WT or RNase L-KO cells either transfected with Lipofactamine RNAiMAX alone or with poly(I:C) for 4 hours (3 biological replicates per condition). For each replicate, an additional RNAiMAX-transfected WT sample was included for IgG control.

first: Xiaowen

last: Mao

first: Sherzod

last: Tokamov

first: Felix

last: Pahmeier

first: Azra

last: Lari

first: Jinyi

last: Xu

first: Eva

last: Harris


title: Canonical BAF complex orchestrates mesenchymal stem cell niche composition and fate via cofactor-guided chromatin remodeling [CUT&Run]

address: 2250 Alcazar Street, CSA103, HSC

overall_design: Control mouse incisor proximal end tissue were collected and digested into cells, then underwent the process following the CUT&RUN protocol.


title: Canonical BAF complex orchestrates mesenchymal stem cell niche composition and fate via cofactor-guided chromatin remodeling [scRNA-seq]

overall_design: Single-cell transcriptomes were obtained from the digested proximal region of mouse incisor of at 4 days post-tamoxifen induction for DKO mice at the age of 1 month.


title: ISL1: A Novel Neuroendocrine Subtype in Small Cell Lung Cancer Predicts Durable Response to Lurbinectedin

city: Indianapolis

first: Misty

last: Shields

state: IN

address: 980 W. Walnut St

institute: Indiana University

summary: Small cell lung cancer (SCLC) is a recalcitrant thoracic malignancy known for acquired chemoresistance, early metastatic spread, and poor overall survival. Treatment with lurbinectedin, a DNA minor groove alkylating agent, provides durable efficacy in a subset of patients. In this study, we aim to identify and validate predictive biomarkers to lurbinectedin in small cell lung cancer patients. Within the ISL1 “high” lines, 1,105 genes were uniquely downregulated following lurbinectedin, including ISL1, RBMS3, PARD3B, SIX1, SOX2-OT, AURKA, and ASCL1. Downregulation of select MYC paralogs was additionally observed in the ISL1 “high” lines. Over 1,100 genes were additionally identified to be uniquely upregulated in the ISL1 “high” lines, including ATF3, BEST1, and DDIT3. ISL1 “low” lines showed significantly fewer unique expression changes following lurbinectedin (35 downregulated, 25 upregulated). Regardless of ISL1 status, 83 genes were globally downregulated, including LSAMP and MACROD2, while only 14 genes were globally upregulated following lurbinectedin, including TONSL, CDT1, and CHTF18.

overall_design: For the RNA-seq, two ISL1 “high” (H209, H187) and two ISL1 “low” (H82, SHP-77) cell lines were treated in biological triplicates with 0.1 nM lurbinectedin (or DMSO vehicle) for 24 h before harvesting for RNA extraction and sownstream RNA-seq.

first: Katherine

last: Minton

first: Tianhao

last: Zhou


title: Canonical BAF complex orchestrates mesenchymal stem cell niche composition and fate via cofactor-guided chromatin remodeling [RNA-Seq]

institute: University of Southern California

overall_design: Transcriptomes were obtained from the digested proximal region of mouse incisor of at 4 days post-tamoxifen induction for DKO mice at the age of 1 month.


title: Pharmacological Depletion  of Polyamines with DFMO in Neuroblastoma cell line SKNBE2

city: Zurich

first: Sarah

last: Cherkaoui

address: August-Forel-Strasse 51

department: Oncology

institute: University Children's Hospital Zurich

summary: Metabolites are central to cellular homeostasis. Whereas much emphasis has been placed on their relevance to meet energetic and biosynthetic demands, metabolic intermediates also function as signaling molecules. Here we show that polyamines, small polycations that are essential for cell biology, regulate the process of alternative pre-mRNA splicing. We find that the inhibition of polyamine synthesis increases the phosphorylation of spliceosomal proteins, concomitant with remarkable perturbation of alternative splicing in cells and tissues. Mechanistically, molecular modeling together with biochemical assays revealed that polyamines bind to acidic phosphorylatable motifs in splicing factors of the U2 snRNP SF3 subcomplex, thus preventing the action of kinases. The molecular process through which polyamines regulate protein phosphorylation is a phenomenon that we define as “metabolic shielding”.

overall_design: The neuroblastoma cell line SKNBE2 was obtained from the Children’s Oncology Group Cell Culture Repository and cultured in RPMI (Gibco). To inhibit polyamine biosynthesis cells were treated for 4 days with 250 μM of DFMO obtained from Pat Woster (Medical University of South Carolina). At sub-confluency cells were washed with ice-cold PBS and RNA was isolated from cell extracts by direct addition of 3-volumes of QIAzol® (Qiagen, Cat. No. 79306). After thorough mixing, RNA was purified using the Direct-Zol RNA Mini Prep Plus kit. Stranded library preparation was performed at the Genomic Platform (UNIGE) following standard protocols. Libraries were sequenced on an Illumina NovaSeq 6000, SR 100 bp.

first: Michael

middle: D

last: Hogarty

first: Raphael

last: Morscher


title: Cytoplasmic mRNA decay by the anti-viral nuclease RNase L promotes transcriptional repression [4sU-seq]

summary: Ribonuclease (RNase) L is an antiviral factor that promiscuously degrades viral and cellular RNA in the cytoplasm. This results in extensive translational reprogramming, altering mRNA processing and export. Here, we reveal that another major consequence of cytoplasmic RNase L activity is the repression of nascent RNA synthesis in the nucleus. This is not associated with altered nuclear RNA stability but instead results from transcriptional repression. For RNA polymerase II, repression is primarily associated with reduced occupancy of serine 2-phosphorylated polymerase in gene bodies, indicating an elongation defect. Prominent among the transcriptionally downregulated loci are immune-related genes, supporting a role for RNase L in tempering innate immune and inflammatory responses. RNase L activation also caused disruption of nucleoli and reduced RNA polymerase I and III transcription. Crosstalk between RNA decay and transcription thereby contributes to the large-scale modulation of gene expression in RNase L-activated cells.

overall_design: Nascent RNA profiling by 4sU-seq of A549 WT or RNase L-KO cells either transfected with Lipofactamine RNAiMAX alone or with poly(I:C) for 4 hours (3 biological replicates per condition).