title: Novel CRISPR-Cas9 BAP1 Knockout Pre-Clinical Tumor Model Recapitulates Human Melanoma Tumorigenesis and Immune Evolution

city: Singapore

first: Mona

middle: Meng

last: Wang

address: 20 College Rd, Singapore

country: Singapore

institute: Singaoire Eye Research Institute

summary: BAP1-deficient melanocytic tumors exhibit strong immunosuppressive features and poor prognosis. Currently, no immune-competent preclinical models exist to study their tumor-immune interactions or test new immunotherapies. This limitation hinders progress in understanding how BAP1 loss drives tumor aggressiveness and immune evasion. To address this, we generated a syngeneic BAP1 knockout melanocyte tumor line using CRISPR-Cas9. We then evaluated its functional and immunological impact in immune-competent mice, including its ability to recapitulate metabolic and immunosuppressive features of human BAP1-deficient melanomas. The selected knockout clone exhibited hallmarks of aggressive skin and intraocular melanomas, including epithelioid morphology, in vivo tumorigenic potential, rapid growth, and key immunosuppressive features, mirroring those observed in human BAP1-deficient melanomas. Cross-species single-cell transcriptome analysis demonstrated strong molecular overlap between BAP1 knockout mouse tumors and high-risk (class 2) human uveal melanomas, highlighting shared pathways in lipid metabolism, transmembrane receptor signaling, and immune modulation. Gene Set Enrichment Analysis confirmed that lipid metabolic reprogramming, previously described in human tumors, is also a key feature of our model, validating its ability to recapitulate human disease biology. This study introduces a syngeneic preclinical model that mimics the immunosuppressive landscape of BAP1-deficient melanocytic tumors, enabling the development and optimization of new combination immunotherapies.

overall_design: This GEO submission includes integrated genomic and transcriptomic datasets generated to investigate the effects of BAP1 loss and tumor anatomical site (ocular versus skin) in murine melanocytic models and syngeneic tumors. Whole-genome sequencing (WGS) was performed on B16F10 cells, primary ocular melanocytes, and Melan-a cells to provide reference genomic backgrounds. Whole-exome sequencing (WES) was conducted on Melan-a (BAP1 wild-type) cells and four independent CRISPR-engineered BAP1 knockout Melan-a clones, with the wild-type Melan-a sample used as the matched reference for somatic variant calling in each knockout clone. Bulk RNA sequencing was performed on Melan-a wild-type cells and the same four BAP1 knockout clones, with biological replicates, to assess transcriptional changes associated with BAP1 loss in vitro. To characterise in vivo tumor ecosystems, single-cell RNA sequencing using the 10x Genomics platform was performed on dissociated syngeneic mouse tumors derived from ocular and cutaneous sites, including one wild-type and one BAP1 knockout tumor from each anatomical location. Together, these datasets enable comparative analyses across genotype, clone, and tumor site to define BAP1-dependent genomic alterations, transcriptional programs, and tumor microenvironment differences.

first: Yuanhan

first: Candice H.E

last: Hua

first: Willie

last: Yu

first: Sarah

last: Coupland

first: Gayoung

last: Park

first: Anita

last: Chan

first: Carlos

middle: R

last: Figueiredo


title: Heart Failure Pleural Fluid Impairs Endothelial Barrier through miR 501-3p Mediated ZO 1 Remodeling

status: Public on Mar 12 2026

city: New Taipei City

first: VIJESH

middle: KUMAR

last: YADAV

address: No. 301號, Yuantong Rd, Zhonghe District, New Taipei City, 235

department: Department of Medical Research and Education, Taipei Medical University - Shuang Ho Hospital, New Taipei City, Taiwan

country: Taiwan

institute: SHH-TMU Taiwan

type: Expression profiling by high throughput sequencing

summary:
Summary:
Heart failure is frequently accompanied by pleural effusion, yet the biological impact of heart failure–associated pleural fluid on vascular endothelial function remains unclear. Here, we show that heart failure pleural fluid impairs endothelial barrier integrity and angiogenic capacity in human umbilical vein endothelial cells. Functional assays revealed increased permeability, reduced migration, and altered tube formation following treatment with patient-derived pleural fluid. Mechanistically, heart failure pleural fluid increased reactive oxygen species production and inflammatory signaling while downregulating tight junction protein ZO-1. Small RNA profiling identified miR 501 3p as a key mediator of these effects. Gain- and loss-of-function experiments demonstrated that miR 501 3p directly regulates ZO-1 expression and contributes to barrier disruption. These findings establish a microRNA-dependent mechanism linking heart failure pleural fluid to endothelial dysfunction and suggest a potential molecular pathway contributing to vascular complications in heart failure.

overall_design: Human umbilical vein endothelial cells (HUVECs) were cultured under standard conditions and divided into two experimental groups: untreated control (Normal) and heart failure–associated pleural fluid–treated (HFPF). For the HFPF group, HUVECs were exposed to heart failure–associated pleural fluid collected from clinically diagnosed heart failure patients. Untreated HUVECs cultured in parallel served as the Normal control group.  Each experimental condition consisted of three independent biological replicates: Normal_1, Normal_2, Normal_3 and  HFPF_1,  HFPF_2, HFPF_3

first: Chieh-Yung

first: Tung-Yu

last: Tiong

first: Ying

last: Chen

first: Yi-Hsuan

last: Lin

first: Vijesh

middle: K

last: Yadav

first: Chih-Ying

last: Changchien

first: Chih‑Feng

last: Chian

first: Chen-Liang

last: Tsai


title: Cross-Species Transcriptomic Integration Reveals a Conserved, MIRO1-Mediated Macrophage-to-T Cell Signaling Axis Driving Immunosuppression in Glioma

city: Palo Alto

first: Xinnan

state: CA

address: 1201 Welch Road, MSLS Building, Rm P151

department: Neurosurgery

country: USA

institute: Stanford University

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Amphiregulin Switches Progenitor Cell Fate for Lineage Commitment During Gastric Mucosal Regeneration

city: Seoul

first: Su-Hyung

last: Lee

state: Seoul

address: 120 Neungdong-ro, Gwangjin-gu

country: South Korea

institute: Konkuk University

summary: Background & Aims: Isthmic progenitors, tissue-specific stem cells in the stomach corpus, maintain mucosal homeostasis by balancing between proliferation and differentiation to gastric epithelial lineages. The progenitor cells rapidly adopt an active state in response to mucosal injury. However, it remains unclear how the isthmic progenitor cell niche is controlled during the regeneration of damaged epithelium. Methods: We recapitulated tissue recovery process after acute mucosal injury in the mouse stomach. BrdU incorporation was utilized to trace newly generated cells during the injury and recovery phases. To define epithelial lineage commitment process during recovery, we performed single cell RNA-sequencing on epithelial cells from the mouse stomachs. We validated the effects of amphiregulin (AREG) on the mucosal recovery, utilizing recombinant AREG treatment or AREG deficient mice.  Results: We determined that an EGFR ligand, AREG, can control progenitor cell lineage commitment. Based on the identification of lineage-committed subpopulations in the corpus epithelium through single cell RNA-sequencing and BrdU incorporation, we showed that isthmic progenitors give rise to epithelial cell lineages through an ordered paradigm during mucosal regeneration. During recovery, AREG treatment promotes repopulation with parietal cells, while suppressing surface cell commitment of progenitors. In contrast, TGF-alpha did not alter parietal cell regeneration but did induce expansion of surface cell populations.  AREG deficiency impairs parietal cell regeneration, but increases surface cell commitment. Conclusions: These data demonstrate that different EGF receptor ligands can distinctly regulate isthmic progenitor-driven mucosal regeneration and lineage commitment.

overall_design: To investigate the cellular dynamics and lineage commitment of gastric epithelial progenitors during mucosal regeneration, we performed single-cell RNA sequencing (scRNA-seq) on mouse stomach corpus tissues. Acute mucosal injury was induced in 6-7 week old C57BL6/J wild-type (WT) mice using a single oral dose of L635 (350 mg/kg). For scRNA-seq, corpus tissues were collected at three distinct time points: untreated normal (PBS control), 1 day post-treatment (acute injury phase), and 3 days post-treatment (recovery phase). Single cells were captured using the PIPseq™ T20 3’ Single Cell Capture and Lysis Kit (Fluent BioSciences) to generate 3’ digital gene expression profiles. This study aims to identify lineage-committed subpopulations and understand the regulatory role of EGFR ligands, particularly Amphiregulin (AREG), in progenitor-driven epithelial recovery.

first: Yoonkyung

last: Won

first: David

last: Gibbs

first: Brianna

last: Caldwell

first: Anna

last: Goldstein

first: Eunyoung

last: Choi

first: James R.

last: Goldenring


title: Genome-wide methylation analysis identifies epigenetic differences in human ILC2s from healthy, atopic, and asthmatic young donors

city: Braunschweig

first: Stefan

last: Floess

address: Inhoffenstr. 7

department: Experimental Immunology

country: Germany

institute: Helmholtz-Centre for Infection Research

type: Methylation profiling by high throughput sequencing

summary: DNA methylation of CpG motifs represents a stable epigenetic mark that critically influences the differentiation, stability and function of immune cell populations. Identifying differentially methylated regions within immune cell lineages contributes to their phenotypic and functional characterization, leading to a better understanding of lineage-specific transcriptional regulation. In this study, we performed a genome-wide methylation analysis of type 2 innate lymphoid cells (ILC2) from healthy (HE), atopic (AT) and asthmatic (AS) young individuals, to investigate inflammation-driven epigenetic changes during human development.

overall_design: ILC2 were isolated from blood of healthy, atopic and asthmatic young human donors (age: 10-16 years) by flow cytometry-based sorting. Genomic DNA was prepared and subjected to genome-wide methylation analysis by enzymatic methyl-sequencing (EM-seq).

first: Matthias

last: Lochner

first: Ayush

last: Jain

first: Elia

middle: C

last: Diem

last: Steglich

first: Ruth

last: Grychtol

first: Anna-Maria

last: Dittrich


title: MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy [eCLIP]

city: Québec

first: Thiery

last: De Serres-Bérard

state: Québec

department: Medicine

country: Canada

institute: Université Laval

summary: The loss of Muscleblind-like (MBNL) protein function, resulting from its sequestration by toxic CUG-expanded DMPK transcripts, is a central pathological mechanism in myotonic dystrophy type 1 (DM1). However, the role of MBNL in neurodevelopmental disorders associated with severe forms of DM1 remains poorly understood. We used enhanced crosslinking and immunoprecipitation (eCLIP) to study MBNL2-RNA binding sites in 70-day-old forebrain organoids derived from an apparently healthy individual, a patient with congenital myotonic dystrophy (CDM) carrying approximately 2,000 CTG repeats, and an isogenic control in which the pathogenic repeat expansion had been removed. Using Skipper, a workflow allowing improved discovery of protein–RNA binding sites, including in annotated repetitive elements, we identified reproducible enriched windows for the DMPK 3′ UTR in CDM organoids compared to the corresponding input controls. In contrast, no significant binding in the same region was detected in either the unaffected or the isogenic control. This finding supports a physical interaction between MBNL2 and the CUG-expanded DMPK mRNA, observed specifically in neural stem cells of late-stage forebrain organoids by immunostaining and fluorescence in situ hybridization (FISH). Our study highlights the sensitivity of neural stem cells to MBNL2 sequestration during cortical development.

overall_design: Forebrain organoids were differentiated from induced pluripotent stem cells (iPSCs) derived either from pediatric patients with CDM carrying approximately 2,000 CTG repeats in the DMPK gene or from an age-matched unaffected individual. Isogenic control lines were also generated by removing the CTG repeat expansion from the DMPK locus in CDM iPSCs. eCLIP experiments were performed in duplicate and compared with matched input controls for each condition.

first: Thiéry

first: Jack

last: Puymirat

first: Grady

last: Nguyen

first: Maya

middle: L

last: Gosztyla

first: Gene

middle: W

last: Yeo


title: MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy [scRNA-Seq]

summary: The loss of Muscleblind-like (MBNL) protein function, resulting from its sequestration by toxic CUG-expanded DMPK transcripts, is a central pathological mechanism in myotonic dystrophy type 1 (DM1). However, the role of MBNL in neurodevelopmental disorders associated with severe forms of DM1 remains poorly understood. We performed single-cell RNA sequencing using the 10x Genomics Chromium platform to investigate the cellular composition and transcriptomic alterations in forebrain organoids derived from an unaffected individual, a patient with congenital myotonic dystrophy (CDM) carrying approximately 2,000 CTG repeats or an isogenic control in which the pathogenic repeat expansion was removed. Our analysis revealed that MBNL2, known to play a key role in the pathogenesis of myotonic dystrophy, is expressed in a subset of neural stem cells in mature forebrain organoids. We identified altered expression of genes involved in neuronal migration and axonal projection specifically in upper-layer cortical neurons of CDM organoids when compared with both the isogenic and the unaffected control. These findings suggest a role for MBNL2 during prenatal cortical development and highlight impaired differentiation of late-born neurons as a potential contributor to the neurodevelopmental abnormalities associated with CDM.

overall_design: Forebrain organoids were differentiated from induced pluripotent stem cells (iPSCs) derived either from pediatric patients with CDM carrying approximately 2,000 CTG repeats in the DMPK gene or from an age-matched unaffected individual. Isogenic control lines were also generated by removing the CTG repeat expansion from the DMPK locus in CDM iPSCs. After 80 days of culture following embryoid body formation, 6–12 organoids per condition were dissociated, and an average of 3460 cells per sample were loaded onto the 10x Genomics Chromium platform to generate single-cell transcriptomic data.


title: SGLT2 inhibition reverses metabolic and inflammatory kidney signatures in youth with type 1 diabetes

city: Seattle

first: Petter

last: Bjornstad

state: Washington

address: 750 Republican St

department: Division of Metabolism, Endocrinology and Nutrition

institute: University of Washington

summary: Sodium-glucose cotransporter-2 (SGLT2) inhibitors slow progression of diabetic kidney disease, but their intrarenal mechanisms remain unclear, particularly in patients with type 1 diabetes (T1D). In a prespecified ancillary study within the placebo-controlled ATTEMPT trial of dapagliflozin in youth with T1D and well-preserved kidney function (N=98), we integrated sequential kidney biopsies, multiparametric kidney MRI, and proteomics. Single-cell RNA-seq of N=16 baseline and N=11 16-week follow-up biopsies (N=27; 214,415 cells) revealed a coordinated network of metabolic, fibrotic, and inflammatory transcriptional changes across nephron, vascular, and immune compartments. These gene shifts paralleled attenuation of hyperfiltration and improvement in glycemic control (HbA1c and time-in-range), implicating 594 transcripts. MRI indicated a reversal of the medullary hyperoxia characteristic of T1D with dapagliflozin. Urine proteomic profiles echoed the transcriptomic patterns. Together, these multimodal data point to metabolic reprogramming, reduced inflammation, and improved oxygen handling as convergent mechanisms of SGLT2-mediated kidney protection. ClinicalTrials.gov: NCT04333823.

first: Ye Ji

first: Phoom

last: Narongkiatikhun

first: Anil

last: Karihaloo

first: Pottumarthi

last: Prasad

first: Lu-Ping

last: Li

first: Kalie

last: Tommerdahl

first: Maninder

last: Sethi

first: Shivani

last: Ramesh

first: Carissa

last: Birznieks

first: Antoine

last: Clarke

first: Yesmino

last: Elia

first: Jacqueline

last: Curtis

first: Cheril

last: Clarson

first: Dylan

last: Weissenkampen

first: Matteo

last: D'Antonio

first: Jairo

last: Arturo Pinzon Cortes

first: Hailey

last: Hampson

first: Long

last: Yuan

first: Sarah

last: van Eeghen

first: Jenny

middle: E

last: Kanter

first: Karin

last: Bornfeldt

first: Tomas

last: Vaisar

first: Patricia

last: Ladd

first: Hiddo

middle: J

last: Heerspink

first: Ian

middle: H

last: de Boer

first: Jesse

middle: A

last: Goodrich

first: Kelly

last: Street

first: Katherine

last: Tuttle

last: Bergmann

first: Cathy

last: Smith

first: Jeffrey

middle: B

last: Hodgin

first: Jennifer

last: Schaub

first: Viji

last: Nair

first: Rajaree

last: Menon

first: Abhjeet

last: Naik

first: Philip

last: McCown

first: Fadhl

last: AlAkwaa

first: Sean

last: Eddy

first: Edgar

last: Otto

first: Nan Hee

last: Kim

first: Robert

middle: G


title: Sex and tissue resolved co-expression networks reveal a female placental–brain axis protective against prenatal PCB exposure

city: Davis

first: Janine

last: LaSalle

state: California

address: 1275 Med Science Dr

institute: University of California, Davis

summary: Background: Neurodevelopmental disorders have a strong male bias that is poorly understood, Placenta is a rich source of molecular information about environmental interactions with genetics (including biological sex), that affect the developing brain. We investigated placentalbrain transcriptional responses in an established mouse model of human-relevant prenatal exposure to polychlorinated biphenyls (PCBs). Results: To understand sex, tissue, and dosage effects in embryonic (E18) brain and placenta RNAseq datasets, we used weighted gene correlation network analysis (WGCNA) to create correlated gene networks that could be compared across sex or tissue. WGCNA revealed that expression within most correlated gene networks were significantly and strongly associated with PCB exposures, but frequently in opposite directions between male-female and placenta-brain comparisons. In both WGCNA and differentially expressed gene analyses, male brain showed more PCB-induced transcriptional changes than male placenta, but the reverse pattern was seen in females. Furthermore, non-monotonic dose responses to PCBs were observed in most gene networks, but were most prominent in male brain. The transcriptomic effects of low dose PCB exposure were significantly reversed by dietary folic acid supplementation across both sexes, but these effects were strongest in female placenta. PCB-dysregulated and folic acid reversed gene networks were commonly enriched in functions in metabolic pathways involved in energy usage and translation, with female-specific protective effects enriched in PPAR, thermogenesis, glycerolipids, and O-glycan biosynthesis, as opposed to toxin responses in male brain. Conclusions: The female protective effect in prenatal PCB exposures appears to be mediated by dose-dependent sex differences in transcriptional modulation of metabolism in placenta.

overall_design: The experiment was designed to test the hypothesis that PCB-induced transcriptional changes in the placental-brain axis will be affected by both dosage and sex. The PCB MARBLES mixture, consisting of PCB 28 (48.2%), PCB 11 (24.3%), PCB 118 (4.9%), PCB 101 (4.5%), PCB 52 (4.5%), PCB 153 (3.1%), PCB 180 (2.8%), PCB 149 (2.1%), PCB 138 (1.7%), PCB 84 (1.5%), PCB 135 (1.3%) and PCB 95 (1.2%), was formulated to mimic the 12 most abundant congeners identified from the serum of pregnant women in the ASD-enriched MARBLES cohort, as previously described.32 C57BL/6J female mice (Jackson Laboratory) aged 6 to 8 weeks were orally exposed to 4 different doses (0, 0.1, 1.0, or 6.0 mg/kg/d) of the PCB mixture in peanut oil (Spectrum Organic) and peanut butter (Trader Joe’s Organic Creamy). The PCB mixture was stored as concentrated stock in peanut oil, then diluted in peanut butter to make dosing mixes for the four dose groups (0, 0.1, 1, and 6 mg/kg/d). The dosing mixes were premade for the entire experiment and stored in the refrigerator and remixed daily. For alterations to folic acid in the chow, mice were fed ad libitum, with the AIN-93G purified diet, containing with or without 6 ppm folic acid supplementation (ENVIGO 190757, 94045, respectively). Females were dosed daily for at least 2 weeks before breeding commenced. Daily dosing then continued through breeding and gestation, up to embryonic day 18 (E18). On E18, pregnant females were euthanized in a CO2 euthanasia chamber. Immediately after euthanasia, embryos were removed, and tissues dissected and flash frozen.

last: Chau

first: Kari

last: Neier

first: Anthony

last: Valenzuela

first: Rebecca

last: Schmidt

first: Blythe

last: Durbin-Johnson

first: Pamela

last: Lein

last: Korf

middle: M


title: MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy

first: Thiery

last: De Serres-Bérard

first: Thiéry

first: Jack

last: Puymirat

first: Grady

last: Nguyen

first: Maya

last: Gosztyla

first: Gene

last: Yeo


title: PPP1CA and RPSA dual inhibition suppresses castration resistance and bone metastasis for prostate cancer by disrupting AR-V7/RANKL signaling

city: Shenyang

first: Wensu

last: Liu

address: 77 Puhe Road, Shenbei District

country: China

institute: China Medical University

summary: Androgen is important in the formation, development and progress of prostate cancer, and deprivation of androgen, which is also named castration, is an effective way in prostate cancer therapies. For patients undergoing castration therapies, castration was gradually becoming ineffective in prostate cancer treatment and therefore resulting in castration-resistance for prostate cancer. Co-IP mass spectrometry, Ribo-seq, RNA-seq and system biology methods were applied to detect castration resistance drivers. Ribosomal drivers were found to be highly expressed and promoting invasion and migration in castration resistant prostate cancer cells and also in bone metastasis prostate cancer cells. Within these ribosomal drivers, RPSA played central roles in promoting castration resistance in assistance of RPL28, RPL4X, RPL11 and RPL23A. RPSA promotes castration resistance through interacting with PPP1CA and AR-V7 to form RPSA-PPP1CA-AR-V7 axis. This axis is bind by RPL23A and RPL28 and assisted by RPL4X. IGF-1 is also engaged in the process of promoting castration resistance and bone metastasis by RPSA-PPP1CA-AR-V7 axis. RPSA inhibitors plus PPP1CA inhibitors have also been proven to significantly restore castration resistance and bone metastasis for prostate cancer. This effect can be reversed by IGF-1 and retinoid acid. For these reasons, we propose that dual inhibition of RPSA and PPP1CA significantly inhibits castration resistance and bone metastasis for prostate cancer.

overall_design: 2 repeats for shNC, shRPL28, shRPL4X,shRPL11, shRPL23A and shRPSA on 22Rv1 cell lines

first: Wenshuo

first: Wei

first: Jing

last: Wan

first: Xiaobei

last: Zhou


title: Bacteroides intestinalis–Driven Arabinoxylan Fermentation Mitigates Inflammatory and Metabolic Dysfunction

city: Urbana

first: Wenyan

last: Mei

state: Illinois

address: 2001 S. Lincoln Avenue

department: Comparative Biosciences

institute: University of Illinois at Urbana-Champaign

summary: Insufficient dietary fiber intake is strongly associated with gut microbiome dysfunction and an increased risk of noncommunicable diseases. Synergistic synbiotics, which pair defined microbial strains with their preferred carbohydrate substrates, offer a promising strategy to restore these functions. However, the rational design of such interventions remains challenging by insufficient understanding of microbial fiber-degrading capacities and the host-relevant bioactivities of fermentation-derived metabolites. Here, we identify human colonic commensal Bacteroides intestinalis (B. intestinalis) as a key microbial mediator of dietary fiber-driven metabolic, immune, and neuronal benefits. We demonstrate that the synergistic interaction between B. intestinalis and its preferred substrate, insoluble wheat arabinoxylan abundant in dietary fiber, enhances the production of anti-inflammatory, antioxidant, and anti-diabetic phenolic compounds and bile acid species. These metabolic effects are accompanied by coordinated transcriptional remodeling in the colon and spleen that improve circadian rhythm regulation, lipid metabolism, and immune defense. Importantly, these beneficial effects are preserved in conventionally raised mice with established high fat diet-induced obesity, where BI and inWAX improves glucose tolerance along with an increased production of neuroactive compounds. Our findings uncover a mechanistic framework linking B. intestinalis-mediated fiber fermentation to gut–liver–brain crosstalk and establish a rational foundation for precision synbiotic design.

overall_design: RNA-seq profiling DSS_cellulose_Spleen, DSS_InWax_Spleen, Water_cellulose_DC, Water_InWax_DC, DSS_cellulose_MC, and DSS_InWax_MC


title: Genome-wide methylation analysis defines the epigenetic identity of human innate lymphoid cells

first: Stefan

last: Floess

summary: DNA methylation of CpG motifs represents a stable epigenetic mark that critically influences the differentiation, stability and function of immune cell populations. Identifying differentially methylated regions within immune cell lineages contributes to their phenotypic and functional characterization, leading to a better understanding of lineage-specific transcriptional regulation. Here, we performed a genome-wide methylation analysis of human innate lymphoid cells (ILCs) isolated from tonsils and blood samples of healthy donors, which allowed us to define specific epigenetic marker regions for ILC1, ILC2 and ILC3.

overall_design: IL1, ILC2, ILC3 and natural killer (NK) cells were isolated from blood and tonsils of healthy human donors by flow cytometry-based sorting. Genomic DNA was prepared and subjected to genome-wide methylation analysis by bisulfite sequencing.

first: Matthias

last: Lochner

first: Ayush

last: Jain

first: Chiawen

last: Lu

first: Elia

last: Diem

last: Steglich


title: Proteosome inhibitor repurposing rescues hypomyelination in HIKESHI-associated Leukodystrophy

city: Aurora

first: Kevin

last: Ess

state: Co

address: 12700 East 19th Avenue

department: Pediatrics

institute: University Colorado Denver

summary: HIKESHI-associated leukodystrophy (HAL) is a lethal genetic neurological condition with most patients dying in childhood. HAL is caused by homozygous mutations in the HIKESHI gene leading to protein loss. HIKESHI serves as a nuclear import carrier for chaperone HSP70 during heat shock response (HSR). As the primary abnormalities are related to white matter, we geneated iPSCs  from affected homozygous HAL patients, non-symptomatic heterozygous first-degree relatives, and healthy unrelated individuals. iPSCs were differentiated into oligodendrocytes, followed by immunofluorescent staining and various assays. Bulk RNASeq revealed various upregulated and downregulated genes during oligodendrocyte development. Immunofluorescence indicates HSP70 and other proteins displayed altered nuclear localization in HIKESHI homozygous cells. Homozygous cells also had much fewer Olig2+ cells, aberrant myelination, and misshapen cells. We conclude that loss of HIKESHI results in dysfunction of oligodendrocyte development and function.

overall_design: RNASeq analysis of HIKHet and HIKHOM oligodendrocytes across 90 day differentiation

first: Sudiksha

last: Rathan-Kumar

first: Matheus

last: Martino-Wojciechowski

first: Tatiana

last: Rabinski

first: Gad

middle: D

last: Vatine


title: Gut–brain axis disruption sustains low intake syndrome in weanling pigs

city: Cerdanyola del Valles

first: Laia

last: Ferreres Serafini

state: Barcelona

address: Edifici V, Travessera dels Turons

country: Spain

institute: Autonomous University of Barcelona

summary: Abrupt weaning imposes highly variable physiological stress on pigs, yet the mechanisms underlying this variability remain poorly understood. We applied an integrative approach combining transcriptomics, gastrointestinal phenotyping, and blood biomarkers to characterize gut–brain axis dynamics at one week post‑weaning (day 7) and at the end of the nursery phase (day 39) in pigs with divergent early performance. Twenty‑four pigs of similar weaning weight (5.65 ± 1.0 kg) were selected from pens showing extreme early feed intake post-weaning and subsequently classified by average daily gain (ADG) as a proxy for individual feed intake (n = 12/timepoint). RNA sequencing of ileal and hypothalamic tissue revealed that low‑ADG pigs at day 7 exhibited impaired intestinal barrier function, suppressed metabolic and immune pathways, and hypothalamic activation of appetite‑suppressing (mTORC1, GLP‑1) and thermogenic signalling, together with endocrine disruption. By day 39, digestive and metabolic pathways were upregulated in the ileum of low‑ADG pigs, yet gut integrity deficits persisted alongside sustained hypothalamic immune activation and disrupted appetite signalling. Blood profiles indicated prolonged metabolic imbalance, characterized by elevated triglycerides, insulin, leptin, and TNF‑α, and reduced PYY. Collectively, these findings define a “low feed intake syndrome”, in which early nutrient deprivation, compromised gut integrity, and dysregulated neuroendocrine signalling converge to perpetuate poor growth and long‑term maladaptation.

overall_design: RNA-seq profiling of the gut-brain axis (ileal and hypothalamic tissue) of piglets with low versus high growth after weaning, on days 7 and 39.

last: Ferreres-Serafini

first: Hubèrt

last: Van Hees

first: Susana

last: Martín-Orúe

first: José

middle: F

last: Pérez

first: Tetske

last: Hulshof

first: Laura

last: Payling

first: Lluís

last: Fabà


title: Conserved enhancer association of piRNAs and the implication in germ cell fate surveillance

city: Taipei City

first: Shau-Ping

last: Lin

state: select a state

address: 4F, No. 81, Chang-Xing St.,

department: Institute of Biotechnology

institute: National Taiwan University

type: Non-coding RNA profiling by high throughput sequencing

summary: We collected fetal testes of gestational week 12-22 abortuses from Taiwan and the USA, to investigate human piRNA profiles correlating to the time window of epigenetic landscape establishment. We identified numerous human piRNAs in second-trimester fetal testes that corresponded to small nucleolar RNAs. Additionally, a substantial proportion of human fetal testicular piRNAs mapped to super-enhancers and typical enhancers, a phenomenon conversed across mouse and chicken species. Notably, many of the pre-pachytene germline piRNAs mapped to enhancers active in various adult somatic lineages, implying they may regulate enhancer activities and safeguard germ cell identity by reducing aberrant expression of somatic genes.

overall_design: Small RNA-seq profiling was conducted on human fetal testes collected from abortuses at gestational week (GW) 12 to 22 due to genietic or other non-gonadal related phenotypic abnormalities. Sample collection was performed at National Taiwan University Hospital under approved IRB protocols.

first: Yen-Tzu

last: Tseng

first: Pin-Jui

last: Kung

first: Hsien-Hen

first: Luca CW

last: Cheng

first: Yi-Tzang

last: Tsai

first: Kai-Wei

last: Chang

first: Hung-Chih

last: Kuo

first: Hong-Nerng

last: Ho

first: Hsin-Fu

last: Chen


title: Single-Cell RNA Sequencing of Galt Gene-Edited Mouse Liver Tissue

city: Guilin

first: Honghao

last: Yu

state: Guangxi

address: Guilin Medical College, Lingui District, Guilin City, Guangxi

institute: Guilin Medical University

summary: This dataset contains single-cell RNA sequencing data from liver tissues of Galt gene-edited (GAL) mice and wild-type (WT) mice.  The samples were collected for the investigation of molecular changes induced by Galt gene mutations, specifically focusing on liver injury.  The dataset includes gene expression profiles of individual cells and enables the study of cell-type-specific responses, immune cell changes, and alterations in key cellular pathways.  This dataset is useful for further understanding the pathophysiology of liver injury associated with Galt gene mutations and provides a resource for research into the molecular mechanisms of galactosemia.

overall_design: Liver tissues from Galt gene-edited (GAL) and wild-type (WT) mice were collected, and single cells were isolated for RNA sequencing. The single-cell suspension was processed using the SeekOne® Digital Droplet Single Cell Library Kit, followed by sequencing on the Illumina NovaSeq 6000 platform.

first: Pengpeng

last: Yue

first: Zhihao

last: Li

first: Ning

last: Wang

first: Yong

first: Lantao

last: Gu

first: Can

last: Fu


title: Heritability and transcriptional impact of JAK3, STAT5A and STAT6 variants in a Tyrolean family

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

summary: The Janus Kinase (JAK) and Signal Transducers and Activators of Transcription (STAT) pathway regulate a range of biological processes, including hematopoiesis. While a major research focus has been on somatic human mutations in disease, less is known about the heritability of germline variants and their physiological impact. Here we identify the rare JAK3P151R, JAK3R925S, STAT5AV494L and STAT6Q633H variants in an extended family spanning three generations and integrate in silico analyses, AlphaFold 3 structural predictions and investigate the immune transcriptomes in probands carrying one or more variants. All four variants are inherited through the germline without any evident clinical or gross physiological manifestations in the carriers. As individual variants, not all persons carrying a specific variant showed the same immune transcriptome. However, the presence of activated basal transcriptomes was limited to individuals carrying one of the four variants above. A next step in understanding the role of germline variants will be to understand how and why other factors including both other germline variants as well as environmental and developmental factors influence the likelihood of expression of an activated basal transcriptome.

overall_design: Total RNA-seq was performed on human blood.


title: Immune and Repair Mechanisms Underlying Congenital Chagas

city: Medellin

first: Sneider

middle: Alexander

last: Gutierrez Guarnizo

state: Antioquia

department: Biology

country: Colombia

institute: Universidad de Antioquia

summary: In this study, we conducted integrative high-throughput analyses of peripheral blood and placental tissue from naturally infected patients in Bolivia, the country with the highest prevalence of Chagas disease and, consequently, the population with the greatest potential for congenital transmission worldwide. We compared T. cruzi-infected and uninfected patients to characterize parasite-associated alterations. Infected mothers were further classified as transmitters or non-transmitters based on the infant’s infection status, determined by serological and molecular tests. Transmitter and non-transmitter mothers were compared to understand the molecular mechanism associated with congenital transmission risk.

overall_design:
We performed three transcriptomic analyses:
1) RNA-seq of maternal peripheral blood, including uninfected controls (n = 11), infected non-transmitter mothers (n = 7), and infected transmitter mothers (n = 5
2) RNA-seq of placental tissue, including uninfected controls (n = 9), infected non-transmitter mothers (n = 4), and infected transmitter mothers (n = 7).
3) Spatial transcriptomics of placental tissue, including uninfected controls (n = 1) infected non-transmitter mothers (n = 1).

first: Monica

last: Mugnier

first: Freddy

last: Tinajeros

first: Robert

last: Gilman

first: Natalie

last: Bowman


title: SETDB1/HUSH modulates Xist RNA levels during establishment of X chromosome inactivation [ChIP-Seq, 2]

city: Oxford

first: Mafalda

last: Almeida

address: South Parks Rd

department: Biochemistry

country: United Kingdom

institute: University of Oxford

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The non-coding RNA Xist mediates X chromosome inactivation (XCI) in mammals, functioning in cis to direct heterochromatin formation over a single X chromosome in cells of early female embryos. Prior studies have determined that Xist transcription and turnover are modulated to maintain the correct level of Xist RNA to inactivate a single X chromosome. The underlying molecular mechanisms are poorly understood. In this study we demonstrate that RNA-dependent recruitment of the H3K9me3 methyltransferase SETDB1 and the HUSH complex across the transcribed Xist locus functions to suppress Xist transcription during establishment of XCI. Thus, degron-mediated acute depletion of SETDB1 or core HUSH subunits abrogates allelic H3K9me3 deposition, increasing Xist transcription, accumulation of Xist RNA, and the rate of X chromosome gene silencing. Our findings support a model in which the SETDB1/HUSH pathway coordinates Xist transcription rates to maintain optimal Xist RNA levels, ensuring the silencing of a single X chromosome.

overall_design: Calibrated native ChIP for H3K9me3 in wild-type iXist-ChrXCast, iXist-ChrX129 and TsixStop mESC and NPC differentiation timnepoints and F121-F1 mESC. Calibrated native ChIP for H3K9me3 in FKBP12F36V-SETDB1 iXist-ChrXCast mESC (clones A12A10, P2F7) and in differentiation timepoints in the presence or absence of SETDB1. Calibrated native ChIP for H3K9me3 in FKBP12F36V-KAP1 (clones A4A11,A4C11,A4F3), FKBP12F36V-MPP8 (clones E10 and H1) and FKBP12F36V-TASOR (clones H4 and F8) iXist-ChrXCast mESC in the absence or presence of KAP1, MPP8 and TASOR respectively.

first: Guifeng

last: Wei

first: Adam

last: Cawte

first: Tatyana

last: Nesterova

first: Neil

last: Brockdorff


title: Sir proteins impede, but do not prevent, access to silent chromatin in living Saccharomyces cerevisiae

first: David

middle: J.

last: Clark

address: 6 Center Drive

department: NICHD

institute: NIH

summary: Gene silencing at the mating type loci in budding yeast depends on the Sir proteins. Sir2, Sir3 and Sir4 are indispensable for silencing, whereas Sir1 has a more limited role. The Sir proteins are also involved in repression at telomeres and ribosomal DNA (rDNA) repeats. Proposed mechanisms for Sir-mediated silencing include limiting access to silenced DNA and inhibition of transcript initiation and/or elongation. Using an inducible M.SssI DNA methyltransferase expression system, we showed previously that the silenced mating type loci are methylated at a much slower rate than the rest of the genome in vivo. Here, we show that, in the absence of Sir2, Sir3 or Sir4, the silenced loci and the telomeric X elements are methylated at a similar rate to the rest of the genome, indicating that these Sir proteins impede access, but do not prevent it. Loss of Sir1 has a minor effect. The rDNA repeats are methylated faster in the absence of Sir2 and, to a lesser extent, of Sir3, but not of Sir4. Our data indicate that steric occlusion is unlikely to be the primary mechanism of silencing, since silenced DNA is accessible in vivo, albeit at a slower rate than elsewhere in the genome.

overall_design: Nanopore long-read sequences. For each time course, methyltransferase expression was induced and samples were collected at 0, 30, 60, 120 and 240 min (5 samples) for M.SssI and at 0, 30, 60, 120, 240 and 480 min (6 samples) for M.CviPI . Time courses were conducted in wild-type, sir1∆, sir2∆, sir3∆ and sir4∆ strains for M.SssI and as well as in the wild-type strain for M.CviPI. Two biological replicate experiments were performed.

first: Kenneth

middle: Y

last: Wu

first: Zhuwei

last: Xu

first: Hemant

last: Prajapati

first: Peter

last: Eriksson


title: Interleukin-36 upregulated type-I interferon responses in systemic lupus erythematosis by promoting the accumulation of self-nucleic acids

city: London

first: Francesca

last: Capon

address: Great Maze Pond

institute: King's College London

summary: Several studies have reported an up-regulation of interleukin (IL)-36 in the serum of patients with systemic lupus erythematosus (SLE). Here, we sought to define the mechanisms whereby IL-36 may contribute to the over-activation of type I Interferon (IFN) responses observed in SLE. We carried out single-cell (sc)RNA-seq in healthy peripheral blood mononuclear cells treated with IL-36 (n=5 donors). We compared the genes and transcriptional networks that were induced by IL-36 with those that were upregulated in a published SLE scRNA-seq dataset (n=33 cases and 11 controls). In follow-up studies, we validated the effects of IL-36 on monocytes by real-time PCR (n=9 donors) and flow-cytometry (n=6).   Classical monocytes were the immune population most affected by IL-36 treatment (n=203 Differentially Expressed Genes). In these cells, IL-36 upregulated transcriptional networks (regulons) driven by IRF7, a key activator of type I IFN responses. A similar upregulation of IRF7 regulons was observed in the monocytes of SLE cases, where measurements of IL-36 and IRF7 activity were significantly correlated (r=0.35, P=0.02). Follow-up studies of human monocytes showed that IL-36 downregulates multiple RNAse genes (RNASE1, RNASE6, RNASET2). IL-36 treatment also increased the percentage of apoptotic cells (45% vs 37% in untreated cells; P=0.001), which are a critical source of self-nucleic acids. We find that IL-36 promotes monocyte apoptosis while downregulating self-nucleic acid clearance. Thus, IL-36 contributes to the accumulation of self-nucleic acids, a key driver of type I IFN responses in SLE.

overall_design:
PBMC samples from healthy donors (n=5) and each sample was split in two. Half the cells were treated with IL-36y for 7 hours and the other half left unstimulated (incubated with PBS). Pooled libraries were sequences on an Illumina HiSeq4000 instrument.

***************************************************************

first: Emma

last: Welsh

first: Daniel

last: McCluskey

first: Patrick

last: Baum

first: Myles

last: Lewis


title: Trans-Histone Crosstalk-Mediated Establishment of Mutually Exclusive H3K79 Methylation Zones [ChIP-Seq]

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

institute: Yonsei University

summary: Histone H3 lysine 79 (H3K79) methylation plays critical roles in various cellular processes, including development and DNA repair, potentially through modulation of chromatin structure and gene expression. Despite its importance, the genome-wide distribution patterns, mechanisms of establishment, and functional distinctions among its mono-, di-, and tri-methylated forms (H3K79me1, me2, and me3) remain largely unclear. Here, we generated genome-wide maps of H3K79me1, H3K79me2, and H3K79me3 using ChIP-seq and found that each methylation state is predominantly associated with a unique subset of genes, which we term state-specific H3K79 methylation zones. These zones are mutually exclusive and are stably maintained even during global transcriptional reprogramming. We further demonstrate that H2B ubiquitination mediated by the Rad6-Bre1 complex is essential for the integrity of these methylation zones. Specifically, deletion of RAD6 leads to the complete loss of the H3K79me3 zone and its conversion into an H3K79me1-enriched region. Interestingly, the H3K79me1 zone is also significantly diminished upon RAD6 deletion, indicating that H2B ubiquitination supports both the maintenance and establishment of specific methylation zones. Similar disruption of the H3K79me1 landscape is observed upon loss of H4K16 acetylation. Functionally, H3K79me1 and H3K79me3 appear to have opposing roles in transcriptional regulation as loss of H3K79 methyltransferase Dot1 results in transcriptional activation of genes within the H3K79me1 zone and repression of genes within the H3K79me3 zone. Together, our findings reveal that distinct H3K79 methylation states define specific and functionally divergent chromatin domains, whose establishment and maintenance depend on trans-histone crosstalk and contribute to opposing transcriptional outputs.

overall_design: Chromatin immunoprecipitation sequencing (ChIP-seq) was performed in yeast to profile genome-wide distributions of H3K79me3, H3K79me2, and H3K79me1. Changes in H3K79me2, H3K79me1, and Dot1 occupancy upon RAD6 deletion were analyzed. Additionally, the dynamics of H3K79 methylation before and after nutrient starvation were examined.

first: Na Hyun

last: Park

first: Hwa-Ryeon

last: Kim

first: Jae-Seok

first: TaeSoo


title: Gene expression profile of HeLa cells overexpressing GFP tagged Nup88

city: Kumamoto

first: Masaki

last: Makise

state: Kumamoto

address: 4-22-1 Ikeda, Nishi-ku

country: Japan

institute: Sojo University

summary: Elevated expression of Nup88 is often observed in various cancers and correlates with poor prognosis.  However, the underlying molecular mechanism by which Nup88 induces cancer malignancy remains unclear.  Considering the possibility that this occurs due to changes in gene expression, we established HeLa R19 cells that stably overexpress either GFP or GFP-tagged Nup88 and screened for genes whose expression changes in a Nup88-dependent manner.  Consequently, we found a significant downregulation of KIF7, which encodes a regulator of the Hedgehog signaling pathway. The co-overexpression of Kif7 in HeLa stable cell line overexpressing Nup88 suppressed Nup88-dependent migration activity, suggesting that the downregulation of KIF7 contributes to Nup88-induced cancer malignancy/cell migration.

overall_design: Total RNA was extracted from a stable HeLa cell line overexpressing GFP or GFP-tagged Nup88 grown in standard culture medium for 48 hr.


title: SETDB1/HUSH modulates Xist RNA levels during establishment of X chromosome inactivation [ChIP-Seq]

first: Mafalda

last: Almeida

overall_design: Calibrated single crosslinked ChIP for RNAPol II, RNA PolII Ser5P, RNA PolII Ser2P in FKBP12F36V-SETDB1 iXist-ChrXCast mouse embryonic stem cells (clones A12A10, P2F7 and G6D2) expressing Xist under a doxycycline inducible promoter in the presence and absence of SETDB1. Double crosslinked ChIP for MPP8 and KAP1 in FKBP12F36V-SETDB1 iXist-ChrXCast mouse embryonic stem cells (clones A12A10 and P2F7) expressing Xist under a doxycycline inducible promoter in the presence and absence of SETDB1.

first: Guifeng

last: Wei

first: Adam

last: Cawte

first: Tatyana

first: Neil


title: Effects of HDAC gene knockdowns in human stem cell derived cardiomyocytes

city: Washington

first: Emilia

last: Entcheva

state: DC

address: 800 22nd Street NW SEH 5000

department: Biomedical Engineering

institute: George Washington University

summary: Histone deacetylases (HDACs) play a major role in a wide range of cellular and developmental processes, often as master regulators of gene transcription. These epigenetic modifiers, which include eleven canonical HDACs and seven sirtuins (SIRTs), are commonly studied in cancer, especially by using nonselective HDAC inhibitor drugs. However, HDACs and SIRTs are also thought to be influential in cardiac function and pathology, yet the specific roles of individual HDACs have not been robustly probed in cardiomyocytes. In this study, we report the transcriptomic effects of individual HDAC/SIRT knockdowns in human induced pluripotent stem cell derived cardiomyocytes.

overall_design: RNA-seq profiling of cardiac cell syncitia after systematic knockdown of inidividual HDAC and SIRT genes

first: Maria

middle: R

last: Pozo

first: Michael

middle: P

last: Pressler

first: Anelia

last: Horvath


title: SETDB1/HUSH modulates Xist RNA levels during establishment of X chromosome inactivation

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

overall_design: Refer to individual Series


title: SETDB1/HUSH modulates Xist RNA levels during establishment of X chromosome inactivation [4sU-seq]

overall_design: 4sU-seq of FKBP12F36V-SETDB1 iXist-ChrXCast mouse embryonic stem cells (clones A12A10, P2F7 and G6D2) expressing Xist under a doxycycline inducible promoter in the presence and absence of SETDB1.

last: Nesterova

last: Brockdorff


title: Comparative Analysis of Oral and Skin Keratinocytes Responses to Oxidative Stress

city: Suzhou

first: Yixuan

last: Zhang

address: No.9 Chongwen Road

institute: Suzhou University

summary: Oxidative stress caused by excessive reactive oxygen species (ROS) disrupts skin and oral epithelial homeostasis and contributes to skin aging, inflammation, periodontitis, and mucosal injury. As the principal defenders in both tissues, keratinocytes may exhibit divergent responses to oxidative stress. However, most existing studies have examined skin or oral keratinocytes in isolation, with few comparative investigations of their tolerance, repair capacity, and antioxidant mechanisms under oxidative stress. In this study, we systematically compared immortalized oral keratinocytes (TIGK) and skin keratinocytes (HaCaT) under hydrogen peroxide (H₂O₂)–induced oxidative stress. Functional analyses, including cell survival, ROS accumulation, wound healing, and proliferation recovery assays, were combined with transcriptomic profiling to evaluate differences in antioxidant and pro-oxidant systems. TIGK exhibited significantly higher survival rates, lower ROS accumulation, and superior migratory and proliferative recovery compared with HaCaT after oxidative insult. Transcriptomic analysis further revealed that TIGK consistently expressed higher levels of antioxidant genes and enzymes. In contrast, HaCaT showed greater ROS accumulation and relatively limited antioxidant defenses. Oral and skin keratinocytes adopt distinct adaptive mechanisms under oxidative stress. The intrinsic redox advantage of oral keratinocytes provides new insights into their rapid wound-healing capacity and may inform strategies to enhance epithelial resilience.

overall_design: Total RNA was extracted from HaCaT and TIGK cells treated with 5 mM H₂O₂ for 3 h or left untreated (n = 3 per group, 12 samples in total)..


title: Impact of ECTV C15 expression on the development of CD8+ effector T cells [d10]

city: Philadelphia

first: Laurence

last: Eisenlohr

state: PA

address: 3615 Civic Center Blvd

department: Pathology and Laboratory Medicine

institute: University of Pennsylvania

summary: Orthopoxviruses, such as variola and Mpox, encode a myriad of immunomodulatory proteins to promote pathogenesis. One notable family is the B22 family of proteins, which are highly conserved surface glycoproteins that potently inhibit T cell activation in vitro and ex vivo.  However, there has been limited work investigating the impact of B22 proteins on both CD4+ and CD8+ T cell responses in vivo. Therefore, we used ectromelia (ECTV) as a natural host-pathogen model to investigate the impact of its B22 protein, C15, on T cell responses in vivo. To broadly investigate the impact of C15 on CD8+ effector (CD62L-CD44+) T cell development during the contraction phase, we performed bulk RNA-seq on splenic CD8+ effector T cells 10 days post-infection with either WT ECTV or ECTV∆C15.

overall_design: 3' mRNA-seq of CD8+ effector (CD62L-CD44+) T cells derived from ECTV WT and ECTV∆C15 infection 10 dpi

first: Stephen

last: Carro

middle: C


title: Impact of ECTV C15 expression on the early immune response in the popliteal lymph node (scRNA-seq)

summary: Orthopoxviruses, such as variola and Mpox, encode a myriad of immunomodulatory proteins to promote pathogenesis. One notable family is the B22 family of proteins, which are highly conserved surface glycoproteins that potently inhibit T cell activation in vitro and ex vivo. Using the model poxvirus, ectromelia (ECTV), our lab has demonstrated that its B22 protein, C15, is capable of inhibiting both CD4+ and CD8+ T cells both in vitro and ex vivo, similar to other B22 proteins. Furthermore, we have also identified an additional function of C15: antagonism of NK cells during early infection. Specifically, C15 antagonizes the engagement of NK cells with infected cells in the popliteal lymph node during the innate immune response to infection. This inhibition by C15 promotes viral dissemination and replication, such that in the absence of C15, viral replication is significantly stunted. To date, there has not been any work investigating the mechanisms underlying this NK cell inhibition. To broadly explore the cell type-specific changes occurring during this critical window, we performed single cell RNA-seq on popliteal lymph nodes at 24 and 48 hours post-infection.

overall_design: scRNA-seq of immune cell populations in the popliteal lymph node 24 and 48 hours post-infection with ECTV WT or ECTV∆C15


title: SETDB1/HUSH modulates Xist RNA levels during establishment of X chromosome inactivation [RNA-Seq]


title: DNTTIP1 Drives Leukemogenesis Through HDAC1-Dependent Epigenetic Silencing of BMF [RNA-Seq, 2]

city: Harbin

first: Huitao

last: Fan

state: Heilongjiang

address: 23 Youzheng street

department: NHC Key Laboratory of Cell Transplantation

institute: The First Affiliated Hospital of Harbin Medical University

summary: Acute leukemia is a highly aggressive malignancy with significant unmet therapeutic needs, partly due to epigenetic dysregulation. Here, we uncover deoxynucleotidyl transferase terminal-interacting protein 1 (DNTTIP1) as a previously unrecognized epigenetic regulator crucial for the survival of leukemic cells. Mechanistically, depletion of DNTTIP1 impairs histone deacetylase 1 (HDAC1) recruitment to chromatin, leading to hyperacetylation of histone H3 lysine 27 (H3K27) at the promoter of BCL2 modifying factor (BMF) and reactivating this pro-apoptotic effector. The upregulated BMF competitively disrupts BCL2-mediated survival pathways, triggering coordinated autophagy and apoptosis. This dual cell death mechanism is critical for leukemia suppression. Our preclinical evidences demonstrate that combined HDAC1 and BCL2 inhibition exerts synergistic anti-leukemic effects, a therapeutic strategy currently under clinical evaluation. Furthermore, we demonstrate that PARP inhibitors profoundly synergize with HDAC1/BCL2 inhibition through interference with DNA damage repair, creating a novel three-pronged therapeutic strategy. Our findings identifies the DNTTIP1-HDAC1-BMF axis as a pivotal epigenetic vulnerability in acute leukemia and reveal its functional roles in sustaining leukemogenesis. This work offers a validated biological framework for advancing this targeted combination therapy into clinical trials.

overall_design: RNA-seq profiling of RS4;11 cells with DNTTIP1 knockdown (sh4) versus empty vector control (pLKO) reveals genome-wide transcriptional alterations induced by DNTTIP1 depletion.

first: Ruolin

last: Xiu

first: Yuzhu

last: Ma

first: Yueying

last: Gao

first: Yao

last: Chen

first: Xinyu

last: Li

first: Yue

last: Wu

first: Meiling

last: Sun

first: Qizhao

first: Shuqian

last: Xu

first: Shengjin

first: Yongsheng


title: DNTTIP1 Drives Leukemogenesis Through HDAC1-Dependent Epigenetic Silencing of BMF [Cut & Tag, RS4;11 , HA-DNTTIP1]

overall_design:
CUT&Tag profiling with an anti-HA antibody in two single-clone RS4;11 cell lines stably overexpressing HA-tagged DNTTIP1 identifies direct genome-wide binding sites of DNTTIP1.
CUT&Tag of HA (DNTTIP1)-targeted in RS4;11 cells


title: Structures of Naked Mole-Rat, Tuco-Tuco, and Guinea Pig Ribosomes: Is rRNA Fragmentation Linked to Translational Fidelity?

city: NEW YORK

first: Joachim

last: Frank

state: NEW YORK

address: 630 WEST 168TH ST.

institute: Columbia University

summary: Ribosomes are central to protein synthesis in all organisms. Among mammals, the ribosome functional core is highly conserved. Remarkably, two rodent species, the naked mole-rat (NMR) and tuco-tuco display fragmented 28S rRNA, coupled with high translational fidelity and long lifespan. The unusual ribosomal architecture in the NMR and tuco-tuco has been speculated to be linked to high translational fidelity. Here we show, by single-particle cryo-electron microscopy (cryo-EM), that despite the fragmentation of their rRNA, NMR and tuco-tuco ribosomes retain their core functional architecture. Compared to ribosomes of the guinea pig, a phylogenetically related rodent without 28S rRNA fragmentation, ribosomes of NMR and tuco-tuco exhibit poorly resolved, certain expansion segments. In contrast, the structure of the guinea pig ribosome shows high similarity to human ribosome. Enhanced translational fidelity in the NMR and tuco-tuco may stem from subtle, allosteric effects in dynamics, linked to rRNA fragmentation.

overall_design: For STRDPOLYA: We use poly-A pull-down to enrich mRNAs from total RNA samples,then proceed with library construction using Illumina TruSeq chemistry. For RIBOZERO: We use ribosomal depletion to remove rRNAs from total RNA samples, then proceed with library construction using Illumina TruSeq chemistry.Libraries are then sequenced using Illumina NovaSeq 6000. We multiplex samples in each lane, which yields targeted number of paired-end 100bp reads for each sample.

first: Cristina

last: Gutierrez-Vargas

first: Swastik

last: De

first: Suvrajit

last: Maji

first: Zheng

last: Liu

first: Zhonghe

last: Ke

first: Martina

last: Nieß

first: Andrei

last: Seluanov

first: Vera

last: Gorbunova


title: DNTTIP1 Drives Leukemogenesis Through HDAC1-Dependent Epigenetic Silencing of BMF [Cut & Tag, RS4;11]

first: Huitao

last: Fan

overall_design:
CUT&Tag profiling of DNTTIP1 knockdown (sh4) versus empty vector control (pLKO) RS4;11 cells reveals altered H3K27ac enrichment.
CUT&Tag of histone modification H3K27ac in RS4;11 cells

first: Ruolin

last: Xiu

first: Yuzhu

first: Yueying

first: Yao


title: Impact of ECTV C15 expression on the development of CD4+ effector T cells

first: Laurence

last: Eisenlohr

summary: Orthopoxviruses, such as variola and Mpox, encode a myriad of immunomodulatory proteins to promote pathogenesis. One notable family is the B22 family of proteins, which are highly conserved surface glycoproteins that potently inhibit T cell activation in vitro and ex vivo.  However, there has been limited work investigating the impact of B22 proteins on both CD4+ and CD8+ T cell responses in vivo. Therefore, we used ectromelia (ECTV) as a natural host-pathogen model to investigate the impact of its B22 protein, C15, on T cell responses in vivo. To broadly investigate the impact of C15 on CD4+ effector (CD62L-CD44+) T cell development, we performed bulk RNA-seq on splenic CD4+ effector T cells 7 days post-infection with either WT ECTV or ECTV∆C15.

overall_design: 3' mRNA-seq of CD4+ effector (CD62L-CD44+) T cells derived from ECTV WT and ECTV∆C15 infection 7 dpi

first: Stephen

last: Carro


title: Human CCR4-NOT is a global regulator of gene expression and is a novel silencer of retrotransposon activation [TT-seq]

city: State College

first: Shardul

last: Kulkarni

address: 463 North Frear Laboratory

institute: Penn State University

summary: CCR4-NOT regulates multiple steps in gene regulation, including transcription, mRNA decay, protein ubiquitylation, and translation. It has been well studied in budding yeast; however, relatively less is known about its regulation and functions in mammals. To characterize the functions of the human CCR4-NOT complex, we developed a rapid auxin-induced degron system to deplete CNOT1 (the scaffold of the complex) and CNOT4 (E3 ubiquitin ligase) in cell culture. To investigate the role of CCR4-NOT in transcription, we used transient transcriptome sequencing (TT-seq) to measure ongoing RNA synthesis. Depletion of either subunit resulted in increased RNA synthesis of several thousand genes. In contrast to most of the genome, a rapid reduction in the synthesis of KRAB-Zinc-Finger-proteins (KZNFs) genes, especially those clustered on chromosome 19, was observed. KZNFs are transcriptional repressors of retro-transposable elements (rTEs), and consistent with the decreased KZNFs expression, we observed a significant and rapid activation of rTEs, mainly Long interspersed Nuclear Elements (LINEs). Our data reveal that CCR4-NOT regulates gene expression and silences retrotransposons across the genome by maintaining KZNF expression. These data establish CCR4-NOT as a global regulator of gene expression, and we have identified a novel mammalian-specific function of the complex, the suppression of rTEs.

overall_design:
To study the roles of human CCR4-NOT complex, we generated auxin inducible degron tagged cells at the genomic locus of CNOT1 and CNOT4 genes.
Cells were treated with auxin to deplete CNOT1 or CNOT4, and total RNA was extracted from the cells to analyze gene expression changes.
We performed RNA-seq to investigate the effects of CNOT1 or CNOT4 depletion on nascent RNA synthesis (TT-seq).
Differential expression analysis was carried out on RNA-seq data obtained from multiple timepoints/treatments.

first: Aswathy

last: Sebastian

first: Joseph

last: Reese


title: Trans-Histone Crosstalk-Mediated Establishment of Mutually Exclusive H3K79 Methylation Zones [RNA-Seq]

city: Seoul

first: Jae Seok

last: Roe

overall_design: Analysis of transcriptional responses in wild type and dot1Δ strains during nutrient starvation.

first: Na Hyun

last: Park

first: Hwa-Ryeon

last: Kim

first: Jae-Seok

first: TaeSoo


title: ADNP regulates chromatin architecture and lineage fidelity during neural differentiation

first: Phillip

last: Wulfridge

state: Pennsylvania

address: 3601 Spruce St

institute: The Wistar Institute

summary: Activity-dependent neuroprotective protein (ADNP) is frequently mutated in autism spectrum disorder and causal in its namesake neurodevelopmental syndrome. In mouse embryonic stem cells (mESCs), ADNP forms the ChAHP complex to function in gene regulation as well as genome organization, where it competes with binding of the architectural protein CTCF. However, it is unclear whether these functions persist in differentiated cells. To shed light on this question, we have established an ADNP-degron cell line to examine CTCF binding, gene expression and chromatin organization upon ADNP loss in neural progenitor cells (NPCs).

overall_design: ChIP, RNA-seq, and Hi-C was performed on ADNP-degron E14 mouse embryonic stem cells and neural progenitor cells. Cells with or without treatment with asunaprevir and dTAG-13 were collected for genomics experiments.

first: Nathaniel

last: Rell

first: John

last: Doherty

first: Kuo-Chen

last: Fang

first: Kavitha

last: Sarma


title: 5’tRNA-derived fragments modulate 𝛽-cell homeostasis and islet macrophage activation in type 2 diabetes [iMAC]

city: Lausanne

first: Cristina

last: Cosentino

address: Rue du Bugnon 9

department: Department of fundamental neurosciences

country: Switzerland

institute: Université de Lausanne

summary: During obesity and type 2 diabetes, pancreatic β-cells face chronic environmental stress, while islet-resident macrophages (iMACs) undergo metabolic reprogramming that exacerbates β-cell dysfunction. Stress-induced cleavage of transfer RNAs (tRNAs) generates tRNA-derived fragments (tRFs), whose role in this context is not fully understood. We identify elevated levels of 5’tRFGlu(CTC) and 5’tRFGly(GCC) in β-cells and iMACs from db/db mice and in islets from type 2 diabetic (T2D) patients. Notably, 5’tRFGlu(CTC) is also induced under prediabetic conditions and inversely correlates with insulin secretion. Lipotoxic stress triggers their production via Angiogenin-mediated cleavage. Blocking 5’tRFGlu(CTC) in islets protects against β-cell apoptosis and restores insulin secretion under palmitate stress. Using a β-cell/macrophage co-culture system, we show that β-cell contact shapes a unique macrophage phenotype (iMAC-like) that shifts upon palmitate exposure—recapitulating in vivo observations. Inhibiting 5’tRFGlu(CTC) in iMAC-like cells prevents this activation switch, reduces β-cell stress, and improves insulin secretion. Mechanistically, 5’tRFGlu(CTC) interacts with RNA-binding proteins to regulate transcriptional and post-transcriptional pathways linked to immune activation, ECM remodeling, neurogenesis, and oxidative stress. Our study identifies 5’tRFs as key mediators of islet microenvironment remodeling in diabetes, offering new insights into intercellular stress signaling in metabolic disease.

overall_design: tRF profiling of Cd45+, F4/80+, Cd11b+ and Cd11c+ islet macrophages from 8 week-old db/db mice (genetic background BKS.Cg-Dock7m+/+LeprdbJ) and wild type controls (genetic background BKS.Cg-Dock7m+/+) isolated by FACS. Small RNA sequencing data were annotated against the dataset from from http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/eukaryota/Mmusc39/Mmusc39-summary.html. High confidence tRNA sequences and mature tRNA sequences were retained, and mtRNA seqences from http://mttrna.bioinf.uni-leipzig.de/mtDataOutput/Search were added. Accesses done in February 2022.


title: Aged Differentiated Cells Reverse into Native Stemness-Like State by Niche Cytokines to Sustain Lifelong Homeostasis and Tissue Repair

city: Haifa

first: Shalini

last: Dimri-Wagh

state: Haifa

address: 1 Efron Street

department: Department of  Genetics and Developmental Biology

country: Israel

institute: Technion Israel Institute of Technology

summary: To study the molecular mechanisms driving dedifferentiation and stem cell plasticity during tissue regeneration, we performed single-cell RNA sequencing at multiple time points-Day 2, Day 5, Day 10, and Day 40,following complete ablation of the limbal stem cell (LSC) population. The primary goal was to characterize the transcriptional reprogramming processes that enable differentiated epithelial cells to reacquire stem cell-like properties and restore the LSC pool. Specifically, we aimed to determine (1) the extent to which dedifferentiated cells recapture native stem cell phenotypes, (2) whether this plasticity is maintained in late differentiated and aged cells, and (3) the niche signals that regulate this process. Our data reveal that differentiated cells undergo extensive transcriptional remodeling, becoming virtually indistinguishable from native LSCs, and functionally sustain long-term tissue homeostasis and repair after repeated injury. Remarkably, this plasticity is retained even in late differentiated and aged cells. Mechanistically, we identify macrophage-derived cytokines as key niche factors promoting dedifferentiation and stemness reacquisition. This dataset provides a comprehensive transcriptional resource of corneal regeneration, offering insights into stem cell plasticity and immune-niche interactions with implications for regenerative medicine and limbal stem cell deficiency therapies.

overall_design: To investigate dedifferentiation during limbal regeneration, the limbal epithelium-including the marginal conjunctiva and peripheral cornea was surgically removed using a rotating ophthalmic Alger brush. At defined time points post-injury (Days 2, 5, 10, and 40), the regenerating limbal epithelial tissue along with the underlying stromal tissue (~0.5 mm) was harvested. Additionally, limbal regions from uninjured eyes were collected as controls. Tissues were enzymatically dissociated using Collagenase A and Trypsin into single-cell suspensions and subjected to single-cell RNA sequencing (scRNA-seq) to profile dynamic transcriptional changes occurring during the dedifferentiation process.

last: Dimri Wagh

first: Swarnabh

last: Bhattacharya

first: Gharam

last: Yassin

first: Ofir

last: Shorer

first: Aya

last: Amitai Lange

first: Anna

last: Altshuler

first: Shira

last: Hadad Porat

first: Keren

last: Yizhak

first: Yuval

last: Shaked

first: Michael

last: Mimouni

first: Beatrice

last: Tiosano

first: Ramez

last: Barbara

first: Ruby

last: Shalom Feuerstein


title: DNTTIP1 Drives Leukemogenesis Through HDAC1-Dependent Epigenetic Silencing of BMF [RNA-Seq, 1]

first: Huitao

last: Fan

overall_design: RNA-seq profiling of RS4;11 cells treated with the HDAC inhibitor MS-275 (1 μM, 48 hours) versus DMSO control reveals genome-wide transcriptional alterations induced by HDAC inhibition.

first: Ruolin

last: Xiu

first: Yuzhu

last: Ma

first: Yueying

last: Gao

first: Yao

last: Chen

first: Xinyu

last: Li

first: Yue

last: Wu

first: Meiling

last: Sun

first: Qizhao

first: Shuqian

last: Xu

first: Shengjin

first: Yongsheng


title: Impact of ECTV C15 expression on the development of CD8+ effector T cells

first: Laurence

last: Eisenlohr

summary: Orthopoxviruses, such as variola and Mpox, encode a myriad of immunomodulatory proteins to promote pathogenesis. One notable family is the B22 family of proteins, which are highly conserved surface glycoproteins that potently inhibit T cell activation in vitro and ex vivo.  However, there has been limited work investigating the impact of B22 proteins on both CD4+ and CD8+ T cell responses in vivo. Therefore, we used ectromelia (ECTV) as a natural host-pathogen model to investigate the impact of its B22 protein, C15, on T cell responses in vivo. To broadly investigate the impact of C15 on CD8+ effector (CD62L-CD44+) T cell development, we performed bulk RNA-seq on splenic CD8+ effector T cells 7 days post-infection with either WT ECTV or ECTV∆C15.

overall_design: 3' mRNA-seq of CD8+ effector (CD62L-CD44+) T cells derived from ECTV WT and ECTV∆C15 infection 7 dpi

first: Stephen

last: Carro


title: 5’tRNA-derived fragments modulate 𝛽-cell homeostasis and islet macrophage activation in type 2 diabetes [beta]

first: Cristina

last: Cosentino

overall_design: tRF profiling of pancreatic beta cells from 8 week-old db/db mice (genetic background BKS.Cg-Dock7m+/+LeprdbJ) and wild type controls (genetic background BKS.Cg-Dock7m+/+) isolated by FACS. Small RNA sequencing data were annotated against the dataset from from http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/eukaryota/Mmusc39/Mmusc39-summary.html. High confidence tRNA sequences and mature tRNA sequences were retained, and mtRNA seqences from http://mttrna.bioinf.uni-leipzig.de/mtDataOutput/Search were added. Accesses done in February 2022.


title: A Single-Cell and Spatial Atlas of Early Human Olfactory Development

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: Merfish 300 gene-panel experiment of human fetal head section spanning olfactory epithelium at post-conceptional weeks 9 and 11

overall_design: Total of 5 sections

first: K

first: Y

last: Mbouamboua

first: P

last: Barbry

last: Giacobini


title: TET3-mediated DNA demethylation contributes to the formation of stable epialleles in tomato

city: Coventry

first: Javier

last: Antunez Sanchez

address: Gibbet Hill Campus

department: Life Sciences

institute: University of Warwick

overall_design: Refer to individual Series


title: Impact of ECTV C15 expression on the early immune response in the popliteal lymph node (bulk RNA-seq)

summary: Orthopoxviruses, such as variola and Mpox, encode a myriad of immunomodulatory proteins to promote pathogenesis. One notable family is the B22 family of proteins, which are highly conserved surface glycoproteins that potently inhibit T cell activation in vitro and ex vivo. Using the model poxvirus, ectromelia (ECTV), our lab has demonstrated that its B22 protein, C15, is capable of inhibiting both CD4+ and CD8+ T cells both in vitro and ex vivo, similar to other B22 proteins. Furthermore, we have also identified an additional function of C15: antagonism of NK cells during early infection. Specifically, C15 antagonizes the engagement of NK cells with infected cells in the popliteal lymph node during the innate immune response to infection. This inhibition by C15 promotes viral dissemination and replication, such that in the absence of C15, viral replication is significantly stunted. To date, there has not been any work investigating the mechanisms underlying this NK cell inhibition. To broadly explore the transcriptional changes occurring during this critical window, we performed bulk RNA-seq on popliteal lymph nodes at 48 hours post-infection.

overall_design: 3' mRNA-seq of immune cell populations in the popliteal lymph node 48 hours post-infection with ECTV WT or ECTV∆C15


title: Differentily expressed genes of homozygotes Cmnor; CmNOR/Cmnor heterozygotes and WT plants

city: Beijing

first: Jinfang

last: Wang

address: No.50 Zhanghua Road, Haidian District

institute: Beijing Academy of Agricultural and Forestry Sciences

summary: Oriental melon, a climacteric fruit prized for its superior quality, faces limited shelf life. Although knockout NON-RIPENING (CmNOR) prolongs storage duration at the expense of quality loss, the potential of its direct agricultural application to reconcile this conflict remains uninvestigated. Through crossing homozygotes Cmnor and wild-type plants, we created CmNOR/Cmnor heterozygotes displaying 6-day delayed ripening and 3-5 day extended shelf life at 20°C storage while preserving fruit quality. Ethylene treatment accelerated softening but failed to restore quality parameters of heterozygotes and homozygotes. Transcriptomic analysis revealed homozygotes showed >10-fold expression variations versus WT in quality-associated genes (e.g., carotenoid biosynthesis), which diminished to ~2-fold differences in heterozygotes. Storage-phase differential genes clustered in water regulation and cell wall modification pathways, with heterozygous-WT expression disparities gradually decreasing over time. The CmNOR dosage effect dynamically modulates interconnected quality and preservation networks, proposing an editing-based solution to overcome the storability-quality dichotomy in climacteric fruits.

overall_design: To explore the differently expressed genes between homozygotes Cmnor; CmNOR/Cmnor heterozygotes and WT flesh during fruit ripening and storage

first: Yong


title: Obesity imprints CD4 T cells via DNA methylation, perpetuating immune dysregulation

city: Birmingham

first: Adam

last: Croft

state: Please Select

address: Birmingham

institute: University of Birmingham

summary: Obesity represents a major global healthcare crisis, with childhood obesity rising at an alarming rate. Children with obesity are highly likely to carry it into adulthood, bringing numerous associated health risks. Even more troubling is the emerging understanding of “obesity memory”, which contributes to the frequent issue of weight regain. Here, we show that obesity imprints CD4 T cells through DNA methylation, leading to a long-time lag, spanning years, before adaptive immune homeostasis is restored after weight loss. Differential DNA methylation analysis highlighted autophagy and immune senescence as key mechanisms underpinning this memory of obesity in CD4 T cells. Additionally, saturated fatty acids, in particular palmitate, drive epigenetic changes in CD4 T cells, perpetuating this altered state. Importantly, we identified molecular targets (i.e., Stk26 and Cdkn1c) underpinning key cell functions (autophagy and immune senescence) that could be targeted to promote a return to immune homeostasis alongside weight loss.

overall_design: Mice were placed either on a 14 week chow diet (CD) – 10% lipid (Test diet, USA, T-5755-1817109),14 week high-fat diet (HFD) – 60% lipid (Test diet, USA, T-58Y1-58126) or had a diet reversal (HFD-RE) with 8 weeks of HFD followed by 6 of chow diet. At week 13, mice were subjected to allogeneic immunisation by intraperitoneal injection with a mixture of splenocytes isolated from WT BALB/c and CBA mice (1:1 ratio, 1.5 x106 cell). Spleens were harvested at the end of week 14. Memory CD4 T cells were isolated from spleens using the EasySep Mouse Memory CD4 T cell isolation kit (Stemcell Technologies) according to the manufacturer’s instructions. Total RNA was isolated from the splenic memory CD4 T cells using the RNeasy micro kit (Qiagen) according to the manufacturer's instructions. Quality control check of RNA was done using the Qubit RNA High Sensitivity (HS) and TapeStation HS assays. 40 ng RNA from each sample was run for mRNA-expression analysis on the nCounter-based NanoString instrument (NanoString Technologies) using the nCounter® Mouse PanCancer Immune Profiling Panel (770 targets) (NanoString technologies).

first: C

last: Mahony

last: Mauro


title: 5’tRNA-derived fragments modulate 𝛽-cell homeostasis and islet macrophage activation in type 2 diabetes [RNAseq_BMDM]

overall_design: Bone marrow derived macrophages were transfected with an antisense of control (ctr) or with antisense targeting 5'tRFGlu(CTC) (Glu) and then polarized into M2 macrophages. Total RNA was purified with miRNeasy micro kit (Qiagen). Illumina Strand mRNA libraries were prepared and sequenced on NovaSeq 6000 sequencer.

first: Romano

last: Regazzi


title: 2′-O-methylation-dependent installation of N2-methylguanosine in the U6 internal stem loop facilitates efficient spliceosome assembly

city: Göttingen

first: Katherine

last: Bohnsack

address: Humboldtallee 23

institute: University Medical Centre Göttingen

summary: The internal stem loop (ISL) of the human U6 snRNA, which catalyzes pre-mRNA splicing, contains LARP7-dependent, snoRNA-guided 2?-O-methylations and an N2-methylguanosine (m2G) that is required for splicing of weak splice sites. Here, we show that installation of m2G72 by the THUMPD2-TRMT112 methyltransferase complex is one of the last maturation events during U6 snRNP biogenesis. We dissect features of THUMPD2 required for association with U6 and present an experimentally validated model of the THUMPD2-TRMT112-U6 complex. Using in vitro methylation assays as well as a newly developed m2G-sensitive deoxyribozyme to monitor U6-m2G72 levels in cellular RNAs, we reveal that 2?-O-methylations within the U6 ISL enhance methylation of G72. We show that m2G72 and the 2?-O-methylations in U6 independently and interdependently influence alternative splicing. Furthermore, our data demonstrate that 2?-O-methylations in the ISL are required for incorporation of U6 into snRNPs whereas m2G72 influences the progression of the U6 snRNP into larger assemblies, highlighting distinct roles of these modifications during spliceosome assembly.

overall_design: mRNA-seq was performed on RNAs from wild-type (WT) or THUMPD2 KO HCT116 cells that had been treated with non-target siRNAs or those targeting LARP7.

first: Nicole

last: Kleiber

first: Lydia

last: Herzel


title: DNTTIP1 Drives Leukemogenesis Through HDAC1-Dependent Epigenetic Silencing of BMF [ATAC-Seq]

first: Huitao

last: Fan

overall_design: Comparative ATAC-seq of DNTTIP1 knockdown (sh4) versus empty vector control (pLKO) RS4;11 cells reveals differential chromatin accessibility patterns.

first: Ruolin

last: Xiu

first: Yuzhu

last: Ma

first: Yueying

last: Gao

first: Yao

last: Chen

first: Xinyu

last: Li

first: Yue

last: Wu

first: Meiling

last: Sun

first: Qizhao

first: Shuqian

last: Xu

first: Shengjin

first: Yongsheng


title: 5’tRNA-derived fragments modulate 𝛽-cell homeostasis and islet macrophage activation in type 2 diabetes - transcriptomic

first: Cristina

last: Cosentino

overall_design: Mouse pancreatic islets were isolated and dispersed. Mouse islet cells were transfected with antisense oligonucleotides (Ctr, 𝛂Glu) and treated with BSA or palmitate (PA). Total RNA was purified with miRNeasy micro kit (Qiagen). Illumina Strand mRNA libraries were prepared and sequenced on Aviti sequencer.


title: An organoid model of the human adrenal cortex identifies drivers of steroidogenesis and zonation [spatial]

city: Basel

first: Quan

address: Grenzacherstrasse 124

institute: Institute of Human Biology (IHB)

summary: The adrenal cortex is the main source of steroid hormones including aldosterone, cortisol and androgens. These hormones play a crucial part in maintaining blood pressure, regulating metabolism and sexual development, respectively. The growth factors and transcriptional networks governing adrenal zonation remain poorly understood. Here, we established organoids derived from primary developing human adrenal cortex tissue. These tissue-resident stem cell-derived organoids display longevity and are composed of mature cells producing different steroid hormones. We use spatial transcriptomics to identify zonated growth factors in tissue, and explore the role of 42 different molecules in controlling cell identity and steroidogenesis using organoids. We find that a combination of WNT, cAMP, BMP/TGFβ and nuclear receptors can regulate cell states representing the different cortical zones. Together, human adrenal cortex organoids represent a complex cellular model to study adrenal biology and disease.

overall_design: Normal fetal and adult adrenal gland tissue.

first: Ninouk

last: Akkerman

first: Laura

last: Gaspa-Toneu

first: Alberto

last: Valdeolivas

first: Irineja

last: Cubela

first: Marion

last: Richardson

first: Nicolas

last: Giroud

first: J Gray

last: Camp

first: Joep

last: Beumer


title: The Ly6Ghigh neutrophil subset occupying the early metastatic niche dictates breast cancer lung metastasis via cathelicidin-induced CD8+ T cell death_CD8+ T cell

city: Chongqing

first: rui

last: wang

state: chongqing

address: No.1, Yi-Xue-Yuan Road, Yu-zhong District

institute: Chongqing Medical University

summary: Lung metastasis is a leading cause of breast cancer (BC)-related mortality, driven by the immunosuppressive traits of the metastatic tumor microenvironment. However, the mechanisms underlying cell-cell crosstalk in shaping immune evasion within the metastatic niche remain poorly defined. Here, we try to decipher the interaction between the lymphocyte antigen 6 complex locus G6Dhigh (Ly6Ghigh) neutrophil subset and cluster of differentiation 8+ T lymphocytes (CD8+ T cells), and their role in promoting pulmonary metastasis of BC.

overall_design: We characterized neutrophil heterogeneity and their functional dynamics using single-cell RNA sequencing (scRNA-seq) and murine models of BC lung metastasis. Genetic tools included cathelicidin antimicrobial peptide knocked out (Cramp)-/- mice to dissect the role of cathelicidin. Spatial co-localization of apoptotic CD8⁺ T cells and neutrophil extracellular traps (NETs) was analyzed via multiplex immunofluorescence while molecular interactions were probed using protein binding assays.

first: Rui

last: Wang


title: The Ly6Ghigh neutrophil subset occupying the early metastatic niche dictates breast cancer lung metastasis via cathelicidin-induced CD8+ T cell death_neutrophil


title: Mechanisms and mouse modeling of tumor dormancy through distinct immune niche formation [D2A1]

city: Bethesda

first: Jonathan

last: Hernandez

address: Building 37

institute: NCI/NIH

summary: Investigate molecular mechanisms of tumor dormancy with myeloid-specific TGFBR2-KO mouse model.

overall_design: Identify differentailly expressed genes between control and SLURP1 treatment in vitro

first: Abdul

last: Ahad

first: Vishal

last: Koparde

first: Jae Young

last: So

first: Li

last: Yang


title: Transcriptomic analysis reveals novel mechanisms underlying  neutrophil activation induced by high salt

city: CABA

first: Ignacio

middle: Gabriel

last: Mazzitelli

state: CABA

address: Paraguay 2155

country: Argentina

institute: INBIRS

summary: Elevated sodium concentrations are commonly observed in tumors and sites of inflammation. Previous studies have shown that high salt levels modulate the phenotype and function of CD4+ and CD8+ T cells, regulatory T cells and macrophages. In this study, we performed transcriptomic studies that revealed profound alterations in the neutrophil transcriptome upon high salt exposure, with changes that significantly exceeded those triggered by conventional agonists. By integrating transcriptomic data with functional assays, our findings indicate that high salt-induced neutrophil activation involves mitochondrial ROS production, which subsequently activates p38 MAPK and engages FOS-, BTK-, and COX2-dependent pathways. Remarkably, the plasticity of the neutrophil transcriptome in response to high salt was further evidenced by the upregulation of genes typically associated with other cell types, including SEMG1, ICAM4, TRIM69, AREG, OSM, and TOB1, suggesting a broader role for neutrophils in different biological processes beyond their participation in innate immunity.

overall_design: RNASeq profiling of human neutrophils exposed 4h to high NaCl (50 mM) abd/or LPS 100 ng/ml

first: Fernando

last: Erra Diaz

first: Jorge

last: Geffner


title: Chromatin architecture reprogramming reveals novel epigenetic dependencies in breast cancer [scRNA-seq]

city: Miami

first: Rodrigo

last: Lucena Borges

state: Florida

address: 1501 NW 10th Avenue

department: Department of Human Genetics

institute: Sylvester Comprehensive Cancer Center

summary: Chromatin architecture plays a key role in development and cancer, yet most studies lack mechanistic depth due to widespread epigenomic remodeling. To address this, we tracked chromatin structure dynamics during the progression of endocrine resistance in ER+ breast cancer using Hi-C, chromatin accessibility, epigenomic, and transcriptomic profiling. We uncovered a critical role for H3K9 methylation and the demethylase KDM4C in driving proliferation of cells fated to become resistant through a non-genomic estrogen-mediated mechanism. These findings highlight the mechanistic contribution of chromatin regulation in therapy resistance and offer a blueprint for studying similar processes in cancer, development, and cell fate decisions.

overall_design: scRNA-seq of Parental T47D cells (ATCC HTB-113) and Primed cells ( 6 months after E2 depletion).

first: Liliana

last: Garcia-Martinez

first: Mengsheng

last: Zha

middle: L

last: Borges

first: Tong

last: Liu

first: Gretter

last: González-Blanco

first: Hao

last: Zhu

first: Zheng

first: Lluis

last: Morey


title: RNA sequencing of aortic valves from dialysis and non-dialysis patients with aortic stenosis

city: Chuo

first: Yosuke

last: Watanabe

address: Shimokato 1110

department: Cardiology

institute: University of Yamanashi

summary: Patients with aortic stenosis (AS) undergoing hemodialysis (HD) often experience faster disease progression and poorer prognosis than non-dialysis patients, yet the underlying mechanisms remain unclear. This study aimed to elucidate clinical and molecular differences between HD and non-HD patients with AS, focusing on transcriptomic profiling of resected aortic valves.

overall_design: RNA sequencing was performed on aortic valves surgically excised from dialysis and non-dialysis patients with aortic stenosis.

first: Satoru

last: Shiraiwa

first: Tran

last: Nguyen

first: Tsuyoshi

last: Kobayashi

first: Atsuhito

last: Nakao

first: Akira

last: Sato

first: Hiroyuki

last: Nakajima


title: Chromatin architecture reprogramming reveals novel epigenetic dependencies in breast cancer [ATAC-seq]

overall_design: ATAC-seq of primed cells (Parental estrogen deprived for 6 months).

last: Wang


title: An organoid model of the human adrenal cortex identifies drivers of steroidogenesis and zonation [scRNA-seq]

first: Quan

last: Xu

overall_design: Adrenal organoids are treated with growth factors.

first: Ninouk

last: Akkerman

first: Laura

last: Gaspa-Toneu

first: Alberto

last: Valdeolivas

first: Irineja

last: Cubela

first: Marion

last: Richardson

first: Nicolas

last: Giroud

first: J Gray

last: Camp

first: Joep

last: Beumer


title: MicroRNA Profiles of Human Follicular Fluid Extracellular Vesicles Reveal Stress Response Pathways and Role in Ovarian Aging

city: Lone Tree

first: Ye

last: Yuan

state: Colorado

address: 10290 RidgeGate Circle

department: Research

institute: Colorado Center for Reproductive Medicine

summary: Advanced maternal age (AMA) patients experience decreased success from assisted reproductive technologies (ART), attributed to quantity and quality of oocytes, which is significantly influenced by the health of surrounding microenvironment. This microenvironment consists of extracellular vesicles in the follicular fluid. Follicular fluid extracellular vesicles (FF-EVs) are important communication mediators between ovarian somatic cells and the oocyte that could be playing a role in the changes of the follicle microenvironment as the ovary ages. To elucidate mechanisms that contribute to the age-related decline of oocyte quality, we characterized EVs and sequenced the small-RNA cargo from young (<32 y.o.) and AMA (>38 y.o.) patients' follicular fluid. We identified 23 differentially expressed microRNAs (DE miRNAs), specifically 12 downregulated and 11 upregulated, in young compared to aged FF-EVs (P value < 0.05, FDR < 0.10, Fold Change > 2). Target gene prediction and pathway analysis indicate up- and downregulated miRNAs target genes associated with oxidative stress response, such as the AGE-RAGE and HIF-1 signaling pathways. Specifically, NFKB1, STAT3, VEGFA, IGF1R, and PIK3R1 targeted by miR-9-5p, miR-223-3p, miR-205-5p, Mir-133a-3p, and miR-222-3p, respectively, and both BCL2 and IGF1 targeted by miR-1-3p. The results of our study reveal EVs and their associated miRNAs could provide a basis for a novel approach to mitigating the negative impacts of oxidative stress during ovarian aging.

overall_design: Human follicular fluid samples were collected from patients during hormone-stimulated oocyte retrieval cycles. Patients were split into two groups: young and aged. The young group consisted of patients under 32 years old, and the aged group consisted of patients over 38 years old. Patients with a BMI greater than 25, endometriosis, or polycystic ovarian syndrome were excluded from the study. Patient follicular fluid was pooled into groups of three to limit individual variation, and EVs were isolated using ultracentrifguation and size-exclusion chromatography. Total RNA was isolated from the EVs and sent to Novogene for small-RNA sequencing.

first: Heather

last: Rogers

first: Ahmed

last: Gad

first: Nico

last: Menjivar

first: Gentry

last: Cork

first: Schoolcraft

last: William

first: Dawit

last: Tesfaye


title: Mechanisms and mouse modeling of tumor dormancy through distinct immune niche formation

first: Jonathan

last: Hernandez

overall_design: Identify differentially expressed genes between dormant and proliferative tumor cells in vivo.

first: Abdul

last: Ahad

first: Vishal

last: Koparde

first: Jae Young

last: So

first: Li

last: Yang


title: Multi-omics analysis of brain metastasis elucidates obesity induced prostaglandin crosstalk in tumor microenvironment restrain CD8T cell expansion

first: Yu

last: Wang

address: No.1 Shuaifuyuan Wangfujing Dongcheng District

department: Department of Neurosurgery

institute: Peking Union Medical College Hospital

summary: Brain metastasis (BrM) is one of the most crucial complications in tumor patients. Obesity contributes to the metabolic remodeling of tumor cells, yet the how obesity impact tumor microenvironment still remains unclear. We utilized scRNA-seq together with TCR seq to decipher the crosstalk with BrM microenvironment

overall_design:
scRNA-seq performed on 9 BrM tumor sample resected form 8 different patients (2 breast cancer, 1 lung adenocarcinoma, 2 lung small cell cancer, 2 renal clear cell cancer from 1 patient, 1 colon adenocarcinoma and 1 rectal cancer, 3 in obese group and 5 in normal BMI group)

***************************************************************
Due to patient privacy concerns, we are not able to submit raw data files.
***************************************************************

first: Zhanao

last: Xu

first: Yuekun


title: Single-Cell Chromatin Accessibility Landscape of Developing Perinatal Mouse Skin: A Multi-Omics Approach to Lineage Specification [scATAC-seq and scRNA-seq]

first: Hanjae

last: Lee

address: 103, Daehak-ro, Jongno-gu

institute: Seoul National University

summary: This study presents a time-series scATAC analysis of developing mouse skin. Motif and footprint analyses at the chromatin level, as well as integrated analysis with single-cell and spatial transcriptomic data, enable an in-depth identification of key transcription factors and driver genes involved in fibroblast differentiation and hair follicle formation. This study demonstrates the utility of scATAC analysis combined with multi-omics approaches in providing a comprehensive understanding of skin development. It serves as a valuable reference for future research on skin development and regeneration, supported by an interactive online portal.

overall_design: Dorsal skin from C57BL/6 mice was isolated at embryonic day 18.5 (E18.5) and postnatal days 0, 2, and 4 (PD0, PD2, PD4), followed by scATAC-seq (E18.5, PD0, PD2, PD4) and scRNA-seq (E18.5).


title: A Pilot Phase II Study of Neoadjuvant Fulvestrant plus Abemaciclib in Women with Advanced Low--Grade Serous Carcinoma

city: Houston

first: Ken

last: Chen

state: TX

address: 7007 Bertner Ave

institute: University of Texas MD Anderson Cancer Center

summary: Purpose: Neoadjuvant chemotherapy shows limited activity in low-grade serous carcinoma (LGSOC) of the ovary, fallopian tube, and peritoneum (LGSOC). Given LGSOC’s similarities to hormone receptor- positive (HR+) breast cancer, including clinical benefit from endocrine therapies, we conducted a phase II pilot study to assess the clinical benefit of neoadjuvant treatment with fulvestrant and abemaciclib for women with advanced LGSOC.  Patients and Methods: Women with untreated, unresectable stage III or IV LGSOC were eligible. Patients received fulvestrant (500 mg IM on day 1 and 15 of the first 28-day cycle, then day 1 of subsequent cycles) and abemaciclib 150 mg orally BID. Pre/perimenopausal patients received goserelin 10.8 mg subcutaneously every 12 weeks for ovarian suppression. Imaging re-assessment was performed every 8 weeks using RECIST 1.1 until deemed resectable. Following interval cytoreductive surgery (ICS), patients received 4 cycles of adjuvant fulvestrant and abemaciclib followed by maintenance letrozole. Patients with progressive disease were removed from the study and received standard chemotherapy. The pPrimary endpoint is best overall response clinical benefit rate (BOR CBR).   Results: Fifteen patients were enrolled and evaluable for efficacy. BOR CBR in the neoadjuvant setting was 100%, with  (9/15 patients (60%) achieving partial response (PR), and 6/15 patients (40%) showing stable disease (SD). One patient with radiologic PR had pathologic complete response at ICS. Nine of fifteen patients (60%) underwent ICS – 5 (55.5%) with complete gross resection, 2 (22.2%) with <1cm residual disease, and 2 (22.2%) with suboptimal cytoreduction. Median time on study prior to surgery was 8.38 months.   Conclusion: Neoadjuvant treatment with fulvestrant and abemaciclib was tolerable and demonstrated unprecedented response and CBGR rates in this pilot study. These results compare favorably withto published outcomes of neoadjuvant chemotherapy in LGSOC.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: We performed GeoMx DSP WTA assay with 2 pairs of samples of pre- and post treatment timepoints and 4 additional patients from post treatment timepoint with fulvestrant and abemaciclib combination therapy.

first: Nejla

last: Ozirmak Lermi

first: Luisa

last: Solis Soto

first: Amir

last: Jazaeri