title: Mapping Individual Chemoresistome in Breast Cancer Patients Unravels Diversity in Dynamic Transcriptional Adaptation

city: Ramat Gan

first: Maya

last: Dadiani

state: Please Select

address: Tel Hashomer

institute: Sheba Medical Center

summary: Tumors are continuously evolving through their course of progression and treatment, a major process contributing to resistance to therapy. Recent studies brought into focus the importance of non-genetic adaptive mechanisms, by which tumors acquire resistance via rewiring transcriptional programs. To dissect these adaptive processes in the individual breast cancer patients, we combined longitudinal transcriptomics with temporal pattern analysis.

overall_design: Matched triplets of archived tumor biopsies from pre-treatment, post-treatment and adjacent normal epithelium were collected from breast cancer patients that underwent neo-adjuvant chemotherapy. Overall, a total of 97 samples from 29 patients were included in this study.

first: Gilgi

last: Friedlander

first: Gili

last: Perry

first: Einav

middle: N

last: Gal-Yam

first: Bella

last: Kaufman


title: Wnt2b Deficiency Causes Abnormal Intestinal Epithelial Development in Humans and Diminished Lgr5+ Stem Cells and Proliferation and in Humans and Mice

status: Public on Nov 01 2025

city: Boston

first: Radhika

middle: Sanjay

last: Khetani

state: MA

address: 401 Park Drive, 3rd floor East

department: Biostatistics

country: USA

institute: Harvard T.H. Chan School of Public Health

type: Expression profiling by high throughput sequencing

summary: Background and aims: Wnt2b is an intestinal canonical Wnt which was previously thought to be fully redundant with other intestinal Wnts. Humans with Wnt2b deficiency have severe phenotypes, however, highlighting the critical importance of Wnt2b. We sought to understand why Wnt2b is critical for intestinal health. Methods: We investigated the intestinal health Wnt2b knock out (KO) mice at baseline. We also assessed the impacts of inflammatory challenge to the small intestine with anti-CD3e antibody and to the colon with dextran sodium sulfate (DSS) administration. In addition, we generated human intestinal organoids (HIOs) and enteroids from Wnt2b deficient patients for transcriptional and histologic analyses. Results: Wnt2b-/- mice were healthy and had normal small intestinal and colonic histology at baseline but decreased intestinal stem cells. Small intestinal response to anti-CD3e was similar to controls. The colons of Wnt2b KO mice were severely affected by DSS compared to controls, and this was due to impaired proliferative responses of stem cells during the early stages of injury. In contrast, HIOs generated from Wnt2b-deficient patients showed a developmental phenotype with abnormal epithelial organization and enriched mesenchymal signature and enteroids showed restricted growth. Conclusion: Wnt2b deficiency in mice more severely impacts the colon than the small intestine and is linked to impaired proliferative capacity. In human Wnt2b deficiency the epithelium is severely disorganized from the early stages of intestinal lineage specification in addition to having diminished intestinal stem cells and proliferation.

overall_design: Two clusters of samples sequenced in two batches and then results cross-analyzed to remove batch-to-batch variability. First batch with 3 samples and 3 controls, second with 4 samples and 4 controls.

first: Amy

middle: E

last: O'Connell

first: Sathuwarman

last: Raveenthiraraj

first: Wanshu

last: Qi

middle: S

first: Nambirajam

last: Sundaram

first: Michael

last: Helmrath

first: David

middle: T

last: Breault


title: Single cell RNA-sequencing shows generation of highly proliferative and robust effector CD8 T cell populations in the tumor.

city: Birmingham

first: Mingyong

last: Liu

state: AL

address: SHEL 531, 1825 University Blvd

department: Clinical Immunology and Rheumatology

institute: University of Alabama at Birmingham

summary: To determine how Entinostat (ENT) treatment affected tumor-infiltrating CD8 T cells, we treated TS/A tumor-bearing mice with vehicle or ENT daily beginning at day 7 and performed single cell RNAseq on CD8 T cells isolated from tumors on day 17. These data suggest that ENT promotes the expansion of a proliferating, progenitor-like CD8+ T cell population that robustly generates effector cells.

overall_design: Single cell analyses of tumor-infiltrating CD8 T cells from entinostat- or vehicle-treated animals

first: Troy

middle: D

last: Randall

first: Tyler

middle: R

last: McCaw

first: Alexander

middle: F

last: Rosenberg


title: RNA-seq analysis in Cal-62 cells treated with Niraparib

city: Tianjin

first: Xiukun

last: Hou

address: Huanhu Road

country: China

institute: Tianjin Cancer Institute and Hospital

summary: To assess the function of Niraparib in thyroid cancer, we performed transcriptome analysis through high-throughput RNA-Seq of DMSO and Niraparib treated Cal-62 cells

overall_design: We treated Cal-62 cells with DMSO and Niraparib and performed the RNA-seq analysis in order to examine the transcriptome after Niraparib treatment

first: Mengran

last: Tian

first: Junya

last: Ning


title: The Peptide Genomic Therapy Increases Antibacterial Immunity and Survival in Sepsis by Reprograming the Gene Orthologs of Human Immunodeficiencies in the Spleen and Lungs

status: Public on Oct 31 2025

city: Nashville

first: Jozef

last: Zienkiewicz

state: TN

address: 1161 21st Ave. South, T2220, MCN

department: Medicine

institute: Vanderbilt University

summary: Sepsis is a life-threatening complication of infections afflicting 49 million patients worldwide with 11 million sepsis-related deaths. In the USA, this growing public health problem concerns 1.7 million adult and pediatric patients. An estimated 1 million patients with asplenia or hyposplenia are particularly vulnerable to sepsis. As the spleen is a major blood-filtering immune organ, we show that its anti-bacterial immunity was increased 9 times by the Peptide Genomic Therapy with the cell-penetrating Nuclear Transport Checkpoint Inhibitor (NTCI) in the preclinical model. Likewise, the antibacterial immunity was increased in the lungs, the frequent site of bacterial infections in spleen-compromised hosts. We also show that the survival increased from 44% to 80%, when the NTCI was added to the antibiotic therapy. Strikingly, the NTCI reprogrammed the expression of the gene orthologs responsible for human immunodeficiencies, aka the Inborn Errors of Immunity (IEI). Among them, the 227 IEI genes were reprogrammed in the spleen and 215 in the lungs, while the mediators of inflammation in blood (IL-6, IL-10, TNFα, Interferon γ, and MCP1) were normalized. Thus, the antibacterial immunity in the spleen and lungs was dramatically increased by the Peptide Genomic Therapy with the NTCI that almost doubled survival in sepsis when added to the antibiotic.

overall_design: We investigated the spleen’s and lungs' genome response to polymicrobial sepsis. We also established an impact of nuclear import blockade on gene expression in sepsis. Sepsis was induced in 8-10-week-old female C57BL/6 mice (Jackson Laboratories, Bar Harbor, ME) by a single intraperitoneal injection of cecal microbiome (CM) stock solution. Mice were treated with saline or with cell-penetrating nuclear transport checkpoint inhibitor (NTCI), cSN50.1 peptide. A control group of mice were challenged with sham (5% dextrose) and treated with saline. A gene expression profiling (RNA-seq) was performed using NGS of spleen total RNA samples from mice euthanized at 26 hours post CM challenge. The comparative gene expression profiling analysis (DESeq2) was performed using RNA-seq data for groups: CM + saline vs. Sham + saline and CM + NTCI vs Sham + saline.

first: Huan

last: Qiao

first: Yan

first: Jacek

last: Hawiger


title: Cooperativity between head-to-head dimerization and head-to-tail multimerization of FoxP3 transcription factor

first: Sun

last: Hur

address: 3 Blackfan St

department: Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital

summary: FoxP3, an essential transcription factor for regulatory T cells (Tregs), forms higher-order multimers on TnG microsatellites in the genome. Although a previous study has shown that FoxP3 can form head-to-head (H-H) dimers on inverted repeats of forkhead motifs (IR-FKHM), in vivo evidence for this configuration was elusive. An unbiased FoxP3 pull-down sequencing approach identified a wide range of sequences supporting H-H dimerization, enabling systematic genomic analysis. This work revealed that FoxP3 binds DNA in Tregs as both H-H dimers and higher-order multimers, often incorporating one half-site of the H-H dimer into TnG repeats. A robust H-H interaction can seed multimerization on adjacent TnG repeats, enhancing assembly even on suboptimal sequences. Unlike other FoxP transcription factors, H-H dimerization is unique to FoxP3. Chimeric construct analyses identified a loop adjacent to the forkhead domain as the determinant for this distinctive function, underscoring a unique synergism between two binding modes.

overall_design:
In vitro pulldown assay using a synthetic dsDNA oligonucleotide library to identify FoxP3-binding motifs. MBP-tagged FoxP3 and FoxP1 were used to pull down DNA sequences with potential binding affinity. The input library was included as a control. Pulldown-enriched DNA was PCR-amplified and sequenced using paired-end 150 bp reads on an Illumina NovaSeq 6000 platform.
Follow-up in vitro pulldown experiment using the same synthetic dsDNA library, focused on comparative binding between FoxP3 and FoxP1. Samples were sequenced using single-end 130-cycle reads on an Illumina NextSeq 2000 platform.

first: Fangwei

last: Leng

first: Ryan

last: Clark

first: Wenxiang

last: Zhang

first: Thibault

last: Viennet

first: Haribabu

last: Arthanari

first: Xi

last: Wang


title: Reduced expression of UPF1 promotes tumor progression through stabilizing COX-2 mRNA in nasopharyngeal carcinoma

city: Guangzhou

first: zixuan

last: chen

state: Guangdong

address: 651 Dongfeng Road East, Yuexiu District, Guangzhou, P.R. China

institute: Sun Yat-sen University Cancer Center

summary: Nonsense-mediated mRNA decay (NMD) is conserved mRNA surveillance pathway that targeted and degraded one-third of aberrant and non-aberrant cellular transcripts. Recently, growing evidences have shown that NMD pathway is implicated in multiple cancer types. However, the activity and function of NMD in nasopharyngeal carcinoma (NPC) remains unclear. Here we demonstrated that the expression level of the core NMD factors UPF1 (up-frameshift) was significantly downregulated in NPC tissues compared with adjacent noncancerous tissues and predicted poor prognosis. Knockdown of UPF1 expression enhanced tumor growth and metastasis of NPC cells in vitro and in vivo. UPF1 down-regulated genes revealed by RNA sequencing were selectively upregulated in NPC tissues. COX-2 and PD-L1 were identified as NMD targets. UPF1 knockdown activated ERK/MAPK and JAK2/STAT3 pathways through stabilizing COX-2 in NPC cells. Importantly, co-culture with UPF1 knockdown NPC cells promotes M2 polarization and migration of macrophages, and suppressed proliferation and activation of CD8+ T cell. Our findings suggested that UPF1 expression level and NMD efficiency were impaired in NPC tissues, which contributed to tumor progression and immune modulation.

overall_design: RNA was extracted from UPF1 overexpressing HK1 cells, UPF1 knockdown (UPF1-KD) 6-10B cells, UPF1 overexpressing 5-8F cells, Emetine treated 5-8F cells and their corresponding control cell lines.

first: Chun

last: Wu

first: Ruowen

last: Xiao

first: Rui

last: Sun

first: Shijuan

last: Mai


title: Effect of FBL depletion on cell morphology

city: Pune

first: Kundan

last: Sengupta

state: Maharashtra

address: Dr.Homi Bhaba road, Pashan

country: India

institute: INDIAN INSTITUTE OF SCIENCE EDUCATION AND RESEARCH,Pune

summary: This study reveals a previously unrecognized role of FBL in maintaining epithelial characteristics. Its depletion led to a marked reduction in Scribble, a key basolateral protein required for stabilizing E-cadherin at the membrane and sustaining Hippo signaling, thereby preventing TAZ activation. Scribble’s bivalent promoter is pre-associated with H3K4me3, H3K27me3, and EZH2. As a nucleolar protein, FBL retains a fraction of EZH2 within the nucleolus, and its loss results in the redistribution of EZH2 into the nucleoplasm, where it engages PRC2-bound promoters, including that of Scribble.Diminished Scribble levels upon FBL knockdown disrupted Hippo signaling, leading to TAZ accumulation and subsequent upregulation of EMT drivers Snail and Foxc2. Additionally, Scribble modulates Akt activity via PHLPP1, and its depletion enhanced Akt-dependent phosphorylation of EZH2, compromising its methyltransferase function. In MCF10A (p53 DN) cells, loss of FBL increased mesenchymal markers (Snail, Twist, Zeb1) while down

overall_design: 0.6 million DLD-1 cells were seeded and transfected with siLacZ and siFBL at final concentration of 50nM, in OptiMEM for 6h. Post-transfection cells were incubated at 5% CO2 and 37C for 72h.

first: Santam

last: Saha

first: AK

last: Balaji

first: Sweety

last: Meel

first: Dimple

last: Notani


title: HDAC inhibition drives treatment duration-dependent changes in proliferation and effector function of tumor-infiltrating CD8 T cells.

first: Mingyong

last: Liu

summary: To determine how Entinostat (ENT) treatment affected tumor-infiltrating CD8 T cells, we treated TS/A tumor-bearing mice with vehicle or ENT daily beginning at day 7 and performed RNAseq on CD8 T cells isolated from tumors on day 10 and day 17. These data show that ENT progressively altered both the function and distribution of infiltrating CD8 T cells.

overall_design: Transcriptomes of tumor-infiltrating CD8 T cells from entinostat- or vehicle-treated animals

first: Troy

last: Randall

first: Tyler

last: McCaw

first: Christopher

last: Scharer


title: Single-cell nucleus ATAC sequencing on colorectal tumor and adjacent nonmalignant tissues

city: Daejeon

first: Inkyung

last: Jung

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: KAIST

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Single-cell ATAC sequencing data were collected from 24 colorectal tumor and 9 adjacent nonmalignant tissues pooled into 15 libraries. This dataset was generated to investigate the global chromatin accessibility profiles of epithelial, stromal, and immune cells in the colorectal cancer microenvironment. Information on the donors, tissues, libraries, and demultiplexed barcodes are provided in the supplementary data of the cited paper.

overall_design: Single-cell chromatin accessibility profiling by high throughput sequencing

first: Andrew

middle: J

last: Lee

first: Woong-Yang

last: Park


title: Comparison of gene expression in HeLa cells after treatment with IFN-b, IFN-g, or VPgEMCV.

city: Kyoto

first: Takashi

last: Fujita

state: Kyoto

address: 53 Shogoin Kawahara-cho, Sakyo-ku

department: Biosystems Science

country: Japan

institute: Kyoto University

summary: We uncovered that cells infected with the encephalomyocarditis virus (EMCV) release soluble factors that induce apoptosis in uninfected cells. These factors were identified as the cytokine TNF-α and the viral protein VPgEMCV, which is necessary for viral RNA synthesis. Intriguingly, we discovered that VPgEMCV also acts as a functional mimic of IFN-γ, activating its canonical signaling pathway. This includes phosphorylation of STAT1 and the induction of IRF-1 and iNOS, leading to increased nitric oxide (NO) production. The synergy of NO accumulation and TNF-α signaling initiates powerful apoptosis. To compare gene sets regulated by IFN-I signaling (IFN-b), IFN-II signaling (IFN-g), and VPgEMCV signaling, we utilized RNA-seq analysis. From the deep sequencing data, we further discovered that VPgEMCV induces a gene expression profile similar to IFN-II signaling (IFN-γ), while also uniquely downregulating a distinct subset of genes. Our findings reveal that this cytokine-mimicry function of VPgEMCV regulates genes to control both viral replication and disease pathogenesis.

overall_design: RNA-seq analysis comparing wildtype HeLa cells treated with IFN-b, IFN-g, or VPgEMCV 24h post-treatment.

first: Yutaro

last: Shirasaka


title: Remodeling of 3D Gene Architecture in Myocardium from Embryonic Development to Early Aging [Hi-C]

city: Chengdu

first: Yuwei

last: Gou

address: No. 211, Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

summary:
Heart-related diseases are increasingly attacking the younger population, and getting more prevalent as the population ages. Better understanding of heart development and aging could help decipher the mechanism of associated heart diseases.
In this study, we reported the application of a typical miniature swine -- Tibetan pig, as human heart model, and illustrated the changes in higher-order chromatin structure and transcription regulation from fetal to sexual maturity and early senescence, as well as the role they play in physiological development and aging.
We observed altered multi-scale structures of the 3D genome from territories and A/B compartments to TADs and loops/PEIs. Changes in territories and A/B compartments indicate high plasticity and disorganization of chromatin structure for the fetal and senescent stages, respectively, compared to the more ordered conformation for the young adult stage, embodied by Von Neumann Entropy (VNE) and compartmentalization strength indexes. From such coarse scale, we also observed that heterochromatin gradually stacked and relaxed during development and senescence, supported by evidence of change in intensity of B-B interactions and correlation between sequence features and A/B compartment switches, across the three critical stages. A finer examination of TAD and loops/PEIs showed that young adults tend to have more accurate transcription regulation through finer control of chromatin structure dynamics, supported by higher correlation of gene expression and TAD connectivity, more space between dynamic boundaries and their targeted genes, and stronger ‘loop skew’ towards A compartments. Another observation of monotonic increase in long-range interactions and decrease in short-range interactions throughout the development and senescent process indicates the gradual loss of plasticity for chromatin conformation.

overall_design: To investigate the changes in the three-dimensional conformation of chromatin during development and aging, as well as the relationship between its trend and transcriptional expression

first: Qianzi

last: Tang


title: PURE-seq Integrates FACS and PIP-seq for Single-Cell Genomics of Ultra-rare Cells

city: San Francisco

first: Sixuan

last: Pan

state: California

address: 1450 3rd Street

department: Bioengineering

institute: UCSF

summary: We used PURE-seq with single-cell RNA-sequencing (scRNA-seq) to study murine long-term hematopoietic stem cells (LT-HSCs) and their transcriptomes in the context of hematopoietic aging.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: First, we used human and mouse cell mixtures to demonstrate the sensitivity and specificity of PURE-seq. We used mixed population of HEK/3T3 or 3T3/PBMC cells with target cell fractions of 10^-3, 10^-4, 10^-5, and 10^-6. Then, we used PURE-seq workflow to study murine LT-HSCs from young, middle-aged, and old mice. We also evaluated murine hematopoietic stem cells (HSCs) and the percentage of long-term HSCs (LT-HSCs) before enrichment, as a comparison to enriched LT-HSCs throuhg PURE-seq.

first: Kai-Chun

last: Chang

first: Inés

last: Fernández-Maestre


title: Gene expression profile at single cell level of CD11b+ cells from E18.5 fetal brain

city: Hefei

first: Qi

middle: wu

last: Bian

state: Anhui

address: Division of Life Sciences and Medicine, 443 Huangshan Road

department: Life sciences and medicine

institute: University of Science and Technology of China

summary: Microglia (MG), the brain-resident macrophages, play key roles in the development and maintenance of brain circuits throughout life.Our previous data demonstrated a correlation between maternal-derived GZMB and the activation of embryonic microglia cells, as well as behavioral abnormalities in offspring. Here, we employ single-cell sequencing technology to analyze the heterogeneity of embryonic microglia cells induced by maternal immune activation, including the role of GZMB in this process

overall_design: We isolated fetal brains from three groups of pregnant mice (E18.5): Ncr1-cre+Saline, Ncr1-cre+polyIC, and Gzmb-cko+polyIC. Subsequently, we isolated CD11b+ cells using MACS from these samples for single-cell sequencing analysis.

first: Qiwu


title: Comparative transcriptomics as a key to understanding the adaptation mechanisms of Baikal sculpins to the deep-water habitat

status: Public on Oct 30 2025

city: Irkutsk

first: Tuyana

last: Sidorova

address: 3, Ulan-Batorskaya

department: Siberian Branch of the Russian Academy of Sciences

country: Russia

institute: Limnological Institute

summary: In this study, the transcriptional profiles of four deep-sea sculpin fish species (Cottoidei) are described for the first time as part of the study of the adaptation of endemic fishes to different habitats in Lake Baikal. These studies will lead to a deeper understanding of the molecular mechanisms that ensure the adaptation of endemic species to specific habitats in Lake Baikal, even at depths of more than 500 m (up to 1600 m).

sample_organism:
Batrachocottus multiradiatus
Comephorus dybowskii
Batrachocottus nikolskii
Comephorus baikalensis

overall_design: To study the effect of habitat depth on the transcriptional profile, a transcriptome analysis was performed for 4 species: m3 - Comephorus dybowski Korotneff, 1905; m4 - Comephorus baicalensis (Pallas, 1776); m6 - Batrachocottus nikolskii (Berg, 1900); m7 - Batrachocottus multiradiatus Berg, 1907. Fish species were collected during trawl surveys on the R/V Vereshchagin in August 2023 and 2024. The work was supported by State project No. 0279-2021-0005 (121032300224-8).

first: Yulia

middle: P

last: Sapozhnikova

middle: V

first: Anastasiya

middle: G

last: Koroleva

first: Evgenia

middle: A

last: Vakhteeva

first: Alexander

last: Epifantsev

first: Vera

middle: M

last: Yakhnenko

first: Sergey

last: Potapov

first: Tatyana

last: Butina

last: Kirilchik

first: Lyubov

last: Sukhanova

first: Ivan

last: Nebesnykh

first: Igor

last: Khanaev


title: DNA Methylation Profiles Predicting Response to Anti-PD-1-based Treatment in Patients with Advanced Gastric Cancer

first: Wei

last: Tang

address: Zhongshan 2nd Street, No. 58

department: Center of Gastrointestinal Surgery

institute: First Affiliated Hospital of Sun Yat-sen University

type: Methylation profiling by genome tiling array

summary: Immunotherapy has shown promise in treating gastric cancer, but predicting patient response remains challenging. In this study, DNA methylation profiles from 30 samples were analyzed using the Infinium MethylationEPIC BeadChip (850K array). A total of 523 differentially methylation probes (DMPs) were identified, from which 20 CpG probes were selected as the most predictive of treatment response. Based on these 20 DMPs, we developed the iMETH model, which accurately predicts patient responses to first-line anti-PD-1-based therapy.

overall_design: Methylation profiling of responders vs. non-responders to anti-PD-1-based treatment in patients with advanced gastric cancer

first: Zhixiong

last: Wang


title: Disruption of histone acetylation homeostasis reveals multilayered chromatin regulation for transcriptional resiliency

city: Los Alamos

first: Eric

last: Small

state: New Mexico

address: Bikini Atoll Rd.

department: Earth and Environmental Sciences Division

institute: Los Alamos National Laboratory

summary: Dysregulation of epigenetic processes leads to a plethora of abnormalities including disease states such as cancer. Therapies focused on epigenetic modulation alter gene expression to correct dysfunction, though the mechanisms and perpetuation of these states is unknown. Here, we use integrated epigenomics and three-dimensional chromatin structure-function analyses after acute histone deacetylase inhibitor cancer drug treatment (suberoylanilide hydroxamic acid in lung cancer cells). Treatment induced substantial (13%) genomic rearrangement that rebounds despite persistent gene expression changes and spreading of acetylation. The chromatin functional landscape (accessibility, active transcription modification, and gene expression) is controlled and locus-specific, while chromatin contacts are globally altered resulting in a moderate weakening of topologically associating domains. Chromatin states are more dynamic at transcriptionally active loci while genes with reduced expression are epigenetically stable suggesting chromatin architectural turnover and nucleosome remodeling is locus-specific and underlies the bidirectional expression changes. Thus, local 3D chromatin and genome structural dynamics is integral for loci regulation in response to epigenomic perturbation. The partial persistence of these altered features may have larger implications for efficacy of epigenetic drugs in amelioration of disease states.

overall_design: We performed multi-omic assessments of human lung carcinoma (A549) cells with and without HDACi drug treatment to identify genome-wide transcriptional, epigenomic, and chromatin structural responses. A concentration of 10 µM SAHA was chosen for subsequent experiments as this treatment considerably altered acetylation on lysine 27 of histone 3 (H3K27ac) while still retaining viable cells at 48 hours post treatment for chromatin structure-function characterization. Time course experiments were conducted in triplicate; control (mock-treated) and treated (10 µM SAHA) A549 cells were collected at 24 and 48 hpt. Genome-wide assays for control and treated paired cells included ChIP-seq (H3ac, H3K27ac, H3K4me3) and RNA-seq, each with three biological replicates, and Hi-C with two biological replicates. ATAC-seq samples from three biological replicates per condition were generated from a separate repeated experiment.

first: Vrinda

last: Venu

first: Cullen

last: Roth

first: Samantha

middle: H

last: Adikari

first: Anna

last: Vlot

first: Kyle

last: Sullivan

first: Chanaka

last: Abeyratne

first: Daniel

last: Jacobson

first: Shawn

last: Starkenburg

first: Karissa

middle: Y

last: Sanbonmatsu

first: Christina

last: Steadman


title: Early transcriptional responses post-recanalization in a mouse model of middle cerebral artery occlusion

city: Edmonton

first: Truong An

last: Bui

state: Alberta

address: 8440 112 Street NW

department: Psychiatry

country: Canada

institute: University of Alberta

summary:
Ischemic stroke is a leading cause of death and disability worldwide. Recanalization therapies for acute ischemic stroke, which include mechanical thrombectomy and rt-PA delivery, are limited as while the operations are successful, many patients experience poor clinical outcomes, termed futile recanalization. Using the murine middle cerebral occlusion (MCAO) model that mimics a large vessel occlusion with recanalization, we performed a comprehensive microarray analysis of blood samples post-MCAO and recanalization in male, female, young adult, and aged mice (N=44). Downstream bioinformatics analysis was then performed in RStudio. We discovered 11 hub genes that are potential genomic markers of early recanalization changes in mice. Vcan, a novel marker, is highly conserved and elevated in mice, rats, and clinical patients. Leukocyte and neutrophil functional activities have significant enrichment in both mice and humans. We identified a range of miRNAs that potentially regulated recanalization responses and NFE4 and MTF1 as the primary transcription factors.
MCAO was performed MCAO mice were euthanized immediately 60 minutes after surgery. In the MCAO+Recan group, the suture was taken out 60 minutes after the onset of occlusion and mice were allowed to recover for an additional 3 hours before euthanasia. Sham mice were subjected to only anaesthesia and the manipulation of surrounding tissues and arteries.

overall_design: Three experimental groups (n=44), sham (SHAM, n=16), 1-hour MCAO (MCAO, N=17), and 1-hour MCAO with 3-hour recovery post-recanalization (MCAO+Recan, n=11), were included in the dataset. Both young (3-6 months old, n=20) and aged (18-24 months old, n=24) male (n=20) and female (n=24) mice were used.

first: Glen

middle: C

last: Jickling

first: Ian

last: Winship


title: DNA Methylation Profiles Predicting Response to Anti-PD-1-based Treatment in Patients with Advanced Gastric Cancer [Targeted Bisulfite-Seq]

type: Methylation profiling by high throughput sequencing

summary: Immunotherapy has shown promise in treating gastric cancer, but predicting patient response remains challenging. In this study, DNA methylation levels at 20 specific CpG probes were measured in 69 tumor samples using targeted bisulfite sequencing (TBS). These CpG probes, previously identified as highly predictive of treatment response, were used to construct and validate a methylation-based prediction model. The resulting iMETH model accurately stratified patients according to their likelihood of responding to first-line anti-PD-1-based therapy.

overall_design:
DNA methylation levels at 20 specific CpG probes were measured in 69 tumor samples using targeted bisulfite sequencing (TBS)
In Sample 'response to ici', ici represents immune checkpoint inhibitor.


title: Shroom3 Affects Neuroepithelial Morphogenesis through Regulating Cytoskeletal Proteins in Cynomolgus Monkey’s Organoids

city: Kunming

first: Peng

last: Li

state: Yunnan

address: No. 727 Jingming South Road, Chenggong District

institute: Kunming University of Science and Technology

summary: The loss of SHROOM3 plays an important role at the neuroepithelial stage, demonstrating the indispensability of SHROOM3 and indicating the great potential of organoids in understanding the mechanism of  neural tube defects (NTDs).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Neuroepithelium cells.


title: Distinct roles of histone H2B ubiquitination at promoters and coding regions of Pol II-transcribed stress genes [MNase-seq]

city: Barcelona

first: Montserrat

last: Vega

state: Barcelona

address: C/ Dr. Aiguader 88, lab 383

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra

summary: Investigate the role of  DUBs in the transcriptional response to oxidative stress

overall_design: Nucleosome profiling using MNase-seq obtained from a wild-type and a ubp8 and ubp16 deleted strains under untreated conditions and after 5 and 15 minutes of 1 mM peroxide treatment

first: Rubén

last: Barrios

first: Rebeca

last: Gracia

first: Susanna

last: Boronat

first: Sarela

last: García-Santamarina

first: Jason

last: C Tanny

first: José

last: Ayté

first: Elena

last: Hidalgo


title: Distinct roles of histone H2B ubiquitination at promoters and coding regions of Pol II-transcribed stress genes [ChIP-seq]

overall_design: ChIP-seq of PolII-HA, Ser2, Ubp8-GFP and Ubp16-GFP obtained from a wild-type and a ubp8 and ubp16 deleted strains under untreated conditions and after 5 and 15 minutes of 1 mM peroxide treatment.

last: C. Tanny


title: Distinct roles of histone H2B ubiquitination at promoters and coding regions of Pol II-transcribed stress genes [RNA-seq]

overall_design: Gene expression profiling using RNA-seq obtained from a wild-type and a ubp8 and ubp16 deleted strains under untreated conditions and after 30 minutes of 1 mM peroxide treatment


title: A human-specific microRNA controls the timing of excitatory synaptogenesis (time course smallRNA)

city: Zurich

first: Gerhard

last: Schratt

address: Winterthurerstrasse 190

department: HEST

country: Switzerland

institute: ETH Zürich

type: Non-coding RNA profiling by high throughput sequencing

summary: Neural circuit development in the human cortex is considerably prolonged in comparison to non-human primates, a trait that contributes to the remarkable cognitive capacity of modern humans. Here, we explore the regulatory role of non-coding RNAs, which dramatically expanded during brain evolution, in synapse development of human-induced pluripotent stem-cell derived neurons. We found that inhibition of a human-specific microRNA, miR-1229-3p, alters the trajectory of human neuronal maturation and enhances excitatory synaptic transmission. Transcriptome analysis following miR-1229 knockdown revealed a downregulation of mitochondrial DNA (mtDNA) encoded genes. We further show that miR-1229 regulates mitochondrial morphology, mtDNA abundance and matrix calcium concentration, and that stimulation of mitochondrial metabolism rescues decreased calcium buffering in miR-1229-3p depleted neurons. Accordingly, miR-1229 directly targets an entire network of genes involved in mitochondrial function and ER-associated protein homeostasis. Our findings reveal an important function of human-specific miR-1229-3p in developmental timing of human synaptogenesis and generally implicate non-coding RNAs in the control of human connectivity and cognition.

overall_design: To investigat gene expression during human neuronal differentiation, we differentiated hiPSC into human neurons following an optimized protocol ("igNeurons"). RNA from these differentiations was extracted at seven time points (Day 0, Day 9, Day 15, Day 21, Day 27, Day 33 & Day 40) and sent for "Ribosomal Depletion"- as well as "SmallRNA"- sequencing.

first: Michael

last: Soutschek


title: A human-specific microRNA controls the timing of excitatory synaptogenesis (time course ribozero)


title: A human-specific microRNA controls the timing of excitatory synaptogenesis (pLNA dataset)

overall_design: To explore gene expression regulation of candidate microRNAs in human neurons, we differentiated hiPSC into human neurons following an optimized protocol ("igNeurons") for 21 days and inhibited those microRNAs (namely miR-181c-5p, miR-1229-3p and miR-3943) from day 9 on. RNA was extracted from 4 independent differentiations and sent for polyA-RNA sequencing. Neurons treated with a control inhibitor (pLNA-Ctrl) as well as untreated neurons ("Empty") were used as control.


title: A human-specific microRNA controls the timing of excitatory synaptogenesis

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

overall_design: Refer to individual Series


title: Rbfox2 selectively governs hematopoietic stem cell self-renewal by regulating proteostasis

city: New York

first: Longfei

last: Gao

state: NY

address: 650 West 168th Street

institute: Columbia University

summary: Self-renewing hematopoietic stem cells (HSCs) generate all blood cells and give rise to long-term reconstitution of the hematopoietic system after transplantation, but the molecular mechanisms that specifically regulate HSCs remain poorly defined. Here we found that HSCs displayed a distinct mRNA alternative splicing pattern and preferentially expressed Rbfox2, an alternative splicing regulator, compared with multipotent progenitors (MPPs). Deletion of Rbfox2 from the hematopoietic compartment specifically depleted HSCs, but not progenitors in the adult bone marrow. Rbfox1 did not function redundantly with Rbfox2 in HSCs. Mechanistically, Rbfox2 loss led to proteostasis stress, including increased protein synthesis rate and accumulated misfolded/unfolded protein contents, in HSCs, but not in progenitors. Small molecules that restore proteostasis rescued HSC defects in Rbfox2-deficient mice. Our work thus reveals that HSCs, but not progenitors, selectively rely on Rbfox2 for their self-renewal and maintenance.

overall_design: We performed RNA-seq on HSCs from 3 control and 3 Rbfox2-deleted mice.

first: Desmond

last: Dickson

first: Huijuan

last: Feng

first: Chaolin

last: Zhang

first: Lei

last: Ding


title: Circadian regulator REV-ERBα is a master regulator of tumor lineage plasticity and an effective therapeutic target [RNA-Seq]

status: Public on Oct 29 2025

city: sacramento

first: Xiong

state: CA

address: 4645 2nd Ave

institute: University of California, Davis

summary: Epigenetic and transcriptional dysregulation plays a fundamental role in tumor lineage plasticity (LP). However, the underlying mechanisms, especially for the initial events of LP development, are still poorly understood. Here, we report that in progression of prostate cancer from adenocarcinoma to treatment-induced neuroendocrine prostate cancer (t-NEPC), anti-AR signaling inhibitors (ARSIs) reprogram the function of a circadian regulator/nuclear receptor REV-ERBα by switching its target gene programs from kinase signaling and metabolic programs to programs of LP, which includes neurogenesis, stem cell and epithelia to mesenchymal transition (EMT) as well as over fifteen LP drivers including POU3F2/BRN2, ASCL1, FOXA2, ONECUT2 and MYCN. Unexpectedly, REV-ERBα facilitates the chromatin occupancy of BRN2, ASCL1 and FOXA1 in their activation of LP programs, thus functioning as a master regulator of ARSI-induced LP driver network. Mechanistically, REV-ERBα induces chromatin accessibility and H3K27ac modification at promoters of LP genes through its recruitment of BRD4 and p300. Overexpression of REV-ERBα alone is sufficient to induce LP and neuroendocrine phenotype and confers cell resistance to ARSI in adenocarcinoma cells. Loss of REV-ERBα potently inhibits NEPC cell growth and abolishes the expression of LP drivers and gene programs. Pharmacological inhibition of REV-ERBα exhibits high potency in blocking the growth of NEPC tumors including patient-derived xenografts.  Our findings reveal that therapy-induced LP development entails a coordinated induction of a network of LP drivers and that REV-ERBα is a novel master regulator of the network and a promising therapeutic target for treatment of advanced prostate cancer such as NEPC.

overall_design: RNA-seq profiling of circadian regulator REV-ERBα inhibition or overexpression in prostate cancer cells and PDX tumors.

first: Yatian

last: Yang

first: Hongye

last: Zou

first: Demin

last: Cai

first: Eva

last: Corey

first: Ronald M

last: Evans

first: Hongwu

last: Chen


title: StealTHY: enabling CRISPR-Cas9 screens in immunocompetent hosts to expose concealed metastatic regulators [CRISPR]

first: Francesc

last: Castro-Giner

address: Otto-Stern-Weg 7

institute: ETH Zurich

summary: CRISPR screens have become standard gene discovery platforms in various contexts, including cancer. Yet, commonly available CRISPR-Cas9 tools are increasingly recognized as unfit for in vivo investigations in immunocompetent contexts, due to the broad immunogenicity of bacterial nucleases and reporters. Here, we show how CRISPR screens with tumor grafts are systematically jeopardized by immunoediting of Cas9-expressing cells in immunocompetent hosts, resulting in iatrogenic clonal dropouts and ultimately compromising target identification.

overall_design: Here, we systematically evaluated the immunogenicity of gold standard CRISPR-Cas9 tools in murine and humanized models of metastatic carcinoma, exploring the specific impact of each constitutive transgenic component on the tumor development, clonality, gene expression features and metastasis formation. In addition,  we introduce a novel platform designed to elude the combined immunogenicity of ectopic Streptococcus pyogenes Cas9 and bacterial proteins like Puromycin-N-acetyltransferase (PuroR), enabling the implementation of fully autologous in vivo CRISPR screens that provide more accurate insights into cancer-immune system interactions.

first: Saini

last: Massimo

first: Castro-Giner

last: Francesc

first: Aceto

last: Nicola


title: RNA-seq analysis of HUDEP-2 cells after erythroid differentiation

status: Public on Oct 26 2025

city: Seoul

first: Heesoo

last: Kim

address: 50 Yonsei-ro, Seodaemun-gu

department: Department of Systems Biology

institute: Yonsei University

summary: To understand the differentially expressed gene of HUDEP-2 cells during erythroid differentiation, we collected cells from each differentiated day and performed RNA-seq.

overall_design: RNA-seq using total RNAs purified from the HUDEP-2 cells at each differentiated days (D0, D1, D2, D3, D4, D5, D6, D7, D8, D12).


title: StealTHY: enabling CRISPR-Cas9 screens in immunocompetent hosts to expose concealed metastatic regulators [paired-end]

overall_design: To learn more about how T-cells are recruited in Cas9-expressing tumors, we carried out RNA-sequencing of tumors at the earliest time point of immune rejection, when Cas9-expressing cells are still predominant, namely between seven and 10 days post-transplantation

first: Massimo

last: Saini

first: Nicola

last: Aceto


title: StealTHY: enabling CRISPR-Cas9 screens in immunocompetent hosts to expose concealed metastatic regulators [single-end]


title: ZEB1, a novel junctional adhesion molecule A regulator, impacts sensitivity of pancreatic cancer-associated fibroblasts to reovirus

city: Solna

first: Bernhard

last: Schmierer

state: (optional)

address: Biomedicum 9B, Solnavagen 9

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: Oncolytic virus (OV) therapy is a promising treatment for various tumors. However, in pancreatic ductal adenocarcinoma (PDAC), the high abundance of cancer-associated fibroblasts (CAFs) can limit OV therapy efficacy by impairing viral spread and anti-tumor immunity. We have previously shown that oncolytic reovirus infection of CAFs depends on the expression of the reovirus entry receptor junctional adhesion molecule A (JAM-A), which is not or lowly expressed in most PDAC CAFs. We propose that increasing JAM-A expression on CAFs will boost viral spread in a tumor. However, there are currently no known regulators of JAM-A expression. Therefore, we performed a genome-wide CRISPR-Cas9 knockout screen to identify novel regulators of JAM-A expression. Ablation of the top negative regulator, zinc finger E-box binding homeobox 1 (ZEB1), in pancreatic fibroblasts led to strong JAM-A upregulation. We show that ZEB1 directly regulates JAM-A expression by binding to the enhancer-box (E-box) regions located within the JAM-A promoter. Importantly, ZEB1 ablation increased the sensitivity of fibroblasts to reovirus infection and subsequent cell death. Our work provides a novel overview of genes regulating JAM-A expression and provides a rational approach of combining ZEB1 inhibition with reovirus therapy to target both CAFs and tumor cells in stroma-rich tumors such as PDAC.

overall_design: Genome-wide CRISPR-KO screen to identify regulators of JAM-A surface expression. RLT-PSC cells stably expressing Cas9 were transduced with the Brunello genome-iwde guide library. At day 7 post transduction, a control sample was taken. The rest of the cells were stained with a JAM-A antibody and top and bottom 15% of cells (staining intensit) were collected by FACS. The screen was performed in two replicates

first: Dam

last: Nicole

first: Harryvan

last: Tom J.

first: Dang

last: Hao

first: Ioannidis

last: Gavriil

first: Schmierer

last: Bernhard

first: Haawinkels

last: Lukas J.A.C.

first: Kemp

last: Vera


title: Human PXR signaling enhances ethanol-induced liver injury in females

status: Public on Oct 25 2025

city: Seattle

first: Julia

middle: Yue

last: Cui

state: WA

address: 4225 Roosevelt Way NE Suite #100

department: Occupational and Health Sciences

institute: University of Washington

summary:
Alcohol-associated liver disease (ALD) results from excessive alcohol consumption and is more severe in females. The prenane X receptor (PXR), a xenobiotic nuclear receptor essential for toxin defense, has been implicated in ALD, but the underlying mechanisms remain unclear. Due to species differences in ligand specificty, humanized PXR (hPXR) mouse models are necessary to investigate its role in the sexual dimorphism of ALD in humans.
Ethanol exposure caused the most severe hepatoxicity in female hPXR mice with microarray analysis identifying 442 genes uniquely regulated by ethanol in female hPXR mice, implicated with ethanol-induced liver damage.

overall_design: Using the 10-day chronic-plus-binge ethanol (NIAAA) model, male and female C57BL/6N Tac wild-type (WT) and hPXR mice were assessed for hepatotoxicity, liver histopathology, protein expression, hepatic transcriptomics, and bioinformatic analyses. Additionally, gene expression and tissue microarray (TMA) analyses were conducted on human ALD samples.

first: Sarah

first: Maxwell

last: Gyamfi


title: Spatial gradients of chromatin accessibility endow embryonic cells with positional information [ATAC-seq]

status: Public on Oct 24 2025

city: Boston

first: Marcos

last: Simoes-Costa

state: Massachusetts

address: 300 Longwood Ave

department: Pathology

institute: Boston Children's Hospital

summary: Embryonic patterning relies on the ability of cells to record and process spatial cues they receive from the environment. In vertebrates, this process is orchestrated by the activation of signal transduction patterns by secreted ligands, which provide cells with positional information. How embryonic progenitors encode these spatial values within their regulatory states has remained a central question in developmental biology. Here, we report that spatial gradients of chromatin activation impart cells with positional values during axial specification. By utilizing spatially-resolved genomic analysis, we identified a set of positional cis-regulatory elements (pCREs) that can predict the location of cells in the developing avian embryo. pCREs are located in the loci of spatially-restricted genes and display graded activation patterns along the embryonic axes. pCRE gradients are established in the early gastrula, and their patterns of accessibility are controlled by the signaling systems involved in axial specification. Our results support the existence of a Cartesian system of chromatin activation that ensures the spatial coordination of cell differentiation in vertebrate embryos.

overall_design: Spatially-resolved transcriptomic and epigenomic analysis of early gastrula embryos

first: Ana

last: Azambuja

first: Megan

last: Rothstein

first: Tatiane

last: Kanno


title: Genome-wide profiling reveals a dual role for histone H2A monoubiquitylation at Polycomb-repressed and enhancer chromatin

city: Toronto

first: Daniel

last: Fusca

state: ON

address: 25 Willcocks Street

department: Department of Ecology and Evolutionary Biology

institute: University of Toronto


title: Analysis of genomic changes induced by the shape of ZnO nanoparticles

status: Public on Oct 23 2025

city: Warszawa

first: Alicja

last: Majewska

address: Nowoursynowska 159

department: Department of Physiology Sciences

country: Poland

institute: Warsaw University of Life Sciences-SGGW Faculty of Veterinary Medicine

summary:
Results of microarray analysis performed to test the effect of ZnO nanoparticle shape on embryonic development in an in ovo model for a dose concentration of 10 ug/ml.
Research was funded from NCN project OPUS UMO-2021/41/B/NZ4/04424 entitled “Influence of the oxide nanoparticles on the organogenesis of chicken embryos”

overall_design: Nanoparticles were administrated into air chamber and after 4 and 5 days embryos were collected for microarray analysis.

first: Bartlomiej

last: Dominiak

first: Julita

last: Rosowska

first: Agnieszka

last: Wal

last: Witkowski

first: Anna

last: Slonska-Zielonka

first: Joanna

last: Cymerys-Bulenda

first: Mikolaj

last: Gralak

first: Marek

last: Godlewski

first: Michal


title: snRNA-seq of centipede antennae (Scolopendra subspinipes mutilans): adult female antennae

status: Public on Oct 22 2025

city: Harbin

first: Wenqi

last: Dong

state: Heilongjiang

address: 26 Hexing Road, Wenzheng Street

institute: Northeast Forestry University

summary: We performed single-nucleus RNA sequencing to characterize the neuronal populations within centipede antennae.

overall_design: To investigate the specific expression receptors in the antennae neurons of centipedes, we collected the antennae of 30 adult female centipedes for snRNA-seq and gene expression analysis.

first: Licheng

last: Yuan

first: Jiangming

last: Shang

first: Jiatong

last: Cheng

first: Yunfei

last: Wang


title: Identification of Three New Rugose Small Colony Variants from a Pseudomonas aeruginosa Biofilm

status: Public on Oct 21 2025

city: Toledo

first: Erin

last: Prestwich

state: Ohio

address: 2801 W. Bancroft St.

department: Medicinal/Biological Chemistry

institute: University of Toledo

summary: Pseudomonas aeruginosa is a gram-negative, pathogenic, bacterium that produces biofilms containing phenotypically distinct subpopulations (Dodson et al., 2022). It was discovered that rugose small colony variants (RSCVs) were isolated with the biofilm subpopulations. RSCVs are hyper-biofilm producing bacterial mutants with increased antibiotic tolerance and are often found in chronic infections. When separating and characterizing the three biofilm cell subpopulations from a single P. aeruginosa PA14 biofilm, we discovered three novel RSCVs (denoted RSCV_1, RSCV_2, and RSCV_3). These RSCVs differed from stationary wild type (WT) PA14, the PA14 biofilm subpopulations, and between the RSCVs themselves. The observed phenotypic changes in the RSCVs included differences in cellular morphology, exopolysaccharide production, biosynthesis of virulence factors, biofilm formation, and antibiotic tolerance. Different molecules were ionized on the cell membranes of RSCVs and stationary phase WT PA14 using matrix assisted laser desorption ionization (MALDI) mass spectrometry. RNA sequencing analysis of stationary phase cells identified a high number of transcripts that were differentially expressed between the RSCVs and WT PA14 as well as between RSCV_1 and RSCV_3. The levels of the intracellular signaling molecule bis-(3′, 5′)-cyclic-dimeric-guanosine monophosphate (cyclic-di-GMP) were higher in all of the RSCVs compared to WT PA14 and significantly lower in RSCV_3 as compared to both RSCV_1 and RSCV_2.  Whole-genome DNA sequencing analysis revealed single-nucleotide deletions and single-nucleotide polymorphisms (SNPs) among the RSCVs and between the RSCVs to WT PA14. The detected differences in the RSCVs have significant implications for biofilm production, antibiotic tolerance, and virulence.

overall_design: Bulk RNA-seq profiling of RSCV_1 (n = 3), RSCV_3 (n = 3), and stationary phase WT PA14 (n = 3).

first: Benjamin

middle: K

last: Smartnick

first: Eric

last: Carlson

first: Chase

middle: N

last: Morse

first: Taylor

last: Dodson

first: Nathan

last: Wamer

first: Avery

last: Horne


title: A deep-learning tool for species-agnostic integration of cancer cell states

first: Jonathan

last: Rub

address: 417 E 68th St

department: Cancer Biology and Genetics

institute: MSKCC

summary: Genetically engineered mouse models (GEMM) of cancer are useful for exploring the development and biological composition of human tumors. Single-cell RNA-sequencing (scRNA-seq) provides a transcriptomic snapshot of cancer to explore heterogeneity of cell states in an immunocompetent context. However, cross-species comparison often suffers from biological batch effect and inherent differences between species decrease the signal of biological insights that can be gleaned from these models. Here, we developed scVital, a computational tool that uses a variational autoencoder and discriminator to embed scRNA-seq data into a species-agnostic latent space to overcome batch effect and identify cell states shared between species. In addition, latent space similarity (LSS) score was concurrently developed as a new metric to evaluate batch correction accuracy by leveraging pre-labeled clusters for scoring instead of the current method of creating new clusters. Using LSS for quantification, scVital performed comparably well relative to other deep learning algorithms and rapidly integrated scRNA-seq data of normal tissues across species with high fidelity. When scVital was applied to pancreatic ductal adenocarcinoma or lung adenocarcinoma data from GEMMs and primary patient samples, scVital accurately aligned biologically similar cell states. In undifferentiated pleomorphic sarcoma, a test case with no a priori knowledge of cell state concordance between mouse and human, scVital identified a previously unknown cell state that persisted after chemotherapy and is shared by a GEMM and human patient-derived xenografts. These findings establish the utility of scVital in identifying conserved cell states across species to enhance the translational capabilities of mouse models.

overall_design: KP GEMM mouse model and patient-derived xenograft models of UPS were treated with either vehicle, short-term doxorubicin (one week), or long-term doxorubicin (3-4 week) and single cell RNA-seq analysis was performe for characterization of cell states.

first: Jason

middle: E

last: Chan

first: Carleigh

last: Sussman

first: Gary

last: Guzman

first: William

last: Tap

first: Cristina

last: Antonescu

first: Samuel

last: Singer

first: Tuomas

last: Tammela

first: Doron

last: Betel


title: Spatial gradients of chromatin accessibility endow embryonic cells with positional information

first: Marcos

last: Simoes-Costa


title: Genome-wide profiling reveals a dual role for histone H2A monoubiquitylation at Polycomb-repressed and enhancer chromatin [ChIP-seq]

first: Daniel

last: Fusca

summary: Histone modifications are an integral component of eukaryotic genome regulation. Polycomb Repressive Complex 1 (PRC1) is responsible for depositing histone H2A lysine 119 mono-ubiquitylation (H2AK119ub) and can work cooperatively with PRC2-mediated histone H3 lysine 27 trimethylation (H3K27me3) to maintain gene repression. However, H3K27me3-independent functions and roles in gene activation have also been described for PRC1. Thus, the extent to which Polycomb complexes and their corresponding histone modifications function together or independently is unclear. Using C. elegans as a model, we investigated the relationship between H2AK119ub and H3K27me3. Here we show that the majority of H2AK119ub and H3K27me3 enrichment across the genome in embryos is distinct, and that the bulk levels of these modifications are regulated independently. We identify many genes related to nervous system development and functionality that have H2AK119ub-enriched promoters and are misregulated in H2AK119ub-deficient mutants, including a subset of genes that are normally H3K27me3-repressed. Surprisingly, we also find an enrichment of H2AK119ub at enhancers, including enhancers proximal to genes which are both up-regulated and down-regulated following the loss of this histone modification. Together, our results indicate a dual role for H2AK119ub in the regulation of both H3K27me3-repressed and enhancer chromatin states.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) of H2AK119ub and H3K27me3 in wild-type worms and mig-32 mutants

first: Kailynn

last: MacGillivray

first: Luomeng

last: Tan

first: Reta

last: Aram

first: Arneet

middle: L

last: Saltzman


title: Loss of FBXO11 establishes a stem cell program in acute myeloid leukemia by dysregulating LONP1

city: Vancouver

first: Aly

last: Karsan

address: 675 West 10th Avenue

institute: Canada's Michael Smith Genome Sciences Centre


title: 5-Formylcytosine Is Not a Prevalent RNA Modification in Mammalian Cells

city: Mainz

first: Alexandr

last: Gopanenko

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology gGmbH (IMB)

summary:
The RNA modification 5-formylcytidine (f5C) is poorly explored in mammals. Low f5C levels reported in mRNA may reflect spurious 5-methylcytidine (m5C) oxidation or targeted demethylation by TET or ALKBH1 dioxygenases. Here we analyze f5C in RNA of mouse embryonic stem cells (mESCs) using LC-MS/MS and chemical-assisted sequencing. We reveal that the previously reported pyridine-borane-sequencing method misidentifies N4-acetylcytidine (ac4C) and unmodified, hyper-reactive cytidines in a CUMC context as f5C. To overcome these limitations, we developed FIBo-seq with enhanced specificity and sensitivity for f5C-sequencing. We find no evidence for a role of TET enzymes in generating f5C, unlike for ALKBH1. Moreover, no f5C sites are detectable in mRNA. Instead, the bulk of mammalian f5C resides in the well-established mitochondrial tRNA Methionine (mt-tRNAMet) and is mediated by ALKBH1. The results argue against an instructive function for f5C outside tRNA in mammals.
This SuperSeries is composed of the SubSeries listed below.

first: Jasmin A.

last: Dehnen

first: Alexandr V.

first: Carola

last: Scholz

first: Michael U.

last: Musheev

first: Christof

last: Niehrs


title: Colonic mucosal gene expression profile associated with neoplastic progression in longstanding ulcerative colitis

status: Public on Oct 20 2025

city: Oslo

first: Yohan

last: Lefol

state: Oslo

address: Sognsvannsveien 20 Rikshospitalet

department: Institute of Clinical Medicine

country: Norway

institute: University of Oslo

summary:
Introduction: Many gene expression studies of colitis-associated colorectal cancer (CA-CRC) in patients with ulcerative colitis (UC) have focused on identification of molecular drivers of progression of UC to CA- CRC. However, they have primarily studied cancerous mucosal biopsies, an approach which primarily may identify the characteristics of the established cancer mucosa and not the early molecular events driving the progression. Long-standing mucosal inflammation is suspected to be one of the main drivers of CA-CRC. Still, not all patients with UC progress and develop cancer. We hypothesise that patients with UC, who have progressed to neoplasia (progressors), have a different molecular profile of inflammation than non-progressors.
Methods: We performed transcriptome profiling on 143 mucosal biopsies from non-neoplastic colonic segments of 14 UC progressors and 30 UC non-progressors. In addition, we performed profiling of lymphocyte infiltration to the mucosa of biopsies taken adjacent to biopsies used for transcriptomic analysis.
Results: We found a characteristic gene expression profile for inflamed mucosa of UC progressors, which primarily is associated with progression of UC to dysplasia or cancer as opposed to long duration of disease. The gene expression profile suggests that the inflamed tissue of UC progressors is negatively enriched for biological processes such as adaptive immune responses and complement system activity and positively enriched for biological processes related to detoxification. Moreover, we found that the microenvironment in the inflamed mucosa of progressors differs from non-progressors by having fewer infiltrating B cells and less lymphoid aggregates.
Conclusions: We found that inflammation of UC patients, who have progressed to dysplasia or cancer, has a different gene expression profile than that of UC non-progressors. Importantly, this profile was primarily associated with progression of disease as opposed to duration of disease. The inflamed mucosa of UC progressors may have lower levels of lymphoid organ-initiating and immune cell- attracting signals and fewer immune cells infiltrating the mucosa. Consequently, progressors may lack the ability to mount sufficient adaptive immune responses necessary to counteract driving forces of malignant transformation in UC.

overall_design: Patients from the prospective Lovisenberg Diakonale Hospital (LDS) and the prospective CA-CRC cohort from Akershus University Hospital (Ahus) were included in the study. In short, this study consists of patients with UC, who are at high risk for CA-CRC e.g., presenting with extension of inflammation proximal to splenic flexure (pancolitis) and at least eight years of disease duration from diagnosis of UC. Non-targeted biopsies were taken from each segment of the colon (ascending, transverse, descending and sigmoid colon as well as rectum). A biopsy was also taken within 2-4 cm of any lesions. Biopsies were preserved in liquid nitrogen. The analysis of gene expression included 14 progressors (five with CA-CRC, two with HGD, seven with LGD) and 30 non-progressors. In total 143 colon biopsies (49 progressor samples and 94 non-progressor samples) were analyzed covering histological non-neoplastic, non-inflamed as well as non-neoplastic, inflamed tissue from right and left colon and rectum. Samples were assigned to groups of non-inflamed and inflamed samples from non-progressor and progressor patients, respectively, resulting in four main sample groups. In addition, inflamed samples were assigned to chronic inflammation and chronic active inflammationfor non-progressors and progressors, respectively, resulting in four inflammation subgroups. All samples were located distant from lesions in the colon with dysplasia or cancer.

first: Lene

last: Alsøe

first: Stephan

last: Brackmann

first: Anna

last: Berit Wennerström

first: Yan

last: Liu

first: Solveig

last: Norheim Andersen

first: Hilde

last: Loge Nilsen


title: Deletion of the X gene, Kdm6a, in microglia reverses the disease-associated microglia transcriptome [CUT&Run]

status: Public on Oct 15 2025

city: Los Angeles

first: Yuichiro

last: Itoh

address: 635 Charles E. Young Drive South

department: Neurology

institute: UCLA

summary: Multiple sclerosis (MS) exhibits a sex difference with the female to male bias nearly 3:1. This may be due to differences in sex hormones, sex chromosomes, or both. Kdm6a is an X chromosome gene that escapes X-inactivation and encodes for a histone demethylase which can modulate autosomal gene expression. Females have two copies of Kdm6a, while males have one copy. Microglia play a key role in the neuropathology of MS. Thus, Kdm6a was selectively deleted in microglia in the MS model, experimental autoimmune encephalomyelitis (EAE), to determine the effect on microglia, neuropathology, and clinical disease. Deletion of the X chromosome gene Kdm6a in microglia ameliorated EAE in females. The transcriptome in microglia Kdm6a knockout mice compared to wild type showed downregulation of disease-associated microglia (DAM) markers and upregulation of resting microglia markers. Gene ontology analyses demonstrated that selective deletion of Kdm6a in microglia caused reversal of the transcriptome changes induced by EAE. In contrast to effects in female mice, selective deletion of Kdm6a in microglia of male mice had no effect on EAE. To complement findings using genetic knockouts, pharmacologic blocking of Kdm6a was done using metformin. Metformin treatment, compared to vehicle, ameliorated EAE in females, with microglia histologically and transcriptionally similar to those from healthy controls. Further in translation, analyses of microglia transcriptomes in MS and healthy controls suggested that blocking Kdm6a may be a novel strategy to target disease-associated microglia in MS women.

overall_design: KDM6A binding sites were identified in microglia with INTACT (isolation of nuclei tagged in specific cell types) approach and CUT&RUN Seq using Tmem119-Cre/ERT2- CAG-Sun1/sfGFP mice.


title: Deletion of the X gene, Kdm6a, in microglia reverses the disease-associated microglia transcriptome

overall_design: Microglia RNAs were isolated from RiboTag mice with Tmem119-Cre/ERT2. For cKO, Kdm6a gene was deleted using Tmem119-Cre/ERT2.


title: Characteristics of Extracellular Vesicle-Derived lncRNAs during the Progression of HBV-Related Hepatocellular Carcinoma

status: Public on Oct 16 2025

city: 天津

first: Yingtang

last: Gao

address: 83 Jintang Road, Hedong District

institute: The Third Central Hospital of Tianjin

summary: Using High-Throughput Sequencing to Conduct Integrated Analysis of the Whole Transcriptome in Blood sEVs from HBV-Associated Liver Disease Cohort

overall_design: Patients with HBV-associated liver diseases—chronic hepatitis B (CHB), liver cirrhosis (LC), benign liver disease (HA), and hepatocellular carcinoma (HCC)—were selected as the study cohort. High-throughput sequencing was utilized to perform comprehensive whole transcriptome analysis (mRNA, miRNA, lncRNA, and circRNA) of small extracellular vesicles (sEVs) isolated from serum .

first: Yanan

last: Ma

first: Cheng

last: Lou

first: Jing

last: liang

first: Chunyue

last: Guo

first: Jinjuan

last: Zhang

first: Chengjun

last: Lu

first: Jiandong


title: Intramuscular Enteric Glia Persist in Hirschsprung Disease and Undergo Neurogenesis in Response to GDNF-NCAM1 Signaling

first: Rhian

last: Stavely

state: MA

address: 185 Cambridge Street, CPZN, 6100

department: Pediatric Surgery

institute: Massachusetts General Hospital

summary:
Background & Aims
Enteric glial cells (EGCs) play vital roles in gut homeostasis and neurogenesis. Hirschsprung disease (HSCR) is a neurocristopathy, yet paradoxically, neural crest-derived enteric glial cells (EGCs) are present within the muscle of the affected region. This study investigates the molecular identity, origins, and neurogenic potential of EGCs in the aganglionic mouse and human colon.
Methods
We utilized single-cell RNA sequencing (scRNA-seq) from aganglionic and ganglionated segments of 10-14 day old Ednrb-null mice (Plp1-GFP;Ednrb-/-) and wild-type controls.
Results
scRNA-seq revealed the absence of GFAP+ intraganglionic (IG) glia in aganglionic colon, while CAMK2b+ extraganglionic (EG) glia and Schwann-like cells (SLCs) were present. EG glia exhibited a transcriptional profile similar to SLCs, suggesting a possible shared embryonic origin.
Conclusions
A subpopulation of extraganglionic EGCs, transcriptionally similar to SLCs, persists in the aganglionic segment of HSCR.

overall_design: Use of 10X Genomics technology to analyze single-cell transcriptomics in single cell suspensions of digested tissue from aganglionic and ganglionic tissue from Plp1-GFP;Ednrb-/- mice.

first: Jessica

last: Mueller

first: Allan

last: Goldstein


title: BAHD1 links H3K27me3 to gene silencing via a conserved BAH reader module and associated corepressor complex in mammalian cells (RNA-Seq)

city: Durham

first: Greg

last: Wang

state: NC

address: 3 Genome Court

department: Duke Department of Pharmacology and Cancer Biology  and Duke Cancer Institute

institute: Duke University School of Medicine, and Department of Biochemistry and Biophysics, UNC at Chapel Hill (adjunct)

summary: Trimethylation of histone H3 lysine 27 (H3K27me3) is crucially involved for gene silencing, (epi)genome organization, cell-fate decision-making and development. To date, functional readout of H3K27me3 is viewed to be achieved mainly through a class of H3K27me3-recognizing chromodomains harbored within the chromobox (CBX) subunit of Polycomb repressive complex 1 (PRC1), which causes chromatin compaction and gene repression partly through histone H2A lysine 119 mono-ubiquitination. We here report that engagement of H3K27me3 by an evolutionarily conserved bromo adjacent homology (BAH) domain harbored within BAH-containing protein 1 (BAHD1) significantly contributes to optimal repression of the H3K27me3-demarcated genes in mammalian cells. BAHD1 assembles a NurD-like transcriptional corepressor complex that contains histone deacetylase 1/2 (HDAC1/2) and MIER1/2/3. Abolishing the BAHD1BAH:H3K27me3 interaction by point mutagenesis interferes with BAHD1 binding to chromatin, resulting in chromatin remodeling at target genes and derepression of Polycomb-related genes. Mice carrying an H3K27me3-association-defective mutation at Bahd1BAH causes marked embryonic lethality, indicating a requirement of this pathway for development. Altogether, this work demonstrates an H3K27me3-initiated signaling cascade that operates through a conserved BAH ‘reader’ module class in mammals.

overall_design: In E14 cell, Bahd1 was depleted using CRISPR-Cas9 system. pPyCAGIZ plasmid containing either wild type GFP-Bahd1 or GFP-Bahd1 (Y637A) mutant cDNA were overexpressed in Bahd1-null E14 cells.

first: Huitao

last: Fan

first: Yiran


title: PhpCNF-Y transcription factor infiltrates heterochromatin to generate  cryptic intron-containing transcripts crucial for small RNA production [Small RNA-Seq]

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

summary: The assembly of repressive heterochromatin in eukaryotic genomes is crucial for silencing lineage-inappropriate genes and repetitive DNA elements. Paradoxically, transcription of repetitive elements within constitutive heterochromatin domains is required for RNA-based mechanisms, such as the RNAi pathway, to target heterochromatin assembly proteins. However, the mechanism by which heterochromatic repeats are transcribed has been unclear. Using fission yeast, we show that the conserved trimeric transcription factor (TF) PhpCNF-Y complex can infiltrate constitutive heterochromatin via its histone-fold domains to transcribe repeat elements. PhpCNF-Y collaborates with a Zn-finger containing TF to bind repeat promoter regions with CCAAT boxes. Mutating either the TFs or the CCAAT binding site disrupts the transcription of heterochromatic repeats. Although repeat elements are transcribed from both strands, PhpCNF-Y-dependent transcripts originate from only one strand. These TF-driven transcripts contain multiple cryptic introns whose predicted splice sites are required for the generation of small interfering RNAs (siRNAs) via a mechanism requiring the spliceosome. Our analyses show that siRNA production by this TF-mediated transcription pathway is critical for heterochromatin nucleation at target repeat loci. This study reveals a mechanism by which heterochromatic repeats are transcribed, initiating their own silencing by triggering a primary cascade that produces siRNAs necessary for heterochromatin nucleation.

overall_design: RNA-sequencing (RNA-seq), Small RNA-Seq in fission yeast.

first: Srivastav

last: Manjit Kumar

first: Folco

last: H Diego

first: Vijayakumari

last: Drisya

first: Nathanailidou

last: Patroula

first: Anil

last: Anupa

first: Jain

last: Shweta

first: Dhakshnamoorthy

last: Jothy

first: O’Neill

last: Maura

first: Andresson

last: Thorkell

first: Wheeler

last: David

first: Grewal

last: Shiv I.S.


title: PhpNF-Y drives heterochromatic transcription to generate splicing machinery-dependent small RNAs [RNA-Seq]

summary: Heterochromatin regions of the genome are transcriptionally repressive in nature. However, constitutive heterochromatin, such as at centromeres and telomeres, coats regions harboring multiple repetitive DNA elements that are preferentially transcribed during S-phase by RNA polymerase II. RNAi machinery processes the transcripts to generate small RNAs (siRNAs) that are crucial for heterochromatin assembly. Despite significant mechanistic advances in the field, the contribution of transcription factor (TF) based mechanisms to repeat element transcription and siRNA production is unclear. Here, we discover that the conserved TF PhpCNF-Y, which contains a histone fold motif, collaborates with a Zn-finger domain-containing factor, Moc3, to access specific sites within the heterochromatin region, regardless of the presence of the repressive histone methylation mark. The cooperative function of the TFs is essential for gaining access to the heterochromatin region, where they bind to specific CCAAT motif sites within the heterochromatic repeat elements cenH and dh. Perturbation of heterochromatin has minimal effect on the binding of the TFs to these specific sites, and they remain bound even outside of the S-phase. We find that PhpCNF-Y and Moc3 mediate the transcription of the repeat elements originating from a bottom strand of cenH, which the spliceosome targets to generate siRNAs in a Swi6HP1-independent manner. This pathway for generating the initial transcripts is crucial for de novo heterochromatin assembly. Collectively, our study uncovers a fundamental transcription factor-based mechanism that gains access to the heterochromatin to enforce transcriptional silencing of repeat elements. Our findings provide significant insights into de novo heterochromatin assembly.


title: Activated Glucocorticoid Receptor is an Estrogen Receptor Silencer in ERα+ metastatic breast cancer [RNA-seq]

city: Basel

first: Mohamed

last: Bentires-Alj

address: Hebelstrasse 20

department: DBM

institute: University Hospital Basel

summary: Estrogen Receptor alpha (ERα)-positive, HER2-negative breast cancers are less aggressive than other subtypes and generally show good patient clinical outcome because they are likely to respond to endocrine therapies. Unfortunately, therapy-resistant metastases may develop and start an inexorable downhill course. ESR1 mutations leading to ligand-independent ERa activation and resistance to endocrine therapy are prevalent in 20 - 55% of patients with ER+ metastatic breast cancer. Here, we found that glucocorticoid receptor (GR) activation  by dexamethasone in ESR1 mutant metastases-bearing mice decreases liver metastases, enhances chemotherapy responsiveness, and prolongs survival. Transcriptomic profiling and proteomics profiling revealed that GR activation not only downregulates estrogen reponse signature but also induces dramatic loss of ER itself, therefore uncovering an estrogen receptor silencing action of GR. ChIP-Seq analysis revealed that prolonged Dex treatment almost completely abrogates ER chromatin binding and that GR binds a subset of ER-related genes including ESR1 itself. This was accompanied by loss of H3K27 acetylation and enhancer acetylation, hence inhibiting transcription. Finally, we found that GR activation in patient-derived organoids reduces the number of ER+ cancer cells and ERα abundance, and predicts good outcome in patients with ER+ breast cancer, using publicly available data. These data imply that administration of synthetic glucocorticoids reduces ER+ cell proliferation, inhibits metastatic ability, enhances chemotherapy efficacy and hence can be beneficial for patients with ER+ metastatic breast cancer, particularly the treatment of refractory ESR1 mutant metastases.

overall_design: MCF-7 ESR1 mutant D538G and Y537S cell lines plated in 6 well plate (2D monolayer), and cultured for 2 days in 2.5% Charcoal stripped FCS, phenol red free DMEM medium were vehicle or Dexamethasone (700 nM) treated for 8h or 24h to activate glucocorticoid receptor.

first: Madhuri

last: Manivannan

first: Charly

last: Jehanno

first: Michal

last: Kloc


title: Activated Glucocorticoid Receptor is an Estrogen Receptor Silencer in ERα+ metastatic breast cancer [ChIP-seq]

overall_design: MCF-7 ESR1 mutant D538G cells plated in 10 cm dishes (2D monolayer), and cultured for 2 days in 2.5% Charcoal stripped FCS, phenol red free DMEM medium were vehicle or Dexamethasone (700 nM) treated for 1h or 24h, in order to assess GR and ER binding to chromatin over different exposure times to Dex.


title: Perimenopausal State Oestradiol to Progesterone Imbalance Drives Alzheimer’s Risk via ERRα Dysregulation and Energy Dyshomeostasis

city: Sha Tin

first: Jacquelyne

last: Sun

state: New Territories

address: Room 612A, Mong Man Wai Building,

department: School of Life Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

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

Sex-biased differences in Alzheimer’s disease (AD) are well documented, but the mechanisms underlying increased vulnerability in postmenopausal women remain unclear. This study aimed to model the effects of perimenopausal hormonal fluctuations on AD pathophysiology. Using a VCD-induced accelerated ovarian failure model in young female C57BL/6J and 3xTg mice, we simulated a perimenopausal state with hormonal changes characterized by elevated oestradiol levels and reduced progesterone levels. Supporting human brain transcriptomic and metabolomic data from the ROSMAP study revealed that impaired oestrogen-related receptor alpha (ERRα) function was a key driver of female sex-biased vulnerability. In female mice, progesterone-guided oestrogen receptor signalling maintained ERRα activity by regulating neuronal cholesterol homeostasis and the TCA cycle. Hormonal imbalances disrupted this mechanism, triggering an aspartate-driven “minicycle,” which increased glutamate release, neuronal excitability, ATP depletion, and energy crisis susceptibility. This study demonstrates how perimenopausal hormonal imbalances exacerbate AD risk via ERRα dysfunction, linking neuronal cholesterol and energy homeostasis to disease vulnerability.

overall_design: Refer to individual Series

first: Kim Hei-Man

last: Chow


title: Deletion of the X chromosome gene Kdm6a in microglia is protective in the multiple sclerosis model [hippocampus]

first: Yuichiro

last: Itoh

state: California

summary: Multiple sclerosis (MS) exhibits a sex difference in susceptibility with females affected more frequently than males. Sexual dimorphisms may be due to differences in sex hormones, sex chromosomes, or both. Regarding sex chromosomes, some X chromosome genes escape X-inactivation and have higher expression in females (XX) compared to males (XY). The Genotype Tissue Expression Project (GTEx) has found that 37% of all genes exhibit sex biased expression which is tissue-specific and cell-specific, but the etiology and ramifications of this sex difference remain unknown. Kdm6a is an X chromosome gene that escapes X-inactivation and encodes for a histone demethylase which can modulate autosomal gene expression. Given the important role of microglia in neurodegenerative diseases, we created a tissue-specific and cell-specific conditional knock out (cKO) of Kdm6a in microglia and induced experimental autoimmune encephalomyelitis (EAE), the most widely used mouse model for MS. Deletion of Kdm6a in microglia ameliorated EAE. Gene expression analysis of spinal cord microglia during EAE in the Kdm6a cKO revealed downregulation of degeneration associated microglial markers and upregulation of resting microglial markers compared to EAE in wild type. Genome wide transcriptome analyses demonstrated reversal of the EAE associated transcriptome in microglia in Kdm6a cKO mice, instead aligning with that of the transcriptome of microglia in healthy mice. Finally, there was a sex difference in the effect of selective deletion of Kdm6a in microglia whereby EAE was abrogated in females more significantly than in males. Together, this demonstrates that the X-escapee Kdm6a is disease promoting in microglia of females with neurodegenerative disease.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hippocampus microglia RNAs

first: Rhonda

last: Voskuhl


title: PhpCNF-Y transcription factor infiltrates heterochromatin to generate  cryptic intron-containing transcripts crucial for small RNA production [ChIP-Seq]

first: Shiv

last: Grewal

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) in fission yeast. Input control and immunoprecipitation samples are provided for each experiment.

first: Srivastav

last: Manjit Kumar

first: Folco

last: H Diego

first: Vijayakumari

last: Drisya


title: Deletion of the X chromosome gene Kdm6a in microglia is protective in the multiple sclerosis model, female and male

overall_design: Comparative gene expression profiling analysis of RNA-seq data for spinal cord microglia RNAs, female and male Tmem119-Cre:RiboTag mice.


title: Deletion of the X chromosome gene Kdm6a in microglia is protective in the multiple sclerosis model, female and male II

overall_design: Comparative gene expression profiling analysis of RNA-seq data for spinal cord microglia RNAs, female and male


title: Deletion of the X chromosome gene Kdm6a in microglia is protective in the multiple sclerosis model

overall_design: Comparative gene expression profiling analysis of RNA-seq data for spinal cord microglia RNAs


title: MODY PDX1P33T: A Mouse Model Reveals Phenotypic Divergence from Human Disease

status: Public on Oct 13 2025

city: Neuherberg

first: Gerhard

last: Przemeck

address: Ingolstaedter Landstr..1

institute: Helmholtz Munich

summary: Introduction: Maturity-onset Diabetes of the Young (MODY) is a rare form of diabetes and arises from mutations in key regulatory genes of the pancreatic beta-cell, leading to their functional impairment and early-onset diabetes. Research into PDX1-MODY, a form of MODY caused by mutations in the PDX1 gene, enhances understanding of gene-specific mechanisms underlying glucose dysregulation and provides insights into possible approaches to restore normal metabolic function. However, no currently published mouse model accurately depicts the genetic cause of PDX1-MODY in human patients.  Methods: Using CRISPR-Cas9 technology, we generated the first mouse model carrying one of the most prevalent pathological PDX1 point mutation found in human patients, P33T, and conducted an 18-week in vivo phenotyping experiment assessing homozygous PDX1P33T and wild-type littermates on both chow and high fat diet (HFD). Additionally, transcriptomic and proteomic analyses were performed on isolated pancreatic islets. Islet architecture was investigated via fluorescent microscopy. Result: Contrary to expectations, our comprehensive phenotypic analysis of the mouse model carrying the homozygous PDX1P33T point mutation revealed no significant differences in metabolic parameters compared to wild-type controls, and no pathological outcomes were observed as seen in human patients. Notably, male PDX1P33T mice exhibited an increase in islet size and number on chow diet but failed to adapt respectively on HFD. Discussion: Our work indicates substantial differences between mouse and human PDX1 function in the pancreas. Further refinement of animal models is necessary to better elucidate the pathophysiology of PDX1-MODY. Ultimately, this study emphasizes the complexities involved in translating human pathologies to animal models, serving as a reminder that findings generated in mice may not always be easily translated to humans.

overall_design: We analysed whole pancreatic islets from homozygous 14-week old PDX1P33T mice, and wt/wt controls

first: Aliona

last: Harten

first: Maximilian

middle: R

last: Schmidtke

first: Florian

last: Giesert

first: David

last: Skerrett-Byrne

first: Raffaele

last: Teperino

first: Martin

last: Hrabě de Angelis


title: Dissecting Gene Regulatory Networks Governing Human Cortical Cell Fate

city: San Francisco

first: Alex

last: Pollen

institute: UCSF

summary: Human cortical neurogenesis involves conserved and specialized developmental processes during a restricted window of prenatal development. Radial glia (RG) neural stem cells shape cortical cell diversity by giving rise to excitatory neurons, oligodendrocytes, and astrocytes, as well as olfactory bulb interneurons (INs) and a recently characterized population of cortical INs. Complex genetic programs orchestrated by transcription factor (TF) circuits govern the balance between self-renewal and differentiation, and between different cell fates. Despite progress in measuring gene regulatory network activity during human cortical development, functional studies are required to evaluate the roles of TFs and effector genes in human RG lineage progression. Here we establish a human primary culture system that allows sensitive discrimination of cell fate dynamics and apply single cell clustered regularly interspaced short palindromic repeats interference (CRISPRi) screening to examine the transcriptional and cell fate consequences of 44 TFs active during cortical neurogenesis. We identified multiple TFs, with novel roles in cortical neurogenesis, including ZNF219, previously uncharacterized, that represses neural differentiation and NR2E1 and ARX that have opposing roles in regulating RG lineage plasticity and progression across developmental stages. We also uncovered convergent effector genes downstream of multiple TFs enriched in neurodevelopmental and neuropsychiatric disorders and observed conserved mechanisms of RG lineage plasticity across primates. We further uncovered a postmitotic role for ARX in safeguarding IN subtype specification through repressing LMO1. Our study provides a framework for dissecting regulatory networks driving cell fate consequences during human neurogenesis.

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: (1) 2D Libraries: Perturb-seq targeting 44 TFs on differentiation D0 and D7: Primary human culture derived from cortical RG were transduced with CRISPRi library targeting 44 TFs with capture sequence on each guide expanded for 7 days (D0) and differentiated for 7 days (D7). Cells were sorted based on GFP expression and captured using 10X Chromium v3.1 HT kit for single cell RNA sequencing. (2) HM2D libraries: Perturb-seq targeting 5 TFs with lineage tracing on differentiation D7: Primary human or macaque culture derived from cortical RG were transduced with CRISPRi library targeting 5 TFs with capture sequence on each guide and STICR static barcode library, expanded for 7 days and differentiated for 7 days. Cells were sorted based on GFP and mCherry co-expression and captured using 10X Chromium v3.1 HT kit. (3) Slice culture libraries: Perturb-seq targeting 5 TFs with lineage tracing on differentiation D12-14: The germinal zone of the developing human brain was locally transduced with CRISPRi library targeting 5 TFs and STICR static barcode library, cultured for 12-14 days. Cells were sorted based on GFP and mCherry co-expression and captured using 10X Chromium v3.1 HT kit. (4) Double knockdown libraries: Perturb-seq targeting ARX and LMO1 on differentiation D7: Primary human culture derived from cortical RG were transduced with CRISPRi library targeting ARX and LMO1 expanded for 7 days (D0) and differentiated for 7 days (D7). Cells were sorted based on GFP and mCherry co-expression and captured using Illumina Single Cell CRISPR Library kit.

first: Jingwen

middle: W

last: Ding


title: KLF5 interacts with RUVBL1/2 to activate classical and basal lineage identities in PDAC [ChIP-seq]

status: Public on Oct 08 2025

city: Cold Spring Harbor

first: Patrick

middle: Joseph

last: Cunniff

address: 1 Bungtown Road

department: Cancer Center

institute: Cold Spring Harbor Laboratory

summary: We identify KLF5 as a lineage master regulator and a dependency in classical and basal subtypes of human PDAC. We integrate proteomic and genetic screens to reveal RUVBL1 and RUVBL2 as transcriptional coactivators of KLF5 in PDAC. We use biochemical and epigenomic methods to validate that KLF5-RUVBL1/2 complexes directly activate lineage identity genes in PDAC.

overall_design: ChIP-seq of KLF5 and RUVBL1/2 in basal-like and classical human pancreatic cancer cell lines.

middle: J

first: Christopher

last: Vakoc


title: Global gene expression in human T cells with targeted disruption of TRAF6 or HOIP

status: Public on Oct 11 2025

city: Parkville

first: Göksu

last: Avar

state: Victoria

address: 30 Flemington Road

department: Biochemistry and Pharmacology

country: Australia

institute: University of Melbourne

summary: We profiled gene expression in human CD4 T cells with CRISPR disruptions of TRAF6 or HOIP. The dataset captures transcriptional outputs linked to CBM-proximal ubiquitin signaling and MALT1 activity, enabling comparison of TCR- and TNFR-driven responses and providing a resource to study how distinct E3 ligases shape NF-κB–related programs.

overall_design:
Primary human CD4⁺ T cells from four donors were edited by CRISPR–Cas9 to disrupt TRAF6 or HOIP (RNF31). Cells were activated via plate-bound TCR/CD28 costimulation for 48 h prior to RNA collection.

##############################################################
Raw data (FASTQ) available on SRA (BioProject Accession PRJNA1277211).
##############################################################

first: Carina

last: Graß

first: Franziska

last: Ober

first: Constanze

last: Sixt

first: Bahareh

last: Moud

first: Irina

last: Antoshkina

first: Frederik

last: Eberstadt

first: Alisa

last: Pulach

first: Antonia

last: Keßler

first: Thomas

last: O’Neill

last: Seeholzer

first: Jan

last: Kranich

last: Brocker

first: Katja

last: Lammens

first: Michael

middle: P

last: Menden

first: Christina

last: Zielinski

first: Daniel

last: Krappmann


title: p53 regulates the expression of histone modifiers to restrict stemness and maintain differentiated luminal identity in breast cancer

city: Rehovot

first: Efrat

last: Shema

state: Israel

address: 234 Hertzel

department: Department of Immunology & Regenerative Biology

country: Israel

institute: Weizmann Institute of Science

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


title: Single-cell Multiomics Analysis Reveals CTCF as a Key Regulator of Lung Morphogenesis and Progenitor Maintenance

status: Public on Oct 09 2025

city: shenzhen

first: Jiang

last: Yamei

address: longfei

institute: The Chinese University of Hong Kong-Shenzhen

summary: Lung development generates a complex tree-like architecture through proximal-distal patterning and branching morphogenesis. However, the gene regulatory programs governing embryonic lung development remain poorly understood. Here, we present a comprehensive single-cell multi-omics atlas of mouse embryonic lungs, integrating gene expression and chromatin accessibility profiles. Through systematic analysis, we identify 13 distinct cell types and map cis-regulatory elements, peak-to-gene linkages, and transcription factors underlying lung development. Leveraging this multi-modal dataset, we uncover lineage-determining transcription factors  driving cell differentiation, including the Activated Protein-1 complex. We further delineate gene regulatory networks involving diverse transcription regulators, including CCCTC-binding factor. Using the Ctcf conditional knockout mouse, coupled with histological and multi-omics analyses, we demonstrate that CCCTC-binding factor  orchestrates lung progenitor maintenance and branching morphogenesis by modulating both gene expression and chromatin accessibility. Thus, our study provides a multi-omics resource and mechanistic insights for transcriptional regulation of lung morphogenesis.

first: Shenfei

last: Sun

first: Yamei

last: Jiang

first: Fujing

last: Huang

first: Wei

last: Wei

first: Mathias

last: Hochgerner

first: Tianmin

last: Xu

first: Xiaoting

last: Wang

first: Kaijun

last: Lin

first: Xinna

last: Zhang

first: Yanli

first: Hua

last: He

first: Miao

last: Yu

first: Xiaofang

last: Tang

first: Xinhua


title: A stress response axis in tumor-associated macrophages dictates phenotype heterogeneity and immunotherapy evasion

status: Public on Oct 10 2025

city: Zurich

first: Florence

last: Vallelian

address: Rämistrasse 100

institute: University Hospital Zürich


title: BAHD1 links H3K27me3 to gene silencing via a conserved BAH reader module and associated corepressor complex in mammalian cells (CUT&RUN)

first: Greg

overall_design: In E14 cell, Bahd1 was depleted using CRISPR-Cas9 system. pPyCAGIZ plasmid containing Wild type GFP-Bahd1 cDNA was overexpressed in Bahd1-null E14 cells.

first: Yiran

last: Guo


title: KLF5 interacts with RUVBL1/2 to activate classical and basal lineage identities in PDAC [CRISPR]

first: Patrick

last: Cunniff

overall_design: FACS-based  CRISPR screens (genome-wide and TF-focused pilot library) to nominate coactivators of KLF5

first: Christopher

last: Vakoc


title: Discovery and characterisation of VPRBP/DCAF1 kinase inhibitor analogues as microtubular destabilising agents with potent anti-myeloma activity

status: Public on Oct 06 2025

city: Melbourne

first: Emily

last: Gruber

state: VIC

address: 305 Grattan St

institute: Peter MacCallum Cancer Centre

summary: Multiple myeloma is a plasma cell malignancy that is susceptible to drugs targeting protein homeostasis such as thalidomide analogues and proteasome inhibitors. Thalidomide analogues modulate the activity of DDB1/CUL4 E3-ligase complexes to perturb substrate recognition and proteasomal degradation thereof. We hypothesised that the cellular pool of DDB1/CUL4 associated factors (DCAFs) may mediate other essential plasma cell processes and offer new targets for therapeutic intervention. Unbiased genetic screening identified DCAF1 (also known as Vpr-binding protein; VPRBP) as essential for myeloma cell survival with a multidomain structure offering several distinct opportunities for drug development. Utilising B32B3, a previously disclosed DCAF1 kinase inhibitor as a template, we developed a series of analogues with enhanced anti-myeloma potency. As anti-myeloma activity did not associate with dephosphorylation of known DCAF1 kinase substrates, we correlated drug-induced cellular phenotypes with whole-genome CRISPR/Cas9 resistance screening to further define mechanistic activity. These studies identified B32B3 analogues as microtubular destabilising agents with potential DCAF1 kinase independent properties and in vivo efficacy in multiple myeloma and lymphoma.

overall_design: RNAsequencing was performed on JJN3 cells that were treated with B32B3 or VPR8 for 6 or 24h.

first: Lev

last: Kats


title: CD8+ T cells in the tumor immune microenvironment modulate resistance to endocrine therapy in hormone receptor-positive breast cancer

status: Public on Oct 07 2025

city: Dallas

first: Fabiana

last: Napolitano

state: TX

address: 6000 Harry Hines Blvd.

institute: Simmons Comprehensive Cancer Center

summary: Enhanced immune infiltration in the tumor immune microenvironment (TIME) is associated with better survival outcomes in patients with triple negative and HER2+ breast cancers. In the hormone-dependent hormone receptor-positive (HR+) subtype, previous studies have identified a subgroup with enhanced immune infiltration. However, the biological significance and role of the TIME in modulating the response to anti-estrogen therapy in breast cancer are not well understood. Herein, using cyclic immunofluorescence and spatial transcriptomics (ST), we dissected the TIME in primary breast cancers that were sensitive or resistant to estrogen deprivation (ED) induced by the aromatase inhibitor letrozole. Stromal tumor-infiltrating lymphocytes (TILs) were increased in ED-resistant vs. ED-sensitive tumors. RNA-sequencing from on-treatment tumors showed differentially regulated pathways, including immune-related gene sets, such as upregulation of IFNɣ and IFNα signaling and allograft rejection. Spatial transcriptomics using GeoMx identified increased antigen processing and immune gene expression signatures in both cancer cells and neighboring immune cells in ED-resistant vs. ED-sensitive tumors. Using CIBERSORT, we uncovered a differential distribution of immune cell subtypes, with CD8+ T cells being enriched in ED-resistant tumors and Tregs in ED-sensitive tumors. The expression of chemokine genes involved in CD8+ T cell recruitment, CXCL9, CXCL10, and CXCL11, was upregulated in ED-resistant primary tumors before and after letrozole treatment. Additionally, CXCL11 levels were higher in media conditioned from HR+ breast cancer cells co-cultured with CD8+ T cells. Both recombinant CXCL11 and co-culture with CD8+ T cells stimulated the growth of HR+ breast cancer cells when deprived of estrogen, akin to the scenario of patients treated with letrozole. Taken together, these data suggest that CD8+T cells in the TIME modulate the response of HR+ breast cancer cells to therapeutic estrogen suppression.

overall_design: To investigate the composition of the TIME in HR+ BC sensitive or resistant to estrogen deprivation (ED), and explore possible mediator of resistance to ED

first: Yunguan

first: Ariella B.

last: Hanker

first: Carlos L.

last: Arteaga


title: CD8+ T cells in the tumor immune microenvironment modulate resistance to endocrine therapy in hormone receptor-positive breast cancer [GeoMx]

first: Ariella

middle: B

first: Carlos


title: KLF5 interacts with RUVBL1/2 to activate classical and basal lineage identities in PDAC [SLAM-seq]

state: NY

overall_design: SLAM-seq following KLF5 degradation or RUVBL1/2 inhibition in basal-like and classical human pancreatic cancer cell lines.


title: KLF5 interacts with RUVBL1/2 to activate classical and basal lineage identities in PDAC [RNA-seq]

overall_design: RNA-seq following KLF5 and RUVBL1/2 manipulation in basal-like and classical human pancreatic cancer cell lines.


title: CD3ε-targeted circRNA-LNP enables One-Step in vivo CAR-T cell therapy with durable solid tumor remission

city: Dongguan

first: Kai

last: Cui

address: No.1 Xincheng Avenue,Songshan Lake Science and Technology Industrial Park

institute: Guangdong Medical University

summary: This study analyzed the transcriptional changes of CAR-T cells after co-culture and cytotoxic activity against gastric cancer cell lines HGC-27 and AGS using RNA sequencing. Compared with control Mock T cells, CAR-T cells co-cultured with HGC-27 showed upregulation of CXCL10, CCL17, IL26, SPHK1, SFN, TRBV7-7, and TRAJ36, while TP53INP1, KLRB1, KLF10, TRIB1, and PIK3CG were downregulated. In the AGS co-culture group, CAR-T cells exhibited upregulation of CCR8, TRAV26-2, TRBV10-1, TRBJ1-6, TRBJ2-6, TRAJ5, and TRAV15, and downregulation of KRT19, CEACAM5, F3, KRT18, and PIK3R2. These findings highlight distinct gene expression signatures of CAR-T cells in different gastric cancer cell contexts.

overall_design:
In this study, anti-Claudin18.2 CAR-T cells were generated and co-cultured with two gastric cancer cell lines (HGC-27 and AGS). The experimental groups consisted of CAR-T cells after co-culture with tumor cells, while the control groups consisted of Mock T cells co-cultured with tumor cells. Biological replicates were included for each group. After cytotoxic co-culture assays, T cells were collected for RNA sequencing. Transcriptome sequencing was performed using the Illumina platform.
D3-C-A = CAR-T cells co-cultured with AGS
D3-M-A = Mock T cells co-cultured with AGS
D3-C-H = CAR-T cells co-cultured with HGC-27
D3-M-H = Mock T cells co-cultured with HGC-27