title: DNMT3A:R882H Is Not Required for Disease Maintenance in Primary Human AML, but Is Associated With Increased Leukemia Stem Cell Frequency [RNA-Seq]

city: Stanford

first: Thomas

last: Koehnke

address: 265 Campus Drive

institute: Stanford University

summary: Genetic mutations are being thoroughly mapped in human cancers, yet a fundamental question in cancer biology is whether such mutations are functionally required for cancer initiation, maintenance of established cancer, or both. Here, we study this question in the context of human acute myeloid leukemia (AML), where DNMT3A:R882 missense mutations often arise early, in pre-leukemic clonal hematopoiesis, and corrupt the DNA methylation landscape to initiate leukemia. We developed CRISPR-based methods to directly correct DNMT3A:R882 mutations in leukemic cells obtained from patients. Surprisingly, DNMT3A:R882 mutations were largely dispensable for disease maintenance. Replacing DNMT3A:R882 mutants with wild-type DNMT3A did not impair the ability of AML cells to engraft in vivo, and minimally altered DNA methylation. Taken together, DNMT3A:R882 mutations are initially necessary for AML initiation, but are largely dispensable for disease maintenance. The notion that initiating oncogenes differ from those that maintain cancer has important implications for cancer evolution and therapy.

overall_design: Bulk RNA-Seq of human leukemic blasts 4 months after re-mutation or correction of DNMT3A:R882H

last: Köhnke

first: Daiki

last: Karigane

first: Ravindra

last: Majeti


title: RNA-sequencing of SVF-derived preadipocytes from inguinal adipose tissue of male mice differentiating under control conditions or treated with CGRP

status: Public on Oct 28 2025

city: ANN ARBOR

first: Jorge

middle: L

last: Ruas

state: Michigan

address: 2800 Plymouth RD, B025-2681 NCRC - Ruas Lab NCRC B025

country: USA

institute: University of Michigan

type: Expression profiling by high throughput sequencing

summary: To investigate the effects of CGRP on adipocyte differentiation, we treated stromal vascular fraction (SVF)-derived preadipocytes from inguinal white adipose tissue (iWAT) of male mice with CGRP during differentiation. RNA-sequencing was performed across a full time course of normal differentiation to identify transcriptional changes induced by CGRP treatment compared to control conditions.

overall_design: RNA sequencing analysis of stromal vascular fraction (SVF)-derived preadipocytes from inguinal white adipose tissue (iWAT) of male mice (n = 3 per group, C57BL/6N) undergoing differentiation under control conditions or with CGRP treatment. Total RNA was extracted using TRI reagent (Sigma-Aldrich, T9424) according to the manufacturer's instructions. RNA was further purified, and DNase treated (Zymo, R1013), and integrity confirmed prior to sequencing (Agilent Technologies, 2100 Bioanalyzer), with an RNA integrity number (RIN) greater than 7 as a threshold. Samples were purified by poly-A enrichment before library preparation using the Illumina NovaSeq X Plus Series platform with a paired-end 150 base pair strategy.

first: Kyle

middle: D

last: Dumont


title: CDK10 suppresses nucleic acid sensors-mediated antitumor immunity [scRNA-Seq]

status: Public on Oct 27 2025

city: wuhan

first: Gaoshan

last: Xu

state: -- Please Select --

address: wuhan

country: China

institute: wuhan university

summary: Cdk10 knockout significantly reduced CT26 tumor growth in immunocompetent BALB/c WT mice. To investigate how Cdk10 influences the tumor immune microenvironment in vivo, we performed single-cell RNA sequencing (scRNA-seq) on WT and Cdk10 KO CT26 tumors derived from immunocompetent BALB/c mice.

overall_design: We subcutaneously inoculated sgControl and sgCdk10 CT26 cells into immunocompetent BALB/c WT mice,and single-cell sequencing was performed


title: DNMT3A:R882H Is Not Required for Disease Maintenance in Primary Human AML, but Is Associated With Increased Leukemia Stem Cell Frequency [scRNA-Seq]

state: CA

overall_design: Single-cell RNA-Seq of human pre-leukemic HSPCs differentiated in vitro for 14 days after re-mutation or correction of DNMT3A:R882H


title: Multi-omics Analysis and Evidence of IL1R1 as a Potential Biomarker for Diabetes-related Intervertebral Disc Degeneration

city: Beijing

first: Lixiang

last: Ding

state: None Selected

address: No. 10, Tieyi Road, Yangfangdian, Haidian District, Beijing

institute: Beijing Shijitan Hospital, Capital Medical University

summary: This study employs 10x Genomics single-cell RNA sequencing (scRNA-seq) to profile cellular changes within the intervertebral discs of diabetic mice. Diabetes mellitus is a systemic inflammatory disease known to drive pathological alterations in multiple organ systems. Here, we specifically investigate the process of diabetes-induced intervertebral disc degeneration. Our findings aim to provide novel insights into the pathogenic mechanisms underlying disc degeneration.

overall_design: We performed single-cell RNA sequencing on nucleus pulposus tissue from ten high-fat-diet-induced diabetic mice. To ensure sequencing data quality, tissues were pooled to create two biological replicate samples: one comprising 5 semaglutide-treated mice and the other comprising 5 untreated control mice.

first: Meng

last: Yi

first: Shijie

last: Liu

first: Yao

last: Zhang

first: Wancheng

last: Lin


title: CDK10 suppresses nucleic acid sensors-mediated antitumor immunity [RNA-Seq]

summary: Cdk10 knockout significantly reduced CT26 tumor growth in immunocompetent BALB/c WT mice.To elucidate the molecular mechanisms by which Cdk10 suppresses anti-tumor immunity, we conducted transcriptomic analyses on WT and Cdk10 KO CT26 cells

overall_design: Total RNA was isolated from sgControl and sgCdk10 CT26 cells using TRIzol Reagent, following the manufacturer's instructions.


title: Targeting IGF2BP1 Enhances Immune Checkpoint Therapy in High-grade Serous Ovarian Cancer

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

country: Germany

institute: Martin Luther University Halle-Wittenberg

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Nutrient stress diverts RRN3 from rRNA transcription to alternative polyadenylation of autophagy mRNAs in ovarian cancer [CRISPR Screen]

city: Tianjin

first: Jianying

last: Lv

state: Tianjin

address: weijin Road No.94

department: School of medicine

institute: Nankai University

summary: Stress-induced alternative processing of mRNA is emerging as an essential mechanism to drive almost every hallmark of cancer. Through a genome-wide screening based on an abnormal transcriptional readthrough event favoring the malignant progression of ovarian carcinoma (OC), we identified novel mRNA processing regulators including RRN3, an essential factor for the transcriptional initiation of rRNA. The long-read RNA sequencing and PAR-CLIP analyses revealed that RRN3 was involved in the usage of alternative polyadenylation (APA) sites, resulting in the altered stability of autophagy-related mRNAs. More interestingly, we discovered that nutrient-deprivation-induced phosphorylation of RRN3 at serine 199 was sufficient to divert RRN3 out of the nucleolus to the nuclear plasma, where RRN3 regulated the APA of autophagy mRNAs, such as OPTN, to enhance their stability and eventually promoted autophagy. Further in vivo experiments showed that nutrient-stress-triggered switch of RRN3 from rRNA transcription to APA regulation was essential for the growth and dissemination of OC in mice.

overall_design: The GeCKO (v2.0) CRISPR library made by Zhangfeng’s lab was purchased from Addgene and amplified using the recommended protocol. The library contains 122,411 sgRNAs targeting 19,050 protein-encoding genes, 1,864 miRNA and 1,000 non-targeting control sgRNAs. A dual-fluorescence transcriptional readthrough (TRT) reporter system was established using pLV-EF1a-MCS-IRES-Bsd vector for the establishment of stable SK-OV-3 cells harboring the TRT reporter sequence (SK-OV-3TRT), in which the majority encoding sequences of COMMD3 and BMI1 were replaced by the mCherry- and EGFP-encoding sequences, respectively, and the sequence in between (including the terminal part of exon 7, intron 7, exon 8 of COMMD3, and the exon 1, intron 1, initial part of exon 2 of BMI1) was kept in frame. Lentivirus carrying the library were prepared according to the manufacturer’s protocol and infected the SK-OV-3TRT cells. The viral titer was estimated and the transduction was performed at a low multiplicity of infection (MOI) around 0.3. After puromycin (2 μg/mL) selection, mCherry+ EGFP- cells were sorted by flow cytometry. The sorted cells (mCherry+ EGFP-) and the parental cells (unsorted cells) were subjected to genomic DNA extraction, PCR-based amplification of sgRNA-encoding sequences and the high-throughput DNA sequencing


title: Targeting IGF2BP1 Enhances Immune Checkpoint Therapy in High-grade Serous Ovarian Cancer [polyA RNA-seq, sorted co-cultures]

summary: High-grade serous ovarian cancer (HGSC) accounts for the vast majority (>70%) of ovarian cancer-associated deaths with minor therapeutic improvements. Among four proposed molecular subtypes of HGSC, the C5 subtype is distinguished by high proliferative potential and elevated immune evasion which is indicated by an unfavorable MHCI/PD-L1 ratio. However, the underlying key drivers of the C5 subtype remained elusive. Here we identify oncofetal RNA-binding proteins (RBPs) promoting the immune evasion of C5-HGSC. The IGF2 mRNA binding protein 1 (IGF2BP1) enhances expression of the E3 ligase MDM2, which induces degradation of IRF1 resulting in reduced MHCI presentation. Concomitantly, IGF2BP1 elevates PD-L1 synthesis by impairing its microRNA-directed silencing. This shifts the intra-tumoral MHCI/PD-L1 ratio, limits immune cell infiltration, and promotes evasion of tumor cells from cytotoxic T cells (CTLs) in human and syngeneic mouse models of ovarian cancer. The small molecule inhibitor BTYNB impairs IGF2BP1-directed regulation of MHCI/PD-L1 ratios, promotes CTL-directed killing as well as activation, and strongly synergizes with immune checkpoint inhibition (ICI) by Nivolumab in vitro and in vivo.

overall_design: Co-culture of ES-2 cells with PBMCs with BTYNB treatment ES-2 cells (2.5x105) we treated with 10 µM BTYNB 24h before HLA-matched human PBMCs in a 1:2 ratio together with CD3/CD28 activation beads (Thermo Fisher) were added for additional 36h. ES-2 cells and PBMCs were separated by FACS sorting before RNA was isolated by TRIZOL. RNA integrity was examined using a BioAnalyzer 2100 (Agilent) before poly(A) RNA enrichment was performed with the poly(A) RNA Selection kit V1.5 (Lexogen). The CORALL Total RNA-Seq V1 (Lexogen) was used for strand-specific library generation. Library preparation and sequencing of paired-end reads was performed on an Illumina NextSeq 1000 platform at the Core Facility Imaging (MLU Halle).

first: Nadine

last: Bley

first: Alexander

last: Rausch


title: Nutrient stress diverts RRN3 from rRNA transcription to alternative polyadenylation of autophagy mRNAs in ovarian cancer

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: RNA polymerase II ChIP-seq  in SK-OV-3 cells(shLacZ/shRRN3) to investigate the influence of RRN3 on Pol II transcription process.


title: Nutrient stress diverts RRN3 from rRNA transcription to alternative polyadenylation of autophagy mRNAs in ovarian cancer [PAR-CLIP]

overall_design: V5-RRN3-expressing SK-OV-3 cells were grown in its complete medium supplemented with 100 μM 4-thiouridine (4-SU) for 14 h before crosslinking.Ten percent of cleared cell lysates were used as the input and the rest were subjected to immunoprecipitation with anti-V5 antibody (Thermo-Fisher Scientific), followed by the elution with V5 peptide (MedChemExpress, Shanghai, China).


title: CDK10 suppresses nucleic acid sensors-mediated antitumor immunity [CRISPR screening]

summary: Given the high druggability of kinases, we utilized a targeted library focused specifically on the kinome for in vivo CRISPR/Cas9 knockout (KO) screening

overall_design: To conduct the screen, lentiviruses carrying the kinome-targeting sgRNAs were used to infect mouse CT26 cancer cells. Following a 7-day selection process to remove uninfected cells, the transduced cells were divided into three groups: in vitro two-dimensional (2D) culture, and in vivo experiments through subcutaneous injection to establish xenograft tumors in either immunodeficient BALB/c nude mice (BALB/c Nude) or immunocompetent wild-type BALB/c mice (BALB/c WT).


title: A catecholamine-independent pathway controlling adaptive adipocyte lipolysis

city: Saint Louis

first: Erica

last: Scheller

state: MO

address: 660 S Euclid Ave

institute: Washington University

summary: Several adipose depots, including constitutive bone marrow adipose tissue, resist conventional lipolytic cues. However, under starvation, wasting or cachexia, the body eventually catabolizes stable adipocytes through unknown mechanisms. Here we developed a mouse model of brain-evoked depletion of all fat, including stable constitutive bone marrow adipose tissue, independent of food intake, to study this phenomenon. Genetic, surgical and chemical approaches demonstrated that catabolism of stable adipocytes required adipose triglyceride lipase-dependent lipolysis but was independent of local nerves, the sympathetic nervous system and catecholamines. Instead, concurrent hypoglycaemia and hypoinsulinaemia activated a potent catabolic state by suppressing lipid storage and increasing catecholamine-independent lipolysis via downregulation of cell-autonomous lipolytic inhibitors including G0s2. This was also sufficient to delipidate classical adipose depots and was recapitulated in tumour-associated cachexic mice. Overall, this defines unique adaptations of stable adipocytes to resist lipolysis in healthy states while isolating a potent catecholamine-independent neurosystemic pathway by which the body can rapidly catabolize all adipose tissues.

overall_design: To identify candidate mechanisms of stable fat lipolysis, we performed RNAseq on caudal vertebrae (CV, stable cBMAT-enriched) from 4- to 5-month-old male and female BMAd-Pnpla2+/+ (WT) mice treated for 9-days with either ICV PBS or 100 ng/hr ICV leptin. Inguinal white adipose tissue (iWAT, responsive fat control) and lumbar vertebrae (LV, no fat control) from the same WT females were included to identify cBMAT-enriched genes. CV samples from age- and sex-matched BMAd-Pnpla2-/- (cKO) mice were also included to isolate the effect of ATGL-mediated fat depletion. To determine which of the differentially expressed lipolysis genes by ICV leptin treatment were reversed with insulin supplementation in vivo, we also included CV samples from age-matched WT males treated with either ICV PBS or 100 ng/hr leptin along with subcutaneous insulin for 9-days.

first: Xiao

first: Sreejith

middle: S

last: Panicker

first: Jordan

middle: M

last: Bollinger

first: Anurag

last: Majumdar

first: Rami

last: Kheireddine

first: Lila

last: Dabill

first: Clara

last: Kim

first: Brian

last: Kleiboeker

first: Fengrui

first: Yongbin

last: Chen

first: Kristann

last: Magee

last: Learman

first: Adam

last: Kepecs

first: Gretchen

middle: A

last: Meyer

first: Jun

first: Steven

last: Thomas

first: Irfan

middle: J

last: Lodhi

first: Ormond

last: MacDougald


title: In vivo intratumoral Heterogeneity in a dish: Scalable Forebrain Organoid Models of Embryonal Brain Tumors for High-Throughput Personalized Drug Discovery

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster


title: Lack of single amino acids transcriptionally tunes sensory systems to enhance microbiota intake

city: Lisbon

first: Gili

last: Ezra

address: Av. Brasília

country: Portugal

institute: Champalimaud foundation

summary: Maintaining sufficient levels of Amino acids (AAs) from the diet is essential for the organism to maintain protein translation and other metabolic processes. Amazingly, the removal of even a single eAA from the diet is sufficient to induce an increase of proteinaceous food intake in Drosophila melanogaster. This process of turning a physiological “need” for any eAA into a psychological “want” driving proteinaceous-food search and consumption still remains poorly understood. Moreover, dietary manipulations of different eAAs have varying effects on metabolism and physiology which depend on the specific eAA depleted. Thus, a systemic analysis of single eAAs effects on the organism is needed. To achieve that, we sequenced RNA from fly heads following exposure to diets depleted of single AAs. We found that depletion of eAAs had different impacts on transcription, however a significant number of regulated transcripts were shared across deprivations, indicating common mechanisms of response to deprivation. Surprisingly chemosensory receptor genes were found amongst the consistently diet-modulated genes, in spite of minimal, if any, change in sensory environment. Genetic manipulations of Or92a confirm its importance for the acceptance of the appropriate food sources, namely , yeast. While Ir76a governs approaches to specific gut bacteria. These results expand the idea that metabolic-internal state can alter sensory processing  already at the transcriptional level, regardless of the sensory environment. Our work uncovers common and unique transcriptional changes induced by all eAA deprivations and reveals novel mechanisms underlying the organism’s behavioral and physiological response to dietary challenges.

overall_design: Each sample is obtained from 10 fly-heads following 3 days on full holidic medium diet or a diet lacking a single eAA

last: Ezra-Nevo

first: Silvia

last: Henriques

first: Daniel

last: Münch

first: Francisco

last: Patricia

first: Celia

last: Baltazar

first: Ana-Paula

last: Elias

first: Bart

last: Deplancke

first: Carlos

last: Ribeiro


title: Gene expression profile at single cell level of Normal Colonic Epithelial Stem Cells (NCE-SC)

city: Kyoto

first: Makoto

middle: Mark

last: Taketo

state: Kyoto

address: Yoshida-Honmachi, Sakyo

department: Kyoto University Hospital

country: Japan

institute: Kyoto University

summary: NCE-SC are inferred as a homogeneous population cultured in the eL-WRN medium (Miyoshi H, Oncotarget 2018;9(31):21950-64.). We used single-cell RNA sequencing (scRNA-seq) to confirm the homogeneity of NCE-SCs.

overall_design: Cultured NCE-SC of human colon were trypsinized, filtered through a strainer and analyzed using scRNA-seq.

first: Fumihiko

last: Kakizaki

first: Hiroyuki

last: Miyoshi

first: M


title: Dual inhibition of FACT and RRM2 suppresses the progression of pancreatic ductal adenocarcinoma driven by the oncohistone H2BG53D

status: Public on Oct 26 2025

city: Hong Kong

first: Tiantian

last: QIN

address: Tat Chee Avenue, Kowloon

institute: City University of Hong Kong

summary: Pancreatic Ductal Adenocarcinoma (PDAC) is a highly lethal cancer with frequent genetic mutations. We previously reported the identification of the histone H2BG53-to-D mutation in PDAC patients and revealed that the mutation destabilizes nucleosomes and promotes cell migration. However, how H2BG53D impacts chromatin and the significance in PDAC development remain largely unknown. Using the genetically engineered mouse models, we demonstrate that H2BG53D accelerates PDAC initiation and metastasis. Moreover, H2BG53D mutation elevates the interaction between nucleosomes and the Facilitates Chromatin Transcription (FACT) complex. FACT depletion reverses transcriptional changes and oncogenic effects induced by H2BG53D mutation. In search of a novel therapeutic strategy for H2BG53D-PDAC, our genome-wide CRISPR/Cas9 screen identified Ribonucleotide Reductase Regulatory Subunit M2 (RRM2) as a druggable target. Remarkably, dual inhibition of RRM2 and FACT exhibits potent cytotoxic effects on PDAC cells in vitro and significantly prolongs the survival of H2BG53D-PDAC mice. This study deciphers the roles and mechanisms of H2BG53D in PDAC progression and proposes a promising therapeutic strategy for this aggressive cancer.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: mouse RNA-seq: KPC and G53D-KPC mice were generated to study the roles of H2BG53D mutation in PDAC development. Primary PDAC tumors and metastases from KPC and G53D-KPC mice were used for this experiment. Gene expression was profiled by RNA-seq. KI cell line RNA-seq: FLAG tagged Wildtype (WT) H2B and H2BG53D knockin PDAC cells were used to study the mechanisms of  H2BG53D on transcriptional alteration and oncogenic phenotype. RNA-seq  were conducted in  in two WT and two H2BG53D cells with or without SPT16 (one subunit of FACT)  depletion. KI cell line CUT&RUN seq: FLAG tagged WildtypeH2B (H2B_WT-FLAG)and H2BG53D-FLAG knockin PDAC cells were used to study the mechanisms of  H2BG53D on transcriptional alteration and oncogenic phenotype.  CUT&RUN seq (targeting FLAG and H2A) were conducted in parental, two WT and two H2BG53D cells with or without SPT16 (one subunit of FACT)  depletion. KI cell line CRISPR screen: FLAG tagged WildtypeH2B (H2B_WT-FLAG) and H2BG53D-FLAG knockin PDAC cells were used to identify the synthetic lethal partner for H2BG53D mutation in PDAC.

first: Kui Ming

last: CHAN


title: Adenophages are an atypical macrophage population in exocrine glands sustained by ILC2-derived GM-CSF

city: Zurich

first: Burkhard

last: Becher

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich


title: Novel lipid nanoparticle adjuvants vaccine for porcine reproductive and respiratory syndrome (PRRS) using in-vitro macrophage assays

status: Public on Oct 25 2025

city: Vancouver

first: Robert

middle: E. W.

last: Hancock

state: British Columbia

address: 2259 - Lower Mall Research Station

department: Department of Microbiology & Immunology

country: Canada

institute: University of British Columbia

summary: A novel triple adjuvant (TriAdj) platform formulated in various cationic lipid nanoparticles (L-TriAdj) was tested in-vitro for use in porcine reproductive and respiratory syndrome virus (PRRSV) vaccines. Gene expression changes in a RAW 264.7 macrophage cell line were evaluated (compared to media control) after 12-hour stimulation with: (i) TriAdj alone, (ii) lipid formulations alone, (iii) L-TriAdj (lipid:TriAdj ratio of 3:2 or 2:1), and (iv) L-TriAdj + PRRSV antigen. Tested L-TriAdj formulations were comprised of (i) dimethyldioctadecylammonium bromide (DDAB) and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) in a 55:45 ratio (abbreviated as DDAB/DOPE), or (ii) DDAB/DOPE with 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), and cholesterol in a 40:30:20:10 ratio (abbreviated as DDAB/DOPE/DSPC/CHOL).

overall_design:
Cultured RAW264.7 macrophage cells were stimulated for 12 hours with TriAdj, L-TriAdj, lipid carriers alone, inactivated PRRSV and whole vaccines (adjuvant+PRRSV).
RNA was isolated and sequenced to evaluate gene expression changes after 12 hour stimulation.

first: Aderonke

last: Ayanniyi

first: Bhavjinder

middle: K

last: Dhillon

first: Adrienne

last: Nagy

middle: E

first: Volker

last: Gerdts

first: Ellen

last: Wasan


title: Colon Cancer Patient-Derived Spheroids and their Stem Cell-Intrinsic mRNA Expression Yield Novel Prognostic Signatures

summary: We characterized colorectal cancer stem cell (CRC-SC)-intrinsic subtypes based on mRNA expression of 57 patient-derived SC lines. We compared their expression profiles with those of normal colonic epithelial stem cells (NCE-SC), and obtained genes relatively underexpressed or overexpressed. First, we found a subgroup of CRC-SC lines in which seven genes were overexpressed despite very low expression in the remaining CRC-SC lines. Importantly, cross-reference of the expression-survival relationship in public databases indicated the Lucky Seven genes to constitute a signature for improved outcome. Likewise, five lead genes were expressed at higher levels than in NCE-SC, representing non-overlapping subtypes. While their expression affected patient outcome singly in each subtype, other related genes overexpressed within the subtype were also associated with better or poorer prognosis. When combined, collective signatures provided novel predictive signatures with much stronger statistical significance. Finally, we integrated the six signatures into a comprehensive signature, which yielded a novel survival prognostic indicator.

overall_design: Six prognostic signatures for colorectal cancer, three favorable and three unfavorable were revealed as a consequence of the 57 patient-derived cancer stem cell lines. Critically, we devised a predictor applicable to any patient via the integration of the six signatures that can be determined using the whole tumor tissue sample.


title: Construction of Human nucleus basalis Organoids and Cholinergic Projections in nbM-cortical Assembloids

city: Nanjing

first: Yan

last: Liu

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

department: School of Pharmacy

institute: Nanjing Medical University

summary: The nucleus basalis, also known as the nucleus basalis of Meynert (nbM), which is considered to be one of the major cholinergic output of basal forebrain, have been found to dynamically modulate activity in the cortex. Dysfunction of nucleus basalis-cortical cholinergic circuit led to cognitive impairment, such as Alzheimer's disease (AD) and Down syndrome (DS). Human nucleus basalis cholinergic neurons derived from human pluripotent stem cells provide powerful tools to study cholinergic neurons-associated diseases and cell therapy. Previous studies reported the generation of 2D human basal forebrain cholinergic neurons which failed to recapitulate the spatial organization, cellular diversity, and crosstalk between different regions. Therefore, a better model to recapitulate human nucleus basalis and cholinergic projections in nbM-cortical is desired. Here we developed a approach for differentiating human pluripotent stem cells into nucleus basalis of Meynert organoids (hnbMOs). We reconstructed hnbM-cortex cholinergic projection by transplanting hnbMOs into immunodeficiency mice to construct chimeric brains and coculturing with human fetal brain. Then we fused hnbMOs with cerebral cortex organoids (hCOs) to form hnbMO-hCO assembloids. We validate the structural and functional connectivity of basal forebrain cholinergic neurons to the cortex in assembloids. An assembloid-chimeric brain was constructed innovatively by transplanting corresponding organoids in the cortex and nbM region to establish a complete human cholinergic projection system. Futhermore, we identified the defects in projection of cholinergic neurons at the morphological and transcriptomic level in Down syndrome patient iPSC-derived assembloids as well as Down syndrome fetal brain tissue. Our work establishes new approach for the study of neurological disorders associated with nbM and nbM-cortical cholinergic neuron circuit.

overall_design: The study presents a novel method for creating nucleus basalis organoids from human pluripotent stem cells to model cholinergic connections to the cortex, helping to investigate neurological disorders linked to this system, particularly in the context of Down syndrome and Alzheimer's disease.


title: Circadian clock control of ribosome composition promotes rhythmic  translation and termination fidelity [RNA-Seq]

city: College Station

first: Deborah

last: Bell-Pedersen

state: TX

address: Mail Stop 3258, BSBW210

department: Biology

institute: Texas A&M University

summary: Ribosome composition can vary depending on cell type, stress or developmental state. Here we describe circadian clock-dependent changes in ribosome composition in Neurospora crassa. Mass spectrometry of ribosomes isolated at different circadian times identified six ribosomal proteins and one ribosome-associated protein with clock-controlled abundance. We confirmed clock control of eL31-HA abundance in purified ribosomes and found that deletion of eL31 altered translation of many mRNAs and inhibited translation rhythms for 42% of rhythmically translated mRNAs. Because eL31 homologs promote translation termination fidelity, we examined ribosome protected footprint (RPF)-seq reads mapping past stop codons over circadian time to reveal clock-dependent and eL31-enhanced rhythms in translation termination fidelity. We further discovered that eL31 promotes proper ion homeostasis and translation elongation fidelity. Taken together these studies demonstrated that the circadian clock governs daily changes in ribosome composition that control rhythms in translation and impact translation fidelity, likely through changes in intracellular Mg2+ levels.

overall_design: RNA-seq (done in parallel with ribosome profiling) of Neurospora crassa ∆eL31(∆ncu08344) mycelia, grown over a circadian time course, 10 time points, 2 replicate experiments for a total of 20 samples

first: Teresa

last: Lamb

first: Kathrina

last: Castillo

first: Rachel

last: Porter

first: Cheng

last: Wu

first: Samuel

middle: O

last: Purvine

first: Griffin

last: Best

first: Ebimobowei

last: Preh

first: Lunda

last: Shen

first: Erika

last: Zenk

first: Scott

last: Baker

first: Matthew

last: Sachs


title: Circadian clock control of ribosome composition promotes rhythmic  translation and termination fidelity [Ribo-Seq]

overall_design: Ribosome protected footprint (RPF)-seq of Neurospora crassa ∆eL31(∆ncu08344) mycelia, grown over a circadian time course, 10 time points, 2 replicate experiments for a total of 20 samples


title: eIF2D promotes 40S ribosomal subunit recycling during intrinsic ribosome destabilization

status: Public on Oct 24 2025

city: Chikusa-ku, Nagoya, Aichi

first: Kazuya

last: Ichihara

address: Furo-cho

institute: Nagoya University

summary: Although eukaryotic initiation factor 2D (eIF2D) is implicated in translation initiation, re-initiation, and ribosome recycling, its precise role remains unclear. Here, we show that eIF2D promotes 40S ribosome recycling during intrinsic ribosome destabilization (IRD), a process in which ribosomes stochastically destabilize while translating proteins with consecutive acidic amino acids at their NH2-terminus. Unrecycled 40S ribosomes accumulate in eIF2D-deficient cells, leading to 80S ribosome stalling. Selective translation complex profiling (TCP-seq) reveals that eIF2D preferentially associates with IRD-prone regions. The winged-helix (WH) domain, unique to eIF2D but absent in MCTS1–DENR, enhances its binding to 40S subunits, but likely clashes with ABCE1 during stop codon-associated recycling. Loss of eIF2D reduces the expression of IRD-inducing proteins, including splicing factors. Together, these findings define a previously unappreciated role for eIF2D in 40S recycling and clarify its mechanistic divergence from the MCTS1–DENR complex.

overall_design: Translatome and transcriptome analysis of eIF2D-deficient HEK293T cells

first: Akinobu

last: Matsumoto


title: CHAMP1 is an essential regulator for human myoblast fusion and muscle development

city: Athens

first: Pengpeng

last: Bi

state: GA

address: 315 Riverbend Rd

institute: University of Georgia

summary: Human skeletal muscle is composed of myofibers, each formed by the fusion of thousands of individual myoblasts. This process requires tightly regulated expression of muscle-specific fusogens, which confer both efficiency and muscle specificity to cell-cell fusion. Currently, the genetic regulation of this process remains poorly understood. Here, we identify CHAMP1, a chromosome alignment factor, as a surprising upstream activator of human myoblast fusion. Genetic deletion of CHAMP1 in human myoblasts led to profound fusion defects in vitro and in vivo following transplantation. Leveraging genomics approach and protein interaction assays, we uncovered a noncanonical role for CHAMP1 as a transcriptional cofactor for MyoD, directly activating the expression of the key muscle fusogen Myomaker. CHAMP1 mutations in human patients cause developmental delay, hypotonia, and muscle weakness, hallmarks of fusion myopathy that are also observed with Myomaker mutations. Importantly, CHAMP1 patient-derived cells exhibit severe fusion defects that can be fully rescued by restoring Myomaker expression. Structure and function analysis identified C2H2-type zinc finger motifs on CHAMP1 protein that are both necessary and sufficient for interaction with MyoD, activation of Myomaker transcription and human myoblast fusion. These findings highlight the muscle-autonomous role of CHAMP1 in muscle development and disease, and point to therapeutic avenues for treating muscle development defect caused by CHAMP1 mutations.

overall_design: RNA-Seq profile of CHAMP1 knock-out (KO) or isogenic rescue (RES) human myoblast at different stages, including myoblast in growth medium (GM), differentiate for 2 days (DM2d), differentiate for 6 days (DM6d).

first: Haifeng

last: Zhang

first: Min

last: Zhou

first: Zheng

first: Zhaoning

last: Wang


title: Active aldehydes accelerate CD8+ T cell exhaustion by metabolic alteration in the tumor microenvironment

first: Kenji

last: Chamoto

address: Yoshida Konoe-cho, Sakyo-ku

department: Department of Immunology and Genomic Medicine

institute: Graduate School of Medicine, Kyoto University

summary: We employed a 10x Genomics single-cell RNA sequencing (scRNA-seq) approach to investigate the characteristics of distinct mitochondrial states within PD1+ CD8+ T cells in tumors. This study demonstrates that mitochondrial status correlates with the depth of exhaustion in PD1+ CD8+ T cells and further characterizes distinct functional stages of exhaustion within the tumor microenvironment (TME).

overall_design:
We conducted single-cell RNA sequencing (scRNA-seq) on the isolated PD1- CD8+ T cells and D1, D2, and D3 populations from PD1+ CD8+ T cells in the MC38 tumor on day14.
Since cellranger multi was executed, the main output files can be found consolidated in GSM9214854 (CD8+ T cells in MC38 tumor, GEX).
The ADT data includes information on cell hashing (hashtags), surface protein markers, and corresponding isotype controls.

first: Yasuharu

last: Haku

first: Koji

last: Kitaoka

first: Koki

last: Ichimaru

first: Tomoko

last: Hirano

first: Jun

first: Kazuhiro

last: Sonomura

first: Asuka

last: Maruo

first: Shuhei

last: Hirose

first: Yu

first: Katsuhiro

last: Ito

first: Tomohiro

last: Kozuki

first: Keiko

last: Yurimoto

first: Mai

last: Kiyono

first: Hidetaka

last: Kosako

first: Toshi

last: Menju

first: Hiroshi

last: Date

first: Takashi

last: Kobayashi

first: Koichi

last: Omori

first: Tomonori

last: Yaguchi

first: Tasuku

last: Honjo


title: RNA-seq analysis for rRNA-depleted RNA in Caenorhabditis elegans.

city: Kobe

first: Hiroki

last: Shibuya

state: Hyogo

address: 2-2-3 Minatojima-minamimachi

department: BDR

institute: RIKEN institute

summary: To investigate the expression of coding and non-coding RNAs, we performed RNA-seq analysis on total RNA from wild-type C. elegans after rRNA depletion.

overall_design: We used two biological duplicates. RNA-seq libraries were prepared by Novogene and sequenced using Illumina Novaseq 6000 (PE150)

first: Michiaki

last: Hamada

first: Masahiro

last: Onoguchi


title: PRC1-mediated H2A.Zub promotes gene expression by preventing H3.1K27me1 incorporation in Arabidopsis

city: Coventry

first: Javier

last: Antunez Sanchez

address: Gibbet Hill Campus

department: Life Sciences

country: United Kingdom

institute: University of Warwick

summary: The PcG complexes guarantee the correct temporal and spatial expression of genes. As such, they are crucial in orchestrating plant developmental phase transitions. While PRC2-mediated H3K27me3 is primarily associated with gene repression, PRC1 has a more versatile role that is not fully understood. Moreover, although PRC1 can monoubiquitinate canonical H2A or its variant H2A.Z, the circumstances under which this occurs remain unknown. Here, we show that in Arabidopsis H2A.Z is the variant that undergoes monoubiquitination during the transition from seed-to-seedling. H2A.Zub incorporation recruits PRC2 to repress seed-specific genes; nevertheless, it also activates gene expression by preventing the incorporation of H3K27me1. Interestingly, the removal of two methyl groups from H3K27me3-marked genes is a prerequisite for H2A.Zub incorporation, placing REF6 activity at the onset of gene reprogramming. Our data also indicate that H2A.Zub plays a role in promoting histone exchange to maintain gene expression patterns. These findings extend our understanding of PRC1-mediated gene regulation.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K27me3 on Arabidopsis seeds 48 hours after imbibition (48 HAI) as well as ChIP-seq for histon variant H2A.Z and histone modifications H3K27me3 and H3K27me1 in Arabidopsis seedlings 10 days after germination (10 DAG).

first: Fernando

last: Baile

last: Antunez-Sanchez

first: Jose

last: Gutierrez-Marcos

first: Myriam

last: Calonje


title: Development of a split-toxin CRISPR screening platform to systematically identify upstream regulators of human myoblast fusion

first: Pengpeng

last: Bi

summary: Muscle defects are a common feature in human developmental disorders and often lead to severe functional impairment. These defects arise from intricate tissue crosstalk and rare genetic mutations, underscoring the need to systematically identify cell-autonomous mechanisms regulating human myogenesis. Despite the clinical significance, our understanding of human development remains limited, due in part to the absence of a scalable genetic approach to study this process. Here, we introduce a rationally designed high-throughput CRISPR screening platform that integrates human myoblast models, muscle-specific CRISPR knockout libraries, and a split-toxin strategy that acts as a functional readout for myoblast fusion—a fundamental step of human myogenesis. This screening strategy enables selection of CRISPR-induced fusion-defective myocytes in a quantifiable manner. Leveraging this platform, our initial genetic screen uncovered a large group of new hits essential for human myoblast fusion. The majority of these hits converge into 23 protein complexes, most of which have not previously been functionally linked to myogenesis in any species. Notably, mutations in 41 of our fusion screen hits cause human diseases presenting abnormal skeletal muscle morphology. Applying a new single-cell CRISPR & RNA-seq approach, we show that majority of these hits control human myoblast fusion as well as influence early-stage myogenic differentiation. Together, this work presents a new systematic approach to study human myogenesis and uncovers promising candidates governing human muscle differentiation and fusion. A broader application of this split-toxin based CRISPR screening platform would accelerate the study of cell-autonomous mechanisms of human muscle development and diseases at scale.

overall_design:
RNA-Seq profile of human myoblast at different stages, including myoblast in growth medium (GM), differentiate for 2 days (DM2d), differentiate for 6 days (DM6d).
Split-pool based single cell CRISPR screen data.


title: Transcriptomic analyses of hMADS cells depleted for hormone-sensitive lipase

city: Toulouse Cedex 4

first: Dominique

last: Langin

address: 1 avenue du Professeur Jean Poulhès

country: France

institute: INSERM

summary: Hormone-sensitive lipase HSL is a major metabolic enzyme of adipocyte as the rate limiting enzyme of lipolysis. Recently, a non enzymatic role of HSL as been described in the regulation of the Carbohydrate Responive Element Binding Protein (ChREBP), controlling adipocyte insulin sensitivity. We aimed at further explore new roles of HSL in the control of adipocyte metabolism through gene expression modulation.

overall_design: HSL-depleted (siHSL) and control (siGFP) hMADS white adipocytes at day14 of differenciation were subjected to low glucose/no insulin treatment, then high glucose and insulin to induce de novo lipogenesis. hMADS beige, and white as control, adipocytes were also studied at day 18 of differentiation

first: Emeline

last: Recazens

first: Jeremy

last: Dufau

first: Claire

last: Naylies

first: Yannick

last: Lippi


title: Screening for the telomerase RNA component in Caenorhabditis elegans by FLAG-TRT-1 eCLIP.

summary: The telomerase RNA component has been unidentified in C. elegans. To identify the telomerase RNA, we generated a C. elegans strain overexpressing FLAG-TRT-1, the catalytic subunit of telomerase, and biochemically screened for FLAG-TRT-1-binding RNAs by enhanced crosslinking and immunoprecipitation (eCLIP) assay.

overall_design: eCLIP studies were performed by Eclipse Bioinnovations Inc (San Diego, www.eclipsebio.com) according to the published single-end CLIP protocol.

first: Jingjing

last: Zhang


title: ATAC-seq and CUT&Tag of memory CD4+ T cells from patients with eosinophilic chronic rhinosinusitis (ECRS)

city: Chiba-shi

first: Hiroyuki

last: Yagyu

state: Chiba

address: 1-8-1, Inohana, Chuo-ku

institute: Chiba University

summary: We complehensively investigated the open chromatin regions and enhancer landscape of CD45RO+ memory CD4+ T cells from PBMCs and nasal polyps of ECRS patients.

overall_design: CD45RO+CD4+ T cells were freshly isolated from PBMCs and nasal polyps and subjected to ATAC-seq and CUT&Tag for H3K27Ac.

last: Kiuchi

first: Eisuke

last: Itakura

first: Kota

last: Kokubo

first: Atsushi

last: Sasaki

first: Chiaki

last: Iwamura

last: Onodera

first: Ami

last: Aoki

first: Takahisa

last: Hishiya

first: Kaori

last: Tsuji

first: Takuto

last: Hiramoto

first: Rie

last: Shinmi

first: Yuri

last: Sonobe

first: Junya

last: Kurita

first: Tomohisa

last: Iinuma

first: Syuji

last: Yonekura

first: Yu

last: Hara

first: Toyoyuki

last: Hanazawa

first: Takeshi

last: Kaneko

first: Toshinori

last: Nakayama

first: Kiyoshi

last: Hirahara


title: Mpox virus OPG175 negatively regulates viral replication via controlling Wnt signaling

first: Kazuo

last: Takayama

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

summary: Mpox virus (MPXV) infection has different case fatality rates and symptoms depending on its clade. However, there has not been sufficient molecular biological analysis of the differences between clades. Here, we investigated whether we can distinguish between clades by focusing on the expression of MPXV genes. The replication efficiency of MPXV clade IIb, responsible for the 2022 Mpox outbreak, was lower than that of clades Ia and IIa. We found that OPG175 was highly expressed in MPXV clade IIb-infected cells. Suppression of OPG175 expression significantly upregulated the infectious titer of MPXV, while OPG175 overexpression significantly decreased the infectious titer of MPXV. We found OPG175 overexpression to enhance the expression of Wnt signaling-related genes and activation of Wnt signaling to decrease the replication efficiency of MPXV. Therefore, high OPG175 expression in MPXV clade IIb-infected cells likely inhibits MPXV replication via activation of Wnt signaling.

overall_design: HEK293 cells were transfected with plasmids-expressing OPG175 or human superoxide dismutase (SOD) 1, and then total RNA was collected and RNA-seq was performed.


title: Screening for H/ACA snoRNAs in Caenorhabditis elegans by GFP-FLAG-DKC-1 eCLIP.

first: Hiroki

last: Shibuya

summary: To identify H/ACA snoRNAs, we generated a C. elegans strain overexpressing GFP-FLAG-DKC-1 and biochemically screened for GFP-FLAG-DKC-1-binding RNAs by enhanced crosslinking and immunoprecipitation (eCLIP) assay.

first: Takefumi

last: Kondo

first: Osamu

last: Nishimura

first: Mitsutaka

last: Kadota


title: scRNA-seq of CD4+ T cells from mouse allergic airway inflammation model and human patients with eosinophilic chronic rhinosinusitis (ECRS)

first: Hiroyuki

last: Yagyu

summary: A unique subpopulation of memory Th2 cells expressing the interleukin-33 receptor ST2 contributes to the pathogenesis of allergic diseases; however, the immune-metabolic mechanisms that induce ST2hi memory Th2 cells in inflamed tissues remain uncertain. Using single-cell RNA-sequencing (scRNA-seq), we revealed active lipid storage and catabolism during ST2hi memory Th2 cell induction in inflamed murine lungs and nasal polyps from patients with ECRS.

overall_design: CD4+ T cells (batch_1) and CD45+ cells (batch_2) were freshly isolated from control and HDM-sensitized mouse lung tissues and subjected to scRNA-seq. For human samples, CD4+ T cells were freshly isolated from nasal polyps and peripheral blood mononuclear cells (PBMCs) of patients with ECRS and subjected to scRNA-seq.

first: Masahiro

last: Kiuchi

first: Eisuke

last: Itakura

first: Kota

last: Kokubo

first: Atsushi

last: Sasaki

first: Chiaki

last: Iwamura

last: Onodera

first: Ami

last: Aoki

first: Takahisa

last: Hishiya

first: Kaori

last: Tsuji


title: ChIP-seq for PPARg, RXRa, and H3K27Ac in inflammation-associated unsaturated fatty acid-supplemented Th2 cells

summary: A unique subpopulation of memory Th2 cells expressing the interleukin-33 receptor ST2 contributes to the pathogenesis of allergic diseases; however, the immune-metabolic mechanisms that induce ST2hi memory Th2 cells in inflamed tissues remain uncertain. We revealed that linoleic and oleic acids increased in the inflamed lungs induced ST2 expression through activating PPARg. Furthermore, this activation of PPARg was dependent on ATGL activity.

overall_design: Each fatty acid complexed to BSA was added to the cell culture medium at a final concentration of 20 µM during the differentiation of Th2 cells from splenic naïve CD4+ T cells. Cells were treated with DMSO or ATGL inhibitor atglistatin (15 µM in DMSO; Sigma-Aldrich) were added to the cell culture medium from day 4. ChIP-seq were conducted on day 5.

first: Takuto

last: Hiramoto

first: Rie

last: Shinmi

first: Yuri

last: Sonobe

first: Junya

last: Kurita

first: Tomohisa

last: Iinuma

first: Syuji

last: Yonekura

first: Yu

last: Hara

first: Toyoyuki

last: Hanazawa

first: Takeshi

last: Kaneko

last: Nakayama


title: ATAC-seq of memory CD4+ T cells from the HDM-sensitized lungs

first: Hiroyuki

last: Yagyu

summary: We complehensively investigated the open chromatin regions of ST2hi memory CD4+ T cells from the HDM-sensitized lungs.

overall_design: ST2loCD44hiCD4+ T cells and ST2hiCD44hiCD4+ T cells were freshly isolated from HDM-sensitized mouse lung tissues and subjected to ATAC-seq.

first: Masahiro

last: Kiuchi

last: Itakura

last: Kokubo

first: Toshinori

first: Kiyoshi

last: Hirahara


title: Quercetin promotes the proliferation and maturation of NK cells by binding to MYH9 and improves cognitive functions in aged mice

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

summary: We implemented transcriptomic analyses of hippocampus of 10M mice; These mice with the treatment of quercetin for 24 days.


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

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

middle: P

last: Azambuja

first: Megan

last: Rothstein

first: Tatiane

last: Kanno


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

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

overall_design: Refer to individual Series


title: Spatial gradients of chromatin accessibility endow embryonic cells with positional information [CUT&RUN]


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


title: Neuronal hyperactivity becomes mTORC1 independent due to epigenetic changes in Tuberous Sclerosis Complex

first: Kellen

last: Winden

state: MA

department: Neurology

summary: Tuberous Sclerosis Complex (TSC) is caused by variants in either TSC1 or TSC2, which cooperate to inhibit the mechanistic target of rapamycin complex 1 (mTORC1). TSC is associated with neurological disorders that have been attributed to disinhibition of mTORC1, but mechanisms connecting dysregulation of mTORC1 to molecular and physiological changes in neurons remain unclear. In this study, we sought to understand transcriptional changes in TSC and identified down-regulation of the immediate early gene, EGR1, in TSC2-deficient excitatory neurons. Furthermore, we found that activity-dependent transcription is impaired in TSC due to abnormalities in epigenetic maturation. Finally, we determined that mTORC1 inhibition started late in neuronal maturation of human neurons is only partially effective in reversing gene expression changes and ineffective in reducing spontaneous neuronal hyperactivity in TSC. These data demonstrate a critical window in early brain development where mTORC1 dysregulation leads to epigenetic changes that contribute to persistent neuronal abnormalities.

overall_design: Control (Tsc2fl/fl SynCre-) and mutant (Tsc2del/fl SynCre+) mice were sacrificed at P30. The frontal cortex was dissected out and processed to obtain nuclei. NucSeq was performed using the inDrops platform.

first: Wardiya

last: Afshar-Saber

first: Juan

last: Ruiz

first: Isabel

last: Gisser

first: Ziqin

last: Yang

first: Leena

last: Mehendale

first: Nicole

last: Teaney

first: Madison

last: Glass

first: Truc

last: Pham

first: Elizabeth

last: Bainbridge

first: Mustafa

last: Sahin


title: Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation

city: Philadelphia

first: YEQIAO

last: ZHOU

state: PA

address: 3600 Civic Center Blvd 14 114

institute: University of Pennsylvania

first: Yeqiao

last: Zhou

first: Robert

middle: B

last: Faryabi


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

first: Marcos

last: Simoes-Costa

first: Ana

last: Azambuja


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

city: Toronto

first: Daniel

last: Fusca

state: ON

address: 25 Willcocks Street

department: Department of Ecology and Evolutionary Biology

institute: University of Toronto

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

last: Saltzman


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

overall_design: RNA-seq in wild-type worms, mig-32 mutants, spat-3 mutants, and mig-32;spat-3 double mutants


title: Meningeal lymphatic ablation reduces ischemic stroke-induced inflammation via reprograming transcriptome profiling in cervical lymph nodes [RNA-seq]

city: Taipei city

first: Gilbert

middle: Aaron

last: Lee

address: 250 Wu-Hsing Street,

country: Taiwan

institute: Taipei Medical University

summary: Meningeal lymphatic system governs immune cell trafficking in the brain via brain-to-cervical lymph node (CLN) pathway. However, the role of meningeal lymphatics in brain–CLN axis after stroke remains unclear. Here, we showed that meningeal lymphatic ablation (MLA) reduced brain infarct and neuronal loss levels and inhibited inflammatory pathways in the hippocampus after MCAO–reperfusion. Single-cell transcriptome analysis demonstrated that MLA reduced monocyte/macrophage and polymorphonuclear cell counts and T and natural killer cell effector function. MLA reprogrammed the transcriptome profile related to chemotaxis and leukocyte migration in CLN LECs and downregulated expression of the CCN1 in floor LECs. Mechanistically, MLA inhibited inflammatory macrophage infiltration by repressing CCN1 and CD147 (thromboinflammatory marker) expression in blood vessels, thus inhibiting detrimental inflammatory responses. Blockade of VEGF-C-mediated signaling in meningeal lymphatic system improved memory function after ischemic stroke. Collectively, MLA reprograms the LEC transcriptome and inhibits CCN1-mediated proinflammatory responses during poststroke brain–CLN signaling.

overall_design: We used RNA-seq analysis to investigate the effects of saline and meingeal lymphatic ablation treatment on hippocampus


title: Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes

status: Public on Oct 23 2025

city: Lyon

first: Aurele

last: Piazza

address: 46 Allee d'Italie

institute: ENS Lyon

summary: Although significant progress has been made in our understanding of DNA replication and spatial chromosome organization in eukaryotes, how they both interplay remains elusive. In particular, from the local structure of two diverging sister-forks to the higher-level organization of the replication machinery into nuclear domains, the mechanistic details of chromatin duplication in the 3D nuclear space remain debated. In this study, we use a computational model of the Saccharomyces cerevisiae genome to explore how replication influences chromatin folding. By integrating both a realistic description of the genome 3D architecture and 1D replication timing, simulations reveal that the colocalization of sister-forks produces a characteristic “fountain” pattern around early origins of replication. We confirm the presence of similar features in vivo in early S-phase with new Hi-C data in various conditions, showing that it is replication-dependent and cohesin-independent. At a larger scale, we show that the 3D genome leads to forks being highly enriched at one pole of the nucleus in early S-phase, before later redistributing more homogeneously, and may favor the higher-order clustering of forks into Replication Foci, as observed in earlier microscopy experiments. Additionally, replication causes temporary chromatin slowdown and reduced mobility due to fork passage and sister chromatid intertwining. Overall, our model offers new insights into the spatial and dynamic organization of chromatin during replication in eukaryotes.

overall_design: Hi-C experiments were performed on S. cerevisiae cultures released from an alpha-factor arrest for 20 minutes.

first: Vinciane

last: Piveteau

first: Aurèle


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


title: Neutrophils after mouse subarachnoid hemorrhage

city: Houston

first: John

middle: P.

last: Hagan

state: Texas

address: 6431 Fannin St.

department: Neurosurgery

institute: UTHealth

summary: Subarachnoid hemorrhage causes an increase in inflammation and may effect neutrophils. Here, we test if there are differences in expression from neutrophils after subarachnoid hemorrhage in mice on days 1 and 3 (compared with a sham control).

overall_design: Comparison of neutrophil gene expression profile after SAH in mice, each sample is a unique mouse

first: Devin

last: McBride


title: Meningeal lymphatic ablation reduces ischemic stroke-induced inflammation via reprograming transcriptome profiling in cervical lymph nodes


title: Targeting CD11b+ regulatory B cells via RAS/RAF/PI3K pathway inhibition augments response to immune checkpoint blockade or CD40 agonism in metastatic melanoma

city: Nashville

first: Chi

last: Yan

state: Tennessee

address: 432A Preston Res Building, 2220 Pierce Ave

institute: Vanderbilt University

summary: Abstract Development of effective second-line treatment options for immune checkpoint blockade (ICB) resistant patients with BRAFWTNRASWT or BRAFWTNRASmut melanoma is crucial. While systemic delivery of agonist CD40 (aCD40) plus anti-PD1 (αPD1) showed activity in patients with ICB-resistant melanoma, the objective response rate was modest (15%), in part due to induction of B regulatory cells (Bregs) which suppress CD8+ effector T cells. We previously reported that RAS/RAF/PI3K-inhibition elevated CD40 expression in melanoma cells and sensitized tumors to ICB. Here, we show that treatment of ICB-resistant BRAFWTNRASWT and BRAFWTNRASmut melanoma tumors with the combination of rigosertib (RGS), a RAS/PI3K/AKT-pathway inhibitor, and/or trametinib (T), a MEK1/2 inhibitor, plus aCD40 overcomes ICB resistance. Overexpression of CD40 in melanoma cells effectively reverses ICB-resistance and induces tumor regression upon aCD40+αPD1 treatment. Mechanistically, RGS+T suppressed aCD40-associated CD11b+PD-L1+ B regulatory cells (B11regs), which promoted CD8+ T-cell killing in melanoma. scRNA-Seq analyses confirmed CD40-associated B11regs across cancer types in patients.  Statement of Significance Addition of aCD40 treatment to PD1 fails to overcome ICB resistance due to aCD40-induction of B11regs and low expression of CD40 in melanoma cells. Our data demonstrate that addition of RAS/RAF/PI3K inhibitors to aCD40 resolves these issues and provides alternative therapeutic options for ICB-resistant BRAFWTNRASWT or BRAFWTNRASmut metastatic melanoma.

overall_design: CD40 overexpression (CD40-OE) and CD40-ctrl clones of 1014 NRAS-mut melanoma cells were generated and injected in C57BL/6 mice. Treatment with 200μg/mouse αPD1 (every 3 days, intraperitoneal), 30μg/mouse aCD40 (every 3 days, intraperitoneal), or 300mg/kg rigosertib (RGS, 5 days a week, oral gavage), starts at day 8 post tumor cell inoculation. Tumor samples were harvested 22 days post-treatment and proceeded with bulk RNA-Seq and TCR-Seq (n=3 per treatment group).

first: Yan

last: Chi

first: Richmond

last: Ann


title: Bulk mRNAseq in control and Plp-CreER_Ddx20 cKO mouse spinal cords

city: Niigata City

first: Norihisa

last: Bizen

address: 757 Ichibancho, Asahimachi-dori, Chuo Ward

department: Graduate School of Medical and Dental Sciences

institute: Niigata University

summary: We sequenced mRNA extracted from the spinal cords of mice at 4 and 4.5 weeks after tamoxifen administration and compared the gene expression levels between the control group and the Ddx20 conditional knockout (Plp-CreER; Ddx20 cKO) group.

overall_design: At 4 and 4.5 weeks after tamoxifen administration, mRNA was extracted from the spinal cords of three control mice and three Ddx20 cKO mice. The extracted mRNA was sequenced using the Illumina NovaSeq 6000 platform to generate mRNA expression profiles.

first: Masataka

last: Ise

first: Hirohide

last: Takebayashi


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

first: Marcos

last: Simoes-Costa

first: Ana

last: Azambuja

first: Megan

last: Rothstein

first: Tatiane

last: Kanno


title: The brain neurovascular epigenome and its association with dementia

city: London

first: Alexander

last: Nott

address: 86 Wood Lane

institute: Imperial College London

summary: Cerebral small vessel disease (SVD) is frequently comorbid with Alzheimer’s disease (AD) and vascular brain endothelial cells (BECs) are enriched for the expression of genes associated with AD genetic risk. However, the gene regulatory landscapes of neurovascular cells and their intersection with genetic risk for disease remains unexplored. Here we have generated gene regulomes for human BECs, mural cells and other brain cell types to show that AD heritability is primarily immune-related and that it shows modest enrichment in BECs. By contrast, genetic risk for SVD is enriched across cells of the neurovascular unit, including astrocytes. Enhancer-to-gene interactomes implicate amyloid processes in both AD and SVD, though the risk genes are mostly distinct for the two disorders. Motifs for putative partners of lineage transcription factors in microglia and BECs were enriched for AD and SVD variants at genes linked to disease pathways. Gene prioritization and enrichment analyses further identified potential repurposable drugs for AD. Our findings highlight novel regulatory mechanisms and therapeutic targets within the neurovascular system.

overall_design:
H3K27ac CUT&Tag on ERG+, NeuN+, NOTCH3+, PU.1+, OLIG2+ and RFX4+ sorted cortical nuclei from aged postmortem tissue.
H3K4me3 CUT&Tag on ERG+, NeuN+, NOTCH3+, PU.1+, OLIG2+ and RFX4+ sorted cortical nuclei from aged postmortem tissue.

first: Kevin

middle: C

last: Ziegler

first: Aydan

last: Askarova

first: Charbel

last: Gergian

first: Reuben

last: Yaa

first: Janna

last: van Dalen

first: Janis

last: Transfeld

first: Filippo

last: Zoppi

first: Jia

last: Du

first: Daniel

last: Clode

first: Fatemeh

last: Rahbar

first: Rebecca

last: Graham

first: Muralidharan

last: Sargurupremraj

first: Stéphanie

last: Debette

first: David

last: Gonda

first: Michael

last: Levy

first: Siddharthan

last: Chandran

first: Sven

last: Falk

first: Marisa

last: Karow

first: Paul

last: Matthews

first: Nicole

middle: G

last: Coufal

first: Alexi


title: Candidate genes underlying hypomelanistic morphs in squamate reptiles

city: Geneva

first: Athanasia

last: Tzika

address: Quai Ernest-Ansermet

department: Genetics and Evolution

institute: University of Geneva

summary: Reptiles exhibit a broad variety of adaptive colours and colours patterns but little is known of the mechanisms responsible for these traits. We focus here on the Hypomelanistic traits of 1 corn snake color morph and 3 leopard gecko color morphs. We use mapping-by-sequencing and and differential expression analysis to identify the causative mutation and identify the genes involved in the phenotypes of these color morphs.

overall_design: Paired-end RNA-Seq of dorsal skin from E40 corn snake embryos WT and Homozygous Hypomelanistic

first: Pierre

last: Beaudier

first: Asier

last: Ullate-Agote


title: Hepatocyte-specific epidermal growth factor receptor (EGFR) deletion attenuates acetaminophen-induced liver injury in mice

city: Pittsburgh

first: Shuchang

last: Liu

address: 203 Lothrop Street

institute: University of Pittsburgh


title: Auxin-induced depletion of human CCR4-NOT subunits reveals opposing functions of CNOT1 and CNOT4 in mRNA metabolism

city: State College

first: Shardul

last: Kulkarni

address: 463 North Frear Laboratory

institute: Penn State University

summary: CCR4-NOT regulates multiple steps in gene regulation, including transcription, mRNA decay, protein ubiquitylation, and translation. Originally discovered in yeast, this complex is highly conserved across eukaryotes, although its composition and functions differ between mammals and yeast. For example, unlike yeast Not4, human CNOT4 (E3 Ubiquitin Ligase) does not form a stable complex with CCR4-NOT, and its functions are less clear compared to its yeast counterpart. To investigate the roles of CNOT1 (the central scaffold subunit) and CNOT4, we developed a rapid auxin-induced degron cell culture system that allows for the acute depletion of these proteins. We studied the effects of their absence on complex integrity, cell growth, and mRNA expression and turnover. Our transcriptome-wide analysis revealed that depleting CNOT1 altered the expression of thousands of transcripts, with the majority showing increased abundance and a general decrease in mRNA decay. Although CNOT4 does not associate with the complex through standard biochemical methods, BioID proximity labelling confirmed its association with the complex in cells. However, depleting CNOT4 did not affect the integrity of CCR4-NOT. In contrast to the effects observed with CNOT1 depletion, reducing CNOT4 levels led to only modest changes in RNA steady-state levels and unexpectedly accelerated global mRNA decay. Finally, we show that the changes in mRNA stability in CCR4-NOT-depleted cells correlated with the codon optimality of the transcripts. Our data suggest that CNOT4 exerts opposite effects on mRNA metabolism compared to CNOT1, and that CNOT4 may have functions distinct from those of complex subunits that promote mRNA degradation.

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

first: Aswathy

last: Sebastian

first: Joseph

last: Reese


title: H3K36 Methylation - a Guardian of Epigenome Integrity [Hi-C]

city: Montreal

first: Jacek

last: Majewski

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

institute: McGill University

summary: H3K36 methylation is a key epigenetic mark with critical roles in development and disease, yet its genome-wide functions remain incompletely understood. Here, we systematically dissect the role of H3K36 methylation using a series of CRISPR-engineered mouse mesenchymal stem cell lines with progressive knockouts of the five H3K36 methyltransferases: NSD1, NSD2, NSD3, SETD2 and ASH1L—culminating in quintuple knockout (QuiKO) cells entirely lacking H3K36me2/3. We demonstrate that H3K36me2 enriched at active cis-regulatory elements predominantly influences enhancer activity and supports the expression of enhancer-dependent genes. Within gene bodies, loss of H3K36me2/3 permits invasion by the repressive H3K27me2/3 modifications, thereby disrupting transcriptional fidelity. Unexpectedly, we uncover a previously undescribed relationship between H3K36me and H3K9me3: upon H3K36me2 depletion, SUV39H1-mediated H3K9me3 redistributes from large constitutive heterochromatic domains into euchromatin, leading to widespread epigenome restructuring and transcriptional changes. This redistribution is accompanied by a collapse of 3D genome organization, including weakened compartment boundaries and a profound loss of long-range interactions. Finally, we validate key findings in two human HNSCC cell lines overexpressing the H3K36M oncohistone, highlighting the conserved role of H3K36 methylation in maintaining epigenome integrity across species and cell types, and providing further mechanistic insights into the downstream consequences of this oncogenic mutation. Together, these data reveal that H3K36me is essential not only for local gene regulation but also for safeguarding the higher-order structure and functional balance of the genome.

overall_design: Hi-C in C3H10T1-2 mouse mesenchymal stem cells and head and neck squamous cell carcinoma (HNSCC) cells to compare the chromatin structure between H3K36me-depleted cells and their respective parental controls.

first: Reinnier

last: Padilla

first: Gerald

last: Shipman

first: Cynthia

last: Horth

first: Michel

last: Gravel

first: Eric

last: Bareke


title: H3K36 Methylation - a Guardian of Epigenome Integrity [ATAC-seq]

overall_design: ATAC sequencing in C3H10T1/2 mouse mesechymal stem cells with successive knockouts of the lysine 36 methyltransferases NSD1, NSD2, SETD2, NSD3 and ASH1L, as well as in HNSCC (head and neck squamous cell carcinoma) cell lines overexpressing H3.3K36M.


title: H3K36 Methylation - a Guardian of Epigenome Integrity

type: Methylation profiling by high throughput sequencing


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.

first: Kim Hei-Man

last: Chow


title: DAP12 deficiency alters microglia-oligodendrocyte communication and enhances resilience against tau toxicity

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

summary: Pathogenic tau accumulation fuels neurodegeneration in Alzheimer’s disease (AD). The role of microglia in tau-driven neurodegeneration is intricate, with DAP12 (DNAX-activation protein 12) triggering microglial immune responses. Mice lacking DAP12 become resistant to tau-induced brain toxicity in tauopathy mice, yet the precise mechanism remains elusive. Our current study uncovers a novel resilience mechanism against tau toxicity conferred by Dap12 deletion. While inactivation of Dap12 elevates tau inclusions, potentially disrupting microglial tau processing, it curbs tau-induced brain inflammation and ameliorates myelin and synapse loss. Tau-induced disease-associated clusters in microglia (MG) and intermediate oligodendrocytes (iOli) are abolished by removal of Dap12. Additionally, AD brains exhibit mouse iOli-like cells spatially correlated with tau pathology. In summary, our study reveals that DAP12 signaling triggers toxic interactions between microglia and oligodendrocytes in tauopathy, mediating tau-induced damage to oligodendrocytes and synaptic loss. Targeting DAP12 signaling presents a promising therapeutic approach for enhancing resilience against tau toxicity in AD.

overall_design: Droplet-based single nuclear RNA sequencing of mouse hippocampus of WT, Dap12+/+ tau+ and Dap12–/–tau+.

first: Hao

last: Chen

last: Fan

first: Qi

last: Guo

first: Man

middle: Y

last: Wong

first: Fangmin

last: Yu

first: Nessa

last: Foxe

first: Winston

last: Wang

first: Aviram

last: Nessim

first: Gillian

last: Carling

first: Bangyan

first: Chloe

last: Lopez-Lee

first: Yige

last: Huang

first: Sadaf

last: Amin

first: Sue-Ann

last: Mok

first: Won-min

first: Bin

last: Zhang

first: Flint

last: Beal

first: Qin

last: Ma

first: Hongjun

last: Fu

first: Wenjie

last: Luo


title: H3K36 Methylation - a Guardian of Epigenome Integrity [CUT&RUN]

first: Jacek

last: Majewski

overall_design: CUT&RUN sequencing for histone modifications H3K4me1, H3K27me3 and H3K9me3 in C3H10T1/2 mouse mesenchymal stem cells.

first: Reinnier

last: Padilla

first: Gerald

last: Shipman

first: Cynthia

last: Horth

first: Michel

last: Gravel

first: Eric

last: Bareke


title: H3K36 Methylation - a Guardian of Epigenome Integrity [ChIP-Seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-Seq) for histone modifications H3K27ac, H3K4me3, H3K27me1/2/3 and H3K9me3 in C3H10T1/2 mouse mesenchymal stem cells. ChIP-Seq for SUV39H1-FLAG and HP1 was also performed in C3H10T1/2 mouse mesechymal stem cells. In human head and neck squamous cell carcinoma (HNSCC) cell lines, ChIP-Seq was performed for H3K9me3, H3K27ac and H3K27me3.


title: H3K36 Methylation - a Guardian of Epigenome Integrity [BiSulfite-seq]

summary: H3K36 methylation is emerging as a key epigenetic modification with strong involvement in genetic disease and cancer. The mechanisms through which H3K36me impacts the epigenome and asserts its functional consequences are far from understood. Here, we use mouse mesenchymal stem cell lines with successive knockouts of the H3K36 methyltransferases: NSD1, NSD2, SETD2, NSD3, and ASH1L, which result in progressive depletion of H3K36me and its complete absence in the quintuple KO cells, to finely dissect the role of H3K36me2 in shaping the epigenome and transcriptome. We show that H3K36me2, which targets active enhancers, is important for maintaining enhancer activity, and its depletion results in downregulation of enhancer-dependent genes. We demonstrate the roles of H3K36me2/3 in preventing the invasion of gene bodies by the silencing H3K27me modifications. Finally, we observe a previously undescribed relationship between H3K36me and H3K9me3: Following the depletion of H3K36me2, H3K9me3 is redistributed away from large heterochromatic domains and towards euchromatin. This results in a drastic decompartmentalization of the genome, weakening the boundaries between active and inactive compartments, and a catastrophic loss of long-range inter-compartment interactions. By studying cells totally devoid of H3K36 methyltransferase activity, we uncover a broad range of crucial functions of H3K36me in maintaining epigenome integrity.

overall_design: Whole genome bisulfite sequencing in C3H10T1/2 mouse mesechymal stem cells to assess methylation levels following successive knockouts of H3K36 methyltransferases NSD1, NSD2, SETD2, NSD3 and ASH1L.


title: Methylome-driven regulation of miRNA expression and its relationship to cardiac dysfunction in idiopathic dilated cardiomyopathy

status: Public on Oct 22 2025

city: Valencia

first: Estefanía

last: Tarazón

address: Avenida Fernando Abril Martorell 106

country: Spain

institute: Instituto de investigación Sanitaria La Fe

summary: Idiopathic dilated cardiomyopathy (iDCM) is a multifactorial disease with a complex pathogenesis involving diverse molecular mechanisms. Among these, epigenetic mechanisms, including both DNA methylation and microRNAs (miRNAs)-mediated regulation, play an important role in determining the disease phenotype. However, the interplay between the DNA methylome and the miRNA transcriptome in iDCM remains largely unexplored. We conducted a cross-cohort multiomic integrative analysis of left ventricular (LV) tissue samples from iDCM patients and control (CNT) donors. DNA methylation profiling was performed using the Infinium MethylationEPIC BeadChip, whereas ncRNA-seq was used to assess transcriptomic changes. We identified a subset of 7 miRNAs exhibiting both differential methylation in their promoter regions and differential expression in their primary and mature forms. Notably, two of these miRNAs, hsa-miR-433-3p (r = 0.671, p < 0.01) and hsa-miR-493-5p (r = 0.585, p < 0.01), which are involved in fibrotic pathways appear to be significantly correlated with the left ventricular ejection fraction (LVEF), an established echocardiographic marker of cardiac function. Importantly, both miRNAs have predicted or validated target genes involved in fibrotic pathways, suggesting a potential link between DNA methylation, miRNA expression, cardiac remodeling, and the disease phenotype. This study enhances our understanding of the epigenetic mechanisms shaping the miRNA transcriptomic landscape in iDCM, revealing suggesting potential roles for these miRNAs in cardiac dysfunction and myocardial fibrosis.

overall_design: We analyzed 50 human heart samples from left ventricular apex of patients diagnosed with idiopathic dilated cardiomyopathy (n=20) and ischemic cardiomyopathy (n=22) undergoing heart transplantation, as well as from control donors (n=8).

first: Esther

last: Roselló-Lletí


title: Meningeal lymphatic ablation reduces ischemic stroke-induced inflammation via reprograming transcriptome profiling in cervical lymph nodes [scRNA-seq]

first: Gilbert

last: Lee

overall_design: We used scRNA-seq analysis to investigate the effects of saline and meingeal lymphatic ablation treatment on brain infiltrating lymphocytes after stroke


title: umami experiment-Analysis of the effect of amino-acids and humic substances on the transcriptome of Arabidopsis

city: Gif sur Yvette

first: Véronique

last: BRUNAUD

address: avenue des sciences

institute: INRAE

summary: 2022_13_qs_umami- umami experiment-Analysis of the effects of biostimulants (amino-acids and humic substances) on plants-Analysis of transcriptomic variations in Arabidopsis seedlings grown in vitro with or without humic substances or amino acid solutions.

overall_design: 3 samples x 3 biological replicats with 1 control and 2 treated (amino-acids and humic substances)

first: Stéphanie

last: Pateyron

first: Christine

last: Paysant-LeRoux

first: Christian

last: Meyer


first: Athanasia

last: Tzika

overall_design: Paired-end RNA-Seq of dorsal skin from E40 leopard geckos embryos WT and Homozygous Hypomelanistic 1, 2 and 3

first: Pierre

last: Beaudier

first: Asier

last: Ullate-Agote


title: Spatially organized progenitors in the zebrafish heart field determine cardiovascular patterning

city: Boston

first: Yunxia

last: Wang

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: Progenitor cells expressing nkx2.5 are specified in the bilateral zebrafish heart field that give rise to distinct components of the cardiovascular system. We have employed a single cell sequencing approach using the inDrops platform to study progenitor cells expressing nkx2.5. After specification, these fields separate into two main sub-populations; a cardiac fraction that migrates to the midline and forms the ventricular myocardium, and a pharyngeal fraction that remains lateral before differentiating into the head muscles, outflow tract, and pharyngeal arch arteries.  This study represents the first multi-omics analysis of pre-migratory populations coordinate.

overall_design: 14- and 20-ss wildtype (TU) and Tg(nkx2.5:ZsYellow) embryos were dissociated by Fluorescence-activated cell sorting (FACSmax) cell dissociation solution and analyzed using scRNA-seq.

first: Hakan

last: Coskun

first: Xinlei

last: Gao

first: Kaifu

last: Chen

first: C

last: Geoffrey Burns

first: Caroline

last: Burns


title: CEP290-deficiency disrupts ciliary axonemal architecture in human iPSC-derived cerebral organoids

city: Zurich

first: Ruxandra

last: Bachmann-Gagescu

address: Winterthurerstrasse 190

institute: University of Zurich

summary: Primary cilia are ubiquitous sensory organelles mediating various signaling modalities essential for development and cell homeostasis. Their dysfunction leads to ciliopathies, human disorders often affecting the central nervous system. CEP290 is a major ciliopathy-associated gene that encodes a centrosomal and ciliary transition zone protein. CEP290 has been implicated in different cellular functions, including cell cycle control, ciliogenesis, and control of ciliary membrane protein content. To investigate CEP290 dysfunction in human neurons, we generated human iPSC-derived cerebral organoids harboring CEP290 mutations. To quantitatively investigate the impact of CEP290 loss on cerebral organoid differentiation, we conducted single-cell RNA-sequencing. We found that CEP290 deficiency does not affect cell cycle progression or organoid formation, despite a tendency for less mature neuronal populations and formation of choroid plexus in mutant organoids.

overall_design: CEP290 CRISPR edited and WT cerebral organoids were harvested and dissociated with three organoids per sample. Samples were analysed using scRNA-seq.

first: Melanie

last: Eschment

first: Olivier

last: Mercey

first: Ellen

last: Aarts

first: Ludovico

last: Perego

first: Joana

last: Figueiro da Silva

first: Affef

last: Abidi

last: Generali

first: Paul

last: Guichard

first: Virginie

last: Hamel


title: H3K36 Methylation - a Guardian of Epigenome Integrity [RNA-seq]

first: Jacek

last: Majewski

overall_design: RNA-sequencing in C3H10T1/2 mouse mesechymal stem cells to perform gene expression analysis following knockouts of lysine 36 methyltransferases (NSD1,NSD2,SETD2,NSD3 and ASH1L) and in HNSCC (head and neck squamous cell carcinoma) cell lines following overexpression of H3.3K36M.

first: Reinnier

last: Padilla

first: Gerald

last: Shipman

first: Cynthia

last: Horth

first: Michel

last: Gravel

first: Eric

last: Bareke


title: Guanine- and cytosine-rich genes are actively transcribed at the nuclear Lmnb1 compartment

city: Cold Spring Harbor

first: Gayan

middle: Indhu

last: Balasooriya

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: Chromatin organization in the mammalian cell nucleus plays a vital role in the regulation of gene expression. The lamina-associated domain at the inner nuclear membrane has been proposed to harbor heterochromatin, while the nuclear interior has been shown to contain most of the euchromatin. Here, we show that a sub-set of actively transcribing genes, marked by RNA Pol II pSer2, are associated with Lmnb1 at the inner nuclear envelop in mESCs and the number of genes proportionally increases upon in vitro differentiation of mESC to olfactory precursor cells. These nuclear periphery-associated actively transcribing genes primarily represent housekeeping genes, and their gene bodies are significantly enriched with guanine and cytosine compared to genes actively transcribed at the nuclear interior. We found the promoters of these gene’s to also be significantly enriched with guanine and to be predominantly regulated by zinc finger protein transcription factors. We provide evidence supporting the emerging notion that the Lmnb1 region is not solely transcriptionally silent.

overall_design: Lmnb1-associated actively transcribing gene in male mESCs and mESC derived OPCs immunoprecipitation by sequential ChIP assay (Lmnb1 and RNA Pol II pSer2) and DNA-sequencing.

middle: I

first: David

middle: L

last: Spector


title: Spatially organized progenitors in the zebrafish heart field determine cardiovascular patterning [MERFISH]

first: Yunxia

last: Wang

summary: Progenitor cells expressing nkx2.5 are specified in the bilateral zebrafish heart field that give rise to distinct components of the cardiovascular system. We performed spatial transcriptomics (MERFISH) to profile 14-ss wildtype (TU) and Tg(nkx2.5:ZsYellow) zebrafish embryos as well as to determine their importance for heart development. Our data provide a blueprint of heart field organization that informs vulnerable aspects of cardiovascular development.

overall_design: 14-ss Tg(nkx2.5:ZsYellow) embryos for heart development were used for analysis.

first: Hakan

last: Coskun

first: Xinlei

last: Gao

first: Kaifu

last: Chen

first: C

last: Geoffrey Burns

first: Caroline

last: Burns


title: Silencing of S100A11 Attenuates Murine Metabolic Dysfunction-associated Steatohepatitis

city: Rochester

first: Harmeet

last: Malhi

state: Mn

address: 200 1st SW

department: GI/Hep research

institute: Mayo Clinic

summary: S100A11 is an alarmin known to be upregulated in MASH; however, its role in MASH pathophysiology remains incompletely defined. In MASH, insulin resistance and subsequent impaired hepatic carbohydrate and lipid metabolism significantly increase de novo lipogenesis causing hepatic steatosis and lipotoxicity. S100A11 promotes steatosis in cell lines. Therefore, we hypothesized that S100A11 drives MASH by upregulating lipid synthesis in the liver. We employed whole body S100A11 knockout (S100a11-/-) mice and liver specific knockdown mice and a MASH inducing diet to address this hypothesis. S100a11-/- mice demonstrated reduced steatosis, inflammation and fibrosis compared to wild type controls. Hepatotropic AAV8 mediated S100A11 silencing in mouse livers significantly attenuated steatosis, inflammation, and fibrosis. Significant dysregulation of carbohydrate and lipid metabolism was identified by Ingenuity Pathway Analysis of bulk-RNA sequencing of S100a11 silenced mouse livers. Candidate gene approach in these pathways identified hexokinase 2 (HK2) as significantly downregulated in the S100a11 knockdown mouse livers. Since hexokinases regulate the crucial stage of glucose flux into downstream metabolic processes, including de novo lipogenesis, we expressed exogenous HK2 in S100a11-/- mice. Overexpression of Hk2 was sufficient to upregulate steatosis under chow fed basal nutrition conditions in S100a11-/- mouse livers. These studies identify S100A11 and HK2 as potential therapeutic targets for MASH.

overall_design: Bulk RNA sequencing of mouse liver following silencing of S100A11 using an AAV8 construct in a dietary MASH model.

first: P. Vineeth

last: Daniel

first: Gyanendra

last: Puri

first: Yixing

last: Luo

first: Naresh

last: Golla

first: Takahito

last: Nishihara

first: Hanna

last: Erickson

first: George

last: Marek

first: Davide

last: Povero

first: Amy

last: Mauer

first: Jun

last: Liu


title: Epigenetic Profiling Reveals Key Super-Enhancer Networks Driving Oncogenesis in HPV-Positive HNSCC

city: Baltimore

first: Fernando

last: Zamuner

state: MD

address: 1550 Orleans Street

department: Department of Otolaryngology - Head and Neck Surgery

institute: Johns Hopkins University, School of Medicine

summary: The objective was to investigate the impact of JQ1, a bromodomain inhibitor, on two cell lines of HPV+ HNSCC by comparing it to a control group that did not receive any treatment (DMSO).

overall_design: For every experiment conducted on the UM-SCC-47 or UPCI-SCC-090 cell line treated with JQ1 or DMSO, we sequenced three repeats, and each of these was performed twice (2 different lanes).

middle: T

first: Daria

middle: A

last: Gaykalova


title: Monitoring the complexity and dynamics of mitochondrial translation

city: Wako city

first: Taisei

last: Wakigawa

state: Saitama prefecture

address: 2-1, Hirosawa

institute: RIKEN

summary: Eukaryotes house the additional protein synthesis system in mitochondria. Given the mitochondrial translation dictates OXPHOS complex abundance and then ATP level in cells, the exhaustive quantitative, and high-resolution delineation of mitoribosome traversal has been awaited. Here, we developed a high-resolution mitochondrial ribosome profiling and unveiled tight regulation of in organello translation. Our approach assessed the stoichiometry and kinetics of mitochondrial translation flux, such as the absolute mitoribosome numbers on a transcript, elongation rate, initiation rate, and lifetime translation round on a transcript. We also surveyed the impacts of all the 34th position modifications on mt-tRNAs, including f5C34, m5C34, τm5U34, τm5s2U34, s2U34, and Q34, as well as t6A37 by the responsible enzyme deletions. Moreover, retapamulin-assisted profiling and disome profiling unveiled cryptic translation initiation sites at sub-cognate codons and the programmed mitoribosome collision sites across the mitochondrial transcriptome, respectively. Our work provides a useful resource to delineate protein synthesis within the bioenergetic powerhouse.

sample_organism:
Homo sapiens
Mus
Mus musculus

platform_organism:
Homo sapiens
Mus
Mus musculus

overall_design: Ribo-Seq, RNA-Seq, Ribo-Calibration, MitoIP-Ribo-seq, MItoIP-Thor-Ribo-Seq, MitoIP-Thor-Disome-Seq.

first: Mari

last: Mito

first: Haruna

last: Yamashiro

first: Kotaro

last: Tomuro

first: Fan-Yan

last: Wei

first: Kazuhito

last: Tomizawa

first: Takeshi

last: Chujo

first: Asuteka

last: Nagao

first: Takeo

last: Suzuki

first: Yuichi

last: Shichino

first: Tsutomu

first: Shintaro

last: Iwasaki


title: Mapping Somatosensory Afferent Circuitry to Bone Identifies Neurotrophic Signals Required for Fracture Healing

first: Aaron

last: James

state: Maryland

address: 720 Rutland Avenue, Ross Bldg., Room 529

institute: Johns Hopkins University

summary: A central feature of bone injury is the sensation of pain, transmitted by nociceptive sensory nerves that innervate the skeleton. Indeed skeletal-innervating peripheral neurons are known to regulate skeletal repair and pathophysiology.  Here, using retrograde peripheral nerve labeling and single cell RNA sequencing (scRNA-seq), we precisely identify the unique molecular signature of skeletal-innervating sensory neurons and the shifting neuronal transcriptomic landscape after bone fracture. Two methods to surgically or genetically denervate fractured bones were used in combination with scRNA-seq to implicate defective mesenchymal cell proliferation and osteodifferentiation as underlying the poor bone repair capacity in the presence of attenuated skeletal innervation. Multi-tissue scRNA-seq and interactome analyses implicated neuron-derived FGF9 as a potent regulator of fracture repair, a finding confirmed by in vitro assessments of neuron-to-skeletal mesenchyme interactions. Identification of FGF9 as a novel,  neuron-derived skeletal growth factor uncovers a potential target for improving tissue repair.

overall_design: To identify skeleton-innervating neurons, an engineered virus with enhanced tropism for peripheral neurons was injected into the midshaft of the  ulnar periosteum of 14-week-old mice (3.5μl AAV-PHP.S-tdTomato). 4 weeks after injection, retrograde labeling of dorsal root ganglion (DRG) neurons with  AAV-PHP.S-tdTomato was evaluated using whole-mount immunohistochemistry, scRNA-Seq and RNAscope (DRGs at C7, C8, T1 levels were used corresponding to the innervation pattern of the forelimb). To characterize temporal transcriptomic responses to ulnar stress fracture  retrogradely labeled whole DRGs were harvested and dissociated at 1-, 14- and 56- days post-stress fracture and subjected to scRNA-Seq. To uncover ulna callus resident cells that may interact with ulna-innervating sensory neurons, callus single-cell transcriptomics atlas from control and denervated callus were generated 14 days post fracture. Denervation of callus was achieved by two methods: surgical neurectomy of ulna neurectomy and chemical inhibition by administrating small molecule 1NMPP1 to TrkAF592A mice. Interaction modalities were performed to reveal potential skeleton-innervating neuron-derived ligands that are involved in fracture repair.

first: Mingxin

last: Xu

first: Zhao

last: Li

first: Masnsen

last: Cherief

middle: W


title: Complex-specific inhibitor for interrogating ATAC histone acetyltransferase complex

city: Hong Kong

first: Sha

last: Liu

address: Pokfulam Road, Hong Kong

department: Department of Chemistry

institute: The University of Hong Kong

summary: Histone acetyltransferases (HATs) modify chromatin to regulate gene expression. Instead of acting alone, HATs function in complexes with other proteins, leading to variations in substrate specificity, genomic localization, and cellular function. To understand the complex-dependent roles of HATs, we present a chemical approach to specifically dissociate ATAC (Ada-two-A-containing) HAT complex from chromatin without perturbing other complexes. Rather than targeting the shared HAT enzyme, we developed chemical probes for an ATAC-specific subunit, YEATS2. The most effective probe, LS-170, specifically reduced the chromatin occupancy of the ATAC complex, decreased the ATAC-dependent histone acetylation level, and downregulated the expression of ATAC-governed genes, leading to significantly suppressed tumor growth in a lung cancer mouse model. This study not only sheds light on the regulatory roles of the ATAC HAT complex in gene transcription, but also provides evidence that the chemical inhibition of the ATAC complex can be a promising therapeutic strategy.

overall_design: H1299 cells were treated with LS-170 or DMSO. RNA-seq was performed with 4 replicates DMSO and 3 replicates LS-170. ChIP-seq were performed in duplicates with matched input control for each condition and antibody.

first: Xiang David


title: Cell-specific delivery of GJB2 restores auditory function in mouse models of DFNB1 deafness and mediates appropriate expression in NHP cochlea

status: Public on Oct 21 2025

first: Erin

middle: Elizabeth

last: Duffy

address: 200 Longwood Ave, Goldenson 405

department: Neurobiology

institute: Harvard Medical School

summary: Mutations in the GJB2 gene cause DFNB1, the most common hereditary hearing loss. GJB2 is expressed by cochlear epithelial cells and fibrocytes, but not by sensory hair cells or neurons. Attempts to treat DFNB1 mouse models with gene therapy have not substantially restored function, as inappropriate expression in hair cells and neurons might compromise their electrical activity. Here, we use ATAC-seq to identify candidate gene regulatory elements (GREs) that can drive cell-type-specific expression of GJB2. HA-tagged GJB2, delivered to a conditional knockout mouse with AAV vectors carrying GREs, is expressed by the appropriate cells, prevents degeneration, and rescues hearing by only 10–20 dB. In a Gjb2 partial knockdown model, a vector lacking HA prevents degeneration and completely restores hearing. In cynomolgus monkey cochleas, human GJB2.HA delivered with similar vectors is located in the appropriate cell types and causes little or no compromise of hearing sensitivity. Together, these findings suggest that GRE-mediated expression of GJB2 can prevent hearing loss in DFNB1 patients.

overall_design: ATAC-seq of bilateral cochleae harvested from neonatal CD1 mice (P2, n=3; P5, n=3; P8, n=4) to determine developmentally relevant gene regulatory elements