title: Blocking Nuclear Receptor Nr4a3 Unlocks the Senescence Barrier to Promote Direct Cardiac Reprogramming

city: wuhan

first: yu

middle: zhang

last: yi

address: donghu street

institute: wuhan university

summary: Direct reprogramming of scar-forming fibroblasts into induced cardiomyocytes (iCMs) offers a regenerative strategy to repair injured myocardium. However, reprogramming efficiency remains low in fibroblasts from adult and aged hearts, and the molecular barriers underlying this resistance remain poorly understood. Here, we used transcriptomic and epigenetic profiling to uncover cellular senescence as a key obstacle limiting fibroblast plasticity and cardiogenic conversion. Fibroblasts from post-neonatal stages exhibited impaired activation of cardiac gene programs and persistent expression of fibrotic and inflammatory signatures. A loss of function screen identified Nr4a3 as a key repressor of cardiac reprogramming, particularly in senescent and aged cardiac fibroblasts (CFs). Nr4a3 overexpression promoted senescence and suppressed iCM reprogramming, whereas Nr4a3 knockdown significantly enhanced iCM induction from both murine and human senescent CFs. Mechanistically, Nr4a3 depletion remodeled the chromatin landscape by shifting it from a fibrotic and inflammatory state to a regenerative cardiac program. We further identified Cxcl14, a senescence-associated secretory phenotype (SASP) factor upregulated by Nr4a3, as a key downstream effector. Blocking Cxcl14 restored reprogramming in otherwise refractory fibroblasts. In vivo, Nr4a3 knockdown enhanced reprogramming-based improvement of heart function following myocardial infarction. These findings demonstrated that cellular senescence is a major barrier to direct cardiac reprogramming and identified Nr4a3 as a central regulator of this block. Targeting Nr4a3 and its downstream effectors may represent a promising therapeutic avenue to enhance cardiac regeneration in aged individuals following injury.

overall_design: To determine the molecular basis by which knockdown Nr4a3 enhances iCM reprogramming, we conducted RNA-seq using shNr4a3-CFs and shNT-CFs collected at  day 7 of treatment.

first: Li

last: Wang

first: Mengxin

last: Liu

first: Zhangyi

last: Yu


title: Linker histone regulates the myeloid versus lymphoid bifurcation of multipotent hematopoietic stem and progenitors

status: Public on Oct 03 2025

city: New Haven

first: Shangqin

last: Guo

state: CT

address: 10 Amistad Street

department: Department of Cell Biology

country: USA

institute: Yale University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Myeloid-biased differentiation of multipotent hematopoietic stem and progenitor cells (HSPCs) occurs with aging or exhaustion. The molecular mechanism(s) responsible for this fate bias remain unclear. Here we report that linker histone regulates HSPC fate choice at the lymphoid versus myeloid bifurcation. Linker histones package nucleosomes and compact chromatin. HSPCs expressing a doxycycline (dox) inducible H1.0 transgene favor the lymphoid fate, display strengthened nucleosome organization and reduced chromatin accessibility at subsets of genomic regions. The genomic regions showing reduced chromatin accessibility host many known marker genes of myeloid biased HSCs. The transcription factor Hlf is located in one of the most differentially closed regions, whose chromatin accessibility and gene expression are reduced in H1.0high HSPCs. Failure to reduce Hlf expression in multipotential HSPCs abrogates the H1.0-endowed lymphoid potential. Furthermore, HSPCs display aspartyl protease dependent H1.0 decreases, especially in response to interferon alpha (IFNa). Aspartyl protease inhibitors preserve endogenous H1.0 levels and promote the lymphoid fate of wild type HSPCs. Thus, our work elucidates a molecular scenario how myeloid bias arises and uncovers a point of intervention for correcting myeloid skewed hematopoiesis.

overall_design: ATAC seq of Lin- Sca1+ cKit+ (LSK) cells isolated from WT or iH1.0-GFP mice treated with Dox water for 3 weeks

first: Kutay

last: Karatepe

first: Bruna

last: Mafra de Faria

first: Jian

last: Zhang


title: Palmitate suppresses CD8+ T cell antitumoral response by disrupting mitochondrial metabolism [ATAC-seq]

status: Public on Oct 06 2025

city: Milano

first: Teresa

last: Manzo

state: Milano

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: IEO

summary: Accumulation of lipids in the tumor microenvironment (TME) is a feature of several solid tumors and increased palmitate (PA) availability fosters tumor progression and metastases. The intrinsic effects of PA on cancer cells are well understood, but its role in modulating CD8+ T cells (CTL) functional performances remains elusive. Here, we found that PA alters the mitochondrial metabolism of CTL and prevents their effector functions in an irreversible manner, resulting in impaired antitumoral immunity. Mechanistically, PA-induced mitochondrial blocking demotes histone acetylation and chromatin accessibility and decreases the transcription of genes promoting DNA replication and production of effector molecule production. We identified the metabolic enzyme Sphingosine Kinase 2 (SPHK2) as a molecular target of PA in establishing CTL dysfunction. Consistently, pharmacological inhibition of SPHK2 restored CTL mitochondrial fitness, effector functions and anti-tumor potential. Thus, we reveal that PA fosters tumor progression by impairing CTL antitumor immunity and highlight the therapeutic potential of inhibiting SPHK2 activity to optimize T cellfunctionality.

overall_design: To investigate the effects of Palmitate on CD8+ T cell function, ATAC-seq of Palmitate-treated vs control cells was carried out after 48 hours of treatment

first: Silvia

last: Tiberti

first: Sara

last: Gennari

first: Martina

last: Romeo

first: Ilir

last: Sheraj

first: Mohamed

middle: F

last: Kassir

first: Juan

last: Fernández-García

first: Carina

middle: B

last: Nava Lauson

first: Roberta

last: Noberini

first: Carlotta

last: Catozzi

first: Tiziano

last: Dallavilla

first: Mattia

last: Ballerini

first: Alessia

last: Loffreda

first: Simona

middle: G

last: Codreanu

first: Stacy

middle: D

last: Sherrod

first: Katrina

middle: L

last: Leaptrot

first: Alexandra

middle: C

last: Schrimpe-Rutledge

first: John

middle: A

last: McLean

first: Martin

middle: H

last: Schaefer

last: Rodighiero

first: Tiziana

last: Bonaldi

first: Sarah-Maria

last: Fendt

first: Besim

last: Ogretmen

last: Sdelci

first: Luigi

last: Nezi


title: Catch and release of sialoglycoRNAs enables sequencing-based profiling across cellular and extracellular material

status: Public on Oct 05 2025

city: Boston

first: Ryan

middle: A.

last: Flynn

state: MA

address: 1 Blackfan Circle

department: Department of Pediatrics

institute: Boston Children’s Hospital

summary: Glycosylated RNAs (glycoRNAs) represent a recently discovered class of small RNAs, but their systematic characterization has been limited by reliance on metabolic chemical reporters and high RNA input requirements. Here we present rPAL sequencing (rPAL-seq), a sensitive and selective platform for de novo discovery of sialoglycoRNAs. rPAL-seq combines enhanced periodate oxidation of sialic acids with a capture–release workflow and optimized library construction using poly(A) extension coupled with template-switching reverse transcription. The method enabled reproducible profiling from less than 100 ng of input RNA, corresponding to less than 2% of the material required by previous approaches. When applied across 13 human cell lines, rPAL-seq identified lineage-associated glycoRNA patterns alongside a conserved core dominated by uridine-rich snRNAs and snoRNAs, with modification signatures implicating glycosylation on acp³U or related uridine-based modifications. Extending to extracellular fractions, rPAL-seq revealed secreted glycoRNA profiles distinct from those of the cellular fraction. rPAL-seq provides a robust, scalable strategy for glycoRNA profiling, opening new avenues for studying this emerging biopolymer.

sample_organism:
Homo sapiens
Canis lupus familiaris
Mus musculus

overall_design: This study aimed to profile sialoglycoRNA from diverse human and animal cell lines using rPAL-seq, a sequencing method first introduced in this study that combines enhanced reductive periodate–aminoxy labeling with sialidase-specific elution. Cells (including HeLa, A549, 293T, Huh7, LPS853, LN308, OCI-AML2, OCI-AML3, Molm13, Jurkat, Jeko1, Nalm6,  DiFi, MDCK, and EMT6) were cultured under standard conditions. Extracellular vesicles (EVs) and non-vesicular extracellular nanoparticles (NVEPs) were isolated from conditioned medium of DiFi and MDCK using previously established protocols. For each biological sample, sialoglycoRNA was captured and processed in 3 parallel groups: IP (VC sialidase–eluted), Control (mock elution with heat-inactivated enzyme), and Input (1% reserved prior to elution). Libraries were prepared using the rPAL-seq workflow and sequenced on an Illumina NovaSeq X platform with single-end 100 bp reads.

first: Ruiqi

last: Ge

first: Dennis

middle: K

last: Jeppesen

first: Sandeep

last: Rai

first: Robert

middle: J

last: Coffey


title: Endothelial BMP6 Drives Hemodynamic-Dependent VSMCs Calcification in Carotid Atherosclerosis

city: zhengzhou

first: Shen

last: Li

address: No. 1 East Jianshe Road

department: The Department of Neurology

country: China

institute: The Department of Neurology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China

type: Expression profiling by high throughput sequencing

summary: Carotid atherosclerosis (CAS) is a major contributor to ischemic stroke, with vascular calcification driving disease progression. However, the molecular mechanisms driving vascular calcification in CAS remain unelucidated. Previous studies have confirmed that bone morphogenetic proteins (BMPs) play essential roles in calcification; however, the regulatory mechanisms of BMP6 signaling in vascular calcification remain unclear. This study aimed to investigate the role of BMP6 in vascular calcification in CAS and the underlying mechanisms. A subset of endothelial cells (ECs) with high BMP6 expression, which interacted with specific vascular smooth muscle cells (VSMCs) via the BMP signaling pathway, was identified using single-cell RNA sequencing of human CAS plaque samples. In vitro experiments demonstrated BMP6-induced osteogenic differentiation of VSMCs. Moreover, BMP6 activated the p-SMAD1/5/8 signaling pathway by binding to the ACVR1–BMPR2 receptor complex, and pharmacological inhibition of this pathway attenuated osteogenic differentiation. Experimental results from endothelium-specific BMP6 knockout (BMP6ECKOApoE-/-) and overexpression (AAV-Cdh5-BMP6) mice confirmed that BMP6 exacerbated vascular calcification, whereas its knockdown reduced calcific lesions. Additionally, disturbed flow conditions upregulated BMP6 expression by suppressing Krüppel-like factor 4 and linking hemodynamic forces to BMP6-mediated calcification. These findings suggest that BMP6 is a key regulator of vascular calcification in CAS, driven by EC–VSMC interactions and hemodynamic stress

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 12 CAS plaques obtained following carotid endarterectomy (CEA) and carotid arteries from mice were isolated by  fluorescence-activated cell sorting and analyzed using ScRNA-seq

first: Shuang

last: Cao

first: Peipei

first: Yongjun

last: Wang

first: Zongping

last: Xia

first: Jie

last: Xu

first: Yuming


title: A single-cell transcriptomic atlas of inner ear morphogenesis in zebrafish

city: Berkeley

first: Ian

last: Swinburne

state: CA

address: Weill Hall, Room 585

department: Molecular and Cell Biology

institute: UC Berkeley

summary: The inner ear constitutes different cell types next to one another: the sensory patches whose hair cells synapse with neurons, the thin channels of three semicircular canals whose perpendicular organization enables detection of directional head rotation, and the endolymphatic duct and sac whose conditional epithelial barrier relieves excess pressure and promotes fluid pressure homeostasis. How the ear’s component cell states are established during development has remained unknown. We use single-cell RNA sequencing to distinguish cell states within the developing ear with wild-type zebrafish embryos and lmx1bb mutants that exhibit defects in canal and sac morphogenesis. We identify the earliest marker for the semicircular canal-genesis zone (ccn1l1), unexpected genes in the endolymphatic sac that suggest a role for tissue contraction in its function (smtnb), parallel gene sets for sensory patches in the neuromast and ear, and a conserved role for cell-cycle pausing (cdkn1bb expression in the canals and sac as previously observed in the developing mouse ear). This atlas provides the most comprehensive transcriptional profiling of the developing inner ear, identifying new molecular leads to understand ear morphogenesis.

overall_design: Blocks of tissue enriched for the inner ear were dissected and collected from wild-type zebrafish at 40, 48, 60, and 72 hours post fertilization (hpf) were collected, and from lmx1bb mutant zebrafish at 60 and 7 hpf. Single-cells were captured and transcriptome libraries were prepared by the single-cell core at Harvard Medical School with established protocols (Klein et al. 2015; Wagner et al. 2018). Libraries were pooled in a manner to evenly distribute samples and prevent overlapping of barcodes. Assembled libraries were then sequenced with paired end reads using 21 flow cells of 75 cycles on an Illumina NextSeq 500. As described previously, cDNA reads were mapped using the GRCz11 zebrafish genome assembly (Wagner et al. 2018).  We provide the raw data (.fastq files) and the entire pooled and filtered data after removing doublets as EarAtlas_FullProcessed.h5ad.  Information about pooling libraries and library indices is provided in Swinburne_EarAtlas_PoolingSamples.xlsx.

first: Akankshi

last: Munjal

first: Kalki

last: Kukreja

first: Sean

last: Megason


title: NAD+ - and EVA1-C-dependent reversal of neurological deficits is mediated by differential alternative RNA splicing in tauopathic animal models

city: Guangzhou

first: Lipeng

last: Mao

state: Guangdong

address: No.601, West Huangpu Avenue

department: Department of Microbiology and Immunology

institute: Jinan University

summary: Aberrant alternative splicing events (ASEs) are emerging as a new hallmark of aging and are linked to age-related neurodegenerative pathologies such as Alzheimer’s disease (AD). AD brains are characterized by abundant intracellular proteinaceous aggregates, including neurofibrillary tangles (NFTs). Although NAD+ and related metabolites can slow down AD progression, the effects of NAD+ on ASEs in AD remain unclear. This study investigates the relationships between NAD+ metabolism, ASEs and AD or AD-like pathologies including tauopathies using deep-learning AI-based algorithms to predict protein structures and protein-protein interactions as well as experimental tauopathy models including hTau.P301S transgenic mice and transgenic hTau[P301L] Caenorhabditis elegans. Mouse transcriptomic data were mined to detect ASEs that were differentially induced in the presence of NAD+ precursor nicotinamide riboside (NR) with specific focus on the Eva1-C locus. The results reveal that the relative abundance of Eva1-C isoforms is sensitive to both the concentration of NR and to tauopathy genotype. NAD+ abundance/metabolic status modulates ASEs and the expression of EVA1-C isoforms, which in turn regulate the interaction with the key proteins, BAG-1 and HSP70, involved in orchestrating protein homeostasis. Importantly, EVA1-C is dramatically reduced in the postmortem entorhinal cortex and hippocampal neurons from 20 Braak 5/6 AD patients compared to 20 of cognitive normal humans. Thus, this study supports the novel idea that NAD+ metabolism modulates abundance of specific mRNA isoforms, and that ASEs influence disease progression in model tauopathies and potentially AD. These results could facilitate future development of NAD+-based splice-switching therapeutics for AD.

overall_design: To better understand how NAD+ precursor, NR, affects the hippocampus of mice in molecular pathways, we performed RNA sequencing in the hippocampal tissue of WT and P301S mice with or without NR treatment. We found that NR changed hippocampal neural activity and homeostasis.

first: Ruixue

last: Ai

first: Xurui

last: Jin


title: Nanomaterial- induced mitochondrial biogenesis enhances intercellular mitochondrial transfer efficiency

city: Bryan

first: Irtisha

last: Singh

state: TX

address: 8447 John Sharp Pkwy MREB II, Suite 4344

department: Cell Biology & Genetics

institute: Texas A&M University

summary: Intercellular mitochondrial transfer, the spontaneous exchange of mitochondria between cells, is a recently described phenomenon crucial for cellular repair, regeneration, and disease management. Enhancing this natural process holds promise for developing novel therapies targeting diseases associated with mitochondrial dysfunction. Here, we introduce a nanomaterial- based approach employing molybdenum disulfide (MoS2) nanoflowers with atomic- scale vacancies to stimulate mitochondrial biogenesis in cells to make them mitochondrial biofactories. Upon internalization, these nanoflowers result in a two- fold increase in mitochondrial mass and enhancing mitochondrial transfer to recipient cells by several- fold. This enhanced efficiency of transfer significantly improves mitochondrial respiratory capacity and adenosine triphosphate production in recipient cells under physiological conditions. In cellular models of mitochondrial and cellular damage, MoS2 enhanced mitochondrial transfer achieved remarkable restoration of cell function. This proof- of- concept study demonstrates that nanomaterial- boosted intercellular mitochondrial transfer can enhance cell survivability and function under diseased conditions, offering a promising strategy for treating mitochondrial dysfunction- related diseases.

overall_design: Paired-end Illumina RNA-seq of sorted smooth muscle cells (SMCs) alone, after coculture with hMSCs (Mito-Transfer), and after coculture with hMSCs pre-treated with MoS2 nanoflowers.

first: John

last: Soukar

first: Kanwar Abhay

first: Ari

last: Aviles

first: Sarah

last: Hargett

first: Harman

last: Kaur

first: Samantha

last: Foster

first: Feng

last: Zhao

first: Vishal

last: Gohil

first: Akhilesh

last: Gaharwar


title: RNA microarray was performed from lung adenocarcinoma cell CL1-0 and CL1-5 that were manipulated LCRMP-1 expression.

status: Public on Oct 02 2025

city: Taipei

first: Yuan-Ling

last: Hsu

address: No.1 Jen Ai road section 1

country: Taiwan

institute: National Taiwan University, College of Medicine

summary: Transcriptomic profiling of CL1-0 and CL1-5 cells with altered LCRMP-1 expression revealed that LCRMP-1 promotes angiogenesis by regulating angiogenesis facotr transcription, implicating its role as a transcriptional co-regulator in lung cancer progression.

overall_design:
CL1-0 LCRMP-1 overexpressing cells (clone  1 and clone 2) were compared with CL1-0 Vector control cells. CL1-5 LCRMP-1 silencing cell was compared with CL1-5 Scramble control cell. Each experimental condition for all cell lines was performed with two biological replicates.
Please note that each sample data was generated from both replicates.

first: Pei-Fang

last: Hung

first: Chi-Chung

last: Wang

first: Yih-Leong

last: Chang

first: Chen-Tu

last: Wu

first: Pei-Shan

first: Xuan-Ren

last: Chen

first: Tse-Ming

last: Hong

first: Pan-Chyr

last: Yang

first: Szu-Hua

last: Pan


title: Overexpression of Meis factors in late-stage retinal progenitors yields complex effects on temporal patterning and neurogenesis.

status: Public on Oct 07 2025

city: Baltimore

first: Patrick

last: Leavey

state: Maryland

address: 733 N Broadway, 332

department: Neuroscience

institute: Johns Hopkins School of Medicine

summary: The vertebrate retina serves as a model for studying neurogenesis and cell fate specification, with retinal progenitor cells following a tightly regulated temporal sequence to generate distinct cell types. Meis1 and Meis2 are transcription factors implicated in early retinal development, but their role in late-stage RPCs remains poorly understood. Here, we investigate whether Meis1 and Meis2 overexpression in postnatal mouse RPCs can alter temporal identity and induce early-born cell types. Using electroporation and single-cell RNA sequencing, we find that while these factors modestly upregulate early-stage gene regulatory network components, they do not repress late-stage transcription factors or induce early-born retinal cells. Meis1 overexpression reduces proliferation and inhibits neurogenesis, whereas Meis2 overexpression  accelerates neurogenic progression without altering fate commitment. Our findings suggest that overexpression of Meis1 and Meis2 modulate largely non-overlapping aspects of temporal identity and neurogenic competence but are insufficient to fully reprogram late-stage progenitors. These results have implications for regenerative strategies aimed at reprogramming retinal cells for therapeutic purposes.

overall_design: Wildtype CD1 murine retinal explants were treated with a pCAGIG- empty control, a pCAGIG-NR2F1, a pCAGIG-NR2F2, or a 50:50 combination of pCAGIG-NR2F1 and pCAGIG-NR2F2 for 2 or 5 days prior to collection and library generation. Retinal explants were lysed into a single cell suspension, GFP+ cells were isolated and run on the 10x Genomics Chromium Single Cell System platform using the Single Cell 3’Reagents Kit v3.1. Libraries were sequenced on Illumina NovaSeq 6000 and processed through the Cell Ranger pipeline using a modified MM10 reference genome with an added loci for GFP transcripts.

first: Clayton

middle: P

last: Santiago

first: Nicole

last: Pannullo

first: Lizhi

last: Jiang

first: Seth

last: Blackshaw


title: CDK7-targeted therapy effectively disrupts cell cycle progression and oncogenic signaling in head and neck squamous cell carcinoma. [PDX]

city: Oviedo

first: Francisco

last: Hermida-Prado

address: Av del Hospital Universitario s/n

department: Head and Neck Lab

country: Spain

institute: Instituto de Investigación Sanitaria del Principado de Asturias

summary: Head and neck squamous cell carcinoma (HNSCC) remains a prevalent and aggressive malignancy, characterized by a lack of targeted therapies and limited clinical benefits. Here, we conducted an optimized whole-genome CRISPR screen across five HNSCC cell lines aimed at identifying actionable genetic vulnerabilities for rapid preclinical evaluation as novel targeted therapies. Given their critical role in cancer, cyclin-dependent kinases (CDKs) were prioritized for further investigation. Among these, CDK7 was identified as an essential and targetable gene across all five cell lines, prompting its selection for in-depth functional and molecular characterization. Genetic and pharmacological inhibition of CDK7 significantly and consistently reduced tumor cell proliferation due to generalized cell cycle arrest and apoptosis induction. Additionally, CDK7 knockout (KO) and selective inhibitors (YKL-5-124 and samuraciclib) demonstrated potent antitumor activity, effectively suppressing tumor growth in HNSCC patient-derived organoids (PDOs), as well as in both cell line- and patient-derived xenograft (PDX) mouse models with minimal toxicity. Mechanistically, CDK7 inhibition led to a broad downregulation of gene sets related to cell cycle progression and DNA repair, and significantly reduced the transcription of essential genes and untargetable vulnerabilities identified by our CRISPR screen. These findings highlight CDK7 as a promising therapeutic target for HNSCC. Our study provides strong evidence of the robust antitumor activity of CDK7-selective inhibition in disease-relevant preclinical models, strongly supporting its progression to clinical testing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from a patient-derived xenograft (PDX) model subcutaneously implanted into the flank of Athymic Nude-Fox1nu mice and treated with vehicle, Samuraciclib (70 mg/kg, 5 doses/week, orally) and YKL-5-124 (10 mg/kg, 5 doses/week, intraperitoneal) for 5 days.

first: Maria

last: Otero-Rosales

first: Irene

last: Pazos

last: Ferrer

first: Monica

last: Alvarez-Fernandez

first: Juana

last: Garcia-Pedrero


title: Exploring Mechano-metabolomic Pathways in CAR T cells

city: Brooklyn

first: Ngoc

middle: Bao

last: Luu

state: NY

address: 6 Metrotech Center, RH 621

institute: New York University

summary: Mechanical force generation at the immunological synapse is a hallmark of CAR T cell cytotoxicity and a key indicator of functional potency, yet the underlying mechanisms are not fully understood. Here, we performed real-time single-cell analysis to quantify the spatiotemporal dynamics of synaptic force and metabolic activity in CAR T cells upon CD19 antigen engagement. We identified a Piezo1–Ca²⁺–Wnt signaling axis that integrates mechanical sensing with cytoskeletal remodeling and metabolic reprogramming. This mechano-metabolic coupling drives CAR T cell activation and varies across different CAR constructs, patient-derived products, and manufacturing conditions. Notably, functional heterogeneity among CAR T cells correlates with differences in their mechanical force profiles and energetic output. Our findings reveal a reciprocal relationship between mechanotransduction and metabolic switching, providing new insight into CAR T cell biology. This framework may inform the development of screening tools and engineering strategies to enhance CAR T cell mechanical fitness, energetic resilience, and therapeutic efficacy.

overall_design: CAR T cells were acitvated by anti-FMC63 Antibody μBeads for 24 hours.

first: Weiqiang


title: Single-cell transcriptomics of Osr1 positive cells from mouse second heart field

city: Houston

first: Ke

last: Zhang

address: 2121 W Holcombe Blvd

department: Center for Epigenetics & Disease Prevention

institute: Texas A&M IBT

summary: Cells from second heart field of mice with mixed B6/129/SvEv background were isolated and single cell sequencing was performed for two stages: E9.5 and E10.5. After dissection, hearts were minced and subjected to cell dissociation using trypsin.

overall_design:
Second heart field were harvested from WT mice at E9.5 and E10.5.

***************************************************************
The raw data were generated by North Dakota IDeA Network of Biomedical Research Excellence Bioinformatic Core which does not share raw data.
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first: Jing

last: Li

first: Lin

last: Liu

first: Linglin

last: Xie


title: scRNA-seq of human CD45+ cells proliferated in the salivary grand or peripheral blood of CD8T cells depleted PBMC-transferred humanized mice

status: Public on Oct 01 2025

city: Yokohama-shi

first: Yuzo

last: Koda

address: 1000 Kamoshida, Aoba-ku, Yokohama-shi, Kanagawa

country: Japan

institute: Mitsubishi Tanabe Pharma Corporation

summary: We found that the transfer of PBMCs depleted of CD8 T cells into immunodeficient mice resulted in the development of Sjögren's syndrome-like salivary gland symptoms without causing GVHD. To characterize the human immune cells infiltrating the salivary glands, we examined the profiles of human immune cells in the salivary glands or peripheral blood of humanized mice by 10x Genomics single-cell RNA sequencing (scRNA-seq). We revealed that human Tph-like cells co-expressing IL-21 and CXCL13 were highly infiltrated in the salivary glands of CD8 T cell-depleted humanized mice.

overall_design: Peripheral blood or salivary glands were collected from immunodeficient mice transplanted with either human PBMCs or PBMCs depleted of CD8 T cells, and mononuclear cells were isolated by density gradient centrifugation. Human CD45+ cells were sorted by fluorescence-activated cell sorting (FACS) using a BD Aria III, and scRNA-seq analysis was performed.

first: Yuki

last: Imura

first: Piruzyan

last: Mariam

first: Sota

last: fujimori

first: Ryota

last: Sato


title: CDK7-targeted therapy effectively disrupts cell cycle progression and oncogenic signaling in head and neck cancer

overall_design: Comparative gene expression profiling analysis of RNA-seq data from FaDu cells treated with vehicle, Samuraciclib (250nM) and YKL-5-124 (250nM) for 72h


title: RNA-seq of Tph and Tfh cells proliferated in the spleens of CD8T cells depleted PBMC-transferred humanized mice

summary: We found that the transfer of PBMCs depleted of CD8 T cells into immunodeficient mice resulted in the proliferation of human Tph/Tfh cells in the spleen. To characterize the Tph/Tfh cells, we examined the comprehensive gene profiles of these cells in the spleen of humanized mice by RNA sequencing (RNA-seq).

overall_design: Spleen was collected from immunodeficient mice transplanted with either human PBMCs depleted of CD8 T cells or HSCs, and mononuclear cells were isolated by density gradient centrifugation. Human Tph/Tfh cells and PD-1/CXCR5 double negative (DN) cells were sorted by fluorescence-activated cell sorting (FACS) using a BD Aria III, and RNA-seq analysis was performed.


title: Aging drives a program of DNA methylation decay in plant organs [EM-Seq]

first: Dawei

last: Dai

address: 2151 Berkeley Way

institute: University of California, Berkeley

type: Methylation profiling by high throughput sequencing

summary: Epigenetic changes are a hallmark of aging in mammals, but their molecular mechanics are poorly understood. DNA methylation is a biomarker for biological age, which may predict age more accurately than date of birth. However, limitations in mammalian models make it difficult to identify mechanisms underpinning age-related DNA methylation changes and dissect causal relationships. Here, we show that the short-lived model plant species Arabidopsis thaliana exhibits a loss of epigenetic integrity during aging, causing DNA methylation decay in repressive chromatin and the expression of transposable elements. We show that the rate of epigenetic aging can be manipulated by extending or curtailing lifespan, and that shoot apical meristems are protected from this aging process. We demonstrate that a program of transcriptional repression suppresses DNA methylation maintenance pathways during aging, and that mutants of this mechanism display a complete absence of epigenetic decay, whilst physical aging remains unaffected. This presents a new paradigm in which a gene regulatory program sets the rate of epigenomic information loss during aging.

overall_design: Refer to individual series

first: Ben

last: Williams


title: Palmitate suppresses CD8+ T cell antitumoral response by disrupting mitochondrial metabolism

first: Teresa

last: Manzo

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

overall_design: Refer to individual Series

first: Silvia

last: Tiberti

first: Sara

last: Gennari

first: Martina

last: Romeo

first: Ilir

last: Sheraj

first: Mohamed

last: Kassir

first: Juan

last: Fernández-García

first: Carina

last: Nava Lauson

first: Roberta

last: Noberini

first: Carlotta

last: Catozzi

first: Tiziano

last: Dallavilla

first: Mattia

last: Ballerini

first: Alessia

last: Loffreda

first: Simona

last: Codreanu

first: Stacy

last: Sherrod

first: Katrina

last: Leaptrot

first: Alexandra

last: Schrimpe-Rutledge

first: John

last: McLean

first: Martin

last: Schaefer

last: Rodighiero

first: Tiziana

last: Bonaldi

first: Sarah-Maria

last: Fendt

first: Besim

last: Ogretmen

last: Sdelci

first: Luigi

last: Nezi


title: Aging drives a program of DNA methylation decay in plant organs [RNA-Seq]

first: Dawei

last: Dai

first: Ben

last: Williams


title: Mapping Hap2/Hap3/Hap5 binding sites in yeast using CPD-seq data

city: Pullman

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

summary: Here, we used the cyclobutane pyrimidine dimer-sequencing (CPD-seq) method to map UV damage footprints associated with transcription factor binding to DNA in yeast. We analyzed CPD-seq data from UV-irradiated wild-type yeast cells that were immediately isolated and analyzed (0hr time point) and compared these data to isolated yeast genomic DNA that was UV-irradiated in vitro (naked DNA control). We analyze these data with a machine learning algorithm to identify binding sites of the Hap2/Hap3/Hap5 transcription factor complex across the yeast genome, based on their UV damage footprint. As a control, we UV-irradiated hap5 mutant cells, which renders the complex unable to bind DNA, and mapped UV damage patterns using CPD-seq.

overall_design: We used the CPD-seq method to map UV-induced cyclobutane pyrimidine dimers (CPDs) at single-nucleotide resolution across the yeast genome, both immediately after UV-irradiation of yeast cells (0hr) and in isolated yeast genomic DNA that was UV-irradiated in vitro.

first: Hannah

middle: E

last: Wilson


title: Transcriptome analysis of Aoham4 and Aoham8 in nematode-trapping fungus Arthrobotrys oligospora

city: Kunming City, Yunnan Province

first: Liu

last: Qianqian

address: No.2 Cuihu North Road, Wuhua District

institute: Yunnan University

summary: Transcriptomic analysis revealed that differentially expressed genes in the absence of Aoham4 and Aoham8 were involved in  carbohydrate metabolism, amino acid metabolism, lipid metabolism, transport and catabolism, energy metabolism, and translation.

overall_design: Examination of differential genes in the WT, ΔAoham4 and ΔAoham8 mutant strains and prediction of multiple cytological processes that may affect trap formation in Arthrobotrys oligospora.

first: Qian-qian

last: Liu

first: Jin-kui

last: Yang


title: Inferring differential dynamics from multi-lineage, multi-omic, and multi-sample single-cell data

city: Ann Arbor

first: Joshua

last: Welch

state: MI

address: 500 S State St

department: DCMB

institute: University of Michigan

summary: Understanding the gene regulatory mechanisms that establish and maintain cell type identities is a central goal in cellular and developmental biology. Single-cell RNA sequencing and multi-omic profiling have revolutionized this field, enabling high-resolution investigation of gene expression dynamics across differentiation stages. RNA velocity, which estimates gene expression changes using mechanistic models, has emerged as a powerful approach for trajectory inference. Recent advances in RNA velocity methods address key limitations such as steady-state assumptions and lack of support for multi-omic data but still fall short in multi-sample integration and differential testing. To overcome these challenges, we introduce MultiVeloVAE, a probabilistic framework for multi-sample RNA velocity inference that integrates single-cell RNA and multi-omic data. MultiVeloVAE models gene expression on a shared time scale, accounts for lineage bifurcations, and enables statistical testing of velocity parameters. Our approach achieves a good balance between batch correction and biological variance conservation and outperforms existing methods in trajectory reconstruction. Using newly generated 10X Multiome datasets from human embryoid bodies and hematopoietic cells, we demonstrate that MultiVeloVAE provides novel insights into chromatin accessibility and gene expression dynamics during development. These results highlight the potential of MultiVeloVAE as a comprehensive tool for de novo multi-omic trajectory analysis and biological discovery.

overall_design:
Human EB, HSPC, and macrophage multi-omic sequences on 10X Genomics platform.

***************************************************************
Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) for controlled access to the personally identifiable sequence data.
***************************************************************

**Raw data for HSPC and Macrophage samples has been deposited to dbGAP phs002915.v2.p1**

first: Chen

last: Li

first: Yichen

last: Gu

first: Maria

last: Virgilio

first: Kun

last: Lee

first: Kathleen

last: Collins


title: Gene expression levels of WT, rep1, and ngs1 mutants of Yarrowia lipolytica grown in GlcNAc medium

city: Wuhan

first: Xiang-Dong

last: Gao

state: Hubei

address: Luojiashan, Wuchang district

institute: Wuhan University

summary: We determined the mRNA levels of genes in Yarrowia lipolytica wild-type, rep1, and ngs1 mutants that carry PACT1-4NAG plasmid in YNB-GlcNAc medium

overall_design: Yarrowia lipolytica WT/pYL27, WT/pYL27-4NAG, rep1/pYL27-4NAG, and ngs1/pYL27-4NAG strains were grown in YNB-GlcNAc medium. Total RNAs were extracted and sequenced (RNA-Seq).

first: Zhen-Hua

last: Wang


title: Transcriptional profiling defines unique subtypes of transit amplifying neural progenitors within the neonatal mouse subventricular zone

status: Public on Sep 30 2025

city: Newark

first: Rebecca

last: Zaritsky

state: NJ

address: 205 South Orange Ave

institute: NJMS - - Newark, NJ

summary: While significant progress has been made in understanding the heterogeneity of Neural Stem Cells (NSCs), our understanding of similar heterogeneity among the more abundant transit amplifying progenitors is lagging. Our work on the neural progenitors (NPs) of the neonatal subventricular zone (SVZ) began over a decade ago, when we used antibodies to the 4 antigens, CD133, LeX, CD140a, and NG2 to perform FACs to classify subsets of the neonatal SVZ as either multi-potential (MP1, MP2, MP3, MP4 and PFMPs), glial-restricted (GRP1, GRP2, and GRP3) or neuron-astrocyte restricted (BNAP). Using RNAseq, we have characterized the distinctive molecular fingerprints of 4 SVZ neural progenitors and compared their gene expression profiles to those of the NSCs. We performed bioinformatic analyses to provide insights into each NP type's unique interactome and the transcription factors regulating their development. Overall, we identified 1581 genes upregulated in at least one NP compared to the NSCs. Of these genes, 796 genes were upregulated in BNAP/GRP1 compared to NSCs; 653 in GRP2/MP3; 440 in GRP3; and 527 in PFMPs. One gene in particular that emerged from our analysis that can be used to distinguish the NPs from the NSCs is Etv1, also known as Er81. Also notable is that the neural stem cells downregulated cilia formation genes as they differentiated to become multipotential progenitors. Among the NPs, both PFMP and GRP3 subtypes differentially expressed genes related to neuron and oligodendrocyte development, including Matn4, Lhfpl3 and Olig2. GRP3s uniquely expressed Etv5, a transcription factor known to promote glial cell fate specification, while PFMPs uniquely expressed Lhx6, a transcription factor that regulates interneuron specification. PFMPs also expressed transcripts for olfactory receptors. Unlike the other NPs, the GRP1 and GRP2 NPs differentially expressed genes for proteins involved in immune function. The present work will serve as an important resource for investigators interested in further defining the transit amplifying progenitors of the mammalian SVZ.

overall_design: RNA sequencing of 8 populations of neural progenitors (Neural Stem cells and 7 intermediate progenitors) isolated from the perventricular zone of P5 mice after FACS.

first: Ekta

last: Kumari

first: Fernando

last: Velloso

first: Seema

last: Hussain

first: Alexander

last: Lemenze

first: Steven

middle: W

last: Levison


title: A non-canonical transcriptional regulation in natural product biosynthesis

city: Shanghai

first: Jinjin

address: 800 Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: TenA-family proteins are widespread bacterial regulators with unknown roles in natural product biosynthesis. This study aimed to functionally characterize LysR2, a TenA-family protein in Actinobacteria, and elucidate its mechanism in regulating the production of lysolipin I. We demonstrate that LysR2 represents a novel type of regulator that controls antibiotic biosynthesis not by direct DNA binding, but through protein-protein interactions, specifically by antagonizing the repressor LysR1. This work reveals an unconventional regulatory strategy, expanding the mechanistic understanding of transcriptional networks in natural product formation.

overall_design: RNA-Seq analysis was performed to identify differentially expressed genes between a lysR2 knockout mutant and the wild-type strain of the producer organism.


title: Accurate quantification of CRISPR effects in pooled FACS screens using Waterbear

city: San Francisco

last: Marson

address: 1650 Owens St

institute: Gladstone-UCSF Institute of Genomic Immunology

summary: CRISPR screens are powerful tools to identify key genes that underlie biological processes. One important type of screen uses fluorescence activated cell sorting (FACS) to sort perturbed cells into bins based on the expression level of a marker gene, followed by guide RNA (gRNA) sequencing. Analysis of these data presents multiple statistical challenges due to multiple factors including the discrete nature of the bins and typically small numbers of replicate experiments. To address these challenges, we developed a robust and powerful Bayesian random effects model and software package called Waterbear. Furthermore, we used Waterbear to explore how various experimental design parameters affect statistical power to establish principled guidelines for future screens. Finally, we experimentally validated our model findings that, when using Waterbear for analysis, high power is maintained even at low coverage and a high multiplicity of infection. We anticipate that Waterbear will be of broad utility for analyzing FACS-based CRISPR screens.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Pooled CRISPR screen followed by FACS to sort CD25 (IL2RA) high or low expressing cells.

first: Harold

last: Pimentel

first: Jacob

last: Freimer

first: Maya

last: Arce

first: Christian

middle: M

last: Garrido

first: Jonathan

last: Pritchard


title: Intestinal epigenomic alterations are associated with a dysregulated nutrient absorption phenotype in obesity [ATAC-Seq]

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

summary: Obesity is an epidemic with myriad health effects, but little is understood regarding individual obese phenotypes and how they may respond to therapy. Epigenetic changes associated with obesity have been detected in blood, liver, pancreas, and adipose tissues. Previous work has found that dietary glucose hyperabsorption occurs in some obese subjects, but detailed transcriptional or epigenomic features of the intestine associated with this phenotype are unknown. This study evaluated differentially expressed genes and relative chromatin accessibility in intestinal organoids to characterize the obese hyperabsorptive phenotype. Methods: Intestinal organoids established from donors classified as lean, obese, or obese hyperabsorptive by body mass index and glucose transport assays were analyzed by RNA-seq, ATAC-seq, and transcription factor footprinting to characterize transcriptional and/or epigenomic features of each phenotype. Organoids from additional lean and obese hyperabsorptive donors were analyzed for specific transcripts by quantitative PCR to validate the predictive value of biomarkers associated with the hyperabsorptive phenotype. Results: Transcriptomic analysis indicated that obese hyperabsorptive subjects have significantly upregulated dietary nutrient absorption proteins and downregulated type I interferon targets. Chromatin accessibility and transcription factor footprinting suggested that enhanced binding of HNF4G promotes the obese hyperabsorption phenotype. Quantitative PCR assessment in a larger subject cohort suggested that intestinal epithelial expression of CUBN, GIP, and SLC2A5 have high correlation with hyperabsorption. Conclusions: The obese hyperabsorption phenotype is characterized by transcriptional changes that support increased nutrient uptake and appear to be driven by differentially accessible chromatin. These observations support obesogenic imprinting on intestinal stem cells (ISCs), the cell population from which organoid cultures are derived and sustained, such that absorptive, metabolic, and innate immune perturbations persist ex vivo in a controlled tissue culture environment. Recognizing that intestinal phenotypes in obesity may differ provides new perspective in considering therapeutic targets and options to manage the disease.

overall_design: Organoid cultures were established from jejunal tissue obtained during upper endoscopy procedures or tissue discarded following bariatric surgeries under approved institutional protocols. Organoids classified as Group 1 were established from lean donors (BMI ≤ 25 kg/m2) and exhibited low intestinal epithelial glucose absorption. Organoids in Group 2 were from obese donors (BMI ≥ 35 kg/m2) and showed elevated intestinal epithelial glucose absorption relative to lean donors. Organoids in Group 3 were from obese donors (BMI ≥ 35 kg/m2) with intestinal epithelial glucose absorption profiles that were similar to lean donors

first: Badurdeen

last: Dilhana

first: Li

last: Zhen

first: Lee

last: Jeong-Heon

first: Ma

last: Tao

first: Bhagwate

last: Aditya Vijay

first: Latanich

last: Rachel

first: Dogiparthi

last: Arjit

first: Ordog

last: Tamas

first: Kovbasnjuk

last: Olga

first: Kumbhari

last: Vivek

first: Foulke-Abel

last: Jennifer


title: DYNAMIC INTERPLAY BETWEEN TUMOR AND MICRO-ENVIRONMENT DURING MULTIPLE MYELOMA DISEASE PROGRESSION

city: Liège

first: Jo

last: Caers

address: Avenue de l'Hôpital

country: Belgium

institute: CHU de Liège

summary: Characterizing the changes between normal, pre-malignant and active disease states increases our understanding of multiple myeloma (MM) pathogenesis and helps further the identification of novel preventive/therapeutic strategies. Here, using single cell multi-modal processing of whole bone marrow (BM) samples, we generated a single cell atlas of the BM from 123 individuals, including healthy volunteers, patients with monoclonal gammopathy of unknown significance (MGUS), smoldering MM (SMM) and active MM. We observed plasma cells alterations and MGUS/SMM early immune dysregulation, which increases as the disease progresses. We show evidence of population shifts in CD8+ T-cells, macrophages and classical dendritic cells. Shifts in CD8+ T-cells and macrophages were further associated with poor overall survival outcomes. We identified ligand-receptor interactions correlated to the downstream changes observed between pre-malignant and MM cells. Our findings show that myeloma tumorigenesis is associated with pathway dysregulation driven by gradual immunophenotypic changes in the tumor and tumor micro-environment.

overall_design:
Using single cell RNA sequencing, surface proteome profiling, and B lymphocyte antigen receptor profiling of unsorted, whole bone marrow aspirates, mononuclear fractions, we generated a cell atlas of the BM micro-environments from 123 individuals to explore tumor micro-environment during MM progression. These subjects included healthy volunteers (HV), and patients with monoclonal gammopathy of unknown significance (MGUS), smoldering MM (SMM) and active MM.
>>>Raw data for human samples not available due to patient privacy concerns<<<

first: Murat

last: Köse

first: Isabelle

last: Bergiers

first: Tine

last: Casneuf


title: Histone methyltransferase PRDM9 promotes survival of drug-tolerant persister cells in glioblastoma [RNA-Seq FPW1 DTPs]

city: Camperdown

first: George

middle: Louis

last: Joun

state: NSW

address: John Hopkins Drive

department: School of Medical Sciences

country: Australia

institute: The University of Sydney

summary: Chemotherapy often kills a large fraction of cancer cells but leaves behind a small population of drug-tolerant persister cells. These persister cells survive drug treatments through reversible, non-genetic mechanisms and cause tumour recurrence upon cessation of therapy. Here, we report a drug tolerance mechanism regulated by the germ-cell-specific H3K4 methyltransferase PRDM9. Through histone proteomic, transcriptomic, lipidomic, and ChIP-sequencing studies combined with CRISPR knockout and phenotypic drug screen, we identified that chemotherapy-induced PRDM9 upregulation promotes metabolic rewiring in glioblastoma stem cells, leading to chemotherapy tolerance. Mechanistically, PRDM9-dependent H3K4me3 at cholesterol biosynthesis genes enhances cholesterol biosynthesis, which persister cells rely on to maintain homeostasis under chemotherapy-induced oxidative stress and lipid peroxidation. PRDM9 inhibition, combined with chemotherapy, resulted in strong anti-cancer efficacy in preclinical glioblastoma models, significantly enhancing the magnitude and duration of the antitumor response by eliminating persisters. These findings demonstrate a previously unknown role of PRDM9 in promoting metabolic reprogramming that enables the survival of drug-tolerant persister cells.

overall_design: FPW1 Glioblastoma Stem Cell line were treated for fourteen days with 25uM CMPD1, to generate drug tolerant persisters (DTP). RNA sequencing was conducted on the persisters, compared to the matched, Day 0 control. N=3 experiments were conducted.

first: Loo

last: Lipin


title: GlyT1 Inhibition by ALX-5407 Attenuates Allograft Rejection Through Suppression of Th1 Cell Differentiation

city: tianjin

first: hu

last: lu

state: State

address: fu kang lu

institute: TMU

summary: Objective: Transplant rejection driven by Th1 cell-mediated immune responses remains a critical challenge. This study aimed to investigate the role of glycine transporter 1 (GlyT1/SLC6A9) in Th1 differentiation and evaluate the therapeutic potential of its inhibitor, ALX-5407, in attenuating allograft rejection. Methods: RNA sequencing, flow cytometry, and qRT-PCR were employed to analyze GlyT1 expression in Th1-polarized CD4⁺T cells. ALX-5407 (0.5–500 nM) was tested in vitro under Th1-polarizing conditions. A murine skin allograft model (BALB/c to C57BL/6) was established to assess graft survival and immune responses. Combination therapy with rapamycin and ALX-5407 was evaluated through histopathology, immunofluorescence, and splenocyte profiling. Mechanistic insights were derived from RNA-seq, KEGG/GO enrichment, and Western blotting. Results: GlyT1 expression was significantly upregulated in Th1 cells and rejection cohorts. ALX-5407 suppressed Th1 differentiation, reducing IFN-γ⁺CD4⁺T cells proportions (p < 0.05) and activation markers (CD25, CD69), while inducing apoptosis via caspase-3 activation and BCL-2 downregulation. Although ALX-5407 monotherapy failed to prolong graft survival, combination with rapamycin synergistically enhanced efficacy (p = 0.018), reduced inflammatory infiltration, and attenuated splenic Th1 polarization. Mechanistically, ALX-5407 inhibited MAPK signaling but activated the PI3K-AKT-mTOR pathway, which rapamycin counteracted to amplify suppression. Conclusions: GlyT1 serves as a metabolic checkpoint in Th1 differentiation, and its inhibition by ALX-5407 attenuates allograft rejection through dual suppression of Th1 function and apoptosis induction. Synergy with rapamycin highlights a novel combinatorial strategy to mitigate rejection with reduced toxicity. These findings position GlyT1 targeting as a promising approach for clinical translation in transplantation immunotherapy.

overall_design: The CD4⁺T cells sorted from the spleen were polarized into Th0 and Th1 subsets under standard conditions for 3 days. For ALX-5407 treatment, cells were exposed to 500 nM ALX-5407 or vehicle (0.1% DMSO) for 72 h.

first: Xiaohan

last: Zhang

first: Weiqi

first: Jianghao

last: Wei

first: Shuai

last: Jin

first: Zhen

last: Wang

first: Hui

first: Gang

last: Feng

first: Jie

last: Zhao


title: RNA-seq data of imbibed vs. mannitol- treated seeds in Arabidopsis thaliana Col - 0 and odr1 - 2 mutant

city: Shenzhen

first: Ling

last: Ding

address: No 7,Pengfei Road,Dapeng District

institute: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences

summary: This study aims to investigate the transcriptomic differences between wild-type Arabidopsis thaliana Col-0 and the odr1-2 mutant in two experimental groups: imbibed seeds (under normal hydration conditions) and seeds subjected to 12-hour mannitol treatment (a common osmotic stress mimic).Using RNA sequencing to compare global gene expression profiles, we seek to identify differentially expressed genes (DEGs) associated with osmotic stress responses, seed imbibition, and the potential regulatory role of the ODR1 gene. Our analysis will clarify how the ODR1 mutation alters transcriptional dynamics under both normal and osmotic stress conditions, thereby providing insights into the molecular mechanisms underlying stress tolerance and seed physiology in Arabidopsis.

overall_design: Transcriptome sequencing was conducted on 12 samples (with three biological replicates per group), derived from Arabidopsis thaliana Col-0 (wild type) and odr1-2 (mutant). All samples were prepared from after-ripened seeds stratified at 4°C for 2 days (to induce dormancy break), followed by two treatments: 12 h imbibition in water or 12 h treatment with 300mM mannitol.


title: Intestinal epigenomic alterations are associated with a dysregulated nutrient absorption phenotype in obesity [RNA-Seq]

first: Aditya

last: Bhagwate

overall_design: Organoid cultures were established from jejunal tissue obtained during upper endoscopy procedures or tissue discarded following bariatric surgeries under approved institutional protocols. Organoids classified as Group 1 were established from lean donors (BMI ≤ 25 kg/m2) and exhibited low intestinal epithelial glucose absorption. Organoids in Group 2 were from obese donors (BMI ≥ 35 kg/m2) and showed elevated intestinal epithelial glucose absorption relative to lean donors. Organoids in Group 3 were from obese donors (BMI ≥ 35 kg/m2) with intestinal epithelial glucose absorption profiles that were similar to lean donors.

first: Badurdeen

last: Dilhana

first: Li

last: Zhen

first: Lee

last: Jeong-Heon

first: Ma

last: Tao

first: Bhagwate

last: Aditya Vijay

first: Latanich

last: Rachel

first: Dogiparthi

last: Arjit

first: Ordog

last: Tamas

first: Kovbasnjuk

last: Olga

first: Kumbhari

first: Foulke-Abel


title: A genome-wide CRISPR screen identifies the TNRC18 gene locus as a novel regulator of inflammatory signaling

city: North Chicago

first: Fedik

last: Rahimov

state: IL

address: 1 N. Waukegan Road

department: Genomics Research Center

institute: AbbVie

summary: Interleukin-1β (IL-1β) is dysregulated in chronic inflammatory diseases, yet the genetic factors influencing IL-1β production remain largely unknown. Myeloid-derived cells are the primary producers of IL-1β, which prompted a genome-wide CRISPR knockout screen in the human myeloid-derived U937 cell model treated with lipopolysaccharide (LPS) to mimic inflammatory conditions and sorted for high and low intracellular IL-1β levels. A total of 295 genes were identified as regulators of IL-1β production, including known mediators such as TLR4, JAK-STAT and IL-10 receptor. Notably, 57 out of the 295 genes overlapped with loci associated with human inflammatory diseases, including the TNRC18 gene locus associated with multiple diseases in the Finnish population. U937 cells engineered with the Finnish-enriched rs748670681 risk allele demonstrated decreased levels of mRNA for TNRC18 and an adjacent gene WIPI2, reduction in LPS-dependent gene activation and cytokine production, but elevation of interferon-responsive gene programs. Transcriptomic profiles for individual knockouts of TNRC18 and WIPI2 attributed the loss of LPS-dependent signaling primarily to TNRC18, which occurs through the modulation of H3K27 acetylation around inflammatory regulatory regions via TNRC18 and its protein interaction network. In contrast, the loss of WIPI2 is characterized by an exacerbation of interferon signaling. Collectively, these findings delineate the global regulatory mechanisms of IL-1β production and provide molecular insights to the role of the rs748670681 variant as a pleiotropic risk factor for inflammatory diseases.

overall_design: To investigate the downstream effects of the TNRC18 and WIPI2 gene knockouts on global gene expression in differentiated U937 myeloid cells, and the effects of the Finnish-enriched risk variant rs748670681 at the WIPI2/TNRC18 gene locus associated with immune-mediated diseases. Genes were knocked out using the CRISPR Cas9 or Cas12a enzymes. The risk alelle T of the rs748670681 SNP was inserted into U937 cells by the HDR-mediated CRISPR/Cas9 editing method. We performed gene expression profiling analysis using data obtained from RNA-seq of U937 cells treated with LPS or vehicle for 24 hours. Comparative gene expression analysis of RNA-seq data were performed between WT and KO cells, and rs748670681-TT and rs748670681-CC cells.

first: Jing

first: Apexa

last: Modi

first: Joshua

last: Stender


title: A genome-wide CRISPR screen identifies the TNRC18 gene locus as a novel regulator of inflammatory signaling [CRISPR Screen]

overall_design: Human monocytic U937 cells that stably express Cas9 and LC3 GFP reporter were infected with the Brunello sgRNA library in three biological replicates. The Brunello CRISPR-Cas9 knockout library contains 76,441 sgRNAs targeting 19,114 protein coding genes with 1,000 non-targeting controls. Cell populations expressing the top and bottom 10% intracellular IL-1β levels were enriched using fluorescence activated cell sorting (FACS). Genomic DNA was isolated, the guide casette was amplifed by PCR, and then sequenced by next generation sequencing.

first: Charles

last: Lu

last: Wang


title: Single Cell RNA-seq of PgrCre/+Srfflox/flox  and Srfflox/flox mouse uterus at gestation day 3.5

city: Research Triangle Park

first: Francesco

middle: John

last: DeMayo

state: North Carolina

address: 111 T W Alexander Dr

department: DIR

institute: NIEHS

summary: Single cell RNA-seq analysis demonstrated dramatic changes in adult PgrCre/+Srfflox/flox endometrial cell populations compared to Srf flox/flox controls. Uterine Srf ablation caused myeloid immune cell infiltration, and differential expression analysis demonstrated that PgrCre/+Srfflox/flox stromal fibroblasts downregulated  progesterone-regulated genes and growth response genes. Proliferating fibroblast populations shifted from G2-M phase-dominant in controls to S-G2 phase-dominant in PgrCre/+Srfflox/flox uteri. PgrCre/+Srfflox/flox epithelial cells overexpressed estrogenic and innate inflammatory genes.

overall_design: Uterine tissues from two mice staged at gestation day 3.5 (3 days after finding vaginal plug) were pooled for each sample, and 2  samples per genotype (from 4 mice per genotype) were sequenced.

first: Ryan

last: Marquardt

first: Sara

last: Grimm

first: San-Pin

last: Wu

first: John

last: Lydon


title: Sequential Platinum and PARP Inhibition Enhances PD1 Immunotherapy Efficacy in Murine Brca2 Mutated Pancreatic Cancer [RNAseq_1]

city: Philadelphia

last: McVey

state: Pennsylvania

address: 3400 Spruce st

institute: University of Pennsylvania

summary: Pancreatic ductal adenocarcinoma (PDAC) is a challenging malignancy to treat, but emerging evidence suggests that specific subtypes may respond more favorably to certain therapies. BRCA-mutated PDAC represents a distinct subtype that is particularly sensitive to DNA-damaging therapies. The current standard of care for advanced BRCA-mutated PDAC involves induction platinum-based chemotherapy followed by maintenance therapy with a poly (ADP-ribose) polymerase inhibitor (PARPi). However, the randomized phase III POLO trial, upon which this standard is based, did not demonstrate an improved overall survival in patients who received olaparib compared to those who received placebo, highlighting the need for new therapeutic approaches. Additionally, there is a lack of robust models that recapitulate the tumor microenvironment of BRCA mutated PDAC, limiting the development of next-generation maintenance treatment options. In this study, we developed a syngeneic and immunocompetent mouse model of Brca2-mutated PDAC.  The model demonstrated high sensitivity to cisplatin plus gemcitabine, but limited efficacy of PARPi monotherapy. Induction with platinum-based chemotherapy sensitized tumors to PARPi maintenance therapy and promoted an exhausted, T cell-inflamed tumor microenvironment. However, resistance emerged which was associated with CDX2 expression and tumor differentiation. The addition of anti-PD1 treatment to PARPi maintenance enhanced tumor regression and prolonged overall survival. These findings provide preclinical support for ongoing clinical trials investigating immunotherapy with PARPi as a maintenance strategy in homologous recombination-deficient PDAC.

overall_design: Bulk RNA sequencing assessing impact of Gemcitabine/Cisplatin or Olaparib in a BRCA2 mutated mouse model

first: Max

last: Wattenberg

first: Gregory

last: Beatty


title: Human Primary Airway Epithelium Response to HCoV-229E Infection

city: Richland

first: Lindsey

middle: N

last: Anderson

address: 3300 Stevens Dr

department: Biological Sciences Division

institute: Pacific Northwest National Laboratory

summary: The purpose of this experiment was to evaluate the human host cellular response to wild-type Human coronavirus strain 229E (HCoV-229E) infection. Sample data was obtained for mock and infected (MOI 3) primary human airway epithelial cells grown in air-liquid interface conditions, processed for RNA sequencing (RNA-Seq) expression analysis.

overall_design: Mock infected and human coronavirus 229E infected samples were collected in primary human airway epithelial cells at 24 hours post infection

first: Amy

last: Sims

first: Hugh

last: Mitchell


title: Microenvironment-Responsive Multifunctional Enzyme-Linked Hydrogel for Diabetic Bone Defects Regeneration

city: Chengdu

first: Zhenyu

last: Luo

address: No.37 Guoxue Road

institute: West China Hospital, Sichuan University

summary: Diabetes mellitus (DM) bone defects face impaired healing due to hyperglycemia, chronic inflammation, and dysregulated bone remodeling, yet existing therapies lack comprehensive strategies targeting these interconnected issues. To address this, a glucose/ROS-responsive multifunctional hydrogel (AAT-ZCG) was designed, integrating tannic acid (TA)-mediated dynamic borate ester bonds and a cascade nanozyme comprising cerium-zoledronic acid-glucose oxidase (ZCG). The hydrogel enables stimuli-responsive release of TA and ZCG within DM microenvironments, depleting glucose via glucose oxidase-mediated catalysis and mitigating inflammation through cerium-mediated ROS scavenging. Moreover, ZCG modulates macrophage polarization, stimulates angiogenesis and enhances osteogenesis. Acidic byproducts trigger ZCG degradation, releasing zoledronic acid to inhibit excessive osteoclast activation. Transcriptomic analysis revealed upregulated forkhead box O1 transcription factor, a key regulator of bone metabolism and inflammation. This all-in-one platform concurrently addresses pivotal mediators in DM bone defects, overcoming limitations of single-target approaches. By consolidating multifunctional responses, AAT-ZCG provides a concise yet effective strategy for DM bone defect regeneration.

overall_design: RNA was extracted from BMSCs used for osteogenic differentiation experiments in vitro from the control and AAT-ZCG groups. All samples underwent quality control. RNA-seq were performed by a sequencing company (Chi Biotech, Shenzhen, Guangdong, China), which also delivered the initial analysis report. Statistical significance was set at P < 0.05, with a fold change of >2 or <0.5 determining significantly differentially expressed genes (DEGs). These DEGs and different metabolites were then subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses.

first: Xiaoxue

last: Fu

first: Weinan

last: Zeng

first: Zongke

last: Zhou


title: Effect of obesity on the neurovascular unit transcriptome in the female mice hippocampus using single nuclei RNA seq

city: Davis

first: Saivageethi

last: Nuthikattu

address: 550 Hutchison Dr

department: Internal Medicine, Cardiovascular division

institute: University of California Davis

summary: Obesity is a global pandemic and a key risk factor for several neurodegenerative diseases including Alzheimer’s disease (AD), Parkinson’s disease, or dementia. The neurovascular unit (NVU), essential for blood-brain barrier (BBB) integrity and comprised of endothelial cells, glial cells (microglia and astrocytes), and neurons, plays an important role in the pathogenesis of neurodegenerative diseases. However, molecular mechanisms underlying the effects of obesity on endothelial and other cells of and its contribution to neurodegeneration remains largely unknown, especially in females. In this study we aimed to decipher in-dept molecular modifications induced by obesity in cells of neurovascular unit by integrative multiomics analysis of endothelial cells, neurons, microglial cells, and astrocytes from the hippocampus of ob/ob female mice. Hippocampus were isolated from ob/ob and C57BL/6J female mice at 17-18 weeks of age. Gene expression profiles of cells of hippocampus were obtained using single nuclei RNA sequencing (snRNAseq) and data analyzed using in-depth bioinformatic analyses.

overall_design: Wild type (C57BL/6J) and ob/ob female mice were fed a standard purified diet AIN-93M, for 8 wks. Mice were sacrificed at 18 weeks of age and hippocampus was dissected from left hemisphere and then stored at -80 degree celcius. Hippocampal nuclei was isolated and single nuclei RNA sequencing was performed. Brain hippocampal endothelial cells, microglial cells, astrocytes, and neuronal cells gene expression was analyzed using a multiomic approach for differential expression of protein and non-protein coding genes, gene networks, functional pathways, and transcription factors.

first: Jennifer

last: Norman

first: Dragan

last: Milenkovic

first: Amparo

last: Villablanca


title: Isoproterenol Infusion Enhances Composition and Function of G-CSF Mobilized Allogeneic Peripheral Blood Hematopoietic Cell Grafts.

city: Tucson

first: Richard

last: Simpson

state: AZ

address: 1501 N Campbell Avenue, CRC building Rm 5340

department: School of Nutritional Sciences & Wellness

institute: University Of Arizona

summary: Graft-versus-host disease (GvHD) and relapse remain critical challenges in allogeneic hematopoietic cell transplantation (alloHCT). Graft composition is pivotal, with naïve T cells increasing GvHD risk and NK cells improving graft-versus-leukemia (GvL) effects. Acute beta-adrenergic receptor activation mobilizes effector lymphocytes, favorably altering circulating immune cell composition. This study investigated whether infusing the non-selective beta-agonist isoproterenol (ISO) after granulocyte colony-stimulating factor (G-CSF) mobilization enhances peripheral blood hematopoietic cell (PBHC) graft composition and outcomes.

overall_design: Blood samples were collected from 10 healthy volunteers (age 27-41 yrs) after five days of G-CSF hematopoietic cell mobilization, before and after infusion with Isoproteranol (ISO). Isolated PBMCs underwent single cell RNA sequencing (scRNAseq) and gene expression analysis was performed on 26 identified clusters

first: Helena

last: Batatinha

first: Grace

last: Niemiro

first: Nicole

last: Pena

first: Giovannah

last: Hoskin

first: Tiffany

last: Zuniga

first: Kyle

last: Smith

first: Forrest

last: Baker

first: Douglass

last: Diak

first: Timothy

last: Kistner

first: Preteesh

last: Mylabathula

first: Michael

last: Seckeler

first: Emmanual

last: Katsanis


title: Hypoglycemia induces metabolic reprogramming and neurodegeneration through SRF/MRTF-A activation in the brain

city: Seoul

first: Minjeong

last: Jang

state: Asia/Oceania

address: 75, Nowon-ro, Nowon-gu, Seoul, Republic of Korea

country: South Korea

institute: Korea Institute of Radiological and Medical Sciences (KIRAMS)

summary: Hypoglycemia, a common complication in diabetic patients receiving insulin or hypoglycemic agents, as well as in individuals undergoing prolonged fasting, can cause brain damage; however, the molecular mechanisms underlying this effect remain poorly understood. To shed light on this issue, we investigated the molecular basis of hypoglycemia-induced neurodegeneration using both in vitro and in vivo hypoglycemic models. Starvation-induced hypoglycemia triggers neurodegenerative features in human neurons and glial cells, mirroring those observed in the brains of hypoglycemic mice. Notably, neurons activated a survival mechanism via serum response factor (SRF) and myocardin-related transcription factor A (MRTF-A)-mediated metabolic reprogramming, utilizing extracellular matrix (ECM) components as alternative energy sources. This adaptation led to excessive production of urea cycle by-products, which in turn induced neurodegeneration, astrocyte reactivity, and microglial activation. Importantly, glucose refeeding reversed these neurodegenerative features by deactivating SRF/MRTF-A signaling. Together, our results uncover a neuron-intrinsic mechanism linking glucose deprivation to reversible neurodegeneration via SRF/MRTF-A, offering potential targets for preventing hypoglycemia-associated brain damage.

overall_design: Total RNA from 3D-cultured ReN cells under hypoglycemic and steady-fed conditions for 24 and 48 hours was isolated using the QIAzol lysis reagent (79306, Qiagen, Germany). RNA quality was assessed using an Agilent 2100 bioanalyzer (Agilent Technologies, Amstelveen, The Netherlands), and RNA quantification was performed using an ND-2000 spectrophotometer (Thermo Inc., DE, USA).

first: Hong Nam

last: Kim


title: Serum response factor is essential for endometrial function and prevention of inflammatory fibrosis

first: Francesco

last: DeMayo

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

overall_design: Refer to individual Series


title: Transcriptional and metabolic stasis define desiccation-induced dormancy in the soil bacterium Arthrobacter sp. AZCC_0090 until water vapor initiates resuscitation

first: Paul

last: Carini

address: 1657 E Helen St

institute: University of Arizona

summary: Microbes inhabiting soils experience periodic water deprivation. The effects of desiccation on DNA, protein, and membrane integrity are well-described. However, the effects of drying and rehydration on the composition of cellular RNA and metabolites are still poorly understood. Here, we describe how slow drying and rehydration with water vapor influence the composition of RNAs and metabolites in a soil Arthrobacter. Drying reduced cultivability relative to hydrated controls, but rehydration of dried cells with water vapor restored cultivability. The fraction of 16S and 23S rRNA to the total RNA pool was constant throughout the experiment, irrespective of treatment. mRNA profiles were invariant in desiccated cells, changing only in response to drying or rehydration. Six transcriptional modules were identified that showed distinct expression patterns in desiccated-rehydrated samples, relative to hydrated controls, including desiccation-responsive and rehydration-specific profiles. Targeted metabolomics also showed a static metabolic state during desiccation. A cluster of metabolites enriched in ribonucleosides and nucleobases was responsive to desiccation and rehydration. Collectively, these results are consistent with the relative stability of mRNA and metabolite profiles in desiccated Arthrobacter. These results imply that stable mRNA in dry dormant cells and intracellular RNA recycling may obscure interpretations of RNA-based environmental analyses that use RNA as a marker of microbial activity.

overall_design: This study examines transcriptional responses to desiccation stress and recovery in Arthrobacter sp. AZCC_0090  through a 16-day time-course RNA-seq experiment. Control samples were maintained at constant 100% relative humidity throughout the experiment, while treatment samples underwent controlled desiccation: 100% RH for days 0-2, gradual drying to 65% RH between days 2-8, further drying to 25% RH between days 8-14, followed by rehydration to 100% RH between days 14-16. RNA samples were collected at four critical time points (days 2, 8, 14, and 16) from both control and treatment groups, yielding eight sample conditions that capture initial desiccation response, progressive dehydration stress, severe desiccation, and cellular recovery upon rehydration.

first: Adriana

last: Gomez-Buckley

first: Christina

middle: R

last: Guerrero

first: Melanie

last: Kridler

first: Isabella

last: Viney

first: Roya

last: Aminitabrizi

first: Malak

last: Tfaily

first: Peter

last: Moma

first: Laura

last: Meredith

first: Ryan

last: Bartelme


title: Extracellular vesicles-mediated transfer of let-7b/7c promotes the proliferation of transition-state spermatogonia in neonatal mouse testis [miRNA-seq]

city: Shenzh

first: Tingting

last: ZHENG

address: Bulan Road

institute: Shenzhen Third People's Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: The self-renewal and differentiation of spermatogonial stem cells (SSCs) play essential roles in spermatogenesis. Extracellular vesicle (EV) is a universal strategy for intercellular communications in stem cell niches. However, the involvement of EVs in regulating the SSCs remains largely unknown. In this study, we have revealed the role of testis EVs isolated from postnatal day 7 (PND7) neonatal mouse testis in guiding spermatogonia into a transit-amplifying state with increased proliferation while retaining their differentiation potential. We profiled the repertoires of proteins and small RNAs by proteomic and small RNA transcriptomic analyses, respectively. We further showed that the EVs secreted by undifferentiated spermatogonia and the Sertoli cell lines, but not from more differentiated germ cell lines, conveyed let-7b/7c miRNA cargoes to spermatogonia, which mediates the effect of EVs on spermatognial transit amplification. Together, this study has deciphered an important intercellular communication within the spermatogonial niche mediated by let-7b/7c cargoes of EVs, providing a new insight into the regulation of SSCs and spermatogenesis.

overall_design: Small RNA sequencing analysis was performed on EVs isolated from postnatal day 7 mouse testis as the experimental group. we analyze tRNA subtypes and expression levels.

last: Zheng

first: Hoi Kei

last: Choy

first: Sze Yan

last: Chan

first: Min

first: Xiaotong

last: Luo

first: Hao

last: Chen

first: Ting

last: Xie

first: Kin Lam

last: Fok


title: A crucial role of the malate aspartate shuttle in metabolic reprogramming in TNF-induced SIRS

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

institute: VIB-UGent

summary: Tumor necrosis factor (TNF) causes a lethal systemic inflammatory response syndrome (SIRS) which is characterized by significant metabolic alterations. Based on liver RNA sequencing, we found that TNF impairs the malate-aspartate shuttle (MAS), an essential redox shuttle that transfers reducing equivalents across the inner mitochondrial membrane thereby recycling cytosolic NAD+. This downregulation of MAS genes in TNF-induced SIRS likely results from loss of HNF4α function, which appears to be the key transcription factor involved. Using Slc25a13-/- mice lacking citrin – a crucial MAS component – we demonstrate that MAS dysfunction exacerbates TNF-induced metabolic dysregulations and lethality. Disruptive NAD+ regeneration leads to diminished mitochondrial β-oxidation, leading to elevated levels of circulating free fatty acids (FFAs) and to hepatic lipid accumulation. Simultaneously, MAS dysfunction promotes glycolysis coupled to lactate production and reduces lactate-mediated gluconeogenesis, culminating in severe hyperlactatemia that triggers VEGF-induced vascular leakage. Overall, MAS dysfunction contributes to metabolic failure and lethality in TNF-induced SIRS, highlighting its potential as a promising, therapeutic target.

overall_design: RNA-seq profiling of WT and Slc25a13 (Citrin) KO mice injected with PBS or TNF (8h post injection)

first: Louise

last: Nuyttens

first: Marah

last: Heyerick

first: Maxime

last: Roes

first: Elise

last: Moens

first: Céline

last: Van Dender

first: Charlotte

last: Wallaeys

first: Tino

last: Hochepied

first: Jolien

last: Vandewalle

first: Claude

last: Libert


title: Extracellular vesicles-mediated transfer of let-7b/7c promotes the proliferation of transition-state spermatogonia in neonatal mouse testis [scRNA-seq]

first: Tingting

last: ZHENG

overall_design: single cell RNA sequencing analysis was performed on primary spermatogonial culture exposed to EVs isolated from postnatal day 7 mouse testis as the experimental group, while exposed to PBS were set as the control group. we analyze their cell clusters and explore the subtype changes.

last: Zheng

first: Hoi Kei


title: A genome-wide CRISPR screen identifies the TNRC18 gene locus as a novel regulator of inflammatory signaling [CUT&Tag]

first: Fedik

last: Rahimov

overall_design: CUT&Tag was performed on two biological replicates per condition using the CUT&Tag-IT Assay Kit (Active Motif, 53172) following manufacturers recommendation. Briefly, 450,000 cells per replicate per condition were bound to the prepared Concanavalin A beads (+spike-in control, Active Motif, 53173) and incubated overnight at 4°C in a rotator with primary antibodies [1 µg of mouse anti-H3K27Ac (1:50, Active Motif, 91193), 1 ug of positive control mouse anti-H3K4me3 (1:50, Active Motif, 91263)]. The samples were then incubated with Rabbit Anti-Mouse secondary antibody (1:100, Active Motif, 53160) for 1 hour at room temperature on a rotator, followed by washes in Dig-Wash buffer. The beads were resuspended with CUT&Tag-IT Assembled pA-Tn5 Transposons and incubated at room temperature on a rotator, followed by washes with Dig-300 buffer. The beads were finally resuspended in tagmentation buffer, and the reactions incubated at 37°C for 60 minutes. The DNA was extracted as detailed in the manufacturer's instructions. Libraries were PCR-amplified using i5 and i7 indexed primers (14 cycles) and primer dimers were removed with AmpureXP bead (Beckman Coulter, A63881) purification. The final libraries were evaluated on Agilent 4200 Tapestation (quality) and Thermo Qubit (quantity) and sequenced on the Illumina NextSeq550 platform (75-bp paired-end reads). Data analysis was performed using HOMER and DeepTools. Briefly, raw FASTQ read pairs were pre-processed where adapter, low-quality sequences, duplicates were removed using cutadapt, rmdup. Preprocessed reads were aligned to human genome (hg38) using Bowtie2 and Drosophila genome (spike in control) to generate the normalization factor. Bedtools were used to sort and index, and HOMER to generate TagDirectory, peak calls and bedgraph for visualization.

first: Rahimov

last: Fedik

first: Ghosh

last: Sujana

first: Shi

last: Manman

first: Stender

last: Joshua


title: GDF15 contributes to thyroid cancer progression and modulates thyroid cancer cell senescence in a p53-dependent manner.

city: jinan

first: jingyu

last: ma

address: Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Lixia, Jinan, Shandong , P.R.China

institute: shandong university

summary: Growth differentiation factor 15（GDF15）displays aberrant expression in multiple malignancies, yet its role and underlying mechanisms in thyroid carcinoma remain unclear. This study aimed to investigate GDF15 expression and functional significance in thyroid cancer, revealing that GDF15 is significantly upregulated and participates in cellular senescence. GDF15 knockdown suppresses proliferation, migration, and invasion of thyroid cancer cells. Transcriptome sequencing demonstrates that GDF15 depletion activates the p53 pathway and induces senescence. Furthermore, our results confirm a protein-level interaction between GDF15 and p53. Given the established importance of p53 in senescence, p53 knockdown partially rescues the enhanced senescence phenotype induced by GDF15 depletion. Consequently, we identify a novel GDF15-p53 regulatory loop wherein GDF15 sustains thyroid carcinogenesis by suppressing p53-dependent senescence. Targeting this axis highlights a promising therapeutic target for thyroid carcinoma, with GDF15 inhibition representing a tumor senescence reactivation strategy.

overall_design: GDF15 expression was knocked down in thyroid cancer cell lines, and the control group was blank control. Set three repetitions for each group.


title: Sequential Platinum and PARP Inhibition Enhances PD1 Immunotherapy Efficacy in Murine Brca2 Mutated Pancreatic Cancer [RNAseq_2]

first: John

last: McVey

overall_design: Bulk RNA sequencing assessing impact of Gemcitabine/Cisplatin followed by maintenance Olaparib or placebo in a BRCA2 mutated mouse model

first: Max

last: Wattenberg

first: Gregory

middle: L

last: Beatty


title: RNA-seq of THESC in SRF-deficient vs Normal Conditions

first: Francesco

last: DeMayo

summary: The transcription factor SRF plays known roles in mitogenic cell response and muscle cell development, and potential roles in endometrial stromal decidualization have been reported. After RNAi-based SRF knockdown in hTERT-immortalized human endometrial stromal cells (THESC), SRF-deficient cells exhibited disrupted cytoskeletal remodeling, cell cycle, and extracellular matrix genes. These data show that SRF is important for endometrial stromal cell homeostasis.

overall_design: THESCs (American Type Culture Collection #CRL-4003) were treated with control non-targeting siRNA or siSRF in triplicate followed by RNA-seq to analyze the impact of SRF deficiency on the transcriptome.

first: Ryan

last: Marquardt

first: Peter

middle: F

last: Lais

first: San-Pin

last: Wu


title: DNA Methylation profiles of self-reported Hispanic subjects in the Northern Manhattan Study

city: Miami

first: Lily

last: Wang

address: 1120 NW 14th St

institute: University of Miami

type: Methylation profiling by genome tiling array

summary: The Northern Manhattan Study (NOMAS) is a community-based cohort designed to investigate the incidence and risk factors of stroke, dementia, and other vascular outcomes. DNA methylation profiles were generated using the Illumina MethylationEPIC v1.0 BeadChip, which assays about 850k CpGs, from blood samples of self-reported Hispanic adults. Eligible participants were stroke-free, aged ≥40 years, and had resided in the Northern Manhattan community for at least three months.

overall_design:
Bisulfite-converted DNA for 322 human blood samples were hybridized to the Illumina MethylationEPIC v1.0 Beadchip;
whole blood from self-reported Hispanic adults, stroke-free at enrollment, with population-level summaries provided in the associated manuscript.
*Please note that only technical sample attributes (Sample_Plate,Sentrix_ID, Batch (collection year: 2019 vs 2021)) are provided, as IRB/participant consent do not permit release of individual-level clinical variables, even in de-identified form*

first: David

last: Lukacsovich

first: Liyong

first: Tatjana

last: Rundek


title: PROM1/CD133 MARKS A PROLIFERATIVE STEM CELL LIKE POPULATION OF BLASTS IN KMT2A REARRANGED INFANT ALL

city: Oxford

first: Joe

middle: Wilson

last: Cross

address: Wellington Square

country: United Kingdom

institute: University of Oxford

summary: Among pediatric acute lymphoblastic leukemias (ALL), KMT2A-rearranged infant ALL (KMT2Ar iALL) carries a particularly poor prognosis due to high rates of treatment-refractory or relapsing disease.  Mechanistically, KMT2Ar drives aggressive disease through epigenetic dysregulation of multiple genes as a direct effect of expression of KMT2A-fusion proteins, most commonly KMT2A::AFF1, in leukemic cells. We previously showed that one of the top 2 most dysregulated genes, PROM1 (Prominin-1), encodes the cell surface protein prominin-1/CD133 and that this is essential for proliferation of KMT2A::AFF1+ cell lines.  Here we show that PROM1 gene expression and cell surface CD133 expression specifically mark a highly proliferative subset of KMT2A::AFF1 blasts both in primary patient samples and in our highly physiologically relevant, primary human fetal liver HSPC-derived KMT2A::AFF1 ALL model (CRISPRKMT2A::AFF1 ALL). CD133+ CRISPRKMT2A::AFF1 blasts, but not CD133- CRISPRKMT2A::AFF1 blasts, exhibit a stem-cell gene expression profile and drive more aggressive disease in vivo. Furthermore, CRISPR-mediated inactivation of PROM1 reduces leukemic proliferation and prolongs survival of mice transplanted with CRISPRKMT2A::AFF1 blasts. These data show that PROM1/CD133 expression has an important functional role in CRISPRKMT2A::AFF1 ALL, and supports targeting PROM1/CD133 by pharmacological or immunotherapy-based approaches in KMT2A::AFF1 iALL.

overall_design: CRISPR-KMT2A::AF4 leukaemias were generated as previously described (Rice et al. doi:10.1038/s41467-021-27270-z). Up to 300,000 CD19+CD133+ and CD19+CD133- blasts were sorted from CRISPR-KMT2A::AF4 leukaemias (n = 3)  and RNAseq libraries generated as previously described (O'Byrne et al. doi:10.1182/blood.2019001289).


title: RNA-seq of ME-HESC in SRF-deficient vs Normal Conditions

summary: The transcription factor SRF plays known roles in mitogenic cell response and muscle cell development, and potential roles in endometrial stromal decidualization have been reported. After RNAi-based SRF knockdown in menstrual effluent-derived primary human endometrial stromal cells (ME-HESC), SRF-deficient cells exhibited disrupted cytoskeletal remodeling, cell cycle, and extracellular matrix genes. These data show that SRF is important for endometrial stromal cell homeostasis.

overall_design: Primary menstrual effluent-derived human endometrial stromal cells (ME-HESCs) were obtained from deidentified archives that were previously banked after non-invasive isolation from menstrual fluids of healthy volunteers with the NIEHS Clinical Research Unit according to IRB approved, published methods and analyzed by RNA-seq at passage number 6. Cells from three distinct human donors were treated with control non-targeting siRNA or siSRF to analyze the impact of SRF deficiency on the transcriptome.


title: Chromatin accessibility (ATAC-seq) analysis on inner ear organ of Corti from WT and Bmi1 KO neonatal mice

city: SHANGHAI

first: yunzhong

last: zhang

state: SHANGHAI

address: 83 fenyang road, xuhui district

department: Department of ENT Institute and Otorhinolaryngology

institute: Eye & ENT Hospital of Fudan University

summary: Clarify changes in chromatin accessibility regions after Bmi1 knockout by performing ATAC-seq on Bmi1 KO and WT organ of Corti from neonatal mice, providing a foundation for integrated analysis of epigenetics and transcriptome sequencing"

overall_design: ATAC-seq data was extracted from OC of WT and Bmi1-/- neonatal mice organ of corti.


title: RNA-seq of PgrCre/+Srfflox/flox  and Srfflox/flox mouse uterus at gestation day 3.5

summary: Upon conditional ablation of Srf in the Pgr-expressing cells of the mouse uterus, PgrCre/+Srff/f (SrfKO) females were infertile, displaying uterine fibrosis and failure to decidualize or support embryo implantation. RNA-seq analysis demonstrated dramatic changes in gestation day 3.5 SrfKO uterine tissues including dysregulation of cytoskeletal remodeling and growth response genes in addition to strong induction of proinflammatory cytokine signaling. These data show that SRF is key for endometrial function and fertility through regulation of inflammatory homeostasis.

overall_design: Four mice of each genotype were staged at gestation day 3.5 (3 days after finding vaginal plug), and RNA was isolated from uterine tissues for sequencing.

last: Lydon


title: H3K27me3 ChIP sequencing on inner ear organ of Corti from WT and Bmi1 KO neonatal mice

summary: We conducted ChIP sequencing for H3k27me3 mark on inner ear organ of Corti from WT and Bmi1 KO neonatal mice, thereby clarifying the epigenetic mechanisms by which Bmi1 impacts auditory cell fate.

overall_design: Comparative CUT&Tag analysis was performed by pulling down with an anti-H3K27me3 antibody and comparing this with a nonspecific negative control Input.


title: Transcriptome sequencing samples of the Bmi1 knockout and wildtype neonatal mouse organ of Corti.

summary: Clarify the transcriptome changes in the inner ear cochlea after Bmi1 knockout

overall_design: Collect  the organ of Corti  from Bmi1 knockout newborn mice and WT mice for RNA extraction and transcriptome sequencing


title: Histone methyltransferase PRDM9 promotes survival of drug-tolerant persister cells in glioblastoma [ChIP-seq]

city: Camperdown

first: George

last: Joun

address: John Hopkins Drive

institute: The University of Sydney

summary: Chemotherapy often kills a large fraction of cancer cells but leaves behind a small population of drug-tolerant persister cells. These persister cells survive drug treatments through reversible, non-genetic mechanisms and cause tumour recurrence upon cessation of therapy. Here, we report a drug tolerance mechanism regulated by the germ-cell-specific H3K4 methyltransferase PRDM9. Through histone proteomic, transcriptomic, lipidomic, and ChIP-sequencing studies combined with CRISPR knockout and phenotypic drug screen, we identified that chemotherapy-induced PRDM9 upregulation promotes metabolic rewiring in glioblastoma stem cells, leading to chemotherapy tolerance. Mechanistically, PRDM9-dependent H3K4me3 at cholesterol biosynthesis genes enhances cholesterol biosynthesis, which persister cells rely on to maintain homeostasis under chemotherapy-induced oxidative stress and lipid peroxidation. PRDM9 inhibition, combined with chemotherapy, resulted in strong anti-cancer efficacy in preclinical glioblastoma models, significantly enhancing the magnitude and duration of the antitumor response by eliminating persisters. These findings demonstrate a previously unknown role of PRDM9 in promoting metabolic reprogramming that enables the survival of drug-tolerant persister cells.

overall_design: Drug Treated glioblastoma stem cell line RKI1, followed by ChIP-seq. Treatment with tubulin inhibitor CMPD1 (10uM) +/- PRDM9 inhibitor MRK-740 (3uM) for 72 hours.

first: Lenka

last: Munoz


title: Histone methyltransferase PRDM9 promotes survival of drug-tolerant persister cells in glioblastoma [RNA-seq]

overall_design: Drug Treated glioblastoma stem cell line RKI1, followed by RNA sequencing. Treatment with tubulin inhibitor CMPD1 (10uM) +/- PRDM9 inhibitor MRK-740 (3uM) for 72 hours, to check changes in gene expression that may be underlying DTP response


title: Histone methyltransferase PRDM9 promotes survival of drug-tolerant persister cells in glioblastoma [RKI1_DTPs_RNAseq]

overall_design: RKI1 Glioblastoma Stem Cell line were treated for fourteen days with 25uM CMPD1, to generate drug tolerant persisters (DTP). RNA sequencing was conducted on the persisters, compared to the matched, Day 0 control. N=3 experiments were conducted.

first: Lipin

last: Loo


title: Nucleophosmin supports WNT-driven hyperproliferation and tumour initiation

status: Public on Sep 29 2025

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

institute: CRUK Scotland Institute

summary: Nucleophosmin (NPM1), a nucleolar protein frequently mutated in haematopoietic malignancies, is overexpressed in several solid tumours with poorly understood functional roles. Here, we demonstrate that Npm1 is upregulated following APC loss in WNT-responsive tissues and supports WNT-driven intestinal and liver tumourigenesis. Mechanistically, NPM1 loss induces ribosome pausing and accumulation at the 5’-end of coding sequences, triggering a protein synthesis stress response and p53 activation, which mediate this anti-tumourigenic effect. Collectively, our data identify NPM1 as a critical WNT effector that sustains WNT-driven hyperproliferation and tumourigenesis by attenuating the integrated stress response (ISR) and p53 activation. Notably, NPM1 expression correlates with elevated WNT signalling and proliferation in human colorectal cancer (CRC), while CRCs harbouring NPM1 deletions exhibit preferential TP53 inactivation, underscoring the clinical relevance of our findings. Being dispensable for adult epithelial homeostasis, NPM1 represents a promising therapeutic target in p53-proficient WNT-driven tumours, including treatment-refractory KRAS-mutant CRC, and hepatic cancers.

overall_design: Bulk RNAseq expression data from mouse small intestine and colon tissues, with genetic modifications in combinations of the genes Apc, Kras, Braf, p53, Alk5, and Notch1.

first: Georgios

last: Kanellos

first: Mark

last: White

first: Megan

last: Mills

first: Andrew

middle: D

last: Campbell

first: Owen

last: Sansom


summary: Chemotherapy often kills a large fraction of cancer cells but leaves behind a small population of drug-tolerant persister cells. These persister cells survive drug treatments through reversible, non-genetic mechanisms and cause tumour recurrence upon cessation of therapy. Here, we report a drug tolerance mechanism regulated by the germ-cell-specific H3K4 methyltransferase PRDM9. Through histone proteomic, transcriptomic, lipidomic, and ChIP-sequencing studies combined with CRISPR knockout and phenotypic drug screens, we identified that chemotherapy-induced PRDM9 upregulation promotes metabolic rewiring in glioblastoma stem cells, leading to chemotherapy tolerance. Mechanistically, PRDM9-dependent H3K4me3 at cholesterol biosynthesis genes enhances cholesterol biosynthesis, which persister cells rely on to maintain homeostasis under chemotherapy-induced oxidative stress and lipid peroxidation. PRDM9 inhibition, combined with chemotherapy, resulted in strong anti-cancer efficacy in preclinical glioblastoma models, significantly enhancing the magnitude and duration of the antitumor response by eliminating persisters. These findings reveal a previously unknown role of PRDM9 in promoting metabolic reprogramming that enables the survival of drug-tolerant persister cells.

overall_design: PRDM9 Knock-out RKI1 glioblastoma stem cell line was treated with +/- 10µM CMPD1 for 72 hours. The KO cell line was compared to Non-Targetted Control (NTC) RKI1 glioblastoma stem cell line, also treated with +/- 10µM CMPD1 for 72 hours, of the same transduction batch and passage number within each biological replicate. There are three biological repeats. We excluded RKI1 n=2 NTC CMPD1 (Sample006) from downstream analysis due to the sample not clustering with the other two NTC CMPD1 repeats.

first: Emma

last: Kempe


title: Transcriptome changes in BeWo cells under chemically induced hypoxia

city: Moscow

first: Ivan

last: Antipenko

address: 11 Pokrovksy Bulvar, Moscow, 109028, Russia

country: Russia

institute: HSE University

summary: Hypoxia is an important condition in placental biology, required for trophoblast differentiation but also associated with various placental pathologies. To model hypoxic response, BeWo b30 choriocarcinoma cells were treated with cobalt chloride (CoCl₂) or an oxyquinoline derivative (4896-3212), both chemical inducers of the HIF1α signaling pathway. Transcriptome profiling was performed to identify gene expression changes under these conditions compared to untreated controls. The dataset provides information on hypoxia-induced transcriptional reprogramming, including genes involved in metabolism, lipid homeostasis, and HIF1α-regulated signaling pathways. These results may contribute to understanding molecular mechanisms of placental adaptation to hypoxia and its role in pathological states.

overall_design: RNA-seq profiling of BeWo b30 cells after 24 h exposure to cobalt (II) chloride or oxyquinoline derivative 4896-3212, both chemical inducers of the HIF-1α signaling pathway

first: Evgeny

last: Knyazev

first: Timur

last: Kulagin

first: Alexander

last: Tonevitsky


title: Derivation of embryonic stem cells from cloned blastocysts using improved somatic cell nuclear transfer in common marmoset

city: Tsukuba

first: Inoue

last: Kimiko

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Research Center

institute: RIKEN

summary: The common marmoset (Callithrix jacchus) is a genetically modifiable non-human primate increasingly used in biomedical research. However, methods to preserve or expand valuable genetic resources in this species remain underdeveloped. Here, we established a method for deriving embryonic stem cells (ESCs) from blastocysts generated by somatic cell nuclear transfer (SCNT) in the marmoset. Injection of mRNA encoding the histone demethylase Kdm4d enabled efficient reprogramming of somatic nuclei, allowing blastocyst formation in 14.5% from fibroblasts. However, nuclear transfer ESCs (ntESCs) were not established from these blastocysts. Combining this method with a G9a histone methyltransferase inhibitor (RK-701) improved blastocyst quality and allowed derivation of ntESC lines, including wildtype and GFP-transgenic lines. These ntESCs exhibited normal karyotypes and pluripotency both in vitro and in vivo. Nuclear and mitochondrial DNA analyses confirmed their nuclear donor origin and cytoplasmic inheritance from recipient oocytes. Transcriptome analysis identified abnormally expressed genes in ntESCs present in a line-dependent and -independent manner, suggesting partial reprogramming resistance that may inform future optimization of SCNT in primates. Our study establishes marmoset SCNT method enabling derivation of ntESCs which may provide a new platform for preserving and engineering marmoset genetic resources.

overall_design: Comparative analysis of gene expression in ESCs derived from IVF, naturally fertilizaed (NAT), and SCNT in common marmoset.

first: Shogo

last: Matoba

first: Satoshi

last: Funaya