title: GATA3 Differentially Regulates the Transcriptome via Its Zinc Finger 2-Modulated Phase Separation

city: Hangzhou

first: Yatao

last: Chen

address: 150 Dongfang Street, Xiasha Street, Qiantang District

institute: Chinese Academy of Sciences

summary: Phase separation (PS) underlies gene control by transcription factors. However, little is known about whether and how the DNA-binding domains (DBDs) regulate the PS for transcription factors to differentially regulate the transcriptome. The transcription factor GATA3, a master immune regulator, is frequently mutated in breast cancer. Here, we report that GATA3 undergoes its DBD-modulated PS to mediate the formation of chromatin condensates. We show that the DBD regulates the GATA3 PS through its zinc finger 2 (ZnF2), which provides positive charges for multivalent electrostatic interactions mainly via two arginine amino acids, R329 and R330. Breast cancer GATA3 with ZnF2-defective mutations, when compared to those without, cause aberrant ZnF2-modulated PS and condensates to remodel the differentially regulated transcriptome, resulting in a favorable prognosis for patients and reduced tumor growth in mice. Thus, GATA3 represents a principle of how a transcription factor differentially regulates the transcriptome via its DBD-modulated PS.

overall_design: Twelve samples from MCF7-GATA3-KO cells stable expressed with four different proteins : GATA3-WT, Zn2-2R-A, X308, and R330 were analyzed and compared with eachother.

first: liming

last: chen

first: yatao

first: yajie

last: wan

first: ziqi

last: wei

first: tan

last: wang


title: Single-cell RNAseq identifies persistent epithelial and immune dysfunction in PwCF by mitigating inter-individual sampling heterogeneity

status: Public on Mar 10 2026

city: Chicago

first: Manu

last: Jain

state: IL

address: 303 E Superio

country: USA

institute: Northwestern University

type: Expression profiling by high throughput sequencing

summary: Nasal epithelium (NE) is used as a surrogate for lower airway epithelium in cystic fibrosis (CF). However, NE is composed of diverse cell types with unique functions; changes to this heterogeneous tissue in disease can be cell-type specific. To explore the impact of tissue heterogeneity, we examine NE gene expression and cell-type heterogeneity using single-cell transcriptomics of people with CF (PwCF) and healthy volunteers (HV). We also compare cell-type abundance in paired single-cell and bulk transcriptomic samples.

overall_design:
Single-cell RNAseq (scRNAseq) was performed on nasal curettage samples from 9 PwCF and 7 HVs. Paired bulk RNAseq samples were obtained from a subeset of 5 PwCF and 5 HVs.

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

first: Thaddeus

last: Cybulski

first: Marc

middle: A

last: Sala

first: Trevor

last: Nicholson

first: Zasu

last: Klug

first: Rachel

last: Nelson

first: Zhan

last: Yu

first: Yuliana

last: Sokolenko

first: Estefani

last: Diaz

first: Suchitra

last: Swaminathan

first: Ziyan

last: Lu

first: Nikolay

middle: S

last: Markov

first: Edward

middle: F

last: McKone

first: Alexander

middle: V

last: Misharin


title: Dissecting the cellular architecture of breast cancer brain metastases reveals prognostically distinct immune landscapes [RNA-Seq]

city: Heidelberg

first: Christel

last: Herold-Mende

department: Department of Neurosurgery

country: Germany

institute: University Hospital Heidelberg

summary: Breast cancer brain metastases (BCBM) are a severe condition with high demand for improved personalized treatment, but a comprehensive understanding of BCBM immune-microenvironment heterogeneity and susceptibility to immunotherapy is lacking. Here, we multimodally profile the immune niche in a vast, clinically well-annotated cohort of 156 BCBM applying tissue cytometry, bulk and single nuclei RNA-sequencing, flow cytometry, and spatial transcriptomics, complemented by functional studies in patient-derived models. Integrative analyses reveal two immune landscapes predicting prolonged patient survival and not deducible from paired primary tumors: 1) BCBM with a high proportion of CD8 tissue-resident-like memory T cells as major players of tumor immune control. 2) BCBM containing tertiary lymphoid structures. Surrogate signatures of these landscapes are prognostic in independent BCBM and primary breast cancer cohorts, are associated with fewer metastases, and predict immunotherapy response. Our work provides critical insights into anti-tumor immunity in BCBM and identifies novel biomarkers with translational relevance.

overall_design:
This dataset comprises bulk RNA sequencing data generated from cryopreserved breast cancer brain metastasis tissues obtained from patients treated at the Department of Neurosurgery, University Hospital Heidelberg. The samples were processed to extract total RNA and subsequently subjected to high-throughput sequencing to capture transcriptomic profiles. These data served as the discovery cohort for the development of the tissue-resident memory T cell (TRM) gene signature, which was derived through a supervised machine-learning approach. The TRM signature was subsequently evaluated and validated in independent external cohorts to assess its robustness and clinical relevance.
All raw sequencing data have been deposited at https://data.ghga.de/dataset/GHGAD28055171876192

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

first: Lena

last: Jassowicz

first: Rolf

last: Warta


title: Genome-wide profiling identifies the genetic dependencies of cell death following EGFR inhibition

city: Worcester

first: Michael

last: Lee

state: MA

address: 55 N Lake Ave

institute: Umass Chan Medical School

summary: EGFR is a proto-oncogene that is mutationally activated in a variety of cancers. Small molecule inhibitors targeting EGFR can effectively slow the progression of disease, and in some settings, these drugs even cause dramatic tumor regression. However, responses to EGFR inhibitors are rarely durable, and the mechanisms contributing to response variation remain unclear. In particular, several distinct mechanisms have been proposed to explain how EGFR inhibition activates cell death, and a consensus has yet to emerge. In this study, we use functional genomics with specialized analyses to infer how genetic perturbations affect the drug-induced death rate. Our data clarify that inhibition of PI3K signaling drives the lethality of EGFR inhibition. Inhibition of other pathways downstream of EGFR, including the RAS-MAPK pathway, promotes growth suppression but not the lethal effects of EGFR inhibitors. Taken together, our study provides a “reference map” for the genome-wide genetic dependencies of lethality in response to EGFR inhibitors.

overall_design: Genome-wide CRISPR KO screen of PC9-Cas9 cells treated with 10 µM erlotinib, 0.1 µM osimertinib, 5 µM osimertinib, or DMSO for 72 hours. T0 samples were taken immediately prior to drugging.

first: Sydney

last: Porto

first: Gavin

last: Birdsall

first: Nicholas

middle: W

last: Harper

first: Megan

middle: E

last: Honeywell

first: Scott

middle: M

last: Leighow

first: Tiana E

last: Naylor

first: Kelly M

last: Ward

first: Mika K

last: Wesley

first: Justin

middle: R

last: Pritchard

middle: J


title: Single-Cell Analyses Identify Independent Aging Processes that Compete to Determine Cellular Fate in Budding Yeast -- scRNA-seq

city: South San Francisco

first: Nathaniel

middle: H

last: Thayer

state: CA

address: 1130 Veteran's Blvd

institute: Calico Life Sciences LLC

summary: Phenotypic heterogeneity is prevalent during aging, yet its underlying molecular drivers remain poorly understood. In budding yeast, two distinct aging trajectories, characterized by either ribosomal DNA (rDNA) instability or mitochondrial decline, have been proposed to be mutually exclusive. Here, we systematically dissect the heterogeneity among aging yeast cells by combining single-cell transcriptomics with longitudinal fluorescence microscopy. Our data reveals distinct transcriptional responses that emerge in aging cells, highlighted by loss of rDNA silencing, a hypoxia response, and the Environmental Stress Response (ESR). Contrary to expectation, we establish that ESR induction is not caused by rDNA instability but is instead a consequence of an early decline in mitochondrial membrane potential (MMP). However, the ESR is merely a biomarker of this decline and not itself a determinant of lifespan. While rDNA instability and mitochondrial dysfunction are anti-correlated as terminal phenotypes, we find that they are not necessarily mutually exclusive and can instead proceed concurrently within individual cells. Targeted genetic perturbations that are specific for one pathway do not impinge on the other, which is in contradiction to the idea of mutual inhibition between the two. We therefore propose a "competing hazards model", where independent aging processes progress in parallel, and the observed mode of death is determined by which process first reaches a catastrophic failure point. Our work untangles the causal links between several aging pathways and provides a new framework for understanding how distinct aging trajectories emerge from independent molecular events.

overall_design: Budding yeast cells (young or aged) were either directly used for single-cell RNA-Seq (timecourse samples) or sorted into subpopulations before scRNA-Seq. SRP40 samples were sorted into high and low fluorescent subpopulations, MMP samples were sorted into high and low MMP ratio subpopulations (as decribed in 10.1083/jcb.202505110).

first: Manuel

last: Hotz

first: Rachel

middle: G

last: Kroll-Ling

first: Daniel

last: Gottschling


title: Single-Cell Analyses Identify Independent Aging Processes that Compete to Determine Cellular Fate in Budding Yeast -- bulk RNA-Seq

overall_design: Budding yeast cells (WT, msn2∆ and msn2∆msn4∆) were harvested as young and aged to perform bulk RNS-Seq.


title: Rapamycin treatment ameliorates HLA-B27-mediated gut inflammation and alters the microbiome in experimental spondyloarthritis

status: Public on Mar 16 2026

city: Bethesda

first: Stephen

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

summary: Rapamycin treatment reduced stool and colon histological scores in B27-Tg rats compared to vehicle-treated B27-Tg controls. Transcriptome analysis revealed that rapamycin reduced expression of key pro-inflammatory cytokines like Il17a, Il17f, Tnf, Il1a, IL1b, and Il22 in B27-Tg colon tissue compared to vehicle-treated B27-Tg controls. Ex vivo treatment of bulk immune cells isolated from B27-Tg rat colon with rapamycin (25 and 50 nM) reduced expression of Il17a, Il17f, Ifng, and Il22 compared to vehicle-treated cells. Rapamycin treatment decreased the abundance of cecum microbiota associated with inflammation in B27-Tg rats. Rapamycin also altered the gut microbiome in WT rats, without associated changes in the tissue transcriptome.  Our study demonstrates that rapamycin treatment substantially reduces HLA-B27-mediated gut inflammation in experimental SpA. Results from this pre-clinical model suggest further evaluation of rapamycin as a therapeutic strategy in HLA-B27 associated diseases is warranted.

overall_design: HLA-B27/human β2-microglobulin transgenic (B27-Tg) rats with gut inflammation were treated with rapamycin (1.5 mg/kg intraperitoneally, 3 times a week) or vehicle for 5 weeks. Healthy age-matched wild type (WT) rats were treated in parallel. Gut inflammation was evaluated via stool scoring and histological assessment. Transcriptome and microbiome analyses were performed on colon tissue and cecal lumen contents, respectively. Bulk immune cells were isolated from the colonic lamina propria of B27-Tg and WT animals, treated with rapamycin ex vivo, and pro-inflammatory cytokine expression was measured using qPCR.

first: Jinny

last: Van Doorn

first: Francesca

last: LiCausi

first: Kelly

last: Zhou

first: Naga

last: Betrapally

first: Eva

last: Gubitz-Hess

first: Antony

last: Cougnoux

first: Stefania

last: Dell’Orso

first: Shamima

last: Islam

first: Robert

last: Colbert

first: Fatemeh

last: Navid


title: Clec3b⁺ fibroblasts are the primary effectors of portal fibrosis following activation via a KLF4/periostin axis [ChIP-Seq]

city: Changchun

first: Chenchen

last: Zhao

state: Jilin Province

address: 5333 Xi’an Road

department: College of Veterinary Medicine

country: China

institute: Jilin University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Portal fibrosis, a determinant of progression in virtually all chronic liver diseases, prototypically develops in biliary diseases. Using single-cell RNA sequencing and genetic cell fate tracing in mouse models, we identified Clec3b⁺ fibroblasts as a distinct subset of portal fibroblasts, which rapidly expand after biliary injury and give rise to the bulk portal myofibroblasts. Mechanistic analyses revealed that Clec3b⁺ portal fibroblasts activation is governed by a Krüppel-like factor 4 (KLF4)/periostin (POSTN) axis, i.e., KLF4 directly binds the Postn promoter and represses its transcription in quiescent fibroblasts, whereas after injury, KLF4 is downregulated, which allows POSTN, acting via αvβ5 integrin, to drive portal fibroblast activation and portal fibrosis. Our findings identify Clec3b+ portal fibroblasts as the primary effectors of portal fibrosis and demonstrate that the KLF4/POSTN signaling axis regulates their activation, offering potential therapeutic targets for inhibiting fibrosis in biliary diseases.

overall_design: To investigate the potential mechanisms by which KLF4 influences the transition of Clec3b-tdT⁺ portal fibroblasts into myofibroblasts, Clec3b-tdT⁺ cells were isolated from the livers of Clec3bCreERT2;R26tdT mice using fluorescence-activated cell sorting (FACS). ChIP-seq was then performed on these Clec3b-tdT⁺ cells following lentivirus-mediated overexpression of Klf4.

first: Lin

last: Lei

first: Wenwen

last: Gao

first: Menglin

last: Liu

first: Guoyue

last: Lv

first: Zhongqi

last: Fan

first: Chantal

last: Housset

first: Fouad

last: Lafdil

first: Axelle

last: Cadoret

first: Sara

last: Lemoinne

first: Yongkang

last: Cheng

first: Jinxia

last: Li

first: Fanrong

last: Kong

first: Xiliang

last: Du

first: Yuxiang

last: Song

first: Guowen

first: Xinwei


title: Ribosome recruitment assays in a synthetic, m¹A methylated pool of mRNA

city: New Haven

first: Sigrid

last: Nachtergaele

state: CT

address: 260 Whitney Ave

department: Molecular, Cellular, and Developmental Biology

institute: Yale University

summary: The transcriptome-wide distribution of N¹-methyladenosine (m¹A) in mRNA remains contested, hindering a clear understanding of regulation of mRNA metabolism by m¹A. Additionally, the enzyme(s) that installs the majority of reported mRNA m¹A sites has yet to be identified. In this study, we characterized TRMT61B, an m¹A methyltransferase known to methylate mitochondrial RNAs, but whose exact sequence preferences have been underexplored. We performed ribosome recruitment assays on a synthetic RNA pool of 5UTR and CDS sequences in vitro methylated by TRMT61B.

overall_design: An RNA pool containing >35,000 human and >500 viral 5′UTR and CDS regions (300 nt total length, including adapter sequences, full 5'UTRs, and truncated endogenous CDS was generated through in vitro transcription of a synthetic DNA oligonucleotide library. RNA was then untreated (no enzyme, NE) or methylated with low (LE) or high (HE) amounts of TRMT61B in a large (640-680 uL) reaction. NE, LE, HE samples were then pooled together and four replicates of Direct Analysis of Ribosome Targeting (DART) was carried out. Sequencing was then carried out on input and 80S-bound RNA fractions, using InduroRT to generate cDNA. DESeq2 was then carried out to compare abundance of individual transcripts in the input vs. 80S-bound RNA samples.

first: Dorthy

last: Fang

first: John

last: Babich

first: Ryan

last: Stanton

first: Isaac

last: Vock

first: Kyrillos

last: Abdallah

first: Mingyi

last: Zhu

first: Richard

first: Matthew

last: Simon

first: Wendy V

last: Gilbert


title: Gene expression profiling of Escherichia coli isolates from aging colonies (Series 2)

city: Paris

first: Claude

last: Saint-Ruf

address: 24 rue du faubourg Saint-Jacques

department: Institut Cochin

country: France

institute: Université paris Cité

summary: This series presents normalized gene expression profiles of three Escherichia coli   K-12 MG1655-derived strains (pygYFP, Y5, and Y6). Strains Y5 and Y6 were originally   isolated from 3-week-old aging colonies, but RNA for transcriptomic profiling was   extracted from 7-day-old colonies regrown under identical conditions.    All samples were hybridized to the NimbleGen GPL9088 one-color microarray platform.   Processed values correspond to RMA-normalized, non-log2 intensities. Raw .pair files   and the processed matrix for these samples are provided.    These data complement Series 1 and constitute a second biological replicate   (B2) for transcriptomic analysis of the parental strain and two evolved isolates   carrying distinct mutations affecting regulatory and stress-response pathways   in aging bacterial colonies.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Three RNA samples were analyzed in this series: one parental control strain   (pygYFP_B2) and two evolved isolates (Y5_B2 and Y6_B2) originally recovered   from 3-week-old aging colonies. For transcriptome profiling, all strains   were regrown under identical conditions and RNA was extracted from 7-day-old   colonies. Each sample was hybridized once to the NimbleGen GPL9088 platform   (one-color Cy3).

first: Adrien

last: Launay

first: Olivier

last: Tenaillon

first: Ivan

last: Matic


title: Mapping TRMT61B-mediated m¹A methylation of a synthetic RNA pool using uMRT

summary: The transcriptome-wide distribution of N¹-methyladenosine (m¹A) in mRNA remains contested, hindering a clear understanding of regulation of mRNA metabolism by m¹A. Additionally, the enzyme(s) that installs the majority of reported mRNA m¹A sites has yet to be identified. In this study, we characterized TRMT61B, an m¹A methyltransferase known to methylate mitochondrial RNAs, but whose exact sequence preferences have been underexplored. We in vitro methylated a synthetic pool of 5UTR and CDS sequences with TRMT61B, and mapped m¹A sites using mutation signatures installed by uMRT.

overall_design: An RNA pool containing >35,000 human and >500 viral 5′UTR and CDS regions (300 nt total length, including adapter sequences, full 5'UTRs, and truncated endogenous CDS was generated through in vitro transcription of a synthetic DNA oligonucleotide library. RNA was thenused for in vitro methylation reactions with TRMT61B, with either no (NE),  low (LE) or high enzyme (HE) amounts. Methylation was carried out in triplicate, with two small (40 uL) and one large (640-680 uL) reaction, with equal ratios of all reaction components. The large reactions were pooled for sequencing and deconvoluted during analysis. Sequencing was carried out using ultraMarathonRT to generate cDNA. Three rounds of sequencing were carried out on each of three replicate samples (2x150 on NovaSeq, 2x250 twice on NextSeq 2000) to get sufficient coverage depth for mutational analysis. After alignment, bam files from the three rounds of sequencing were merged by sample and then run through an ad-hoc mutational analysis pipeline to look for increased mutation rates in LE and HE enzymes vs. NE.

last: Li


title: Gene expression profiling of Escherichia coli isolates from aging colonies (Series 1)

summary: This series presents normalized gene expression profiles of three Escherichia coli K-12 MG1655-derived strains (pygYFP, Y5, and Y6). Strains Y5 and Y6 were originally isolated from 3-week-old aging colonies, but RNA for transcriptomic profiling was extracted from 7-day-old colonies regrown under identical conditions. All samples were hybridized to the NimbleGen GPL9088 one-color microarray platform, and processed values correspond to RMA-normalized, non-log2 intensities. These data compare the parental strain to two evolved isolates carrying distinct regulatory and stress-response mutations, and can be used to study diversification and adaptive strategies emerging in aging bacterial colonies.

overall_design:
Three RNA samples were analyzed in this series: one parental control strain (pygYFP_B1) and two evolved isolates (Y5_B1 and Y6_B1) that were originally recovered from 3-week-old aging colonies. For transcriptome profiling, all strains were regrown under identical conditions and RNA was extracted from 7-day-old colonies. Each sample was hybridized once to the NimbleGen GPL9088 platform.
*** This submission (Series 1 of BioProject PRJNA1355247) does not include raw NimbleGen files because the original *.pair* files from this older experiment are no longer available. ***


title: Immunoprecipitation of m¹A methylated mRNA upon TRMT61B overexpression

summary: The transcriptome-wide distribution of N¹-methyladenosine (m¹A) in mRNA remains contested, hindering a clear understanding of regulation of mRNA metabolism by m¹A. Additionally, the enzyme(s) that installs the majority of reported mRNA m¹A sites has yet to be identified. In this study, we characterized TRMT61B, an m¹A methyltransferase known to methylate mitochondrial RNAs, but whose exact sequence preferences have been underexplored. We integrated in vivo overexpression of TRMT61B and in vitro methylation of a synthetic pool of diverse human RNA sequences to characterize the sequence preferences of TRMT61B target RNAs.

overall_design: RNA-seq profiling of U2OS cells was collected for transiently overexpressing TRMT61B or a control plasmid, with and without m1A-IP treatment. Normalized counts tables were generated using DESeq2, and mutational calling was carried out using bakR.


title: Single-cell transcriptomic profiling of the developing zebrafish heart.

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Cardiac development is a complex process where bilateral precursors undergo migration, proliferation, and differentiation to form a multi-chambered organ that sustains life.  While scRNA-seq technology has advanced significantly, a comprehensive analysis of vertebrate heart development from early to late developmental stages is still lacking.  We profiled over 34,000 cells from resected zebrafish hearts spanning 10 developmental stages from 25 hours to 60 days post-fertilization.  We identified and sub-clustered all known cardiac cell types, revealing distinct proliferation dynamics.  We also analysed the cardiac interactome, focusing on the ligand-receptor interactions between myocardial and endocardial cells.  By investigating later stages, we discovered novel marker genes, which appears to be enriched in trabecular cardiomyocytes. This zebrafish heart atlas enhances our understanding of vertebrate heart development and represents a valuable resource for future studies.

overall_design: For each condition, hearts (number depending on developmental stage) were dissected, dissociated and analyzed by scRNA-seq.

first: Marco

last: Tarasco

first: Thomas

last: Juan

first: Yousef

last: Alayoubi

first: Agatha

last: Ribeiro da Silva

first: Radha

last: Kulkarni

first: Marga

last: Albu

first: Annika

last: Nürnberger

last: Guenther

first: Mario

last: Looso

first: Didier

last: Stainier


title: Single cell and spatial sequencing analysis of cancer associated fibroblasts in the brain metastasis tumor microenvironment [Multiome]

status: Public on Mar 09 2026

city: Los Angeles

first: Bodour

last: Salhia

address: 1450 Biggy Street

department: Department of Cancer Biology

institute: University of Southern California

summary: Brain metastasis (BM) remains largely incurable. Cancer-associated fibroblasts (CAFs) can either support or inhibit tumor growth in the tumor microenvironment (TME), yet their roles in BM remain under-described. Here we report a single-cell and spatial sequencing analysis of human BM tissues and define four transcriptionally distinct CAF subpopulations. BM CAF subpopulations are characterized by either extracellular matrix (ECM), immune, contractile, or neural features, and show distinct spatial distributions within the BM TME. Further analyses reveal that BM CAFs engage extensively in cell-cell communication and adopt distinct cell states, including an ECM CAF cell state marked by high levels of immunoglobulin superfamily containing leucine rich repeat expression (ISLR-CAFs). Functionally, ISLR-CAFs reduce BM tumor cell viability in vitro, consistent with a tumor-inhibitory role. These findings highlight the heterogeneity and plasticity of CAFs in BM, emphasizing the importance of precision in defining stromal contributions to disease progression and therapeutic response.

overall_design: In this study, we performed single-cell Multiome sequencing (scMultiome-seq; RNA and ATAC) on nine human BM tissue samples to evaluate cellular heterogeneity within the TME. Seven samples were from lung-to-brain metastases (LBM) and two from breast-to-brain metastases (BBM)

last: Simon

first: David

middle: N

last: Buckley

first: Zeyi

last: Yang

first: Chikako

last: Matsuba

first: Ben

middle: Y

last: Tew

first: Gerald

middle: C

last: Gooden

first: Kyle

last: Hurth

first: Steven

last: Toms

middle: D

last: Tran

first: Gabriel

last: Zada

middle: P

last: Salomon


title: DNA methylation stochasticity is linked to transcriptional variability and identifies convergent epigenetic disruption across genetically-defined subtypes of AML [CellCulture_WGBS]

city: Baltimore

first: Andrew

last: Feinberg

address: 855 North Wolfe Street

department: Center for Epigenetics

institute: Johns Hopkins University

type: Methylation profiling by high throughput sequencing

summary: Epigenetic regulators are frequently mutated in acute myeloid leukemia (AML). We investigated DNA methylation stochasticity in genetic subtypes of AML using WGBS data and publicly-available ERRBS data, and identified transcriptional dysregulation and altered chromatin accessibility related to methylation entropy using single-cell RNA-seq and single-cell ATAC-seq data. We demonstrated that the hypomethylating drug decitabine (DAC) leads to reduction of DNA methylation entropy specifically in IDH2-mutant AML cells.

overall_design: WGBS of IDH2-mutant isogenic TF-1 cells and parental TF-1 erythroleukemia cells treated with decitabine (DAC) or DMSO control.

first: Eleanor

last: Hilgart

first: Michael

last: Koldobskiy


title: Unveiling the Developmental and Tumor Suppressive Roles of the p53 variant, p53psi

city: Toronto

first: Liam

last: Hendrikse

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

summary: Through alternative splicing, the TP53 gene can generate multiple protein isoforms with distinct biochemical properties. Among the thirteen splicing isoforms described to date, the p53psi isoform has been identified as a variant that is shorter than full-length p53 as it lacks nuclear localization, oligomerization and part of the DNA binding domains due to the use of an alternative 3' splice site in intron 6. Several TP53-truncating mutations, including those producing p53psi, have been detected in a significant proportion of human tumors. However, the mechanistic roles of these truncated p53 proteins remain poorly understood. Here, we describe the generation and analysis of a genetically engineered mouse model that expresses the p53psi protein in place of the full-length p53 protein. In the C57/BL6J genetic background, mice heterozygous for the targeted p53psi allele (p53KI/+) appear phenotypically normal, survive to adulthood, and reproduce. However, heterozygote mating fails to yield viable p53psi homozygote knock-in (p53KI/KI) pups, indicating that forced p53psi expression disrupts embryogenesis. Timed mating studies revealed that homozygous p53psi expression is embryonically lethal at day E16.5. Embryos at E14.5-16.5 were pale, reduced in size, and exhibited exencephaly, a defect typically associated with a failure in neural tube closure. Mouse embryonic fibroblasts (MEFs) derived from p53psi embryos and transformed with the E1A and H-RasV12 oncogenes formed tumors with a decreased growth rate compared to their p53null counterparts, suggesting that p53psi retains at least some tumor-suppressive functions. Our mechanistic studies suggest that p53psi modulates tumorigenesis by triggering senescence. These findings provide new insights into the role of the p53psi variant, paving the way for a better interpretation of TP53 mutational patterns in human cancers.

overall_design: Comparative RNA-seq profiling of E1a/RASV12-transformed murine embryonic fibroblasts (MEFs) derived from p53psi and p53null background embryos.

first: Chiara

last: Gorrini

first: Parameswaran

last: Pamachandran

first: Tak

last: Mak


title: SLC1A5 prevents aortic aneurysm and dissection by glutaminolytic-epigenetic orchestration of vascular smooth muscle cell homeostasis [RNA-seq]

status: Public on Mar 15 2026

city: Guangzhou

first: Zhiping

last: Liu

state: Guangdong

address: No. 855, East Xingye Avenue

institute: Jinan University

summary: Glutamine is carried into and out of cells by glutamine transporters such as SLC1, SLC7 and SLC38 families, and cytoplasmic glutamine subsequently catabolized to glutamate that provides biosynthetic precursors. To identify the candidate glutamine transporters or glutamate metabolism regulators that contributed to the pathogenesis of Aortic aneurysm and dissection (AAD), we used RNA sequencing analysis in Ang II perfusion-induced AAD in Apoe-/- mice and discovered that several key genes associated with glutamine transports and metabolism were considerably reduced in AAD, particularly Slc1a5.

overall_design: RNA-sequencing of aortas without adventitial tissues from 8 saline-infused Apoe-/- mice or 8 Ang II-infused Apoe-/- mice for 7 days.

first: Pinglian

first: Zhechang

last: Gao

first: Weile

last: Ye

first: Ke

last: He

first: Suowen

last: Xu

first: Jiaojiao

last: Wang


title: DNA methylation stochasticity is linked to transcriptional variability and identifies convergent epigenetic disruption across genetically-defined subtypes of AML [PrimaryAML_scATACseq]

summary: Epigenetic regulators are frequently mutated in acute myeloid leukemia (AML). We investigated DNA methylation stochasticity in genetic subtypes of AML using WGBS data and publicly-available ERRBS data, and identified transcriptional dysregulation and altered chromatin accessibility related to methylation entropy using single-cell RNA-seq and single-cell ATAC-seq data.

overall_design: Single-cell ATAC-seq of primary patient acute myeloid leukemia samples and normal CD34+ and GMP progenitor samples.


title: The m5C orchestrator NSUN7 drives SPARC/HMGB1 axis–mediated inflammation to exacerbate kidney injury [MeRIP-Seq]

city: Hefei

first: Yuhang

last: Dong

address: Meishan Road NO.81

institute: Anhui Medical University

summary: Growing evidence indicates that kidney inflammation is a major contributor to the pathogenesis of various renal diseases, including acute kidney injury (AKI). Although RNA modifications have been implicated in regulating kidney inflammation, their precise roles remain largely unknown. Here, we show that kidney inflammation and injury were associated with elevated RNA 5-methylcytosine (m5C) modifications, primarily driven by the m5C “writer” NOP2/Sun RNA methyltransferase family member 7 (NSUN7). Both global and kidney-specific deletion of Nsun7 in mice reduced m5C abundance, attenuated inflammatory responses, and decreased macrophage infiltration, underscoring its proinflammatory role in the kidney. Mechanistically, we identified secreted protein acidic and cysteine-rich (SPARC) as a major downstream effector of NSUN7. SPARC upregulation amplified inflammatory responses in renal tubular epithelial cells by interacting with high mobility group box 1 and further promoted proinflammatory macrophage infiltration via tubular-macrophage crosstalk. Notably, therapeutic silencing of Nsun7 using a kidney-specific DNA tetrahedral molecular carrier developed for this study effectively alleviated inflammation and improved renal outcomes in AKI models. Collectively, our findings identify NSUN7 as a key driver of renal inflammation via SPARC regulation and underscore its potential as a therapeutic target in inflammatory kidney diseases.

overall_design: To identify specific targets of NSUN7 in renal inflammation, we conducted RNA-seq and MeRIP-seq analyses in cisplatin-stimulated HK2 cells with or without silencing of NSUN7

first: Xiaoming

last: Meng


title: Medullary cavity expansion is mediated by distinct cell populations during fetal bone development

city: Fukuoka

first: Shinichiro

last: Sawa

address: 3-1-1 Maidashi, Higashiku

country: Japan

institute: Kyushu University

summary: Single cell RNA-sequencing was performed to examine the transcriptomic identity of RANKL-expressing cells during fracture healing in mice. RANKL fate-mapping mice were used to isolate tdTomato-labeled cells from tibiae at post-fracture day 14.

overall_design: Tnfsf11-tTA; LC1; R26-tdTomato mice  were treated with doxycycline in the drinking water from embryonic day 0 to postnatal day 14.  A fracture was surgically induced in the right tibia at postnatal day 21. Tibiae were isolated at post-fracture day 14, and single-cell suspensions were prepared. CD45.2-Ter119-CD31-tdTomato+ cells were sorted from four mice and pooled. Sorted cells were subjected to single-cell RNA sequencing using the 10x Genomics　Chromium Single Cell 3′ Gene Expression v3.1 platform.

first: Eriko

last: Sumiya


title: Engineering of Amino Acid-Derived Ionizable Lipids Enables Inhaled Base Editing for Therapeutic Gene Correction in the Lung

first: Fanglin

last: Gong

state: ON

address: 144 College St

institute: University of Toronto

summary: CRISPR-based gene editing holds promise for treating genetic diseases, yet its application to lung disorders has been hindered by the challenges of pulmonary delivery. Inspired by the modularity and biocompatibility of amino acid-derived chemistries, we report the combinatorial synthesis of 960 ionizable lipids incorporating chemically diverse backbones from both proteinogenic and non-proteinogenic α-amino acids. Through high-throughput screening and structure-function analysis, we identify CHCha-10, a cyclohexyl amino acid-derived lipid that forms biodegradable nanoparticles capable of efficiently delivering mRNA-based gene editors to lung epithelial cells. Following intratracheal administration, CHCha-10 nanoparticles exhibit enhanced mucus penetration, and epithelial-specific transfection in both mice and ferrets. As a functional application, we demonstrate the first instance of in vivo base editing in the lung via inhalation. Delivery of adenine base editor mRNA and guide RNA targeting the CFTR G542X mutation restores CFTR expression and chloride channel function in G542X human airway epithelial cells, mouse-derived intestinal organoids, and the lungs of cystic fibrosis mice.

overall_design: Amplicon sequencing results of the Cftr locus from treated B6-Tg(CFTRG542X)Cwr (CFTR G542X) mice lung. Mice were intratracheally administered CHCha-10 LNPs encapsulating ABE/A9. Lung tissues were harvested 3 days post-dosing, and genomic DNA was extracted to assess base-editing efficiency.


title: Transcriptomic and proteomic analyses show minimal role for mast cell ST2 in primary Heligmosomoides polygyrus bakeri infection

city: Dundee

first: Henry

last: McSorley

address: Dow Street

department: Cell Signalling & Immunology

country: United Kingdom

institute: University of Dundee

summary: The IL-33/ST2 pathway is important as part of the type 2 immune response against helminth infections. Mast cells express the highest levels of the IL-33 receptor subunit ST2 of any immune cell, and mast cells can mediate type 2 immune inflammation, however the role of IL-33-driven mast cell responses in helminth infection is poorly understood. We sought to determine the role of mast cell ST2 expression during Heligmosomoides polygyrus bakeri (Hpb) infection by generating mast cell conditional ST2 knockout (MCPT5Cre x ST2f/f, cKO) mice. These mice have normal frequencies of mast cells at steady state, but show specific and strong (albeit incomplete) knockdown of ST2 expression on mast cells. On Hpb infection, faecal egg and adult worm burden were similar between cKO and littermate controls, as were mast cell degranulation markers, serum IgE and goblet cell hyperplasia. Therefore, we conclude that mast cell ST2 does not play a dominant role in Hpb infection. To further investigate the immune response to infection in cKO and littermate controls, transcriptomic and proteomic changes were assessed in duodenal tissues in infected versus naïve mice in cKO and control mice. Minimal transcriptomic and proteomic changes were seen between genotypes, whereas substantial changes were seen between naïve and infected mice, regardless of genotype. Hpb infection induced local increases at the transcript and protein level for mast cell proteases (MCPT1 and MCPT2), resistin-like molecules (RELMα and RELMβ), and markers such as the phospholipase PLA2G4C and the pore-forming protein gasdermin C. Bulk proteomic analysis was also searched against the Hpb genome to identify Hpb proteins present in the duodenal tissues. A list of 60 Hpb proteins of interest were identified in infected duodenal samples, of which 18 contain a signal peptide and are present in the excretory/secretory products of Hpb (HES) (likely secretory products including immunomodulatory proteins); 28 proteins are present in HES but do not contain a signal peptide (likely excretory products); and 14 proteins are not present in HES (likely proteins present in the remnants of Hpb within the duodenum). This work thus provides datasets for changes in the mouse intestine due to Hpb infection, at both the transcript and protein level, as well as a dataset of Hpb proteins detectable in the mouse duodenum at day 14 of infection.

overall_design: Bulk RNA-seq profiling of duodenal tissue from MCPT5Cre x ST2f/f and MCPT5WT x ST2f/f mice, either naïve or at day 14 of Heligmosomoides polygyrus bakeri infection

first: Nicole

last: Ong

first: Suzanne

last: Hodge

first: Christa

last: Baker

first: Danielle

last: Smyth

first: Tania

last: Frangova


title: DNA methylation stochasticity is linked to transcriptional variability and identifies convergent epigenetic disruption across genetically-defined subtypes of AML [PrimaryAML_WGBS]

first: Andrew

last: Feinberg

overall_design:
WGBS of primary patient acute myeloid leukemia samples and normal CD34+, CMP, GMP, and MEP samples.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

first: Eleanor

last: Hilgart

first: Michael

last: Koldobskiy


title: Herpes simplex virus type 1 (HSV-1) R-loops are targets for APOBEC-mediated mutagenesis

city: Debrecen

first: Márton

last: Miskei

address: Egyetem tér 1.

department: Department of Molecular Biotechnology and Microbiology

country: Hungary

institute: University of Debrecen

summary: APOBEC3 enzymes are key components of antiviral immunity that introduce mutations into viral genomes. We show that R-loops serve as preferred substrates for APOBEC3 mutagenesis during herpes simplex virus type 1 infection. APOBEC3 enzymes are recruited to viral R-loops, where they generate clustered C-to-T mutations in genes critical for viral assembly. Importantly, R-loops alone are not mutagenic, and APOBECA3 enzymes do not edit HSV-1 without an R-loop; mutagenesis occurs when R-loops and APOBEC3 enzymes interact. These findings identify endogenous R-loops formed during the HSV-1 life cycle as focal vulnerabilities and highlight R-loop–APOBEC3 coupling as a mechanism for antiviral mutagenesis.

overall_design: ChIP-seq and DRIP-seq experiments to determine the APOBEC binding site and R-loops on the HSV-1 genome.

first: Marton

first: Lorant

last: Szekvolgyi


title: Nuclear Speckles enable processing of RNA from GC-rich Isochores [Df1 RNA-Seq]

city: Berlin

first: IBRAHIM

middle: AVSAR

last: ILIK

state: Berlin

address: Ihnestraße 63-73

institute: Max-Planck-Institut für molekulare Genetik

summary: Nuclear Speckles are large, multi-component condensates in the mammalian nuclei that are thought to be involved in various stages of gene expression, including transcription, splicing, and export. Investigating the direct role of Speckles in these processes have been intractable due to their heterogeneous, multi-component nature. Here we show that Speckles are necessary for the splicing of GC-rich, levelled intron/exon architecture. Acute removal of Speckles leads to a drastic downregulation of GC-rich genes which are clustered within GC-rich isochores. Genes outside these domains are physically away from Speckles and are not affected from loss of Speckles. Animal genomes that do not have GC-rich isochores, do not have GC-rich levelled intron/exon architecture and do not have Speckles. Our results suggest that the expansion of Speckles core proteins’ intrinsically disordered domains during vertebrate evolution facilitated GC-content elevation in Amniotes by creating a condensate necessary to splice the by-products of this process: GC-rich, levelled intron/exon architecture.

overall_design: Gene expression profiling of Df1 (Chicken) cells subject to SON-depletion  or control treatment.. Libraries were prepeared from pA(+)-selected RNA, 6 libraries in total.

first: Michal

last: Malszycki

first: Ibrahim

last: Ilik

first: Lisa

last: Martina

first: Tugce

last: Aktas


title: Wnt-materials sustain H3K14-acetylation in human skeletal stem cells for tissue engineering and bone repair [CUT&Tag]

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

institute: Zhejiang University

summary: Engineering functional tissues for transplantation requires insight into epigenetic mechanisms that regulate stem cell fate. We have developed the Wnt-induced osteogenic tissue model (WIOTM), a platform that recapitulates human osteogenesis, and identified acetylation of histone H3 at lysine 14 (H3K14ac) as a critical epigenetic regulator in human skeletal stem cells (hSSCs). In WIOTM, localized Wnt signals drive asymmetric cell division (ACD), yielding a proximal hSSC with high H3K14ac and a distal daughter with reduced H3K14ac that migrates into the 3D collagen matrix and initiate osteogenic differentiation. Disrupting H3K14ac in hSSCs abrogates ACD and WIOTM formation. To test whether hSSCs maintain H3K14ac in vivo, we formed the WIOTM on Wnt-functionalized polymer bandages and transplanted them into calvarial defects. The WIOTM contributed to bone repair, and human cells adjacent to the bandages retained high H3K14ac despite the injury environment. These findings establish WIOTM as both a mechanistic and translational platform for regenerative medicine.

overall_design: CUT&Tag for histone modifications H3K14ac and H3K27me3 in hSSCs cultured on Inactive and Active Wnt.


title: Nuclear Speckles enable processing of RNA from GC-rich Isochores [Fish_RNAseq]

overall_design: Gene expression profiling of Fathead minnow (fish) EPC cells cells subject to human SON-overexpression  or control treatment.. Libraries were prepeared from pA(+)-selected RNA, 6 libraries in total.

middle: A


title: Nuclear Speckles enable processing of RNA from GC-rich Isochores [4sU]

overall_design: Nascent transcription profiling of HCT116 cells subject to SRRM2-depletion, SON-depletion, SRRM2+SON-depletion or control treatment. Libraries were prepeared from 4sU-labelled RNA, 8 libraries in total.


title: Wnt-materials sustain H3K14-acetylation in human skeletal stem cells for tissue engineering and bone repair [RNA-Seq]

overall_design: RNA-Seq in hSSCs cultured on Inactive and Active Wnt.


title: Nuclear Speckles enable processing of RNA from GC-rich Isochores [RNA-Seq]

overall_design: Gene expression profiling of HEK293 cells stably expression various SON variants in endogenous-SON-depleted cells.. Libraries were prepeared from pA(+)-selected RNA, 27 libraries in total.


title: Wnt-materials sustain H3K14-acetylation in human skeletal stem cells for tissue engineering and bone repair [ATAC-Seq]

overall_design: ATAC-Seq in hSSCs cultured on Inactive and Active Wnt.


title: Exposed phosphatidylserine is a non-classical inhibitory molecule during CD8 T cell exhaustion [scRAN-seq]

city: Tampa

first: Christopher

middle: Bernardo

last: Medina

state: FL

address: 3011 W Holly Dirve

department: Immunology

institute: Moffitt Cancer Center

summary: In cancer and chronic infection CD8 T cell exhaustion is hallmarked by expression of inhibitory surface receptors such as PD-1, TIM-3, CTLA-4, LAG-3, and TIGIT. Thus, inhibitory receptor focus has been limited to surface expressed proteins and an expansion into different classes of inhibitory molecules is needed. In this study we identify the lipid metabolite phosphatidylserine (PS) as a regulator of T cell exhaustion. PS localizes to the inner plasma membrane of live cells but is externalized to the outer membrane of apoptotic cells where it can function as a potent inhibitory ligand. However, the role of PS on live immune cells is less clear4. We show that live, exhausted, antigen specific CD8 T cells externalize PS during chronic lymphocytic choriomeningitis virus (LCMV) infection. PS exposure is initiated upon T cell activation and chronic antigen stimulation led to continued externalization. PD-1+ Tcf1+ stem-like, Tim-3+ transitory, and Tim3+ terminally differentiated/exhausted cells all expose PS. Furthermore, transcriptomic and lipidomic analyses identified increased PS metabolism during exhaustion. To evaluate the inhibitory function of exposed PS in exhaustion we treated chronically infected mice with the PS-targeting antibody (mch1N11)5 and found that monotherapy alone expanded the PD-1+ LCMV-specific CD8 T cell immune response. Most significantly, PD-1+ Tcf1+ stem-like CD8 T cells downregulated quiescence-associated gene modules and increased proliferation and self-renewal after treatment. Mechanistically, we found that exposed PS from exhausted T cells could suppress co-stimulatory molecule expression on neighboring dendritic cells to limit PD-1+ CD8 T cell proliferation. Combination of PS-targeting with aPD-L1 synergized to further increase the CD8 T cell effector response and improve viral control. Lastly, we identify that CD8 tumor infiltrating lymphocytes from human clear cell renal cell carcinoma (ccRCC) and human non-small cell lung cancer (NSCLC) patient tumors similarly expose PS indicating its translational potential. In fact, clinical trials combining PS-targeting antibodies and PD-L1 antibodies have recently been used in combination therapies. Therefore, our work details live PS CD8 T cell biology and provides a potential mechanism of action by which exposed PS facilitates suppressive T cell – DC interactions to function as a ‘non-classical’ inhibitory molecule during exhaustion.

overall_design: LCMV Cl. 13 chronically infected mice were treated with control IgG or mch1N11 PS-targeting antibodies every 3 days at 200ug per injection IP for one week. Spleen were isolated post-treatment and CD11b+ (Tcell/NKcell/Bcell lineage neg) cells were isolated from respective groups and used for scRNAseq

middle: B

first: Rafi

last: Ahmed


title: Nuclear Speckles enable processing of RNA from GC-rich Isochores [Pore-C]

summary: Nuclear Speckles are large, multi-component condensates in the mammalian nuclei that are thought to be involved in various stages of gene expression, including transcription, splicing, and export. Investigating the direct role of Speckles in these processes have been intractable due to their heterogeneous, multi-component nature. Here we show that Speckles are necessary for the splicing of GC-rich genes with short introns clustered within GC-rich isochores (levelled intron/exon architecture). Acute removal of Speckles leads to a drastic downregulation of this class of  genes, whereas genes outside these domains are physically away from Speckles and are not affected from loss of Speckles. Animal genomes that do not have GC-rich isochores, do not have GC-rich levelled intron/exon architecture and do not have Speckles. Our results suggest that the expansion of Speckles core proteins’ intrinsically disordered domains during vertebrate evolution facilitated GC-content elevation in Amniotes by creating a condensate necessary to splice the by-products of this process: GC-rich, levelled intron/exon architecture.

overall_design: HCT116 cells, Pore-C

first: Michał

last: Małszyck

first: İbrahim

last: Avşar Ilık

first: Daniela

last: Salgado Figueroa

first: Nirmalya

last: Dasgupta

first: Menşura

last: Feray Çoşar

first: Keun-Tae

last: Kim

first: Gil Daniel

last: Bregieiro Carraco

first: Beatrix

last: Fauler

first: David

last: Meierhofer

first: Thorsten

last: Mielke

first: Hiroo

last: Imai

first: Cantaş

last: Alev

first: Ferhat

last: Ay

first: Tuğçe

last: Aktaş


title: Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption

city: San Francisco

first: Elphege

last: Nora

address: 555 Mission Bay Boulevard South

department: Cardiovascular Research Institute

institute: University of California San Francisco

summary: Genome folding is not static, but emerges from dynamic processes that control transcription, replication, recombination, and repair. DNA loop extrusion by cohesin is central to genome organization, yet it remains unclear how cells can tune extrusion kinetics to achieve precise and functional chromosome folding patterns. Here we show that extrusion rate acts as a tunable biophysical parameter in cells, quantitatively dialed by the respective dosage of the cohesin cofactors NIPBL and PDS5. Modulation of extrusion rate can offset changes in cohesin lifetime to buffer steady-state chromosome structure and transcriptional states, even in the face of abnormal extrusion dynamics. These findings provide a long-sought mechanistic basis for the genetic interactions between cohesin cofactors and for the molecular origin of haploinsufficiency in cohesinopathies, such as Cornelia de Lange syndrome.

overall_design: Stranded mRNA-seq in mouse embryonic stem cell lines. Cells harbor an auxin-inducible degron or dTAG-inducible (FKBP12) degron on endogenous PDS5A, PDS5B, WAPL, NIPBL alleles and were treated with  dTAG/IAA (PDS5A or PDS5B or WAPL or NIPBL depletion). WT parental cells are E14Tg2a (129 X,Y background).

first: Rini

last: Shah

first: Elphège


title: Sequence-specific RNA recognition drives Restrictor-mediated termination of extragenic transcription [eCLIP]

city: Milano

first: Gaurav

last: Mandana

address: Via Adamello 16

country: Italy

institute: European Institute of Oncology

summary: Mammalian genomes harbour hundreds of thousands of RNA Polymerase II (Pol II) landing pads, enhancers and promoters, from which transcription can initiate bidirectionally. Nevertheless, processive transcription is largely restricted to the small gene-containing fraction of the genome. A highly conserved and essential metazoan complex, Restrictor, composed of WDR82 and ZC3H4, restrains processive Pol II activity at thousands of extragenic transcription units, thus representing a critical enforcer of genome utilization. However, because of the widespread recruitment of Restrictor to both genic and non-genic transcription sites, the identification of the mechanistic basis for its exquisite selectivity for extragenic transcription has remained elusive thus far. Here, we show that while WDR82 tethers Restrictor to sites of transcription initiation, the three C3H1-type zinc fingers of ZC3H4 make sequence-specific interactions with short motifs selectively enriched at the 5’ end of extragenic transcripts, with such interactions being required for transcription termination. Hence, while Restrictor recruitment relies on WDR82-dependent tethering to the initiating Pol II, its selectivity mainly arises from sequence-specific RNA recognition.

overall_design: eCLIP was carried out in the indicated experimental conditions in a HCT-116 cell line engineered to endogenously modify ZC3H4 with the addition of a Flag-Tag. Endogenous ZC3H4 was precipitated using an anti-FLAG antibody while HA-ZC3H4 expressed from lentiviral vectors was immunoprecipitated by anti-HA.

first: Danilo

last: Polizzese

last: Madappa Mandana

first: Viviana

last: Piccolo

first: Marta

last: Russo

first: Sara

last: Polletti

first: Elena

last: Prosperini

first: Gioacchino

last: Natoli


title: Sequence-specific RNA recognition drives Restrictor-mediated termination of extragenic transcription [HCT116_4sU-RNAseq]

overall_design: 4sU-RNA seq in a HCT-116 human cell line genetically modified to introduce the AID degron at the C-terminus of ZC3H4. Data were generated with or without Auxin-induced depletion of ZC3H4.


title: Sequence-specific RNA recognition drives Restrictor-mediated termination of extragenic transcription [RBNS]

overall_design: To investigate the binding specificity of ZC3H4, we conducted RNA Bind-n-Seq (RBNS) experiments using either a ZC3H4 fragment including the three C3H1 zinc fingers or WDR82-ZC3H4 in complex.


title: Sequence-specific RNA recognition drives Restrictor-mediated termination of extragenic transcription [ChIP-Seq]

overall_design: The genomic distribution of ZC3H4 was analyzed by ChIP-seq and compared with that of RNA polymerase II phosphorylated at either Ser5 or Ser2 of the CTD. Genomic distribution of mutant ZC3H4 constructs was also analyzed by ChIP-seq.


title: Sequence-specific RNA recognition drives Restrictor-mediated termination of extragenic transcription [HeLa__4sU-RNAseq]

overall_design: 4sU-RNA seq was performed in HeLa cells following acute CRISPR/Cas9-mediated domain-specific deletion of ZC3H4, where two single guide RNAs were used to precisely excise functional domains while preserving the open reading frame

first: DDanilo

first: DGaurav

first: DMarta

first: DSara

first: DElena

first: DGiuseppe

last: Ciossani

first: DSilvia

last: Monzani

first: DLuigi

last: Scietti

first: DSimona

last: Rodighiero

first: DFrancesco

last: Gualdrini

first: DViviana

first: DGioacchino


title: Re-analysis of PRO-seq data from HCT116 cells (GSE129501)

first: Gaurav

summary: This submission provides processed PRO-seq coverage tracks (bigWig files) from the re-analysis of public data (GSE129501, samples GSM3714462 and GSM3714463) from HCT116 human colorectal carcinoma cells. Data were aligned to the hg38 reference genome (GENCODE release 33; https://www.gencodegenes.org/human/release_33.html)  and normalized using bamCoverage (PMID: 27079975). These processed files are intended for visualization and downstream analysis of nascent transcription.

relation:
Reanalysis of: GSM3714462
Reanalysis of: GSM3714463
SubSeries of: GSE300453

overall_design:
Publicly available PRO-seq datasets from wild-type HCT116 cells (GSE129501) were downloaded and re-processed to generate normalized genome-wide coverage tracks (bigWig) on the hg38 reference genome.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************


title: Immune Dynamics in Palmoplantar Pustulosis Unveiled by Single-Cell and High-Resolution Spatial Transcriptomics [Spatial Transcriptomics]

city: Seoul

first: Hanjae

last: Lee

address: 103, Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

summary: Palmoplantar pustulosis (PPP) is a chronic and relapsing inflammatory skin disorder marked by the appearance of sterile pustules on the palms and/or soles, with an underlying pathogenesis that remains only partially understood. In this study, we mapped the immune landscape underlying PPP progression using single-cell RNA sequencing (scRNA-seq) integrated with high-resolution spatial transcriptomics (ST). Keratinocytes and fibroblasts in PPP showed enhanced activation of the JAK–STAT signaling pathway, alongside a progressive accumulation of myeloid dendritic cells and Th17 cells across disease stages—from healthy control (HC) to non-pustular lesion (NPL), and then to pustular lesion (PL). Cell–cell interaction analysis revealed CCL19–CCR7 signaling between fibroblastic reticular cell (FRC)-like fibroblasts and LAMP3⁺/CCR7⁺ migratory dendritic cells, as well as CCL22/CCL17–CCR4 signaling between these dendritic cells and CD4⁺ T cells, including Th17 subsets. These interactions were spatially validated, with dendritic cells localized both within pustules and in the upper dermis. Within the CCL19⁺ dermal compartment, activated antigen-presenting cells and lymphocytes coalesced into a lymphoid-like immune structure. Moreover, pustular and surrounding keratinocytes emerged as key sources of CXCL1/6/8–ACKR1 signaling, promoting neutrophil infiltration via endothelial engagement. These coordinated cellular interactions contribute to the establishment of a spatially organized and densely populated immune niche during PPP progression. Lastly, transcriptome-based drug prediction analysis highlighted JAK inhibitors and phosphodiesterase-4 (PDE4) inhibitors as promising therapeutic candidates capable of targeting multiple components of PPP pathology. Overall, this work provides an integrative view of immune dynamics in PPP and offers potential avenues for more targeted and effective therapies.

overall_design: Spatial sequencing libraries were generated using the Visium HD Human Transcriptome Kit (10x Genomics, 1000675) according to the manufacturer’s instructions at Macrogen Inc. (Seoul, Korea). FFPE tissue blocks with DV200 values greater than 30% were selected for library preparation, and 5 μm sections were used.


title: Immune Dynamics in Palmoplantar Pustulosis Unveiled by Single-Cell and High-Resolution Spatial Transcriptomics [scRNA-seq]

overall_design:
Full-thickness human skin samples from patients with PPP were obtained from the sole via punch biopsies, and healthy sole skin was collected as dog-ear tissue during surgical excision of an atypical nevus.

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


title: Sequence-specific RNA recognition drives Restrictor-mediated termination of extragenic transcription [TTseq]

overall_design: Nascent transcriptomes were analyzed in multiple experimental conditions to characterize Restrictor-mediated transcriptional regulation of extragenic transcription

first: Danilo

first: Viviana

first: Marta

first: Sara


title: Re-analysis of PRO-cap data from HCT116 cells (GSE219977)

summary: This submission provides processed PRO-cap coverage tracks (bigWig files) from the re-analysis of public data (GSE219977, samples GSM6783554 and GSM6783555) from Homo sapiens HCT116 genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, (insertion) using CRISPR targeting H. sapiens SUPT16H. Data were aligned to the hg38 reference genome (GENCODE release 33; https://www.gencodegenes.org/human/release_33.html)  and normalized using bamCoverage (PMID: 27079975). These processed files are intended for visualization and downstream analysis of nascent transcription.

relation:
Reanalysis of: GSM6783554
Reanalysis of: GSM6783555
SubSeries of: GSE300453

overall_design:
Publicly available PRO-cap datasets from wild-type HCT116 cells (GSE219977) were downloaded and re-processed to generate normalized genome-wide coverage tracks (bigWig) on the hg38 reference genome.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************


title: Breast Cancer samples of Mexican patients

city: Ciudad de Mexico

first: Martha-Eugenia

last: Ruiz-Tachiquin

state: Ciudad de Mexico

address: Av. Cuauhtemoc No.330, Col. Doctores, Alcaldia Cuauhtemoc

department: Unidad de Investigacion Medica en Enfermedades Oncologicas

country: Mexico

institute: Instituto Mexicano del Seguro Social

type: Genome binding/occupancy profiling by SNP array

type: Genome binding/occupancy profiling by genome tiling array

summary: Breast Cancer is a multifactorial disease with an important genetics background, example copy number variants (CNV). Microarray data analysis were performed to identify CNV that could be contributing to those Mexican patient's clinical phenotypes and genotypes

overall_design: Affymetrix CytoScan HD arrays were performed according to the manufacturer's instructions. Copy Number Analysis of Cytoscan Affymetrix arrays was performed with ChAS software for adult samples, five adyacent tumor tissue, four leukocites and five tumor tissue.

last: Ruiz-Tachiquín

first: Violeta

last: Larios-Serrato


title: Neuregulin-1 facilitates myelin regeneration through microglia-mediated mechanisms in a mouse model of chronic demyelination

city: Winnipeg

first: Soheila

last: Karimi-Abdolrezaee

state: MB

address: 629-Basic Medical Sciences Building, 745 Bannatyne Avenue

department: Department of Physiology and Pathophysiology

institute: University of Manitoba

summary: Failure in remyelination is a key feature of progressive multiple sclerosis (MS) that drive neurodegeneration and accumulation of disabilities. Microglia crucially facilitate oligodendrocyte remyelination in MS lesions through myelin phagocytosis, and subsequent cholesterol metabolism and release. However, microglia lose this capacity in chronic demyelinated lesions, as they acquire a dysfunctional phenotype characterized by intracellular accumulation of lipid droplets due to impaired cholesterol processing of myelin debris. Given the abundance of microglia in chronic MS lesions, revitalizing their pro-remyelination capacity represents a critical repair strategy for progressive MS. Here, we reveal that dysregulation of neuregulin-1 underlies impaired remyelination in chronically demyelinated brain lesions. Therapeutic restoration of neuregulin-1 supports remarkable myelin regeneration by augmenting microglia capacity for clearance of myelin debris, cholesterol metabolism and efflux. Altogether, we demonstrate the promise of neuregulin-1 as an endogenous target to facilitate microglia reparative functions in progressive MS in which there is an unmet critical need for new treatments.

overall_design: The samples are microglia isolated from corpus callosum of mice using magnetic-activated cell sorting (MACS) of CD11b+ cells. Each sample is the result of pooling of the brains of 2 mice. The treatment groups include: 1- Control mice. 2- Cuprizone for 10 weeks + 2 weeks of recovery period and Vehicle (0.1% BSA in saline) treatment. 3- Control mice. 2- Cuprizone for 10 weeks + 2 weeks of recovery period and Neuregulin 1 beta 1 (30µg/kg/day) treatment.


title: Nuclear Speckles enable processing of RNA from GC-rich Isochores [SON_Halo_4sU_pulse]

first: IBRAHIM

last: ILIK

overall_design: Gene expression profiling of HCT116 cells subject to control vs SON-depletion. Libraries were prepared from cells incubated with 1mM 4sU for 15 minutes. Ribo-depleted total RNA was used to construct 4 libraries in total.

first: Lisa

last: Martina

first: Michal

last: Malszycki

first: Tugce

last: Aktas

first: Ibrahim

last: Ilik


title: Nuclear Speckles enable processing of RNA from GC-rich Isochores [SON_Halo_pSR_SF3B1_FLASH]

overall_design: FLASH libraries of p-SR (mAb 1H4) and SF3B1 in HCT116_SON-HaloTag cells that were either treated with DMSO as a control or HaloPROTAC-3 for 16hr to deplete SON protein.


title: Nuclear Speckles enable processing of RNA from GC-rich Isochores [SON_Halo_SRRM2_dTAG_PoreC]

overall_design: Pore-C data of HCT116 cells subject to SON-depletion for 0, 6, 12 or 18hrs.

first: Daniela

last: Salgado Figueroa

first: Ferhat

last: Ay


title: Nuclear Speckles enable processing of RNA from GC-rich Isochores [SON_Halo_SRRM2_dTAG_pA]

overall_design: Gene expression profiling of HCT116 cells subject to SRRM2-depletion, SON-depletion, SRRM2+SON-depletion or control treatment.. Libraries were prepeared from pA(+)-selected RNA, 12 libraries in total.


title: DNA methylation stochasticity is linked to transcriptional variability and identifies convergent epigenetic disruption across genetically-defined subtypes of AML [scRNAseq]

first: Andrew

last: Feinberg

summary: Epigenetic regulators are frequently mutated in acute myeloid leukemia (AML). We applied the CPEL method to publicly-available ERRBS data to investigate DNA methylation stochasticity in genetic subtypes of AML, and identified transcriptional dysregulation related to methylation entropy using single-cell RNA-seq data.

overall_design: Single-cell RNA-seq of primary patient acute myeloid leukemia samples and normal CD34+ progenitor samples.

first: Eleanor

last: Hilgart

first: Michael

last: Koldobskiy


title: Nuclear Speckles enable processing of RNA from GC-rich Isochores [SON_Halo_CR_Ser2P]

overall_design: Profiling of RNAPII ser2p in HCT116 cells subject to SON-depletion, or control treatment using CUT & RUN.


title: Nuclear Speckles enable processing of RNA from GC-rich Isochores [SON_Halo_Fractionation]

overall_design: Gene expression profiling of HCT116 cells subject to control vs SON-depletion. Libraries were prepeared from ribo-depleted total RNA (whole-cell extract), nuclear RNA or cytoplasmic RNA, 18 libraries in total.


title: Nuclear Speckles enable processing of RNA from GC-rich Isochores [SON_Halo_4sU_chase]

overall_design: Gene expression profiling of HCT116 cells subject to control vs SON-depletion. Libraries were prepeared from cells incubated with 1mM 4sU for 15 minutes, then chased with medium without 4sU for 45 minutes. Ribo-depleted total RNA was used to construct 4 libraries in total.


title: Nuclear Speckles enable processing of RNA from GC-rich Isochores [SON_Halo_CR_H3K9_H327me3]

overall_design: Profiling of H3K9me3 and H3K27me3 in HCT116 cells subject to SON-depletion, or control treatment using CUT & RUN.


title: Nuclear Speckles enable processing of RNA from GC-rich Isochores [HCT116_wt_TRA2AB_KD_pA]

overall_design: Gene expression profiling of HCT116 cells subject to TRA2A/B  or control siRNA for 48hrs. Libraries were prepeared from pA(+)-selected RNA. Control siRNA treatment of this experiment was published: GSM7824617, GSM7824618, GSM7824619


title: Medullary cavity expansion is mediated by distinct cell populations during fetal bone development [scRNA-seq]

first: Shinichiro

last: Sawa

summary:
Single-cell RNA-sequencing was performed to examine the transcriptional landscape of murine fetal primary ossification center in early bone and bone marrow development.
We particularly focused on the identification of potential osteoclast-inducing cells in the developing bone and aimed to analyzed its cellular fates.

overall_design:
For whole bone analyses, cells were sorted from bone and bone marrow of embryonic day 15.5 (E15.5) or 9-week-old mice.
For analysis of early primary ossification center, tdTomato positive cells were sorted from the diaphysis of Tnfsf11-tTA; LC1; R26-tdTomato mice or Col10a1-Cre; R26-tdTomato mice at E15.5.
For cell lineage tracing experiments, tdTomato positive cells were sorted from bone and bone marrow of E17.5 or postnatal day 3 Tnfsf11-tTA; LC1; R26-tdTomato mice which were treated with doxycycline from E15 onwards.
Sorted cells were subjected to scRNA-sequencing based on 10x Genomics Chromium Single Cell 3' Gene Expression Profiling version 3.1 platform.

first: Eriko

last: Sumiya


title: Medullary cavity expansion is mediated by distinct cell populations during fetal bone development

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

overall_design: Refer to individual Series


title: Medullary cavity expansion is mediated by distinct cell populations during fetal bone development [bulk RNA-seq]

summary: RNA-sequencing was performed to examine the transcriptional characteristics of cells involved in osteoclast induction in murine fetal bone.

overall_design:
For analysis of cells marked by CD55 and CD90, tdTomato positive cells isolated from the diaphysis of embryonic day 15.5 (E15.5) Tnfsf11-tTA; LC1; R26-tdTomato mouse bones were further subdivided into CD55+CD90+, CD55+CD90-, CD55-CD90+ and CDCD-CD90- populations and sorted respectively. Two biological replicates were obtained.
For analysis of cells marked by RANKL-tdTomato and Csf1-EGFP, diaphyseal cells isolated from E15.5 Csf1-VCre; Tnfsf11-tTA; LC1; R26-tdTomato; R26-VSV-EGFP mouse bones were subdivided into tdTomato+EGFP+, tdTomato+EGFP-, tdTomato-EGFP+ and tdTomato-EGFP- populations and sorted respectively. Three biological replicates were obtained.
RNA from 14-200 cells were reverse transcribed and amplified for library construction using SMART-Seq kit (Takara Bio).


title: H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs [ChIP-seq]

city: Montreal

first: Jacek

last: Majewski

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

institute: McGill University

summary: Polycomb Repressive Complex 2 (PRC2) deposits H3K27me3 to recruit canonical PRC1 (cPRC1) that establishes repressive heterochromatin. Higher order cPRC1-mediated chromatin interactions characterize early development and resolve during cell differentiation. Here, we use two opposing models of H3K27me3 dysregulation to elucidate how these long-range loops affect gene expression and cellular phenotypes. Aggressive gliomas driven by histone H3 Lys-27-Met (H3K27M) mutations or EZH-Interacting Protein (EZHIP) expression confine H3K27me3 deposition to PRC2 nucleation sites, while loss of the H3K36 methyltransferase NSD1 in pluripotent stem cells leads to its unrestrained spread from these sites.  In H3K27M mutant tumours, focal H3K27me3 deposition concentrates chromatin occupancy of cPRC1 complexes, which results in long-range chromatin interactions anchored in polycomb bodies, mirroring patterns found in stem cells. Conversely, spread of H3K27me3 due to NSD1 loss dilutes cPRC1 deposition and disrupts polycomb body architecture. In H3K27M cells, H3K27me3 confinement sustains repression of genes tethered to the polycomb bodies, promoting self-renewing progenitor states required for tumour development. Maintenance of progenitor states depends on cPRC1 interaction with H3K27me3, as chemical allosteric modulation of chromodomains alleviates repression of transcription and promotes differentiation. These results suggest that H3K27me3 spread from CGIs modulates cPRC1 gene expression programs to orchestrate developmental transitions through the maintenance or dissolution of repressive 3D loop architecture at polycomb bodies. Imbalances in the spread of H3K27me3 altering chromatin architecture in disease including H3K27M-expressing neoplasms or following NSD1 loss contribute to explain pathogenic states.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Hi-C, ChIP-seq, bulk and single-cell RNA-seq on isogenic model systems with altered H3K27me3 spread

first: Nada

last: Jabado

first: Chao

last: Lu


title: H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs [RNA-seq]

overall_design: Hi-C, ChIP-seq, bulk and single-cell RNA-seq on model systems with altered H3K27me3 spread


title: tRNA m1A modification enhances anti-tumor immunity in macrophages by promoting translation of key interferon associated genes

city: anonymity

first: anonymity

last: anonymity

state: anonymity

address: anonymity

department: anonymity

institute: anonymity


title: Peripheral modulation of Pumilio in intestinal stem cells and the corpus allatum affects sleep latency in Drosophila

status: Public on Mar 08 2026

city: San Juan

first: Jose

middle: L

last: Agosto-Rivera

state: Puerto Rico

address: 14 Ave. Universidad Ste. 1401

department: Biology

institute: University of Puerto Rico, Rio Piedras

summary: While central circuits governing sleep are well-studied, the contribution of signaling from peripheral tissues remains a critical yet less understood aspect of sleep regulation. The highly conserved RNA-binding protein Pumilio (Pum) is a post-transcriptional regulator expressed in multiple tissues that influence systemic physiology, but its role in modulating basal sleep has not been established. Although Pumilio’s function in central neurons has been linked to sleep homeostasis following deprivation, whether it regulates sleep through peripheral mechanisms remains unknown. Here, we use conditional genetic tools in the fruit fly Drosophila melanogaster to demonstrate that genetic manipulation of Pumilio targeting the intestinal stem cells (ISCs) and the endocrine corpus allatum (CA) regulates the transition to sleep. Reducing Pumilio function in either the ISCs or the CA independently and significantly accelerates nighttime sleep onset, while overexpression produces the opposite effect. This behavioral change is accompanied by widespread transcriptional alterations in the head, characterized by a robust upregulation of genes involved in cellular stress responses. Our findings reveal a previously unrecognized gut-endocrine-brain signaling axis and identify peripheral post-transcriptional regulation as a key input to the central control of sleep behavior.

overall_design: RNA-seq profiling by high-throughput sequencing of Drosophila heads (10 per sample) following transgene expression at 29°C using the TARGET system. Comparative analysis between pum knockdown and mCherry control groups.

first: Josué

last: Rodríguez-Cordero

first: Marialena

last: Dorta-Avilés

first: Imilce

last: Rodriguez-Fernandez

first: Alfredo

last: Ghezzi

first: José

last: Lizardi-Ortiz


title: H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs [Hi-C ]


title: A low-input Micro-C protocol for high-resolution 3D genome mapping

city: shenzhen

first: Chongren

last: Pei

state: guangdong

address: Gaoke Innovation Center, Guangming District

department: Institute of Molecular Physiology

institute: Shenzhen Bay Laboratory

summary: Standard Micro-C protocols typically require millions of cells, which limits their application to rare cell populations. Here, we present an optimized low-input Micro-C workflow that requires only 100,000 cells. By comparing 30 G of sequencing data from 100,000 cells with that from 5 million G1E-ER4 cells, we demonstrate that all key architectural features—compartments, TADs, and chromatin loops—are reliably detected. Applying this method to investigate acute CTCF degradation, we observed the loss of loops and TAD boundaries in CTCF-degraded samples, consistent with previous reports. Our optimized protocol enables nucleosome-resolution 3D genome mapping for sample-limited studies.

overall_design: To evaluate the feasibility of performing Micro-C (micrococcal nuclease chromosome conformation capture) using 100,000 G1E-ER4 cells, the following experimental procedure was conducted. Cells were first cross-linked with formaldehyde and EGS, followed by chromatin digestion with MNase. The digested chromatin, fragmented into nucleosome, was then ligated using T4 DNA ligase in the presence of biotin-labeled nucleotides. After reverse cross-linking, DNA was purified with DNA clean beads. Biotin-containing DNA fragments were subsequently pulled down using streptavidin C1 beads to construct the DNA library for sequencing.

first: Fengnian

last: Shan

first: Sijian

last: Xia

first: Fei

last: Ling


title: Muscleblind-like proteins dimerize by forming disulfide bonds to influence regulation of alternative splicing

city: Atlanta

first: Adam

last: Kosti

state: GA

address: 615 Michael St

department: Cell Biology

institute: Emory University

summary: Muscleblind-like (MBNL) RNA-binding proteins (RBPs) possess modular domains that contribute to their regulation of alternative splicing and RNA localization. MBNL dimerization may play a role in these functions, but the mechanism is not well understood. Here we identify a cysteine residue in the unstructured carboxy-terminal domain of MBNL1 that enables dimerization by forming intermolecular disulfide bonds. We also demonstrate that MBNL2 likewise dimerizes by forming disulfide bonds between multiple cysteines in its carboxy-terminal tail. Nucleocytoplasmic fractionation revealed a greater proportion of MBNL1 dimer in the nucleus, suggesting a nuclear function for the MBNL1 dimer. We investigated a connection between MBNL1 dimerization and MBNL1-mediated regulation of alternative splicing. To accomplish this, we mutated the MBNL1 cysteine in question to alanine (C325A) and performed RNAseq. We uncovered numerous novel splicing events sensitive to MBNL1 dimerization.

overall_design: RNA-seq profiling of WT MEFs, Double Knockout (DKO) MBNL1/2 MEFs, DKO MEFs transfected with WT-MBNL1 and DKO MEFs transfected with MBNL1 that has a conserved cysteine mutated to an alanine.

first: Luke

last: Knudson

first: Gary

last: Bassell


title: LIF induced tumor plasticity establishes an immunosuppressive myeloid niche in LKB1 mutant lung cancer [antiLif_CITEseq]

status: Public on Mar 07 2026

city: New York

first: Yuan

last: Hao

address: Laura and Isaac Perlmutter Cancer Center

institute: NYU Langone Health

summary: Single Cell RNA-seq analysis (5' CITE-seq) of immune Cells from Murine Lkb1 mutant KP Lung Tumors  with deletion of Lif or Lifr (Figure 3)

overall_design: Eight weeks after tumor initiation, mice with Lkb1 mutant tumors were treated with an isotype control or anti-LIF therapy for 3 weeks. 11 weeks after tumor initiation, immune cells from the lungs of KP GEMM mice were isolated (sorted live, CD45 positive, extravascular CD45 negative). 10% sorted tumor cells were spiked in (GFP positive CD45 negative). 2 samples per lane individually hashed. N=2 per tumor genetic condition.

first: Ray

last: Pillai

first: Ali

last: Rashidfarrokhi

first: Aristotelis

last: Tsirigos

first: Sergei

last: Koralov

first: Thales

last: Papagiannakopoulos


title: LIF induced tumor plasticity establishes an immunosuppressive myeloid niche in LKB1 mutant lung cancer [sgLif_CITEseq]

summary: Single Cell RNA-seq analysis (5' CITE-seq) of immune Cells from Murine Lkb1 mutant KP Lung Tumors  with deletion of Lif or Lifr (Figure 3 and Figure 4)

overall_design: 11 weeks after tumor initiation, immune cells from the lungs of KP GEMM mice were isolated (sorted live, CD45 positive, extravascular CD45 negative). 10% sorted tumor cells were spiked in (GFP positive CD45 negative). 2 samples per lane individually hashed. N=2 per tumor genetic condition.


title: Expression profiling by high throughput sequencing of breast cancer

city: Guiyang

first: Tao

last: Wang

state: Guizhou

address: #83 zhongshandong road

institute: Guizhou Provincial People's Hospital

summary: This study comprises 158 clinical samples diagnosed as breast carcinoma in situ. Total RNA was extracted from fresh-frozen tissue specimens and subjected to high-throughput RNA sequencing to characterize the transcriptomic landscape and identify molecular signatures associated with disease progression and heterogeneity.

overall_design:
Gene expression profiling analysis of RNA-seq data for breast cancer.

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


title: LIF induced tumor plasticity establishes an immunosuppressive myeloid niche in LKB1 mutant lung cancer [10x_scRNAseq]

summary: Single Cell RNA-seq analysis (3' 10x) of immune Cells from Murine Lkb1 wildtype or mutant KP Lung Tumors (Figure 1A, 1B, 1C)

overall_design: Immune cells from the lungs of KP GEMM mice were isolated (sorted live, CD45 positive, extravascular CD45 negative). 2 samples per lane individually hashed. N=2 per tumor genetic condition.


title: LIF induced tumor plasticity establishes an immunosuppressive myeloid niche in LKB1 mutant lung cancer [RNA-seq]

summary: Bulk RNA-seq of sorted Lkb1 wildtype (sgNeo) and Lkb1 mutant (sgLkb1) tumor cells

overall_design: 11 weeks after tumor initiation, tumors were sorted (GFP positive CD45 negative) and Bulk RNA-seq was performed.


title: Characterization of the effect of hepatocyte nuclear factor 4 (Hnf4) silencing in enterocytes on gene expression in the developing Drosophila larval midgut

city: Cologne

first: Gilles

last: Storelli

address: Joseph Stelzmannstrasse 26

department: CECAD Research Center

institute: University of Cologne

summary: The main objective of this study was to characterize the effects of Hnf4 silencing in enterocytes (ECs) on the Drosophila midgut during larval development. Larval midguts from control animals and animals expressing Hnf4 RNAi in ECs were collected on day three and four after egg laying, corresponding to the late L2 and early L3 stages, respectively. Midguts were then processed for RNA extraction and mRNA sequencing. Our mRNA-seq study reveals significant changes in the transcriptome of control midguts between days three and four of larval development, with increased expression of numerous genes involved in lipid metabolism. Silencing Hnf4 largely suppresses this transcriptional switch, highlighting the role of this nuclear receptor in inducing intestinal lipid metabolism during larval development.

overall_design: Hnf4 silencing in ECs was achieved by expressing a UAS-Hnf4 RNAi transgene using the EC-specific mex-GAL4 driver. To do this, mex-GAL4 females (RRID:BDSC_ 91368) were crossed with UAS-Hnf4 RNAi males (RRID:BDSC_64988), and the resulting offspring (“mex_Hnf4i”) were used in the experiments. The progeny of the cross between mex-GAL4 females and attP40 males (RRID:BDSC_36304) were used as controls (“mex_attp40”). Embryos were collected after an overnight egg-laying period, and transferred in batches of 40 to polystyrene vials containing a yeast-only diet. Larvae were then collected three and four days later for midgut dissection (“D3” and “D4”, respectively). These time points correspond to the late L2 and early L3 stages, respectively. Total RNA was extracted from 30 midguts for the D3 larvae, and 10 midguts for the D4 larvae. mRNA sequencing was performed on four biological replicates per genotype and time point.

first: Clara

last: Lefranc

first: Arnaud

last: Fichant


title: Longitudinal analysis of lipid changes in the sciatic nerve caused by overexpression of PMP22 in models of CMT1A.

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

summary: Charcot-Marie-Tooth type 1A (CMT1A), a prevalent progressive demyelinating peripheral neuropathy is caused by a duplication of the peripheral myelin protein (PMP22) gene. PMP22 is crucial for formation of compact myelin, but the mechanism by which PMP22 overexpression results in CMT1A pathogenesis remains elusive. To investigate these mechanisms, we analyzed the C3 and C22 mouse models, carrying 5 and 10 additional copies of the human PMP22 gene, at five developmental stages (3, 5, 7, 9, and 12 weeks of age). We focused on alterations in lipid synthesis associated with PMP22 overexpression and disease progression, and found a clear gene-dosage effect. In addition, we examined mice on the C3 background with a Schwann cell–specific c-Jun knockout. Our findings suggest potential avenues for dietary interventions, to improve myelination in CMT1A.

overall_design: RNA-seq was performed on whole sciatic nerves from two mouse models of CMT1A, the C22 (10 additional copies of human PMP22) and C3 (5 additional copies of human PMP22) and their respective controls at five time points (3, 5, 7, 9, and 12 weeks). In addition, we also collected th esciatic nerve and conducted RNA-seq on the whole sciatic nervest for C3-PMP22 c-JunP0Cre mice, these have in addition to increased hPMP22 copies also a schwann cell specific knock-out of cs-Jun.

first: Tom

last: Hellings

first: Naima

last: Lamzira-Arichi

first: Jeroen

last: Vreijling

first: Davy

last: Cats

last: Kuipers

first: Rico

last: J E Derks

first: Marieke

last: Heijink

first: Niek

last: Blomberg

first: Iulia

last: Sidorov

first: Martin

last: Giera

first: Frank

last: Baas

first: Kees

last: Fluiter


title: DNA methylation stochasticity is linked to transcriptional variability and identifies convergent epigenetic disruption across genetically-defined subtypes of AML

status: Public on Mar 06 2026

city: Baltimore

first: Andrew

last: Feinberg

state: MD

address: 855 North Wolfe Street

institute: Johns Hopkins University


title: PMEPA1 mediates resistance to mTOR inhibitors in triple-negative breast cancer via dual modulation of TGF-β signaling and PI3K/AKT activation

city: hyderabad

first: Ramesh

last: Ummanni

state: Telangana

address: Tarnaka

department: Applied Biology

country: India

institute: CSIR-Indian Institute of Chemical Technology

summary: Acquired resistance to mammalian target of rapamycin inhibitors (mTORi) severely limits their clinical efficacy in triple-negative breast cancer (TNBC), a subtype devoid of targeted therapeutic options. To model acquired resistance, we established two mTORi-resistant TNBC cell lines, MDA-MB-231/DREVE and MDA-MB-231/DRRIDA, through chronic exposure to everolimus and ridaforolimus, respectively. These resistant cells exhibited sustained mTOR signaling, evasion of G1 arrest, enhanced migratory potential, and anchorage-independent growth. Transcriptome profiling by whole RNA Sequencing coupled with GSEA analyses revealed convergent activation of the PI3K/AKT axis and upregulation of TGF-β and KRAS signaling, alongside suppression of IL-2-mediated responses. Integrative analysis identified PMEPA1, a known modulator of TGF-β signaling, as a key driver of resistance. PMEPA1 expression was elevated in resistant cells and correlated with poor survival in TNBC patients. We demonstrated that PMEPA1 confers resistance to mTORi by suppressing canonical SMAD signaling while promoting activation of the PI3K/AKT/mTOR pathway through PTEN downregulation. Targeted silencing of PMEPA1 restored drug sensitivity, reversed epithelial–mesenchymal transition (EMT), and impaired stem-like properties. Pharmacological inhibition of upstream TGF-β signaling with galunisertib downregulated PMEPA1 and synergistically restored mTORi sensitivity in in-vitro and xenograft models, leading to significant tumor regression. Histological analysis confirmed reduced proliferation, angiogenesis, and PMEPA1 expression while necrotic foci increased in combination treated tumors. These findings establish PMEPA1 as a dual modulator of canonical and non-canonical TGF-β signaling, and a critical mediator of mTORi resistance in TNBC. Targeting the TGF-β/PMEPA1 axis represents a promising strategy to overcome resistance and improve outcomes in patients with mTORi-refractory TNBC

overall_design: RNA-sequencing was performed on MDA-MB-231/WT and two resistant derivatives, MDA-MB-231/DREVE (cultured in 20 μM Everolimus) and MDA-MB-231/DRRIDA (cultured in 30 μM Ridaforolimus), to profile transcriptional changes associated with acquired mTOR inhibitor resistance

first: Chithrapournami

last: M S

first: Biswajit

last: Biswas

first: Andugulapati

middle: S

last: Balagi


title: Metasasis-associated wound repair promotes reciprocal activation of the lung epithelium and breast cancer metastases during metastatic outgrowth

city: Aurora

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

summary: When tumor cells colonize distant organs during metastasis, they interact extensively with surrounding cells. These interactions often change the behavior of surrounding cell populations which collectively induce a pro-tumor microenvironment that permits tumor cell outgrowth into overt, clinically detectable metastatic disease. The lung is one of the most common sites of breast cancer (BC) metastasis, and alveolar epithelial cells are the most common cell type in the lung. A gap in our ability to treat patients with established lung metastases lies in our lack of knowledge regarding how the lung microenvironment is remodeled during metastatic outgrowth and how this contributes to disease progression. Immunocompetent preclinical mouse models of BC metastasis were used to study late-stage lung metastatic outgrowth, the stage at which most patients are diagnosed with metastatic disease. A custom imaging panel was developed to quantify lung wound repair and inflammation, and single-cell RNA-sequencing (scRNAseq) was performed on mouse lungs with high or low metastatic burden to identify cell-type specific genes altered during metastatic outgrowth. No-contact co-culture experiments were used to examine reciprocal paracrine interactions between lung type II alveolar epithelial (AT2) cells and BC cells. A chronic wound repair-related phenotype developed within the lung microenvironment during metastatic outgrowth, which was characterized by an increased number and activation of AT2 cells surrounding growing metastases. scRNAseq of lungs with a high versus low metastatic burden showed that metastatic outgrowth significantly changed AT2 gene expression, resulting in a modified secretome. No-contact co-culture experiments indicated that BC-derived secreted factors alter AT2 gene expression, while AT2-derived secreted factors promoted TNBC growth. We investigated the possible mechanism(s) responsible for these effects and found that AT2 secreted factor genes, regulated by the cAMP response element-binding protein (CREB), contribute to BC proliferation. Targeting CREB signaling with the phosphodiesterase 4 (PDE4) inhibitor roflumilast reduced AT2-BC reciprocal interactions in vitro and metastatic outgrowth in vivo. Our studies demonstrate the potential for targeting metastasis-associated wound repair and lung epithelial cell activation with PDE4 inhibitors. This strategy may be an effective way to treat and manage metastatic BC progression in established, clinically detectable disease.

overall_design: Induced pluripotent stem cells (iPSC) cells were differentiated into lung type II alveolar epithelial cells (iAT2) following the protocol outlined in Tamò et al. 2018. Transwell plates with 0.4µm pores were used to investigate paracrine interactions between cell lines (no contact co-culture). iAT2 cells were no contact co-cultured with TNBC cells (SUM159PT or MDA-MB-453) for 5 days. Control iAT2 cells were cultured alone.

first: Jessica

last: Christenson

first: Nicole

last: Spoelstra

first: Michelle

last: Williams

first: Kathleen

last: O'Neill

first: David

last: Orlicky

first: Jennifer

last: Wagner

first: Li Wei

last: Kuo

first: Lyndsey

last: Crump

last: Richer


title: Multiomics immune profiling of a patient-relevant orthotopic lung cancer model using SEPARATE-Seq.

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

summary: Relevant pre-clinical models are essential for driving progress in cancer therapy research. Here, we developed a pre-clinical study framework using an injectable orthotopic lung adenocarcinoma (LUAD) model (ORTHO) that replicates key features of human LUAD patients and is dissectible into tumoural and non-tumoural adjacent tissue, in analogy with patient samples. We also present SEPARATE-Seq, a technique enabling the partitioning of vascular and intratissue immune cells along with scRNA-Seq. By applying both SEPARATE-Seq and spatial transcriptomics to our dissectible ORTHO model, we confirmed that our model replicates key immune features of human LUAD patients. Similarly to these patients, we observed NK-cell dysfunction and neutrophil dichotomy, and uncovered that these are driven by their vascular/intratissue or tumour/adjacent location, highlighting the need for these spatial distinctions. Additionally, we reveal that several immune populations are restricted to specialised, local niches within the tumour, including a ring of lipid-associated TAMs lining the tumour edge and hubs of interferon-stimulated cells. Overall, our resource, available through an interactive tool, provides a comprehensive multiomics immune characterisation of a reproducible pre-clinical LUAD mouse model.

overall_design: Cell line scRNA-Seq: In vitro cultured cells from LLC-Thy1.1 cell lines: (i) not passaged (P0) or (ii) passaged twice in vivo (P2). P0 and P2 samples were multiplexed using both cell multiplexing oligonucleotide (CMO) and hashtag oligos (HTO). Cells were sorted for 7-AAD- singlets.    ORTHO/SUBCUT CITE-Seq: 7-AAD-CD45+Thy1.1- sorted immune cells, isolated from (i and ii) tumours or adjacent tissue of the ORTHO LLC-Thy1.1 P2 mouse model, (iii) lung tissue from HBSS mock-inoculated mice, or (IV) from subcutaneous LLC-Thy1.1 P2 mouse tumors. Individual murine samples were multiplexed using HTO hashing (4 mice per sample type), and the vascular cells of each murine sample were labeled using STREP-tags (binding to IV injected CD45-biotin antibody).

first: Bardet

last: Pauline

first: Allonsius

last: Lize

first: Laoui

last: Damya


title: In vivo CRISPR screens of Toxoplasma gondii targeting proteins of the apical complex and the pellicle.

city: Suita

first: Yuta

last: Tachibana

state: Osaka

address: 3-1, Yamadaoka

department: Research Institute for Microbial Diseases (RIMD)

institute: Osaka University

summary: We performed in vivo CRISPR screens of Toxoplasma targeting proteins of the apical complex and the pellicle during mouse infection.

overall_design: This apical-pellicle library targeting 309 genes which consisted 3090 gRNAs targeting proteins of the apical complex and the pellicle together with dispensable and essential control genes.

first: Masahiro

last: Yamamoto


title: Next Generation Sequencing Facilitates Quantitative Analysis of  Macrophage and Leukemia Cell Transcriptomes  in Mouse Iron-overload  MLL-AF9 Acute Myeloid Leukemia

city: Nanjing

first: feifei

last: yang

address: Changle Road 68

institute: Nanjing first hospital,Nanjing medical university

summary: The goals of this study aim to reveal functional and phenotypic diversity of  Macrophage and Leukemia Cell in response to the Iron-overloaded microenvironmental cues  in mouse acute myeloid leukemia

overall_design: Anasizy the transcriptomes of Macrophage and Leukemia cell in Mouse Iron-overload acute myeloid leukemia

first: Feifei

last: Yang


title: Effect of depletion of HNRNPC on multiple myeloma cells

summary: The goals of this study aim to reveal functional changes mediated by HNRNPC in multiple myeloma cells

overall_design: Anasizy the transcriptomes of multiple myeloma cells


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

status: Public on Mar 05 2026

city: Palo Alto

first: Xinnan

last: Wang

state: CA

address: 1201 Welch Road, MSLS Building, Rm P151

department: Neurosurgery

institute: Stanford University

summary: We generated bulk RNA sequencing (RNA-seq) data from human glioma surgical resections treated ex vivo with a MIRO1-binding compound (MR3) or vehicle control. Fresh tumor specimens were processed and cultured under controlled conditions prior to RNA extraction and high-throughput transcriptomic profiling to characterize treatment-associated gene expression changes within the tumor microenvironment (TME). The dataset captures global transcriptional programs from tumor tissue, reflecting contributions from malignant cells as well as stromal and immune components present in the resections. These data enable analysis of MIRO1-dependent transcriptional regulation in human glioma and facilitate cross-species integration with murine single-nucleus RNA-seq datasets. This resource supports investigation of mitochondrial-associated transcriptional programs and their impact on immune microenvironment remodeling in human glioma.

overall_design: Bulk RNA-seq profiling of human glioma tumor core specimens treated ex vivo with 10 μM MIRO1-binding compound (MR3) or vehicle control (DMSO) for 24 hours, with snap-frozen tissues collected for transcriptomic analysis.

first: Menghan

last: Li

first: Zehui

last: Du