title: Ex vivo modelling of lung tissue resident antimicrobial responses

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

institute: University of Geneva

summary: Tissue resident host responses to microbial infections in the respiratory tract are highly dynamic in space and time and rely on the interaction of a multitude of cell types. To model these multicellular responses reliably in cell culture, we compare here the global transcriptional antimicrobial response to infection with influenza A virus (IAV) in precision cut lung slices (PCLS), volume defined organ discs largely maintaining the cellular composition and 3D architecture of the donor lung. To permit a fair comparison of host responses in an isogenic background we first challenged mice in vivo and murine PCLS (mPCLS) and assess host transcriptomic changes by unbiased RNAseq. While core antiviral responses overlapped substantially, mPCLS lacked certain features—such as type II interferon expression—likely due to the absence of infiltrating immune cells responses. Importantly, when expanding our findings to immune experienced human precision cut lung slices (hPCLS), we find a much broader antiviral response after IAV challenge, including type I, II and III interferons, suggesting the presence of responsive tissue resident lymphocytes. To prove specificity of this response we infected hPCLS with Streptococcus pneumoniae. Ex vivo tissues responded with a distinct proinflammatory gene profile including IL1A, IL1B and IL17 expression. Blocking of IL-1β signaling partially inhibited the proinflammatory response, suggesting cellular crosstalk and a complex and specific antimicrobial reaction in this ex vivo model. In conclusion diversified tissue resident immune cell compartment distinguishes the human ex vivo model, making it an ideal system for microbiological and immunological research.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Lung samples from mouse or human infected in vivo or ex vivo (PCLS model) with Influenza A H1N1 strain were processed to RNA extraction for bulk RNAseq. This allowed us to compare the early host response between the in vivo situation and the ex vivo modelling.

first: Helena

last: Choltus

first: Niccolo

last: Bianchi

first: Nelli

last: Heikkila

first: Fedor

last: Bezrukov

first: Nina

last: Leitner

first: Beryl

last: Mazel-Sanchez

first: Veronique

last: Serre Beinier

first: Wolfram

last: Karenovics

first: Yannick

last: Nissille

first: Benoit

last: Bedat

first: Virginie

last: Prendki

first: Alexander

last: Lobrinus

first: Christiane

last: Eberhardt

first: Simone

last: Beccatini

first: Mirco

last: Schmolke


title: DNMT1 loss leads to hypermethylation of a subset of late replicating domains by DNMT3A.

status: Public on Mar 26 2026

city: Edinburgh

first: Duncan

last: Sproul

state: Mid Lothian

address: Crewe Road South

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

type: Methylation profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: DNMT1 loss leads to hypermethylation of a subset of late replicating domains by DNMT3A (H3K36me2 native ChIP-seq)

summary: Loss of DNA methylation is a hallmark of cancer that is proposed to promote carcinogenesis through gene expression alterations, retrotransposon activation and induction of genomic instability. Cancer-associated hypomethylation does not occur across the whole genome but leads to the formation of partially methylated domains (PMDs). However, the mechanisms underpinning PMD formation remain unclear. PMDs replicate late in S-phase leading to the proposal that they become hypomethylated due to incomplete re-methylation by the maintenance methyltransferase DNMT1 during cell division. Here we investigate the role of DNMT1 in the formation of PMDs in cancer by conducting whole genome bisulfite sequencing (WGBS), repli-seq and ChIP-seq on DNMT1 knockout HCT116 colorectal cancer cells (DNMT1 KO cells). We find that DNMT1 loss leads to preferential hypomethylation in late replicating, heterochromatic PMDs marked by the constitutive heterochromatic mark H3K9me3 or the facultative heterochromatic mark H3K27me3. However, we also observe that a subset of H3K9me3-marked PMDs gain methylation in DNMT1 KO cells. We find that, in DNMT1 KO cells, these hypermethylated PMDs remain late replicating but gain DNMT3A localisation. This is accompanied by loss of heterochromatic H3K9me3 and specific gain of euchromatic H3K36me2. Our observations suggest that hypermethylated PMDs lose their heterochromatic state, enabling their methylation by DNMT3A and the establishment of a hypermethylated, non-PMD state, despite their late replication timing. More generally, our findings suggest that the de novo DNMTs play a key role in establishing domain level DNA methylation patterns in cancer cells.

overall_design: This series contains H3K36me2 native ChIP-seq from human cancer cell lines. HCT116 cells and derivatives lacking DNMT1 were grown before chromatin was extracted and H3K36me2 levels analysed by native ChIP-seq.


title: DNMT1 loss leads to hypermethylation of a subset of late replicating domains by DNMT3A (repli-seq)

overall_design: This series contains repli-seq from human cancer cell lines. HCT116 cells and derivatives lacking DNMT1 were grown before replication timing was profiled using repli-seq.


title: DNMT1 loss leads to hypermethylation of a subset of late replicating domains by DNMT3A (WGBS)

overall_design: This series contains WGBS from human cancer cell lines. HCT116 cells and derivatives lacking DNMT1 were grown before genomic DNA was extracted and DNA methylation levels analysed by Whole Genome Bisuflite sequencing (WGBS).


title: Transcription Elongation Factor SPT6 Maintains Epidermal Homeostasis and Suppresses Skin Inflammation in Mice

city: Guangzhou

first: Jingting

last: Li

address: No 1, Zhongshan 2 Road, 12th Floor

department: Institue of Precision Medicine

country: China

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: We employed single-cell RNA sequencing (scRNA-seq) using 10x Genomics technology to investigate the impact of Supt6 epidermis-specific knockout on epidermal homeostasis in mice. The histone chaperone SPT6 is a central regulator of genomic stability. Our previous studies have shown that SPT6 promotes epidermal differentiation by regulating transcriptional elongation in human epidermal stem/progenitor cells, but its in vivo role remains unclear. Our research has discovered for the first time that the transcriptional elongation factor SPT6 regulates skin inflammation, hair follicle development, and wound healing, providing a novel therapeutic target for clinical treatment of psoriasis and related skin disorders.

overall_design: single cell RNA-seq of wild-type mice and Supt6 KO mice epidermis, collected on the 5th day after the final tamoxifen injection.

first: Yushuang

last: Sun


title: Ectopic MYC Expression Reprograms Epigenetic Landscapes and Transcription Factor Networks to Drive Differentiation Block and Malignant Transformation in AML [RNA-Seq]

city: New York

first: BiNGS

last: Core

address: 3 E 101st St

country: USA

institute: Icahn School of Medicine at Mount Sinai

summary: Overexpression of MYC is a common convergent consequence of genetic driver mutations in acute myeloid leukemia (AML). However, despite extensive research, the mechanisms by which this proto-oncogene promotes leukemogenesis remain incompletely understood. Here, we developed models of deregulated MYC expression in human pluripotent stem cell (hPSC)-derived myelopoiesis. We show that MYC overexpression from the endogenous locus maintaining physiological regulation is insufficient for leukemogenesis. Rather, constitutive MYC overexpression from ectopic alleles is necessary for driving and sustaining leukemia-associated phenotypes. These phenotypes depend on the widespread disruption of epigenetic landscapes imposed by MYC overexpression, which in turn underlies a differentiation arrest and dysregulation of the BACH1 transcription factor network, identified here as a mediator of these changes. Our findings shed new light into the mechanisms underlying MYC-induced malignant transformation and leukemogenesis, suggesting novel therapeutic targets for AML.

overall_design: A total of 22 RNA-Seq libraries from human embryonic stem cell-derived hematopoietic progenitor cells (HPCs) with ectopic MYC expression (+Dox, 10 samples consisting of 2 replicates each for 5 timepoints during HPC culture: days 12, 14, 16, 18 and 20) and control without ectopic MYC expression (-Dox, 12 samples consisting of 2 replicates each for 6 timepoints during HPC culture: days 10, 12, 14, 16, 18 and 20).

first: David

last: Dominguez-Sola

first: Eirini

last: Papapetrou

first: Saul

last: Carcamo


title: Ectopic MYC Expression Reprograms Epigenetic Landscapes and Transcription Factor Networks to Drive Differentiation Block and Malignant Transformation in AML [ATAC-seq]

overall_design: A total of 44 ATAC-Seq libraries from human embryonic stem cell-derived hematopoietic progenitor cells (HPCs) with (+Dox) or without (-Dox) ectopic MYC expression.


title: SPT6 maintains epidermal homeostasis by inhibiting an NF-κB- positive feedback loop to prevent excessive inflammation

city: Ghuangzhou

address: NO.2 Zhongshan Road

department: Institute of Precision Medicine

institute: The First Affiliated Hospital of Sun Yat-sen University

summary: Keratinocytes are increasingly recognized as central regulators of cutaneous immune responses and key contributors to maintaining immune homeostasis. However, whether and how epidermal stem and progenitor cells (EPSCs) actively suppress proinflammatory signaling pathways to prevent excessive inflammation and maintain epidermal immune quiescence remains unclear. Here, we generated a conditional knockout mouse model (K14-CreERT; Supt6fl/fl) to investigate the role of SPT6, a transcription elongation factor, in epidermal and immune homeostasis. Loss of SPT6 in basal keratinocytes led to spontaneous, psoriasis-like skin inflammation, characterized by epidermal hyperplasia, immune cell infiltration, parakeratosis, and hyperkeratosis. SPT6-deficient mice also exhibited significantly delayed wound healing accompanied by impaired Wnt signaling. Moreover, single- cell RNA sequencing revealed distinct keratinocyte subpopulations with inflammatory signatures, elevated NF-κB signaling, and suppressed Wnt signaling. Mechanistically, SPT6 suppresses NF-κB signaling by binding to an enhancer of the RELA gene and preventing its positive transcriptional feedback loop. These findings support a new paradigm in which the default state of the skin may be primed for inflammation, and active suppression by factors such as SPT6 is required to maintain epidermal homeostasis. Taken together, the results of our study reveal a previously unrecognized role for SPT6 as a key regulator of epidermal immune quiescence and tissue integrity.

overall_design: RNA-seq of wild-type mice and Supt6 KO mice, collected on the 10th day after the final tamoxifen injection.


title: A new mRNA antigen vaccine induces potent B and T cell responses and in vivo protection against SARS-CoV-2

city: La Jolla

first: Jing

last: Wen

state: CA

address: 3147 Biomedical Sciences Wy

department: CMM

institute: UCSD

summary: We designed a new SARS-CoV-2 mRNA vaccine G1-C. We immunized mice with 2 doses of GFP, RBD, and G1-C vaccines and then analyzed vaccine-induced immune response in vivo.

overall_design: We immunized mice with 2 doses of GFP, RBD, and G1-C vaccines. 14 days after the booster, we isolated bone marrow cells and performed single-cell RNA sequencing of 9 samples from GFP, RBD and G1-C groups to assess differential gene expression.

first: Jaesu

last: Moon

first: Luca

last: Tucciarone

first: Shania

last: Bu

first: Tariq

middle: M

last: Rana


title: Maternal Microbiome-Derived Propionic Acid: A Key Regulator of Offspring Myelinogenesis Through Histone Lactylation-Mediated cGMP-PKG Activation

city: Xi'an

first: Yuan

last: Zhang

address: No. 620, West Chang'an Avenue, Chang'an District

institute: Shaanxi Normal University

summary: The maternal gut microbiome plays a crucial role in regulating offspring neurodevelopment through microbial metabolite signaling, yet its influence on central nervous system (CNS) myelinogenesis, a pivotal process for neural circuit maturation, remains poorly understood. Here, using antibiotic-induced maternal dysbiosis models, we identify propionic acid (PA), a short-chain fatty acid (SCFA) derived from the maternal microbiome, as a key epigenetic modulator of oligodendrocyte precursor cell (OPC) differentiation. Maternal antibiotic-induced gut dysbiosis led to significant hypomyelination in offspring, an effect that could be rescued by postnatal PA supplementation. PA not only enhanced developmental myelination but also promoted remyelination following lysolecithin-induced demyelination by inducing OPC maturation. Mechanistically, PA induced histone H4K12 lactylation (H4K12la), thereby activating transcription of cGMP-PKG signaling components (e.g., Gna12) and upregulating Sox family transcription factors essential for oligodendrocyte differentiation. These findings establish a propionate-H4K12la-cGMP-PKG axis that links maternal microbial metabolism to offspring myelination, revealing SCFA-driven epigenetic regulation as a promising therapeutic avenue for CNS disorders.

overall_design: Neonatal C57BL/6 mouse brain tissue (postnatal days 0–3, mixed sex) was rapidly dissociated in HBSS. OPCs were isolated using the Neural Tissue Dissociation Kit Ran and CD140a (PDGFRα) MicroBead Kit, seeded into poly-D-lysine–coated 6-well plates, and maintained in DMEM/F12 containing 20 ng/mL PDGF-AA, 2% B27, 20 ng/mL bFGF, 2 mM GlutaMAX, and 1% N2. After 24 h, the proliferation medium was replaced with DMEM/F12 containing 2% B27 and 1% N2, supplemented with either propionic acid (PA, 10 μM) or vehicle to induce differentiation. Two biological replicates were prepared for each condition. After 48 h, cells were trypsinized, and 1 × 10⁵ cells per sample were collected for library construction.

first: Yan

first: Bing

last: Han

first: Xuan

last: Wang

first: Yarou

last: Zou

first: Xing


title: Dual RNA-seq analyses provide insights into the biology of the fish pathogen Piscirickettsia salmonis

city: Santiago

first: Veronica

last: Cambiazo

address: Av. El Libano 5524

country: Chile

institute: Instituto de Nutrición y Tecnología de los Alimentos (INTA)

summary: Piscirickettsia salmonis is a facultative intracellular pathogen and the causative agent of piscirickettsiosis, a systemic infection of salmonid fish, with high impact on the salmonid aquaculture in Chile. After invasion, P. salmonis actively replicates in macrophages and monocytes, and its ability to enter and multiply within host cells is essential for pathogenesis. The ability of P. salmonis to subvert the functions of macrophages contributes to bacteria survival and dissemination within the host. Here, we adapted dual RNA-sequencing to define how P. salmonis remodel their gene expression in tandem with that of infected the host cell, a macrophage-like cell line from Salmo salar head kidney, known as SHK1. We found that SHK1 cells increased lysosomal content and activity to defend against invading bacteria, while P. salmonis upregulated gene functions related to virulence, including type IV secretion system (T4SS), iron acquisition, transport and efflux systems.

sample_organism:
Piscirickettsia salmonis
Salmo salar

platform_organism:
Piscirickettsia salmonis
Salmo salar

overall_design: SHK-1 cells infected with P. salmonis CGR02 at day 4 (stationary growth phase), SHK-1 control cells, and P. salmonis CGR02 in exponential phase grown in axenic medium were sequenced using RNA-seq. The transcriptome of SHK-1 infected cells was compared with the SHK-1 control cells, and the intracellular transcriptome of P. salmonis was compared with P. salmonis in exponential phase grown in axenic medium.

first: Pamela

last: Aravena

first: Christian

last: Hodar

first: Daniel

middle: E

last: Palma

first: Javiera

last: Ortiz


title: Integrated Transcriptomic and Proteomic Analysis of the Immune Response in Hyalomma anatolicum to Bacterial Invasion

status: Public on Mar 25 2026

city: Urumqi

first: Ercha

last: Hu

state: Xinjiang

address: East nongda Rd 311，Sayibak district

department: College of Veterinary Medicine

institute: Xinjiang Agricultural University

summary:
Background: Hyalomma anatolicum is a multi-host ectoparasite that carrys and transmits a variety of zoonotic pathogens. Understanding the immune response of ticks to bacterial infections is of research significance for deciphering their immune defense mechanisms and harnessing tick - derived molecules.
Methods: In the current study, transcriptomic and proteomic analyses on H. anatolicum injected with Staphylococcus aureus (SA group), Proteus mirabilis (PM group) or phosphate buffered saline (PBS group) were performed.
Results: In pairwise comparisons among the experimental groups, we identified 9,776 (SA/PBS), 10,230 (PM/PBS), and 1,309 (SA/PM) differentially expressed genes (DEGs), as well as 175 (SA/PBS), 277 (PM/PBS), and 223 (SA/PM) differentially expressed proteins (DEPs), respectively. Subsequent KEGG pathway analysis revealed that these DEGs and DEPs were significantly enriched in a range of pertinent pathways, including the immune system and apoptosis, Toll and IMD signaling pathways, MAPK signaling pathway, and NF - κB signaling pathway. The RT - qPCR detection data exhibited a concordant trend with the RNA - seq data, indicating a substantial alignment in the observed results. Notably, the defensin and lectin gene families emerged as potentially pivotal components within the innate immune defense system of ticks.
Conclusion: Overall, in this study, genes, proteins, and signaling pathways integral to the immune defense of H. anatolicum were identified, offering substantial potential for future research focused on harnessing its intricate immune defense mechanisms for antimicrobial applications.

overall_design: To investigate the gene expression profiles of H. anatolicum in response to bacterial challenges, transcriptome and proteome sequencing were conducted in this study. Specifically, female H. anatolicum ticks, collected from the same breeding experiment two weeks post - molting, were first immersed in sterile phosphate - buffered saline (PBS) solution and gently agitated for 15 s to clean their surfaces for three times. After thorough drying on sterile medical gauze, the ticks were positioned under a dissecting microscope with their ventral side exposed upwards. Each tick was then individually injected with either S. aureus suspended in phosphate-buffered saline (500 nL containing 10⁷ CFU) or P. mirabilis suspended in PBS (500 nL containing 10⁷ CFU), and a small amount of sterile petrolatum was picked up with a sterile needle and quickly applied to seal the wound upon needle withdrawal. This was accomplished through a puncture into their fourth coxal segment using a precision microsyringe (Hamilton Bonaduz, LTD, Switzerland). The control group received an equivalent volume of PBS (500 nL, 10 mM) to allow for comparative analysis of responses during bacterial invasion.

first: Jianlong

last: Li

first: Tingxiang

last: Luo

first: Zhen

last: Ma

first: Depeng

last: Yang

first: Sen

first: Yongchang

first: Bayinchahan

last: Gailike

first: Qingyong

last: Guo

first: Zhengxiang


title: Rhabdomyosarcoma transcriptomics upon PAX3-FOXO1 rescue with other fusion proteins

city: Durham

first: Seth

last: Zimmerman

state: NC

address: 308 Research Dr.

institute: Duke University

summary: PAX3-FOXO1 is the commonly identified oncofusion gene found in rhabdomyosarcoma. However, other rare fusions are also seen. Here, we have knocked down PAX3-FOXO1 in a fusion-positive RMS cell line (RH4) with shRNA targeting the breakpoint and rescued cell growth with 7 fusions found in this cancer. RNA sequencing was then used to asess how each fusion alters transcription by comparing the RNA sequencing to a PAX3-FOXO1 knock down cell.

overall_design: Samples include RNA from RH4 cells transduced with a doxycycline induced shRNA targeting PAX3-FOXO1 (sh4) and either a vector encoding a control TurboID-NLS or each fusion tagged with the TurboID fused to the C-Terminus. A negative control was also included which consisted of RH4 cell transduced with a scrambled shRNA and TurboID-NLS. All cells were grown in the presense of Doxycycline.  Each sample was generated in technical triplicate


title: The genotoxic stress sensor ZBP1 drives tau pathology

city: Charlottesville

first: Jessica

middle: M.

last: Thanos

state: VA

address: 409 Lane Road

institute: University of Virginia

summary: To gain a more comprehensive and unbiased assessment of how ZBP1 signaling affects microglial, astrocytic, and neuronal biology in tauopathy, we performed single-nucleus RNA sequencing (snRNA-seq) on pooled hippocampi from 9-month-old PS19 and PZKO (PS19, ZBP1 KO) mice.

overall_design: Snap-frozen hippocampi were collected from 9-month-old male PS19 and PZKO mice and submitted to GENEWIZ (Azenta Life Sciences) for nuclei isolation, library preparation, and RNA sequencing.

first: Olivia

middle: C

last: Campbell

first: Nick

middle: R

last: Natale

first: Ana

last: Royo Marco

first: Michael

middle: A

last: Puchalski

first: John

last: Lukens


title: Quantitative transcriptome and proteome maps of classical nonclinical species [b3]

city: Groton

first: Darien

last: Capunitan

state: CT

address: 255 Shennecossett Rd

institute: Pfizer

summary: The distribution of expression of target genes can provide insights that advance understanding of target availability to aid therapeutic development purposes. The increase of use of biologics and novel modalities, combined with the opportunities of alternative to in vivo experimental methods in safety evaluation of new therapeutics. A detailed understanding of expression levels in target tissues is essential to selecting nonclinical species with the highest translational potential. We quantified the relative RNA and proteinlevels across more than 40 normal tissues and 5 nonclinical species several tissues in human. We identified patterns of cross-species and methodology relationships that can aid in the broader understanding of nonclinical experimental design. We observedexpression profile similarity across tissues that favors species similarity, except for select nervous system and immune tissues. In exploring tissue specificity, we identified ubiquitous transcripts that encode tissue-specific proteins. We also assessed discordance between RNA and protein enrichment and revealed potential sites of synthesis and action of secreted proteins. These data and their relationships are foundational assets in toxicology study design and provide insights into biological regulation in drug discovery.

sample_organism:
Macaca fascicularis
Canis lupus familiaris
Rattus norvegicus

overall_design: Rna-seq proflining of tissue samples from pre-clinical animals (minipigs, cynomolgus monkeys, beagle dogs, Wistar Han rats, CD1 and C57BL6 mouse) Snap frozen tissue samples were collected from 3 male and 3 female animals (minipig, cynomolgus monkeys and dogs) and for rodents, 5 male and 5 female animals were used for tissue collection.Frozen human tissue samples (3 males and 3 females) were obtained from Pfizer Tissue Bank.  Rodent tissue samples from Rat and Mouse (7 to 9 weeks old, n=5/gender) were pooled & analyzed by gender. Samples (n=3/gender, 6 samples/tissue type/species) from human, cyno, dog, and pigs were pooled by tissue type only.

first: Elias

last: Oziolor

first: Liang

last: Xue

first: Dennis

last: Pelletier

first: Emi

last: Kimoto

first: Joel

middle: D

last: Federspiel

first: Mark

last: Sheehan

first: Seda

last: Arat

first: Leah

last: Newman

first: Sophia

last: Lee

first: Jessie

last: Qian

first: Steven

last: Kumpf

first: Thomas

last: Lanz

first: Mathew

last: Martin

first: Nagappan

last: Mathialagan


title: Quantitative transcriptome and proteome maps of classical nonclinical species [b2]

sample_organism:
Macaca fascicularis
Canis lupus familiaris
Mus musculus
Rattus norvegicus


title: Quantitative transcriptome and proteome maps of classical nonclinical species

sample_organism:
Macaca fascicularis
Homo sapiens
Canis lupus familiaris
Sus scrofa
Mus musculus
Rattus norvegicus


title: Quantitative transcriptome and proteome maps of classical nonclinical species [b1]

platform_organism:
Macaca fascicularis
Homo sapiens
Canis lupus familiaris
Sus scrofa
Mus musculus
Rattus norvegicus


title: MECOM promotes leukemia progression and inhibits mast cell differentiation through functional competition with GATA2 (CordBlood_RNA-seq)

city: Shimotsuke

first: Kohei

last: Iida

state: Tochigi

address: Yakushiji 3311-1

department: Regenerative medicine

country: Japan

institute: Jichi medical university

summary: MECOM is a transcription factor critical for the maintenance of hematopoietic stem cells (HSCs) and the pathogenesis of myeloid leukemia. Germline mutations clustered in the C-terminal zinc finger domain (ZFD) of MECOM are known to cause MECOM-associated syndromes, involving bone marrow failure and skeletal anomalies. However, the molecular consequences of these mutations and the precise downstream mechanisms of MECOM remain elusive. Here, we demonstrate that the C-terminal ZFD serves as the dominant DNA-binding module of MECOM, and that disease-associated mutations abrogate its DNA-binding capacity. Mechanistically, we reveal that MECOM functionally antagonizes GATA2 via C-terminal ZFD-mediated DNA binding and recruitment of the corepressor CtBP. This repression promotes myeloid leukemogenesis while suppressing mast cell differentiation. Furthermore, we generated a knockin mouse model harboring a C-terminal ZFD mutation, which successfully recapitulated the clinical phenotypes of MECOM-associated syndromes, including reduction of HSCs and B cells. Collectively, our findings define C-terminal ZFD mutations as loss-of-function mutations with impaired DNA binding, uncover the MECOM-GATA2 axis as a key regulatory pathway, and provide a valuable mouse model for understanding MECOM-associated syndromes.

overall_design: RNA-seq profiling human CD34+ umbilical cord blood cells transduced with pMYS-IRE-GFP vector, wild-type MECOM, or mutant MECOM (MECOM-R750 or MECOM-DL/AS). GFP+ cells were sorted 48 hours after transduction, and were cultured for 4 days.

first: Tomoya

last: Isobe

first: Shuhei

last: Asada

first: Tomohiro

last: Yabushita

first: Susumu

last: Goyama


title: MECOM promotes leukemia progression and inhibits mast cell differentiation through functional competition with GATA2 (HEK293T_ChIP-seq)

overall_design: ChIP-seq of MECOM with AM tag in HEK293T cells transduced with pMYS-IRE-GFP vector, wild-type MECOM, or mutant MECOM (MECOM-R750 or MECOM-DL/AS).


title: PD-1 signaling and PD-1 blockade-mediated tumor control are established at microvillar T cell contacts

city: Oxford

first: Simon

last: Davis

address: MRC Weatherall Institute of Molecular Medicine

department: Radcliffe Department of Medicine

institute: University of Oxford

summary: To investigate the differences between nivolumab_mIgG1 and nivolumab_mIgG1_D265A, and to identify the context in which antibody agonism might impact therapy, we employed a single-cell RNA sequencing approach using 10x Genomics to study the immune populations of tumors, and draining lymph nodes (dLN), and non-draining lymph nodes (non-dLN).

overall_design: Nine samples derived from three mice and three anatomical sites (tumor, dLN, and non-dLN) were multiplexed and sequenced in a single run to minimize batch effects. All samples were FACS sorted for live CD45+ cells. Mouse 1 was treated with nivolumab_mIgG1_D265A, mouse 2 was treated with nivolumab_mIgG1, and mouse 3 was treated with MOPC21 (isotype control). Sample 1: CD45+ cells (immune cells) isolated from tumour from mouse 1; Sample 2: CD45+ cells (immune cells) isolated from dLN from mouse 1; Sample 3: CD45+ cells (immune cells) isolated from non-dLN from mouse 1; Sample 4: CD45+ cells (immune cells) isolated from tumour from mouse 2; Sample 5: CD45+ cells (immune cells) isolated from dLN from mouse 2; Sample 6: CD45+ cells (immune cells) isolated from non-dLN from mouse 2; Sample 7: CD45+ cells (immune cells) isolated from tumour from mouse 3; Sample 8: CD45+ cells (immune cells) isolated from dLN from mouse 3; Sample 9: CD45+ cells (immune cells) isolated from non-dLN from mouse 3. Sequencing reads were aligned to the mouse reference genome (mm10-1.2.0) using Cell Ranger (10x Genomics, v8.0.1). Quality control filtering was applied to exclude cells with low sequencing depth (<500 UMIs), low gene complexity (<200 detected genes), or high mitochondrial gene content (>20%).

first: Sumana

last: Sharma

first: Yuan

last: Lui

first: Martin

last: Fellermeyer

first: Edward

last: Jenkins


title: Dominant Malignant Clones Leverage Lineage Restricted Epigenomic Programs to Drive Ependymoma Development [snMultiome]

city: Memphis

first: Stephen

middle: C.

last: Mack

state: Tennessee

address: 262 Danny Thomas Place

institute: St. Jude Children’s Research Hospital

summary: ZFTA-RELA (ZR) is the most recurrent genetic alteration seen in pediatric supratentorial ependymoma (EPN) and is sufficient to initiate tumors in mice. Despite the oncogenic potential of ZR, it is observed nearly exclusively in childhood EPN, with tumors located distinctly in the supratentorial region of the central nervous system (CNS). We hypothesized that specific chromatin modules accessible during brain development would render distinct cell lineage programs at direct risk of transformation by ZR. To this end, we performed combined single nucleus ATAC and RNA (snMultiome) sequencing of the developing mouse forebrain, as compared to ZR-driven mouse and human EPN. We demonstrate that specific developmental lineage programs present in transient progenitor cells and regulated by PLAG/L family transcription factors (TF) are at risk of neoplastic transformation. Binding of this chromatin network by ZR or other PLAG/L family motif targeting fusion oncoproteins lead to persistent chromatin accessibility at oncogenic loci and oncogene expression. Cross-species analysis of mouse and human ZR EPN reveals significant cell type heterogeneity mirroring incomplete neurogenic and gliogenic differentiation, with a small percentage of cycling progenitor-like or radial glial-like cells that establish a putative tumor cell hierarchy. In vivo lineage tracing studies reveal neoplastic clones that aggressively dominate tumor growth and establish the entire EPN cellular hierarchy. These findings unravel developmental epigenomic states critical for fusion oncoprotein-driven transformation and elucidate how these states continue to shape tumor progression.

overall_design:
Human brain tumors, including PLAG/L fusion–associated tumors and ependymomas, were prepared for 10x Multiome (snATAC + snRNA) sequencing.

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

first: Hua

last: Sun

first: Alisha

middle: S

last: Kardian


title: Dominant Malignant Clones Leverage Lineage Restricted Epigenomic Programs to Drive Ependymoma Development

overall_design: ZFTA-RELA fusion mouse IUE models were prepared for TrackerSeq (scRNA) sequencing.


title: Dominant Malignant Clones Leverage Lineage Restricted Epigenomic Programs to Drive Ependymoma Development [10X Multiome]

type: Non-coding RNA profiling by high throughput sequencing

overall_design: The forebrains from a healthy mouse at E12.5,E16.5,E18.5,P0,P1,P6, and YAP1-Fusion mouse IUE models were prepared for 10xMultiome (snATAC + snRNA) sequencing.


title: Dendritic cells accelerate CAR T cells in irradiated tumors through chimeric synapses [CITE-seq]

first: Laszlo

last: Halasz

state: NY

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

summary: Sustaining Chimeric Antigen Receptor (CAR) T cell activity in the tumor microenvironment (TME) is a major challenge that continues to hinder the advancement of this therapy for solid tumors. Here we report dramatically enhanced longevity of CAR T cells targeted to irradiated orthotopic lung tumors, leading to durable control in a syngeneic mouse model. CAR T cells robustly infiltrated into irradiated tumors where they maintained elevated expression of cytotoxic effector genes and demonstrated enhanced cytotoxicity. Remarkably, enhanced CAR T cell persistence in irradiated tumors was critically dependent on dendritic cells through a surprising mechanism. Dendritic cells that underwent “antigen-dressing” of tumor-derived target antigens could activate CAR T cells through the chimeric receptor, while resident and infiltrating myeloid subsets that also underwent antigen-dressing did not, suggesting that DCs were unique amongst myeloid cells in the capacity to maintain CAR T cells. Furthermore, tumor irradiation did not enhance CAR T cell activity through depletion of tumor associated macrophages alone, as targeted depletion of CSF1R-dependent myeloid cells had no measurable impact on CAR T cell persistence or tumor control. Rather, these data indicate that tumor irradiation generates conditions conducive for CAR T cells and antigen-dressed dendritic cells to engage effectively. The discovery that a well-tolerated dose of radiation bolsters CAR T cell persistence in solid tumors marks a pivotal advance with significant translational potential, and demonstrates for the first time the indispensable role dendritic cells have in sustaining CAR T cell activity against solid tumors.

overall_design: CITE-seq of WT mouse lung immune cells (CD45+) treated with chemo (n=3) and chemo + radiotherapy (n = 5).

first: Ishibashi

last: Maki

first: Matthew

last: Park

first: Ahmed

last: Jalal

first: Sophia

last: Navarre


title: DNMT1 loss leads to hypermethylation of a subset of late replicating domains by DNMT3A (histone ChIP-seq)

first: Duncan

last: Sproul

overall_design:
This series contains histone ChIP-seq from human cancer cell lines. HCT116 cells and derivatives lacking DNMT1 were grown before chromatin was extracted and histone modification levels analysed by ChIP-seq.

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


title: Effect of CHOP deficicncy of PTPMT1KO regulatory T cells

city: Cologne

first: Mauro

last: Corrado

address: Joseph-Stelzmann-Str. 26

country: Germany

institute: University of Cologne

summary: CD4 T cells were isolated from Wt, PTPMT1 DT, CHOP KO and PTPMT1 DT CHOP DKO mice. Cells were activated in vitro and differentiated into regulatory T cells for 4 days. At this time point cells were harvested and analysed by proteomics.

overall_design: Four gorups of samples: Wt, PTPMT1 KO,  CHOP KO,  DKO Treg samples


title: Genome-wide association mapping for cardiomyocyte ploidy identifies Shroom3 as responsible for hyperpolyploidy and ventricular dilation [bulkRNA-Seq]

city: Milwaukee

first: Anooj

last: Arkatkar

state: WI

address: 8701 W Watertown Plank Rd.

department: Cell Biology, Neurobiology, and Anatomy

institute: Medical College of Wisconsin

summary: Cardiomyocyte (CM) polyploidy is widely observed across the animal kingdom and various ploidy states are associated with cardiac injury responses, including regeneration and heart failure. However, our understanding of the comprehensive mechanisms governing CM ploidy and its relationship with heart physiology has been hindered by a lack of experimental tools. To address this issue and uncover novel genetic regulators, we surveyed CM ploidy across a new genetic resource known as the Hybrid Rat Diversity Panel and founnd significant variation in ploidy phenotypes across the panel. Using select rat strains with divergent displays of CM ploidy, we found that hyperpolyploidization (≥8N) positively correlates with various physiological parameters namely left ventricular dilation and reduced ejection fraction. Genome-wide association mapping identified several loci significantly associated with frequency of hyperpolyploid CMs. Investigation of genes harboring damaging protein coding variants within these loci identified enrichment of cytoarchitectural genes, of which the ACTIN-binding protein, Shroom3, was found to be strongly and specifically expressed in CMs and harbors 7 damaging protein coding variants. CM-specific deletion of Shroom3 resulted in increased hyperpolyploidization and promoted left ventricular dilation and reduced ejection fraction. Furthermore, functional characterization of single nucleotide variants resulting in amino acid changes within SHROOM3 confirmed two protein coding variants that disrupted SHROOM3-ACTIN interaction and led to altered expression of cell cycle genes. This study elucidates the genetic determinants of CM ploidy phenotypes and solidifies a correlative relationship between CM ploidy and left ventricular function. Importantly, CM intrinsic expression of at least one gene mapped in this study, Shroom3, is confirmed to regulate CM hyperpolyploidization and cardiac function.

overall_design: RNA-seq profiling of neonatal rat ventricular cardiomyocytes (NRVCMs) transduced with GFP, Shroom3 1073S, or Shroom3 1073G adenovirus vectors

first: Alexandra

middle: L

last: Purdy

first: Amirala

middle: B

last: Nik

first: Prottoy

last: Hasan

first: Michael

last: Flinn

first: Priyanka

last: Choudhury

first: Cheyret

last: Wood

first: Akiko

last: Takizawa

first: Lynn

last: Malloy

first: Monika

last: Tutaj

first: Brian

last: Link

first: Timothy

middle: F

last: Plageman Jr

first: Anne

last: Kwitek

first: Melinda

last: Dwinell

first: Laura

last: Saba

first: Caitlin

last: O'Meara

first: Michaela

last: Patterson


title: Alveolar macrophages serve as an early viral sponge inducing long-lived functional enhancement

status: Public on Jun 01 2026

city: Iowa City

first: Jennifer

middle: Rachelle

last: Bermick

state: IA

address: 431 Newton Road, 505 EMRB

department: Pediatrics

institute: University of Iowa

summary: Respiratory syncytial virus infection results in chromatin accessibility changes in murine alveolar macrophages.

overall_design: ATACseq was performed on CD45+Ly6G-SiglecF+CD11c+ Tomato+ (directly RSV infected) and Tomato- (not directly RSV infected) murine alveolar macrophages 30 days following initial RSV infection.


title: Androgen activity in the male embryonic hindbrain drives lethal PFA ependymoma [mm_MF_Dev_scRNA_batch2]

city: Toronto

middle: D.

last: Taylor

state: Ontario

address: 555 University Ave

department: DSCB

country: Canada

institute: The Hospital for Sick Children

summary: In this study, we examine transcriptional sex differences between developing male and female hindbrain cells and their role in PFA pathogenesis, primarily in the poor prognosis of male patients.

overall_design: Male and female mouse hindbrain structures from 8 developmental stages were processed for single-cell RNA sequencing.


title: Androgen activity in the male embryonic hindbrain drives lethal PFA ependymoma [mm_FCG_scRNA_batch2]

overall_design: Four Core Genotype mouse cerebellum from 2 developmental stages were processed for single-cell RNA sequencing.


title: Genome-wide association mapping for cardiomyocyte ploidy identifies Shroom3 as responsible for hyperpolyploidy and ventricular dilation

first: Anooj

last: Arkatkar

summary: Cardiomyocyte (CM) polyploidization has been associated with cardiac injury responses, including regeneration and heart failure. However, our understanding of the comprehensive mechanisms governing CM ploidy and its influence on heart physiology has been hindered by a lack of experimental tools. To address this issue and uncover novel genetic regulators, we surveyed CM ploidy across a new genetic resource known as the Hybrid Rat Diversity Panel and find significant variation in ploidy phenotypes across the panel. Using select rat strains with divergent displays of CM ploidy, we found that hyperpolyploidization (≥8N) positively correlates with various physiological parameters namely left ventricular dilation and reduced ejection fraction. Genome-wide association mapping identifies several loci significantly associated with frequency of hyperpolyploid CMs. Investigation of genes harboring damaging protein coding variants identified enrichment of cytoarchitectural genes, of which the ACTIN-binding protein, Shroom3, was found to be strongly and specifically expressed in CMs and harbor 7 damaging protein coding variants. Indeed, CM-specific deletion of Shroom3 increased hyperpolyploidization in adult mice, while also promoting left ventricular dilation and reducing cardiac function. Furthermore, functional characterization of single nucleotide variants resulting in amino acid changes within SHROOM3 confirmed two protein coding variants that disrupted SHROOM3-ACTIN interaction. This study elucidates the genetic determinants of CM ploidy phenotypes and solidifies a relationship between CM ploidy and left ventricular function. Importantly, CM intrinsic expression of at least one gene mapped in this study, Shroom3, is confirmed to regulate CM hyperpolyploidization and cardiac function.

overall_design: Single nucleus RNA sequencing on nuclei extracted from ventricles of uninjured rat hearts at 8 weeks of age across 3 strains of the HRDP (BN-Lx, F344, and M520; N=2 hearts per strain)

first: Alexandra

last: Purdy

last: Bakhshiannik

last: O’Meara


title: Hijacking innate immunity to enhance mRNA therapeutics

city: Guangzhou

first: Shu

last: Meng

state: Guangdong

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Science Research

institute: Guangzhou National Laboratory

summary: The therapeutic success of in vitro-transcribed (IVT) mRNA depends on its stability and efficient translation. However, IVT mRNA is highly susceptible to immune-mediated degradation, limiting its efficacy. Here, we co-transfected IVT mCherry mRNA with immune suppressor M or SOCS1 mRNA in human umbilical vein endothelial cells (HUVECs) for 6h and 24h to explore whether hijacking innate immunity could enhance expression and half-life of IVT mRNA. Subsequently, RNA-seq was performed to investigate the transcriptomic changes in HUVECs after transfecting IVT mRNA. We sought to clarify the potential mechanism underlying degradation of IVT mRNA.

overall_design: HUVECs were transfected with IVT mCherry mRNA, IVT mCherry mRNA + Luc, IVT mCherry mRNA + M, and IVT mCherry mRNA + SOCS1, respectively. Then, HUVECS were collected at 6h and 24h after transfection. Control group was also included. We got three replicates for each time point and each group. Total RNA were extracted and subjected to rRNA depletion-based RNA-seq profiling.

first: Tinghong

last: Zhang

first: Jinling

last: Qin

first: Xing

last: Peng


title: Anatomical diversity of the adult corticospinal tract revealed by single cell transcriptional profiling.

city: New Haven

first: William

middle: Ben

last: Cafferty

address: 300 George Street

department: Neurology

institute: Yale University

summary: The corticospinal tract (CST) forms a central part of the voluntary motor apparatus in all mammals. Thus, injury, disease, and subsequent degeneration within this pathway result in chronic irreversible functional deficits. Current strategies to repair the damaged CST are sub-optimal in part due to underexplored molecular heterogeneity within the adult tract. Here we combine spinal retrograde CST tracing with single-cell RNA sequencing in adult male and female mice to index corticospinal neuron (CSN) subtypes that differentially innervate the forelimb and hindlimb.  We exploit publicly available datasets to confer anatomical specialization among CSNs and show that CSNs segregate not only along the forelimb and hindlimb axis but also by supraspinal axon collateralization. These anatomically defined transcriptional data allow us to use machine learning tools to build classifiers that discriminate between CSNs and cortical layer 2/3 and non-spinally terminating layer 5 neurons in M1, and separately identify limb specific CSNs. Utilizing these tools, CSN subtypes can be differentially identified to study postnatal patterning of the CST in vivo, leveraged to screen for novel limb-specific axon growth survival and growth activators in vitro, and ultimately exploited to repair the damaged CST after injury and disease.

overall_design: Adult corticospinal tract neurons (CSNs) were labeled via either bilateral intraspinal (cevical for forelimb, lumbar for hind limb) injection of retrogradeAAV-GFP, or via expression of tdTomato in rbp4-cre:Ai14 transgenic mice. FACS of marcodissected layer 5 of M1 regions differentiated CSNs (GFP or tdtomato+) from non-CSNs (controls) for single cell RNA sequencing.

first: Noa

last: Golan

first: Daniel

last: Ehrlich

first: James

last: Bonanno

first: Rory

last: O'Brien

first: Matias

last: Murillo

first: Sierra

last: Kauer

first: David

last: van Dijk


title: Effect of PTPMT1 deficiency on regulatory T cells

first: Mauro

last: Corrado

summary: CD4 T cells were isolated from Wt and PTPMT1 DT mice. Cells were activated in vitro and differentiated into regulatory T cells for 4 days. At this time point WT and KO cells were harvested and analysed by proteomics.

overall_design: Two gorups of samples: 4 Wt treg samples and 4 KO Treg samples


title: The Deubiquitinating Enzyme Otub2 Modulates Pancreatic Beta-Cells Function and Survival

city: Rehovot

first: Sima

last: Lev

address: 234 Herzl St.

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

summary: We have previously shown that otubain 2 (OTUB2), a deubiquitinating enzyme, inhibits caspase-3/7 activity in primary human islets; promotes insulin secretion and inhibits cytokine-induced nuclear factor-κB (NFκB) activity. In the present work we show that overexpression of Otub2 in MIN6 cells inhibits NFκB activity and the expression of its target genes MCP-1 and iNOS. Consequently, both the basal and the cytokine-induced apoptosis of cultured MIN6 cells and dispersed human islets were inhibited. Overexpression of Otub2 in MIN6 cells increase the mRNA levels of NKx6.1 and Glut2 and concomitantly increased glucose-stimulated insulin secretion (GSIS) (by 2-3-fold). The beneficial effects of Otub2 on β-cell function was demonstrated by the phenotype of   Otub2-/+ and Otub2-/- mice, which manifested impaired glucose tolerance and increased expression of NFkB target genes (e.g. IP-10, MCP-1 and IL-1b).  RNAseq analysis of pancreata derived from OTUB2 KO mice revealed reduced expression of genes that down regulate K+ transporters (e.g. Ank2, Cacna1a and Kcnab1) combined with an increase in oxidative phosphorylation related genes. Given that closure of K+ channels is crucial for insulin secretion, these results could account, at least in part, for the impaired GSIS in the OTUB2 KO mice. Indeed, mass-spectrometry analysis of proteins co-immunoprecipitated with Otub2 revealed the voltage-gated potassium channel subunit Kv9.3 as a major Otub2 binding-partner. Additional binding partners included the Peg3 and Camk2d proteins, which promote NFκB signaling and β-cell death. Hence, by deubiquitinating proteins in complexes that contain Peg3 and Camk2d, Otub2 might inhibit propagation of NFκB signaling and β-cell apoptosis. Collectively our findings implicate Otub2 as a key regulator of b cell function, mainly affecting NFkB signaling and the K+ channels that regulate insulin secretion.

overall_design: RNA sequencing was perfomed on RNA extracted from pancreas and liver of OTUB2 knock-out mice (homozygote, heterozygotes) and WT mice.

first: Yehiel

last: Zick

first: Michal

last: Oshri

first: Yaron

last: Vinik


title: Single cell multiome  atlas of pediatric ependymoma

first: Stephen

last: Mack

summary: ZFTA-RELA is the most recurrent genetic alteration seen in ependymoma, and sufficient to initiate tumors when expressed during mouse brain development. Despite ZFTA-RELA’s potent oncogenic potential, ZFTA-RELA gene fusions are observed exclusively in ependymoma and have never been documented in any other adult or pediatric malignancy. We hypothesized that specific chromatin modules accessible during brain development would render specific cells-of-origin at increased risk of transformation by ZFTA fusion proteins. To this end we performed integrated single cell ATAC and RNA-seq analysis (referred to as scMultimome) in mouse and human ependymoma tumors driven by the ZFTA-RELA fusion. We demonstrate that specific epi-developmental programs present in radial glia and regulated by Plagl1 are at direct risk of transformation. Oncoprotein engagement of this chromatin module leads to persistent oncogene expression, a failure to halt cellular proliferation, and initiate terminal cellular differentiation. Surprisingly, ependymomas exhibit significant heterogeneity across lineage differentiation programs, and continued activation of Plagl1 networks in differentiated cell types such as tumor neuronal-like cells contribute to tumor progression. These findings implicate specific chromatin modules in cells of origin as critical mediators of ependymoma initiation. Persistent activation and erosion of developmetn lineage programs serve as drivers of tumor development and contribute to the cellular heterogeneity of the tumor microenvironment.

overall_design: The forebrains from a healthy mouse at E14.5, a GBM mouse IUE model, and three ZFTA-RELA ependymomas mouse IUE models were processed for 10xMultiome (snATAC + snRNA) sequencing.

first: Hua

last: Sun

first: Alisha

last: Kardian


title: Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning

city: Amsterdam

first: Mikhail

last: Magnitov

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

summary: Most genetic variants in the human genome reside in non-coding regions, where they can perturb regulatory elements, influence gene expression, and contribute to various phenotypes and diseases. However, identifying such functionally relevant genetic variation remains challenging. Here we integrate personal genomics, allele-specific gene regulation, and deep learning predictions to map the impact of non-coding variation in its native allelic and regulatory context. We identify and validate hundreds of cell-type-specific transcription factor binding events disrupted by genetic variants, providing mechanistic insights underlying allele-specific gene regulation. Using this framework, we discover a rare variant that modulates PIK3R5 gene expression by disrupting an OCT2 binding site within a distal enhancer. Our study establishes a generalisable strategy for interpreting non-coding regulatory variation, enabling systematic dissection of variant effects across diverse biological systems and offering an alternative framework to investigate the disease mechanisms.

overall_design: 10X linked-reads sequencing, chromatin confirmation capture (Hi-C), chromatin accessibility (ATAC-seq), and gene expression (TT-seq) in GM12878 (NA12878), GM18983 (NA18983), HG01241, HG02601, and HG03464 lymphoblastoid cell lines.

first: Elzo

last: de Wit


title: Dendritic cells accelerate CAR T cells in irradiated tumors through chimeric synapses [RNA-seq]

city: New York

first: Laszlo

last: Halasz

overall_design:
To investigate the transcriptomic profiles of CAR T cells from irradiated tumors versus unirradiated tumors, we sorted CAR T cells from mice with established lung tumors, half that were irradiated before adpotive transfer and half that were unirradiated. The CAR T cells were further sorted into CD4+ CAR T cells and CD8+ CAR T cells. CD4+ CAR T cells sorted from the irradiated and unirradiated mice were pooled by treatment conditions due to lower cell count. CD8+ CAR T cells were left separated by mice, for a total of five samples from the irradiated group and five samples from the unirradiated group.
We then performed RNA-seq gene expression profiling analysis using data from five samples of CD8+ CAR T cells from the irradiated mice, five samples of CD8+ CAR T cells from the unirradiated mice, pooled CD4+ CAR T cells from five irradiated mice, and pooled CD4+ CAR T cells from the five unirradiated mice.
We then performed comparative gene profiling RNA-seq analysis was performed between CD8+ CAR T cell samples from five mice with irradiated tumors and CD8+ CAR T cell samples from five mice with unirradiated tumors; similarly, comparative analysis was performed between CD4+ CAR T cells from irradiated tumors and CD4+ CAR T cells from unirradiated tumors.

first: Ishibashi

last: Maki

first: Ahmed

last: Jalal

first: Sophia

last: Navarre


title: Androgen activity in the male embryonic hindbrain drives lethal PFA ependymoma [mm_FCG_scRNA_batch1]

first: Michael

last: Taylor


title: Androgen activity in the male embryonic hindbrain drives lethal PFA ependymoma [mm_MF_Dev_scRNA_batch1]


title: Recovery from Heart Failure: Microvascular Mechanisms

city: Boston

first: Krishan

last: Gupta

state: MASSACHUSETTS

address: 300 Longwood Avenu, Boston children's Hospital

institute: Boston Children's Hospital/Harvard Medical School

summary:
Background: Heart failure (HF) is a significant global health problem. Left-ventricular assist device (LVAD) implantation serves as a bridge for patients awaiting heart transplantation. Intriguingly, LVAD support often improves cardiac histology and function, sometimes enough to avoid transplantation after LVAD removal. However, the cellular programs underlying this recovery remain unclear.
Methods: Myocardial tissues were obtained from patients with HF at the time of LVAD implantation (pre-LVAD) and explantation (post-LVAD) for histological analysis and single-nucleus RNA sequencing (snRNA-seq). A murine model of HF recovery, combined with lineage tracing studies, was employed to define cellular sources of vascular repair. Cardiac function, fibrosis, and vascular density were assessed using echocardiography, histology, and fluorescent microsphere perfusion. A patient-derived cardiac non-myocyte culture system was established to interrogate mechanisms of cell-fate regulation.
Results: Post-LVAD myocardial tissues exhibited reduced fibrosis and increased capillary density compared to pre-LVAD samples. Across samples, fibroblast abundance inversely correlated with endothelial cell abundance, consistent with enhanced angiogenesis during recovery. SnRNA-seq identified a fibroblast subset predisposed to undergo mesenchymal-to-endothelial transition, acquiring an endothelial cell identity. Additionally, non-myocytes from pre-LVAD hearts proliferated poorly and failed to form vascular structures, whereas non-myocytes from post-LVAD hearts displayed greater proliferative and angiogenic capacity, forming vessel-like structures, reinforcing the association of HF recovery with angiogenic reprogramming. Mechanistically, knockdown of c-Myc by siRNA shifted post-LVAD non-myocytes to a pre-LVAD-like state, while c-Myc overexpression by mRNA in pre-LVAD cells induced a post-LVAD-like phenotype, implicating c-Myc as one contributor to this fate switch. A model of heart failure recovery in mice mimicked the histological and functional changes in patients, with physiological evidence of increased microvascular perfusion, associated with a fibroblast-to-endothelial transition documented by lineage tracing.
Conclusions: HF recovery involves reduced fibrosis and enhanced microvascularization, partly driven by fibroblast-to-endothelial cell fate transition. c-Myc functions as one regulator of this transition, offering a mechanistic entry point to develop regenerative therapies in HF.

overall_design: We isolated nuclei from frozen human heart tissue samples and constructed 3’ single cell gene expression libraries (Next GEM v3.1) using the 10x Genomics Chromium system. The libraries were sequenced with ~200 million PE150 reads per sample on Illumina NovaSeq. After sequencing, clean reads were analyzed with human reference genome GRCh38 using Cell Ranger v6.1.2. Introns were included in the analysis.

first: Rajul

middle: K

last: Ranka

first: Shuang

last: Li

first: Alexander

last: Lu

first: Keith

last: Youker

first: Kaifu

last: Chen

first: John

middle: P

last: Cooke


title: Expression data from CD4+CD25- T cells of VAVcreKeapfl/fl mice

status: Public on Mar 24 2026

city: Aachen

first: Christopher

middle: Thomas

last: Neullens

address: Pauwelsstraße 30, 52074

institute: RWTH Aachen University Medical Faculty

summary: The transcription factor NRF2 regulated oxidative stress responses. Deletion of Keap1 results in constitutive NRF2 activation. We analyzed the consequences of NRF2 activation for gene expression in T cells.

overall_design:
Genome-wide transcriptome analysis for VAVcreKeapfl/fl and WT CD4+CD25- T cells were performed using Gene Chip® Mouse Gene 2.0 arrays

**Submitters state that the complete processed data files were not available due to file loss.**

first: C

first: K

last: Ohl


title: Xenium spatial transcriptomic profiling of mouse lung following pharmacologic inhibition of lactate transport during fibrotic remodeling

city: Providence

first: William

last: Oldham

state: RI

address: 55 Claverick Street

department: Medicine

institute: Brown University

summary: Lactate transport is an important regulator of cellular metabolism and may contribute to fibroblast activation and extracellular matrix remodeling during pulmonary fibrosis. To define the spatial transcriptional landscape associated with pharmacologic inhibition of lactate transport during fibrotic lung remodeling, we performed spatial transcriptomic profiling of mouse lung tissue using the 10x Genomics Xenium Analyzer. Lung sections from mice with bleomycin-induced pulmonary fibrosis treated with inhibitors of monocarboxylate transport were analyzed using the Xenium Prime 5K Mouse Pan Tissue & Pathways panel to generate cell-resolved spatial gene expression maps. The resulting dataset provides spatially resolved transcriptional profiles across epithelial, stromal, endothelial, and immune compartments of the injured lung, enabling analysis of fibroblast activation states and spatial microenvironments associated with fibrotic remodeling.

overall_design: Pulmonary fibrosis was induced in C57BL/6N mice (10–12 weeks old) by intratracheal administration of bleomycin (1.2 U/kg). Beginning on day 7 after injury, mice received pharmacologic inhibition of lactate transport consisting of the MCT1 inhibitor AZD3965 (100 mg/kg twice daily) and the MCT4 inhibitor VB124 (30 mg/kg once daily) administered by oral gavage. Control animals received vehicle alone. Animals were sacrificed 21 days after bleomycin administration and lungs were harvested. The left lung was inflation-fixed and processed for formalin-fixed paraffin-embedded (FFPE) tissue preparation. Lung sections from eight samples were distributed across two Xenium slides to minimize batch effects. Slides were processed according to the Xenium Prime in situ gene expression workflow and hybridized with the Xenium Prime 5K Mouse Pan Tissue & Pathways panel. Spatial transcript detection and imaging were performed on the 10x Genomics Xenium Analyzer, and transcript coordinates were assigned to segmented cells to generate cell-level gene expression profiles for downstream analysis.

first: David

last: Ziehr

first: Fei

first: Ce

last: Gao

first: Sean

last: Prell

first: Kevin

last: Wei

middle: M


title: MECOM promotes leukemia progression and inhibits mast cell differentiation through functional competition with GATA2

city: Tokyo

first: Mayuko

last: Nakanishi

address: 4-6-1 Shirokanedai, Minato-ku

institute: The University of Tokyo

summary: MECOM is a transcription factor critical for the maintenance of hematopoietic stem cells (HSCs) and the pathogenesis of myeloid leukemia. Germline mutations clustered in the C-terminal zinc finger domain (ZFD) of MECOM are known to cause MECOM-associated syndromes, involving bone marrow failure and skeletal anomalies. However, the molecular consequences of these mutations and the precise downstream mechanisms of MECOM remain elusive. Here, we demonstrate that the C-terminal ZFD serves as the dominant DNA-binding module of MECOM, and that disease-associated mutations abrogate its DNA-binding capacity. Mechanistically, we reveal that MECOM functionally antagonizes GATA2 via C-terminal ZFD-mediated DNA binding and recruitment of the corepressor CtBP. This repression promotes myeloid leukemogenesis while suppressing mast cell differentiation. Furthermore, we generated a knockin mouse model harboring a C-terminal ZFD mutation, which successfully recapitulated the clinical phenotypes of MECOM-associated syndromes, including reduction of HSCs and B cells. Collectively, our findings define C-terminal ZFD mutations as loss-of-function mutations with impaired DNA binding, uncover the MECOM-GATA2 axis as a key regulatory pathway, and provide a valuable mouse model for understanding MECOM-associated syndromes.

overall_design: RNA-seq profiling of SLAM-LSK (CD150+, CD48-, Lineage-, ScaI+, cKiT+) cells derived from bone marrows of wild type or MecomWT/R751W C57BL6 mice.

first: Kohei

last: Iida

first: Susumu

last: Goyama


title: Spatial analysis revealed localization of osteblastogenesis-inhibitory factors in Giant Cell Tumor of Bone

city: Chuo-ku

first: Masaki

last: Shimada

state: Kumamoto

address: 1-1-1 Honjo

department: Department of Orthopaedic Surgery

institute: Kumamoto University

summary: Giant cell tumor of bone (GCTB) is an intermediate malignant tumor characterized by osteolytic lesions. Although surgical resection is the mainstay of treatment, the postoperative recurrence is frequently seen, and the tumor can arise in surgically challenging locations such as the pelvis. GCTB tumor cells are not giant cells, but rather stromal cells surrounding giant cells. However, currently available pharmacological therapies are limited to indirect inhibition of bone resorption by giant cells. The mechanisms underlying the marked osteolysis and the insufficient osteogenesis—despite the usual reactive stimulation of bone formation—remain poorly understood. In this study, we employed spatial transcriptomic approaches to visualize gene expression within the tumor microenvironment of GCTB. The resulting data, integrated with immunohistochemical analyses, revealed region-specific cellular distributions and characteristic gene expression patterns, providing new insights into the survival strategies of this tumor.

overall_design: The 5 µm section of the formalin-fixed paraffin-embedded (FFPE) tumor block was placed on a standard glass slide. Deparafinization, H&E staining and imaging were performed. After decrosslinking was conducted, probe hybridization and ligation were also performed.

first: Takeshi

last: Miyamoto


title: RbFox2 is a RhoBTB1-Cullin-3 Target in Vascular Smooth Muscle Regulating Arterial Stiffness through the Cytoskeleton

city: Wauwatosa

first: Ibrahim

last: Vazirabad

state: Wisconsin

address: 8915 W Connell Ave

department: Physiology

summary: The RhoBTB1-Cullin3 (CUL3) pathway in smooth muscle cells (SMCs) controls the ubiquitination of target proteins and through this blood pressure (BP) and arterial stiffness. We performed proximity labelling coupled with mass spectrometry to identify RhoBTB1 interacting partners in A7R5 SMCs. We identified 59 proteins which bound to the C-terminal half of RhoBTB1, the region identified as essential for its adapter function to deliver substrates to CUL3. We examined one of these proteins in detail - RbFox2. Co-immunoprecipitation validated the interaction of RbFox2 with RhoBTB1. Expression of RbFox2 was elevated in response to inhibition of the ubiquitination-proteasomal pathway, CUL3-deficiency, and RhoBTB1 inhibition by either siRNA or angiotensin II (ANG). RbFox2 was ubiquitinated in a RhoBTB1- and CUL3-dependent manner suggesting it is regulated through the RhoBTB1-CUL3-dependent ubiquitin-proteasome pathway. Inhibition of RbFox2 impaired the actin cytoskeleton in A7R5 cells and in primary SMC from RbFox2Flox mice and decreased the levels of globular and filamentous actin. ANG increased BP and arterial stiffness of RbFox2Flox mice, but the progression of arterial stiffness was halted after SMC-specific RbFox2 deletion despite a continued rise in BP. We conclude that RhoBTB1 and its target RbFox2 is an important regulator of arterial stiffness through its actions to regulate the cytoskeleton.

overall_design: A7R5 cells were grown in Dulbecco’s modified Eagle medium supplemented with 5% fetal bovine serum and 1% penicillin–streptomycin and maintained at 37°C with 5% CO2. The A7R5 cells were transfected with RbFox2 siRNA and matched scrambled control siRNA.

first: Gaurav

last: Kumar

first: Nisita

last: Chaihongsa

first: Daniel

middle: T

last: Brozoski

first: Daria

last: Golosova

middle: Y

first: Ko-Ting

first: Kelsey

last: Wackman

first: Ravi

last: Singh

first: Curt

last: Sigmund


title: An Optimised Translating Ribosome Affinity Purification (TRAP) Protocol for Low-Abundance Drosophila tissues

city: Cambridge

first: Alex

last: Whitworth

address: Hills road

department: MRC MBU

institute: University of Cambridge

summary: Localised protein translation, from subcellular localised mRNAs, has emerged as an important process of spatially-restricted cellular changes. This is especially important in cells with extremely elaborated architectures such as neurons. We present a highly sensitive TRAP protocol optimised for the specific isolation of ribosome-bound mRNAs in Drosophila from limited input samples, which enabled the isolation of axonal mRNAs from larval and adult (leg) motor neurons. RNA-seq revealed a set of axonally translated transcripts, including mRNAs encoding multiple ribosomal and mitochondrial proteins. Notably, these are among the types of transcripts found in axons of other species, indicating that axonal translation is conserved in Drosophila. Our optimised low-input TRAP method will allow the study of local translation to be explored in conjunction with Drosophila genetic manipulations, facilitating in-depth investigation of axonal translation across genetic backgrounds, developmental stages, and experimental conditions such as models of human disease. Moreover, it can be used for rare or genetically challenging genotypes and can be adapted to other tissues and model systems that may benefit from a sensitive TRAP protocol.

overall_design: Translating Ribosome Affinity Purification (TRAP) was used to identify neuronal mRNAs from Drosophila heads and axonal mRNAs from adult legs and larval motor neurons expressing Flag-GFP-RpL10 under DIP-γ-GAL4 (adult neurons) or OK371-GAL4 (larvae). Control genotype was UAS-Flag-GFP-RpL10/+. Three biological replicates were performed per condition (two for leg control).

first: Leonor

last: Miller-Fleming

first: Wing Hei

last: Au


title: Inference of cell-cell communication in human fetal liver from high definition spatial profiling using Renoir

city: Houston

first: Narein

last: Rao

state: Texas

address: 6100 Main St

department: Computer Science

institute: RICE University

summary: We developed Renoir, an algorithm for charting the ligand-target activities across a spatial topology. To validate this method, we generated 10x Genomics Visium HD datasets from human fetal liver samples (13 PCW and 14 PCW) and applied Renoir on these datasets. Renoir identified hepatocyte-macrophage interactions in these samples.

overall_design: Two fetal liver samples (FFPE) were used for the generation of 10x Genomics Visium HD datasets.

first: Ankur

last: Sharma

first: Archita

last: Mishra

first: Jerry

last: Chan

first: Florent

last: Jinhoux

first: Hamim

last: Zafar


title: Cellular stress-induced eccrine gland dysfunction as a potential mechanism in acquired idiopathic generalized anhidrosis

city: Hamamatsu

first: Tetsuya

last: Honda

address: 1-20-1 Handayama, Chuo-ku

institute: Hamamatsu University School of Medicine

summary: Acquired idiopathic generalized anhidrosis (AIGA) is a rare disorder characterized by systemic anhidrosis or hypohidrosis of unknown etiology. Corticosteroid pulse therapy is widely used for its treatment. We analyzed skin lesions from AIGA patients before and after corticosteroid pulse therapy through single-cell RNA sequencing analyses.

overall_design: Biopsies were taken from anhidrotic skin areas before corticosteroid therapy and from adjacent sweat-recovered areas after therapy.

first: Reiko

last: Kageyama

first: Keiko

last: Sakamoto

first: Satoshi

last: Nakamizo

first: Masahiro

last: Nakagawa

first: Kenji

last: Kabashima

first: Keisuke

last: Nagao


title: An Artemisia scoparia extract and rosiglitazone have distinct but overlapping effects on adipocyte function.

city: Baton Rouge

first: Jacqueline

last: Stephens

state: LA

address: 6400 Perkins Road

institute: Louisiana State University

summary: The effects of the PPAR-gamma agonist rosiglitazone (ROSI) on adipocyte gene expression have been extensively studied. Like ROSI, both SCO and a bioactive derivative, capillartemesin 7 (CAP7) inhibit lipolysis induced by the inflammatory cytokine TNF-alpha; they appear to do so through PPARg-dependent mechanisms that are overlapping but not identical to those engaged by ROSI. To compare the transcriptional effects of SCO, CAP7, and ROSI, we performed a comparative gene expression profiling analysis of RNA-seq data from fully differentiated adipocytes that were treated with DMSO vehicle, SCO, CAP7, or ROSI, in the presence or absence of TNFa. Gene ontology and pathway analyses were performed to provide guidance for developing additional hypotheses to investigate mechanism of action underlying the ability of SCO and CAP7 to reduce TNFa-induced lipolysis and affect overall adipocyte function.

overall_design: Fully differentiated 3T3-L1 adipocytes were treated with DMSO vehicle, SCO, CAP7, or the PPARgamma agonist, rosiglitazone (ROSI), in the presence or absence of TNFa. Four replicates per condition were included. ROSI was used as control to compare specific affects on PPARgamma target gene expression.

first: Anik

last: Boudreau

first: Allison

middle: J

last: Richard

first: Lindsey

last: Yoo


title: Killer cell immunoglobulin-like receptors delineate distinct phenotypes and functions in human γδ T cells [RNA-seq]

city: Ottawa

first: Alexandre

last: Blais

state: ON

address: 451 Smyth Road

institute: University of Ottawa

summary: Killer cell immunoglobulin-like receptors (KIRs) are a diverse family of HLA class I-specific receptors that shape immune responses, primarily through NK cells. Beyond NK cells, subsets of T cells, notably γδ T cells, express KIRs, but their roles remain unclear. Here, we demonstrate that KIR⁺γδ T cells are significantly more abundant in CMV-seropositive healthy adults, particularly within the Vδ2⁻ subset. These cells exhibit a TEMRA phenotype, are predominantly CD16⁺CD57⁺, hallmarks of a highly differentiated state, and express multiple NK cell-associated receptors. KIR+γδ T cells display enhanced cytotoxic potential, with higher levels of granzyme B and perforin than their KIR- counterparts. Using Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and transcriptional analyses, we show that KIR- and KIR+ γδ T cells reveal distinct molecular signatures, with KIR+γδ T cells transcriptionally and epigenetically aligning with terminally differentiated effector memory T cells, while KIR- cells retain a naïve-like phenotype. These findings suggest that CMV infection drives the differentiation of γδ T cells into potent, KIR-expressing cytotoxic effectors. This adaptive mechanism may bolster immune defense while maintaining self-tolerance, highlighting a previously unappreciated role for KIRs in shaping γδ T cell immunity.

overall_design: Peripheral blood KIR- and KIR+ γδ T cell subsets from healthy adult humans were separately sorted using flow cytometry. Total RNA was then extracted and subjected to short-reads high-throughput sequencing. Six biological replicates for each subset were profiled.

first: Mahya

last: Razmi

first: Yeganeh

last: Almasi

first: Marilee

last: Larrivée

first: Jonathan

last: Angel

first: Zakia

last: Djaoud


title: Killer cell immunoglobulin-like receptors delineate distinct phenotypes and functions in human γδ T cells [ATAC]

overall_design: Peripheral blood KIR- and KIR+ γδ T cell subsets from healthy adult humans were separately sorted using flow cytometry. ATAC-seq libraries were then prepared using the OMNI-ATAC protocol descibed by Corces et al (Nature Methods, 2017). Six biological replicates for each subset were profiled.


title: Elimination of senescent cells with senolytic host-directed therapy reduces tuberculosis progression in mice.

city: Baltimore

first: Somnath

last: Shee

state: MD

address: 1550 Orleans St, CRB2 Building, Room-176

department: Medicine, Infectious diseases

institute: Johns Hopkins University

summary: By eliciting lung necrosis, which enhances aerosol transmission, Mycobacterium tuberculosis (Mtb) sustains its long-term survival as a human pathogen. In studying the necrotic granuloma lesions unique tocharacteristic of Mtb-infected B6.Sst1S mice, we found that lung myeloid cells display elevated senescence markers including cell cycle arrest proteins p21 and p16, the DNA damage marker γH2A.X, senescence-associated β-Galactosidase activity, and senescence-associated secretory phenotype (SASP) proteins. These same markers were also elevated in Mtb-infected aged wild type (WT) mice but not in young WT mice. Global transcriptomics data revealed activation of pro-survival (PI3K, MAPK) and anti-apoptotic pathways in TNFα- treated and Mtb- infected B6.Sst1S BMDMs. As senescent cells have been postulated shown to be long-lived, non-dividing cells which release tissue damaging signaling molecules, we treated Mtb-infected mice with a cocktail of three senolytic drugs (dasatinib, quercetin, and fisetin) designed to kill senescent cells. Senolytic drug treatment prolonged survival and reduced Mtb lung counts in B6.Sst1S and aged WT mice to a greater degree than young WT mice and concomitantly reduced lung senescence markers. These findings indicate that (1) Mtb infection may induce lung myeloid cells to enter a senescent state and that these cells play a causal role in disease progression, and (2) Senolytics merit consideration for human clinical trials against tuberculosis (TB)Senolytics should be tested in human clinical trials against TB.

overall_design: To compare the gene expression in stressed bone marrow- derived macrophages (BMDMs) from young B6.Sst1S mice (female; 8-12 weeks old) relative to young WT C57BL/6 (B6)- BMDMs, we performed bulk RNA- sequencing on BMDMs subjected to (1) 10 ng/ml TNFα treatment (48 hours only), and (2) Mtb H37Rv (MOI=10; 24 hours) infection only.

first: Wiiliam

last: Bishai


title: Resistance to neoadjuvant talazoparib in triple-negative breast cancer mediated by BRN2-induced ATR/STAT3 pathways or Shieldin 2 subclone expansion

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

summary: Intrinsic and acquired resistance to poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) remains a major barrier in treating homologous recombination (HR) repair-deficient tumors, including those with germline or somatic BRCA1/2 mutations. Although PARPi are FDA approved for adjuvant treatment of locally advanced or metastatic breast cancer in patients with germline BRCA1/2 mutations, emerging data support their use as monotherapy in the neoadjuvant setting. Promising safety profiles of newer-generation PARPi further support this potential. However, resistance mechanisms specific to the neoadjuvant setting are poorly understood. To address this gap, we leveraged resources from a phase II neoadjuvant clinical trial (NCT03499353), analyzing tumors from patients with germline BRCA1/2 mutant  breast tumors before and after six months of talazoparib monotherapy. Whole-transcriptome analyses were performed on these samples. Additionally, we established orthotopic patient-derived xenograft models from a subset of the patient tumors and conducted whole-exome and whole-transcriptome analysis. This integrative approach revealed both known and novel PARPi resistance mechanisms. In one case, overexpression of BRN2, encoding a transcription factor that plays a critical role in neurogenesis, led to activation of ATR/RAD51 and STAT3 pathways, restoring homologous recombination  (HR) repair. BRN2-driven resistance could be reversed with ATR and STAT3 inhibitors, resensitizing cells to talazoparib. In another, an HR repair proficient tumor subclone lacking Shieldin 2 expression expanded during treatment and accounted for intrinsic resistance. Our findings highlight the need to determine intrinsic and anticipate acquired resistance pathways in treatment-naïve tumors and support combining PARPi with targeted agents to improve outcomes in the neoadjuvant setting.

overall_design:
RNA-Seq profiling of PDX tumors established from breast cancer tumors from patients with germline BRCA mutations, before and after treatment with PARP inhibitor.

***************************************************************
These samples are derived from patient tissue, and we do not have consent to share the raw sequence data in a database that is not controlled  access.
***************************************************************

first: Noor

last: Abdulkareem

first: Yan

last: Jiang

first: Yuan

last: Qi

first: Xuan

last: Liu

first: Xiaomei

last: Zhang

first: Shirong

last: Cai

first: Jiansu

last: Shao

first: Sabrina

last: Jeter-Jones

first: Amanda

last: Rinkenbaugh

first: Chun-Chun

last: Cheng

first: Faiza

last: Hancock

first: Jill

last: Schwartz

first: Jennifer

last: Litton

first: Helen

last: Piwnica-Worms


title: Elimination of senescent cells with senolytic host-  directed therapy reduces tuberculosis progression in mice

first: Somnath

last: Shee

overall_design: To compare the gene expression in stressed bone marrow- derived macrophages (BMDMs) from young B6.Sst1S mice (female; 8-12 weeks old) relative to young WT C57BL/6 (B6)- BMDMs, we performed bulk RNA- sequencing on BMDMs subjected to 10 ng/ml TNFα pretreatment (18 hours), followed by Mtb H37Rv (MOI=10; 24 hours) infection in the continued presence of TNFα.


title: RNA N6-Methyladenosine (m6A) regulates cell cycle progression in Diffuse Midline Glioma (DMG) and confers sensitivity to FTO inhibition

city: Sydney

first: Samuel

middle: Ernest

last: Ross

state: NSW

address: The University of Sydney

country: Australia

institute: The University of Sydney

summary: The epitranscriptome has not previously been evaluated in DMG. Given the pivotal role of m6A in normal OPC biology, investigating its dysregulation in DMG could uncover new therapeutic options and improve our understanding of the disease's underlying mechanisms. Here, for the first time, we perform direct RNA-sequencing on patient-derived DMG cultures to generate transcript and base-resolution m6A landscapes of DMG. Furthermore, we interrogate the therapeutic benefits of  the Fat mass and obesity associated (FTO) player inhibitor FB23-2 in DMG using direct RNA sequencing and RNA sequencing

overall_design: To investigate the m6A landscape of DMG, we have peformed direct RNA-sequencing on normal patient cells, SU-DIPGXIII, SU-DIPGXVII, and FB23-2 treated SU-DIPGXVIII cultures. Additionally, to investigate the effects of FTO inhibition, we have peformed RNA sequencing on SU-DIPGXIII, SU-DIPGXVII, and HSJD-DIPG007 cultures after 24 hour treatments with DMSO or FB23-2 at ~IC50 concentration.

middle: E


title: Therapeutic reactivation of hippocampal progenitors reverses cognition decline in progressive brain demyelination

city: Winnipeg

first: Soheila

last: Karimi

state: Manitoba

address: 745 Bannatyne Avenue

department: Physiology and Pathophysiology

institute: University of Manitoba

summary: Chronic brain demyelination and neurodegeneration are pathological hallmarks of progressive multiple sclerosis (MS) that underlie cognitive impairments. Neural precursor cells (NPCs) that reside in the hippocampus support cognition through adult neurogenesis. However, with MS chronicity, hippocampal neurogenesis declines that results in memory and learning impairments. Currently, the underlying mechanisms that drive NPC senescence in chronic MS are largely unknown. Here, we have linked downregulation of Neuregulin-1beta 1 (Nrg-1β1) to hippocampal neurodegeneration, neurogenic decline and memory impairment in mice with chronic brain demyelination. Nrg-1β1 is a key factor for neural differentiation that we previously reported its downregulation in chronic human MS lesions. Here, extensive in vivo and in vitro characterizations revealed that therapeutic restoration of Nrg-1β1 can reactivate NPCs and foster hippocampal repair by neurogenesis, synapse reassembly and remyelination that reverses memory impairments. Transcriptomics of NPC progenies confirmed upregulation of genes associated with myelination, synaptic resilience, and cellular homeostasis, underscoring the potential of Nrg-1β1 in activating regenerative mechanisms within the chronically demyelinated hippocampus. Moreover, in comparison with Siponimod, a leading disease modifying therapy for secondary progressive MS, Nrg1β1 treatment achieved multifaceted and greater reparative effects. These new findings introduce Nrg1β1 as a disease relevant candidate with promising therapeutic potential for progressive MS.

overall_design: The samples are hip-NPC (GFP+)  isolated from hippocampus of mice using magnetic-activated cell sorting (MACS). Each sample is the result of one mouse brain. The treatment groups include: 1- Cuprizone for 10 weeks + 4 weeks of spontaneous recovery period (Vehicle) (0.1% BSA in saline) treatment. 2-  Cuprizone for 10 weeks + 4 weeks of recovery period and Neuregulin 1 beta 1 (60µg/kg/day) treatment.


title: A hierarchical Rorc(γt) cis-regulatory cascade orchestrates differentiation of RORγt⁺ innate immune cells [BulkRNA-seq_ChILP]

city: Fukuoka

first: Shinichiro

last: Sawa

address: 3-1-1 Maidashi, Higashiku

institute: Kyushu University

summary: Although ILC3s are known to differentiate in RORγt-dependent manner, besides ILC3s, RORγt-dependent developmental program is shared among several lymphocytes.However, little is known about the regulatory mechanism of RORγt expression specific to ILC3s. Our data newly idetified cell lineage-specific and two-step regulation of RORγt expression in ILC3 including LTi cells.

overall_design: To confirm the maturation of LTi cells with the upregulation of RORγt expression, we performed Bulk-RNA seq on LTi progenitor cells sorted from the E14.5 fetal liver based on their levels of RORγt expression. Additionally, we further subdivided the RORγt high population based on the expression of CD127 and MHC class II to confirm their heterogeneity

first: Takuma

last: Fukui

first: Miyuki

last: Watanabe

first: Satoshi

last: Kojo

first: Eriko

last: Sumiya


title: A hierarchical Rorc(γt) cis-regulatory cascade orchestrates differentiation of RORγt⁺ innate immune cells [scRNA-seq]

overall_design: To confirm the maturation of LTi cells with the upregulation of RORγt expression, we performed scRNA seq on LTi progenitor cells sorted from the E14.5 fetal liver based on their levels of RORγt expression.


title: Deciphering lineage decision of hematopoietic stem cells at homeostasis and aging

city: Chengdu

first: Yujun

last: Deng

address: No. 17, Section 3, Renmin South Road, Chengdu

institute: Sichuan University

summary: To revealed the mechanism of long-term hematopoietic stem cells (LT-HSCs) lineage decision and bias during aging, we applied scRNA sequencing with three sub-clusters within the compartment in different age groups, namely CD150hiSca1hi LT-HSCs, CD150hiSca1lo LT-HSCs and CD150lo LT-HSCs. These three LT-HSC subsets encompass a spectrum of lineage specification and commitment cell states, which were further segregated into 6 different clusters. Characterization of the self-renewal capacity and lineage potential of the quiescence HSC subpopulation by transplantation assays revealed the identity of bona fide HSC (Meg3+-HSC), which expanded dramatically started at middle-age, with dynamic transcriptional activities associated with protein modification and platelets activation.

overall_design: For 10x scRNA-seq or CITE-seq, CD150hi Sca1hi, CD150hi Sca1lo, and CD150lo LT-HSC from mice of different ages were sorted by using FACS AriaTM III sorter.

first: Ni

last: Wei

first: Huiwen

last: Zhan

first: Min

last: Liu

first: Pengbo

last: Guan

first: Yusi

last: Xie

first: Lunzhi

last: Dai

first: Hongbo

last: Hu

first: Huiyuan

last: Zhang


title: RNA-seq analysis of human NSCLC cell lines treated with 9α,11α-dihydroxy-kaurenoic acid (AL-X)

status: Public on Mar 23 2026

city: Taichung

first: Po-Chen

last: Chu

address: No. 100, Sec. 1, Jingmao Rd., Beitun Dist.

country: Taiwan

institute: China Medical University

summary: Non-small cell lung cancer (NSCLC) remains a leading cause of cancer-related mortality worldwide. In this study, we performed bulk RNA sequencing to investigate the transcriptomic effects of 9α,11α-dihydroxy-kaurenoic acid (9α,11αOH-KA, also referred to as AL-X) in human NSCLC cells. A549, HCC827, and H1975 cell lines were treated with 10 μg/mL 9α,11αOH-KA or vehicle (DMSO) for 48 hours. Total RNA was extracted and subjected to paired-end sequencing using the Illumina platform. This dataset provides a comprehensive resource for understanding the molecular mechanisms underlying mitochondrial dysfunction and anti-cancer effects induced by 9α,11αOH-KA in NSCLC.

overall_design: Three human NSCLC cell lines (A549, HCC827, and H1975) were treated with DMSO (control) or 10 μg/mL 9α,11αOH-KA for 48 hours. Total RNA was extracted and used for library preparation and paired-end RNA sequencing (Illumina platform).

first: Yu-Chi


title: Single-cell RNA-seq profiling of the DHT-induced androgenetic alopecia (AGA) mouse model treated with anti-DKK3 antibody

city: Incheon

first: Jong-Hyuk

last: Sung

address: 32 Songdogwahak-ro

country: South Korea

institute: Epi Biotech Co., Ltd.

summary: Androgenetic alopecia (AGA) is characterized by progressive hair follicle miniaturization and remodeling of the skin microenvironment. To investigate cellular changes associated with AGA and the effects of DKK3 blockade, we performed single-cell RNA sequencing (scRNA-seq) of dorsal skin from a DHT-induced mouse model. Three experimental groups of male C3H/HeN mice were analyzed: vehicle control, DHT-treated AGA model, and DHT-treated mice receiving anti-DKK3 neutralizing antibody. Single-cell transcriptomic profiling identified cell population changes associated with DHT exposure and their modulation by anti-DKK3 treatment. This dataset provides a single-cell atlas of dorsal skin in the AGA model and following DKK3 inhibition.

overall_design: Dorsal skin samples were collected from three groups of male C3H/HeN mice: vehicle control, DHT-treated AGA model, and DHT-treated AGA model with anti-DKK3 neutralizing antibody.

first: Minsoo

last: Noh

first: Seungchan

last: An

first: Hyunju

last: Kim

first: Mei

last: Zheng

first: In Guk

last: Park

first: Leegu

last: Song


title: Nuclear Speckle Dynamics are Controlled by Polyphosphate Inhibition of CLK Proteins

city: Sant Cugat del Vallés

first: Samuel

last: Bru

state: Barcelona

address: Josep Trueta, s/n

department: Biomedical Sciences

country: Spain

institute: Universitat Internacional de Catalunya

summary: Nuclear speckles (NS) are membrane-less nuclear organelles that act as critical hubs for pre-mRNA splicing. Defects in splicing are linked to several human diseases, including cancer, Alzheimer's disease, and dystrophies. While CLK kinases regulate the mobilization of splicing factors from NS, the molecular mechanisms underlying NS assembly and dissolution remain unclear. Using an adaptation of the Biotinylation by Antibody Recognition (BAR) technique, we identified polyphosphate (polyP) as a novel and essential regulator of NS dynamics. Polyphosphate, a highly conserved polyanion composed of a chain of phosphate molecules, is involved in several functions in mammalian cells. Here, we show that polyP interacts with the NS core component SRRM2, and its depletion disrupts NS organization releasing splicing factors into the nucleoplasm. RNA-seq analysis reveals that polyP depletion increases exon exclusion, particularly in transcripts with multiple isoforms, highlighting its role in splicing regulation. Mechanistically, we demonstrate that polyP acts as a physiological inhibitor of CLK3 kinase, preventing the phosphorylation of SR proteins and thereby maintaining NS stability. Our findings not only expand our understanding of NS biology but also provide new insights into the polyP involvement in splicing-related diseases.

overall_design: This study investigates the transcriptomic changes in HEK293T cells under two different experimental setups: overexpression and knockdown. In the first group, cells were transfected with either an empty pWPI plasmid (control) or pWPI vectors carrying NUDT3, PRUNE1, or CLK3 (n=4 replicates per condition). In the second group, cells were transfected with siScramble (control) or siSRRM2 (n=2 replicates per condition). All cells were harvested 48 hours post-transfection for total RNA extraction. Sequencing was performed by Macrogen using the Illumina NovaSeq 6000 platform, generating 150 bp paired-end reads with a depth of approximately 100 million reads per sample.

first: Blanca

last: Lázaro

first: Francisco

last: Tadeo

first: Andrea

last: Rodríguez

first: Lucía

last: Ayuso-Molina

first: Joan

last: Martínez-Láinez

first: Eva

last: Quandt

first: Maribel

last: Bernard

first: Filipy

last: Borghi

first: Adolfo

last: Saiardi

first: Jonàs

last: Juan-Mateu

first: Javier

last: Jiménez

first: Josep

last: Clotet


title: Promoter mutagenesis and a massively parallel reporter screen of the MAPT locus identifies cis-regulatory elements and genetic variation effects

city: Huntsville

first: Jesse

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

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

overall_design: Refer to individual Series

first: Nicholas

first: Rebecca

last: Hauser


title: WTAP tetramer ensures m⁶A writer assembly and faithful mitosis

city: Anhui

first: shan

last: zhang

address: No. 443, Huangshan Road

institute: University of Science and Technology of China

summary: The m6A methyltransferase complex (“writer”) regulates mRNA stability and translation, but how its assembly is orchestrated remains incompletely understood. Wilms’ tumor 1-associating protein (WTAP) is a conserved regulatory subunit essential for m⁶A deposition and cell proliferation, yet its structural organization and mechanistic contributions remain elusive.Our live-cell imaging demonstrates that WTAP is required for accurate chromosome segregation, and MeRIP-seq analysis identifies WTAP-dependent m⁶A regulation as a critical determinant sustaining the expression of mitotic regulators, including KIF20A. Together, our study defines a tetrameric scaffold function for WTAP that is essential for writer complex integrity and highlights its pivotal role in linking m⁶A methylation to cell cycle progression.

overall_design: We performed MeRIP sequencing to identify genes related to cell growth and chromosome segregation whose m6A modifications are regulated by WTAP knockdown in comparison to the control group


title: Effect of TRAP-1 and control compounds on gene expression in BxPC-3 cells

city: Palo Alto

first: Steven

last: Corsello

state: California

address: 240 Pasteur Drive

department: Stanford School of Medicine

institute: Stanford University

summary: TRAP-1 is a transcriptional activator of p53. To determine the downstream effects of TRAP-1 on gene expression, we perfromed mRNAseq on BxPC-3 cells treateted with the drug, negative controls, and positive controls.

overall_design: BxPC-3 cells were seeded into a 6-well plate (5x10^5 cells / well), cultured overnight, treated with the indicated compounds for either 2 or 4 h, and harvested with TRIzol (Invitrogen). Total RNA was extracted using the Direct-zol RNA MicroPrep kit (Zymo Research) according to the manufacturer's instructions. For sequencing library preparation, polyA-containing transcript were enriched, prepared into paired-end libraries, and sequenced on an Illumina NovaSeq using paired-end 150-bp read length by Novogene. Gene-level expression was quantified from RNA-seq using the nf-core/rnaseq pipeline (version 3.18.0). Salmon (version 1.10.3) was used to generate gene-level read counts.

first: Nick

middle: A

last: Phillips

first: Xijun

last: Zhu


title: Restoration of lysosomal membrane integrity in cell models of Pompe disease depends on fatty acid synthase and its product palmitic acid

city: Paris

first: Ganna

last: Panasyuk

address: 156-160 Rue Vaugirard, Faculté de Médecine Paris Descartes,, 4th Floor - Lab-408/Office-404,, 4th Floor - Lab-408/Office-404,

country: France

institute: Inserm U1151/CNRS UMR 8253, Necker Enfants Malades Institute (INEM)

summary: Lysosomal storage disorders (LSDs) are rare inherited diseases caused by mutations in lysosomal proteins, leading to substrate accumulation and lysosomal dysfunction. Whether this build-up compromises lysosomal membrane integrity remains an open question. In this study, we aimed to investigate the presence of lysosomal membrane damage in LSD cells and to identify mechanisms that could reveal potential therapeutic strategies for amelioration of cellular physiology. Methods: Primary skin fibroblasts from Pompe disease patients were used to evaluate lysosomal integrity and function. Pharmacologic and metabolite treatments were applied in loss-of-function and rescue analyses, and transcriptomics analysis was done under these conditions. Results: In Pompe disease, caused by mutations in the acid alpha-glucosidase gene, glycogen accumulation, palmitate treatment improved lysosomal function in fibroblasts from patients, with no significant effect at transcriptional level. Conclusions: These findings open to novel therapeutic opportunities for improvement of lysosomal function through development of treatments that target fatty acid metabolism.

overall_design: Skin fibroblasts of a Pompe disease patient were treated for 24 hours with BSA-palmitate (200 µM) compared to treatment by fatty acid-free BSA (BSA), followed by PE-100 Poly-A enriched RNA-seq  (n=2-3 replicates).

first: Edouard

last: Le Guillou

first: Arianna

last: Segaloni

first: Alexis

last: Gadault

first: Nathaniel

last: Henneman

first: Min

last: Su

first: Ivan

last: Nemazanyy

first: Catia

last: Oliveira Dias

first: Nesrine

last: Hifdi

first: Valérie

last: Nivet-Antoine

first: Michael

last: Laemmerhofer

first: Karim

last: Hnia

first: Catherine

last: Caillaud


title: RNF25 confers tolerance to azacytidine-induced mRNA damage by curbing activation of the integrated stress response [TTchem-seq]

city: Munich

first: Julian

last: Stingele

address: Butenandtstraße 1

institute: LMU Munich

summary: Excessive RNA damage activates cellular stress responses, triggering cell death. However, pathways that negatively regulate RNA damage responses are largely uncharacterized. Using genetic screens, we here find that the ubiquitin ligase RNF25 provides tolerance to RNA damage caused by the nucleoside analogue azacytidine, a chemotherapeutic agent used to treat acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). Mechanistically, azacytidine is incorporated into mRNA, where it causes lesions that stall elongating ribosomes , leading to cytotoxic activation of the GCN2-dependent integrated stress response (ISR). RNF25 prevents ISR hyperactivation by ubiquitylation of ribosomal protein eS31, suppresses cell death upon azacytidine tretament. Our study reveals an mRNA damage tolerance mechanism that determines cellular survival in response to azacytidine, highlighting RNA damage-induced stress response as a potentially critical component of chemosensitivity in AML and MDS.

overall_design: TT-chem Seq with HAP1 cells treated or not for 1h or 5h with 1uM RNAPI inhibitor  (BMH-21), 100uM RNAPII inhibitor (DRB) or 20uM RNAPIII inhibitor (ML-60218).

first: Diana

last: van den Heuvel

first: Martijn

last: Luijsterburg

first: Marlis

last: Fischaleck

first: Alexander

last: Graf

first: Stefan

last: Krebs


title: RNF25 confers tolerance to azacytidine-induced mRNA damage by curbing activation of the integrated stress response [RNA-seq]

overall_design: RNA-Seq with HAP1 AAVS1, RNF25 KO, GCN2 KO, RNF25 GCN2 DKO, ZNF598 KO and eS31 K113R cells treated or not with azacytidine or halofuginone.

first: Carla

last: Engel

first: Shubo

last: Zhao

first: Julia

last: Philippou-Massier


title: RNF25 confers tolerance to azacytidine-induced mRNA damage by curbing activation of the integrated stress response [Ribo-seq]

overall_design: Ribo-Seq with HAP1 WT cells pre-treated with 1 µM GCN2i for 1 h, followed by 2 h treatment with 20 µM aza-C and GCN2i and 2 h recovery with GCN2i.

last: Bagaric

first: Jonathan

last: Bohlen