title: Transport stress induces immune dysregulation and exacerbates Mycobacterium tuberculosis infection in mice

city: wuhan

first: xiaojuan

last: gou

address: 1 Shizishan Street, Hongshan District, Wuhan City, Hubei Province

department: College of Veterinary medicine

institute: Huazhong Agricultural University

summary: While transport stress (TS) is a well-known factor impacting immune function and infection, its cellular and molecular mechanisms remain elusive. In this study, we investigated the effects of TS on immune responses and its role in exacerbating Mycobacterium tuberculosis (Mtb) infection in mice. Behavioral assessments revealed that TS induced anxiety-like behaviors in mice. Concomitantly, TS disrupted hypothalamic-pituitary-adrenal (HPA) axis homeostasis, altered hormone secretion patterns, and led to dysregulation of stress response genes (Egr1, Fos) and circadian regulators (Dbp, Per3). Single-cell RNA sequencing of the spleen revealed severe immune dysfunction, characterized by inhibition of Th17 differentiation, IL-17 signaling, and antigen presentation. Importantly, TS affects the crosstalk between the HPA axis and the spleen through ligand-receptor interactions, such as Pomc-Oprm1 and Gdf15-Tgfbr2. Furthermore, TS exacerbated the severity of Mtb infection, increased bacterial loads in the lungs and spleen, and attenuated infection-induced upregulation of immune genes (Tnfα, Il12b). Mechanistically, TS impairs adaptive immunity (Th1/Th2 differentiation) while amplifying neurotransmitter-related signaling, ultimately compromising host defenses. These findings highlight TS as a key contributor to neuroendocrine immune dysregulation, leading to increased susceptibility to infection. Addressing stress-related immune dysfunction may be crucial for improving outcomes in tuberculosis and other infectious diseases.

overall_design:
Research Objective
This study aims to investigate the effects of transport stress on immune regulation in mice and its role in the progression of Mycobacterium tuberculosis infection, and to reveal how stress-induced immune dysregulation exacerbates the pathological progression of tuberculosis.

Bacteria strains
Mycobacterium tuberculosis H37Ra was cultured at 37°C under static conditions in Middlebrook 7H9 broth (Becton Dickinson, New Jersey, USA, 271310) supplemented with 10% oleic albumin dextrose catalase (OADC, Becton Dickinson, New Jersey, USA), 0.05% Tween 80, and 0.5% glycerol or on solid Middlebrook 7H11 agar plates (Becton Dickinson, New Jersey, USA) supplemented with 10% OADC and 0.5% glycerol. For mouse immunization, H37Ra cultures were centrifuged at 3,000 g for 10 min to pellet the bacteria. The pellet was resuspended in PBS to achieve 3×106 bacteria/mL and passed through an insulin syringe several times to disperse the bacteria.

Animals
Male C57BL/6 mice, aged 4-6 weeks and weighing 18–20 g, were purchased from Huazhong Agricultural University Experimental Animal Center. The mice were group-housed (5 per cage) in polycarbonate cages with free access to food and water under a 12 h light/dark cycle at 22-25°C and 50-70% of relatice humidity. The C57BL/6J mice were divided into four groups (control, TS, Mtb, and Mtb+TS groups), with 10 mice in each group. The control group was immunized with PBS and not subjected to restraint stress (TS). The Mtb group was immunized with H37Ra and not subjected to TS. The TS group was immunized with PBS and subjected to TS. The Mtb_TS group was immunized with H37Ra and subjected to TS (Fig 1 and Fig 4).All procedures complied with NIH guidelines (NIH Publication No. 85-23) and were approved by the Huazhong Agricultural University Ethics Committee (HZAUMO-2023-0234). Experimenters were blinded to group assignments throughout behavioral assessments.

TS in mice
Mice were subjected to daily transport stress stimulations for 8 consecutive days (3 h;8:30to 11:30)using standardized restraint procedures.Minimal handing was used to insert a group of 10 mice into the restraint device, consisting of a closed transparent 500 mL plastic bottle, to restric its activity. Large breathing holes around the bottle provide adequate ventilation. The bottles containing the mice were transferred to a temperature-controlled shaker and shaken at 90-120 rpm/min at 35-36 °C. The mice were dried and placed in their original cages with free access to food and water after TS.

Statistical analysis
Data were presented as mean ± SEM. Statistical analysis were performed using two-tailed Student’s t-tests to compare two-group or Analysis of Variance (ANOVA) for the multiple-group comparisons. by using GraphPad Prism 9.0 (La Jolla, CA, USA). Significant difference was shown as *, **, *** and **** when p values < 0.05, < 0.01, < 0.001, and < 0.0001, respectively. Additionally, RNA-seq data from the hypothalamus, pituitary, and adrenal glands were analyzed for differentially expressed genes using DESeq2. For single-cell RNA-seq data of the spleen, the BD Rhapsody™ Whole Transcriptome Analysis (WTA) pipeline (v1.11) was used for scRNA-seq data preprocessing, Seurat (v4.4.0) was employed for quality control and clustering, and CellChat (version 1.6.1) was utilized for cell-cell communication analysis.

first: Xiaojuan

last: Gou

first: Yingying

last: Lei


title: Expression Analysis (RNA-Seq) of adult Myelodysplastic Syndromes (MDS)/Acute Myeloid Leukemia (AML) with isolated monosomy 7 compared to controls

status: Public on Mar 26 2026

city: Perugia

first: Cristina

last: Mecucci

address: Piazzale Menghini n.9

department: Department of Medicine, Hematology and Bone Marrow Transplantation Unit

country: Italy

institute: University of Perugia

type: Expression profiling by high throughput sequencing

summary: Monosomy 7 is one of the most frequent aneuploidies in myeloid malignancies, associated to heterogeneous phenotypes. Its poor prognosis differentiates it from  aberrations leading to partial/complete loss of 7q region.  Underlying pathogenic mechanisms are still undetermined. We performed a comprehensive epi-genomic study of karyotypically isolated monosomy 7 in adult Myelodysplastic Syndromes/Acute Myeloid Leukemias.

overall_design:
mRNA profiles of 18 monosomy 7 cases (Mon7), 28 controls (13 bone marrow samples from non-neoplastic cytopenias, normal bone marrow morphology and normal karyotype -CTL; 5 dic(1;7)(q10;p10) cases -DIC; 10 MDS and AML with normal karyotype - nkMN), and of CD34+ separated cells from one monosomy 7 case and one AML with normal karyotype.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Anair

middle: G

last: Lema Fernandez

first: Carlotta

last: Nardelli


title: Thalamic NRXN1-Mediated Input to Human Cortical Progenitors Drives Excitatory Neurogenesis

status: Public on Mar 25 2026

city: Los Angeles

first: Aparna

last: Bhaduri

state: CA

address: 615 Charles E Young Dr S

department: Biological Chemistry

country: USA

institute: University of California, Los Angeles

summary: According to the protocortex hypothesis, extrinsic thalamic signaling is necessary for refining cortical areas and cell types, but the mechanism by which these inputs shape human cortex development remains largely unexplored. We fuse cortical and thalamic organoids to study this process. Using single-nuclei RNA-sequencing and cellular imaging, we discover that thalamic signals during a progenitor-rich critical period drive developmental gene expression changes and shift cell fate toward increased excitatory neurogenesis. We find NRXN1 mediates thalamic axon contact with primate-enriched outer radial glia; genetic perturbation of NRXN1 reduces these contacts and significantly attenuates upper-layer neurogenesis. These findings underscore the influence of thalamic input on human cortical radial glia specification, and suggest a novel mechanism for thalamic regulation of human outer radial glia cell fate.

overall_design: 10X GEMX single-cell (sc) and single-nuclei (sn) RNA-sequencing of thalamocortical and corticocortical assembloids generated from multiple stem cell lines. In addition to baseline snRNA-seq of assembloids, several conditions were also assayed 1) severed cortex from thalamocortical assembloids, 2) cortical halves of assembloids that have been infected with CellTag virus for lineage tracing, and 3) Assembloids with genetic knockout of NRXN1 on the thalamic side versus non-targeting control.

first: Claudia

middle: V

last: Nguyen


title: Decoding a combinatorial RNA polymerase II CTD grammar that specifies protein-coding gene transcription and mRNA export

city: Austin

first: Qian

last: Zhang

state: TX

address: 2515 Speedway

institute: The Unibersity of Texas at Austin

type: Non-coding RNA profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The effects of the loss of SMARCB1 on DNA damage repair

city: Boston

first: Huy

state: MA

address: 450 Brookline Ave

department: Radiation Oncology

institute: Dana-Farber Cancer Institute

summary: SMARCB1 is the core subunit of BAF complex. However, the role of SMARCB1 in DNA damage repair remains unclear. Here, we performed an RNA sequencing study in the SMARCB1 knockout cells to identify in RNA expression and splicing following loss of SMARCB1.

overall_design: To investigate the genome-wide effects of SMARCB1 loss, we generated SMARCB1 knockout cells in the RPE TP53 -/- background and performed RNA sequencing with RPE p53-/- parental and SMARCB1 knockout cells.

first: Shuhei

last: Asada

first: Guangli

last: Zhu

first: Alan

middle: D

last: D’Andrea


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

first: Tomoya

last: Isobe

first: Tomohiro

last: Yabushita

first: Susumu

last: Goyama


title: Elucidating Salinity Stress and Engineered Solutions on Trichloroethene Bioremediation using a Consortium containing Dehalococcoides mccartyi

city: Berkeley

first: Lisa

last: Alvarez-Cohen

address: Davis Hall

department: Department of Civil and Environmental Engineering

institute: University of California, Berkeley

summary: Groundwater salinization threatens contaminant bioremediation worldwide, yet how syntrophic microbial consortia—central to these processes—respond to salinity stress remains poorly understood. Using a defined trichloroethene-dechlorinating consortium comprising Dehalococcoides mccartyi strain 195 (Dhc195), Desulfovibrio vulgaris Hildenborough (DvH), and Pelosinus fermentans R7 (PfR7), we show that functional resilience under salinity is governed by syntrophic dependencies rather than the tolerance of keystone organisms alone. Under chronic salinity, dechlorination became incomplete above 16 g/L NaCl despite stable Dhc195 and DvH, reflecting impaired vitamin B12 supply by PfR7. Co-amendment with glycine betaine and vitamin B12 sustained function under chronic moderate salinity up to ~18 g/L NaCl, but not during acute salinity upsurge greater than 21 g/L NaCl. Axenic cultures showed uncoupling of Dhc195 growth and dechlorination at high salinity, while transcriptomic analyses indicated a shift toward survival-oriented, amino acid–based adaptation during acute stress. Consortium metabolomics further highlighted membrane remodeling and altered metabolic exchange under salinity stress. Together, these findings demonstrate that sustaining bioremediation in salinizing aquifers requires community-level strategies that explicitly account for syntrophic vulnerability rather than organism-centric tolerance.

overall_design: RNA-seq profiling of WT Dhc195 cells 12 hours and 18 hours after introduction of two salinity perturbations

first: Mohan

last: Sun


title: Construction and Evaluation of an Acid-Responsive Antibacterial Coating with Laser-Induced Micro/Nano-Structured Titanium Surface Loaded LAMA3 pDNA@ZIF-8 Nanoparticles for Enhanced Soft Tissue Integration

city: Xi'an

first: Qiang

last: Miao

state: Shaanx

address: Changle West Road

country: China

institute: Air Force Medical University

summary: Unlike natural teeth, dental implants exhibit distinct peri-implant structures characterized by only about one-third of the hemidesmosomal attachments and the absence of periodontal ligament fiber insertion, which compromise their long-term success. Guided epithelial ingrowth via laser-induced microgrooves combined with enhanced hemidesmosome formation through LAMA3 gene transfection represents a promising strategy to improve soft tissue integration. In this study, a micro/nano-textured surface was fabricated on titanium implants by laser patterning followed by anodization to promote directional cell growth. A layer-by-layer self-assembled coating composed of ZIF-8-encapsulated LAMA3 plasmid was constructed on this micro/nano-surface. This coating exhibited acid-responsive release behavior and demonstrated antibacterial activity. More importantly, it effectively delivered the LAMA3 plasmid into cells and upregulated the expression of hemidesmosome-related proteins integrin α6 and integrin β4, both in vitro and in a rat implantation model. RNA sequencing revealed that the coating modulated global gene expression profiles and subsequently influenced cellular functions. In immortalized keratinocytes, differentially expressed genes were enriched in the MAPK signaling pathway, which was further validated by protein expression analysis after MAPK blockade. These findings indicate that our functional coating endows dental implants with favorable prospects for enhancing soft tissue sealing, offering a novel strategy to improve the long-term stability of oral implants.

overall_design: The micro/nano Lama3 pDNA@ZIF-8 coated specimens were designated as the experimental group, and pure titanium sheets served as the control. HaCaT cells were seeded onto the specimens. After 3 days of culture at 37 °C, total RNA was extracted and subjected to transcriptome sequencing to profile global gene expression changes.

first: YiFei

first: ChuFan

last: Ma


title: Microvascular endothelial scavenger receptor class B type I protects against heart failure with preserved ejection fraction by inhibiting T-cell cardiotropism

city: Shanghai

first: Yufei

last: Wu

address: Siping Campus,1239 Siping Road, Yangpu District, Shangha.

institute: School of Medicine, Tongji University

summary: Cardiac microvascular endothelial cells (CMECs) dysfunction is a well-recognized mediator of heart failure with preserved ejection fraction (HFpEF), but the underlying mechanism remains unclear. Here we find that scavenger receptor class B type I (SR-B1) is predominantly expressed in CMECs and decreased significantly in HFpEF. Endothelial-specific SR-B1 deficiency exacerbates cardiac pathological remodeling and diastolic dysfunction in HFpEF, which can be prevented by endothelial SR-B1 reconstitution through adeno-associated virus serotype 1 (AAV1)-mediated delivery in endothelial-specific SR-B1-deficient mice. Single-cardiac-endothelial-cell transcriptomics and lineage-tracing system reveal that inflammatory CMECs subcluster activation is responsible for the deteriorating HFpEF progression induced by endothelial SR-B1 loss, rather than endothelial-to-mesenchymal transition. Mechanistically, SR-B1 loss drives increased CXCL10 secretion, which orchestrates CMECs activation and CXCR3-positive T-cell cardiotropism to promote diastolic dysfunction—a process associated with endothelial IRF1 activation. Most importantly, the SR-B1-CXCL10-CXCR3 axis is activated in human HFpEF cardiac tissue, and the elevated CXCL10 level in plasma is independently associated with a higher HFpEF prevalence. This study uncovers that activation of SR-B1–CXCL10-CXCR3 axis in CMECs aggravates HFpEF pathogenesis through accumulation of CXCR3-positive T-cells in hearts.

overall_design: R26-stop-tdTomato mice were crossed with endothelial-restricted SR-B1 deletion to generate triple-transgenic and endothelial lineage tracing mice, including NC Sfl/fl/RΔEC vs NC Sfl/+/RΔEC or HFpEF Sfl/fl/RΔEC vs HFpEF Sfl/+/RΔEC mice. Red Fluorescent Protein (RFP)-positive cells from isolated cardiac left ventricle were obtained from FACS, then subjected to single-cell RNA sequencing.

first: Lemin

last: Zheng


title: Inactive b1-integrin acts as a cell junction-localized molecular scaffold for Angiopoietin2-TIE2-FOXO1 signaling [RNA-Seq]

city: Helsinki

first: Pipsa

last: Saharinen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: Transcriptome profiling of lymphatic endothelial cells (LECs) treated with R&D angiopoietin-2 (rhAng2) for 3 or 6 hours to investigate early transcriptional responses.

overall_design: Lymphatic endothelial cells (LECs) were stimulated with multimeric Ang2 for either 3 h or 6 h. Control cells were treated with BSA for the corresponding time periods. Following stimulation, cells were collected for downstream scRNA-seq analysis.

first: Klaudia

last: Lewna

first: Shraman

middle: K

last: Bohra

first: Keerthana

last: Ganesh


title: Inactive b1-integrin acts as a cell junction-localized molecular scaffold for Angiopoietin2-TIE2-FOXO1 signaling

summary: Transcriptome profiling of lymphatic endothelial cells (LECs) treated with multimeric angiopoietin-2 (Ang2) for 3 or 6 hours to investigate early transcriptional responses.


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

city: New York

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: 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.

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

first: Hua

first: Alisha

middle: S

last: Kardian


title: PD-1 signaling and anti-PD-1 antibody-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

country: United Kingdom

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: The processed data of mrpl13 mutant and sibling. (zebrafish)

city: Qingdao

first: xinkai

last: cheng

address: No. 5 Yushan Road

institute: zebrafish liver

summary: The liver is the largest metabolic organ in the human body, performing functions as metabolism, secretion, immunity, and detoxification. Due to the high energy demand, liver cells are rich in mitochondria. Mitochondrial homeostasis is crucial for liver development and function, yet the molecular pathways linking mitochondrial dysfunction to liver defects remain incompletely understood. In this study, using the zebrafish model, we show that loss of Mrpl13, a component of the mitochondrial ribosomal subunit, results in pronounced abnormalities in liver development. The deficiency of Mrpl13 disrupts mitochondrial homeostasis, as evidenced by fragmentated mitochondria, impaired energy metabolism, excessive reactive oxygen species, and lipid accumulation in liver cells. Notably, loss of Mrpl13 triggers mTORC1 signaling, and treatment with the mTORC1 inhibitor rapamycin significantly alleviates liver developmental defects, suggesting that mTORC1 signaling mediates the role of Mrpl13 in regulating mitochondrial homeostasis and liver development. Overall, our findings reveal a regulatory axis involving Mrpl13, mTORC1, and mitochondrial homeostasis during liver development, providing a theoretical basis for exploring therapeutic strategies for liver defects associated with mitochondrial dysfunction.

overall_design: Liver transcriptome sequencing conducted on mrpl13 mutants and sibling (7 dpf).

first: Xinkai

last: Cheng


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

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.

last: Sun


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.

middle: M

first: Olivia

last: Campbell

first: Nick

middle: R

last: Natale

first: Ana

last: Royo Marco

first: Michael

middle: A

last: Puchalski

first: John

last: Lukens


title: Accelerated cerebromicrovascular senescence contributes to cognitive decline in a mouse model of paclitaxel (Taxol)-induced chemobrain [Spatial Transcriptomics]

city: Oklahoma City

first: Roland

last: Patai

state: Oklahoma

address: 975 NE 10th street

department: Department of Neurosurgery

institute: University of Oklahoma Health Campus

summary: Chemotherapy-induced cognitive impairment ("chemobrain") is a frequent side-effect in cancer survivors treated with paclitaxel (PTX). The mechanisms responsible for PTX-induced cognitive impairment remain obscure, and there are no effective treatments or prevention strategies. Here, we test the hypothesis that PTX induces endothelial senescence, which impairs microvascular function and contributes to the genesis of cognitive decline. We treated transgenic p16-3MR mice, which allows the detection and selective elimination of senescent cells, with PTX (5 mg/kg/day, 2 cycles; 5 days/cycle). PTX-treated and control mice were tested for spatial memory performance, neurovascular coupling (NVC) responses (whisker-stimulation-induced increases in cerebral blood flow), microvascular density, blood-brain barrier (BBB) permeability and the presence of senescent endothelial cells (by flow cytometry and single-cell transcriptomics) at 6 months post-treatment. PTX induced senescence in endothelial cells, which associated with microvascular rarefaction, NVC dysfunction, BBB disruption, neuroinflammation, and impaired performance on cognitive tasks. To establish a causal relationship between PTX-induced senescence and impaired microvascular functions, senescent cells were depleted from PTX-treated animals (at 3 months post-treatment) by genetic (ganciclovir) or pharmacological (treatment with the senolytic drug ABT263/Navitoclax) means. In PTX treated mice, both treatments effectively eliminated senescent endothelial cells, rescued endothelium-mediated NVC responses and BBB integrity, increased capillarization and improved cognitive performance. Our findings suggest that senolytic treatments can be a promising strategy for preventing chemotherapy-induced cognitive impairment.

overall_design: The authors performed spatial transcriptomics to assess the anatomical distribution of senescent cells in the brains of paclitaxel (PTX)-treated p16-3MR mice. Mice were treated with PTX or vehicle and, following a 6-month post-treatment period with or without senolytic interventions (GCV or ABT263), brains were collected and sectioned for spatially resolved transcriptomic analysis. Tissue sections were processed to capture whole-transcriptome mRNA expression while preserving histological context, enabling the mapping of senescence-associated gene expression (e.g., Cdkn2a) to specific brain regions. This approach allowed comparison of the spatial distribution and abundance of senescent cells across experimental groups, including cortex, white matter, and hippocampus.

first: Anna

last: Csiszar

first: Zoltan

last: Ungvari

first: Tripti

last: Gautam

first: Tamas

last: Kiss


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

first: Stephen

last: Mack

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

first: Hua

first: Alisha

last: Kardian


title: Comparative transcriptomic profiling of human 3D endometrial stromal organoids under distinct decidualization stimuli

city: Pitscataway

first: Shuo

last: Xiao

state: NJ

address: 170 Frelinghuysen Rd, Room 404

department: Pharmacology & Toxicology

institute: Rutgers University

summary: Endometrial stromal decidualization is a hormone-regulated process essential for establishing uterine receptivity and supporting embryo implantation. Three-dimensional (3D) endometrial organoid systems provide a physiologically relevant platform to study this process; however, how different stimulatory conditions influence decidualization responses in 3D culture remains incompletely characterized. In this study, we generated 3D human endometrial stromal organoids and subjected them to four experimental conditions: vehicle control, cyclic adenosine monophosphate (cAMP) stimulation, combined estrogen–progesterone–cAMP (EPC) treatment, and co-culture with in vitro–grown follicles derived from mouse ovary. Organoids were cultured for 6 days under each condition, followed by bulk RNA sequencing. Principal component analysis (PCA) revealed clear separation between control and stimulated groups, with cAMP, EPC, and follicle co-culture conditions showing distinct but partially overlapping transcriptional profiles. Differential gene expression analysis identified both shared and condition-specific transcriptional changes across the four treatments. Pathway-level analysis using gene set variation analysis (GSVA) further demonstrated common decidualization-associated biological processes alongside stimulus-specific functional responses. This dataset provides a comprehensive resource for investigating how distinct biochemical and paracrine stimuli regulate decidualization in 3D endometrial organoid systems. It enables comparative analysis of canonical cAMP-driven responses, hormone-mediated signaling, and follicle-derived paracrine effects on endometrial stromal decidualization.

overall_design: Human primary endometrial stromal cells were seeded into agarose-based 3D Petri Dish molds to generate Endo-organoids and cultured for 6 days under four conditions: vehicle control, cAMP alone (0.5 mM), EPC treatment consisting of estradiol (E2, 10 nM), progesterone (P4, 1 μM), and cAMP (0.5 mM), or co-culture with four in vitro–grown ovarian follicles in the presence of cAMP (0.5 mM). Endo-organoids collected after 6 days of treatment were subjected to bulk RNA sequencing analysis to compare shared and stimulus-specific transcriptomic responses under distinct decidualization-related conditions.

first: Shichao

last: Liu

first: Yubing

first: Jiyang

last: Zhang

first: Tingjie

last: Zhan

first: Qiang

first: Nataki

last: Douglas

first: Xiaoqin

last: Ye


title: Quantitative transcriptome and proteome maps of classical nonclinical species

city: Groton

first: Darien

last: Capunitan

state: CT

address: 255 Shennecossett Rd

institute: Pfizer

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


title: Plasma Extracellular Vesicle Modulate Immune Cell Transcriptional Responses Following Acute Myocardial Infarction

first: Naveed

last: Akbar

state: England

address: Division of Cardiovascular Medicine, Radcliffe Department of Medicine, HS04

summary: Plasma extracellular vesicles (EVs) increase during acute myocardial infarction (MI), correlate with myocardial injury, and mobilise immune cells from the spleen to the circulation. These cells are transcriptionally activated even before tissue recruitment, yet the mechanisms driving this priming are unclear. We show that plasma EVs isolated at hospital presentation with MI are enriched in miRNA‑320b. Endothelial cells upregulate miRNA‑320b in EVs following inflammatory stimulation. Target gene pathway analysis revealed enrichment in adhesion and cytokine signalling. Endothelial EVs promoted monocyte adhesion and induced IL6 and TNF mRNA expression in macrophages while dampening cytokine secretion. RNA-sequencing of MI patient neutrophils and monocytes confirmed significant enrichment of miRNA‑320b targets. Peripheral blood mononuclear cells treated with MI EVs showed similar gene regulation. These findings suggest that EV‑mediated transfer of miRNA‑320b primes immune cells for adhesion and cytokine signalling. Understanding this axis may enable therapeutic immunomodulation of immune cells to improve repair following MI.

overall_design: RNA-sequencing of peripheral blood monocytes from STEMI and NSTEMI patients and peripheral blood mononuclear cells (PBMCs) treated with plasma-extracellular vesicles from STEMI and NSTEMI patients.

first: Adam

last: Braithwaite

first: Tafadzwa

last: Kufazvinei


title: Overcoming T cell tolerance to tumor self-antigens through catch-bond engineering - TCR156wt and S32M

first: Zhiyuan

last: Mao

state: California

address: 675 Charles E. Young Dr. South

department: Microbiology Immunology & Molecular Genetics

summary: T cells are often weakly responsive to tumor self-antigens because of central tolerance, which constrains their ability to eliminate tumors. Affinity-matured T cell receptors can exhibit enhanced tumor killing properties but in therapeutic settings have been accompanied by off-target cross-reactivity and toxicity, because high-affinity TCRs antigen specificity is altered compared to naturally selected TCRs. Here, we exploited the physiological biophysical mechanism of TCR activation through mechanical force, by engineering to a weakly reactive TCR specific for a non-mutated human prostate tumor associated antigen (TAA), Prostatic Acid Phosphatase (PAP). We isolated a catch bonding “hotspot” whose mutation enhanced T cell activity by increasing TCR-pMHC bond lifetime, whilst maintaining physiological affinities and antigen fine-specificities. T cells expressing these engineered TCRs showed vastly superior expansion and tumor killing properties in vitro and in vivo, as well as enhanced effector phenotypes and proliferation in the tumor, as measured by single-cell RNA-seq. High resolution structures and molecular dynamics simulations of the TCR-pMHC complexes reveal the structural hotspot in TCR CDR1 is primed for peptide interaction in the catch bond engineered TCR. These studies establish catch bond engineering as a viable biophysically-based strategy to convert tolerized anti-tumor T cells into potent TCR-T killers.

overall_design: To evaluate the antigen recognition patterns of TCR156wt and S32M, yeast library expressing HLA-A*0201 presenting highly diverse antigens were selected against TCR tetramers. After 3-4 rounds of selection, the libraries were deep-sequenced to identify the contact residues to the TCRs.

first: Xiaojing

last: Chen

first: Kenan

last: Garcia

first: Owen

middle: N

last: Witte


title: Regulation of basal and TNFa-induced fibroblast gene expressions by peptidylarginine deiminase 2

first: Mohammad Aslam

last: Saifi

address: 60 Fenwood Rd

department: Medicine

institute: Brigham and Women's Hospital

summary: Objective: Peptidylarginine deiminases (PADs) modulate immune cell function and contribute to the development of rheumatoid arthritis (RA), which frequently co-occurs with interstitial lung disease (ILD). Fibroblasts exhibit organ-specific function and play pathogenic roles in RA and ILD. This study aims to examine the cell-autonomous role of PADs in regulating gene expression of fibroblasts from various organs. Methods: Fibroblasts of various organs and thioglycolate elicited peritoneal cells were harvested from wild type, PAD2-deficient, or PAD4-deficient mice. Primary human lung fibroblasts were subjected to CRISPR-mediated PAD2 ablation. Bulk RNA sequencing was performed to identify PAD2-regulated genes. Differential expression was subsequently confirmed, and basal and TNFα-induced gene expression were measured, using quantitative PCR, flow cytometry, and/or ELISA. Results: PAD2 transcript levels in lung fibroblasts increased with age, a trend not observed in fibroblasts from other organs. While PAD2 deficiency had a limited impact on the overall transcriptome of lung fibroblasts, it consistently reduced the expression of Podoplanin (PDPN) and TNFRSF1b across fibroblasts from all mouse organs and human lung fibroblasts. Lung fibroblasts exhibited the highest IL-6 expression among all sources of fibroblast. Notably, PAD2 deficiency, but not PAD4 deficiency, attenuated TNFα-induced IL-6 expression in fibroblasts from lung and synovium but not other organs. Conclusion: PAD2 is expressed in lung fibroblasts in an age-dependent manner and cell-autonomously regulates TNFα-induced gene expression of fibroblasts based on their organ origin, particularly lung and synovium. These findings suggest a novel pathogenic role for PAD2 in rheumatoid arthritis (RA) and offer a plausible explanation for the observed lung-synovium connection.

overall_design: WT and PAD2KO neonatal fibroblasts were isolated, FACS separated and subjected to bulk RNA seq

first: Mohammad

first: Flavien

last: Marguerie

first: Mari

last: Kamiya

first: Hung

last: Nguyen

first: Edy

middle: Y

last: Kim

first: Ho

last: IC


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

city: Toronto

first: Michael

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

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) 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

middle: L

last: Purdy

first: Amirala

last: Bakhshiannik

first: Prottoy

last: Hasan

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: Anne

middle: E

last: Kwitek

first: Melinda

last: Dwinell

first: Laura

last: Saba

first: Caitlin

last: O’Meara

first: Michaela

last: Patterson


title: Overcoming T cell tolerance to tumor self-antigens through catch-bond engineering

city: Los Angeles

first: Zhiyuan

last: Mao

institute: University of California, Los Angeles

overall_design:
Single cell sequencing data of Tumor infiltrating lymphocytes expressing different T cell receptors (TCRs).
To evaluate the tumor infiltrating lymphocytes (TILs) of TCR-engineered human T cells, 5 million TCR-engineered T cells were injected into NSG mice bearing PC3-A2-PAP tumors. The animals were sacrificed 9 days after T cell injection. Tumors were harvested to extract TILs. TILs were then single-cell sequenced.

first: Xiaojing

last: Chen

first: Kenan

last: Garcia

first: Owen

last: Witte


title: Transcriptome sequencing analysis of Cyp4f3b gene interference in human gallbladder carcinoma cells gbc-sd

city: Kunming

first: xiang

middle: wen

last: lan

address: 300 Bailong Temple, Panlong District, Kunming, Yunnan 650224, China

institute: Southwest Forestry University

summary: This study aimed to investigate the molecular mechanism underlying the effects of Cyp4f3b gene interference on the biological behaviors of human gallbladder carcinoma cells gbc-sd. Three replicate cell samples from each group (sh-NC control group and sh-Cyp4f3b interference group) were subjected to total RNA extraction and quality control, sequencing library construction and evaluation, RNA-seq sequencing and filtering, reference sequence alignment, gene expression level analysis, and differential expression analysis. Differentially expressed genes and significantly enriched signaling pathways were systematically identified to provide molecular evidence for clarifying the role of Cyp4f3b in gallbladder carcinogenesis and progression.

overall_design: sh-NC sh-Cyp4f3b


title: Aβ suppresses oligodendrocyte differentiation in vivo or vitro via inflammatory activation and cytoskeletal contraction.

city: shanghai

first: Wenxiu

last: Dai

address: No. 746, Zhongshan Middle Road, Songjiang District, Shanghai

institute: Shanghai Jiao Tong University

summary: Aβ disrupts oligodendrocyte lineage cells through a dual mechanism inflammatory activation and cytoskeletal compromise leading to maturation blockade  and hypomyelination independent of axonal damage. These findings position oligodendrocyte dysfunction as a key component of AD white matter pathology and identify potential therapeutic targets.

overall_design: RNA-seq analysis of primary OPC in wild-type adult rats with and without treatment of Aβ.

first: Daopeng

last: Li

first: Liang

last: Zhang


title: ADAMTS9-AS2 acts as an epigenetic brake to constrain DNMT3B-mediated CADM2 silencing in esophageal squamous cell carcinoma metastasis

city: Xinxiang

first: Fangfang

last: Shen

address: No. 599 hualan east street

institute: The Third Affiliated Hospital of Xinxiang Medical University

type: Methylation profiling by genome tiling array

summary: Introduction: Metastatic recurrence drives dismal survival in esophageal squamous cell carcinoma (ESCC), yet epigenetic mechanisms underlying metastasis remain poorly defined. While DNMT1 and DNMT3A contribute to ESCC pathogenesis, DNMT3B’s role is enigmatic despite frequent dysregulation. Methods: Integrated methylome-transcriptome profiling comprised genome-wide methylation screening in 5 paired ESCC tumor and adjacent normal tissues. Parallel mRNA microarray profiling quantified expression levels of DNMT3B, CADM2, and ADAMTS9-AS2 in ESCC tumors. RIP, ChIP, and pyrosequencing in ESCC cells validated molecular interactions. Results: ADAMTS9-AS2 downregulation promoted ESCC proliferation, migration, and invasion. Mechanistically, ADAMTS9-AS2 directly bound DNMT3B, preventing its occupancy at the CADM2. Rescue experiments confirmed CADM2 overexpression reversed ADAMTS9-AS2 knockdown-induced oncogenic phenotypes. Clinically, DNMT3B overexpression in lymph node-positive tumors correlated with metastatic progression. Discussion: ADAMTS9-AS2 functions as an epigenetic brake by sequestering DNMT3B, thereby blocking CADM2 epigenetic silencing and metastasis in ESCC. Targeting this axis offers potential therapeutic strategies against ESCC.

overall_design: Genome-wide DNA methylation profiling was performed using Illumina methylation microarrays (850K CpG sites). Genomic DNA extracted from 5 paired ESCC tumor and adjacent normal fresh-frozen tissues underwent bisulfite conversion using the EZ DNA Methylation-Lightning Kit (Zymo Research). Converted DNA was amplified, fragmented, and hybridized to the BeadChip according to the manufacturer’s protocol. Arrays were scanned on an Illumina iScan system, and raw intensity data were processed using the ChAMP package in R (v4.0.3) for quality control, normalization (BMIQ), which inherently adjusts for technical variations and potential batch effects, and β-value calculation. Differentially methylated positions (DMPs) were identified with a threshold of |Δβ|≥0.2 and adjusted P<0.05, with P-values adjusted for multiple testing using the Benjamini-Hochberg false discovery rate (FDR) method as a standard procedure. Whole transcriptome profiling was performed using Agilent SurePrint G3 Human GE v3 microarrays (8×60K) on 5 paired ESCC tumor and adjacent normal tissues. Total RNA was extracted with TRIzol reagent (Invitrogen), quantified (NanoDrop), and quality-controlled. RNA amplification, labeling with Cy3/Cy5 dyes (Quick Amp Labeling Kit), and hybridization followed manufacturer protocols. Arrays were scanned on an Agilent G2565CA scanner. Raw data were processed with Feature Extraction Software, normalized by quantile method, and subsequently adjusted for potential batch effects using the ComBat function from the sva package in R. Processed data were analyzed using the limma package. Differentially expressed genes (DEGs) were identified with |log2FC|≥2 and adjusted P<0.05, employing the Benjamini-Hochberg FDR method for multiple testing correction.

first: Fang-Fang


title: Transcriptome sequencing data sets of a marine ammonia-oxidizing archaeon Nitrosopumilus zosterae NM25 to hydrogen peroxide

city: Fujisawa

first: Tatsunori

last: Nakagawa

address: 1866 Kameino

institute: Nihon University

summary: Marine ammonia-oxidizing archaea are known to lack the catalase gene that functions as a scavenger at high concentrations of hydrogen peroxide. Therefore, nearly isolated ammonia-oxidizing archaea require the addition of a hydrogen peroxide scavenger to their culture medium, despite being aerobic. To understand the transcriptomic response to hydrogen peroxide stress, we performed RNA-Seq analysis under two different conditions: one without the addition of a hydrogen peroxide scavenger and one with the addition of a hydrogen peroxide scavenger as a control.

overall_design: RNA-seq profiling of marine ammonia-oxidizing archaeon Nitrosopumilus zosterae NM25 in the absence and presence of the hydrogen peroxide scavenger alpha-ketoglutarate after 10 days of incubation.

first: Yuki

last: Tsuchiya

first: Reiji

last: Takahashi


title: Arginine Metabolism Supports De Novo Pyrimidine Biosynthesis to Block DNA Damage and Maintain Epstein-Barr Virus Latency

city: Boston

first: Shaowen

last: White

address: 181 Longwood Ave, Channing Labs Room 861

summary: Incompletely understood mechanisms serve to maintain Epstein-Barr virus (EBV) latency in most B-cell states, in which viral oncogene(s) are expressed but lytic antigens are repressed. Shortly after EBV's discovery and even before it was named, early pioneers Werne and Gertrude Henle identified that restriction of extracellular arginine de-represses EBV lytic antigens within Burkitt lymphoma tumor cells. However, for nearly 60 years, it has remained unknown how arginine metabolism supports EBV latency. To gain insights, we performed an amino acid restriction screen in Burkitt cell lines. This confirmed that arginine restriction was sufficient to trigger EBV reactivation in Burkitt B-cells and gastric carcinoma models. Arginine restriction strongly impaired de novo pyrimidine biosynthesis, and CRISPR or chemical genetic blockade of pyrimidine biosynthesis enzymes induced EBV immediate early and early lytic gene expression. However, arginine restriction blocked EBV lytic DNA replication and consequently also late gene expression, suggesting an abortive lytic cycle. Arginine restriction triggered DNA damage, which was an important driver of arginine restriction-driven EBV reactivation. Arginine restriction and DNA hypomethylation synergistically increased EBV reactivation. Together, our results highlight arginine and pyrimidine metabolism as potential targets for EBV lytic antigen induction therapy in B and epithelial cell contexts.

overall_design: RNA-seq profiling of EBV+ Burkitt cell P3HR-1 cultured in replete or arginine-free media for 5 days. Three biological replicates were included for each media condition.

first: White

last: Shaowen

first: Liao

last: Yifei

first: Yin

last: Wang

first: Li

last: Shunji

first: Burton

last: Eric

first: Gewurz

last: Benjamin


title: Effect of triazine thiols on steady-state mRNA levels in iPSC-derived hepatocytes

city: Charleston

first: Stephen

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

summary: We previously reported that triazine thiols reduce apolipoprotein B (ApoB) secretion from human iPSC-derived hepatocytes (HLCs) and from humanized mice. To determine whether these compounds affected hepatocyte mRNA levels, we performed bulk RNA sequencing of HLCs treated with the triazine thiol DL-1 or with vehicle (DMSO) for 24 hours. Treatment with triazine thiols only modestly affected steady-state mRNA levels. Of 335 differentially expressed genes, none were directly related to ApoB synthesis, lipoprotein assembly, or secretory pathways. The the most affected mRNAs encoded proteins involved in metallothionein induction, suggesting a metal stress response likely unrelated to the compound’s effects on lipid metabolism. These results imply that DL-1 reduces APO-B secretion through post-transcriptional mechanisms.

overall_design: Hepatocytes were generated from iPSCs and treated with either DMSO (vehicle) or 2 µg/ml of the triazine thiol DL-1 for 24 hrs. Samples were collected and subjected to RNA-seq. Data were generated from biological triplicates.

first: Carla

last: Martinez-Morant

first: Jui-Tung

last: Liu

first: Yu-Lin

last: Jiang

first: Josef

last: Blaszkiewicz


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: Sensory neuron dysfunction in dorsal root ganglia during disease onset in the SOD1G93A mouse model for ALS

city: Suita

first: Akira

last: Nishiura

state: Osaka

institute: The University of Osaka

summary: Amyotrophic lateral sclerosis (ALS) is primarily characterized by motor neuron degeneration, but accumulating evidence suggests that sensory neurons are also affected. To investigate early sensory neuron dysfunction in ALS, we performed bulk RNA sequencing of dorsal root ganglia (DRG) isolated from SOD1-G93A transgenic mice and wild-type controls at disease onset. This dataset provides transcriptomic profiles that reveal molecular alterations associated with ALS-related sensory neuron pathology.

overall_design: Bulk RNA-seq was performed on dorsal root ganglia from SOD1-G93A transgenic mice and wild-type littermates to compare gene expression changes associated with ALS disease onset.

first: Nishiura

last: Akira

first: Seki

last: Soju


title: Methionine and choline deficiency rewires transcriptional programs to recapitulate molecular features of human MASH

city: San Antonio

first: Xiaoli

last: Sun

address: 7703 Floyd Curl Dr

department: Pharmacology

institute: University of Texas Health Science Center at San Antonio

summary: Metabolic dysfunction-associated steatohepatitis (MASH) is a leading cause of cirrhosis and liver related mortality, but it remains unclear how nutrient stresses drive coordinated transcriptional remodeling in the pathogenesis of MASH. Clinical studies reported that methionine and choline deficiency (MCD) promotes chronic liver diseases. Multiple types of MCD diets have been adopted to establish MASH mouse models. However, how methionine and choline deficiency modulates cell-intrinsic transcriptional responses across parenchymal and nonparenchymal liver cell types, and whether these effects recapitulate human MASH, remains unclear. Here, we generated a customized MCD cell culture medium to induce nutrient stress in HepG2 cells, endothelial cells, bone marrow derived macrophages, and hepatic stellate cells (HSCs). RNA sequencing was performed to characterize transcriptional regulations in response to MCD. Across cell types, lack of methionine and choline induced transcriptional program of inflammatory and stress response and suppressed metabolic pathways and cell-cycle progression, suggesting a  proliferation pause as a compensatory stress-adaptive response that preserves cell viability and essential functions.  In addition to these shared responses, MCD stress also caused distinct cell type-specific outputs that could contribute to the pathogenesis of MASH. Integrated analysis of these datasets with human MASH liver single nucleus transcriptomic data demonstrated that MCD condition recapitulates multiple pathophysiological features of human MASH, including the elevated inflammation, enhanced hepatocyte death, disrupted redox balance, altered metabolic homeostasis, and HSC activation. These findings not only uncover how MCD stress promotes MASH progression, but also provide a conceptual basis to guide future use of MCD diet-induced models in MASH studies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Transcriptional profiling of methionine/choline deficiency–induced responses across liver-relevant cell types using in vitro culture models, including HepG2 hepatocytes, immortalized human endothelial cells, immortalized bone marrow–derived macrophages, and immortalized human hepatic stellate cells.


title: Patient-derived orthotopic xenograft models recapitulate the peritoneal dissemination of pancreatic cancer and delineate its transcriptional and regulatory programs [scRNA-seq]

city: Tokyo

first: Kohei

last: Kumegawa

address: 3-8-31 Ariake, Koto-ku

institute: Japanese Foundation for Cancer Research

summary:
BACKGROUND & AIMS: The mechanisms of peritoneal dissemination in pancreatic ductal adenocarcinoma (PDAC) remain unclear partly owing to the lack of patient-derived models that recapitulate this process. This study aimed to establish an orthotopic model of PDAC peritoneal dissemination and to uncover the transcriptional and regulatory programs underlying this process.
METHODS: Organoids were established from primary pancreatic tumors and malignant effusions of patients with PDAC and orthotopically transplanted into the pancreas of immunodeficient mice to generate patient-derived orthotopic xenograft (PDOX) models. Subsequently, the organoids were rederived from pancreatic and peritoneal lesions of a representative model (PDOX12) and orthotopically reimplanted to assess the dissemination capacity. Single-nucleus RNA sequencing (snRNA-seq) and single-cell ATAC sequencing (scATAC-seq) were performed to analyze the tumors from these models.
RESULTS: The organoids that were derived from malignant effusions reproducibly generated peritoneal metastases after orthotopic implantation. To dissect this process more precisely, we focused on one representative model (PDOX12) and rederived organoids from its pancreatic and peritoneal lesions. These organoids generated matched PDOX models that differed only in dissemination potential when reimplanted orthotopically. The results of snRNA-seq revealed a distinct subpopulation enriched in the high-dissemination model, which was characterized by the coordinated activation of genes involved in cytoskeletal dynamics, extracellular matrix remodeling, and plasticity-related signaling—suggesting a dissemination-primed state. Integration with scATAC-seq identified STAT3, SMAD3, and SOX2 as potential upstream regulators of this gene program.
CONCLUSIONS: This study established PDOX models that isolate the peritoneal dissemination phenotype and reveal the transcriptional and regulatory programs driving this process.

overall_design:
scRNA-seq profiling of patient derived organoids from the patients with pancreatic cancer

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

first: Takaaki

last: Furukawa

first: Reo

last: Maruyama


title: Patient-derived orthotopic xenograft models recapitulate the peritoneal dissemination of pancreatic cancer and delineate its transcriptional and regulatory programs [RNA-seq]

overall_design:
RNA-seq profiling of patient derived organoids from the patients with pancreatic cancer

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


title: Prolonged KRAS-MAPK Inhibition Induces Interferon-mediated Epithelial-to-Mesenchymal Transition and Reveals Therapeutic Opportunities [cut and run-ChipSeq]

first: Ashenafi

last: Bulle

state: Missouri

address: 660 S Euclid Ave

department: Molecular Oncology

institute: Washington University School of Medicine

summary: Direct targeting of KRAS to inhibit the MAPK cascade is poised to transform the therapeutic landscape of pancreatic ductal adenocarcinoma (PDAC). However, analyses of PDAC samples from patients treated with KRASG12C inhibitors have revealed secondary mutations restoring MAPK signaling and promoting epithelial-to-mesenchymal transition (EMT) as key mechanisms of acquired resistance. Here, we show that human PDAC specimens and patient-derived cell lines treated with the ERK inhibitor ulixertinib display upregulation of EMT-associated and inflammatory gene programs, particularly those linked to the interferon response. Using the GeneRep-nSCORE computational framework to reconstruct and rank regulatory networks enriched in ERKi and KRASi-resistant PDAC cells, we identified TRIM22, an interferon-inducible E3 ubiquitin ligase, as a critical mediator of EMT and treatment resistance. Mechanistically, TRIM22 promotes proteasomal degradation of IκBα, leading to activation of NF-κB signaling, a known driver of EMT. Notably, we identify TACSTD2, encoding Trophoblast Cell Surface Antigen 2 (TROP2), as an NF-κB target gene upregulated following EMT. Functionally, combining ulixertinib or the KRAS inhibitor MRTX1133 with the TROP2-directed antibody-drug conjugate sacituzumab govitecan significantly suppressed the growth of PDAC patient-derived xenografts. Together, our work identifies TRIM22 as a molecular link between interferon signaling and EMT and reveals TROP2 as a druggable vulnerability to sustain the therapeutic efficacy of KRAS-MAPK pathway inhibitors.

overall_design: cut and run-ChipSeq analysis of Pa01C cell treated with Ulixertinib or MRTX1133  in comparison to DMSO treatment group

first: Kian-Huat

last: Lim


title: RNA-seq profiling of cochlea in wild-type mice and NEU4 mutant at P7

city: jinan

first: Shu

middle: hui

last: Kong

state: Huaiyin District

address: 4# Duanxing West Road, Huaiyin District, Jinan, Shandong, 250021

institute: Shandong Provincial ENT Hospital

summary: Using the constructed NEU4 gene knockout model, explore the impact of functional impairment of this gene on inner ear development and hearing.


title: Patient-derived orthotopic xenograft models recapitulate the peritoneal dissemination of pancreatic cancer and delineate its transcriptional and regulatory programs [scATAC-seq]

overall_design:
scATAC-seq profiling of mouse-engrafted patient derived organoids from the patients with pancreatic cancer

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


title: Highlights of Tuft Cells in Mouse and Human Salivary Glands

city: Chicago

first: George

last: Chlipala

state: IL

address: 900 S. Ashland Ave

department: Research Informatics Core

institute: University of Illinois Chicago

summary: Tuft cells (TCs) are rare chemosensory epithelial cells that regulate mucosal homeostasis in several organs, but their role in salivary glands (SGs) remains unclear. This study investigated TC features in both mouse and human SGs. In mouse samples, transmission electron microscopy (TEM), histological analysis, bulk RNA-sequencing and proteomic analyses were performed on submandibular glands (SMGs) from female and male C57BL/6J (wild-type) and C57BL/6J-Pou2f3-/- mice, which lack TCs. Moreover, human minor SG biopsies were evaluated by immunostaining and Poisson regression to identify clinical, serological, and histopathological features correlated with TC abundance. TEM analysis confirmed conserved TC ultrastructure—apical microvilli, a tubulovesicular system, and cytospinules—in both female and male mouse SMGs. Moreover, TC loss was associated with sex-specific transcriptional remodeling (1742 differentially expressed genes in females versus 175 in males), morphological alterations and sex-specific saliva proteomic remodeling. In human minor SG biopsies, TC counts were correlated with salivary flow, serological and histopathology features. In summary, these findings suggest that TCs are regulators of epithelial integrity and potential biomarkers of SG dysfunction.

overall_design: This study compared tuft cells (TCs) across mouse and human salivary glands. In mice, female and male C57BL/6J wild-type and Pou2f3−/− (TC-deficient) submandibular glands were analyzed to test effects of genotype and sex on TC structure/localization (TEM, POU2F3/KRT8 staining), gland architecture (histology), transcriptome (bulk RNA-seq), and salivary function/composition (saliva flow and proteomics). In humans, minor salivary gland biopsies from Sjögren’s disease and non-Sjögren sicca cohorts were immunostained to quantify TC abundance and modeled against salivary flow, autoantibodies, and histopathology features.

first: Michael

last: Rusiniak

first: Lara

last: Shimagami

first: Victor

middle: Z

last: Drummond

first: Mariana

last: Santos

first: Fernanda

last: Castro

first: Chao

last: Xue

first: Ming

last: Zhang

first: Jun

last: Qu

first: Mark

last: Maienschein-Cline

first: Tarcilia

last: Silva

first: Silvia

middle: F

last: Sousa

first: Harim

last: Tavares dos Santos


title: Prolonged KRAS-MAPK Inhibition Induces Interferon-mediated Epithelial-to-Mesenchymal Transition and Reveals Therapeutic Opportunities [scRNAseq-Ulixertinib]

overall_design: scRNAseq analysis of KPPC mice treated with ulixertinib  in comparison to DMSO treatment group


title: Prolonged KRAS-MAPK Inhibition Induces Interferon-mediated Epithelial-to-Mesenchymal Transition and Reveals Therapeutic Opportunities.

overall_design: Bulk RNAseq analysis of Pa01C, Pa02C, Pa03C and Pa14C cells following ulixertinib treatment in comparison to DMSO treatment group


title: Psoriasis-like disease prevents squamous skin tumor development by neutrophil-driven inflammation

city: Vienna

first: Katharina

last: Rindler

address: Waehringer Guertel 18-20

department: Dermatology

country: Austria

institute: Medical University of Vienna

summary: Psoriasis is a chronic inflammatory skin disease affecting millions of people worldwide. Although growing evidence links chronic inflammation with increased cancer risk, the association between psoriasis and cutaneous squamous cell carcinoma (cSCC) is still elusive. Using cell transplantation and chemical-induced models of cSCC combined with inducible genetically engineered mouse models (GEMMs) of psoriasis, we investigated how chronic skin and systemic inflammation affects squamous skin tumor initiation and progression. Here we show that in the context of severe psoriasis-like disease, neutrophil-dependent inflammation prevents squamous skin tumor development. Cellular and molecular analyses of psoriasis-like skin at the tumor initiation stage revealed a marked infiltration of CD54–expressing neutrophils, associated with the release of cytotoxic granules and neutrophil extracellular traps (NETs), as well as enhanced senescence and the expression of senescence-associated secretory phenotype (SASP) in keratinocytes. Furthermore, single-cell RNA sequencing demonstrated that inflammatory N1-like neutrophils mediate re-programming of the cell-cell communication networks, while keratinocytes displayed diminished responsiveness to mitogenic signals, including EGF and WNT. Importantly, neutrophil depletion ameliorated psoriasis-like inflammation, abolished the senescence-like phenotype in keratinocytes and restored tumor growth. We propose that the release of neutrophil granules and NETs in psoriasis-like skin eliminate tumor cells and/or mediate oxidative and inflammatory stress-induced senescence in keratinocytes, thereby preventing tumor growth. Taken together, we have defined an innate control of skin tumorigenesis in psoriasis-like disease, which will be relevant for developing cancer prevention strategies.

overall_design: The DKO*K15 mice and their respective Cre-negative controls were generated by genetic crosses of the junBf/f and c-junf/f  alleles with the K15-CrePR1 in mixed C57BL/6. Psoriasis-like disease was induced in 8-week-old mice by intraperitoneal injections of 2 mg Mifepristone (RU486) (Merck) for 5 consecutive days. Mice were treated with DMBA and TPA to induce skin tumorigenesis. Briefly, the back skin of 6-week-old mice was shaved 24 hrs before treated once with 50 μg of DMBA (Sigma-Aldrich) and then 3 times per week with 4 μg of TPA (Sigma-Aldrich) for the duration of 15 weeks. Papilloma growth was monitored weekly and tissue samples were collected 48 hrs post last TPA application. Skin samples were harvested in PBS, cut in small pieces using a scalpel and digested with 100 μg/ml LiberaseTM (Roche) and 100 μg/ml of DNase I (Sigma-Aldrich) for 1 hr at 37 °C. 30,000 cells per sample were processed for single-cell RNA sequencing on a Chromium X Instrument using the GEM-X Single Cell 5’ Reagent Kit (10X Genomics, Pleasanton, CA) and a single-cell gel bead emulsion was generated. cDNA amplification and library preparation were performed according to the manufacturer’s instructions. Quality and concentration of libraries were determined using Qubit dsDNA HS kit (Invitrogen) and TapeStation D1000 (Agilent). Libraries were sequenced on one NovaSeq SP flow cell (Illumina) with the 150bp paired-end configuration.

first: Panagiota

last: Tsokkou

first: Martin

last: Holcmann

first: Kamil

last: Mieczkowski

first: Lisa

last: Shaw

first: Matthias

last: Farlik

first: Maria

last: Sibilia

first: Erwin

last: Wagner


title: miRNA expression profiling of visceral adipose tissue-derived extracellular vesicles in nicotine-treated ApoE-/- mice

city: Harbin

first: LI

last: YANCHAO

state: Heilongjiang

address: 2nd Affiliated Hospital of Harbin Medical University, No. 157 Baojian Road, Nangang District, Harbin, Heilongjiang, China.

department: Cardiology Organization

institute: The Second Affiliated Hospital of Harbin Medical University

summary: This study profiles the miRNA expression of visceral adipose tissue-derived extracellular vesicles (VAT-EVs) in ApoE-deficient (ApoE-/-) mice subjected to different dietary and treatment conditions. Mice were fed either a high-fat diet (HFD) or a high-fat diet combined with nicotine administration (HFD+Ni). Epididymal white adipose tissue (eWAT) was used as a representative visceral fat depot for EV isolation. High-throughput small RNA sequencing was performed to characterize the miRNA cargo of VAT-EVs and to identify differentially expressed miRNAs between the two groups. The resulting dataset provides a resource for investigating nicotine-associated alterations in EV-mediated miRNA signaling in the context of metabolic and inflammatory processes.

overall_design: Extracellular vesicles were isolated from epididymal white adipose tissue (eWAT) of mice in two experimental groups (HFD and HFD+Ni). Small RNA libraries were constructed from EV-derived RNA and sequenced to profile miRNA expression. Comparative analysis was performed between the two groups.

first: Yanchao

last: Li

first: Xuedong

last: Wang

first: Jingbo

last: Hou


title: Mitochondrial potential as a biomarker of T cell fitness and function in cancer immunotherapy

city: Nashville

first: John

last: Karijolich

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

summary: Checkpoint inhibitors have transformed cancer treatment, yet predicting responses remains challenging. Mitochondrial quality decreases in tumor infiltrating lymphocytes and correlates with impaired anti-tumor immunity in animal models. Mitochondrial membrane potential (MMP) increases with T cell activation but may also indicate cellular dysfunction. Here we assessed the MMP of tumor-associated T cells as an indicator of cell phenotypes and immunotherapy responses in Non-Small Cell Lung Carinoma and clear cell Renal Cell Carcinoma patients. Primary tumors were collected followed by analysis of peripheral blood mononuclear cells (PBMC) prior to and after three weeks on treatment with immune checkpoint inhibition (ICI). PBMC T cells were analyzed for MMP using tetramethylrhodamine ethyl ester (TMRE) and sorted into high and low populations. TCRβ and single cell RNA sequencing of primary tumors identified and characterized peripheral blood T cell clones associated with the tumor microenvironment. As anticipated, ICI therapy increased the frequency of effector T cells in patients who experienced clinical benefit. TMREhigh peripheral blood T cells with tumor-matching TCRβ sequences had elevated oxidative phosphorylation gene signatures. Gene signatures of stress and exhaustion, such as Tigit and Cmc1, were also elevated in the TMREhigh CD8 T cell populations while gene expression patterns in TMRElow cells suggested mitochondrial fitness and cell longevity. Importantly, clinical benefit from ICI was negatively correlated with the TMREhigh CD8 T cell gene expression signature. These findings highlight the presence of a T cell population of with elevated MMP that correlates with T cell exhaustion-like states and failed response to immunotherapy.

overall_design: Peripheral blood was isolated piror to treatment and 3-6 weeks post-initaition of therapy in patients undergoing standard of care treatment with ipilimumab and nivolumab for kidney cancer and patients with lung cancer on a clinical trial receiving treatment with nivolumab and novel VEGF tyrosine kinase inhibitor, vorolanib (NCT#03583086). For single cell experiments, kidney and lung patient PBMCs were FACS sorted using BD FACS Aria II by cell singlets (FSC-A vs FSC-H and SSC-A vs SSC-H), lymphocytes, viable, CD3+, TMRE low and TMRE high. TMRE low and high populations were separated based on TMRE modal distributions.

first: Paul

last: Lindau

first: Jeffrey

last: Rathmell

first: Kathryn

last: Beckermann


title: Milk Fat Globule EGF and Factor V/VIII Domain Containing (MFGE8) as a Novel Player in Equine Endometrial Fibrosis

city: Neustadt am Rübenberge

first: Claudia

last: Klein

state: Lower Saxony

address: Höltystraße 10

department: Biotechnology

country: Germany

institute: Friedrich-Loeffler-Institut

summary: Effects of TGF β1 and MFGE8 on equine endometrial fibroblasts in vitro were investigated by single cell sequencing. Single cell sequencing revealed a certain degree of heterogeneity among cultured fibroblasts. TGF β1 exposure of fibroblasts confirmed its profibrotic effects by altered expression of transcripts associated with extracellular matrix remodeling, the upregulation of growth factors, e.g. platelet-derived growth factor B, while downregulating interferon alpha, beta, and gamma signaling. MFGE8 treatment effects were subtler, including decreased profibrotic leukemia inhibitory factor expression and an upregulation of interferon alpha and beta signaling in a subset of cells. In a fibroblast subpopulation, upregulation of phosphatase and tensin homolog signaling, indicated an antifibrotic effect of MFGE8.

overall_design: Equine endometrial fibroblasts (n=4) were seeded onto collagen-coated hydrogels 12-well plates. From 48 hours to 72 hours (treatment phase), cells were incubated using cell culture medium containing 0.1% BSA and and received either (1) no further supplementation (control) (2) were supplemented with 10 ng/ml human recombinant TGF-β1 or (3) were supplemented with 10 ng/ml mouse recombinant MFGE8. Following 24 hours of incubation, cells were harvested and processed for single cell sequencing using the Chromium Next GEM Single Cell 3’Reagent Kits v3.1, Dual Index (10x Genomics, CA, USA). Resulting libraries were subjected to paired-end (100 bp) sequencing as multiplexed pools on a NovaSeq 6000 using an S4 Reagent Kit v1.5 4XP (290 pM, 200 cycles; Illumina, CA, USA).

first: Elena

last: zu Klampen

first: Gregor

last: Neufeld


title: Single-cell transcriptome profiling of hematopoietic stem and progenitor cells in mice

city: Chengdu

first: chen

last: li

address: Renmin South Road

institute: Sichuan Univercity

summary:
The regulatory dynamics of transcription start sites (TSS) within mouse bone marrow hematopoietic stem cells are not yet fully understood. To address this, our research employed 5' scRNA-seq to ensure thorough capture of TSS data, an outcome not readily achievable with conventional 3' scRNA-seq. This technique enables the precise characterization of the transcriptome for each respective stage of cellular differentiation [CITE-seq].
To complement our 5' CITE-seq data, we also generated a 3' single-cell RNA sequencing dataset. While 5' sequencing is optimal for TSS analysis, 3'-based scRNA-seq is a robust and widely-used method for defining cell states and quantifying gene expression. This dataset serves as a foundational reference, allowing for direct comparison with the vast majority of public scRNA-seq data and providing a benchmark for validating the cellular heterogeneity within our HSPC population [3scRNAseq].
To achieve a comprehensive understanding of the transcriptomic landscape, we employed single-cell Oxford Nanopore (scONT) sequencing. This long-read, full-length transcript sequencing approach overcomes the limitations of short-read methods, enabling the identification and quantification of distinct transcript isoforms. This dataset provides critical auxiliary validation for our findings from the 5' and 3' platforms and offers deeper insights into the role of alternative splicing and isoform usage during hematopoiesis [scONT].

overall_design: Lineage-negative (Lin⁻) hematopoietic stem and progenitor cells (HSPCs) from the bone marrow of C57BL/6J mice were isolated by magnetic-activated cell sorting (MACS) and analyzed using CITE-seq、3‘ scRNA-seq and scONT.

first: Zijie

last: Xu


title: Integrated Perturb-seq and Computational Modeling Identifies KAT6A-Menin-DOT1L Synergy and Associated Gene Program as Therapeutic Targets in Acute Myeloid Leukemia [Perturb-seq]

city: Birmingham

first: Changde

last: Cheng

state: Alabama

address: 1824 6th Ave S, WTI 510G

department: Department of Medicine - Hematology & Oncology

institute: The University of Alabama at Birmingham

summary:
Background:
Acute myeloid leukemia (AML) is a heterogeneous malignancy characterized by genetic and epigenetic dysregulation. Despite advances in targeted therapies against individual epigenetic regulators, clinical responses are often transient due to complex compensatory mechanisms. Identifying functional interactions between chromatin regulators and their associated transcriptional programs represents a promising strategy to overcome resistance and enhance therapeutic efficacy.

Results:
Using Perturb-seq combined with computational modeling and machine learning approaches, we systematically investigated 16 key epigenetic regulators across the Menin-MLL, Polycomb, and histone acetyltransferase complexes in MOLM-13 cells. Single-cell transcriptomic analysis of 31,015 cells revealed 17 distinct gene programs with differential impacts on AML pathogenesis. We identified strong synergy between KAT6A and the Menin-DOT1L axis in regulating oncogenic pathways, particularly gene program P-15 (Pro-Differentiation Program), which significantly correlates with favorable clinical outcomes in both TCGA and Beat-AML cohorts. Notably, P-15 showed high expression in NPM1-mutated AML and remission-stage patients but was suppressed in TP53-mutated cases with poor prognosis. Validating our computational predictions, dual inhibition of Menin (VTP-50469) and KAT6A (WM119, a preclinical compound) demonstrated significant therapeutic synergy in MOLM-13 cells, reducing the IC50 from 35nM to 12nM. Conversely, PCGF1 disruption conferred resistance to DOT1L inhibition, revealing a novel mechanism of therapeutic resistance. Bulk RNA-seq analysis of combination treatments confirmed that dual KAT6A-Menin inhibition uniquely modulates specific gene modules associated with myeloid differentiation.

Conclusions:
Our integrated experimental-computational approach, distinct from prior studies examining individual epigenetic regulators in isolation, identifies the KAT6A-Menin-DOT1L axis as a critical regulator of AML transcriptional programs in MLL-rearranged leukemia and reveals gene program P-15 as both a favorable prognostic biomarker and potential therapeutic target. These findings provide mechanistic insights into epigenetic regulation in AML and establish a framework for developing rational combination therapies targeting cooperative epigenetic dependencies while preventing compensatory resistance mechanisms.

overall_design: Perturb seq against 16 AML target genes.

first: Sajesan

last: Aryal

first: Rui

last: Lu


title: Conversion of Th17 into exTh17 sustains rheumatoid-like IL-17-independent inflammatory arthritis [Xenium]

city: los angeles

first: yizhou

last: wang

address: 8700 beverly blvd

institute: cedars-sinai medical center

summary: T helper 17 (Th17) cells are found in peripheral blood and synovial fluid of rheumatoid arthritis (RA) patients, however IL-17-targeted interventions have shown limited efficacy in established RA. While it is known that inflammation can induce Th17 transdifferentiation into Th1- or Tr1-like IL-17-negative exTh17 cells, the role of exTh17 in arthritis is not known. Here, we explore the premise that exTh17 cells promote joint inflammation in autoimmune arthritis. To assess the potential immunophenotypic dynamics and role of exTh17 in inflammatory arthritis, we performed Th17 lineage tracing studies in the SKG mouse model of RA. We show that in arthritic mice, synovial Th17 transdifferentiate into IFNγ- and IL-10- exTh17 which become the most prominent CD4+ population in chronic arthritis. SKG exTh17 cells are more arthritogenic than Th17, and able to sustain synovial inflammation that is IL-17-independent but enriched with IL-6 and TNF, two RA-promoting cytokines. Synovial exTh17 present a unique gene signature, including upregulation of CD44 and S1PR4. This gene signature has correlates in the profile of CD4+ T cells found in human RA synovium. We further demonstrate that crosstalk between Th17 and fibroblast-like synoviocytes via S1P signaling promote Th17-exTh17 conversion. Additionally, CD44 is necessary for the arthritogenic effect of exTh17. Our study suggests that the fibroblast-like synoviocyte expansion, which occurs during RA progression, can drive progressive conversion of Th17 into exTh17 which sustains inflammation with features of human established RA. The results offer new insights that could be potentially useful for future precision therapy approaches to RA.

overall_design: Spatial Transcriptomic (Xenium 10X) on Rheumatoid Arthritis (RA) Human Synovium from RA patients

first: Martina

last: Zoccheddu

first: Kensuke

last: Suga

first: Mattias

last: Svensson

first: Paramita

last: Dutta

first: Amara

last: Seng

first: Sanaz

last: Panahandeh

first: Hadijat-Kubura

last: Moradeke Makinde

first: Myungja

last: Ro

first: Yizhou

first: Hyobin

last: Kim

first: Zbigniew

last: Mikulski

first: Katarzyna

last: Dobaczewska

first: Francesca

last: Ingegnoli

first: Ruth

last: Minsha

last: Seagrist

first: Mary

last: Carns

first: Kathleen

last: Aren

first: Salina

last: Dominguez

first: Angela

last: Denn

first: Roberto

last: Caporali

first: Pietro

last: Simone Randelli

first: David

last: McBride

first: Arthur

last: Mandelin

first: Carla

last: Cuda

first: Zhiping

middle: P

first: Jason

middle: H

last: Moore

first: Nisarg

middle: J

last: Shah

first: Kyoung

last: Won

first: Deborah

last: Winter

first: Ferhat

last: Ay

first: Harris

last: Perlman

first: Nunzio

last: Bottini


title: Expression data from Insulin Degrading Enzyme-Knocked Down alpha pancreatic cells (mouse)

city: Palencia

first: Sergio

last: Díez-Hermano

state: Palencia

address: C/Felipe II, 10, 2C

country: Spain

institute: University of Valladolid

summary:
Insulin-degrading enzyme (IDE) is a protein with proteolytic and non-proteolytic functions that regulates primary cilium.We hypothesize that IDE deficiency alter expression of genes involved in the formation of the primary cilium . To test this hypothesis we performed microarray studies in mouse alphaTC1.9 cells with a partial deficiency of IDE gene. Results show that IDE knocdown led to regulation of genes involved in cellular functions related to primary cilium.
We used microarrays to explore whether expression of genes related to cilliogenesis is affected by reduced expression of IDE gene in alpha pancreatic cells

overall_design: We used control mouse alpha cells (alphaTC1.9) and A-IDE-KD cells generated using the siRNAIDE. Microarray analyses were performed on the ClariomTM S Array (Thermofisher). Data were acquired on the GeneChipTM 3000 instrument (Affymetrix) and highthroughput automated processing was performed using the GeneTitan™ Microarray System (Thermofisher).

first: G

last: Perdomo

first: S

last: Diez-Hermano


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

middle: B

last: Ehrlich

first: James

last: Bonanno

first: Rory

last: O'Brien

first: Matias

last: Murillo

first: Sierra

last: Kauer

last: van Dijk


title: 5-ethynyluridine perturbs nuclear RNA metabolism to promote the nuclear accumulation of TDP-43 and other RNA binding proteins

city: Houston

first: Eric

last: Van Nostrand

state: TX

address: 1 Baylor Plaza Rm T334

department: Therapeutic Innovation Center

institute: Baylor College of Medicine

summary: TDP-43, an essential nucleic acid binding protein and splicing regulator, is disrupted in neurodegeneration and an urgent therapeutic target. We and others demonstrated that TDP-43 nuclear localization and function depend on the abundance of its nuclear pre-mRNA binding partners and its recruitment into large ribonucleoprotein complexes, which restricts TDP-43 nuclear efflux and maintains the critical nuclear pool of TDP-43. To further investigate the interplay between TDP-43 and nascent RNAs, we set out to employ 5-ethynyluridine (5EU), a widely used uridine analog that enables ‘click chemistry’ labeling of nascent RNAs. Unexpectedly, 5EU induced the nuclear accumulation of TDP-43 and other nuclear RNA binding proteins (RBPs) and attenuated TDP-43 nuclear exit. RNA FISH demonstrated 5EU-induced nuclear accumulation of polyadenylated and GU-rich RNAs. TDP-43 eCLIP confirmed that 5EU stabilizes TDP-43 binding to intronic sites, and TDP-43 function in cryptic exon repression remained intact. There was no major change in RNA stability, but RNA-seq demonstrated a marked alteration in RNA splicing, which is less efficient in 5EU-treated cells. Thus, 5EU perturbs nuclear RNA metabolism leading to nuclear RNA and RBP accumulation. These findings have critical implications for studies utilizing 5EU and identify a novel mechanistic inroad to support TDP-43 homeostasis.

overall_design: Two replicates each of TDP43 eCLIP were performed for cells either untreated, treated with Pol II inhibitor NVP2, treated with 5-ethynyluridine, or pre-treated with 5-ethynyluridine followed by subsequent treatment with NVP2.

first: Lindsey

last: Hayes

first: Benjamin

last: Zaepfel

first: Lauren

last: Duan

first: Anne

last: Starner

first: Mason

last: Bartels

first: Rebekah

last: Rothacher

first: Sophie

last: Martin

first: Rachel

last: French

first: Zhe

last: Zhang

first: Irika

last: Sinha

first: Jonathan

last: Ling

first: Shuying

last: Sun

first: Yuna

last: Ayala

first: Jeff

last: Coller

first: Liliana

last: Florea

first: Petr

last: Kalab


title: Synovial Th17 transdifferentiation into exTh17 sustains chronic IL-17-independent  inflammatory arthritis

first: yizhou

last: wang

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

overall_design: Refer to individual Series


title: RNA-Seq analysis of  tumor and matched normal samples from colorectal cancer patients.

city: Singapore

first: Oleg

last: Grinchuk

address: 61 Biopolis Dr, Proteos

country: Singapore

institute: IMCB

summary: Tumour cells often downregulate human leukocyte antigen (HLA) class I to evade cytotoxic T lymphocyte (CTL) immunity. Although natural killer (NK) cells target MHC-I-deficient cells, many cancers bypass NK cell-mediated killing through additional immune evasion strategies. Using CRISPR-Cas9 screening, GPC2, a cell surface protein, was identified as a key suppressor of NK cell activity against HLAnull cancer cells. GPC2 is upregulated in several cancers, correlating with poor patient outcomes. In colorectal cancer, GPC2 was found to be inversely correlated with HLA class 1 expression.

overall_design: The whole RNA-seq dataset included 2 batches: the first dataset included 40 samples (20 tumour and 20 matched normal) for 20 CRC patients and the second data set comprised of 33 samples (19 tumour and 14 matched normal) for 14 CRC patients.

first: Gloryn

last: Chia

middle: V

first: Malini

last: Rethnam

first: Yi

last: Ren

first: Sharmistha

last: Kundu


title: Effect of CHOP deficicncy of PTPMT1KO regulatory T cells

city: Cologne

first: Mauro

last: Corrado

address: Joseph-Stelzmann-Str. 26

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: Conflict resolution between the replisome and Pol II [bTMP-seq]

city: Montreal

first: Yajie

last: Huang

state: Quebec

address: 900 saint-Denis

institute: CRCHUM

summary: The replisome and RNA polymerase II (Pol II) use the sample DNA template during the S phase. Inevitably, there is a conflict between these two machineries when they try to pass each other to accomplish their respective tasks. How such a conflict is resolved, especially in mammalian cells, is a quintessential biological question of which we only have a limited understanding. Using several recently developed techniques, we determined in vivo the replication fork speed, direction, and interruption when the replisome met Pol II. Based on nsRNA-seq of the mouse embryonic fibroblasts (MEFs), we revealed that a tiny fraction of all the genes, i.e., about 1.5 %, downregulated their transcription during the S-phase compared to the G1 phase. A moderate 20% reduction of II density in the S-phase-enriched  MEFs compared to asynchronous MEFs was observed. These two means represent the means of temporal segregation from replication. A moderate and significant bias (about 17% difference) was found favoring the co-directional forks over head-on forks. The encounter between the replisome and Pol II was quite eventful. About 21% of the forks were aborted in the Pol II-dense TSS region. Although the majority of the forks could still pass the TSS region, they hesitated and slowed down when the tips of the forks approached the Pol II dense region. Paradoxically, the forks traveled faster in genome regions dotted with more Pol IIs as long as their tips were not near the latter, probably due to a higher degree of chromatin negative supercoiling near Pol IIs. Our study demonstrated that the mammalian cells relied on multiple measures, such as temporal segregation, co-direction preference, and fork abortion, to mitigate the danger of replication-transcription conflict, but all these measures operated only as auxiliaries. The majority of the forks could pass Pol IIs unscathed, indicating the existence of a so-far unidentified, very efficient conflict resolution mechanism.

overall_design: bTMP-seq of Armc5 knock-out and wild-type mouse embryonic fibroblasts from E13.5 mice.

first: Hongyu

last: Luo

first: Jiangping

last: Wu