title: Two distinct SWI/SNF complexes direct chromatin-linked transcriptional programs in Toxoplasma [RNA-Seq]

city: Cambridge

first: Dominic

last: Schwarz

address: 455 Main St

department: Biology

institute: Massachusetts Institute of Technology

summary: Chromatin remodeling complexes dynamically modify DNA accessibility to mediate changes in gene expression during eukaryotic cell cycle progression, developmental transitions, and environmental adaptation. Higher eukaryotes have multiple remodeler subtypes based on the incorporation of different ATPases; however, the coordination and functional specificity of these diverse complexes is not well understood. Apicomplexan parasites such as Toxoplasma gondii have a limited set of chromatin remodelers offering a divergent setting in which to explore the function of homologous complexes. These parasites have selectively retained the Myb domain–containing proteins with homology to chromatin-associated regulators like SNF2h and SWI3. Here, a comprehensive analysis of the Myb protein family in Toxoplasma defines the composition of two SWI3 complexes with mutually exclusive ATPase homologous—TgSNF2a and TgSNF2b. Integrating transcriptomics with a custom chromatin-profiling strategy, we show that TgSNF2a is essential for the timely transcription of genes, while TgSNF2b ensures global transcriptional competency and fidelity throughout the cell cycle and developmental transitions. Cell cycle–resolved chromatin profiling conclusively shows the shift from TgSNF2b to TgSNF2a occupancy when regulated genes transition from being poised to being actively transcribed. Our findings demonstrate that TgSNF2a and TgSNF2b perform distinct yet interdependent regulatory roles shaped by their chromatin context. This work uncovers ancestral principles of chromatin regulation and offers new insight into the functional diversification of SWI/SNF complexes across eukaryotes.

overall_design: Transcriptomic profiling following auxin-induced conditional knockdown of nuclear-localized, fitness-conferring Myb proteins and the SWI/SNF helicases TgSNF2a and TgSNF2b at 6, 12, or 24 hours post-treatment, each tagged with a minimal auxin-inducible degron (mAID).

first: Sebastian

last: Lourido


title: Stromal and Endothelial Transcriptional Changes during Progression from MGUS to Myeloma and after Treatment Response [scRNA-seq]

status: Public on Apr 26 2026

city: Pamplona

first: Itziar

last: Cenzano

state: Navarra

address: Avenida de Pio XII, 55

country: Spain

institute: CIMA Universidad de Navarra

type: Expression profiling by high throughput sequencing

summary: The role of the non-immune bone marrow microenvironment (BME) in the transition from monoclonal gammopathy of undetermined significance (MGUS) into clinically active multiple myeloma (MM) remains incompletely defined. To address this, we transcriptionally profiled endothelial cells (EC), mesenchymal stem cells (MSC), and MM cells at single-cell resolution from genetically engineered mouse models (BIc1 and MIc1) that recapitulate MGUS to MM progression. Our analysis of the BIc1 model revealed distinct transcriptional alterations in EC and MSC, uncovering stage-specific BME-PC interactions shaping disease progression. Interestingly, we identified an interferon (IFN)-related myeloma signature in both EC and MSC that was reversed after treatment with bortezomib (Velcade), lenalidomide (Revlimid), and dexamethasone (VRd).

overall_design: We performed single-cell RNA sequencing (scRNA-seq) on FACS-sorted non-hematopoietic bone marrow cells and GFP+ plasma cells (PC) from BIcγ1 and MIcγ1 murine models that recapitulate human MGUS and MM, with YFPcγ1 mice as controls. In BIcγ1 mice carrying humanized CRBN, a VRd treatment arm (bortezomib, lenalidomide, dexamethasone; oral gavage, 20 weeks) was included to assess therapy-induced BME remodeling. For each experiment, bone marrow cells from 4–6 mice were pooled, and ~15,000 cells per sample were processed using the 10x Genomics Single Cell 3′ v3.1 workflow. Libraries were sequenced on an Illumina NextSeq 2000.

first: Felipe

last: Prosper


title: Transcriptome Analysis of Palmitic Acid-treated Human Primary Hair Follicle Stem Cells

city: Guangzhou

first: shizhao

last: liu

address: guangzhou avenue north

country: China

institute: southern medical university

summary: The effect of palmitic acid (PA) on human primary hair follicle stem cells (HFSCs) remains unclear. In this study, HFSCs were treated with PA or vehicle control, and transcriptome sequencing was performed to investigate the molecular alterations. Our results indicate that PA treatment activates peroxisome proliferator-activated receptor (PPAR) and other related signaling pathways. This dataset provides a comprehensive transcriptional profile of PA-treated HFSCs, offering insights into the potential regulatory mechanisms of PA in hair follicle biology and serving as a resource for further studies on lipid metabolism and stem cell function.

overall_design: The study was designed with two experimental groups: untreated control hair follicle stem cells (HFSCs), and HFSCs treated with palmitic acid (PA). Each group included three independent biological replicates.


title: Two distinct SWI/SNF complexes direct chromatin-linked transcriptional programs in Toxoplasma [CUT&Run]

state: MA

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Chromatin profiling of Toxoplasma gondii SWI/SNF complexes using parasites expressing C-terminally 2xALFA-tagged TgSWI3, TgSNF2a, or TgSNF2b. It should be noted that in previous versions of this manuscript, TgSNF2a was designated as TgBRG1, TgSNF2b as TgBRM and TgTFIIIB as TgBDP1.


title: Aging restricts maturation of CXCL13+ T follicular helper cells in human immunity

status: Public on Apr 27 2026

city: Palo Alto

first: Mark

middle: M

last: Davis

state: California

address: 240 Pasteur Drive

institute: Stanford

summary: Secondary lymphoid organs are concentrated sites of adaptive immune responses, but how these structures change over the lifespan is unclear. Recent work has revealed unique alterations to T follicular helper (Tfh) cells in older individuals. However, the gene-regulatory control of Tfh cell development in the context of aging has not been explored. Here, we characterized Tfh cells from human tonsil tissue, finding impaired B cell help, reduced tissue organizational cues, and restricted development with age. Maturation of Tfh cells in older adults was limited by gene-expression programs acquired during early differentiation of naïve CD4T cell precursors, including targets of critical transcriptional regulators like TCF7 and LEF1. Collectively, these results suggest that the transcriptional control of naïve CD4T cell differentiation has a lasting impact on subsequent Tfh maturation. Therefore, the state of the naïve CD4T cell pool during human aging can impair the ability to mount a protective adaptive immune response.

overall_design: Cryopreserved tonsil and PBMC single-cell suspensionsn from human donors were thawed and CD3+ T cells were magnetically enriched. Cells were stained with TotalSeqC antibodies against CD3, CD4, and CD8, along with either a tonsil- or PBMC-specific antibody barcode. Labeled tonsil and PBMC samples for each donor were then combined, and Individual gene expression (GEX), Antibody Dependent Tag (ADT), and T Cell Receptor (TCR) libraries were prepared and sequenced.

first: Nathan

middle: A

last: Bracey

first: Casey

last: Beppler

first: Tatjana

last: Bilich


title: Two distinct SWI/SNF complexes direct chromatin-linked transcriptional programs in Toxoplasma.

overall_design:
Chromatin profiling of synchronized Toxoplasma gondii parasites expressing SWI/SNF complex components TgSNF2a or TgSNF2b C-terminally tagged with 2xALFA. It should be noted that in previous versions of this manuscript, TgSNF2a was designated as TgBRG1 and TgSNF2b as TgBRM.

Please note that the sample titles have been updated on April 27, 2026.


title: Identification of Aging-Related Signature Genes in Temporomandibular Joint Degeneration Based on Bioinformatics

city: Beijing

first: Xinyi

last: Wang

state: Ms.

address: Haidian district

department: Prosthodontics

institute: Peking University School and Hospital of Stomatology

summary: Background: Temporomandibular joint (TMJ) degenerative diseases are increasingly affecting elderly populations, with aging being a significant risk factor driving the TMJ changes. This study aims to explore the shared characteristics between aging and TMJ degenerative diseases at the tissue level, and to identify aging-related signature genes in TMJ degenerations using bioinformatics approaches. Methods: Young (2 months of age, n=7) and aged (18 months of age, n=6) mice’s condyles were used to construct an aging dataset. Overlapping genes were selected from differentially expressed genes in the TMJOA dataset, aging dataset and mechanical stimulation dataset.  Temporomandibular joint osteoarthritis-associated and aging-related differentially expressed genes (TMJOA-ARDEGs) were identified through Weighted gene co-expression network analysis. Functional enrichment analysis and Protein-Protein Interaction networks were employed. Machine learning was applied to select Hub temporomandibular joint osteoarthritis-associated and aging-related differentially expressed genes (Hub TMJOA-ARDEGs). An age-related TMJOA mouse model (18 months of age) was established and grouped based on the micro-CT and the modified Mankin scores. The expression changes of key Hub TMJOA-ARDEGs were verified by immunohistochemical staining. The Mann-Whitney U test was used in non-normally distributed data, presented as [median (interquartile range)]. Results: Fifty-two TMJOA-ARDEGs were identified, with functional enrichment analysis revealed that these genes participate in circadian rhythm and apoptosis. Eight Hub TMJOA-ARDEGs were identified, ANK1, MELTF, FERMT3, MDFI, CXCL14, EPHA3, SMOC2 and NR1D1. Based on the micro-CT, 12 TMJs of aged mice were divided into the TMJOA group (n=6) and the healthy group (n=6). Micro-CT revealed bone resorption in the TMJOA group compared to the healthy group, with a decrease in BV/TV (p<0.05) and an increase in Tb.Sp (p<0.05). The modified Mankin scores showed that the TMJOA group had a score of 5.61 (2.28), higher than the healthy group's score of 0.83 (1.28), p<0.01. These results confirm the validity of the model grouping. Among the Hub TMJOA-ARDEGs, NR1D1 is a key gene involved in regulating circadian rhythm. In immunohistochemical staining, the expression level of NR1D1 showed significantly elevated expression in osteoarthritis mice (p<0.01). Conclusion: NR1D1, a negative feedback regulator in the circadian rhythm loop, is a characteristic gene associated with both aging and TMJ degenerative diseases.

overall_design: We used bulk RNA sequencing to detect differences in gene expression between young (2 months old, n=7) and aged (18 months old, n=6) mice in temporomandibular joint cartilage. RNA was extracted directly from the mandibular condylar cartilage.

first: Ziyang

last: Xia

first: Minda

first: Yanzhang

last: Zhou

first: Ting

last: Jiang

first: Jingwen

last: Yang


title: Oncolytic vaccinia virus JX-594 demonstrates subtype-specific efficacy and predictive biomarkers in gastric cancer cell lines

city: 강남구

first: Inho

last: Park

state: 서울특별시

address: Dept. of Pathology, Gangnam Severance Hospital, 20, Eonjuro 63gil

department: Yonsei University College of Medicine

country: South Korea

institute: Yonsei University College of Medicine

summary: This project investigates the therapeutic potential of the oncolytic vaccinia virus JX-594 in gastric cancer. We analyzed 49 molecularly characterized GC cell lines and xenograft models, and performed transcriptomic profiling to identify subtype-specific responsiveness and explore predictive biomarkers that may guide clinical application.

overall_design: RNA-seq was performed for 49 molecularly characterized gastric cancer cell lines. Total RNA was extracted using the RNeasy Mini Kit (Qiagen), quality-assessed with NanoDrop and Bioanalyzer, and sequenced on the Illumina HiSeq 2500 platform using 2×100 bp paired-end reads.

first: Jee Hung

last: Kim

first: YeLin

first: Youkeun

last: Shin

first: Woo Sun

last: Kwon

first: Tae Soo

first: Namhee

last: Lee

first: Keunhee

last: Oh

first: Chan

first: Hei-Cheul

last: Jeung

first: Sun Young

last: Rha


title: scRNA-Seq of CD45+ cells in B16F10 tumor after adoptive cytotoxic T lymphocyte immunotherapy

city: Osaka

first: Koji

last: Nagaoka

address: 377-2 Ohno-Higashi, Osaka-Sayama

department: Department of Immunology

country: Japan

institute: Kindai University Faculty of Medicine

summary: Although adoptive cell transfer (ACT) with tumor-specific CD8⁺ T cells induces initial tumor regression, tumors often relapse due to incomplete eradication and immune evasion. To investigate the mechanisms of tumor regrowth after ACT, we performed single-cell RNA sequencing (scRNA-seq) of tumor-infiltrating immune cells in a murine melanoma model. B16F10 melanoma-bearing C57BL/6 mice were treated with gp100-specific Pmel-1 cytotoxic T lymphocytes (CTLs). Tumors were harvested on days 3, 7, and 14 post-transfer, and CD45⁺ immune cells were isolated for 10x Genomics Chromium-based scRNA-seq. This dataset supports the analysis of immune cell states during tumor progression after ACT.

overall_design: C57BL/6 mice were subcutaneously inoculated with B16F10 melanoma cells. On day 9 after tumor inoculation, mice received intravenous adoptive transfer of in vitro-activated gp100-specific Pmel-1 cytotoxic T lymphocytes (CTLs). Tumors were harvested on days 3, 7, and 14 following ACT. Tumors from individual mice were enzymatically dissociated into single-cell suspensions, and CD45⁺ immune cells were isolated from each sample using magnetic bead-based selection. Equal numbers of CD45⁺ cells from three mice were pooled at each time point and subjected to single-cell RNA sequencing using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index).

first: Kazuhiro

last: Kakimi


title: CD24+ human dental papilla cells as translational seed cells for dentin-pulp regeneration via BMP2/SIRT1 metabolic axis

city: chengdu

first: Cheng

last: Liang

state: sichuan

address: 14, Section 3, South Renmin Road, Chengdu, Sichuan, China

institute: Sichuan University West China School of Stomatology

summary: Regeneration of the dentin-pulp complex is a central goal in dental tissue engineering, essential for restoring both structural integrity and biological function of damaged teeth. However, the inherent heterogeneity of dental stem cells limits our understanding of lineage-specific subsets critical for efficient odontogenesis and regenerative outcomes. Here, we identify a distinct subpopulation of human dental papilla cells (hDPCs) marked by CD24 expression. CD24⁺ hDPCs exhibit robust odontogenic differentiation capacity, preferential localization to odontoblast-generating regions during tooth development, and accumulation beneath reparative dentin in carious teeth. Functionally, CD24⁺ hDPCs drive coordinated regeneration of well-vascularized pulp and structurally integrated dentin tissues in both ectopic murine and preclinical in situ minipig models, significantly outperforming conventional dental pulp stem cells. Mechanistically, we delineate a BMP2-driven metabolic axis in which elevated BMP signaling sustains SIRT1 expression and promotes mitochondrial metabolism. Inhibition of BMP signaling disrupts this axis, activating WNT signaling, reducing SIRT1 expression, compromising antioxidant and autophagic responses, and consequently diminishing odontogenic capacity. Furthermore, BMP signaling in CD24⁺ hDPCs induces VEGF expression, enhancing endothelial cell recruitment and neovascularization via paracrine effects. CD24 also acts as a downstream marker of odontogenic BMP signaling, reflecting BMP pathway activation and correlating with odontogenic potential, although it does not directly mediate differentiation. Together, our findings characterize CD24⁺ hDPCs as a regeneration-competent subpopulation that integrates mitochondrial metabolism and signaling crosstalk to enable coordinated dentin and pulp regeneration, representing a translationally relevant cell source for dental tissue engineering.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Gene expression profiling of CD24⁻ and CD24⁺ hDPCs in vitro culture and regenerated pulp tissue at 2 weeks post-implantation.

first: Zhi

last: Liu

first: Jie

last: Li

first: Cong

last: Han

first: Yu

last: Gao

first: Bohuai

first: Qiuyu

last: Chen

first: Fei

last: Bi

first: Weimin

last: Wu

first: Tiantian

last: Hu

first: Jingyi

last: Zhang

first: Ding

last: Bai

first: Yiping

first: Weidong

last: Tian

first: Tian


title: FBXL6 promotes bladder cancer progression by stabilizing ENO1 through K63-linked ubiquitination

city: Wuhan

last: Xiao

address: Donghu Road 169

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

summary: Ubiquitin-mediated post-translational modifications play critical roles in tumor progression, yet their regulatory mechanisms in bladder cancer (BLCA) remain incompletely understood. Here, we identified FBXL6, belonging to the F-box protein family, as a potential oncogenic driver in BLCA through integrative bioinformatic analysis of multiple public datasets and validation in clinical specimens. Functional analyses demonstrated that FBXL6 accelerates both the in vitro proliferation and migration of BLCA cells and the in vivo progression of tumors and metastatic spread. Mechanistically, transcriptomic profiling and metabolic analyses suggested that FBXL6 regulates glycolysis, with particular involvement of the glycolytic enzyme ENO1. While ENO1 mRNA remained largely unchanged upon FBXL6 knockdown, Western blot analysis revealed corresponding changes in ENO1 protein levels, indicating post-transcriptional regulation. Co-immunoprecipitation assays confirmed a physical interaction between FBXL6 and ENO1, and domain-mapping analysis revealed that the leucine-rich repeat (LRR) region of FBXL6 mediates ENO1 binding. Moreover, ubiquitination assays demonstrated that FBXL6 enhances K63-linked polyubiquitination of ENO1, leading to its stabilization. Restoration of ENO1 expression partially rescued the suppressed proliferation and migration induced by FBXL6 knockdown, as demonstrated by rescue assays. Overall, our data support a novel model in which FBXL6 facilitates BLCA progression through K63-linked stabilization of ENO1, highlighting its potential value in targeted therapy for bladder cancer.

overall_design: To uncover the underlying mechanism by which FBXL6 promotes BLCA tumor growth and metastasis, RNA-seq analysis was performed on T24 cells transfected with siNC or siFBXL6.

first: Ruoyu

last: Huang

first: Xinghuan

last: Wang


title: Histone H4 lysine 20 tri-methylation safeguards breast cancer lineage fidelity and unfolded protein response [scRNA-seq]

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave. S1070

institute: Dana-Farber Cancer Institute

summary: Triple-negative breast cancer (TNBC) is a breast cancer subtype with worse prognosis and limited therapeutic options, partly due to significant epigenetic heterogeneity both within and between tumors. We previously reported that histone H4 lysine 20 trimethylation (H4K20me3) is the most variable histone modification in TNBC. H4K20me3 showed an opposing genomic distribution to other H4 acetylations and was essential for histone integration with a subset of distal intergenic genomic regions. Unlike H3K9me3, H4K20me3 exhibited greater heterogeneity across tumors and normal mammary glands. Regions uniquely enriched for H4K20me3 have higher epigenetic and transcriptional activity. Inhibition of the H4K20me3 methyltransferase, KMT5B/5C using A-196 led to substantial H4K20me3 loss and H4K20me1 gain at regions associated with lineage-specificity, stress response, and cell cycle regulation. A-196 treatment moderately suppressed tumor growth in vivo, inducing mesenchymal transition and unfolded protein response (UPR) in cancer cells, and increased proinflammatory macrophage infiltration into the tumor microenvironment. Integrated multi-omic analysis revealed that mesenchymal TNBCs, with the lowest H4K20me3 levels, have more active chromatin at UPR genes and stronger responses to ER stress inducers. Consistently, KMT5B/5C inhibition in basal TNBC induced mesenchymal-like features, heightened ER stress response and the associated cell proliferative suppression through increased G1 arrest, driven by the de novo recruitment of the transcriptional repressor E2F4. Combining A-196 with the HSP90 inhibitor 17AAG synergistically reduced TNBC tumor growth. Overall, our study identifies H4K20me3 as a facultative heterochromatin mark regulating lineage identity and UPR in TNBC, offering novel epigenetic therapeutic strategies targeting KMT5B/5C.

overall_design: Exponentially growing cells (4T1 and EMT6) were resuspended in ice cold PBS and 50% Matrigel (BD Biosciences) and orthotopically injected into the inguinal mammary fat pads in a 50 μl volume of 6-week-old female Balb/c mice. Mice were randomized after all mice developed palpable tumors to ensure no pre-treatment tumor volume differences. Compounds were administered as below: Vehicle (90% corn oil+10% DMSO) and A-196 (25mg/kg daily oral gavage). Animals were euthanized, and tumors were harvested when tumors in the control group reached ~ 2 cm3 size.

first: Li

last: Zheqi

first: Polyak

last: Kornelia


title: Histone H4 lysine 20 tri-methylation safeguards breast cancer lineage fidelity and unfolded protein response [Bulk RNA-seq]

overall_design: For in vitro experiment, SUM149 cells were treated with or without 1μM A196 for 5 days and subjected for 1μM Tunicamycin treatment for 12 hours. For in vivo xenograft experiment, exponentially growing cells were resuspended in ice cold PBS and 50% Matrigel (BD Biosciences) and orthotopically injected into the inguinal mammary fat pads in a 50 μl volume of 6-week-old female female NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice. Mice were randomized after all mice developed palpable tumors to ensure no pre-treatment tumor volume differences. Compounds were administered as below:  A-196 (25mg/kg daily oral gavage),  17AAG (12.5mg/kg, 5 days/week intraperitoneal injection) or their combination. All compounds were dissolved in 90% corn oil + 10% DMSO. Animals were euthanized, and tumors were harvested when tumors in the control group reached ~ 2 cm3 size


title: Histone H4 lysine 20 tri-methylation safeguards breast cancer lineage fidelity and unfolded protein response

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

overall_design: Refer to individual Series


title: Histone H4 lysine 20 tri-methylation safeguards breast cancer lineage fidelity and unfolded protein response [ChIP-seq/ATAC-seq]

overall_design: For in vitro experiment, cells were profield under three different designs: 1) baseline charaterization without any treatment; 2) 0,1% DMSO (vehicle) or 1μM A196 treatment for 5 days; 3) wiuth or without pretreatment of 1μM A196 treatment for 5 days and further in the presence or absence of 1μM Tunicamycin treatment for 12 hours.


title: Tumor-Suppressing Multi-Enterobacteria enhance the anti-PD-1/PD-L1 efficacy in microsatellite stable colorectal cancer

first: xiaoting

last: Su

state: Hubei

address: Tongji Hospital, No. 1995, Jiefang Avenue, Wuhan, Hubei

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Gut microbiome significantly influences immunotherapy responses in colorectal cancer (CRC) treatment. While individual enterobacteria have been identified as enhancers of anti-PD-1/anti-PD-L1 therapy, the synergistic effects of multiple enterobacteria remain underexplored. To fill the gap, we introduced Tumor-Suppressing Multi-Enterobacteria (TSME), a consortium of nine beneficial intestinal probiotic strains, and investigated its impact on the anti-PD-1/anti-PD-L1 therapy for microsatellite stable (MSS) CRC. Using a tumor-bearing mouse model and genomic sequencing techniques, our research demonstrated that TSME significantly improved therapy efficacy by optimizing tumor immune microenvironment. Specifically, the addition of TSME notably increased CD8+ T infiltration, modulated cytokine profiles, and up-regulated crucial immune-related pathways, including TNF and JAK-STAT. Additionally, TSME altered intestinal microbial composition, enriching beneficial bacteria such as Akkermansia and Alistipes. These findings suggest that the well-engineered multi-enterobacteria could significantly enhance the effectiveness of immunotherapy for MSS CRC by synergistically modulating the immune and microbial landscapes.

overall_design:
To explore the synergistic effect of tumor suppressing multi-enterobacteria (TSME) in enhancing the anti-PD-1/PD-L1 efficacy in microsatellite stable colorectal cancer (MSS CRC), we developed a a murine model by inoculating mice with CT26 cells.
To assess the changes in gene expression linked to the treatment, we performed RNA sequencing on mouse tumor tissues from various treatment groups.
To examine alterations in the gut microbiota resulting from the combined administration of αPD-L1 and TSME in CT26 tumor-bearing mice, we isolated DNA from the fecal samples of these mice and conducted 16S rDNA sequencing analysis.

first: Xiaoting

first: Mingsheng

first: Zhou

first: Fang


title: CTCF-binding sites demarcate chromatin domains enriched with H3K9me2 or H3K9me3 and restrict the spreading of these histone modifications in human cells

city: Busan

first: Jin

last: Kang

address: 2, Busandaehak-ro 63beon-gil, Geumjeong-gu

department: Department of Molecular Biology

institute: Pusan National University

summary: CTCF-binding sites are frequently found at the boundaries of chromatin domains enriched with specific histone modifications in vertebrate genomes, where they function as barriers that limit the spreading of these modifications. However, the role of CTCF-binding sites in chromatin domains marked by H3K9me2 or H3K9me3 remains poorly understood. In this study, we analyzed CTCF-binding sites and the distribution of H3K9me2 and H3K9me3 around these sites in human K562 cells, and investigated the spreading of these modifications following CTCF depletion. Genome-wide analysis revealed that certain CTCF-binding sites are located at the boundaries of chromatin domains enriched with H3K9me2 or H3K9me3. Upon loss of CTCF binding, both modifications spread to neighboring chromatin at over half of boundaries delimiting highly and distinctly enriched domains. Boundaries where such spreading did not occur (non-spreading boundaries) were flanked by regions with a more active chromatin state compared to those where spreading occurred (spreading boundaries). Gene transcription was significantly reduced in neighboring regions where H3K9me2 or H3K9me3 had spread. Further comprehensive analysis revealed that this transcriptional reduction was specifically associated with the spread of H3K9me2 rather than H3K9me3. These findings suggest that CTCF-binding sites demarcate chromatin domains enriched with H3K9me2 or H3K9me3 and act as barriers to the propagation of these modifications in mammalian cells. Notably, the spread of H3K9me2 appears to play a specific role in transcriptional repression.

overall_design: H3K9me2, H3K9me3, and H3K9ac ChIP-seq and total RNA-seq were performed in control and/or CTCF knockdown (CTCFi) K562 cells.

first: AeRi

last: Kim


title: mRNA expression profiling of A549 cells treated with TSA at different time points

first: Lifei

last: Ma

address: 5 Dong Dan San Tiao

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Cellular senescence (CS) refers to a stable arrest of the cell cycle characterized by an altered profiles of gene expression networks. However, a reliable strategy to quantify senescent levels is lacking. Here we developed a machine learning-based tool (Predictive Cellular Senescence Model, PreCSenM) that addresses this issue by defining senescent levels as CS score through incorporating senescent features from multiplatform data. While applying this model to predict clinical outcomes in patients with lung adenocarcinoma (LUAD), PreCSenMo identified that HDAC inhibitors (HDACi) can trigger LUAD cellular senescence. To reveal the transcriptional profiling dynamics of HDACi-induced senescence in lung cancer cells, we performed RNA-seq of A549 treated with TSA at different time points.

overall_design: Transcriptional profiling of A549 cells which exposed to growth medium containing TSA (300 nM) under different conditions (Control, 6, 12, 24, and 48 h). Duplicate experiments for each condition were performed to obtained samples for RNA-seq.

first: Huiyang

last: Li

first: Xiaoman

first: Houzao


title: Gene expression profiling from human WPMY1 cells with control or WNT5A knockdown.

city: Minato-ku

first: Takahashi

last: Sayuri

state: Tokyo

address: 4-6-1 Shirokanedai

institute: The University of  Tokyo

summary: WPMY1 cells stably transduced with control or WNT5A shRNA were established. Total RNA was isolated from 5x 10^6 cells of each

overall_design: To test the effect of depleting WNT5A on the gene expression of myofibroblast stromal cells, human WPMY1 cells were transduced with lentivirus for shRNA targeting WNT5A or non-targeting control shRNA.

first: Sayuri

last: Takahashi


title: Epigenetic profiling of A549 cells treated with TSA [ATAC-seq]

summary: Cellular senescence (CS) refers to a stable arrest of the cell cycle characterized by an altered profiles of gene expression networks. However, a reliable strategy to quantify senescent levels is lacking. Here we developed a machine learning-based tool (Predictive Cellular Senescence Model, PreCSenM) that addresses this issue by defining senescent levels as CS score through incorporating senescent features from multiplatform data. While applying this model to predict clinical outcomes in patients with lung adenocarcinoma (LUAD), PreCSenMo identified that HDAC inhibitors (HDACi) can trigger LUAD cellular senescence. To reveal the epigenetic profiling dynamics of HDACi-induced senescence in lung cancer cells, we performed ATAC-seq of A549 treated with TSA.

overall_design: Epigenetic profiling of A549 cells which exposed to growth medium containing TSA (300 nM) under different condition (Control and 12h).

first: Hou-Zao

last: Chen


title: Epigenomic-transcriptional network during neural crest cell differentiation [DNA methylation]

city: Saitama

first: Kyosuke

last: Mukae

state: Kitaadachi-gun

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

institute: Saitama Cancer Center

summary: Neural crest cells (NCCs) originate from the neural tube during early embryogenesis, and they are a pivotal cell population involved in vertebrate development. NCCs are mainly divided into cranial NCCs (cNCCs) and trunk NCCs (tNCCs), which subsequently differentiate into diverse tissues and organs. Proper differentiation and fate determination into NCCs are essential for normal development and survival of individuals, and abnormal differentiation of NCCs can lead to various diseases such as cardiac disorders and tumors. Epigenetic mechanisms, including histone modification and DNA methylation, are crucial for regulating NCC differentiation. However, the specific mechanisms of DNA methylation underlying the differentiation of cNCCs and tNCCs remain poorly understood. This study aimed to address this knowledge gap by comparing the differentiation mechanisms of cranial and trunk NCCs derived from human induced pluripotent stem cells. Through integrated analysis of the transcriptome and DNA methylome data, we found that along with differentiation, DNA demethylation upstream of the transcription start sites of myocyte enhancer factor 2C (MEF2C) in cNCCs and thyroid hormone receptor alpha-2 (THRA2) in tNCCs led to increased expression of these genes. Furthermore, MEF2C and THRA2 were found to potentially regulate NCC markers. Our findings contribute to a detailed understanding of regulatory mechanisms of DNA methylation in normal NCC differentiation and may provide insights into the pathogenesis of NCC-related diseases such as neuroblastoma.

overall_design: Genomic DNA was isolated from iPSCs, cNCCs, and tNCCs of 414C2, 201B7, and 604A3 cells using a proteinase K (FUJIFILM) method with subsequent purification by phenol-chloroform (NIPPON GENE, Tokyo, Japan). After RNase treatment and additional purification, genome-wide DNA methylation analysis was conducted using an Infinium MethylationEPIC BeadChip v.1.0 (Illumina, San Diego, CA, USA). Each sample was analyzed once because of the high analytical reproducibility of this microarray. The microarray assessed the degree of methylation of 862,927 probes with a β-value ranging from 0 (unmethylated) to 1 (fully methylated). To reduce the data size for convenient handling, neighboring probes (CpG sites) were assembled into a genomic block consisting of probes within 500 bp using MACON. A genomic block was annotated based on its relative location from the transcription start site (TSS) and against a CpG island. All 862,927 probes were assembled into 551,478 genomic blocks, and 538,523 blocks on the autosomes were used for methylation analysis. The DNA methylation level of each genomic block was calculated as the mean β value of all probes within the genomic block.

first: Takehiko

last: Kamijo

first: Naoko

last: Hattori

first: Satoshi

last: Yamashita

first: Toshikazu

last: Ushijima


title: TCF7L2 Promotes Abdominal Aortic Aneurysm through Smooth Muscle Cell-Mediated Extracellular Matrix Remodeling [RNA-seq]

status: Public on Apr 25 2026

city: Ann arbor

first: Yongjie

last: Deng

address: 2800 Plymouth Rd. NCRC blg26, Rm355s

institute: University of Michigan

summary: Abdominal aortic aneurysm (AAA) lacks effective pharmacological therapies. Here, we investigate transcription factor 7-like 2 (TCF7L2), a genetic locus associated with both thoracic and abdominal aortic aneurysms, to elucidate its role in AAA pathogenesis. Integrating summary-data-based Mendelian randomization (SMR) with single-cell RNA sequencing (scRNA-seq) of human and mouse aortas, we identify TCF7L2 as a gene enriched in vascular smooth muscle cells (VSMCs) and causally linked to AAA development. Smooth muscle cell-specific TCF7L2 knockout significantly attenuates AAA formation across three distinct murine models (Ang II infusion-, BAPN/Ang II co-administration-, and elastase-induced AAA), independent of systemic blood pressure or lipid levels. Mechanistic studies reveal that TCF7L2 directly upregulates MMP14 and downregulates TIMP3 expression, driving MMP2-mediated extracellular matrix (ECM) degradation. Concurrently, TCF7L2 represses integrin β1 (ITGB1) expression, reducing VSMC adhesion to the ECM. Collectively, these findings identify TCF7L2 as a key driver of pathological vascular remodeling in AAA, suggesting that targeting TCF7L2 may offer a novel therapeutic strategy for limiting AAA progression.

overall_design: RNA-seq profiling of human aortic smooth muscle cells (HASMCs) transfected with control siRNA or TCF7L2-targeting siRNA under vehicle-treated conditions, with 4 biological replicates per group.

first: Yaozhong

last: Liu

first: Yang

last: Zhao

first: Hongyu

first: Guizhen

first: Zhenguo

last: Wang

first: Xu

last: Zhang

first: Chao

last: Xue

first: Wei

last: Huang

first: Tianqing

last: Zhu

first: Haocheng

last: Lu

first: Yanhong

last: Guo

first: Lin

last: Chang

first: Ida

last: Surakka

first: Eugene

first: Jifeng


title: Epigenomic-transcriptional network during neural crest cell differentiation [gene expression]

first: Kyosuke

last: Mukae

overall_design: Total RNA was extracted from iPSCs, cNCCs and tNCCs, and a microarray analysis was performed using the Agilent platform of 8x60 K design ID G4851B (Agilent Single Color. 39494, Agilent Technologies). Two hundred nanograms of total RNA was labeled with Cyanine3 using a Low Input Quick-Amp Labeling Kit (one color, Agilent Technologies) according to the manufacturer’s instructions. Purified labeled total RNA was hybridized to the expression microarray. Hybridization, the scanning of microarrays, and data extraction from scanned images were conducted according to Agilent protocol version 6.9.

first: Takehiko

first: Mik

last: Ohira


title: Autophagy mutant cells accumulates proteins involved in cell proliferation desiccation and rehydration in Physcomitrium patens

summary: Autophagy is the process responsible for degrading cytoplasmic components in lysosomes and vacuoles. It has been widely accepted that autophagy contributes to cellular survival against stress, since autophagy-deficient (atg) mutants are predominantly more sensitive to environmental stress, including nutrient starvation, than their wild-type (WT) counterparts. However, Physcomitrium atg mutants are able to survive from desiccation stress compared with WT under presence of ABA. The molecular mechanism is not understood. In this study, comparative proteomic and microarray expression analysis were performed for WT and atg mutant protonemal colonies of Physcomitrium. Integrated analysis showed that signaling pathways involved in MYB, MAPK were activated, and that protective proteins such as LEA and antioxidant-related proteins were not differentially expressed between WT and atg mutant. This suggests that atg mutant was highly tolerant to desiccation stress by activating cell proliferation during both dehydration and rehydration processes. Also, yeast microarray analysis using publicly available data showed that signaling pathways involved in cell proliferation, such as MYB, were activated in rehydration. This shows that activation of cell proliferation is important for inducing desiccation tolerance. This study has provided new evidence that autophagy is involved in the relationship between desiccation tolerance and cell proliferation, but we have not been able to pinpoint its direct effect. Further work is needed to elucidate the dynamics of proteins in autophagy and induction of desiccation tolerance.

overall_design: Total RNAs were extracted from WT and atg5 colonies of 7-day-old protonema (hydration), 24h after ABA (ABA), 24h after dehydration (dehydration) and 24h after rehydration (rehydration). A microarray-based expression profile was performed using the custom microarrays of two color for Physcomitrium (4 × 44 K format) of Agilent platform (Agilent Technologies, California, USA). Briefly, 400 ng of total RNA was labelled with cyanine3 or cyanine5 using a low input quick-amp labelling kit according to the manufacturer’s instructions.


title: TCF7L2 Promotes Abdominal Aortic Aneurysm through Smooth Muscle Cell-Mediated Extracellular Matrix Remodeling [ChIP-Seq]

first: Yongjie

overall_design: ChIP-seq analysis of TCF7L2 occupancy in human aortic smooth muscle cells with matched IgG controls.

first: Yaozhong

first: Yang

last: Chen


title: Loss of the E3 ubiquitin ligase MARCHF6 alters hepatic lipid metabolism and drives spontaneous hepatosteatosis

city: Amsterdam

first: Sebastian

last: Hendrix

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: UMC Amsterdam location AMC

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) and its progressive form, steatohepatitis (MASH), feature excessive hepatic fat accumulation, yet the relative contributions of dietary vs. endogenous fats and their interactions has remained enigmatic. Here, we identify the endoplasmic reticulum–associated E3 ubiquitin ligase MARCHF6 as a pivotal regulator of hepatic lipid metabolism. Global or hepatocyte-specific deletion of Marchf6 induced spontaneous accumulation of triglycerides and cholesteryl esters under chow-fed conditions, revealing a cell-autonomous hepatic defect independent of caloric excess. Mechanistically, loss of MARCHF6 stabilized its substrate squalene epoxidase (SQLE), enhancing sterol pathway flux while concomitantly activating the SREBP1-driven lipogenic transcriptional program and increasing lipoprotein clearance. Accordingly, lipidomic analyses demonstrated remodeling of the hepatic lipidome towards polyunsaturated, long-chain neutral lipids, consistent with increased lipogenesis-driven NADPH consumption. In line with this, pharmacological inhibition of the oxidative pentose phosphate pathway reduced lipid accumulation in MARCHF6-deficient human hepatocytes. Congruently, transcriptomic data from human MASLD/MASH patients revealed reduced hepatic MARCHF6 expression alongside an increase in that of the lipogenic genes SREBF1, FASN, and SCD1. Overall, these data establish MARCHF6 as a multifaceted gatekeeper that integrates sterol turnover, NADPH usage, and lipogenesis to maintain hepatic lipid homeostasis

overall_design: RNA seq profiling of total liver tissue of 10 week old WT C57Bl/6J mice and C57Bl/6J mice with liver specific knockout of Marchf6 (deletion of Exon2). Mice were kept on standard chow diet.

first: Vinay

last: Sachdev

first: Nienke

last: van Loon

first: Jenina

last: Kingma

first: Roelof

last: Ottenhoff

first: Josephine

last: Tan

first: Marlene

last: van den Berg

first: Suzanne

last: Duijst

first: Aldo

last: Jongejan

first: Johannes

last: Levels

first: Patrick

last: Rensen

first: Sander

last: Kooijman

first: Jan-Freark

last: de Boer

first: Folkert

last: Kuipers

first: Katharina

middle: B

last: Kuentzel

first: Dagmar

last: Kratky

first: Yun

last: Kwon

first: Anja

last: Zeigerer

first: Noam

last: Zelcer


title: The effects of high-thoracic spinal cord injury on the heart transcriptome

city: Kelowna

first: Christopher

middle: Roy

last: West

state: BC

address: Reichwald Health Sciences Centre, 1088 Discovery Ave

department: Cellular and Physiological Sciences

country: Canada

institute: University of British Columbia

summary: It is becoming increasingly recognized that high-level spinal cord injury (SCI) is associated with altered heart structure and function as well as a significantly elevated risk for heart disease.   Despite this knowledge, we know remarkably little about the temporal molecular changes that occur in the heart following SCI and how these relate to functional decline. In the present study, we addressed this shortcoming by combining bulk RNA sequencing (RNA-seq) of left ventricle (LV) tissue with matching in vivo cardiac function assessments (i.e., pressure-volume loops obtained via LV catheterization) from the same animals.  We studied rats at either the acute (1 and 3d post-SCI) or chronic (12wk post-SCI) stage of SCI to establish temporal patterns and compared findings to sham-injured rats. We found that SCI induces marked, time-dependent changes in cardiac gene expression and function. Acute (1–3d) and chronic (12w) SCI display distinct, often opposing transcriptomic signatures, with thousands of genes differentially expressed versus SHAM. Acute SCI is characterized by suppressed immune, inflammatory, cell cycle, and stress-response pathways with altered metabolism. Chronic SCI shows upregulated immune signaling, impaired oxidative phosphorylation, extracellular matrix remodeling, and stress responses. Functionally, cardiac systolic dysfunction occurs early post-SCI and persists to the chronic phase. Reduced systolic function is strongly correlated with changes in immune, hypoxia, and cholesterol-related genes at the acute time-points, and with immune and hormone-signaling pathways at the chronic time-point. Collectively, our data provide novel insight into the cardiac transcriptome post-SCI and identify the molecular pathways that most strongly correlate to functional decline.

overall_design: RNA-seq data of left-ventricular (LV) tissue (mid-ventricular, free-wall, flash frozen) obtained from male Wistar rats. LV samples were collected from these groups: 1) SHAM, no spinal cord injury (SCI), high-thoracic durotomy only; 2) 1 day following high-thoracic complete transection SCI (1d SCI); 3) 3 days following high-thoracic complete transection SCI (3d SCI); 2) 12 weeks following high-thoracic complete transection SCI (12w SCI). N=6 per group.

first: Mary

middle: P

last: Fossey

first: Brian

last: Hayes

first: Erin

last: Erskine

first: Malihe-Sadat

last: Poormasjedi-Meibod

first: Anne

last: Haegert

first: Funda

last: Sar

first: David

middle: J

last: Granville

first: Amrit

last: Singh

middle: R


title: Transcriptomic profile of the hippocampus of rat strains with contrasting nervous system excitability

city: Калининград

first: Irina

last: Shalaginova

state: Калининградская область

address: Черняховского 36-11

country: Russia

institute: Pavlov Institute of Physiology

summary: Bulk RNA sequencing of the hippocampus in male rats from two selectively bred strains differing in nervous system excitability: LT (low threshold, high-excitability) and HT (high threshold, low-excitability). The aim was to characterize baseline interstrain transcriptomic divergence in intact animals and identify major functional themes associated with inherited differences in excitability.

overall_design: Hippocampal tissue was collected from intact 5-month-old male rats of two selectively bred strains, LT and HT, with 5 biological replicates per group. Total RNA was extracted from the whole hippocampus, poly(A)+ RNA libraries were prepared, and single-end 50-bp sequencing was performed on the Illumina HiSeq1500 platform. Differential expression was assessed between LT and HT samples.


title: Detachment-induced gene expression changes in four lung adenocarcinoma cell lines, H2009, LC-2/ad, H2228, and HCC4006.

city: Shimotsuke

first: Toshiro

last: Niki

state: Tochigi

department: Department of Pathology

institute: Jichi Medical University

summary: The aims of the study was to analyze gene expression changes induced by detachment from culture plate. Of the genes upregulated in detached state, we focused on MUC21, a membrane-anchored mucin, that was previously shown to exhibit anti-adhesive property. Using MUC21-KO cells, we demonstrated that MUC21 play a critical role in the growth and survival of lung adenocarcinoma cells both in attached and detached state.

overall_design: Lung adenocarcinoma cell line, H2009, LC-2/ad, H2228, and HCC4006, were plated onto ultra-low attachment culture plate and RNA was extracted at day 1 and day 7 using the RNeasy Mini Kit. RNA exrtracted from cells in standard cultured condition (in attched state) was used as controls. The RNA samples were then subjected to RNA sequencing. There were no replicates for each sample (n=1).

first: Ryotaro

last: Sakio

first: Daisuke

last: Komura

first: Shumpei

last: Ishikawa


title: mRNA profile of 6 lung adenocarcinoma cell lines

summary: To obatain mRNA profiles of 6 lung adenocarcinoma cell lines

overall_design:
Cell were cultures under standard culture conditions and total RNA was extracted using the RNeasy Mini Kit. There were no replicate samples (n=1).
*** Submitters state that raw data CEL files have been lost and therefore are not included***


title: pH Gradient Drives Redox Reactions in the Nucleolar Caps to Modulate Nucleolar Integrity and Function

city: Xiamen

first: Fan

last: Wu

address: 4221 Xiang'an South Road

institute: Xiamen University

summary: Enzymatic catalysis has long been thought of as the primary driver of redox processes in living cells. Biomolecular condensates, formed via phase separation, exhibit unique physicochemical properties that distinguish them from the surrounding milieu. Emerging evidence indicates that the electrochemical properties of biomolecular condensates can participate in a plethora of pathophysiological processes by potentiating chemical reactions, including redox reactions. Nevertheless, the regulatory mechanisms governing the electrochemical equilibrium of biomolecular condensates and their influence on the emergent physicochemical functions, especially in cellulo, remain poorly understood. Here, we demonstrate that specific nucleolar stressors induce the formation of highly alkaline nucleolar caps, which generate an interfacial pH gradient that drives spontaneous redox reactions. Non-enzymatic reactive oxygen species (ROS) production depends on positively charged constituents within the nucleolar caps and correlates strongly with the pH microenvironment. Excessive ROS accumulation directly modulates the partition and diffusion of proteins rich in cysteine and methionine, whereas scavenging ROS markedly accelerates the recovery of nucleolar multiphase organization and functionality upon stress removal. Collectively, our findings propose a non-enzymatic redox mechanism operating within cellular condensates and highlight the critical role of physical interfaces in orchestrating the chemical dynamics of biomolecular condensates.

overall_design: RNA profiling of U-2 OS cells expressing SRSF1 wild-type and its mutant S-A


title: Tumor sialylation controls effective anti-cancer immunity in breast cancer

city: Vienna

first: Stefan

last: Mereiter

address: Dr. Bohr-Gasse 3, IMBA

country: Austria

institute: IMBA

summary: Breast cancer is the most prevalent cancer among women, yet immune checkpoint inhibitors remain largely ineffective in the majority of patients. To better understand the mechanisms underlying immune evasion in breast cancer, we analyzed two independent clinical cohorts and identified a negative association between tumor sialylation and T cell infiltration across molecular subtypes, most prominently in luminal B tumors. In preclinical models, both genetic and pharmacologic inhibition of tumor cell sialylation reshape the tumor microenvironment by reducing neutrophil and PMN-MDSC infiltration, while CD8⁺ effector and Tcf7⁺ memory T cells are increased within the mammary tumors. Mechanistically, sialylation enhances the serum half-life of granulocyte colony-stimulating factor (G-CSF), a key driver of neutrophilic immunosuppression, and dampens tumor cell immunogenicity by limiting MHC-I surface expression. Disruption of sialylation sensitizes resistant mammary tumors to CD8⁺ T cell-mediated killing and synergizes with anti-PD-1 therapy in multiple breast cancer models. Analysis of patient datasets further reveals a sialylation gene signature enriched in breast tumors, especially of the luminal B subtype, that correlates with increased neutrophils and poor CD8⁺ T cell infiltration. Our findings establish tumor cell sialylation as a central regulator of immune evasion in breast cancer, offering a therapeutic vulnerability to unlock anti-tumor immunity and improve responsiveness to immune checkpoint inhibitors.

overall_design: Single cell transcriptomic analyses were performed to characterize the immune cells of the tumor microenvironment in 4T1 tumors either proficient or deficient in sialylation.


title: Detachment-induced gene expression changes in lung adenocarcinoma cell lines, A549 and H441.

summary: The aims of the study was to analyze gene expression changes induced by detachment from culture plate.

overall_design:
Lung adenocarcinoma cell line, A549 and H441, were plated onto ultra-low attachment culture plate and RNA was extracted at day 1 and day 7 using the RNeasy Mini Kit. A549 and H441 cells that were cultured and maintained on ultra-low attachment culture plate for more than 2 months were designated A549-FL and H441-FL, respectively. RNA was extracted from A549-FL and H441-FL cells, both in standard culture and in ultra-low attachment culture. The RNA samples were then subjected to Agilent microarray analysis. There were no replicates for each sample (n=1).

In the normalized expression data, ID_REF represents the Agilent FeatureNum. Annotation information linking FeatureNum to probes and genes is provided in the supplementary file GSE319366_RAW.tar.


title: Human Nail Single-Cell Landscape Identifies KRT19+ NSCs and SOX2/SOX9-WNT Regulated Differentiation

city: Shanghai

first: SHIHUI

last: LIN

state: Shanghai

address: No. 639 Zao Zhi Ju Road, Huangpu District, Shanghai, China

institute: Shanghai Jiao Tong University School of Medicine

summary: Nail stem cells (NSCs) are crucial for nail growth and fingertip regeneration, yet their identity and regulatory mechanisms remain unclear. Here, we used single-cell RNA sequencing to construct a spatiotemporal landscape of nine clusters of human nail epithelial cells. Through analysis of their bidirectional differentiation, we identified a KRT19+ subpopulation capable of differentiating into both nail structure and peri-nail epithelium. Our findings reveal that SOX2-controlled WNT signaling is inhibited in the proximal nail matrix, activated in the distal nail matrix, and subsequently downregulated by SOX9 towards the nail bed, guiding the orderly OFF-ON-OFF regulation of KRT19+ NSC differentiation into nail structure epithelium. In vivo validation using mouse models and human samples confirmed the regenerative capacity of KRT19+ NSCs. This study is the first to identify KRT19+ NSCs using a human nail single-cell atlas and elucidate their key regulatory mechanisms, providing a foundation for nail and digit regeneration therapies.

overall_design:
Human nail tissue samples were collected from pediatric patients undergoing duplicated thumb (preaxial polydactyly) excision surgery. Informed consent was obtained from guardians, and the study was approved by the Ethics Committee of Shanghai Ninth People’s Hospital (IRB: SH9H-2021-T391-2), in accordance with the Declaration of Helsinki. Inclusion criteria included age between 8 months and 2 years (with one subject aged 18 days), absence of familial genetic history, and normal nail growth.Single-cell suspensions were prepared by combining proximal nail fold, nail matrix, and nail bed tissues in a 2:2:1 ratio, yielding ≥20,000 total cells at 700–1000 cells/μL. Single-cell library preparation followed the 10x Genomics v3.1 protocol. Specifically, 75 μL of Master Mix with cell suspension, 40 μL of barcoded gel beads, and 280 μL of oil were loaded onto a Chromium Chip B and processed using a Chromium Controller. Generated GEMs were reverse transcribed to ss-cDNA, purified, and PCR amplified to produce ds-cDNA. Libraries were then fragmented, end-repaired, ligated with adapters, and indexed by PCR. Sequencing was performed on an Illumina NovaSeq 6000 platform.

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

first: Xia

last: Fang

first: Shihui

last: Lin


title: Heat Stress-Induced Phenotypic and Transcriptomic Shifts in Dairy Cows: Functional Validation of DNAJB1 as a Key Thermo-tolerant Gene

city: Edinburgh

first: Du

last: ninghui

address: Old College, South Bridge, Edinburgh, EH8 9YL, UK

country: United Kingdom

institute: School of Science and Engineering，University of Edinburgh

summary: This study analyzed phenotypic, physiological, and molecular changes in heat-stressed Holstein cows using transcriptomics and metabolomics to identify heat-tolerance markers. A high-temperature environment of 35°C ± 1°C with 60% humidity was simulated and maintained for 14 days in a climate-controlled chamber. During this period, physiological parameters, production performance, and blood biochemical indicators of the cows were measured. The results demonstrated that under heat stress conditions, respiratory rates increased, milk yield significantly decreased, and overall production performance declined substantially. Building on the successful establishment of the heat tolerance model, subsequent genetic analyses were conducted on control and heat-stressed individuals. RNA-seq analysis of heat-stressed cows revealed heat response pathways and the core gene DNAJB1, which were not observed in the control group. Functional validation through qPCR and CRISPR/Cas9 editing confirmed the critical role of DNAJB1 in heat tolerance, thereby establishing its reliability as a molecular marker.

overall_design: The Holsteins in the high-temperature group were maintained at a temperature of 35°C ± 1°C in an environment with 60% humidity, while the Holsteins in the control group were set at a temperature of 20°C ± 2°C and 50% humidity.

first: Ninghui

last: Du


title: RNA-seq data of MV4-11, Kasumi-1, and KG-1 cells treated with HDAC8 inhibitor 22d 10 μM and control

city: MONROVIA

first: Yahuei

last: Kuo

state: CA

address: 1218 S 5TH AVE

department: Hem Malignancies Trans Sci

institute: City of Hope National Medical Center

summary: We performed RNA sequencing on MV4-11, Kasumi-1, and KG-1 leukemia cell lines treated with HDAC8 inhibitor 22d at 10 μM and their respective control groups. The sequencing reads were processed to generate gene-level count matrices. This dataset provides processed count data for downstream gene expression analysis and comparison between treated and control conditions.

overall_design: Three human leukemia cell lines (MV4-11, Kasumi-1, and KG-1) were cultured under standard conditions. Cells were treated with HDAC8 inhibitor 22d at 10 μM for 12 hours, with untreated cells serving as controls. Each condition included three biological replicates.  Total RNA was extracted from each sample using standard protocols, and RNA quality was assessed by Bioanalyzer. Sequencing libraries were prepared using the Illumina TruSeq RNA Library Prep Kit and sequenced on an Illumina NovaSeq 6000 platform to generate paired-end reads of 150 bp.  Raw reads were aligned to the human reference genome (GRCh38) using STAR aligner. Gene-level counts were generated using featureCounts.  The dataset includes processed gene-level count matrices for all samples, which are suitable for downstream differential expression analysis and gene expression profiling.

first: Wancheng

last: Guo

first: Lianjun

last: Zhang

first: Yu-Hsuan

last: Fu

first: Ya-Huei


title: Lactate and lactylation of RNA splicing factors triggered metabolic code reverse central dogma modulates totipotency development

city: Hong Kong

first: Yingzhe

last: Ding

state: Shatin NT.

address: Rm503,Li Ka Shing Medical Science Build.,Prince of Wales Hosp.,30-32 Ngan SHing St.

department: Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: Totipotent cells mark the inception of mammalian development and are present in the body for an extremely brief duration. Exploring the regulation of stem cell totipotency would help us to understand the mammalian embryo development and accelerate its application on regeneration medicine. Here using high responsive lactate probe-Fila, we revealed that high lactate signal was related to stem cell totipotency, and supplement of lactate captured totipotent stem cell from naïve or primed stem cells significantly both in human and mouse. Then, we discovered that the high Kla intensity was a character of totipotency in embryo cells and cell lines, and the Kla intensity decreased following the totipotency development. Moreover, using high throughput lactylome and proteome analysis, we found the highest Kla intensity and sites in totipotent stem cells both on the cellular and subcellular. Notably, we revealed that Kla proteins participated in almost fundamental biological pathways such as RNA splicing, DNA repair and chromatin organization et al., and the Kla proteins related to these pathways represented a dynamic change during the totipotency development. We further focused on the most enrichment pathway RNA splicing, and revealed that the high Kla level on RNA splicing factors inhibited the splicing efficiency to activate the totipotent genes and silence the pluripotent genes, respectively. Finally, we screened and identified the Kla on six critical RNA splicing factors were essential for totipotency. Our work highlights lactate as a master and conservative metabolite, and reveals “lactate triggered-metabolic codon reversed central dogma” that involves the lactate driven Kla on RNA splicing factors to regulate the pre-mRNA splicing efficiency in the context of totipotency development.

overall_design: RNA-seq was performed in two cell like cells (2CLCs),embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs),Mouse Embryonic Fibroblast(MEFs) cells and 0mM,60mM,80mM sodium lactate treated ESCs.

first: Xingguo

last: Liu

first: Keshi

last: Chen

first: Linpeng

last: Li


title: Expression data from HeLa-Cas9 cells after TLN1 or KD2 loss-of-function

city: Heidelberg

first: Marie

last: Buck-Wiese

address: Im Neuenheimer Feld 267

department: BioQuant

country: Germany

institute: Universität Heidelberg

summary:
To compare on- and off-target effect of transfected antibodies to gene-editing and RNAinterference, Cas9-expressing HeLa cells were transfected with biomolecules for each method via solid-phase reverse transfection
and RNA expression was profiled 48h post-transfection.

overall_design: Cells were seeded on reverse transfection coating containing biomolecules targeting TLN1 or KD2 for a multi-level loss of function. 48h post transfection total RNA was isolated from three independent replicates and pooled for expression profiling.

first: Sally

last: Liechocki

first: Vytaute

last: Starkuviene


title: Wnt signaling restores evolutionary loss of regenerative potential in Hydra

city: Davis

first: Sergio

middle: Esteban

last: Campos

address: One Shields Ave

department: Molecular and Cellular Biology

institute: University of California Davis

summary: The regenerative potential of animals varies widely, even among closely-related species. In a comparative study of regeneration across the Hydra genus, we found that while most species exhibit robust whole-body regeneration, Hydra oligactis and other members of the Oligactis clade consistently fail to regenerate their feet. To investigate the mechanisms underlying this deficiency, we analyzed transcriptional responses during head and foot regeneration in H. oligactis. Our analysis revealed that the general injury response in H. oligactis lacks activation of Wnt signaling, a pathway essential for Hydra vulgaris foot regeneration. Notably, transient treatment with a Wnt agonist in H. oligactis triggered a foot-specific transcriptional program, successfully rescuing foot regeneration. Our transcriptional profiling also revealed dlx2 as a likely high-level regulator of foot regeneration, dependent on Wnt signaling activation. Our study establishes a comparative framework for understanding the molecular basis of regeneration and its evolutionary loss in closely-related species.

overall_design: The experimental design of this study included transcriptional profiling of H. oligactis head and foot regeneration, all timepoints, tissues and treatment included at least 3 biological samples each composed of tissue extracted from ~30 animals. A first batch of Illumina sequencing was comprised of 4 biological replicates of homeostatic head and foot tissue and 3 biological replicates of head and foot regenerating tissue at 0, 3, 12 and 48 hours after a transverse bisection at the midpoint of the body column. Regenerating tissue was collected by cutting 1/3 of the body column adjacent to the wound site. Homeostatic heads and feet and 0 hpa head and foot regenerating tissue were treated for 30 seconds with 0.05% DMSO, while 3, 12 and 48 hpa samples were left in 0.5% DMSO for 3 hours before washing. In addition, this first sequencing batch included at least 3 biological replicates of foot regenerating tissue treated with Alsterpaullone 5 uM for 3 hours after amputation and collected at 3, 12 and 48 hours hpa. A second RNA-sequencing batch was comprised of 2 biological replicates of homeostatic head and foot tissue and 3 biological replicates of head and foot regenerating tissue collected at 0 and 24 hpa after 0.05% DMSO treatment and foot regenerating tissue collected at 24 hpa after treatment a 3 hours treatment with 5uM Alsterpaullone. In total this dataset is comprised of 60 RNA-seq samples.

middle: E

first: Celina

last: Juliano


title: CNOT3 maintains ILC2 integrity by destabilizing Tbx21 and Rorc mRNAs [RNA-seq]

city: Akita

first: Megumi

last: Tatematsu

department: Department of Medical Biology

institute: Akita University Graduate School of Medicine

summary: Immune responses are initiated by activation of innate lymphoid cells (ILCs), T-bet-dependent natural killer and ILC1 cells, GATA-3-dependent ILC2 cells, and RORγt-dependent ILC3 cells. Despite accumulated knowledge of translational regulation in ILCs, comprehensive impact of mRNA decay on ILCs has not been clarified yet. CNOT3 is a main subunit of the CCR4-NOT complex which mainly destabilizes mRNAs by poly (A) deadenylation in eukaryotes. Here, we showed that CNOT3 is required for cell survival of all ILCs and that the absence of CNOT3 promoted T-bet and RORγt expression due to increased stability of Tbx21 and Rorc mRNAs in ILC2 cells and enabled them to produce granzyme B and IL-22. Likewise, Th1 and Th17 skewing was induced in CD4 T cells lacking CNOT3. Furthermore, CNOT3 in each ILC subset contributes to their type-specific immune responses. Thus, the CCR4-NOT complex controls ILC differentiation by inhibiting the potential for type 1 and 3 immunity.

overall_design:
To investigate roles of CCR4-NOT complex in ILCs, we compared expression profile of NK cells, ILC2s and ILC3s from  control and Cnot3 conditional KO mice.
RNA-seq data of spleen NK cells from Cnot3f/f mice and Cnot3f/f Il7r-Cre mice (biological triplicates). RNA-seq data of lung ILC2s from Cnot3f/f mice and  Cnot3f/f Il7r-Cre mice (biological triplicates). RNA-seq data of small intestine ILC2s from Cnot3f/f mice and Cnot3f/f Il7r-Cre mice (biological triplicates). RNA-seq data of small intestine CCR6+ ILC3s from Cnot3f/f mice and  Cnot3f/f Il7r-Cre mice (biological triplicates).


title: CNOT3 maintains ILC2 integrity by destabilizing Tbx21 and Rorc mRNAs [RIP-seq]

overall_design:
RIP-sequence was performed using anti-Cnot3 antibody to distinguish direct target mRNAs of CCR4-NOT complex in ILC subsets.
RIP-seq data of spleen NK cells for bindings of Cnot3 (bilogical triplicates).RIP-seq data of lung ILC2s for bindings of Cnot3 (bilogical duplicates). RIP-seq data of small intestine ILC2s for bindings of Cnot3 (bilogical duplicates). RIP-seq data of small intestine ILC3s for bindings of Cnot3 (bilogical duplicates).


title: A novel nanobody-based TCR-like CAR-T therapy targeting PRAME for the treatment of acute myeloid leukemia

first: Xintong

state: Please select your state

address: Ruijin second road

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Chimeric antigen receptor (CAR) T-cell immunotherapy in acute myeloid leukemia (AML) remains challenging, primarily due to the lack of specific cell surface antigens that are highly expressed on leukemic blasts but largely absent on hematopoietic stem/progenitor cells and healthy tissues. TCR-like CAR-T therapy targeting intracellular antigens provides a novel strategy for the treatment of AML. In this study, we aimed to develop nanobodies targeting the intracellular antigen PRAME and to establish a novel nanobody-based TCR-like CAR-T cell therapy directed against the peptide-MHC complex PRAME425-433/HLA-A2.

overall_design: To investigate the molecular mechanisms underlying anti-PRAME TCR-like CAR-T cell-mediated killing of AML cells, we performed bulk RNA-Seq on antigen-specific stimulated CAR-T cells following co-culture with THP-1 or OCI-AML3 cells at a 1:1 effector-to-target (E:T) ratio for 24 hours. Untransduced T cells and anti-PRAME CAR-T cells that did not receive antigen stimulation were used as controls.

first: Jianfeng

first: Xue

first: Xuejiao

last: Yang

first: Jianqing

last: Mi

first: Wenbo

last: Wang

first: Yueying


title: Generation of synthetic kidneys from expandable kidney progenitors [Days 5 and 9]

city: Los Angeles

first: Zhongwei

address: 1425 San Pablo St

department: Keck medicine

institute: University of Southern California

summary: Kidney is the central organs responsible for maintaining the homeostasis of our body, the sophisticated structure and cell composition underpin kidney’s function. Here we report the generation of mouse synthetic kidneys (SK) from expandable nephron progenitor cells (NPC) and ureteric bud (UB). Unexpectedly, versatile renal interstitial cells can be induced in synthetic kidneys. Mechanistically, a portion of NPCs go through transdifferentiation and become interstitial progenitor cells (IPCs) in SK context, then further differentiate into various renal interstitial cells. These kidney progenitors-derived synthetic kidneys highly resembled postnatal mouse kidneys in terms of high-order patterning and showed essential renal physiological functions.

overall_design: Cell populations profiling analysis of kidney explants collected at Day 5 and D9 time points through 10x Genomics scRNA-seq assays

first: Biao

last: Huang

first: Zipeng

last: Zeng

first: Jincan

last: He

first: Sunghyun

last: Kim

first: Kari

last: Koppitch

first: Jinjin

first: Chennan

first: Nils

middle: O

last: Lindström

first: Andrew

last: McMahon


title: Degradation of AGO2 by TRIM25 drives cancer progression and chemotherapy resistance

city: 上海市

first: Jianxiu

last: Yu

state: 上海市

address: Room 202, Building 7, 280 South Chongqing Road,

department: Department of Biochemistry and Molecular Cell Biology

type: Non-coding RNA profiling by high throughput sequencing

summary: AGO2, as a key member of the RISC complex, is underexpressed in a variety of tumor cells. It is shown that the E3 ligase TRIM25 is highly expressed in a variety of tumor cells and mediates the degradation of the ubiquitin-proteasome pathway of AGO2. This effect of TRIM25 on AGO2 promotes tumor progression and resistance of tumor cells to chemotherapeutic agents. The specific mechanism is that TRIM25 regulates the level of miR-148b-5p in cells through AGO2, and then regulates the downstream ABCC1. Based on the above results, targeting miR-148b-5p provides a new strategy for the treatment of tumors.

overall_design: mRNA expression profiles and miRNA expression profiles in H1299 stable cell lines

first: Zihan

last: Zhou


title: Transcriptional activation of the PKLR gene by novel erythroid-specific regulatory elements [ChIP-Seq]

city: Busan

first: AeRi

address: 2, Busandaehak-ro 63beon-gil, Geumjeong-gu

institute: Pusan national university

summary: We proposed that newly identified transcription regulatory elements act as enhancers for the PKLR gene transcription in erythroid cells.

overall_design: Histone H3K27ac ChIP-seq was performed in control, GATA1 or TAL1-depleted (GAi or TAi) cells

first: Yew Woon


title: Differential gene expression during biofilm dispersal by gluocse starvation

city: Basel

first: Knut

last: Drescher

state: BS

address: Spitalstrasse 41

department: Biozentrum

country: Switzerland

institute: University of Basel

summary: In this study we determined the gene expression of whole genome during glucose starvation of biofilms followed by RNA-sequencing.

overall_design: mRNA profiles of V.cholerae wild type in different conditions. The biofilms were grown in microfluidic chambers, dispersal was induced by glucose starvation, and RNA-samples were taken 1hr after induction. Two indepent biological replicates for each condition are provided. Each biological replicates was from 2 techincal replicates which later were combined due to low sample volume

first: Praveen

middle: K

last: Singh

first: Nikolai

last: Peschek

first: Kai

last: Papenfort


title: Formation mechanism of agar-like zona pellucida and its adverse effects on human oocytes

city: Fuzhou

first: Zhiren

last: Liu

state: Fujian

address: 20 Chazhong Road

institute: the First Affiliated Hospital of Fujian Medical University

summary: Agar-like zona pellucida (ZP) is a type of ZP abnormality that adversely affects oocyte maturation, fertilization, and developmental potential. However, the mechanisms underlying its formation and its detrimental effects on oocytes remain elusive. Through comprehensive analyses including whole-exome sequencing, transcriptome sequencing, Q-PCR, scanning electron microscopy, and transmission electron microscopy, our study found that the c.2785G>C mutation in ATRX may represent a genetic factor contributing to the agar-like ZP formation. Moreover, while mutations in ZP1-4 genes were not essential for agar-like ZP formation per se, an increased proportion of ZP1 protein among the four ZP proteins contributed to this phenomenon. Additionally, up-regulation of PMP22 may also be implicated in agar-like ZP formation and exert deleterious effects on oocyte development. Our findings enhance our understanding of agar-like ZP and provide a theoretical foundation for its treatment in assisted reproduction. Furthermore, our study demonstrates potential applications in contraception as the agar-like ZP effectively inhibits conventional fertilization of oocytes.

overall_design: (1) The MI oocytes with an agar-like ZP were obtained from these patients, namely Cases t2, t3, t4, A, B, C, D, E, F and G. For transcriptome sequencing analysis, Cases t2-t4 each provided agar-like ZP oocytes. For Q-PCR analysis, Cases F and G offered one MI agar-like ZP oocyte each. SEM was performed on six MI agar-like ZP oocytes from Cases C and D. TEM was conducted on five MI agar-like ZP oocytes obtained from Case E.(2) The MI oocytes possessing a normal ZP were procured from four patients, namely Cases 1, 2, 3, and 4. The normal MI oocytes acquired from Cases 1 and 2 were chosen as control groups for Cases F and G in Q-PCR analyses. Case 3 provided six normal MI oocytes for SEM analysis, while Case 4 contributed five normal MI oocytes for TEM examination.(3) Genomic DNA was extracted from peripheral blood samples of cases A, B, C, D, E, F, G, 1 and 2 for whole-exome sequencing (WES).

first: Mingting

last: Jiang


title: Prevotella disiens Disrupts Endometrial Function via p38 MAPK-Mediated WNT Inhibition and Tryptophan Metabolism Dysregulation

city: Chongqing

first: Shen

last: Zhang

address: No. 288 Tianwen avenue, Nanan district

department: Obstetrics and Gynecology Department

institute: The Second Affiliated Hospital of Chongqing Medical University

summary:
Background: Recurrent implantation failure poses a challenge in assisted reproductive technology, often linked to an imbalance in the endometrial microbiome. Prevotella disiens, a bacterium found in the reproductive tract, is associated with reduced implantation success, but its effects on the endometrium are not well understood. This study uses hormone-responsive endometrial organoids to explore how Prevotella disiens alters endometrial function at a molecular level, aiming to uncover mechanisms contributing to implantation failure.
Results: Endometrial organoids exposed to Prevotella disiens showed structural damage and significant changes in gene expression, unlike those treated with Lactobacillus species. Key findings include activation of the p38 MAPK pathway, suppression of WNT signaling, and increased expression of tryptophan metabolism genes. Metabolomic analysis revealed elevated kynurenine pathway metabolites in these organoids. Additionally, higher p38 MAPK and kynurenine pathway gene expression, and lower WNT pathway gene expression were observed in endometrial biopsies from patients with Prevotella disiens colonization. Blocking p38 MAPK in endometrial organoids reversed WNT suppression and normalized tryptophan metabolites.
Conclusions: Prevotella disiens disrupts endometrial function by activating p38 MAPK, which inhibits WNT signaling and alters tryptophan metabolism, potentially hindering embryo implantation. These findings highlight the endometrial microbiome’s influence on reproductive success and point to p38 MAPK as a possible target for improving outcomes in assisted reproductive technology.

overall_design: Human endometrial organoids were derived from patient tissues and cultured under hormonal conditions mimicking the implantation window using estrogen and progesterone stimulation. The organoids were then co-cultured with either Lactobacillus crispatus, Lactobacillus iners, Prevotella disiens, or left untreated as a control for 24 hours. Three independent organoid cultures were prepared for each treatment group, serving as biological replicates. Total RNA was extracted from each sample for RNA sequencing to analyze the transcriptional responses to different microbiota treatments.

first: Jiashuo

first: Xiaoqin

first: Huijia

last: Chen

first: Heng

last: Zou


title: STING Acts as a Rheostat of the Unfolded Protein Response to Regulate Antigen Presentation during Inflammation.

status: Public on Apr 24 2026

city: Montréal

first: Lilia

last: Rodriguez

state: Québec

address: 2900, boul. Édouard-Montpetit

institute: University of Montreal

summary: A growing body of evidence supports the contribution of the long-lasting adaptive immune system in Parkinson’s disease (PD). We showed that the PD-associated protein PINK1 negatively regulates the presentation of mitochondrial antigens (MitAP) on MHC-I molecules. In vivo evidence indicated that MitAP activation in mice, in the absence of PINK1, led to cytotoxic CD8+ T cell stimulation and severe motor impairments, reversible by L-DOPA. We show here that following TLR4 activation, MitAP is engaged through a pathway involving cGAS-STING, which acts as a rheostat to dampen the unfolded protein response (UPR). Without STING, the stress response is amplified, leading to a translational attenuation that inhibits the expression of XBP1s, a transcription factor required for MitAP. STING activity also regulates the repertoire of peptides displayed at the cell surface during inflammation, highlighting a potential role in immunosurveillance. These findings establish STING and the UPR as key immune regulators targetable for therapeutic intervention during autoimmune diseases and PD.

overall_design: RNA-seq profiling of mouse RAW cells treated with LPS or not (control) for 6 hours.

first: Michel

last: Desjardins

first: Ahmed

last: Fahmy

first: Ali

last: Ahmadi

first: Joël

last: Lanoix

first: Tyler

last: Cannon

first: Moustafa

middle: N

last: Elemeery

first: Camberly

last: Hernandez Paredes

first: Benoit

last: Barrette

first: Eric

last: Bonneil

first: Yong

last: Zhong Xu

first: Maha

last: Ibrahim

first: Guillermo

last: Arango-Duque

last: Audemard

first: Sébastien

last: Lemieux

last: Chevet

first: Erwin

last: Schur

first: Philippe

last: Pierre

first: Samantha

last: Gruenheid

first: Pierre

last: Thibault

first: Heidi

last: McBride


title: The DUTRENEO trial: bulk prospective biomarker-guided therapy selection and spatial transcriptomic dissection of immunotherapy response in muscle-invasive bladder cancer

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

institute: CNIO

summary: Predictive biomarkers for immune checkpoint inhibitors (ICI) have largely been identified retrospectively, but their clinical utility remains unproven in prospective settings. Here, we report the results of DUTRENEO, a prospective, randomized phase 2 trial testing whether a retrospective, well-validated, 18-gene tumor inflammation signature (TIS) could guide neoadjuvant ICI therapy in muscle-invasive bladder cancer. The trial failed to meet its primary endpoint, demonstrating that bulk gene expression stratification does not sufficiently enrich for responders in this setting. To understand the biological determinants of this failure, we generated a single-cell spatial transcriptomics dataset profiling 377 genes in ~5.4 million cells across large tissue areas. This high-resolution profiling revealed that response to ICI is governed by spatial architectures invisible to bulk assays, specifically the proximity of CD8⁺ T cells to cancer cells and the localized co-expression of checkpoints within epithelial-rich neighborhoods. Furthermore, we identified fibroblast-rich communities as a key feature of immune exclusion in non-responders. We derived a quantitative framework for the design of future clinical trials incorporating spatial analyses, demonstrating that reducing the annotation panel to ≥77 genes and sampling ≥3 mm tissue diameter preserves predictive spatial signal while enabling scalable throughput. These findings elucidate the architectural constraints that limit bulk biomarkers and provide a quantitative framework to embed spatial profiling into clinical studies.

overall_design: Transurethral Resection of Bladder Tumor (TURBT) FFPE samples. Patients’ tumours were classified as immune-hot (hot, for simplicity) or immune-cold (cold, for simplicity) based on the score of the TIS signature. Patients with hot tumours were randomized to receive ICI or NAC whereas patients with cold tumours received standard NAC.

first: Francisco

middle: X

last: Real

first: Mustafa

last: Sibai

first: Eduard

last: Porta-Pardo

first: Enrique

last: Grande


title: circRNA_013145–miR-185-5p–RhoA Axis: A Novel Mechanism in the Pathophysiology of Diabetes-induced Erectile Dysfunction

city: zhejiang

first: Runrun

last: Zhang

address: 548 Binwen Road, Binjiang District, Hangzhou City, Zhejiang

institute: Zhejiang Chinese Medical University

summary: This study investigated circRNA expression profiles in penile tissues of DMED rats using high-throughput microarray

overall_design: We have completed the Arraystar Rat circRNA Array analysis of the 8 samples that you submitted. Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were hybridized onto the Arraystar Rat circRNA Array (8x15K, Arraystar). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

first: Wenhan

last: Huang

first: Jianxiong

last: Ma


title: A spatial in situ hybridization platform for T cell receptor variable gene-based clonotype analysis in tissue

city: Hamburg

first: Cedric

last: Ly

address: Falkenried 94

institute: UKE

summary: Resolving T cell clonality at single-cell spatial resolution remains a major challenge. Here, we developed an in situ hybridization panel comprising probes for immune and tissue cell types alongside comprehensive coverage of TRAV, TRBV, TRGV, and TRDV gene segments, enabling unbiased spatial mapping of T cell clones in situ. As a proof of principle, we applied this approach to human kidney biopsies from patients with ANCA-associated glomerulonephritis and controls. Combinatorial TRV gene expression allowed identification of T cell clones and their spatial organization. Confined clusters of clonally related αβ T cells were found in proximity to increased numbers of antigen-presenting cells, consistent with local immune activation, while γδ T cells occupied distinct peripheral niches. Although paired αβ chain detection is currently limited, this method establishes a scalable framework for spatially resolved clonotype analysis and provides a broadly applicable tool to investigate tissue-level immune organization across diseases.

overall_design: Processing of human samples, cell surface staining, and FACS sorting were performed as previously described (33). Samples were measured and FACS-sorted on an AriaFusion or AriaIIIu (BD Biosciences, Heidelberg, Germany). ScRNA-seq of human samples was performed using the Chromium Next GEM Single Cell 5’ Kit v2 (10x Genomics, PN-1000265) and the Human TCR Amplification Kit (10x Genomics, PN-1000253) according to manufacturer’s instructions.

first: Darius

last: Schaub

first: Robin

last: Khatri

first: Zeba

last: Sultana

first: Annika

last: Boxnick

first: Zheng

last: Song

first: Tobias

last: Huber

first: Thorsten

last: Wiech

first: Eva

last: Tolosa

first: Ulf

last: Panze

first: Stefan

last: Bonn

first: Christian

last: Krebs

first: Immo

last: Prinz


title: Chronic Reduction of Topoisomerase IIβ Alters Neural Circuit Function and Behavior in Mice

city: Tokyo

first: Chiaki

last: Ohtaka-Maruyama

address: 2-1-6 Kamikitazawa, Setagaya-ku

department: Developmental Neuroscience Project

institute: Tokyo Metropolitan Institute of Medical Science

summary: The purpose of this study is to investigate the transcriptomic alterations associated with reduced Top2b expression in the adult mouse brain. We performed bulk RNA-sequencing on whole brain tissues from 3.5-month-old wild-type and Top2b-low expressing homozygous mice to identify differentially expressed genes and underlying molecular pathways.

overall_design: Bulk RNA-sequencing was performed on whole brain tissues derived from 3.5-month-old wild-type mice (n=3) and Top2b-low expressing homozygous mice (n=3). Transcriptome profiles were compared between the two genotypes to assess the effect of Top2b downregulation in the adult brain.

first: Xianghe

first: Tomohiro

last: Iguchi

first: Soichiro

last: Ide

first: Shintaro

last: Yamada

first: Ngo Thi To

last: Trinh

first: Yumiko

last: Hatanaka

first: Midori

last: Yamaguchi

first: Hiroshi

last: Shitara

first: Masato

middle: T

last: Kanemaki

first: Hideya

last: Kawaji

first: Kimiko

last: Fukuda

first: Hiroyuki

last: Sasanuma


title: Compare the differences in gene expression of TAMs in mouse tumor tissues treated with AdV-Fe3O4@PACM and AdV-iCD47-Fe3O4@PACM.

city: Nantong

first: Jie

last: Dong

address: Qixiu road 19

institute: Nantong University

summary: Oncolytic adenoviruses (AdVs) represent a promising immunotherapeutic approach against cancer, yet their clinical translation is hindered by rapid systemic clearance, poor tumor accumulation, limited extravasation across the endothelial barrier, and an immunosuppressive tumor microenvironment. To overcome these challenges, we developed a biomimetic nanocomplex, AdV-iCD47-Fe₃O₄@PACM, consisting of an oncolytic adenovirus chemically conjugated with chemically modified CD47 siRNA and loaded with Fe₃O₄ nanoparticles, all encapsulated within a palmitoylated cancer cell membrane (PACM). Upon intravenous administration, the PACM coating enables immune evasion and prolonged circulation. Application of an external magnetic field promotes active tumor targeting via Fe₃O₄, while palmitic acid moieties transiently increase vascular permeability by downregulating tight junctions, facilitating nanocomplex extravasation into the tumor interstitium. Once inside tumor cells, the oncolytic AdV induces direct cytolysis, and the released chemically modified siRNA achieves sustained CD47 silencing, blocking the “don’t eat me” signal and enhancing macrophage-mediated phagocytosis. This dual mechanism—direct oncolysis combined with innate immune checkpoint blockade—elicits a robust antitumor immune response. Both in vitro and in vivo evaluations demonstrate that the AdV-iCD47-Fe₃O₄@PACM platform effectively overcomes key barriers of systemic delivery and immunosuppression, offering a promising strategy for enhanced cancer immunotherapy.

overall_design: The MC38 bearing mice were i.v. injected with 5×10^8 IFU of AdV-Fe3O4@PACM or AdV-iCD47-Fe3O4@PACM three times.24 hours after treatment, TAMs were isolated using anti-F4/80 MicroBeads , and total RNA from TAMs was extracted using RNeasy mini plus kit and stored at −80°C. Transcriptome RNA- seq analysis was performed using the Illumina NovaSeq 6000 sequencing platform.


title: MERFISH data on seven mouse brain with Abeta pathology

city: Watertown

first: Borislav

last: Dejanovic

address: 100 Forge Rd

institute: Vigil Neuroscience

summary: Microglia adopt various spatially resolved gene and functional profiles in amyloidosis mice, for example the relative enrichment of DAMs proximal to plaques. To spatially resolve these transcriptional changes and identify microglial populations responsive to TREM2 small molecule agonism, multiplexed error-robust fluorescence in situ hybridization (MERFISH) was conducted on sagittal brain sections from VG-3909–treated 5xFAD;hTREM2 mice, 12 hours post-oral dosing. Simultaneous immunostaining using an anti-amyloid antibody enabled spatial correlation of microglial transcriptomes with amyloid plaque localization. The custom MERFISH panel comprised 500 genes, included cell-type markers and microglia-focused genes.

overall_design: Brains were collected from four 5xFAD;hTREM2 mice dosed with 30mg/kg VG-3909 and compared to brains from three vehicle-treated animals. The imaged RNA species were detected, decoded and assigned to individual cells.


title: ID2 secures cDC1 specification by antagonizing E proteins at a pleiotropic Zeb2 enhancer [CUT&RUN]

city: St. Louis

first: Feiya

last: Ou

state: MO

address: 4939 Children's Place

department: Pathology & Immunology

institute: Washington University in St. Louis

summary: The transcriptional regulator ID2 is required for type 1 classical dendritic cell (cDC1) specification, yet the mechanism has remained obscure. We previously identified the Zeb2 -165-kb enhancer as key to normal hematopoiesis, controlled by competing CEBP and NFIL3 inputs during myeloid dendritic cell divergence. Here, we uncover an unprecedented role for E proteins in myelopoiesis and demonstrate that ID2 promotes cDC1 development by antagonizing E protein activity at E-boxes within the Zeb2 enhancer. Deleting these E-boxes abolishes lymphoid B cell and plasmacytoid dendritic cell (pDC) development while skewing myelopoiesis toward cDC1s. Remarkably, E-box deletion rescues cDC1 development in Id2-deficient mice. These findings support a two-step model in which NFIL3 transiently represses Zeb2, followed by ID2-mediated inhibition of E proteins to stabilize cDC1 fate specification. Further, this work defines a paradigm of “site-specific pleiotropy,” wherein distinct transcription factor motifs–E-boxes and CEBP sites–within a single enhancer direct diverse cell fates.

overall_design: CUT&RUN was performed for CEBPa in sorted bone marrow Lin- KIThi-int FLT3+ cells from Zeb2 -165-kb enhancer variants (WT, DC, and DE).

first: Kenneth

last: Murphy


title: Identification and quantification of intracellular N-acetylglucosamine modified glycoRNAs

city: Nanjing

first: Yunlong

last: Chen

address: No. 163, Xianlin Avenue, Qixia District

department: School of Chemistry

institute: Nanjing University

summary: GlycoRNAs are recently discovered glycoconjugates, their different components and distributions are urgently-to-study issues. Here, we design a general paradigm to study glycoRNA from multiple perspectives. Using the metabolic labelling technology and the designed fluorescent DNA probes, the GlcNAc modified Y5 RNA is identified to be mainly in nucleus by FRET imaging. After it is collected by a target-specific capture procedure, the component of GlcNAc conjugated ribonucleotide can be determined by gel electrophoresis and MALDI-TOF analysis. The levels of intracellular GlcNAc modified Y5 RNA in different cell lines are in situ quantified with a GlcNAc-specific in situ hybridization-mediated proximity ligation assay with single-cell and single-molecule resolution. These findings innovate the distribution and quantitation information of glycoRNAs, which greatly promotes the functional research of glycoRNAs.

overall_design: Total RNAs from the Ac4GlcNAz metabolically labelled and then RNase treated HeLa cells were extracted with a traditional procedure using Trizol reagent. The azide-containing RNAs (50 µg) was digested with Pro. K for 45 min. Following digestion, the sample was incubated with click reaction reagents containing alkyne-biotin at 55 °C for 20 min. The resulting RNA was purified, and 200 ng aliquot was reserved as the input control. Streptavidin modified magnetic beads were blocked at 25 °C for 1 h and subsequently washed twice. The purified RNA from the click reaction was then incubated with the blocked streptavidin modified beads for 2 h at 4 °C with rotation. Post-incubation, the bead-bound complexes were subjected to sequential washes. Bound RNA was eluted from the beads using streptavidin elution buffer during 10 min reaction to yield the immunoprecipitated sample. Both the input and immunoprecipitated RNA samples were then processed for PANDORA-seq library construction and sequencing. The sncRNA annotation was performed using the SPORTS1.1 software package.

first: Yi

last: Ren

first: Yuexuan

last: Meng

first: Huipu

last: Liu

first: Guangming

last: Li

first: Jiahui

last: Sun

first: Huangxian

last: Ju


title: ID2 secures cDC1 specification by antagonizing E proteins at a pleiotropic Zeb2 enhancer [CUTAC]

overall_design: CUTAC was performed for H3K4me2 and H3K4me3 in sorted bone marrow common monocyte progenitors (cMoPs) from Zeb2 -165-kb enhancer variants (WT and DE).


title: Macrophage-fibroblast crosstalk shapes wound repair signaling in vitro

city: Irvine

first: Wendy

middle: F

email: wendy.liu@uci.edu, enriqud2@uci.edu

state: California

address: 419 S. Circle View Drive

department: Biomedical Engineering

institute: University of California Irvine

summary: Wound healing requires coordinated interactions between macrophages and fibroblasts, yet how contact-dependent signaling integrates with paracrine pathways to regulate their reciprocal behavior is not well defined. Here, we investigated macrophage-fibroblast communication using complementary 2D and 3D in vitro wound healing models combined with live-cell calcium imaging and single-cell RNA sequencing (scRNA-seq). We show that bone marrow-derived macrophages (BMDMs) promote fibroblast scratch closure in a contact-dependent manner independent of connexins, whereas fibroblasts reciprocally regulate macrophage cytokine secretion through distinct mechanisms. Direct cell-cell contact with fibroblasts enhanced macrophage IL10 production via connexin 43 (Cx43)-dependent signaling, whereas TNFα secretion was suppressed through paracrine interactions. We further demonstrate that fibroblast-macrophage contact induces connexin-dependent intermittent calcium signals selectively in macrophages. ScRNA-seq revealed that wounding reshapes macrophage and fibroblast populations, uncovering dynamic regulation of cell adhesion molecules (CAMs) and intercellular signaling pathways. Together, these findings reveal the integration of contact-dependent calcium and connexin signaling with transcriptional remodeling to coordinate macrophage-fibroblast behavior during healing.

overall_design: RNA-seq profiling of cocultured bone marrow-derived macrophages (BMDMs) and NIH/3T3 fibroblasts in a collagen gel, comparing intact gels to those with a 0.2 mm puncture to model in vitro wounding.

first: Maksim

middle: V

last: Plikus

first: Daniela

last: Enriquez-Ochoa

first: Raji

last: Nagalla

first: Yingzi

first: Christian

last: Guerrero-Juarez


title: Effect of 4EHP (nCBP) mutation on gene expression during heat stress responses in Arabidopsis thaliana

city: MEXICO CITY

first: TZVETANKA

middle: DIMITROVA

last: DINKOVA

state: DISTRITO FEDERAL

address: CIRCUITO EXTERIOR, CIUDAD UNIVERSITARIA DELEGACION COYOACAN

department: BIOCHEMESTRY

country: Mexico

institute: UNIVERSIDAD NACIONAL AUTONOMA DE MEXICO, FACULTAD DE QUIMICA

summary: Translation initiation factors of the eIF4E family play a crucial role in regulating translation and the cellular metabolism of mRNAs. In this study, we show that loss of the class II eIF4E known as 4EHP (nCBP) confers enhanced basal and acquired thermotolerance and causes a mild flowering delay without major root defects. Under heat stress, 4EHP-GFP re-localizes from a diffuse cytosolic pattern to cytoplasmatic foci, where it co-localizes with canonical stress granule (SG) markers. Transcriptomic analysis under control, acclimation and heat stress conditions reveals that 4EHP limits the accumulation of a specific subset of heat-responsive mRNAs, especially those encoding several heat shock proteins (HSPs), which remain constitutively expressed in 4ehp-1 mutant under control conditions and during heat stress. Our results indicate that 4EHP regulates chaperone production, via heat-responsive SG regulatory pathway for the corresponding mRNAs.

overall_design: RNAseq profiling of wild type Col-0 (WT) or 4ehp-1 mutant (HP) Arabidopsis thaliana 7-days-old plantlets under control (22 ºC), acclimation (38 ºC) and heat stress after acclimation (45 ºC) temperatures.

first: Marlon

last: Pulido-Torres

first: Karen

last: Quiroz-Nuñez

first: Eduardo

last: Dorado-Cruz

first: Susana

last: De la Torre-Díaz

first: Abraham

last: León-Domínguez

first: Jorge

last: Herrera-Díaz

first: Oliver

last: Herzog

first: Héctor

last: Quezada

first: Manuela

last: Nájera-Martínez

first: Magdalena

last: Weingartner

first: Tzvetanka

middle: D

last: Dinkova


title: Ngn3 reprograms late retinal progenitor cells through transcriptional and epigenetic mechnisms [RNA-Seq]

city: Guangzhou

first: SHUYI

last: CHEN

state: Guangdong

address: 54 S. Xianlie Rd

department: State Key Laboratory of Ophthalmology

institute: Zhongshan Ophthalmic Center, SYSU

summary: Ngn family transcription factors exhibit potent capacity to promote neurogenesis under diverse cellular context. Using in vivo electroporation on newbone mouse pups retinas, we demonstrate that overexpression of Ngn3 (Ngn3-OE) reprogramms the differentiation competent status of late retinal progenitor celle (RPC), promoting rod photoreceptor differentiation while repressing the fates of Müller glial cell and other interneurons. Herein, we perform RNA-seq and ATAC-seq to investigate the underlying molecular mechanism by which Ngn3 reprogramms late RPCs.

overall_design: Ngn3-overexpressing plasmids were introduced into late-stage RPCs via in vivo electroporation in postnatal day 1 (P1) mouse pups. Following electroporation, GFP-labeled electroporated late RPCs were isolated using fluorescence-activated cell sorting (FACS). Isolated cells were then processes for RNA-seq and ATAC-seq.

first: Shuyi

last: Chen