title: Autophagy-Dependent Regulation of YAP1 by STK38 governs recruitment of differentiated cells as progenitor cells during regeneration

city: Houston

first: Jason

last: Mills

state: TX

address: 1 Baylor Plaza

department: Gastroenterology

institute: Baylor College of Medicine

summary: Paligenosis is a conserved process that enables mature cells to reenter the cell cycle in response to tissue injury, progressing through stages of autodegradation, gene expression changes, and proliferation. The Hippo signaling pathway, particularly YAP1, plays a key role in regulating this process, with Serine/Threonine Kinase 38 (STK38) identified as a key regulator that inhibits YAP1 in uninjured cells but is degraded via autophagy during injury. This degradation of STK38 leads to YAP1 activation, which drives cellular plasticity and proliferation.  Additionally, the secretory maturation factor MIST1 helps preserve STK38 function, suggesting a broader, evolutionarily conserved role for autophagy in tissue regeneration.

overall_design: This study involves four groups of mice: 1.HDTAM-treated Atp4b-DTR mice – Transgenic Atp4b-DTR mice received high-dose tamoxifen (HDTAM) for 2 days to induce chief cell paligenosis. The gastric corpus was harvested 24 hours after the final injection. 2.DT-treated Atp4b-DTR mice – Atp4b-DTR mice were treated with diphtheria toxin (DT) for 2 days to induce reversible parietal cell ablation. The gastric corpus was harvested 24 hours post-treatment.3.Control Atp4b-DTR mice – Atp4b-DTR mice without DT treatment.4.Wild-type controls – Wild-type B6 mice without HDTAM treatment. The gastric corpus was dissociated into single cells using a combination of mechanical and chemical techniques. Three mice were used per group/condition.

first: Yongji

last: Zeng

first: Steven

last: Bark


title: TGF-β1 Inhibits IL-1β-Induced Chemokine Expression in Human Synovial Fibroblasts

status: Public on Mar 15 2026

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

country: USA

institute: Washington University in St. Louis School of Medicine

type: Expression profiling by high throughput sequencing

summary: Purpose: Fibroblast-like synoviocytes (FLSs) play a crucial role in maintaining joint homeostasis by secreting matrix components and lubricin [1, 2]. However, under inflammatory conditions, FLSs contribute to tissue damage, leading to osteoarthritis (OA) [3]. The specific genes and pathways driving this inflammatory response in FLSs remain poorly understood. This study aims to elucidate the transcriptome-wide responses of FLSs to IL-1β, a master proinflammatory cytokine, and to investigate the modulatory effects of TGF-β1 on the expression of chemokine transcripts in a model of inflammatory arthritis.  Methods: Normal FLSs were isolated from synovial explants obtained from patients undergoing anterior cruciate ligament reconstruction surgery. The isolated cells were expended and exposed to IL-1β (10 ng/mL) for 24 hours to simulate inflammatory arthritis. Changes in gene expression were assessed by RNA-seq and validated through Fluidigm multiplex real-time PCR [4]. In a separate experiment, FLSs were pre-treated with IL-1β as above and subsequently exposed to TGF-β1 (10 ng/mL) for an additional 48 hours to evaluate its potential modulatory effects on the expression of chemokines as determined by Fluidigm multiplex real-time PCR.  Results: IL-1β-treated FLSs showed a significant upregulation of numerous chemokines, including CCL20, CCL5, CXCL8, CXCL6, CXCL4, CXCL1, CXCL3, and CXCL2. Additionally, transcripts associated with inflammatory arthritis, such as CSF2, CSF3, MMP12, IL1B, and LIPM, were elevated (Table 1). Expression of KRT14, KRT19, KRT18, and several other anabolic and matrix genes was significantly reduced with IL-1β-treatment (Table 1). The genes highly expressed in IL-1β-treated cells were enriched for NFkB signaling, cytokine and chemokine signaling, TNF signaling, and necroptosis, whereas genes lowly expressed were enriched for the immune system. TGF-β1 treatment exhibited strong anti-inflammatory effects, modulating the expression of numerous chemokines and inflammatory mediators, thereby counteracting the IL-1β-induced inflammatory response in FLSs (Fig. 1). Moreover, the expression of the chemokine transcription factor C/EBPβ was also high (about twofold) in  IL-1β-treated cells, which was reduced by half after TGF-β1 treatment, suggesting that TGF-β1 exerts its anti-chemokine effects through transcriptional repression of C/EBPβ in FLSs.  Conclusions: This is the first study to examine the effects of IL-1β treatment in FLS derived from patients with ACL tears. Our data show that IL-1β significantly influences the expression of CC and CXC chemokine transcripts in FLSs, mirroring findings in chondrocytes, where human adult chondrocytes exhibit increased expression of CC and CXC chemokines [5]. Our finding that TGF-β1 effectively mitigates the inflammatory responses induced by IL-1β, potentially through suppression of transcription factor C/EBPβ, is novel. It highlights the potential of TGF-β1 as a therapeutic target for OA-related inflammatory conditions. These findings warrant further mechanistic studies to understand the inflammatory dynamics of FLSs in inflammatory arthritis.

overall_design: Normal FLSs were isolated from patients undergoing ACL reconstruction. Cells were treated with IL-1β (10 ng/mL). Total RNA was subjected to RNA-seq.

first: Lei

last: Cai

first: Robert

last: Brophy

first: Tycksen

last: Eric

first: Muhammad Farooq

last: Rai


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

city: Guangzhou

first: Zhiping

last: Liu

state: Guangdong

address: No. 855, East Xingye Avenue

country: China

institute: Jinan University

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

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

first: Pinglian

last: Yang

first: Zhechang

last: Gao

first: Weile

last: Ye

first: Ke

last: He

first: Suowen

last: Xu

first: Jiaojiao

last: Wang


title: Mechanisms by which whole genome doubling drives breast tumor evolution [scRNA-seq]

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave. S1070

institute: Dana-Farber Cancer Institute

summary: Whole genome doubling (WGD) is one of the most common genetic alterations in human cancer generally associated with poor clinical outcome, yet the underlying mechanisms have not been delineated. Here we developed an experimental model of WGD using murine mammary tumor cell lines in immunocompetent mice and found that WGD triggers immune evasion characterized by reduced infiltration of CD8+ T cells. Via comprehensive cellular and molecular characterization of WGD+ and WGD- tumors at the single cell level, we determined that WGD+ cancer cells have diminished antigen presentation due to muted response to IFN stimulation in part due to epigenetic silencing of transcriptional regulators of MHCI genes via the PRC2 complex. WGD+ tumors also have lower alpha-ketoglutarate/succinate ratio that might lead to the observed increase in histone H3 lysine 27 trimethyl levels associated with repressive chromatin. Lastly, WGD+ tumors are more responsive to anti-PD-L1 blockade and to EED inhibitors and this is associated with increased antigen presentation and CD8+ T cell infiltration. Our results have important implications for the treatment of patients with WGD+ breast cancer.

overall_design: TA3 cell lines that engineered for WGD- and WGD+ was used for mouse orthgotopic injection into the ingunal mammar gland of NSG and A/J mice. And the tumors were collected at the desired time points (day14 or day8).

first: Pierre

last: Foidart

first: Zheqi

last: Li

first: Marco

last: Seehawer


title: Mechanisms by which whole genome doubling drives breast tumor evolution [bulk RNA-Seq]

summary: Triple-negative breast cancers (TNBC) account for 10-15% of all breast cancers. The combination of chemotherapy and Immunotherapy (ICI: immune checkpoint inhibitor) is now a standard in stages II-III TNBC while this regimen is used only in a subset of advanced TNBC tumors presenting a high expression of PD-L1. However, whole exome sequencing of tumors in clinical trials investigating ICI for treatment of various solid tumors other than breast cancer indicate that tumors which undergone a WGD (whole genome doubling) are more sensitive to immune checkpoints inhibitors. Almost all human cells are diploid. Nevertheless, a WGD happens when regulation system maintaining the diploid status fail. The WGD+ cells are tetraploid, oncogenic and facilitate tumorigenesis. The WGD occurs in 44% of breast cancers and has been correlated to advanced cases, lower survival and higher resistance to chemotherapies and targeted therapies. Therefore it is crucial todefine the role of WGD towards the immune escape/control of TNBC and response to ICI.  The first step of this work was to generate different cells line in both WGD- and WGD+ status. Using a technique of membrane homofusion of parentals cells, we obtained a WGD in three different basal murine mammary tumor cell lines (67NR, 168fARN, TA3Hauschka) and one human TNBC cell (SUM 159). The acquisition of WGD was then confirmed by flow cytometry (FACS) (DNA quantity by Hoechst staining) and karyotyping. The TA3Hauschka cell line is of particular interest since it is the only murine cell line which is diploid in parental state.   By injection of WGD+ or parental DP cells in mammary fat pads of syngeneic immunocompetent strain or immunocompromised (NSG) mice, we observed a plateau of tumoral growth only for immunocompetent mice injected with WGD- cells while the WGD+ tumors escaped to spontaneous immune control. No difference of growth was seen in NSG mice between WGD- and WGD+ tumors. On tumor sections, a much more pronounced necrosis was seen in WGD- tumors comparatively to WGD+ tumors in syngeneic mice while the necrosis was mild and similar for both WGD+ and WGD- tumors in NSG mice. Immunofluorescence staining demonstrated an important neutrophilic infiltration of WGD+ while the WGD- tumors had strong T-cell lymphoid infiltrates frankly superior to the lymphoid infiltration of WGD+ tumors. These differences of infiltrates have been confirmed on digested tumors by both FACS and single cells RNA expression (scRNA) analyses. The FACS analysis also showed that the WGD+ tumors had an immunosuppressive pattern with notably higher levels of Tregs cells. To validate the hypothesis that WGD- are controlled by the infiltration of cytotoxic CD8 cells (leading to higher necrosis) while WGD+ tumors induce an immunosuppressive field, we performed an in vivo experiment investigating depletion of CD8 and neutrophils (anti-CD8 and anti-Ly6G antibodies) and a treatment by anti-PD-L1 antibodies (ICI). The treatment by isotypes antibodies confirmed the immune control of only the WGD- tumors. Anti-CD8 treatment led to an important increase in WGD- tumors growth but hadn’t any impact on WGD+ tumors while anti-Ly6G antibodies had no significative impact on WGD- and WGD+ tumors. The treatment by anti-PD-L1 antibodies was significantly more efficient to reduce the growth of WGD+ tumors than WGD- tumors. ScRNA analysis of WGD- and WGD+ untreated tumors revealed that WGD+ tumors have a significative decrease of presentation of MHCI complex.  Therefore, this study highlights the potential role of biomarker of response to immune checkpoint inhibitor of whole genome doubling in TNBC.

overall_design: TA3 cell lines that engineered for WGD- and WGD+ was used for mouse orthgotopic injection into the ingunal mammar gland. And the tumors were collected at the desired time points and subjected for RNA extraction and transcriptomic profiling. For the first experiment, TA3 WGD- and WGD+ cells were injected into NSG and A/J mice following treatment of vehicle or YM-155 for 14 days. For the second experiment, TA3 cells were injected into A/J mice and trated with isotype antibody or antibodies against PD-L1 or aCD8 for 14 days. For the thrid experiment, TA3 cells were injected into A/J mice and tumors were collected at day8 and day14 respectively.


title: Mechanisms by which whole genome doubling drives breast tumor evolution

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: SS-31 protects against paraquat-induced lung injury and fibrosis via inhibition of the MAPK signal pathway

city: Harbin

first: Quankuan

last: Gu

state: Heilongjiang Province

address: Department of Critical Care Medicine

institute: the First Affiliated Hospital of Harbin Medical University

summary:
Aims: To explore the therapeutic effect of SS-31 on lung injury and lung fibrosis caused by paraquat (PQ).
Methods: In vivo experiments involved the intraperitoneal injection of PQ solution into C57BL/6 mice to induce lung injury and fibrosis. Subsequently, SS-31 solution was administered intraperitoneally on a daily basis to investigate its protective effects against PQ-induced lung injury and fibrosis. In vitro use of PQ caused inflammatory responses in  A549 cell line, and the therapeutic effects of SS-31 were explored by treatment with different concentrations of SS-31 in A549. The SS-31 pathway of action was explored and validated by RNA sequencing.
Results: In vivo, SS-31 reduced PQ-induced mortality, acute lung injury, lung fibrosis and apoptosis in mice. The same results were obtained iin vitro experiments. SS-31 was found to inhibit the MAPK pathway by RNA sequencing. The mechanism was further validated by verifying MAPK pathway proteins and applying MAPK pathway agonists.
Innovation and Conclusion: In vivo and in vitro experiments demonstrated that SS-31 reduces lung injury and fibrosis induced by PQ. It works through inhibition of the MAPK signaling pathway.

first: Peiyao

last: Luo

first: Jianpeng

first: Huanhuan

first: Xianyong

first: Yang

last: Chong

first: Jiannan

last: Zhang

first: Yiqi

first: Mingbo

last: Zhao

first: Wei

first: Xianglin

last: Meng

first: Mingyan


title: An infectious murine model for hepacivirus-associated fibrosis and hepatocellular carcinoma

city: New York

first: Brad

last: Rosenberg

state: New York

address: 1 Gustave L Levy Pl

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

summary: The NrHV-HCC model represents the first immunocompetent infectious system that faithfully recapitulates the multistage progression from chronic viral hepatitis to spontaneous hepatocellular carcinoma, bridging a long-standing translational gap between mechanistic mouse studies and human liver cancer. By mirroring the immunopathological, molecular, and sex-associated features of chronic HCV infection, this model provides an unparalleled platform to investigate virus-host interactions underlying fibrosis and oncogenesis. High HCC penetrance and the genetically tractable C57BL/6 background further enhance experimental utility, enabling precise mechanistic dissection and genetic manipulation in a physiologically relevant setting. The capacity to study spontaneous tumor development in the context of natural infection allows for rigorous testing of antifibrotic and anti-cancer strategies, while the persistence of oncogenic potential after viral clearance raises important questions about irreversible disease reprogramming and elevated cancer risk following viral cure - issues of direct relevance to patients cured of HCV.

overall_design: To investigate the transcriptional and mutational landscape of NrHV infected mice and resultant tumors, mock or NrHV infection was established in C57BL/6 mice depleted for CD4 T cells at days -4 and 14 post infection. "Bulk" RNA sequencing (RNA-Seq) was performed on liver/tumor tissue gathered at from both experimental cohorts to assess transcriptional changes over time. To study the mutational landscape, we performed Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT), a custom hybridization capture–based assay encompassing all genes that are druggable by approved therapies or are targets of experimental therapies being investigated in clinical trials at Memorial Sloan Kettering Cancer Center (MSKCC), as well as frequently mutated genes in human cancer (somatic and germline mutations).

first: Mariana

last: Noguiera Batista

first: Juliano

last: Bordignon

first: Ana

last: Luiza Pamplona Mosimann

first: Charles

last: Rice


title: Multi-omics characterization of SIRT3 metabolism and its adaptation to the presence of amyloid-beta oligomers in nasal epithelial cells

status: Public on Mar 14 2026

city: Pamplona

first: Paz

last: Cartas Cejudo

address: Irunlarrea, 3

country: Spain

institute: Navarrabiomed

summary: Sirtuins (SIRTs) are nicotinamide adenine dinucleotide (NAD⁺)-dependent deacetylases that regulate cellular homeostasis in a multifactorial manner. Although alterations in SIRT signaling are evidenced in both olfactory dysfunction and Alzheimer’s disease (AD), the specific role of sirtuin 3 (SIRT3) in olfactory metabolism remains unknown. Here, we have evidenced a partial interdependency between SIRT3 and SIRT5 deacetylase members in human nasal epithelial cell cultures (hNECs). A multi-omic integrative approach applied to conditions of SIRT3 silencing or overexpression revealed that hNEC metabolism is markedly more sensitive to reduced SIRT3 levels, identifying specific transcripts and phosphorylation sites belonging to inflammatory and redox mediators that are tightly regulated by SIRT3 in hNECs. Following exposure to oligomeric Aβ peptide, phosphoproteomic alterations promoted an activation trend of stress-induced senescence and apoptotic signaling in SIRT3-silenced hNECs, whereas induced activation of mitotic phase–related pathways, Hippo signaling, and glycogen metabolism were evidenced in SIRT3-overexpressing hNECs. From a translational point of view, a dissimilar sex-dependent profile in serum SIRT protein levels (SIRT1 and SIRT6) was observed across multiple neurological disorders including AD, mixed dementia, frontotemporal lobar degeneration and amyotrophic lateral sclerosis. These data shed new light on novel SIRT-dependent mechanisms associated with neurodegeneration, underscoring that the maintenance of optimal SIRT3 protein levels may partially counteract the detrimental effects induced by Aβ oligomers in AD at olfactory level.

overall_design: RNAseq profiling of human nasal epithelial cells with silencing, overexpression and Abeta oligomer.

last: Cartas-Cejudo

first: Marina

last: De Miguel

first: Silvia

last: Romero-Murillo

first: Leire

last: Extramiana

first: Joaquín

last: Fernández-Irigoyen

first: Enrique

last: Santamaría


title: A structurally dynamic chromosome 11 locus from Oryza rufipogon L. confers broad-spectrum recessive resistance to bacterial blight

city: Beijing

first: Muhammad

last: Sohaib Shafique

state: Beijing

address: 12-Zhongguancun south street, Haidian District

department: Institute of Crop Sciences

institute: Chinese Academy of Agricultural Sciences

summary: Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most destructive diseases affecting rice production worldwide. In this study, the wild rice accession Oryza rufipogon Wild173 (UP36) exhibiting strong resistance to multiple Xoo strains was investigated in comparison with the susceptible rice cultivar Longjing-31 (CK2). To explore the molecular mechanisms underlying bacterial blight resistance, transcriptome sequencing (RNA-seq) was performed on leaf tissues collected from resistant and susceptible plants following inoculation with the Xoo strain PXO99A. Comparative transcriptomic analysis was conducted to identify differentially expressed genes associated with defense responses. The dataset provides insights into transcriptional reprogramming during pathogen infection and facilitates the identification of candidate genes and defense-related pathways involved in bacterial blight resistance in rice. These data provide valuable resources for understanding host–pathogen interactions and for improving disease resistance in rice breeding programs.

overall_design: Leaf samples of the resistant wild rice accession Oryza rufipogon UP36 were collected at 0 h and 48 h after inoculation with Xanthomonas oryzae pv. oryzae (Xoo) strain PXO99A for transcriptome analysis. Total RNA was extracted from leaf tissues and used for RNA-seq library construction. For each time point, three independent biological replicates were prepared, resulting in a total of six samples. Libraries were sequenced using a paired-end strategy, generating R1 and R2 FASTQ files for each replicate. This dataset was generated to investigate transcriptional changes associated with bacterial blight resistance in UP36 following Xoo infection. The experiment design is consistent with the manuscript description that RNA-seq was performed on leaf tissues collected after Xoo inoculation to analyze defense-related transcriptional responses in UP36.

first: Zhiyuan

last: Ji

first: Shafique

last: Muhammad Sohaib


title: AURKA inhibitor VIC-1911 induces mitotic defects and functional BRACness, sensitizing prostate cancer to PARP inhibition

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

summary: VIC-1911, formerly known as TAS-119, is a next-generation, ATP-competitive AURKA inhibitor with high selectivity over AURKB and AURKC. In this study, we demonstrate that VIC-1911 potently and selectively inhibits AURKA signaling in diverse prostate cancer (PC) cell models, including both androgen receptor (AR)-positive and AR-negative cell lines. VIC-1911 treatment suppressed AURKA phosphorylation and downstream effectors at nanomolar concentrations without affecting AURKB/C activity, resulting in mitotic defects, DNA double-strand breaks (DSBs), and apoptosis. Transcriptomic profiling and immunofluorescence analysis revealed robust activation of DNA damage response pathways and the p53 pathway, consistent with mitotic catastrophe-induced genotoxic stress. Functionally, VIC-1911 significantly inhibited PC cell proliferation and tumor growth in xenograft models, including castration-resistant and AR-negative tumors. Given its ability to induce DNA damage, we evaluated the combinatorial effect of VIC-1911 with PARP inhibitors (PARPi). The combination exhibited synergistic anti-tumor effects in vitro and in vivo, leading to enhanced mitotic abnormalities, γH2AX accumulation, and cleaved PARP expression, even in homologous recombination (HR)-proficient settings. Importantly, VIC-1911 monotherapy and its combination with PARPi were well tolerated in vivo. These findings position VIC-1911 as a promising therapeutic agent for advanced prostate cancer, either as monotherapy or in combination with PARPi to broaden clinical efficacy beyond HR-deficient tumors

overall_design: To investigate thethe gene expression profiles induced by treatmetn with AURKA inhibitor, PARP inhibitor, or their combination in prostate cancer cells we performed RNA-seq analysis of cells treated with either vehicle (VEH), VIC-1911 (AURKAi), OLA (PARPi), or their combination (COMBO).

first: Galina

last: Gritsina

first: Qi

last: Chu

first: Jonathan C

last: Zhao


title: P2X4 Drives Sex-Specific Neuroprotection in Autoimmune Neuroinflammation

city: Leioa

first: Maria

last: Domercq

state: Bizkaia

address: Barrio Sarriena, s/n

department: Neurosciences

institute: Achucarro Basque Center for Neuroscience

summary: Microglia critically influence multiple sclerosis (MS) pathophysiology through debris clearance, myelin repair, and modulation of neuroinflammation. These processes are partly regulated by ATP-gated ion channel P2X4, predominantly expressed in microglia. We previously reported that ivermectin (IVM), a positive allosteric modulator of P2X4, promotes myelin phagocytosis, remyelination, and functional recovery in experimental autoimmune encephalomyelitis (EAE). Here, we dissected the cellular basis of P2X4-mediated effects using P2X4mCherryIN knock-in (P2X4KI) mice, in which P2X4 is replaced by a non-internalized variant (P2X4KI), leading to increased surface localization at the plasma membrane. Constitutive and myeloid-specific P2X4KI (Cd11b-P2X4KI) mice showed significant amelioration of EAE motor deficits, although exclusively in females. Despite equivalent P2X4 expression, function, and IVM responsiveness between sexes, progesterone potentiated P2X4 currents and prolonged channel deactivation, revealing direct hormonal modulation of P2X4 gating. Notably, ovariectomy abolished P2X4-mediated protection in females, confirming the requirement of female hormones. These findings identify microglial P2X4 as a critical modulator of neuroinflammatory outcomes and uncover a previously unrecognized hormone–P2X4 interaction that underlies sex-specific disease modulation. Targeting this pathway may enable precision therapies for MS.

overall_design: RNA-seq was performed on total microglial populations, isolated by fluorescence-activated cell sorting (FACS), from spinal cords of WildType and Cd11b-P2X4KI mice

first: Paloma

last: Mata

last: Bosch-Juan

first: Eric

last: Bué-Grabot


title: SMYD3 promotes immune evasion in clear cell renal cell carcinoma via SREBP1-mediated transactivation of CD47

city: Jinan

first: Zhengfang

last: Liu

address: 107 Wenhua Xilu

institute: Qilu Hospital of Shandong University

summary: The field of immunotherapy for clear cell renal cell carcinoma (ccRCC) is rapidly expanding over the past decade, but limited success to date. Cancer cell-intrinsic features (e.g., genetic aberrations, dysregulation of signaling pathway) play a pivotal role in orchestrating the composition and functional state of immune landscape, which in turn impact tumor progression and response to immunotherapy. However, the underlying mechanism of crosstalk between renal cancer cell and immune cell is largely unknown. Here we discovered that cancer cell-intrinsic SET and MYND domain-containing protein 3 (SMYD3) dysregulation orchestrated an immunosuppressive microenvironment and impaired responses to PD-1 blockade by reprograming the infiltration of immune cells in tumor microenvironment (TME) of ccRCC. Mechanistically, SMYD3, a chromatin regulator, cooperated with Sp1 to transcriptionally promote sterol regulatory element-binding protein 1 (SREBP1) expression by modifying H3-K4 di-/trimethylation and consequently activating the transcription of CD47. CD47, a bridge between innate and adaptive immunity, acted as the downstream effector molecule of the SMYD3 signal to promote the infiltration of Th2 cells, protecting renal cancer cell from immune attack. In summary, we elucidated a critical role for cancer cell-intrinsic SMYD3-SREBP1-CD47 signal in the regulation of the immune microenvironment in ccRCC, and provided a potential strategy to manipulate the tumor immune milieu in favor of antitumor immunity.

overall_design: To gain insights into immune landscape changes induced by SMYD3 in renal cell carcinoma, we performed single-cell RNA sequencing (scRNA-seq) on FACS-sorted CD45+ immune cells from tumors in BALB/c mouse orthotopically engrafted with control and SMYD3-knockdown RENCA tumors.

first: Xiumei

first: Bo

last: Han

first: Shouzhen

last: Chen


title: Single-cell sequencing data of aged male mice treated with Dasatinib plus Quercetin (DQ)

city: Changsha

first: xiao

middle: qiao

last: ni

address: No. 87, Xiangya Road

institute: Xiangya hospital central south university

summary: Single-cell sequencing data on thymus, bone marrow, liver, muscle and adipose of aged male mice treated with Dasatinib plus Quercetin (DQ)

overall_design: Treated 18/19-month-old male mice with dasatinib combined with quercetin (DQ), and thymus, bone marrow, liver, muscle and adipose (including white adipose tissue and brown adipose tissue) were collected for single-cell RNA-seq (thymus, bone marrow and liver) and single-nucleus RNA-seq (muscle and adipose).


title: Disrupting SOX2 Self-Association and Condensates to Overcome Chemotherapeutic Drug Resistance in Lung Squamous Cell Carcinoma [Cut & Run, 2]

city: GuangZhou

first: Wen

last: Yulin

address: No.190 Kaiyuan Avenue

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS)

summary: Chemotherapy remains one of the most important treatments for lung squamous cell carcinoma (LSCC), yet overcoming chemotherapeutic drug resistance poses a significant challenge. The high frequency of SOX2 copy number amplification observed in LSCC patients underscores its potential role as a regulator in this context. Our investigation reveals a strong correlation between SOX2 amplification and expression levels in LSCC patients. Notably, overexpression of SOX2 confers resistance to chemotherapeutic drugs in LSCC cell lines. We elucidate that SOX2 undergoes phase separation, forming condensates that sequester chemotherapeutic agents used in LSCC treatment, thereby exacerbating chemotherapeutic drug resistance in LSCC cells. To address this, we design a small peptide containing 16 amino acids conjugated with 8 arginine, specifically targeting α-helix within HMG domain to disrupt SOX2 self-association. Our data demonstrate that this peptide effectively prevents SOX2 droplet formation, consequently reversing chemotherapy tolerance in LSCC without compromising SOX2 transcriptional activity. Collectively, our findings unveil a novel mechanism of chemotherapy resistance in LSCC mediated by SOX2 phase separation and propose a promising peptide-based therapeutic strategy to combat chemoresistance in LSCC.

overall_design: CUT&Run of SOX2 in NCI-H520 cells in ultrapure water control group and after 12 hours of 10 μM Hx1R8 treatment group.

first: Juehan

last: Wang

first: Yulin

last: Wen

first: Sainan

last: Huang

first: Yanjiang

first: Hongjie

last: Yao


title: Reception of conspecific cues alter testicular gene expression and improve fertility: evidence in boreal chorus frogs (Pseudacris macalata)

city: Ottawa

first: Jeffrey

last: Ethier

state: Ontario

address: 75 Laurier Ave E

department: Biology

country: Canada

institute: University of Ottawa

summary: The evidence for the social modulation of reproduction in vertebrates is established but poorly defined for many taxa despite the link between social cues and endocrine function. It is unclear if physiological effects, such as increased sex hormone concentration or gamete maturation, impact reproductive outcomes, such as fertilization rates or viability of offspring. We investigated the effect of conspecific signals on the calling behaviour, reproductive output, and gonadal gene expression in boreal chorus frogs (Pseudacris maculata). Using breeding trials in a captive setting, we found that broadcasts of conspecific signals nearly doubled the duration of calling activity and increases the proportion of viable eggs by over 13%. We then used RNA-sequencing techniques to demonstrate exposure to broadcasts of chorus behaviour increased the expression of genes associated with steroidogenesis, spermatogenesis, and gonadal development in male chorus frogs within 6 hours. Several gene pathways were similarly affected in male chorus frogs receiving hormone injections to induce sperm development and release, implying there are parallels in hypothalamic-pituitary-gonadal axis stimulation produced by reception of conspecific cues and hormonal induction. We provide some of the first evidence of amphibian social signals causing rapid molecular linked to fertility regulation.

overall_design: We compared the testicular gene expression profiles of male chorus frogs 6 hours after exposure to broadcasts of one of three intensities of conspecific calls: a small chorus of approximately 10–12 males (“Low Chorus”), a large chorus of approximately 100 males (“High Chorus”) or a recording of the natural breeding environment with no calling males (“Wind”). We also compared testicular gene expression profiles of male frogs 6 hours after injection with either a hormone mixture that effectively induces spawning (Amphiplex method) or saline vehicle (Saline).

middle: P

first: Hyoji

last: Lee

first: Stacey

middle: A

last: Robinson

first: Vance

middle: L

last: Trudeau


title: Disrupting SOX2 Self-Association and Condensates to Overcome Chemotherapeutic Drug Resistance in Lung Squamous Cell Carcinoma [RNA-Seq, 2]

overall_design: Gene expression profiling of NCI-H520 cells in ultrapure water control group and after 12 hours of 10 μM Hx1R8 treatment group.


title: Z-RNA drives Tau-mediated neurodegeneration of Alzheimer’s disease [ChIP-Seq]

city: Xiamen

first: Boxin

last: Zhang

address: 良渚实验室1369号

institute: 良渚实验室

summary: Tau aggregates lead to progressive neurodegeneration in Alzheimer’s disease (AD). Neuron death is one of the hallmarks of neurodegeneration. However, the pathological influence of neuronal death is undetermined, and the connection between Tau aggregates and neuronal death remains elusive. Here we demonstrated the essential role of neuron death in Tau-related neurodegeneration. Tau-neurons died in necroptosis, dependent on ZBP1 sensitized by Z-RNAs (an unusual left-handed conformation). Those endogenous Z-RNAs were transcripts of reactivated transposable elements (TEs) originally silenced in heterochromatin.

overall_design: Chromatin immunoprecipitation DNA-sequencing(ChIP-seq) for histone modifications H3K9me3 in hippocampus.


title: Identification of genes regulated by knockdown of HSF1 or CBFA2T2

city: Ube

first: MITSUKAI

last: FUJIMOTO

state: Yamaguchi

address: 1-1-1 Minami-Kogushi

department: Graduate School of Medicine

country: Japan

institute: Yamaguchi University

summary: To examine whether the HSF1–CBFA2T2 complex regulates gene expression in human melanoma MeWo cells, DNA microarray analysis was performed.

overall_design: mRNA expression profiles were analyzed in human melanoma MeWo cells with shRNA-mediated knockdown of HSF1 or CBFA2T2, with scrambled shRNA (SCR) used as a control. DNA microarray analysis was performed using the Clariom S Array Human GeneChip (Thermo Fisher Scientific).

first: Mitsuaki

last: Fujimoto

first: Ryosuke

last: Takii

first: Akira

last: Nakaki


title: Z-RNA drives Tau-mediated neurodegeneration of Alzheimer’s disease [bulkRNA-seq]

summary: Tau aggregates lead to progressive neurodegeneration in Alzheimer’s disease (AD) (ref). Neuron death is one of the hallmarks of neurodegeneration (ref). However, the pathological influence of neuronal death is undetermined, and the connection between Tau aggregates and neuronal death remains elusive. Here we demonstrated the essential role of neuron death in Tau-related neurodegeneration. Tau-neurons died in necroptosis, dependent on ZBP1 sensitized by Z-RNAs (an unusual left-handed conformation). Those endogenous Z-RNAs were transcripts of reactivated transposable elements (TEs) originally silenced in heterochromatin.

overall_design: The gene expression profiling analysis for the hippocampus of 10-month-old WT, PS19 and PS19 Zbp1+/- mice.


title: Z-RNA drives Tau-mediated neurodegeneration of Alzheimer’s disease

overall_design: ZBP1 was pull down by corresponding antibodies.The immunoprecipitated RNA was purified for RNA sequencing.

first: Yuenan

last: Zhou


title: Chromatin-intrinsic mechanisms determine orientation-specific class switch recombination [3C-HTGTS]

first: Xuefei

address: No.5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center (BIOPIC)

institute: Peking University

summary: Activation-induced cytidine deaminase (AID)-initiated immunoglobulin heavy chain (Igh) class switch recombination (CSR) replaces donor Cμ constant region exons (CHs) with a downstream acceptor CH to generate different functional antibody isotypes. However, mechanisms governing orientation-specific productive CSR remain incompletely understood. Through analysing the characteristics of evolved constant regions and constructing diversified constant regions to recapitulate productive CSR in jawed vertebrates to systematically dissect productive CSR determinants, we found that switch topological configuration (STC), including transcriptional orientation, chromatin distance, and chromatin domain of Igh, determines orientation-specific joining of AID-initiated breaks for productive CSR. Long-distance CHs under co-oriented transcription within Igh domain foster predominantly deletional joining-mediated productive CSR. In contrast, oppositely transcribed and short-distance CHs affect end-joining bias via promoting diffusion-mediated inversional joining for CSR with lower efficiency. Moreover, AID-initiated breaks in different domains, facilitate more diffusion-mediated orientation-unbiased end-joining for non-productive CSR. Our findings uncover chromatin-intrinsic mechanisms safeguarding orientation-specific productive CSR throughout evolution.

overall_design: We performed CSR-HTGTS-Seq, 3C-HTGTS,  PRO-Seq and ChIP-seq in different mutants of CH12F3 cells to study roles of chromatin configuration in orientation-specific end joining of AID-initiated breaks in IgH class switch recombination.

first: Sha

last: Luo

first: Ruoling

last: Qiap

first: Hialiang

last: Zha


title: Chromatin-intrinsic mechanisms determine orientation-specific class switch recombination [PRO-seq]


title: Single-cell sequencing data of aged male mice treated with Vehicle or Dasatinib plus Quercetin (DQ)

first: xiao

last: ni

summary: Single-cell sequencing data on bone marrow, thymus, liver, muscle and adipose

overall_design: Treated 18 or 19-month-old mice with Vehicle or dasatinib combined with quercetin (DQ), and after 2 months, bone marrow, thymus, liver, muscle and adipose (including white adipose tissue and brown adipose tissue) were collected for single-cell RNA-seq (thymus,  bone marrow and liver) and single-nucleus RNA-seq (adipose and muscle).


title: Mechanisms by which whole genome doubling drives breast tumor evolution [CUT&Run]

first: Kornelia

last: Polyak

summary: Triple-negative breast cancers (TNBC) account for 10-15% of all breast cancers. The combination of chemotherapy and Immunotherapy (ICI: immune checkpoint inhibitor) is now a standard in stages II-III TNBC while this regimen is used only in a subset of advanced TNBC tumors presenting a high expression of PD-L1. However, whole exome sequencing of tumors in clinical trials investigating ICI for treatment of various solid tumors other than breast cancer indicate that tumors which undergone a WGD (whole genome doubling) are more sensitive to immune checkpoints inhibitors. Almost all human cells are diploid. Nevertheless, a WGD happens when regulation system maintaining the diploid status fail. The WGD+ cells are tetraploid, oncogenic and facilitate tumorigenesis. The WGD occurs in 44% of breast cancers and has been correlated to advanced cases, lower survival and higher resistance to chemotherapies and targeted therapies. Therefore it is crucial todefine the role of WGD towards the immune escape/control of TNBC and response to ICI.  The first step of this work was to generate different cells line in both WGD- and WGD+ status. Using a technique of membrane homofusion of parentals cells, we obtained a WGD in three different basal murine mammary tumor cell lines (67NR, 168fARN, TA3Hauschka) and one human TNBC cell (SUM 159). The acquisition of WGD was then confirmed by flow cytometry (FACS) (DNA quantity by Hoechst staining) and karyotyping. The TA3Hauschka cell line is of particular interest since it is the only murine cell line which is diploid in parental state.   By injection of WGD+ or parental DP cells in mammary fat pads of syngeneic immunocompetent strain or immunocompromised (NSG) mice, we observed a plateau of tumoral growth only for immunocompetent mice injected with WGD- cells while the WGD+ tumors escaped to spontaneous immune control. No difference of growth was seen in NSG mice between WGD- and WGD+ tumors. On tumor sections, a much more pronounced necrosis was seen in WGD- tumors comparatively to WGD+ tumors in syngeneic mice while the necrosis was mild and similar for both WGD+ and WGD- tumors in NSG mice. Immunofluorescence staining demonstrated an important neutrophilic infiltration of WGD+ while the WGD- tumors had strong T-cell lymphoid infiltrates frankly superior to the lymphoid infiltration of WGD+ tumors. These differences of infiltrates have been confirmed on digested tumors by both FACS and single cells RNA expression (scRNA) analyses. The FACS analysis also showed that the WGD+ tumors had an immunosuppressive pattern with notably higher levels of Tregs cells. To validate the hypothesis that WGD- are controlled by the infiltration of cytotoxic CD8 cells (leading to higher necrosis) while WGD+ tumors induce an immunosuppressive field, we performed an in vivo experiment investigating depletion of CD8 and neutrophils (anti-CD8 and anti-Ly6G antibodies) and a treatment by anti-PD-L1 antibodies (ICI). The treatment by isotypes antibodies confirmed the immune control of only the WGD- tumors. Anti-CD8 treatment led to an important increase in WGD- tumors growth but hadn’t any impact on WGD+ tumors while anti-Ly6G antibodies had no significative impact on WGD- and WGD+ tumors. The treatment by anti-PD-L1 antibodies was significantly more efficient to reduce the growth of WGD+ tumors than WGD- tumors. ScRNA analysis of WGD- and WGD+ untreated tumors revealed that WGD+ tumors have a significative decrease of presentation of MHCI complex.  Therefore, this study highlights the potential role of biomarker of response to immune checkpoint inhibitor of whole genome doubling in TNBC.

overall_design: TA3 cell lines that engineered for WGD- and WGD+ was used for mouse orthgotopic injection into the ingunal mammar gland. And the tumors were collected at the desired time points and subjected for RNA extraction and transcriptomic profiling. For the first experiment, TA3 WGD- and WGD+ cells were injected into NSG and A/J mice following treatment of vehicle or YM-155 for 14 days. For the second experiment, TA3 cells were injected into A/J mice and trated with isotype antibody or antibodies against PD-L1 or aCD8 for 14 days. For the thrid experiment, TA3 cells were injected into A/J mice and tumors were collected at day8 and day14 respectively.

first: Pierre

last: Foidart

first: Zheqi

last: Li

first: Marco

last: Seehawer


title: Effect of  WFDC21P knockdown in BT549 cells.

city: Foshan

first: Yi

last: Wang

address: Guicheng Street

institute: Sun Yat-Sen University

summary: We identify a long noncoding RNA, WFDC21P (lnc-DC), which corelates to anti-tumor immunity in triple negative breast cancer (TNBC). To investigate the pathway that mediates the role of WFDC21P in TNBC, we knock down WFDC21P in BT549 cells with two siRNAs and perform RNA-seq analysis.

overall_design: Comparative gene expression profiling of RNA-seq data for BT549 cells and its knockdown derivatives (siNC, siWFDC21P-1, siWFDC21P-2). Triplicate experiments were performed for the RNA-seq analysis.

first: Zean

first: Man-Li


title: Z-RNA drives Tau-mediated neurodegeneration of Alzheimer’s disease [RNA-Seq]

first: Boxin


title: Chromatin-intrinsic mechanisms determine orientation-specific class switch recombination [ChIP-Seq]


title: Chromatin-intrinsic mechanisms determine orientation-specific class switch recombination [CSR-HTGTS-Seq]

first: Ruolin

last: Qiao

first: Hailiang


title: Tff2 marks gastric corpus progenitors that give rise to pyloric metaplasia/SPEM following injury

first: Hualong

last: Zheng

state: NY

department: Department of Medicine

institute: Columbia University Medical Center

summary: Pyloric metaplasia, also known as spasmolytic polypeptide-expressing metaplasia (SPEM), arises in the corpus in response to oxyntic atrophy, but its origin and role in gastric cancer remain poorly understood. Using Tff2-CreERT knockin mice, we identified highly proliferative Tff2+ progenitors in the corpus isthmus that give rise to multiple secretory lineages, including chief cells. While lacking long-term self-renewal ability, Tff2+ corpus progenitors rapidly expand to form short-term SPEM following acute injury or loss of chief cells. Genetic ablation of Tff2+ progenitors abrogated SPEM formation, while genetic ablation of GIF+ chief cells enhanced SPEM formation from Tff2+ progenitors. In response to H. pylori infection, Tff2+ progenitors progressed first to metaplasia and then later to dysplasia. Interestingly, induction of KrasG12D mutations in Tff2+ progenitors facilitated direct progression to dysplasia in part through the acquisition of stem cell-like properties. In contrast, Kras-mutated SPEM and chief cells were not able to progress to dysplasia. Tff2 mRNA was downregulated in isthmus cells during progression to dysplasia. Single-cell RNA sequencing and spatial transcriptomics of human tissues revealed distinct differentiation trajectories for SPEM and gastric cancer. These findings challenge the conventional model of stepwise progression through metaplasia and instead identify Tff2+ progenitor cells as potential cells of origin for SPEM and possibly for gastric cancer.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed on sorted Tff2+ progenitors and their progeny from Tff2-CreERT; Rosa26-tdTomato mice to investigate their differentiation trajectories. Two experimental groups were analyzed: Low-Dose Tamoxifen (LDT) and High-Dose Tamoxifen (HDT). The LDT group included six mice, with Tff2+ progenitors collected on Day 1 and mature progeny on Day 28, yielding a total of 20,649 cells with 74% viability. The HDT group also included six mice, with Tff2+ progenitors collected on Day 1 and SPEM cells on Day 5, yielding 22,068 cells with 83% viability. Cells were sorted via flow cytometry based on EpCAM+ and tdTomato+ markers, and libraries were prepared using the 10x Genomics Chromium platform.

first: Ruhong

last: Tu

first: Biyun

first: Jin

last: Qian

first: Feijing

last: Wu

first: Yosuke

last: Ochiai

first: Hiroki

last: Kobayashi

first: Quin

middle: T

last: Waterbury

first: Leah

middle: B

last: Zamechek

first: Changming

last: Huang

first: Ping

first: Yoku

last: Hayakawa

first: Timothy

middle: C


title: Targeted inhibition of de novo lipogenesis induces cancer cell senescence

city: Salt

first: Javier

middle: Abel

last: Menendez

state: Girona

address: Dr Castany s/n. Parc hospitalari Marti i Julia

institute: Girona Biomedical Research Institute

summary: Conventional chemotherapeutic agents and radiation induce accelerated senescence in cancer cells, a phenomenon known as therapy- induced senescence (TIS). Here, we investigated whether TIS can also be induced by targeted inhibition of de novo lipogenesis, which we term fatty acid synthesis therapy-induced senescence (FASTIS). SKBR3 breast cancer cells were treated for 7 days with clinically relevant inhibitors of the key lipogenic enzymes acetyl-CoA carboxylase (ND-646) and fatty acid synthase (TVB-3166) as well as with the well-established, mechanistically distinct TIS inducers bleomycin (an antibiotic that promotes oxidative stress), alisertib (an Aurora A kinase inhibitor that promotes mitotic stress), doxorubicin (a topoisomerase II inhibitor and DNA intercalator that induces DNA damage stress), and palbociclib (a CDK4/6 inhibitor that induces replication stress). To understand the unique versus shared molecular changes of the FASTIS phenotype induced by fatty acid synthesis inhibitors compared to other TIS inducers, we performed mRNA-Seq experiments to provide a comprehensive, high-resolution view of the underlying coding transcriptomes. To account for potential artifacts due to cell subpopulations entering a quiescent state to survive nutrient deprivation after 7 days, parallel mRNA sequencing was also performed in untreated (proliferative) cells at days 0 and 7.

overall_design: RNA-seq profiling of SKBr3 cells treated with de novo lipogenesis inhibitors (ND-646 and TVB-3166) or well-established senescence inducers (bleomycin, alisertib, doxorubicin, palboclib) at days 0 and 7.

first: Àngela

last: Llop-Hernández

first: Sara

last: Verdura

first: Travis

last: Van der Steen

first: José Antonio

last: Encinar

first: Begoña

last: Martin-Castillo

first: George

last: Kemble

first: Elisabet

last: Cuyàs

first: Ruth

last: Lupu

first: Javier A.


title: Senataxin promotes recombination fidelity during antigen receptor gene diversification

city: Paris

first: Ludovic

last: Deriano

address: 25-28 Rue du Docteur Roux

department: Immunology

country: France

institute: Institut Pasteur

summary: Immunoglobulin (Ig) and T cell receptor (TCR) V(D)J gene recombination relies on non-homologous end-joining (NHEJ), which repairs DNA double-strand breaks (DSBs) introduced by the RAG1/2 nuclease complex. Functional redundancies exist between NHEJ and the ATM kinase-dependent chromatin DSB response, likely masking the activity of additional factors. Here, we performed targeted CRISPR/Cas9 knockout screens (+/- ATM kinase inhibition) in pro-B cells and identified Senataxin (SETX) as a novel player in V(D)J recombination. We show that SETX supports V(D)J recombination, particularly when the ATM kinase is inhibited or in an XLF-deficient background. Furthermore, we show that SETX suppresses the formation of aberrant coding end-to-signal end hybrid joints during V(D)J recombination, both in vitro and in vivo. Finally, SETX prevents the aberrant joining of AID-induced DNA ends during class switch recombination (CSR). Overall, our work reveals an important role for SETX in promoting recombination fidelity and suppressing genome instability during antigen receptor gene diversification.

overall_design: RNA-seq profiling of WT and Setx-/- v-Abl pro-B cell clones after 45h ABLki treatment. N = 3 biological replicates for each cell line.

first: Alice

last: Libri

first: Jinglong

last: Wang

first: Timea

last: Marton

first: Wei

last: Yu

first: François

last: Dossin

first: Gabriel

last: Balmus

first: Bernardo

last: Reina-San-Martin

first: Richard

last: Frock

first: Chloé

last: Lescale


title: Disrupting SOX2 Self-Association and Condensates to Overcome Chemotherapeutic Drug Resistance in Lung Squamous Cell Carcinoma [RNA-Seq]

first: Wen

last: Yulin

overall_design: Gene expression profiling of NCI-H520 cells in PBS control group and after 48 hours of 2 μM cisplatin treatment group.

first: Juehan

first: Yulin

last: Wen

first: Sainan

last: Huang

first: Yanjiang

last: Liu

first: Hongjie

last: Yao


title: Comparative analysis of gene expression in HDV-infected dHepaRG cells upon treatment with IFN-α-2a or IFN-λ1

status: Public on Mar 13 2026

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

summary: Hepatitis D virus (HDV) causes the most severe form of chronic viral hepatitis, often leading to advanced liver disease and hepatocellular carcinoma. Viral cure is rarely achieved in infected patients. Interferon-alpha (IFN-α)-based therapies show suboptimal efficacy and low rates of sustained response, as reflected by their limited effect on HDV replication in vitro. Here, we show that HDV infection induces cellular resistance to IFN-α, marked by impaired STAT1 phosphorylation and reduced expression of interferon-stimulated genes (ISGs) in hepatocyte-like cells. This refractoriness depends on virus-induced innate immune activation, highlighting the role of HDV-induced ISG expression in regulating IFN signalling. We identify USP18 as a key mediator of IFN-α resistance in infected cells. Notably, ISG expression in response to type III IFN (IFN-λ) remains intact, consistent with USP18’s selective inhibition of IFN-α signalling. Collectively, these findings reveal the molecular mechanism of IFN-α resistance in HDV-infected hepatocytes and provide a rationale for developing novel therapies against this major public health threat.

overall_design: For transcriptomic analyses, differentiated HepaRG (dHepaRG) cells were either inoculated with HDV virions at a multiplicity of infection (MOI) of approximately 100 viral genome equivalents (vge) per cell for 6 days or left non-infected. Cells were then treated for 8 h with either IFN-alpha-2a (500 IU/mL) or IFN-lambda-1 (100 ng/mL). As controls, non-infected dHepaRG cells were treated for 8 h with IFN-alpha-2a (500 IU/mL) or IL-29/IFN-lambda-1 (100 ng/mL). Additional control conditions included infection of dHepaRG cells for 8 h with Sendai virus (SeV, Cantell strain; AVS Bio) at 10 hemagglutination units (HAU)/mL or with encephalomyocarditis virus (EMCV, Sigean strain; kindly provided by Labib Bakkali-Kassimi, Anses, France) at an MOI of 0.70 vge/cell. Cells were lysed and total intracellular RNA was extracted using the Monarch Nucleic Acid Purification Kit (New England Biolabs).

first: Claudie

last: Eber

first: Roxanne

last: Fouillé

first: Julie

last: Lucifora

first: Eloi

middle: R

last: Verrier


title: ChIP-Seq with reference exogenous genome (ChIP-Rx) of MYC in parental U2OS cells

city: Pittsburgh

first: Da

last: Yang

state: PA

address: 3501 Terrace

department: School of Pharmacy

institute: University of Pittsburgh

summary: Emerging evidence suggests that MYC binds RNAs, but its functional consequences remain unclear. Here, we integrate multi-omics data and reveal that MYC broadly binds enhancer RNAs (eRNAs), which exhibit high cancer- and tissue-specific expression in cancer cell lines and patient tumors. Moreover, we developed a computational pipeline to identify potential cis-regulatory MYC-eRNA target genes, with most predicted eRNA-target pairs supported by RNA polymerase II-mediated chromatin interaction data. Among these, we functionally characterized MERG1 as an oncogenic eRNA that promotes breast cancer tumorigenesis. Mechanistically, MERG1 interacts with MYC to enhance its occupancy at the GREB1 promoter, driving chromatin remodeling and epigenetic activation. This process specifically amplifies GREB1 expression and promotes tumor progression. Finally, nanoparticle-mediated delivery of antisense oligonucleotides targeting MERG1 suppresses MYC-mediated breast cancer growth. These results advance our understanding of the enhancer-driven regulation of gene expression and tumorigenesis and provide insights into the regulatory landscape of MYC in cancer.

overall_design: Chromatin immunoprecipitation assays followed by sequencing (ChIP-Seq) with reference exogenous genome (ChIP-Rx) of MYC in parental U2OS cells. NIH3T3 cells (mouse) were used as the reference exogenous genome. Two biological replicates were sequenced for each cell.

first: Sihan

last: Li

first: Zehua

last: Wang


title: Disrupting SOX2 Self-Association and Condensates to Overcome Chemotherapeutic Drug Resistance in Lung Squamous Cell Carcinoma [CUT&Run]


title: Transcriptional profiling of CRP-V5 and K52Q-V5 Vibrio cholerae C6706 grown in M9 minimal medium with maltose or trehalose as sole carbon source

city: Boston

first: Renato

last: Santos

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: RNA-seq was performed to compare the transcriptomes of Vibrio cholerae C6706 strains expressing V5-tagged wild-type CRP (CRP-V5) or the acetylation-mimicking mutant K52Q-V5 during growth in M9 minimal medium supplemented with 0.8% maltose or 0.8% trehalose as the sole carbon source. Overnight cultures grown in LB were washed and resuspended in the respective M9 media, then cultivated for approximately 3 hours to mid-exponential phase. Total RNA was extracted and subjected to stranded total RNA sequencing with ribosomal RNA depletion. This dataset complements ChIP-seq and RNA-seq data previously deposited under GSE310654 by examining CRP-dependent transcriptional responses under carbon source-specific conditions.

overall_design: Vibrio cholerae C6706 strains carrying chromosomally integrated CRP-V5 or K52Q-V5 were grown overnight in LB medium, washed in PBS, and resuspended in M9 minimal medium with 0.8% maltose or 0.8% trehalose. Cultures were grown to mid-exponential phase (~3 hours) at 27°C with shaking at 200 rpm. Total RNA was extracted using the irect-zol RNA Miniprep Kit (Zymo), DNase-treated, and sequenced using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus on a NovaSeq X Plus (paired-end 150 bp). Three biological replicates were generated per condition (2 genotypes × 2 carbon sources = 4 conditions, 12 samples total).


title: Widespread non-Mendelian inheritance of DNA methylation patterns in mice.

city: Baltimore

first: Adam

last: Davidovich

state: Maryland

address: 855 N. Wolfe Street

institute: Johns Hopkins University

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Single-nucleus transcriptomic profiling of mouse hearts following angiotensin II-infused with or without bisphenol F (BPF) treatment.

first: Qingtao

last: Meng

address: No.10, West Tou Tiao, Youan Men Wai, Fengtai District

institute: capital Medical University

summary: Bisphenol F (BPF) is a widely used substitute for bisphenol A (BPA) in plastic manufacturing; however, its potential toxicity remains insufficiently characterized. In this study, we investigated the impact of BPF exposure on the intestinal barrier and cardiovascular system. Based on prior untargeted metabolomic analysis, we revealed that BPF can be converted into N-acetylputrescine (NAP) through a microbiota-associated metabolic process. Further experiments demonstrated that BPF exposure stimulated intestinal epithelial cells to secrete spermidine/spermine N1-acetyltransferase 1 (Sat1), an enzyme involved in this conversion. To identify the cell types and signaling pathways associated with BPF exposure under hypertensive conditions, we conducted snRNA-seq of heart tissues from angiotensin II-infused mice and angiotensin II-infused mice pretreated with BPF exposure. The raw sequencing data and processed expression matrices are provided in this submission.

overall_design: snRNA-seq of mouse heart tissues from angiotensin II-infused mice (n = 5) and angiotensin II-infused mice treated with BPF expose (n = 5).

first: Jing

first: Jie

last: Xu

first: Huanzhuo

last: Mai

first: Guolei

last: Niu

first: Shenshen

last: Wu

first: Xianan

last: Zhang

first: Jiahao

last: Zhu

first: Michael

last: Aschner

first: Rui

last: Chen


title: RNA binding proteins Pcbp1 and Pcbp2 are indispensable for B cell development [scRNA-seq]

city: Hangzhou

first: Xing

last: Chang

state: Zhejiang

address: No. 600 Dunyu Road, Sandun Town, Xihu District

department: School of Life Sciences

institute: Westlake University

summary: B-cell development in the bone marrow is a tightly regulated process requiring precise control of gene expression at both transcriptional and post-transcriptional levels. Here, we identify the RNA-binding proteins Pcbp1 and Pcbp2 as essential, redundant regulators of early B lymphopoiesis. While a single deficiency of either Pcbp1 or Pcbp2 results in only a partial blockade at the pro-B to pre-B transition, their combined deletion causes a near-complete arrest. Using single-cell RNA sequencing, we identify the developmental bottleneck to the pro-B VDJ A stage—characterized by active D-JH rearrangement—with a failure to generate Lambda pre-B or immature B cells. Mechanistically, Pcbp1/2 deficiency triggers multifaceted cell-intrinsic defects: loss of Ebf1-driven lineage identity, mitochondrial dysfunction, and accumulation of proteotoxic stress. These defects converge to block early progenitor survival and expansion, ultimately preventing B cells from progressing beyond the pre-B stage. Our findings establish Pcbp1 and Pcbp2 as critical post-transcriptional regulators that couple metabolic fitness with lineage integrity, uncovering an RBP-dependent checkpoint essential for B cell lymphopoiesis.

overall_design: To elucidate the molecular basis of the developmental arrest in the Pcbp1/2-dKO background, we performed single-cell RNA sequencing (scRNA-seq) on bone marrow B220+ cells. Bone marrow B220+Dump- cells (gated to exclude CD4, CD8a, Ly6G/6C, NK1.1, and CD11c) were sorted from two WT mice (Mb1-Cre Pcbp1 +/+ Pcbp2+/+) into early (CD43+) and late (CD43-) progenitor fractions at a 1:1 ratio, while total B220+Dump- cells were collected for sequencing from three Pcbp1/2-dKO mice (Mb1-Cre Pcbp1 fl/fl Pcbp2 fl/fl).

first: Li

last: Lin

first: Tuan

last: Qi

first: Geng


title: The metabolic cofactor Coenzyme A enhances alternative macrophage activation via MyD88-linked signaling [RNA-seq]

city: Los Angeles

first: Anthony

last: Jones

state: CA

address: 650 Charles E Young Dr. South, Room 23-305

department: Department of Molecular and Medical Pharmacology

institute: University of California, Los Angeles

summary: Metabolites and metabolic co-factors can shape the innate immune response, though the  pathways by which these molecules adjust inflammation remain incompletely understood. Here we show that the metabolic cofactor Coenzyme A (CoA) enhances IL-4 driven alternative macrophage activation [M(IL-4)] in vitro and in vivo. Unexpectedly, we found that perturbations in intracellular CoA metabolism did not influence M(IL-4) differentiation. Rather, we discovered that exogenous CoA is a weak TLR4 agonist which primes macrophages for increased receptivity to IL-4 signals and resolution of inflammation via MyD88. Mechanistic studies revealed MyD88- linked signals enhance IL-4 responsiveness, in part, by reshaping chromatin accessibility to enhance transcription of IL-4-linked genes. The results identify CoA as a host metabolic co-factor that influences macrophage function through an extrinsic TLR4-dependent mechanism and suggest that damage-associated molecular patterns (DAMPs) can prime macrophages for alternative activation and resolution of inflammation.

overall_design: RNA-seq profiling of bone marrow-derived macrophages treated with Vehicle, IL-4, IL-4 in combination with Coenzyme A for  48hrs

middle: E

first: Ajit

middle: S

last: Divakaruni


title: miRNA Expression data from human heatstroke patients

city: Thuwal

first: Maria

middle: de los Angeles

last: Gomez

address: 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia

department: Bioengineering

country: Saudi Arabia

institute: KAUST

type: Non-coding RNA profiling by high throughput sequencing

summary: This study examined miRNA responses to heat exposure in peripheral blood mononuclear cells from 19 patients with heat stroke and 19 controls.

overall_design: We enrolled 19 non-heat stroke (NHS) pilgrims, friends, or relatives of heat stroke patients living in the same environmental heat as a control group. We obtained blood samples from control subjects upon enrolment and heat stroke patients on arrival to the cooling unit, before cooling (Heatstroke T0) and after cooling (Heatstroke T1).

first: Abderrezak

last: Bouchama

first: Saeed

last: Al Mahri


title: The metabolic cofactor Coenzyme A enhances alternative macrophage activation via MyD88-linked signaling [ATAC-seq]

overall_design: ATAC-seq profiling of bone marrow-derived macrophages treated with Vehicle, IL-4, IL-4 in combination with the TLR2 agonist Pam3CSK4 for  12 or 24hrs


title: RNA binding proteins Pcbp1 and Pcbp2 are indispensable for B cell development [scRNA-seq ko]

last: Li


title: Lactylation Converts ABHD6 into a Mitochondrial Regulator that Drives Lenvatinib Resistance in Hepatocellular Carcinoma

city: Nantong

first: Long

last: Hu

address: Chongchuan DistrictNantong University No.9 Seyuan Rd

institute: nantong university

summary: Hepatocellular carcinoma (HCC) frequently develops resistance to lenvatinib, a frontline tyrosine kinase inhibitor. Resistance arises from heterogeneous mechanisms involving metabolic reprogramming and mitochondrial adaptation, implicating regulators of these processes as potential therapeutic targets.

overall_design: Here, we identified α/β hydrolase domain containing 6 (ABHD6) as a critical driver of lenvatinib resistance by perturbing mitochondrial dynamics. Ligand-binding at the S148 catalytic site allosterically controlled a molecular switch between canonical enzymatic and non-canonical scaffolding functions of ABHD6, and the pro-resistance function was independent of catalysis but required an unoccupied catalytic site. In resistant HCC, the Warburg effect elevated lactate, leading to K245 lactylation of ABHD6. This modification triggered the mitochondrial translocation of ABHD6, where it functioned as a scaffold that competitively bound the fission regulator FIS1 and displaced DRP1. Disruption of the fission machinery stabilized hyperfused mitochondria, thereby conferring lenvatinib resistance by suppressing drug-induced apoptosis and ROS generation. Both inhibiting lactate production and enforcing occupancy of the S148 site with substrates or a specific inhibitor blocked formation of the ABHD6-FIS1 complex, reactivated mitochondrial fission, and restored lenvatinib sensitivity. This study identified a lactate-driven functional switch in ABHD6 and established that targeting this allosteric mechanism is an effective therapeutic strategy to overcome lenvatinib resistance.

first: Zhiyuan

last: Tang


title: ST36 acupoint implantation of an astragaloside IV–glycyrrhizic acid drug eluting suture enhances immune function in weaned lambs by modulating the Treg/Th17 balance

city: Lanzhou

first: Ke

last: Zhou

state: Gansu

address: No. 1 Yingmen Village Gansu Agricultural University

institute: National Natural Science Foundation of China

summary: Weaning is a critical period in young animals and is often accompanied by immunosuppression and intestinal immune imbalance caused by stress and nutritional transition. In this study, an astragaloside IV- and glycyrrhizic acid-loaded drug-eluting suture system (A.G.-ES) was developed to improve the stability and practicality of immune-enhancing intervention, and its immunomodulatory effects after implantation at the Zusanli acupoints (ST36) were evaluated in both cyclophosphamide-induced immunosuppressed mice and weaned lambs. In mice, colon histology, flow cytometry of gut-associated lymphoid tissues, proteomics, and qPCR were used to investigate the underlying mechanisms. In lambs, complete blood counts, immunoglobulin levels, and single-cell transcriptomic profiles of peripheral blood mononuclear cells were assessed. The results showed that A.G.-ES alleviated colonic mucus layer injury, increased goblet cell numbers and mucus secretion, and promoted restoration of the Treg/Th17 balance in immunosuppressed mice. Proteomic analysis further showed that A.G.-ES regulated key molecules related to intestinal mucosal barrier function and immune regulation. In weaned lambs, A.G.-ES increased WBC, LYM, RBC, HCT, HGB, IgM, and IgG levels and reshaped PBMC immune cell composition with enhanced T cell-related immune pathway activity. These findings indicate that ST36 implantation of A.G.-ES may improve immune function during weaning and has potential for veterinary application.

overall_design: PBMCs were isolated from sheep whole blood using HISTOPAQUE 1083 lymphocyte separation medium, collected from the intermediate layer, and analyzed by single-cell RNA sequencing.

first: Hai

first: Zhizhen

last: Zhao


title: HIV-1 Amplifies IL-8 Response Of Human Stellate Cells To Gram-Positive Microbial Products Via H4K5 Histone Acetylation

city: Bethesda

first: Laurence

last: Zhang

address: 9000 Rockville pike

institute: NIH/Kelly

summary: Patients living with Human Immunodeficiency Virus (PLWH) develop accelerated liver fibrosis, but the exact mechanism remains unknown. Unlike gram-negative bacterial products, the impact of gram-positive microbial products in Human Immunodeficiency Virus 1 (HIV-1) associated liver inflammation and fibrosis remains poorly understood. In this study, we investigated the effect of lipoteichoic acid (LTA), a major gram-positive bacterial component, on HSCs in the context of HIV-1 infection. Our data revealed that HIV-1 infection sensitizes HSCs to LTA stimulation, leading to an amplified IL-8 response mediated through histone acetylation that may accelerate liver fibrosis progression in PLWH. As microbial translocation persists despite effective antiretroviral therapy, these findings underscore the need for targeted strategies to mitigate liver fibrosis in HIV-1 infected patients.

overall_design: Total RNA from Lx2 cells treated with medium, HIV-1BaL (MOI = 0.1), and/or LTA (1 μg/mL) was sequenced (n = 3 per group). RNA quality was assessed by a Nano Drop 2000 Bioanalyzer, and RNA-Seq was performed by Mount Sinai NGS Core. Reads were aligned with STAR, quantified with HTSeq, and analyzed with DESeq2 using hg19 annotation.CHIP-seq was analyzed using a pipeline of bowtie2, macs callpeak2, samtools, bedtools, and deeptools

first: Lumin

first: Rabab

middle: O

last: Ali

first: Naichaya

last: Chamroonkul

first: Parissa

last: Tabrizia

first: Myron

last: Schwart

first: Ganesh

last: Gunasekaran

last: Isabel Fiel

first: Thomas

last: Schiano

first: Steven

last: Ward

first: Meena

last: Bansal


title: Effects of RRAGD p.(Ser76Leu) variant in human induced pluripotent stem cell-derived cardiomyocytes gene expression

city: Nijmegen

first: Sara

last: van Katwijk

address: Geert Grooteplein Zuid 28

department: Medical BioSciences

country: Netherlands

institute: Radboudumc

summary: RRAGD p.(Ser76Leu) has been associated with dilated cardiomyopathy. To study the effects of this variant on cardiomyocyte gene expression profile, we generated a human induced pluripotent stem cell-derived cardiomyocyte (hiPSC-CM) model carrying heterozygous mutation of the variant. After bulk-RNA seq, we showed that 124 genes were upregulated and 48 genes were downregulated in RRAGD p.(Ser76Leu) hiPSC-CMs compared to RRAGD WT hiPSC-CMs. Further analyses revealed that pathways related to muscle development were downregulated, while pathways associated with actin cytoskeleton regulation were upregulated.

overall_design: First, heterozygous RRAGD p.(Ser76Leu) variant was introduced into the hiPSCs using CRISPR-Cas9. Then, these hiPSCs were differentiated into cardiomyocytes. After 80 days in culture, total RNA was extracted from RRAGD p.(Ser76Leu) and RRAGD WT hiPSC-CMs. These RNA's were then subjected to bulk RNA-seq. RNA samples from four differentiation rounds were sequenced per cell line.

first: Anastasia

last: Adella

first: Pieter

last: Leermakers

first: Joost

last: Maartens

last: Hoenderop

first: Jeroen

last: de Baaij


title: Disrupting SOX2 Self-Association and Condensates to Overcome Chemotherapeutic Drug Resistance in Lung Squamous Cell Carcinoma

city: GuangZhou

first: Wen

last: Yulin

address: No.190 Kaiyuan Avenue

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS)


title: HIV Transgenic Mouse Monocytes Display Increased In Vivo Migration Across the Blood Brain Barrier Associated with Increased Expression of Genes Associated with Mononuclear Leukocyte Migration

city: Bronx

first: Harris

last: Goldstein

address: 1300 Morris Park Avenue

department: Pediatrics

institute: Albert Einstein College of Medicine

summary: Soon after HIV acquisition, circulating HIV-infected monocytes cross the blood-brain barrier (BBB) and infect resident brain microglia and other susceptible cells, establishing a potential viral reservoir. Despite supressive antiretroviral therapy, these HIV-infected cells mediate a neuroinflammatory process causing HIV-associated neurocognitive deficites (HAND) in at least 20% of people with HIV. Continued migration of HIV-infected monocytes into the brain may further exacerbate neuroinflammation and replenish viral reservoirs. To ascertain how HIV infection facilitates monocyte passage across the BBB in vivo, we developed a novel mouse model to quantify circulating monocytes supporting HIV production that migrated into the brain. We demontrate that significantly more monocytes from HIV-transgenic mice, capable of supporting HIV production, crossed the BBB compared to control transgenic mouse monocytes. This difference was particularly pronounced after recipient mice were treated with lipopolysaccharide (LPS). To explore the underlying mechanism, we compared the transcriptomes of HIV transgenic mouse monocytes and control mouse monocytes and identified multiple differentially expressed genes linked to mononuclear leukocyte trafficking, including several associated with monocyte chemotaxis. We also evaluated the effect of substance use in combination with HIV infection on monocyte migration across the BBB into the brain by treating HIV transgenic mice with either morphine or methamphetamine. Short-term exposure to either drug did not significantly alter the migration of HIV-transgenic monocytes across the BBB.

overall_design: RNA-seq profiling of WT (CCC mice) and HIV (JRCCC mice) CD11b monocytes in the presence and absence of LPS treatment (3 mg/kg; 24 hour treatment)

first: Sydentricker

last: Agnes

first: Lee

last: Danica

first: Voss

last: Adilyn

first: Zheng

last: Jian

first: Hur

last: Hong

first: Kandpal

last: Manoj

first: Goldstein

last: Harris


title: Prenatal Heat Calls Program DNA Methylation in the Embryonic Zebra Finch Brain

city: Clemson

first: Prakrit

last: Subba

state: SC

address: 132 Long Hall, 230 Parkway Drive

department: Biological Sciences

institute: Clemson University

summary: Zebra finch embryos can detect prenatal acoustic cues that may help prepare them for post-hatch environmental conditions, but the molecular mechanisms underlying this developmental programming remain poorly understood. We used reduced representation bisulfite sequencing (RRBS) to profile DNA methylation in whole brains of embryonic day 14 zebra finch embryos exposed prenatally to either heat call playback or control call playback from embryonic day 10 through embryonic day 13. The study included embryos from both treatment groups, and samples failing RRBS quality control were excluded before downstream analysis, resulting in a final cohort of 35 embryos. Differential methylation analysis identified CpG sites associated with prenatal heat call exposure in genes and pathways related to nuclear receptor signaling, protein phosphorylation, synaptic organization, and GABAergic signaling. A recurrent signal across analytical models was intronic hypermethylation in RBFOX2, a gene involved in RNA splicing and neuronal development. These data indicate that prenatal acoustic experience is associated with locus-specific epigenetic variation in the embryonic brain and provide a molecular framework for understanding acoustic developmental programming in a warming environment.

overall_design: Fertilized eggs from zebra finches were collected and incubated under controlled conditions, and embryos were assigned using a within-clutch balanced design to one of two prenatal acoustic treatments: control playback or heat call playback. Acoustic playbacks were delivered daily from embryonic day 10 to embryonic day 13 for 9 hours per day, and whole brains were collected on embryonic day 14 for DNA methylation profiling. Genomic DNA from whole brain tissue was used to prepare RRBS libraries with MspI and TaqI digestion, and libraries were sequenced on an Illumina HiSeq 2000 using 50 bp single-end reads. After quality control exclusion of five low-quality samples, the final dataset consisted of 20 control embryos and 15 heat call-exposed embryos. Reads were quality filtered, aligned to the zebra finch reference genome bTaeGut1.4.pri (GCF_003957565.2), and per-CpG methylation ratios were calculated for downstream differential methylation analysis.

first: Natalie A

last: Shay

first: Katerina

last: Palios

first: Michael G

last: Emmerson

first: Elisabetta

last: Versace

first: Katherine L

last: Buchanan

first: Mylene M

last: Mariette

first: David F

last: Clayton

first: Julia M

last: George


title: Expression data from retinoic acid induced newborn rat epidermal keratinocytes

city: Tokyo

first: Akihito

last: Ishigami

address: 35-2 Sakae-cho, Itabashi-ku

institute: Tokyo Metropolitan Institute for Geriatrics and Gerontology

summary:
Epidermal keratinization is a tightly regulated process essential for skin barrier function, requiring coordinated control of keratinocyte proliferation and differentiation. Retinoic acid, a bioactive metabolite of vitamin A, is known to promote keratinocyte proliferation while suppressing differentiation; however, the molecular mechanisms underlying this dual regulation remain incompletely understood.
We analyzed retinoic acid-induced changes in proliferative characteristics and keratinization-associated differentiation, assessed global gene expression profiles. (Microarray)

overall_design: Cells were treated with 5 µM all-trans retinoic acid or vehicle control. Medium was replaced every 24 h, and cells were cultured for up to 5 days.


title: AADAT-Driven Metabolic Control of Malate and CoQ₁₀ Shapes Immune Evasion in Triple-Negative Breast Cancer

city: Houston

first: Arun

last: Sreekumar

state: Texas

address: One Baylor Plaza

department: Molecular and Cell Biology

institute: Baylor College of Medicine

summary: Compared to other subtypes of breast cancer, triple-negative breast cancers (TNBC) have fewer treatment options and exhibit a worse prognosis. Through integrated transcriptomic, metabolomic, immunohistochemical, spatial, and clinical analyses, we identify the mitochondrial enzyme, α-aminoadipate aminotransferase (AADAT) as a previously unrecognized metabolic immune checkpoint in TNBC. AADAT mRNA and protein were significantly upregulated in human TNBC, and high AADAT expression was associated with reduced intra-tumoral CD8⁺ T-cell density and inferior survival. Genetic silencing of AADAT in orthotopic murine TNBC models curtailed primary tumor growth and distant metastasis in a CD8⁺ T-cell–dependent manner, enhanced effector T-cell activation, and sensitized tumors to dual PD-1/CTLA-4 blockade. Mechanistically, unbiased metabolomics showed increased malate levels after AADAT knockdown. Additionally, 4-hydroxyphenylpyruvate, an essential precursor for coenzyme Q₁₀ (CoQ₁₀) biosynthesis, decreased following AADAT knockdown, suggesting an impaired mitochondrial electron transport chain. CoQ₁₀ supplementation restored metabolic balance and reversed malate accumulation caused by AADAT knockdown, indicating that AADAT helps maintain CoQ₁₀-supported redox homeostasis, thereby preventing malate buildup and export. Notably, malate addition directly boosted CD8⁺ T-cell oxidative metabolism, increased the NAD⁺/NADH ratio and reactive oxygen species, and augmented TNF-α and IFN-γ production. In vivo, malate supplementation in drinking water phenocopied AADAT knockdown, restored the response to paclitaxel plus anti–PD-1 therapy in multiple independent syngeneic TNBC models with de novo or acquired resistance to immunotherapy, reduced tumor burden, and prolonged survival. In patient cohorts, higher spatially clustered intra-tumoral malate is associated with co-localization of functional CD8⁺ T cells, decreased exhausted T-cell neighborhoods, and superior post-chemotherapy outcomes. These data position AADAT as a central metabolic orchestrator of immune escape in TNBC and nominate oral malate as a readily translatable adjuvant to reverse chemo-immunotherapy resistance in TNBC.

overall_design: The CD8+T-cells harvested from the spleen of OT-1 mice, are co-cultured with tumor cells (E0771-ova+) in a ratio of 1:5 (Tcell:Tumor cell). There was a shRNA used to knockdown AADAT (induced by Doxycycline) referred as iKD1, in the tumor cells . The cells are referred as E0771-ova+-iKD1. Also, to analyze if Malate phenocopies the impact of AADAT knockdown on T-cell activity, Control tumor cells (with no Doxycycline treatment) were treated with Malate. So, the conditions of co-culture were as follows: 1. Control-iKD1+Tcells;  2. AADAT-iKD1+Tcells; 3. Control-iKD1+Tcells + Malate. All three conditions were plated in 3 separates plates, providing n=3 for each condition. After the co-culture and treatment, the T-cells were isolated from the co-culture cell suspension and subjected to RNA sequencing.

first: Megha

last: Chatterjee


title: Mechanisms of Huatanqushihuoxue Formula (HQHF) in Ameliorating MAFLD 1 via Transcriptomic Analysis and Ferroptosis Regulation

city: Zhengzhou

first: wanyi

last: zhu

state: Henan

address: No.19,Renmin Road,Jinshui Districtt

institute: The First Affiliated Hospital of Henan University of Chinese Medicine

summary: Background: Metabolic dysfunction-associated fatty liver disease(MALD) is a prevalent condition with limited therapeutic options.Huatangushihuoxue Formula (HQHF) demonstrates efficacy against MAFLD, yet its broader clinical application is hindered by an unclear mechanism of action. Purpose:This study aimed to elucidate the therapeutic mechanisms and molecular targets of HQHF in MAFLD. Study design and Methods: MAFLD was induced in mice via a 26 high-fat diet (HFD). After HQHF intervention, systematic evaluations were conducted.Transcriptome analysis of liver tissues was performed, followed by Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses  of differentially expressed genes. Key targets were identified using Cytoscape.Experimental validations included protein immunoblotting, immunohistochemistry, quantitative PCR. and immunofluorescence.Finally, a preliminary analysis of the single-cell sequencing data was conducted. Results: Transcriptome analyses indicated that HQHF's therapeutic effects are centrally mediated through the regulation of oxidative stress and ferroptosis. Experimental validation confirmed that HQHF alleviates oxidative stress and inhibits ferroptosis to treat MALD. Furthermore, eight key target genes were identified: Tnfaip3, Cx3cll, ICAM-1, CCND1, MAPK13,VDAC2, ATF4, and c-Myc. HQHF was verified to regulate the expression of these genes, which are involved in MAFLD pathophysiology.

overall_design: Male C57BL/6 mice with diet-induced MAFLD were randomly divided into a normal control group, an HFD model group and low-, medium- and high-dose HQHF groups (n = 9 per group). After 12 weeks of HFD feeding and model validation, HQHF was administered by gavage, and liver tissues and serum were collected for histology, biochemical measurements and transcriptomic/single-cell RNA-seq analyses focusing on ferroptosis-related mechanisms.

first: Sutong

last: Liu

first: Lihui

last: Zhang

first: Weichen

last: Ma

first: Wanyi

last: Zhu

first: Qing

last: Zao

first: Minghao

first: Kaiqi

last: Su

first: Wenxia

last: Zhao


title: EBV INFECTION OUTCOMES DETERMINED BY MONOCYTE AND TREG-DRIVEN IMMUNE DYNAMICS IN AN EX VIVO PBMC MODEL [RNA-Seq Mock]

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Epstein-Barr virus (EBV) infects >95% of the adult population with diverse outcomes ranging from benign latency to cancers and autoimmune diseases. Immunological control of EBV infection is known to be an important determinant of EBV infection outcomes. However, species-specific viral tropism and limited infection models have impeded mechanistic insights into early host–immune control of EBV infection. Here, we use ex vivo infection of peripheral blood mononuclear cells (PBMCs), rather than routinely used B cell enriched culture systems, to study immune and viral dynamics during primary EBV infection. We combined bulk RNA sequencing, EBV transcript enrichment, and flow cytometry to characterize cellular responses across Days 1, 7–8, and 14 post-infection. Early infection triggered a monocyte-specific antiviral response marked by changes in the expression of genes associated with lipid metabolism (LIPA, lysosomal acid lipase) and chemotaxis (CCR1 and CCR2). Inhibitors of LIPA increased EBV titers during primary infection, indicating that LIPA is part of an early monocyte-driven antiviral response. At later timepoints post-infection, donor-dependent variability in lymphoblastoid cell line (LCL) outgrowth was associated with divergent immune states. Donors that failed to generate LCLs demonstrated increased frequencies of CD8+ T cells and reduced numbers of regulatory T cells (CD4⁺CD25⁺FOXP3⁺). EBV transcriptomics revealed that LCL-failed donors exhibited elevated early lytic gene expression but did not establish a type III latency program.  Our findings suggest that individual variations in immune cell composition and gene expression may account for differences in the immune response to EBV.  These findings define temporal immune and viral signatures that predict transformation outcome and highlight intact PBMCs as a tractable model to study EBV pathogenesis in a genetically diverse, human-specific context.

overall_design: Cryopreserved peripheral blood mononuclear cells (PBMCs) from healthy donors (n = 5) were thawed into RPMI 1640 medium (Cat# 11875085, Gibco) supplemented with 10% fetal bovine serum (FBS), 1% GlutaMAX (Cat# 35050061, Gibco), and antibiotics (100 U/mL penicillin and 100 µg/mL streptomycin; Cat# 15140122, Gibco). Following thawing, cells were rested overnight at 37 °C with 5% CO₂ before infection. Cells were plated at a density of 1 × 10⁶ cells/mL in 12-well plates. Infection was performed using the Mutu I strain of Epstein–Barr virus (EBV) at a multiplicity of infection (MOI) = 1. Parallel mock-infected controls were prepared using the same medium without virus. Samples were collected from both conditions (mock and EBV-infected) at multiple timepoints post-infection to capture dynamic transcriptional and immunological responses. Each biological replicate (donor) was processed independently to control for donor variability.

first: Leena

last: Yoon

first: Lauren

middle: N

last: MacMullen

first: Leonardo

last: Muñoz

first: Alina

last: Gu

first: Jamie

last: Bregman

first: Mary

last: Campion

first: Avi

last: Srivastava

first: Rena

last: Xian

first: Richard

middle: F

last: Ambinder

first: Andrew

last: Kossenkov

first: Samantha

last: Soldan

first: Paul

middle: M

last: Lieberman


title: A scalable human-zebrafish xenotransplantation model reveals gastrosome-mediated processing of dying neurons by human microglia

city: Zurich

first: Izaskun

last: Mallona

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

summary: Microglia engulf dying neurons through efferocytosis, a critical function in both development and disease. How microglia process the engulfed neuronal material—especially lipids—remains poorly understood, despite its central role in neurodegeneration. Thus, we developed HuZIBRA, a scalable in vivo xenotransplantation model in which human iPSC-derived microglia-like cells (iMGLs) are introduced into the developing zebrafish brain (zf-hiMG), a system characterized by high levels of neuronal cell death and amenable to precise genetic and pharmacological manipulation. We show that human microglia-like cells recognize and engulf apoptotic zebrafish neurons, indicating conserved efferocytic mechanisms. In these cells, engulfed neuronal material accumulates into a distinct, lipid-rich intracellular compartment, the gastrosome, which we also observed in iMGLs placed in a human brain-like environment. The size of the human gastrosome dynamically reflects neuronal cell death levels and is regulated by key genes, including TREM2 and SLC37A2. Pharmacological inhibition of the cholesterol transporter NPC1 induces gastrosome expansion and lipid accumulation, recapitulating pathological features of Niemann-Pick disease type C. Thus, HuZIBRA provides a powerful in vivo platform to uncover cell-autonomous adaptive responses of human microglia to apoptotic and metabolic stress, with the gastrosome emerging as a key integrator of neuronal debris processing and disease-relevant lipid metabolism.

overall_design: RNA-seq profiling of iPSC‑derived microglia, including wild‑type controls and mutant lines for Slc37a2 and TREM2, at different timepoints, with biological replicates.

first: Ambra

last: Villani

first: Francesca

last: Peri


title: Integrated Analysis of Proboscis Ultrastructure and Olfactory Receptor Genes under Different Foraging Conditions in Apis cerana cerana

city: Jinzhong

first: chang

last: song

address: No.1 Mingxian South Road, Taigu District

department: College of Animal Science and Technology

institute: Shanxi Agricultural University

summary: The proboscis of Apis cerana cerana is primarily recognized as a feeding organ; however, its potential role in close-range chemical perception during foraging remains insufficiently understood. While antennal olfaction has been extensively investigated, whether the proboscis contributes to volatile signal detection and how it responds transcriptionally under different foraging conditions are still unclear. This study aimed to integrate ultrastructural and transcriptomic analyses to elucidate the morphological basis and olfactory-related molecular responses of the proboscis under distinct foraging states.

overall_design: Scanning electron microscopy revealed a highly organized glossal architecture, with longitudinal ridge–groove structures in the mid-region and densely distributed hair-like sensilla in the distal glossa and flabellum, forming a spatial gradient of structural specialization. Transcriptome profiling identified 1,549 and 1,652 differentially expressed genes (DEGs) in pear- and rapeseed-foraging bees, respectively, compared with non-foraging controls, whereas only 89 DEGs were detected between floral sources, indicating that foraging state is the primary driver of transcriptional remodeling. Enrichment analyses showed that DEGs were predominantly associated with cellular processes and signal transduction pathways. Six candidate odorant receptor (OR) genes were identified in the proboscis, and phylogenetic analyses revealed both conserved orthologous relationships and lineage-specific divergence.

first: Chang

last: Song


title: Maternal-Fetal Immune Conflict in a Mouse Model of Neurodevelopmental Disorders.

city: Boston

first: Brian

last: Kalish

address: 220 Longwood Ave

department: Neurobiology

institute: Boston Children's Hospital

summary: In order to understand effect of Maternal Immune Activation (MIA) on placenta, we performed single-nucleus sequencing of placenta of pregnant mice at E13.5, treated with MIA and PBS (Control).We investigated stress-induced alterations in gene expression and the corresponding enrichment of Gene Ontology terms.

overall_design: We performed single nuclei sequencing on placenta samples extracted from E13.5 pregnant mice treated with PBS (control; n=3), and Maternal Immune activation (MIA; n=3). Placenta only from male embryos were used in this study.

first: Irene

last: Martin

first: Bharti

last: Kukreja

first: Paige

last: Henderson

first: Qianyu

last: Lin

first: Daniel

last: DiMartino

first: Valerie

last: Bagan

first: Justin

last: Park

first: Lucas

last: Cheadle


title: EHMT2-mediated chromatin reprogramming in 5-fluorouracil (5-FU) resistant colorectal cancer

city: Daejeon

first: In Hwan

last: Tae

address: 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: This study generated transcriptomic datasets to investigate the role of EHMT2 in acquired 5-fluorouracil resistance in colorectal cancer models. RNA sequencing was performed in parental and 5-FU resistant HCT116 cell lines under genetic and pharmacological modulation of EHMT2. These datasets support the findings described in the associated manuscript and provide a resource for further investigation of transcriptional mechanisms underlying chemoresistance.

overall_design: This submission includes RNA-seq samples derived from the HCT116 colorectal cancer cell line. Samples represent parental (wild-type) and 5-fluorouracil resistant cells (5fu or 5fuR) subjected to genetic modulation of EHMT2, including siRNA-mediated knockdown and corresponding siRNA control conditions. Independent biological replicates are included for each condition to enable comparative analysis of transcriptional changes associated with acquired chemoresistance.


title: EBV INFECTION OUTCOMES DETERMINED BY MONOCYTE AND TREG-DRIVEN IMMUNE DYNAMICS IN AN EX VIVO PBMC MODEL [RNA-Seq EBV enrich]

first: Priyankara

last: Wickramasinghe

overall_design: RNA-seq of human PBMCs infected with EBV (control, non-enriched) and EBV-captured (EBVc, probe-enriched) conditions. Two biological replicates were collected for each condition, each with two technical replicates. Sequencing performed as paired-end polyA RNA-seq on Illumina NovaSeq X.

first: Leena

last: Yoon

first: Lauren

last: MacMullen

first: Leonardo

last: Muñoz

first: Alina

last: Gu

first: Jamie

last: Bregman

first: Mary

last: Campion

first: Avi

last: Srivastava

first: Rena

last: Xian

first: Richard

last: Ambinder

first: Andrew

last: Kossenkov

first: Samantha

last: Soldan


title: Sensitive monitoring of enhancer and noncoding RNA transcription via ribozyme-assisted RNA editing

city: Beijing

first: Yangming

last: Wang

address: No.5 Yiheyuan Road, Haidian District

department: College of Future Technology

institute: Peking University

summary: The primary goal of this study is to provide tools for understanding transcriptional regulation of native genomic elements that combine high sensitivity, quantitative output, and broad applicability. Existing methods often have limited dynamic range, disrupt host RNAs, or fail to detect short-lived transcripts. Here, we present ribozyme-processed ADAR-engaging RNA-directed editing (REDDIT), a technology that converts transcriptional events into reporter protein translation via precise A-to-I RNA editing. REDDIT sensitively detects transcription from protein-coding genes, long noncoding RNAs (lncRNAs), primary microRNAs (pri-miRNAs), and enhancer RNAs (eRNAs), including low abundance and short-lived species, while minimally perturbing host gene expression, RNA processing, and the global editome. We apply REDDIT to monitor the naïve-to-primed transition in human embryonic stem cells (hESCs) and convert it into a transcription recorder that permanently logs transient and combinatorial transcriptional inputs when paired with Cre recombinase. Finally, by adapting REDDIT for high-throughput screening, we uncover multiple signaling pathways that regulate lncRNA and eRNA biogenesis. REDDIT therefore provides a scalable platform for quantitative monitoring and retrospective analysis of endogenous transcriptional dynamics across diverse genomic contexts.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
RNA-seq profiling of a cell lines that stably express the mCherry-TAG-GFP reporter (REDDIT_hESC_ctrl) and corresponding knock-in cell lines (REDDIT_NANOG, REDDIT_MIR302, REDDIT_ACTB_intron1, REDDIT_ACTB_polyA, REDDIT_SOX2_polyA); RNA-seq profiling of a cell lines that stably express the mCherry-TAG-GFP reporter (REDDIT_mESC_ctrl) and corresponding knock-in cell lines (REDDIT_lncenc1); RNA-seq profiling of REDDIT_MIR302 cells at Day 0, Day 5, Day 12, Day 14-high, Day 14-low, Day 20 of cardiomyocyte differentiation; RNA-seq profiling of wildtype mESC treated with DMSO (WT_mESC_DMSO_48h or WT_mESC_DMSO_7 days) and UNC0638 (WT_mESC_UNC0638_48h or WT_mESC_UNC0638_7 days); RNA-seq profiling of wildtype hESC treated with DMSO (WT_hESC_DMSO) and RepSox (WT_hESC_RepSox); GRO-seq profiling of wildtype hESC treated with DMSO (GRO_WT_hESC_DMSO) and RepSox (GRO_WT_hESC_RepSox).
The editing efficiency of the premature stop codon in the mCherry-TAG-GFP reporter was assessed through RNA sequencing and amplicon analysis. RNA libraries were constructed from NANOG-REDDIT hESCs during the process of neural induction, and mRNA sequences flanking the premature stop codon were amplified and analyzed following transfection with different ART RNA designs.

first: Jing

first: Jia-Zhen

first: Lu-Feng

last: Hu


title: A Chemical-Genetic Interaction Matrix Reveals Drug Mechanism and Genetic Architecture

city: Toronto

first: Micheal

middle: D

last: Tyers

address: 555 University Avenue

institute: The Hospital for Sick Children

summary: This dataset contains the RNA-seq data associated with a CRISPR/Cas9 study for which the screen results (sgRNA reads) are included in the GEO record GSE15547. Specifically, this dataset contains the RNA-seq results used to assess absolute gene expression in Nalm-6 cells, results for 3 PPP3CA knockout polulations, 3 PPP3R1 knockout populations, one FK-506 (tacrolimus) treated population and ERCC spike-in experiments on PABIR1 (formerly FAM122A) knockout cells, each with their own wild type and/or DMSO-treated control samples.

overall_design: RNA-seq profiling of wild type, mutant or compound-treated Nalm-6 cells. ERCC spike-in experiments are meant to assess differences in overall transcription rate.

first: Jasmin

last: Coulombe-Huntington

first: Thierry

last: Bertomeu

first: Caroline

last: Huard

first: Daniel

last: St-Cyr

first: Corrine

last: St-Denis

last: Chatr-Ayamontri

first: Mike