title: Tumor-stromal crosstalk and macrophage enrichment is associated with chemotherapy response in bladder cancer

city: Aachen

first: Janik

last: Riese

address: Pauwelsstraße 30

department: Institute of Pathology

institute: UK Aachen

summary: This dataset provides a spatial transcriptomic atlas of bladder cancer tissue treated ex vivo with standard chemotherapy. Tumor specimens from eight bladder cancer patients were excised and treated for 48 hours with gemcitabine and cisplatin (GemCis) or medium control (MSC), followed by formalin fixation and paraffin embedding. Spatial gene expression profiling was performed using the NanoString GeoMx Digital Spatial Profiler Whole Transcriptome Atlas (WTA), capturing expression of over 18,000 transcripts. Tumor regions were identified by cytokeratin (CK) staining and analyzed alongside adjacent stroma (CK-negative). Chemotherapy treatment led to significant transcriptomic alterations, including downregulation of pathways related to substance uptake (e.g., endocytosis) and metabolism (e.g., glycolysis), and upregulation of cell death pathways. Cellular deconvolution using xCell revealed stromal M2 macrophage enrichment in chemotherapy-resistant samples, suggesting a microenvironmental contribution to resistance.

overall_design: Fresh tumor tissue from eight patients with bladder cancer was obtained and divided into two conditions: treatment with gemcitabine/cisplatin (GemCis) or medium control (MSC), incubated for 48 hours ex vivo. Post-treatment, tissues were formalin-fixed, paraffin-embedded, and processed using the NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) assay. Regions of interest (ROIs) were selected based on immunohistochemical cytokeratin (CK) staining to distinguish tumor cells (CK-positive) from stroma (CK-negative). Two technical replicates per condition and region were collected. Standard GeoMx WTA workflow was applied, with downstream analysis including differential expression, pathway analysis, caspase-3 immunohistochemistry for treatment response classification, and xCell-based deconvolution to profile immune cell populations. The resulting data provide spatial resolution of transcriptomic changes in response to chemotherapy and insights into mechanisms of chemoresistance in bladder cancer.

first: Sophie

last: Leypold

first: Michael

last: Rose

first: Lancelot

last: Seillier


title: Coreopsis tinctoria: A Natural Remedy Against UVA-Induced Photodamage in HaCaT via Nrf2/HO-1 Mediated Endoplasmic Reticulum Stress Alleviation

status: Public on Dec 31 2025

city: SHENZHEN

first: JIANGMING

last: ZHONG

address: Shennan rd 9996, 518000, Shenzhen, Guangdong, P.R. China.

country: China

institute: Shenzhen Hujia Technology Co., Ltd.

type: Expression profiling by high throughput sequencing

summary: Solar ultraviolet (UV) radiation includes UVB (290-320 nm) and UVA (320-400 nm) wavelengths. While UVA is less energetic than UVB, it causes significant damage to both dermal and epidermal layers through acute and chronic exposure, leading to the accumulation of misfolded proteins and triggering endoplasmic reticulum (ER) stress. Mild exposure may activate a protective unfolded protein response, but prolonged exposure can result in cellular apoptosis. UVA radiation induces ER stress primarily through reactive oxygen species (ROS) production, activating downstream signaling pathways. Thus, identifying compounds that alleviate UVA-induced ER stress is crucial. Coreopsis tinctoria (CT), a traditional remedy from Xinjiang, China, contains bioactive compounds like flavonoids and polysaccharides, known for their antioxidant and anti-inflammatory effects.This study aims to evaluate the effectiveness of CT extract in reducing UVA-induced skin photodamage in human keratinocytes (HaCaT) by alleviating ER stress and apoptosis.We conducted transcriptomics analysis on UVA-exposed HaCaT cells, with and without CT extract treatment. Gene Ontology (GO) enrichment analysis highlighted differentially expressed genes associated with the ‘response to ER stress’ and ‘cellular response to misfolded proteins’ in the CT-treated cells compared to untreated UVA-irradiated cells. Western blotting, RT-qPCR, and immunofluorescence confirmed that markers related to ER stress, such as CHOP, pIRE1, and ATF6, were significantly downregulated following CT treatment. Additionally, apoptosis-related markers, including BCL2, cleaved-caspase 3, and cleaved-caspase 9, were reduced, and apoptosis assays using flow cytometry corroborated these findings. Notably, the application of tunicamycin, an ER stress inducer, negated the protective effects of CT against UVA-induced apoptosis and inflammation. Meanwhile, we identified the crosstalk pathway of Nrf2/HO-1 and ER stress by CT in eliciting the downstream antioxidant and detoxification targets. Furthermore, high-performance liquid chromatography (HPLC) analysis identified marein as the active compound responsible for the observed alleviation of ER stress following UVA exposure.These findings suggest that CT may serve as a promising therapeutic agent for protecting human keratinocytes from UVA-induced damage by mitigating ER stress and apoptosis.

overall_design: RNA-seq profiling of HaCaT (Human Keratinocyte) cells subjected to UVA irradiation. After UVA irradiation with the addition of CT, we wanted to investigate whether CT had the ability of anti-photodamage in HaCaT (Human Keratinocyte) cell, especially in ER stress. Then we performed gene expression profiling analysis using data obtained from RNA seq of 3 different treated ways (control group (NC), UVA treated group, UVA and CT co-treated group) in Hacat cell.

first: Zhong

last: Jiangming

first: Liang

last: Ling

first: Nie

last: Xin

first: Zhao

first: Li

last: Menggeng

last: Mingjie

first: Wu

last: Xuanmin

first: Shu

last: Peng


title: Host MTDH orchestrates liver lipid metabolism and CD8+ T cells to suppress antitumor immunity [Hepatocytes]

city: Plainsboro

first: Yong

last: Wei

state: NJ

address: LTL227 Wathington Road

department: Molecular Biology

country: USA

institute: Princeton University

summary: Cancer affects the function of distant organs beyond metastasis, conversely, dysfunction in distant organs can also impact tumor progression. However, the mechanisms underlying these interactions remains poorly understood. Here, we uncover that metadherin (MTDH), previously identified as a cancer metastatic gene, expressed in different host tissues, manipulates systemic lipid metabolism to control CD8+ T cell-mediated antitumor immunity. Genetic ablation of MTDH in host tissues significantly suppresses tumor growth and lung metastasis. Mechanistically, MTDH loss in hepatocytes prevents tumor environment-driven dysfunction of lipid metabolism. MTDH deficiency in hepatocytes increases PPARa-mediated lipid oxidation, resulting in reduced systemic lipid levels. Moreover, reduced systemic lipid levels metabolically reprogram MTDH knockout (KO) tumor-infiltrating CD8+ T cells by increasing mitochondrial biogenesis and resistance to lipid peroxidation-induced death. This increased metabolic fitness enhances the effector function of MTDH KO tumor-infiltrating CD8+ T, triggering ASCL4-depedent ferroptosis in tumor cells, contributing to tumor suppression. Targeting host MTDH efficiently synergizes with anti-PD-1 therapy across colorectal and metastatic breast cancer models, providing a promising therapeutic strategy for immunotherapy non-responsive cancers. Thus, our study identifies MTDH as an essential bridge connecting tumor and distant liver communications through metabolic reprogramming, revealing a previously unknown mechanism by which cancer is regulated as a systemic disease.

overall_design: Hepatocytes from age-matched WT and MTDH KO mice were collected. After treatment with TNFa, TGFb, or Kupffer cells conditioned media treated with Py8119-EVPs, total RNA were extracted  and processed to RNA sequencing. Three biological replicates of each group were collected.

last: Tang

first: Yibin

last: Kang


title: Exosomal SNHG26 derived from drug-resistant tongue squamous cell carcinoma cells inhibits the anticancer effect of NK cells in the microenvironment

city: Nanchang

first: Jiaxuan

last: Qiu

state: Jiangxi

address: 17 Yongwai Zheng Street

institute: The First Affiliated Hospital of Nanchang University

summary: Cisplatin resistance is a common occurrence among patients diagnosed with tongue squamous cell carcinoma (TSCC), resulting in a bleak prognosis. The immune microenvironment, specifically the involvement of Natural killer (NK) cells, plays a significant role in the development of drug-resistant tumor cells and subsequently impacts patient prognosis. However, the precise interaction mode and the underlying mechanisms governing this process remain elusive.

overall_design: In this study, a variety of research subjects were utilized, including clinical samples, patient-derived organoids (PDO), TSCC/NK cell co-culture system, patient-derived tumor xenograft (PDX) models, and humanized mice. Various methods were employed, such as drug sensitivity testing, single cell and transcriptome sequencing analysis, gene regulation, DNA/RNA/protein interaction experiments, to investigate and confirm the cascade reaction of TSCC cisplatin resistance-induced NK-related immunosuppression.

first: Qingkun

last: Jiang


title: mRNA profiling of human effector Type 1 T helper (Th1) cells for autoimmune gene signatures using the nCounter Nanostring platform [Metabolism Panel]

city: Rochester

first: Adebowale

last: Bamidele

state: Minnesota

address: Medicine, 200 First Street SW, Guggenheim 10

department: Medicine

institute: Mayo Clinic

summary: Human naïve CD4 T cells were purified from healthy volunteers' peripheral blood using commercially available kits and differentiated into effector Th1 in vitro by culturing for 6 days in the presence of anti-CD3 and CD28 antibodies (2 µg/ml each) and IL-12 (20 ng/ml). Human effector Th1 cells were harvested on day 6 post-differentiation and treated with either vehicle, LY (0.0125 µM), or Methyl Pyruvate (MePyr, 5 mM) in complete RPMI media for 24 hours.

overall_design: Gene expression profiling. Effector Th1 cells from four biological replicates (donors) were used and treated separately as indicated in the summary. An equal amount of total RNA from each replicate was used for gene expression analysis.

first: Shravan

middle: K

last: Mishra

middle: O


title: Host- and echinocandin-induced stresses exert profound cell wall changes in Candida parapsilosis, conferring echinocandin tolerance and retaining fitness

city: Merced

first: Clarissa

last: Nobile

state: California

address: 5200 N Lake road

department: Molecular and Cell Biology

institute: University of California MERCED

summary: In this study, we compared transcriptomic changes in four serial isolates of Candida parapsilosis from a single patient over three time points (90 minutes, 8 hours and 24 hours) and two growth conditions (biofilm and planktonic). The later serial isolates have increased fitness and are resistant to echinocandins compared to the initial strain. Using RNA-Seq, we identified strain-specific changes in expression of specific biological processes and cellular components including fungal-type cell wall and transmembrane transport.

overall_design: RNA-Seq profiling of Candida parapsilosis serial isolates Cp9, Cp10, Cp11 and Cp12 derived from the bloodstream infection of a single patient, grown under planktonic and biofilm conditions  for 90 minutes, 8 hours and 24 hours.

first: Farnaz

last: Daneshnia

first: Liuyang

last: Cai

first: Deepika

last: Gunasekaran

first: Isah

last: Gautam

first: Austin

middle: M

last: Perry

first: Pegah Mosharaf

last: Ghahfarokhy

first: Arefeh

last: Ebadati

first: Julieta

last: Munoz

first: Dorian

last: Padilla

first: Süleyha

last: Hilmioglu-Polat

first: Shenglin

last: Mei

first: Daneil

middle: J

last: Floyd

first: Miquel Àngel

last: Schikora-Tamarit

first: Diego

last: Funtes

first: María

last: Artigués-Lleixà

first: Louise

middle: A

last: Walker

first: Samuel Martins

last: Gonçalves

first: Sebastian

last: Jusuf

first: Mostafa

last: Salehi

first: Agostinho

last: Carvalho

first: Jigar

middle: V

last: Desai

first: David

middle: S

last: Perlin

first: Carol

last: Munro

first: Alex

last: Hopke

first: Tuo

last: Wang

first: Toni

last: Gabaldon

first: Wenjie

last: Fang

last: Mansour

first: Amir

last: Arastehfar


title: Increased AIF-1-mediated p38 MAPK Phosphorylation in the Mid-secretory Endometrium Impairs Endometrial Receptivity in Women with Recurrent Implantation Failure

city: shanghai

first: mingjuan

last: zhou

address: No.1665 Kongjiang Road, Yangpu District

department: Department of Obstetrics and Gynecology

institute: The affiliated Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University

summary: Summary answer: AIF-1 is significantly upregulated in the endometrial stromal cells of women with RIF, inhibiting cell proliferation and decidualization via the p38 MAPK phosphorylation, thereby reducing endometrial receptivity.

overall_design: Using the T-HESC stromal cell line as the research model, transfection experiments were performed to construct two sample groups: the experimental group (transfected with an allograft inflammatory factor 1/AIF1 overexpression plasmid) and the control group (transfected with a nonsense sequence vector plasmid), followed by mRNA high-throughput sequencing analysis.

first: Mingjuan

last: Zhou

first: Jingru

last: Duan

first: Xiaowei

first: Hanfei

last: Zhu

first: Dan

last: Zhang

first: Bufang

last: Xu

first: Aijun


title: Diwu Yanggan capcules alleviate hepatocellular carcinoma progression by regulating YAP signaling

city: Wuhan

first: Yu

address: No. 16, West Huangjiahu Road, Hongshan District

institute: Hubei University of Chinese Medicine

summary: Hepatocellular carcinoma (HCC) is a highly malignant tumor with poor prognosis, and its progression typically follows a stepwise pathological process of "hepatitis-liver fibrosis-cirrhosis-HCC." Due to the complex pathogenesis and prolonged disease course, effective early intervention strategies remain limited, highlighting the critical need for novel preventive and therapeutic approaches.In our previous study, the Chinese herbal compound DWYG was found to significantly ameliorate liver fibrosis and reduce the incidence of cirrhosis. Given that fibrosis and cirrhosis are well-established risk factors for HCC development, we hypothesize that DWYG may exert preventive effects against HCC by interrupting this pathological progression.To test this hypothesis, we will establish a DEN/CCl4-induced primary HCC mouse model to systematically evaluate the interventional effects of DWYG on hepatocarcinogenesis. Furthermore, RNA sequencing (RNA-seq) and molecular biology techniques will be employed to elucidate the underlying mechanisms.

overall_design: Twenty-four 2-week-old male C57BL/6 mice were randomly divided into four groups (n=6 per group): one control group and three HCC model groups. The model groups received intraperitoneal (i.p.) injections of diethylnitrosamine (DEN, 0.67% v/w), while the control group received equivalent volumes of normal saline. Starting at 8 weeks of age, the model groups were administered carbon tetrachloride (CCl4, 20% in olive oil, i.p.) twice weekly until the end of the experiment. At 17 weeks of age, two model groups began receiving DWYG treatment: one group received the clinical equivalent dose (medium-dose group, DWYG-M) and the other received twice the clinical equivalent dose (high-dose group, DWYG-H). All mice were sacrificed at 22 weeks of age for liver tissue collection. From each group, two randomly selected liver samples were subjected to RNA sequencing (RNA-seq) to analyze differentially expressed genes and investigate underlying molecular mechanisms.


title: Hyperactive Alternative RNA Splicing Facilitates Immune Escape in Small Cell Lung Cancer [RNA-Seq]

city: Chengdu, Cihna

first: Xiangmeng

last: Luo

state: Sichuan

address: No.17 Renmin road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

summary: The mechanisms driving cancer immune escape remain incompletely understood. In this study, we reveal that alternative RNA splicing is hyperactivated in small cell lung cancer (SCLC), particularly in the classic neuroendocrine subtypes, and is associated with poor prognosis. ASCL1, a defining transcription factor of SCLC, directly binds to and upregulates the expression of most splicing factors, including PRMT5. Elevated levels of these splicing factors correlate with an increase in skipped exon (SE) and mutually exclusive exon (MXE) events. Notably, the skipped exons in SCLC exhibit strong immunogenicity and are associated with immune suppression. Genetic or pharmacological inhibition of PRMT5 significantly suppresses SCLC progression both in vitro and in vivo. Transcriptome analyses demonstrate that PRMT5 deficiency reduces the prevalence of SEs and MXEs and thus maintains exons with high immunogenicity. Consistent with these findings, GSK3368715, a clinically safe PRMT5 inhibitor, synergizes with anti-PD1 antibody to treat SCLC by repressing alternative RNA splicing and enhancing immune responses. Taken together, we propose that hyperactive alternative RNA splicing, which excludes exons with strong immunogenicity, serves as a key mechanism for immune escape in SCLC, which highlights a potential therapeutic vulnerability for this aggressive disease.

overall_design: Bulk RNAseq in mouse normal lung organoids, SCLC organoids and SCLC organoids treated with GSK.

first: Yucui

last: Shang

last: Liu

first: Chong

last: Chen


title: Role of ALDH18A1 in regulating the progression of Metabolic dysfunction-associated steatohepatitis

city: Hangzhou

first: Sike

last: Yu

address: No.1 Xiangshan Branch Lane, Xihu District

institute: Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences

summary: Metabolic dysfunction-associated steatohepatitis (MASH) continues to be a considerable health problem. We identify Aldehyde dehydrogenase 18 family, member A1 (ALDH18A1) as a key factor in MASH aggravation via promoting liver proline accumulation. Silencing of the liver-specific Aldh18a1 gene mitigates MASH, while overexpression of ALDH18A1 exacerbates the phenotype of MASH. Mechanistically, under MASH pathological conditions, ALDH18A1 may affect hepatic lipid metabolism through increasing proline synthesis in hepatocytes. Our results indicate that the overexpression of the enzyme-inactive mutant of ALDH18A1 at the cellular level does not promote lipid accumulation in hepatocytes, in contrast to the overexpression of the wild-type ALDH18A1. Moreover, our observations of inhibited cellular mitochondrial respiratory function due to ALDH18A1 overexpression demonstrated that the overexpression of ALDH18A1, which drives higher proline concentration, is associated with impaired mitochondrial respiratory function. The results indicate that the suppression of hepatic proline production may be beneficial for the advancement of new MASH therapeutics.

overall_design: To explore the changes in lipid metabolism and mitochondrial function pathways, transcriptomic analysis was performed in liver tissues from mice fed a CDAHFD diet and those from mice fed a normal diet.

first: Zan

last: Lyu


title: FOXF2 regulates pericyte function required for pericyte-endothelial signaling during neonatal hyperoxic lung injury [CUT&Tag]

city: Chengdu

first: Hua

last: He

address: 2222 Xinchuan Rd

institute: West China Second University Hospital Sichuan University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Pulmonary vascular development is essential for alveolarization, and disruption of this process contributes to bronchopulmonary dysplasia (BPD) pulmonary pathology. Proper vascular development requires an orchestration of many cell types within the lung. However, the mechanisms by which pericytes support the endothelium in the postnatal lung remain poorly understood. Here, we identify FOXF2 as a critical transcription factor that governs pericyte maturation and function during postnatal lung development and regeneration. FOXF2 expression in pericytes increases postnatally and is selectively downregulated following neonatal hyperoxic injury. Pdgfrb-CreER mediated Foxf2 deletion in pericytes leads to pericyte hyperplasia, impaired migration, reduced expression of angiogenic factors such as ANGPTL4, and exacerbated alveolar simplification in a neonatal murine model of BPD. Transcriptomic and genomic studies demonstrate that FOXF2 maintains chromatin accessibility at pro-angiogenic loci and modulates paracrine signaling essential for endothelial regeneration. Loss of FOXF2 disrupts pericyte–endothelial crosstalk, impairing angiogenesis and alveolar repair during injury. Our study identifies FOXF2 as a central transcriptional regulator of pericyte-driven vascular niche function in the neonatal lung and underscores the pathogenic role of dysfunctional pericytes in BPD.

overall_design: CUT&Tag and Cleavage Under Targeted Accessible Chromatin (CUTAC, a low salt version of CUT&Tag) using FOXF2 and H3K4me2 antibodies were performed on CD140b+ cells, sorted by MACS, isolated from the lungs of wild type mice, Foxf2 KO (Foxf2f/f; Pdgfrb-CreER) and littermate control mice at postnatal day 7.


title: FOXF2 regulates pericyte function required for pericyte-endothelial signaling during neonatal hyperoxic lung injury [scRNA-seq]

overall_design: Single-cell RNA sequencing (scRNA-seq) libraries were generated from CD45⁻ cells sorted from control and Foxf2 cKO lungs using the Chromium Next GEM Single Cell 5' Reagent Kit v2 (10x Genomics).


title: Gene expression analysis of patient-derived engineered organoid model of thyroid cancer (TC)

city: shenzhen

first: Huang

last: Yibin

address: Engineering Biological Industry Innovation Centre, No.229 Gongchang Road, Xinhu Street, Guangming District

institute: SynOrg Biotechnology (Shenzhen) Co., Ltd.

summary: Inter-tumor heterogeneity is a major hurdle in thyroid cancer (TC) precision therapy. The use of non-engineered organoids (NEOs), derived from primary tissue, as a potent tool for cancer drug screening is limited by their dependence on inefficient manual procedures. Here, we establish droplet-engineered organoids (DEOs) derived from TC patients using microfluidic technology, which recapitulates histopathology and genomic landscape of parental tumors, and preserve the drug sensitivity differences of patients. Furthermore, we reveal NF-κB pathway as a major mediator of advanced DEOs generation. A NF-κB inhibitor and anti cancer drugs are screened, exhibiting a marked anti-proliferative effect. Together, our study demonstrates a microfluidic-based approach for rapid construction of TC DEOs and investigates the maturation mechanisms, providing an ideal in vitro model and novel insights for the development of therapeutic strategies against thyroid carcinoma.

overall_design: RNA-seq profiling of thyroid cancer tissue (TC_M), early-stage thyroid cancer organoids (TCDEO_E) and late-stage thyroid cancer organoids (TCDEO_L)

first: Xiaoyong

last: Dai

first: Yongde

last: Cai

first: Yingshi

last: Su

first: Yibin

last: Huang

first: Hengyuan

last: Gao


title: Next Generation Sequencing Facilitates Quantitative Analysis of Cornea Tissues from Lut Treated and Vehicle Control Treated EDE Mice

city: Shanghai

first: qian

last: yu

address: 1665 Kong Jiang Road

institute: Xinhua Hospital affiliated to Shanghai Jiao Tong University School of Medicine

summary: We had one goal to perform this study: transcriptome of cornea tissues from Lut treated and vehicle control treated EDE mice

overall_design: Comparison of transcriptome of cornea tissues from Lut treated and vehicle control treated EDE mice

first: Qian


title: Single-cell transcriptomic and m6A methylation analysis reveals platelet-mediated immune regulatory mechanisms in sepsis

city: Tianjin

first: Weiwei

last: Qian

address: 154 Anshan Road, Heping District

department: Department of Emergency

summary: Sepsis is a life-threatening syndrome characterized by a dysregulated host response to infection and systemic inflammation, with a highly heterogeneous and complex immunopathology. Immune imbalance plays a central role in its progression. In recent years, the immunomodulatory functions of platelets have garnered increasing attention, revealing roles beyond their classical functions in hemostasis and thrombosis. Concurrently, N6-methyladenosine (m6A)—the most prevalent internal modification in eukaryotic mRNA—has been implicated in the regulation of immune responses and cell fate decisions. However, its role in sepsis remains poorly understood. In this study, we integrated single-cell RNA sequencing (scRNA-seq) data from the GSE167363 dataset and m6A methylome profiles of peripheral blood mononuclear cells (PBMCs) from sepsis patients. Then, a comprehensive analysis of immune cell composition, developmental trajectories, intercellular communication, and epigenetic modifications across healthy controls, survivors, and non-survivors was conducted. Our findings revealed a progressive enrichment of platelets during sepsis progression, along with a potential phenotypic reprogramming of B cells, T cells, and Tregs toward platelet-like characteristics.

overall_design: This study utilized the publicly available scRNA-seq dataset GSE167363, which includes peripheral blood mononuclear cell (PBMC) samples from 10 patients with Gram-negative sepsis (survivor group: n = 6; non-survivor group: n = 4) and 2 healthy controls (HCs). Additionally,PBMCs from six sepsis patients (survivor group: n = 3; non-survivor group: n = 3), recruited from the Department of Emergency Medicine, Tianjin Medical University General Hospital, were used for m6A methylation sequencing.

first: Yuanyuan

first: Xinyang

last: Zhao

first: Yuxin

last: Dong

first: Jian

last: Zhou

first: Songtao

last: Shou


title: NRF1-mediated Innate Immune Response Drives Cellular Senescence and Aging

city: TIANJIN

first: hong

last: lei

address: WEIJIN STREET

institute: nankai university

summary: Senescent cell accumulation in organs is a hallmark of aging, leading to diminished regenerative capacity and organ dysfunction. Aberrant innate immune responses contribute significantly to cellular senescence, yet the precise interplay between innate immunity and senescence remains poorly characterized. Here, we elucidate the pivotal role of nuclear respiratory factor 1 (NRF1) in orchestrating innate immune responses that drive senescence and the senescence-associated secretory phenotype (SASP). NRF1 deficiency delayed cellular senescence and ameliorated age-related deterioration in multiple organs. Mechanistically, NRF1 enhanced SASP by transcriptionally regulating TBK1 and IRF3, critical nodes in innate immunity essential for senescence induction. Conversely, NRF1 deficiency suppressed innate immune activation, thereby attenuating inflammation associated with senescence and aging. Additionally, DNA damage activated ATM kinase, which phosphorylated NRF1 at Ser393, augmenting the NRF1-TBK1/IRF3-type I interferon axis and exacerbating cellular senescence. Furthermore, NRF1 knockdown treatment effectively mitigated aging phenotypes and extended lifespan in aged mice. Collectively, our findings underscore the essential role of the ATM-NRF1-TBK1/IRF3-type I interferon axis in DNA damage-induced senescence, suggesting that targeted NRF1 modulation holds therapeutic promise for improving the aging process.

overall_design: RNA sequencing (RNA-Seq) was performed to compare the transcriptome of NRF1-knockout (KO) Primary MEF with wild-type (WT) Primary MEF upon proliferation (Prol), or senescence (Sen).

first: Hong

last: Lei

first: Yijia

last: Long

first: Tian

first: Jiaojiao

last: Zhang


title: Single cell RNA-seq of myeloid immune cells in melanoma-draining lymph nodes

city: Mannheim

first: Volker

last: Ast

address: Theodor-Kutzer-Ufer 1-3

department: NGS Core Facility

country: Germany

institute: University Hospital Mannheim

summary: Tumor-draining lymph nodes are crucial for tumor immunity and immunotherapy outcomes. In this study, myeloid immune landscapes were profiled in lymph nodes draining either immunotherapy-sensitive or immunotherapy-resistant melanoma in mice.

overall_design: Myeloid immune cells expressing CD11b and/or CD11c were isolated from tumor-draining inguinal and axillary lymph nodes collected from mice bearing YUMM1.7 and YUMMER1.7 melanoma. Tumor-free animals served as naive control. Lymph nodes from multiple mice were pooled for each of the samples. Cells were subsequently subjected to single cell RNA-sequencing.

first: Lothar

middle: C

last: Dieterich


title: Differential regulation of genes in response to exogenous ganglioside GM2 treatment in Cancer cells.

city: Kolkata

first: Kaushik

last: Biswas

state: WB

address: Block EN-80 Sector V, Salt Lake, College More

department: Department of Biological Sciences

country: India

institute: Bose Institute

summary: Gangliosides have been implicated in various diseases including but not limited to cancer. Overexpression of one of these gangliosides, namely ganglioside GM2 has been associated with several cancers like Glioblastoma (GBM), Renal Cell Carcinoma (RCC) and several others. Despite the definite role of GM2 in tumor-induced host immune suppression has been extensively studied, not much was known regarding its involvement in the alteration of tumor cell behaviour. Our laboratory established that ganglioside GM2 plays a pivotal role in promoting migration and invasion of cancer cells and in inducing epithelial-mesenchymal transition (EMT) primarily by acquiring anoikis resistance and anchorage independence. Our initial data indicates that GM2's pro-tumorigenic function may be elaborated through modulation of a diverse, yet distinct signaling pathways. To address this, we undertook this task of mapping the differential regulation of genes in response to exogenous GM2 treatment in HeLa cells.

overall_design: RNA-seq profiling of GM2 treated (1hour treatment in serum starved condition) and non treated condition (only serum starved condition) in HeLa wild type cells.

first: Barun

last: Mahata

first: Elora

last: Khamrui

first: Aishwarya

last: Ray

first: Arijita

last: Sarkar

first: Zhumur

last: Ghosh


title: The role of Treg-mediated IL-6R signaling in epithelial cell biology

first: Jessica

last: Hohenstein

state: MN

address: 200 1st St SW

summary: IL-6 has been shown to be crucial in promoting inflammation in the context of IBD. Our previous work demonstrated an impairment of the FOXP3-mediated interactions necessary for Tregs to suppress immune responses following incubation with IL-6. However, the precise role of IL-6 and its receptor (IL-6R) signaling in Tregs and the impact on other cell types during IBD pathogenesis remains to be studied. Here  we demonstrate that loss of the IL-6R on Tregs negatively impacts intestinal epithelial cell homeostasis, and suggests the alterations could be contributing to an exacerbated phenotype in an in vivo model of colitis.

overall_design: RNA-seq profiling of cololnic IECs isolated from water or 2% DSS-treated conditional Treg IL-6RaKO mice and Treg WTcre mice (controls).

first: Emily

middle: E

last: Klatt

first: Brooke

middle: R

last: Druliner

first: Feda

middle: H

last: Hamdan

first: William

last: Faubion Jr


title: Granulocyte Derived Resistin Induces Classical Monocyte Repartition and Immune Suppression in CMML

city: Mancehster

first: Kiran

last: Batta

address: Paterson Building, Wilmslow Rd

department: Division of Cancer Research

country: United Kingdom

institute: University of Manchester

summary: Chronic myelomonocytic leukemia (CMML) is a clonal malignancy characterized by overlapping myeloid dysplasia and proliferation with persisting monocytosis. Characteristic repartitioning of classical monocytes is now a supporting diagnostic criterion (WHO5), though its mechanistic basis remains unknown. While monocytes are the cardinal malignant cell type in CMML, as a stem cell neoplasm the disease clone comprises most lineages and differentiation stages including granulocytes.  To investigate the pathogenic contribution of granulocytes in CMML maintenance and progression, we have performed molecular and functional characterization of CMML granulocytes. Compared with healthy age-matched controls, CMML granulocytes exhibited defective maturation with reduced granularity and phagocytic capacity. Transcriptome analysis revealed activation of pathways linked to proliferation, Myc activity and inflammation. Notably, RETN, which encodes inflammatory mediator Resistin, was upregulated 100-fold in CMML granulocytes; but not differentially expressed in CMML PBMNCs, sorted monocytes, or stem and progenitor cells compared to their healthy counterparts. Accordingly, Resistin protein levels were 10-fold higher in plasma from CMML patients and higher plasma Resistin levels correlate with poor overall survival. Remarkably, exposure of healthy monocytes to exogenous recombinant Resistin induced classical monocyte repartition, recapitulating the pattern seen in CMML, and inhibited macrophage differentiation. Transcriptome analysis of Resistin treated monocytes revealed that Resistin induces gene signatures related to immune suppression and myeloid-derived suppressor cell phenotype. We found SEMA4A to be a downstream target of Resisin and is overexpressed in CMML monocytes.  Consistent with known roles for SEMA4A, CMML patients displayed higher percentage of T-regs and elevated Th2/Th1 ratio compared with healthy controls, apparently corresponding with associated Resistin levels. Furthermore, we demonstrated that Resistin directly induces the T-reg expansion and skews the Th2/Th1 ratio by binding to monocytes. In conclusion, we showed that immature granulocytes in CMML produce high levels of Resistin, which contributes to classical monocytosis phenotype and immune suppression.

overall_design: Granulocytes were isolated from 5 ml peripheral blood of healthy and CMML donors using EasySep™ Direct Human Neutrophil Isolation Kit (Stem Cell Technologies, 19666), following manufacturer's recommendations. Isolated granulocytes were washed twice in PBS and subjected to RNA isolation and RNA-seq

first: Nathan

last: Hull


title: The H19/miR-760/BST2 axis orchestrates breast cancer tumorigenesis and metastasis

city: Lille

first: Kekely

middle: Boanerges

last: Klouyovo

address: Bd du Professeur Jules Leclercq

country: France

institute: CANTHER UMR9020 CNRS U1277 Inserm

summary: The long non-coding RNA H19 has been widely attested as a promotor of breast cancer by favoring proliferation, migration, invasion, and tumor growth. In this study, we attempted to decipher molecular mechanisms underlying the oncogenic activities of H19. Transcriptomic analyses revealed that H19 overexpression correlates with increased BST2 expression at both transcriptional and protein levels in breast cancer cell lines. Functional assays demonstrated that BST2 overexpression mimics the oncogenic effects of H19 by enhancing tumor cell aggressiveness in vitro and tumor growth in vivo. Interestingly, we also observed a reciprocal regulation, where BST2 expression modulates H19 levels, suggesting a cross-regulatory mechanism. Further mechanistic studies identified miR-760 as a key post-transcriptional regulator orchestrating this interplay. Using luciferase reporter assays and miRNA modulation strategies, we found that miR-760 directly targets both H19 and BST2, thereby regulating their expression in a coordinated manner. Our findings uncover a novel H19/miR-760/BST2 regulatory axis that enhances breast cancer progression and suggest that this axis could be studied to identify potential targets for therapeutic intervention.

first: Eric

last: Adriaenssens

first: Léa

last: Mabille


title: HMGB3 promotes brain metastasis in lung adenocarcinoma by recruiting SSBP1 for nuclear translocation to remodel mitochondrial metabolism

first: Huanhuan

last: Cui

address: 270 Dong'an Road

institute: Fudan University Shanghai Cancer Center

summary: Background: Brain metastasis, a leading cause of death in patients with lung adenocarcinoma (LUAD), arises from tumor cells adapting to the brain’s unique microenvironment of the brain through metabolic remodeling regulated by key oncogenes. Here, we aimed to determine the role of high mobility group protein B3 (HMGB3) in regulating tumor cell metabolism to promote the progression and brain metastasis in LUAD. Methods: In this study, a LUAD cell model predisposed to brain metastasis was developed in this study, and differentially expressed genes HMGB3 was identified. HMGB3 expression in LUAD was then validated through a series of in vitro and in vivo experiments, including western blotting, single-cell RNA sequencing (scRNA-seq), and immunohistochemistry (IHC). Tissue microarray (TMA) and LUAD brain metastasis clinical samples were used to explore the expression of HMGB3 and its clinical significance in LUAD. Additionally, we performed gene enrichment analysis on scRNA-seq and bulk RNA-seq, along with western blotting, to identify the pathways through which HMGB3 may cause brain metastasis. We then used coimmunoprecipitation and mass spectrometry to identify protein single-stranded DNA binding protein 1 (SSBP1), which interacts with HMGB3. Finally, gain and loss-of-function and rescue experiments were conducted to study SSBP1’s roles in LUAD cells. Results: HMGB3 upregulation in LUAD primary tumors and brain metastases associated with poor prognosis independent of metastasis. HMGB3 enhanced the migration, invasion, and epithelial-mesenchymal transition (EMT) capabilities of LUAD cells in vitro and promotes the occurrence and development of brain metastasis in vivo. Mechanistically, HMGB3 recruited SSBP1, inducing its nuclear translocation and reprogramming mitochondrial metabolism, thereby increasing cytoplasmic reactive oxygen species (ROS) levels, which activated the phosphatidylinositol 3-kinase–protein kinase B (PI3K-Akt) pathway by downregulating phosphatase and tensin homolog (PTEN), enhancing tumor cell proliferation, migration, invasion, and EMT. Conclusions: This study demonstrated that HMGB3 functions as a driver gene in the brain metastasis of LUAD, promoting metabolic adaptation of tumor cells to the brain microenvironment through the regulation of mitochondrial metabolism, thereby offering potential therapeutic targets for LUAD brain metastases.

overall_design: A xenograft model of brain metastasis was generated using 4-week-old male BALB/c nude mice. To address potential injection failures and allow humane euthanasia of severely ill mice, 10–12 mice were assigned to each group, ensuring that eight mice were used for the final analysis. Mice were anesthetized using 1% pentobarbital in phosphate-buffered saline (PBS), fixed supine, and disinfected. The left ventricle was located by gently pressing the chest (second to third intercostal spaces) and marked. A 1 mL syringe was prepared with a 200 μL air gap, filled with 200 μL of cell suspension containing cells (H2030) at a concentration of 5 × 10^⁴ cells/mL, and then air bubbles were removed. The syringe was inserted vertically 3–5 mm at the marked point; bright red blood flow confirmed left ventricle entry, and 100 μL of cell suspension was injected within 10 s. The needle was slowly withdrawn, and the bleeding was stopped by applying pressure. Mice were allowed to recover on a warming pad and housed in a specific pathogen free environment. Five weeks later, the mice were euthanized using CO2, then soaked in 75% ethanol, and dissected using sterile tools to extract the brain and isolate the tumor masses, which were then minced and enzymatically digested using collagenase I/II and trypsin. The digested tissue was neutralized with complete medium, centrifuged at 1,000 rpm for 5 min, then resuspended in complete medium, and plated in culture dishes. Cells are incubated at 37°C with 5% CO₂ for 24–48 h, after which tumor cells with parental morphology were observed, medium was replaced, and cells are expanded. Once the cell number expanded to 106, the first-generation LUAD brain metastasis cells (Lbrm1) were subjected to a second round of intracardiac injection using the same method. After the next round of brain metastatic tumors formation, H2030-Lbrm2 cells were primarily cultured using the same method. Ultimately, we obtained H2030-Lbrm1, Lbrm2, Lbrm3, Lbrm4, Lbrm5, and Lbrm5, which were designated as H2030-Lbrm and used for in vitro experiments as they had highest brain metastasis properties. To downregulate the expression of HMGB3, HMGB3-targeting small interfering RNA (siRNA) siHMGB3: 5'-GCAGAUAAAGUGCGCUAUGAU-3' along with a negative control (siNC), were synthesized by Tsing Ke (Shanghai, China). The transfection experiments for siRNA were performed according to the manufacturer’s guidelines for Lipo3000 as follows. Cells (H2030-Lbrm) were seeded in six-well plates at 70%–80% confluence. Transfection complexes including 250 µL Opti-MEM I, 7 µL lipofectamine 3000, and 15 pmol siRNA, incubated for 10–20 min, and added to each well. The medium was replaced after 6 h, and the cells were cultured for 48–72 h.

first: Yuechao

last: Yang

first: Sen

last: Li

first: Weiguo

last: Hu

first: Liangdong

first: Yiqun

last: Cao


title: Hyperactive Alternative RNA Splicing Facilitates Immune Escape in Small Cell Lung Cancer [scRNA-Seq]

first: Xiangmeng

last: Luo

overall_design: sc-RNAseq in Anti-PD1 (n=2) and Anti-PD1+GSK (n=2) mouse SCLC groups.

first: Yucui

last: Shang

first: Yu

last: Liu

first: Chong

last: Chen


title: Omics analysis reveals striking effects of progesterone receptor on mitochondria and mitochondria-mediated apoptosis independent of caspases in Breast Cancer cells

city: Singapore

first: Valerie Chun Ling

last: Lin

address: 60, Nanyang Dr

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary: The role of progesterone receptor (PR) in breast cancer remains controversial with conflicting reports from both clinical and laboratory studies. To address these discrepancies, we conducted an integrated omics analysis using MCF-7 cells with elevated PR expression (MCF-7PR) through transfection. Treatment with the pure PR agonist R5020 induced strong antiproliferative and proapoptotic effects. Quantitative proteomics identified 4,915 PR-regulated proteins and 678 phosphorylated peptides, with nearly 100% verifiable rate by Western blotting analysis. The proteomics data was closely correlated with transcriptomic data. Key pathways upregulated included hypoxia, p53 signaling, TNFA signaling via NFKB, epithelial-mesenchymal transition, and KRAS signaling, while E2F targets, G2/M checkpoint, and mitotic spindle assembly were downregulated. R5020 broadly suppressed cell cycle regulators, including CDKs, cyclins, DNA replication proteins, and components of the Ndc80 and chromosomal passenger complexes. Concurrently, it elicited significant changes in 200 mitochondrial proteins, upregulating many proapoptotic factors (e.g., BNIP3, NIX, AIF/AIFM1, AIFM2, ENDOG, HtrA2/Omi) and downregulating anti-apoptotic proteins (BCL-2, BCL-XL), leading to mitochondrial outer membrane permeability and caspase-independent apoptosis. Consistent with previous reports, we observed significant upregulation of pro-growth proteins such as EGFR, IRS2, and CCND1. However, these changes were functionally inconsequential, partly due to inhibitory phosphorylation, as IRS2 phosphorylation at S306 increased 4-fold. In conclusion, this omics study achieved to date the most comprehensive understanding of PR-regulated proteins and molecular networks, revealing a predominantly anti-proliferative and proapoptotic role with significant mitochondrial involvement. Our findings suggest that pure PR agonists warrant evaluation as first-line endocrine therapy for breast cancer with high PR expression.

overall_design: RNA profiling of MCF-7 cells overexpressing with PR (MCF-7PR) under ETOH (vehicle control) or PR-agonist R5020 treatment for 96 hours

first: Qian Yee

last: Woo

first: Pheck Khee

last: Lau

first: Bernett TK

last: Lee

first: Natasa

last: Bajalovic

first: Shi Hao

first: Kye Siong

last: Leong

first: Kai Yee

last: Pow

first: Simra

last: Hanan

first: Wei

last: Meng

first: Soak Kuan

last: Lai

first: Valerie CL


title: Rorippa islandica is a genetically accessible dicot model system to study flooding tolerance

city: Groningen

first: Hans

last: van Veen

address: Nijenborgh 7

department: GELIFES

country: Netherlands

institute: University of Groningen

summary: Most crop species cannot survive flooding events for a long period of time. However, within the Cardamineae tribe of the Brassicaceae family, there exist several wild species with high flooding tolerance.  Here, Rorippa islandica was identified as a genetically accessible diploid species with high submergence tolerance. Another diploid species from the same genus, R. stylosa, showed similar submergence sensitivity compared with Arabidopsis. Both species exhibited a strong and partially overlapping transcriptomic response to submergence within the first 48 hours of stress, including carbon-starvation and ethylene-responsive marker genes. We demonstrate that R. islandica can be transformed via floral dip, but with rather low frequency. The successful CRISPR-Cas9-mediated knockout of RiBCA3 confirms the suitability of this species for genetic transformation. However, although it was hypothesized that RiBCA3 might have an important function in carbon fixation under water, no differences in submergence survival or underwater photosynthesis were observed between wildtype and bca3 knockout lines. The molecular mechanisms of submergence tolerance of Rorippa islandica are therefore not understood yet. The data indicate that illumination and therefore photosynthesis-associated processes must be the basis for superior submergence survival. This work suggests that Rorippa islandica is a promising dicot model to further investigate the underlying tolerance mechanisms.

sample_organism:
Rorippa islandica
Rorippa pyrenaica

platform_organism:
Rorippa islandica
Rorippa pyrenaica

overall_design: Submergence experiments were conducted in transparent plastic boxes, filled with tap water the day before. Control plants were kept in empty boxes. After 24 and 48 hours young healthy leaves were harvested for RNAsequenicing for both Rorippa stylosa and Rorippa islandica. Plants were grown in pots 3 to 4 weeks prior start of the experiment.

first: Malte

last: Bartylla

first: Emma

last: Düthorn

first: Jana

middle: T

last: Müller

first: Markus

last: Wirtz

first: Rashmi

last: Sasidharan

first: Angelika

last: Mustroph


title: GDF15 Expression in Thermogenic Adipocytes Regulates Energy Homeostasis in a Sex-dependent Manner

city: Iowa City

first: Renata

last: Pereira

state: Iowa

address: 169 Newton Rd

department: Internal Medicine

institute: University of Iowa

summary: Diet-induced obesity (DIO) induces growth differentiation factor 15 (GDF15) in various tissues, leading to increased GDF15 serum levels. The liver is the primary source of circulating GDF15 during DIO, but other tissues are also required. We investigated whether brown adipose tissue (BAT) contributes to GDF15 circulating levels and whether Gdf15 induction in BAT regulates systemic metabolism during DIO. We generated mice with selective Gdf15 deletion in thermogenic adipocytes (KO) and subjected them to 12 weeks of high-fat diet (HFD) feeding. Although in ad-libitum fed conditions GDF15 serum levels were unchanged between genotypes regardless of sex, female KO mice demonstrated reduced food intake, increased mitochondrial fatty acid oxidation in BAT, and were resistant to DIO, which was prevented by ovariectomy. Conversely, male KO mice demonstrated increased food intake, reduced mitochondrial respiratory capacity, and increased fibro-inflammation in BAT, resulting in increased body weight and fat mass accrual. Together, our data show that Gdf15 expression in BAT is required to regulate energy metabolism in mice in a sex-dependent manner.

overall_design: RNA-seq profiling of brown adipose tissue from male or female mice fed a high fat diet for 12-weeks. Mice either had an intact GDF15 gene or it was knocked out specifically in the brown adipose tissue.

first: Jayashree

last: Jena

first: Eric

last: Weatherford


title: Transcriptome aequencing of Pyrocoelia pectoralis

city: Weifang

first: Wang

last: Guobao

address: No.5147 Dongfeng East Street

institute: Weifang University

summary: The intriguing reaction of bioluminescence in the fireflies depends on the luciferin metabolism in luminous organs

first: Guobao

last: Wang


title: ⁶⁰Co-γ radiation-induced GDH64 NtCYC mutation enhances the glandular trichome density and aroma quality of tobacco via physiological, biochemical, and molecular mechanisms

city: Guiyang

first: kai

last: pi

state: Guizhou

department: Key Laboratory for Tobacco Quality Research Guizhou Province

institute: Guizhou University

summary: Background: Tobacco leaves are the core raw materials for cigarette production, and their quality has direct and significant impacts on the sensory qualities of cigarette products. Cembrane diterpenoid alcohols are the main precursors of the aroma and fragrance components of tobacco leaves, accounting for approximately 60% of their chemical composition and considerably contributing to their aroma. Initially, we used ⁶⁰Co-γ radiation to induce mutagenesis in the tobacco wildtype variety, GDH64, to obtain the aphid-resistant mutant, MuGHD64. Cembrane diterpenoid alcohol levels were significantly increased in MuGHD64, indicating altered aromatic quality of its tobacco leaves. However, characteristic traits of and molecular mechanisms underlying the increased cembrane diterpenoid alcohol levels in MuGHD64 remain unknown. Therefore, MuGHD64 and GDH64 were investigated in this study. Results: Physiological and biochemical indicator levels were measured in MuGHD64 and GDH64, and transcriptome sequencing was performed to determine the mechanisms responsible for the increased cembrane diterpenoid alcohol levels in MuGHD64. Notably, cembratriene-ol and -diol levels were significantly higher in MuGHD64 than in GDH64. Additionally, MuGHD64 exhibited optimal chemical component levels and improved coordination. Its sensory quality indicators, such as aroma quality and intensity, sweetness, smoothness, and fineness, were superior to those of GDH64. Leaf surface secretory trichome density was significantly higher in MuGHD64 than in GDH64 at all stages. Levels of the cembrane diterpenoid alcohol metabolic precursors, isopentenyl and geranylgeranyl diphosphates, were also significantly higher in MuGHD64 than in GDH64. Transcriptome sequencing revealed that differentially expressed genes were mainly enriched in the metabolic processes related to terpenoid biosynthesis, sesquiterpenoid biosynthesis, isoprenoid biosynthesis, diterpenoid metabolism, diterpenoid biosynthesis, terpenoid skeleton biosynthesis, and plant hormone signal transduction. Cloning and sequencing of the cembratriene-ol synthase gene, NtCYC, revealed that the coding sequence of MuGHD64 harbored nucleotide substitutions at eight sites, resulting in six amino acid alterations. This significantly increased the gene expression levels, enhancing cembratriene-ol synthesis. Consequently, cembratriene-ol and -diol levels were significantly elevated, markedly improving the aroma quality of MuGHD64. Conclusions: Overall, this study revealed new genetic resources for the enhanced synthesis of cembratriene-ol, providing a foundation for breeding aroma-rich high-quality tobacco plants.

overall_design: MuGDH64 and GDH64 were the experimental materials used in this study. MuGHD64 was obtained via radiation mutagenesis breeding through ⁶⁰Co-γ irradiation of GDH64. Among the stable mutant strains, MuGHD64 was identified as an aphid-resistant mutant. Field experiments were conducted using a randomized block design with three replicates, each consisting of four rows, with 15 plants per row. Trials were conducted at the Tobacco Research Base of Guizhou University (106°16′E, 26°06′N) in 2022 and 2023. The tobacco field had yellow soil with loose texture and moderate fertility. Seedlings were propagated using the floating seedling method, and field cultivation and management were performed according to the local high-quality flue-cured tobacco cultivation techniques. MuGHD64 and GDH64 samples were collected at 40, 55, 70, and 85 d post-transplantation. In each plot, three healthy tobacco plants with uniform growth were randomly selected, and 9th to 11th leaves from the bottom were collected from each plant. Using a punch sampler, leaf portions were collected from each plant, mixed, placed in a centrifuge tube, immediately treated with liquid nitrogen, and stored at –80 °C for physiological indicator and transcriptome sequencing analyses. After middle leaf maturation, 9th to 11th leaves of MuGHD64 and GDH64 were harvested, dried, ground, and stored for cembrane diterpenoid alcohol measurement, with some portions used for sensory quality evaluation.

first: Yang

last: Chen

first: Ying

last: Huang


title: Ptbp1 facilitates cytoskeletal organization through the mTOR-PKCα pathway in Sertoli cells thereby supporting spermatogenesis

city: Minato

first: Manabu

last: Ozawa

state: Tokyo

address: 4-6-1, Shirokanedai

department: Institute of Medical Science

country: Japan

institute: The University of Tokyo

summary: Spermatogenesis is a highly coordinated process to produce mature spermatozoa. Somatic lineage Sertoli cells located in seminiferous tubule provide structural and paracrine support for spermatogenesis. Proper regulation of the Sertoli cell cytoskeleton dynamics is essential for this function; however, its regulatory mechanisms remain unclear. We show that the RNA-binding protein PTBP1 maintains cytoskeletal integrity in Sertoli cells via mTORC2 signaling. Sertoli cell–specific Ptbp1 deletion in mice results in germ cell loss, disrupted blood–testis barrier, and male infertility. Transcriptomic analysis of purified Sertoli cells revealed the dysregulation of cytoskeletal- and adhesion-related genes. RIP-seq demonstrated that PTBP1 binds to Rictor mRNA, which is a core mTORC2 component. PTBP1 loss reduced RICTOR protein levels and downstream PKCα activation, impairing the cytoskeletal structure. Rescue of cytoskeletal defects in PTBP1-deficient TM4 cells by constitutively active PKCα confirmed the functional relevance of the mTORC2–PKCα axis. These findings identify PTBP1 as a post-transcriptional regulator of mTORC2 signaling that supports Sertoli cell architecture and spermatogenesis, providing mechanistic insights into the regulation of male fertility.

overall_design: RNAseq of FACSed Sertoli cells; PTBP1-immunoprecipitated RNAseq

first: Hideto

last: Mori

first: Masafumi

last: Muratani

first: Takuya

last: Yamamoto


title: Enhancer-associated LncRNA-ITGA2 promotes vascular smooth muscle remodeling by mediating ITGA2 promoter-enhancer interactions

city: Xi'an

first: XIAN

last: GUO

address: Xinyi Road

institute: Air Force Medical University

summary: We investigated the function of Lnc-RNA-ITGA2, which comprises a single exon and is located on chromosome 5 within the first intronic region of the ITGA2 gene, as critical regulator of VSMC phenotypes in vitro.

overall_design: To study the functional phenotype and downstream pathway genes after LncRNA-ITGA2 overexpression in VSMCs, we conducted transcriptome sequencing analysis on VSMCs transfected with Ad-lncRNA-ITGA2 and Ad-GFP.


title: CircFKBP8(5S,6)-encoded protein promotes stress susceptibility in mice by downregulating dopamine D3 receptor expression and its downstream AMPK/mTOR/ULK1 autophagy signalling

city: Nanjing

first: Dandan

last: Xu

state: Jiangsu Province

address: No.87 Dingjiaqiao

institute: Southeast University

summary: Major depressive disorder (MDD) is a serious mental disorder, yet the mechanism by which circular RNAs (circRNAs) are involved in the pathogenesis of MDD by encoding proteins is unknown. Our previous study found that circFKBP8 (5S, 6) relies on its encoded proteins, namely cFKBP8, to promote susceptibility to chronic unpredictable mild stress (CUMS) in mice, but the precise molecular mechanisms are unknown. Here we found that overexpression of circFKBP8 (5S, 6) or cFKBP8 in neurons of the prelimbic cortex (Prl) of CUMS mice downregulated the expression level of DRD3 and its downstream AMPK/ULK1 (Ser555) and AMPK/mTOR/ULK1 (Ser757) pathways, which resulted in downregulation of neuronal autophagy levels. Interestingly, both activation and overexpression of DRD3 ameliorated the exacerbation of depressive-like behaviors induced by circFKBP8 (5S, 6) or cFKBP8, activated both the AMPK/ULK1 (Ser555) pathway and the AMPK/mTOR/ULK1 (Ser757) pathway, and upregulated neuronal autophagy levels. In conclusion, circFKBP8 (5S, 6) or cFKBP8 promote susceptibility to CUMS in mice, at least in part, by down-regulating DRD3 expression and its downstream AMPK/mTOR/ULK1 signaling pathway-mediated neuronal autophagy.

overall_design: 6-8 week male mice were randomly assigned to receive one of the following viral injections (bilateral prelimbic cortex tissues ; coordinates: AP +1.9 mm, ML ±0.3 mm, DV -2.5 mm from bregma): Vehicle control: rAAV-hSyn-bGH-polyA-CMV-EGFP (AAV/9), circFKBP8(5S,6) overexpression: rAAV-hSyn-circFKBP8-bGH-polyA-CMV-EGFP (AAV/9), cFKBP8 overexpression: rAAV-hSyn-peptide-3×Flag-P2A-EGFP-hGH-polyA (AAV/9). Neuronal overexpression of circFKBP8(5S,6) or its encoded protein cFKBP8 was confirmed 2 weeks post-injection. Mice subsequently underwent 5 weeks of chronic unpredictable mild stress, after which prelimbic cortex tissues were collected for RNA sequencing analysis.

first: Zihan

first: Gaojia

last: Zhang

first: Jiao

last: Jiao

first: Yujia

last: Cao

first: Mengyu

last: Liu

first: Yan

last: Kong

first: Zhijun


title: Epigenetically modulating macrophage subpopulations promotes long-term allograft survival in a mouse heart transplant model

city: Houston

first: Ge

last: Deng

state: Texas

address: 6670 Bertner Avenue, R7-217

institute: Houston Methodist Hospital and Houston Methodist Research Institute

summary: Despite much-improved protocols that broadly suppress the adaptive immune cells, most allografts are still lost to chronic rejection, in which macrophages have been prominently featured in the graft. In both clinical and pre-clinical studies, the graft-infiltrating macrophages often acquire diverse effector activities, especially the M2-biased programs, to mediate graft damage. But the precise mechanisms that regulate such programs remain incompletely defined. In the present study, we took a genome-wide approach to profile the epigenomic changes of M2-biased macrophages and identified the bromodomain and extra-terminal domain family protein-4 (BRD4) as a critical epigenetic regulator of M2 cells. Further in vitro studies revealed that either blocking BRD4 using a chemical inhibitor or conditional deletion of Brd4 in myeloid cells profoundly inhibited the induction of M2 cells. Importantly, in a fully MHC-mismatched heart transplant model, in which treatment with low doses of CTLA-4Ig led to the development of chronic rejection, inhibition of BDR4 in transplant recipients resulted in long-term heart allograft survival, which was associated with diminished intra-graft M2 cells and absence of histological features of chronic rejection. Together, our data suggest that macrophages can be epigenetically modified in favor of transplant survival and that BRD4 seems a promising therapeutic target for blocking chronic allograft rejection.

overall_design: Bone marrow derived macrophages (BMDM) was stimulated with IL-4 to polarize into M2 with or without JQ1 treatment and  BRD4 or H3K27Ac ChIP seq was performed to explore the role of chromatin reader BRD4 in macrophage M2 polarization.

first: Xiaojun

last: Su

first: Si

last: Sun

first: Guangchuan

first: Samson

last: Hennessy-Strahs

first: Junhui

last: Li

first: Zhuyun

last: Mao

first: Rafik

last: Ghobrial

first: Xiang

last: Xiao

first: Wenhao

first: Xian


title: Aging-dependent reduction of KAT7 (HBO1) activity impairs imMKCL-based platelet production by promoting immune properties

city: Kyoto

first: Koji

last: Eto

address: 53 Kawahara-cho, Shogoin Kawahara-cho, Sakyo-ku

department: CiRA

institute: Kyoto University

summary: The master cell bank (MCB) system is essential for regenerative cell therapy. We have developed iPSC-based immortalized megakaryocyte progenitor cell lines (imMKCLs) as an MCB for iPSC-platelet (iPSC-PLT) transfusion. However, imMKCLs exhibit both thrombopoietic and immune-skewed properties, with enhanced immune activity impairing platelet producibility. The link between immune properties and thrombopoietic efficiency remains unclear. Here, we demonstrate that G1 and G2/M interphases in proliferating imMKCLs contribute to platelet generation, while lysine acetyltransferase 7 (KAT7) suppresses immune-biased dominancy to maintain these interphases. KAT7 inhibition with WM3835 increases G0 cells, mimicking imMKCL aging, and induces cGAS-STING activation, chromatin instability, TNF-α, IFN-β and pro-inflammatory cytokine secretion. Additionally, TNF-α treatment recapitulates the transition to G0 seen with KAT7 loss. These findings identify KAT7 as a key regulator of imMKCL proliferation by preventing immune-skewed properties, highlighting its potential as a quality control marker in iPSC-PLT manufacturing.

overall_design: RNA-seq profiling of imMKCLs at proliferation phase (present of doxcycline) with or without KAT7 inhibitor (WM3835)

first: Wei-Yin

last: Qiu

first: S

last: Nakamura

first: T

first: K


title: The effect of miR192-LNP on the regulation of innate immune response

city: Kumamoto

first: Ken

last: Takashima

state: Kumamoto

address: 1-1-1, Honjo, Chuo-ku

department: Department of Immunology

institute: Kumamoto University

summary: Previously, we demonstrated that microRNA-192 (miR-192) is an aging-associated immune-regulatory microRNA suppressing the hyperinflammatory state observed in the elderly (Tsukamoto T et al., iScience, 2020). In this study, we utilized lipid nanoparticle (LNP) technology to deliver miR-192 into the macrophage cells  and investigated its mechanism of inflammation regulation and potential therapeutic applications. Murine macrophage RAW264.7 cells were pretreated with miR-192-LNP for 24 hours, followed by stimulation with lipopolysaccharide (LPS). To assess the impact of miR-192-LNP on the innate immune response against LPS, we performed bulk RNA sequencing (RNA-seq) to analyze gene expression alterations.

overall_design: To examine the effect of miR-192-containing lipid nanoparticles (LNPs) on the innate immune response, RAW264.7 cells were pretreated with miR-192-LNP or negative control miRNA (NC)-LNP (containing 100 pmol miRNA) for 24 hours, followed by stimulation with 200 ng/mL LPS for an additional 24 hours. Gene expression profiles were obtained by RNA sequencing (RNA-seq) from six experimental groups: nonLNP_-, NC-LNP_-, miR192-LNP_-, nonLNP_LPS, NC-LNP_LPS, miR192-LNP_LPS), each with three biological replicates.

first: Yuriko

last: Takagi

first: Tasuku

last: Nishimura

first: Takahisa

last: Kouwaki

first: Hiroyuki

last: Oshiumi


title: Transcriptome aequencing of Clania variegata

first: Wang

last: Guobao

overall_design: De novo transcriptome sequencing to identify the neuropeptides and neuropeptide receptors of Clania variegata

first: Guobao

last: Wang


title: Enhancing Immunotherapy Outcomes: Spatial Multi-Omics Predictive Models for Non-Small Cell Lung Cancer [GeoMx DSP]

city: New Haven

first: Thazin

middle: Nwe

last: Aung

address: 310 Cedar Street

institute: Yale University

summary: Non–small cell lung cancer (NSCLC) has an increasing number of targeted and systemic therapies allowing subsets of patients to achieve long–term durable benefit. Fundamental to understanding responses to a given therapy is comprehensive molecular characterization of the underlying tumor immune microenvironment (TIME). The TIME may inform models to predict immunotherapy outcomes and features to delineate therapeutic responses and clinical endpoints. We hypothesize that an integrated multi–omics approach will uncover interactions within the NSCLC TIME and identify novel biomarkers that are predictive of immunotherapy responses, thus aiding precision oncology. To develop a spatially resolved TIME model for NSCLC immunotherapy, we utilized a multi–omics approach, combining spatial mapping of protein expression at the single–cell resolution by Phenocycler Fusion (PCF) and multi–cellular readout whole transcriptome  profiling at cellular compartment resolution by Digital Spatial Profiling (DSP–GeoMx–WTA). This approach facilitated a detailed examination of the TIME in NSCLC samples from patients undergoing first–line immunotherapy. We studied two independent cohorts of advanced NSCLC tissue samples, treated with PD–1–based immunotherapies. We derived gene signatures from cell type signatures to predict treatment outcomes using a multistage Least Absolute Shrinkage and Selection Operator (LASSO) approach. Our spatial proteomic analysis identified three distinct cell types, proliferating tumor cells, granulocytes, and vessels, associated with resistance to immunotherapy. A high proportion of these cell types demonstrated a hazard ratio (HR) of 3.8 (p = 0.004) in the Yale training cohort and 1.8 (p = 0.05) in the UQ validation cohort. In the response cell–type model, higher levels of M1 macrophages, M2 macrophages, and CD4 T cells had an HR of 0.4 (p = 0.019) in the training cohort and 0.49 (p = 0.036) in the validation. In the transcriptomic analysis, gene signatures derived from these cell types predicted outcomes with high accuracy. The resistance gene model, which included 8 genes associated with epithelial–mesenchymal transition (EMT) and cell migration, showed an HR of 5.3 (p < 0.001) in the Yale training cohort, 2.2 (p = 0.036) in the UQ validation cohort, and 1.7 (p = 0.042) in the Greek validation cohort. Conversely, the response gene model, consisting of 8 genes associated with immunomodulation, had an HR of 0.22 (p = 0.005) in the Yale training cohort, 0.38 (p = 0.034) in the UQ validation cohort, and 0.56 (p = 0.041) in the Greek validation cohort. Multivariable analysis, adjusting for age, sex, disease stage, prior chemotherapy, type of immunotherapy, line of immunotherapy, histology, and smoking status, confirmed that the resistance signature remained significantly associated with worse outcomes, while the response signature remained associated with improved outcomes in both the UQ and Greek cohorts. This research highlights the potential of a multi–omics cell typing and gene expression profiling approach in advancing NSCLC treatment toward precision oncology. By offering insights into the TIME and unveiling novel biomarkers, our model seeks to define resistance and to improve prediction of response to treatment.

overall_design: This study investigates the tumor immune microenvironment (TIME) in non–small cell lung cancer (NSCLC) using a multi-omics approach to develop a predictive model for immunotherapy outcomes. We analyzed three independent cohorts: a Yale training cohort (n = 48), a University of Queensland (UQ) validation cohort (n = 45), and a Greek validation cohort (n = 42), all consisting of advanced NSCLC tissue samples from patients treated with PD-1-based immunotherapy. To characterize the TIME, we combined single-cell spatial protein mapping using Phenocycler Fusion (PCF) with Digital Spatial Profiling (DSP-GeoMx-WTA) for whole transcriptome analysis at compartment-level resolution. Spatial proteomic analysis was used to identify distinct immune and stromal cell populations, while transcriptomic profiling provided gene expression data across different cellular compartments. A Least Absolute Shrinkage and Selection Operator (LASSO) approach was applied to derive gene signatures predictive of treatment outcomes. Multivariable statistical analyses were performed to assess the relationship between identified cell types, gene expression patterns, and clinical variables such as age, sex, disease stage, prior chemotherapy, immunotherapy type, histology, and smoking status. The DSP–GeoMx–WTA raw and processed RNA sequencing data of Yale discovery cohort were made available with the accession number GSE271689. The DSP–CTA raw RNA sequencing data of UQ validation cohort is available under the assession number GSE221733.

first: James

last: Monkman

first: Jonathan

last: Warrell

first: Ioannis

last: Vathiotis

first: Roy

last: Herbst

first: Arutha

last: Kulasinghe

first: David

last: Rimm


title: Asymmetric Division in a Two-Cell-Like State Rejuvenates Embryonic Stem Cells

city: Guangzhou

first: Man

last: Zhang

state: Guangdong

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

department: Department of Basic Research

institute: Guangzhou Laboratory

summary: An intriguing question in biology is whether all cells age. Embryonic stem cells (ESCs) stand out as rare normal cells capable of indefinite in vitro passage. However, it remains unclear how ESC lineage immortality is achieved and whether individual ESCs are immortal. Using long term live-cell imaging to follow fates of single ESCs, we show here that lineage renewal of ESCs can be attributed to a sporadic state characterized by the expression of markers found in two-cell embryos. During this state, cells undergo asymmetric divisions, giving rise to one dying branch, and one that reverts to the pluripotent state. Importantly, the latter lineage exhibits signs of rejuvenation, including reduced DNA damage and enhanced chimeric efficiency. These findings underscore the crucial role of asymmetric cell division in maintaining the long-term health of the ESC lineage against mounting damage within individual cells.

overall_design: To trace the fate of 2C-like cells, we established a mouse embryonic stem (mES) cell line expressing a MERVL promoter driven GFP reporter (MERVL::GFP) to mark the 2C-like state, and H2B-mIFP to track cells. The MERVL::GFP signal strongly correlates with endogenous MERVL-Gag protein staining.

first: Mingwei

last: Min


title: Enhancer-associated LncRNA-ITGA2 promotes vascular smooth muscle remodeling by mediating ITGA2 promoter-enhancer interactions [CUT&TAG]

first: XIAN

last: GUO

summary: The proliferation and migration of VSMCs significantly contribute to vascular remodeling. Recent studies have suggested that enhancer-associated long noncoding RNAs (elncRNAs) play crucial roles in regulating gene expression and cell fate. However, the specific elncRNAs implicated in VSMC dysfunction and their regulatory mechanisms remain poorly understood. This study used multiomics profiling, including CUT&Tag, promoter capture Hi-C (PCHi-C), and microarray analysis, to identify LncRNA-ITGA2 as a novel elncRNA highly expressed in PDGF-induced proliferative human VSMCs. We used CUT&Tag technology to identify enhancer regions labeled by H3K4me1, and overlap lncRNA gene loci in LNCipedia database to identify enhancer-associated long noncoding RNAs (elncRNAs). By integrating the CUT&Tag data of H3K4me1 and H3K27ac, the dynamic regulatory network of enhancers was systematically analyzed, providing a key epigenetic basis for subsequent functional studies and target discovery.


title: Early malaria immune signatures in naïve adults experimentally infected with P.falciparum reveal high and low responders.

city: Barcelona

first: Gemma

last: Moncunill

state: Barcelona

address: Rosselló 153

department: Malaria

country: Spain

institute: ISGlobal

summary: The immune response to Plasmodium falciparum (Pf) is complex and varies across individuals. A controlled human malaria infection (CHMI) study using Pf sporozoites (PfSPZ) was conducted to optimize administration methods and investigate early immune responses. Naïve volunteers were infected via intramuscular (IM) or direct venous inoculation (DVI), with varying parasitemia rates and pre-patent periods. Blood transcriptional profiling identified two distinct immune response profiles: high responders, with stronger and faster transcriptomic activation, and low responders, with weaker responses. These profiles correlated with differences in antibody levels, cytokine/chemokine responses, and dendritic cell phenotyping. High responders exhibited lower innate immune activation but stronger baseline T and B cell signatures. Understanding these early immune mechanisms may help identify pathways to enhance effective and lasting malaria immunity.

overall_design: This series consists of 88 human samples from 22 individuals, analyzed at four different time points (D-1: before challenge, D01: 1 day post-challenge, D07: 7 days post-challenge, and M0: day of malaria diagnosis), using the Human Transcriptome 2.1 Arrays platform.

first: G

first: C

last: Sanchez

last: Gómez-Pérez

first: M

last: Vidal

last: Campo

first: A

last: Jimenez

first: D

last: Barrios

first: E

last: James

first: P

last: Billingsley

first: B

last: Mordmüller

last: Sim

last: Legarda

last: Kremsner

last: Hoffman

last: Alonso

last: Dobaño


title: RNA structure directs RNA partitioning and is actively disrupted inside stress granules to enable cellular recovery

first: Jovi

last: Lim

address: 60 Biopolis St

institute: Genome Institute of Singapore

summary: RNA structures play important roles in liquid-liquid phase separation. However, how it is regulated during stress response and stress granule formation is still under studied. Here, we performed in vivo RNA structure probing before and after sodium arsenite treatment, and in stress granules. While RNAs generally become more double-stranded upon stress, they maintain their single-strandedness inside stress granules. We showed that RNA single-strandedness enables increased inclusion inside stress granules and that stress granule-enriched RNAs form fewer intra- and intermolecular RNA-RNA interactions. Additionally, several RNA binding proteins including SRSF1 are enriched in differential structure regions.  eCLIP analysis revealed that SRSF1 binds to single-stranded regions along RNAs, and increased SRSF1 binding enabled better inclusion of RNAs in stress granules, whereas depletion of SRSF1 decreased stress granule formation under low amounts of stress. We also observed the active unwinding of RNAs inside stress granules by helicases, including DDX3X, and showed that inhibition of DDX3X results in slower dissolution of stress granules during recovery. Our study reveals the existence of multiple mechanisms to maintain RNA single-strandedness inside stress granules and to allow reversibility of stress granule formation, highlighting the importance of regulating RNA structure to enable cellular plasticity and response.

overall_design: To study dynamic changes in RNA structures and RNA-RNA interactions during arsenite stress, we performed in vivo click Selective 2-Hydroxyl Acylation and Profiling Experiment (icSHAPE) and proximity ligation sequencing (SPLASH). Specifically, we stressed HeLa cells with sodium arsenite (NaAsO2) for an hour and then allowed the cells to recover for 1 or 2 hours by removing sodium arsenite from the media. At each of these time points (untreated, 1-hour arsenite stress, 1-hour recovery, and 2-hour recovery), we treated the cells with the SHAPE compound, NAI-N3, to map local secondary structures. As both intra and inter-molecular RNA-RNA interactions are possibly involved in the process of biomolecular condensate formation, we performed SPLASH to determine the intra- and inter molecular RNA-RNA interactions in untreated and stressed cells. Additionally, we also performed ribosome profiling (Ribo-seq) to study the translation efficiency of the cellular transcripts during stress and recovery.

first: Bowen

last: Zhu

first: Yu

last: Zhang

first: Wen Ting

last: Tan

first: Jiayi

first: Joy

last: Xiang

first: Roland

last: Huber

first: Anthony

last: Khong

first: Yue

last: Wan


title: Next Generation Sequencing Facilitates Quantitative Analysis of keratocytes sorted from Prrx1-creERT;Ptch1 and ctrl mice

city: Shanghai

first: qian

last: yu

address: 1665 Kong Jiang Road

institute: Xinhua Hospital affiliated to Shanghai Jiao Tong University School of Medicine

summary: We had one goal to perform this study: transcriptome of keratocytes sorted from Prrx1-creERT;Ptch1 and ctrl mice

overall_design: Comparison of transcriptome of keratocytes  sorted from Prrx1-creERT;Ptch1 and ctrl mice

first: Qian

last: Yu


title: Next Generation Sequencing Facilitates Quantitative Analysis of Epithelial cells sorted from Prrx1-creERT;Ptch1 and ctrl mice

summary: We had one goal to perform this study: transcriptome of Epithelial cells sorted from Prrx1-creERT;Ptch1 and ctrl mice

overall_design: Comparison of transcriptome of Epithelial cells sorted from Prrx1-creERT;Ptch1 and ctrl mice


title: Host MTDH orchestrates liver lipid metabolism and CD8+ T cells to suppress antitumor immunity [Tumor]

city: Plainsboro

first: Yong

last: Wei

address: LTL227 Wathington Road

department: Molecular Biology

institute: Princeton University

summary: Cancer affects the function of distant organs beyond metastasis, conversely, dysfunction in distant organs can also impact tumor progression. However, the mechanisms underlying these interactions remains poorly understood. Here, we uncover that metadherin (MTDH), previously identified as a cancer metastatic gene, expressed in different host tissues, manipulates systemic lipid metabolism to control CD8+ T cell-mediated antitumor immunity. Genetic ablation of MTDH in host tissues significantly suppresses tumor growth and lung metastasis. Mechanistically, MTDH loss in hepatocytes prevents tumor environment-driven dysfunction of lipid metabolism. MTDH deficiency in hepatocytes increases PPARa-mediated lipid oxidation, resulting in reduced systemic lipid levels. Moreover, reduced systemic lipid levels metabolically reprogram MTDH knockout (KO) tumor-infiltrating CD8+ T cells by increasing mitochondrial biogenesis and resistance to lipid peroxidation-induced death. This increased metabolic fitness enhances the effector function of MTDH KO tumor-infiltrating CD8+ T, triggering ASCL4-depedent ferroptosis in tumor cells, contributing to tumor suppression. Targeting host MTDH efficiently synergizes with anti-PD-1 therapy across colorectal and metastatic breast cancer models, providing a promising therapeutic strategy for immunotherapy non-responsive cancers. Thus, our study identifies MTDH as an essential bridge connecting tumor and distant liver communications through metabolic reprogramming, revealing a previously unknown mechanism by which cancer is regulated as a systemic disease.

overall_design: Py8119 cells were injected into mice with vary Mtdh status, i.e wild type vs Knockout. Tumors were harvested and CD45- tumor cells iwere sorted and harvested for transcriptome profiling using bulk RNAseq. Pair samples are used for the experiment.

last: Tang

first: Yibin

last: Kang


title: Metformin as an early intervention for melanocyte senescence through autophagy-redox balance

city: Suwon

first: Jin Cheol

last: Kim

address: 206, World cup-ro, Yeongtong-gu

country: South Korea

institute: Ajou University School of Medicine

summary:
To investigated the functional characteristics and molecular mechanisms underlying senescence in UV irradiated melanocytes.
We performed gene expression profiling analysis using data obtained from scRNA-seq of UV-irradiated senescent melanocytes.

overall_design: Gene expression profiling analysis of scRNA-seq data for UV-irradiated primary normal human melanocytes (HEMn-MP, Gibco, C1025C)

first: Jincheol

first: Taejun

last: Park

first: Heeyoung


title: Alterations in chromatin architecture promote totipotent-like features in a DUX-dependent manner

city: Bethesda

first: Sergio

last: Ruiz Macias

state: Maryland

address: 37 Convent Dr, Room 1112B

department: Center for Cancer Research

institute: National Cancer Institute

summary: 2-cell like cells (2CLC) are a transiently cycling population of cells with totipotent-associated features. Interestingly, CTCF depletion leads to 2CLC conversion in mouse ESC. However, the mechanism underlying this reprogramming or whether totipotent-like conversion depends on chromatin structural alterations or to CTCF-specific effects is unclear. We demonstrate that 2CLC conversion mediated by CTCF loss depends on the transcription factor DUX and correlates with nucleolar integrity. We show that depletion of the cohesin release factor WAPL in ESC also promotes 2CLC reprogramming which is increased by CTCF co-depletion. Single-cell RNAseq/ATACseq analyses in CTCF/WAPL-depleted ESC revealed that chromatin accessibility precedes 2C-associated gene expression. Finally, although distinct transcriptional changes were associated to WAPL or CTCF depletion in human ESC, we did not detect any similarity in their transcriptome with those of early stages of human embryo development suggesting a lack of conservation. Our work revealed an intertwined link between higher-order chromatin organization and totipotency in mice.

overall_design: Multiome analysis from mouse ESC ESC-CTCF/WAPL-AID treated with IAA for 0, 24, 48 and 72 hours. Single nuclei were extracted from cells and joint snRNA and scATAC libraries were prepared using the 10x Genomics Platform.

first: Ruiz

last: Sergio

first: Vega-Sendino

last: Maria

first: Kelly

last: Michael

first: Taukulis

last: Ian


title: TET-dependent signaling of β-cell underlies intrauterine hyperglycemia-induced glucose intolerance in offspring [RRBS]

first: Jiahang

last: Mo

address: No.131 Dong'an Road

department: Institute of Reproduction and Development

institute: Obstetrics and gynecology Hospital of Fudan University

type: Methylation profiling by high throughput sequencing

summary: Epidemiologically, gestational diabetes mellitus (GDM) increases offspring’s diabetes risk. Intrauterine hyperglycemia (IHG) is a typical characteristic of GDM, impairing offspring’s glucose tolerance and insulin secretion, but the underlying mechanisms remain unclear. Here, we found IHG downregulates DNA demethylases Tet2/3 in fetal pancreatic islets. Pancreas-specific Tet2/3 double knockout (DKO) recapitulates the IHG effects.

overall_design: To investigate the mechanisms of impairing offspring’s glucose tolerance and insulin secretion in IHG offspring. Pancreatic islets from Tet2/3 double knockout mouse was analyzed using RRBS.


title: Toxicogenomics weight of evidence to demonstrate a CAR-mediated MoA for cyclobutrifluram-related mouse liver tumors

city: Bracknell

first: Liam

last: Doonan

state: Berkshire

address: Jealott's Hill International Research Centre

institute: Syngenta

summary: Transcriptomics and metabolomics provide useful data to identify the mode of action for chemical-induced murine liver tumors and to exclude alternative modes of action. This data was incorporated into a mode of action assessment, for the murine liver hepatocellular carcinomas associated with 80-week dietary exposure to CD-1 mice of the novel complex II succinate dehydrogenase inhibitor (SDHI), cyclobutrifluram.   The assessment was conducted using the framework developed by the International Programme on Chemical Safety (IPCS) and the International Life Science Institute (ILSI), based on activation of the constitutive androstane receptor (CAR) and subsequent downstream events. Cyclobutrifluram activated human and mouse CAR in an in vitro transactivation assay.  Dietary administration of cyclobutrifluram was associated with time and/or dose-dependent liver weight increases, minimal to moderate hepatic centrilobular hypertrophy, induction of CAR-related enzyme activity, specifically CYP2B and CYP3A, and hepatocellular proliferation.  Transcriptomic assessment of the liver identified gene expression profiles consistent with CAR activation.  Metabolomic assessment indicated that cyclobutrifluram induced similar biochemical changes to the known CAR activator phenobarbital.  Alternative hypotheses to CAR-induced hepatic tumors were assessed and considered to be non-relevant.  The transcriptomic and particularly the metabolomic assessments indicated that cyclobutrifluram did not have activity other than that related to CAR induction.

overall_design: Gene expression in mouse liver control and following exposure to cyclobutrifluram 120, 400 and 800 ppm, or positive control for CAR activation phenobarbital 850ppm 10 animals for each condition and timepoint (3, 8 and 29 days) were used (150 samples total).

first: Fang

last: Zhang

first: Caleb

last: Lord

first: Aniko

last: Kende

first: David

last: Cowie

middle: B

first: Kathryn

last: Bailey

first: Emily

last: Scorgie

first: Elizabeth

middle: F

last: McInnes

first: Angela

last: Hofstra


title: Hepatic Metabolic Adaption During Prolonged Cyclic Calorie Restriction

city: Hong Kong

first: Man Yuen

last: LEE

address: Hunghom

department: Department of Applied Biology and Chemical Technology

country: Hong Kong

institute: The Hong Kong Polytechnic University

summary: The liver plays a crucial role in metabolic processes, and its response to fasting or intermittent fasting has been extensively studied. However, the effects of non-fasting calorie restriction (CR) on hepatic changes remain underexplored. The current data revealed new hepatic metabolic changes that do not follow traditional fasting patterns, demonstrating the liver's high metabolic adaptability to dietary content and eating habit changes.

overall_design: In this study, we designed a weekly intermittent calorie restriction cycle: 50% reduction on days 1 and 4, 70% on days 2 and 3, and unrestricted eating on days 5 to 7. This pattern mimics feasible non-linear CR observed in humans. To evaluate metabolic outcomes, high-fat diets (HFD) were utilized to induce obesity and related metabolic disorders, providing a robust model for assessing the efficacy of CR interventions. Liver samples from the ad libitum (AL) control group and low-calorie (LC, Day3 of the cycle) and refeeding (RF, Day7 of the cycle) phases from the calorie-restricted group were examined via RNAseq.

first: Leo

last: Lee

first: Thomas

middle: Y

last: Leung


title: Effect of Top2α depletion on the transcripional profile of HPV31-positive HaCaT (HaCaT31)cells

city: Chongqing

first: Yanfei

last: Liu

address: No.1 Yixueyuan Road, Yuzhong District,

department: Institute of Life Sciences

institute: Chongqing Medical University

summary: To explore the downstream targets of Top2α and the potential mechanisms of how TOP2A regulates HPV replication, RNA-seq was applied to HPV-positive cells with Top2α knockdown.

overall_design: HaCaT31 cells were transduced with viruses expressing Top2α shRNA and subsequently selected for stable expression of the shRNA using puromycin. The knockdown cells and the scramble cells were then compared to identify potential downstream targets of Top2α.

first: Shiyuan

last: Hong


title: Physiological and transcriptomic responses in brown trout, Salmo trutta, to multiple stressors: pesticide mixtures, elevated water temperature and the proliferative kidney disease

city: Lausanne

first: Rébecca

last: Beauvais

address: EPFL-ENAC-IIE-GE, Station 2

country: Switzerland

institute: Swiss Centre for applied ecotoxicology

summary: Contamination with pesticides, increased temperature and the presence of pathogens is a multiple stressor scenario relevant to surface water ecosystems globally. This study investigated the effects of these three environmental stressors and their combinations on juvenile brown trout, Salmo trutta. After acclimation to 12 or 15°C, fish were exposed for 14 days to one (at 12°C) or two (at 15°C) sublethal concentrations of a pesticide mixture (fluopyram, epoxiconazole, diuron, chlorpyrifos, λ-cyhalothrin). Following exposure, the fish were transferred for three months into clean water, with half of the individuals being exposed to spores of T. bryosalmonae, the causative agent of  proliferative kidney disease (PKD).  After 14 days of exposure, pesticides showed no impact on survival, growth, hematocrit, or organ indices but significantly altered the transcriptome (RNA-Seq) and gene expression in the brain and liver. A significant decrease in basal oxygen consumption was observed 2.5 months after fish were exposed to the high concentration of pesticides at 15°C, raising concerns that sublethal effects of pesticides may be limiting ecological fitness longer than expected. Susceptibility to PKD, assessed from infection prevalence, parasite intensity and kidney somatic index, was not affected by pesticide pre-exposure. No interactions between temperature and pesticide exposure were observed on apical, physiological, or qPCR endpoints. However, transcriptomic analysis revealed that the number of differentially expressed genes (DEGs) induced by pesticides was greater at 15°C. Interestingly, the number of DEGs affected by temperature in the brain was strongly reduced in the presence of pesticides.

overall_design: RNA-Seq profiling of liver (30 samples) and brain (30 samples) tissues of 6-month old brown trout exposed 14 days to 1 pesticide mixture at 12°C or 2 different pesticide mixtures at  15 °. RNA-Seq profiling of liver tissues of 6-month old brown trout exposed 4 days  to spores of Tetracapsuloides bryosalmonae, inducing the proliferative kidney disease and collected after 44 days exposure in clean water (12 samples).

first: Anne-Sophie

last: Voisin

first: Kristina

last: Rehberger

first: Melanie

last: Fasel

first: Helmut

last: Segner

first: Inge

last: Werner


title: Bulk RNA-Seq of primary human bronchial epithelial cells after transfection with different Cas9 formats

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

institute: Berlin Institute of Health, Charité Medical University of Berlin

summary: The goal of this study was to assess the immunogenicity of different Cas9 formats and subsequently its impact on gene editing efficacies. We investigated the impact of unmodified and pseuoduridine-modified Cas9 mRNA and Cas9 RNP on the innate immune response of NHBE cells by analysing the transcription profiles of NHBE cells after the different treatments.

overall_design: 1-factorial design; primary human bronchial epithelial cells were treated with either of 3 conditions (Cas9 RNP, unmodified Cas9 mRNA, pseudo-uridine modified Cas9 mRNA) or untreated (controls).

first: Sarah

last: Hedtrich

last: Weiner 3rd


title: Enhancer-associated LncRNA-ITGA2 promotes vascular smooth muscle remodeling by mediating ITGA2 promoter-enhancer interactions [RNA-seq]

city: Xi'an

first: XIAN

last: GUO

address: Xinyi Road

institute: Air Force Medical University

summary: To characterize the effects of PDGF-BB on long non-coding RNA (lncRNA) expression in vascular smooth muscle cells (VSMCs). Primary human VSMCs were cultured and treated with PDGF (20 ng/mL) or vehicle control (Veh) for 24 hours. Then we conducted lncRNA-seq and observed an increased in LncRNA-ITGA2 transcript reads following PDGF-BB treatment. This result is consistent with our microarray findings.


title: TET-dependent signaling of β-cell underlies intrauterine hyperglycemia-induced glucose intolerance in offspring [scRNA-seq]

first: Jiahang

last: Mo

summary: Epidemiologically, gestational diabetes mellitus (GDM) increases offspring’s diabetes risk. Intrauterine hyperglycemia (IHG) is a typical characteristic of GDM, impairing offspring’s glucose tolerance and insulin secretion, but the underlying mechanisms remain unclear. Here, we found IHG downregulates DNA demethylases Tet2/3 in fetal pancreatic islets. Pancreas-specific Tet2/3 double knockout (DKO) recapitulates the IHG effects. scRNA-seq analysis shows IHG or DKO downregulates β-cell signature while upregulating δ-cell signature.

overall_design: To investigate the mechanisms of impairing offspring’s glucose tolerance and insulin secretion in IHG offspring. Pancreatic islets from Tet2/3 double knockout mouse and IHG offspring was analyzed using scRNA-seq.


title: Multi-faceted nanodrug reinforcing metalloimmunotherapy for hepatocellular carcinoma

first: Yanteng

last: Xu

address: 600# Tianhe Road

department: Centre for Nanomedicine

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

summary: Hepatocellular carcinoma (HCC) is a major cause of cancer-related deaths, with limited options for unresectable cases. Immunotherapies show promise but are hindered by the immunosuppressive tumor microenvironment (TME). This study developed cobalt-Lenvatinib combination nanoclusters (Co+Len@OVA) to enhance HCC immunotherapy. These nanoclusters, formed by self-assembling ovalbumin, Lenvatinib, and cobalt ions, effectively inhibited HCC progression and reduced immunosuppression. They accumulated at tumor sites, inducing immunogenic cell death and activating the STING-IFNβ pathway, leading to a potent antitumor immune response. Additionally, they normalized tumor vasculature, improving anti-PD1 antibody retention and penetration. Combining Co+Len@OVA with anti-PD1 therapy significantly reduced HCC tumor volume more effectively than conventional treatments. Our study shows that Co+Len@OVA nanoclusters offer a promising treatment for HCC, particularly when surgery is not an option. They combine cobalt-mediated metalloimmunotherapy with Lenvatinib and boost the effectiveness of anti-PD1 therapy.

overall_design: Mice with in-situ Hepa1-6-luc cell-derived HCC were randomly allocated into six treatment groups: Control, OVA+anti-PD1, Lenvatinib+anti-PD1, Len@OVA+anti-PD1, Co+Len@OVA+anti-PD1, and Co@OVA+anti-PD1. These mice received tail vein injections of drug-loaded nanoclusters (2 mg/mL) or free Lenvatinib (equivalent to the nanocluster concentration) along with anti-PD1 (50 μg per injection) every 4 days, while the nanoclusters or free Lenvatinib were administered every 3 days. On day 14, tumor tissues from the Control, Lenvatinib+anti-PD1, and Co+Len@OVA+anti-PD1 groups (n = 3 per group) were harvested for mRNA extraction using TRIzol reagent. Sequencing libraries were prepared, and 2×150bp double-end sequencing was conducted using Illumina Novaseq™ 6000.

first: Yongwei

last: Hu

first: Wei

first: Linsen

last: Ye

first: Yang

last: Yang


title: ANGPT1 as a Prognostic Biomarker in a Large-Scale Pan-cancer Analysis

city: Guiyang

first: Dan

last: Ma

address: No. 9 Beijing Road, Guiyang City, Guizhou Province

department: Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D

institute: Guizhou Medical University

summary: Angiopoietin 1 (ANGPT1) plays a significant role in tumorigenesis, prognosis, and chemoresistance across various cancers. This study demonstrated that ANGPT1 expression is heterogeneous among tumor types, with high expression linked to poor prognosis in multiple cancers and associated with immune infiltration, tumor mutation burden, and drug sensitivity. In acute myeloid leukemia (AML), ANGPT1 was markedly upregulated in patients compared to healthy controls and further elevated in non-responders versus complete remission cases. Functional assays confirmed its role in promoting AML cell proliferation, highlighting ANGPT1 as a promising prognostic biomarker and therapeutic target in AML and other malignancies.

overall_design: Bone marrow mononuclear cells were collected from newly diagnosed, treatment-naïve acute myeloid leukemia (AML) patients for RNA sequencing (RNA-seq).

first: Qian

last: Kang

first: Junzhao

last: Wan

first: Min

last: Zhang

first: Yunsheng

last: Ran

first: Ping

last: Liu

first: Zhen

last: Zhou


title: RNA transcriptome sequencing of Skin Cutaneous Melanoma cell line A375 and SK-MEL-28 treated with siNC or siLINC01291

city: Guangzhou City

first: Minna

state: Guangdong Province

address: 1838 Guangzhou Avenue North

institute: Southern Medical University

summary: To figure out the role of long non-coding RNA LINC01291 in Skin Cutaneous Melanoma and the underlying mechanism, RNA transcriptome sequencing was performed to globally characterize LINC01291-regulated transcriptome changes. LINC01291 knockdown by siRNA in melanoma cells. A375 and SK-MEL-28 cells treated with siNC served as control.

first: Ke

last: Wang

first: MIin

first: Yanjie

last: Kuang

first: Jun

first: Liang

first: Li