title: Myosin 5b Deficiency Alters Liver Proliferation, Zonation and Bile Acid Composition

city: Ladson

first: Rachel

last: Edens-Valentine

state: SC

address: 9675 Spencer Woods Rd

institute: Medical University of South Carolina

summary: Background: Myosin 5b (Myo5b) is a motor protein critical for trafficking proteins to the apical surface of intestinal epithelial cells. Inactivating mutations in MYO5B cause Microvillus Inclusion Disease (MVID), a congenital diarrhea disorder that often leads to liver cholestasis. While Myo5b’s role in the intestine is well characterized, its function in the liver remains unclear. Methods & Results: To define the hepatic consequences of Myo5b loss, we analyzed germline Myo5b knockout (KO) mice. Bulk RNA-seq of KO livers revealed significant transcriptomic alterations, notably downregulation of genes linked to cell proliferation. Immunostaining confirmed reduced Ki67, phospho-histone H3, and cyclin D1 expression, along with impaired growth of liver organoids in Myo5b deficient mice. Histology and lipid staining showed steatosis and enlarged lipid droplets, with gene signatures favoring lipogenesis and ketogenesis in mice lacking Myo5b. Myo5b KO livers also displayed disrupted zonated gene expression and loss of zone 1 and zone 3 markers. Bile acid profiling revealed reduced hepatic bile acid levels, decreased expression of classical pathway genes (Cyp7a1, Cyp7b1), and compensatory upregulation of Cyp27a1. In the ileum, we observed mislocalization of the apical bile acid transporter ASBT and decreased levels of basolateral OSTβ, leading to impaired enterohepatic recycling and increased luminal bile acids. Conclusions: These findings reveal a previously unrecognized role for Myo5b in liver proliferation, metabolic zonation, and bile acid homeostasis, highlighting its importance in maintaining hepatobiliary function.

overall_design: Neonatal CD1 mice harboring a germline deletion of Myosin 5b and control (wildtype or heterozygous) mice were euthanized between the ages of 3-8 days old. For RNAseq, the entire liver was collected in Trizol and stored at -80 ºC prior to RNA extraction. mRNA was isolated using Trizol extraction and QIAGEN RNA easy kit according to the manufacturer’s instructions. mRNA was extracted from the entire liver of 4 Myo5b KO and 4 control littermates and RNAseq was performed by MedGenome. RNAseq data was used for differential gene expression analysis, pathway analysis, and principal component analysis. Differential gene expression and pathway analysis were performed with RStudio (2024.04.2+764) using the DESeq2 R package (1.46.0)

first: Piper

last: McKee

last: Stubler

first: Renata

last: do Nascimento

first: Charulekha

last: Packirisamy

first: Casper

last: van Altena

first: Lauren

last: Giordano

first: Colleen

last: LeBlanc

first: Selene

last: Shore

first: Jessica

last: Hartman

first: Robin

last: Muise-Helmericks

first: Andrew

last: Percy

first: Thomas

last: Horvath

first: Kristen

last: Engevik

first: Melinda

first: Amy

middle: C


title: APOBEC3B effect on Hepatocellular carcinoma

status: Public on Jan 12 2026

city: Nanjing

first: Duowei

last: Wang

state: JIANGSU

address: Longmian Road 639

country: China

institute: China Pharmaceutical University

type: Expression profiling by high throughput sequencing

summary: Analysis of Hepatocellular carcinoma (HCC) with overexpression of  APOBEC3B. Results provide insight into the role of APOBEC3B in the regulation of tumor microenvironment.

overall_design: Liver Tissues mRNA profiles of control and APOBEC3B overexpression mice were generated by deep sequencing, in duplicate.

first: Yong

last: Yang


title: Transcriptome Sequencing Analysis of Human Colorectal Cancer Cell Lines After ECM1 Knockdown

status: Public on Jan 11 2026

city: Chongqing

first: Huihui

last: Xiao

address: shapingba

institute: Chongqing university

summary: To investigate the regulatory role of ECM1 in CCL20 expression in colorectal cancer, this study employed the human colorectal cancer SW620 cell line. Stable knockdown of ECM1 gene expression was achieved via shRNA, and single-cell transcriptome sequencing technology was used to systematically compare the transcriptomic differences between the ECM1 knockdown group (SW620-shECM1) and the negative control group (SW620-shNC). Sequencing analysis revealed that ECM1 knockdown significantly affected multiple signaling pathways, among which the TNF-α signaling pathway was notably activated, and the expression and activity of the key transcription factor JUNB underwent significant changes. Further mechanistic studies demonstrated that ECM1 regulates the transcription and expression of the downstream chemokine CCL20 by modulating the TNF-α/JUNB signaling axis. This study is the first to reveal the molecular mechanism by which ECM1 regulates CCL20 through the TNF-α-JUNB pathway in colorectal cancer at the single-cell level, providing a new perspective for understanding the role of ECM1 in the tumor microenvironment and immune regulation.

overall_design: The human colorectal cancer SW620 cell line was used to explore ECM1's regulatory role in CCL20 expression. Stable ECM1 knockdown was established in SW620 cells using shRNA (SW620-shECM1 group), with a negative control group (SW620-shNC) set simultaneously. Single-cell transcriptome sequencing was performed to compare transcriptomic differences between the two groups, focusing on analyzing changes in signaling pathways and key molecule expression related to ECM1-mediated CCL20 regulation.


title: Analysis of three-dimensional enhancer network regulated by CTCF in CD4+ T cells [ATAC-seq]

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

country: South Korea

institute: Yonsei University College of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Purpose: We aim to analyze genome-wide changes in RNA expression, histone modifications, chromatin structure, and 3D genome organization in CD4+ T cells following CTCF depletion.
Conclusions: CTCF controls gene expression via 3D enhancer network in CD4+ T cells

overall_design: ATAC-seq analysis for CTCF-WT and CTCF-KO CD4+ T cells with biological replicates

first: Eun-Chong

last: Lee

first: Sugyung


title: Hypoxia restores the acidosis-induced inhibition of cancer cell dissemination

city: Baltimore

first: Konstantinos

last: Konstantopoulos

state: MD

address: 3400 N Charles St, Croft Hall G65

department: Chemical and Biomolecular Engineering

country: USA

institute: Johns Hopkins University

summary: Acidosis is a hallmark of the tumor microenvironment and has been linked to aggressive cancer behavior, characterized by increased migration, invasion, and metastasis. We herein demonstrate that short-term exposure (24-72 h) to acidic extracellular pH (pHe=6.4) suppresses cell proliferation, metabolism, dissociation from tumor spheroids, and migration in vitro as well as extravasation in chick embryos and mice. Acidosis acutely inhibits motility by downregulating the activity of sodium-hydrogen exchanger isoform-1 (NHE1), which in turn suppresses phosphatidylinositol 3‑kinase (PI3K)/Akt. PI3K/Akt inhibition blocks Yes-associated protein (YAP) translocation to the nucleus, reducing NHE1 and integrin-linked kinase (ILK) expression. The resulting reduction in NHE1-/ILK-dependent migration and ATP production is rescued by hypoxia across cell types. While certain cancer cells can adapt to long-term (>3 weeks) acidosis and acquire an aggressive phenotype, acidosis-induced adaptation is not universal and depends on the cell’s ability to restrain reactive oxygen species overproduction via fatty acid oxidation.

overall_design: RNA-seq profiling of MDA-MB-231 cells incubated with medium of extracellular pH=7.4 or 6.4 for 24 h or 10 weeks.


title: RBP4 inhibits tongue squamous cell carcinoma progression through inhibition of the PI3K/AKT signaling pathway and promotion of macrophage M1-type polarization

city: Beijing

first: Huayuan

last: Liu

state: Beijing

address: New Student Apartment Building, No. 17, South Panjiayuan, Chaoyang District, Beijing

institute: Chinese Academy of Medical Sciences Cancer Hospital

summary: Tongue squamous cell carcinoma (TSCC) is a common type of oral mucosal epithelial malignancy that can severely affect patient quality of life. Therefore, novel therapeutic strategies for TSCC are needed. This study aimed to investigate the role and mechanism of action of retinol-binding protein 4 (RBP4) in TSCC progression and its effect on tumor-associated macrophages. To this end, TSCC cell lines with RBP4 over-expression and knockdown were constructed, and effects of RBP4 expression on the proliferation and inva-sive abilities of TSCC cells were verified using ex vivo experiments. Furthermore, a tumor cell-macrophage co-culture model was established to assess the effect of RBP4 on macrophage polarization. RBP4 overex-pression reduced the phosphorylation of the PI3K/Akt/mTOR pathway and inhibited tumor cell proliferation by regulating Snail levels; RBP4 inhibited TSCC cells from undergoing epithelial-mesenchymal transition. In addition, RBP4 promoted the activation of NF-κB signaling pathway, leading to macrophage polarization toward M1 type and inhibiting TSCC growth. We found for the first time that RBP4 affects the prolifera-tion and migration of TSCC cells by inhibiting the activation of the PI3K-Akt signaling pathway, and that RBP4 promotes the M1-type polarization of tumor-associated macrophages, which contributes to their on-cogenic effects.

overall_design: Transcriptome sequencing was performed by Genechem, based on the Illumina sequencing platform for transcriptome sequencing (RNA-Seq) of a recombinant human RBP4 protein-treated M0 macrophage cell model. A KEGG pathway enrichment analysis was performed using the R software “clusterProfiler” pack-age after obtaining the differential genes based on gene expression analysis.

first: Ying

last: Yan

last: Miao

first: Xiaofeng


title: Uridine Diphosphate Drives Myeloid Differentiation and Functional Reprogramming Through Dynamic Transcriptional Networks

city: Catanzaro

first: Giuseppe

last: Fiume

address: Viale Europa, Campus "S. Venuta", Ed. Bioscienze,Germaneto

department: Department of Experimental and Clinical Medicine

country: Italy

institute: University of Catanzaro "Magna Graecia"

summary:
PBMC were stimulated with UDP (100 micromolar) or left untreated (NT) for the indicated points. RNA was extracted and subjected to Nanostring nCounter Immunology Panel
The expression of around 500 genes of immunological relevance was analyzed in the different samples.

overall_design: Gene expression profiling by Nanostring Immunological Panel was performed on PBMC  stimulated with UDP (100 micromolar) or left untreated (NT) for the indicated points.

first: Caterina

last: Giordano

first: Emilio

last: Straface

first: Debora

last: Gentile


title: The Mechanism of Gene Regulation in Recurrent Vulvovaginal Candidiasis (RVVC Group)

city: Kunming

first: xiang

middle: wen

last: lan

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

institute: Southwest Forestry University

summary: Kunming mice were infected with Candida albicans, and transcriptome sequencing and analysis were performed to investigate the mechanism by which gene X mediates recurrent vulvovaginal candidiasis (RVVC) through the Y signaling pathway, thereby providing novel insights and potential therapeutic targets for the treatment of RVVC.

overall_design: Establish mouse models of vulvovaginal candidiasis (VVC) and recurrent vulvovaginal candidiasis (RVVC). Perform high-throughput transcriptome sequencing on vaginal epithelial tissues from the control, VVC, and RVVC groups, followed by screening for differentially expressed genes (DEGs).


title: Aging-associated differences in mammary tumor-initiating populations and immune evasion pathways in breast cancer [bulk_RNA_seq]

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave. S1070

institute: Dana-Farber Cancer Institute

summary: Aging is a major risk factor for breast cancer, yet how it shapes tumor development, molecular phenotype, and immune evasion remains incompletely understood. Deciphering how aging influences cancer development is critical for improving risk assessment, prevention, and treatment. Here, using a N-nitroso-N-methylurea (NMU)-induced rat mammary tumor model that recapitulates key features of human breast cancer, we integrated bulk and single-cell transcriptomics, whole-exome sequencing, and histopathological analysis to dissect age-associated differences in tumorigenesis. We found that age at NMU exposure critically influences tumor incidence, mutational burden, subtype, and immune microenvironment. Tumors arising in aged rats originate from luminal progenitor-like cells with increased genomic instability, suppressed immune infiltration, and impaired antigen presentation linked to loss of heterozygosity at Chr 20p. These age-associated epithelial and immune changes were conserved in human breast cancers, where loss of the homologous Chr 6p region correlated with reduced lymphocyte infiltration and shorter relapse-free survival. These findings reveal that aging alters the tumor-initiating cell population and promotes immune-evasive tumor states through chromosomal instability-driven antigen presentation defects. Our work provides mechanistic insight into the reduced efficacy of immunotherapy in older patients.

overall_design: To induce mammary tumors, rats of different ages (1-, 3-, 6-, 12-, 20-month-old) received two intraperitoneal injections of 50 mg/kg N-Nitroso-N-methylurea (NMU) at a one-week interval. Tumor growth was monitored regularly using caliper measurements. The maximum allowable tumor burden of 4 cm was not exceeded in any experiment. Rats were euthanized by CO₂ inhalation, and tumors were collected and snap frozen in liquid nitrogen. RNA was isolated using RNeasy Mini Kit (Qiagen) with on-column DNA digestion. Two tumors (1m-4 and 6m-1) were excluded from library preparation due to extended postmortem intervals, as the animals were discovered several hours after death. Libraries preparation with poly(A) selection and 150-bp paired-end sequencing on an Illumina HiSeq platform were performed by GENEWIZ (USA; www.GENEWIZ.com).

first: Pengze


title: Effect of Meflin overexpression on the fibroblast transcriptome in a three-dimensional culture using cell accumulation technique

city: Nagoya

first: Akihiro

last: Sakai

state: Aichi

country: Japan

institute: Nagoya university

summary: We previously reported that Meflin, encoded by the immunoglobulin superfamily containing leucine-rich repeat (ISLR) gene, is a marker for tumor-restraining cancer-associated fibroblasts. However, the functional roles of Meflin in fibroblasts remain unclear. To investigate the functional impact of Meflin expression in fibroblasts, RNA sequencing was performed on Meflin-overexpressing NHDF-Ad cells cultured under conditions that better mimic the in vivo tumor microenvironment, using a cell accumulation technique that accurately recapitulates the fibrotic stroma observed in aggressive human cancers. Meflin overexpression resulted in the downregulation of PDPN, a well-established marker of tumor-promoting CAFs, and upregulation of DPT and COL15A1, which are markers of universal fibroblasts that resemble normal fibroblasts and are considered a potential source of diverse fibroblast subtypes.These findings suggest that high-level expression of Meflin is crucial for skewing CAFs toward a more universal fibroblast–like state.

overall_design: RNA-seq profiling of Meflin-overexpressing NHDF-Ad cells and control NHDF-Ad cells cultured either alone or co-cultured with MDA-MB-468, a triple-negative breast cancer cell line, in a three-dimensional culture system using the cell accumulation technique.

first: Shinji

last: Mii

first: Atsushi

last: Enomoto


title: Aging-associated differences in mammary tumor-initiating populations and immune evasion pathways in breast cancer

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

overall_design: Refer to individual Series


title: Gut-Brain Axis Regulates Liver Anti-Tumor Immunity

city: Bethesda

first: Tim

last: Greten

address: Building 10, Room 2B38B

department: Thoracic and GI Malignancies Branch

institute: NIH

summary: Hepatic immunosuppression contributes to high mortality in liver cancer. Nerve activity has been implicated in peripheral immune response and tumor growth. Whether cholinergic neuroimmune interactions shape hepatocellular carcinoma (HCC) remains uncertain. Hepatic vagotomy significantly reduced primary and metastatic liver tumors in mice. These vagotomized livers exhibited anti-tumor immunity, notably elevated inflammatory and cytotoxic CD8+ T cell subsets. Pharmaceutical or genetic disruption of ACh activity regulated CD8+ T cell function via AChR Chrm3, while tumor growth was rescued in Rag1KO mice or following CD8+ T cell depletion. Beyond tumor-specific outcomes, vagotomy improved cancer-associated fatigue and anxiety-like behavior. As microbiota transplantation from HCC donors was sufficient to impair behavior, we performed microbiome sequencing throughout cohousing and microbiota transplantation studies. Tumor, rather than vagotomy, robustly altered fecal bacterial composition, increasing Desulfovibrionales and Clostridial taxa. This tumor microbiota was sufficient to promote anti-tumor CD8+ T cell immune features only within vagotomized, but not vagal-intact, tumor-free mice. We identify gut-brain ACh signaling as a critical, dynamic, and targetable arc to modulate liver immunity and cancer outcomes.

overall_design: Eight samples were prepared for scRNA-seq. Solid RIL175 tumors were excised from Sham Vagatomy (SV) and Hepatic Vagatomy (HV) livers (n = 3 / group) 21 d following tumor initiation.  RIL175 tumor-bearing mice (n = 3 SV, 3 HV mice) from non-tumorous liver and matched (pooled) tumors.

first: Bauer

last: Kylynda

first: Trehan

last: Rajiv

first: Ma

last: Chi

first: Greten

last: Tim


title: Aging-associated differences in mammary tumor-initiating populations and immune evasion pathways in breast cancer [exome_seq]

overall_design: To induce mammary tumors, rats of different ages (1-, 3-, 6-, 12-, 20-month-old) received two intraperitoneal injections of 50 mg/kg N-Nitroso-N-methylurea (NMU) at a one-week interval. Tumor growth was monitored regularly using caliper measurements. The maximum allowable tumor burden of 4 cm was not exceeded in any experiment. Rats were euthanized by CO₂ inhalation, and tumors were collected and snap frozen in liquid nitrogen. Whole-exome sequencing libraries were prepared using the Agilent SureSelectXT Target Enrichment System following the manufacturer’s protocol. DNA from the liver of an untreated healthy rat served as a normal control. Briefly, 3 µg of genomic DNA extracted from rat tumors was sheared to the desired fragment size using ultrasonication, followed by end-repair, A-tailing, and adapter ligation. The adapter-ligated DNA was hybridized to biotinylated RNA baits targeting exome regions, and captured DNA fragments were enriched using streptavidin-coated magnetic beads. After PCR amplification, the final libraries were quantified, assessed for quality using a Bioanalyzer, and sequenced on an Illumina platform to generate paired-end reads.


title: Aging-associated differences in mammary tumor-initiating populations and immune evasion pathways in breast cancer [scRNA-Seq]

overall_design: To induce mammary tumors, rats of different ages (1-, 3-, 6-, 12-, 20-month-old) received two intraperitoneal injections of 50 mg/kg N-Nitroso-N-methylurea (NMU) at a one-week interval. Tumor growth was monitored regularly using caliper measurements. The maximum allowable tumor burden of 4 cm was not exceeded in any experiment. Rats were euthanized by CO₂ inhalation, and tumors were harvested as previously described. Briefly, tumors were enzymatically digested in DMEM/F12 medium containing 2 mg/mL collagenase IV, 2 mg/mL hyaluronidase, and 2 mg/mL bovine serum albumin (BSA) at 37ºC for 1–2 hours, followed by freezing in cryopreservation medium (90% fetal bovine serum (FBS) and 10% dimethyl sulfoxide) in liquid nitrogen. For mammary tumor scRNA-seq, viable cells were resuspended in PBS with 0.04% BSA at a cell concentration of 1000 cells/μL. 10,000 cells were loaded onto a 10x Genomics Chromium™ instrument (10x Genomics) according to the manufacturer's instructions. The scRNA-seq libraries were prepared according to the Chromium Next GEM Single Cell 5’ HT v2 protocol (10x Genomics). Quality control for amplified cDNA libraries and final sequencing libraries were performed using Bioanalyzer High Sensitivity DNA Kit (Agilent). The pooled libraries were sequenced on Illumina NovaSeq X plus platform.


title: Evaluation of targeted and immune combination therapies in a rat model of hormone receptor-positive breast cancer  [scRNA]

summary: Breast cancer hormone receptor (HR) estrogen and progesterone (ER/PR) positive tumors were generated in an outbred rat model (Sprague-Dawley) through the injection of the carcinogen N-nitrosomethylurea (NMU). These tumors were treated with immune checkpoint blockade (anti PD-L1) in combination with targeted therapies, including an TBK1/IKBKE inhibitor, a KMT5B/C inhibitor, a TGF-b inhibitor, and a selective estrogen receptor degrader (SERD). This dataset includes single-cell RNA sequencing (scRNA-seq) data from tumors subjected to various treatment setups. Whole-tumor digestion was performed to preserve a comprehensive representation of the tumor microenvironment. The study aims to identify mechanisms that sensitize HR postive tumor subtypes to immune checkpoint blockade therapy.

overall_design: Tumors were induced by intraperitoneal injection of 50 mg/kg NMU on days 46 and 53 of age. Treatment with NIS793 (a TGFBR inhibitor), IKBKEi (a TNK1/IKBKE inhibitor), A196 (a SUV420H1/SUV420H1 inhibitor), Fulvestrant (an estrogen receptor antagonist), ⍺PD-L1, or a combination of targeted therapy with immune checkpoint blockade (ICB) was initiated when tumors reached 8 mm in size, more than one tumor was detected, or a tumor remained unchanged in size for more than three days. Rats were randomly assigned to treatment groups, and tumor size was measured every other day using calipers.

first: Ernesto

last: Rojas Jimenez

first: Triet

last: Bui

first: Marco

last: Seehawer

first: Jun

last: Nishida


title: The role of hippocampal niche exosomes in rat hippocampal neurogenesis after fimbria-fornix transection

city: nantong

first: wen

last: li

address: qixiu road 19

institute: Nantong University

summary: Exosomes transfer signaling molecules such as proteins, lipids, and RNAs to facilitate cell–cell communication and play an important role in the stem cell microenvironment. In previous work, we demonstrated that rat fimbria–fornix transection (FFT) enhances neurogenesis from neural stem cells (NSCs) in the subgranular zone (SGZ). However, how neurogenesis is modulated after denervation remains unknown. Here, we investigated whether exosomes in a denervated hippocampal niche may affect neurogenesis.  Using the FFT rat model, we extracted hippocampal exosomes and used RNA sequencing to identify noncoding RNA expression profiles.

overall_design: The rat hippocampal tissue (denervated and untreated) was quickly harvested on ice. It was then digested with 0.125% trypsin at 37 °C for 30 min and the serum without exosomes was added to stop digestion. The Total Exosome Isolation Kit (from plasma) (Invitrogen, USA) was added to the supernatant after 4 °C, 3000g, 30 min centrifugation for an overnight stand. Then, after 4 °C, 10,000g, 1 h centrifugation, the precipitation was resuspended with 50 μl DPBS, and exosomes were harvested for the following experiments. high-throughput sequencing ofexosomes from hippocampal niche.

first: Guohua

last: Jin

first: Xiang

last: Cheng

first: Wen

last: Li


title: Next Generation Sequencing to evaluate effects of MiR26b on atherosclerotic mouse vessels

city: Maastricht

first: Han

address: P. Debyelaan 25

country: Netherlands

institute: Maastricht University

summary: In this study, Apoe-/- control mice and Apoe-/-MiR26b-/- mice were placed on a HFD for 4 weeks. Aortic arch and thoracic aorta from these mice were used to perform NGS analysis.

overall_design: Aortic arch and thoracic aorta isolated from Apoe-/- control mice and Apoe-/-MiR26b-/- mice after 4 weeks HFD.

first: Emiel

middle: P

last: Van der Vorst

first: Linsey

middle: J

last: Peters


title: RNA-Seq of VUMC-DIPG10 and HSJD-DIPG007 human diffuse intrinsic pontine glioma cells treated with a copper chelator

city: Bologna

first: Daniele

last: Mercatelli

address: Via Irnerio 45

department: Pharmacy and Biotechnology

institute: University of Bologna

summary: We report the application of RNA-sequencing of VUMC-DIPG10 and HSJD-DIPG007 human diffuse intrinsic pontine glioma cells treated with copper chelator Tetraethylenepentamine (TEPA) for 24 hours. We show transcriptome changes following copper chelation vs. control untreated cells.vs. control samples

overall_design: VUMC-DIPG10 and HSJD-DIPG007 human diffuse intrinsic pontine glioma cells treated with copper chelator at 24 hours in vitro

first: Federica

last: Saletta

first: Federico

last: Giorgi

first: Orazio

last: Vittorio


title: Wnt/β-catenin signaling restrains developmental beige adipocyte thermogenesis and its inhibition imprints long-term energy expenditure_Inguinal white adipose tissue from 4- and 8-week-old male mice

status: Public on Jan 10 2026

city: Chengdu

first: Ganran

last: Xu

address: No. 14, Section 3, Renmin South Road, Wuhou District

department: West China School of Stomatology

institute: Sichuan University

summary: Beige adipocytes that emerge during the peri-weaning period support sympathetic nervous system (SNS)-independent thermogenesis, yet the mechanisms governing this spontaneous beiging remain unclear.

overall_design: Here, by integrating transcriptomic profiling with adipocyte-targeted Ctnnb1 deletion in mice, we identify the canonical Wnt signaling as an endogenous brake on developmental beige thermogenesis. Peri-weaning inguinal fat from adipocyte Ctnnb1 knockout mice exhibits enhanced beige adipocyte biogenesis, with increased thermogenesis-related gene expression and mitochondrial oxidative capacity, which programs durable activation of adaptive thermogenesis and augmented whole-body energy expenditure into adulthood. Mechanistically, suppression of Wnt/β-catenin signaling induces a non-canonical Wnt5a-Ca2⁺-AMPK axis that promotes triglyceride lipolysis and subsequent PPAR-driven fatty acid oxidation, thereby fueling mitochondrial respiration. Genetic or pharmacological disruption of this axis blunts thermogenic responses induced by β-catenin inhibition in both murine and human subcutaneous adipocytes, indicating that Wnt5a-Ca2⁺-AMPK axis is required for the cell-autonomous activation of beige fat. These results reveal Wnt/β-catenin signaling as a developmental constraint on beige adipocyte formation and suggest an SNS-independent route to sustainably raise energy expenditure and improve metabolic health.


title: Wnt/β-catenin signaling restrains developmental beige adipocyte thermogenesis and its inhibition imprints long-term energy expenditure_Primary adipocytes differentiated in vitro, 4- and 8-week-old male mice


title: Comprehensive multi-omics analyses elucidate the mechanism of male sexual dysfunction induced by chronic prostatitis/chronic pelvic pain syndrome in the experimental autoimmune prostatitis rat model

first: Mengchi

last: Yu

address: No. 300 Guangzhou Road, Gulou District

institute: The First Affiliated Hospital of Nanjing Medical University

summary: Chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) is a condition characterized by persistent pain in the genitourinary tract. Men with CP/CPPS are significantly more susceptible to sexual dysfunction compared to the general population. While an association exists between CP/CPPS and sexual dysfunction, the underlying mechanisms remain poorly understood. This study sought to elucidate the underlying central mechanisms linking autoimmune prostatitis to sexual dysfunction by employing an integrated multi-omics approach in a well-established rodent model.

overall_design: An experimental autoimmune prostatitis (EAP) model was induced by injecting a mixture of rat prostate protein and Freund's adjuvant. Comprehensive assessments were conducted, including histopathological evaluation of prostate and penile tissues via H&E and Masson's trichrome staining, quantification of serum cytokines and neurochemicals using ELISA, functional assessment of erectile capability by measuring intracavernous pressure/mean arterial pressure (ICP/MAP) ratio, and detailed mating behavior analysis. Brain tissues from rats were collected for comprehensive transcriptomic profiling and non-targeted metabolomic analyses.

first: Jiaochen

last: Luan


title: Title update

first: Maxim

middle: Batkovič

last: Tomashevsky

address: 9000 Rockville Pike

department: NLM

institute: NčBi

summary: summary

overall_design: design


title: Spatial genome organization is associated with nematode programmed DNA elimination [Hi-C Parascaris univalens]

city: Knoxville

first: Jianbin

last: Wang

state: TN

address: 1311 Cumberland Avenue, Ken and Blaire Mossman Building Rm 309

institute: The University of Tennessee

summary: Programmed DNA elimination (PDE) is a notable exception to genome integrity, characterized by significant DNA loss during development. In many nematodes, PDE is initiated by DNA double-strand breaks (DSBs), which lead to chromosome fragmentation and subsequent DNA loss. However, the mechanism of nematode programmed DNA breakage remains largely unclear. Interestingly, in the human and pig parasitic nematode Ascaris, no conserved motif or sequence structures are present at chromosomal breakage regions (CBRs), suggesting the recognition of CBRs may be sequence-independent. Using Hi-C, we revealed that Ascaris CBRs engage in three-dimensional (3D) interactions before PDE, indicating that physical contacts between break regions may contribute to the PDE process. The 3D interactions are established in both Ascaris male and female germlines, demonstrating inherent genome organization associated with the CBRs and to-be-eliminated sequences. In contrast, in the unichromosomal horse parasite Parascaris univalens, transient pairwise interactions between neighboring CBRs that will form the ends of future somatic chromosomes were observed only during PDE. Intriguingly, we found that Ascaris PDE, which converts 24 germline chromosomes into 36 somatic ones, induces specific compartmentalization changes. Remarkably, Parascaris PDE generates the same set of 36 somatic chromosomes, and the 3D compartment changes following PDE are consistent between the two species. Overall, our findings suggest that CBRs spatially demarcate the retained and eliminated DNA and may contribute to their spatial organization during Ascaris PDE. We also demonstrated that the 3D genome reorganization of the somatic chromosomes in these nematodes following PDE is evolutionary and developmentally conserved.

overall_design: Hi-C was performed using samples from different embryonic and larvals stages of Parascaris univalens.

first: James

middle: R

last: Simmons


title: Role of mitofusins in oocyte development

city: São Carlos

first: Marcos

middle: Roberto

last: Chiaratti

state: SP

address: Rod. Washington Luis km 235

department: Departamento de Genética e Evolução

country: Brazil

institute: Universidade Federal de São Carlos

summary: We performed RNA sequencing (RNAseq) analysis to determine the effect of single (Mfn1-/- or Mfn2-/-) and double (Mfn1-/- and Mfn2-/-; Mfn1&2-/-) knockouts of mitofusins on oocyte gene expression profile. We found that in comparison with the wild-type (WT) control, 161 (Mfn1-/-), 538 (Mfn2-/-) and 474 (Mfn1&2-/-) genes were differentially expressed in knockout oocytes at the germinal-vesicle stage (FDR<0.05 and log fold change > 1 or < -1). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of genes exclusively down-regulated in each group indicated an over-representation in Mfn1-/- oocytes of Rap1 signaling pathway and PI3K-Akt signaling pathways. In comparison, these pathways were found to be up-regulated across Mfn2-/-, Mfn1&2-/- and WT oocytes. Our findings provide new insights into the roles of mitofusins in oocytes, shedding light on the potential mechanism of infertility associated with Mfn1 deficiency.

overall_design: Germinal-vesicle (GV) arrested oocytes were collected from Mfn1-/-, Mfn2-/- and Mfn1&2-/- mice aged 21-23 days. Pools of 50 oocytes from each group were used in triplicates for RNA sequencing.

first: F

middle: H

last: Sugiyama

first: K

middle: F

last: Carvalho

first: C

last: Macabelli

first: P

last: Tizioto

first: L

middle: L

last: Coutinho

first: R

last: Nociti

first: M


title: The hedgehog co-receptors cdon and boc function synergistically to regulate zebrafish craniofacial development

city: Easton

first: Ezra

last: Lencer

state: PA

address: 746 High Street

department: Department of Biology

institute: Lafayette College

summary: Craniofacial development is a complex developmental process that involves formation of the skeleton, muscle, and tendons. Defects in craniofacial development lead to common hereditary disorders such as orofacial clefting or holoprosencephaly. Among genetic factors regulating craniofacial development, dysregulated hedgehog signaling is commonly associated with craniofacial skeletal defects. Here, we characterize craniofacial phenotypes associated with two hedgehog signaling co-receptors, cdon and boc, in zebrafish. Pedigree analyses have previously linked both CDON and BOC to microform holoprosencephaly skeletal defects, and mutations of Cdon and Boc in mouse result in midline craniofacial phenotypes. However, a detailed analysis of craniofacial phenotypes associated with cdon and boc in zebrafish has not been completed. Our studies show that cdon and boc operate synergistically to promote craniofacial cartilage, tendon, and muscle development in zebrafish. Using RNA-seq and HCR in situ hybridization we show that mutations of cdon and boc result in misregulation of chondrogenesis gene expression including Indian hedgehog ligand, tendon associated thrombospondin genes, and FOX transcription factors. Our data are consistent with a model whereby cdon and boc together modify hedgehog activity in the head, and establishes a foundation for using zebrafish to further understand the role of cdon and boc in craniofacial hereditary disorders such as holoprosencephaly.

overall_design: RNA-seq profiling of heads of wildtype and double homozygous mutant cdon/boc embryos at 30 hours post fertillization and at 4 days post fertilization.

first: Ryan

last: Nickens

first: Sophia

last: Guitar

first: Bryan

last: Zepeda

first: Julaine

last: Roffers-Agarwal

first: Kristin B.

last: Artinger


title: Effect of FADS2 overexpression on gene expression of adipose stem cells

city: wuhan

first: sen

last: ren

state: hubei

address: donghu road

department: Department of Neurosurgery

institute: Zhongnan Hospital of Wuhan University

summary: In the current investigation, an RNA-seq analysis was conducted to examine the differentially expressed genes in aged ASCs (O-ASCs) following the overexpression of FADS2. The analysis revealed that 84 genes were significantly upregulated, while 516 genes were downregulated in oe-FADS2 O-ASCs compared to the oe-NC control group. GSEA indicated significant enrichment in pathways such as unsaturated fatty acid biosynthesis, the p53 signaling pathway, and the MAPK signaling pathway. GO analysis demonstrated that the differentially expressed genes were primarily localized to the nucleus and extracellular regions, with molecular functions encompassing metal ion binding and DNA binding activities, among others. Additionally, these genes were implicated in biological processes including angiogenesis, inflammatory response, and regulation of transcription mediated by RNA polymerase II. KEGG pathway analysis further highlighted enrichment in pathways associated with viral infection, cytokine-cytokine receptor interactions, the NOD-like receptor signaling pathway, and the IL-17 signaling pathway.

overall_design: A comparative RNA-seq was conducted on a cohort comprising three  oe-FADS2 O-ASCs and three oe-NC O-ASCs

first: Sen

last: Ren

first: Yu

last: Yan


title: Gene expression profiles of GM-CSF cultured bone marrow cells treated with HCQ or cGAMP.

city: Tokyo

first: Hideo

last: Negishi

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

department: Vaccine Science

institute: The Institute of Medical Science, The University of Tokyo

summary: We performed RNA sequencing (RNA-seq) of granulocyte-macrophage colony-stimulating factor (GM-CSF) cultured bone marrow cells (GM-BMCs) treated with hydroxychloroquine (HCQ) or cyclic guanosine monophosphate–adenosine monophosphate (cGAMP) to compare the gene expression profiles between HCQ and cGAMP treatments in GM-BMCs.

overall_design: Bone marrow cells were isolated from the legs of mice and cultured in RPMI 1640 (Nacalai Tesque, Kyoto, Japan) containing 10% foetal bovine serum (FBS) (Sigma-Aldrich, St. Louis, MO, USA) and 10 ng/ml of GM-CSF (PeproTech, Cranbury, NJ, USA). Red blood cells (RBCs) were lysed with RBC lysis buffer (Thermo Fisher Scientific, Waltham, MA, USA) before culture. After 4 days, additional GM-CSF (10 ng/ml) was added and used for the experiment on days 6–7. GM-BMCs were treated with HCQ (100 μM) or cGAMP (5 μg/ml) for the indicated time periods and subjected to RNA-seq analysis.

first: Yusuke

last: Wada

first: Tatsuma

last: Ban

first: Tomoya

last: Hayashi

first: Ken

last: Ishii


title: Post-COVID impairment of memory T cell responses to community-acquired pathogens can be rectified by activating cellular metabolism

city: Chicago

first: Lavanya

last: Visvabharathy

state: IL

address: 5812 S. Ellis Ave.

department: Surgery

institute: University of Chicago

summary: Infection rates involving bacterial and viral pathogens have increased precipitously after the COVID-19 pandemic. While it has been speculated that higher infection rates resulted from increased hospitalizations throughout the pandemic or greater use of antibiotics, precisely why rates remain high today has remained unexplained. Mitochondrial dysfunction is known to occur post-COVID and may disrupt immune responses. Within T cells, SARS-CoV-2 infection is linked to low mitochondrial membrane potential, increased mitochondrial apoptosis, and decreased mitochondrial respiration, which together impact cellular activation and function beyond the acute phase of illness. Here, we demonstrate that decreased mitochondrial function in T cells post-COVID may contribute to higher infection susceptibility by metabolically immobilizing T cell memory responses. Using donor-matched peripheral blood samples from 31 COVID-naïve individuals who subsequently contracted COVID-19, we tracked how influenza A (IAV), Staphylococcus aureus (SA), and Varicella-zoster virus (VZV) T memory cell responses are impacted by COVID-19 infection. We found that gene expression linked to T cell activation decreased but mitochondrial redox-pathway genes increased in CD4 memory T cells post-COVID. However, mitochondrial flux and reactive oxygen species production were limited in a plurality of post-COVID memory T cells after stimulation with IAV, SA, and VZV. Furthermore, we found a disordered relationship between memory T cell mobilization of glycolysis, fatty acid metabolism, and oxidative phosphorylation pathways post-COVID which was partially rescued by pharmacological activation of mitochondrial pathways within antigen-specific T cells. Collectively, these findings indicate that COVID-19 infection may have lasting effects on inhibiting T cell memory responses to commonly encountered community-acquired pathogens, with significant implications for the clinical care of immunologically vulnerable populations in the post-pandemic era.

overall_design: PBMCs from matched donors pre- and post-COVID were stimulated with overlapping peptides of VZV-Orf4 antigen overnight. CD4+CD45RO+ memory T cells were purified by negative selection and total RNA was isolated using the Qiagen RNEasy Mini kit. RNA was then sent to the NUSeq Core for library prep + sequencing.

first: Jason

last: Shapiro


title: Effect of GBA1 deficiency in human iPSC-derived dopaminergic neurons and astrocytes

city: Seattle

first: Colby

last: Samstag

state: WA

address: 300 Ninth Ave

institute: University of Washington

summary: Mutations in the gene glucosidase, beta acid 1 (GBA1) are the strongest genetic risk factor for Parkinson’s disease (PD) and associate with faster disease progression.  GBA1 is expressed in all cell types of the central nervous system, with some evidence supporting higher expression in glial cells than neurons.  To elucidate possible divergent functions in neurons versus glia, we differentiated human iPSCs generated from an individual with PD heterozygous for the GBA1 pathogenic null variant IVS2+1 (GBA1IVS/+),Mutations in the gene glucosidase, beta acid 1 (GBA1) are the strongest genetic risk factor for Parkinson’s disease (PD) and associate with faster disease progression.  GBA1 is expressed in all cell types of the central nervous system, with some evidence supporting higher expression in glial cells than neurons.  To elucidate possible divergent functions in neurons versus glia, we generated human iPSCs from fibroblasts from an individual with PD carrying the GBA1 c.115+1 G>A, also known as IVS2+1 G>A variant (GBA1IVS/+). This intronic GBA1 variant is associated with severe neuronopathic Gaucher’s disease and interrupts the canonical splice site following exon 2, leading to nonsense mediated decay and is therefore considered a null allele.  An isogenic GBA1+/+ Rev control was generated by CRISPR/Cas9 genome editing to revert the GBA1 IVS2+1 G>A variant back to wildtype, and in the genome editing process, an iPSC clone homozygous for GBA1 IVS2+1 G>A was also generated (GBA1IVS/IVS). A matched control iPSC clone that remained unedited after CRISPR/Cas9 genome editing, maintaining heterozygosity for GBA1 IVS2+1 G>A, was also isolated (GBA1IVS/+ A4).Transcriptomic analysis of GBA1-deficient neurons and astrocytes revealed cell-type specific profiles. GBA1deficiency in neurons downregulated genes associated with immune response and upregulation of cholesterol synthesis, while GBA1 deficiency in astrocytes downregulated genes associated with translation and upregulated genes involved in extracellular matrix biogenesis, suggestive of gliosis. The transcriptomic profile of GBA1-deficient astrocytes was consistent with neurotoxic reactive astrocytes. Together, these findings indicate that GBA1deficiency has cell type-specific effects, where neurons have increased vulnerability to alterations in endolysosomal trafficking leading to α-synucleinopathy while GBA1 deficiency in astrocytes leads to increased neurotoxic reactivity but not impairment in endolysosomal trafficking and development of a-synuclein pathology.

overall_design: RNAseq profiling of dopaminergic neurons and astrocytes differentiatied from 3 iPSC clones generated from an individual with Parkinson's disease heterozygous for the GBA1 c.115+1G>A (IVS2+1), 1 clone homozygous for GBA1 IVS2+1 that is isogenic to the hereozygous GBA1 IVS2+1 clones, 1 clone with wildtype GBA1 that is isogenic to the heterozygous IVS2+1 clones, 1 clone isogenic to the heterozygous IVS2+1 clones that underwent the same CRISPR/Cas9 gene editing process that resulted in the homozygous GBA1 IVS2+1 clone and the GBA1 WT clone but was not edited by CRISPR/Cas9, and 3 iPSC clones generated from a healthy age- and sex-matched individual unrelated to the individual with Parkinson's disease heterozygous for GBA1 IVS2+1.

first: Marie

middle: Y

last: Davis


title: Wnt/β-catenin signaling restrains developmental beige adipocyte thermogenesis and its inhibition imprints long-term energy expenditure_Inguinal white adipose tissue (iWAT) from 4-week-old male mice

first: Ganran

last: Xu


title: Single-cell gene expression profiles of GM-CSF cultured bone marrow cells treated with HCQ or cGAMP.

summary: We performed single-cell RNA sequencing (scRNA-seq) of granulocyte-macrophage colony-stimulating factor (GM-CSF) cultured bone marrow cells (GM-BMCs) treated with hydroxychloroquine (HCQ) or cyclic guanosine monophosphate–adenosine monophosphate (cGAMP) to reveal a divergence of the gene expression pattern in interferon β (IFNβ)-expressing cells between HCQ and cGAMP treatments.

overall_design: Bone marrow cells were isolated from the legs of mice and cultured in RPMI 1640 (Nacalai Tesque, Kyoto, Japan) containing 10% foetal bovine serum (FBS) (Sigma-Aldrich, St. Louis, MO, USA) and 10 ng/ml of GM-CSF (PeproTech, Cranbury, NJ, USA). Red blood cells (RBCs) were lysed with RBC lysis buffer (Thermo Fisher Scientific, Waltham, MA, USA) before culture. After 4 days, additional GM-CSF (10 ng/ml) was added and used for the experiment on days 6–7. GM-BMCs were treated with HCQ (100 μM) or cGAMP (5 μg/ml) for 6 h and subjected to scRNA-seq analysis.


title: Genetic inactivation of the Translin/Trax RNase activity alters small RNAs including miRNAs, disrupts gene expression and impairs distinct forms of hippocampal synaptic plasticity and memory

city: Iowa City

first: Junko

last: Kasuya

state: IA

address: 169 Newton Rd

department: Neuroscience and Pharmacology

institute: University of Iowa

overall_design: Refer to individual Series


title: Single-cell gene expression profiles of lung cells from HCQ-treated mice.

summary: We performed single-cell RNA sequencing (scRNA-seq) of lung cells from hydroxychloroquine (HCQ)-treated mice to examine HCQ-induced IFN-I response in the lung.

overall_design: Mice were treated with 50 mg/kg of HCQ (TCI) on days 0, 1, and 2. Lungs were harvested on day 3, lung cells were isolated using the gentleMACS Dissociator (Miltenyi Biotec) according to the manufacturer’s standard protocol, and the cells were subjected to scRNA-seq analysis.


title: Genetic inactivation of the Translin/Trax RNase activity alters small RNAs including miRNAs, disrupts gene expression and impairs distinct forms of hippocampal synaptic plasticity and memory [Trax bulk mRNAseq]

summary: Neurons utilize RNA interference in the reversible translational repression of synaptically localized mRNAs, enabling rapid translation in response to synaptic activity. Two evolutionarily conserved proteins, Translin and Trax, form an RNase complex which processes miRNAs, tRNAs and siRNAs. To determine the specific role of the RNase activity of this complex in brain function, we employed a mouse line harboring a point mutation in Trax (E126A) that renders the Translin/Trax RNase inactive. At the molecular level, we found alterations in the levels of multiple small RNAs including miRNAs, tsRNAs and substantial downregulation of gene expression at the mRNA level in the hippocampus of TraxE126A mice. At the synaptic level, TraxE126A mice exhibit deficits in specific forms of long-term hippocampal synaptic plasticity. At the behavioral level, TraxE126A mice display impaired long-term spatial memory and altered open-field and acoustic-startle behavior. These studies reveal the functional role of Translin/Trax RNase in the mammalian brain.

overall_design: Hippocampal mRNA-seq profiling of 14-17 weeks old Trax[E126A] mutant was compared to their control littermates.

first: Mahesh

middle: S

last: Shetty

first: Xiuping

last: Fu

first: Marisol

last: Lauffer

first: Satya

middle: M

last: Tadinada

first: Tania

last: Chatterjee Chowdhury

first: Jay

last: Baraban

first: Ted

last: Abel


title: Effect of recombinant human CD26/DPPIV protein or Sitagliptin (DPPIV enzyme inhibitor) on CD3 T cells at day 2 after in vitro cell culture

city: Hefei

first: Liang

last: Wang

state: Anhui

address: 96 Jinzhai Road

institute: University of Science and Technology of China

summary: To examine the impacts of recombinant human CD26/DPPIV protein and Sitagliptin on donor T-cell activation

overall_design: we performed in vitro cell culture assays on T cells selected from PBMCs of healthy donor by adding PHA-L (1.25 μg/mL, control group), PHA-L + recombinant human CD26/DPPIV protein (1000 ng/mL, sCD26 group) or PHA-L + Sitagliptin (DPPIV enzyme inhibitor, 200 μg/mL, Sitagliptin group) for 2 days

first: Yue

last: Wu

first: Yiwen

last: Hou

first: Xiaoyu

last: Zhu

first: Cheng

last: Zhan


title: Shared cellular characteristics of dysfunctional stromal cell differentiation underpin impaired healing in two models of perturbed fracture healing

city: Ann Arbor

first: Kurt

last: Hankenson

state: MI

address: 109 Zina Pitcher Pl.

department: Department of Orthopaedic Surgery

institute: University of Michigan

summary: 10% of the fifteen million bone fractures each year that occur in the US fail to heal, which leads to significant loss of function, morbidity, and mortality. However, very little is known about the cellular and molecular mechanisms underpinning inferior healing. Two perturbed fracture models, surgically induced ischemia and the genetic deletion of the self-antigen CD47, were studied to identify unifying cellular and molecular mechanisms. C57Bl/6 wild-type (WT) mice with intact vasculature (WT Intact), WT mice with induced ischemia (WT Ischemic), and CD47-null mice with intact vasculature (CD47-KO) underwent transverse tibial fractures. Single-cell RNA-sequencing (scRNAseq) was performed during the inflammatory stage  (4 days post-fracture) and the stromal stage (7 days post fracture) to assess transcriptomic alterations in perturbed fracture calluses.

overall_design: Tibial fractures were performed at 18(±2) weeks of age in C57 Bl/6 mice. A hypodermic needle was first placed as an intramedullary nail followed by tibial fracture using a three-point bend apparatus. Alternatively, mice underwent ischemic fracture by isolation and ligation of the left femoral artery prior to fracture described above. We additionally fractured CD47-null mice on a Bl/6 background. Fracture calluses were harvested at 4 and 7 days post fracture. Periosteum was harvested as well from uninjured WT and CD47-null mice. This represents 8 conditions (1) WT intact vasculature 4 days post-fracture, (2) WT Ischemic 4 days post-fracture, (3) CD47-null intact vasculature 4 days post-fracture, (4) WT intact vasculature 7 days post-fracture, (5) WT Ischemic 7 days post-fracture, (6) CD47-null intact vasculature 7 days post-fracture, (7) WT periosteum, and (8) CD47-null periosteum. For each fracture condition, we sequenced a single biological replicate made up of 8 pooled calluses (equal male/female).

first: Christina

middle: A

last: Capobianco

first: Michelle

last: Song

first: Easton

last: Farrell

first: Alexander

last: Knights

first: Karen

last: Kessell

first: Alexis

last: Donneys

first: Tristan

last: Maerz

middle: D


title: SOX4 regulates STAT6 to modulate MTHFD2 Expression and Impacts Drug Resistance in Hepatocellular Carcinoma

city: Taoyuan

first: Jang-Hau

last: Lian

address: No. 5, Fuxing Street

country: Taiwan

institute: Chang Gung Memorial Hospital

type: Methylation profiling by high throughput sequencing

summary: SOX4 overexpression in hepatocellular carcinoma (HCC) is linked to poor prognosis, modulating gene expression via epigenetic mechanisms. This study reveals SOX4 interacts with DNA demethylases to reduce STAT6 promoter methylation, enhancing STAT6 transcripts. SOX4-STAT6 regulates MTHFD2, critical for NADPH and purine synthesis. Elevated SOX4, STAT6, and MTHFD2 levels correlate with immunotherapy resistance and poor outcomes in HCC. Targeting STAT6 and MTHFD2 in TKI-resistant HCC tumors suppressed growth, highlighting the therapeutic potential of disrupting the SOX4/STAT6/MTHFD2 axis in HCC progression and drug resistance.

overall_design: Analyze the DNA methylation sequence of Hep3B and Hep3B SOX4 knockout cells to understand how SOX4 regulates gene expression through DNA methylation.

first: Chia-Lung

last: Tsai

first: Ming-Chin

last: Yu

first: Chi-Neu


title: Genetic inactivation of the Translin/Trax RNase activity alters small RNAs including miRNAs, disrupts gene expression and impairs distinct forms of hippocampal synaptic plasticity and memory [Trax microRNAseq]

first: Junko

last: Kasuya

overall_design: hippocampal microRNA-seq profiling of 14-17 weeks old Trax[E126A] mutant mice was compared to their control littermates.

first: Mahesh

last: Shetty

first: Xiuping

last: Fu

first: Marisol

last: Lauffer

first: Satya

last: Tadinada

first: Tania

last: Chatterjee Chowdhury

first: Jay

last: Baraban

first: Ted

last: Abel


title: Cocaine, via ΔFosB, remodels gene expression and excitability in ventral hippocampus

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Ventral hippocampus (vHPC) CA1 pyramidal neurons send glutamatergic projections to nucleus accumbens (NAc), and this vHPC-NAc circuit mediates cocaine seeking and reward, but it is unclear whether vHPC-NAc neuron properties are modulated by cocaine exposure to drive subsequent behavior. The immediate early gene transcription factor ΔFosB is induced throughout the brain by cocaine and is critical for cocaine seeking, but it’s function in vHPC-NAc neurons is not understood. We now show that circuit-specific knockout of ΔFosB in vHPC-NAc neurons impaired cocaine reward expression and forced abstinence-induced seeking. We also found that vHPC-NAc excitability was decreased by experimenter-administered repeated cocaine and cocaine self-administration, and this cocaine-induced excitability decrease was mediated by ΔFosB expression. To uncover the mechanism of this change in circuit function, we used circuit-specific translating ribosome affinity purification (TRAP) to assess cocaine-induced, ΔFosB-dependent changes in gene expression in vHPC-NAc. We found that cocaine causes a ΔFosB-dependent increase in the expression of calreticulin, an ER-resident calcium-buffering protein. Calreticulin expression mediated vHPC-NAc excitability and was necessary for cocaine reward. These findings uncover a novel, non-canonical mechanism by which cocaine increases calreticulin in vHPC leading to decreased vHPC-NAc excitability and drive cocaine seeking and reward.

overall_design: TRAP experiment conducted on saline/coc/cocFlox groups

first: Andrew L.

last: Eagle

first: Marie A.

last: Doyle

first: Chiho

last: Sugimoto

first: Megan

last: Dykstra

first: Hayley M.

last: Kuhn

first: Ian

last: Maze

first: Michelle S.

last: Mazei-Robison

first: Alfred J.

last: Robison


title: Replication Timing Uncovers a Novel Two-Compartment Arrangement of Maize Interphase Euchromatin.

city: Tallahassee

first: Hank

last: Bass

state: FL

address: 222 S Copeland St

department: Biological Sciences

institute: Florida State University

summary: The time within S phase when a given genomic region replicates is measurable and referred to as Replication Timing (RT). We previously proposed a "mini-domain" chromatin fiber RT model for maize euchromatin's spatial architecture. 3D quantitative cytology showed that euchromatin is subdivided into two compartments during S-phase, distinguished by chromatin condensation and replication timing: Early-S and Middle-S. A key gap remains in understanding whether this compartmentalization is a general feature throughout the cell cycle, which could greatly impact our knowledge of genome architecture and gene regulation. To investigate this, we conducted two orthogonal assays, Hi-C for genome-wide interaction data and 3D FISH for direct visualization of chromatin organization. The Hi-C-derived eigenvalues and insulation scores significantly concord with Early-S and Middle-S regions. Early-S regions showed negative insulation scores with more long-range contacts, whereas Middle-S regions displayed the opposite, positive insulation scores with fewer long-range contacts. Compared to Middle-S regions, the Early-S regions showed much stronger correlations with epigenomic signatures of open and transcriptionally active chromatin. Oligo FISH painting with RT-specific probes demonstrated that Early-S and Middle-S regions occupied adjacent but largely non-overlapping nucleoplasmic regions throughout all stages of interphase, including G1. These findings validate our model while establishing that the global "A" compartment of euchromatin actually consists of two spatially and epigenetically distinct substructures – now referred to as Early-S and Middle-S compartments. Given the strong correlation between replication timing and Hi-C data from root tips, we examined the conservation of Hi-C architecture in both root tip and earshoot tissues and found them to be remarkably similar. Overall, our findings highlight the importance of replication timing as a conserved feature of chromatin architecture, reflecting broader principles of genome organization.

overall_design: Hi-C experiment in maize root tip and earshoot

first: Hafiza-Sara

last: Akram

first: Emily

middle: E

last: Wear

first: Leigh

last: Mickelson-Young

first: Zachary

last: Turpin

first: Linda

last: Hanley-Bowdoin

first: William

last: Thompson

first: Lorenzo

last: Concia

middle: W


title: Lysine-specific histone demethylase 1A (KDM1A/LSD1) inhibition attenuates DNA double strand break repair and augments efficacy of temozolomide in glioblastoma II

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

summary: Patient-derived primary GSCs were established from discarded specimens obtained from glioblastoma (GBM) patients undergoing surgery at UT Health San Antonio. We examined global transcriptional changes by RNA-sequencing using patient derived glioma stem cells (GSCs) treated with either vehicle, KDM1A inhibitor (NCD38) or temozolomide (TMZ) , or combination of NCD38+TMZ. Patient-derived GSCs (GSC082209) were treated with vehicle or NCD38 (3 µM) or TMZ (50 µM) or NCD38+TMZ for 24 hours. The RNA was isolated and utilized for RNA-seq analysis.

overall_design: Patient derived GSC08 cells were treated with vehicle or NCD38 (3 µM) or TMZ (50 µM) or NCD38+TMZ for 24 hours. The RNA was isolated and utilized for RNA-seq analysis.  Total RNA was isolated using RNeasy mini kit according to the manufacturer's instructions (Qiagen, Valencia, CA).  Illumina TruSeq RNA Sample Preparation was performed following the manufacturer's protocol. Samples were run on an Illumina HiSeq 3000 in duplicate. The combined raw reads were aligned to UCSC hg19, and genes were annotated by Tophat. Genes were annotated and quantified by the HTSeq-DESeq pipeline.

first: Salvador

last: Alejo

first: Yidong

last: Chen

first: Gangadhara

last: Sareddy


title: Nanobody-tethered transposition for dual profiling of chromatin accessibility and DNA methylation

city: guagnzhou

first: tang

last: guorun

address: xingang

institute: Sun Yat-sen University

summary: DNA methylation and histone modifications are critical epigenetic regulators that orchestrate gene expression and modulate various physiological and pathological processes. However, existing methodologies for simultaneous profiling of these epigenetic marks often require high cell input and suffer from data loss due to bisulfite conversion. In this study, we present advanced multimodal chromatin profiling methods, MethylTag and Multi-MethylTag, that address these challenges by integrating Tn5 transposase with methylated adaptors and optimizing post-bisulfite library preparation. These methods enable high-resolution, multi-dimensional chromatin profiling with reduced cell input and improved data integrity. We validated these techniques in various human and mouse cell lines, revealing complex interactions between DNA methylation and histone modifications. Our findings highlight the utility of these approaches in enhancing epigenetic research and deepening our understanding of the regulatory mechanisms underlying gene expression.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: In the 5mC-CUT&Tag method, Tn5 transposase is coupled with protein A/G (pA/G-Tn5) and preloaded with methylated P5 adaptors30. This pA/G-Tn5 complex is directed to specific histone modifications via primary and secondary antibodies, facilitating the incorporation of methylated P5 adaptors at the 5’ ends of nearby DNA fragments. During the subsequent bisulfite treatment, unmethylated cytosines (C) are converted to uracils (read as thymine (T) during sequencing), while 5-methylcytosines (5mC) and the methylated adaptors remain unchanged. Post-bisulfite treatment, the ligation of the 3’ adaptor ensures that the library can be efficiently amplified by PCR, which reduces the high duplication rates and information loss often caused by DNA template breakage during bisulfite conversion. Additionally, fragmented λDNA with methylated adaptors is included as a spike-in control before bisulfite treatment to monitor the C-to-T conversion rate without affecting the amplification and sequencing.

first: Jizhou

last: Liu

first: Guorun

last: Tang

first: Ziang

last: Lu

first: Zhiying

last: Wang

first: Yelin

last: Lan

first: Guanzheng

last: Luo

first: Xiaocheng

last: Weng

first: Yafen

first: Xiang

last: Zhou

first: Jindi


title: Lysine-specific histone demethylase 1A (KDM1A/LSD1) inhibition attenuates DNA double strand break repair and augments efficacy of temozolomide in glioblastoma

summary: Patient-derived primary GSCs (GSC082209) were established from discarded specimens obtained from glioblastoma (GBM) patients undergoing surgery at UT Health San Antonio. We examined global transcriptional changes by RNA-sequencing using patient derived glioma stem cells (GSCs) that are transduced with KDM1A gRNA to knockout KDM1A. For KDM1A knockout, Scramble  and KDM1A-specific gRNA  were transduced into GSCs possessing TET-inducible Cas9. Cas9 stimulation was done by treating GSCs with 50 ng/mL doxycycline for 14 days, after which cells were validated for KDM1A knockout.The RNA was isolated and utilized for RNA-seq analysis.

overall_design: KDM1A knockout (KO) GSCs were generated using CRISPR/Cas9 system. Total RNA was isolated using RNeasy mini kit according to the manufacturer's instructions (Qiagen, Valencia, CA).  Illumina TruSeq RNA Sample Preparation was performed following the manufacturer's protocol. Samples were run on an Illumina HiSeq 3000 in duplicate. The combined raw reads were aligned to UCSC hg19, and genes were annotated by Tophat. Genes were annotated and quantified by the HTSeq-DESeq pipeline.


title: Molecular characterization of patient derived glioblastoma cell line

summary: Patient-derived primary GSCs (GSC082209) was established from discarded specimens obtained from glioblastoma (GBM) patient undergoing surgery at UT Health San Antonio. The specimens were collected in accordance with the Declaration of Helsinki and approved by the Institutional Review Board (or Ethics Committee) of UT Health San Antonio. Patients provided informed consent for surgery and use of their tissues for research. Deidentified fresh tissue was collected intraoperatively, dispersed into single cells, and cultured briefly in a neurobasal media for expansion and purification followed by intracranial injection in nude mice. Patient derived GSCs were cultured as neurospheres in neurobasal medium (Invitrogen, Carlsbad, CA) supplemented with B27 serum-free supplement, EGF (20 ng/mL), bFGF (20 ng/mL), LIF (10 ng/mL) and heparin (5 µg/mL). The RNA was isolated and utilized for RNA-seq analysis. GSC082209 was subtyped based on established TCGA gene expression-based molecular classifications.

overall_design: Total RNA from GSC082209 cells was isolated using RNeasy mini kit according to the manufacturer's instructions (Qiagen, Valencia, CA).  Illumina TruSeq RNA Sample Preparation was performed following the manufacturer's protocol. Samples were run on an Illumina HiSeq 3000. The combined raw reads were aligned to UCSC hg19, and genes were annotated by Tophat. Genes were annotated and quantified by the HTSeq-DESeq pipeline.


title: A Prevalent Disease-Associated SNP in the Human ID3 Gene Regulates E-Protein Activity and Cellular Proliferation [VMSC RNA-Seq]

status: Public on Jan 09 2026

city: Charlottesville

first: Brett

last: Ransegnola

state: VA

address: 755 Walker Square, Apt 2D

institute: UVA SOM

summary: The helix-loop-helix transcription factor ID3 is a critical regulator of tissue development and homeostasis. Aberrations in ID3 are strongly associated with numerous human disease processes including Burkitt’s lymphoma. We previously identified that a single nucleotide polymorphism (SNP) in ID3 at rs11574 is associated with increased vascular disease burden in three independent cohorts; however, the mechanisms by which this SNP alters ID3 function and impacts vascular cells are unknown. Here, we show that the minor allele of rs11574 specifically disrupts ID3’s ability to bind the E-protein E12. Computational analysis and confirmatory biochemical experiments revealed that rs11574’s effects on ID3:E12 dimerization are dependent upon a key residue within E12’s unique loop domain. Functionally, the disruption of ID3:E12 binding promotes E12 binding to and activation of the p21 promoter. Isogenic human cell lines harboring the rs11574 minor allele exhibited decreased cell proliferation and altered expression of genes involved in proliferation. RNAseq revealed distinct roles for E12 and E47 in transcriptional regulation of vascular smooth muscle cells (VSMCs). Primary human VSMCs from subjects with the rs11574 minor allele exhibited reduced mitogen-stimulated proliferation. Taken together, these results provide the first characterization of altered molecular and cellular functions of this disease-associated SNP in ID3 at rs11574.

overall_design: Bulk mRNAseq of primary murine vascular smooth muscle cells WT/KO for E12 and WT/KO for E47. n=2 independent extractions. Cells were revived from cryorecovery and lysed for RNAseq in Trizol.

first: Christopher

last: Henderson

first: James

last: Garmey

first: Ali

last: Khan

first: Rédouane

last: Aherrahrou

first: Michael

last: Purdy

first: Shijie

last: Wu

first: Andrea

first: Jennifer

last: Kirby

last: Lipinski

first: Vicki

last: Gordon

first: Mark

last: Yeager

first: Mete

last: Civelek

first: Coleen

last: McNamara


title: Downstream genes and pathways of PPT1 in hepatocellular carcinoma

city: Wuhan

first: Xing-Xing

last: He

state: Hubei

address: 1095# Jie-Fang Avenue

department: Institute of Liver and Gastrointestinal Diseases

institute: Tongji Hospital

summary: To explore the mechanism and downstream pathways of PPT1 in hepatocellular carcinoma (HCC). We performed microarray assay to identify the downstream genes of PPT1. As a result, we obtained 476 (291 upregulation and 185 downregulation) differentially expressed genes significantly affected by PPT1 knockdown. Function enrichment analysis showed that these genes were enriched in “cell metabolism” and “signal transduction” pathways which are possibly related with lysosomal function. Real-time quantitative RT-PCR was performed to verify the microarray results. In conclusion, the expression profile of many genes were significantly affected by PPT1 knockdown, which helps to further explore the mechanism of the effects of PPT1 in HCC.

overall_design: PLC/PRF/5 cells transfected with si-PPT1 -1 or siRNA-NC were used to synthesize double-stranded complementary DNA (cDNA), which was labeled and hybridized on the SurePrint G3 Human Gene Expression Microarray 8×60K v2 (Agilent Technologies, Santa Clara, CA, USA). Processed slides were scanned with the Agilent G2565CA Microarray Scanner (Agilent Technologies) after hybridization and washing. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed lncRNAs and mRNAs between two samples were identified through Fold Change filtering and Student’s t-test. The normalized intensity for each lncRNA and mRNA was presented as a log2-transformed pattern, fold changes >2 and p-values <0.05 were selected as significantly differentially expressed.

first: Jiao

last: Bao

first: Xiang-Yuan

first: Yun

last: Gan

first: Meng-Die

last: Cao

first: Yuan

last: Yuan


title: Post-transcriptional regulation of proliferation and quiescence

city: Glasgow

first: Holly

last: Hall

address: Garscube Estate, Switchback Road, Bearsden

country: United Kingdom

institute: Cancer Research UK Scotland Institute

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


title: Stiffness sensing fuels matrix-driven metabolic reboot for kidney repair and regeneration [Visium]

city: Pittsburgh

first: Shuchang

last: Liu

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: Kidney repair after acute kidney injury (AKI) relies on a finely tuned extracellular matrix (ECM) that provides both structural integrity and mechanical cues. As primary ECM architects, fibroblasts and pericytes rapidly mobilize to the injury site post-AKI, yet the ECM-driven repair mechanisms remain inadequately understood. Leveraging data-independent acquisition-based proteomics, spatial transcriptomics, genetic and pharmaceutical models, and tissue engineering, we profiled the proteome landscape of decellularized kidney matrix scaffold post-AKI and highlighted microfibrillar-associated protein 2 (Mfap2) as a key core matrisome component. Sourced primarily from fibroblasts and pericytes, Mfap2 loss disrupts kidney architecture and metabolic balance, aggravating AKI. Global proteomics revealed that Mfap2 knockout downregulates tubule-derived 3-hydroxy-3-methylglutaryl-CoA synthase 2 (Hmgcs2) via estrogen receptor 2 (Esr2)-mediated transcriptional repression and elevated post-translational succinylation. Phosphoproteomics further uncovered a shift in mechanical signaling, where Mfap2 deficiency hyperactivates mitogen-activated protein kinases, driving large tumor suppressor kinase 1 (Lats1) in tubular cells without altering integrin receptor activity. Mechanistically, Lats1 suppression amplifies Esr2 transcription without affecting its ubiquitin-mediated degradation, functioning independently of the canonical Yap/Taz signaling. Remarkably, Esr2 agonists restored kidney function in Mfap2-deficient models. These findings position Mfap2 as a key regulator of ECM stiffness and mechanical signaling, orchestrating metabolic reprogramming and a pro-repair microenvironment essential for kidney repair and regeneration.

overall_design: Heterozygous Mfap2 mice (Product name: S-KO-03113, Strain name: C57BL/6JCya-Mfap2em1) were obtained from Cyagen (Santa Clara, CA). Male and female Mfap2 heterozygous mice were mated to generate Mfap2-wild type (WT) and Mfap2-knockout (KO) offspring. Kidney MFAP2 WT slide and MFAP2 KO slide were pooled into one spatial transcritpomics imaging for analysis.

last: Gui

first: Yuanyuan

last: Wang

first: Wenxue

last: Li

first: Jia-Jun

first: Kelly

last: Zheng

first: Jianzhong

first: Henry Wells

last: Shaffer

first: Cameron

last: Jones

first: Samantha Mae

last: Mallari

first: Yanbao

last: Yu

first: Silvia

first: Yansheng

first: Dong

last: Zhou


title: Post-transcriptional regulation of proliferation and quiescence (total_RNAseq)

summary: mRNA profiles of proliferating and quiescent human fibroblasts


title: DAXX governs the silencing of LINE1 during spermatogenesis in mice [RNA-seq]

first: shen

last: jin

address: No. 299, Bayi Road, Wuchang District, Wuhan City

institute: Wuhan university

summary: The suppression of transposable elements in germline is critical for safeguarding fertility. Here we identify that the DAXX, a potent transcription repressor and an H3.3 chaperone, is indispensable for transposable elements silencing during spermatogenesis. Male mice with conditional knockout of Daxx in germ cells mediated by Ddx4-cre display delayed meiotic progression, deformed and reduced production of sperms, and an age-dependent decline in fertility. The ablation of DAXX results in activation of evolutionarily young LINE1 and ERVs subfamilies. Further study found that reduced H3K9me3 modification and DNA methylation of young LINE1, especially L1Md_A, L1Md_Tf and L1Md_Gf.In summary, this study identifies DAXX as a previously unknown regulator of spermatogenesis and demonstrates that it functions as an epigenetic regulator to maintain the silencing of the young LINE1

overall_design: This study aims to perform RNA-seq profiling to compare the testes of p8 wild-type mice and their knockdown counterparts, thereby exploring gene expression changes during meiosis and sperm development.

first: Zejia

first: Chaoyang

last: Xiong

first: Jin

last: Shen

first: Chen

last: Tan

first: Dupeng

last: Ma

first: Jun

last: Chen

first: Rong

first: Qi

last: Sun

first: Weihao

last: Gong

first: Wenming

first: Mengya

last: Huang

first: Li

first: Yueqiu

first: Guohong

first: Mengcheng

last: Luo


title: A Prevalent Disease-Associated SNP in the Human ID3 Gene Regulates E-Protein Activity and Cellular Proliferation [HEK293T RNA-Seq]

first: Brett

last: Ransegnola

overall_design: Bulk mRNAseq of HEK293T cell lines either homozygous for the major allele of rs11574 (maj/maj), homozygous for the minor allele/risk allele (min/min) or heterozygous (HET) 48hr after release from 24hr serum starvation.

first: Christopher

last: Henderson

first: James

last: Garmey

first: Ali

last: Khan

first: Rédouane

last: Aherrahrou

first: Michael

last: Purdy

first: Shijie

last: Wu

first: Andrea

first: Jennifer

last: Kirby

last: Lipinski

first: Vicki

last: Gordon

first: Mark

last: Yeager

first: Mete

last: Civelek

first: Coleen

last: McNamara


title: Post-transcriptional regulation of proliferation and quiescence (mRNAdecay)

first: Holly

last: Hall

overall_design: For serum starvation growth conditions cells were seed one day prior to serum starvation. Cells were washed twice with PBS and the media replaced with either 10% or 0% FBS containing DMEM for 72 hours. proliferating and quiescent cells were incubated for nine hours in complete medium containing 100 µM s4U. This medium was exchanged every three hours. The chase consisted of two PBS washes and replacement of complete media supplemented with 1 mM uridine. Cells were harvested with direct application of Trizol reagent at hours 0, 2, 4 and 8 post-removal of s4U. Samples with and without treatment of IAA were collected, to ensure baseline mutation rate did not exceed IAA treatment. QuantSeq 3’mRNA-seq library were generated and sequenced. The resulting data was processed using SLAMdunk pipeline. Three biological replicates of both proliferating and quiescent samples were processed for each indicated timepoint.


title: Integrated chromatin and transcriptomic profiling reveals sex-specific mechanisms of gene regulation in hepatic nutrient responses

city: Los Angeles

first: Zhengyi

last: Zhang

address: Westwood

institute: UCLA

summary: The three-dimensional organizing of the genome plays an important role in cellular function. Alterations between open and closed chromatin states contributes to DNA binding, collaborative transcriptional activities and informs post-transcriptional processing. The liver is the primary site orchestrating metabolic control, needing to mount a rapid adaptive response to environmental challenges. Here, we leveraged ATAC-seq to interrogate the chromatin architecture in liver under different dietary cues. We mapped over 120,000 nucleosome peaks, revealing a remarkably preserved hepatic chromatin landscape across feeding conditions. Stringent analysis of nucleosome rearrangements, unexpectedly, nominated sex as the most dominant factor segregating changes in chromatin accessibility. Lipid-rich diet led to a more accessible chromatin confirmation at promoter regions in female mice along with enrichment of promoter binding CCAAT-binding domain proteins. Male liver exhibited stronger binding for nutrient sensing nuclear receptors. Integrative analysis with gene expression and lipid composition corroborates a role for chromatin states in informing functional differences in metabolic traits. We uncouple the influence of gonadal and sex-chromosomal factors using the Four Core Genotype mouse model. Leveraging our framework, we provide mechanistic evidence underlying the regulation for the critical sex-dimorphic GWAS gene, Pnpla3. In summary, we provide a comprehensive epigenetic resource in murine liver that uncovers the complexity of chromatin dynamics in response to diet and sex.

overall_design: Wild-type mice were obtained from The Jackson Laboratory and were fed ad libitum on either a standard chow diet, Western diet (WD: Research Diets, D12079B), or high-fat diet (HFD: Research Diets, D12492). For the ATAC-seq experiments, mice were subjected to diet treatments for 2 weeks. 75,000 nuclei were extracted and centrifuged at 500 g for 5 min at 4°C and used for the transposition reaction. ATAC-Seq libraries were constructed using the Nextera Tn5 Transposase and DNA library preparation kit (Illumina) as described (Buenrostro et al. 2015). We performed size selection usign AMPure XP magnetic beads. Libraries were sequenced at the Broad Stem Cell Research Center Sequencing Core (BSCRC) at UCLA.

first: Tamer

last: Sallam


title: TDP-43 dysfunction leads to the accumulation of cryptic transposable element-derived exons in iPSC derived neurons and ALS/FTD patient tissues [brain isoseq]

first: Oliver

last: Tam

address: 435 E 30th St

department: Institute for Systems Genetics

institute: NYU Grossman School of Medicine

summary: TDP-43 is an RNA and DNA binding protein that plays major roles in regulating RNA processing.  In particular, TDP-43 dysfunction leads to the accumulation of cryptic splice isoforms that result from improperly spliced mRNAs. In addition to its role in regulating splicing, TDP-43 is also known to regulate the expression of transposable elements (TEs). TEs are mobile genetic elements which comprise a significant proportion of the human genome, but are normally silenced in healthy somatic cells. TEs are interspersed throughout the genome, both in gene-depleted regions and interspersed within gene introns and gene regulatory sequences. We used optimized long-read RNA sequencing assays to generate catalogs of mis-spliced and mis-expressed genes and TEs in human neurons depleted for TDP-43. In addition to known TDP-43 driven cryptic isoforms, we identified hundreds of TDP-43 dependent spliced RNAs formed as part of cryptic gene-TE fusion events that result from mis-splicing of TE sequences into gene transcripts. Among these TDP-43 dependent gene-TE cryptic transcripts (crypTEs), we found: TEs that provide alternate gene promoters/5’UTRs, TEs that act as cassette exons inside host gene mRNAs, as well as TEs that provide alternate transcript 3’ ends. These cryptic gene-TE fusions are predicted to induce: aberrant expression of ALS relevant genes, nonsense mediated decay (NMD) products, as well as novel peptides from gene-TE fusions within the gene coding sequence. We further verified that many of these crypTE transcripts are detected in ALS/FTD cortical tissues with TDP-43 pathology. In short, TDP-43 dependent CrypTE events represent a large reservoir of ALS/FTD relevant transcripts and peptides that are not captured by standard assays and analyses.

overall_design: Long read RNA (Isoseq) libraries generated from 8 human donor prefrontal cortex samples (BA46), across a range of non-neuropathological sudden-death controls, ALS patients, and ALS patients who exhibit cognitive impairment on a standardized screening exam.

first: Isobel

last: Bolger

first: Regina

last: Shaw

first: Claudio

last: Roque

first: Chris

last: Jackson

first: Hemali

last: Phatnani

first: Molly

last: Gale Hammell


title: Metabolic surgery mitigates early kidney injury in obese youth with diabetes by suppressing mTORC1/JAK–STAT signaling

first: Phillip

middle: John

last: McCown

address: 1500 E. Medical Center Drive

department: Internal Medicine - Nephrology

institute: University of Michigan Medicine

summary: Background Youth with type 2 diabetes (T2D) and severe obesity face high risk of diabetic kidney disease, which metabolic bariatric surgery (MBS) can mitigate. This study explores structural and molecular changes in kidneys after vertical sleeve gastrectomy (VSG), a form of MBS. Methods Paired analyses, including metabolic profiling, kidney volume assessment, histological evaluation, and single-cell RNA sequencing (scRNAseq) on kidney biopsies from five youth with T2D and obesity pre- and 12 months post-VSG in the IMPROVE-T2D (Impact of Metabolic surgery on Pancreatic, Renal and cardiOVascular hEalth in youth with T2D) cohort. Circulating proteomics with kidney transcriptomics, were linked using data from an independent cohort of youth with obesity, with or without T2D, undergoing MBS in Teen-Longitudinal Assessment of Bariatric Surgery (Teen-LABS, n=64). Results Post-VSG, participants lost weight and had improvements in insulin sensitivity and metabolic parameters. Kidney changes included reduced renal hyperfiltration, total kidney volume, mesangial matrix area, and microalbuminuria. scRNAseq in proximal tubule (PT) and thick ascending limb cells indicated repression of glycolysis, gluconeogenesis, and tricarboxylic acid cycle genes, with upregulation of AMP-activated protein kinase (AMPK) and Forkhead box O3 (FOXO3). Decreased metabolic signaling aligned with reduced ribosomal phosphorylated S6K (pS6K), suggesting attenuated mTORC1 activity. JAK-STAT pathway activation in PT was diminished, correlating with lower circulating ligands from Teen-LABS proteomic data. Conclusion MBS/VSG prompts kidney molecular adaptations, providing potential targets for non-surgical interventions against obesity- and diabetes-associated kidney disease.

overall_design:
Single cell RNA-seq (scRNA-seq) datasets derived from 10x Genomics processing of segments of kidney biopsied material, preserved in CryoStor, were generated individually and then integrated with harmony-based integration in Seurat v4. Raw data not provided due to patient privacy concerns as a result of small sample size.

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

last: Menon

first: Abhijit

last: Naik

first: Fadhl

last: Alakwaa

first: Matthias

last: Kretzler

first: Petter

last: Bjornstad


title: RNA-binding proteins Zfp36l1 and Zfp36l2 protect against premature thymic involution.

city: North York

first: Vinothkumar

last: Rajan

state: ON

address: 2075 Bayview Ave, Room # M7-413

country: Canada

institute: Sunnybrook Research Institute

summary: The thymus is a primary lymphoid organ that undergoes progressive age-associated involution, leading to reduced T cell output and impaired adaptive immunity. In this study, we employed scRNA-Seq as well as other approaches to reveal that medullary thymic epithelial cells (mTECs) produce excessive proinflammatory cytokines in the absence of Zfp36l1 and Zfp36l2, two RNA-binding proteins of TTP family. Consequently, FOXN1, a master regulator of pro-lymphopoietic genes in thymic epithelial cells, was down-regulated in young mice, which leads to premature thymic involution in knockout mice. These findings reveal a protective role for TTP family proteins in regulating cytokine levels within the thymic microenvironment and preventing premature thymic involution.

overall_design: Thymic epithelial cells (TECs) from 3 postnatal day 6 conditional double knockout mice that specifically delete Zfp36l1 and Zfp36l2 in TECs and 3 floxed control mice were isolated by fluorescence-activated cell sorting (FACS) and analyzed by scRNA-Seq

first: Jianxun

last: Han

first: Juan Carlos

last: Zúñiga-Pflücker


title: LONP-1 deficiency causes dysregulated protein synthesis within mitochondria that is restored by mitoribosomal mutations

city: Worcester

first: Junhui

last: Li

state: MA

address: 364 Plantation St

institute: University of Massachusetts Medical School

summary: Mitochondrial homeostasis is maintained by multiple molecular chaperones and proteases located within the organelle. The mitochondrial matrix-localized protease LONP-1 degrades oxidatively damaged or misfolded proteins. Importantly, LONP-1 also regulates mitochondrial DNA replication. Here, we show that mutations in C. elegans that impair LONP-1 function cause dysregulation of mitochondrial DNA replication, mitochondrial RNA transcription and protein synthesis within the mitochondrial matrix. LONP-1 deficient worms had reduced levels of oxidative phosphorylation proteins despite increased mt-DNA encoded protein synthesis. Via a forward genetic screen, we identified three mutations that restored mitochondrial function and the rate of development in lonp-1 mutants to levels comparable to those in wildtype worms. Interestingly, all three suppressor mutations were found in genes encoding mitochondrial ribosome proteins. A point mutation in the small mitochondrial ribosome protein MRPS-38 restored oxidative phosphorylation in lonp-1 mutant worms. Combined, our results suggest that LONP-1 regulates mitochondrial protein synthesis and that the suppressor mutations within MRPS-38 or MRPS-15 enhance oxidative phosphorylation complex assembly by slowing translation.

overall_design: Worms were collected at the L4 stage. RNA was extracted using Trizol reagent.

first: Levi

last: Ali

first: Avijit

last: Mallick

first: Cole

last: Haynes


title: Heterogeneity and plasticity of the naive CD4+ T cell compartment [human CITEseq]

city: Lebanon

first: J. Louise

last: Lines

state: NH

address: DHMC

institute: Dartmouth College

summary: While naive CD4+ T cells have historically been considered a homogenous population, recent studies provide evidence that functional heterogeneity exists. Using scRNAseq, we identified five transcriptionally distinct naive CD4+ T cell subsets that emerge within the single positive stage in the thymus: a quiescence cluster (TQ), a memory-like cluster (TMEM), a TCR-reactive cluster (TTCR), an IFN-responsive cluster (TIFN), and an undifferentiated cluster (TUND). Elevated expression of transcription factors KLF2, Mx1, and Nur77 within the TQ, TIFN, and TTCR clusters, respectively, enabled enrichment of these subsets for functional validation. Sorted subsets displayed distinctive functional responses upon stimulation. Furthermore, treatment of mice with inflammatory stimuli reduced cytokine production of naive T cells ex vivo. In SLE patients, IFN-induced gene expression was markedly elevated within the TIFN cluster. Our data demonstrate that naive T cells are shaped by their host environment, with functional biases manifesting upon activation. These findings highlight the importance of understanding how naive T cell heterogeneity may be distorted in cancer, autoimmunity, and infectious diseases.

overall_design: naive CD4 T cells were enriched from mouse spleen, LN or blood by fluorescence activated cell sorting, and then were processed for scRNAseq.

first: Alia

last: Sajani

first: Evelien

last: Schaafsma

first: Walburga

last: Croteau

first: Mohamed

last: ElTanbouly

first: Elizabeth

middle: C

last: Nowak

first: Chao

last: Cheng

first: Christopher

last: Burns

first: Mary Jo

last: Turk

first: Randolph

last: Noelle

first: Louise


title: Heterogeneity and plasticity of the naive CD4+ T cell compartment [mouse CITEseq]


title: Heterogeneity and plasticity of the naive CD4+ T cell compartment [Bulk RNAseq]


title: NKG2D Upregulation Enhances T and NK Cell Cytotoxicity, Sensitizes Tumors to Combined αPD1 and αVEGF Therapy, and Contributes to Hearing Loss Prevention in Vestibular Schwannoma Model

city: Columbus

first: Long-Sheng

last: Chang

address: 575 Children's Crossroad

institute: Abigail Wexner Institute at Nationwide Children's Hospital

summary: Background: NF2-related schwannomatosis (NF2-SWN) is a debilitating condition that calls for robust treatment options. NF2-SWN is characterized by bilateral vestibular schwannomas (VSs), which grow over time and can result in irreversible sensorineural hearing loss, significantly affecting the quality of life for those affected. At present, there are no FDA-approved medications specifically for treating VS or related hearing loss. VS management involves radiotherapy or surgical resection, while bevacizumab, an anti-vascular endothelial growth factor monoclonal antibody (αVEGF), has been used off-label in NF2-SWN to shrink the tumor. However, not all patients respond and the effect is not always durable. There is a critical need for effective medications that can stop VS growth and associated hearing loss. While immune checkpoint inhibitors have transformed cancer therapy, their potential has not been thoroughly explored in non-malignant tumors such as VS. Methods: We characterize the effects of combined anti-programmed cell death protein-1 (αPD1) and αVEGF treatment on tumor growth and hearing function in two syngeneic, immune-competent VS models. Results: Combining αVEGF with αPD1 treatment significantly enhances the antitumor efficacy of each monotherapy. Specifically, i) αVEGF augments αPD1 efficacy by normalizing tumor vasculature to improve drug delivery and immune cell infiltration, and by activating the antitumor cytotoxicity of T and NK cells via NKG2D upregulation; and ii) combined αPD1 with αVEGF treatment effectively controls the growth of tumors that progressed despite αVEGF treatment. Conclusion: These findings provide a strong foundation for the αPD1 with αVEGF combination therapies to treat patients with NF2-SWN.

overall_design: Single cells were extracted from 3 NF2-mutated treatment-naïve schwannomas and 1 bevacizumab-treated schwannoma from an NF2 patient that was on bevacizumab for almost 10 years scRNA libraries were prepared using the 10x Genomics platform.

first: Natalie

last: Wu


title: Mineralocorticoid Receptor Antagonism Reduces Atrial Arrhythmias Post- Cardiac Surgery and Attenuates Atrial Stress Responses to Cardioplegic Arrest

city: Rochester

first: Ieng Lam

last: Lei

state: MN

address: 321 3rd Ave Sw

institute: Mayo Clinic

summary: We performed snRNA-seq in the left ventricle of human heart from normal control, AF patients, and perfused heart tissue after stored with HTK or HTK+canrenone

overall_design: Nuclei were isolated from the snap frozen tissues, and sequencing in Singleron Platform.

first: Ienglam

first: Paul

last: Tang


title: Targeting UGCG sensitizes AML cells to Venetoclax through RAB32-mediated endoplasmic reticulum-mitochondria communication

city: Guangzhou

first: hui

last: zeng

address: 106 Zhongshan 2nd Rd

institute: Guangdong Provincial People's Hospital

summary: UDP-glucose ceramide glucosyltransferase (UGCG) is an enzyme that glycosylates ceramide and blunts its pro-apoptotic activity in cancer cells. Targeting UGCG sensitizes solid cancer cells to chemotherapy. However, whether targeting UGCG can increase the sensitivity of AML cells to Venetoclax remains unclear. Here, we found that the inhibition of UGCG genetically or with its inhibitor Eliglustat efficiently suppressed growth and promoted apoptosis in AML cells. Moreover, Eliglustat in combination with Venetoclax increased apoptosis, reduced AML cell viability, and inhibited AML effectively both for primary AML cells and  xenograft models. Mechanistically, the combination induced ceramide accumulation which activated the endoplasmic reticulum (ER) stress-GRP78/PERK/CHOP axis. Interestingly, combinatory treatment activated RAB32, which led to mitochondrial fission through ER-mitochondria communication and DRP1 activation. These findings demonstrate that targeting UGCG in combination with Venetoclax is a new combinatory strategy to treat AML, and provide new insights for ceramide-mediated cell death in anti-cancer therapies.

overall_design: both including DMSO, 48 h ELI and ABT at the indicated concentrations alone or in combination treatment groups

first: Sun

last: Xiaofan

first: Li

last: Yue

first: Pan

last: Danqi

first: Du

last: Juan

first: Zeng

last: Hui


title: Multiplexed TrAEL-seq captures DNA replication dynamics in mammalian cells

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

summary: TrAEL-seq was used to detect replication forks and DSBs in PC9 and DLD1 cells in response to Hydroxyurea, DRB Triptolide, Cerelasertib or Palbociclib treatement.

overall_design: PC9 and DLD1 cells, untreated and treated with Hydroxyurea, DRB Triptolide, Cerelasertib or Palbociclib treatment.

first: Alex

last: Whale

first: Kieron

last: May

first: Jonathan

last: Houseley


title: Increased susceptibility to 4-HNE-induced toxicity and impaired development in a model of ALDH4A1 deficient pediatric epilepsy carrying the S352L variant

city: Stanford

first: Benjamin

last: Kraemer

address: 736 Serra Street

institute: Stanford University

summary: Certain human mutations in the mitochondrial aldehyde dehydrogenase 4A1 (ALDH4A1) lead to a severe, pediatric form of epilepsy and developmental abnormalities, yet the precise molecular mechanism leading to the clinical phenotypes remains unexplained. ALDH4A1 metabolizes glutamic-γ-semialdehyde (GSA). Mutations in ALDH4A1, which lead to inactive enzyme variants, cause GSA to accumulate and vitamin B6 inactivation. Patients with severe ALDH4A1 deficiency have pediatric epilepsy and are resistant to prescribed therapies. We develop knock-in cell culture and mouse models of the S352L variant to help characterize this human pathology. The knock-in models show that ALDH4A1 is necessary for clearing a non-canonical substrate, 4-hydroxynonenal (4-HNE) without becoming inactivated like the main clearance mechanism of 4-HNE, ALDH2, and that ALDH4A1 deficiency alters transcriptional profiles in genes that regulate brain development, including LGI1 and FOXB1. Protein levels including those in the proline metabolic pathway (e.g., spermine synthase) are also downregulated in both S352L iPSCs and the brains of S352L homozygous mice. This work identifies additional metabolic and transcriptional pathways regulated by ALDH4A1, and potential pathways that can be targeted to treat patients with ALDH4A1 deficiency.

overall_design: RNA-seq profiling of wildtype 802-30F iPS cells and their S352L homozygous KI counterparts under basal conditions.

first: Gwangbeom

last: Heo

first: Che-Hong

last: Chen

first: Daria

last: Mochly-Rosen


title: ACSL5 Mediates Adaptation to the Palmitic Acid-Enriched Pulmonary Microenvironment to Enhance Metastatic Breast Cancer Cell Survival and Lung Metastasis

city: Chongqing

first: Shaojie

last: Cheng

state: -- None selected --

address: No.1, Yi-Xue-Yuan Road, Yu-Zhong District

institute: Chongqing Medical University

summary: Metastasis accounts for 90% of cancer-related death. Distant metastasis follows a non-random pattern, termed “organotropism”, for instance, breast cancer (BC) preferentially metastasizes to the lung, bone, brain, and liver. The lung is a common site for BC metastasis, yet the underlying mechanisms and treatment strategies for lung metastasis remain unclear. To uncover the molecular mechanisms underlying the lung-tropic metastasis of breast tumors, we performed transcriptome sequencing on primary tumors and lung metastases.

overall_design: The transcriptome sequencing studies were performed by deep sequencing for HCC1806-LM3, HCC1806-PRI, LT1T2, PT1T2 and PT3 cells.

first: Shanchun

first: Chao

last: Chang

first: Xiaoqi

last: Liu

first: Manran


title: Gene expression in ACSL5-wildtype and ACSL5-deficient LM3 cells with PA treatment

summary: Metastasis accounts for 90% of cancer-related death. Distant metastasis follows a non-random pattern, termed “organotropism”. The lung is a common site for BC metastasis, yet the underlying mechanisms and treatment strategies for lung metastasis remain unclear.

overall_design: To investigate the role of ACSL5 mediate lung-tropic metastasis of breast tumors, we performed high-throughput sequencing in ACSL5-wildtype and ACSL5-deficient LM3 cells treated with or without PA.


title: TDP-43 dysfunction leads to the accumulation of cryptic transposable element-derived exons in iPSC derived neurons and ALS/FTD patient tissues [i3N RNAseq]

city: New York

first: Oliver

last: Tam

overall_design: Cortical neurons were induced from pluripotent stem cells (i3N), and were treated with sgRNA targeting TDP-43, 5-Azacytidine treatment, or both. RNA was collected from these i3N cultures and gene expression was compared.

first: Isobel

last: Bolger

first: Regina

last: Shaw

first: Kathryn

last: O'Neill

first: Karthick

last: Natarajan

first: Molly

last: Gale Hammell


title: Multiplexed TrAEL-seq captures DNA replication dynamics in mammalian cells [Bcells]

first: Laura

last: Biggins

summary: TrAEL-seq was used to detect DSBs in mouse B cells activated by treatment with Lipopolysaccharide (LPS)

overall_design: Untreated and LPS activated B cells

first: Alex

first: Claudia

last: Ribeiro de Almeida


title: TDP-43 dysfunction leads to the accumulation of cryptic transposable element-derived exons in iPSC derived neurons and ALS/FTD patient tissues [i3N isoseq]

overall_design: Cortical neurons were induced from pluripotent stem cells (i3N), and were treated with sgRNA targeting TDP-43, 5-Azacytidine treatment, or both. RNA was collected from these i3N cultures and sequenced to identify full length transcripts.