title: Gcn2 deficiency triggers anemia and hypoxic intolerance in zebrafish

status: Public on Jan 30 2026

city: Qingdao

first: Chengdong

last: Liu

state: Shandong

address: 5 Yushan Rd

country: China

institute: Ocean University of China

type: Expression profiling by high throughput sequencing

summary: The Integrated Stress Response (ISR) is a critical signaling network that maintains intracellular homeostasis and enables cells to adapt to diverse stress conditions. While the ISR has been linked to ferroptosis, its physiological function in regulating hypoxic adaptation remains poorly understood. Here, we identify General Control Nonderepressible 2 (GCN2) is essential for maintaining redox homeostasis and suppressing ferroptosis. Gcn2-deficient zebrafish exhibit hypersensitivity to hypoxia, with increased mortality associated with excessive heme degradation and mitochondrial damage. Loss of Gcn2 leads to upregulation of hmox1a, reduced erythrocyte numbers, and elevated levels of free ionic iron, collectively contributing to the development of anemia. Mechanistically, loss of Gcn2 downregulates the amino acid transporter chaperone slc3a2b, resulting in disturbed cysteine metabolism. This defect impairs glutathione biosynthesis, triggering ferroptosis characterized by elevated oxidative stress and iron-dependent lipid peroxidation. GCN2-deficient also induces ferroptosis in HeLa cells. Our findings elucidate a critical role for GCN2 in protecting against ferroptosis and promoting hypoxic tolerance.

overall_design: RNA-seq profiling of wild-type and gcn2-deficient zebrafish larvae under normoxic and hypoxic conditions, Three days post-fertilization (3 dpf) wild-type and gcn2-deficient zebrafish larvae were exposed to either normoxic or hypoxic conditions for 8 hours. Each condition included three biological replicates. Total RNA was extracted and subjected to poly(A)-selected RNA sequencing.


title: Effects of SLC2A1 knockdown in intrahepatic cholangiocarcinoma (ICC) cancer-associated fibroblasts (CAFs) on endothelial sprouting under normal and hypoxic conditions

city: HANGZHOU

first: Jianing

last: Fan

address: NO. 3 EAST QINGCHUN ROAD

institute: Sir Run Run Shaw Hospital

summary: Hypoxia is a critical determinant of endothelial sprouting. We here demonstrate that hypoxia-driven remodeling of the ICC tumor microenvironment promotes the emergence of a distinct CAF subset, termed tumor-like CAF (tCAF). We further identify SLC2A1 in tCAFs as a potential key regulator that facilitates endothelial sprouting, although the underlying molecular mechanisms remain to be elucidated. Collectively, our data provide a molecular basis for the aggressive vascular invasive phenotype of ICC and delineate a hypoxia–tCAF–endothelial cell signaling axis, highlighting SLC2A1 as a potential therapeutic target for disrupting tumor angiogenesis in ICC.

overall_design: RNA sequencing analysis of wild-type ICC CAF cells and their shSLC2A1 knockdown cells under normal and hypoxic conditions.


title: Single-cell transcriptomic analysis of KLF15-mediated cardiac protection in heart failure

city: Göttingen

first: Laura

last: Zelarayan

address: Robert-Koch-Str 40

country: Germany

institute: University Medical Center Göttingen

summary: Single-cell RNA sequencing of mouse hearts subjected to transverse aortic constriction (TAC) or sham surgery to characterize the temporal progression of cardiac remodeling from homeostasis through compensated hypertrophy to pathological heart failure. Hearts were harvested at three timepoints (5 days, 8 weeks, and 16 weeks) post-surgery to capture progressive cellular and transcriptional changes during pressure overload-induced heart failure.

overall_design: Mice underwent TAC or sham surgery. Hearts were harvested at 5 days (TAC n=5, Sham n=5), 8 weeks (TAC n=3, Sham n=3), and 16 weeks (TAC n=3, Sham n=3) post-surgery (total 22 animals). Single cells were isolated via Langendorff perfusion. For the 5D and 16W timepoints, cardiomyocyte-enriched (CM) and non-cardiomyocyte-enriched (NCM) fractions were processed separately. Cells were distributed on ICELL8 250v nanowell chips and processed for scRNA-seq. Live cells were selected using Hoechst 33342 and propidium iodide staining. Libraries were prepared using the ICELL8 System and sequenced on Illumina HiSeq 4000.

first: Eric

last: Schoger

first: Rosa

last: Kim

first: Federico

last: Bleckwedel


title: Effect of intrauterine growth restriction on the transcriptome of microglia in hippocampus

city: Shanghai

first: Zhu

last: wei

address: siping road 1239

institute: tongji university

summary: Microglia exhibit an overactivated phenotype in a variety of FGR animal models. Further studies have shown that the excessive activation of microglia can last from the perinatal period to adolescence. Although there has been some research on the function of microglia in perinatal period, there is still a lack of research on the function and mechanism of microglia in adolescence. Our data fill the gap in the transcriptome changes of microglia in the hippocampus during adolescence and provide a basis for understanding the functions and mechanisms of microglia in the hippocampus during adolescence.

overall_design: RNA-seq profiling of hippocampus microglia in control and FGR mice at postpartum three week


title: RUVBL2 transcriptionally regulates the mitophagy pathway in gallbladder cancer cells

first: Chuanxin

last: Yang

address: 600 Yishan Road

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Gemcitabine resistance in gallbladder cancer poses a significant challenge to patient prognosis. This study identified RUVBL2 as a critical factor contributing to gemcitabine resistance in gallbladder cancer. Further analysis, combining ChIP-seq and gene enrichment studies, revealed that RUVBL2 regulates the mitophagy pathway. This regulation helps maintain intracellular redox homeostasis in gallbladder cancer cells following gemcitabine treatment.

overall_design: In the human gallbladder cancer cell line NOZ (with two biological duplicates), ChIP assay was performed using an antibody against RUVBL2, followed by high-throughput sequencing.

first: Jian

last: Wang


title: Spatial transcriptomic analysis of CLDN6-positive solid and small cluster areas in human ovarian cancer

city: Yokohama

first: Shinichi

last: Onishi

state: Kanagawa

address: 216,Totsuka-cho, Totsuka-ku

country: Japan

institute: Chugai pharmaceutical co., Ltd.

summary: To investigate the intratumoral heterogeneity of CLDN6 expression in epithelial ovarian cancer (EOC), we performed spatial transcriptomic analysis on clinical specimens. CLDN6-positive cells were observed to form two morphologically distinct patterns: solid tumor areas and dispersed small tumor cell clusters. Using the NanoString GeoMx Digital Spatial Profiler, we compared the gene expression profiles of these two areas within the same tumors. The analysis revealed that small cluster areas showed higher expression of genes related to epithelial-mesenchymal transition (EMT) and extracellular matrix (ECM) remodeling compared to solid areas. These findings suggest that morphologically distinct CLDN6-positive areas represent cell populations with different molecular characteristics, highlighting the plasticity of EOC.

overall_design: Formalin-fixed, paraffin-embedded (FFPE) tissue sections from two patients with ovarian serous adenocarcinoma were analyzed by spatial transcriptomics using the NanoString GeoMx Digital Spatial Profiler. Regions of interest (ROIs) were selected from CLDN6-positive/Pan-CK-positive areas, categorized as either 'solid tumor areas' or 'dispersed small tumor cell clusters'. Gene expression profiles of Pan-CK-segmented areas within these ROIs were compared to characterize the molecular differences between the two morphological patterns.

first: Chie

last: Kato

first: Etsuko

last: Fujii

first: Nami

last: Yabuki

first: Hitomichi

last: Terashima

first: Atsuhiko


title: Metformin enhances TRAIL-mediated antitumor activity of liver natural killer cells in mice

city: Hiroshima

first: Tomoaki

last: Bekki

address: Kasumi1-2-3, Minamiku

institute: Hiroshima University

summary: Metformin exerts antitumor activity across multiple cancers, largely attributed to anti-inflammatory effects and the AMP-activated protein kinase (AMPK)-mediated inhibition of mammalian target of rapamycin (mTOR). However, the effects of metformin on intrahepatic immunity remain poorly defined. We previously demonstrated that mTOR inhibition augments the antitumor function of liver natural killer (NK) cells by upregulating tumor necrosis factor-related apoptosis-inducing ligand (TRAIL). Here, we investigated whether metformin modulates TRAIL expression on liver NK cells. Compared with vehicle control, metformin increased the proportion of TRAIL+ liver NK cells, enhanced the cytotoxicity of liver NK cells against TRAIL-sensitive tumor targets, and suppressed tumor growth in vivo. Mechanistically, metformin increased, by downregulating Eomes expression, the proportion of liver-resident NK cells (also known as type 1 innate lymphoid cells) which are an immature, TRAILhigh subset. Moreover, activation of the AMPK signaling axis may contribute to metformin-induced promotion of TRAIL+ liver NK cells. These findings indicate that metformin potentiates the antitumor activity of liver NK cells via TRAIL upregulation, supporting its potential repositioning as an immunomodulatory adjuvant for liver cancer.

overall_design: RNA-seq profiling of liver NK cells from metformin-treated wild-type mice

first: Masahiro

last: Ohira

first: Yuki

last: Imaoka

first: Kouki

first: Hiroaki

last: Niitsu

first: Yuka

last: Tanaka

first: Tsuyoshi

last: Kobayashi

first: Hideki

last: Ohdan


title: Gene expression in NIH:OVCAR-3 xenograft tumor treated with vehicle or carboplatin

first: Naoki

last: Kimura

address: 216 Totsukacho, Totsuka-ku, Chugai Life Science Park Yokohama

institute: Chugai Pharmaceutical Co.,ltd

summary: Gene expression differences in OVCAR3 xenograft tumors after vehicle or carboplatin treatment were successfully identified

overall_design: NIH:OVCAR-3 tumor bearing HuNOG mice were administrated saline (vehicle) or carboplatin (30 mg/kg) and used for gene expression analysis


title: Gene expression in NIH:OVCAR-3 xenograft tumor treated with vehicle or carboplatin [Progression]


title: RNA-seq of immortalized human podocytes treated with calcineurin inhibitors

city: New York

first: Evren

middle: U

last: Azeloglu

state: NY

address: 1 Gustave L. Levy Place

department: Nephrology

country: USA

institute: Icahn School of Medicine at Mount Sinai

summary: Human podocytes were treated with 100 nM of thecalcineurin inhibitors cyclosporine A, tacrolimus, or voclosporin. RNA-sequencing was performed to measure gene expression changes relative to DMSO-treated control samples.

overall_design: Differentiated immortalized human podocytes were treated with 100 nM of either cyclosporine A (CSA), tacrolimus (TAC), voclosporin (VCS), or DMSO control. RNA was isolated 24 hours after treatment, and RNA-seq was performed with 3 replicates for each condition.

first: Jonathan

last: Haydak

first: Jacob

last: Wright


title: Gene expression in NIH:OVCAR-3 cells treated with chemotherapeutic drugs

summary: Difference of gene expression in NIH:OVCAR-3 cells after treatment of chemotherapies

overall_design: NIH:OVCAR-3 cells treated with chemotherapeutic drugs were harvested and used for gene expression analysis


title: spaTransfer: transfer learning for single-cell and spatial transcriptomics data using non-negative matrix factorization [DG]

city: BALTIMORE

first: Xin Zhi

last: Fang

state: MD

address: 615 N Wolfe St

department: Biostatistics

institute: Johns Hopkins University

summary: Recent advances in spatially-resolved transcriptomics have enabled profiling of gene expression  in a spatial context, which has led to the generation of large-scale single-cell and spatial atlases  with computationally-derived cell type or spatial domain labels. An increasingly important  task with these data has become the transfer of cell type or spatial domain annotations from a  given reference (or source) atlas into a new target tissue or sample. The reference and target  datasets could be at different resolutions or measured on different experimental platforms. Here,  we present a method to perform cross-platform transfer learning that takes as input single-cell  or spatial domain labels from a reference atlas or dataset and transfers the labels to a target  dataset at a similar or different resolution. Specifically, we use non-negative matrix factorization  (NMF) on the reference data to identify factors associated with labels of interest and project  these factors into the target dataset to label each new observation. We use a multinomial model  with the factors as covariates and labels as the response to predict labels in the target dataset.  In contrast to existing approaches, the advantage of our approach is interpretability, without  compromising on accuracy. We demonstrate the performance of the method in two human brain  tissues and show that our model identifies spatially coherent domains in the target datasets with  concordance of marker gene expression. We implement spaTransfer in open-source software as  an R package (github.com/cindyfang70/spaTransfer).

overall_design: The DG data shown in this study came from four donors of differing ages (N=1 infant,  N=1 teen, N=1 adult, N=1 elderly). Cryosections from fresh frozen DG tissue samples were  mounted onto Xenium slides with two tissue samples from different donors on each slide. The infant and  adult samples were mounted onto three slides and the teen and elderly were mounted onto another three  slides. Sectioning specifications for these samples are listed in the 10x Genomics protocol CG000579 (Rev  C). Slides with frozen tissue sections were shipped on dry ice to 10x Genomics, where the samples were  processed in two separate batches.

first: Cindy

first: Kelsey

middle: D

last: Montgomery

first: Sarah

middle: E

last: Maguire

first: Anthony

last: Ramnauth

first: Boyi

last: Guo

first: Ryan

middle: A

last: Miller

first: Annie

middle: B

last: Nguyen

first: Joel

last: Kleinman

first: Thomas

middle: M

last: Hyde

first: Heena

middle: R

last: Divecha

first: Keri

last: Martinowich

first: Kristen

last: Maynard

first: Stephanie

middle: C

last: Page

last: Hicks


title: spaTransfer: transfer learning for single-cell and spatial  transcriptomics data using non-negative matrix factorization

overall_design: The dlPFC data shown in this study were collected from 4 adult neurotypical donors. Cryosections from dlPFC tissue samples were mounted onto Xenium slides with 3 tissue sam-  ples from 3 donors on each slide. We collected adjacent replicates across the 2 Xenium slides for 2 donors.  Sectioning specifications for dlPFC samples are listed in the 10x Genomics protocol CG000579 (Rev C).


title: Transcriptomic analysis in relation to adventitious rooting of different petunia species

city: Erfurt

first: Sindy

last: Chamas

address: Kuehnhaeuser Strasse 101

institute: Erfurt Research Centre for Horticultural Crops, University of Applied Sciences Erfurt

summary: Excision-induced adventitious rooting of cuttings is a key developmental process for vegetative propagation of many crops, that involves a phytohormone-controlled reprogramming and redifferentiation of specific cells in the stem base. Even though the important role of auxin as inductor of adventitious roots is widely accepted, the endogenous control of auxin action at whole cutting level and the interaction with other hormones are not completely understood. Comparing the genome-sequenced Petunia species P. axillaris and P. inflata, we monitored the transcriptome of phytohormone-related genes in different cutting sections by a phytohormone-targeted microarray. Expression of 17 selected auxin-related genes was quantified in the same RNA samples by RT-qPCR.

sample_organism:
Petunia axillaris
Petunia integrifolia subsp. inflata

overall_design: Gene expression in five different tissues (basal leaves, upper leaves, shoot apex, upper shoot and stem base) of Petunia cuttings was measured at 0, 0.5, 2, 24 and 72 hours post excision. Three replicates were taken for each time point and tissue. Cuttings from two Petunia species (P. axillaris and P. inflata) were used for this experiment.

first: Uwe

last: Druege

first: Katharina

last: Federspiel


title: Kupffer Cell Calibration of T Cell Responses via VSIG4-CD5 Interaction Promotes Tumor Evasion [bulkRNA]

city: Hefei

first: xia

last: zhou

address: huang shan Road 443

institute: university of science and technology of china

summary: Liver metastasis often resists T cell-based immunotherapy, indicating an adaptation of metastatic tumors towards reduced immunogenicity in the liver. Here we demonstrate that VSIG4, an immune checkpoint molecule predominantly expressed on Kupffer cells, plays an opposing role in determining the growth of liver metastases with varying antigenicity by modulating cognate TCR signaling through its interaction with CD5. Mechanistically, VSIG4-CD5 engagement impedes activation of low-affinity CD8+ T cells while enhancing responses of high-affinity CD8+ T cells by rescuing them from activation-induced cell death. This bi-directional regulation favors growth of metastatic tumor clones with low antigenicity, and fosters an T cell-unfavorable immune landscape as metastatic liver cancer progresses. Blockade of VSIG4-CD5 interaction with a newly generated anti-VSIG4 nanoantibody sensitizes liver metastases to anti-PDL1 therapy, achieving remarkably synergistic efficacy in mice. Our findings provide mechanistic insights into cancer immunoediting in liver metastasis and propose a promising approach for treating immunologically cold tumors.

overall_design: B16F10 cells were injected into WT and VSIG4 ko mice. 7 days latter, Kupffer cells from tumor-bearing WT and VSIG4 ko mice were isolated and sorted by FACS, Further RNA-seq were performed and analyzed.

first: Xia

last: Zhou

first: Wei

last: Liu

first: Jing

last: Hu

first: Qi

last: Yao


title: Targeting the Cancer-Retina Antigen PDE6G with mRNA-LNP Vaccine Elicits Potent Anti-Tumor Immunity Against Breast Cancer

city: 杭州

first: wei

last: zhang

state: 浙江省

address: 浙江省杭州市钱塘区下沙街道东方街150中国科学院杭州医学研究所

institute: 浙江工业大学

summary: The development of effective mRNA vaccines for breast cancer has been constrained by the lack of highly immunogenic and tumor-specific antigens. Here, we identify PDE6G, an immune-privileged retina-enriched antigen aberrantly overexpressed in breast tumors, and develop a PDE6G mRNA-LNP vaccine. Vaccination elicited robust CD8+ T cell responses, promoted clonal expansion of effector and IFN-competent T cell subsets, and suppressed tumor growth without detectable toxicity. Single-cell RNA  sequencing (scRNA-seq) revealed that vaccination of PDE6G mRNA-LNP reshapes the tumor immune microenvironment (TIME) by expanding antigen-presenting Cd74+ tumor-associated macrophages (TAMs) while reducing immunosuppressive Maf+ macrophages, and enhancing crosstalk between macrophages and CD8+ T cells. Moreover, combining PDE6G mRNA-LNP with PD-1 blockade further improved anti-tumor efficacy. These findings establish cancer-retina antigens as promising vaccine targets and demonstrate that PDE6G mRNA-LNP coordinates adaptive immunity and tumor microenvironment remodeling, providing a safe and potent strategy for breast cancer immunotherapy.

overall_design: PDE6G-expressing tumor models (experimental group) were immunized with PDE6G mRNA-LNP vaccine

first: Yue

last: Zhao

first: Yichun

last: Pan

last: Zhang

first: Zhao

last: Zuo


title: Kupffer Cell Calibration of T Cell Responses via VSIG4-CD5 Interaction Promotes Tumor Evasion [TCR-Seq]

overall_design: B16F10 cells were injected into WT and VSIG4 ko mice. 14 days latter, CD8+ T cells from tumor-bearing WT and VSIG4 ko mice were isolated and sorted by FACS, Further RNA-seq were performed and analyzed.


title: Gene expression in NIH:OVCAR-3 cells cultured in different cell density conditions

first: Naoki

last: Kimura

summary: Difference of gene expression in different cell culture condition was successfully identified

overall_design: NIH:OVCAR-3 cells were cultured under low density, medium density, and high density. After one week of culture, cells were harvested and used for gene expression analysis


title: Unraveling cetuximab response in head and neck cancer with APHRODYTHE, a multi-omics patient-derived xenograft platform

city: Derry

first: Mary-Kate

last: Riley

address: 26 Knightsbridge

country: United Kingdom

institute: Queen's University Belfast

summary: The anti-EGFR antibody cetuximab is an established therapy for head and neck squamous cell carcinoma (HNSCC), yet robust predictive biomarkers of response remain elusive. To address this gap, we established APHRODYTHE, a resource of 79 HPV-negative HNSCC patient-derived xenografts (PDXs), including 61 with genomic annotation, 52 with RNA-seq profiling, and 63 tested with cetuximab in a population-scale preclinical trial. APHRODYTHE faithfully recapitulated the mutational, copy number, and transcriptional landscapes of human HNSCC, enabling systematic discovery of response determinants. Integrated multi-omics analyses revealed that tumors with pronounced squamous differentiation and keratinization were more likely to respond, whereas high Sonic Hedgehog (SHH) pathway activity was associated with intrinsic resistance. Cetuximab-sensitive tumors were also enriched for EGFR amplification, elevated EGFR ligand expression, and mutations in NOTCH1, FAT1, and ATM. Immunohistochemistry validated keratinization markers as candidate predictors of benefit with potential clinical applicability. Functionally, SHH pathway activation conferred antibody resistance, while pharmacologic SHH inhibition restored cetuximab sensitivity in resistant models. Together, these findings position APHRODYTHE as a robust translational platform, identify squamous keratinization and SHH activity as complementary biomarkers for patient stratification, and motivate SHH inhibition as a rational combination strategy to enhance cetuximab efficacy in HNSCC.

overall_design:
RNA-seq proflling of primary head and neck squamous cell carcinoma biopsies from human samples and patient-matched PDX models

***************************************************************
Not uploading raw FastQ files to GEO due to patient privacy concerns for PDX and human samples
***************************************************************

first: Eugenia

last: Zanella

first: Francesco

last: Sassi

last: Craig

first: Elena

last: Grassi

first: Shauna

last: Lambe

first: Valentina

last: Vurchio

first: Francesca

last: Cottino

first: Martina

last: Ferri

last: Galimi

first: Vincenzo

last: Landolfo

first: Eliano

last: Cascardi

last: Maldi

first: Pamela

last: Arcella

first: Fiorenza

last: Enrico

first: Giovanni

middle: N

last: Berta

first: Marco

last: Merlano

first: Danilo

last: Galizia

first: Paola

last: Cassoni

first: Stefano

last: Bondi

first: Erika

last: Crosett

last: Succo

first: Anna

last: Sapino

first: Caterina

last: Marchiò

first: Jacqueline

last: James

first: Sarah

middle: L

last: Maguire

first: Simon

last: McDade

first: Andrea

last: Bertotti

first: Livio

last: Trusolino


title: Effect of intrauterine growth restriction on the DNA methylation of microglia in hippocampus

first: Zhu

last: wei

type: Methylation profiling by high throughput sequencing

summary: Early-life exposures (spanning from the gamete stage to childhood) to adverse environmental factors can exert long-term effects on offspring health through epigenetic modifications, significantly increasing susceptibility to chronic diseases such as neuropsychiatric disorders in adulthood. Previous studies have shown that fetal growth restriction can lead to excessive activation of microglia in the individual's brain, but there is still a lack of research on its epigenetic mechanisms. Our data supplements the changes in DNA methylation of microglia in the hippocampus of individuals with fetal growth restriction, and explores the epigenetic basis of microglial activation

overall_design: WGBS profiling of hippocampus microglia in control and FGR mice at postpartum three week


title: Single-cell multiomics uncovers an endothelial mechanosensitive PIEZO1-IL-33 axis driving pulmonary fibrosis

city: Chengdu

first: Bisen

last: Ding

address: Renmin South Road

institute: State Key Laboratory of Biotherapy

summary: Pulmonary fibrosis (PF) represents a progressive interstitial lung disease marked by excessive extracellular matrix deposition and architectural distortion. Vascular endothelial cells (ECs) critically contribute to fibrogenesis through paracrine secretion of pro-fibrotic mediators, yet their mechanobiological regulation remains elusive. UsingThrough integrated single-cell multi-omics profiling of human PF specimens and experimental fibrosis models induced by bleomycin or silica (Bleomycin/SiO2-induced), we identify identified mechanosensitive Piezo1 upregulation in ECs as a hallmark of fibrotic progression. Endothelial-specific Piezo1 knockout significantly attenuates attenuated Bleomycin-induced fibrotic remodeling, establishing its pathogenic necessity. Mechanistically, Piezo1 activation promotes promoted PF development by inducing a pro-fibrotic molecule interleukin-33 (IL-33) secretion via CAPN2-mediated STAT3 phosphorylation. These findings suggest that the endothelial PIEZO1-CAPN2-STAT3-IL-33 axis is a promising therapeutic target for PF intervention.

overall_design: Lung tissues of Saline or Silica or Bleomycin induced mice were obtained for both scRNA-seq and scATAC-seq (n=3 per group).

first: Lanlan

last: Zhang

first: Ruijie

last: Hou


title: Effect of intrauterine growth restriction on the chromatin accessibility of microglia in hippocampus

summary: Early-life exposures (spanning from the gamete stage to childhood) to adverse environmental factors can exert long-term effects on offspring health through epigenetic modifications, significantly increasing susceptibility to chronic diseases such as neuropsychiatric disorders in adulthood. Previous studies have shown that fetal growth restriction can lead to excessive activation of microglia in the individual's brain, but there is still a lack of research on its epigenetic mechanisms. Our data supplements the changes in chromatin accessibility of microglia in the hippocampus of individuals with fetal growth restriction, and explores the epigenetic basis of microglial activation

overall_design: ATAC-seq profiling of hippocampus microglia in control and FGR mice at postpartum three week


title: Danggui Niantong granules in the treatment of rheumatoid arthritis - a mechanistic approach using ceRNA networks

city: Guangzhou

first: Yisi

last: Cai

address: No. 1023 South Shatai Road, Baiyun District

department: School of Traditional Chinese Medicine

institute: Southern Medical university

summary: This project aims to explore the changes in ceRNA expression profiles of mh7a after the use of Danggui Niantong granules. In conclusion, this study provides evidence that DGNTG exhibits anti-RA effects associated with its inhibition of  synoviocyte proliferation, migration and invasion. To explore the underlying mechanism, we constructed a ceRNA network based on transcriptomic data from DGNTG-treated MH7A cells.

overall_design: CeRNA microarray analysis of MH7a cells in control group and Danggui Niantong granule-treated group

first: Yanyan

last: Song

first: Xiaoling

last: Zeng

first: Gang

last: Liu

first: Lixia

last: Yuan


title: Single-cell RNA sequencing of hippocampal microglia in Fetal growth restriction mouse

summary: Microglia exhibit an overactivated phenotype in a variety of FGR animal models. Further studies have shown that the excessive activation of microglia can last from the perinatal period to adolescence.  In recent years, breakthroughs in single-cell sequencing technologies have revealed the high heterogeneity of microglia, and previous studies have identified multiple pathological microglial subpopulations in neuropsychiatric disorders. Nevertheless, in the context of FGR-associated cognitive impairment in offspring, the mechanistic contributions of hippocampal microglia, their heterogeneity at single-cell resolution have not been elucidated.

overall_design: scRNA-seq of hippocampal microglia in postpartum three week Control and FGR mice


title: Effect of intrauterine growth restriction on the H3K4me3, H3K9ac, H3K27ac and H3k9me3 histione modification of microglia in hippocampus

summary: Early-life exposures (spanning from the gamete stage to childhood) to adverse environmental factors can exert long-term effects on offspring health through epigenetic modifications, significantly increasing susceptibility to chronic diseases such as neuropsychiatric disorders in adulthood. Previous studies have shown that fetal growth restriction can lead to excessive activation of microglia in the individual's brain, but there is still a lack of research on its epigenetic mechanisms. Our data supplements the gap of  changes of H3K4me3, H3K9ac, H3K27ac and H3K9me3 histone modification  of microglia in the hippocampus of individuals with fetal growth restriction, and explores the epigenetic basis of microglial activation

overall_design: ULI-NChIP-seq profiling of hippocampus microglia in control and FGR mice at postpartum three week


title: Mild SARS-CoV-2 maternal infection in mice induces transient offspring neurodevelopmental aberrance

city: New Haven

first: Matthew

last: Yuen

state: Connecticut

address: 100 College

department: Neuroscience

institute: Yale School of Medicine

summary: Maternal viral infection during pregnancy has been identified as a risk factor for psychiatric disorders and neurodevelopmental abnormalities in offspring. With cumulative SARS-CoV-2 infections now numbering in the hundreds of millions globally, there is a need to evaluate the effects of maternal SARS-CoV-2 infection on offspring brain development and behavior. We developed a mouse model of mild SARS-CoV-2 infection during pregnancy, where SARS-CoV-2 infection is restricted to the respiratory tract. These mice did not exhibit weight loss despite detectable local and systemic immune responses, including placental inflammation. Characterization of the offspring cerebral cortex revealed transient transcriptomic changes at post-natal day 5 (P5), but no gross alterations in the cytoarchitecture, synaptic density, or microglia abundance. Moreover, we did not detect any significant changes in open field nor novel object recognition tests in P50 offspring born to SARS-CoV-2-infected dams. These results suggest that mild SARS-CoV-2 infection induces transient perturbations to offspring brain development but does not appear to result in long-lasting structural or behavioral deficits.

overall_design: SARS-CoV-2 infection or mock infection (PBS) of pregnant dams at embryonic day (E)10. Bullk RNA sequencing of the cerebral cortex of offspring at E15, postnatal day (P) 5, and P30. In addition, bulk RNA sequencing of the placenta 4 days post infection (E14). Included here are both biological replicates (unique mouse litters) and technical replicates (offsprings within a given mouse litter).

first: Wesley

last: Tung

first: Helen

first: Hyesun

last: Cho

first: Peiwen

last: Lu

first: Harvey

last: Kliman

first: Robert

last: Homer

first: Alexa

last: Herrerias

first: Nikkita

last: Salla

first: Arianna

last: Rodriguez Rivera

first: Yuting

first: Kartik

last: Pattabiraman

first: Akiko

last: Iwasaki


title: Comparative transcriptomic analysis of in vivo–derived and IVF porcine embryos at the 4-cell, blastocyst, and hatched blastocyst stages

city: Cheongju

first: Cheng-Lin

last: Zhan

address: Chungdae-ro 1, Seowon-Gu

country: South Korea

institute: Chungbuk National University

summary: Early embryonic development is highly sensitive to both developmental stage and culture environment, and in vitro fertilization (IVF) is known to induce transcriptional and epigenetic alterations that may compromise embryo quality and developmental competence. To systematically characterize stage-specific and origin-dependent transcriptional differences, we performed RNA sequencing of porcine embryos derived in vivo and by IVF at key preimplantation stages. Transcriptomes were generated from in vivo–derived blastocysts and hatched blastocysts, IVF-derived blastocysts and hatched blastocysts, as well as IVF-derived 4-cell embryos. Comparative analyses enable the dissection of transcriptional programs associated with early cleavage, blastocyst formation, hatching, and culture-induced perturbations. This dataset provides a comprehensive resource for investigating developmental stage transitions, IVF-associated transcriptional dysregulation, and molecular determinants of embryo quality during porcine preimplantation development.

overall_design: RNA-seq was performed on porcine preimplantation embryos collected at defined developmental stages. Experimental groups included: (i) in vivo–derived blastocysts, (ii) in vivo–derived hatched blastocysts, (iii) IVF-derived blastocysts, (iv) IVF-derived hatched blastocysts, and (v) IVF-derived 4-cell embryos. Total RNA was extracted from pooled embryos within each group and subjected to high-throughput RNA sequencing. The resulting transcriptomic profiles were used to compare developmental stage–dependent gene expression dynamics and to assess the impact of IVF culture conditions on embryonic transcriptional programs.

first: Xiangshun

last: Cui

first: Chenglin

first: Songhee

last: Lee

first: Dongjie

last: Zhou

first: Xiaohan

last: Li

first: Minghong

last: Sun

first: Gyuhyun


title: Unravelling WRN helicase: Structural Insights Reveal Conformational States and Opportunities for MSI-H Cancer Drug Discovery

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

institute: The Babraham Institute

summary: Werner syndrome helicase (WRN) is a RecQ-family DNA helicase essential for genome maintenance and is a synthetic lethal target in microsatellite instability-high (MSI-H) cancers. Despite its therapeutic promise, the conformational dynamics that enable WRN to unwind DNA, and how inhibitors disrupt this activity, remains poorly understood. Here, we present crystal structures of apo WRN and WRN bound to single-stranded DNA (ssDNA), capturing key conformations in the helicase catalytic cycle. These structures reveal how WRN engages DNA through conserved polar and aromatic interactions, and how domain rearrangements, including an ordering of the aromatic-rich loop (ARL), drive directional translocation. Biochemical and biophysical data demonstrate how nucleotide and inhibitor binding remodel these conformations and suggest that known clinical inhibitors (HRO761 and VVD-133214) function by locking WRN in inactive, ‘off-DNA’ states. Resistance emerged rapidly in vitro, through acquired point mutations as well as altered WRN expression. Together, our findings provide a structural framework for the WRN structural cycle and support the development of next-generation ‘on-DNA’ inhibitors to overcome resistance

overall_design: Samples were collected to charactersie the changes in gene expression of cell lines after acute or chronic treatment of WRN inhibitors to identify changes. One million cells of 3 biological replicates were washed with PBS and snap-frozen in dry ice. Samples were collected from HCT116, 0.1% DMSO treated HCT116, HRO761 and VVD-133214 chronically treated HCT116 in the early (HRO761: 1uM; VVD-133214: 600nM) and late (HRO761: 13uM; VVD-133214: 3uM) stages of resistance development, and HRO761 and VVD-13321 acute treated HCT116. For acute treatment, the 0.1% DMSO HCT116 cell line was grown in 13uM HRO761 or 3uM VVD-13321 for one passage.

first: Catherine

middle: T

last: Fletcher

first: Abigail

last: Mornement

first: Charlotte

last: Barrett

first: Peter

last: Canning

first: Prakash

last: Rucktooa

first: Sophie

last: Huber

first: Christopher

last: Cooper

first: Conor

last: Scully

first: Andrew

middle: S

last: Dore

first: Daniel

last: Rohle

first: Geoffrey

last: Smith

first: Sarah

last: Skerratt

first: Amanda

middle: J

last: Kennedy


title: Type I interferon responses mediated by CD14⁺ monocytes drive CD4⁺ T-cell activation in PWH

city: Paris

first: Beatrice

last: Jacquelin

address: 28, rue du Dr Roux

country: France

institute: Institut Pasteur

summary: T-cell activation is a key feature of chronic HIV infection and is predictive of non-AIDS-defining comorbidities in people with HIV (PWH) receiving antiretroviral therapy (ART). Monocytes from PWH display distinct transcriptional programs, yet their role in T-cell activation remains unclear. In this study, we investigated how the response of CD14⁺ monocytes from PWH to type I interferon (IFN-1) influences T-cell activation. Ex vivo transcriptional profiles and in vitro IFN-1 responses of CD14⁺ monocytes were compared between PWH and uninfected individuals (UI). We identified distinct ex vivo transcriptional signatures in CD14⁺ monocytes from PWH versus UI, as well as differential responses to IFN-1. T cells from ART-treated PWH exhibited persistent activation, which correlated positively with IFN-1-stimulated gene expression. In vitro IFN-1 exposure led to increased proportions of activated CD4⁺ T cells in PWH—but not in UI—an effect reproduced by the transfer of IFN-1-primed CD14⁺ monocytes. Finally, JAK inhibitors effectively blocked IFN-1-mediated T-cell activation. Our findings underscore the role of IFN-1-primed CD14⁺ monocytes in sustaining chronic T-cell activation during HIV infection and highlight JAK inhibitors as a potential therapeutic strategy.

overall_design: A total of samples from 11 people living with HIV (PLH) and 4 healthy donors (HD) were included in this gene expression study.

first: Léo

last: Plaçais

first: Béatrice

first: Martin

last: Dutertre

first: Vanessa

last: d’Urbano

first: Annamaria

last: Paolini

first: Marie

last: Bitu

first: Christelliah

last: Mouanga

first: Oscar

last: Haigh

first: Katia

last: Bourdic

first: Delphine

last: Desjardins

first: Michaela

last: Müller-Trutwin

first: Christine

last: Bourgeois

first: Olivier

last: Lambotte

first: Nicolas

last: Noel


title: Targeted innate immune inhibition therapy compared to antibiotics for recurrent acute cystitis

city: Lund

first: Ines

last: Ambite

address: Klinikgatan 28

department: Laboratory Medicine

country: Sweden

institute: Lund University

summary: Cystitis is a bacterial infection of the bladder that occurs in about half of women at least once in their lifetime. Antibiotics such as nitrofurantoin are used to treat cystitis but antibiotic resistance is a concern, especially for recurrent infections. Here we report an open label, randomized, single-center, phase 2 study to analyze the acute and long-term safety and efficacy of the IL-1 receptor antagonist anakinra, compared to nitrofurantoin, in recurrent cystitis. Thirty adult female patients with a documented history of recurrent cystitis and a current acute cystitis episode were randomized in a 2:1 ratio to treatment with anakinra (n=20) or nitrofurantoin (n=10) for five days. Primary and secondary efficacy end points were reached, defined as the reduction in typical symptoms, measured by the acute cystitis symptom score (ACSS, day 5), longitudinal symptom scores, recurrence rates, quality of life gene, expression analysis and microbiology at follow-up on days 15, 30 and at six months. Symptom scores were decreased in the anakinra (P<0.001), and nitrofurantoin (P<0.001) arms after five days and remained low after 15, 30 days and 6 months. Recurrences were less frequent after 6 months in both treatment groups compared to the 6-month pre-enrolment history (P<0.001 for anakinra and P=0.004 for nitrofurantoin) and the quality of life was increased, without adverse effects. Immune gene expression was rapidly inhibited in the anakinra treated patients but not in the nitrofurantoin group. Targeted innate immune inhibition therapy shows non-inferiority to nitrofurantoin in patients with recurrent acute cystitis (German Clinical Trials Register, DRKS00025964; EudraCT, 2019-004209-28).

overall_design: Expression data from RNA samples of recurrent cystitis patients. RNA was extracted from blood of patient treated with anakinra or nitrofurantoin. Blood samples were collected longitudinally throughout the clinical study.

first: Catharina

last: Svanborg

first: Florian

last: Wagenlehner


title: Trans-regulation of heterochromatin underlies genetic variation in 3D genome contacts

city: Bar Harbor

first: Christopher

middle: Lee

last: Baker

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

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

overall_design: Refer to individual Series


title: Simtuzumab attenuates Loxl2-mediated extracellular matrix remodeling and preserves cardiac function in LMNA mutation-induced dilated cardiomyopathy

city: Hamburg

first: Sonia

last: Singh

address: Martinistr. 52

institute: University Medical Center Hamburg-Eppendorf

summary: Background | Dilated cardiomyopathy (DCM) caused by LMNA mutations is a severe cardiac condition marked by arrhythmias, contractile dysfunction, and excessive myocardial fibrosis, which collectively impair left ventricular function and increase the risk of heart failure. While the disease has been well characterized, a lack of insight into the pathogenesis has impeded the development of therapies. Methods | Here, we employed induced pluripotent stem cells (hiPSCs) derived from a patient carrying a LMNA point mutation (c.665A>C, p.His222Pro), alongside a murine model carrying the same mutation, to investigate the functional and molecular abnormalities driving DCM. Results | We demonstrated that LMNA patient-derived cardiomyocytes (hiPSC-CMs) and engineered heart tissues (hiPSC-EHTs) exhibited elevated diastolic calcium levels and reduced sensitivity to external calcium, respectively, as well as hypocontractility. These cells also displayed nuclear shape abnormalities in 2D and 3D, a hallmark of LMNA-associated DCM, associated with disrupted chromosome spatial organization and altered gene expression profiles. Transcriptomic analysis revealed dysregulation of extracellular matrix remodeling and significant upregulation of Loxl2 in mutated hiPSC-CMs, hiPSC-EHTs, and mice. Treatment with Simtuzumab, a Loxl2 inhibitor, effectively prevented cardiac dysfunction and fibrosis in vivo. Conclusion | Taken together, our findings underscore the crucial role of Loxl2 as a therapeutic target and suggest that its inhibition could be a promising strategy to preserve cardiac function in LMNA-associated DCM.

overall_design: RNA-seq profiling of wild-type and LMNA H222P human induced pluripotent stem cell-derived engineered heart tissues

last: Kervella

first: Charlotta

last: Behrens

first: Cécile

last: Peccate

first: Zoheir

last: Guesmia

first: Fiorella

last: Grandi

first: Nathalie

last: Mougenot

first: Anne

last: Forand

first: Azzouz

last: Charrabi

first: Guy

last: Brochier

first: Ramaroson

last: Andriantsitohaina

first: Thomas

last: Eschenhagen

first: Albano

last: Meli

first: Antoine

last: Muchir


title: Distinct Control of Histone H1 Expression within the Histone Locus Body by CRAMP1 [ChIP-seq]

city: Chicago

first: SHASHANK

last: SRIVASTAVA

state: IL

address: 303 E Superior St, SQE Lab 7-400

institute: Northwestern University

summary: Proper histone gene expression is critical for cell viability and maintenance of genomic integrity. Multiple histone genes are organized into three genomic loci encode replication-coupled core and linker histones. Histone gene expression and transcript processing are orchestrated in the histone locus body (HLB) within the nucleus. We identified human CRAMP1 as a selective regulator of the linker histone H1 expression. CRAMP1 was recruited to the HLB in RPE1hTERT cells. Affinity purification showed that CRAMP1 physically associates with the HLB component GON4L (also known as YARP). We demonstrated that the PAH domains of GON4L interact with CRAMP1. CRAMP1 disruption resulted in a loss of histone H1 expression and a reduction in H1 protein levels. CRAMP1 occupies unmethylated promoters of replication-coupled linker histone genes that reside within the histone locus body and replication-independent histone H1 loci, which reside in a region of the genome without other histone genes. Together, these data identify CRAMP1 as a novel and selective regulator of histone H1 gene expression.

overall_design: To determine chromatin binding patterns of CRAMP1, we created RPE-1 PKO hTERT-immortalized cells that express a V5-tagged CRAMP1 construct.  ChIP-seq  was conducted in the above cells using a V5 antibody.

first: Vadlamani

last: Pranathi

first: Daniel

last: Foltz


title: A novel CasRx-based approach identifies TRA2B as a critical splicing regulator of AR-V7 in advanced prostate cancer

city: Newcastle upon Tyne

first: Luke

last: Gaughan

address: Paul O'Gorman Building, Framlington Place

institute: Newcastle University

summary: To determine by RNA-Seq global transcriptomic changes resulting from siRNA knockdown of splicing regulators TRA2A, TRA2B, or both TRA2A and TRA2B, in the castrate resistant prostate cancer cell line CWR22Rv1.

overall_design: CWR22Rv1 cells were transfected with 25 nM siRNA targeting either TRA2A (siTRA2A), TRA2B (siTRA2B), both TRA2A and TRA2B (siTRA2A/TRA2B) or a scrambled/non-targeting siRNA (siScr). 72 hours later, total RNA was extracted and sent for paired-end RNA-Seq.

first: Nicholas

last: Brittain


title: KG1a phenotypic subsets under normoxia and hypoxia

city: Brighton

first: Chris

last: Pepper

address: Falmer

institute: University of Sussex

summary: We set out to investigate the transcriptional signatures of two phenotypically distinct subsets found in the KG1a cell line - CD34+/CD38dim/CLL-1dim and CD34+/CD38bright/CLL-1bright under both normoxic and hypoxic conditions.

overall_design: We set out to explore how normoxia and hypoxia affected two phenotypically distinct subsets found in the KG1a cell line - CD34+/CD38dim/CLL-1dim and CD34+/CD38bright/CLL-1bright

first: Kim

last: Sharp

first: Eleni

last: E. Ladikou

first: Emma

last: Kennedy

first: John

last: Jones

first: Fabio

last: A. Simoes

first: Simon

last: A. Mitchell

first: Andrea

last: G. S. Pepper


title: Transcriptomic profiling of HCT116 and HT29 colorectal cancer cells after piR-37524 inhibition

city: Hong Kong

first: Jiaxi

last: Li

state: Hong Kong (SAR)

address: FLAT G,8/F,SUN ON BUILDING,490 QUEENS ROAD WEST

department: surgery

country: Hong Kong

institute: The university of Hong Kong

summary: Piwi-interacting RNA 37524 (piR-37524) is a novel oncogenic non-coding RNA overexpressed in colorectal cancer (CRC), associated with tumor progression, metastasis, and poor clinical outcomes. To elucidate the downstream transcriptional regulatory network of piR-37524, we performed RNA sequencing on two human CRC cell lines (HCT116 and HT29) transfected with a piR-37524-specific inhibitor or negative control (NC). Total RNA was extracted 48 hours post-transfection, and libraries were sequenced on an Illumina HiSeq 2500 platform. KEGG enrichment analysis revealed DEGs were significantly associated with TNF signaling pathway, TGF-beta signaling pathway, and microRNAs in cancer which  are key pathways involved in CRC cell proliferation, migration, and epithelial-mesenchymal transition. Intersection analysis of upregulated DEGs across both cell lines identified TNFAIP3 as a potential direct target of piR-37524. This transcriptomic dataset provides comprehensive insights into the gene regulatory network mediated by piR-37524 in CRC cells, supporting its role as a therapeutic target via the TNFAIP3/NF-κB/EMT axis. The data will facilitate further exploration of piRNA-driven oncogenic mechanisms in CRC and the development of novel diagnostic or therapeutic strategies.

overall_design: RNA-seq profiling of HCT116 and HT29 colorectal cancer cells transfected with piR-37524-specific inhibitor or negative control, with three biological replicates per group.

first: Deepak

last: Iyer

first: Siming

last: Sui

first: Zheng

last: Huang

first: Wai-Yan

last: Sin

first: Abraham

last: Man

first: Wai-Lun

last: Law

first: Chi-Chung

last: Foo

first: Lui

last: Ng


first: Bisen

last: Ding

overall_design: Human lung tissues were obtained from five Normal individuals and four IPF patients.

first: Lanlan

last: Zhang

first: Ruijie

last: Hou


title: An RNA polymerase III tissue and tumor atlas uncovers context-specific activities linked to 3D epigenome regulatory mechanisms

city: Urbana

first: Ruiying

last: Cheng

address: B520 Chemical & Life Sciences Laboratory

department: School of Molecular & Cellular Biology

institute: The University of Illinois Urbana-Champaign

summary: RNA polymerase III (Pol III) produces a plethora of small noncoding RNA species involved in diverse cellular processes, from transcription regulation and splicing to RNA stability, translation, and proteostasis. Though Pol III activity is broadly coupled with cellular demands for protein synthesis and growth, a more precise understanding of gene-level dynamics and context-specific expression patterns remains missing, in part due to multiple challenges related to sequencing and mapping Pol III-derived small ncRNAs. Here, we establish a predictive multi-tissue map of Pol III activity across 19 tissues and 22 primary cancers by comprehensively profiling the chromatin accessibility of canonical Pol III-transcribed gene classes. Our framework relies on the unique relationship between gene accessibility and Pol III transcription, inferring activity through uniform binary classification of ATAC-seq enrichment at Pol III-transcribed genes. By characterizing multi-context gene uniformity, we provide a definition of the core Pol III transcriptome, broadly active across specialized tissues, and catalog genes with varied levels of context specificity. Our genomic Pol III atlas uncovers variable levels of activity across tissues, including sharp contraction of the Pol III transcriptome in heart and brain tissues and frequent expansion across diverse cancers. We show that both tissue- and tumor-specific genes are significantly enriched within lamina-associated domains (LADs), and that aberrant expression of nuclear lamin proteins is sufficient to induce Pol III- emergent patterns at tumor-specific genes. Together, these findings link Pol III dynamics to subnuclear compartment- alization and provide a resource for better understanding Pol III expansion and small RNA biogenesis in cancer.

overall_design: H1 stem cells and H1-derived cardiomyocytes were harvested (~10 million cells per ChIP experiment) and resuspended in growth media at 1 × 106 cells/mL and cross-linked with rotation at room temperature in 1% formaldehyde for 10 min. Cross-linking was quenched with the addition of 200 mM glycine and an additional 5 min of rotation at room temperature. Cross-linked cells were then spun down and resuspended in 1× RIPA lysis buffer, followed by chromatin shearing via sonication (3 cycles using a Branson sonicator: 30 s on, 60 s off; 20 additional cycles on a Bioruptor sonicator: 30 s on, 30 s off). Individual ChIP experiments were performed on pre-cleared chromatin using antibody-coupled ChIP grade Protein G magnetic beads (Cell Signaling Technology). POLR3A antibody was obtained from ThermoFisher Scientific (PA5-58170). 5 ug of antibody per ChIP was coupled to 18 uL of beads and rotated overnight with sheared chromatin at 4°C. Beads were then washed 5× in ChIP wash buffer (Santa Cruz), 1× in TE, and chromatin eluted in TE + 1% SDS. Cross-linking was then reversed by incubation at 65°C overnight, followed by digestion of RNA (30 min RNase incubation at 37°C) and digestion of protein (30 min proteinase K incubation at 45°C). ChIP DNA was then purified on a minElute column (Qiagen), followed by DNA library preparation (NEBNext Ultra II DNA Library Prep Kit for Illumina) and size selection of 350-550 bp fragments via gel extraction (Qiagen).

last: Lizarazo

first: Sihang

last: Zhou

first: Rajendra

last: K C

first: Yawei

last: Shen

first: Qing

last: Liu

first: Kevin

last: Van Bortle


title: Trans-regulation of heterochromatin underlies genetic variation in 3D genome contacts IV

first: Christopher

last: Baker

summary: Background Genetic variation drives phenotypic diversity and disease susceptibility. Trans-acting genetic variation coordinates genome-wide chromatin changes, yet the molecular mechanisms underlying this regulation remain largely unknown. Here, we use the power of mouse genetics to investigate how genetic variation at trans-acting loci regulates 3D chromatin interactions. Results Genetically variable 3D interactions were identified using HiChIP to map H3K27ac-associated regulatory elements in C57BL/6J (B6) and DBA/2J (D2) embryonic stem cells (ESCs). We identified 4,962 strain-differential interactions (~5% of total interactions), 71% of which overlapped chromatin accessibility quantitative trait loci (caQTL), establishing that chromatin interaction variation is predominantly heritable. These differential interactions showed coordinated changes in chromatin state and gene expression, with stronger interactions associated with increased accessibility and transcription. Notably, loci regulated in trans exhibited a unique chromatin signature where weaker interactions were enriched for H3K9me3-marked heterochromatin. This pattern was 20-fold more enriched at trans-regulated targets compared to cis, implicating heterochromatin in trans-regulation of 3D genome structure. Analysis of F1 hybrids revealed dominant repressive effects, consistent with heterochromatin-mediated trans-regulation. To causally test this mechanism, we generated reciprocal congenic mouse strains carrying a Chr13 trans-QTL region on otherwise inbred genetic backgrounds. Integrated multiomic profiling of congenic ESC lines demonstrated that this single locus coordinates changes in H3K9me3, H3K27ac, chromatin accessibility, and 3D contact frequency at hundreds of distal genomic regions. Remarkably, 73-83% of differential interactions at Chr13 trans-QTL targets changed in the predicted direction, demonstrating that heterochromatin-mediated trans-regulation coordinately regulates hundreds of regulatory loci. Conclusions This work establishes heterochromatin formation as a mechanism by which genetic variation at trans-acting loci coordinates changes across chromatin accessibility, histone modifications, and 3D genome organization, providing a framework for understanding how early developmental chromatin states could generate phenotypic variation while preserving essential developmental programs.

overall_design: ChIP-seq of the histone modification H3K27ac and H3K9me3 in C57BL/6J and DBA/2J, B6.D2-(rs30079041-rs51756099)/Bakr (QJ), and D2.B6-(rs29224292-rs51756099)/Bakr (XE) mouse embryonic stem cells (2 or 3 biological/technical replicates each)


title: Autophagy enhancement ameliorates tau burden and neurofilament pathology in sporadic PSP-RS neurons

city: Catanzaro

first: Barbara

last: Puccio

address: Viale Europa

department: Dept of Surgical and Medical Sciences

country: Italy

institute: Magna Graecia University of Catanzaro

summary: Progressive supranuclear palsy, Richardson’s syndrome subtype (PSP-RS), is a tauopathy marked by early axonal pathology and neurodegeneration. Modeling sporadic PSP-RS in human neurons remained a major challenge. Here, we generated midbrain dopaminergic (mDA) neurons from induced pluripotent stem cells (iPSCs) derived from idiopathic PSP-RS patients and healthy controls. Combined transcriptomic and proteomic analysis revealed reduced dopaminergic differentiation and synaptic function, alongside increased phosphorylated and oligomeric Tau, neurofilament accumulation, axonal swelling, and endoplasmic reticulum disorganization. These alterations coincided with impaired autophagic flux and elevated levels of phosphorylated mTOR. Pharmacological inhibition of mTOR restored autophagy and reduced neurofilament and tau pathology. Collectively, our findings implicate mTOR-dependent autophagy dysfunction as a key driver of early axonal pathology of PSP-RS and highlight autophagy modulation as a promising therapeutic avenue.

overall_design: RNA-seq profiling of iPSC-derived dopaminergic neurons from pHC and spPSP at DIV60

first: Raffaele

last: Covello

first: Giorgia Lucia

last: Benedetto

first: Stefania

last: Scalise

first: Caterina

last: Gabriele

first: Desirèe

last: Valente

first: Clara

last: Zannino

first: Pietro Hiram

last: Guzzi

first: Andrea

last: Quattrone

first: Marco

last: Gaspari

first: Aldo

first: Elvira Immacolata

last: Parrotta

first: Giovanni

last: Cuda


title: Trans-regulation of heterochromatin underlies genetic variation in 3D genome contacts I

overall_design: ATAC-seq in C57BL/6J, DBA/2J, B6.D2-(rs30079041-rs51756099)/Bakr (QJ), and D2.B6-(rs29224292-rs51756099)/Bakr (XE) mouse embryonic stem cells (2 or 3 technical replicates each)


title: Trans-regulation of heterochromatin underlies genetic variation in 3D genome contacts II

overall_design: H3K27ac HiChIP C57BL/6J and DBA/2J mouse embryonic stem cells (2 biological replicates each)


title: Distinct Control of Histone H1 Expression within the Histone Locus Body by CRAMP1 [BiSulfite-seq]

first: SHASHANK

last: SRIVASTAVA

overall_design: To evelaute the methyation state of the histone gene promoter, actively proliferating RPE1hTERT cells treated with non-targetting (NT) siRNA were subjected reduced representation bisulfite sequencing.

first: Justin

last: Bodner

first: Qianli

first: Benjamin

last: Singer

first: Daniel

last: Foltz


title: Trans-regulation of heterochromatin underlies genetic variation in 3D genome contacts III

first: Christopher

last: Baker

overall_design: H3K27ac Dovetail MNase HiChIP in C57BL/6J and DBA/2J, B6.D2-(rs30079041-rs51756099)/Bakr (QJ), and D2.B6-(rs29224292-rs51756099)/Bakr (XE) mouse embryonic stem cells (2 technical replicates each)


title: Decoding human tRNA modifications and crosstalk by enhanced single-read analysis

first: Mahdi

last: Assari

state: Illinois

address: 1380 E HYDE PARK BLVD APT 806

department: Chemistry

institute: The University of Chicago

summary: tRNA modifications regulate gene expression and protein synthesis. Human tRNAome contains ~40 chemical modification types distributed on average at 13 sites in cytosolic tRNA and 6 sites in mitochondrial tRNA. tRNA modifications display dynamic patterns dependent on cell type and cell state, underscoring the need for advancing methodologies to assess their variations and crosstalks transcriptome-wide. Here, we develop enhanced single-read analysis of tRNA crosstalks (eSLAC), an integrative platform that combines the NGS sequencing method of multiplex small RNA sequencing (MSR-seq), expanded capability to measure pseudouridine (Ψ), 5-formylcytidine (f5C), and N4-acetylcytidine (ac4C), and a single-read analysis pipeline that examines the modification-modification and modification-charging crosstalks. We achieve assessments of over 60% of all human tRNA modification sites and assign Ψ sites to three Ψ writer enzymes. Both Ψ-Ψ and Ψ-charging have strong positive crosstalks. Applying polysome tRNA profiling, we identify differential tRNA isodecoder utilization and tRNA Ψ variations in the E-site versus A and P sites on the polysome. Our approach establishes a foundation for revealing the interconnectedness and the functional complexity of the tRNA modome.

overall_design: Wild-type (WT) cells were analyzed with no treatment (NT), bisulfite treatment (BS), or picoborane treatment (PB) to assess baseline and chemically-induced modification signatures. To dissect the role of specific pseudouridine synthases, bisulfite-treated samples from PUS1, TRUB1, and PUS7 knockout (KO) lines were included. Polysome-associated and input (total) RNA fractions from WT cells were also analyzed with and without bisulfite treatment to evaluate ribosome-associated tRNA modifications. All conditions were performed with biological replicates to ensure robustness in differential modification detection.

first: Brandon

last: Chew

first: Marek

last: Sobczyk

first: Chenyou

last: Zhu

first: Hoang Anh

middle: V

last: Tran

first: Dominika

last: Rudzka

first: Wen

last: Zhang

first: Tao

last: Pan

first: Mohammad Amin

last: Bayat Tork


title: Mechanistic Study on METTL3-Mediated m6A Modification of PDE4D in Zearalenone-Induced Testicular Injury in Mice

city: Harbin

first: Lige

last: Bao

state: Heilongjiang

address: 600 Changjiang Road, Xiangfang District, Harbin 150030, P. R. China

institute: Northeast Agricultural University

summary: Zearalenone (ZEA) is a non-steroidal estrogenic mycotoxin that causes marked testicular injury and male reproductive toxicity, but the involvement of RNA N6-methyladenosine (m6A) modification in this process remains unclear. In this study, we used Balb/c mice and mouse Sertoli TM4 cells to investigate whether ZEA-induced testicular damage is mediated by m6A dysregulation. Global m6A levels and the expression of m6A regulators were first examined, revealing that ZEA exposure significantly decreased overall m6A methylation and downregulated the methyltransferase METTL3 in mouse testes and TM4 cells. We then performed MeRIP-seq (m6A-seq) combined with RNA-seq on testes from control and ZEA-treated mice to profile ZEA-induced changes in the m6A epitranscriptome and transcriptome. Integrated analysis identified 615 differential m6A peaks and 529 differentially expressed genes, with 76 genes showing both altered m6A modification and mRNA expression. KEGG pathway enrichment indicated prominent involvement of the cAMP signaling pathway, tight junctions and inflammatory signaling. Among these candidates, phosphodiesterase 4D (PDE4D) emerged as a key m6A-regulated target. ZEA increased PDE4D expression while reducing its m6A level, whereas METTL3 overexpression enhanced m6A modification on PDE4D, promoted PDE4D mRNA decay, restored cAMP content and reactivated the cAMP–PKA–CREB anti-inflammatory pathway. Functionally, METTL3 overexpression or PDE4D knockdown alleviated ZEA-induced inflammatory cytokine upregulation, disruption of blood-testis barrier–related junction proteins and TM4 cell proliferation arrest. These data demonstrate that ZEA impairs testicular function at least in part by suppressing METTL3-mediated m6A modification of PDE4D and inhibiting the cAMP–PKA–CREB pathway, providing an epitranscriptomic mechanism for ZEA-induced male reproductive toxicity.

overall_design: This submission includes total testicular RNA samples from male Balb/c mice assigned to vehicle control and zearalenone (ZEA)–exposed groups (n = 3 biological replicates per group). Testes were collected from individual mice after in vivo exposure, and RNA from each mouse was used to generate both m6A-enriched (MeRIP-seq) and matched input (RNA-seq) libraries. Vehicle-treated samples serve as reference controls for ZEA-treated samples to assess the effects of ZEA exposure on testicular m6A methylation and gene expression.

first: Jiaqi

last: Hu

first: Yongze

last: Huang

first: Yitong

last: Lu

first: Jiaxin

first: Zhiyong

last: Wu

first: Jichang

last: Li


title: Comprehensive analysis of tonsillar gene expression and the tonsillar microbiota in patients with palmoplantar pustulosis and pustulotic arthro-osteitis

city: Shinjuku

first: Satomi

last: Kobayashi

state: Tokyo

address: 2-5-1 Nakaochiai

institute: Seibo International Catholic Hospital

summary: Background: Tonsillectomy improves or cures symptoms in patients with palmoplantar pustulosis (PPP) and suppresses disease progression in patients with pustulotic arthro-osteitis (PAO), highlighting the important role of tonsils in the pathogenesis of PPP/PAO.  Objective: To identify active inflammatory pathways in the tonsil tissue of patients with PPP/PAO, and to clarify the characteristics of tonsillar microbiota.  Methods: We assessed gene expression in tonsil tissue removed from Japanese adults with PPP/PAO or recurrent tonsillitis (RT)/sleep apnea syndrome (SAS) using microarray and quantitative reverse transcription polymerase chain reaction analysis. We also performed a comprehensive analysis of the tonsillar microbiota (tonsillar crypts) using next-generation sequencing. Potential associations between tonsillar gene expression and bacterial composition were evaluated.  Results: Twenty-five tonsils from patients with PPP/PAO and 15 tonsils from patients with RT/SAS were included. The gene expression of inflammatory cytokines and molecules involved in the Th17, Th2, and Treg pathways was significantly higher in the tonsillar tissue of patients with PPP/PAO than in patients with RT/SAS. There were no significant differences in genus-level tonsillar microbiota between the two groups. Correlation analysis revealed a significant positive correlation between Streptococcus spp. and the expression of Th17 and Th2 pathway genes. Correlation patterns were similar between the PPP/PAO and RT/SAS groups for Streptococcus spp. but differed for the other genera.  Conclusion: The tonsils of patients with PPP/PAO are in a complex inflammatory state, with enhanced Th17, Th2, and Treg responses. Members of the Streptococcus genus may be involved in the induction of inflammatory characteristics in PPP/PAO.

overall_design: This observational study was conducted from July 2020 to November 2022. Tonsil tissue removed at Seibo International Catholic Hospital from Japanese adult patients as part of their PPP/PAO, recurrent tonsillitis (RT), or sleep apnea　syndrome (SAS) treatment was used. Gene expression analysis was performed to identify molecular variations in inflammatory pathways in the tonsillar crypt tissue of patients with PPP/PAO using patients with RT/SAS as a comparator. A comprehensive analysis of the tonsillar microbiota was conducted to elucidate the tonsillar bacterial composition of patients with PPP/PAO. A correlation analysis was conducted to evaluate potential associations between tonsillar gene expression and bacterial composition.

first: Masato

last: Komai


title: Distinct Control of Histone H1 Expression within the Histone Locus Body by CRAMP1

first: SHASHANK

last: SRIVASTAVA

overall_design: To evaluate the acute gene expression changes that occur dependent on CRAMP1 activity we used HEK293T cells that contain a degron tag at the endogenous locus.  TT-seq  was conducted following degradation of CRAMP1 by dTAG addition at defined times.

first: Shashank

last: Srivastava

first: Daniel

last: Foltz


title: SARS-CoV-2 Variant-Dependent Alterations in Nasopharyngeal Microbiota and Host Inflammatory Response

city: Santiago

first: mario

middle: Alberto

last: maulen

state: Región Metropolitana

address: Amunategui 425, depto 31

department: Facultad de Ingenieria

country: Chile

institute: Universidad San Sebastian

summary: SARS-CoV-2 infection alters both the nasopharyngeal microbiota and host inflammatory environment. In this study, nasopharyngeal samples collected in Chile during different phases of the pandemic were analyzed using 16S rRNA gene sequencing (V3–V4) and RT-qPCR quantification of IL-2, TNF-α, IFN-γ and IL-1ra. Machine-learning models (Random Forest and K-Nearest Neighbors) were applied to integrate microbial community profiles, cytokine expression, and SARS-CoV-2 variants (Gamma, Lambda, Delta). The results show variant-dependent immunomicrobial signatures characterized by TNF-α-driven inflammation and the expansion of opportunistic bacterial genera such as Acinetobacter, Prevotella, and Staphylococcus. These findings provide a comprehensive overview of the interplay between viral infection, microbiome structure, and inflammatory responses and highlight the utility of combining microbiome and cytokine profiling with machine-learning approaches to discriminate infection outcomes across SARS-CoV-2 variants.

overall_design: Nasopharyngeal swab samples were collected in Chile between April 2021 and August 2021 for SARS-CoV-2 diagnosis and variant identification. Samples were tested by RT-qPCR, and variants (Gamma, Lambda, Delta) were determined using Hydrolysis Probe–based assays. Bacterial community profiling was performed by sequencing the V3–V4 region of the 16S rRNA gene using Illumina MiSeq technology. Raw reads were demultiplexed and processed using the DADA2 pipeline for quality filtering, denoising, chimera removal, and generation of amplicon sequence variants (ASVs). The resulting ASV table, taxonomic assignments (SILVA-138), and sample metadata constitute the processed data provided in this submission. The study aims to characterize variant-associated changes in nasopharyngeal microbial communities during SARS-CoV-2 infection.

first: Mario

last: Maulén

first: Ignacio

last: Pezoa

last: León

first: Ela

last: Dominguez

first: Alberto

last: Martin

first: Waldo

last: Díaz-Vásquez


title: Distinct Control of Histone H1 Expression within the Histone Locus Body by CRAMP1 [ATAC-seq]

overall_design: To determine chromatin binding patterns of CRAMP1, we created RPE-1 PKO hTERT-immortalized cells that express a V5-tagged CRAMP1 construct.  ChIP-seq  was conducted in the above cells using a V5 antibody.

first: Vadlamani

last: Pranathi


title: Caspase inhibition restores dopaminergic identity through the PKA–CREB–BDNF axis in Parkinson’s disease neurons

first: Barbara

last: Puccio

summary: The progressive loss of dopaminergic identity in midbrain neurons is a hallmark of Parkinson’s disease (PD), contributing to synaptic dysfunction and neurodegeneration. While a subset of PD cases is linked to genetic mutations, the majority are sporadic (sPD) and of unknown etiology. Current therapies offer only symptomatic relief and do not prevent neurodegeneration, underscoring the urgent need for disease-modifying strategies targeting actionable molecular pathways. Here, we used human induced pluripotent stem cell (hiPSC)-derived midbrain dopaminergic neurons (mDAs) from sporadic PD patients to investigate early alterations in neuronal identity, plasticity, and survival. We found that PD-derived mDAs exhibit upregulation of phosphorylated α-synuclein, marked reductions in dopaminergic markers (TH, NURR1), deficient dopamine handling, and impaired synaptogenesis. Transcriptomic and protein analyses revealed sustained activation of apoptotic caspases (caspase-3, -7) and downregulation of the PKA–CREB–BDNF signaling axis, which underpins dopaminergic differentiation and synaptic maturation. Pharmacological inhibition of caspases with Q-VD-OPh restored pCREB, BDNF, and downstream dopaminergic markers, leading to morphological recovery and functional synaptic rescue. Inhibition of PKA with H89 abrogated these effects, positioning the caspase–PKA–CREB cascade as a critical regulator of dopaminergic identity in PD neurons. These findings define a novel non-apoptotic role for caspases in disrupting the transcriptional program of mDAs and identify a druggable pathway capable of rescuing key aspects of dopaminergic function in a patient-derived cellular model. This work provides a mechanistic rationale for targeting caspase signaling in early-stage PD.

overall_design: RNA-seq profiling of iPSC-derived dopaminergic neurons from pHC and spPD at DIV60

first: Giorgia Lucia

last: Benedetto

first: Raffaele

last: Covello

first: Stefania

last: Scalise

first: Caterina

last: Gabriele

first: Desirèe

last: Valente

first: Clara

last: Zannino

first: Pietro Hiram

last: Guzzi

first: Pierangelo

last: Veltri

first: Andrea

last: Quattrone

first: Verdon

last: Taylor

first: Marco

last: Gaspari

first: Aldo

first: Elvira Immacolata

last: Parrotta

first: Giovanni

last: Cuda


first: Simon

last: Lizarazo

address: 505 S Goodwin Ave

department: Molecular and Integrative Physiology

institute: University of Illinois Urbana Champaign

type: Non-coding RNA profiling by high throughput sequencing

overall_design: HEK293 (ATCC) were cultured in complete Dulbecco’s Modified Eagle’s Medium (DMEM) (Corning) supplemented with 10% fetal bovine serum ( Corning) and 1% Penicillin-Streptomycin. Cells were maintained in 10-cm dishes by seeding 1 x 10^6 cells with complete medium every 2-3 days. Cells were maintained in a humidified atmosphere at 37 C with 5% CO2. For ATAC-Seq, 100,000 cells were collected following overexpression of eGFP, LMNA, LMNB1, or LMNB2. Libraries were prepared using the ATAC-Seq Kit (Active Motif) according to the manufacturer’s protocol. For small RNA-Seq, cells from the same overexpression conditions (eGFP, LMNA, LMNB1, or LMNB2) were recollected, and total RNA enriched for small RNAs was extracted using the mirVana PARIS Kit (Thermo Fisher Scientific) following the manufacturer’s instructions. Libraries were prepared and sequenced on the NovaSeq X Plus (Illumina) platform. All sequencing was performed at the University of Illinois, Roy J. Carver Biotechnology Center.

first: Sihang

last: Zhou

first: Ruying

last: Cheng

first: Rajendra

last: K C

first: Yawei

last: Shen

first: Qing

last: Liu

first: Kevin

last: Van Bortle


title: DBSOMA: A Machine Learning Method that Identifies Chemical Modulators of Transcriptional States Uncovers Effectors of Beta-Cell Maturation

city: Brookline, MA

first: Timothy

middle: Robert

last: Kunz

state: MA

address: 120 Babcock St, Apt 2

department: Stem Cell and Regenerative Biology

institute: Harvard

summary: There are currently few high-throughput ways to determine the aptness of applying the transcriptional readout of a biological perturbation to specific systems. Herein we use density analysis of transcriptional correlations to computationally predict whether a given perturbation readout is relevant to Stem Cell derived islet (SC-Islet) maturation. The approach, Denisty Based Self-Organizing Map Analysis (DBSOMA), first learns patterns of gene expression represented in scRNA-seq sets by clustering genes with the Self-Organizing-Map (SOM) algorithm. Perturbation expression profiles and other gene lists are then projected onto the SOM grid, where the degree of clustering is determined by the Density-Based Spatial Clustering of Applications with Noise (DBSCAN) algorithm. Filtering based on the degree of structure and the degree of overlap with a desired state yields candidate perturbagens for use in that system. Here we applied DBSOMA to SC-Islet maturation and identified known and novel regulators of β-cell maturation.

overall_design: The DBSOMA tool was used to predict compounds from among L1000 transcriptional response signatures which may affect beta cell maturation in vitro. A subset of these predicted compounds were then incorporporated into the standard SC-islet differentiation protocol in planar cultures. After treatment through stage 5 and a week a of stage 6, whole islet cultures were submitted for bulk RNA sequencing by Admera Health.


title: RNA-seq analysis of gene expression regulated by CRAMP1

first: SHASHANK

last: SRIVASTAVA

overall_design: To evelaute the gene exprseion changes that occur dependent on CRAMP1 activity we created HEK293T cells thata contain a degraon tag at the endogenous locus.  RNA-seq  was conducted following degradation of CRAMP1 by dTAG addition at defined times.

first: Shashank

last: Srivastava

first: Daniel

last: Foltz


title: Single Cell Transcriptome Signatures of Sarcoidosis in Lung Immune Cell Populations

city: Denver

first: Camille

last: Moore

state: CO

address: 1400 Jackson St.

institute: National Jewish Health

summary: Rationale: To identify cell specific molecular changes associated with sarcoidosis risk and progression, we aimed to characterize the cellular composition, gene expression patterns, and cell-cell interactions in BAL cells from patients with sarcoidosis (both progressive and non-progressive) and healthy controls. Methods: Single cell RNA-seq data were collected on 12 sarcoidosis and 4 control participants. We combined scRNA-seq data from these participants with our previously collected data on 4 sarcoidosis and 10 control participants for a final sample size of 16 sarcoidosis cases (8 progressive and 8 non-progressive) and 14 controls. Following initial preprocessing in Cell Ranger, data were quality controlled, combined, and clustered in Seurat. We tested differences in cell proportions by disease group using F-tests on cell proportions and differences in gene expression using pseudobulk analysis. Cell to cell communication and pathway analysis were performed using CellChat. Results: We identified five macrophage populations: resident, high metallothionein (MT) resident, recruited, profibrotic recruited, and proliferating macrophages. Each subpopulation displayed unique gene expression profiles, with notable differential expression of genes and pathways linked to sarcoidosis in resident macrophages, recruited macrophages, and proliferating macrophages. We also observed changes in gene expression associated with disease progression in resident and recruited macrophages. In non-macrophages cells, we observed a significant reduction in the number of B cells in sarcoidosis patients compared to controls. Among T cell populations, we identified specific transcriptional alterations at gene and pathway level. Additionally, we observed distinct differences in cell-to-cell interactions of macrophages and T cells between sarcoidosis patients and healthy controls. Conclusions: These findings underscore the complexity of immune cell involvement in sarcoidosis and highlight potential cellular and molecular targets for further investigation.

overall_design: All sarcoidosis subjects met the ATS/ERS criteria (DOI: 10.1164/rccm.202002-0251ST) for tissue biopsy confirmation of diagnosis of sarcoidosis. The non-progressive phenotype was defined as having either acute (i.e. consistent with Lofgren’s syndrome) or non-acute disease presentation, no new organ involvement, lung function testing with <10% decline in FVC or FEV1, <15% decline in DLCO, and stable chest imaging within 2 years after BAL. The progressive phenotype had a non-acute disease presentation; lung function testing with ≥10% decline in FVC or FEV1; or ≥15% decline in DLCO; worsening chest imaging; and/or if they required initiation of systemic immunosuppressive treatment any time up to 2 years after BAL.

first: Shu-Yi

last: Liao

first: Cheyret

last: Wood

first: Arunangshu

last: Sarkar

first: Jonathan

last: Cardwell

first: Kristyn

last: MacPhail

first: Margaret

last: Mroz

first: Christina

last: Riley

first: Kara

last: Mould

first: Clara

last: Restrepo

first: Li

last: Li

first: Lisa

last: Maier

first: Ivana

last: Yang


title: Plasminogen small RNA cargo promotes immunogenicity and inhibits enzymatic activity [7369-DM]

city: Nashville

first: Danielle

last: Michell

state: TN

address: 2220 Pierece Ave

department: Department of Medicine

institute: Vanderbilt Univ. Medical Center

summary: Plasminogen (Plg), the pro-enzyme of the serine-protease plasmin, is a lipoprotein-like particle in biofluids. Plg transports (oxidized) phospholipids and has the ability to accept free cholesterol from macrophages, two processes normally observed with lipoproteins. We have previously reported the biological functions of cell-free small RNA (cf-sRNA) circulating on lipoproteins. We hypothesized that Plg also transports functional cf-sRNAs. Indeed, both human and bovine Plg samples were observed to transport sRNAs (25-60nt in length) in plasma. Small RNA sequencing analyses found that Plg carries both host and non-host (microbial) sRNA. Plg samples were observed to accept sRNAs from donor macrophages in efflux studies and were observed to have moderate affinity (Kd=µM range) towards candidate host and microbial sRNAs, as quantified by microscale thermophoresis. Using PCR and bulk RNA sequencing, we discovered that Plg-sRNAs confer, in large part, Plg’s pro-inflammatory cytokine responses in macrophages. RNase treatments of both human and bovine Plg were found to significantly increase Plg’s enzymatic activity, as observed through both activity assays and clot lysis assays. Collectively, results from this study suggest that Plg is a novel circulating lipoprotein-like ribonucleoprotein and support that sRNA cargo negatively regulate Plg’s enzymatic function and enhance Plg’s immunogenicity. Therefore, Plg-sRNA cargo and its receptors present new therapeutic targets to control fibrinolysis, as well as wound and systemic inflammation.

overall_design: sRNA sequencing of human high density lipoproteins (HDL) and lysine purified plasminogen (PLG) from healthy donors and those with familial hypercholesterolemia

first: Michell

last: Danielle L.

first: Vickers

last: Kasey C.


title: Transcription factor REST regulates activation and growth of human Hepatic Stellate Cells

city: Solna

first: Vladimir

middle: S.

last: Shavva

address: Solnavägen 30

department: Department of Medicine, Solna

institute: Karolinska Institutet

summary: Activation of hepatic stellate cells (HSC) is a key component in the progression of metabolic dysfunction-associated steatotic liver disease (MASLD) to metabolic-associated steatohepatitis (MASH) and hepatocellular carcinoma (HCC). Targeting HSC activation to prevent MASH and HCC pathogenesis showed promise in mouse models, suggesting that development of therapeutic strategies to abrogate HSC activation could be a promising approach to combat liver disease. Metabolic alterations were suggested to play a pivotal role in HSC activation, yet the mechanisms linking these processes have not been fully elucidated. Here we observe a key role of the RE1-silencing transcription factor (REST) in linking HSC activation, lipid utilization, and mitochondrial metabolism, suggesting that REST is a mechanistic link between HSC metabolism and activation.

overall_design: Primary human Hepatic Stellate Cells isolated from four donors were activated by plating and transfected with scrambled siRNA or siRNA targeting REST. RNA was isolated 12 days following transfection and plating.


title: Plasminogen small RNA cargo promotes immunogenicity and inhibits enzymatic activity

overall_design: Total RNA sequencing of bone marrow-derived macrophages treated with PLG exposed to Rnases

first: Danielle L

first: Kasey C

last: Vickers


title: Sensory nerve-derived CGRP controls osteoclastogenesis by limiting macrophage bioenergetics in bone repair

city: Gold coast

first: Jiaying

last: Liu

address: G40, parkland drive

country: Australia

institute: Griffith university

summary: Bone healing is a tightly orchestrated, multiphase process that requires coordinated interactions between immune cells and skeletal cells. Sensory nerves act as intrinsic effectors of the inflammatory response, whose role in osteoimmunology during healing remains poorly defined. Using a bone healing model with sensory denervation, it’s shown that sensory nerves protect bone repair by suppressing excessive osteoclastogenesis. During the acute inflammatory phase, sensory nerves are upstream regulators of macrophage activation. At the molecular level, calcitonin gene-related peptide (CGRP), a sensory neuron–derived neuropeptide, is identified to modulate macrophage activation by restricting key functions such as migration, phagocytosis, and pro-inflammatory cytokine production. Importantly, CGRP rapidly constrains adenosine triphosphate (ATP) synthesis with limited mitochondrial respiration in activating macrophages, accompanied by downregulating genes associated with oxidative phosphorylation and mitochondrial complex components. Following the metabolic checkpoint, macrophages exposed to CGRP show attenuated osteoclastogenic capacity, with decreased secretion of multiple key factors that support osteoclast differentiation and survival. Together, these findings indicate the neuro–immune–metabolic axis in bone healing, where sensory nerve–derived CGRP influences macrophage bioenergetics and thereby contributes to osteoimmunological regulation. It emphasizes the potential of incorporating sensory signals into therapeutic strategies, particularly those targeting immunometabolism in bone regeneration.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: RNA-seq profiling of the healing tissue from periodontal bone defect on day 3, day 7 and day 14 with normal sensory innervation, as well as periodontal healing tissue with sensory denervation on day 3, 7 and day14.

first: Ting

last: Zhang

first: Lili

first: Kevin

last: Dudley


title: Effect of SRPK1 knockdown on gene expression of HEK293T cell line

city: Beijing

first: Xiao-Hui

last: Tan

address: 8, Xishiku Street, Xicheng District

institute: Peking University First Hospital

summary: To investigate the effect of SRPK1 on gene expression of HEK293T, we used SRPK1 shRNA to stably reduce the expression of SRPK1 via lentiviral transduction, which was then subjected to RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HEK293T with stable knockdown of SRPK1 or not.

first: Rui-Li

last: Guan


title: Resistance to BRAF inhibitors drives melanoma sensitivity to Chk1 inhibition

city: Rio de Janeiro

first: Patricia

last: Abrao Possik

state: RJ

address: Rua Andre Cavalcanti 37

country: Brazil

institute: Brazilian National Cancer Institute

summary: BRAF inhibitor-resistant melanomas (BRAFiR) acquire (epi)genetic and functional alterations that enable them to evade alternative treatments. Identifying these alterations is critical to advancing treatment strategies. Here, we explored the effect of Chk1 inhibition (Chk1i) on BRAFiR cells, revealing higher sensitivity compared to treatment-naïve cells both in vitro and in vivo. Using FUCCI-labeling and time-lapse microscopy, we show that S phase progression is required for Chk1i-induced cytotoxicity in BRAFiR cells, but not in treatment-naïve cells. Replication stress markers, including reduced BrdU incorporation and increased phospho-RPA and γH2AX, were exclusive to BRAFiR cells exposed to Chk1i. Untreated BRAFiR cells exhibited upregulated DNA replication genes, reduced ongoing replication fibers and increased origin firing, suggesting intrinsic replication changes. MAPK pathway reactivation in treatment-naïve cells mimicked BRAFiR traits, increasing sensitivity to Chk1i. These findings indicate that Chk1i exploits elevated replication stress in BRAFiR, highlighting its therapeutic potential in overcoming MAPK inhibitor resistance in melanoma.

overall_design: RNA-seq profiling of 888mel melanoma cell lines and their BRAFi-resistant derivatives treated for 6 and 12 hours with the Chk1 inhibitor GDC0575

middle: G

last: Carvalho

last: Possik

first: Juliana

last: Kenski

first: Daniel

last: Moreira

first: Mariana

last: Boroni


title: Colorectal cancer-derived osteopontin rewires macrophages into a pro-metastatic M2 state via the PI3K/AKT/CSF1-CSF1R axis

city: GuangZhou

first: xiaoxia

last: Liang

address: 26 Yuancun Er Heng Road

institute: Sixth Affiliated Hospital of Sun Yat-sen University

summary: Metastasis remains the primary cause of mortality in colorectal cancer (CRC), with a 5-year survival rate of approximately 14%, despite advancements in treatment. SPP1+ tumor-associated macrophages (TAMs) are implicated in promoting tumor growth, angiogenesis, and immune evasion. Osteopontin (OPN), encoded by the SPP1 gene, is a critical regulator of TAMs M2 polarization and CRC metastasis. However, the mechanisms by which CRC-derived OPN interacts with M2-TAMs to promote metastasis remain unclear. Here, We found that OPN is highly expressed in metastatic CRC and is associated with poor prognosis. However, knockdown or overexpression of OPN in CRC cells did not directly affect tumor cell invasion and metastasis, which is inconsistent with previously reported trends. Additionally, OPN expression levels were positively correlated with M2-like TAMs infiltration. Using an in vitro co-culture system, we found that CRC-derived OPN induces M2-like polarization of TAMs, and the two mutually promote chemotactic migration. Mechanistically, high OPN expression activates the PI3K/AKT signaling pathway in macrophages, promoting the secretion of CSF1, which induces M2-like polarization of macrophages to facilitate tumor metastasis. Finally, in a mouse metastasis model, blocking the CSF1/CSF1R axis with a CSF1R inhibitor reduced the recruitment of M2-TAMs and CRC tumor metastasis.Our study demonstrates that the OPN/CSF1/CSF1R/PI3K/AKT axis plays a crucial role in CRC metastasis. Blocking CSF1/CSF1R reduces M2-TAM infiltration and tumor metastasis, thereby enhancing the therapeutic efficacy for metastatic CRC.

overall_design: RNA-seq profiling of THP-1 cells treated with PMA and co-cultured with conditioned medium (CM) from SW480 cells with OPN knockdown derivatives (shNC and sh) for 48 hours.


title: Runx1 transcriptional regulation of microglia critically modulates opioid analgesia and withdrawal in humans and rodents

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

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

overall_design: Refer to individual Series


title: Hyperactive PI3K-delta in Th1 and Th2 differentiation [RNA-seq]

city: Bethesda

first: Tom

last: Hill

state: Maryland

address: NIHBC 10 - CLINICAL CENTER BG RM 11N244A, 10 CENTER DR

institute: NIAID

summary: We are examining the consequences of activating mutations in PI3K-delta in Th1 vs. Th2 differentiation. Using the house dust mite (HDM) model of allergic airway inflammation, which drives potent Th2 responses in vivo, we have found mice expressing hyper-activated PI3K-delta show impaired Th2 differentiation and instead favor Th1 cell differentiation. We would like to further investigate this aberrant CD4 differentiation profile using scRNA-seq to characterize PI3K-delta regulated aspects of type II immunity.

overall_design: Investigate differences between AIL2 mutants & controls, in Th0, Th1 & Th2 stimulated cells

first: Swartzberg

last: Pamela

first: Golec

last: Dominic

first: Gazzinelli-Guimaraes

last: Pedro

first: Chauss

last: Daniel

first: Yu

last: Kang

first: Hill

last: Tom

first: Nagashima

last: Hir/oyuki

first: Nivelo

last: Luis

first: Cannons

last: Jennifer

first: Perry

last: Jillian

first: Joshi

last: Ilin

first: Periera

last: Nicolas

first: Cruz

last: Anthony

first: Marcus Silva Oliveira

last: Fabrício

first: Druey

last: Kirk

first: Lack

last: Justin

first: Nutman

last: Thomas

first: Villarino

last: Alejandro

first: O'Shea

last: John

first: Afzali

last: Behdad


title: Myocardial Fibroblasts are a Primary Source High Molecular Weight Hyaluronan Production in the Failing Heart

city: Louisville

first: Richa

last: Singhal

state: KY

address: 580 S Preston Street, Baxter II Building, Office 321B

department: Medicine

institute: University of Louisville

summary: Background: The extracellular matrix provides organizational context for solid organs. During disease, such as acute myocardial infarction, the composition of the extracellular matrix changes remarkably. One of the most notable changes in the extracellular matrix is in the accumulation of collagen; however, hyaluronan rivals collagen in terms of its abundance. Yet, the extent to which specific cells and enzymes may contribute to such accumulation has been largely unexplored. Here, we hypothesized that activated cardiac fibroblasts produce hyaluronan via hyaluronan synthase 2 (HAS2). Methods and Results: Using immunofluorescence, biochemical extraction, and ELISA, we show that hyaluronan accumulates following myocardial infarction and persists through at least four weeks. Our analyses of failing heart RNA sequencing data suggest fibroblasts are the cells most changed in expression of HAS2. Given these insights, we used HAS2 gain- and loss-of-function approaches to examine the extent to which activated cardiac fibroblasts produced hyaluronan. TGF-induced activation of fibroblasts caused a significant increase in Has2 mRNA and concomitant accumulation of hyaluronan greater than 1 MDa in size. Deletion of Has2 abrogated TGF-induced production of hyaluronan. In addition, overexpression of Has2 was sufficient to cause an increase in hyaluronan accumulation in the absence of TGF-induced activation. Given the magnitude of hyaluronan production, and that hyaluronan has been reported to have biologic activity, we then queried whether the primary functions of fibroblasts (proliferation, migration, and collagen production) were impacted by hyaluronan treatment. Our data indicated negligible impacts of Has2 on proliferation, migration, and collagen production. Exposing fibroblasts to exogenous hyaluronan also had minimal impact on fibroblasts. We also assessed whether fibroblast-borne Hyal2 plays a role in degradation of hyaluronan, and our data indicated little impact of Hyal2 on hyaluronan accumulation (or even any impacts on the transcriptional profile of fibroblasts). Conclusion: Activated fibroblasts produce high molecular weight hyaluronan, and the production of hyaluronan depends on Has2. The robust production of hyaluronan by fibroblasts does not appear to impact fibroblast function.

overall_design: Cardiac fibroblasts were treated with adenovirus to force deletion of Hyal2 as well as overexpression of Hyal2.

first: Steven

middle: P

last: Jones

first: Danielle

last: Little

middle: A


title: Myocardial Fibroblasts are a Primary Source High Molecular Weight Hyaluronan Production in the Failing Heart [RNASeq_Has2_overexpression]

overall_design: Cardiac fibroblasts were treated with adenovirus to force overexpression of Has2.


title: Restoration of endogenous transcription factor activity by nuclease-deficient Cas9VPR prevents cardiac failure upon stress II

city: Göttingen

first: Laura

last: Zelarayan

address: Robert-Koch-Str 40

institute: University Medical Center Göttingen

summary: Cardiac remodeling is linked to maladaptive transcriptional networks, but identifying and targeting key factors with potential to reverse these processes is still a challenge. We employed network-based analysis of single cell heart transcriptomes to compute the transcription factor activities triggering heart failure. We found that the regulation of KLF15 activity is a major driver of cardiomyocyte failure. Through the use of CRISPR/nuclease-deficient (d)Cas9-based transcriptional regulation, we demonstrated that restoration of endogenous Klf15 expression and activity in cardiomyocytes was sufficient to mitigate pathological transcriptional reprogramming and preserved cardiac function in mice and human myocardial models. We also showed that KLF15 is a downstream targetable factor in the broad TGFβ-mediated stress response in human cardiomyocytes, controlling transcriptional embryonalization. Lastly, we engineered a therapeutically applicable mini-dCas9VPR variant suitable for adeno-associated viral delivery, eliciting endogenous KLF15 transcriptional activation in human cardiomyocytes. This case study presents a therapeutic strategy for restoring the stress-induced downregulation of essential genes to prevent heart failure with broader implications for other disease contexts.

overall_design: Engineered heart muscle (EHM) were generated by combining CRISPRa hiPSC-cardiomyocytes (3.85x10^5) transduced with either non-targeted control gRNAs (NT) or KLF15 gRNAs and with human foreskin fibroblasts (1.65x10^5) in a bovine collagen matrix. These EHM were cast into a 48-well plate (myriamed GmbH) and cultured initially in IMDM (Gibco) supplemented with 4% B27 minus insulin, 100 ng/mL IGF-1, 5 ng/mL VEGF165, 10 ng/mL FGF-2, 100 U/mL penicillin, 100 µg/mL streptomycin, and 5 ng/mL TGF-β1 for 3 days. From day 4 onwards, TGF-β1 was removed. Starting from day 14, the medium was switched to alpha-MEM (Gibco) with 4% B27 minus insulin, 1% MEM non-essential amino acids, 100 ng/mL IGF-1, 5 ng/mL VEGF165, 10 ng/mL FGF-2, 100 U/mL penicillin, and 100 µg/mL streptomycin. On day 28, EHM were either cultured on flexible, silicone poles (control, healthy = Flex) or subjected to mechanical stress by culturing them on rigid metal poles (stressed = Fix) for an additional 7 days. Total RNA was extracted for RNA sequencing to analyze gene expression changes under the different experimental conditions (NT vs. KLF15 gRNA and Flex vs. Fix).

first: Eric

last: Schoger

first: Federico

last: Bleckwedel

last: Zelarayán