title: Hfq orchestrates a robust RNA-RNA interaction network in Acinetobacter baumannii. [RNA-Seq]

city: Iowa City

first: Michael

middle: J

last: Gebhardt

state: IA

address: 431 Newton Road, 200A EMRB

department: Department of Microbiology and Microbiology

institute: University of Iowa

summary: A key challenge for understanding the role(s) played by short, non-coding RNAs (sRNAs) in bacteria is identifying the mRNA targets regulated by the sRNAs. Because the Hfq protein mediates the interactions between many sRNAs and the corresponding target mRNAs, one apporach to identify the mRNA targets of sRNAs is to capture sRNA:mRNA interactions occuring on Hfq by exposing cells to UV-irradiation, which forms cross-links between nucleic acids and proteins. We subjected cells of A. baumannii  strain AB5075 and a derivative of AB5075 harboring a C-terminal VSV-G epitope on Hfq to UV-irradiation, immune-precipitated the Hfq-RNA complexes, ligated neighboring RNA molecules together with RNA Ligase, and then purififed the resulting RNAs. These RNAs were converted into cDNA libraries and sequenced using the Illumina NextSeq platform and then subjected to RIL-seq analysis pipeline (version 0.78) to identify chimeric RNA molecules.

overall_design: Total RNA-seq data files to accompany the RIL-seq data on WT AB5075 and a derivative thereof that carrys a chromosomally-encoded Hfq-VSVG for two different growth conditions

first: Simon

last: Dove


title: Ototoxicity-induced c-Fos activation underlies regenerative capacity in vestibular sensory epithelia

status: Public on Dec 02 2025

city: SHANGHAI

first: yunzhong

last: zhang

state: SHANGHAI

address: 83 fenyang road, xuhui district

department: Department of ENT Institute and Otorhinolaryngology

country: China

institute: Eye & ENT Hospital of Fudan University

type: Expression profiling by high throughput sequencing

summary: Transcriptomic changes in neonatal mouse utricles ex vivo cultured samples following AAV-PHP.eB-mediated Fos plasmid transfection.

overall_design: Expression profiling by high-throughput sequencing performed on the Fos overexpression group and the gentamicin-only injury group, respectively.


title: CAR NK cell production from human cord blood cells is enhanced by stimulation of the IL15 receptor on NK progenitor cells

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: Human cord blood (CB)-derived CAR NK cells have demonstrated significant anti-tumor efficacy in clinical trials. We recently reported that CB-derived CAR NK cells are  mainly derived from CD7+CD56-CD34-HLA-DR-Lin- NK precursors. Here we show that CAR NK cell production from human CB cells can be enhanced by stimulation of the IL15 receptor on NK precursors. In CB CD56-CD34-HLADR-Lin- cells, the IL15 receptor was expressed exclusively on the CD7+ NK cell precursors but not on the CD7- population. The production of mature NK cells from the purified NK cell precursors or CD3- CB cells was significantly enhanced by using K562 feeder cells expressing membrane-bound (mb) IL15 in addition to 4-1BB ligand and mbIL21. The in vitro and in vivo anti-tumor efficacy of CAR NK cells generated using K562 feeder cells expressing 4-1BBL, mbIL15 and mbIL21 was comparable to that of CAR NK cells generated using the K562 feeder cells expressing only 4-1BBL and mbIL21. These results suggest that the use of K562 feeder cells expressing mbIL15 in addition to 4-1BBL and mbIL21 increases the yield of CAR NK cell production from CB cells, while the clinical efficacy and safety of the CAR NK cells generated should be tested in the future.

overall_design: RNA-seq profiling of CD7+CD56-CD34-HLADR-Lin-  cells and CD7-CD56-CD34-HLADR-Lin- cells

first: Yosuke

last: Kogue

first: Naoki

last: Hosen


title: STING-induced programmed necrosis modulates the collagen-rich immunosuppressive microenvironment in meningiomas

city: Chicago

first: Mark

last: Youngblood

state: IL

address: 676 N. St. Clair Street; Suite 2210

department: Department of Neurological Surgery

country: USA

institute: Northwestern University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Hfq orchestrates a robust RNA-RNA interaction network in Acinetobacter baumannii. [RIL-Seq]

overall_design: Applying RIL-seq to WT AB5075 and a derivative thereof that carrys a chromosomally-encoded Hfq-VSVG for two different growth conditions


title: A spatiotemporal atlas of orchiectomy-induced modulation of cellular composition and gene expression in the mouse prostate [scRNA-seq]

city: Ann Arbor

first: Evan

middle: T

last: Keller

state: Michigan

address: 1109 Geddes Avenue

department: Urology

institute: University of Michigan

summary: Mice models are commonly used to further our understanding of the function of the prostate and response to androgen depletion. We used both spatial transcriptomics and single cell transcriptomics to determine how the mouse prostate degrades after castration. We identified changes in each of the prostate lobes that couuld be tracked over time as well as changes in the immune profile and of the composition of fibroblasts within the prostate. In addition to several previously identified fibroblast subtypes that we were able to show were altered in response to androgen depletion, we identified a novel fibroblast subtype present only in the castrated prostate.

overall_design: Mice were castrated and prostates isolated and used for 10x Chromium single cell sequence fifteen days later

first: Greg

last: Shelley

first: May

last: Alison

first: Allison

last: May

first: Jinlu

last: Dai

first: Sethu

last: Pitchiaya

first: Arvind

last: Rao


title: Obesity-driven inflammation enables triple-negative breast cancer progression through immunosuppression

city: Chapel Hill

last: Coleman

state: NC

address: 135 Dauer Dr

institute: University of North Carolina

summary: control and obese,  C57BL6J mice with or without sulindac treatment were injected with E0771, metMWntlung, or metMWntliver cells and tumor growth was monitored

overall_design: total RNA was isolated from each tumor and analyzed by microarray

middle: F

first: Stephen

middle: D

last: Hursting


title: Whole-genome sequencing and analysis of a novel strain Streptococcus oralis CRC211 from colorectal tumor

city: Shanghai

first: yunjie

last: shi

address: No 800，Xiangyin Road

institute: Naval Medical University

summary: This study provides a comprehensive genomic characterization of Streptococcus oralis CRC211, a novel bacterial strain isolated from colorectal tumor tissue, through whole-genome sequencing and comparative analysis. The high-quality assembled genome (15.03 Mb, 40.94% GC content) contains 2 prophage regions spanning 160.5 kb, which may facilitate horizontal transfer of virulence genes. Functional annotation identified 3,674 genes, with significant enrichment in metabolic pathways (amino acid and carbohydrate metabolism) and virulence factors (116 genes in VFDB), including adhesins and biofilm-associated proteins that likely promote tumor colonization. Comparative genomic analysis revealed CRC211 shares 92.29% average nucleotide identity with reference S. oralis strains, while pan-genome analysis demonstrated an open genome structure with 1,222 conserved core genes. The strain also carries 75 antimicrobial resistance genes, suggesting potential clinical relevance. Notably, the genomic profile indicates adaptations for nutrient acquisition and immune evasion in the tumor microenvironment. These findings establish CRC211 as a CRC-associated strain with distinct genomic features that may contribute to tumor progression, providing crucial insights for future investigations into its oncogenic mechanisms and potential applications in microbiota-based diagnostics or therapeutics for colorectal cancer.

first: Yunjie

last: Shi

first: Ling

last: Liu

first: Weiliang

last: Hou

first: Hao

last: wang


title: Exosomal Non-Coding RNAs Drives Multiple Myeloma Progression

city: Indiana University

first: Reza

last: Shahbazi

address: 980 W Walnut st

institute: Indiana University

summary: This study aimed to investigate gender-specific dysregulation of exosomal non-coding RNAs (ncRNAs) and their regulated mRNAs in multiple myeloma (MM). Exosomes were isolated from six MM cell lines (LP1, NCI-H929, JJN-3, U-266, KMS-11, and ANBL-6), bone marrow aspirates from 24 MM patients (8 female and 16 male), and 7 healthy controls. Exosome characterization using NanoSight NS300 confirmed consistent size distribution and concentration across samples. RNA sequencing was performed on exosomal RNA cargo to profile long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and mRNAs, enabling analysis of their regulatory roles in MM pathogenesis.

overall_design: RNA-Seq profiling was performed on exosomal RNA isolated from six multiple myeloma (MM) cell lines (LP1, NCI-H929, JJN-3, U-266, KMS-11, and ANBL-6), bone marrow aspirates from 24 MM patients (8 females and 16 males), and 7 healthy control samples.

first: Samaneh

last: Maleknia

first: Sanam

last: Rezaei Benam

last: Ahmann

first: Rafael

last: Fonseca

first: Diane

last: Jelinek


title: Generation of human blastoids from three-dimensionally cultured primed human pluripotent stem cells

city: Kyoto

first: Kaori

last: Mutsuda-Zapater

address: Yoshidahonmachi, Sakyo Ward

institute: Kyoto university

summary: A human blastoid, which is an artificial human blastocyst, and has a potential as great tool to investigate fundamentals during the development and establish in vitro models to study the pregnancy failure and birth deficiency, without the use of a human embryo. In 2021, although some methods to generate blastoids have been reported, they used human naïve pluripotent stem cells, which often show genomic instability during in vitro culture. Here, we introduce the simple, robust and scalable method to generate human blastoids from more stable human primed embryonic stem cells. By using non-cell-adhesive hydrogel, hESC aggregates received the chemophysical cellular environment, and forming the asymmetric blastoid structure with the cellular distribution like a human blastocyst. The obtained blastoids also showed the capability the implantation in vitro. This model will enable to elucidate the underlying mechanisms of human pre- and post-implantation process, leading to assisted reproductive technology.

overall_design: We analyzed cDNA profiles StepOnePlus from RNAs in individual KhES1 human embryonic stem cells and human blastoids generated from KhES1 cells using Illumina Next seq 500.

first: Satoshi

last: Imamura

first: Xiaopeng

last: Wen

first: Shiho

last: Terada

first: Kyoko

last: Sawada

first: Kei

last: Saito

first: Ken-ichiro

last: Kamei


title: Protamine expression in somatic cells condenses chromatin and disrupts transcription without altering DNA methylation

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

summary: Protamines play a crucial role in nuclear condensation during spermiogenesis, a process associated with significant chromatin remodeling and replacement of histones by protamines. While much research has focused on the function of protamines in sperm development and fertility, their effects in non-sperm cells remain largely unexplored. In this study, we investigated the impact of overexpressing murine and human protamine 1 and 2 (PRM1 and PRM2) on nuclear architecture, histone eviction, DNA methylation, and transcription in HEK293T cells and mesenchymal stromal cells (MSCs). Overexpression of protamines resulted in nuclear condensation and particularly PRM1 showed notable enrichment in nucleoli and cycle abnormalities. Immunofluorescence staining indicated a significant reduction in specific histone modifications (H3K9me3, H3K4me1, and H3K27Ac) in response to protamine expression, especially in MSCs. Interestingly, despite these changes in nuclear organization, the methylome remained largely stable upon protamine expression. However, particularly expression of protamines significantly diminished transcription, especially of the ribosomal genes upon PRM1 expression. Our studies indicate that PRM1 and PRM2 condense distinct genomic regions in somatic cells, resulting in widespread silencing of gene expression.

overall_design: HEK293T cells were transfected with empty vector, human PRM1-EFGP, or  human PRM2-EGFP. Three days after transfection cells were sorted and high EGFP cells were used to isolate total RNA and perform RNA-Seq analysis.

first: Deepika

last: Puri

first: Alexandra

last: Bott

first: Monica

last: Varona Baranda

first: Esra

last: Dursun Torlak

first: Gina Esther

last: Merges

first: Hubert

last: Schorle


title: T cell-mediated SIV dissemination into the CNS: a single-cell transcriptomic analysis

city: Omaha

first: Howard

middle: S

last: Fox

state: Nebraska

address: 42nd and Emile

institute: University of Nebraska Medical Center

summary: HIV infection disrupts immune function in both the periphery and central nervous system by depleting CD4+ T cells and inducing uncontrolled inflammation. CNS infection is initiated when infected blood leukocytes, thought to be monocytes and/or CD4+ T cells, infiltrate the brain and facilitate viral entry. However, the composition and phenotypic characteristics of these "Trojan horse" cells during acute infection remain poorly understood. To address this gap, we performed single-cell RNA sequencing (scRNA-seq) on the brain and blood of rhesus macaques 12 days post-inoculation (p.i.) with simian immunodeficiency virus (SIV). Our analysis of brain immune cells revealed a distinct cell cluster co-expressing both myeloid and lymphoid genes, raising the possibility that brain myeloid cells may engulf CD4+ T cells entering the brain from the blood, and that the lymphocytes represent the Trojan horse. To examine this finding, we conducted scRNA-seq on a macrophage–T cell (Mac-T) coculture system. Interestingly, we identified a substantial population of Mac-T cells under different culture conditions. Furthermore, our analysis suggested that specific chemokines could serve as markers to distinguish Mac-T cells from technical doublet artifacts in scRNA-seq data. Beyond this intriguing cell population, our study identified additional lymphocyte subsets and uncovered phenotypic T cell shifts during acute infection. Notably, we observed a sharp decline in proportion of CD4+ memory T cells alongside an expansion of proliferating CD4+ cytotoxic T cells in both the blood and brain. These cytotoxic CD4+ T cells exhibited high expressions of viral entry receptors (e.g., CD4 and CCR5) and adhesion molecules (e.g., LFA-1 and VLA-4), and had the highest number and proportion of infected cells in the brain, suggesting their role as "Trojan horse" cells that facilitate viral dissemination into the CNS. Additionally, their elevated expression of cytotoxic molecules indicates potential pathogenic effects on the brain. Comparative transcriptomic analysis further revealed that brain lymphocytes were more mature than their blood counterparts, with naïve T cells being nearly absent in the brain. To further examine these findings and assess their temporal dynamics, we integrated publicly available scRNA-seq data from brain lymphocytes at 21 days p.i. This analysis corroborated our key observations and highlighted progressive changes in lymphocyte phenotypes and transcriptomic profiles over time. Overall, this study provides a comprehensive transcriptomic characterization of brain lymphocytes and blood CD4+ T cells during acute SIV infection, identifying a candidate lymphocyte phenotype that can contribute to CNS infection

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: For studying brain lymphocyte responses in acute SIV infection, 92T was non-infected control samples and other three (93T, 94T, 95T) were in acute-infected group. The rhesus macaques in the acute-infected group were infected with Simian Immunodeficiency Virus (SIV) for 12 days.  For studying monocyte-derived macrophages (MDMs) and jurkats cocultivation, we had four different groups: NoApop, CD95, Campto, NoCoCul groups. The MDMs and jurkats were cocultured in NoApop, CD95, and Campto groups. For NoCoCul groups, the jurkats and MDMs were mixed before library preparation to assess the artefactual dual capture.  In CD95 and Campto groups, the jurkats were induced apoptosis by CD95 or camptothecin prior to cocultivation.

first: Meng

last: Niu

first: Benjamin

middle: G

last: Lamberty

first: Katy

last: Emanuel

first: Xiaoke

last: Xu


title: Comprehensive analysis of aberrant alternative splicing and RNA binding proteins regulators associated with age-related sensorineural hearing loss

city: Chongqing

first: Wei

last: Yu

address: No. 83, Xinqiaozheng Street, Shapingba District, Chongqing, China

institute: The Second Affiliated Hospital of Army Military Medical University of the People's Liberation Army of China

summary: The mechanisms of RNA binding proteins (RBPs) regulate alternative splicing(AS) in age-related sensorineural hearing loss (SNHL) is unclear.We used RNA-seq data from the database to identify AS events and differentially expressed RNA binding proteins (DERBPs) among Control, Age8 and Age12 group in the mouse models of age-related SNHL. GO database and KEGG pathway were used to analysis the function, the co-expression relationship between regulated alternative splicing(RAS) and DERBPs were established to investigate the mechanism of RBPs regulating AS in age-related SNHL. An age-related SNHL mouse model was successfully reconstructed and cochlear tissues were obtained for experimental validation of the RNA-seq data. AS regulation significantly different in age-related SNHL. The Chronological group exhibited 198 RAS, 1012 differentially expressed genes (DEGs), and 25 DERBPs. Diseased group identified 187 RAS, 523 DEGs, and 14 DERBPs. The reconstructed animal model of age-related SNHL confirmed the enrichment of RAS in the positive regulation of GTPase activity pathway and the validated transcriptome expression of Isg15, Myom1, and Acan were found to be consistent with the trend observed in the data analysis. Besides, co-expression analyses of Isg15 and Uap1 trends were consistent with experimentally validated trends and they were negatively correlated. Isg15 may affect the mechanism of age-related SNHL by regulating Uap1, which requires further investigation.

overall_design: We established age-related mouse models and employed whole transcriptome sequencing data to identify genes associated with age-related sensorineural hearing loss, including both mRNA and long non-coding RNA (lncRNA) genes.

first: Zeping

last: Qin

first: Xinyu

last: Liang

first: Xianbai

last: Zhu

first: Guojing

last: Tan

first: Baiyang

last: Ren

first: Yanghong

last: Xiang

first: Can

last: Zou

first: Xueqin

last: Zhou

first: Hongyang

last: Wang

first: Anchun

last: Deng


title: Adipocyte-specific Mlkl knockout mitigates obesity-induced metabolic dysfunction by enhancing mitochondrial functions.

city: Paris

first: Jérémie

last: Gautheron

address: 27 rue Chaligny

country: France

institute: Inserm, Sorbonne Université

summary: Obesity is a global epidemic characterized by chronic low-grade inflammation and metabolic dysfunction, with adipose tissue playing a pivotal role in these processes. The mixed lineage kinase domain-like pseudokinase (MLKL) is a critical mediator of necroptosis but also exhibits noncanonical roles in metabolic regulation. This study aimed to investigate the adipocyte-specific functions of MLKL in obesity. Using adipocyte-specific Mlkl knockout (MlklAdi-KO) mice, we observed reduced susceptibility to high-fat diet (HFD)-induced obesity, enhanced glucose tolerance, and improved insulin sensitivity. MlklAdi-KO mice showed elevated energy expenditure independent of changes in food intake or locomotor activity, correlating with increased mitochondrial function and reduced lipid accumulation in white adipose tissue (WAT). Transcriptomic analyses of WAT revealed significant modulation of pathways linked to oxidative phosphorylation, inflammation, and lipid metabolism. Furthermore, metabolomic profiling highlighted reductions in TCA cycle intermediates, acylcarnitines, and pro-inflammatory amino acids in MlklAdi-KO mice under HFD conditions. These findings were accompanied by improved hepatic lipid profiles and decreased steatosis, underscoring systemic benefits of adipocyte-specific Mlkl deletion. Mechanistically, Mlkl deficiency altered adipocyte differentiation, potentially via modulation of Wnt10b and transcriptional regulators such as Foxa1. These results position MLKL as a promising therapeutic target for obesity and related metabolic disorders, emphasizing the need for future studies using conditional knockout and overexpression models to explore its cell-specific and noncanonical functions in metabolic regulation.

overall_design: RNA-seq profiling of epididymal adipose and liver tissue of AdipoCre Mlkllox/lox mice and their WT littermates after 16 weeks of Normal Chow Diet or High Fat Diet.

first: Juliette

last: Tokgozoglu

first: Valeria

middle: V

last: Pistorio


title: Isolation and characterization of an islet-associated CD45- MHC class II+ cells using single cell RNA sequencing.

city: La Jolla

first: Alain

last: Domissy

state: CA

address: 10550 North Torrey Pines Road

department: Immunology

institute: The Scripps Research Institute

summary: MHC-II is expressed in normal murine and human islets by cells that are located at the periphery of the islet and associated with the efferent vasculature. These cells are non-hematopoietic in origin based on their non-expression of CD45, and split in two families, vascular and fibroblastic, based on their gene transcription profiles, their morphology, and their location.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Fresh human islets (IIDP, Prodo laboratories) were washed once with PBS prior to digestion with trypsin EDTA (Corning) for 20 minutes on ice with light shaking every 5 minutes68. Islets were gently dissociated with a P1000 pipette prior to stopping the enzymatic reaction with DMEM-10% serum. Cell suspensions were filtered through 0.7μm nylon screens. Dissociated islets were stained with antibodies against HLA-DR-Bv421 (L243, BioLegend) and CD45-FITC (HI30, BioLegend) in FACS buffer with 2% serum. PI-/CD45-/HLA-DR+ or PI-/CD45+/HLA-DR+
Mice Pancreata were perfused with 0.5mg/mL of collagenase P (Sigma-Aldrich) through the common bile duct and digested at 37ºC for 17min. After several washes, pancreatic slurry was passed through a 0.419mm wire mesh strainer. A density gradient was established by layering histopaque1077 (Sigma-Aldrich) and serum-free RPMI, and sample loaded on top. After centrifugation at 600 g for 20 min, islets were collected at the histopaque/media interface, washed and hand-picked under a dissecting microscope. An average of 300-400 islets were recovered per mouse. For making single cell suspension, islets were digested with trypsin-EDTA and washed extensively before being counted.Dissociated islets were stained with antibodies against MHC II-PE (OX-6, BioLegend) and CD45-FITC in FACS buffer with 2% FBS. PI-/CD45-/MHC II+ or PI-/CD45+/MHC II+ cells were sorted into semi-skirted 96 well PCR plates with 5ul of RT solution per well.

first: Luc

last: Teyton

first: Don

last: Clarke


title: Obesity-driven inflammation enables triple-negative breast cancer progression through immunosuppression [scRNA-Seq]

first: Michael

last: Coleman

summary: control and obese,  C57BL6J mice with or without sulindac treatment were injected with E0771 cells and tumor growth was monitored

overall_design: whole tumors were dissociated by cold protease, and subjected to 10x genomics scRNAseq analysis

first: Stephen

last: Hursting


title: Colony morphology altered by Myh9 deficiency uncoupled from pluripotency

city: hangzhou

first: kuang

last: junqi

address: No.18 Shilongshan Road

institute: westlake University

summary: The naïve mouse embryonic stem cells, characterized by high nuclear/cytoplasmic ratio, and dome-shaped colonies with smoothly contoured edges, exhibit self-renewal and pluripotency. However, it is unclear about the biological significance of dome-like morphology in relation to pluripotency. Here, we generate stable ES cell lines with a flat morphology, capable of sustained monolayer growth and efficient single-cell clonogenic capacity, by knocking out non-muscle myosin heavy chain IIA. Notably, even when deprived of the typical dome-like colony morphology, the ES cells retain their self-renewal capacity and pluripotency to differentiate into the three germ layers. Our data disprove the long-standing paradigm in stem cell field that the dome-shaped colony architecture is intrinsically linked to naïve pluripotency, instead demonstrating that core pluripotency circuitry operates independently of this morphological constraint.

overall_design: We analyzed the transcriptome in mESCs upon Myh9 deficiency.

first: Junqi

last: Kuang

first: Duanqing

last: Pei


title: Macropinocytosis and vascularization detrmine response to mTOR inhibitors in lung squamous cell carcinomas

city: Los Angeles

first: Milica

last: Momcilovic

address: 10833 LeConte Ave

institute: University of California Los Angeles

summary: Resistance to small molecule inhibitors targeting key metabolic pathways in lung tumors remains a significant challenge in personalized cancer therapy. In this study, we investigated the mechanisms of resistance to the small molecule mTOR inhibitor TAK228 across lung squamous cell carcinoma (LUSC) cell lines, xenograft models, and patient-derived xenografts (PDXs). Our findings reveal that LUSC cells adapt to mTOR inhibition by engaging macropinocytosis, a form of endocytosis that facilitates enhanced uptake of extracellular nutrients, thereby increasing amino acid availability. Co-inhibition of both mTOR and macropinocytosis using small molecule inhibitors effectively reduced tumor growth. Additionally, we identified angiogenesis as a key mechanism limiting the efficacy of mTOR inhibition in vivo. Notably, prolonged treatment of PDXs with TAK228 and the glutaminase inhibitor CB-839 led to upregulation of vascularization, which coincided with a rebound in tumor growth despite the continued presence of both inhibitors. These findings highlight adaptive mechanisms that contribute to resistance to targeted therapies and provide insight into potential clinical strategies to overcome resistance in lung cancer.

overall_design: RNA-Seq profiling of (a) H1703 xenografts treated with Vehicle or TAK228 or TAK228+EIPA; (b) H2170 xenografts treated with Vehicle or TAK228; (c) PDX005 treated with Vehicle or TAK228+CB839.


title: BRD4 and MYB Inhibition Overcomes Venetoclax Resistance in EVI1-rearranged Acute Myeloid Leukemia

city: Kobe

first: Weijia

last: Zang

address: Hyogo, Kobe, Chuo Ward, Minatojima Minamimachi, 6 Chome−３−7

department: Department of Hematology-Oncology

institute: Foundation for Biomedical Research and Innovation at Kobe

summary: EVI1-rearranged acute myeloid leukemia (AML) with inv(3)(q21q26) or t(3;3)(q21q26) represents a distinct and aggressive subtype characterized by poor prognosis and limited treatment options. However, the optimal strategy to overcome resistance to conventional therapy remains elusive. Building upon observations correlating EVI1 overexpression with reduced sensitivity to venetoclax, a BH3-mimetic inhibitor, we investigated the mechanisms of resistance to venetoclax in combination with hypomethylating agents in inv(3)/t(3;3) AML cells. Utilizing novel murine models recapitulating inv(3) AML with concomitant SF3B1 mutations, we conducted comprehensive phenotypic and transcriptomic analyses in the presence or absence of venetoclax-containing therapy. Despite initial therapeutic responses, manifested as partially prolonged survival and myeloid differentiation, resistant leukemic cells demonstrated enhanced dependency on BRD4 and MYB pathways with a dormant phenotype. Notably, inhibition of either BRD4 or MYB significantly augmented the efficacy of venetoclax and hypomethylating agents in both murine and patient-derived AML models harboring inv(3) and SF3B1 mutations. These findings elucidate the transcriptional dynamics underlying venetoclax resistance and propose alternative therapeutic strategies targeting BRD4 and MYB as promising avenues for improving outcomes in patients with EVI1-rearranged AML. Our work highlights the necessity for innovative combination therapies to address the multifaceted mechanisms of resistance in this high-risk leukemia subtype.

overall_design: Vehicle, VEN/DAC treatment group, and VEN/DAC resistance group mouse c-Kit+ cells were sorted by MACS. RNA was extracted, then Poly(A)- selected, and stranded DNA libraries were prepared.

first: Yui

last: Koike

first: Koutarou

last: Nishimura

first: Daichi

last: Inoue


title: Mechanisms of Activation and Serotonin release from Human Enterochromaffin Cells

city: Cambridge

first: Fiona

last: Gribble

state: Cambridgeshire

address: Box 289 Addenbrooke's Hospital, Hills Road

department: Medical Research Laboratories

country: United Kingdom

institute: University of Cambridge

summary: Gastrointestinal (GI) enterochromaffin (EC) cells are specialised sensors of luminal stimuli. They secrete most of the body’s serotonin (5-HT), and are critical for modulating GI motility, secretion, and sensation, while also signalling satiety and intestinal discomfort. The aim of this study was to investigate mechanisms underlying the regulation of human EC cells, and the relative importance of direct nutrient stimulation compared with neuronal and paracrine regulation.

overall_design: Intestinal organoids from human duodenal biopsies were modified using CRISPR-Cas9 to specifically label EC cells with the fluorescent protein Venus. EC cells were purified by fluorescence-activated cell sorting for analysis by bulk RNA sequencing.

first: Christopher

middle: A

last: Smith

first: Constanza

last: Alcaino

middle: M


title: The outer retina in young P23H retinitis pigmentosa mice overexpresses critical components of synaptic transmission

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research

summary: To determine the gene expression changes in the retina of 1-month-old P23H/Gnat2-KO versus Gnat2-KO mice, we generated single-cell suspensions, and performed scRNA-Seq (10X Genomics).

overall_design: One retina from two male and two female mice per group (total n=4 per group; groups: Gnat2-KO and P23H/Gnat2-KO mice) were pooled to prepare two single-cell suspensions at a final concentration of 1,000 cells/µl. Freshly dissociated cells (~10,000) were loaded into a 10x Genomics Chromium Single Cell system using v3 chemistry following the manufacturer's instructions.

first: Henri

last: Leinonen


title: Genetic Alterations in KEAP1-NRF2 system Induced by Anti-Cancer Treatments Contribute to Cisplatin Resistance in Head and Neck Squamous Cell Carcinoma

city: Sendai

first: Yuki

last: Nakayama

address: 2-1 Seiryo-machi,Aoba

department: Biochemistry and Molecular Biology

institute: Tohoku Medical Megabank Organization, Tohoku University

summary: Cisplatin (CDDP) is widely used in the chemotherapy of head-and-neck squamous cell carcinoma (HNSCC), but its efficacy is limited in recurrent cases. This highlights the need for a deeper understanding of the mechanisms underlying the CDDP resistance. We hypothesized that chemoradiotherapy with CDDP may induce hyperactivation of NRF2, contributing to CDDP resistance. To investigate this, we first examined NRF2 expression in clinical HNSCC samples by immunohistochemistry and assessed the occurrence of somatic mutations in KEAP1 and NRF2 genes using public databases. We found that high NRF2 expression was associated with poorer prognosis compared to low expression. Furthermore, recurrent HNSCC cases following post-operative chemoradiotherapy exhibited higher NRF2 accumulation than their corresponding primary tumors. Database analysis also revealed occurrence of frequent mutations in KEAP1 associated with CDDP treatment. We then assessed the role of NRF2 in HNSCC malignancy utilizing seven parent (P) HNSCC cell lines and their CDDP-resistant (CR) derivatives. Of these P-CR pairs, three CR cell lines exhibited NRF2 upregulation. Two of them carried KEAP1 mutations and one carried an NRF2 mutation, both present in P and CR lines. These NRF2-high CR lines showed elevated expression of NRF2 target gene and activation of xenobiotic metabolism and reactive oxygen species pathways. Treatment with mitomycin C (MMC), known for its synthetic lethal activity against NRF2-activated cancer cells, showed strong cytotoxicity in NRF2-high CR lines. These findings indicate that the KEAP1-NRF2 system plays a critical role in the development of CDDP resistance and that MMC represents a promising therapeutic option for NRF2-high/CDDP-resistant HNSCC.

overall_design: RNA-seq profiling of Head and neck squamous cell carcinoma cell lines and their cisplatin (CDDP)-resistant derivertives.

first: Keiko

last: Taguchi

first: Masayuki

last: Yamamoto


title: Integrative profiling of liver cancer reveals lysine metabolic reprogramming and patient stratification with distinct immune microenvironment and therapeutic responses

city: Xi'an, Shaanxi Province

first: Yungang

last: Xu

state: Shaanxi

address: Xi'an, Shaanxi Province

institute: Xi'an Jiaotong University

summary: Liver cancer is a major global health challenge with high aggressiveness and recurrence rate. Metabolic reprogramming is one of the cancer hallmarks and allows tumor cells to adapt to drastic changes, supporting their rapid growth, survival, and proliferation under various conditions. Several amino acids have been found to undergo metabolic reprogramming in tumors and thus being potential anti-tumor targets. However, the characterization and implication of lysine metabolic reprogramming in tumors remains largely unexplored. Therefore, we carried out transcriptomics, proteomics, single-cell omics, immunohistochemistry, and multiplex immunofluorescence profiling on tumor and adjacent normal tissues obtained from 30 hepatocellular carcinoma patients to characterize the lysine metabolism in liver cancer and investigate its implications for tumor prognosis, immune microenvironment, and immunotherapy responses. Integrative analyses and quantitative evaluations revealed the reprogrammed lysine metabolism and inter-patient heterogeneity in liver cancer. The patients with lower lysine metabolism in tumors had worse prognoses and a predominance of immunosuppressive TIME, including increased infiltration of myeloid-derived suppressor cells, Tregs, TIM3+CD8+, and LAG3+CD8+T cells. These immunosuppressive cells contribute to immunotherapeutic resistance and promote tumor progression. Collectively, we highlighted the significance of lysine metabolism in shaping TIME and therapeutic responses of liver cancer, offering new insights into clinical molecular subtyping and potential therapeutic strategies.

overall_design: We performed scRNA-seq on tumor and adjacent tissues from four pairs of hepatocellular carcinoma patients using the 10x Genomics platform, and one pair of samples also underwent scTCR-seq.

first: Xinlan

last: Lu

first: Min

last: Qiang

first: Rufeng

last: Li

first: Chen

last: Guo

first: Kang

first: Yufei

last: Yao

first: Jiayi

last: Wang

first: Changcheng

first: Kangsheng

last: Tu

first: Yule

last: Chen


title: Optogenetic mitochondrial preconditioning enhances cardiomyocyte survival under stress

city: Columbus

first: Lufang

last: Zhou

state: Ohio

address: 460 W 12th Ave, BRT

institute: Ohio State University

summary: Mitochondria play a central role in preconditioning-mediated cytoprotection, yet the specific role of mitochondrial membrane potential (ΔΨm) in this process remains incompletely understood. In this study, we employed a next-generation, mitochondrial-targeted optogenetic system (mOpto) to induce precisely controlled (partial and transient) ΔΨm depolarization and investigate its role in enhancing cardiomyocyte resilience to stress. Human AC16 cardiomyocytes expressing mOpto were subjected to low-intensity LED illumination for preconditioning, followed by exposure to stressors including FCCP, H2O2, or simulated ischemia-reperfusion. mOpto-preconditioned cells exhibited significantly improved viability, attenuated ΔΨm depolarization, and reduced reactive oxygen species (ROS) production compared to non-preconditioned controls. Notably, this cytoprotective effect occurred independently of canonical ROS signaling and mitochondrial ATP-sensitive potassium channel (mitoKATP) activation. Transcriptional analysis revealed coordinated mitochondrial and metabolic reprogramming, including upregulation of genes involved in lipid biosynthesis, mitochondrial quality control, energy homeostasis, and a shift toward mitochondrial fusion. Importantly, mOpto preconditioning conferred similar cytoprotective effects in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), underscoring the translational potential of this approach. These findings demonstrate that mOpto-mediated transient ΔΨm depolarization induces a preconditioning effect that enhances cardiomyocyte resilience through the establishment of a mitochondrial "memory" and dynamic remodeling of mitochondrial function.

overall_design: RNA-Seq profiling of AC16 cells, including Control and expressing mOpto subjected to FCCP treatment with and without preconditioning

first: Seulhee

last: Kim

first: Hwayeon

last: Lim

first: Patrick

last: Ernst

first: Li

last: Zhu

first: Jiashuai

last: Zhang

last: Xie

first: Xiaoguang

last: Liu


title: Oxidative stress and GPX2 control pancreatic vs non-pancreatic cell fate in human endoderm

city: Poznan

first: Katarzyna

last: Blaszczyk

state: Wielkopolska

address: ul. Uniwersytetu Poznańskiego 6/1.87

department: Faculty of Biology, Institute of Molecular Biology and Biotechnology, Department of Gene Expression

institute: Adam Mickiewicz University

summary: The role of oxidative stress in cell fate decisions during human endoderm development remains poorly understood. Here, we show that GPX2, a key enzyme in the reactive oxygen species (ROS) scavenging pathway, plays a crucial role in directing pancreatic versus non-pancreatic cell fate decisions during in vitro human endoderm differentiation. Using hPSCs with GPX2 loss-of- or gain-of-function, we observed that GPX2-deficient cells exhibit a strong propensity to differentiate into liver-like cells, even under pancreatic-promoting conditions. Single-cell RNA sequencing, ATAC sequencing, and follow-up analyses revealed that GPX2 deficiency disrupts posterior foregut patterning, leading to the emergence of multilineage progenitors capable of generating liver- and intestine-like lineages. Phenotype rescue experiments demonstrated that manipulating oxidative stress levels by either inhibiting or promoting ROS production could mimic or revert the effects of GPX2 deficiency, respectively. Our findings highlight the critical role of oxidative stress in modulating developmental trajectories and suggest that GPX2 acts as a gatekeeper of pancreatic cell fate by influencing the expression of PDX1 and other lineage-specifying factors.

overall_design: Comparative gene expression profiling analysis of RNA-seq, scRNA-seq and ATAC-seq data for iCas9 hPSCs and its GPX2 KO derivative in different stages of differentiation towards stem cells derived beta cells.

first: Joanna

last: Szpotkowska

first: Wojciech

last: Szlachcic

first: Maja

last: Baginska

first: Magdalena

last: Socha

first: Malgorzata

last: Borowiak


title: Metabolic Reprogramming in Primary Endocervical Cells Infected by Chlamydia trachomatis

city: Kuala Lumpur

first: Heng Choon

last: Cheong

address: Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya

country: Malaysia

institute: Universiti Malaya

summary: Genital infection by Chlamydia trachomatis is the most common bacterial sexually transmitted disease worldwide, posing a significant threat to reproductive health. Its ability to persist silently in the host often delays treatment, leading to chronic inflammation and complications such as pelvic inflammatory disease, ectopic pregnancy, and infertility in females. Despite progress in understanding C. trachomatis pathogenesis, studies in primary cells remain limited. This study explored the interaction between C. trachomatis and primary human endocervical cells, revealing extensive host transcriptional changes, including strong inflammatory responses (IFN-α, IFN-γ, TNF-α), suppression of E2F targets, DNA repair, G2M checkpoint, and oxidative phosphorylation, indicating mitochondrial dysfunction. Downregulation of electron transport chain genes and phenotypic analysis showed selective TCA cycle impairments in succinate and citrate utilization. Further research is needed to uncover the mechanisms behind C. trachomatis-mitochondria interactions.

overall_design: RNA-seq profiling of primary endocervical cells (PCS-480-011) infected by C. trachomatis for 8, 24, and 40 hours.

first: Sofiah

last: Sulaiman

first: Li-Yen

last: Chang

first: Won Fen

last: Wong


title: FAM49B suppresses ovarian cancer cell growth through regulating MAPK signaling

city: Dalian

first: ning

last: shen

address: 9 Western Section,Lvshun South Street,Lvshunkou District

institute: Dalian Medical University

summary: The family with sequence similarity 49 member B (FAM49B, also known as CYRI-B) has recently attracted interest as a new player in cancer development. Upregulation of FAM49B expression has been observed in ovarian cancer tissues. Here we show that knockdown of FAM49B significantly increased ovarian cancer growth the in vitro, ovo and xenograft model. Transcriptomic analysis of FAM49B-depleted and control cells revealed that the MAPK pathway was upregulated upon FAM49B silencing. Supporting the transcription analysis, we found that knockdown of FAM49B enhanced the activation of EGFR and downstream MEK-ERK signaling, whereas FAM49B overexpression exhibited opposite trends. Overall, our data show that FAM49B acts as a suppressor of cancer cell growth in ovarian cancer through regulating MAPK signaling.

overall_design: Ovarian cancer OVCAR8 cells with stable knockdown of FAM49B and shCON as a negative control.  shCON and shFAM49B cells were extracted for RNA sequencing

first: Songshu

last: Meng

first: Sha

last: Du


title: Lamin A/C-EZH2 interaction in modulating Epithelial-to-mesenchymal Transistion in breast cancer cells

city: Pune

first: Kundan

last: Sengupta

state: Maharashtra

address: Dr. Homi Bhabha Road

department: Biology

country: India

institute: Indian Institute of Science Education and Research PUNE

summary: Epithelial-to-mesenchymal transition (EMT) is a developmentally conserved cell biological program adopted by cancer cells to metastasize to different organs. In this process, compact, cobblestone-shaped epithelial cells transform into more slender-shaped mesenchymal cells. Throughout metastasis, cells reside at various stages along the E-M spectrum. Epithelial cells are not necessarily converted to mesenchymal cells, as cells in the E-M continuum exhibit greater survival advantages and better metastatic ability than complete mesenchymal forms. During metastasis, epithelial cells traverse through narrow capillaries, inducing nucleus rupture. The nucleus is protected by type V intermediate filament proteins, Lamins, in the inner nuclear membrane, providing structural integrity, facilitating genome organization, and acting as an impediment to cell migration. Therefore, Lamin expression is downregulated to facilitate nuclear compliance during EMT, serving as a precursor for metastasis. Here, we aim to address the mechanism of Lamin downmodulation and its role in genome organization during EMT. We have attempted to address these questions in three independent and well-established breast cancer cell lines representing cells at specific stages of the EM spectrum, providing a paradigm to elucidate the role of Lamins in genome organization and function during EMT.

overall_design: RNA-Seq profiling of MCF10A cells upon Lamin A/C knockdown. siRNA for Lamin A/C was used and control non-targeting LacZ was used.

first: Balaji

last: AK

first: Santam

last: Saha


title: Single-Cell Transcriptomics on Young and Aged Bone Marrow Megakaryocyte Progenitor Cells

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: Aging associates with platelet hyperreactivity and thromboinflammation, which markedly contribute to cardiovascular disease and thrombotic events.  Here, we studied the characteristics of megakaryocyte progenitor cells (MkP) in a mouse model of aging. Single-cell RNAseq was performed on bone marrow samples from young (3 months) and old (>24 months) male and female mice.

overall_design: Young (3-month-old) and old (>24-month-old) C57BL/6 mice (6 females and 6 males per group) were purchased from Jackson Laboratory. All animal care and experiments were approved by the Institutional Animal Care and Use Committee of the University of Zurich. Femora and Tibiae were harvested and cleaned of muscle and tissue. Bone marrow (BM) was isolated and erythrocytes were removed by incubation with RBC lysis buffer. To enrich MkP cells, BM cells were stained with CD41+ and CD42d+ antibodies and sorted using MACS, followed by a BD FACS Aria III 4L. scRNA-seq dataset for each sample was generated using the Chromium system (10X Genomics). Libraries were sequenced on the Illumina NovaSeq 6000 platform. Raw data files were processed using the Cell Ranger 7.2.0 pipeline.

first: Pratintip

last: Lee

first: Soheil

last: Saravi

first: Juerg

middle: H

last: Beer

first: Christian

last: Wolfrum


title: Single nucleus RNA-seq of Kdr-FACS cells from late embryonic mouse kidney

city: Dallas

first: Thomas

last: Carroll

address: 6000 Harry Hines Blvd.

institute: UT Southwestern

summary: Here, we performed single nuclear RNA sequencing (snucRNA-Seq) to interrogate embryonic renal endothelial cells. We identified nine different endothelial cell types, and validated expression of novel candidates using multiplex RNAScope.

overall_design: Nuclei were obtained from digestion of whole kidneys. Kdr expressing cells were isolated via FACS and analyzed with snRNA-seq.

first: Peter M.

last: Luo

first: Neha

last: Ahuja

first: Ondine

last: Cleaver


title: Protective effect of mesaconate on autoimmune hepatitis via suppression of inflammatory response and oxidative stress

city: Tianjin

first: Zhang

last: Qian

address: No. 22 Qixiangtai Road, Heping District

institute: Tianjin Medical University

summary: Autoimmune hepatitis (AIH) is a severe immune-mediated inflammatory liver disease that currently lacks feasible drug treatment. Existing evidence suggests that mesaconate (MSA) exhibits immunomodulatory capacities, however, its role in AIH remains unclear. Here, we constructed a mouse model of AIH by administering concanavalin A (ConA) and conducted prophylactic administration to investigate the pharmacological effect of MSA on AIH and the underlying mechanisms of action. We found that pretreatment with MSA can effectively mitigate ConA-induced AIH by dampening the inflammatory response, oxidative stress, and apoptosis, both in vivo and in vitro. The underlying protective mechanism is associated with the inhibition of the IFN-γ-JAK1/2-STAT1 signaling pathway by MSA. Overall, our research not only validates the therapeutic potential of MSA for the management of AIH for the first time, but also provides a novel perspective and a promising therapeutic candidate for the future treatment of autoimmune disorders.

overall_design: Mice were randomized into three groups: (1) Normal control, (2) ConA, (3) MSA + ConA. The normal control group received an equivalent volume of sterile phosphate-buffered saline (PBS) via tail vein injection. ConA and MSA were dissolved in sterile PBS to achieve the specified concentrations. The ConA group received a single dose of ConA (20 mg/kg body weight, 4 mg/ml in PBS, Sigma-Aldrich, China) via tail vein injection. The MSA + ConA group received an intraperitoneal injection of MSA (250 mg/kg body weight, 50 mg/ml in PBS, Sigma-Aldrich, China) 6 hours before ConA injection. Twelve hours post-ConA administration, mice were euthanized, and  liver tissues (n=3) for RNA-Seq.

first: Qian

last: Zhang

first: Wei

last: Hong

first: Tao

last: Han


title: Regional information in dental mesenchyme

city: Seoul

first: Han-Sung

last: Jung

address: 50, Yonsei-ro, Seodaemun-gu

department: Dental School

country: South Korea

institute: Yonsei University

summary: Positional information plays a crucial role in embryonic pattern formation, yet its role in tooth development remains unexplored. In this study, we investigated the regional specification of lingual and buccal dental mesenchyme during tooth development.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data between cap and bell stage, lingual and buccal part of dental mesenchyme at cap and bell stage, and lingual and buccal part of dental mesenchyme which were cultured in vitro at cap stage.
- (Cap/Bell stage)_"W" means whole tooth germ
- "L" means lingual
- "B" means buccal

first: Eun-Jung

last: Kim


title: Lactate-mediated histone lactylation promotes melanoma angiogenesis

city: Xi’an

first: mao

last: zhao

address: No 127 of West Changle Road

institute: Xijing Hospital, Air Force Medical University

summary: The pathogenesis of cancer is rather complicated and includes multiple aspects, with metabolic reprogramming and angiogenesis as the leading hallmark characteristics. Recent reports have unveiled that the glycolytic metabolite lactate could modify histone lactylation level to epigenetically regulate gene expressions and biological processes in cancer, while the role of lactate-mediated histone lactylation in tumor angiogenesis remains elusive. By taking advantage of melanoma as the model, we demonstrate that lactate-mediated histone lactylation promotes tumor angiogenesis via IL-33/ST2 axis.

overall_design: In order to identify the key  key genes regulating angiogenesis through histone lactylation，Transwell chamber is used to co-culture HUVECs with human melanoma cell line A2058 for 72 hours to establish TA-HUVECs,Then TA-HUVEC treated with NALA (10 mM) and/or A-485 (10 μM) for 48h.

first: Mao

last: Zhao


title: Circulating miRNAs in obese heart failure patients: Case control study

city: Porto Alegre

first: Santiago Alonso

last: Tobar Leitao

state: Rio Grande do Sul

address: Rua Ramiro Barcelos 2350

department: Experimental Research Center

country: Brazil

institute: Hospital de Clínicas de Porto Alegre

summary: The main objective of this study was to identify differentially expressed circulating miRNAs in HF-obese (BMI ≥30 kg/m2 and % body fat > 25% in men and > 35% in women) and HF-lean patients (BMI < 25 kg/m2 and % body fat ≤22% in men and ≤32% in women). This case-control study was carried out using plasma samples from 20 HF patients (18-80 years with LVEF <45%) and from 10 healthy controls (blood donors) for microarray. The miRNAs were extracted with Trizol-LS reagent (396 μL plasma, 4 μL Cel-miR-39-3p, and 1.2 μL of Trizol-LS) and then analyzed on the miRNA 4.0 Affymetrix GeneChip array following the manufacturer's instructions. Raw data were normalized using Robust Microarray Average (RMA), batch effects were adjusted with Surrogate Variable Analysis (SVA), and differential expression analysis was performed with the Limma R package.

overall_design: Case-control study: 20 heart failure patients (10 obese HF patients and 10 lean HF patients)

first: Doiglas

last: Soares

first: Amanda

last: Lopes

first: Mariana

last: Recamonde-Mendoza

first: Rodrigo

last: Bueno

first: Raquel

last: Calloni

first: Nadine

last: Clausell

first: Santiago

last: Leitao

first: Andreia

last: Biolo


title: Maternal postpartum sedentary life exacerbates the metabolic cost of moderately fat rich diet in male mice

city: New York

first: Miklos

last: Toth

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Profound social and economic changes in recent generations have led to reduced physical activity and increased calorie intake, leading to a higher incidence of metabolic disease. These effects may propagate across generations amplifying the impact on descendants. Here we found that limited physical activity of dams brought about increased liver weight and lipid accumulation in the male offspring on a moderate fat calorie western-like diet from weaning to adulthood, while maternal voluntary exercise on running wheels during the postpartum period was sufficient to prevent the development of the phenotype in the otherwise sedentary offspring. Elevated fatty acid (FA) and reduced acylcarnitine levels in the liver of offspring of exercising mothers suggested increased FA flux for oxidation that with elevated mitochondrial β-oxidation indicated a maternally programmed mechanism to cope with increased fat calories. Finally, single-nucleus transcriptional profiling indicated dysregulated lipid metabolism in hepatocytes and upregulation of phagocytosis related genes in Kupffer cells/macrophages and collagen genes in and stellate cells, signs of liver damage in the offspring of sedentary but not exercising mothers. A similar combination of maternal sedentary lifestyle and increased fat calory intake from childhood could contribute to the increased incidence of obesity in recent generations.

overall_design: Exercise of mother (Run, Sed) x Diet (21%, 13%)

first: Katherine

last: Lopez

first: Madelyn

middle: R

last: Baker

first: Qiuying

last: Chen

first: Michele

last: Alves-Bezerra

first: Baran

last: Ersoy

first: Judit

last: Gal Toth

first: Faten

last: Taki

first: David

middle: E

last: Cohen

first: Steven

last: Gross


title: CD271 orchestrates skin structure, differentiation, and inflammation via PI3K/Akt and PKCα/ERK pathways

city: Modena

first: Elisabetta

last: Palazzo

address: Via del Pozzo

country: Italy

institute: Unimore

summary: The involvement of the neurotrophin network in pathological skin conditions by their common neurotrophin receptor CD271 has become recently evident. CD271 mediates various cellular responses in keratinocytes, and in vitro analysis shows that it is implicated in human interfollicular keratinocyte stem cells-transient amplifying cell switch. However, no in vivo models are available to dissect the complexity of these mechanisms, including the effect on the inflammatory response. We characterize novel mouse models, CD271cKO and CD271ciKO, where CD271 is conditionally absent in keratinocytes during development or after topical induction, respectively. We identified substantial skin changes by histology, transcriptomic, and molecular analysis, including epidermal hyperproliferation and “activated” keratinocyte signature, linked to PI3K/Akt and mitogenic pathways. KO keratinocyte displays upregulation of Ki67, PCNA, KRT5, KRT6, and P-ERK, as well as IL1α, IL8, and TGFβ. KO skin showed significant recruitment of CD45, CD4, and CD8+ cells, and release of inflammatory cytokines     . Overall, our data defines CD271 as a crucial regulator of skin homeostasis and inflammation. Our models represent exceptionally useful tools for characterization and, subsequently, development of therapies for skin conditions characterized by modulation of keratinocyte homeostatic balance.

overall_design: RNAseq profiling of CD271 conditional KO mouse skin versus Wild-type at day 1 after birth.

first: Marika

last: Quadri

first: Cristina

last: Pellegrini

first: Mirco

last: Mastrangelo

first: Maria Concetta

last: Fargnoli


title: LINC01198 activates Hippo signaling to stimulate IL-1β autocrine for enhancing vemurafenib resistance in melanoma by associating with TAOK1/2

city: GUANGZHOU

first: JIEYU

last: LIU

address: Shatainanlu

institute: South Medical University

summary: To identify the genes, especially LncRNA ,that play important roles in vemurafenib resistance in melanoma, high-throughput sequencing was performed.

overall_design: A375 cell line and A375 vemurafenib_resistence cell line that we constructed

first: Li

last: Ma

first: Liang

last: Zhou

first: Jieyu

last: Liu

first: Xiaoting

last: Liang

first: Ke

last: Wang


title: Species-Specific Regulatory Complexes Shape Quan􀆟ta􀆟ve Resistance to a Necrotrophic Pathogen in Wild Tomatoes.

city: Kiel

first: Severin

last: Einspanier

address: Hermann-Rodewald-Straße 9

department: Department of Plant Pathology and Protection

institute: Christian-Albrechts-University Kiel

summary: Wild relatives of crop species possess diverse levels of quantitative disease resistance (QDR) to biotic stresses, yet the genomic and regulatory mechanisms underlying these differences are not well understood. In particular, how QDR against a generalist necrotrophic pathogen evolved and whether it is driven by conserved or species-specific regulatory networks remains unclear. Here, we examined the transcriptomic responses of five diverse wild tomato species that span a gradient of QDR. we initially hypothesized that conserved regulatory modules might control QDR. Instead, Using differential gene expression analysis and weighted gene co-expression network analysis (WGCNA), we find instead that species-specific regulatory features, encompassing both infection-induced and constitutively expressed genes, predominantly shape QDR levels. Although we identified an ethylene response factor (ERF-D6) among candidate genes for QDR-regulation, it did not fully account for the phenotypic variation. To further dissect the evolutionary basis of these regulatory patterns, we performed phylotranscriptomic analyses on gene co-regulatory networks. Strikingly, QDR-associated gene sets were enriched for evolutionarily older genes, suggesting that ancient gene functions have been co-opted rather than derived from recent gene family expansions. These results provide new insights into the evolutionary and regulatory complexity governing QDR and underscore the importance of species-specific gene regulation in shaping resistance against a cosmopolitan necrotrophic pathogen.

sample_organism:
Solanum chilense
Solanum pimpinellifolium
Solanum pennellii
Solanum habrochaites
Solanum lycopersicoides

overall_design: QuantSeq 3' Sequencing (gene-expression profiling) experiment with five wild Solanum species (S. Chilense, S. Habrochaites, S. Penellii. S. Lycopersicoides, S. Pimpinellifolium) contrasting one susceptible and one more resistant genotype in Sclerotinia sclerotiorum infected and mock-conditions. Samples from detached leaves were collected relative to lesion development during the lesion expansion.

first: Remco

last: Stam


title: B-cell-Specific Wwox Deletion Promotes Plasmablastic Tumor Development and Pro-Inflammatory Signatures in a Myeloma Mouse Model

city: Houston

first: Yue

last: Lu

state: TX

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: Deletions and translocations affecting WWOX accompanied by loss of expression are frequently observed in B cell neoplasms and are linked to poor prognosis. Our previous research showed that Wwox deletion early in B cell development induces genomic instability, neoplastic transformation, and monoclonal gammopathies in mice. In this study, by crossing Cd19 Wwox knockout (KO) with Vk*MYC myeloma model mice, we generated a model with concurrent Wwox deletion and MYC activation, reproducing two common oncogenic alterations in B and plasma cell cancers. We observed that Vk*MYC:Wwox KO mice exhibited significantly reduced survival rates primarily due to the development of plasmablastic plasmacytomas and lymphomas. Transcriptome profiling from bone marrow derived Cd138+ plasma cells and plasmablastic tumors revealed enrichment of biofunctions related to tumorigenic phenotype and inflammation activation upon Wwox deletion in Vk*MYC mice. Wwox KO plasmablastic tumors displayed mutations affecting classical cancer genes, DNA damage response (DDR) genes, as well as overexpression of Aid/Apobec family members associated to hypermutation and DDR mutational signatures. These findings illustrate the significant pathobiological effects of B cell specific Wwox deletion and support a relevant role for WWOX loss of function in B cell neoplastic progression towards more aggressive phenotypes.

overall_design: RNA sequencing analysis of Vk*MYC:Wwox WT-BM (n=3), Vk*MYC:Wwox KO-BM (n=3), and Vk*MYC:Wwox KO-PBT (n=4) samples to evaluate comparative gene expression changes between Vk*MYC:Wwox WT-BM vs KO-BM and Vk*MYC:Wwox KO-BM vs KO-PBT groups.

first: Tabish

last: Hussain

first: Matthew

last: Bramble

first: Bin

first: Martin

middle: C

last: Abba

first: Marta

last: Chesi

first: C. Marcelo

last: Aldaz


title: Broncho brushing samples from healthy donors and Job's Syndrome patients

city: Chapel Hill

first: Ling

last: Sun

address: 125 Mason Farm RD 7230K Marsico Hall 7230K Marsico Hall

institute: UNC at Chapel Hill

summary: To find the DEGs between healthy donors and Job's Syndrome patients, we extracted RNA from broncho brushing samples collected from healthy donors and Job's Syndrome patients.

overall_design: Gene expression profiling analysis was performed on RNA obtained from the healthy donors and Job's Syndrome patients' broncho brushing samples

first: Hong

last: Dang

first: Gang

last: Chen

first: Alexandra

last: Freeman

first: Kenneth

middle: N

last: Olivier

first: Chevalia

last: Robinson


title: Single-cell analysis defines highly specific leukemia-induced neutrophils and links MMP8 expression to recruitment of tumor associated neutrophils during FGFR1 driven leukemogenesis

city: Augusta

first: John

last: Cowell

state: GA

address: 1410 Laney-Walker Blvd

institute: Augusta University

summary: Leukemias driven by activated, chimeric FGFR1 kinases typically progress to AML which have poor prognosis. Mouse models of this syndrome allow detailed analysis of cellular and molecular changes occurring during leukemogenesis. We have used these models to determine the effects of leukemia development on the immune cell composition in the leukemia microenvironment during leukemia development and progression. Single cell RNA sequencing (scRNA-Seq) was used to characterize leukemia associated neutrophils and define gene expression changes in these cells during leukemia progression. scRNA-Seq revealed six distinct subgroups of neutrophils based on their specific differential gene expression. In response to leukemia development, there is a dramatic increase in only two of the neutrophil subgroups. These two subgroups show specific gene expression signatures consistent with neutrophil precursors which give rise to immature polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs). Analysis of gene expression in these precursor cells identified pathways that were specifically upregulated, the most pronounced of which involved matrix metalloproteinases Mmp8 and Mmp9, during leukemia progression. Pharmacological inhibition of MMPs using Ilomastat preferentially restricted in vitro migration of neutrophils from leukemic mice and led to a significantly improved survival in vivo, accompanied by impaired PMN-MDSC recruitment. As a result, levels of T-cells were proportionally increased. In clinically annotated TCGA databases, MMP8 was shown to act as an independent indicator for poor prognosis and correlated with higher neutrophil infiltration and poor pan-cancer prognosis. We have defined specific leukemia responsive neutrophil subgroups based on their unique gene expression profile, which appear to be the precursors of neutrophils specifically associated with leukemia progression. An important event during development of these neutrophils is upregulation MMP genes which facilitated mobilization of these precursors from the BM in response to cancer progression, suggesting a possible therapeutic approach to suppress the development of immune tolerance.

overall_design: BBC2 SCLL cells were transplanted into wild type Balb/C micen. Peripheral blood samples were collected from naive mice and leukemic mice at day 11 with intermediate stage and day 14 with late stage disease. The leukocytes were processed for scRNA-Seq libraries using the Chromium Controller (10X Genomics) and the Chromium 3′ Single Cell mRNA-seq V3 reagents. The scRNA-Seq libraries were sequenced using an Illumina NovaSeq 6000 System.

first: Tianxiang

last: Hu

first: Huidong

last: Shi


title: Neurovascular mitochondrial susceptibility impacts blood-brain barrier function and behavior

city: Philadelphia

first: Jorge

middle: I.

last: Alvarez

state: PA

address: 310 S University Ave Room H434

department: Pathobiology

institute: University of Pennsylvania

summary: Maintenance of blood-brain barrier (BBB) integrity is critical to optimal brain function, and its impairment has been linked to multiple neurological disorders. A notable feature of the BBB is its elevated mitochondrial content compared to peripheral endothelial cells, although the functional implications of this phenomenon remain unknown. Here we studied BBB mitochondrial function in the context of the 22q11.2 deletion syndrome (22qDS), a condition associated with a highly increased risk for neuropsychiatric disease. As the 22q11.2 deletion includes 6 mitochondrial genes, and because we have previously identified BBB impairment in 22qDS, we addressed the hypothesis that mitochondrial deficits contribute to BBB dysfunction and impact behavior in this condition. We report mitochondrial impairment in human induced pluripotent stem cell (iPSC)-derived BBB endothelial cells from 22qDS patients, and in BBB endothelial cells from a mouse model of 22qDS. Remarkably, treatment to improve mitochondrial function attenuates mitochondrial deficits and enhances BBB function in both the iPSC and mouse 22qDS models. This treatment also corrected social memory in the mouse model, a deficit previously associated with BBB dysfunction. As BBB integrity correlated with social memory performance, together our findings suggest that mitochondrial dysfunction in the BBB influences barrier integrity and behavior in 22qDS.

overall_design: RNAseq profiling of brain enodthelial total RNA isolated from 22qDS untreated mice and 22qDS mice given 0.5% bezafibrate-enriched chow.

first: Alexis

last: Crockett

first: Hania

last: Kebir

first: Maria

last: Velez-Colón

first: Cen

last: Li

first: Frances

last: Smith

first: Stewart

last: Anderson

middle: I


title: Androgen regulated ECD overexpression promotes prostate cancer tumorigenesis through increased glycolysis

city: Omaha

first: Timothy

middle: Edward

last: Reznicek

address: S 45th St

department: Genetics Cell Biology & Anatomy

institute: University Of Nebraska Medical Center

summary: Prostate cancer (PC) is the second most common cancer in men worldwide. Androgen receptor (AR)-mediated signaling is essential for PC tumorigenesis and use of AR inhibitors is the first line of therapy until patients develop androgen-resistant PC. Here, we report that the mammalian orthologue of the drosophila ecdysoneless (ECD) mRNA and protein are overexpressed in PC patient tissues as compared to hyperplastic prostate tissues, and its overexpression predicts shorter survival in patients. RNA-seq analysis of mouse tumors revealed increase mRNA levels of several glycolytic genes in ECD-overexpressing tumors. Our results support a novel role of androgen regulated ECD overexpression in PC tumorigenesis through direct ECD binding and stabilization of mRNAs of key glycolytic genes.

overall_design: Total RNA-seq of modified human LNCaP xenografted tumors after 37 days. LNCaP cells were modified to overexpress ECD and compared with control LNCaP tumors.

first: Mohsin

last: Raza

first: Asher

last: Rajan

first: Benjamin

middle: B

last: Kennedy

first: Farshid

last: Oruji

first: Sameer

last: Mirza

first: Jordan

last: Rowley

first: Glen

last: Kristianse

first: Bhopal

last: Mohapatra

first: Hamid

last: Band

first: Vimla


title: KAT6A acetylation mediates metabolic adaptation to growth and mitochondrial metabolism through AMPK

city: Newark

first: Michinari

last: Nakamura

state: NJ

address: 185 South Orange Ave, Medical Science Building G609

department: Cell Biology and Molecular Medicine

institute: Rutgers New Jersey Medical School

summary: We have previously demonstrated that a ketogenic diet alleviates cardiac pathology under high blood pressure. Here we show that lysine acetyltransferase 6A (KAT6A) is acetylated in the hearts of mice fed a ketogenic diet under hypertension, which enhances its interaction with AMPK regulatory subunits. RNA-sequencing analysis demonstrated that the KAT6A-K815Q acetylation-mimetic mutant stimulates AMPK signaling in cardiomyocytes. Moreover, the KAT6A-K815Q acetylation-mimetic mutant mitigated phenylephrine-induced mitochondrial dysfunction and cardiomyocyte hypertrophy via AMPK activation in vitro.

overall_design: Primary rat neonatal cardiomyocytes were transfected with adenovirus-harboring human KAT6A-wild type (WT), -K815R (acetylation-resistant mutant), -K815Q (acetylation-mimetic mutant), or LacZ as a control for two days. Total RNA was isolated using TRIzol. n=3


title: Exploiting nanopore sequencing advances for tRNA sequencing of human cancer models

city: Amsterdam

first: Arno

last: Velds

address: Plesmanlaan 121

department: Genomics Core Facility

country: Netherlands

institute: The Netherlands Cancer Institute

summary: tRNAs are important regulators of protein synthesis, and dysregulation of their abundance and modifications status is involved in many human diseases, including cancer. Despite the rapid development of novel tRNA sequencing approaches, due to tRNAs stable secondary structure and abundant modification sites, human tRNA landscape has remained mostly unexplored. Here, we evaluated the new nanopore RNA004 chemistry that is combined with an upgraded Dorado RNA base-caller model for tRNA quantification and site-specific modification determination in human cancer models. We demonstrate that this technology is sensitive to changes in tRNA expression between cancer cell types and response to external stress conditions, with highly reproducible results. We also show that analysis of base-calling error rate confirms the presence of known modifications, among them is the cancer-associated tRNAPhe-Wybutosine modification by TRMT12 (TYW2) . Furthermore, utilizing the new feature of RNA004 chemistry for the detection of common modifications, we show site-specific identification of m5C and pseudouridine at their annotated positions as well as in their known tRNA isoacceptors. We also reveal unique new modification sites and pinpoint a possible limitation of this method in differentiating between m1A and m6A chemical isomers. Overall, RNA004 tRNA-seq has the potential to improve human tRNAome characterization of tRNA abundance and  site-specific modifications simultaneously.

overall_design: Human tRNA quantification and modification analysis by Oxford Nanopore Direct RNA sequencing

first: Adva

last: Kochavi

first: Roderick

last: Beijersbergen

first: Reuven

last: Agami


title: Butyrate-LncRNALy6C-RUNX3 axis determines gut resident macrophages by NR4A1 mediated ERK1/2/MAPK pathway

first: Yunhuan

last: Gao

address: No. 94, Weijin Road, Nankai District, Tianjin, China

institute: Nankai University

summary: Gut resident macrophages play a critical role in maintaining gut homeostasis. These resident macrophages may come from peripheral blood inflammatory monocytes. However, the mechanism (s) for the differentiation of inflammatory monocytes into gut resident macrophages maintain to be further understood. We here found that transcription factor RUNX3 play a critical role in the process of inflammatory monocytes into resident macrophages. RUNX3flow/flowlyz2-Cre mice had decreased resident macrophages, increased ZFP36, which could cause degradation of cytokines and chemokines in the resident macrophages of colon tissues. RUNX3 could promote the expression of NR4A1, which could induce the differentiation of inflammatory monocytes into resident macrophages. Single cell population analyses found that ERK1/2/MAPK pathway played a critical role in NR4A1 mediated differentiation of gut resident macrophages. Notably, RUNX3 expression could be promoted by butyrate through lncRNALy6C. Interestingly, high levels of lncRNALy6C, RUNX3, NR4A1 and ZFP36 could be detected in the resident macrophages of healthy individuals. Thus, there exists a butyrate-LncRNA6C-RUNX3-NR4A1-REK1/2 MAPK axis to maintain gut homeostasis through increasing resident macrophages and promoting ZFP36 expression in the macrophages.

overall_design: BMDMs were treatment with 500 µM Butyrate for 24h. One days later, all cells with or without Butyrate treatment were collected for RNA extraction. Total RNA was extracted using an RNeasy mini kit (QIAGEN, CA). RNA-seq libraries were prepared with the TruSeq sample preparation kit (Illumina, CA).


title: Tumor-infiltrating lymphocytes-derived CD8+ clonotypes infiltrate the tumor tissue and mediate tumor regression in glioblastoma [RNA-Seq]

city: Solna

first: Lucas

last: Arruda

address: Nanna Svartz väg  4

country: Sweden

institute: CuraCell AB

summary: IL-2/IL-15/IL-21-expanded TILs achieved complete tumor regression in a hypermutated glioblastoma patient, overcoming the immunosuppressive microenvironment. This case highlights a novel approach for treating gliomas using tailored adoptive cell therapy strategies.

overall_design: Tumor samples were submited to WES, RNA seq and TCR NGS before and after TIL infusions. TIL products and blood samples during treatment had CD4 and CD8 T-cells sorted and TCR sequenced.


title: Tumor-infiltrating lymphocytes-derived CD8+ clonotypes infiltrate the tumor tissue and mediate tumor regression in glioblastoma [WES]


title: Integrative transcriptome-wide association reveals PRKCG-linked GABAergic dysfunction in FXTAS

city: Atlanta

first: Yulin

last: Jin

address: 615 Micheal Street

department: Human Genetics

institute: Emory University

summary: This SuperSeries is composed of the SubSeries listed below: GSE285979, GSE286170

overall_design: Refer to individual Series

first: Peng


title: scRNA-seq of lung cells from murine model of ozone induced asthma exacerbation

city: Columbus

first: Rodney

last: Britt

state: Oh

address: 575 Childrens Crossroad

department: Center for Perinatal Research

institute: Nationwide Children's Hospital

summary: Ozone (O3) inhalation triggers asthmatic airway hyperresponsiveness (AHR), but the mechanisms by which this occurs are unknown. Previously, we developed a murine model of dust mite, ragweed, and aspergillus (DRA)-induced allergic lung inflammation followed by O3 exposure for mechanistic investigation. In this model, mice exposed to DRA or O3 alone do not develop AHR, but the two exposures combined have a synergistic effect and the DRA+O3 exposure group develops significant AHR.  The present study used single cell RNA-sequencing for unbiased profiling of cells within the lungs of mice exposed to DRA, O3, or DRA+O3, to identify the components that contribute to AHR. Inflammation is generally considered the underlying cause of AHR, so immune cells were of specific focus.

overall_design: Lung cells from C57BL/6J mice from 4 different exposure groups (untreated controls, DRA allergen mixture, ozone exposed, and DRA+ozone) were analyzed by scRNA-seq. There are two replicates for each exposure group; 1 male (cells from 3 mice pooled) and 1 female (cells from 3 mice pooled).

first: Jess

middle: L

last: Ray

first: Josh

last: Walum

last: Britt Jr.

first: Joshua

last: Englert

first: Megan

last: Ballinger


title: Dual-functional Brain-targeting Liposomes with iRGD Modification for Co-delivery of Osimertinib and Bortezomib to Combat Radioresistant Glioblastoma

city: 广州市

first: Cuiying

last: Xie

state: 广东省

address: 广州大道北1838号南方医院菜鸟驿站

institute: Southern Medical University

summary: Rationale：Glioblastoma (GBM) is a highly aggressive brain tumor, often associated with the activation of EGFR and NF-κB signaling pathways in radioresistant GBM cells. Concurrently targeting these pathways presents a promising strategy to overcome radioresistance and enhance therapeutic efficacy. Methods：We established a radioresistant glioblastoma stem cell (GSCs) model by exposing U87-derived GSCs to 5 Gy irradiation for 13 cycles. After differentiation and colony formation selection, we obtained a radioresistant cell line (Diff cells). These model cell lines mimic the progression of recurrence in GBM. Transcriptomic analysis of Diff cells, GSCs, and U87 cells, combined with public datasets from The Cancer Genome Atlas (TCGA), was conducted to identify key signaling pathways involved in radioresistance. Based on these findings, we designed a novel dual-functionalized nanoliposome (iRGD-OB-LP) for the co-delivery of Osimertinib and Bortezomib to simultaneously inhibit the EGFR and NF-κB pathways. The physicochemical properties, cellular uptake, and drug release profiles of iRGD-OB-LP were characterized, and its targeting capability, antitumor activity, and radiosensitization potential were evaluated both in vitro and in vivo. Results: We successfully established GSCs from U87 cells and induced radioresistance in these GSCs. The Diff cells derived from GSCs retained radioresistant characteristics and exhibited significant resistance to radiotherapy-induced cell death. Transcriptomic analysis of Diff cells, GSCs, and U87 cells, along with TCGA data, identified EGFR and NF-κB (RelA/p65) as key pathways involved in radioresistance. iRGD-OB-LP demonstrated efficient tumor-specific targeting, cellular uptake, and sustained drug release. In vitro, iRGD-OB-LP effectively inhibited EGFR and NF-κB pathway activation, prolonged DNA damage induced by radiotherapy, reduced tumor cell stemness, and enhanced radiotherapy-induced apoptosis. In vivo, studies using an orthotopic GBM mouse model revealed that iRGD-OB-LP successfully crossed the blood-tumor barrier, accumulated at tumor sites, and synergistically enhanced the efficacy of radiotherapy, as evidenced by suppressed tumor growth and prolonged survival. Conclusion: In this study, we established Diff cells as a radioresistant model derived from GSCs and identified EGFR and NF-κB (RelA/p65) as critical pathways in sustaining the radioresistant phenotype through RNA sequencing and TCGA data analysis. The iRGD-OB-LP nanoplatform offers a promising strategy for targeted delivery of dual inhibitors to simultaneously inhibit EGFR and NF-κB, overcoming GBM radioresistance. This innovative approach highlights a potential strategy to improve radiotherapy outcomes in GBM treatment.

overall_design: RNA-Seq profiling the wildtype U87, radioresistant GSCs, and differentiated cells (Diff).

first: Jieyi

last: Wu

first: Han

last: Yang

first: Ancheng

last: Gu

first: Wanwen

last: Cao

first: Xiangcao

last: Yao

first: Zhiyong

last: Li

first: Yuchun

last: Niu

first: Jianlong

first: Zhongyuan

last: Xu

first: Bohong

last: Cen


title: Tumor-infiltrating lymphocytes-derived CD8+ clonotypes infiltrate the tumor tissue and mediate tumor regression in glioblastoma [TCR]

first: Lucas

last: Arruda


title: Th17 cell recruitment in IgA nephropathy

city: Tianjin

first: Yena

last: Zhou

address: 94 Weijin Road

summary: Palmitoylation, a vital post-translational modification of proteins, has remained largely unexplored in immune-associated kidney diseases. This study is the first to reveal that palmitoylation plays a pivotal role in IgA nephropathy (IgAN) by regulating the activity of the transcription factor TEA Domain Transcription Factor 4 (TEAD4), thereby driving Th17 cell recruitment. Moreover, our findings suggest that inhibiting palmitoylation could act as a "braking" mechanism to slow disease progression. By analyzing clinical samples from IgAN patients and mouse models, we observed a significant positive correlation between the extent of Th17 cell infiltration in renal tissues and disease severity. Mechanistic investigations demonstrated that, under an inflammatory microenvironment, damaged renal tubular epithelial cells upregulate the expression of the chemokine CCL20 via TEAD4, thereby promoting Th17 cell recruitment. Notably, we identified that TEAD4 activity is regulated by its palmitoylation status, rather than changes in its protein expression levels. Further analysis identified zinc finger DHHC-type palmitoyltransferase 14 (ZDHHC14) as the critical enzyme mediating TEAD4 palmitoylation. ZDHHC14 was found to be highly expressed in the renal tissues of both IgAN patients and mouse models. Knockdown of ZDHHC14 significantly reduced CCL20 expression and diminished Th17 cell infiltration. In vivo therapeutic experiments confirmed that the ZDHHC inhibitor 2-bromopalmitate (2-BP) effectively alleviated Th17 cell infiltration and renal interstitial fibrosis, substantially delaying disease progression in IgAN mice. This study provides the first comprehensive insight into the regulatory mechanism of TEAD4 palmitoylation in IgAN progression. It further proposes a novel therapeutic approach targeting palmitoylation to modulate Th17 cell recruitment, offering critical theoretical foundations and potential clinical applications for the precise treatment of immune-mediated kidney diseases.

overall_design: RNA-seq profiling of IgAN mouse kidney and control mouse kidney at 24w

first: Chuyue

last: Zhang

first: Jikai

last: Xia

first: Qun

last: Liu

first: Xiangmei

last: Chen

first: Ying

last: Zheng

first: Xiaoniao


title: Ischaemic preconditioning blunted myocardial DNA methylation and regulated myocardial transcriptome in ischaemic reperfusion settings

city: Melbourne

first: Abdul Waheed

last: Khan

state: Vic

address: 99 Commercial Road

department: Diabetes

country: Australia

institute: Monash University

summary: Background.  Ischemic preconditioning (IPC) reduces infarct size but may increase the extent of reversible cardiac dysfunction (myocardial stunning). DNA methylation is thought to regulate IPC-induced gene expression, impacting inflammation, oxidative stress, apoptosis, and DNA repair pathways. Aims.  This study aimed to identify transcriptomic changes associated with IPC and elucidate the role of DNA methylation in regulating these changes, thereby distinguishing the mechanisms underlying IPC-mediated protection from necrosis and myocardial stunning. Methods. A rat model of cardiac ischemia-reperfusion (I/R) injury was used, with IPC induced by two 5-minute ischemia-reperfusion cycles followed by 13.5 minutes of ischemia, and a control group undergoing 13.5 minutes of ischemia without IPC. Myocardial samples were collected at early (T1) and 4-hour (T2) post reperfusion, representing stunned myocardium in the IPC group and necrosis in the control group. RNA sequencing, DNMT activity assay and promoter methylation analyses of differentially expressed genes (DEGs) were performed to assess transcriptomic and epigenetic changes. Results. IPC reprogrammed the cardiac transcriptome, with 53 DEGs at T1 and 166 at T2, including key regulators of inflammation (Nfkbia), DNA repair (Gadd45b), and stress responses (Cebpd, Jun). Long non-coding RNAs (lncRNAs) were also enriched. IPC reduced global DNMT activity, promoting hypomethylation of protective genes such as Cebpd, Nfkbia, Gadd45b, Jun, and Aplod1 at T1, while selectively hypermethylating maladaptive genes like Tmem200c and Fgfr4 despite persistent reduced global DNMT activity at T2. Conclusion. IPC reprograms the cardiac transcriptome through dynamic DNA methylation changes, potentially mediating protection against myocardial necrosis as an adaptive response.

overall_design: RNA seq profilling of myocardial tissue of rats that underwent ischaemia-reperfusion injury with or without ischaemic preconditioning using temporary left anterior descending artery ligation (LAD) at the base line (T1) and 4 hours (T2) post reperfusion.

first: Shafaat

last: Hussain

first: Ahmed

last: Elmahdy

first: Yalda

last: Kakaei

first: Aaron

last: Espinosa

first: Abhishek

last: Jha

first: Elmir

last: Omerovic

first: Karin

last: Jandeleit-Dahm

first: Bjorn

last: Redfors

first: Maxwell

last: Scott


title: Induction of Senescence During Postpartum Mammary Gland Involution supports tissue remodeling and promotes postpartum tumorigenesis

city: Paris

first: Jérémy

last: Chantrel

state: Ile-de-France

address: 25-28 rue du Dr. Roux

department: Developmental and Stem Cell Biology

institute: Institut Pasteur

summary: Cellular senescence is an evolutionarily conserved stress response which contributes to tissue repair and tumor suppression, yet its accumulation is also linked to aging and disease. Whether physiological senescence can be exploited by oncogenic events to promote tumorigenesis is unknown. Postpartum mammary gland involution is a major adult tissue-remodeling event, resembling wound healing, and is closely associated with postpartum breast cancer (PPBC). Here, we show that during mammary gland involution in mice, a p16-dependent senescence response is induced in alveolar luminal cells. Eliminating senescent cells disrupts tissue remodeling and delays involution, demonstrating their physiological importance. However, in a PPBC model where oncogenic activation coincides with involution, removing involution-associated senescent cells extended tumor latency. Mechanistically, senescent cells enhance tumor cell plasticity via the senescence-associated secretory phenotype (SASP), fostering metastasis. Our findings reveal that senescence, while required for postpartum tissue remodelling, can be hijacked to facilitate tumorigenesis, defining senescence as a unifying mechanism linking tissue repair to tumorigenesis.

overall_design: Bulk RNAseq data include mammary gland from wild type females at different involution timepoints (Inv0, Inv1, Inv3, Inv7)

first: Aurélie

last: Chiche

first: Lamia

last: Djoual

first: Elsa

last: Charifou

first: Shuoyang

last: Wang

first: Laurianne

last: Temime

first: Marielle

last: Saclier

first: Shaoxiang

first: Han

last: Li


title: Chronic kidney disease progression in IgA nephropathy

first: Yena

last: Zhou

overall_design: RNA-seq profiling of fibroblast co-culture with/without Th17 cells

first: Chuyue

last: Zhang

first: Jikai

last: Xia

first: Qun

last: Liu

first: Xiangmei

last: Chen

first: Ying

last: Zheng

first: Xiaoniao


title: LIMCH1 inhibits antitumor immunity by upregulating PDL1 in triple-negative breast cancer

first: Minghan

last: Qiu

state: Tianjin

address: Department of Oncology, Tianjin Union Medical Center of Nankai Univercity, 190 Jieyuan Street, Hongqiao District, Tianjin, China.

department: Department of Oncology

summary: Breast cancer is one of the most common malignancies worldwide, with triple-negative breast cancer (TNBC) being a highly aggressive subtype that has shown the greatest benefit from immunotherapy among breast cancer types. LIMCH1, a LIM-domain protein involved in cytoskeletal regulation, has recently been implicated in tumor progression but remains poorly characterized in breast cancer. This study demonstrated that LIMCH1 is overexpressed in breast cancer and associated with poor prognosis. Functional assays revealed that LIMCH1 promotes proliferation and migration while inducing immune evasion through PD-L1 upregulation via the MAPK pathway in TNBC. High LIMCH1 expression correlated with reduced CD4+ and CD8+ T-cell infiltration, an immunosuppressive tumor microenvironment, and lower anti-PD1 therapy efficacy. These findings highlight LIMCH1 as a key driver of tumor progression and immune escape in breast cancer, suggesting its potential as a prognostic biomarker and therapeutic target for precision immunotherapy

overall_design: RNAseq was performed on 4T1 cells with stable LIMCH1 overexpression and their empty vector controls.

first: Ming

last: Gao


title: Inhibition of integrated stress response promotes primordial follicle activation via the mTOR pathway

city: guangzhou

first: Weiyong Wang

address: 382 Outer Ring East Road, Guangzhou Higher Education Mega Center

institute: south china university of technology

summary: Background: The integrated stress response (ISR) is a conserved signaling network that enables cells to cope with stress and maintain homeostasis. Accumulating evidence from both human and animal studies suggests that chronic stress has been implicated as a significant factor in the development of premature ovarian insufficiency (POI). The aim of this study was to investigate the effects of targeted ISR inhibition by ISRIB on primordial follicle activation and explore its underlying mechanisms in a mouse model.  Methods: This study used intraperitoneal injection to investigate the effects of ISR activity and its inhibitor ISRIB on primordial follicle activation in vivo. Newborn ICR mice were randomly assigned to the Control, Corticosterone, ISRIB, and Corticosterone + ISRIB groups. Mouse and human ovarian tissues were cultured in vitro and treated with ISRIB and/or a proto-oncogenic receptor tyrosine kinase (KIT) inhibitor. Various methods were used to assess differences in follicle counting, ISR activity, cell proliferation, cell apoptosis, and the mTOR pathway.  Results: ISR activity was present in normal newborn mouse ovaries and significantly increased in corticosterone-induced stress mouse ovaries. Excessive ISR activity induced by corticosterone reduced the number of primordial follicles, which could be partially reversed by ISRIB. In vitro treatment with ISRIB inhibited the protein levels of p-eIF2α and ATF4, while promoting granulosa cell proliferation and primordial follicle activation, and increasing the levels of phosphorylated mTOR (p-mTOR), phosphorylated protein kinase B (p-Akt), and KIT ligand (KITL). The KIT inhibitor ISCK03 significantly decreased the phosphorylation levels of Akt and forkhead box O3a (FOXO3a), as well as the number of growing follicles induced by ISRIB. In both in vivo injection and in vitro ovarian tissue culture models, ISRIB promoted primordial follicle activation via the mTOR pathway in pre-granulosa cells.  Conclusion: The results suggest that inhibiting ISR can prevent primordial follicle depletion caused by excessive ISR activity. ISRIB has been shown to promote primordial follicle activation in mouse and human ovaries via the mTOR pathway. These results suggest that ISRIB may be a potential therapeutic option for infertility in stress-induced POI patients.

first: Tiantian

last: Hao

first: Weiyong

first: Ziyong

last: Zhao

first: Zehua

last: Deng

first: Yashuang

last: Weng

first: Meijia

first: Yuezhou


title: Folate receptor β performs a checkpoint function in activated macrophages

city: West Lafayette

first: Sagar

last: Utturkar

state: IN

address: 201 S University St

department: Institute for Cancer Research

institute: Purdue University

summary: Macrophages and monocytes are essential components of the immune system that distinguish themselves from all other cells in the body by expressing a beta isoform of the folate receptor (FRβ). Because FRβ does not bind folate until the macrophage/monocyte is exposed to immunosuppressive cytokines, the question naturally arose whether FRβ might perform an immune-related function. We report here that FRβ knockout mice display autoimmune symptoms that can include alopecia, enlarged spleens, and dermatitis. We further show that bone marrow-derived macrophages from KO mice exhibit strong upregulation of pro-inflammatory genes and downregulation of anti-inflammatory genes. Exogenous inflammatory stimuli are also more intense in FRβ KO mice, and syngeneic tumors (TRAMP C2, MC38) grow much slower in FRβ-depleted mice.  Analysis of these tumors further reveals that CD69+ T-cell populations are increased while PD1+ T-cells, PD-L1+ TAMs and PD-L1+ MDSCs are decreased in the malignant lesions. Because FRβ deletion or blockade of FRβ with a monoclonal antibody impairs a macrophages' ability to suppress T-cell activation, and since FRβ expression correlates inversely with human cancer patient survival, we conclude that FRβ performs a checkpoint function specifically in macrophages and MDSCs.

overall_design:
To investigate the role of FRβ, we generated a FRβ knock out (KO) mouse model that lacks functional FRβ and then compared the FRβ KO macrophages with the wild type (WT) ones.
Next, we isolated bone marrow derived macrophages from WT and FRβ KO mice and performed a total RNA-sequencing.
Finally, the differential gene expression and the relative changes in gene expression were analyzed in the WT and FRβ KO macrophages.

first: Fenghua

first: Md Yusuf

last: Al-Amin

first: Philip

last: Low


title: Ret finger protein deficiency attenuates adipogenesis in high fat diet-induced obese mice

city: Hwasun

first: Nakwon

last: Choe

state: Seoyang-ro 322

address: Baekseo-ro 160

department: Pharmacology

institute: Chonnam Univ. Med. Sch.

summary: Ret finger protein (RFP, also known as TRIM27) is a multifunctional protein involved in tumor suppression and transcriptional regulation. While our previous studies revealed RFP's inhibitory role in myogenesis through MyoD regulation, its function in lipid metabolism remained unknown. Here, we investigated the effects of RFP deficiency on adipose metabolism in high-fat diet (HFD)-induced obesity. RFP knockout mice showed significantly reduced weight gain and fat accumulation, along with improved glucose levels and insulin sensitivity compared to wild-type controls. These metabolic improvements were replicated in adipocyte-specific RFP knockout mice. In vitro studies using 3T3-L1 adipocytes demonstrated that RFP regulates adipogenic gene expression through interaction with PPAR-γ and interference with its transcriptional activity. Our findings identify RFP as a key regulator balancing skeletal muscle and adipocyte maturation, suggesting that RFP inhibition could be a potential therapeutic target for obesity and metabolic disorders.

overall_design: To explore how RFP deficiency affects gene expression, we subjected wild-type and RFP KO mice to a 12-week high-fat diet (HFD) regimen and utilized epididymal white adipose tissue (eWAT) for mRNA sequencing analysis.

first: Yun-Gyeong

last: Lee

first: Anna

last: Jeong

first: Yongwoon

last: Lim

first: Sera

last: Shin

first: Hosouk

last: Joung

first: Hye Jung

last: Cho

first: Kwang-Il

last: Nam

first: Gwang Hyeon

last: Eom

first: So-Young

last: Park

first: Byung-Hyun

first: Duk-Hwa

last: Kwon

first: Hyun

last: Kook


title: Excitation-contraction coupling, cardiomyocyte electrophysiology, and transcriptome changes in two translational HFpEF murine models: Aetiology and sex-dependent differences

city: Seattle

first: Jennifer

last: Davis

state: WA

address: 850 Republican St, Brotman #343

department: Lab Medicine and Pathology

institute: University of Washington

summary: Heart failure (HF) with preserved ejection fraction (HFpEF) comprises heterogenous clinical phenotypes and presence of various co-morbidities. Recent two-hit translational animal models, including the hypertensive, nitrosative-stressed mice fed with high-fat diet and L-NAME (HFD+L-NAME) and the obese-diabetic leptin receptor-deficient db/db mice with excess aldosterone (db/db+Aldo), may phenocopy select subgroups of HFpEF. We systematically compared mechanisms of excitation-contraction coupling (ECC), electrophysiology, and gene transcription in these key preclinical HFpEF models and between sexes to advance translation. We performed morphometry, echocardiography, cellular electrophysiology, intracellular Ca2+ imaging, and RNA-sequencing. The multiorgan HFpEF phenotype showed key differences between the 2 models, db/db+Aldo mice were markedly obese, had severe hyperglycaemia and hepatomegaly, whereas male HFD+L-NAME mice had more pronounced cardiac hypertrophy. Diastolic dysfunction was more severe in db/db+Aldo mice and worse in females therein, whereas female sex was protective in HFD+L-NAME. Marked proarrhythmic action potential (AP) changes (AP prolongation, increased short-term variability and alternans threshold) occurred in db/db+Aldo (in both sexes), these AP changes were less severe in male HFD+L-NAME and absent in female HFD+L-NAME. In line with these, differential ionic current and Ca2+ handling changes occurred between these two HFpEF models and between sexes in each model. RNA-sequencing revealed highly distinctive gene expression profiles between HFpEF models. We conclude that marked differences exist in cardiomyocyte ECC, electrophysiology, and gene expression between HFD+L-NAME and db/db+Aldo mice and between sexes. This indicates that a combination of translational HFpEF models that mimic select HFpEF sub-phenogroups are needed to better understand HFpEF mechanisms for therapeutic drug development.

overall_design: RNAseq of whole heart samples from two groups. The first group (HFD-LNAME group) has WT mice treated with normal chow (Control - HFD-LName) and WT mice treated with high fat diet (HFD) with L-NAME (Treated - HFD-Lname). The second group (DBDB-Aldo) has WT mice treated with SHAM minipumps (Control - DBDB Aldo) and db/db mice treated with aldosterone minipumps (Treated - DBDB Aldo).

first: Bers

last: Donald

first: Heygi

last: Bence

first: Bailey

last: Logan