title: Coordinated Gene Family Evolution Shapes the Genome of Dimorphic Organisms

city: Murcia

first: Carlos

last: Lax

address: Facultad de Biología

department: Genetics and Microbiology

country: Spain

institute: University of Murcia

summary: Dimorphic organisms possess the remarkable ability to encode within their genomes the information necessary to alternate between two distinct life forms, a choice unavailable to most monomorphic species. However, the evolutionary solution that allows for the integration of genetic information from two divergent life forms into a single dimorphic organism remains unresolved. Here, we investigated this phenomenon using species of Mucorales fungi that are not only capable of growing as either yeast or mycelium but also able to transition reversibly between these forms depending on environmental cues. We have discovered that hundreds of gene families have undergone convergent evolution to adapt their paralogs to the dimorphic lifestyle. This adaptation manifests as the functionalization of paralogs and expression, with some paralogs expressed in the yeast form and others in the mycelial form. Although each of these dimorphic gene families performs distinct and specialized functions, they are all coordinately regulated to achieve differential expression of yeast and mycelium paralogs. Furthermore, distinct gene families with related functions have organized their paralogs into head-to-head (H2H) structures, further enhancing the coordination of their differential expression. This striking coordinated regulation is controlled by two new genes identified in this study (dkl and dfl). Loss of function of these genes results in global dysregulation of gene expression and the consequential loss of dimorphism. Dimorphic gene families, H2H marker loci, and the dfl gene are conserved across various dimorphic species but are absent in closely related monomorphic species. Collectively, dimorphic gene families, their genomic organization, and their specific regulation represent a novel evolutionary mechanism that integrates and optimizes the genetic information required for two distinct life forms within a single organism.

overall_design: RNA-seq experiment to analyze the differences in gene expression at the mRNA levels in the yeast-to-hyphae and from mycelium-to-yeast transitions in M. lusitanicus. Total RNA was extracted using the NYZ total RNA kit (NYZtech) and subjected to on-column DNase I treatment (Sigma). Three biological replicates were analyzed for each expression experiment.

first: Ghizlane

last: Tahiri

first: Maria Isabel

last: Navarro-Mendoza

first: Gabriel

last: Navarro del Saz

last: Peréz Arques

first: Victor

last: Garre

first: Francisco

last: E. Nicolás


title: Epigenomic and Transcriptomic Alterations Precede Amyloidosis in the Hippocampus of an Alzheimer's Mouse Model [BiSulfite-seq]

status: Public on Nov 20 2025

city: Portland

first: Mariam

last: Okhovat

state: Oregon

address: 3030 S Moody Ave.

department: Medicine

country: USA

institute: Oregon Health and Science University

type: Methylation profiling by high throughput sequencing

summary: Detecting and understanding Alzheimer's disease (AD) in its early stages is essential for uncovering the initial mechanisms behind its neuropathology and devising effective interventions. In this study, we leveraged the humanized AppNL-G-F mouse which exhibits early-onset amyloid pathology along a predictable timeline, to investigate molecular changes in the hippocampus and blood before the onset of severe neuropathology and independent of aging. Employing a multi-omics approach, we identified alterations in chromatin accessibility, gene expression, and DNA methylation associated with early amyloidosis. Chromatin accessibility changes were prominent in excitatory neurons during early pathology, with a later shift to inhibitory neurons, potentially reflecting compensatory mechanisms to mitigate excitatory neuron dysregulation. Despite broadly comparable hippocampal cell composition, transcriptomic comparisons between wild-type and AppNL-G-F mice revealed major gene expression differences, particularly in pathways related to mitochondrial function and protein biosynthesis, preceding severe amyloid plaque deposition. In later stages, upregulation of immune and neuroinflammatory pathways was observed, aligning with established neuroinflammatory processes in AD. Additionally, we identified extensive DNA methylation differences in both the blood and hippocampus of AppNL-G-F mice during early and late stages of pathology. Many differentially methylated regions in the blood, even at early pathology stages, were associated with cis-regulatory elements in the brain and were located near differentially expressed genes in the hippocampus. These regions were enriched in pathways related to brain function, such as neuron development and synaptic processes, indicating a link between blood methylation patterns and brain function. This suggests the potential utility of blood methylation as a biomarker for early amyloidosis detection. Notably, we identified five candidate biomarker genes, including Rbfox1 and Camta1, with epigenetic dysregulation detectable in both the brain and blood prior to severe amyloid accumulation. Our study, leveraging a unique AD mouse model and a multi-omics approach, highlights epigenetic signatures of AD before the onset of clinical symptoms, providing a foundation for future research into early diagnosis and therapeutic strategies, as well as potential biomarkers.

overall_design: WGBS libraries were prepared using gDNA from both blood and hippocampus tissues of wildtype and APP_nlgf mice across three developmental stages (postnatal week 3, week 8, and week 24) and both sexes (n=5 per sex/age/genotype combination). For each tissue and time point, regions of significant differential methylation (DMRs) were identified by comparing the two genotypes, with sex included as a covariate in the analysis.

first: Lucia

last: Carbone

first: Brett

last: Davis


title: Epigenomic and Transcriptomic Alterations Precede Amyloidosis in the Hippocampus of an Alzheimer's Mouse Model [RNA-seq]

type: Expression profiling by high throughput sequencing

overall_design: Bulk hippocampus from male and female AppNL-G-F and wild-type mice was collected across three postnatal time points (week 3, 8 and 24; W3, W8 and W24) for a total of 60 samples (5 replicates per age/sex/genotype). Males and females were combined to serve as biological replicates. Gene expression patterns were compared between the two genotypes at each of the three time points, by using sex as co-variate.


title: Epigenomic and Transcriptomic Alterations Precede Amyloidosis in the Hippocampus of an Alzheimer's Mouse Model

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: scATAC-seq libraries were prepared after pooling of n=5 biological replicates per genotype (wildtype and APP_nlgf), age (postnatal week 3, week 8, and week 24) and sex (male and female). For each tissue and time point, regions of significant differential methylation (DMRs) were identified by comparing the two genotypes, with sex included as a covariate in the analysis.


title: Human CRX Regulates Photoreceptor Cells Development via Bidirectional Transcriptional Control in Retinal Organoids

city: Guangzhou

first: Xiufeng

last: Zhong

address: 54 xianlie Rd

department: Zhongshan Ophthalmic Center

country: China

institute: Sun Yat-sen University

summary: CRX (cone-rod homeobox) is a key regulator of retinal photoreceptor development, yet its human-specific functions remain poorly understood due to scarce human retinal tissues and significant species differences. Here, we established a human CRX-mCherry fluorescent reporter retinal organoid (RO) model to dissect CRX-mediated gene regulation. Using FACS, RNA-seq, and CUT&Tag-seq, we identified CRX target genes and revealed its dual regulatory role: it activates photoreceptor-specific genes (e.g., RP1L1, linked to inherited retinal degeneration) in a dose-dependent manner, while suppressing non-photoreceptor genes (e.g., PCDH8 and PROX1). Notably, we first generated the human CRX CUT&Tag dataset, providing direct insights into CRX’s genome-wide regulatory landscape in photoreceptor cell development. These findings demonstrate that CRX functions as both a transcriptional activator and repressor, ensuring photoreceptor-specific gene expression and preventing aberrant cell fate transitions. Our study provides critical insights into the role of human CRX in retinal development and implications for retinal degenerative diseases.

overall_design: We established a CRX-mCherry reporter fluorescent hiPSC line, which was subsequently differentiated into retinal organoids (ROs). On day 90 (D90), ROs were dissociated into single cells through enzymatic digestion. The cell suspension was then subjected to fluorescence-activated cell sorting (FACS) to isolate mCherry-positive and mCherry-negative cell populations. These two distinct populations were collected separately for RNA-seq analysis (designated as mN and mP). Furthermore, we performed ChIP-seq on D90 CRX-mCherry ROs to investigate CRX binding sites across the genome. Two experimental conditions were established: (1) a negative control group without CRX antibody (designated as -Ab), and (2) an experimental group with CRX antibody (designated as +Ab) to specifically capture CRX-associated chromatin regions.

first: Yuan

last: Wang

first: Bingbing

last: Xie

first: Xiaojing

last: Song

first: Guanjie

last: Gao

first: Yuanyuan

last: Guan

first: Dandan

last: Zheng

first: Ping

last: Xu


title: HIV-Induced Sialoglycans on Infected Cells Promote Immune Evasion from Myeloid Cell-Mediated Killing

city: Chicago

first: Shalini

last: Singh

state: IL

address: 300 E. Superior Street

department: Department of Medicine (Infectious Diseases)

institute: Northwestern University

summary: Sialic acid-containing glycans (sialoglycans) on pathological cells interact with Siglecs, glyco-immune checkpoint receptors expressed on myeloid cells such as monocytes and neutrophils. This interaction suppresses the cytotoxic functions of these immune cells. We show that HIV infection reprograms the glycosylation machinery of infected cells to increase the expression of specific sialoglycan ligands for Siglecs-3, -7, and -9. These ligands engage Siglecs on myeloid cells, impairing their ability to target HIV-infected cells. Selective disruption of these interactions using 10-1074-Sia, an HIV-specific antibody conjugated to sialidase—an enzyme that removes sialic acids—significantly enhances monocyte- and neutrophil-mediated killing of HIV-infected cells in autologous assays. Treatment with 10-1074-Sia in humanized mice infected with HIV reduces viral load and decreases inflammation. These findings reveal a novel immune evasion mechanism exploited by HIV to evade myeloid cell immune surveillance and highlight the potential of targeting sialoglycan-Siglec interactions to improve immune clearance of HIV-infected cells.

overall_design: RNAseq profilling of monocytes co-cultured with HIV-TYBE infected primary CD4 T cells (E:T=10:1) in the presence of 10-1074, 10-1074-Sia or Isotype antibody

first: Mohamed

last: Abdel-Mohsen


title: CTCF couples long-range loop extrusion and diffusion to mediate a diverse Igk repertoire [HTGTS-VDJ-Seq]

city: East Lansing

first: Yu

last: Zhang

state: MI

address: 567 Wilson Rd, Biomedical and Physical Sciences Building, Rm 5176

department: Microbiology, Genetics and Immunology

institute: Michigan State University

summary: Dynamic genome folding is important for V(D)J recombination at the immunoglobulin kappa (Igk) locus, which recombines Jk and Vk gene segments across a 3.2 Mb region in both deletional and inversional orientations. Chromatin loop extrusion and diffusion are considered two key mechanisms underlying Igk folding, but how they coordinate remains unclear. Here we show that CTCF is a key regulator coupling loop extrusion and diffusion during Igk V-J rearrangement, promoting recombination in both orientations across long genomic distances. Mechanistically, the CTCF N-terminus promotes long-range loop extrusion that facilitates distal Vk usage by stabilizing cohesin against WAPL release, and also forms loop barriers enabling chromatin diffusion for inversional Vk joining. In CTCF N-terminal-deficient B cells, defects in inversional Vk joining are not restored by WAPL depletion but are instead largely rescued by a dCas9-blockade targeted to the Vk-Jk intergenic region, mimicking the CTCF barrier. Our findings thus highlight how CTCF coordinates distinct genome-folding mechanisms through its dual roles in cohesin stabilization and extrusion barrier formation to ensure the generation of a diverse Igk repertoire.

overall_design: We performed HTGTS-V(D)J-Seq in v-Abl transformed pro-B cells and the various mutant derivatives to study the molecular basis of CTCF's role in Igk recombination

first: Emma

last: Bush


title: Neuronal GDF-15 delivery alters peripheral CD4+ T cell phenotype

city: Hamburg

first: Jana

last: Sonner

state: Hamburg

address: Martinistr. 52

department: ZMNH

country: Germany

institute: UKE

summary: In this study we investigated the immunomodulatory properties of GDF-15 in the context of neuroinflammation. We exploited neuronal gene therapy to overexpress GDF-15 within the central nervous system, which protected mice from developing any clinical signs of neuroinflammation in the experimental autoimmune encephalitis (EAE) model. We discovered that GDF-15 delivery modulated the peripheral T cell response and prevented immune cells from transmigrating into the central nervous system.

overall_design: Female C57BL/6J mice were injected with an rAAV (PHP.eB) capsid to express eGFP or murine GDF-15 under the control of the human Synapsin 1 promoter to restrict expression to neurons. Three weeks later EAE was induced in half of the animals using MOG35-55/CFA and pertussis toxin. During the preclinical phase (day 9 post immunisation) EAE animals and healthy controls were sacrificed and spleens collected. CD4+ T cells were enriched using the MojoSort Mouse CD4 T Cell Isolation Kit.


title: Debranching enzyme DBR1-mediated lariat RNA turnover requires ALBA proteins in Arabidopsis

city: Shanghai

first: Haoran

last: Ge

address: Songhu Road 2005

institute: Fudan university

summary: Lariat RNAs, generated as by-products of RNA splicing from excised introns, must be removed. RNA debranching enzyme (DBR1) is the core factor responsible for lariat RNA removal. However, the mechanism by which DBR1 debranches lariat RNAs remains unclear. Here, we demonstrate that six ALBA (Acetylation Lowers Binding Affinity) proteins interact with DBR1 to enhance its debranching activity and facilitate DBR1's accessibility to lariat RNAs, thereby promoting lariat RNA turnover. Similar to dbr1, alba mutants exhibit pleiotropic developmental defects and accumulate lariat RNAs. ALBAs bind to lariat RNAs via their C-terminal RGG/RG-rich repeats and assist DBR1 in binding to these RNAs. The N-terminal ALBA domain mediates the interaction with DBR1 and enhances its enzymatic activity. Cold stress induces lariat RNA accumulation by attenuating the ALBA–DBR1 interaction, which in turn reduces the induction of cold-responsive genes by impairing their transcription. Together, these findings uncover that lariat RNA turnover requires ALBA proteins.

overall_design: Lariat RNA-seq for four genotypes plants under normal condition or cold treatment was performed with 3 biological replicates each. Lariat RNA-seq for transgenic plants  and albah was performed with 3 biological replicates each. RIP-seq for GFP and ALBA5 in Col-0 and dbr1-2 was performed with 2 biological replicates each. RIP-seq for DBR1(H85A) in Col-0 and alba456 was performed with 2 biological replicates each.

first: Qi

last: Tang

first: Jingjing

last: Wu

first: Binglian


title: NNMT promotes tubular senescence and fibrosis in chronic kidney disease (db/m and db/db mice kidney)

city: Amsterdam

first: Alessandra

last: Tammaro

state: AZ

address: Meibergdreef 05

department: Department of pathology

country: Netherlands

institute: Amsterdam University Medical Center

summary: Diabetic kidney disease is the leading cause of chronic kidney disease. db/db mice, which carry a deletion mutation resulting in a dysfunctional leptin receptor, exhibit hyperphagia, obesity, and elevated insulin levels, making them a widely used preclinical model of diabetic kidney disease. At 16 weeks of age, db/db mice showed enriched transcriptomic signatures of cellular senescence in their kidneys compared to control db/m mice.

overall_design: 2 groups of 8 (db/m) and 9 (db/db) animals. Kidney tissue from 16-week old male BKS.Cg-Dock7m +/+ Leprdb/J HE/HE (db/m) and BKS.Cg-Dock7m +/+ Leprdb/J WT/HO (db/db) mice.

first: Lucie

last: Chanvillard

first: Hildo

last: Lantermans

first: Christopher

last: Wall

first: Jonathan

last: Thevenet

first: Loes

last: Butter

first: Loic

last: Tauzin

first: Nike

last: Claessen

first: Stefan

last: Christen

first: Giulia

last: Lizzo

first: Sonia

last: Karaz

first: José Luis

last: Sanchez-Garcia

first: Sylviane

last: Métairon

first: Valentina

last: Ferro

first: Sofia

last: Moco

first: Daniel

last: Raalte

first: Joris

middle: J

last: Roelofs

first: Matthew

last: Sanders

first: Jerome

middle: N

last: Feige

first: Vincenzo

last: Sorrentino


title: PABPN1-C5 Axis Promotes Hepatocellular Carcinoma Progression via NF-kB Activation

first: Siyao

last: Guo

address: No.58 Zhongshan Er Road

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: RNA polyadenylation is a key post-transcriptional modification essential for gene expression regulation. However, the role and mechanism of polyadenylation and its key molecule, polyadenylate binding protein nuclear 1 (PABPN1), in hepatocellular carcinoma (HCC) remain poorly understood. This study investigates the role of PABPN1 and its regulatory genes in HCC progression to identify potential therapeutic targets. Analysis of The Cancer Genome Atlas (TCGA) dataset and an independent HCC cohort revealed significant upregulation of PABPN1 in HCC patients, which correlates with poor prognosis. Loss-of-function studies using HCC cell lines and conditional knockout mouse models demonstrated that targeting PABPN1 inhibited HCC progression. Conversely, overexpression of PABPN1 promoted HCC development in vitro and in a hydrodynamic transfection hepatocarcinogenesis mouse model. Mechanistic investigations showed that PABPN1 modulates C5 mRNA polyadenylation and stability, with the PABPN1-C5 axis driving NF-kB activation and recruiting polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) to promote HCC progression. Therapeutic targeting of the PABPN1-C5 axis using the C5a receptor inhibitor CCX168 significantly inhibited HCC progression in both in vitro and in vivo models. This study identifies PABPN1 as a critical regulator of HCC development and sheds light on the post-transcriptional regulation of complement components in cancer. Targeting the PABPN1-C5 axis represents a promising strategy for HCC treatment.

overall_design: RNA-seq profiling of control and PABPN1-depleted HCC cells.

first: Canfeng

last: Zhang

first: Shuibin

last: Lin


title: TCF21 orchestrates epithelial-to-mesenchymal transition and cytoskeleton reorganization in uterine development and endometriosis

city: Beijing

first: Jie

last: Li

address: 8 Xishiku Rd., Xicheng District

institute: Peking University First Hospital

summary: TCF21 expression is upregulated in ectopic endometrial tissues and stromal cells in endometriosis patients and contributes to the pathogenesis of endometriosis. To explore TCF21-dependent gene regulation, Cleavage Under Targets and Tagmentation (CUT&Tag) was conducted and revealed that TCF21 transcriptionally activated a cohort of genes in endometriotic stromal cells.

overall_design: CUT&Tag using antibody against TCF21 in primary endometriotic stromal cells

first: Jingwen

last: Zhu

first: Jing

last: Liang

first: Qing

last: Xue


title: 5-HT Reuptake Blockade Disrupts Genomic Stability-Based proteostasis to Induce Pyroptosis via Remodeling Histone Serotonylation [RNA-seq]

city: Xiamen

first: aicun

last: li

address: South Xiang'an Road 4221-120, Xiang'an Campus, Xiamen University, Xiang'an District

institute: Xiamen University

summary: The dual challenges of limited therapeutic options caused by de novo or acquired resistance and psychological distress in melanoma patients necessitate innovative treatment strategies. In this study, we identify Paroxetine Hydrochloride (PH), an FDA-approved antidepressant, as a novel therapeutic agent for BRAFV600E-mutated melanoma, including BRAFi/MEKi-resistant cases. Furthermore, our findings unraveled that PH acts as an unrecognized pyroptosis inducer. By triggering pyroptosis, PH remodels the tumor microenvironment to synergize with anti-PD-1 therapy while maintaining a favorable safety profile. Mechanistically, PH impedes serotonin reuptake, leading to epigenetic reprogramming through reduced histone serotonylation at the promoters of DNA repair genes. The impairment of DNA damage repair pathways in turn triggers genomic instability, proteostasis imbalance, and endoplasmic reticulum stress, ultimately inducing pyroptosis. Our findings uncover the underlying mechanism by which 5-HT drives melanoma progression and highlight PH as a promising candidate with multiple clinical potentials for melanoma treatment.

overall_design: RNA-seq was perform to obtain Paroxetine Hydrochloride-dependent transcriptomic signatures

first: Aicun

first: Zhicheng

last: Gong

first: Xiao

last: Lu


title: Transcriptomic changes in paired eutopic and ectopic endometrium of ovarian endometriosis

summary: The pathogenesis and mechanisms underlying endometriosis are still not fully understood. Emerging studies highlight that altered genes expressions may play a role in disease onset and progression. This research investigates critical genes gain further insight into the molecular basis of endometriosis. Through high-throughput sequencing, we performed paired expression analyses of mRNAs, microRNAs and lncRNAs in ectopic and paired eutopic endometrial tissues from five patients with ovarian endometriosis.Our findings shed new light on the regulatory networks involved, potentially guiding future strategies for replacement therapy in endometriosis.

overall_design: Five pairs of ectopic and eutopic endometrium were sent for whole-transcriptome sequencing. In brief, samples of eutopic endometrium and ectopic endometrioma from the cyst walls were obtained immediately from 5 patients, ages 23 to 40 years old, who underwent hysteroscopy combined with laparoscopy for endometriosis, forming five pairs of self-control groups. All women had regular menstrual cycles and were not taking hormone therapy. According to the preoperative history, the menstrual phase was confirmed, and all samples were in the proliferative phase. The samples were sequenced using the Illumina HiSeq 2000/2500 platform, and 50-bp single-end reads were generated. Sequencing and data collection were conducted by Novogene Bioinformatics Technology Co., Ltd. (Beijing, China).

first: Xiaoqing

last: Wang


title: Ion-coupled Transfersome Complexes for Enhanced Transdermal NAD+ Repletion and Defense Against Cellular Senescence Signatures

city: Gwangju

first: Yunju

last: Jo

address: 123, Cheomdangwagi-ro

country: South Korea

institute: Gwangju Institute of Science and Technology

summary: To investigate the cullular mechanism of NAD+ and NAD+ liposome againist various aging models

overall_design: Seung-Hyun, Jun

first: Seongsu

last: Kang

first: Sanghyun

last: Ye

first: Jiwon

last: Park

first: Dongryeol

last: Ryu


title: Gene expression profile at single cell level of tumor-infiltrating NK (tuNK) from CT26_b2m-/- tumor received IL-21 treatment or IL-21 and IL-15 combination treatment.

city: Lausanne

first: Yi

address: Rte Csntonale, Station9, MED1 2926

country: Switzerland

institute: EPFL

summary: NK cells are considered as dominant killing while tumor cells downregulating MHC-I expression to avoid recognition, but NK cell function are impaired in the tumor microenvironment. We used single cell RNA sequencing to analyze the NK cell performance in tumor with IL-21 treatment.

overall_design: TuNK were isolated from  CT26_b2m-/- tumor by MACS enrichment and FACS according to the gating strategy CD45+CD3-NKp46+ and analyzed using scRNAseq.

first: Li

last: Tang


title: Circular RNA circTNK2 contributes to immune evasion and acts as a nanotherapeutic target in tamoxifen-resistant ER-positive breast cancer

city: Nanchang

first: Boxuan

last: Zhou

state: Jiangxi

address: 17th Yongwai Street, Donghu District

department: Department of Breast Disease Center

institute: Nanchang University

type: Non-coding RNA profiling by high throughput sequencing

summary: circTNK2, a circular RNA, is significantly overexpressed in tamoxifen-resistant breast cancer tissues and is linked to poor prognosis. circTNK2 encodes a novel 487-amino acid protein, termed C-TNK2-487aa, which inhibits the recruitment of natural killer (NK) cells. Mechanistic studies reveal that C-TNK2-487aa interacts with STAT3 and promotes its phosphorylation in ER-positive breast cancer cells. The increased phosphorylated STAT3 then competes with STAT1 binding, inhibiting the formation of STAT1 homodimers required for CXCL10 transcription, ultimately leading to immune evasion. Additionally, circTNK2 binds to SRSF1 and promotes tamoxifen resistance and breast cancer cell proliferation. Co-delivery of circTNK2 antisense oligonucleotides (ASO) and CXCL10 plasmid DNA mediated by BC-targeting ZIF-8 nanoparticles markedly suppresses breast cancer growth, reverses tamoxifen resistance, and increases tumor infiltration of CD56+ NK cells in vivo. These findings underscore the critical role of the circTNK2-encoded peptide in tamoxifen resistance and immune evasion, providing a therapeutic vulnerability in treating tamoxifen-resistant breast cancer.

overall_design:
To investigate the roles of circRNAs in ER-positive, tamoxifen-resistant breast cancer, we collected three tamoxifen-sensitive and three tamoxifen-resistant ER-positive breast cancer tumor samples.We conducted circRNA expression profiling using circRNA-seq data from these samples.Comparative analysis of circRNA expression profiles revealed differentially expressed circRNAs between the two groups.
To elucidate how C-TNK2-487aa contributes to the progression of ER-positive breast cancer, we established MCF7-Pa cells (MCF7 parental, tamoxifen sensitive cell line) that overexpress either circTNK2IRES-Mut or circTNK2. We then performed gene expression profiling using RNA-seq data from these modified cells, with two biological replicates for each group. Comparative analysis of gene expression profiles identified differentially expressed genes (DEGs) between the two groups.

first: Runxin

last: Wu

first: Shi-Yuan

last: Cheng


title: RNA-seq profiling of mouse lung endothelial cells to investigate ENG-dependent and ENG-independent BMP9-induced target genes.

city: Cambridge

first: Jingxu

last: Guo

address: Papworth Road

country: United Kingdom

institute: University of Cambridge

summary: The aim of this experiment is to dissect endoglin (ENG)-dependent and ENG-independent BMP9 target genes. We have shown previously (PMID: 31431534) that BMP9 in complex with soluble endoglin (sENG:BMP9) has compromised signalling in Eng knockout (KO) mouse lung endothelial cells (MLECs), but not in wild type (WT) MLECs, suggesting sENG:BMP9 signalling in WT MLECs is mostly ENG-dependent. Hence we designed this experiment to compare  sENG:BMP9 signalliing in WT cells with prodomain bound BMP9 (pro:BMP9) signalling in Eng-KO cells to tease out ENG-dependent and ENG-independent BMP9 target genes.

overall_design: MLECs were isolated from four independent Eng fl/fl:Rosa26-CRE:Immorto mice. Eng KO MLECs were generted by tamoxifen induction in vitro, along with vehicle treated cells to obtain wild type (WT) control. Treatment in WT cells include PBS-treatment and sENG:BMP9 treatment. Treatment in KO cells include PBS-treatment and pro:BMP9 treatment. All samples were processed in parallel for RNA extraction and RNAsequencing.

first: Wei

last: Li


title: 5-HT Reuptake Blockade Disrupts Genomic Stability-Based proteostasis to Induce Pyroptosis via Remodeling Histone Serotonylation [ChIP-seq]

first: aicun

overall_design: ChIP-seq performed in this study was designed to uncover the role of  H3-5HT/H3K4me3 mediated regulation of gene transcription.


title: NNMT overexpression promotes tubular senescence and fibrosis in human chronic kidney disease (young, old and NAM-supplemented old mice kidney) [Series_4]

first: Alessandra

last: Tammaro

summary: Aging is a major risk factor for chronic kidney disease. Aged mice (21 months old) exhibited enriched transcriptomic signatures of fibrosis and cellular senescence in their kidneys compared to young mice (4 months old), and dietary supplementation with nicotinamide (NAM) was insufficient to reverse these disease signatures.

overall_design: 3 groups of 6 (young) or 8 (old, old+NAM) animals. Kidney tissue from 4 months old (young) and 21 months old (old) wild-type (WT) C57BL/6JRj male mice. Some old animals supplemented with nicotinamide (NAM) mixed with the diet at a dose of 200 mg/kg bw/day, 1.6g/kg food for 14 weeks.

first: Lucie

last: Chanvillard

first: Hildo

last: Lantermans

first: Christopher

last: Wall

first: Jonathan

last: Thevenet

first: Loes

last: Butter

first: Loic

last: Tauzin

first: Nike

last: Claessen

first: Stefan

last: Christen

first: Giulia

last: Lizzo

first: Sonia

last: Karaz

first: José Luis

last: Sanchez-Garcia

first: Sylviane

last: Métairon

first: Valentina

last: Ferro

first: Sofia

last: Moco

first: Daniel

last: Raalte

first: Joris

last: Roelofs

first: Matthew

last: Sanders

first: Jerome

last: Feige

first: Vincenzo

last: Sorrentino


title: NNMT overexpression promotes tubular senescence and fibrosis in human chronic kidney disease (Nnmt overexpressing TEC cells) [Series_3]

first: Alessandra

last: Tammaro

summary: Renal tubular epithelial cells (TECs) are increasingly recognized as the central locus of chronic kidney disease and renal fibrosis. Here, we used conditionally immortalized TECs (expressing SV40 large T antigen at permissive conditions, 33°C with IFNγ, and behaving like normal primary cultures after 7 days in restrictive conditions, 37°C without IFNγ) and genetically overexpressed Nnmt (Nnmt-OE) by means of lentiviral transduction of a mock or Nnmt expression construct. In the TGFβ model mimicking the senescent and pro-fibrotic changes in TECs, Nnmt overexpression resulted in an aggravated phenotype.

overall_design: 12 samples, 3 replicates, 4 conditions. Cells transduced with a mock or Nnmt expression construct and selected on puromycin. Some samples treated for 48h with TGFβ 10 ng/mL.

first: Lucie

last: Chanvillard

first: Hildo

last: Lantermans

first: Christopher

last: Wall


title: Unique DNA methylation signature may not specifically characterize BLBS across distinct genetic variants

city: Philadelphia

first: Kelly

last: Clark

state: PA

address: 3501 Civic Center Blvd

department: Human Genetics

institute: Children's Hospital of Philadelphia

type: Methylation profiling by genome tiling array

summary: Bryant-Li-Bhoj syndrome (BLBS) is a mixed neurodevelopmental/neurodegenerative syndrome caused by germline variants in the genes encoding Histone 3.3 (H3.3). Here, we assess DNA methylation differences between BLBS patient-derived and unaffected control tissues (dermal fibroblasts and blood samples) using the Illumina EPICv2 methylation microarray. Our 8 dermal fibroblast samples and 12 blood samples represent 19 of the 70 unique causative BLBS variants. After multiple testing correction, no CpG probes showed statistically significant methylation differences in either of these tissues. The lack of significant DNA methylation changes identified at this time in BLBS supports evaluation of other causes of dysregulation, as well as re-evaluation for more subtle methylation changes when more samples become available.

overall_design: We profiled DNA methylation using the Illumina EPIC v2 whole genome methylation microarray in 2 replicates each of 8 BLBS patient-derived and 6 control dermal fibroblast lines, and 1 replicate each of 12 BLBS patient-derived and 12 control whole blood samples.


title: NNMT overexpression promotes tubular senescence and fibrosis in human chronic kidney disease (NNMT inhibition in TEC cells) [Series_1]

summary: Renal tubular epithelial cells (TECs) are increasingly recognized as the central locus of chronic kidney disease and renal fibrosis. Here, we used conditionally immortalized TECs (expressing SV40 large T antigen at permissive conditions, 33°C with IFNγ, and behaving like normal primary cultures after 7 days in restrictive conditions, 37°C without IFNγ), stimulated with TGFβ to mimic the senescent and pro-fibrotic phenotypic shift of TECs during kidney disease. Co-treating the cells with the selective and membrane-permeable small molecule 5-amino-1-methylquinolinium iodide (NNMTi) significantly protected against senescence and epithelial-to-mesenchymal transition in TGFβ-stimulated TECs.

overall_design: 12 samples, 3 replicates, 4 conditions. Control, TGFβ 10 ng/mL, NNMTi (5-amino-1-methylquinolinium) 50 µM, TGFβ + NNMTi. Cells treated for 48h.

first: Jonathan

last: Thevenet

first: Loes

last: Butter

first: Loic

last: Tauzin

first: Nike

last: Claessen

first: Stefan

last: Christen


title: Nuclear exosome targeting complexes modulate 3D chromatin interactions  genome-wide

city: Toulouse

first: Olivier

last: Cuvier

address: 118 route de Narbonne

department: LBME

country: France

institute: CNRS

summary: Three-dimensional chromatin contacts are thought to be largely determined by loop exclusion driven by CTCF and the cohesin complex. Recent evidence also suggests a role for RNA in shaping genome architecture. Nuclear RNA exosome, together with targeting complexes, PAXT and NEXT, control the decay of noncoding RNAs (ncRNAs), notably enhancer-associated RNAs (eRNAs) and promoter upstream transcripts (PROMPTs). We mapped the chromatin recruitment sites of ZCCHC8 (NEXT), ZFC3H1 (PAXT) and MTR4 helicase, as well as the ncRNAs accumulating upon their depletion. While NEXT and PAXT map to both TSSs and enhancers, MTR4 was associated with enhancers that show preferential long-range contacts with promoters. Loss of MTR4 or ZFC3H1 led to the accumulation of cohesin at target enhancers and TSSs. Chromatin conformation capture analysis revealed that MTR4 modulates the 3D genome landscape. Contacts at anchor points were increased while intraloop contacts were decreased following loss of MTR4 suggesting that MTR4 facilitates loop extrusion. These data highlight a key interplay between cohesin-mediated enhancer-promoter interactions and the regulation of ncRNAs by nuclear RNA exosome that is consistent with a role for RNA in genome folding.

overall_design: Long-range chromatin interactions were detected by Hi-C in control or MTR4 depleted cells

first: Charbel

last: Akkawi

first: Alexandre

last: Heurteau

first: Stephane

last: Schaak

first: Julie

last: Bossuyt

first: Rosemary

last: Kiernan


title: NNMT promotes tubular senescence and fibrosis in chronic kidney disease

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

overall_design: Refer to individual Series


title: NNMT overexpression promotes tubular senescence and fibrosis in human chronic kidney disease (NAM and SAM supplementation in TEC cells) [Series_2]

summary: Renal tubular epithelial cells (TECs) are increasingly recognized as the central locus of chronic kidney disease and renal fibrosis. Here, we used conditionally immortalized TECs (expressing SV40 large T antigen at permissive conditions, 33°C with IFNγ, and behaving like normal primary cultures after 7 days in restrictive conditions, 37°C without IFNγ), stimulated with TGFβ to mimic the senescent and pro-fibrotic phenotypic shift of TECs during kidney disease. Co-treating the cells with nicotinamide (NAM) did not prevent the senescence and epithelial-to-mesenchymal transition in TGFβ-stimulated TECs, while co-treating with S-adenosyl methionine (SAM) attenuated this dysfunctional phenotype.

overall_design: 18 samples, 3 replicates, 6 conditions. Control, TGFβ 10 ng/mL, nicotinamide (NAM) 1mM, TGFβ + NAM, S-adenosyl methionine (SAM) 0.5mM, TGFβ + SAM. Cells treated for 48h.

first: Giulia

last: Lizzo

first: Sonia

last: Karaz

first: José Luis

last: Sanchez-Garcia

first: Sylviane

last: Métairon

first: Valentina

last: Ferro

first: Sofia

last: Moco

first: Daniel

last: Raalte

first: Joris

last: Roelofs

first: Matthew

last: Sanders

first: Jerome

last: Feige

first: Vincenzo

last: Sorrentino


title: Functional and multi-omic aging rejuvenation with GLP-1R agonism [bulk RNA-seq]

city: Hong Kong

first: Andrew

middle: J.

last: Kwok

address: 30-32 Ngan Shing Street, Shatin, New Territories

department: Medicine and Therapeutics

country: Hong Kong

institute: Chinese University of Hong Kong

summary: Identifying readily implementable methods that can effectively counteract aging is urgently needed for tackling age-related degenerative disorders. Here, we conducted functional assessments and deep molecular phenotyping in the aging mouse to demonstrate that glucagon-like peptide-1 receptor agonist (GLP-1RA) treatment attenuates body-wide age-related changes. In male mice treated with a GLP-1RA from 11 months of age for 30 weeks, we observed improvements in physical and cognitive performance, alongside age-counteracting effects that are prominently evident at multiple omic levels. These span the transcriptomes and DNA methylomes of various tissues, organs and circulating white blood cells, as well as the plasma metabolome. Importantly, the beneficial effects are specific to the aging mice, not young adults, and are achieved with a relatively low dosage of GLP-1RA which has a negligible impact on food consumption and body weight. In older mice treated with a GLP-1RA from 18 months of age for 13 weeks, the molecular rejuvenation effects are even more prominent and generally dependent on hypothalamic GLP-1R, pointing to a brain-body axis of aging modulation. We benchmarked the GLP-1RA age-counteracting effects against those of mTOR inhibition, a well-established anti-aging intervention, observing a strong resemblance across the two strategies. Our findings have broad implications for understanding the mechanistic basis of the clinically observed pleiotropic effects of GLP-1RAs, the design of intervention trials for age-related diseases, and the development of anti-aging-based therapeutics.

overall_design: Poly A enriched bulk RNA-seq was carried out on a range of tissues body-wide under different age, drug treatment (exenatide, rapamycin) conditions, and hypothalamic GLP-1R knockdown conditions.

first: Andrew J.

first: Junzhe

last: Huang

first: Ho

last: Ko


title: Functional and multi-omic aging rejuvenation with GLP-1R agonism

platform_organism:
Macaca mulatta
Homo sapiens
Mus musculus
Rattus

overall_design: DNA methylation assays were carried out by the Clock Foundation using a HorvathMammalMethylChip320 methylation array containing loci from the Infinium Mouse Methylation BeadChip (i.e., mm285k array62) and the mammalian methylation array (i.e., mm40k array60).


title: Function and transcriptional profiles comparison between tumor-infitlrating NK cell (tuNK) and splenic NK cell (spNK) [RNA-seq]

first: Yi

last: Wang

summary: Natural killer (NK) cells, a type of potent cytotoxic lymphocytes, are particularly promising for the treatment of cancers that lose or downregulate major histocompatibility complex class I (MHC-I) expression to evade T cell-mediated immunotherapy. However, the hostile and immune suppressive tumor microenvironment (TME) greatly hinders the function of tumor-infiltrating NK cells limiting the therapeutic efficacy against solid tumors. Here, we show that a fusion protein of interleukin-21 (IL-21−Fc), as a direct in vivo intervention, can safely and effectively reprogram NK cell metabolism and enhance their effector function in the TME. Our research demonstrates that combining IL-21−Fc with IL-15 superagonist (IL-15SA) or NK cell transfer leads to the eradication of MHC-I-deficient tumors and confers durable protection in syngeneic and xenograft tumor models. Mechanistically, we uncover that IL-21−Fc enhances NK cell effector function by upregulating glycolysis in a lactate dehydrogenase A (LDHA)-dependent manner. These findings not only underscore the considerable potential of IL-21−Fc as an in vivo therapeutic intervention to bolster NK cell-based immunotherapy, but also unveil an innovative strategy of metabolic reprogramming for NK cell rejuvenation within tumors.

overall_design: To explore and compare the transcriptomic profiles of the intratumoral and splenic NK cells, in addition to assess the function of NK cells within the TME. We established a subcutaneous (s.c.) MHC-I-deficient tumor model by inoculating BALB/c mice with CT26_β2m-/- murine colorectal carcinoma cells and performed bulk RNA-seq of sorted tissue-infiltrating NK cells.

first: Li

last: Tang

first: Yugang

last: Guo


title: Lamin A/C-regulated cysteine catabolic flux modulates stem cell fate through epigenome reprogramming [ES_ChIP_seq_H3K9me3_LA]

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

institute: Medical Faculty Mannheim/University of Heidelberg

summary: Spatiotemporal changes in the nuclear lamina and cell metabolism shape cell fate, yet their interplay is poorly understood. Here, we identify lamin A/C as a key regulator of cysteine catabolic flux essential for proper cell fate and longevity. Its loss in naïve mouse pluripotent stem cells leads to upregulation of the cysteine generating and catabolizing enzymes, cystathionine γ-lyase (CTH) and cystathionine β-synthase (CBS), thereby promoting de novo cysteine synthesis. Increased cysteine flux into acetyl-CoA fosters histone H3K9 and H3K27 acetylation, triggering a transition from naïve to primed pluripotency and abnormal cell fate and function. Conversely, the toxic gain-of-function mutation of Lmna, encoding lamin A/C and associated with premature aging, reduces CTH and CBS levels. This reroutes cysteine catabolic flux and alters the balance between H3K9 acetylation and methylation, crucially impacting germ layer formation and genome stability. Importantly, modulation of Cth and Cbs rescues the abnormal cell fate and function, restores the DNA damage repair capacity, and alleviates the senescent phenotype caused by lamin A/C mutations, highlighting the potential of modulating cell metabolism to mitigate epigenetic diseases.

overall_design: Control, Lmna KO and Lmna G609G/G609G  Nkx2-5-GFP mES cell lines were cultured on feeder condition in DMEM high glucose supplemented with 15% FCS and 1000 U/ml LIF. ESCs  were harvested to perform for H3K9me3 ChIP-seq.

first: Julio

last: Cordero

first: Yinuo


title: Genetic and dietary determinants of gut microbiome-bile acid interactions in BXD recombinant inbred mouse population

first: Xiaoxu

last: Li

address: Station 15 - CH

summary: Transcriptome data measured by microarray in proximal colon of  the BXD mouse genetic diversity model under a standard chow or a high fat diet at a postprandial state.

overall_design: At 29 weeks of age, previous euthanasia, mice were fasted overday and refed with their respective diet for 4h following their physiological cycle. Multi-organ were flash-frozen and bio-banked for future use, the assoiacted datasets are mentioned in the paper. In this study, proximal colon samples were collected and immediately frozen in liquid nitrogen for RNA extraction and RNEasy cleanup. Each dietary and strain cohort consisted of ~5 animals which were prepared independently then pooled evenly by µg RNA before the Affymetrix arrays were run.

first: Johan

last: Auwerx

first: Kristina

last: Schoonjans

first: Alessia

last: Perino

first: Hao


title: Lamin A/C-regulated cysteine catabolic flux modulates stem cell fate through epigenome reprogramming [ES_ChIP_seq_H3K9ac_H3K27ac_LA]

overall_design: Control, Lmna KO nd CTH OE Nkx2-5-GFP mES cell lines were cultured on feeder condition in DMEM high glucose supplemented with 15% FCS and 1000 U/ml LIF. ESCs  were harvested to perform for H3K9ac and H3K27ac ChIP-seq.


title: MYC-Driven Gliosis Impairs Neuron-Glia Communication in Amyotrophic Lateral Sclerosis

city: Trento

first: Manuela

last: Basso

address: via sommarive 9

department: CIBIO

country: Italy

institute: University of Trento

summary: Chronic activation of glial cells leads to the dysfunction and degeneration of motor and cortical neurons in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) with an unknown mechanism. To shed light on the molecular pathogenetic processes underlying the exordium and contribution of gliosis to disease onset and progression, we used cells, mice, and patient-derived cells modeling TDP-43, SOD1, and C9orf72-linked and sporadic ALS. Our data reveal a sequential disease progression, starting with enhanced glial reactivity and proliferation, and transitioning into inflammation with upregulation of pro-inflammatory genes. Using mouse genetics, we show that expression of mutant TDP-43 in astrocytes is necessary to cause gliosis and behavioral abnormalities. Mechanistically, we show that glial MYC gain-of-function drives neurodegeneration by promoting the release of astrocytic EVs that nonetheless fail to provide trophic support to surrounding neurons. Our research reveals a novel functional role for MYC in glia-to-neuron miscommunication in ALS.

overall_design: RNA-seq was performed on purified astrocytes (ACSA+), purified oligodendrocytes (O4+) isolated from cortices and spinal cords of TDP-43Q331K mice. Purified microglia (Cd11b+) was obtained from the same mouse model but from cortices only. Samples were collected from mice at either 3, 6, or 10 months. Moreover, samples from omomyc treated astrocytes are included.

first: Paolo

last: Fioretti

first: Anna

last: Barbieri

first: Alice

last: Migazzi


title: Dynamic expression of Erg controls fetal-to-adult maturation of the hematopoietic system

city: Boston

first: Mayuri

last: Yano

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital


title: Dynamic expression of Erg controls fetal-to-adult maturation of the hematopoietic system [ChIP-seq]

summary: Adults and children are affected by different types of blood diseases.  We hypothesize that this is due to differences in normal blood formation between infants, children, and adults.  Our laboratory focuses on understanding these age-related differences in blood formation as a foundation upon which to improve understanding of blood diseases.  In this project, we extend our previous work to understand how hallmarks of young versus mature blood formation – for example, the types of mature blood cells produced – are controlled at the genetic level.  I will use a combination of mouse models, genetic manipulation, and genetic profiling to test our hypothesis that the key blood stem cell factor Erg controls the age state of blood formation.

overall_design: To understand how Erg controls programs regulating the fetal to adult hematopoietic transition, we performed RNA sequencing (RNA-seq) and chromatin immunoprecipitation (ChIP) for the active histone mark lysine 27 acetylation (H3K27Ac) on lineage negative HSPCs of defined genotypes. RNA-seq and ChIP-seq were performed to compare the transcriptome between wild-type (WT) fetal liver, WT bone marrow, and Erg+/-  bone marrow lineage negative cells by negative selection using biotinylated lineage antibodies and streptavidin beads.

first: Mayrui

last: Tanaka-Yano

first: R

middle: G

last: Rowe

first: Edroaldo

last: Lummertz da Rocha

first: Berkley

last: Gryder


title: Single-cell transcriptomics reveals species-dependent immune infiltration of T cells in Huntington's disease neurodegeneration

city: GuangZhou

first: Jiawei

address: No. 601 West Huangpu Avenue, Tianhe District,

department: Guangdong-Hong Kong-Macau Institute of CNS Regeneration (GHMICR)

institute: JINAN University

summary: Immune infiltration of T cells in the brain has been observed in various pathological conditions, but whether this phenomenon occurs in Huntington disease (HD) remains unknown. To address this question, we conducted an investigation using HD knock-in pigs, which exhibit selective neurodegeneration similar to HD patients. Single-cell transcriptomes identified that glial cells are the most abundant cell type in the human and pig striatum, while neurons outnumber glial cells in the mouse striatum. HD knock-in pigs recapitulate the loss of specific types of striatal neurons (iSPN and dSPN) observed in HD patients, a phenomenon not observed in HD knock-in mice. The increased IFN-activated microglia subgroup in HD knock-in pigs was found to secrete CCL8 chemokines to recruit CD8+ T cells. These T cells release perforin and granzyme, leading to the degeneration of striatal neurons. Although HD-KI mouse striatum does not show elevated CCL8, administration of CCL8 resulted in an increase in CD8+ T cells and a reduction in neuronal cells. These findings suggest that species-dependent abundance of glial cells and the effects of mutant huntingtin on glial cells contribute to microglia-driven immune infiltration of CD8+ T cells, ultimately playing a critical role in the selective neurodegeneration in HD.

overall_design: To determine the single cell atlas of the striatum of HD-KI pigs and whether T cell immune infiltration occurs in HD, we performed single cell transcriptome sequencing on HD-KI pigs

first: Yingqi

last: Lin

first: Sen

last: Yan


title: Neferine improves cardiac remodeling induced by hypertension by modulating multiple signaling pathways --heart

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

summary: The goals of this study is to compare the differently expressed genes in heart tissue of WKY and SHR with or withoutneferine treatment. The SHRs were randomly divided into 2 groups: SHR, and SHR +neferine (10mg/kg/d) groups . WKY rats  were set as control. Rats in WKY and SHR groups were  intragastrically with double distilled water (dd H2O), while rats in  SHR + neferine (10mg/kg/d) group were intragastrically with 10 mg/kg/d of neferine for 10 weeks.  Then the  heart tissues were used to identify differentially expressed genes among different groups.

overall_design: RNA sequencing was performed with heart tissue of rats in 3 groups: WKY, SHR, SHR +neferine (10mg/kg/d) treated  to identify the differently expressed genes and related pathway.

first: Aling

last: Shen

first: Meizhu

last: Wu

first: Zhi

last: Guo


title: Dynamic expression of Erg controls fetal-to-adult maturation of the hematopoietic system [RNA-seq]


title: c-Abl-induced Wnt/β-catenin activation and Ksp-tdTomato+ PDGFRα+ tubular epithelial cells promote renal fibrosis in mice through epithelial-to-mesenchymal transition

first: Qianyi

last: Bao

address: 800 Dongchuan RD. Minhang District, Shanghai, China

institute: Bio-X Institutes, Shanghai Jiao Tong University

summary: Renal fibrosis is a common pathological manifestation of chronic kidney disease (CKD). Epithelial-to-mesenchymal transition (EMT) plays an essential role during renal fibrosis. Here we found the increased expression of c-Abl, a nonreceptor tyrosine kinase, in the tubular epithelial cells (TECs) of patients with CKD and renal fibrosis mouse models. c-Abl deficiency in TECs attenuated kidney fibrosis in mice. c-Abl overexpression in TECs in vitro promoted EMT, accompanied by the activation of the Wnt/β-catenin signaling which in turn promotes the expression of c-Abl, thereby forming a positive feedback loop. We further found that during renal fibrosis, a group of TECs undergo a partial EMT program, resulting in PDGFRα expression in the Ksp cell lineage. The primary functions of Ksp-tdTomato+ PDGFRα+ cells were to recruit macrophages by secreting chemokines and to create an inflammatory microenvironment by secreting inflammatory factors. c-Abl deletion in TECs reduced the number of Ksp-tdTomato+ PDGFRα+ cells and decelerated EMT progression. In fibrotic mouse models, the c-Abl inhibitors nilotinib and GNF5 ameliorated EMT, inflammation, and fibrosis. Together, our findings suggest that c-Abl-dependent Wnt/β-catenin signaling activation and Ksp-tdTomato/PDGFRα double-positive cells drive renal fibrosis through partial EMT, providing new insights into the pathogenesis of CKD and a new therapeutic target.

overall_design: c-AblloxP/loxP mice were bred with transgenic Ksp-Cre mice to generate a tubular epithelial cell (TEC)-specific knockout c-Abl mouse line. In male mice (8 weeks old; c-Ablflox/flox and c-AblEpi-cKO mice), UUO was maintained for 14 days. The mRNA transcriptome of mouse kidney tissues was examined. Fibrotic kidney tissues from the c-Ablflox/flox group and c-AblEpi-cKO mice kidney tissues were compared. The goal was to identify the effect of c-Abl knockdown in TECs of renal fibrosis on gene expression during kidney fibrosis.

first: Anyu

last: Wang


title: TDP-43 nuclear loss in FTD-ALS causes widespread alternative polyadenylation

city: Stanford

first: Yi

last: Zeng

address: 300 Pasteur Drive

institute: Stanford University

summary: In frontotemporal dementia and amyotrophic lateral sclerosis, the RNA-binding protein TDP-43 is depleted from the nucleus. TDP-43 loss leads to cryptic exon inclusion but a role in other RNA processing events remains unresolved. Here, we show that loss of TDP-43 causes widespread changes in alternative polyadenylation, impacting expression of disease-relevant genes (e.g., ELP1, NEFL, and TMEM106B), providing evidence that alternative polyadenylation is a new facet to TDP-43 pathology.

overall_design: To investigate the role of TDP-43 regulated alternative polyadenylation in FTD and ALS, we differentiated human stem cells to cortical neurons, used shRNA to knock down TDP-43, and then performed RNA-seq and 3' end-seq to examine the impact of TDP-43 knockdown on alternative polyadenylation and corresponding gene expression changes.

first: Anastasiia

last: Lovchykoval

first: Tetsuya

last: Akiyama

first: Chang

last: Liu

first: Caiwei

first: Vidhya

middle: M

last: Jawahar

first: Odilia

last: Sianto

last: Calliari

first: Mercedes

last: Prudencio

first: Dennis

middle: W

last: Dickson

first: Leonard

last: Petrucelli

first: Aaron

middle: D

last: Gitler


title: USP51-GRP78 axis promotes doxorubicin-resistance by regulating the activity of ABCB1 in TNBC

city: Tian Jin

first: Yang

last: Ou

address: Weijin road

institute: Nankai university

summary: Background: Resistance to chemotherapy remains an obstacle for triple-negative breast cancer (TNBC) patients. The core components of the ubiquitin-proteasome system have been demonstrated to regulate chemoresistance of TNBC. As a novel DUB, ubiquitin-specific peptidase 51 (USP51) plays a pivotal role in chemotherapeutic resistance in multiple malignancies. Herein, we sought to better understand how USP51 performs a cell-intrinsic role in mediating chemotherapeutic resistance in TNBC. Methods: Western blotting, RNA-sequencing and CCK8 assay were used to determine the important DUB for chemoresistance of breast cancer. Coimmunoprecipitation and pulldown analyses, protein deubiquitination assay, immunohistochemistry and molecular biology methods were then used to determine the significance of USP51 in TNBC chemoresistance and associated signaling pathways in several different cell lines, mouse models and patient tissue samples. Ubiquitin-7-amido-4-methylcoumarin (Ub-AMC)-based deubiquitinase activity, cellular thermal shift and surface plasmon resonance (SPR) analyses were performed to investigate the activity of USP51 inhibitors. Results: To identify the critical DUB involved in breast cancer chemoresistance, we established doxorubicin-resistant Cal51 and MDA-MB-231 by multiple dose exposure. We found ectopic USP51 in doxorubicin-resistant cells compared with parental cell. Moreover, USP51-interfered chemoresistant tumor cells exhibited impaired cell viability as well as increasing DNA damage and apoptosis after treated with doxorubicin. Inversely, ectopic USP51 not inactive mutant USP51C372S enhanced cell viability and decreased DNA damage and apoptosis after treated with doxorubicin. At the molecular level, GRP78 was identified as a bona fide substrate of USP51. Importantly, knockdown USP51 increased doxorubicin-induced DNA damage and apoptosis, which was recovered by overexpressing GRP78 in vitro and in vivo. In addition, the activity of ABCB1, the main efflux pump of doxorubicin, was enhanced by GRP78. Consistently, the expression of USP51, GRP78 and ABCB1 were correlated with doxorubicin-resistance in TNBC patients. Finally, we explored a small molecular inhibitor of USP51, WCY-4-1, which confered chemosensitization in TNBC. Conclusion: These findings collectively indicated that USP51 enhances the activity of ABCB1 by deubiquitinating and stabilizing GRP78, which leads to decreased accumulation of doxorubicin as well as decreased DNA damage and apoptosis in TNBC. Our results also revealed that inhibition of USP51 impairs doxorubicin-resistance in TNBC.

overall_design: To identify the DUB regulated doxorubicin-resistance of breast cancer, Cal51 and doxorubicin-resistant Cal51R cell lines were send to perform RNA sequencing.


title: The Zeb1-Cxcl1 axis impairs the antitumor immune response by inducing M2 macrophage polarization in breast cancer I

summary: Zeb1, a classic epithelial-mesenchymal transition (EMT) regulator, has recently been found to be involved in M2 macrophage polarization in the tumor immune microenvironment, thereby promoting tumor development. However, the underlying mechanism of Zeb1-induced M2 macrophage polarization remains largely unexplored. To identify the potential role of Zeb1 in remodeling the tumor immune microenvironment in breast cancer, we crossed the floxed Zeb1 allele homozygously into PyMT mice to generate PyMT;Zeb1cKO (MMTV-Cre; PyMT;Zeb1fl/fl) mice. We found that the recruitment of M2 macrophages was significantly reduced in tumors from PyMT;Zeb1cKO mice, along with weakening of the tumor suppressive effect. Mechanistically, Zeb1 plays a crucial role in transcriptionally promoting the expression of Cxcl1 in tumor cells and enhancing the secretion of Cxcl1 in serum. Eventually, Cxcl1 activated the JAK-Stat3 signature via Cxcr2 and then induced the M2 polarization of macrophages, which leads to T cell inactivation and impairs the antitumor immune response in breast cancer. Our results revealed the important role of Zeb1 in the remodeling of the breast cancer tumor microenvironment, suggesting a novel therapeutic intervention for the treatment of advanced cancers.

overall_design: To identify the molecular mechanism that mediates Zeb1-induced M2-like TAM polarization, shZeb1/231 and shCtrl/231 cell lines was obtained to perform RNA sequencing.


title: Lamin A/C-regulated cysteine catabolic flux modulates stem cell fate through epigenome reprogramming

first: Gergana

last: Dobreva


title: Lamin A/C-regulated cysteine catabolic flux modulates stem cell fate through epigenome reprogramming [bulkPolyA_RNA_seq_LA_ES]

overall_design:
Total RNA was isolated  from ES_shControl , ES_shControl Lmna_KO, ES_shCth Lmna_KO, and CTH OE Nkx2-5-GFP mES cell lines
Total RNA was isolated from ES_shCbs_Lmna_KO Nkx2-5-GFP mES cell lines to process for polyARNA-seq

first: Julio

last: Cordero

first: Yinuo


title: Transplantation of human glial progenitor cells into adult Huntington Disease mice rescues neuronal architecture and aspects of behavior

city: Rochester

first: Steven

last: Goldman

state: NY

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

summary: Glial pathology is a significant contributor to disease pathogenesis in Huntington disease (HD), and neonatal glial replacement can delay disease progression and rescue aspects of behavior in mouse models of HD. Here we asked if the transplantation of normal human glial progenitor cells (hGPCs) into adult HD mice might similarly ameliorate phenotype. We found that the introduction of hGPCs into the striata of adult R6/2 HD mice significantly ameliorated their motor and cognitive phenotypes, extended their survival, and rescued aspects of medium spiny neuronal dendritic architecture. To establish the basis for this effect, we used retrograde labeling of striatal MSNs with glycoprotein-deleted rabies virus in hGPC-engrafted adult R6/2 mice to discover that the dendritic architecture of striatal MSNs was partially restored in adult-engrafted mice. These findings suggest that glial replacement may delay disease progression in HD, and that this is associated with the dynamic reorganization of medium spiny neuron dendritic architecture.

overall_design: WT mice or R62 mice (HD model) (n=2) were transplanted with human glia to investigate neuronal changes in response to glial transplantation. Unengrafted mice for both WT and R62 were used as control.

first: Carlos

middle: B

last: Villanueva

middle: A

first: Ashley

last: Tate

first: Signe

middle: S

last: Lorenzen

first: Abdellatif

last: Benraiss

first: Nguyen

middle: P

last: Huynh

first: Benjamin

last: Mansky


title: Effects of lipopolysaccharide (LPS) or interferon gamma (IFNy) treatment on wild type or PILRA knock-out iPSC-derived human microglia after 24 hours

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

summary: To study the effect of PILRA loss-of-function immune signaling pathways, we treated wildtype and PILRA knock-out (KO) iPSC-derived microglia (iMGs) with lipopolysaccharide (LPS) or interferon gamma (IFNy) for 24 hours and performed bulk RNA-seq analysis.

overall_design: iPSC-derived microglia (iMG) with either wildtype or PILRA knock-out genotypes were treated with either 1) LPS, 2) IFNg or 3) left untreated for 24 hours. The experiment was repeated five times, starting with freshly seeded iMG on different days.

first: David

last: Tatarakis

first: Tanya

last: Weerakkody

first: Kathryn

last: Monroe

first: Mathew

last: Blurton-Jones


title: The Zeb1-Cxcl1 axis impairs the antitumor immune response by inducing M2 macrophage polarization in breast cancer II

overall_design: To identify the molecular mechanism that mediates Zeb1-induced M2-like TAM polarization, EpCAM+ breast cancer epithelial cells were isolated from PyMT and PyMT;Zeb1cKO tumors to perform RNA sequencing.


title: Dual developmental effects of ARX poly-alanine mutations in human cortical excitatory and inhibitory neurons

city: San Antonio

first: Jenny

last: Hsieh

state: Texas

address: One UTSA Circle

department: Department of Neuroscience, Developmental and Regenerative Biology

institute: University of Texas at San Antonio

summary: Infantile spasms (IS), a severe childhood epilepsy with an incidence of 1.6–4.5 per 10,000 live births, often lead to lifelong intellectual disability. Up to 5% of affected males carry mutations in the Aristaless-related homeobox (ARX) gene. The lack of human-specific models for developmental epilepsy limits progress, making organoids a promising alternative. We use human cortical (CO) and ganglionic eminence organoids (GEO) to model poly-alanine expansion (PAE) mutations in ARX. PAE mutations increase cortical progenitor proliferation and accelerate early cortical development. ARX expression is upregulated in patient-derived COs at 30 DIV, correlating with altered cell cycle gene expression. We observe enhanced, cell-autonomous interneuron migration, which is rescued by CXCR4 inhibition. ARXPAE assembloids exhibit early network hyperactivity. These findings highlight the utility of human brain organoids in uncovering ARXPAE-driven mechanisms and represent a critical step toward developing targeted therapies for IS and related developmental epilepsies.

overall_design:
Human iPSC derived cortical organoids and ganglionic eminence organoids at 2 developmental timepoints (30DIV and 120DIV) were dissociated , single cell suspension was made and 10X genomics was used to perform single cell RNA sequencing
DIV = Days in vitro
Mapped to GRCh38 human assembly

first: Vanesa

last: Nieto-Estevez

first: Parul

last: Varma

first: Sara

last: Mirsadeghi

first: Jimena

last: Caballero

first: Sergio

last: Gamero-Alameda

first: Ali

last: Hosseini

first: Marc

last: Silvosa

first: Drew

last: Thodeson

first: Sonal

last: Goswami

first: Zane

middle: R

last: Lybrand

first: Michele

last: Giugliano

first: Christopher

last: Navara


title: Nutrigenomic profiling identifies ZIP10 (SLC39A10) as a regulator of erythroid zinc homeostasis with genetic associations to anemia risk

status: Public on Nov 19 2025

city: Seoul

first: Moon-Suhn

last: Ryu

address: 50 Yonsei-ro, Seodaemun-gu, Samsung Hall 611

institute: Yonsei University

summary: To determine the physiological roles of ZIP10 and zinc in erythroid progenitor cells, Zip10 was depleted via nucleofector-mediated siRNA delivery into cells and cellular zinc was restricted by DTPA treatment. The transcriptome profiles acquired from RNA-seq were compared with those of control cells.

overall_design: Comparative gene expression profiling of control G1E-ER4 cells and those deficient in cellular zinc, ZIP10, or both (n = 3 biological replicates per group)

first: Juyoung

last: Kim


title: A receptor kinase complex refines cambium activity in Arabidopsis

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

institute: Durham University

summary: The largest reservoir of terrestrial biomass is the wood within plant stems. Consisting of xylem cells, wood is derived from the cambium, a stem cell population that is maintained by non-cell autonomous signalling. The central component of this system is PXY, a receptor protein present on the plasma membrane of cambium cells. Here, we show that PXY protein interacts with a second membrane-localised receptor kinase, ER, to promote cambium fate. Combinatorial mutations between ER, ERL1 and ERL2 and receptor kinases of a second family, PXY, PXL1, and PXL2, show severe cambial defects, but the mechanism underpinning these phenotypes is not known. Here we discovered that PXY and PXL proteins form protein complexes with ER family members. In genetic analyses, plant lines in which PXY signalling was constitutively active had dramatic phenotypic changes that required the presence of ER or ERL2. Our results demonstrate that PXY signalling mediated cambium regulation depends on ER signalling and explains ER function in the cambium. Because the cambium produces xylem, which constitutes the wood in vascular plants, our findings position PXY-ER complexes at the centre of the accumulation of this versatile biomaterial and essential carbon sink.

overall_design: RNA-Seq profiling of 7-day-old wild type, er mutant and XVE:ER transformed er mutant at 0h, 3h and 8h Estradiol induction.

first: Qing

last: He

first: Peter

last: Etchells


title: Antigen-reactive CD4 T cells after SARS-CoV-2 vaccination show divergent phenotypic states with or without restimulation [mixed samples]

city: Erlangen

first: Kilian

last: Schober

state: Bavaria

address: Maximiliansplatz 2

department: Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene

institute: Universitätsklinikum Erlangen

summary: Understanding T cell fate requires precise knowledge of antigen reactivity. For CD4+ T cells, conventional identification of antigen reactivity by peptide restimulation relies on cellular activation, but thereby also introduces a phenotypic bias. However, by performing single-cell RNA and TCR sequencing on both antigen-stimulated and unstimulated samples, clonotypes can be tracked across conditions to identify antigen-reactive CD4+ T cells and simultaneously assess their phenotypes in the unperturbed state. Using this “reverse phenotyping” strategy, complemented by DNA-barcoded peptide–HLA class II multimers, we here investigated the longitudinal phenotypic evolution of SARS-CoV-2 spike–reactive CD4+ T cells after repeated mRNA vaccination. Without stimulation, reactive clones showed more Th-neutral features and less of an activated Th1-like state than would be assessed after antigen restimulation, yet retained a distinct transcriptional state into the memory phase. These results uncover durable imprints in antigen-reactive CD4+ T cells and highlight that cell state classification can differ fundamentally when judged by phenotype versus function.

overall_design: Antigen-specific T cells after SARS-CoV-2 mRNA vaccination were identified by in vitro-restimulation using a peptide mix spanning the full-length SARS-CoV-2 spike glycoprotein. In vitro re-stimulated and unstimulated cells (non-naive CD4 and CD8 T cells) were sorted by FACS and subjected to 5' scRNAseq on a 10x Genomics platform

first: Katharina

last: Kocher

first: Felix

last: Drost

first: Christine

last: Schülein

first: Bernd

last: Spriewald

first: Benjamin

last: Schubert


title: Antigen-reactive CD4 T cells after SARS-CoV-2 vaccination show divergent phenotypic states with or without restimulation [separate samples]


title: RNAseq of colonic epithelial and lamina propria-derived Tregs

city: Amsterdam

first: Lisanne

last: Lutter

address: De Boelelaan 1117

institute: Amsterdam University Medical Center

summary: Local tissue adaptation by immune cells is of especially high importance in the small and large intestines, the largest mucosal barrier surface in the body. Recent work on tissue resident T cells has focused on CD8+ “tissue resident memory cells” or Trm. However, the human colon also contains different populations of CD4+ T cells, in mice referred to as “intraepithelial lymphocytes” and “lamina propria lymphocytes”. Our results uncover a pattern of compartmentalized tissue adaptation of human colonic CD4+ T cells in the steady state. This pattern is lost during active Inflammatory Bowel Disease, with potential detrimental effects on barrier maintenance and continued inflammation.

overall_design: RNA-seq profiling of sorted Tregs derived from the epithelium and lamina propria of colonic biopsies of patients with Crohn's disease and one control tissue from a patient with colorectal cancer.

first: Femke

last: van Wijk

first: David

last: Hoytema van Konijnenburg


title: IL-15 neutralization reduces acute lentivirus inflammation and signaling in the brain

city: Iowa City

first: Chen

middle: Sabrina

last: Tan

state: IA

address: 200 Hawkins Dr.

department: Medicine

institute: University of Iowa

summary: In this study, we investigated the impact of IL15 on the brain’s immune and inflammatory milieu during acute SIV infection of rhesus macaques. Given the ongoing issue of HIV-associated neurocognitive disorders (HAND) in people living with HIV and the role of inflammation in its pathogenesis, understanding the brain’s immune response to lentiviral infections is crucial. We found that SIV infection stimulated a resident brain immune response in control animals, characterized by increased astrocyte activation and enhanced ramification of microbial morphology. However, animals treated with anti-IL15 antibodies (aIL15) prior to SIVmac239X infection showed significantly reduced brain inflammation without altering SIV levels in brain tissues. Specifically, aIL15 treatment resulted in 1) decreased overall microglial cell populations; 2) altered T lymphocyte dynamics in the brain; 3) reduced proinflammatory cytokine (IL6) expression in microglia; and 4) increased anti-inflammatory cytokine (TGF-β) expression in brain macrophages. RNA transcription profiles of aIL15-treated animals revealed an overall reduction in inflammatory signaling, alongside upregulation of genes associated with M1 macrophage signaling pathways. These results suggest that peripheral modulation of IL15 can attenuate neuroinflammation during acute lentiviral infection and may be therapeutic in conditions such as HAND. Our findings highlight the potential for targeting peripheral immune factors to modulate central nervous system inflammation in lentiviral infections.

overall_design: 11 adule male rhesus macaques were used. 8 were infected with SIVmac239. 3 were sacrificed on day 7, 5 were sacrificed on day 14. 3 were uninfected controls. Brain tissue from the frontal cortex and blood was sampled at necropsy. Basal ganglia and thalamus tissue were also collected from one animal.

first: Daniel

last: Ram

first: Raja

last: Gopalakrishnan

first: Malika

last: Aid

first: Kyle

last: Kroll

first: Eunice

middle: K

last: Gikundiro

first: Caitlin

last: Davis

first: Marco

last: Hefti

first: Kimberly

middle: L

last: Fiock

first: Brook

last: Tilahun

first: Yvette

last: Umotoniwase

first: Rhianna

last: Jones

first: Griffin

last: Woolley

first: Valerie

last: Varner

first: Michelle

last: Lifton

first: Steven

middle: E

last: Bosinger

first: Dan

middle: H

last: Barouch

first: Brandon

middle: F

last: Keele

first: R. Keith

last: Reeves

first: Sabrina


title: Bovine endometrial organoids: A new tool to study conceptus-maternal interactions in mammals

city: Leeds

first: LeedsOmics

last: UoLeeds

state: West Yorkshire

address: Clarendon Way

department: Cross-faculty

institute: University of Leeds

summary: In cattle, communication between endometrium and conceptus during the peri-implantation period is crucial for successful pregnancy. Understanding these interactions is vital as most early pregnancy loss occurs during this time. A major challenge in understanding uterine function and early pregnancy is lack of appropriate in-vitro models. Two-dimensional models are available, but do not recapitulate the endometrium’s complex multicellular structure. Here, we describe a hormonally responsive organoid model of the bovine endometrium, developed as a tool for studying endometrial function and early pregnancy. Bovine glandular epithelial cells were isolated from reproductive tracts and cultured in an extracellular matrix hydrogel (Cultrex 2) at 38.5°C, 5% CO (n=3). RNA was extracted and qPCR confirmed the presence of gland markers: leukemia inhibitory factor, mucin-1, insulin-like growth factor binding protein-1, kruppel-like factor-5 and forkhead box protein-A2. Organoids were imaged at specific time-points to monitor growth and passaged 3 times in 1:2 or 1:3 ratios after growing for a minimum of 10 days per passage. Morphologically, organoids were spherical and fast-growing at passages 0 and 1, but this declines following passage 2. Bovine endometrial organoids (n=3, passage 0) were treated with 1000 ng/ml recombinant ovine Interferon Tau (IFNT) or 10 μg/ml progesterone (P4) for 24 hours and analysed by RNASeq to assess hormone responsiveness. Differential expression analysis by DeSeq2 negative binomial distribution model followed by Wald test and Benjamini-Hochberg correction identified 373 transcripts significantly upregulated (padj<0.05 or log2fold change >0.05) in response to P4 treatment, with downstream analysis showing significant overrepresentation (FDR<0.05) of genes associated with positive regulation of protein localisation to plasma membrane and cell periphery. Of the 240 genes significantly downregulated by P4 these were significantly overrepresented (FDR<0.05) in biological processes of cilium and cytoskeleton organisation. IFNT treatment resulted in significant upregulation of 414 genes and downregulation of 119 genes. The largest cluster associated with differentially expressed genes in response to IFNT is defence to virus and interferon signalling. There were 30 genes altered by both P4 treatment and IFNT treatment. Organoids were also shown to express conserved microRNAs, and it was possible to culture them in a microfluidics device - making them a useful model for a multitude of potential investigations. This model provides a tool to investigate bovine endometrial function and peri-implantation communication, subsequently allowing species comparison to understand diversity in reproductive strategies.

overall_design: Bovine endometrial organoid cultures were treated with control (media only), vehicle control (EtOH), Progesterone, PBS, PDI, CAPG, and Interferon tau for 24 hours and RNASeq carried out to assess hormone/protein responsiveness

first: Jessica

middle: C

last: Edge

first: Olga

last: Amelkina

first: Haidee

last: Tinning

first: Gianluca

last: Giovanardi

first: Elena

last: Mancinelli

first: Samantha

last: Gardner

first: Elton

last: Vasconcelos

first: Virginia

last: Pensabene

first: Karen

last: Forbes

first: Mary

middle: J

last: O'Connell

first: Peter

last: Ruane

first: Niamh

last: Forde


title: Interaction of adjuvants, sex, and the microbiome on SIV vaccine-induced immunity and protective efficacy in rhesus macaques

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

institute: Northwestern University

summary: Mucosal priming of rhesus macaques with replicating Adenovirus SIV-recombinants and systemic boosting with ALVAC-SIV plus envelope protein or DNA encoding SIV genes plus envelope protein elicited strong immunologic responses in both compartments. Following repeated low-dose intrarectal SIV challenges, significant acquisition delay compared to adjuvant controls was not observed. However, delayed acquisition in both vaccine arms and adjuvant controls compared to naïve controls led to identification of transcriptomic signatures associated with protective innate immunity. Vaccinated females but not males exhibited significantly lower acute viremia compared to same-sex controls, confirming our previously reported sex-difference in SIV vaccine outcomes. The rectal microbiome of females and males responded differently to the prime-boost regimen and differentially associated with viremia control and systemic and mucosal humoral immunity. We conclude that the impact on protective efficacy of vaccine-induced microbiome alteration in males and females and trained immunity are factors of significant importance in vaccine outcome.

overall_design: Sixty rhesus macaques were vaccinated with Ad5+ALVAC-SIV vaccine (n=25), Ad5+DNA-SIV vaccine (n=25) or empty Ad5 vector+adjuvant (n=10). Whole blood samples wre collected pre-vaccination, 24 hours after the 2nd immunization (wk12, 2nd Ad5 priming) and 24h after the 4th immunization (wk36, 2nd DNA or ALVAC boost). In total, the dataset comprises of 180 samples.

first: Rafick

last: Sekaly

first: Marjorie

last: Guroff


title: RNA-sequencing analysis of tumor tissues from two Drosophila yki variants

city: hangzhou

first: qiaoran

last: li

address: Qinchun Road 79

institute: The First Affiliated Hospital, School of Medicine，Zhejiang University

summary: In this study, we demonstrated that tumor-bearing flies exhibit enhanced avoidance of bitter substances, and it is correlated with the severity of the tumor in our genetic models. To identify tumor-secreted cytokines uniquely upregulated in the malignant tumor model (GMR>ykiSA) compared to the mild tumor model (GMR>ykiWT), we performed RNA-sequencing analysis on both types of yki-induced tumor tissues.

overall_design: 3 samples each for GMR-Gal4 control (duizhao) head tissue and GMR>ykiSA, GMR>ykiWT tumor head tissue were used to extract the RNA. Each sample contains 50-80 heads.

first: Qiaoran

last: Li

first: Pumin

last: Zhang

first: Benjiang

last: Qiao


title: Lamin A/C-regulated cysteine catabolic flux modulates stem cell fate through epigenome reprogramming [04scRNA_seq_D10]

city: Mannheim

first: Gergana

last: Dobreva

address: Ludolf-Krehl-Str. 7-11

institute: Medical Faculty Mannheim/University of Heidelberg

summary: Spatiotemporal changes in the nuclear lamina and cell metabolism shape cell fate, yet their interplay is poorly understood. Here, we identify lamin A/C as a key regulator of cysteine catabolic flux essential for proper cell fate and longevity. Its loss in naïve mouse pluripotent stem cells leads to upregulation of the cysteine generating and catabolizing enzymes, cystathionine γ-lyase (CTH) and cystathionine β-synthase (CBS), thereby promoting de novo cysteine synthesis. Increased cysteine flux into acetyl-CoA fosters histone H3K9 and H3K27 acetylation, triggering a transition from naïve to primed pluripotency and abnormal cell fate and function. Conversely, the toxic gain-of-function mutation of Lmna, encoding lamin A/C and associated with premature aging, reduces CTH and CBS levels. This reroutes cysteine catabolic flux and alters the balance between H3K9 acetylation and methylation, crucially impacting germ layer formation and genome stability. Importantly, modulation of Cth and Cbs rescues the abnormal cell fate and function, restores the DNA damage repair capacity, and alleviates the senescent phenotype caused by lamin A/C mutations, highlighting the potential of modulating cell metabolism to mitigate epigenetic diseases.

overall_design: Day10 EBs differentiated shControl, shControl Lmna-/-, shCth Lmna-/- mESCs were digested with Collagenase I.

first: Yonggang

last: Ren

first: Yinuo

last: Wang

first: Julio

last: Cordero Henriquez


title: DDX6 undergoes phase separation to modulate metabolic plasticity and drug resistance in AML [CRISPR Screen]

city: Duarte

first: Rui

last: Su

state: CA

address: 1500 E Duarte Rd

institute: City of Hope

summary: Chemoresistance in acute myeloid leukemia (AML) is a major cause of poor prognosis and frequent relapse among patients. Under stress conditions such as chemotherapy or radiotherapy, processing bodies (PBs) and stress granules (SGs) can sequester essential mRNAs and proteins to modulate leukemia cell survival. However, the precise role(s) of PBs and SGs in AML pathogenesis and chemotherapy response remains unclear. To systematically identify PB/SG-associated genes that are critical for AML survival, we selected 101 genes encoding RNA-binding proteins that are localized within PBs and SGs, and constructed a customized CRISPR library targeting these genes for both in vitro and in vivo CRISPR screening with AML cell line (Mono-Mac-6) and patient-derived xenograft (PDX) cells.

overall_design: In the pilot experiment, the infection efficiency of 2,084 gRNAs was maintained at 0.2–0.3. Subsequently, the CRISPR library (containing 2,084 gRNAs) was introduced into Cas9-expressing Mono-mac-6 AML monoclonal cells and patient-derived xenograft (PDX) AML cells via lentiviral transduction, ensuring an infection efficiency of 0.2–0.3. Transduced AML cells were then selected with blasticidin (10 μg/mL) and puromycin (Mono-mac-6: 0.5 μg/mL; PDX-1: 16 μg/mL) for 3–5 days to obtain positively transduced populations. Cells collected after selection were designated as day 0 (baseline) samples. For the in vitro screening, both Mono-mac-6 and PDX cells were used (three biological replicates, 2 × 10⁶ cells per replicate). For the in vivo screening, PDX cells were used (six biological replicates, 2 × 10⁶ cells per replicate). For the in vivo CRISPR screen, PDX cells were injected into immunodeficient mice. After 28 days, bone marrow cells were harvested, and human CD45⁺ PDX cells were isolated using magnetic bead sorting as endpoint samples for sequencing (six replicates, 2 × 10⁶ cells per replicate). For the in vitro CRISPR screen, both Mono-mac-6 and PDX cells were continuously cultured for 28 days (maintaining ≥10,000-fold total cell expansion), after which cells were collected as endpoint samples for sequencing (three replicates per group, 2 × 10⁶ cells per replicate).

first: Chun-Wei (David)

last: Chen

first: Hongjie

last: Bi

first: Anthony

last: Chan


title: Nutrigenomic profiling identifies ZIP10 (SLC39A10) as a regulator of erythroid zinc homeostasis with genetic associations to anemia risk I

first: Moon-Suhn

last: Ryu

summary: To determine the effects of heme synthesis inhibition via different pathways in erythroid progenitor cells, heme synthesis was inhibited by 50 µM DTPA treatment (a zinc chelator), 50 µM DFO treatment (a  iron chelator), or 0.2 mM succinylacetone (SA, a ALAD inhibitor) for 24 hours in differentiating G1E-ER4 cells. G1E-ER4 Cells were divided into four groups: untreated control, 50 µM DTPA treatment, 50 µM DFO treatment, and 0.2 mM SA. The transcriptome profiles acquired from RNA-seq were compared with those of control cells.

overall_design: Comparative gene expression profiling of control G1E-ER4 cells and those deficient in cellular zinc, cellular iron, or ALAD activity (n = 3 biological replicates per group)

first: Juyoung

last: Kim


title: KLF5 controls subtype-independent highly interactive enhancers in pancreatic cancer to regulate cell survival [HiChIPseq]

city: Stuttgart

first: Steven

last: Johnsen

address: Auerbachstrasse 112

institute: Robert Bosch Center for Tumor Diseases

summary: Pancreatic ductal adenocarcinoma (PDAC) remains a highly lethal cancer with a 5-year survival rate of 13%. Despite recent molecular stratification of tumors into distinct classical and basal-like cell states, most tumors are heterogeneous and contain both subtypes. Therefore, therapeutic approaches targeting only one subtype are unlikely to be effective as standalone PDAC treatments. Here, we integrated chromatin accessibility (ATAC-seq), genome-wide occupancy (ChIP-seq) for epigenetic status (H3K27ac) and H3K4me3-anchored chromatin topology (HiChIP) to uncover subtype-independent highly interactive enhancers that interact with essential genes in PDAC. Motif analysis revealed these common enhancers were bound by KLF5 with subsequent depletion leading to decreased cell viability via induction of apoptosis. To elucidate the transcriptional and epigenetic mechanisms by which KLF5 functions in PDAC, we employed rapid depletion of KLF5 with dTAG technology and profiled the effects on the open and active chromatin landscape and transcription with nascent RNA and mRNA-seq over time. Enhancer inactivation via KRAB domain Zim3-dCas9 fusion protein confirmed KLF5-bound enhancers regulate target genes, including the anti-apoptotic gene BCL2L1. Multiplex immunofluorescence confirmed co-staining of KLF5 and Bcl-xL in patient samples and overexpression of Bcl-xL rescued the induction of apoptosis after KLF5 depletion. Taken together, this study provides new insights into common mechanisms to target highly heterogeneous PDAC tumors.

overall_design: To investigate KLF5-dependent mechanisms of cell survival in pancreatic cancer, we performed H3K4me3-anchored HiChIPseq in PDAC cell lines under normal conditions.

first: Thomas

last: Ekstrom


title: PAXT/NEXT targeting of RNA exosome regulates antisense transcripts through cohesin-mediated long-range contacts [RNA-seq]

city: Montpellier

first: Rosemary

last: Kiernan

address: 141 rue de la cardonille

institute: UMR9002 CNRS-UM

summary: Here, we mapped the binding sites of PAXT/ZFC3H1, NEXT/ZCCHC8 and their shared MTR4 helicase subunit. Our data highlight a key interplay between cohesin-mediated long-range interactions in 3D and ncRNA regulation by MTR4 helicase and nuclear RNA exosome.

overall_design: Analysis of upregulated ncRNAs upon depletion of MTR4 using siRNA in HeLa cells followed by RNA-seq.

first: Xavier

last: Contreras

first: Alexandre

last: Heurteau

first: Olivier

last: Cuvier


title: Refined cellular activity expression signatures provide a targeted framework to quantify phenotypic intra-tumour heterogeneity in single-cell data

city: Lyon cedex 08

first: Pierre

last: Martinez

address: 28 rue Laennec

institute: Cancer Research Centre of Lyon

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

overall_design: Refer to individual Series


title: A two-component system signaling hub controls enterococcal membrane remodeling in response to daptomycin

city: Genève

first: Kimberly

last: Kline

address: 1 Rue Michel Servet

institute: University of Geneva

summary: Daptomycin resistance in Enterococcus faecalis is due to consecutive acquisition of two types of mutation: a primary mutation that constitutively activates the LiaFSR two component system followed by secondary mutations in phospholipid biosynthetic genes. Here, we study how E. faecalis remodels its membrane composition in response to the antibiotic as part of a cell envelope stress response. We show that cell membrane remodelling is due to LTA synthesis by LtaS1. LTA production is under the control of the two component systems LiaFSR, SapRS, and BsrRS and contributes to baseline daptomycin resistance. We propose an updated model of how E. faecalis responds to daptomycin and provide a framework to understand the sequential acquisition of mutations that lead to clinical high-resistance daptomycin resistance.

overall_design: We wanted to understand a) if membrane remodelling in wild-type E. faecalis is regulated on the transcriptional level, and b) uncover the LiaFSR regulon during daptomycin stress. Thus, we determined transcriptional changes in wild-type, ∆liaR, and ∆liaFSR strains exposed to daptomycin. We included three biological replicates of each strain and treated with a subinhibitory concentration of daptomycin for 15 min prior to RNA-Seq analysis. Untreated cultures were used as controls.

first: Cristina

last: Colomer Winter

first: Zeus

last: Nair

first: Jerome

last: Chua

first: Soukayna

last: Jabli

first: Mélanie

last: Roch

last: von Rohr

first: Amaury

last: Cazenaeve-Gassiot

first: Roberto

last: Sierra

first: Joachim

last: Kloehn

first: Diego

middle: O

last: Andrey

first: Markus

last: Wenk

first: Shu Sin

last: Chng


title: Nutrigenomic profiling identifies ZIP10 (SLC39A10) as a regulator of erythroid zinc homeostasis with genetic associations to anemia risk II

first: Moon-Suhn

last: Ryu

summary: To determine the physiological roles of zinc in erythroid progenitor cells, cellular zinc was restricted by 50 µM DTPA treatment (a zinc chelator) for 24 hours in differentiating G1E-ER4 cells. G1E-ER4 cells induced for differentiation by beta-estradiol were divided into two groups: control and 50 µM DTPA treatment. A sample from cells untreated with beta-estradiol was also included as an undifferentiated group.

overall_design: Comparative gene expression profiling of G1E-ER4 cells differentiating under control zinc and zinc restriction (n = 3 biological replicates per treatment), and undifferntiating cells without zinc intervention (n = 1)

first: Juyoung

last: Kim


title: KLF5 controls subtype-independent highly interactive enhancers in pancreatic cancer to regulate cell survival [ChIPseq]

first: Steven

last: Johnsen

overall_design: To investigate KLF5-dependent mechanisms of cell survival in pancreatic cancer, we performed ChIPseq after dTAG treament in clonal L36pl cells with endogenous knockin of GFP-FKBP12 into the KLF5 locus after dTAG treatment for H3K27ac, H3K4me3, KLF5. We also performed ChIPseq for CTCF, H3K27ac, and dNP63 under normal conditions in PDAC cell lines.

first: Thomas

last: Ekstrom


title: Brain Molecular Mechanisms in Rasmussen Encephalitis

city: New York

first: Ziyan

last: Lin

department: Applied Bioinformatics Laboratories

institute: NYU Grossman School of Medicine

summary: Objective: Identify molecular mechanisms in brain tissue of Rasmussen encephalitis (RE) when compared to people with non-RE epilepsy (PWE) and control cases using whole exome sequencing (WES), RNAseq, and proteomics. Methods: Frozen brain tissue (ages 2-19 years) was obtained from control autopsy (n=14), surgical PWE (n=10), and surgical RE cases (n=27). We evaluated WES variants in RE associated with epilepsy, seizures, RE, and human leukocyte antigens (HLAs). Differential expression was evaluated by RNAseq (adjusted p<0.05) and label-free quantitative mass spectrometry (false discovery rate<5%) in the three groups. Results: WES revealed no common pathogenic variants in RE, although several rare and likely deleterious variants of unknown significance (VUS; ANGPTL7/MTOR, SCN1A, FCGR3B, MTOR) and more common HLA VUS in >25% RE cases (HLA-DRB1, HLA-DQA2) all with allele frequency <5% in the general population. RNAseq in RE vs. PWE (1516 altered transcripts) revealed significant activation of crosstalk between dendritic and natural killer cells (p=7.94x10-6, z=2.65), in RE vs. control (7466 transcripts) neuroinflammation signaling activation (p=6.31x10-13, z=5.07), and in PWE vs. control (945 transcripts) phagosome formation activation (p=2.00x10-13, z=5.61). Proteomics detected fewer altered targets. Significance: In RE, we identified activated immune signaling pathways and immune cell type annotation enrichment that suggest roles of the innate and adaptive immune responses, as well as HLA variants that may increase vulnerability to RE. Follow up studies could evaluate cell type density and subregional localization associated with top targets, clinical history (neuropathology, disease duration), and whether modulating crosstalk between dendritic and natural killer cells may limit disease progression.

overall_design: RNAseq. Comparisons were made from frozen brain tissue for RE, PWE, and control. RNA was isolated from brain (10mg) with miRNeasy Purification of Total RNA (Qiagen), using Qiazol with handheld pestle-equipped device, 22-gauge needle. RNA quality and concentration was determined by Agilent Bioanalyzer. Libraries were created by NYU GTC with Illumina Stranded Total RNA Prep with Ribo-Zero Plus (Cat.20040529), and sequenced on Illumina NovaSeq6000 with S2 100-cycle flow cell, 50bp paired-end.

first: Dominique

last: Leitner

first: Orrin

last: Devinsky


title: IL-22 from enteroendocrine cells promotes early-life gut motility via microbiota in zebrafish

city: Paris

first: Pedro

last: Hernandez

address: 11-13 rue Pierre et Marie Curie, BDD building

department: Genetics and Developmental Biology

institute: Institut Curie

summary: The gut microbiota, immune system, and enteric nervous system interact to regulate adult gut physiology. Yet the mechanisms establishing gut physiology during development remain unknown.  We report that in developing zebrafish, enteroendocrine cells produced IL-22 in response to microbial signals before lymphocytes populate the gut. In larvae, IL-22 shaped the gut microbiota, increased Lactobacillaceae abundance and ghrelin expression to promote gut motility. Impaired motility and ghrelin expression were restored in il22-/- zebrafish by transfer of microbiota from wild-type zebrafish or by monoassociation with Lactobacillus plantarum. IL-22-deficient mice had impaired gut motility and reduced ghrelin expression in early life too, indicating a conserved function. Thus, before immune system maturation, enteroendocrine cells regulate early-life gut function by controlling the microbiota via IL-22.

overall_design: RNA-seq profiling of dissected guts from 7-day post-fertilization WT and il22-/- zebrafish larvae, under conventional, axenic, and co-housing conditions

first: Rabahi

last: Soraya

first: Hernandez

last: Pedro P


title: Maintenance of gene expression homeostasis by systems-level feedback loops in response to changes in RNA polymerase II dosage

city: Copenhagen

first: Jesper

middle: Q

last: Svejstrup

address: Blegdamsvej 3B

department: ICMM

country: Denmark

institute: University of Copenhagen

summary: Transcription is regulated by sequence-specific transcription factors and enzymes allowing access to genes in chromatin. However, recent data indicate that the abundance of RNA polymerase II (RNAPII) may itself under certain circumstances represent an additional, crucial determinant of transcription regulation. Here, we titrated the cellular dosage of human RPB1, the largest RNAPII subunit, using the dTAG system to more generally assess the importance of RNAPII levels. Unexpectedly, cells are extremely sensitive to RPB1 dosage, with a mere 30% reduction sufficient to perturb cell proliferation, cell cycle progression, and global transcription. Using a combination of sequencing and proteomic approaches, we uncover the existence of multiple feedback loops between transcriptional initiation, promotor-proximal pause release, transcript elongation, splicing, and mRNA half-life, which facilitate the maintenance of gene expression homeostasis. Together, our data suggests that gene expression is highly sensitive to RPB1 dosage and that the cellular levels of RNAPII must be tightly regulated.

overall_design: To investigate the effect of RPB1 abundance on promoter-proximal pausing, we modulated RPB1 levels by treating RPB1 degron cells with 4 concentrations of dTAGv-1. After 16 hours, cells were harvested and we performed an in vitro nuclear run-on reaction, followed by extraction of biotinylated RNA (PRO-seq), to gain insight into the genome-wide occupancy of transcription-competent RNA polymerases at a single-nucleotide resolution.

first: Anouk

middle: M

last: Olthof

first: Melvin

last: Noe Gonzalez

first: Nanna

last: Poulsen

first: Nicolas

last: Nieto Moreno

first: Theodora

last: Bautu

first: Simona

last: Cugusi


title: PAXT/NEXT targeting of RNA exosome regulates antisense transcripts through cohesin-mediated long-range contacts

first: Rosemary

last: Kiernan