title: The retrotransposon-derived capsid genes PNMA1 and PNMA4 maintain reproductive capacity

first: Luke

last: Berchowitz

state: NY

department: Genetics & Development

institute: Columbia University

summary: Almost half of the human genome consists of retrotransposons, ‘parasitic’ sequences that insert themselves into the host genome via an RNA intermediate. While most of these sequences are silenced or mutationally deactivated, they can present opportunities for evolutionary innovation: mutation of a deteriorating retrotransposon can result in a gene that provides a selective advantage to the host in a process termed domestication1–3. The PNMA family of gag-like capsid genes were domesticated from an ancient vertebrate retrotransposon of the Metaviridae clade at least 100 million years ago4,5. There are six full-length PNMA genes in humans and five in mice5. PNMA1-3 were originally identified as autoantigens that cause paraneoplastic neurological syndrome (PNS). PNMA4-6 were identified based on homology with PNMA1-3 but are not implicated in PNS6,7. We reasoned that the conservation of PNMA genes is unlikely to be based on their autoantigenic properties. While Pnma5 is implicated in oocyte development via an unknown mechanism8, little is known about the non-pathological roles of the other genes. PNMA1 and PNMA4 are positively regulated by the master germ cell transcription factors MYBL1 and STRA8, and their transcripts are bound by the translational regulator DAZL during gametogenesis9. This developmental regulation of PNMA1 and PNMA4 expression in gonadal tissue suggested to us that they might serve a reproductive function. Through the analysis of donated human ovaries, genome-wide association studies (GWAS), and genetic mouse models, we find that PNMA1 and PNMA4 are necessary for the maintenance of a normal reproductive lifespan. These proteins self-assemble into capsid-like structures that exit human cells, and we observed large PNMA4 particles in mouse male gonadal tissue that are consistent with capsid formation.

overall_design: Lysate was prepared from eight testes (collected at 3 months) from either wild type or control (lacking Pnma4) mice (3 biological replicates each). Lysate was fractionated by velocity (38,000 rpm, 3 hours) over a double sucrose cushion (25% and 70%). The 70% meniscus was further fractionated by isopycnic centrifugation on an iodixanol step gradient. PNMA4 was IPed from iodixanol fractions 8 and 9, RNA was extracted IP beads, and sequenced.

first: Wood

first: Cullen

last: Harrison

first: Berchowitz

last: Luke


title: Succinate facilities CD4+ T cell infiltration and CCL1 production to promote myofibroblast activation and obstruction-induced renal fibrosis

status: Public on Jun 25 2025

city: Quanzhou

first: wei

last: zhang

address: NO. 1028 Anji South Road, Fengze District

country: China

institute: quanzhou first hospital affiliated to fujian medical university

type: Expression profiling by high throughput sequencing

summary: To understand the roles of succinate in CD4+ T cells, we performed RNA sequencing of isolated spleen CD4+ T cells treated with or without cell membrane permeable dimethyl succinate, which can enter into T cells and increase intracellular succinate concentration. The treatment led to upregulation of genes associated with T cell activation, including cell shape, inflammatory response, meiotic nuclear division, and leukocyte migration. These results suggest that succinate promotes CD4+ T cell activation.

overall_design: Bulk RNA sequencing was performed in spleen CD4+ T cells treated with or without three days of dimethyl succinate.

first: Wei Zhang

last: Yuandong Tao


title: CSF1-R inhibition attenuates posttraumatic osteoarthritis and quadriceps atrophy following ligament injury I

city: Lexington

first: Alexander

middle: Romano

last: Keeble

state: KY

address: 900 S Limestone st

country: USA

institute: University of Kentucky

summary: Knee osteoarthritis contributes substantially to worldwide disability. Post-traumatic osteoarthritis (PTOA) develops secondary to a joint injury, such as ligament rupture, and there is increasing evidence suggesting a key role for inflammation in the etiology of PTOA and associated functional deficits. Colony stimulating factor 1 receptor (CSF1-R) has been implicated in the pathogenesis of musculoskeletal degeneration following anterior cruciate ligament (ACL) injury. We sought to assess the efficacy CSF1-R inhibition to mitigate muscle and joint pathology in a mouse model of PTOA. Four-month-old mice were randomized to receive a CSF1-R inhibitor and studied for 7 or 28 days after joint injury. Additionally, we profiled synovial fluid samples for CSF1-R from patients with injury to their ACL. Transcriptomic analysis of quadriceps muscle and articular cartilage in CSF1-R inhibitor-treated animals at 7 days after injury revealed elevated chondrocyte differentiation within articular cartilage and enhanced metabolic and contractile gene expression within skeletal muscle. At 28 days post-injury, CSF1-R inhibition attenuated PTOA severity and mitigated skeletal muscle atrophy. Patient synovial fluid CSF1-R levels correlated with matrix metalloproteinase 13, a prognostic marker and molecular effector of PTOA. Our findings support an opportunity for CSF1-R targeting to mitigate the severity of PTOA and muscle atrophy after joint injury.

overall_design: Comparative gene expression profiles were assessed in murne cartilage before and after ACL transection. One group received a CSF1-R inhibitor, the other received a placebo control

middle: R

first: Nicholas

middle: T

last: Thomas

first: Peyton

last: Balawender

first: Camille

last: Brightwell

first: Sara

last: Gonzalez-Velez

first: Madeline

last: O’Daniel

first: Caitlin

middle: E

last: Conley

first: Austin

middle: V

last: Stone

first: Darren

middle: L

last: Johnson

first: Brian

last: Noehren

first: Cale

middle: A

last: Jacobs

first: Christopher

middle: S

last: Fry

first: Allison

middle: M

last: Owen


title: Epigenetic silencing and CRISPR-mediated reactivation of Tight Junction Protein Claudin 10 B (CLDN10B) in Skin Cancer.

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

summary: The kidney's tubular system relies on cell polarity and tight junctions to maintain structure and function and disruptions contribute to diseases like cancer. Loss of tight junction proteins such as Claudins, can actively contribute to tumorigenesis. We aimed to identify biomarkers for renal carcinoma, after kidney transplantation and conventional kidney tumors. We identified the epigenetic silencing of the Claudin 10 gene isoform B (CLDN10B) through DNA hypermethylation in renal cancers, including clear cell- (ccRCC), papillary - (pRCC) and post-transplantation renal carcinoma (PT-RCC). In contrast, CLDN10A, was hypomethylated in ccRCC and pRCC. Differential methylation of the Isoforms discriminates RCC from other malignancies. The epigenetic alteration of CLDN10B significantly correlated with reduced patient survival and advanced tumor staging. CLDN10B overexpression or induction significantly inhibited migration, cell cycle progression, and cellular growth. Using a CRISPR-based epigenetic editing reactivated CLDN10B to its endogenous level using VP160 and TET1 by promoter demethylation and significantly demonstrated its tumor-suppressive effects in 2D and 3D cell models. Our findings suggest that CLDN10B acts as a tumor suppressor, and its epigenetic regulation may represent a therapeutic target for RCC. Ultimately, understanding CLDN10B’s regulation and function could provide new insights into renal cancer treatment.

overall_design: For dynamic 3D cell culture, 1.5 million inducible HEK293 TREx cells were transferred into flasks. After 6 hours, cells were induced with 2 mg/mL of doxycycline and analyzed by microscopy 72 h later.

first: Antje

last: Richter


title: KChIP3 promotes Alzheimer's disease by impairing long-term potentiation and memory

city: Mexico City

first: David

last: Valle-Garcia

address: Av. Insurgentes Sur 3877, La Fama, Tlalpan

country: Mexico

institute: National Institute of Neurology and Neurosurgery

summary: Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by β -amyloid (βA) peptide accumulation, neuroinflammation, increased synaptic pruning, and cognitive decline. Effective treatments for AD are still lacking. This study investigates the role of potassium channel interacting protein 3 (KChIP3) in AD using the 5XFAD murine model. We found increased KChIP3 levels in the hippocampus of 5XFAD mice, correlating with βA 40 accumulation and neuroinflammation. Genetic deletion of KChIP3 in 5XFAD mice significantly reduced βA plaque formation, proinflammatory cytokine levels, and reactive gliosis in the hippocampus. Transcriptomic and proteomic analyses revealed restored synaptic markers and reduced microglial DAM1 phenotype in 5XFAD/KChIP3 -/- mice. KChIP3 deficiency improved dendritic tree complexity and synaptic plasticity, enhancing learning and memory in 5XFAD mice. Mechanistically, KChIP3 deletion restores immune response balance by modulating microglial phenotype upregulating CD47, CD200, and C1q levels. Our findings, along with recent computational studies using human data, suggest KChIP3 as a potential therapeutic target in AD, addressing neuroinflammation and synaptic dysfunction. Further research is needed to explore its potential as a diagnostic and prognostic biomarker.

overall_design: RNA-seq from hippocampus samples derived from control (WT) 5xFAD, Kcnip3 KO and 5xFAD/Kcnip3 KO adult animals

first: Karla

middle: F

last: Meza-Sosa

first: Eladio

last: Cortes-Flores

first: Gustavo

last: Martinez-Pedraza

first: Leonor

last: Perez-Martinez


title: Covalent Binding of Thioredoxin to TXNIP is Required for Diet-induced Hepatic Insulin Resistance  in the Liver

city: Cambridge

first: Richard

middle: Theodore

last: Lee

state: MA

address: 7 Divinity Avenue

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: Among vertebrate animals, mammals have retained a unique molecular change that allows an intracellular arrestin domain-containing protein to bind covalently to thioredoxin. This interaction of Thioredoxin-Interacting Protein (TXNIP) with thioredoxin can only occur when thioredoxin is in the reduced state, allowing TXNIP to "sense" the cellular oxidized environment1. Here we show that a single cysteine in TXNIP mediates the development of hepatic insulin resistance in the setting of a high fat diet (HFD). Mice with exchange of TXNIP Cysteine 247 for Serine (C247S) showed improved whole-body and hepatic insulin sensitivities compared to wildtype (WT) controls following an 8-week HFD. The inhibition of the TXNIP-thioredoxin interaction under chow and HFD also regulated plasma and liver lipids and reduced free fatty acid accumulation in the livers following HFD.  These data show that mammals have a single amino acid enabling interaction of redox state with TXNIP that mediates insulin resistance in the setting of a high-fat diet. This reveals a potential evolutionarily-conserved mechanism for hepatic insulin resistance in metabolic syndromes.

overall_design: Livers from Wildtype, TXNIP C247S mutant and TXNIP KO mice on 8 weeks high-fat diet are collected and processed for Bulk RNA seq

first: Sezin

last: Dagdeviren

first: Megan

last: Hoang

first: Steven

middle: J

last: Blair


title: The Structural Variations of Rapeseed BnaC3.LEAFY with Agronomic Effects on the Timing of Inflorescence Formation and Flower Opening

city: Hangzhou

first: Mengjie

last: Gong

address: Yuhangtang Road-866

institute: Zhejiang University

summary: Rapeseed (Brassica napus L.) is a globally significant oil-producing crop, and its structural variations (SVs) are fundamental to the enhancement and domestication of important agronomic traits. However, the effects of SVs on agronomic traits in allotetraploid rapeseed are still largely unexplored. Here, we conducted a whole-genome identification of SVs based on 300 re-sequenced rapeseed accessions and found 42,384 high-quality SVs consisted of 34,442 deletions, 6,653 insertions, 828 duplications and 461 inversions. Onset of inflorescence formation and subsequent flower opening at the proper time is crucial for successful propagation. To uncover significant SVs associated with inflorescence development, we performed genome-wide association study based on SVs (SV-GWAS) and identified seven significant SVs. Through analysis of each SV and referencing previous studies, we explored the SV in the second intron of LEAFY on Chromosome C3 (BnaC3.LFY), which is one of homologs of Arabidopsis floral identification gene LFY (AtLFY). BnaC3.LFY Hap1 is significantly related to early inflorescence development due to increased gene expression of BnaC3.LFY. By the CRISPR/Cas9 application in the wild-type spring accession Westar, multiple deletions in intron 2 region of BnaC3.LFY were received and the phenotype of delayed flowering opening was observed. Additionally, we discovered the conserved function of the second intron in Arabidopsis. This study demonstrates the whole-genome layout of SVs in Brassica napus genomes and highlights the conserved role of the second intron of BnaC3.LFY in influencing the timing of inflorescence formation and flower opening, with significant agronomic implications.

overall_design: To compare the two distinct haplotypes of BnaC3.LFY, we selected 3 representative Hap 1 (R5044, R5159 and R5161) and Hap 2 (R4168, R4210, R4817) accessions for transcriptome analysis.

first: Huiqi

last: Zhang


title: Distinct Transcriptomic Signatures in Pulmonary Tissue Resident and Vascular “Resident-Like” T Cells in Nonhuman Primates

city: Covington

first: Alexandra

last: Melton

address: 18703 Three Rivers Road

institute: Tulane National Primate Research Center

summary: Abstract Intravascular staining (ivs) provides an innovative method for distinguishing tissue-resident lymphocytes from those within the organ’s vasculature, a distinction that is particularly important in highly vascularized organs such as the lung. Cells that stain positive for the infusion antibody (ivs+) have generally been considered lingering blood contaminants; however, recent studies have shown that these cells may not be as transitory as originally thought. Here, we utilized ivs staining to differentiate and isolate T cells from both the lung interstitium (ivs-) and lung vasculature (ivs+) of rhesus macaques (RhM). We then characterized and compared these T cell populations via single-cell RNA sequencing (scRNAseq) and flow cytometry. We found that ivs- T cells exhibit a core gene signature resembling that of tissue-resident memory T cells (Trms), whereas ivs+ T cells represent a distinct population with a unique phenotype and transcriptional profile. Notably, CD8+ T cells were enriched within the lung vasculature (ivs+ subset) and predominantly exhibited an effector phenotype, highlighted by increased cytotoxicity. Moreover, these pulmonary vascular “resident-like” CD8+ T cells (ivs+) demonstrated a gene expression profile enriched in transcripts typically associated with a tissue-resident phenotype, as well as cell adhesion markers and pathways involved in vascular/platelet interactions. In Simian Immunodeficiency Virus (SIV) infected RhMs, pulmonary ivs+ CD8+ T cells displayed enhanced effector responses compared to Trms. Our findings suggest that ivs+ T cells in the pulmonary vasculature represent a unique, “resident-like” population with potent effector functions, highlighting their potential significance in pulmonary immunity.

overall_design: Thawed PBMC, lung, and bronchial lymph node (BLN) cells were stained in 15 mL conical tubes with live/dead and surface cocktails with 2x the typical antibody concentration. Cells were washed in FACS buffer and resuspended in RPMI-1640 without phenol red supplemented with 10% FBS. Cells were sorted using fluorescence-activated sorting (FACS) to isolate CD3+ T cells from blood and BLN as well as CD3+ ivs- and CD3+ ivs+ cells from lung using the BD FACSAria (BD Bioscience) or MACSQuant Tyto (Miltenyi Biotec). CD3+ ivs- and CD3+ ivs+ cells from lung, as well as CD3+ T cells from blood and BLN, were processed for single-cell RNA sequencing (scRNAseq) following the 10x Genomics® Single Cell Protocols – Cell Preparation Guide for the “preparation of limited samples.”

first: E

last: Potter

first: Toni

last: Penney

first: Clara

last: Krzykwa

first: Lori

last: Rowe

first: Hunter

first: Diogo

last: Magnani

first: Jay

middle: K

last: Kolls

first: Robert

first: Nicholas

last: Maness


title: ZNFX1 suppresses apoptosis-associated mRNA stability in cardiomyocyte to protect against myocardial infarction (hypoxia)

city: Harbin

first: Yang

last: Shi

state: Heilongjiang

address: No.157 Baojian Rd, Harbin, HEILONGJIANG

department: Department of Pharmacology

institute: Harbin medical university

summary: Aims: Cardiomyocytes apoptosis is the predominant pathological feature following myocardial infarction (MI) and significantly impacts disease progression and outcomes. Zinc finger NFX1-type containing 1 (ZNFX1), an RNA helicase family member, remains relatively understudied in molecular biology and its role in cardiovascular diseases remains unclear. This study aims to explore the involvement of ZNFX1 in MI and uncover its mechanisms underlying cardiomyocyte apoptosis. Methods and results: Male C57BL/6 mice were administered AAV9-ZNFX1 or AAV9-sh-ZNFX1 with the cTNT promoter via tail vein injection for the purpose of cardiomyocyte-specific ZNFX1 overexpression or knockdown. Concurrently, left anterior descending coronary artery ligation (LAD) was performed to induce MI. Echocardiography was utilized to evaluate the cardiac function. Triphenyl tetrazolium chloride (TTC), Hematoxylin and eosin (HE) and Masson's trichrome staining were used to evaluate the cardiac infarction and cardiac remodeling. TUNEL assay, flow cytometry, western blot and quantitative reverse transcription PCR (qRT-PCR) were employed to evaluate apoptosis. The cardiomyocyte viability was quantified using the CCK-8 assay. RNA sequencing (RNA-seq) and RNA immunoprecipitation assays (RIP) were employed to investigate the interaction between ZNFX1 and apoptosis-associated genes. The expression of ZNFX1 was decreased in MI myocardium and hypoxia-treated cardiomyocytes. Overexpression of ZNFX1 significantly attenuated cardiac dysfunction, reduced infarct size, inhibited collagen deposition and alleviated cardiac hypertrophy which was ascribed to MI in mice, whereas knockdown of ZNFX1 produced the opposite effects. RNA-seq identified apoptosis as a possible regulated pathway of ZNFX1, overexpression of ZNFX1 represses the cardiomyocyte apoptosis that gives rise to MI while knockdown of ZNFX1 deteriorates it. Mechanically, ZNFX1 binds with mRNA of apoptosis genes that contain highly structured 3'UTR and prompts their decay.   Conclusion: ZNFX1 plays a protective role in MI by degrading mRNA of apoptosis-related genes, which often possess highly structured 3'UTRs. This highlights ZNFX1 as a potential novel molecular target for treating cardiac dysfunction associated with MI. Keywords: ZNFX1, apoptosis, mRNA stability, helicase activity, UPF1, myocardial infarction

overall_design: The mouse hearts were separately harvested from MI and MI+ZNFX1 groups and the primary cardiomyocytes were harvested from hypoxia and hypoxia+ZNFX1 groups. The RNA libraries were sequenced using the Illumina NovaseqTM 6000 platform, conducted by LC Bio-Technology CO., Ltd. (Hangzhou, China). Briefly, the heart RNA samples were isolated and purified by TRIzol (ThermoFisher Scientific). The amount and purity of RNA samples were controlled by NanoDrop ND-1000 (NanoDrop, DE). Also, RNA integrity was tested by Bioanalyzer 2100 (Agilent). mRNA containing PolyA (polyadenylate) was captured by Oligo (dT) magnetic beads (Dynabeads Oligo (dT), ThermoFisher Scientific) through two rounds of purification. Finally, Illumina NovaseqTM 6000 was used to sequence in PE150 mode according to standard procedures. FPKM values for each gene were determined based on gene length and the number of reads mapped. Differential expression analysis was carried out using the DESeq2 R package (version 1.20.0). Genes with a P value less than 0.05 and a fold change greater than 2 were identified as differentially expressed. Gene Set Enrichment Analysis (GSEA) was conducted using tools available on OmicStudio (https://www.omicstudio.cn/tool). The heatmap was generated using the R (https://www.r-project.org/) on the OmicStudio platform (https://www.omicstudio.cn/tool).


title: ZNFX1 suppresses apoptosis-associated mRNA stability in cardiomyocyte to protect against myocardial infarction


title: Identification of Asporin as a HER3 ligand that exposes a therapeutic vulnerability in metastatic prostate cancer [VCaP_EnzaResistant_9817-HYW]

city: Nashville

first: Hong Yuen

last: Wong

state: Tennessee

address: 2220 Pierce Ave # PRB648, Preston Research Building

department: Medicine

institute: VUMC

summary: Cancer-associated fibroblasts (CAF) are part of the tumor microenvironment that enable cancer cells to establish metastases, but the mechanisms of these interactions are not fully known. Herein, we identify a novel paracrine mechanism in which CAF-secreted asporin (ASPN) activates ErbB signaling and subsequent migration of adjacent metastatic prostate cancer cells. Our data support that ASPN binds directly to HER3 to induce HER2/HER3 heterodimerization and activation of the PI3-kinase and MAP-kinase pathways. Genetic and therapeutic inhibition of HER2/HER3 ablated ASPN-induced signaling and migration. Small molecule and antibody-drug conjugates targeting HER2/HER3 demonstrated efficacy in vitro, with near complete resolution of tumors in vivo. Clinically, over 50% of human prostate cancer metastases show expression of HER2/HER3, along with ASPN expressing CAF.  Collectively, these findings support ASPN functions as a HER3 ligand to induce cellular migration which can be targeted with anti-HER2/HER3 therapies, highlighting the potential clinical benefit for patients with metastatic prostate cancer.

overall_design:
For cells treated with recombinant proteins: Cells were plated in triplicate in 6 well plates (500,000-750,000 cells/well) and allowed to adhere for 24-48 hours. Cells were starved in serum and calcium-free media (Vanderbilt Cell Culture Core) for 6-12 hours prior to addition of recombinant proteins. Total RNA was extracted from cells after 0, 12, or 24 hrs of treatment.
For drug resistant cells: Cells were plated in triplicates in T25 flasks, cultured to a confluency of ~70%, and harvested for total RNA extraction.

first: Amanda

middle: B

last: Hesterberg

first: Hong

middle: Y

first: Paula

last: Hurley


title: The impact of inactivation of the GH/IGF axis during aging on healthspan

city: New York

first: Shoshana

last: Yakar

address: 345E 24th Street

institute: New York University

summary: Several mouse lines with congenital growth hormone (GH) / insulin-like growth factor-1 (IGF1) axis disruption have shown improved health and extended lifespan. The current study investigated how inactivating this axis, specifically during aging, impacts the health span. We used a tamoxifen-inducible global GH receptor (GHR) knockout mouse model starting at 12 months and followed the mice until 24 months of age (iGHRKO12-24 mice).   We found sex- and tissue-specific effects, with some being pro-aging and others anti-aging. Measuring an array of cytokines in serum revealed that inactivation of the GH/IGF1 axis at 12 months did not affect systemic inflammation during aging. On the other hand, hypothalamic inflammation was significantly reduced in iGHRKO12-24 mice, evidenced by GFAP+ (glial fibrillary acidic protein, a marker of astrocytes) and Iba-1+ (a marker for microglia). Liver RNAseq analysis indicated feminization of the male transcriptome, with significant changes in the expression of monooxygenase, sulfotransferase, and solute-carrier-transporter gene clusters. Finally, we found impaired bone morphology, which was more pronounced in male iGHRKO12-24 mice and correlated with the onset age of GH/IGF1 inactivation. We conclude that inhibiting the GH/IGF1 axis during aging only partially preserves the beneficial health span effects observed with congenital GH deficiency.

overall_design: Comparative gene expression profiling analysis and GO analyis of floxed GHR mouse liver samples with RNA-seq

first: Sher

last: Poudel

first: Ryan

last: Ruff

first: Zhiming

last: He

first: Manisha

last: Dixit

first: Gozde

last: Yildirim

first: Hashan

last: Jayarathne

first: Dulmalika

middle: H

last: Manchanayake

first: Jelena

last: Basta-Pljakic

first: Silvana

last: Duran-Ortiz

first: Mitchell

last: Schaffler

first: John

last: Kopchick

first: Marianna

last: Sadagurski


title: Identification of Asporin as a HER3 ligand that exposes a therapeutic vulnerability in metastatic prostate cancer [LNCaP_EnzaResistant_9445-HYW]

first: Hong Yuen


title: Identification of Asporin as a HER3 ligand that exposes a therapeutic vulnerability in metastatic prostate cancer [NRG1_MyCCaP_10722-AH]

first: Amanda


title: Changes of methylation at enhancers appear to be essential for HIV infection progression

city: Szczecin

first: Tomasz

last: Wojdacz

state: Zachodniopomorskie

address: Unii Lubelskiej 1

department: Independent Clinical Epigenetics Laboratory

country: Poland

institute: Pomeranian Medical University

type: Methylation profiling by genome tiling array

summary: We studied the influence of the European HIV-1 subtype B (most common in the Western and central Europe) and subtype A6 (prevalent in Eastern Europe including Ukraine and Russia) on host methylome during infection progression and in virus subtype specific manner. Our results show that regardless of virus subtype in the beginning of the infection HIV related methylation changes more frequently affect parts of the genome with low expression activity including heterochromatin and quiescent regions. However, the analysis of the methylomes of blood cells of PLWH at stage four of the infection showed that with the infection progression genomic regulatory elements that harbour infection related methylation changes are enhancers. We further showed that the effect of each of the virus subtype on host methylome is to a large extent similar and in general involve hypomethylation of loci associated with key pathways involved in viral infection. But our results also indicate that each of the virus subtype appears to at least to some extent affect host methylome in virus subtype specific manner. Most importantly we showed that progression related methylation changes that we identified are reversed with ART therapy.

overall_design: The study included 24 antiretroviral treatment naïve people with HIV, representing four equally sized (n = 6) groups stratified based on virus subtype (A6 and B) and WHO HIV disease stage (I/HIV and IV/AIDS).

first: Olga

last: Taryma-Leśniak

first: Jan

last: Bińkowski

first: Kaja

last: Mielczak

first: Bogusz

last: Aksak-Wąs

first: Malwina

last: Karasińska-Cieślak

first: Marta

last: Sobalska-Kwapis

first: Dominik

last: Starpargiel

first: Miłosz

last: Parczewski


title: Identification of Asporin as a HER3 ligand that exposes a therapeutic vulnerability in metastatic prostate cancer (NRG1)

last: Wong

overall_design: For cells treated with recombinant proteins: Cells were plated in triplicate in 6 well plates (500,000-750,000 cells/well) and allowed to adhere for 24-48 hours. Cells were starved in serum and calcium-free media (Vanderbilt Cell Culture Core) for 6-12 hours prior to addition of recombinant proteins. Total RNA was extracted from cells after 0, 12, or 24 hrs of treatment.  For drug resistant cells: Cells were plated in triplicates in T25 flasks, cultured to a confluency of ~70%, and harvested for total RNA extraction.

last: Hesterberg

first: Hong

first: Paula

last: Hurley


title: Transcriptomic analysis reveals the cell membrane defense regulated by LiaX-FRS system in Lacticaseibacillus paracasei L9 under bile salt stress

city: Changsha

first: Ning ning

last: Yan

state: Hunan

address: Changsha University of Science & Technology

institute: 长沙理工大学

summary: By comparing the transcriptome results of the control strain and the mutant strain under bile salt stress, the genes with large differential expression changes were analyzed in depth and combined with experiments to explore how the mutant genes were regulated by stress to cope with bile salt stress

overall_design: The mutants were cultured with MRS Broth (HuanKai Microbial, Guangdong, China) at 37oC with the addition of 10 μg/mL erythromycin (EM). 0.05% glycine deoxycholate (GDCA, Sigma-Aldrich, Germany )was added in the medium to perform bile salt stress when needed.

first: Xiayin

last: Ma

first: Ningning

first: Yanmei

last: Wang


title: Erianin inhibits the progression of pancreatic cancer by directly targeting AKT and ASK1

city: Tianjin

first: Minghan

last: Qiu

state: Tianjin

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

department: Department of Oncology

summary: Erianin, a natural product extracted from Dendrobium, possesses multiple pharmacological properties, including antioxidative and antitumor activities. The objective of this study was: to evaluate the anti-pancreatic cancer activity of erianin and explore its underlying mechanisms.To further explore the potential molecular mechanisms of erianin in pancreatic cancer, we performed RNA Sequencing analysis to identify DEGs under erianin stimulation in SW1990 cells.

overall_design: SW1990 cells were treated with 100nM Erianin for 48 hours, with an equal concentration of DMSO as the control.

first: Ruxue

last: Liu

first: Zhen

last: Yang

first: Huaqing


title: Intestinal Epithelial C/EBPβ Deficiency Impairs Colitis-Associated Tumorigenesis by Disrupting CXCL1 /CXCL2/CXCL5-CXCR2-Mediated Neutrophil Infiltration [RNA-seq ]

city: Nanjing

first: li

last: mingyue

address: 163 Xianlin Avenue

institute: Nanjing university

summary: To investigate the function of intestinal-specific cebpb loss in the infiltration of neutrophils, we performed transcriptomic sequencing to compare global gene expression in the colon tissues from AOM/DSS mice models.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT control, WT AOM/DSS, and CebpbΔIEC AOM/DSS.

first: Mingyue

last: Li

first: Xintong

first: Wenjie

last: Hu


title: RSK1 modulates the translatome of glioblastoma cells in an isoform-specific manner

city: Ottawa

first: Martin

last: Roffe

state: ON

address: 401 Smyth Rd

country: Canada

institute: CHEO Research Institute

summary: The p90 ribosomal S6 kinase (RSK) family, downstream targets of Ras/ERK signaling, encompass four human isoforms (RSK1-4). Glioblastoma (GBM) predominantly expresses RSK1 and RSK2. Notably, RSK1 is markedly upregulated in a subset of GBMs associated with dismal prognosis and immune infiltration, whereas RSK2 expression remains consistent across cases. We verified that GBM-derived cell lines recapitulate RSK isoform expression profiles and estimated their stoichiometry. Through the generation of RSK1 and RSK2 knockout (RSK1KO and RSK2KO) as well as double knockout (DKO) GBM cells, we investigated isoform-specific functions of RSK. Surprisingly, contrary to conventional belief, we found that mTORC1 is not activated by RSK isoforms. Instead, eIF4B phosphorylation at S422 was RSK-dependent rather than mTORC1/S6K-dependent, with RSK1 exerting a more pronounced effect. Intriguingly, RSK1 and RSK2 displayed differential effects on translation, with RSK1 maintaining translation of specific mRNAs under conditions of reduced overall translation due to mTORC1 inhibition, unlike RSK2. Finally, we verified that while the translatome of RSK1KO cells show a downregulation of mRNAs affecting cell cycle, DNA replication and repair, RSK2 depletion impacted mitochondrial and respiratory genes. Notably, DKO cells exhibited compounded phenotypes, underscoring the existence of isoform-specific gene regulation programs orchestrated by RSK. Collectively, our findings offer mechanistic insights crucial for unraveling the role of RSK1 in GBMs.

overall_design: In order to define RSK-isoform specific functions, we applied the CRISPR/Cas9 technique to edit the genome of glioblastome-derived LN18 cells (LN18CRISPR) and thus generate knockout cells for RSK1 (RSK1KO) or RSK2 (RSK2KO), and also double-knockout cells for both RSK1 and RSK2 (DKO). Cells were pre-treated with Torin1 (or DMSO) before serum stimulation for 6 hours. Total and polysome-associated (poly) mRNA were analyzed by microarray.


title: AP2X-1 is a negative regulator of Toxoplasma gondii sexual commitment

city: Lanzhou

first: JinLei

address: yanchangbao

institute: LVRI

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Toxoplasma gondii is a ubiquitous protozoan with a complex life cycle involving transitions between different hosts and developmental stages, each adapted to a unique niche within its host. However, the regulatory mechanisms controlling these life cycle transitions remain poorly understood. In this study, we characterized the AP2 factor AP2X-1, which is expressed during the tachyzoite and bradyzoite stages, but not in the mature merozoite stage. Knockout of ap2X-1 significantly impaired tachyzoite invasion and replication, while increasing the frequency of bradyzoite differentiation. As a component of the HDAC3/MORC complex, knockout of ap2X-1 led to the upregulation of bradyzoite and sexual stage-specific genes. Single-cell sequencing revealed that ap2X-1 knockout strains behaved as a mixed population of tachyzoites, bradyzoites, merozoites, and sporozoites. CUT&Tag analysis revealed substantial overlap between AP2X-1 and HDAC3/MORC complex binding at the promoters of bradyzoite and sexual stage-specific genes. Additionally, ATAC-seq analysis demonstrated that AP2X-1 modulates chromatin compaction and accessibility, suggesting that AP2X-1 recruits the HDAC3/MORC complex to repress bradyzoite differentiation and sexual commitment. The loss of ap2X-1 resulted in significant attenuation of T. gondii virulence and reduced the formation of brain cysts in vivo. These findings identify AP2X-1 as a critical negative regulator of T. gondii sexual development.

overall_design:
We report genome-wide AP2X-1 profiles in Toxoplasma gondii using CUT&TAG

We report  chromatin compaction and accessibility of AP2X-1 in Toxoplasma gondii using ATAC-Seq.

first: Li-Xiu

last: Sun

first: Meng

first: Tian-Yu

last: Zhang

first: Hany M

last: Elsheikha

first: Xiao-Nan

last: Zheng

first: Zhi-Wei

first: Bao-Quan

last: Fu

first: Xing-Quan

last: Zhu

first: Guo-Hua

first: Jin-Lei


title: Microengineered transplantation of human solid tumors for in vitro studies of CAR T immunotherapy

city: Philadelphia

first: Dan Dongeun

last: Huh

state: Pennsylvania

address: 210 S 33rd Street 315S Skirkanich Hall

department: Bioengineering

institute: University of Pennsylvania

summary: Despite its proven efficacy for hematologic malignancies, chimeric antigen receptor (CAR) T cell therapy has met with limited success in treating solid tumors. While this represents a significant clinical challenge in cancer immunotherapy, preclinical efforts to assess and improve the efficacy and safety of CAR T therapy are hindered by our limited ability to model, probe, and modulate the complexity of cancer-immune interactions in solid tumors. Here, we present a microengineered platform for in vitro reproduction, real-time imaging, and in-depth analysis of malignant human solid tumors during CAR T therapy. Using a compartmentalized device with an externally accessible interface, this system makes it possible to engineer three-dimensional organotypic constructs composed of human tumor explants that can be vascularized and perfused with blood-borne immune cells in a controlled manner. We first present a microphysiological model of adenocarcinoma tumors in the human lung infused with CAR-T cells to demonstrate its capabilities to reproduce the three essential steps of targeting solid tumors, including CAR T cell recognition of tumor-associated antigens, infiltration, and survival and effector function in the tumor microenvironment. Using flow cytometry and single-cell RNA sequencing, we probe how the phenotype of CAR T cells changes during their recruitment and persistence. Furthermore, we use the sequencing data to discover a therapeutic target that can be pharmacologically inhibited in our model to significantly increase CAR T cell trafficking and their anti-tumor effects, for which we also present specific biomarkers identified by untargeted metabolomics analysis. This work provides a potentially powerful approach for mechanistic studies and preclinical screening of adoptive cell therapies for cancer and other complex diseases.

overall_design: The microengineered solid tumor models with vascularized tumor explants were infused with CAR T cells and analyzed using single cell RNA-sequencing.

first: Dan

middle: D

first: Haijiao


title: The TET protein family interactor PROSER1 sustains hematopoietic stem cell function [ChIP-Seq]

city: Dundee

first: Kasper

middle: Dindler

last: Rasmussen

address: Dow Street

department: Division of Molecular, Cellular, and Developmental Biology (MCDB)

country: United Kingdom

institute: School of Life Sciences, University of Dundee

summary: Ten-Eleven-Translocation (TET) enzymes are epigenetic regulators important for prevention of hematological malignancies. PROSER1, a known TET protein interactor, has a critical role in modulating TET-mediated DNA demethylation during development. However, the potential involvement of PROSER1 in regulation of hematopoiesis and leukemogenesis remains unknown. Here, we demonstrate that the leukemia suppressive functions of TET2 are preserved in the absence of PROSER1. Nonetheless, we find that loss of PROSER1 partially recapitulates the aberrant enhancer DNA methylation phenotype observed upon TET2 knockout, suggesting that PROSER1 and TET2 play both cooperative and distinct roles in the regulation of DNA methylation in hematopoiesis. Importantly, using serial hematopoietic stem cell (HSC) transplantation assays, we find progressive exhaustion of HSC activity and reduction in hematopoietic lineage output upon loss of PROSER1. Our findings imply that, beyond the established role of TET2 loss-of-function mutations in promoting HSC expansion and leukemic transformation, accurate TET activity, regulated by PROSER1, is equally important to prevent HSC exhaustion and sustain normal hematopoiesis.

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) in wildtype and PROSER1 KO immortalised hematopoietic progenitor cells (HOXB8-FL) for the following histone modifications: H3K27ac, H3K4me1, H3K27me3. Enzymatic methyl-seq (EM-seq) in wildtype, PROSER1 KO and TET2 KO HOXB8-FL cells. RNA-seq in LSK cells (Lin-Sca1+cKit+) FACS purified from lethally irradiated recipient mice transplanted with wildtype or PROSER1 knockout bone marrow.

first: Elena

last: Knatko

first: Anna

last: Fleming

first: Xiang

first: Phoebe

last: Crawley

first: Ieva

last: Budriunaite


title: Effect of MICT1 depletion on gene expression in differentiated brown adipocytes.

city: Berkeley

first: Danielle

last: Yi

state: CA

address: 220 Morgan Hall

institute: UC Berkeley

summary: Using high throughput sequencing, we report  gene expression profiling in mouse brown adipocytes upon forskoln treatment in contorl (Scr) and MICT1-CRISPR KO pool.

overall_design: Gene expression profiling induced by loss of MICT1 in mouse brown adipocytes

first: Hei

last: Sul


title: Pharmacological inhibition of tyrosine protein-kinase 2 reduces islet inflammation and delays type 1 diabetes onset in mice

city: Indianapolis

first: Carmella

last: Evans-Molina

state: Indiana

address: 16 Tech Innovation Bldg 1; 1210 Waterway Blvd Ste 4100

department: Pediatrics

institute: Indiana University School of Medicine

summary: Tyrosine protein-kinase 2 (TYK2), a member of the Janus kinase family, mediates inflammatory signaling through multiple cytokines, including interferon-α (IFNα), interleukin (IL)-12, and IL-23. Missense mutations in TYK2 are associated with protection against type 1 diabetes (T1D), and inhibition of TYK2 shows promise in the management of other autoimmune conditions. Here, we evaluated the effects of specific TYK2 inhibitors (TYK2is) in pre-clinical models of T1D. First, human β cells, cadaveric donor islets, and iPSC-derived islets were treated in vitro with IFNα in combination with a small molecule TYK2i (BMS-986165 or a related molecule BMS-986202). TYK2 inhibition prevented IFNα-induced β cell HLA class I up-regulation, endoplasmic reticulum stress, and chemokine production. In co-culture studies, pre-treatment of β cells with a TYK2i prevented IFNα-induced activation of T cells targeting an epitope of insulin. In vivo administration of BMS-986202 in two mouse models of T1D (RIP-LCMV-GP mice and NOD mice) reduced systemic and tissue-localized inflammation, prevented β cell death, and delayed T1D onset. Transcriptional phenotyping of pancreatic islets, pancreatic lymph nodes (PLN), and spleen during early disease pathogenesis highlighted a role for TYK2 inhibition in modulating signaling pathways associated with inflammation, translational control, stress signaling, secretory function, immunity, and diabetes. Additionally, TYK2i treatment changed the composition of innate and adaptive immune cell populations in the blood and disease target tissues, resulting in an immune phenotype with a diminished capacity for β cell destruction. Overall, these findings indicate that TYK2i has beneficial effects in both the immune and endocrine compartments in models of T1D, thus supporting a path forward for testing TYK2 inhibitors in human T1D.

overall_design: To understand the impact of TYK2 inhibition across target tissues and obtain insight into their effects on T1D pathogenesis, we used a GeoMx spatial whole transcriptomic atlas (WTA) to evaluate islets, spleen, and PLN from RIP-LCMV-GP mice at days 3 and 7 post-inoculation and islets and PLN from NOD mice treated with vehicle or TYK2i.

first: Farooq

last: Syed

first: Preethi

last: Krishnan


title: Analysis of genome-wide DNA methylation patterns in peripheral blood of healthy individuals

first: Tomasz

last: Wojdacz

summary: Genome-wide DNA methylation patterns were quantified in peripheral blood samples collected from 24 healthy individuals using the Illumina Infinium HumanMethylationEPIC BeadChip

overall_design: In this study, we recruited 24 individuals with no symptoms of the disease. From each participant we collected peripheral blood sample for DNA extraction and performed DNA methylation analyses using Illumina Infinium HumanMethylationEPIC BeadChip.

first: Olga

last: Taryma-Leśniak

first: Jan

last: Bińkowski

first: Katarzyna

last: Sokolowska

first: Konrad

last: Borowski


title: Identification of Asporin as a HER3 ligand that exposes a therapeutic vulnerability in metastatic prostate cancer (ASPN)

first: Hong Yuen

last: Wong

first: Amanda

last: Hesterberg

first: Hong

first: Paula

last: Hurley


title: The TET protein family interactor PROSER1 sustains hematopoietic stem cell function

first: Kasper

last: Rasmussen

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The TET protein family interactor PROSER1 sustains hematopoietic stem cell function [Emseq]

first: Elena

last: Knatko

first: Anna

last: Fleming

first: Xiang

last: Li

first: Phoebe


title: 5-ALA photodynamic metabolite-powered zero-waste “ferroptosis amplifier” for enhanced hypertrophic scar therapy

status: Public on Jun 24 2025

city: Chongqing

first: Tao

last: Chen

address: No.426, Songshi North Road, Yubei District

institute: Stomatological Hospital of Chongqing Medical University

summary: Hypertrophic scar (HS) is a somatopsychic disease that significantly affects quality of life. 5-aminolevulinic acid (5-ALA)-mediated photodynamic therapy (PDT) holds promise for HS treatment, while challenges like poor transdermal delivery and rapid metabolism into non_xfffe_photosensitive heme restrict its effectiveness. Inspired by the natural phenomenon of a whale fall nourishing life, this study innovatively repurposes 5-ALA metabolic waste, heme, as a “whale-like” energy source to drive ferroptosis, thus establishing a zero-waste therapy. This is achieved by encapsulating 5-ALA and baicalin within human H-ferritin (HFn), subsequently incorporated into polyvinylpyrrolidone (PVP) microneedles (FAB@MN). The FAB@MN exhibits excellent targeting towards hypertrophic scar fibroblasts (HSFs) with pH-responsive programmed drug release. Upon application, 5-ALA is converted into PpIX to initiate PDT. Subsequently, baicalin is released, triggering ferroptosis while also synergizing with the ROS and heme accumulated during PDT to overstimulate the HO-1-heme metabolic axis. This activation releases Fe2+ and CO, further potentiating ferroptosis. Moreover, the enhanced ferroptotic response driven by FAB@MN induces mitophagy, leading to increased Fe²⁺ release from the mitochondria. Unlike conventional PDT only focuses on immediate effects, this approach uses 5-ALA photodynamic waste to fuel a sustained ferroptosis response post-PDT, offering new avenues for HS treatments.

overall_design: This research project has been approved by the Ethics Committee of Chongqing Medical University (CQHS-REC-2024-058). Nine HS tissues and the matched normal skin tissues were provided by patients undergoing surgical treatment, and each patient has voluntarily signed an informed consent form. All participants in this study did not have any known systemic diseases and were not receiving any treatments that could potentially affect the study results. In brief, tissues were first cut into 3 mm-thick slices, and then digested overnight with 0.25% neutral protease II. Subsequently, the epidermal layer was peeled off, and further digestion was carried out for 4-6 hours at 37°C with 0.2% Collagenase II. After digestion, cells were filtered and collected using a cell strainer with a 75μm pore size, then resuspended in Dulbecco's Modified Eagle Medium (DMEM) containing 10% FBS and cultured at 37°C in an atmosphere of 5% CO2. The method of isolating fibroblasts from normal skin was similar to the aforementioned process for obtaining HSFs with minor modifications. HSFs were seeded at a density of 1 × 10^5 cells/well in a 24-well plate and cultured for 24 hours in DMEM containing 10% FBS. Subsequently, the cells were treated with FAB NPs for 4 hours, followed by 10 mins of illumination, and then incubated for another 24 hours. Total RNA was extracted using TRIzol reagent (Invitrogen, USA), and the integrity of the RNA was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). RNA samples were prepared using total RNA as a template. Initially, mRNA was extracted from total RNA using magnetic beads coated with poly-T oligonucleotides. This mRNA was then fragmented under high temperatures in the presence of divalent cations, using a 5X First Strand Synthesis Reaction Buffer. The synthesis of the first cDNA strand was achieved using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-). This was followed by the synthesis of the second cDNA strand using DNA Polymerase I and RNase H. Exonuclease and polymerase activities were employed to transform remaining overhangs into blunt ends. Subsequent to the adenylation of the 3' ends of the DNA fragments, adapters containing hairpin loop structures were attached, setting the stage for hybridization. cDNA fragments ranging in size from 370-420 bp were isolated using the AMPure XP system (Beckman Coulter, Beverly, USA). Amplification of these fragments was then carried out using Phusion High-Fidelity DNA Polymerase, along with universal PCR primers and an Index (X) Primer. The PCR products were purified within the AMPure XP system, and the library's quality was evaluated using an Agilent Bioanalyzer 2100 system. Indexed samples were clustered on the cBot Cluster Generation System using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer's guidelines. Post-clustering, the library was sequenced on the Illumina Novaseq platform, producing 150 bp paired-end reads and thereby acquiring the sequence data of the fragments.

first: Yuan

first: Shan

last: Wang

first: Congxiu

last: Mao

first: Qinyi

last: Lu

first: Xingyu

last: Zhu

first: Dongqi

last: Fan

first: Yiping

last: Liu

first: Xu

first: Jinglei

last: Zhan

first: Zixin

last: Yang

first: Ping

last: Ji

first: Qingqing

last: He


title: Identification of Asporin as a HER3 ligand that exposes a therapeutic vulnerability in metastatic prostate cancer [ASPN_MyCCaP_10111-AH]

first: Hong Yuen

last: Wong

first: Amanda

last: Hesterberg

first: Hong

first: Paula


title: Aging Reprograms the Rhythmic Transcriptome in the Retina

city: HangZhou

first: Wang

last: Zhijie

state: ZheJiang

address: No. 618, Fengqi East Road

department: Department of Retina Center

institute: Eye Hospital and School of Ophthalmology

summary: Aging is a significant risk factor for various retinal degenerative diseases. However, its impact on diurnal transcriptional profile of the retina remains largely unexplored. Addressing this knowledge gap is crucial given the rising prevalence of age-related retinal diseases.

overall_design: We conducted high-throughput RNA sequencing on retinal samples collected at 4-hour intervals (n = 24 per group) from young (6-week-old) and aged (20-month-old) C57BL/6 mice maintained under a 12h:12h light-dark cycle. Differential expression analysis was performed using edgeR (FDR < 0.05, |FC| > 1.5). Rhythmicity analysis was conducted using the MetaCycle package, which integrates JTK_CYCLE and Lomb-Scargle algorithms, while differential rhythmicity analysis was performed using the CircaCompare package.

first: Zhijie

first: Lifeng

first: Lin

first: Mengai

last: Wu

first: Bin

last: Zheng

first: YuanYuan


title: Experimment of DNA methylation seqencing for 12 Alzheimser patients and 12 normal cognitve subjects of Japanese.

city: Obu

first: Risa

last: Mitsumori

state: Aichi

address: 7-430, Morioka-cho

department: Research Institute

country: Japan

institute: National Center for Geriatrics and Gerontology

summary: To investigate the diffrential methylation region (DMR) in the whole blood between Alzheimer's patientis and normal cognitive subjects, methylation seqencing were performed.

overall_design: Total 24 of subjects were included in this study: 12 Alzheimer's disease patients and 12 normal cognitive patients. Genomic DNA (gDNA) was extracted from peripheral blood by using a Maxwell RSC Instrument (Promega, USA) with Maxwell RSC Buffy Coat DNA Kit (Promega, USA).

first: Kayoko

last: Sawamura

first: Kimi

last: Yamakoshi

first: Akinori

last: Nakamura

first: Yutaka

last: Arahata

first: Shumpei

last: Niida

first: Daichi

last: Shigemizu

first: Koichi

last: Ozaki

first: Nobuyoshi

last: Shimoda


title: Gene expression data comparing HIV exposed and HIV unexposed freshly isolated umbilical cord blood derived CD34+ haematopoietic stem/progenitor cells

city: Pretoria

first: Candice

middle: Laverne

last: Hendricks

state: Gauteng

address: 15 Bophelo Road, Prinshof Campus, University of Pretoria, Gezinaa

department: Medical Immunology

country: South Africa

institute: University of Pretoria

summary:
Umbilical cord blood (UCB) is a donor source for haematopoietic stem cell transplantation but only HIV unexposed and uninfected cord blood has been used to date. HIV exposed and uninfected cord blood could potentially be considered as a donor source in HIV endemic countries, provided the functioning of these CD34+ Haematopoietic stem cells (HSPCs) is comparable to HIV unexposed cells.
We performed gene expression analysis on umbilical cord blood CD34+ HSPCs to determine if any differences exist between HIV unexposed and HIV exposed cohorts with mothers taking newer antiretroviral drugs.

overall_design: Umbilical cord blood was obtained from term HIV exposed and unexposed infants. After obtaining a pure mononuclear cell population, magnetic isolation was employed to enrich for CD34+ HSPCs. RNA was extracted from the CD34+ HSPCs on the day of isolation. This was followed by hybridisation on Affymetrix microarrays.

first: Michael

last: Pepper

first: Melvin

last: Ambele

first: Juanita

last: Mellet


title: Short chain fatty acids regulate the chromatin landscape and distinct gene expression changes in human colorectal cancer cells

city: Cleveland

first: Leah

last: Gates

state: OH

address: 10900 Euclid Avenue

institute: Case Western Reserve University

summary: Short chain fatty acids (SCFAs) are small metabolites that are produced through the activity of microbes and have important roles in human physiology. These metabolites have varied mechanisms in interacting with the host, of which one such mode is decorating the chromatin landscape. We previously detected specific histone modifications in the mouse gut that can be derived from SCFAs and are regulated by the microbiota. However, the roles of these SCFAs on chromatin and how they impact gene regulation in human cells is largely unknown. Now, our studies demonstrate these microbiota-dependent histone posttranslational modifications (PTMs) are associated with alterations in gene regulation in human cells. We show that histone butyrylation on H3K27 is detected in human colon samples. Furthermore, histone acetylation, butyrylation, and propionylation on H3K9 and H3K27 are responsive to levels of SCFAs in human colon cancer cell lines and are associated with active gene regulatory elements. In addition, treatment of human cancer cell lines with individual metabolites or combinations of SCFAs replicating the intestinal lumen environment result in distinct and overlapping gene program changes, with butyrate largely driving gene regulatory effects of SCFA combinations. Lastly, we define butyrate effects on gene expression that are independent of HDAC inhibition and are dependent on p300/CBP, suggesting potential gene programs regulated by histone butyrylation. Together, these results demonstrate that SCFAs are key regulators of the chromatin landscape and gene programs in human colorectal cancer cells.

overall_design: One experiment includes ChIP-seq of histone acyl modifications in HCT-116 cells treated with either butyrate or propionate. Other experiments are RNA-seq data from HCT-116 or Caco-2 cells treated with different short chain fatty acids or inhibitors targeting HDACs or p300/CBP. All RNA-seq samples are provided in biological triplicate.

first: Leah A.

first: Matthew R

last: Paul

first: Thomas S

last: Carroll


title: Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks

city: Amsterdam

first: Xabier

last: Vergara

state: North Holland

address: Plesmalaan 121

department: Molecular Genetics

country: Netherlands

institute: Netherlands Cancer Institute

summary: Lamina-associated domains (LADs) are large genomic regions that contact the nuclear lamina (NL). Double-strand breaks (DSBs) in LADs are known to be repaired more slowly and with different pathway preferences compared to other chromatin contexts. However, little is known about the chromatin changes at LADs that occur during DSB repair. Here, we report that a single DSB inside a LAD can cause detachment from the NL over several megabases. This profound spatial rearrangement is transient and reverts within 48 hours. Preventing this detachment slows down repair kinetics and renders repair incomplete, indicating that NL detachment is required for efficient repair of DSBs in LADs. NL detachment is dependent on gH2AX and ATM, while it is antagonized by DNAPKcs activity. Remarkably, gH2AX also antagonizes NL interactions at chromosome ends. Taken together, our data indicate that gH2AX accumulation in LADs induces large scale rewiring of genome-NL interactions, allowing for efficient repair of DSBs.

overall_design: We used pADamID to profile NL interactions as well as yH2AX after inducing DSBs in LADs. The data we are submitting mainly included pA-DamID data from human cell lines (RPE-1 and K562) transfected with either a gRNA targetting a LAD or tracr only control.

first: Anna

middle: G

last: Manjon

first: Marco

last: Novais-Cruz

first: Marcel

last: de Haas

first: Ayoub

last: Ouchene

first: Tom

last: van Schaik

first: Stefano

last: Manzo

first: Bas

last: van Steensel

first: Rene

last: Medema


title: The deubiquitinase USP17 regulates the expression of the oncogenic driver β-catenin in colorectal cancer

city: Montreal

first: Marc

last: Servant

state: Quebec

address: P.O. Box 6128, Downtown Station

department: Faculty of Pharmacy

institute: Université de Montréal

summary: Aberrant activation of the Wnt/β-catenin signaling pathway is a hallmark of colorectal cancer (CRC). Here, we identify the deubiquitinating enzyme USP17 as a critical regulator of β-catenin stability in CRC. We demonstrate that USP17 directly interacts with and deubiquitinates β-catenin, preventing its degradation and enhancing its stability. CRISPR/Cas9-mediated knockout of USP17 in CRC-derived cell lines significantly reduced β-catenin levels and suppressed epithelial-mesenchymal transition (EMT), as evidenced by distinct morphological changes and altered expression of classical EMT markers. USP17 depletion reduced the proliferation of CRC cell lines and impaired CRC tumor growth in vivo. Conversely, USP17 overexpression in immortalized rat enterocytes elevated β-catenin levels and enhanced KRAS-induced cell proliferation. RNA sequencing and quantitative proteomic analysis of USP17-depleted CRC cells revealed significant suppression of the transcriptional coactivator function of β-catenin, impacting key oncogenic-related pathways. Our findings establish USP17 as a key regulator of β-catenin signaling and highlight its potential as a candidate therapeutic target in CRC.

overall_design: To gain mechanistic insight into how USP17 promotes CRC tumorigenesis, we performed bulk RNA sequencing of COLO 320DM cells transfected with independent USP17-targeting siRNA duplexes or non-silencing controls (siNT and L2)

first: Mariana

last: Acevedo

first: Florence

last: Dô

first: Firas

last: El-Mortada

first: Pierre-Luc

last: Tanguay

first: Laure

last: Voisin

first: Thibault

last: Houles

first: Geneviève

last: Lavoie

first: David

last: Allard

first: Philippe

middle: P

last: Roux

first: John

last: Stagg

first: Samuel

last: Doré

first: Logan

last: Walsh

first: Jimmy

last: Fourtounis

first: Eric

last: Bonneil

first: Sylvain

last: Meloche


title: Isoform-Specific Gene Regulation by Progesterone Receptors Drives Divergent Phenotypes in Breast Cancer Cells [RNA-Seq]

city: Minneapolis

first: Noelle

middle: E

last: Gillis

state: Minnesota

address: 2231 6th ST SE, CCRB

institute: University of Minnesota

summary: Exposure to progesterone is a recognized risk factor for breast cancer, and PGR polymorphisms are associated with various malignancies. The two progesterone receptor (PR) isoforms, full length PR-B and truncated PR-A, are expressed from the PGR gene in breast tissue and play crucial roles in normal physiology and breast cancer progression. An imbalance in the expression ratio of these isoforms, favoring increased levels of PR-A, is common in breast cancer and is associated with resistance to tamoxifen in Luminal A-type tumors. Notably, PRs have recently been implicated in promoting endocrine resistance and driving the expansion of cancer stem-like cell (CSC) populations. Despite this insight, the isoform-specific molecular and epigenetic mechanisms underlying PR action in ER+ breast cancers remain understudied. Phenotypic studies of T47D cell lines that express exclusively PR-A or PR-B showed that PR isoforms regulate divergent cell fates. PR-B expressing cells have a higher proliferation rate, while PR-A expressing cells produce more mammospheres. We profiled progesterone-driven gene expression in cells grown in both adherent (2D) and mammosphere (3D) growth conditions and found differential gene regulation by PR-A and PR-B that is consistent with the observed divergent phenotypes. We then performed CUT&RUN to identify the genomic binding patterns unique to each PR isoform and their suite of target genes. Our findings indicate that PR-A acts as a regulator of the cell cycle and senescence, while PR-B plays a pivotal role in metabolism and intracellular signaling. Our genomic profiling of PRs in this model system has unveiled novel isoform-specific functions of PR. This work has shifted our prior understanding of the role of PRs in gene regulation, offering potential insights for therapeutic interventions in ER+ breast cancer.

overall_design: RNA-seq was performed on T47D cell lines expressing PR-A or PR-B exclusively. Cells were treated with 10 nM R5020 or vehicle control. Cells were grown in adherent (2D) or mammosphere (3D) condtions.

first: Carol

last: Lange


title: Isoform-Specific Gene Regulation by Progesterone Receptors Drives Divergent Phenotypes in Breast Cancer Cells [CUT&Run]


title: Translational buffering tunes gene expression in mouse and human

city: Austin

first: Can

last: Cenik

state: Texas

address: 2500 Speedway

department: Department of Molecular Biosciences

institute: University of Texas

summary: Translational buffering refers to the regulation of ribosome occupancy to offset the effects of transcriptional variation. While previous work reported translational buffering in a limited set of conditions, it remains unknown whether this is an intrinsic property of specific genes across a large number of different cell types. To identify genes exhibiting this phenomenon on a global scale and across different experimental conditions, we uniformly analyzed 1515 matched ribosome profiling and RNA-seq datasets from human and mouse tissues or cell lines. This resource enabled us to determine the set of genes exhibiting translational buffering by comparative analysis of variation at ribosome occupancy and the RNA levels across cell types and the relationship between mRNA abundance and translation efficiency. We demonstrate that translational buffering is a conserved property of genes using homologous gene pairs from humans and mice. Genes exhibiting translational buffering have lower variation in protein abundance in cancer cell lines, primary human tissues and mouse samples. Moreover, we observed that translationally buffered genes are more likely to be haploinsufficient and triplosensitive suggesting a demand for stringent dosage limits in these genes. We hypothesized two models of translational buffering, namely “differential accessibility model” and “change in translation initiation rate model”. Our experiment suggests that some transcripts conform to the former and others align with the alternate model. Overall, our work broadens the catalog of genes subjected to translational buffering, underscores the characteristics of genes that demonstrate this phenomenon and additionally provides an insight into the rationale driving this effect.

overall_design: Ribosome profiling along with matched total and translating RNA -seq from HEK293T cells

first: Shilpa

last: Rao

first: Aden

last: Le

last: Persyn


title: FBXO11-Mediated Proteolysis of BAHD1 Relieves PRC2-dependent Transcriptional Repression in Erythropoiesis

city: Suzhou

first: Peng

last: Xu

state: Jiangsu

address: Office3625 Building703, RENAI ROAD No.199, INDUSTRIAL PARK DISTRICT

department: Suzhou Medical College

institute: Soochow University

summary: The histone mark H3K27me3 and its reader/writer Polycomb repressive complex 2 (PRC2) mediate widespread transcriptional repression in stem and progenitor cells. Mechanisms that regulate this activity are critical for tissue development but poorly understood. Here we show that the E3 ubiquitin ligase FBXO11 relieves PRC2-mediated repression during erythroid maturation by targeting its newly identified substrate BAHD1, an H3K27me3 reader that recruits transcriptional co-repressors. Erythroblasts lacking FBXO11 are developmentally delayed, with reduced expression of maturation-associated genes, most of which harbor bivalent histone marks (activating H3K4me3 and repressive H3K27me3), bind BAHD1, and fail to recruit the erythroid transcription factor GATA1. The BAHD1 complex interacts physically with PRC2 and depletion of either component restores FBXO11-deficient erythroid gene expression. Previous studies showed that FBXO11 promotes B-cell development and inhibits lymphomagenesis by degrading the transcriptional repressor BCL6. We show that in aggressive B-cell lymphoma lines, depletion of FBXO11 causes the accumulation of both BCL6 and BAHD1, and that suppression of BAHD1 slows cell expansion. Our studies identify BAHD1 as a novel effector of PRC2-mediated repression and reveal how a single E3 ubiquitin ligase eliminates PRC2 repression at developmentally poised bivalent genes during erythropoiesis. The FBXO11-BAHD1 regulatory axis may function in other developmental pathways, including B-lymphopoiesis and lymphomagenesis.

overall_design: The goals of this study are to compare the transcriptomes in wild type HUDEP-2 and FBXO11 -/- HUDEP-2 erythroblast. We further compare the transcriptomes in BAHD1shRNA or shLuciferase treated FBXO11 KO HUDEP-2 cells. Finally we intergrate the RNA-seq data with CHIP-Seq data (H3K4me1, H3K27ac) to support our hypothesis.

first: Beisi

first: Xing

last: Tang


title: Multi-omics Identifies Tumor-Intrinsic SREBP1 Driving Immune Exclusion in Hepatocellular Carcinoma

city: Pittsburgh

first: Rebekah

last: Dadey

state: PA

address: 5115 Centre Avenue

department: Hematology/Oncology

institute: University of Pittsburgh

summary: Immune checkpoint inhibitors (ICI) have improved patient outcomes in hepatocellular carcinoma (HCC); however most patients do not experience durable benefit. The non-T cell-inflamed tumor microenvironment (TME), characterized by limited CD8+ T cell infiltration, reduced dendritic cell function, and low IFNγ-associated gene expression, is associated with lower likelihood of response to ICI.  To nominate new therapeutic targets for overcoming ICI resistance in HCC, we conduced single cell RNAseq using 10X Genomics on 6 primary HCC tumors.

overall_design:
Cells were isolated from HCC tumors using Millitenyi Gentle MACS digestion protocols and single cell suspensions were subjected to 5' 10X single cell RNAseq from 10X Genomics using 5' chemistry. Indicated samples were sequenced at the University of Pittsburgh Medical Center Genome Core or at Novogene (or both). We aimed for 50,000 reads/cell in an estimated 10,000 cells per sample. We utilized Cell Ranger software (v7.0) for alignment to the human reference sequence (GRCh38)

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

first: Jason

last: Luke

first: Riyue

last: Bao


title: BET bromodomain inhibitors attenuate transcription of a subset of IL-1-induced NF-κB target genes that promote inflammation in β-cells

city: Milwaukee

first: Joshua

last: Nord

state: WI

address: 8701 W Watertown Plank Rd

institute: Medical College of Wisconsin

summary: Cytokine-stimulated transcription of NF-κB target genes is linked to the development of multiple inflammatory and autoimmune diseases. Inhibitors of bromodomain and extraterminal domain (BET) epigenetic reader proteins attenuate inflammatory gene transcription and delay the onset of several inflammatory diseases, including autoimmune diabetes. Our previous studies showed that BET bromodomain inhibitors disrupt the interaction between BET family member BRD4 and NF-κB transcription factor p65 in β-cells, thus attenuating cytokine-stimulated NF-κB-dependent gene and functional changes. However, the role of NF-κB in developing inflammatory disease is controversial, as NF-κB inhibition can promote disease progression in some contexts. NF-κB target genes play both physiological and pathophysiological roles in regulating the cellular response to cytokines. Here, using cytokine-stimulated pancreatic β-cells as an inflammatory disease model, we show that NF-κB-dependent gene products that participate in inflammation are sensitive to BET bromodomain inhibition. In contrast, gene products that maintain cellular homeostasis or protect β-cells from stressors are largely insensitive to BET bromodomain inhibition. These studies define a novel and selective role for BET bromodomain-containing proteins in regulating inflammatory gene activation.

overall_design: INS 832/13 rat insulinoma cells treated with BET bromodomain inhibitor (+)-JQ1 (dissolved in DMSO). DMSO was used as a control.

first: Savannah

last: Makowski

first: Paul

last: Sidlowski

first: Karina

middle: L

last: Bursch

first: John

last: Corbett

first: Brian

middle: C

last: Smith


title: ICOS-driven Cholesterol and Cortisol Biosynthesis Shape IL-10 Production in ILC2s to Regulate Airway Hyperreactivity

city: Los Angeles

first: Yoshihiro

last: Sakano

address: 1450 Biggy street

department: Molecular Microbiology & Immunology

institute: Unversity of Southern California

summary: Group 2 innate lymphoid cells (ILC2) induce type 2 inflammation in the lungs in response to allergens. Here, we investigated the regulatory mechanism of IL-10 production by ILC2s on the development of airway hyperreactivity (AHR), with a particular focus on the role of ICOS. Our findings demonstrate that inhibition of ICOS in pulmonary ILC2s significantly promotes IL-10 production. Lack of ICOS reprograms ILC2 steroid metabolism, resulting in increased cholesterol and cortisol biosynthesis and Glucocorticoid receptor (GR) activation. Consequently, this reprogramming regulates MAF and NFIL3 activation, thereby promoting IL-10 production. We notably found that in vivo GR inhibition or ILC2-specific GR deficiency exacerbated the development of AHR in multiple mouse models. Finally, we extended our findings to a human setting and demonstrated concordant results between murine models and human ILC2s. Taken together, our results therefore indicate that ICOS negatively regulates IL-10 production in ILC2s by controlling cholesterol and cortisol biosynthesis.

overall_design: mRNA profiles of mouse lung ILC2s from WT and ICOS KO mice were generated by deep sequencing, in duplicates, using a NextSeq 500.


title: Transplant immunosuppressant therapies induce unique functional changes in and re-shape gut immune homeostasis

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

summary: Current immunosuppressants effectively suppress adaptive and innate immune responses, but their broad, antigen-non-specific effects often result in significant complications. Here we investigated understudied immunosuppressant effects of four major immunosuppressant classes including tacrolimus, prednisone, mycophenolate mofetil (MMF), and Fingolimod (FTY), on the gut microbiome, metabolic pathways, lymphoid architecture and lymphocyte trafficking. Despite their distinct mechanisms of action, all drugs induced progressive alterations from moderate early changes to substantial alterations in the gut microbiome composition and metabolic pathways with prolonged treatment, converging to a shared dysbiotic state. This was accompanied by significant metabolic alterations and distinct phases of intestinal transcriptional responses. Time-dependent changes in lymph node (LN) reorganization and cellular composition were also observed, showing compartmentalized immune regulation in mesenteric and peripheral lymphoid tissues. Together, these findings highlight the underappreciated complexity and temporal dynamics of immunosuppressant effect, linking drug-induced changes in gut microbiome and compartmentalized immune regulation in lymphoid tissues. Notably, MMF and FTY demonstrated most robust immunomodulatory properties, and were able to suppress alloantigen-induced inflammation through mediating regulatory T cells and LN remodeling. Understanding these relationships provides new opportunities for refining immunosuppressive strategies to mitigate treatment-related complications in transplant patients, ultimately improving long-term organ transplant outcomes.

overall_design: intestinal transcriptome at days 7 and 30 of  C57BL/6 mice daily with four immunosuppressants [TAC (tacrolimus), the glucocorticoid prednisone (PRED), mycophenolate mofetil (MMF), and Fingolimod (FTY)], respectively, using untreated mice as controls.

first: Bing

last: Ma

first: Jonathan

last: S Bromberg

first: Yang

last: Song


title: Distinct Molecular Patterns in R6/2 HD Mouse Brain: Insights from Spatiotemporal Transcriptomics

city: Irvine

first: Ricardo

last: Miramontes

address: 845 Health Sciences Rd

institute: UC Irvine

summary: Huntington’s disease (HD) is a progressive neurodegenerative disease marked by widespread cellular disruption. To understand disease mechanisms by investigating transcriptional differences, we and others have utilized bulk and single cell transcriptomics which provide cell type information but limited spatial information. We therefore utilized 10x Genomics Visium spatial transcriptomics integrated with matched single nuclei-RNA-seq in the HD R6/2 mouse brain (postnatal day 0, 4- and 12-week) to examine disease trajectories across regions in a rapidly progressing model. Our data suggests regional, temporal and cell type specific regulatory pathways that establish distinct gene expression changes in brain. Synaptic dysfunction is observed broadly throughout the brain. We observed early dysregulation of the transcription factor Tcf-4 that may drive cortical changes. Mitochondrial deficits are the earliest changes, beginning at P0 in striatum prior to overt symptom onset together with increased expression of striatal identity genes that then become progressively downregulated. Finally, we identified a time-dependent dysregulation of neuropeptide Y signaling and potential interaction with the cAMP/PKA pathway, which may be involved in early imbalance between Drd1 and Drd2 neuron vulnerability.

overall_design: 10x Genomics FLEX snRNAseq was conducted on a rapidly progressing Huntington's disease mouse model, R6/2, and non-transgenic controls at three time points: postnatal day 0, presymptomatic 4-week and symptomatic 12-week (n=3 Males/group/genotype).

first: Mara

last: Burns

first: Jie

last: Wu

first: Madhu

last: Saddala

last: Reidling

first: Vivek

last: Swarup

first: Albert

last: La Spada

first: Ryan

last: Lim

first: Leslie

last: Thompson


title: Epithelium intrinsic zinc sensing maintains host-microbiome symbiosis via modulation of Tuft and Paneth cell lineages [rna-seq_mtf_ko_sio_zn]

city: Providence

first: Geongoo

last: Han

address: 171 Meeting St.

institute: Brown University

summary: Zinc (Zn) is widely recognized as an essential diet-derived micronutrient for optimal growth due to its crucial role in cell proliferation, differentiation, and apoptosis[1-3]. Yet the precise role of Zn in barrier sites such as the intestinal epithelium that is constantly renewing and remodeling remains poorly defined. To address how Zn impacts epithelial lining and gut homeostasis, we generated mice defective in Zn sensing by deleting Metal-responsive Transcription Factor 1 (MTF1) specifically in the intestinal epithelial cells (IECs).  MTF1 is a highly conserved Zn-dependent transcription factor that regulates cellular Zn homeostasis [4]. Mice deleted for MTF1 in intestinal epithelial cells (MTF1 ΔIEC) had altered Zn homeostasis that coincided with significant increase in inflammatory immune response to microbes, indicating a critical role of IEC intrinsic Zn sensing in regulating immune homeostasis in the gut. MTF1 deletion resulted in loss of specialized secretory cell lineages such as Paneth and Tuft cells, compromised barrier function against commensal bacteria, and altered susceptibility to helminth and viral infections. MTF1-dependent Zn sensing proved essential for differentiating specialized epithelial cell lineages from newly proliferated intestinal stem cells. Ex vivo experiments using small intestinal organoids (SIOs) demonstrated that Zn treatment promoted the differentiation of proliferating epithelial cells into specialized cell lineages in wild-type organoids, an effect which is absent in MTF1ΔIEC SIOs. This study provides compelling evidence for the fundamental role of Zn in promoting the differentiation of specialized intestinal epithelial cell lineages, which are key to interactions with diverse microbes and maintaining immune homeostasis in the gut.

overall_design: To investigate the role of zinc in the small intestine, we used small intestinal organoids. The small intestinal organoids from MTF1 Cre- and Cre+ mice were harvested and processed for bulk RNA -seq.

first: Rebecca

last: Yunker

first: Kellie

last: Baldaro

first: Li

last: Zhang

first: Sanghyun

last: Lee

first: Shipra

last: Vaishnava


title: Affymetrix OncoScan SNP arrays for profiling somatic copy-number alterations of Indolent Primary Renal B-Cell Lymphomas

city: Lübeck

first: Axel

last: Künstner

address: Ratzeburger Allee 160

department: LIED

institute: University of Lübeck

type: Genome binding/occupancy profiling by SNP array

summary: Molecular profiling of indolent primary renal B-Cell lymphomas identifies unique pathogenetic mechanisms and parallels with lymphomas from other origins. Here, we used Affymetrix OncoScan CNV arrays to characterise somatic copy number variations in 33 pr-iNHL cases.

overall_design: Total DNA was extracted and prepared for OncoSan CNV arrays from 33 FFPE prDLBCL cases following the manufacturer protocol.

first: A

first: N

last: Gebauer

first: H

last: Busch


title: Epithelium intrinsic zinc sensing maintains host-microbiome symbiosis via modulation of Tuft and Paneth cell lineages [rna-seq_mtf_ko_si]

overall_design: To investigate the role of zinc in the small intestine, we generated mice defective in Zn sensing by deleting Metal-responsive Transcription Factor 1 (MTF1) specifically in the intestinal epithelial cells (IECs) using Cre-lox system. The small intestine of Cre- and Cre+ mice were harvested and processed for bulk RNA -seq.


title: Combined Th2 and Th17/22 cytokines models atopic dermatitis pathophysiology in vitro

city: Nijmegen

first: Jo Huiqing

last: Zhou

address: Geert Grooteplein 26/28

institute: Radboud University

summary: In atopic dermatitis (AD), epidermal disease hallmarks are driven by a complex cutaneous inflammatory milieu that varies between patients. How these variable inflammatory signatures translate to patient-specific disease endotypes is poorly understood, which hampers the personalized use of targeted drugs. We here employed primary and immortalized keratinocyte-derived human epidermal equivalents stimulated with T helper (Th)2, -17 and -22 cytokines, to unravel which AD-associated cytokines drive specific epidermal disease hallmarks. Th2 cytokines IL-4 and IL-13 were main inducers of a pro-inflammatory and hyperproliferative response. The presence of IL-17A or IL-22 in the Th2 milieu caused spongiosis, impaired keratinocyte differentiation (loss of FLG, IVL, KRT2) and epidermal barrier defects (altered CLDN1, CLDN4, transepithelial impedance). Transcriptomic analyses revealed upregulation of proliferation genes by Th2 cytokines, and activation of different immune pathways upon Th2 cytokines alone and combination of Th2 and Th17/22 cytokines. Downregulation of epidermis development was most apparent upon combined exposure to Th2 cytokines and IL-22. Single-cell spatial transcriptomics showed expansion of keratinocytes expressing high level of proliferation  genes in all epidermal layers, and downregulation of terminal differentiation genes in the upper epidermal layers. Our in vitro AD model using Th2 + IL-22 showed the highest transcriptome resemblance with in vivo AD lesional epidermis and we identified IL-22 specific alteration of epidermis development by lipid mediators like ACER1 and AKR1C3. Finally, we revealed that Aryl Hydrocarbon Receptor (AHR) ligands partially restored the barrier defects caused by Th2 and IL-22, whereas combination of AHR ligand Tapinarof with Janus Kinase (JAK) inhibitor I had an even greater restoring effect. Thus, specific combinations of cytokines upregulated in AD skin drive differential disease hallmarks highlighting the importance of personalized medicine and the need for prediction models in the targeted treatment of AD patients.

overall_design: Human epidermal equivalents generated from normal human epidermal keratinocytes (NHEK) or immortalized N/TERT-2G keratinocytes were stimulated for de last 72 hours at the air-liquid interphase (ALI) with Th2 cytokines (IL-4 and IL-13) with and without IL-17A or IL-22.

first: Luca

last: Meesters

first: Janou

middle: A

last: Roubroeks

first: Huiqing

first: Ellen

last: van den Bogaard


title: In vitro generation of a ureteral organoid from pluripotent stem cells

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

summary: The ureter is the outlet for urine produced by the kidney. Recent advances in stem cell biology have enabled the in vitro generation of kidney organoids from pluripotent stem cells (PSCs), but they lack the ureter, which hinders the smooth drainage of urine. By mimicking the in vivo developmental process of ureteral stromal progenitors (SPs) from the posterior intermediate mesoderm, we report here in vitro induction protocols for ureteral SPs from mouse and human PSCs. When the induced SPs were combined with ureteral epithelia derived from mouse embryos, the elongated, multilayered ureteral structure was reconstituted, exhibiting peristaltic constriction. The ureter-like spherical organoids entirely derived from mouse PSCs can also be generated by combining the induced SPs and the epithelial progenitor, the ureteric bud. Furthermore, ureteral SPs induced from TBX18-deficient human PSCs recapitulate the disease state of a congenital anomaly of the urinary tract. Therefore, our induction protocols for ureteral SPs will be useful for the elucidation of ureteral development and disease, and will be an important step towards functional kidney organoids with urine flow.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Kidney mRNA profiles of embryonic day E11.5, E13.5, E15.5, E17.5, postnatal day 0 and day7 at single cell resolution. mRNA profiles of  Induced stromal progenitors from mouse ESCs and cultured ureters at single cell resolution

first: Yutaro

last: Ibi

first: Koichiro

last: Miike

first: Tomoko

last: Ohmori

first: Chen-Leng

last: Cai

first: Ryuichi

last: Nishinakamura


title: Distinct Molecular Patterns in R6/2 HD Mouse Brain: Insights from Spatiotemporal Transcriptomics [Spatial Transcriptomics]

first: Ricardo

last: Miramontes

overall_design: 10x Genomics Visium spatial transcriptomics was conducted on brain tissue of a rapidly progressing Huntington's disease mouse model, R6/2, and non-transgenic controls at three time points: postnatal day 0, presymptomatic 4-week and symptomatic 12-week (n=2-3 Males/group/genotype).

first: Mara

last: Burns

first: Jie

last: Wu

first: Madhu

last: Saddala

first: John

last: Reidling

first: Vivek

last: Swarup

first: Albert

last: La Spada

first: Ryan

last: Lim

first: Leslie

last: Thompson


title: Synthetic hypomorphic alleles to study MUTE-dependent molecular transitions in stomatal development.

city: Toledo

first: Montaña

last: Mena

state: Toledo

address: Avda. Carlos III s/n

department: Environmental Sciences

country: Spain

institute: UCLM

summary: Stomatal abundance sets the plant potential for gas exchange, impacting photosynthesis and transpiration, and ultimately, plant survival and growth. Stomata originate from cell lineages initiated by asymmetric divisions of protodermal cells, producing meristemoids that develop into guard cell pairs. The transcription factors SPEECHLESS, MUTE, and FAMA are essential for stomatal lineage development, sequentially driving cell division and differentiation events. Their absence produces stomataless epidermis, hindering analysis of their roles during lineage development.  MUTE drives the transition from proliferating meristemoids to stomata commitment. We aim to explore the molecular mechanisms underlying MUTE activity, using partial loss-of-function alleles predicted to impair DNA-binding and potentially alter the expression of MUTE transcriptional targets. We engineered mutant allele coding sequences, generated Arabidopsis lines carrying these alleles and analyzed their epidermal and transcriptional phenotypes using microscopy and RNAseq. Synthetic alleles driven by the MUTE promoter rescued the stomataless phenotype of the seedling-lethal mute-3 mutant, enabling stomata differentiation and resulting in viable, fertile plants.  Further examination of the developmental consequences of MUTE partial loss-of-function revealed arrested lineages, reduced stomatal abundance and altered stomatal spacing. Transcriptomic analysis of very young cotyledons from complemented lines indicated that some MUTE targets, but not others, require an intact MUTE bHLH domain. Comparison with existing lineage cell-specific transcriptional profiles showed that lineage development in the mutant lines was delayed compared to the wild-type but followed similar gene networks. These synthetic alleles provide new insight into MUTE ability to accurately and timely specify stomata formation.

overall_design:
To explore the molecular mechanisms underlying MUTE activity we designed two MUTE variants carriyng specific mutations in the bHLH domain: MUTEv5 (substitution Arg10>Trp10) and MUTEPPP (substitutions Hys3>Pro3, Glu7>Pro7 and Arg11>Pro11 ). These synthetic alleles and the wild-type allele driven by the MUTE promoter were mobilized into the mute-3 background to generate homozygous MUTEv5 and MUTEPPP lines, with MUTE lines used as the reference.
For gene expression profiling we selected lines representative of the distinct quantitative epidermal phenotypes exhibited by the synthetic alleles. For MUTEv5, we chose line #2 with a moderate clustered stomata phenotype, and line #5 that showed a severe phenotype of arrested lineages. As a representative of the MUTEPPP lines, line #3 was chosen.  As a control, MUTE line #1 was used. RNA-seq data were obtained from three independent biological replicates, each consisting of 50 seedlings collected at 2 days post-germination.
Comparative gene expresión profiling análisis of RNA-seq data for lines MUTE#1, MUTEv5#2, MUTEv5#5 and MUTEPPP#3.

first: Jonatan

last: Illescas-Miranda

first: Carmen

last: Fenoll


title: Characterization of genome-modified Caenorhabditis elegans expressing the human cytochrome P450 (CYP1A1 and CYP1A2) pathway

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

institute: King's College London

summary: Polycyclic aromatic hydrocarbons (PAHs), such as benzo[a]pyrene (BaP), are produced by the incomplete combustion of organic matter and thus are present in tobacco smoke, charbroiled food and diesel exhaust. The nematode Caenorhabditis elegans lacks the genetic components of the classical mammalian cytochrome P450 (CYP)-mediated BaP-diol-epoxide metabolism pathway thus CYP1A1 or CYP1A2 together with human epoxide hydrolase (EPHX) was introduced into the worm genome, thereby allowing to study potential physiological, genomic and transcriptional changes after BaP exposure in these CYP-humanised C. elegans strains. Strain and exposure specific changes in the transcriptome were identified by means of RNAseq.  thereby demonstrating the amenity of introducing human genes into the C. elegans genome and their utility to serve as a model for environmental carcinogenesis and pharmacological research.

overall_design: RNA sequencing (RNASeq) was carried out via the Illumina NovaSeq platform to define the transcriptomic fingerprints in C.elegans exposed to no, a low (40 µM) or high (640 µM) concentrations of benzo[a]pyrene from synchronized L1 stage to L4 stage. Three strains were used and the transcriptomic responses compared, namely a background strain, or strains that were genome-modified to express either the human CYP1A1 and EPHX or CYP1A2 and EPHX .

first: Yuzhi

last: Chen

first: Volker

middle: M

last: Arlt


title: High Dimensional Analysis of Sputum Cell Transcriptomes Identifies novel pathways associated with Clinical Phenotypes of Asthma

city: New Haven

first: Xiting

last: Yan

state: Connecticut

address: 300 Cedar Street, Ste S441D

department: Internal Medicine

institute: Yale School of Medicine

summary:
Background: Asthma is a chronic inflammatory disease of the airways driven by interactions among structural cells of the airway, the immune system, and the environment. Characterization of cells isolated from the sputum has been used to study the pathogenesis of asthma and optimize treatment regimens, but the cellular transcriptomes and intercellular communication changes in the sputum of asthma are not well understood.
Methods: Single cell RNA sequencing was applied to cells isolated from the sputum from 16 patients with asthma and 8 non-asthmatic normal controls.  Cell identity was determined by analysis of curated cell marker genes combined with SingleR annotation. Cell specific gene expression and communication networks were compared between asthma and controls and were correlated with asthma phenotypes.
Findings: 15 different cell populations were identified, including several types of macrophages, monocytes, dendritic cells, and lymphocytes as well as several rare (<2%) cell types such as mast cells, innate lymphoid cells, and bronchial epithelial cells. Analysis of the intercellular communications demonstrated that signaling pathways are generally more active in asthma compared to control.  CD4+ cells and dendritic cells had the largest increase in outgoing signals to other cell types. One of the strongest signal was the ADAM12 and CCL22 ligand-receptor pathways showing the strongest shift between asthma and controls.
Interpretation: Analysis of cellular transcriptomes in the sputum demonstrates innate and adaptive mechanisms are increased in asthma. Increased expression of ADAM12 suggests a critical role in the pathogenesis of asthma.

overall_design: Cells from sputum samples of asthma patients and normal controls were isolated and analyzed using the 10x Genomics Chromium 3' single-cell RNA sequencing kit.

first: Geoffrey

last: Chupp

first: Qing

last: Liu


title: Epigenetic modulation elicits an NK cell-mediated immune response in urothelial carcinoma

city: chiayi

first: Michael

middle: W Y

last: Chan

state: chiayi

address: No. 168, Section 1, Daxue Road, Minxiong Township

department: Dept of Biomedical sciences

country: Taiwan

institute: National Chung Cheng University

summary: Urothelial carcinoma of the bladder, the second most prevalent cancer within the urothelial system, often evades immune recognition by natural killer (NK) cells, but studies have shown that cyproheptadine (CPH), an anti-histamine drug, exhibits anticancer effects in this carcinoma. Co-culturing CPH-treated cells with NKG2D-expressing NK92 cells resulted in enhanced NK-mediated lysis of UC cells, with RNA-seq analysis revealing increased expression of the NKG2D ligand ULBP2 in CPH-treated cells. We hypothesize that cyproheptadine as a epigenetic modifier enhances NK-mediated cytotoxicity by restoring NKG2D ligands and CCL3 and as a control we used entinostat a known FDA approved HDAC1/3 inhibitor. Targeting NK cells offers a promising strategy against urothelial carcinoma. Further analysis showed epigenetic regulation of ULBP2 expression with increased H3K27Ac active mark enrichment in CPH-treated cells. Overexpression of ULBP2 led to increased NK-mediated lysis, while knockdown reduced it in CPH-treated urothelial carcinoma cells. Additionally, CPH treatment enhanced the anti-tumor effect in a mouse model, likely due to increased NK and NKT cell infiltration. In summary, CPH triggers an innate immune response against urothelial carcinoma by promoting NK cell-mediated cytotoxicity through ULBP2 and CCL3 restoration.

overall_design: To investigate differentially expressed genes after cyproheptadine treatment. We treated MB49 cells with cyproheptadine for 48hrs and extracted RNA using RNA extraction kit (Rneasy mini kit: cat no.74104 and 74106). Then extracted RNA was sequenced using sequenced on an Illumina NovaSeq 6000 platform

middle: W

first: Himani

last: Kumari


title: YY1 stabilizes super enhancer-promoter loops and gene expression during mesenchymal stem cell aging (ChIP-Seq)

city: Qingdao

first: Luyang

last: Sun

address: 189 Songling Road

institute: QIBEBT

summary: Stem cell aging leads to a progressive functional decline in self-renewal and differentiation capacity. How chromatin architecture impacts the gene expression changes that underlie altered stem cell function remains to be fully understood. Here, by integrative analyses of transcriptomic, epigenomic and Hi-C data in young and old in vitro aged human mesenchymal stem cells (MSCs), we identified super enhancer (SE)-promoter pairs and delineated changes in these loops during aging. SE target genes are associated with GO categories involved in key MSC functions and are enriched among genes with altered expression during aging, suggesting that changes in SE activity contribute to the functional decline of aged MSCs. YY1 is highly enriched at promoters and SEs and is lost from these regions in old cells. Loss of YY1 from SE-promoter loops correlates with reduced Hi-C contacts, and YY1 knockdown in young cells recapitulates age-associated transcriptomic changes, particularly among SE target genes. Our analyses provide novel insights into the role of altered chromatin loops in stem cell aging and highlight the function of YY1 in maintaining super enhancer-promoter loops and promoting gene expression stability during this process.

overall_design: YY1 and CTCF ChIP-seq of young and old ucMSCs

first: Brenna

middle: S

last: McCauley

first: Haiyang

first: Weiwei

last: Dang


title: YY1 stabilizes super enhancer-promoter loops and gene expression during mesenchymal stem cell aging (RNA-Seq)

overall_design: RNA-seq analysis between YY1 KD and control ucMSCs.


title: YY1 stabilizes super enhancer-promoter loops and gene expression during mesenchymal stem cell aging (Hi-C)

overall_design: HiC analysis between young and old MSC.


title: YY1 stabilizes super enhancer-promoter loops and gene expression during mesenchymal stem cell aging

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

overall_design: Refer to individual Series


title: Mutational signatures of genome-modified Caenorhabditis elegans expressing the human cytochrome P450 (CYP1A1 and CYP1A2) pathway

type: Genome variation profiling by high throughput sequencing

summary: Polycyclic aromatic hydrocarbons (PAHs), such as benzo[a]pyrene (BaP), are produced by the incomplete combustion of organic matter and thus are present in tobacco smoke, charbroiled food and diesel exhaust. The nematode Caenorhabditis elegans lacks the genetic components of the classical mammalian cytochrome P450 (CYP)-mediated BaP-diol-epoxide metabolism pathway thus CYP1A1 or CYP1A2 together with human epoxide hydrolase (EPHX) was introduced into the worm genome, thereby allowing to study potential physiological, genomic and transcriptional changes after BaP exposure in these CYP-humanised C. elegans strains. Whole genome sequencing revealed a higher frequency of T>G base substitution mutations in worms expressing human CYP1A1;EPHX thereby demonstrating the amenity of introducing human genes into the C. elegans genome and their utility to serve as a model for environmental carcinogenesis and pharmacological research.

overall_design: Whole genome sequencing was carried out via the Illumina NovaSeq platform to detect SNPs, InDels, SVs and CNVs  in C.elegans exposed to no, a low (40 µM) or high (640 µM) concentrations of benzo[a]pyrene from synchronized L1 stage to L4 stage. Three strains were used , namely a background strain, or strains that were genome-modified to express either the human CYP1A1 and EPHX or CYP1A2 and EPHX .