title: Reconstitution of the uterine immune milieu after transplantation (scRNA-seq)

city: Huddinge

first: Dan

last: Sun

address: Alfred Nobels allé 8

department: MedH

country: Sweden

institute: Karolinska Institutet

summary: Maintenance of tissue-specific immunity is important for immunological fitness, but its establishment have been difficult to assess in humans. Here, we investigated reconstitution of the human uterine immune system by studying women undergoing uterus solid organ transplantation (UTx) or hematopoietic stem cell transplantation (HSCT). Through single-cell identification based on SNPs and disparate HLA expression using single-cell RNA sequencing or high-parameter flow cytometry, donor vs recipient cell origin was determined, and features of these cells were studied. Endometrial immune cell reconstitution occurred after both UTx and HSCT, at the transcriptomic, phenotypic, and spatial level. This occurred despite tacrolimus-induced calcineurin-mediated NFAT pathway inhibition, which affected de novo induction of tissue-residency features in vitro. Intriguingly, after HSCT, immune cells of male origin could reconstitute the endometrium. Collectively, our results proved insights into tissue immune system persistence and reconstitution capabilities in an organ undergoing continuous regeneration.

overall_design: Samples from in total three UTX and two HSCT patients were subjected to single-cell RNA sequencing (scRNAseq, via 10x Genomics platform according to manufacturer’s protocol). For the first UTX sample, we performed a targeted fluorescence-activated cell sorting (FACS) to obtain distinct leukocyte subsets from either recipient (B cells) or donor peripheral blood (monocytes), as well as T and NK cells from recipient tissue. Cells were then combined for scRNAseq. The other UTX and HSCT samples were sorted as alive CD45+ mononuclear cells from either tissue or peripheral blood before being subjected to scRNAseq.

first: Benedikt

last: Strunz

first: Martin

middle: A

last: Ivarsson

first: Corinna

last: Mayer

first: Christoph

last: Ziegenhain

first: Ylva

last: Crona-Guterstam

last: Solders

first: Johan

last: Mölne

first: Andreas

last: Björklund

first: Nicole

last: Marquardt

first: Helen

last: Kaipe

first: Angelique

last: Flöter-Rådestad

first: Sebastian

last: Gidlöf

first: Mats

last: Brännström

first: Niklas

middle: K

last: Björkström


title: CRISPR-RfxCas13d screening uncovers Bckdk as a post-translational regulator of the maternal-to-zygotic transition in teleosts [RNA ppp4r2a_phf10]

status: Public on Aug 22 2025

city: Kansas City

first: Ariel

middle: Alejandro

last: Bazzini

state: Missouri

country: USA

institute: Stowers Institute for Medical Research

type: Expression profiling by high throughput sequencing

summary: The Maternal-to-Zygotic transition (MZT) is a reprograming process encompassing zygotic genome activation (ZGA) and the clearance of maternally-provided mRNAs. While some factors regulating MZT have been identified, there are thousands of maternal RNAs whose function has not been ascribed yet. Here, we have performed a proof-of-principle CRISPR-RfxCas13d maternal screening targeting mRNAs encoding protein kinases and phosphatases in zebrafish and identified Bckdk as a novel post-translational regulator of MZT. Bckdk mRNA knockdown caused epiboly defects, ZGA deregulation, H3K27ac reduction and a partial impairment of miR-430 processing. Phospho-proteomic analysis revealed that Phf10 (Baf45a), a chromatin remodeling factor, is less phosphorylated upon Bckdk depletion. Further, phf10 mRNA knockdown also altered ZGA and Phf10 constitutively phosphorylated rescued the developmental defects after bckdk mRNA depletion. Altogether, our results demonstrate the competence of CRISPR-RfxCas13d screenings to uncover new regulators of early vertebrate development and shed light on the post-translational control of MZT mediated by protein phosphorylation.

overall_design: Transcriptomic analysis of the mRNA knockdown of phf10 and ppp4r2a compared to control embryos injected only with RfxCas13d at 4hpf


title: CRISPR-RfxCas13d screening uncovers Bckdk as a post-translational regulator of the maternal-to-zygotic transition in teleosts [RNA Medaka]

overall_design: Transcriptomic analysis of the mRNA knockdown of BCKDK in Medaka embyros compared to embryos injected only with RfxCas13d protein


title: Transcriptional profiling of  colon cancer tumors in mice with Trim21 gene Knock out

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: NO. 199 Renai Road

country: China

institute: Soochow University

summary: To investigate the biological function Trim21 in the colon cancer, we compared the gene expression profiles of colon tumor tissues from Trim21 +/+ and Trim21 -/- mice treated with the carcinogen azoxymethane (AOM) and the proinflammatory agent dextran sulfate sodium (DSS).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for colon tumor tissues from AOM/DSS-treated Trim21 +/+ and Trim21 -/- mice.

first: Hua

last: Wu


title: Loss of Nuclear Receptor Nr4a3 Alleviates Cellular Senescence to Promote Adult Direct Cardiac Reprogramming (ATAC-Seq)

city: wuhan

first: ZHANGYI

middle: ZHANGYI

last: YU

state: hubei

address: donghu street

department: Frontier Science Center for Immunology and Metabolism

institute: wuhan university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Direct cardiac reprogramming of fibroblast to cardiomyocytes represents a potential means of restoring cardiac function following injury.   However, aged and adult fibroblast are less efficient for reprogramming compared with neonatal fibroblast. In this study, through the joint analysis of RNAseq and ATACseq, we found that compared with Neo-iCM, cardiac related features were down-regulated with aging, while fibrosis and SASP related genes were significantly up-regulated with aging. Single-cell transcriptomics reveals a bifurcated trajectory of aged iCM reprogramming. Then, we screened 51 transcriptomic and epigenomic regulators of the barriers to aged-iCM reprogramming and found that Nuclear receptor subfamily 4 group A member 3 (Nr4a3), an pro-inflammatory transcription factor, induced cellular senescence to inhibit direct reprogramming during aging. Mechanistically, knockdown of Nr4a3 enhanced direct cardiac reprogramming by promoting cardiac gene programs and inhibiting fibrosis pathway and secretes SASP. In addition, knockdown of Nr4a3 promoted human reprogramming in primary ventricular human cardiac fibroblasts (HCFs) and improved heart function after MI.

overall_design:
To comprehensively decipher why iCM reprogramming is dramatically hindered in adult and aged CFs, we investigated the global epigenetic changes of iCMs from neonatal to advanced age.
To determine the molecular basis by which knockdown Nr4a3 enhances iCM reprogramming, we conducted ATAC-seq using shNr4a3-iCMs and shNT-iCMs collected at reprogramming day 7.

first: Li

last: Wang

first: Mengxin

last: Liu

first: Zhangyi

last: Yu


title: Effect of metformin in the mouse ileum gene expression

city: seoul

first: jungho

last: nam

address: 50-1, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

country: South Korea

institute: yonsei univ

summary: Metformin is first line treatment for type 2 diabetes, however its exact mechanisms remain incompletely understood. Furthermore, the role of glucose transporter in intestine are highlighted to investigate metabolic change. We here report RNA change after metformin treatment in ileum tissue. We are going to focus on change of glucose transporter and relate factor of those changes. In previous study metformin increases expression of GLUT1/GLUT2 in ileum and metformin plays role as complex1 inhibitor so we are going to find target of metformin-induced glucose metabolic increasment

overall_design: To investigate metformin-induced changes in ileum, we prepare 2 group that orally gaveaged vehicle or metformin 300mg/kg daily/6days after 6days we gave 600mg/kg orally treatment lastly before sacrifice. 2hours after last treatment gavaged mouse sacrificed and ileum tissue collected. Each group has 3 animals and total RNA has extracted by each tissue.

first: JungHo

last: Nam

first: ChanWoo

last: Kang

first: JuHun

last: Oh

first: EunKyung

first: Soo hyun

last: Lee

first: Cheol Ryong

last: Ku


title: RNA-seq analysis of differentially expressed genes between WT and shTRIM21 RKO cells.

summary: To investigate the biological function TRIM21 in the colorectal cancer, we established RKO cell lines in which the TRIM21 gene has been knocked down by shRNA. We used a lentiviral shRNA technique to knockdown TRIM21 expression in RKO cells. A scrambled shRNA (shRNA/Control) was used as a control. We then performed RNA-Seq with Cloud-seq Biotech Inc. (Shanghai, China) to analyze gene expression changes in RKO cells. For each sample, three independent biological replicates were performed.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for RKO cells and its KD derivatives (shTRIM21).


title: FXR1 dominates mRNA export fate via riboregulation during hESC differentiation

city: Beijing

first: Zhongyang

last: Chen

address: No.5, Dongdan Santiao, Dongcheng District

institute: School of Basic Medicine, Peking Union Medical College (PUMC)

summary: mRNA export is required for its translation into functional protein, facilitated by the interaction between mRNA transporters and nuclear pore complex (NPC). However, only a few mRNA transporters associated with NPC were identified. Here, we comprehensively depicted NPC interactome in human embryonic stem cells (hESCs), from which we identified a series of novel mRNA transporters. Among them, FXR1 functioned as a cytoplasmic mRNA acceptor, promoted the release of G-quadruplex containing mRNA from its export receptor, simultaneously mediated the localization of nucleoporins mRNA on nuclear pore. FXR1 bound G-quadruplex or nucleoporin AGAA RNA via its RGG and KH domain respectively, which in turn weakened or enhanced its binding to nuclear pore, thus resulted in mRNA release or localization. More importantly, the decline of FXR1 and nuclear pore activity helped hESCs to achieve fate transition by impeding the nuclear export of transcribed RNAs, which was required for hESC differentiation.

overall_design: RNA-seq and eCLIP-seq datasets.

first: Jiabin

first: Yanni

last: Ma

first: Jia


title: RNA-seq in MaV208 WT and mutant Saccharomyces cerevisiae yeast strains treated with DMSO, TSA, or E6R

city: New Orleans

first: Tina

middle: M

last: O'Grady

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

summary: As part of a larger study identifying novel HDAC complex inhibitors, WT cells were treated with DMSO, 20 μM TSA or 50 μM E6R to investigate changes in gene expression levels. Also, cultures of rpd3Δ and sin3Δ mutant strains treated with DMSO were investigated.

overall_design: Saccharomyces cerevisiae WT MaV208 cells were treated in triplicate (three biologically independent samples per group) with DMSO, 20 μM TSA or 50 μM E6R, then RNA was harvested and sequenced. Also, RNA was harvested from Saccharomyces cerevisiae sin3Δ and rpd3Δ mutant strains treated with DMSO (three biologically indpendent samples per group) and RNA-seq was performed.

first: Julien

last: Olivet

first: SoonGang

last: Choi

first: Tong

last: Hao

first: David

middle: E

last: Hill

first: Franck

last: Dequiedt

first: Jean-Claude

last: Twizere

first: Marc

last: Vidal


title: Loss of Nuclear Receptor Nr4a3 Alleviates Cellular Senescence to Promote Adult Direct Cardiac Reprogramming

first: ZHANGYI

last: YU

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

overall_design: Refer to individual Series


title: ChIP-Seq in Saccaromyces cerevisiae via Sin3-(3xHA)

summary: As part of a larger study involving novel HDAC complex inhibitors, cultures were treated with 0.6% DMSO, 400 μM TSA, or 400 μM E6, then ChIP-Seq was performed via Sin3-(3xHA)

overall_design: Cultures of sin3∆ S. cerevisiae cells expressing a Sin3-(3xHA) protein were treated with DMSO, TSA or E6. ChIP-sequencing was performed with an established ChIP-grade anti-HA antibody. Two biologically independent replicates (independent pull-downs) were collected for each treatment.


title: Unbiased identification of nanoparticle cell uptake mechanism via a genome-wide CRISPR/Cas9 knockout screen

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: A major bottleneck in nanocarrier and macromolecule development for therapeutic delivery is our limited understanding of the processes involved in their uptake into target cells. This includes their active interactions with membrane transporters that co-ordinate cellular uptake and processing. Current strategies to elucidate the mechanism of uptake, such as painstaking manipulation of individual effectors with pharmacological inhibitors or specific genetic knockdowns, are limited in scope and biased towards previously studied pathways or the intuition of the investigators. Furthermore, each of these approaches present significant off-target effects, clouding the outcomes. We set out to demonstrate that an unbiased whole-genome screening approach using pooled CRISPR/Cas9 libraries can provide a robust and rapid approach to identify novel effectors of material uptake. We develop a methodology termed fast-library of inserts (FLI)-seq for library preparation and quantitative readout of pooled screens that shows improved technical reproducibility and is easier to perform than existing methods. In this proof-of-concept study we use this approach FLI-seq to identify a solute carrier protein family member SLC18B1 as a candidate transporter for polymeric micelles.

overall_design: Data includes a benchmarking experiment (containing 22 total samples, including infection replicate 1 (with 12x, 25x, 35x, 50x, 70x, 100x, and 200x cell coverage samples each with technical replicates A and B) and infection replicate 2 (with 12x, 17x, 25x, 35x, 50x, 70x, 100x, and 200x cell coverage samples), and a micelle uptake screen (with two infection replicates)

first: Eric

middle: L

last: Van Nostrand

first: Sarah

last: Barnhill

first: Alexander

last: Shishkin

last: Nelles

last: Byeon

first: Thai

last: Nguyen

first: Yiu-Chueng

last: Wong

first: Nathan

middle: C

last: Gianneschi

middle: W


title: Infants with perinatal HIV from the TARA cohort, pre-ART

status: Public on Aug 21 2025

city: Miami

first: Akshay

last: Iyer

state: FL

institute: University of Miami

summary: This study investigated immune correlates of viral control in infants with perinatally acquired HIV prior to initiation of antiretroviral therapy (ART). Peripheral blood mononuclear cells (PBMC) were collected at a pre-ART time point and analyzed by single-cell RNA sequencing to profile immune cell composition and transcriptional states. Infants were stratified into high and low viral load groups based on plasma HIV RNA levels at the time of sampling. Transcriptomic profiles were compared between groups to identify cell types, gene expression programs, and immune pathways associated with lower viral load, with the goal of defining candidate immune mechanisms that may contribute to spontaneous control of HIV replication in early life.

overall_design: Investigate gene expression (GEX), protein expression (FB/ADT), and T-cell/B-cell clonality in PBMC from infants that aquired HIV perinatally  at 1-2 month old prior to starting ART.

first: Lesley

last: De Armas

first: Savita

last: Pahwa


title: Transcriptomic Profiling of Immune Cell-Enriched Regions in Triple-Negative Breast Cancer Using Targeted RNA Sequencing

city: Bangkok

first: Suparada

last: Khanaruksombat

address: 2 Wanglang

department: Immunology

country: Thailand

institute: Faculty of Medicine Siriraj Hospital, Mahidol University

summary: Triple-negative breast cancer (TNBC), characterized by the lack of hormone receptors and HER2 expression, remains a challenging subtype due to the absence of effective targeted therapies. Tumor budding (TB), a histopathological feature reflecting invasive potential, has recently emerged as a valuable prognostic marker across various cancers, including TNBC. Identifying transcriptomic alterations associated with high TB is critical for understanding mechanisms of tumor progression and immune evasion. In this study, we employed TempO-Seq, a high-throughput targeted RNA sequencing technology, to profile gene expression in immune cell-enriched regions of breast cancer tissues. Our objective was to uncover immune-related biomarkers and gene signatures specific to high TB cases, with the ultimate goal of informing prognostic stratification and potential therapeutic targets in aggressive breast cancer subtypes.

overall_design: This study analyzed transcriptomic profiles from 15 formalin-fixed, paraffin-embedded (FFPE) breast cancer tumor specimens, including 13 triple-negative breast cancer (TNBC) cases, one HER2-positive case, and one luminal subtype. Tumor budding (TB) status was assessed histologically and used as a stratification variable. Among all samples, 12 exhibited high TB and 3 showed low TB features. Specifically, within the TNBC subset, 11 samples were categorized as high TB and 2 as low TB. Spatially distinct immune cell–enriched tumor regions were microdissected for targeted RNA sequencing using the TempO-Seq platform, enabling focused evaluation of immune-related gene expression signatures in relation to TB status.

first: Simran

last: Venkatraman

first: Pranisa

last: Jamjuntra

first: Doonyapat

last: Sa-Nguanraksa

first: Somchai

last: Chutipongtanate

first: Malee

last: Warnnissorn

first: Peti

last: Thuwajit

first: Rutaiwan

last: Tohtong

first: Thuwajit

last: Chanitra


title: RNA-seq of bilateral frontal cortex tissues in mice treated with HDAC complex inhibitors

first: Tina

last: O'Grady

summary: As part of a larger study of novel HDAC complex inhibitors, wild-type and Hdac2 cKO (pyramidal neurons, frontal cortex) mice were treated with Vehicle or 50 mg/kg E6R and RNA expression in the bilateral frontal cortex was analyzed.

overall_design: Wild-type or Hdac2 cKO mice (n=5 or 6) were treated with Vehicle or 50 mg/kg E6R for 10 days. RNA was extracted from the bilateral front cortex and sequenced.

first: Julien

last: Olivet

first: Salvador

last: Sierra

first: Mario

last: de la Fuente Revenga

first: Mikhail

middle: G

last: Dozmorov

first: Tong

last: Hao

first: Franck

last: Dequiedt

first: Jean-Claude

last: Twizere

first: Marc

last: Vidal

first: Javier

last: González-Maeso


title: RNA-seq in human neuroblastoma SK-N-BE(2)-C cells treated with DMSO, TSA or E6R

summary: As part of a larger study identifying novel HDAC complex inhibitors, cells were treated with 0.8% DMSO, 1 μM TSA, or 25 μM E6R to investigate changes in gene expression levels.

overall_design: SK-N-BE(2)-C cells were treated in triplicate (three biologically independent samples per group) with 0.8% DMSO, 1 μM TSA, or 25 μM E6R, then RNA was harvested and sequenced

first: SoonGang

last: Choi

first: David

last: Hill


title: Smart-seq2 single-cell RNA sequencing of human pancreatic islets

first: Ping

last: Chen

department: Department of Laboratory Medicine

summary: Previous study (Segerstolpe Å et.al., Cell Metab . 2016) has revealed the single-cell landscape of human pancreatic islets from 10 human individuals. Here, we have performed Smart-seq2 scRNA-seq of additional 4 healthy and 6 T2D individuals.

overall_design: single-cell RNA-seq

first: Åsa

last: Segerstolpe

first: Pernilla

last: Eliasson

first: Rickard

last: Sandberg


title: E7386 enhances lenvatinib’s antitumor activity in preclinical models and human hepatocellular carcinoma.

city: Barcelona

first: Ana

last: Hernández de Sande

address: C/ del Rosselló, 153

country: Spain

institute: IDIBAPS

summary: To study the antitumor and antiangiogenic activity of combining E7386 (an oral protein-protein interaction inhibitor targeting CREB-binding protein (CBP)/β-catenin) with lenvatinib and explore a novel mechanism of action of E7386 that boosts antitumor response.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
We transcriptomically profiled four HCC cell lines treated with DMSO or E7386
We transcriptomically profiled HCCs obtained from genetically engineered mouse models overexpressing MYC-lucOS;CTNNB1 and treated with Vehicle, E7386, Lenvatinib or E7386+Lenvatinib

first: Agavni

last: Mesropian

first: Albert

last: Gris-Oliver

first: Ugne

last: Balaseviciute

first: Amaia

last: Lujambio

first: Josep M

last: Llovet


title: Single-nucleus RNA-seq of peripheral blood mononuclear cells from multiple sclerosis patients and healthy controls

city: Campinas

first: Natalia

last: Munhoz Alves

state: SP

address: Rua Engenheiro Humberto Soares Camargo, 08

country: Brazil

institute: University of Campinas (UNICAMP)

summary: Multiple sclerosis (MS) is a chronic immune-mediated disease of the central nervous system marked by neuroinflammation and demyelination. Emerging evidence suggests that circulating immune cells contribute to disease activity, heterogeneity of clinical course, and treatment response. Here we provide single-nucleus transcriptomes of peripheral blood mononuclear cells (PBMCs) from individuals with MS and healthy controls. The dataset enables cell-type–resolved interrogation of peripheral immune states associated with MS, including comparisons of cell-state frequencies and gene-expression programs between groups, exploration of inflammatory pathways and ligand–receptor interactions, and discovery of candidate biomarkers. This resource supports integrative analyses with external MS cohorts and facilitates hypothesis generation on mechanisms of immune dysregulation in MS.

overall_design: Whole blood was collected from patients diagnosed with multiple sclerosis and from healthy control donors. PBMCs were isolated by Ficoll density-gradient centrifugation. Nuclei were extracted from PBMCs (10x Genomics protocol CG000365) and loaded on a Chromium Next GEM controller for single-nucleus capture and library construction using the Single Cell 3′ v3.1 Dual Index kit. Libraries were sequenced on an Illumina instrument. Resulting data were processed to obtain per-cell (nucleus) UMI count matrices for downstream analyses and group comparisons (MS vs control).

first: Alessandro

last: dos Santos Farias

first: Marcelo

last: Mori

first: Tereza

last: Fontes Cal

last: Brunetti Silva

first: Breno

last: Bandoni Ferrari


title: Deciphering Host Stress Responses for Predictable Heterologous Gene Expression in E. coli

city: Kgs. Lyngby

first: Christoffer

last: Rode

address: Søltofts Plads, Building 220

country: Denmark

institute: Technical University of Denmark

summary: Predictable expression of heterologous genes remains a key challenge in biotechnology, largely due to cellular stresses imposed on the production host. Here, we systematically dissect stress responses across Escherichia coli strains expressing diverse proteins under varying promoters and translation efficiencies. Using independent component analysis on new and existing large transcriptomic datasets, we identify distinct responses to transcriptional and translational stresses: excessive heterologous mRNA triggers a cold shock response that controls mRNA stability (cspA-I, deaD), while protein production activates a heat shock response involving proteolysis and chaperone functions. We further identify a broad adaptation response, consistently co-activated with the heat shock response during protein production, that provides stationary phase regulation (rspAB) and osmoregulation (betABIT). Targeting these latter functions through strain and media modifications significantly increases eGFP production. Other host stress responses depend on the protein being expressed; for example, we find production of cysteine-rich proteins to uniquely activate functions regulating iron- and redox homeostasis and oxidative stress responses. This work demonstrates a holistic, systems-level view of cellular stresses to heterologous gene expression by considering transcriptional, translational, and product-specific contributions, paving the way toward predictable and optimized expression strategies.

overall_design: RNA-Seq profiling of Escherichia coli hosts containing expression plasmids for different heterologous genes and with variable ribosome binding site strengths.

first: Philip

last: Beulig

first: Mathias

last: Jönsson

first: Morten

middle: H

last: Nørholm

first: Leonie

middle: J

last: Jahn

first: Daniel

last: Zielinski

first: Bernhard

middle: O

last: Palsson

first: Emre

last: Özdemir

first: Lei

last: Yang


title: Engineered thoracic spinal cord organoids for transplantation after spinal cord injury

city: Shanghai

first: Yanjing

last: Zhu

address: No.727 Zhongshan Road

institute: Tongji University

summary: Human iPSC-derived thoracic spinal cord organoids were transplanted into spinal cord injury mice, and spinal cord tissue was collected after 7 weeks. The transplantation resulted in functional recovery and neural circuit remodeling in the injured mice.

overall_design: Human iPSC-derived thoracic spinal cord organoids (21 days) were transplanted into spinal cord injury mice, and spinal cord tissue for spatial transcriptomics (ST-Seq) was collected after 7 weeks. During the induction of spinal cord organoids from iPSCs, RNA was extracted from 3 or 4 biological replicates at 2 weeks, 3 weeks, and 8 weeks for RNA sequencing. Untreated iPSCs were also collected and subjected to RNA-seq.

first: Ruiqi

last: Huang

first: Liqun

last: Yu

first: Liming

last: Cheng

first: Rongrong


title: Frataxin deficiency drives cardiac dysfunction and transcriptional dysregulation in Friedreich ataxia iPSC model

city: Fitzroy

first: Jarmon

last: Lees

state: VIC

address: 9 Princes Street, Fitzroy, Victoria, Australia

country: Australia

institute: St Vincent's Institute Of Medical Research

summary: Friedreich ataxia (FRDA) is a progressive neuromuscular degenerative disorder caused by GAA repeat expansions in the FXN gene, leading to frataxin deficiency and multisystem pathology. Cardiomyopathy is the leading cause of mortality in FRDA patients. To investigate the cellular and molecular mechanisms underlying FRDA-associated cardiac dysfunction, we employed induced pluripotent stem cell (iPSC) lines derived from three FRDA patients, each paired with an isogenic control line generated through CRISPR/Cas9-mediated excision of the pathogenic GAA repeat expansion. Correction of the mutation restored FXN expression to levels comparable to healthy donor iPSCs, and all lines differentiated efficiently into cardiomyocytes. Functional analysis revealed significant contractile abnormalities in FRDA cardiomyocytes and multicellular cardiac microtissues, including prolonged contraction and relaxation times and faster beating rates, consistent with clinical observations of cardiac contractile dysfunction. FRDA cardiomyocytes also exhibited pathological features such as increased cell size, irregular calcium transients, elevated mitochondrial reactive oxygen species levels, increased mitochondrial fission and increased cell death. These phenotypes were exacerbated by pathological levels of iron supplementation in culture media, highlighting the heightened sensitivity of frataxin-deficient cardiomyocytes to iron-induced metabolic stress. RNA sequencing revealed a distinct transcriptional profile associated with frataxin deficiency. MEG3 and PCDHGA10 were consistently dysregulated across all three FRDA-iPSC lines and may represent early molecular markers of FRDA cardiomyopathy. Together, these findings establish a robust human iPSC model of FRDA cardiomyopathy that captures early disease phenotypes and reveals novel molecular targets. This preclinical human model provides valuable insight into the pathogenesis of FRDA and provides a platform for developing early-stage therapeutic interventions.

overall_design: RNA-seq profiling of 3x Friedriech ataxia patients' cardiomyocytes and their isogenic corrected control cardiomyocytes differentiated from iPSCs.

first: Haoxiang

last: Zhang

first: Lebei

last: Jiao

first: Anne

last: Kong

first: Ren

last: Phang

first: Li

last: Li

last: Su

first: Anthony

middle: S

last: Mukhtar

first: Alice

last: Pébay

first: Mirella

last: Dottori

first: Louise

last: Corben

first: Martin

last: Delatycki

first: Roger

last: Peverill

first: Stephen

last: Wilcox

first: Jeffrey

last: Pullin

first: Jarny

last: Choi

first: Davis

last: McCarthy

first: Jill

last: Napierala

first: Marek

first: Shiang

middle: Y

last: Lim


title: Radiosensitizing effect of THBS1 knockdown in radioresistant head and neck carcinoma cell lines

city: SEOUL

first: Minji

last: An

address: 52, Ewhayeodae-gil, Seodaemun-gu

institute: Ewha Womans University

summary: This study aimed to investigate the radiosensitizing effects of THBS1 knockdown in radioresistant head and neck squamous cell carcinoma (HNSCC) cell lines. Using siRNA-mediated silencing of THBS1 in CAL27 and Detroit 562 cells, we examined transcriptomic changes associated with enhanced sensitivity to proton beam irradiation. Bulk RNA-seq was performed to profile genome-wide expression patterns in control and THBS1-depleted cells, providing insights into gene expression programs linked to THBS1-mediated radioresistance and potential therapeutic targets.

overall_design: RNA-seq profiling of two radioresistant HNSCC cell lines, CAL27 and Detroit 562, and their siRNA-mediated THBS1 knockdown derivatives, with three biological replicates per group, totaling 12 samples.

first: Changhoon

first: Wankyu

last: Kim

first: Arang

last: Son


title: ChIP-seq of LNCaP cells for AR

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

summary: Chromatin immunoprecipiation is used to infer transcription factor activity. In this project, we performed ChIP-seq in LNCaP prostate cancer cells with antibodies against the androgen receptor to identify its binding sites under hormone-replete conditions.

overall_design: Chromatin was extracted from LNCaP prostate cancer cells and immunoprecipitated with antibodies against AR. DNA was sequenced to identify AR binding sites. Enriched DNA was normalized against input.

first: David

last: Takeda


title: STING induces ZBP1-mediated necroptosis independently of TNFR1 and FADD

city: Cologne

first: Gianmaria

last: Liccardi

address: Joseph Stelzmann strasse 52, Institute of Biochemistry

country: Germany

institute: Uniklinik, University of Cologne

summary: Conditional deletion of Caspase-8 in epidermal keratinocytes (Casp8E-KO) causes necroptosis-driven lethal dermatitis1-7. Here, we discover that Casp8 loss leads to accumulation of cytosolic DNA responsible for the activation of a cyclic-GMP-AMP synthase (cGAS)/stimulator of interferon (IFN) gene (STING)-mediated transcriptional program. Genetic and biochemical evidence indicate that STING upregulates both Z-DNA binding protein-1 (ZBP1), and mixed lineage kinase domain-like (MLKL). Combined Casp8-deficiency- and STING-activation-driven accumulation of Z-nuclei acids, activates ZBP1 and triggers formation of a ZBP1–RIPK1–RIPK3 complex independently of FADD-RIPK1-RIPK3 complex enabling necroptosis execution. Genetically, we reveal a functional overlap between STING and ZBP1 as drivers of lethal dermatitis independently of TNFR1, uncovering a novel aetiology of necroptotic inflammation. Since gain-of-function mutations in human STING cause STING-Associated Vasculopathy with onset in Infancy (SAVI), we assessed the role of STING-induced necroptosis in SAVI’s aetiology. Chronic activation of STING in patients orchestrates a necroptotic transcriptional program which is confirmed in the N153S-SAVI preclinical mouse model where immune cell–driven pathology and lethality are remarkably rescued by RIPK3 co-deletion. These findings establish STING-driven ZBP1-mediated necroptosis as a central pathogenic mechanism in both Casp8-deficient inflammation and SAVI and suggest that targeting the ZBP1-RIPK3-MLKL axis holds therapeutic potential for interferonopathies characterised by excessive necroptosis.

overall_design: Comparative gene expression from skin of p5 mice in Casp8E-KO , Casp8E-KO ;  Tnfr1-/- , Casp8E-KO ;  StingE-KO, Casp8E-KO ;  Sting-/-  , Casp8E-KO/wt. TP = Time point= P5.

first: Konstantinos

last: Kelepouras

first: Julia

last: Saggau

first: Debora

last: Bonasera

first: Christine

last: Kiefer

first: Federica

last: Locci

first: Hassan

last: Rakhsh-Khorshid

first: Louisa

last: Grauvogel

first: Ana

last: Abreu Varanda

last: Peifer

first: Elena

last: Loricchio

first: Antonella

last: Montinaro

first: Marijana

last: Croon

first: Aleksandra

last: Trifunovic

first: Giusi

last: Prencipe

last: Insalaco

first: Fabrizio

last: De Benedetti

first: Henning

last: Walczak


title: Macrophages orchestrate elimination of Shigella from the intestinal epithelial cell niche via TLR-induced IL-12 and IFN-γ

city: Berkeley

first: Kevin

middle: D

last: Eislmayr

state: California

address: 415 Weill Hall

institute: UC Berkeley

summary: Bacteria of the genus Shigella replicate in intestinal epithelial cells and cause shigellosis, a severe diarrheal disease that resolves spontaneously in most healthy individuals. During shigellosis, neutrophils are abundantly recruited to the gut, and have long been thought to be central to Shigella control and pathogenesis. However, how shigellosis resolves remains poorly understood due to the longstanding lack of a tractable and physiological animal model. Here, using our newly developed Nlrc4–/–Casp11–/– mouse model of shigellosis, we unexpectedly find no major role for neutrophils in limiting Shigella or in disease pathogenesis. Instead, we uncover an essential role for macrophages in the host control of Shigella. Macrophages respond to Shigella via TLRs to produce IL-12, which then induces IFN-γ, a cytokine that is essential to control Shigella replication in intestinal epithelial cells. Collectively, our findings reshape our understanding of the innate immune response to Shigella.

overall_design: RNA sequencing of bead-enriched EpCAM+ epithelial cells isolated from the colon and cecum of 6 mice 48h post-infection  with Shgiella and 5 non infected animals


title: N460S on PB2 and I163T on nucleoprotein synergistically enhance the replication and pathogenicity of influenza B virus

city: Guangzhou

first: yuting

last: Ye

address: Guangzhou Dongfengxi road

institute: Guangzhou Medical University

summary: Influenza B virus (IBV), though often overshadowed by influenza A viruses (IAVs), remains a significant global public health concern, particularly during seasons when it predominates. However, the molecular mechanisms underlying IBV pathogenicity remain largely unknown. In this study, we analyzed polymerase polymorphisms in an IBV isolated from a single patient’s oropharyngeal swab and identified two plaque colonies with distinct replication and pathogenicity phenotypes, associated with the PB2:N460S and NP:I163T substitutions. Using reverse genetics, we generated recombinant IBV mutants to evaluate the impact of these substitutions. The results showed that while neither mutation alone significantly affected viral replication or pathogenicity, their combination markedly enhanced both. Transcriptomic analysis of infected lung tissues revealed heightened immune activation, including upregulation of antiviral and immune-related genes, contributing to excessive inflammation and disease severity. Mechanistically, both substitutions increased protein expression and strengthened PB2-NP interaction, but only together did they enhance polymerase activity. Structural modeling suggested that PB2:460 is positioned at the PB2-NP interface, whereas NP:163 is not, indicating an indirect functional interplay. These findings provide new insights into the molecular determinants of IBV pathogenesis, highlighting the synergistic effect of PB2:N460S and NP:I163T in enhancing viral fitness and exacerbating disease outcomes.

overall_design: Mice lungs intranasally infected with the recombinant influenza B viruses rgPB2460N/NP163I or rgPB2460S/NP163T were harvested at 5 dpi for RNA sequencing. Control mice were inoculated with 50 μl of PBS only. Total RNA was extracted using the Tissue RNA Purification Kit PLUS (EZBioscience). RNA libraries for mRNA sequencing were prepared with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB), following the manufacturer's instructions.

first: Weiqi

last: Pan

first: Yu

last: Gao


title: Gene expression and chromatin accessibility profiles at the single-nucleus level of the antennae of Harpegnathos saltator

city: New York

first: Bogdan

last: Sieriebriennikov

state: NY

address: 100 Washington Sq E

institute: New York University

summary: We performed multiome sequencing of the antennae of Harpegnathos saltator to identify potential regulatory element controlling the expression of odorant receptor genes.

overall_design: Nuclei were isolated from dissociated antennae and subjected to 10X multiome sequencing.

first: Olena

last: Kolumba

first: Aurore

last: de Beaurepaire

first: Jennifer

last: Wu

first: Eva

last: Bardol

first: Valentina

last: Fambri

first: Yuwei

last: Zhong

first: Ildar

last: Gainetdinov

first: Danny

last: Reinberg

first: Hua

last: Yan

first: Claude

last: Desplan


title: Estrogen Receptor 1 Signaling in Hepatic Stellate Cells Designates Resistance to Liver Fibrosis [ChIP-seq]

city: Shenzhen

first: Haoyue

last: Zhang

address: Gaoke Innovation Center, Guangqiao Road, Guangming District, Shenzhen

institute: Shenzhen Bay Lab

summary: The prevalence and severity of liver fibrosis appear higher in men than in premenopausal women, while postmenopausal women exhibit the worsened disease. However, the pathophysiological mechanism underlying such clinical observations remains incompletely understood. Here, we show that sex hormone depletion in adult female mice exaggerates the model of liver fibrosis, while estradiol replacement in castrated male mice is sufficient to mitigate the disease severity. Transcriptomic analyses and immunohistochemistry then demonstrate that both human and mouse hepatic stellate cells (HSCs), the primary cell type responsible for extracellular fibrous depositions, predominantly express the estrogen receptor 1 (ESR1). Of importance, genetic deletion of ESR1 in mouse HSCs markedly promotes liver fibrosis. Moreover, chromatin immunoprecipitation followed by sequencing (ChIP-seq) and in vitro manipulations reveal that ESR1 can directly target the expression of fibrosis-related genes in HSCs. Together, this study has elucidated a critical aspect of ESR1 signaling in the sexual dimorphism of liver fibrosis.

overall_design: First, we selected female C57/B6J mice and simulated menopause through ovariectomy, combined with methionine-choline deficient (MCD) diet to induce a metabolic dysfunction-associated steatohepatitis (MASH) model. We then performed HE staining, Sirius Red staining, immunofluorescence staining, and histochemical analysis on liver tissues to evaluate the regulatory role of estrogen in liver fibrosis within the MASH model. Next, we established a hormone-deficient model in male mice via castration surgery to eliminate the effects of endogenous sex hormones on the experiment. We then implanted 17β-estradiol implants in combination with the choline-deficient, methionine-limited diet to further confirm that estrogen, rather than other substances secreted by the ovaries, influenced liver fibrosis. Subsequently, we identified the types of estrogen receptors expressed in hepatic stellate cells (HSCs) of both humans and mice through immunofluorescence staining and transcriptome sequencing. Building on this, we specifically knocked out the estrogen receptor alpha (ERα) gene in HSCs of female mice, induced MASH with MCD diet, and again conducted HE staining, Sirius Red staining, immunofluorescence staining, and histochemical analysis on liver tissues to determine whether estrogen directly influences the progression of liver fibrosis by regulating the expression of fibrosis-related factors in HSCs. Finally, we conducted in vitro 17-estradiol induction on HSCs to assess transcriptome changes and performed ChIP-seq analysis using estrogen receptor antibodies to establish the direct regulatory role of estrogen as a transcription factor on fibrosis-related genes in HSCs.

first: Jing

last: Yang

first: Tianhao

last: Li

first: Fuhai

last: Liu


title: Zika virus exploits autophagy for replication in human trabecular meshwork and autophagic inhibition at autolysomal maturation ameliorates Zika-induced ocular complications.

city: Columbia

first: Pallav

last: Singh

address: CE720 Clinical Support and Education

department: Institute for Data Science and Informatics

institute: University of Missouri

summary: Zika virus (ZIKV) infection causes severe ocular and neurological pathologies in infants following in-utero exposure. ZIKV is also the lone member of Flavivirus, which is known to cause congenital glaucoma. However, the cellular and molecular basis of congenital ZIKV ocular infection and glaucoma are not well understood. Autophagy has been shown to play dual roles in viral infection and glaucoma pathogenesis. However, how ZIKV interferes with autophagic pathways in the trabecular meshwork (TM) and whether autophagy contributes to ZIKV-induced ocular complications remains elusive. In this study, we investigated the role of autophagic pathways in ZIKV pathogenesis in the anterior segment (AS) of the eye utilizing a primary human trabecular meshwork (HTMC) and a IFNAR1-/- mouse model of ocular ZIKV infection. Our results from this study show that ZIKV permissively infects HTMC, induces a dysregulated immune response, and triggers autophagic activity in TM and mouse AS tissue. Our data suggest that although ZIKV initially activates autophagy in TM, it impairs the overall autophagic flux during the course of infection by modulating the VSP39-HOPS complex and STX17-SNARE complex to avoid autolysosomal maturation. We discovered that ZIKV utilizes late-endosomes/lysosomes for their replication and spread in TM. We further demonstrated that modulation of autophagy at the autolysosomal maturation stage with an FDA-approved drug, hydroxychloroquine, or Bafilomycin A1, inhibits ZIKV replication in TM and ameliorates ZIKV-induced ocular pathology in the mouse eyes.Our study is the first to demonstrate the mechanistic insight by which ZIKV manipulates autophagic activity in TM and ocular milieu, and we suggest that the precise modulation of autophagy could be a potential therapeutic avenue for developing new strategies to treat ZIKV-induced ocular complications.

overall_design: HTMC cells were either mock treted or Infected with Zika Virus in presence and absence of Hydroxychloroquine (HCQ) and Rapamycin (Rapa) and RNAseq was performed.

first: Pawan

first: Faraz

last: Ahmad

first: Trupti

last: Joshi


title: Telomere dysfunction in renal epithelial cells leads to kidney fibrosis

city: Madrid

first: Ruth

last: Álvarez-Díaz

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology

institute: Spanish National Cancer Research Center (CNIO)

summary: Renal tubular epithelial cells (TECs) are critical mediators of renal fibrogenesis. Telomere dysfunction has been associated with renal injury and fibrosis. However, the role of telomere dysfunction specifically in TECs in the onset and progression of renal fibrosis remains poorly understood. To investigate the impact of telomere dysfunction on renal injury and fibrosis, we generated mice depleted for the shelterin component TRF1 specifically in TECs. Genetic ablation of Trf1 caused decline in renal function, tubular injury and tubulointerstitial fibrosis eight weeks after TRF1 depletion, concomitant with excessive accumulation of extracellular matrix (ECM), cell cycle arrest at G2/M phase, and telomeric damage. Trf1Δ/Δ mice activated regenerative repair mechanism, increasing the risk of of chronic kidney disease (CKD) progression following acute kidney injury (AKI), supporting proliferation-mediated telomere shortening in tubular cells. Mechanistically, Trf1 deletion upregulated Ras–Raf–Mek–Erk, PI3k/Akt/mTOR and p38 pathways. At humane endpoint, Trf1Δ/Δ mice displayed elevated urinary albumin-to-creatinine ratio (uACR), associated with augmented interstitial fibrosis and tubular atrophy eventually leading to CKD. In folic acid (FA)-induced nephropathy, depletion of Trf1 in TECs mitigated the fibrogenic phenotype of CKD. Collectively, our study underlies the important role of TECs in the development and progression of renal fibrosis and CKD associated to dysfunctional telomeres.

overall_design: Tamoxifen (TMX) (Sigma Aldrich, T-5648-1G) was intraperitoneally (i.p.) injected to six-to eight-week-old male and female Trf1+/+ KFP+/t Cre+/t and Trf1lox/lox KFP+/t Cre+/t mice for three times a week for 8 weeks until the sacrifice.

first: Sarita

last: Saraswati

first: Osvaldo

last: Graña-Castro

first: María

last: Blasco


title: Reduced type I interferon response in plasmacytoid dendritic cells is associated with asthma in school-aged children

city: Nedlands

first: Jonatan

last: Leffler

state: WA

address: 15 Hospital Ave

institute: Telethon Kids Institute

summary: Allergic sensitisation and reduced ability to respond to viral infections may contribute to virus-induced wheeze and asthma development in young children. Plasmacytoid dendritic cells (pDC) are rare immune cells that produce type I interferons (IFN-I) and play a key role in orchestrating immune responses against viruses. To further evaluate the function of pDC in children with asthma, we studied a subset of 71 children from the Early Life Lung Function (ELLF) cohort at the age of 7-years. As part of the ELLF study, participants were characterised for atopic sensitisation, viral infection history and lung function testing. pDC responses to a TLR7/8 agonist were assessed in the presence or absence of anti-IgE using an in vitro assay. Responses were evaluated utilising flow cytometry, multiplexed cytokine assays and transcriptional analysis of isolated pDC. pDC responses varied considerably across individuals and those who responded with IFN-I following stimulation showed lower proportion of asthma compared to those who responded with TNF-only. A TNF-only response was associated with increased atopy and reduced upregulation of IFN-associated genes. Anti-IgE stimulation reduced pDC activation and the reduction was associated with baseline expression of the IgE receptor (FceR1). A reduction in a gene module centralised around genes such as TPM2, LILRA4 and CLEC4C was also observed. Together, these findings suggest that pDC responses are variable, associated with asthma and appear influenced by environmental stimuli. This response thus appears to be an important aspect of asthma pathology in children.

overall_design: RNASeq of isolated plasmacytoid dendritic cells (pDC). Peripheral blood mononuclear cells from 24 children (age 7 yrs) with or without asthma from the ELLF cohort were stimulated in vitro with R848 (TLR7/8 agonist) with or without pre-incubation of anti-IgE to induce IgE crosslinking. Following stimulation for 16h, pDC were stained and isolated for RNASeq using flow cytometry assisted cell sorting.

first: Isabelle

last: Coenen

first: Anya

last: Jones

first: Alice

middle: A

last: White

first: Mari

last: Takashima

first: Wen

last: Ray Lee

first: Matthew

last: Wong

first: Dwan

last: Vilcins

first: Ulrich

last: Kadolsky

first: Ali

last: Sadiq Cheema

first: Alka

last: Saxena

first: Anthony

last: Bosco

first: Keith

last: Grimwood

first: Peter

last: Sly

first: Deborah

last: Strickland


title: Pre-clinical proof-of-concept of anti-fibrotic activity of caveolin-1 scaffolding domain peptide LTI-03 in ex vivo precision cut lung slices from patients with Idiopathic Pulmonary Fibrosis

city: Los Angeles

first: Yago

last: Jannini-Sa

address: 8700 Beverly Blvd. AHSP Room A9401

department: Medicine / Lung Institute

institute: Cedars-Sinai Medical Center

summary: Human lung tissues from idiopathic pulmonary fibrosis (IPF) patients undergoing lung transplantation and non-IPF donors were obtained via the European IPF Registry (euIPFreg) sites Vienna and Giessen and delivered via the European IPF Biobank or the UGMLC Biobank, a member of the DZL platform biobanking. The study protocol was approved by the Ethics Committee of the Justus-Liebig University School of Medicine (No. 111/08: European IPF Registry and 58/15: UGMLC Giessen Biobank), and informed consent was obtained in written form from each subject (a comprehensive list of patient data and applied assays is provided in Table 2). Lung biopsy cores were obtained exclusively from 8 patients undergoing lung transplant for treatment of IPF and processed for PCLS culture as previously described18. All patients were male, an average of 61.5 years of age (std dev 6.56 years), and had a clinical diagnosis of IPF alone, or IPF with secondary pulmonary hypertension (PH). Usual interstitial pneumonia (UIP) was the main pathological finding on all explant tissue.

overall_design: LTI-03 was added in PCLS culture media at 0.3, 5.0, or 10 μM for treatments. The inactive control peptide CP at 10 μM while Nintedanib was prepared in a 1 mM stock solution with sterile filtered DMSO and used at 1 μM. PCLS were treated every 12hrs and supernatant and tissue was harvested 12 hours following the last of either three (day 2) or nine treatments (day 5).

first: BreAnne

last: MacKenzie

first: Poornima

last: Mahavadi

first: Brecht

last: Creyns

first: Ana Lucia

last: Coelho

first: Milena

last: Espindola

first: Clemens

last: Ruppert

first: Brian

last: Windsor

last: Aigner

first: Cory

last: Hogaboam

first: Andreas

last: Guenther


title: The toxicity and mechanisms of pyrotinib on male reproductive system

city: Zhenjiang

first: Jie

last: Yang

address: 301 Xuefu Road

institute: Jiangsu University

summary: While Pyrotinib has proven effective in treating HER2-positive breast cancer, its impact on male patients is not well-studied. This research examines the potential toxicity of Pyrotinib on the male reproductive system using mouse Leydig cells. Our results indicate that 24 hours of Pyrotinib treatment significantly increased apoptosis and decreased cell viability. Clonogenic assays showed a marked reduction in colony formation, and flow cytometry analysis revealed that 67.2% of the treated cells were in the G1 phase, suggesting hindered progression into the S phase. Western blot analysis demonstrated an initial rise in phosphorylated AKT and ERK, which was followed by a notable decline in these phosphorylated proteins after extended treatment, indicating the involvement of specific pathways in the drug's effects. Transcriptome sequencing identified a downregulation of 197 genes due to Pyrotinib treatment, with these genes enriched in processes related to chromatin and mitosis, particularly in pathways linked to the cell cycle. These findings imply that Pyrotinib inhibits cell proliferation through various molecular mechanisms, underscoring the necessity for further research into its safety and effects on male reproductive health.

overall_design: TM3 cells in the logarithmic growth phase were dissociated and counted, then seeded into 6-well plates at a density of 500,000 cells per well. The treatment group received 100 nM Pyrotinib, while the control group was treated with 0.1‰ DMSO, with three replicates for each group. After 48 hours of treatment, RNA was extracted using TRIzol reagent (Santa) and sent to Beijing Novogene Co., Ltd. for transcriptome sequencing.

first: Xiao

last: Hu

first: Zhongjian

last: Pan

first: Peng

last: Zheng

first: Jian

last: Tan

first: Zhipeng

last: Xu

first: Huaming

last: Tang

first: Jianpeng


title: Astrocyte-enriched murine cortical and white matter transcriptional profiles after stroke in spatially-defined zones of post-stroke reactivity

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary:
Zones of reactive astrocytes after stroke were defined in both white matter and cortical stroke models using a combination of phenotyping and morphology. These zones were then excised via laser capture microscopy in mGFAP-77.6-Cre/Ribotag mice and astrocytic ribosomes were immunopreciptated to generate astrocyte-enriched zone-specific transcriptomic profiles.
RNA extracted from cleared lysate (input) was used to assess astrocytic enrichment in white matter and cortex in both the uninjured brain and in the combined first three zones of reactivity after stroke, comparing expression profiles to matched immunoprecipitated ribosome-associated RNA.

overall_design: Enrichment cohorts: uninjured white matter and uninjured cortex, both cleared lysate (input) RNA and ribosomally-associated immunoprecipitated RNA (IP), 5 per group. Post-stroke zones 1-3 white matter and cortex, both cleared lysate (input) RNA and ribosomally-associated immunoprecipitated RNA (IP), 3 per group. To assess enrichment, IP samples were compared to input from the same cohort. Astrocyte-enriched post-stroke samples: IP samples from each of 5 zones per stroke model and their respective uninjured control (also used in enrichment analyses); 4-5 samples per zone. To assess stroke-induced changes in gene expression, each post-stroke zone was compared to the uninjured samples from that brain region.

first: Amy

last: Gleichman

first: S

middle: T

last: Carmichael


title: Bisphenol AP promotes the development of bleomycin-induced pulmonary fibrosis by regulating macrophage function

first: Ze

last: Chen

state: -- Please Select --

address: 910 Hengshan Road

institute: International Peace Maternity and Child Health Hospital

summary: Bisphenol AP (BPAP), a structural analogue of bisphenol A (BPA), has been frequently detected in humans. The presence of BPAP is linked to various adverse health outcomes, including metabolic diseases and mood disorders. However, the effects by which BPAP contributes to lung diseases remain inadequately understood. This study utilized the mouse macrophage cell line RAW 264.7 and bleomycin induced pulmonary fibrosis model (PF) of C57BL/6 mice to explore the effects of BPAP. Functional experiments demonstrated that BPAP exposure inhibited macrophage proliferation and enhanced oxidative stress. Additionally, BPAP exposure enhanced the phagocytic and chemotactic functions of macrophages.

overall_design: To explore the molecular mechanisms underlying the effects of BPAP on macrophages, RNA-seq was conducted to identify the differentially expressed genes (DEGs) in response to BPAP exposure.

first: Jiuru

last: Zhao

first: Zhiwei

last: Liu


title: Chromatin profiling of the Harpegnathos saltator antennae

first: Bogdan

last: Sieriebriennikov

summary: We have profiled the antennae of Harpegnathos saltator for H3K27ac, H3K27me3, and H3K4me3.

overall_design: We have isolated nuclei from the antennae of Harpegnathos saltator and performed CUT&RUN against H3K27ac, H3K27me3, H3K36me3 and H3K4me3.

first: Olena

last: Kolumba

first: Aurore

last: de Beaurepaire

first: Jennifer

last: Wu

first: Eva

last: Bardol

first: Valentina

last: Fambri

first: Yuwei

last: Zhong

first: Ildar

last: Gainetdinov

first: Danny

last: Reinberg

first: Hua

last: Yan

first: Claude

last: Desplan


title: Functional investigations of p53 acetylation enabled by heterobifunctional molecules

city: LA JOLLA

first: Christopher

last: Parker

address: 10550 North Torrey Pines Road SR311E

institute: Scripps Research

summary: Post-translational modifications (PTMs) dynamically regulate the critical stress response and tumor suppressive functions of p53. Among these, acetylation events mediated by multiple acetyltransferases lead to differential target gene activation and subsequent cell fate. However, our understanding of these events is incomplete, due to, in part, the inability to selectively and dynamically control p53 acetylation. We recently developed a heterobifunctional small molecule system, AceTAG, to direct the acetyltransferase p300/CBP for targeted protein acetylation in cells. Here, we expand AceTAG to leverage the acetyltransferase PCAF/GCN5 and apply these tools to investigate the functional consequences of targeted p53 acetylation in human cancer cells. We demonstrate that recruitment of p300/CBP or PCAF/GCN5 to p53 results in distinct acetylation events and differentiated transcriptional activities. Further, we show that chemically induced acetylation of multiple hotspot p53 mutants results in increased stabilization and enhancement of transcriptional activity. Collectively, these studies demonstrate the utility of AceTAG for functional investigations of protein acetylation.

overall_design: To investigate transcriptome changes induced by AceTAGp300/CBP-1 and AceTAGPCAF/GCN5-4.

first: Li

first: Soumya

last: Singha Roy

first: Appaso

last: Jadhav

first: Wesley

last: Wang

first: Pei

first: Timothy

last: Bishop

first: Michael

last: Erb


title: ZMYND11 Functions in Bimodal Regulation of Latent Genes and Brain-like Splicing to Safeguard Corticogenesis [RNA-seq]

city: Cincinnati

first: Jason

last: Tchieu

address: 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

summary: While the identification of pathogenic variants linked to neurodevelopmental (NDD) and autism spectrum disorders (ASD) has advanced rapidly, the mechanisms underlying these genetic risks remain unclear. Here, we leveraged a human pluripotent stem cell model to uncover the neurodevelopmental consequences of mutations in ZMYND11, a newly implicated risk gene. ZMYND11, known for its tumor suppressor function, encodes a histone-reader that recognizes sites of transcriptional elongation and acts as a co-repressor. Our findings reveal that ZMYND11 deficient cortical neural stem cells exhibit upregulation expression of latent developmental pathways, leading to impaired production of secondary neural progenitors and neurons. In addition to its chromatin-related functions, we found ZMYND11 orchestrates a brain specific isoform switch that affects migration and proliferation of cortical neural stem cells. We further demonstrated that brain specificity is likely to involve the activity of the splicing regulator RBFOX2. Finally, we extended our findings to 10 additional lines with different chromatin-related NDD/ASD risk factors and identified a subset displaying similar activation of developmental pathways and splicing dysregulation, which could partially be rescued by leveraging the transcriptional repression and splicing coordination of ZMYND11. Collectively, our work highlights the critical role of ZMYND11 in regulating developmental signals and alternative splicing, offering novel insights into the molecular pathology of ZMYND11-associated NDDs. Moreover, these findings suggest broader convergence with other genetic risk factors for NDD/ASD, presenting potential therapeutic avenues for intervention.

overall_design: To investigate the role of ZMYND11 in corticogenesis, we performed RNA-seq on WT and ZMYND11 mutant human embryonic stem cells and d18 cortical neural stem cells, WT d18 cortical neural stem cells that overexpressed FLAG-ZMYND11 or not for 3 days, and d18 cortical neural stem cells differentiated from a subset of Autistic mutants (termed "Class I") and isogenic controls (UMOD edited).

first: Xuyao

last: Chang


title: Activation of OSM-STAT3 Epigenetically Regulates Tumor-Promoting Transcriptional Programs in Cervical Cancer [ATAC-Seq]

status: Public on Aug 20 2025

city: Cheongju-si

first: Junho

last: Noh

state: Chungcheongbuk-do

address: 1, Chungdae-ro, Seowon-gu

department: Biological science and biotechnology

institute: Chungbuk National University

summary: Despite improvements in preventative strategies, such as regular screenings with Pap tests and human papillomavirus (HPV) tests as well as HPV vaccinations, effective treatment for advanced cervical cancer remains poor. Deregulation of STAT3 is an oncogenic factor that promotes tumorigenesis and epithelial-to-mesenchymal transition (EMT) in various cancers. Oncostatin M (OSM), a pleiotropic cytokine, induces STAT3 activation, exacerbating cervical cancer. However, the mechanism by which the OSM-STAT3 axis epigenetically regulates tumor-progression-related genes in cervical cancer is not well understood. Here, we show that OSM-mediated STAT3 activation promotes pro-tumorigenic gene expression programs, with chromatin remodeling in cervical cancer. Reanalysis of scRNA-seq data performed in cervical cancer uncovered an interaction between the oncostatin M receptor (OSMR) on tumor cells and OSM induced by tumor-associated macrophages (TAMs). Our gene expression profiling (bulk RNA-seq) shows that OSM-induced genes were involved in hypoxia, wound healing, and angiogenesis, which were significantly inhibited by SD-36, a STAT3-selective degrader. Additionally, ATAC-seq experiments revealed that STAT3 binding motifs were preferentially enriched in open chromatin regions of the OSM-STAT3-regulated genes. Among the 50 candidate genes that were regulated epigenetically through the OSM-STAT3 axis, we found that the expression levels of NDRG1, HK2, PLOD2, and NPC1 were significantly correlated with those of OSMR and STAT3 in three independent cervical cancer cohorts. Also, higher expression levels of these genes are significantly associated with poor prognosis in cervical cancer patients. Collectively, our findings demonstrate that the OSM-STAT3 signaling pathway regulates crucial transcriptomic programs through epigenetic changes and that selective inhibition of STAT3 may be a novel therapeutic strategy for patients with advanced cervical cancer.

overall_design: To investigate the OSM-STAT3 signaling pathway in cervical cancer cells, we treated HeLaS3 cells individually or simultaneously with OSM and the STAT3 degrader SD36.

first: Chaelin

last: You

first: Keunsoo

last: Kang

first: Kyuho


title: E2F2 transcription factor promotes a cholestatic MASH phenotype by regulating hepatobiliary metabolism through miR-34a-5p

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background and Aims: Metabolic dysfunction–associated steatotic liver
disease (MASLD) affects a heterogeneous group of patients. Among them, those
with a cholestatic profile show worse outcomes. Here, we investigated whether
E2F2 is involved in MASLD-associated cholestasis and, if so, the role of miRNAs.
Methods: E2f2-knockout (E2f2 AQ5 −/−) and wild-type (WT) mice were fed a cholinedeficient
high-fat diet (ChD-HFD) or an HFD after injection of diethylnitrosamine
(DEN-HFD) to induce metabolic dysfunction–associated steatohepatitis (MASH).
E2F2 was overexpressed in the liver by AAV8. Cholestasis was induced by bile
duct ligation or by a 3,5-diethoxycarbonyl-1,4-dihydrocollidine-enriched diet.
MicroRNA sequencing was performed. Two biopsy-proven MASLD patient
cohorts were used.
Results: E2F2 deficiency resulted in increased synthesis and excretion of cholesterol,
phosphatidylcholine, and bile acids, reducing their storage in the liver
while increasing their presence in feces. This was consistent with increased
expression of genes involved in biliary lipid metabolism, reduced inflammation and
fibrosis, and the generation of a distinct miRNA profile, thereby preventing MASH.
Liver-specific induction of E2F2 in vivo hampered the transcriptional program
involved in biliary lipid metabolism and upregulated miR-34a-5p, which was
downregulated in E2f2−/− mice. The protective effects observed in E2f2−/− mice
were lost when a miR-34a-5p mimic was used. Hepatic miR-34a-5p levels were
elevated in patients with advanced fibrosis, inflammation, steatosis score, cholelithiasis,
and increased serum bile acids and biliary lipids. E2f2 deficiency conferred
protection against cholestatic liver injury.
Conclusions: E2F2 deficiency protects against MASH and cholestasis, preventing
cholesterol accumulation, fibrosis, and inflammation through modulation ofmiR-
34a-5p. This could provide therapeutic benefits for patients with cholestatic MASH.

overall_design: Liver samples from male E2f2-deficient and wild-type (WT) mice were analysed after administering DEN-HFD treatment, which involved an intraperitoneal injection of diethylnitrosamine (DEN) at 25 mg/kg to 14-day-old mice, followed by a high-fat diet (HFD).

first: Maider

last: Apodaka-Biguri

first: André

last: Simão

first: Francisco

last: González-Romero

first: Daniela

last: Mestre

first: Pedro

last: Rodrigues

first: Igor

last: Aurrekoetxea

first: Beatriz

last: Gómez-Santos

first: Xabier

last: Buqué

first: Ane

last: Nieva-Zuluaga

first: Mikel

last: Ruiz de Gauna

first: Idoia

last: Fernandez-Puertas

first: Ainhoa

last: Iglesias-Ara

first: Juan-José

last: Lozano

first: José

last: García-Marín

first: Luis

last: Bujanda

first: Jesús

last: Banales

first: César

last: Martín

first: Lorena

last: Mosteiro

first: Gaizka

last: Errazti

first: Wing-Kin

last: Syn

last: Castaño

last: Zubiaga

first: Rui

last: Castro

first: Patricia

last: Aspichueta


title: Chromatin remodeler CHD7 regulates neurogenic gene expression via controlling chromatin accessibility and modifications of histone marks H3K27me3 and H3K4me3

city: Shanghai

first: Chenxi

last: He

address: 131 Dong'an Rd, Mingdao Bldg, Rm 512

institute: Fudan University

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

overall_design: Refer to individual Series

first: Zhuxi

last: Huang

first: Fei

last: Lan

first: Weijun

last: Feng


title: Estrogen Receptor 1 Signaling in Hepatic Stellate Cells Designates Resistance to Liver Fibrosis

first: Haoyue

last: Zhang

first: Jing

last: Yang

first: Tianhao

last: Li

first: Fuhai

last: Liu


title: Exploring the Differential Host Responses to DSS and UC-Derived Microbiota in a Mouse Model of Colitis

city: Kosice

first: Maria

last: Rynikova

address: Srobarova 2

country: Slovakia

institute: Pavol Jozef Safarik University in Kosice

summary: Ulcerative colitis (UC) is a chronic inflammatory condition of the colon, characterized by recurring mucosal inflammation. Current evidence suggests that dysbiosis may drive the disease, but mechanistic links remain incompletely understood. To further investigate the host-microbiome interactions, three UC-induction methods were used on a pseudo germ-free mouse model: (1) DSS, (2) fecal microbiota transplantation (FMT) from a UC patient, and (3) combination of both DSS and FMT simultaneously. Disease severity (DAI), immune cell profiles (flow cytometry), colon transcriptomics (RNA sequencing), and microbiota composition (16S rRNA sequencing) were assessed. Our study revealed distinct effects of DSS and FMT on experimental colitis. DSS had a more pronounced impact on disease severity, while FMT exerted a stronger influence on several immune populations and downregulation of genes associated with tight junctions and mucins. Microbiome analysis demonstrated distinct compositional profiles across all experimental groups. The combined FMT and DSS model exhibited features of both induction methods, resulting in exacerbated clinical scores, barrier dysfunction, and inflammatory responses. Our study provides valuable insight into host–microbiome interactions in UC and introduces a dual-hit approach that may more accurately recapitulate its multifactorial pathogenesis than DSS alone.

overall_design: RNA-seq transcriptomic profiling of colon mucosal cells before (day 0) and after treatment (day 5) with either DSS, UC FMT or both

first: Sona

last: Gancarcikova

first: Stanislav

last: Lauko

first: Dagmar

last: Mudronova

first: Petra

last: Adamkova

first: Martin

last: Janicko

first: Vlasta

last: Demeckova


title: Single-cell analysis of human airway epithelium reveals cell type-specific responses to Aspergillus and Coccidioides

city: Boston

first: Jatin

last: Vyas

state: MA

address: 55 Fruit Street

institute: Massachusetts General Hospital

summary: Respiratory fungal infections pose a significant threat to human health, but animal models do not fully recapitulate human disease, necessitating advanced models to study human-fungal pathogen interactions. In this study, we utilized primary human airway epithelial cells (hAECs) to recapitulate the lung environment in vitro and investigate cellular responses to two diverse, clinically significant fungal pathogens, Aspergillus fumigatus and Coccidioides posadasii. To understand the mechanisms of early pathogenesis for both fungi, we performed single-cell RNA sequencing of infected hAECs. Analysis revealed that both fungi induced cellular stress and cytokine production. However, the cell subtypes affected and specific pathways differed between fungi, with A. fumigatus and C. posadasii triggering protein-folding-related stress in ciliated cells and hypoxia responses in secretory cells, respectively. This study represents one of the first reports of single-cell transcriptional analysis of hAECs infected with either A. fumigatus or C. posadasii, providing a vital dataset to dissect the mechanism of disease and potentially identify targetable pathways.

overall_design: Human airway epithelial cells were differentiated using standard air-liquid interface procedures and infected with 10^7 colony forming units of either Aspergillus fumigatus or Coccidiodes posadasii. Following infection, a single-cell suspension was generated and cells were sequenced

first: Alfred

last: Harding

first: Arianne

last: Crossen

first: Jennifer

last: Reedy

first: Kyle

last: Basham

first: Olivia

last: Hepworth

first: Yanting

first: Viral

last: Shah

first: Manalee

middle: V

last: Surve

last: Simaku

first: Geneva

middle: N

last: Kwaku

first: Kristine

last: Nolling  Jensen

first: Hannah

last: Brown  Harding

first: Yohana

last: Otto

first: Rebecca

last: Ward

first: Bruce

last: Klein

first: Jayaraj

last: Rajagopal

first: Pritha

last: Sen

first: Adam

last: Haber


title: Single-Cell RNA-Seq Study Showing the Effect of Healthy and Cencer Cells on HSCs

city: Indiana University

first: Reza

last: Shahbazi

address: 980 W Walnut st

institute: Indiana University

summary: Hematopoietic stem cells (HSCs) are highly sensitive to signals from their surrounding microenvironment, yet the precise effects of healthy versus malignant cells on HSC behavior remain poorly understood. In this study, we applied single-cell RNA sequencing (scRNA-seq) to profile HSCs exposed to either exosomes from healthy primary cells or cancer-derived cells. Our analyses revealed distinct transcriptional programs induced by each condition.

overall_design: Single-cell RNA profiling were performed on primary CD34 cells treated with exosomes.

first: Samaneh

last: Maleknia

first: Sanam

last: Rezaei Benam


title: Differential expression of Organ Transplant Rejection related genes after xenokidney from 1KO.1TG vs. 3KO.7TG donor pigs

city: Durham

first: Jean

last: Kwun

state: NC

address: 207 Research Dr, Jones 362

department: Surgery

institute: Duke University

summary:
Animals received 3KO.7TG showed a distinct pattern of gene expression compared to those received 1KO.1TG
After weaning immunosuppression, Animals received 3KO.7TG showed elevation of genes related to neutrophil degranulation, coagulation pathway, B cell, and PC.

overall_design: In this study presented here, renal xenografts from animals received 1KO.1TG and 3KO.7TG donor pigs were used to acquire expression profiles of a total of 758 genes using nanostring - nCounter Human Organ Transplant Panel


title: Repeats Mimic Pathogen-Associated Patterns Across a Vast Evolutionary Landscape [J2-RIP-Seq]

first: John

last: LaCava

address: 1230 York ave

institute: The Rockefeller University

summary: An emerging hallmark of many human diseases is transcription of typically silenced repetitive DNA containing pathogen-associated molecular patterns (PAMPs).  These PAMPs engage the innate immune system via pattern recognition receptors (PRRs) – a phenomenon known as “viral mimicry.” We propose a statistical physics framework to quantify viral mimicry by measuring “selective forces” that enrich PAMPs compared to a genome-wide reference distribution. We validate our predictions by identifying repeats that bind different PRRs and show viral mimicry in different repeat families across eukaryotic genomes, suggesting shared mechanisms drive emergence and retention. We propose two non-exclusive evolutionary hypotheses. The first ‘repeat-centric’ hypothesis posits PAMPs are integral to the repeat lifecycle and are therefore enriched as they mediate repeat expansion. The second ‘organism-centric’ hypothesis proposes viral mimicry functions as a cell-intrinsic feedback mechanism for sensing and reacting to transcriptional dysregulation, which provides a selective pressure to maintain PAMPs in genomes.

overall_design: J2-RIP-Seq of untreated POP92 cell line; RNA-Seq controls are under GEO series GSE145639( samples GSM4322694 and GSM4322693)

first: Daniel

last: De Carvalho

first: Håvard

last: Lindholm

first: Sajid

last: Marhon

first: Amir

last: Hosseini

first: Raymond

last: Chen

first: Benjamin

last: Greenbaum

first: Siyu

last: Sun


title: Gene expression profiles at single cell level of Kenyon cells in adult Drosophila melanogaster females

first: Bogdan

last: Sieriebriennikov

address: 100 Washington Sq E

institute: New York University

summary: Kenyon cells are grouped into 3 classes and 7 molecularly defined subtypes. While single-cell transcriptomes for the 3 classes were available from brain-level atlases, here, we take a targeted approach to distinguish between the subtypes.

overall_design: To generate an adult Kenyon cell data set and annotate the seven molecularly defined cell subtypes (Aso et al., 2014), we single-cell sequenced seven genotypes that simultaneously expressed GFP in all Kenyon cells and mtdTomato in a defined Kenyon cell subtype(s). To generate such flies, the OK107-QF2>QUAS-GFP, UAS-mtdTomato line (BDSC# 66472) was crossed with each of the following subtype-specific split-GAL4 lines (Aso et al., 2014; Shih et al., 2019): γm and γd  (BDSC #68265), γd (BDSC #68256), α′/β′m (BDSC #68322), α′/β′ap (BDSC #68370), α/βp (BDSC #68383), α/βc (BDSC #68255), α/βs (BDSC #68267). The brains of adult female F1 progeny with the respective OK107-QF2>QUAS-GFP, GAL4-AD∩GAL4-DBD>UAS-mtdTomato genotype were dissected, visually checked for mtdTomato fluorescence in the mushroom body, dissociated into single cells, and stained with the DNA dye DRAQ5. Specifically, brains were dissected for up to 60 minutes in Schneider’s medium and placed on ice. Optic lobes were removed during dissection. After all dissections were completed, collagenase and dispase were added to a final concentration of 2mg/mL each along with 45 uM Actinomycin D, and samples were incubated at 26C for 1 h without agitation. Samples were washed 2-3 times with DPBS+0.04% BSA, dissociated by trituration and passed through a 20 um PluriStrainer. Cells were stained with 5 uM DRAQ5 before being subjected to flow cytometry on a FACS Aria II (New York University Genomics Core). Forward scatter area and width were used to gate single cells, and cells were sorted into DPBS+0.04% BSA. Specifically, DRAQ5+,GFP+ cells were FAC-sorted to enrich the samples for Kenyon cells. mtdTomato expression was not used for sorting. Given the prior knowledge that different classes of Kenyon cells separate well during the analysis of single-cell data, the brains of flies where the subtypes of different classes were labeled (e.g. γd, α′/β′ap, and α/βs) were pooled in different combinations before the dissociation to minimize batch effects. Each brain pool corresponds to one library and includes at least 8 brains. Single-cell libraries were prepared using the 10X Chromium Next GEM Single Cell 3’ Kit v3.1.


title: Targeting HSPB1 Reduces Tumor Growth and Abrogates Treg-Mediated Tumor Immunosuppression

city: shanghai

first: Songguo

last: Zheng

address: No.621 Zhongshan 2nd Road, Songjiang District, Shanghai

institute: Shanghai Jiaotong University

summary: Colorectal cancer (CRC) shows limited responsiveness to immune-checkpoint blockade, highlighting the need for further investigation. The intratumoral Treg/CD8⁺ T-cell ratio serves as a predictive biomarker for therapeutic efficacy. Here, we first demonstrate that targeting HSPB1 lowers this ratio and confers therapeutic benefit in CRC. Methods. Candidate genes were identified by integrative single-cell transcriptomics and spatial transcriptomics, followed by survival analyses of TCGA cohorts. Functional interrogation was performed using CRISPR-Cas9 engineered knockout cell lines. Subcutaneous tumor models were established, and the immune microenvironment was characterized by multiparametric flow cytometry. Mechanistic validation was achieved through bulk RNA-seq and complementary functional assays. Results. Single-cell profiling identified HSPB1 as a determinant of the intratumoral Treg/CD8⁺ T-cell ratio, and TCGA analysis showed its prognostic relevance in CRC. Spatial transcriptomics revealed colocalization of HSPB1-expressing tumor cells with Tregs. Subcutaneous tumor models demonstrated that CRISPR-mediated HSPB1 deletion or pharmacologic inhibition markedly suppressed tumor growth and reprogrammed the Treg-dominated microenvironment. In vitro polarization assays confirmed that targeting HSPB1 selectively restrains Treg differentiation without affecting Th17. Integrated transcriptomic and functional studies further elucidated that HSPB1 orchestrates CCL20–CCR6 mediated Treg recruitment, thereby shaping the immunosuppressive milieu within colorectal tumors.Conclusions. Targeting HSPB1 exerts dual anti-tumor effects by directly suppressing neoplastic proliferation and concurrently alleviating Treg-mediated immunosuppression within the tumor microenvironment.

overall_design: SW480 cells were infected with lentiviruses encoding CRISPR/Cas9 sgNC or sgHSPB1. Forty-eight hours post-infection, the cells were subjected to puromycin selection for 72 h. The surviving cells were then harvested for RNA extraction and subsequent RNA-seq analysis.

first: Qi

last: Hu

first: Yang

last: Lu


title: An Allele Agnostic Mutant KRAS Inhibitor Demonstrates Broad Spectrum Tumour Growth Inhibition in Pancreatic Ductal Adenocarcinoma

city: New York

first: Anirban

last: Maitra

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

summary: Mutations in KRAS are a dominant driver of pancreatic ductal adenocarcinoma (PDAC), with over 40% of PDAC patients presenting with KRASG12D mutations. The recent development of small molecule inhibitors targeting KRASG12D, has enabled effective targeting of mutant KRAS signaling and suppression of PDAC; however, the contribution of the tumor microenvironment (TME) to the therapeutic efficacy of KRASG12D inhibition and mechanism/s of resistance to KRASG12D suppression remain to be elucidated. Here, we employed spatial transcriptomics to evaluate cancer cell intrinsic and extrinsic responses to KRASG12D inhibition with panKRASi (BI-2493). In panKRASi-treated immune-replete models, we observe increased intratumoral CD8+ effector T cells and decreased infiltration of myeloid cells, along with remodeling of the tumor microenvironment (TME). In addition, both Cxcl9 and Cxcl10 expression were upregulated in KPCYG12D tumors upon panKRASi treatmen. To dissect the involvement of CAF subtypes in the panKRASi response, we utilized a RCTD deconvolution approach to evaluate their abundance, showing no significant differences in the overall CAF subtype population but a visible increase in the myCAFs population under panKRASi treatment. Focus on cancer-intrinsic mechanisms we reported a switch in cellular identity towards the gene expression of classical signatures in panKRASi treated tumors in both canonical Moffit signature and metaprogram-derived signature. In addition, a decrease in cell cycle-related pathways (E2F targets, G2M checkpoints) and EMT signature was reported for panKRASi treated samples combined with a clear switch from glycolysis to oxidative phosphorylation under treatment with a decrease in p53 and TNF⍺ signaling via NFⲕΒ.

overall_design: Pancreas tissue from mice treated with vehicle or panKRASi was collected in formalin and processed into paraffin blocks after 14 days of treatment. Two different tumor areas/mice for a total of four mice per group (vehicle/panKRASi) were combined into a TMA of 4x4. 5 um thick sections were generated, stained with H&E, and scanned with an Zeiss Axio Scan.Z1 prior entering the 10x CytAssist pipeline for spatial transcriptomics.

first: Francesca

last: Paradiso

first: Yunhe

last: Liu

first: Kimal

middle: I

last: Rajapakshe

first: Andre

last: Faustino


title: Transcriptional response to varying air humidity in Arabidopsis

first: yangxuan

last: liu

address: 300 Fenglin Road

institute: CAS Center for Excellence in Molecular Plant Science (CEMPS), Chinese Academy of Sciences

summary: To investigate the molecular mechanism of plant response to air humidity, wild-type plants and pip2;5, a mutant defective in water transport, were subjected 24 hours of high and low air humidity treatments. The results showed that genes related to hypoxia response, ethylene pathways, and ABA responses were differentially expressed in the pip2;5 mutant compared to the wild type.

overall_design: The inflorescence meristems of wild-type and pip2;5 plants under various humidity conditions were dissected for transcriptome analysis.

first: Yimin

last: Zhu

first: Yangxuan

first: Weibing

last: Yang


title: Gene expression profiling of colorectal cancer tissues, matched normal tissues, colorectal cancer cell lines, and primary cultures (2D organoids)

city: Osaka

first: Norikatsu

last: Miyoshi

address: 3-1-69, Ohtemae, Chuo-ku

department: Innovative Oncology Research and Regenerative Medicine

country: Japan

institute: Osaka International Cancer Institute

summary: We performed a comprehensive gene expression analysis of human colorectal cancer (CRC) tissues, matched adjacent normal mucosa, established CRC cell lines, and primary cultures derived from patient tumors (2D organoids). This dataset aims to identify genes and signaling pathways preferentially expressed in cancer cells and to explore clinically relevant mechanisms through comparative analysis of primary cultures and patient tissues.

overall_design: Gene expression was profiled using the Agilent SurePrint G3 Human GE v3 8x60K microarray platform. The study included four sample types: 1. Colorectal cancer tissues from patients, 2. Matched adjacent normal colorectal tissues, 3.Established CRC cell lines, 4.Primary cultures derived from patient tumors, maintained as 2D organoids.

first: Shiki

last: Fujino


title: Cyclic di-AMP drives secondary differentiation in Chlamydia trachomatis

city: Omaha

first: Jeonghoon

last: Lee

state: Nebraska

address: 985900 Nebraska Medical Center

department: Pathology, Microbiology, and Immunology

institute: University of Nebraska Medical Center

summary: The obligate intracellular bacterium Chlamydia alternates between two functional forms during its developmental cycle: elementary body (EB) and reticulate body (RB). However, the molecular mechanisms governing the transitions between these forms are unknown. Here, we present evidence cyclic di-AMP (c-di-AMP) is a key factor in triggering the transition from RB to EB (i.e., secondary differentiation) in the chlamydial developmental cycle. We made strains producing different levels of c-di-AMP, which we linked to changes in secondary differentiation status. Increases in c-di-AMP resulted in an earlier increase in transcription of EB-associated genes, and this was further manifested in earlier production of EBs. In contrast, when c-di-AMP levels were decreased, secondary differentiation was delayed. Based on these data, we conclude there is a threshold level of c-di-AMP needed to trigger secondary differentiation in Chlamydia. This is the first study to define a mechanism of secondary differentiation in Chlamydia.

overall_design: The transformants of dacAop and dacA-KD were infected into HeLa cells. At 10 hpi, the constructs were induced or not with 5 nM aTc.  RNA samples were prepared from dacAop-infected cells and dacA-KD-infected cells at 16 hpi and 24 hpi, respectively. 20 μg RNA samples were treated with DNase to remove DNA contamination by using DNA-free Turbo kit (Thermo) according to the manusfacturer’s instruction. Ribosomal RNA was depleted from samples using the MICROBEnrich (Thermo) and MICROBExpress kits (Thermo) following the manufacturer’s instructions. RNA samples were processed for sequencing by the UNMC Genomics Core Facility.

first: Scot

middle: P

last: Ouellette

first: Junghoon


title: Defining Functional Hub Genes in Basal-like Breast Cancer Networks

city: Torino

first: Aurora

last: Savino

state: Piemonte

address: via Nizza, 52

country: Italy

institute: Università di Torino

summary: The behaviour of complex biological systems emerges from the coordinated activity of networked molecular components. In this context, gene regulatory networks (aka gene coexpression networks) offer insights into the regulation of gene expression programs. In cancer, aberrant gene expression underlies molecular and clinical features, and identifying key networked transcriptional regulators may enable targeted therapeutic interventions. However, computationally inferred regulatory nodes have so far hardly been experimentally validated. Here we combined gene expression network analysis with gene perturbation experiments to test whether computationally identified hub genes act as upstream regulators of their coexpression modules in breast cancer. To better capture the context-dependent nature of gene regulation and minimize confounding effects from inter-subtype heterogeneity, we also constructed subtype-specific networks. Using the METABRIC transcriptomic dataset of primary breast tumours, we identified clinically-informative gene modules in the highly aggressive basal-like subtype. Candidate regulatory hubs were prioritized based on network centrality, and their functional relevance was assessed both in silico and in vitro. CRISPR-mediated knockout of selected hub genes resulted in coordinated down-regulation of module genes and impaired cellular functions, demonstrating causal links between hub gene function, module expression and phenotypic outcome. Moreover, we observed a significant correlation between the transcriptional impact of each knockout and its functional effects—highlighting the biological relevance of coexpression modules and supporting the hypothesis that their structure reflects functional dependencies.

overall_design: Cas12a based inactivation of E2F3 or TFDP1 genes in Hs578T, MDA-MB-231 and MDA-MB-468 basal-like breast cancer cell lines. After transduction with Cas12a and 3x sgRNA array encoding vector, cells were cloned by limiting dilution. Two independent clones were analysed for each cell line/gene and compared with cells transduced with the empty vector.

first: Lidia

last: Avalle

first: Valeria

last: Poli


title: Newly discovered base barrier cells provide compartmentalization of choroid plexus, brain and CSF

city: Zwijnaarde

first: Roosmarijn

middle: E.

last: Vandenbroucke

state: Gent

address: Technologiepark-Zwijnaarde 71

department: VIB Center for Inflammation Research

country: Belgium

institute: VIB-UGent

summary: The choroid plexus (ChP) is a highly understudied structure of the central nervous system (CNS). The structure hangs in the brain ventricles, is composed of an epithelial cell layer, which produces the cerebrospinal fluid (CSF) and forms the blood-CSF barrier. It encapsulates a stromal mix of fenestrated capillaries, fibroblasts and a broad range of immune cells. Here, we report that the ChP base region harbors unique fibroblasts that cluster together, are connected by tight junctions and seal the ChP stroma from brain and CSF, thereby forming ChP base barrier cells (ChP BBCs). ChP BBCs are derived from meningeal mesenchymal precursors, arrive early during embryonic development, are maintained throughout life and are conserved across species. Moreover, we provide transcriptional profiles and key markers to label ChP BBCs and observe a striking transcriptional similarity with meningeal arachnoid barrier cells (ABCs). Finally, we provide evidence that this fibroblast cluster functions as a barrier to control communication between CSF and the ChP stroma and between the latter and the brain parenchyma. Moreover, loss of barrier function was observed during an inflammatory insult. Altogether, we have identified a novel barrier that provides functional compartmentalization of ChP, brain and CSF.

overall_design: We performed scRNA-Seq to investigate the cellular heterogeneity within the Choroid Plexus of mice of various ages. After an initial analysis, we focused in on the various Fibroblast subsets present in our dataset and compared them to various cell types from other public datasets.

first: Daan

last: Verhaege

first: Clint

last: De Nolf

middle: E


title: Loss of UXS1 Selectively Depletes Pyrimidines and Induces Replication Stress in KEAP1-Mutant Lung Cancer [RNA-seq]

city: South San Francisco

first: Melat

middle: T.

last: Gebru

address: 1170 Veterans Blvd

department: Oncology

institute: Calico Life Sciences LLC.

summary: Kelch-like ECH associated protein 1 (KEAP1) is the third most commonly mutated gene in non-small cell lung cancer (NSCLC) and is associated with poor prognosis. Here, we investigated synthetic lethal interaction genes in KEAP1-mutated cancer cells and identified a dependency on UDP xylose synthase 1 (UXS1), which converts UDP-glucuronic acid (UDP-GlcA) to UDP- xylose in the proteoglycan synthetic pathway. UDP glucose dehydrogenase (UGDH), a transcriptional target of NRF2 that converts UDP-glucose to UDP-GlcA, was highly expressed in KEAP1-mutant tumors. Upon UXS1 knockdown, depletion of UDP-xylose occurred in both KEAP1-mutant and wildtype (WT) cells, whereas UDP-GlcA accumulated to a greater extent in the KEAP1-mutant setting. The resulting shortage of available UDP and other pyrimidines slowed S-phase progression and stalled DNA replication fork marks, causing cells to undergo prolonged cell-cycle exit or apoptosis. Dependency on UXS1 was rescued by knocking out UGDH to prevent UDP-GlcA accumulation and UDP depletion. DNA replication stress in UXS1-depleted cells sensitized them to clinical cell-cycle checkpoint inhibitors. Further, CRISPR screening experiments identified genes that modulate UXS1 dependency. While liver had the highest normal tissue expression of UGDH, UXS1 knockout in the liver did not result in hepatotoxicity. Taken together, these data demonstrate that UXS1 is a selective dependency in KEAP1-mutant tumors and loss of UXS1 creates additional therapeutically exploitable vulnerabilities in KEAP1-mutant tumors.

overall_design: Transcriptome profiling of NCI-H2122 and A549 control NTC and UXS1 knockdown cells 5 and 6 days after induction of knockdown by doxycycline treatment respectively.

first: Timothy

last: Hoffman

first: David

last: Stokoe


title: ProCTLA-4 in anti-tumor immunity

city: Beijing

first: Wenyan

last: Wang

address: Tsinghua Road

institute: Tsinghua

summary: We developed a prodrug of the anti-CTLA4 antibody, named ProCTLA-4. ProCTLA-4 elicits anti-tumor immune responses with reduced toxicity compared to current CTLA4 blockade therapies. Moreover, compared to currently used Probody Therapeutics targeting CTLA-4, ProCTLA-4 offers significant advantages for enhanced efficacy. Thus, our design establishes an alternative paradigm for antibody therapeutics that enables reduction of irAEs while simultaneously increasing therapeutic efficacy.

overall_design: We isolated intratumoral live CD45+ immune cells and investigated the transcriptional signatures at the single-cell level following CTLA-4/ProCTLA-4 antibody treatment.

first: Weian

last: Cao

first: Junfan

last: Chen

first: Yutong

last: Fu

first: Yang-Xin


title: Cerebrovascular p16INK4A expression induces cerebral small vessel disease-related phenotypes

city: Jacksonville

first: Yingxue

last: Ren

address: 4500 San Pablo Rd S

institute: Mayo Clinic

summary: Cerebral small vessel disease (cSVD) is the most common cause of vascular cognitive impairment and dementia (VCID) and highly associated with Alzheimer’s disease pathogenesis. There is an urgent need to establish relevant animal models for cSVD. As aging is the strongest risk factor for these diseases, cerebrovascular senescence is implicated in cSVD pathogenesis. We investigated how AAV-based expression of senescence marker CDKN2A/p16INK4A in cerebrovascular endothelial cells influences cSVD phenotypes in adult wild-type mice. A single intraperitoneal injection of the AAV carrying CDKN2A/p16INK4A caused blood-brain barrier impairments, neurovascular uncoupling, and reduction of cerebral blood flow, accompanied with behavioral changes in mice. While single cell RNA-sequencing and immunostaining revealed the upregulation of VCAM1 in cerebrovascular endothelial cells, in vivo two-photon excitation microscopy detected aggravated leukocyte adhesions to capillaries. Our findings demonstrate the contributions of p16INK4A in cerebrovascular endothelial cells to cSVD and VCID pathogenesis through new mouse model.

overall_design: We used single cell RNA sequencing to investigat how AAV-based expression of senescence marker CDKN2A/p16INK4A in cerebrovascular endothelial cells influences cSVD phenotypes in adult wild-type mice.

first: Keiji

last: Kawatani

first: Takahisa

last: Kanekiyo


title: Bulk Affymetrix Exon array analysis of prostate tissues prior to treatment with neoadjuvant ADT plus enzalutamide

city: Bethesda

first: Adam

last: Sowalsky

address: 37 Convent Drive Building 37 Room 1062B

institute: National Cancer Institute

type: Expression profiling by genome tiling array

summary:
The purpose of this study was to profile bulk tissue gene expression on Affymetrix microarrays prior to therapy
Processing of samples on this microarray platform enables direct comparison to thousands of previously-described specimens.

overall_design: Biopsies were acquired prior to therapy, without microdissection. RNA was extracted and processed for Affymetrix Human Exon GeneChips.

first: William

middle: L

last: Dahut

middle: G


title: Activation of OSM-STAT3 Epigenetically Regulates Tumor-Promoting Transcriptional Programs in Cervical Cancer [RNA-Seq]

city: Cheongju-si

first: Junho

last: Noh

address: 1, Chungdae-ro, Seowon-gu

institute: Chungbuk National University

summary: Despite improvements in preventative strategies, such as regular screenings with Pap tests and human papillomavirus (HPV) tests as well as HPV vaccinations, effective treatment for advanced cervical cancer remains poor. Deregulation of STAT3 is an oncogenic factor that promotes tumorigenesis and epithelial-to-mesenchymal transition (EMT) in various cancers. Oncostatin M (OSM), a pleiotropic cytokine, induces STAT3 activation, exacerbating cervical cancer. However, the mechanism by which the OSM-STAT3 axis epigenetically regulates tumor-progression-related genes in cervical cancer is not well understood. Here, we show that OSM-mediated STAT3 activation promotes pro-tumorigenic gene expression programs, with chromatin remodeling in cervical cancer. Reanalysis of scRNA-seq data performed in cervical cancer uncovered an interaction between the oncostatin M receptor (OSMR) on tumor cells and OSM induced by tumor-associated macrophages (TAMs). Our gene expression profiling (bulk RNA-seq) shows that OSM-induced genes were involved in hypoxia, wound healing, and angiogenesis, which were significantly inhibited by SD-36, a STAT3-selective degrader. Additionally, ATAC-seq experiments revealed that STAT3 binding motifs were preferentially enriched in open chromatin regions of the OSM-STAT3-regulated genes. Among the 50 candidate genes that were regulated epigenetically through the OSM-STAT3 axis, we found that the expression levels of NDRG1, HK2, PLOD2, and NPC1 were significantly correlated with those of OSMR and STAT3 in three independent cervical cancer cohorts. Also, higher expression levels of these genes are significantly associated with poor prognosis in cervical cancer patients. Collectively, our findings demonstrate that the OSM-STAT3 signaling pathway regulates crucial transcriptomic programs through epigenetic changes and that selective inhibition of STAT3 may be a novel therapeutic strategy for patients with advanced cervical cancer.

overall_design: To investigate the OSM-STAT3 signaling pathway in cervical cancer cells, we treated HeLaS3 cells individually or simultaneously with OSM and the STAT3 degrader SD36.

first: Chaelin

last: You

first: Keunsoo

last: Kang

first: Kyuho


title: Transcriptomic Analysis Reveals TME-Mediated Macrophage IFIT1 Upregulation and CX3CR1 Suppression Drive Osteosarcoma Progression

city: Nangning

first: Keyi

address: No. 22 Shuangyong Road, Qingxiu District

institute: Guangxi Medical University

summary: Osteosarcoma (OS) is one of the most common bone tumors which prognosis of patients is unsatisfactory. Due to the stagnancy in conventional treatments, researchers begin to find therapeutic targets from tumor microenvironment (TME) and tumor associated macrophages (TAM). We aim to investigate the influence of the effects of OS TME on gene expression of macrophages which may provide reference to OS treatment. RNA sequencing was performed on BMMs cultured with or without K7M2 CM for 48 hours to analyze gene expression changes.

overall_design: Transcriptome sequencing was performed on BMMs, BMMs after 48 h of K7M2 CM intervention, and BMMs after 48 hours of K7M2 CM + DTM intervention

first: Huanyang

last: He

first: Jiamin

last: Liang

first: Yuangang

last: Su

first: Jinmin

last: Zhao

first: Qian

last: Liu