title: SNCA triplication disrupts proteostasis and extracellular architecture prior to neurodegeneration in human midbrain organoids [RNA-seq]

city: Belfast

first: Sarah

last: Maguire

address: 97 Lisburn Road

department: PGJCCR

institute: Queen's University Belfast

summary: Synucleinopathies, including Parkinson’s disease, are characterized by α-synuclein (SNCA) aggregation and progressive neurodegeneration, yet the early molecular events linking SNCA gene dosage to disrupted proteostasis remain poorly understood. Here, we used human midbrain organoids derived from induced pluripotent stem cells (iPSC) carrying an SNCA triplication (SNCA Trip) and the isogenic corrected line (SNCA Isog) to dissect early pathogenic mechanisms in a 3D human model of synucleinopathy. We combined immunohistochemistry, immunoblotting, tandem mass tag proteomics, bulk RNA sequencing, and ribosome profiling to systematically characterize molecular alterations in SNCA Trip organoids at day 50 (D50) and day 100 (D100) of maturation. SNCA Trip organoids exhibited increased α-synuclein accumulation, neuromelanin deposition, and activation of mTORC1 (p-rpS6), ERK1/2, AKT and p-eIF2α signalling pathways by D100. Proteomic and transcriptomic analyses revealed upregulation of cytoskeletal, synaptic, and axonal development pathways, alongside significant downregulation of extracellular matrix (ECM) components and upregulation of perineuronal net (PNN) genes. Ribosome profiling showed minimal global translational changes but uncovered selective translational buffering of neuronal and ECM-associated transcripts. Confocal imaging confirmed progressive disorganization of pericellular and interstitial ECM structures around neurons in SNCA Trip organoids. Our findings demonstrate that SNCA triplication induces early proteostatic disruption and extracellular matrix remodelling prior to neurodegeneration and suggest that altered gene expression and ECM homeostasis may contribute to disease initiation and progression. Targeting these early aberrant mechanisms may offer new therapeutic opportunities for synucleinopathies, such as Parkinson’s Disease.

overall_design: Ribosome sequencing was performed in D100 human midbrain organoids. Samples incuded isogenic (n=3) and SNCA triplication (n=3) genotypes, each replicate comprising 3 pooled organoids. Total RNA was extracted using the RNeasy Micro Kit (Qiagen, #74004)

first: Elpida

last: Statoulla

first: Maria

last: Zafeiri

first: Kleanthi

last: Chalkiadaki

first: Georgia

last: Voudouri

first: Karmel

middle: S

last: Gkika

first: Christos

last: Papazoglou

first: Thomas

last: Durcan

first: Arkady

last: Khoutorsky

first: Seyed

last: Mehdi Jafarnejad

first: Alexander

last: Dityatev

middle: G

last: Gkogkas


title: Bacterial extracellular vesicles from Streptococcus mutans drive OSCC progression through β-catenin signaling

status: Public on Apr 09 2026

city: Harbin

first: Yong

last: Fang

state: Hei longjiang

address: 157 Health Road, Nangang District, Harbin City

department: Department of Microbiology

country: China

institute: Harbin medical university

type: Expression profiling by high throughput sequencing

summary: Oral squamous cell carcinoma (OSCC) is an aggressive malignancy in which microbial dysbiosis is increasingly recognized as a contributing factor, yet the pathogenic potential of bacterial extracellular vesicles (EVs) remains poorly defined. To determine whether Streptococcus mutans–derived EVs (SmEVs) influence OSCC progression, we isolated and characterized SmEVs from ATCC 35668 and examined their effects in CAL-27 cells and a nude-mouse xenograft model. SmEVs were readily internalized by OSCC cells and enhanced proliferative, migratory, and invasive capacities in vitro. Transcriptomic analysis revealed that SmEV exposure reshaped the CAL-27 gene expression landscape and prominently enriched the Wnt/β-catenin signaling pathway, accompanied by increased activation of β-catenin, TCF7, and FOSL1/Fra-1 in both cultured cells and xenograft tumors. DIA proteomics identified a broad array of SmEV proteins, and in silico docking highlighted several abundant, cancer-associated candidates with strong predicted interactions with β-catenin. In vivo, co-administration of SmEVs accelerated tumor growth and reinforced activation of the β-catenin axis. Collectively, these findings provide the first evidence that S. mutans–derived EVs promote OSCC progression through β-catenin–driven transcriptional programs and identify specific vesicular proteins as candidate mediators, offering new insights into microbe-derived factors as potential diagnostic or therapeutic targets in OSCC.

overall_design: We performed mRNA sequencing analysis on the oral cancer cell line CAL-27 with or without the action of Streptococcus mutans extracellular vesicles.

first: Guoding

last: Cao

first: Yichen

last: Jiang

first: Xinhang

last: Li

first: Ran

last: Liu

first: Kaili

first: Fikadu

last: Balcha

first: Mingyang

last: Ding

first: Meng

last: Yuan

first: Ting


title: RNA-seq of placentas from FNDC5-deficient and wild-type mice at gestational day 17.5

city: Toronto

first: Sascha

last: Drewlo

address: 2075 Bayview Ave.

country: Canada

institute: Sunnybrook Research Institute

summary: Fibronectin type III domain–containing protein 5 (FNDC5), the precursor of the myokine irisin, has been implicated in metabolic regulation and pregnancy outcomes, but its role in placental development is not well understood. To investigate how FNDC5 deficiency affects the placental transcriptome, we performed mRNA sequencing on placentas collected at gestational day 17.5 from FNDC5 knockout (FNDC5-/-) and wild-type mice. Total RNA was isolated from whole placentas, poly(A)+-selected, and used to generate strand-specific libraries with the NEBNext Ultra II Directional RNA Library Prep Kit, followed by paired-end sequencing on an Illumina NovaSeq 6000. These data enable identification of FNDC5-dependent changes in placental gene expression associated with alterations in fetal–placental growth and maternal body weight.

overall_design: Placental tissue was collected at gestational day 17.5 from pregnant dams carrying FNDC5 knockout (KO) or wild-type (WT) conceptuses. RNA-seq libraries were prepared from 12 placentas in total (n = 6 WT, n = 6 KO) and sequenced as paired-end reads. Differential expression analysis compares KO versus WT placentas to identify genes and pathways altered by loss of FNDC5.


title: Functional redundancy between UTY and UTX in regulating the localization of transcription factors involved in pluripotency [ChIP-seq]

city: Yokohama

first: Tomohiko

last: Akiyama

state: Kanagawa

address: 3-9 Fuku-ura

department: School of medicine

country: Japan

institute: Yokohama city university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The Y chromosome retains a limited number of protein-coding genes, yet their biological significance remains poorly understood. Here, we find UTY, a Y-linked homolog of the histone demethylase UTX, plays an essential regulator of pluripotency in human embryonic stem cells. Despite its low expression and weak enzymatic activity, UTY co-localizes with UTX at active cis-regulatory elements and contributes to the regulation of core pluripotency genes such as NODAL and LEFTY. Through genome-wide occupancy and transcriptome analyses of knockout cell lines, we show that UTY and UTX function redundantly to maintain proper localization of key transcription factors including OCT4 and SOX2. Dual loss of UTY and UTX leads to their mislocalization, widespread transcriptional dysregulation, and loss of pluripotency, without changes in H3K27 methylation. Instead, these effects are associated with changes in histone acetylation and altered chromatin accessibility, likely driven by recruitment of ATP-dependent chromatin remodelers, pointing to a non-enzymatic mechanism. Our findings uncover a novel role for UTY in stabilizing transcription factor binding and maintaining cell identity, demonstrating that even the evolutionarily compact Y chromosome retains critical regulatory functions in early human development.

overall_design: Chromatin immunoprecipitation DNA sequencing for H3K27ac and H3K27me3 in WT and UTX/UTY-KO hES cells


title: SNCA triplication disrupts proteostasis and extracellular architecture prior to neurodegeneration in human midbrain organoids [Ribo-seq]

first: Sarah

last: Maguire

country: United Kingdom

overall_design: Ribosome sequencing was performed in D100 human midbrain organoids wuth RiboLace kit. Samples incuded isogenic (n=3) and SNCA triplication (n=2) genotypes, each replicate comprising 10 pooled organoids. Organoids were pre-treated with cycloheximide prior to lysis.

first: Elpida

last: Statoulla

first: Maria

last: Zafeiri

first: Kleanthi

last: Chalkiadaki

first: Georgia

last: Voudouri

first: Karmel

last: Gkika

first: Christos


title: Sodium Channel Isoform Diversity Underlies Chamber-Specific Cardiac Excitability [bulk RNA-seq]

city: Iowa City

first: Jared

middle: M.

last: McLendon

state: Iowa

address: 180 South Grand Ave, CPB 554

department: Pharmaceutical Sciences and Experimental Therapeutics

country: USA

institute: University of Iowa - College of Pharmacy

summary: Sodium channels are essential for cardiac conduction and excitability. The sodium current is primarily carried by the voltage gated sodium channel isoform NaV1.5. Using a novel NaV1.5 chimeric construct (NaV1.5-GX), our study reveals a unique chamber-specific distribution of non-NaV1.5 sodium channel isoforms, and we performed bulk RNA sequencing of murine ventricles to assess if acute NaV1.5 inhibition changed the trascriptional profile of the ventricular myocytes.

overall_design: mRNA sequencing was performed on bulk murine ventricles from wild type and mutant mice, 4 hours after treatment with an intraperitoneal injection of either DMSO (vehicle control, n=3 WT, n=4 GX) or MRL5 (GX family compound that potently inhibits the NaV1.5-GX channel in mutant mice, n=2 WT, n=4 GX).

first: Christian

last: Anderson

middle: M


title: Loss of schizophrenia risk gene XPO7 disrupts neuronal excitability and network regularity via altered Na+ channel dynamics in human neurons

city: Cambridge

first: Lei

last: Cui

state: MA

address: 75 Ames st. room 8115b room 8115b

institute: Broad Institute of MIT and Harvard

summary: Schizophrenia is a highly heritable psychiatric disorder, yet the molecular mechanisms by which genetic risk contributes to disease pathophysiology remain largely unknown. In this study, we investigate the functional consequences of XPO7 loss of function (LoF) in human induced pluripotent stem cell (iPSC)-derived neurons, focusing on its role as a schizophrenia risk gene identified through recent large-scale exome sequencing analyses. By integrating high-precision electrophysiological measurements with transcriptomic, proteomic, and imaging approaches, we demonstrate that XPO7 LoF alters Na+ channel properties and availability, disrupts neuronal excitability, and impairs the synchrony and regularity of network activity. These functional deficits are accompanied by widespread molecular dysregulation affecting nucleocytoplasmic transport, ion channel function, and synaptic composition. Among the dysregulated proteins is Nav1.2, a voltage-gated sodium channel encoded by the schizophrenia-associated gene SCN2A, which exhibits aberrant subcellular distribution in XPO7 LoF neurons, characterized by increased somatic accumulation and reduced synaptic localization. Together, these findings position XPO7 as a critical regulator of neuronal excitability and connectivity, linking channelopathy to cellular phenotypes relevant to schizophrenia pathophysiology.

overall_design: RNA-seq on isogenic human iPSC-derived excitatory neurons carrying either heterozygous or homozygous XPO7 loss-of-function (LoF) mutations. Samples were collected at three stages of neuronal differentiation (Day 28, Day 42, and Day 56) to capture transcriptional changes across development. Parental (wildtype) iPSC-derived neurons were included as controls.

first: Jen

middle: Q

last: Pan


title: LY6D Identifies Persistent Tumor-Initiating Cells Driving Pancreatic Tumorigenesis

city: Shanghai

first: Juanjuan

last: Shi

address: 160 Pujian Rd Shanghai 200127 P. R. China

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

summary: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy driven by oncogenic KRAS and inflammation-induced cellular heterogeneity, yet the mechanisms underlying tumor-initiating cells (TICs) emergence and maintenance remain unclear. Our study establishes LY6D as a marker of persistent TICs that orchestrate pancreatic cancer progression across all disease stages. Single-cell RNA sequencing of inflammation-driven PDAC models reveals that LY6D+ TICs specifically originate from KRAS-mutant acinar-to-ductal metaplasia (ADM) lesions under inflammatory conditions, maintaining conserved stemness properties and exhibiting a distinctive oxidative phosphorylation (OXPHOS) dependency throughout tumor evolution. Moreover, genetic ablation of Ly6d in KrasG12D pancreata delays tumorigenesis, while forced Ly6d expression enhances tumorigenic potential and metastatic capability. Mechanistically, LY6D-despite lacking intracellular domains-scaffolds lipid raft-associated kinase networks and  FOSL1-dependent epigenetic reprogramming to establish a stable pro-tumorigenic state. Clinically, LY6D+ cells are enriched in human PDAC and exhibit conserved stemness and epithelial-mesenchymal transition (EMT) properties. Strikingly, LY6D expression levels demonstrate PDAC-restricted prognostic power. Our work defines LY6D as pan-stage TICs marker linking cellular plasticity to PDAC initiation and progression, offering new avenues for early detection and interception of this lethal ma

overall_design: To investigate the mechanism of pancreatic cancer tumorigenesis, we performed Single-cell RNA sequencing of caerulein induced chronic pancreatitis in Ly6d conditional knockout-Kras G12D mutation and control Kras G12D mutation mouse models.

first: Jing

last: Xue


title: Strong Concordance of DNA Methylation Measures Between Venous and Capillary Blood - Implications for Human Epigenome Studies

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 117-2194 Health Sciences Mall

department: Faculty of Medicine

institute: University of British Columbia

type: Genome binding/occupancy profiling by genome tiling array

summary: DNA methylation is tissue specific, which has profound implications for data analysis. While both capillary and venous blood samples are whole blood, they are not identical in their clinical profiles. Here we assess the congruency of DNA methylation from 20 individuals with matched venous and capillary blood draw DNA methylation.  We used DNA methylation profiles from Illumina EPIC v2 arrays assess the differences of these blood sources in quality control approches, in predicted immune cell proportions,  in DNA methylation based predictors including epigenetic clocks and lifestyle predictors, and performed an examplar EWAS

overall_design: Bisulphite converted DNA from 40 blood samples, either capillary or venous blood from 20 matched individuals, were hybridized to the Illumina Infinium HumanMethylationEPIC version 2.0 microarray to evaluate: i) Differences in DNA methylation profiles between venous and capillary blood draws, and ii) Differences in DNA methylation-data based predictors calculated from either venous or capillary blood. Thereafter an EWAS of age and sex was conducted.

first: Hannah-Ruth

last: Engelbrecht

first: Chaini

last: Konwar

first: Beryl

middle: C

last: Zhuang

first: Kristy

last: Dever

first: Julie

middle: L

last: MacIsaac

first: Tran

middle: K

last: Toan

first: Kim

last: Korinek

first: Zachary

last: Zimmer


title: Estrogen Impacts NOD2-Dependent Regulation of Intestinal Homeostasis

city: Edmonton

first: Edan

last: Foley

state: Alberta

address: 116 st and 85 ave

department: Medical Microbiology and Immunology

institute: University of Alberta

summary: To investigate how NOD2 deficiency impacts gut homeostasis at the cellular level, prior to the onset of inflammation, we perform single-cell RNA sequencing on whole intestines from adult co-housed, in-crossed WT and nod2-/- siblings; minimizing impacts of environmental and genetic variability

overall_design: Five adult WT TL and five adult nod2-/- cohoused incrossed siblings with equal sex distribution were selected. Adult zebrafish intestines were dissected, dissociated into a single cell suspension, and processed for single-cell RNA sequencing.

first: Mckenna

last: Eklund


title: IRF7 links HK1-dependent histone lactylation to fibroblast activation and cardiac fibrosis [CUT&Tag]

city: Nanjing

first: yujia

last: xue

address: Longmian Avenue 639

institute: China Pharmaceutical University

summary: In response to a myriad of stimuli quiescent resident cardiac fibroblasts undergo metabolic, morphological, and functional alterations to transition to myofibroblasts and mediate cardiac fibrosis. In the present study we investigated the contribution of interferon regulatory factor 7 (IRF7) to fibroblast activation and cardiac fibrosis. IRF7 knockdown in quiescent cardiac fibroblasts potentiated whereas IRF7 over-expression suppressed myofibroblast transition. Consistently, targeted deletion of IRF7 fibroblasts/myofibroblasts similarly exacerbated cardiac fibrosis and dampened heart function in animal models of heart failure. Integrated transcriptomic analysis uncovered Hexokinase 1 (Hk1) as a downstream target for IRF7. Congruently, genetic deletion or pharmaceutical inhibition of HK1 protected the mice from adverse cardiac remodeling. Mechanistically, HK1 contributed to cellular lactate pool to promote histone H3K9 lactylation thus licensing the transcription of pro-fibrogenic molecules. Finally, the relevance of the IRF7-HK1 axis was authenticated in human heart specimens. In conclusion, our data unveil a previously unrecognized IRF7-HK1 axis that contributes to metaboloepigenetic reprogramming of fibroblast activation and cardiac fibrosis. Targeting this axis might yield novel therapeutic solutions for the intervention of heart failure.

overall_design: Mouse primary cardiac fibroblasts were induced to undergo Hk1 knockdown by transfection with SiRNA, followed by TGF-β treatment.

first: Ming

last: Kong

first: Chenghao

last: Zhu

first: Yujia

first: Wenxuan

last: Hong

first: Guoqing

last: Zhang

first: Dingsheng

last: Jinag

first: Yong

last: Xu

first: Junli

last: Guo


title: Uridine Modulates Gene Expression Programs During RANKL-Induced Osteoclastogenesis in RAW264.7 Cells

city: Hefei

first: sijie

last: bian

address: Huaihai Avenue

department: Department of Orthopaedics

institute: The First Affiliated Hospital of Anhui Medical Universit

summary: Uridine has been implicated in the regulation of metabolic and redox processes, yet its transcriptional effects during osteoclast differentiation remain unclear. This dataset profiles global gene expression in RAW264.7 cells under three conditions: untreated control, RANKL-induced osteoclastogenesis, and RANKL combined with uridine treatment. The results reveal uridine-responsive transcriptional changes involving osteoclast differentiation, oxidative stress regulation, and PI3K/Akt–FoxO–related pathways, providing mechanistic insight into uridine-mediated modulation of osteoclastogenesis.

overall_design: This study analyzed nine RNA-seq samples from RAW264.7 murine macrophages. Three experimental conditions were included: untreated control, RANKL-induced osteoclast differentiation, and RANKL combined with uridine treatment. Each condition contained three biological replicates. Total RNA was collected after 3 days of culture and sequenced to evaluate transcriptional changes associated with uridine-mediated regulation of osteoclastogenesis.

first: Sijie

last: Bian


title: A circuit of mechanically regulated transcription factors balances regenerative and fibrotic memory of mesenchymal stromal cells [RNA-seq]

city: Charlottesville

first: Andrew

last: Miller

state: Virginia

address: 415 Lane Rd.

department: Biomedical Engineering

institute: University of Virginia

summary: Therapeutic mesenchymal stromal cells (MSCs) are used to support the healing of severe injuries such as skin burn wounds. However, the pivotal expansion from donor biopsies on conventionally stiff culture surfaces activates MSCs into scar-promoting myofibroblasts. We previously coined the term mechanical memory to describe that priming of MSCs on scar-stiff culture substrates imprints myofibroblast features that persist even after a switch to skin-soft substrates. We now unravel mechanisms and factors that, conversely, suppress myofibroblast activation upon priming in skin-soft expansion culture. Such ‘soft memory’ factors are poised to preserve MSC regenerative features while suppressing fibrogenesis. Mechanically primed MSCs were compared by RNA- and assay for transposase-accessible chromatin (ATAC)-sequencing. The promoters of genes that were highly accessible and upregulated upon soft priming and memorized after switch to stiff substrates were significantly enriched for motifs predicted to bind the transcription factor HOXA11. Knockdown of HOXA11 resulted in enhanced expression of fibrogenic and osteogenic genes in soft-primed MSCs and reduced expression of anti-fibrotic factors, including the transcription factor SALLl1. SALL1 is a potent suppressor of pro-fibrotic genes such as Postn, Col8a1, Grem2, Thps1 and Thps2, and the transcription factor Gata6. GATA6, in turn, emerges as a keeper of stiff-induced myofibroblast memory by maintaining the accessibility of pro-fibrotic genes even after switch to soft substrates. By manipulating the SALL1-GATA6 transcriptional circuit in culture, we produced therapeutic MSCs that suppress fibrosis in an animal model of hypertrophic skin scarring. We propose that similar control over myofibroblast memory will enhance the success of therapeutic MSC applications in organ repair.

overall_design: RNA-sequencing of rat bone marrow-dervied mesenchymal stromal cells (MSCs) cultured on 2kPa or 100kPa gelatin-coated silicone elastomer substrates for 1, 3, or 5 passages. Passages were performed once per week. To evaluate the role of mechanical memory in the maintenance of the chromatin accessibility landscape, MSCs were cultured on 2kPa or 100kPa substrates for 3 passages and transferred to 100kPa (2T100_4) or 2kPa substrates (100T2_4) for 2 additional passages, respectively.

first: Fereshteh

last: Younesi

middle: E

first: Natalie

last: Andonian

first: Li

last: Diao

first: Thomas

middle: H

last: Barker

first: Boris

last: Hinz


title: Spatial transcriptomics for intrathoracic adhesion in mice

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

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

summary: Intrathoracic adhesions (IAs) complicate thoracic surgery, causing risks such as bleeding, prolonged operative time, and postoperative air leakage. Severe adhesions (>10% pleura) often necessitate conversion from VATS to open thoracotomy due to dissection difficulties and pleural damage. Given the increasing role of lung segmentectomy and re-lobectomy for small or recurrent NSCLC, reoperations with IA are expected to rise, highlighting the need for effective IA prevention. This study aimed to establish such a murine IA model, evaluate pathological and gene expression changes, and identify targets to prevent lung–chest wall adhesions.

overall_design: B6 mice were anesthetized with ketamine, and intrathoracic adhesions were induced. On day 6 after adhesion induction, lung tissues were harvested, fixed in 4% formaldehyde, and embedded in paraffin blocks. Sections were cut at 5 µm intervals, and the samples were subsequently subjected to Visium spatial transcriptomic analysis.

first: Tomohisa

last: Sakaue

first: Yu

last: Mori

first: Hironori

last: Izutani


title: A circuit of mechanically regulated transcription factors balances regenerative and fibrotic memory of mesenchymal stromal cells [ATAC-Seq]

overall_design: ATAC-sequencing of rat bone marrow-dervied mesenchymal stromal cells (MSCs) cultured on 2kPa or 100kPa gelatin-coated silicone elastomer substrates for 1, 3, or 5 passages. Passages were performed once per week. To evaluate the role of mechanical memory in the maintenance of the chromatin accessibility landscape, MSCs were cultured on 2kPa or 100kPa substrates for 3 passages and transferred to 100kPa (2T100_4) or 2kPa substrates (100T2_4) for 2 additional passages, respectively.


title: Effects of ASH2L deficiency on the differentiation and thermogenic capacity of primary adipocytes

first: Yajie

last: Hu

state: Shanghai

address: 825 Zhangheng Road, Pudong New District, Shanghai, China.

department: Human Phenome Institute

institute: Fudan University

summary: Adipocyte development and thermogenesis are tightly regulated by epigenetic mechanisms, which may represent potential therapeutic targets for metabolic disorders such as obesity. In this study, we identified Ash2l, a core component of the COMPASS histone methyltransferase complex, as a critical regulator that promotes adipogenesis and thermogenesis. Our ChIP-seq analysis revealed that Ash2l exerts its function by modulating the expression of genes marked by broad Ash2l peaks near transcription start sites, many of which are closely associated with adipogenesis and thermogenic processes.

overall_design: ChIP-seq of Ash2l (Absent, small, or homeotic disc 2-like protein) in BAT primary adipocytes

first: Jialin

last: Zhao

first: Chenxi

last: Xiao

first: Shenhan

first: Jun

last: Chang

first: Xinhua

last: Liu


title: Autoinhibition of ASXL1 Condensation via Opposing-Charge Blocks in Its Disordered Region

city: Guangzhou

first: Xiao

last: Fang

address: No. 1 Panfu Road, Yuexiu District

institute: Guangzhou First People's Hospital

summary: Long intrinsically disordered regions (IDRs) are prevalent in chromatin regulators, yet how they encode regulatory logic remains unclear. Here, we show that ASXL1, a frequently mutated scaffold protein in myeloid malignancies, employs a charge-based autoregulatory mechanism to control phase separation. Truncations within ASXL1’s long linker IDR (llIDR) remove a negatively charged segment that normally inhibits condensate formation by electrostatically masking the positively charged ASXM1 domain. Loss of this charge block shifts ASXL1 into a condensate-competent state, promoting liquid-like assembly and facilitating recruitment of the chromatin reader BRD2. These aberrant condensates alter BRD2’s genomic localization, disrupt heterochromatin organization, and impair neutrophil differentiation. Pharmacological disruption of condensates partially restores nuclear morphology, suggesting therapeutic tractability. Our findings define a tunable electrostatic switch within ASXL1’s IDR and provide a general framework for understanding how charge patterning in IDRs governs nuclear condensation and lineage fidelity.

overall_design: ChIP-seq data for ASXL1 and BRD2 in U2OS ASXL1-TR-BioID and ASXL1-LTR-BioID stable cell lines; ChIP-seq data for BRD2 in U2OS ASXL1-TR and ASXL1-LTR knock-in cells; CUT&Tag data for ASXL1 in U2OS ASXL1-TR and ASXL1-LTR knock-in cells; and ATAC-seq data in U2OS wild-type, ASXL1-FL, ASXL1-TR, and ASXL1-LTR knock-in cells.


title: Transcriptome analyses of Arabidopsis natural accessions Col-0 and IP-Svi-0 at different tempearatures

city: Seoul

first: Zeeshan

last: Nasim

address: Anam-ro 145, Seongbuk-Gu

department: School of Life Sciences and Biotechnology

country: South Korea

institute: Korea University

summary: Plants are sessile organisms; thus they developed sophisticated endogenous mechanisms to detect and respond to various environmental cues . Our planet has diverse light and temperature conditions, to adopt in such a wide range of climatic conditions plants must have phenotypic plasticity. In addition to phenotypic plasticity plants also have variations in ontogenetic trajectory that results from genetic and epigenetic modifications leading to differential growth response to varying environment. To ensure successful adaptation and survivability in diverse climatic conditions a number of genetic polymorphisms are accumulated in various natural accessions of Arabidopsis. In this study, we investigated the reasons of photoperiod and temperature insensitive early flowering phenotype of San Vicente (IP-Svi-0) which was collected from San Vicente, Spain (Latitude: 43.39; Longitude: -7.39). Our RNA seq analysis showed decreased expression of MAF1-3 and 5

overall_design: To investigae differentially expressed genes in IP-Svi-0 natural accession and identifying imporant genes involved in its early flowering, we performed RNA sequencing of two different IP-Svi-0 and Col-0 seedlings at different temperatures.

first: Nasim

last: Zeeshan

first: Karim

last: Nouroz

first: Ahn

last: Ji-Hoon


title: Pulmonary fibroblast subsets demonstrate differentially enriched signaling pathways during fibrosis resolution and repair

city: Denver

first: Elizabeth

last: Redente

state: CO

address: 1400 Jackson Street

department: Pediatrics

institute: National Jewish Health

summary: The lungs have a remarkable capacity to undergo homoeostatic repair and regeneration after injury, which often occurs in patients with acute respiratory distress syndrome (ARDS) and in the single-dose bleomycin mouse model. Fibroblasts are critical mediators of fibrotic disease and RNA sequencing has identified significant heterogeneity within pulmonary fibroblast populations. However, the contribution of distinct fibroblast subsets to the repair process has been understudied compared to their role in fibrosis initiation and progression. Therefore, we sought to define the transcriptional landscape of three phenotypically-defined fibroblast subsets that occupy discrete spatial locations in naïve lungs. Using TdTomato-lineage tracing approaches, we identified and interrogated collagen1a1+ (Col1a1) fibroblasts, perilipin 2+ (Plin2) alveolar fibroblasts, and -smooth muscle actin+ (Acta2) myofibroblasts during fibrosis development and resolution after single-dose bleomycin. Quantification of fibroblast numbers showed that all three subsets expand during fibrosis and contract towards naïve levels with resolution. Principal component and gene-set enrichment analyses indicated that each subset undergoes major transcriptomic shifts during fibrosis development, converging on a similar pro-fibrotic transcriptional profile. However, during resolution, Plin2+ and Acta2+ fibroblasts revert towards a pre-fibrotic transcriptional state, whereas Col1a1+ fibroblasts acquire a distinct program that suggests suggesting an active role in mediating the repair processes.

overall_design: Bluk RNA-seq: Col1a1: Naïve (3 reps), 3wk bleo (3 reps), 8wk bleo (3 reps); Acta2: Naïve (3 reps), 3wk bleo (3 reps), 8wk bleo (3 reps); Plin2: Naïve (3 reps), 3wk bleo (3 reps), 8 wk bleo (2 reps)

first: Foster

last: Daniel G.

first: Javkhlan

last: Nomin

first: Black

last: Bart P.

first: Vestal

last: Brian E.

first: Riches

last: David W.H.

first: Redente

last: Eliabeth F.


title: STAT4 drives optimal expansion and transcriptional repression of type I interferon pathway in inflammatory ILC2

city: Rome

first: Mattia

last: Laffranchi

address: Viale Regina Elena 291

department: Molecular Medicine

country: Italy

institute: La Sapienza University of Rome

summary: Innate immune cells respond rapidly to environmental cues through signal-regulated transcription factors (SRTF) that sense changes in the tissue microenvironment.  Signal Transducer and Activator of Transcription (STAT) proteins are critical regulators of cytokine signaling and determine polarized immune responses. Herein, we reveal that activated type 2 innate lymphocytes (ILC2) express STAT4, a SRTF canonically linked to type 1 immunity. STAT4 expression is induced in ILC2s upon activation by the alarmin IL-25 and linked with generation of inflammatory ILC2s (iILC2s), a subset characterized by a mixed type 2/type 3 cytokine profile. Despite elevated STAT4 expression, iILC2s do not acquire type 1 features, such as IFN-g production or T-bet expression and do not respond to IL-12 stimulation. Instead, STAT4 is activated downstream of type I interferons and supports the maintenance of the iILC2 pool. Transcriptomic analysis of Stat4-deficient ILC2s reveals enhanced type I interferon signaling and impaired proliferation, suggesting that STAT4 functions to antagonize interferon-driven suppression. Our data uncover a novel regulatory axis in which IL-25-induced STAT4 expression equips ILC2s to modulate interferon responses, thus sustaining inflammatory effector populations during immune activation. These findings broaden the understanding of ILC2 activation and suggest new avenues for modulating innate lymphocytes in inflammatory diseases.

overall_design: For bulk RNA-seq experiments 30-50,000 ILC2 were FACS-sorted as L/D-CD3ε- CD19-NK1.1, KLRG1+ cells from the lungs of IL-25-treated (3 days) Rag2-/- and Rag2-/-Stat4-/- mice. Four replicates for Stat4-sufficient and -deficient ILC2 were generated.

first: Giuseppe

last: Pietropaolo

last: Sciumé


title: Quantitative Proteomics Reveals the Role of Lysine Lactylation in Lenalidomide-Resistance in Multiple Myeloma Cells [RNA-Seq]

city: Yantai

first: Xinlong

last: Guo

state: Shandong province

address: No. 198, Binhai East Road, Muping District, Yantai City, Shandong Province, China

department: Shandong Laboratory of Yantai Drug Discovery

institute: Bohai Rim Advanced Research Institute for Drug Discovery

summary: Multiple myeloma (MM) is a hematologic malignancy characterized by abnormal plasma cell proliferation, with lenalidomide emerging as a primary treatment. However, prolonged use often leads to drug resistance, underscoring the need to understand resistance mechanisms. Protein post-translational modifications (PTMs) play crucial roles in disease development, including chemoresistance. Here, we investigate the involvement of new types of PTMs, focusing on lysine lactylation (Kla), in lenalidomide resistance. We observed elevated Kla levels in lenalidomide-resistant MM cells, implicating its role in resistance. Through quantitative proteome, lactylome, and acetylome analysis, we identified 7493 proteins, 1241 Kla sites, and 9313 lysine acetylation (Kac) sites, thereby revealing differential protein expression and PTM profiles in lenalidomide-resistant cells. Proteomic analysis revealed that a serious of chemoresistance related proteins were upregulated, and a number of CRL4CRBN regulatory factors were downregulated. Lactylome analysis revealed that numerous chemoresistance related proteins exhibited increased Kla levels in lenalidomide-resistant MM cells, suggesting that Kla played an important role in the development of lenalidomide-resistance in LenR MM cells. Notably, histone H4K8la were associated with upregulation of chemoresistance-related genes CDK6 and ECHS1. Our findings shed light on the epigenetic mechanisms underlying lenalidomide resistance in MM, offering insights for overcoming chemoresistance.

overall_design: RNA-seq profiling of wildtype (WT) and lenalidomide-resistant (LenR) MM.1S cells.

first: Xuelian

last: Ren

first: Cong

last: Yan

first: He

last: Huang


title: m6a and NuRD complexes regulate monocytic differentiation and resistance to BCL2/BCL2L1 inhibitors in AML

city: Portland

first: Daniel

last: Bottomly

address: 3181 S.W. Sam Jackson Park Rd.

institute: Oregon Health and Science University

summary: Frontline use of the BCL2 inhibitor, venetoclax, for acute myeloid leukemia (AML) has resulted in broad improvements in patient outcome. A major remaining challenge is the development of venetoclax resistance, frequently driven by compensatory transcriptional programs that promote cell survival and differentiation. These changes reduce dependence on BCL2 in favor of alternative anti-apoptotic BCL2 family members such as MCL1 or BCL2L1 (BCL-XL). Using CRISPR-based genome-wide perturbation screens, we investigated the genetic dependencies of venetoclax and the BCL2/BCL2L1 dual inhibitor AZD4320. We identified the N6-methyladenosine (m6A) writer RBM15, and the Nucleosome Remodeling and Deacetylase (NuRD) complex interactor ZMYND8 as novel mediators of resistance to both venetoclax and AZD4320. Loss of RBM15 or ZMYND8 induced drug resistance, concurrent with alterations in BCL2 family expression and monocytic differentiation. Accordingly, in AML patient samples we found reduced expression of the respective m6a or NuRD complexes was significantly associated with monocytic differentiation and ex vivo resistance to the same drugs. These findings provide critical insights into previously undescribed mechanisms of BCL2 family inhibitor resistance in AML.

overall_design: Using a genome-wide CRISPR screen on OCI-AML2 cells, we performed comparisons of sgRNA read counts between DMSO and AZD4320 at Day 14.  Genes that were significantly depleted (enriched) relative to DMSO controls were deemed candidates for enhancing drug sensitivity (resistance).

first: Jackson

last: Brim-Edwards

first: Karen

last: Morris

first: Quinlan

last: Morrow

first: Stephen

last: Kurtz

first: Cristina

last: Tognon

first: Shannon

last: McWeeney

first: Tamilla

last: Nechiporuk

first: Kevin

last: Watanabe-Smith

first: Jeffrey

middle: W

last: Tyner


title: Quantitative Proteomics Reveals the Role of Lysine Lactylation in Lenalidomide-Resistance in Multiple Myeloma Cells [CUT&Tag]

summary: Multiple myeloma (MM) is a hematologic malignancy characterized by abnormal plasma cell proliferation, with lenalidomide emerging as a primary treatment. However, prolonged use often leads to drug resistance, underscoring the need to understand resistance mechanisms. Protein post-translational modifications (PTMs) play crucial roles in disease development, including chemoresistance. Here, we investigate the involvement of new types of PTMs, focusing on lysine lactylation (Kla), in lenalidomide resistance. We observed elevated Kla levels in lenalidomide-resistant MM cells, implicating its role in resistance. Through quantitative proteome, lactylome, and acetylome analysis, we identified 7493 proteins, 1241 Kla sites, and 9313 lysine acetylation (Kac) sites, thereby revealing differential protein expression and PTM profiles in lenalidomide-resistant cells. Proteomic analysis revealed that a serious of chemoresistance related proteins were upregulated, and a number of CRL4-CRBN regulatory factors were downregulated. Lactylome analysis revealed that numerous chemoresistance related proteins exhibited increased Kla levels in lenalidomide-resistant MM cells, suggesting that Kla played an important role in the development of lenalidomide-resistance in LenR MM cells. Notably, histone H4K8la were associated with upregulation of chemoresistance-related genes CDK6 and ECHS1. Our findings shed light on the epigenetic mechanisms underlying lenalidomide resistance in MM, offering insights for overcoming chemoresistance.


title: The molecular architecture of incidental meningiomas

city: San Francisco

first: Minh

middle: P

last: Nguyen

state: California

institute: University of California, San Francisco

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Functional redundancy between UTY and UTX in regulating the localization of transcription factors involved in pluripotency [RNA-seq]

city: Yokohama

first: Tomohiko

last: Akiyama

address: 3-9 Fuku-ura

institute: Yokohama city university

summary: The Y chromosome retains a limited number of protein-coding genes, yet their biological significance remains poorly understood. Here, we find UTY, a Y-linked homolog of the histone demethylase UTX, plays an essential regulator of pluripotency in human embryonic stem cells. Despite its low expression and weak enzymatic activity, UTY co-localizes with UTX at active cis-regulatory elements and contributes to the regulation of core pluripotency genes such as NODAL and LEFTY. Through genome-wide occupancy and transcriptome analyses of knockout cell lines, we show that UTY and UTX function redundantly to maintain proper localization of key transcription factors including OCT4 and SOX2. Dual loss of UTY and UTX leads to their mislocalization, widespread transcriptional dysregulation, and loss of pluripotency, without changes in H3K27 methylation. Instead, these effects are associated with changes in histone acetylation and altered chromatin accessibility, likely driven by recruitment of ATP-dependent chromatin remodelers, pointing to a non-enzymatic mechanism. Our findings uncover a novel role for UTY in stabilizing transcription factor binding and maintaining cell identity, demonstrating that even the evolutionarily compact Y chromosome retains critical regulatory functions in early human development.

overall_design: RNA-sequencing analysis for WT and UTX/UTY-KO hES cells


title: Functional redundancy between UTY and UTX in regulating the localization of transcription factors involved in pluripotency


title: Targeted gene expression panel for incidental meningiomas

summary: A previously published custom Nanostring nCounter panel of 75 meningioma related genes and reference genes was performed on human  FFPE meningioma samples. This was done as part of a study of the molecular architecture of incidental meningiomas.

overall_design: 129 human meningiomas samples were processed for this study

first: David

middle: R

last: Raleigh


title: Dual-targeting PARP and LIN28B alleviates the accumulation of malignant serous effusion by decreasing vascular permeability

city: shanghai

first: yan

last: fang

address: dongchuan Street 800

institute: shanghai jiaotong university

summary: Malignant serous effusion (MSE) is a common and severe complication in advanced malignancies, associated with poor prognosis and high recurrence rates. To date, no standardized treatments are available for MSE management, posing significant clinical challenges. Here, we identify aberrant LIN28B expression and dysregulation of DNA repair pathways in MSE patient samples and preclinical models. We developed a nanoparticle delivery system incorporating LIN28B siRNA (siRNA/DSSP@lip-PEG-FA) to specifically inhibit LIN28B function. Combined with the PARP inhibitor BMN673, this nanoparticle system significantly alleviates MSE accumulation and prolongs survival in preclinical models without systemic cytotoxicity. Mechanistically, single-cell RNA sequencing (scRNAseq) reveals that this combination therapy markedly remodels the immune microenvironment by decreasing M2 macrophages and increasing neutrophil components with altered subtypes. Notably, Arg1-positive neutrophils, which produce pro-inflammatory cytokines to increase vascular permeability, are diminished by the combination treatment. Furthermore, In vitro and in vivo experiments demonstrate that our approach inhibits vascular leakage and strengthens the rigidity of tight junction, suggesting suppression of vascular permeability. Together, our findings establish dual-targeting of PARP and LIN28B as a promising therapeutic strategy for MSE management in advanced cancers, with the potential to improve patient quality of life.

overall_design: ascites (n = 2) from mice treated with LIN28B siRNA and BMN673 and PBS were extracted and analysis by 10× Genomics single-cell RNA sequencing (scRNA-seq).

first: Yan

last: Fang

first: Yao

last: Lin

first: Jianfeng

last: Shen


title: Dissecting the cell-type specific role of a dominant resistance gene during viral infection [scRNA-Seq]

city: Ningbo

first: zhang

middle: yu

last: hong

address: No. 818, Fenghua Street

institute: Ningbo University

summary: Plant viruses cause widespread crop epidemics, with resistance (R) genes playing key roles in plant defense by triggering responses that limit viral replication and spread. However, given the diversity of plant cell types and their developmental paths, the specific roles of R genes in distinct cell types remain unclear. Using tomato brown rugose fruit virus (ToBRFV), which partially overcomes the tobamovirus resistance gene Tm-22, this study employed single-cell RNA sequencing to explore infection dynamics and Tm-22-mediated responses at the cellular level. Results indicated that upon ToBRFV infection, the Tm-22 gene and the tm-2 allele, which carries a recessive form of Tm-22, differentially regulate the composition of cell types in tomato leaves. Tm-22 does not fully inhibit viral entry or movement during the early stages but selectively restricts viral replication or accumulation in certain cell types. ToBRFV differentially modulates signaling pathways depending on cell type and genotype, including Tm-22 and tm-2 homozygotes. Pseudotime analysis revealed that during mesophyll cell development in Tm-22 plants, ToBRFV reverses expression of BR positive regulators, but not negative ones; silencing these BR positive regulators increased infection in Tm-22 plants while suppressing it in tm-2 plants, linking BR signaling to Tm-22-dependent resistance. This study offers the first cell-type-specific insight into R gene function, showing how Tm-22 restrains ToBRFV accumulation through BR signaling pathways. It provides a valuable framework for future single-cell investigations of resistance genes, enhancing our understanding of plant-virus interactions.

overall_design: Four sample from ToBRFV or the pcb-GUS control inoculated tm-2 tomato plants and Tm-22 tomato plants. Comparative gene expression profile analysis of scRNA-seq data for Tm-22 and tm-2 plants either pcb-GUS (mock) inoculated  or ToBRFV inoculated . Including four comparison groups, tm-2-Mock vs. Tm-22-Mock, Tm-22-ToB vs. Tm-22-Mock, tm-2-ToB vs. tm-2-Mock, and tm-2-ToB vs. Tm-22-ToB.

first: Yuhong

last: Zhang

first: Shan

last: Bu

first: Luyou

last: Wang

first: Jiayi

last: Liu

first: Junchen

last: Xu

first: Jiejun

last: Peng

first: Fei

last: Yan

first: Jian

last: Wu


title: Functional redundancy between UTY and UTX in regulating the localization of transcription factors involved in pluripotency [ChIP-seq_dualcross]

overall_design: Dual-crosslink chromatin immunoprecipitation DNA sequencing for transcription and chromatin related factors in WT and UTX/UTY-KO hES cells


title: LY6D Identifies Persistent Tumor-Initiating Cells Driving Pancreatic Tumorigenesis [ATAC-seq]

city: Shanghai

first: Juanjuan

last: Shi

address: 160 Pujian Rd Shanghai 200127 P. R. China

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

summary: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy driven by oncogenic KRAS and inflammation-induced cellular heterogeneity, yet the mechanisms underlying tumor-initiating cells (TICs) emergence and maintenance remain unclear. Our study establishes LY6D as a marker of persistent TICs that orchestrate pancreatic cancer progression across all disease stages. Single-cell RNA sequencing of inflammation-driven PDAC models reveals that LY6D+ TICs specifically originate from KRAS-mutant acinar-to-ductal metaplasia (ADM) lesions under inflammatory conditions, maintaining conserved stemness properties and exhibiting a distinctive oxidative phosphorylation (OXPHOS) dependency throughout tumor evolution. Moreover, genetic ablation of Ly6d in KrasG12D pancreata delays tumorigenesis, while forced Ly6d expression enhances tumorigenic potential and metastatic capability. Mechanistically, LY6D-despite lacking intracellular domains-scaffolds lipid raft-associated kinase networks and  FOSL1-dependent epigenetic reprogramming to establish a stable pro-tumorigenic state. Clinically, LY6D+ cells are enriched in human PDAC and exhibit conserved stemness and epithelial-mesenchymal transition (EMT) properties. Strikingly, LY6D expression levels demonstrate PDAC-restricted prognostic power. Our work defines LY6D as pan-stage TICs marker linking cellular plasticity to PDAC initiation and progression, offering new avenues for early detection and interception of this lethal malignancy.

overall_design: To investigate the mechanism how ly6d affect the pancreatic cancer initiation and development, we performed ATACseq in Ly6d low cells and Ly6D high cells, as well as the Ly6D WT cells and Ly6D overexpression cells to validate the chromatin accessibility.

first: Jing

last: Xue


title: LY6D Identifies Persistent Tumor-Initiating Cells Driving Pancreatic Tumorigenesis [RNA-seq]

overall_design: To investigate the mechanism how ly6d affect the pancreatic cancer initiation and development, we performed RNAseq in Ly6d WT cells and Ly6D overexpression cells to validate the transcriptomics.


title: Analysis of the mechanism of acquisition of chemotherapy resistance in colorectal cancer cell lines

first: Daisuke

last: Motooka

summary: Although anticancer drugs such as fluorouracil and oxaliplatin are widely used in the treatment of colorectal cancer, they are ineffective when cancer cells acquire drug resistance. The treatment strategy for colorectal cancer that has acquired drug resistance has become a problem in chemotherapy. To investigate the cause of drug resistance, we created drug-resistant strains of colon cancer cell lines by mixing a small amount of anticancer drug in the culture medium and culturing them for a long period of time, and explored the genetic changes by RNA-sequence.

overall_design: The colorectal cancer cell lines HCT116, SW480, and DLD1 were exposed to a non-lethal dose of fluorouracil(5 - 70μM) and oxaliplatin(5 - 35μM) and cultured for about 6 months for RNA-seq analysis.

first: Yoshinao

last: Chinen

first: Tsuyoshi

last: Hata

last: Okuzaki

first: Yuichiro

last: Doki


title: Species-specific oxygen sensing governs the initiation of vertebrate limb regeneration [scRNA-seq]

city: Tübingen

first: Can

last: Aztekin

address: Max-Planck-Ring 9

department: TheFriedrich Miescher Laboratory

country: Germany

institute: The Max Planck Society for Biology

summary: Why mammals cannot regenerate limbs, unlike amphibians, presents a longstanding puzzle in biology. We show that exposing ex vivo amputated embryonic mouse limbs to subatmospheric oxygen environment, or stabilizing oxygen-sensitive HIF1A enables not only rapid wound healing, but alters cellular mechanics, and reshapes the histone landscape to prime regenerative fates. Conversely, regenerative Xenopus tadpole limbs display low oxygen-sensing capacity, robust wound healing, a regenerative histone landscape, and glycolytic programs even under high oxygen. This reduced oxygen-sensing capacity, in stark contrast to mammals, associates with decreased HIF1A-regulating gene expressions. Our findings thus uncover species-specific oxygen sensing as a unifying mechanism for limb regeneration initiation across vertebrates, reveal how aquatic subatmospheric habitats may enhance regenerative capabilities, and identify targetable barriers to unlock latent limb regenerative programs in adult mammals.

sample_organism:
Xenopus laevis
Mus musculus

platform_organism:
Xenopus laevis
Mus musculus

overall_design: RNA-seq profiling of mouse and Xenopus cells extracted from limb explants cultured under different conditions at 1 or 3 dpa (days post-amputation).

first: Georgios

last: Tsissios

first: Marion

last: Leleu


title: LY6D Identifies Persistent Tumor-Initiating Cells Driving Pancreatic Tumorigenesis [scRNA-seq]

overall_design: To investigate the mechanism of pancreatic cancer tumorigenesis, we performed Single-cell RNA sequencing of caerulein induced chronic pancreatitis in Kras WT and Kras G12D mutation mouse models.


title: Fusion-positive rhabdomyosarcoma oncofusions share a common interactome

city: Durham

first: Benjamin

middle: Kakimoto

last: Lau

state: NC

address: 3 Genome Court

institute: Duke University

summary: The sole reoccurring oncogenic mutation in the pediatric cancer of fusion-positive rhabdomyosarcoma is a reciprocal translocation giving rise to a transcriptional oncofusion comprised of the N-terminus of the PAX3 transcription factor encoding DNA-binding domains fused in-frame to the C-terminus of the FOXO1 transcription factor encoding a transactivation domain. However, a host of new translocations have been detected in this cancer that are known or predicted to encode a protein comprised of the same PAX3 or its paralog PAX7 N-terminus, but with very different C-terminal fusion partners. How such different oncofusions cause the identical cancer was unknown. Here we show that these oncofusions are functionally interchangeable and engage a common interactome of proteins and activate a core shared transcriptional program. Interestingly, this common interactome contains the C-terminal fusion partners or their paralogs of all tested oncofusions, as well as the C-terminal fusion partner of a novel oncofusion. We thus suggest that oncofusions originate in rhabdomyosarcoma from the same DNA-binding domain fused to proteins within a common interactome, which in turn engages a core set of genes giving rise to this cancer.

overall_design: We used CUT&Tag to assess genome-wide binding of PAX3-FOXO1 and its cofactors in RF4 cells. Specifically, CUT&Tag for anti-Flag was used to probe endogenous PAX3-FOXO1, as well as for PAX3-FOXO1’s cofactors (INO80D, MAML1 and NCOA1), in RF4-flag cells harboring a Flag tag knockin to endogenous PAX3-FOXO1 allele; additionally, CUT&Tag for anti-V5 was used to probe various rhabdomyosarcoma-associated oncofusions in the shP3F1 RF4-flag cells with an ectopically expressed, V5-tagged PAX3-FOXO1, PAX3-INO80D, PAX3-MAML1 or PAX3-NCOA1.

first: G. Greg


title: LTBP4 Deficiency Inhibits NLRP3 Inflammasome Activation in Cardiomyocytes and Attenuates Heart Failure

first: Jieyu

last: Guo

address: 138 Yixueyuan Rd,

institute: fudan university

summary: The complex mechanisms underlying the roles of inflammation in heart failure remain incompletely understood. In this study, we elucidate the significant role of LTBP4 in heart failure. LTBP4 was capable of promoting the interaction between NLRP3 and NEK7 and activating the NLRP3 inflammasome signaling pathway. The 1574-1624 amino acids of LTBP4 were essential for this process. Inhibition of LTBP4 improves heart function post-TAC, highlighting its potential as a new therapeutic target for heart failure.

overall_design: To explore the role of myocardial LTBP4 in heart remodeling after transverse aortic constriction (TAC), RNA sequencing was performed on WT and cardiomyocyte-specific Ltbp4 inducible knockout mice (Ltbp4cko) mice hearts post-TAC.

first: Dan

last: Meng

first: Siyu

last: Ma


title: Blocking Interaction of Apurinic/apyrimidinic Endonuclease and DNA Secondary Structure G-quadruplex Suppresses Triple-Negative Breast Cancer Metastasis

city: Omaha

first: Jordan

last: Rowley

state: NE

address: 3828 Jones St, Apt 202

institute: University of Nebraska Medical Center

summary: Triple-negative breast cancer (TNBC) is the most aggressive and highly metastatic breast cancer. Recent genome-wide analyses have identified significant alterations in non-canonical four-stranded DNA secondary structures, G-quadruplexes (G4), within promoter and enhancer regions of genes linked to metastatic TNBC. The mechanistic link between G4 DNA and TNBC metastasis, however, remains unclear. Using CRISPR to genetically abrogate G4 folding at the endogenous  gene promoters in TNBC cells, we demonstrate that loss of G4 structure in CXCL1 gene promoter significantly reduces CXCL1 expression, consequently a significant decrease in cell migration and invasion, as well as in vivo tumorigenesis and lung metastasis. Mechanistically, G4 recruits APE1, a multifunctional protein that enhances transcription factors binding through its redox-effector function and activates key metastasis-associated genes. Further, APE1 deletion or disruption of its binding to G4 with TMPyP4, a G4 ligand, suppresses gene expression, tumor growth, and lung metastasis. Our study provides the first genetic evidence of G4's role in tumor progression and metastasis and identifies the G4:APE1 axis as a novel therapeutic target to target TNBC primary tumor and metastasis.

overall_design: Our study reveals a novel mechanistic link between G4 structure and APE1 to regulate expression of pro-metastatic genes in TNBC progression and distant metastasis. Importantly, we demonstrate that disrupting the G4:APE1 axis using a pharmacological inhibitor significantly impairs metastatic potential, highlighting a promising and targetable therapeutic approach for TNBC metastasis.

first: Achyuth

last: Kalluchi

first: Chen

last: Yingling

first: Bhakat

last: Kishor


title: CRISPR/Cas-based activation of PPARGC1A boosts endogenous mitochondria and enhances cardiac function and recovery after myocardial infarction

city: Houston

first: Isaac

middle: B

last: Hilton

state: TX

address: 6500 Main St

department: Bioengineering

institute: Rice University

summary: Insufficient energy supply, defined by reduced mitochondrial capacity and altered substrate metabolism, has emerged as a key pathological factor in the development of heart failure (HF) after myocardial infarction (MI). Although current therapeutic strategies of revascularization and afterload reduction have been transformative, no strategy directly augments myocardial energy production. In mammalian cells, mitochondrial biogenesis is orchestrated by the activity of multiple genes encoded by both the nuclear and mitochondrial genomes. While the activation of PPARGC1A, a key driver of mitochondrial biogenesis, can increase cellular mitochondria, supraphysiological levels of PPARGC1A result in adverse tissue remodeling and heart function. CRISPR activation (CRISPRa) technologies present a unique opportunity to address these shortcomings, as they enable tunable control over endogenous target gene expression in cells and in vivo. Here, we demonstrate that transcriptional activation of PPARGC1A using CRISPRa increases cellular mitochondria in diverse human cell types. This effect is mediated through the activation of transcriptional programs driving mitochondrial biogenesis, mitochondrial function, and cellular bioenergetics. These activated transcriptional programs synergize to increase ATP production and reserve capacity in human cardiomyocytes. CRISPRa targeting of PPARGC1A in vivo increases cardiac mitochondria to recover heart ejection fraction in an acute-MI model. Furthermore, CRISPRa acts on adult human heart samples to increase PPARGC1A protein levels and cellular mitochondria, elevating general mitochondrial function in both normal and HF-diagnosed hearts. Altogether, these results provide the first proof-of-concept demonstration that endogenous gene activation via CRISPRa can improve heart function after myocardial infarction.

overall_design: RNA-seq profiling of untransduced AC16 cells and CRISPRa targeting PPARGC1A transduced cells 72 hours post-transduction

first: Mario

last: Escobar

first: Ravi

last: Ghanta


title: Structural basis for Lamassu-based antiviral immunity and its evolution from DNA repair machinery

city: New York

first: Samuel

last: Sternberg

address: 701 W. 168th Street, HHSC 726

institute: Columbia University

summary: Bacterial immune systems exhibit remarkable diversity and modularity, as a consequence of the continuous selective pressures imposed by phage predation. Despite recent mechanistic advances, the evolutionary origins of many antiphage immune systems remain elusive, especially for those that encode homologs of the Structural Maintenance of Chromosomes (SMC) superfamily, which are essential for chromosome maintenance and DNA repair across domains of life. Here, we elucidate the structural basis and evolutionary emergence of Lamassu, a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor. Using cryo-EM, we determined structures of the Vibrio cholerae Lamassu complex in both apo- and dsDNA-bound states, revealing unexpected stoichiometry and topological architectures. We further demonstrate how Lamassu specifically senses dsDNA in vitro and phage replication origins in vivo, thereby triggering the formation of LmuA tetramers that activate the Cap4 nuclease domain. Our findings reveal that Lamassu evolved via exaptation of the bacterial Rad50-Mre11 DNA repair system to form a compact, modular sensor for viral replication, exemplifying how cellular machinery can be co-opted for novel immune functions.

overall_design: E. Coli ChIP-seq profiling to identify LmuB protein binding site from Lamassu defense system. Samples include a number of time points post lambda phage infection as well as induction conditions in order to identify optimal conditions for identifying the binding site.

first: Matthieu

last: Haudiquet

first: Arpita

last: Chakravarti

first: Zhiying

last: Zhang

first: Josephine

last: Ramirez

first: Alba

last: Herrero del Valle

first: Paul Dominic

last: Olinares

first: Rachel

last: Lavenir

first: Massilia

last: Aït Ahmed

first: M. Jason

last: de la Cruz

first: Brian

middle: T

last: Chait

first: Aude

last: Bernheim

first: Dinshaw

last: Patel


title: LIN28B siRNA+BMN673

first: yan

last: fang

summary: Malignant serous effusion (MSE) is a common and severe complication in advanced malignancies, associated with poor prognosis and high recurrence rates. To date, no standardized treatments are available for MSE management, posing significant clinical challenges. Here, we identify aberrant LIN28B expression and dysregulation of DNA repair pathways in MSE patient samples and preclinical models. We developed a nanoparticle delivery system incorporating LIN28B siRNA (siRNA/DSSP@lip-PEG-FA) to specifically inhibit LIN28B function. Combined with the PARP inhibitor BMN673, this nanoparticle system significantly alleviates MSE accumulation and prolongs survival in preclinical models without systemic cytotoxicity. Mechanistically,bulk RNA sequencing (RNAseq) of A2780 reveals that this combination therapy markedly remodels the immune microenvironment by decreasing M2 macrophages and increasing neutrophil components with altered subtypes. Notably, Arg1-positive neutrophils, which produce pro-inflammatory cytokines to increase vascular permeability, are diminished by the combination treatment. Furthermore, In vitro and in vivo experiments demonstrate that our approach inhibits vascular leakage and strengthens the rigidity of tight junction, suggesting suppression of vascular permeability. Together, our findings establish dual-targeting of PARP and LIN28B as a promising therapeutic strategy for MSE management in advanced cancers, with the potential to improve patient quality of life.

overall_design: RNA-seg profling of wildtype A2780 cells treated with PARP inhibitor BMN673 and LIN28B siRNA (siRNA/DSSP@lip-PEG-FA)

first: Yan

last: Fang

first: Yao

last: Lin

first: Jianfeng

last: Shen


title: Screening Genes related to Bur Lignification Development in field sandbur (Cenchrus pauciflorus Benth.) Based on Full-Length Transcriptome Sequencing

city: tongliao

first: zhao

last: jaiwei

address: No. 996 West Xilamulun Street, Keerqin District, Tongliao City, Inner Mongolia Autonomous Region

department: inner mongolia university for nationalities

summary: Full-length transcriptome of field sandbur (Cenchrus pauciflorus Benth.) was constructed, and high-throughput sequencing was conducted on mixed samples from four stages (BS1-BS4) of bur development and the root, stem, and leaf organs using the PacBio platform. After quality control and redundancy removal, 266,986 isoforms were obtained, of which 245,910 were annotated to seven major functional databases, accounting for 92.11%. This result showed the highest similarity with other grass species in the Trib. Paniceae R. Br., such as Setaria viridis. A total of 155,474 coding sequences (CDS) with coding capability were predicted, including 3,957 isoforms that have the ability to code for transcription factors. KEGG functional distribution analysis indicated that the number of genes involved in cellular anatomical entities reached 125,020; KOG annotation identified 4,889 genes involved in the synthesis, transport, and metabolism of secondary metabolites. Within the phenylpropanoid biosynthesis pathway, 1,900 isoforms were identified as participating in the lignin biosynthesis pathway of bur, and these genes may be candidate genes for lignification development in the bur. This study lays the foundation for elucidating the molecular mechanisms underlying the lignification development of the invasive plant field sandbur in the Horqin grassland.

overall_design: The total RNA is first synthesized using BGI's patented UMI base PCR cDNA Synthesis Kit to form the first strand cDNA. The first strand cDNA is then amplified by PCR to form the second strand cDNA. After the double strand DNA is amplified by secondary PCR, it can be used for SMRBell library construction and sequencing.

first: Yujie

last: Chen


title: Effect of 3T3-L1 adipocytes co-culture with MCF7 breast tumor cells.

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

summary: In breast cancer, the tumor microenvironment includes adipocytes. When in contact with breast tumor cells, adipocytes undergo lipolysis and dedifferentiation. These changes in the adipocytes support breast tumor cell migration and invasion. This study asseses the changes in gene expression in co-cultured adipocytes and MCF7 cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We used the 3T3-L1 cell line, and differentiated it in adipocytes. The adipocytes were untreated (d3T3L1) or in direct co-culture with MCF7 cells (d3T3L1 + MCF7) for three days. In parallel, MCF7 cells were untreated (MCF7) or in direct co-culture with adipocytes (MCF7 + d3T3L1) for three days. The experiment was performed in triplicates, hence the numbers 1, 2 or 3 after each sample name. The direct co-culture was performed using the Boyden chamber system.

first: Antonio

last: García de Herreros

first: Laura

last: Garrido Jiménez


title: Single-cell and spatial transcriptomics uncover the role of B chromosomes in driving plant invasiveness

city: Helsinki

first: Cui

last: Wang

address: PL 65 (Viikinkaari 1)

country: Finland

institute: University of Helsinki

summary: Invasive plants can significantly disrupt native biodiversity, yet the genetic mechanisms driving their success remain poorly understood. This study investigates the genetic basis of invasiveness in the common reed (Phragmites australis), a resilient grass species that became invasive in North America following its introduction from Europe. By integrating whole-genome sequencing with bulk, single-cell, and spatial transcriptomics, we constructed a comprehensive single-cell atlas of the common reed's shoot system. UMAP analysis revealed 19 distinct cell clusters within the shoot, which were annotated using Gene Ontology (GO) enrichment to identify key cell types, including mesophyll, epidermal, bundle sheath, differentiating vascular cells, shoot apical meristems, and a cell cycle-associated cluster. We inferred key genes involved in the specification of several tissues, such as epidermal cells and ground meristems. For gene expression analysis, shoot tissues from three individuals of the invasive North American population and three from the native European population were included. Comparative transcriptomic analysis revealed significant upregulation of genes associated with the light-harvesting components of photosynthesis in several tissues of the invasive population, while genes involved in the respiratory burst related to defense responses were notably downregulated.

overall_design: Shoot tissue of one individual from the invasive population NAint61 was used for spatial transcriptomics to confirm the cell types.

first: James

last: Ord

first: Mengxiao

last: Yan

first: Yunfei

last: Cai

first: Hongjin

last: Shao

first: Lele

first: Jarkko

last: Salojärvi

last: Liu

first: Weihua

last: Guo


title: The spatially resolved kidney transcriptome signatures in rat models of trauma-induced acute kidney injury

city: Paris

first: Pierre

last: Isnard

address: 156-160, rue de Vaugirard

country: France

institute: INEM

summary: Acute kidney injury (AKI) is a severe complication of trauma, particularly in cases involving hemorrhagic shock (HS) and rhabdomyolysis (RM). To elucidate the molecular mechanisms underlying trauma-induced AKI, we developed three rat models: HS, RM, and their combination (RM-HS). RM-HS resulted in the most severe phenotype, including high mortality, profound metabolic dysfunction, and extensive renal injury. Bulk and spatial transcriptomics revealed RM as the dominant driver of transcriptional changes, with significant involvement of hypoxia, reactive oxygen species (ROS), unfolded protein response (UPR), and apoptosis pathways. Region-specific analyses highlighted the corticomedullary junction (CMJ) as a critical site of injury, where lipid metabolism dysregulation and ferroptosis were prominent. Notably, perilipin 2 (PLIN2) emerged as a key marker of RM and RM-HS, correlating with metabolic dysfunction and injury severity. These findings provide mechanistic insights into trauma-induced AKI and identify PLIN2 as a potential biomarker and therapeutic target for mitigating kidney damage in trauma patients.

overall_design: Spatial transcriptomics (ST) analysis was performed on a subset of samples (n = 3 animals per group: RM-HS, HS, RM, and Sham), totaling 12 samples. Formalin-fixed, paraffin-embedded rat (Rattus norvegicus) kidney sections were processed using NanoString GeoMx DSP ST to investigate region-specific transcriptional programs associated with trauma-induced AKI.

first: Nicolas

last: Libert


title: Loss-of-function mutations in the gene encoding PTH4 cause change of mineral homeostasis, distorted bone development and altered transcription in the kidney of teleost fish

city: Vigo

first: Luis

last: Méndez Martínez

address: Eduardo Cabello Nº6

institute: Instituto de Investigaciones Marinas (IIM-CSIC)

summary: Pth4 is an ancient parathyroid hormone synthesized by hypothalamic neurons and lost in eutherian mammals. To investigate its role in mineral homeostasis and skeletal development, we generated a pth4 knockout (pth4ko) zebrafish strain using CRISPR/Cas9 and performed transcriptomic analysis across six key tissues: brain, kidney, intestine, gills, scales, and bone. The loss of Pth4 resulted in significant disruptions in calcium and phosphate balance, skeletal abnormalities, and tissue-specific transcriptional changes. Dysregulation of mineral homeostasis genes such as fgf23, phex, and slc34a1a, was observed, particularly in the kidney. Additionally, genes encoding extracellular matrix components (col1a1a, col10a1a, col11a1) and matrix metalloproteinases (mmp9, mmp13a, mmp2) were also differentially expressed in bone, indicating altered bone and scale remodeling. These findings suggest that Pth4 participates in regulating calcium and phosphate balance and bone health in zebrafish possibly through interactions with the FGF23-Klotho axis, thereby contributing to a more comprehensive understanding of the mechanisms underlying mineral regulation and the roles of the PTH family in vertebrate skeletal development.

overall_design: For this study 4 pth4ko fish and 4 WT fish were used. Six tissues were sampled from each fish: intestine, brain, kidney, gills, scales and bone. Samples were collected for each tissue from each fish resulting in a total of 48 samples. We then performed differential gene expression analysis comparing the pth4 knockout samples with the WT samples for each tissue

last: Méndez-Martínez

first: Paula

last: Suarez-Bregua

last: Guerrero-Peña

first: Elisa

last: Barreriro-Docío

first: Carolina

last: Costas-Prado

last: Cobelo-García

first: Josep

last: Rotllant


title: 53BP1 orchestrates sequence feature of RAG targets to balance DNA repair outcomes during V(D)J recombination [VDJ-HTGTS-Seq]

city: Beijing

first: Xuefei

last: Zhang

address: No.5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center (BIOPIC)

institute: Peking University

summary: RAG endonuclease initiates V(D)J recombination by cleaving recombination signal sequences (RSSs), subsequently repaired by classical nonhomologous end-joining (c-NHEJ). However, 53BP1, as a key DNA damage response (DDR) factor promoting c-NHEJ, is dispensable for V(D)J recombination. Here, we report that 53BP1 orchestrates sequence strength of RAG targets to shape end-joining features during V(D)J recombination. Deficiency of 53BP1, rather than other DDR factors, specifically increases junctional microhomology (MH) of cryptic RSS (cRSS) recombination instead of RSS recombination. Depletion of RIF1 or Shieldin, downstream factors of 53BP1, partially mimics the phenotypes of 53BP1-deficiency. Notably, loss of RNF168, rather than other classical resection and alternative end-joining factors, is sufficient to fully rescue 53BP1-deficiency-mediated increase of junctional MH during cRSS recombination. Remarkably, RAG mutant and RSS score analyses indicate that sequence strength of RAG targets determines the unique roles of 53BP1 in balancing end-joining outcomes. Our findings provide deeper mechanistic insights into DNA damage repair for RAG cleaved on- and off-targets during V(D)J recombination.

overall_design: We performed VDJ-HTGTS-Seq, 3C-HTGTS, ChIP-seq, and  PRO-Seq in different mutants of v-Abl transformed pro-B cell lines to study roles of 53BP1 in V(D)J recombination.

first: Sha

last: Luo

first: Hailiang

last: Zha

first: Zifan

last: Yang

first: Zhichen

last: Wan

first: Ruoxi

last: Kong

first: Ruolin

last: Qiao


title: DNA methylation profiling of incidental meningiomas

first: Minh

last: Nguyen

summary:
Background: The prevalence of incidentally discovered meningiomas is increasing. Clinical and radiographic models help predict growth patterns and need for intervention, but there is an unmet need to understand the molecular architecture of incidental meningiomas to improve risk stratification and guide treatment planning.
Methods: A cohort of incidental meningiomas from consecutive patients who presented to a neurosurgical clinic at a single institution were analyzed using serial magnetic resonance imaging volumetrics, IMPACT risk groups, targeted gene expression profiling, DNA methylation profiling, and copy number profiling. All adult patients with asymptomatic, incidental intracranial meningioma on imaging examination were included. Volumetric growth, treatment-free survival, and symptom-free survival from time of detection were compared using the Kaplan-Meier method, Cox proportional hazards regression, and competing risks regression analyses.
Results: The study cohort was comprised of 238 consecutive incidental meningiomas, 81% from women with a median age at detection of 59 years. Median meningioma volume at detection was 3.83 cm3, median annual and percent volumetric growth rate were 0.3 cm3 and 19.7%, respectively, median volumetric doubling time was 4.3 years, and the median clinical and MRI follow-up were 9.1 and 6.7 years, respectively. The rate of symptomatic progression was 15.5%, and 93.7% of incidental meningiomas were treated during follow-up, with a median time-to-treatment of 1.06 years. IMPACT risk groups stratified treatment-free (p<0.0001) and symptom-free survival (p=0.0007), and only 5% of incidental meningiomas recurred after treatment. Targeted gene expression profiling and DNA methylation profiling revealed that most incidental meningiomas were low molecular risk, although incidental meningiomas from the Hypermitotic DNA methylation group were larger at the time of detection (p=0.0237). Cell cycle genes were suppressed in incidental meningiomas compared to 1434 previously-published non-incidental meningiomas, and incidental meningiomas showed lower copy number alteration burden and distinct patterns of chromosomal alteration compared to non-incidental meningiomas. Molecular high-risk incidental meningiomas had favorable postoperative outcomes compared to propensity-matched non-incidental meningiomas from the same molecular groups.
Conclusions: Incidental meningiomas have excellent clinical outcomes after treatment but are overwhelmingly molecularly low risk and slow growing. These data indicate that the majority of incidental meningiomas can be safely followed with serial imaging surveillance. Molecular profiling of incidental meningiomas sheds light on early stages of meningeal tumorigenesis and suggests that early treatment of appropriately selected patients may improve long-term clinical outcomes for molecularly high-risk incidental meningiomas.

overall_design: DNA methylation profiles of 131 incidental meningiomas collected between 1998 and 2019 at a single institution

first: David

last: Raleigh


title: Species-specific oxygen sensing governs the initiation of vertebrate limb regeneration

city: Geneva

first: Hanrong

last: Hu

address: B1 0 266.045 (Campus Biotech bâtiment B1)

department: Brain Mind Institute

country: Switzerland

institute: EPFL

overall_design: CUT&Tag of mouse and xenopus limb explants cultured at hypoxic or atmospheric oxygen levels

first: Kelly

first: Aztekin

last: Can


title: 53BP1 orchestrates sequence feature of RAG targets to balance DNA repair outcomes during V(D)J recombination [ChIP-seq]

overall_design: We performed VDJ-HTGTS-Seq, 3C-HTGTS, ChIP-seq, CUT&RUN, and  PRO-Seq in different mutants of v-Abl transformed pro-B cell lines to study roles of 53BP1 in V(D)J recombination.


title: Histon lactylation drives HAS2 expression in gastric cancer tumorigensis after H.pylori infection

city: Nanjing

first: Han

last: Chen

state: Jiangsu

address: #300 Guzhou Road, Gulou District

institute: Nanjing Medical University

summary: Histone lactylation, an epigenetic modification, promotes tumor growth and immune evasion in various cancers. Our study found increased pan-lysine lactylation and H3K18la in gastric tissues, linked to poor prognosis. Inhibiting glycolysis and silencing lactate dehydrogenase reduced H3K18la, boosting CD8+ T-cell activity against gastric cancer. H3K18la activated HAS2 transcription, enhancing MYC nuclear transport and PD-L1 expression..Our data provide a molecular framework for Histone lactylation in the process of gastric cancer.

overall_design: RNA-seq profiling of AGS cells (control) and AGS cells treated with 2-DG at day 5; AGS cells and GES cells at day 5

first: Xiaoying

last: Zhou


title: Species-specific oxygen sensing governs the initiation of vertebrate limb regeneration [multiomics]

first: Can

last: Aztekin

overall_design: Multiome-seq: Single nuclei were extracted from mouse limbs at intact (no amputation), 6 hpa (hours post-amputation), 1 dpa (days post-amputation), and 3 dpa. Joint snRNA-seq and snATAC-seq libraries were prepared using the 10x Genomics platform.

first: Georgios

last: Tsissios

first: Marion

last: Leleu


title: A role for miR-4488 in conditional suppression of ER stress-associated pro-inflammatory responses

city: Rehovot

first: Ester

last: Feldmesser

state: Rehovot

address: POB 25

department: Life Science Core Facilities

country: Israel

institute: Weizmann Institute

summary: ER stress underlies numerous severe pathologies. We have metabolically perturbed normal fibroblasts in order to study the biological roles of microRNAs (miRs) under mild and extended ER stress. We now report that miR-4488 quenches inflammation-associated gene expression in such metabolically perturbed cells. Furthermore, we define miR-4488 as a non-canonical miRNA derived from the expansion segment ES7L of the 28S ribosomal RNA. Generation of miR-4488 requires Dicer, but not Drosha. Moreover, its generation involves the autophagy-lysosome route and is inhibited when this pathway is blocked, thus unveiling an anti-inflammatory role for lysosomes engaged at the onset of stress. Mechanistically, miR-4488 suppresses the expression of NFKB2 and RELB, whose mRNAs specifically associate with miR-4488 exclusively upon stress. This selectivity suggests that miR-4488 may have promise for treating mild ER stress-associated diseases.

overall_design: For the mRNA expression array analysis, total RNA derived from miR-CTRL or miR-4488-transfected HFF were used.

first: Dan

last: Michael

first: Alexander

last: Maman

first: Moshe

last: Oren


title: AML-PDXs Accelerate Development of Novel Drug Combinations for KMT2A-rearranged Acute Myeloid leukemia

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

institute: università di padova

summary: In pediatric acute myeloid leukemia (AML) the achievement of complete remission with standard treatments is obtained in most cases, but relapse still occurs in 30% of patients with greater incidence found in those patients showing high-risk AML genetic features. There is, therefore, an urgent need to identify novel effective therapies for children with relapsed-refractory leukemia. We established 26 AML patient-derived xenografts (PDXs), through sequential engraftment in NSG mice, including 14 high-risk genetic subtypes. Results confirmed AML-PDXs robustly resemble the original AML in terms of immunophenotype, genomic, and transcriptomic profiles, offering a comprehensive view of the disease complexity, useful to tailor therapies. In particular, by whole-exome sequencing, we evidenced a high intra-tumoral heterogeneity and we identified variants of each founder clone being perpetuated from patient-AML blasts to PDX. Then, we explored the efficacy of several drugs predicted to target these genomic variants in a three-dimensional in vitro culture and demonstrated that targeting variants of theWnt/β-cateninpathway is a promising strategy to reduce AML subclone fitness. By RNA-sequencing we observed thatKMT2A-rearranged AML and AML-PDXs shared aberrantly activated metabolic and stem expression signatures and documented that both IACS-010759 and Asparaginase, tailored to target transcriptome aberrancies, if combined with Venetoclax, mediated a significantly prolonged PDXs survival compared to Venetoclax used as single agent. Overall, our data indicate that AML-PDX models are unique tools for capturing AML heterogeneity, offering the possibility to target cancer cells in their multiple aspects, this increasing the chance to fully eradicate leukemia cells.

overall_design: To investigate the transcriptomic similarity between patient AML and AML-PDX, we performed RNA-sequencing of blasts derived from patients and paired PDXs. These data were further dissected to deconvolute cell type composition and unravel peculiar altered pathways in KMT2A-r AML.

first: Ambra

last: Da Ros

first: Silvia

last: Bresolin

first: Martina

last: Pigazzi


title: Effects of MyD88 inhibitor in mice with IL-33-induced allergic airway inflammation

city: Wenzhou

first: Hui

last: Zhang

state: Zhejiang

address: Xueyuan west road number 109

institute: The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University

summary: Analysis of gene expression changes in ILC2s-mediated asthmatic mice treated intratracheally with MyD88 inhibitor. IL-33 can stably induce ILC2s-mediated airway inflammation and AHR in a mouse model entirely independent of acquired immune system. This work focused on investigating the influence of MyD88 in governing ILC2s-driven allergic airway disease.

overall_design: C57BL/6 mice were randomly assigned to three groups: control group (CON), IL-33 model group (IL-33), and LM8 treatment group (IL-33+LM8). Mice in the IL-33 model and LM8 treatment groups underwent intratracheal challenges with rmIL-33 (0.5 µg per mouse) on days 0, 1, 2, and 3. In the LM8 treatment group, mice were intraperitoneally injected with LM8 solution (10 mg/kg each mouse) prior to IL-33 challenge. Mice in the control group received challenges with phosphate buffered saline. Transcriptome sequencing analysis was conducted on fresh lung tissues from mice. Genes that increased in IL-33-induced asthmatic mice and declined with MyD88 inhibitor was extracted.

first: Lijiao

last: Gao

first: Weiting

last: Pan

first: Yali


title: Effect of adiponectin receptor agonist AdipoRON on breast cancer cell lines

city: Yokohama

first: Shinya

last: Sato

state: Kanagawa

address: 2-3-2, Nakao, Asahi-Ku

institute: Kanagawa Cancer Center Research Institute

summary: Various adipocyte-derived adipokines reportedly regulate cancer growth, but their underlying mechanisms and cancer types suited for therapeutic interventions remain unknown. We analyzed adipokine receptor expression across cancer types and found that breast cancer cells express remarkably high levels of Adiponectin receptor 1. Adiponectin receptor stimulation decreased the proliferation and migratory ability of hormone receptor (HR)-positive and triple-negative breast cancer cell lines while activating apoptosis. Combination treatment with adiponectin receptor stimulants and existing drugs additively inhibited cell proliferation. Gene expression analysis revealed that adiponectin receptor stimulation regulates ferroptosis as well as ER expression in breast cancer cell lines. In conclusion, adiponectin receptor stimulation suppresses tumor growth across genetic breast cancer subtypes.

overall_design: RNA-Seq profiling of breast cancer cell lines (MCF7, T47D, MDA-MB-231 and MDA-MB-468) with or without AdipoRON treatment


title: Single Cell RNA-seq of optimized Human Ventral Spinal Organoids Generated from hESCs

city: cambridge

first: Andras

last: Lakatos

state: cambridgeshire

address: Cambridge Centre For Brain Repair, Ed Adrian Building

institute: University of Cambridge

summary: Single Cell RNA-sequencing of DIV100 Spinal Organoids generated from H9-hESCs cultured at the air-liquid-interface.

overall_design: 3 samples prepared from 3 separate slices from 3 separate organoids. Spinal organoids were sliced at DIV25 and further cultured till DIV100 where they were dissociated and processed for single cell sequencing using the 10X platform.

first: George

last: Gibbons


title: Massively parallel assessment of gene regulatory activity at human cortical structure associated variants

city: Chapel Hill

first: Jason

last: Stein

address: 116 Manning Drive, CB# 7250 Room 7202A, Mary Ellen Jones Building

department: Genetics

institute: UNC Chapel Hill

summary: Genetic association studies have identified hundreds of largely non-coding loci associated with inter-individual differences in the structure of the human cortex, though the specific genetic variants that impact regulatory activity are unknown. We implemented a Massively Parallel Reporter Assay (MPRA) to measure the regulatory activity of 9,092 cortical structure associated DNA variants in human neural progenitor cells during Wnt stimulation and at baseline. We identified 918 variants with regulatory potential from 150 cortical structure associated loci (76% of loci studied), of which >50% showed allelic effects. Wnt stimulation modified regulatory activity at a subset of loci that functioned as condition-dependent enhancers. Regulatory activity in MPRA was largely induced by Alu elements that were hypothesized to contribute to cortical expansion. The regionally specific impact of genetic variants that disrupt motifs is likely mediated through the levels of transcription factor expression during development, further clarifying the molecular mechanisms altering cortical structure.

overall_design: Massively parallele reporter assay (MPRA) on cortical structure associated variants in primary human neural progenitor cells (phNPCs)

first: Nana

last: Matoba

first: Jessica

last: McAfee

first: Alvaro

middle: A

last: Beltran

first: Jesse

last: Raab

first: Hyejung

last: Won


title: Chromatin accessibility of different Kupffer cell subsets in a mycobacterial infection

city: Freiburg

first: Philipp

last: Henneke

state: Baden-Württemberg

address: Breisacher Straße 115 B

department: Institute for Infection Prevention and Control (IIK)

institute: University Hospital Freiburg

summary:
Kupffer cells can be distinguished in three subpopulations during mycobacterial infection based on the expression of Tim4 and the fluorochrome tdTomato within Clec4fCre-tdTomato-NLS: ROSA26EYFP mice: KChigh are double positive, KClow lack the expression of tdTomato, and Tim4- KCs lack the expression of Tim4 but are tdTomato positive.
These subpopulations differ in their origin and tissue localization. The aim of this ATAC sequencing was to profile the subsets with regard to their chromatin accessibility.

overall_design: Kupffer cell subsets from Clec4fCre-tdTomato-NLS: ROSA26EYFP mice 4 weeks after i.v. injection of BCG (denominated as high, low, or Tim) or PBS (samples named PBS) were isolated and sorted by flow cytometry.

first: Jana

last: Neuber

first: Samuel

last: Wald

first: Sebastian

last: Preißl


title: Macrophage accumulations on the injured pulmonary surface accelerate intrathoracic adhesions

city: Toon

first: Tomohisa

last: Sakaue

address: Shitsukawa

department: Cardiovascular and Thoracic Surgery

institute: Ehime University

summary: We established a novel mouse model of intrathoracic adhesions (IA) to investigate the molecular mechanisms underlying IA formation. RNA sequencing analysis was performed to explore these mechanisms. A 200 μL talc solution was administered into the left thoracic cavity, and the mice were sacrificed at 30 minutes, 3 days, and 9 days post-administration. IA tissues, including the left lung parenchyma and chest wall, were harvested and homogenized using QIAzol lysis reagent. Total RNA was extracted, and the FASTQ file data were trimmed and mapped using the GLC Genomics Workbench. Differential gene expression and enrichment analyses were performed using RNAseq Chef version 1.1.2. According to the bulk RNA analysis, we observed a significant upregulation of genes associated with inflammatory cytokines and macrophage surface markers, including Il6, Ccl2, Il1β, Tgfβ1, Cd163, Cd68, and Cd86, at day 3. Meanwhile, genes related to the extracellular matrix (ECM) and its production processes were significantly upregulated at day 9. Cnet plot showed that the TNF-α and NF-κB signaling pathways were activated during the early phase, while epithelial-mesenchymal transition occurred during the completion phase of IA formation. Ingenuity Pathway Analysis (IPA) on day 3 revealed activation of leukocyte trafficking, maturation, and emigration, along with agranulocyte adhesion and diapedesis.

overall_design: Bulk RNA-seq profiling for talc-induced intrathoracic adhesion (IA) tissues of left thoracic cavities in mice at day 0, 3 and 9 after talc administration.

first: Yu

last: Mori

first: Hironori

last: Izutani


title: Expression study of granuloma macrophages in the mouse liver

summary: Kupffer cells can be distinguished in three subpopulations during mycobacterial infection, based on the expression of Tim4 and the fluorochrome tdTomato within Clec4fCre-tdTomato-NLS: ROSA26EYFP mice. These subpopulations differ in their origin and tissue localization. The aim of this bulk RNA sequencing was to profile the subsets and identify marker genes, as well as to interfer functional differences.

overall_design: Kupffer cell subsets from three Clec4fCre-tdTomato-NLS: ROSA26EYFP mice 4 weeks after i.v. injection with BCG-BFP or PBS were isolated and sorted by flow cytometry.


title: EZH2 Blockade Reverses Doxorubicin Resistance by Disrupting Metabolic and DNA Repair Networks in Breast Cancer

status: Public on Apr 08 2026

city: Tianjin

first: Chen

last: Wenlong

state: 天津市

address: No. 23 Pingjiang Road, Hexi District

institute: 天津医科大学第二医院

summary: Background: Doxorubicin (DOX) resistance remains a major obstacle to effective chemotherapy in breast cancer. However, the pharmacologically actionable regulators sustaining this resistant phenotype and its therapeutic vulnerabilities remain incompletely defined. Methods: DOX-resistant breast cancer cell models were established and treated with the EZH2 inhibitors tazemetostat or GSK126, alone or in combination with DOX. Cell viability, oxidative stress, DNA damage, and mitochondrial function were assessed in vitro. Transcriptomic profiling was performed to identify pathway alterations. A pH-responsive liposomal system for delivery of DOX and tazemetostat was developed and evaluated in vivo. Results: EZH2 was highly expressed in breast cancer and correlated with poor clinical outcomes. DOX treatment induced adaptive upregulation of EZH2 in both sensitive and resistant cells. Pharmacological inhibition of EZH2 markedly restored DOX sensitivity and exhibited strong synergistic cytotoxicity in resistant models. EZH2 blockade enhanced DOX-induced oxidative stress and DNA damage, with concomitant suppression of multiple DNA repair pathways and increased γH2AX accumulation. Transcriptomic and functional analyses revealed disrupted mitochondrial function and energy metabolism, characterized by loss of mitochondrial membrane potential and ATP depletion. In vivo, combined EZH2 inhibition and DOX significantly suppressed tumor growth, while pH-responsive liposomal delivery further enhanced antitumor efficacy and reduced systemic toxicity. Conclusion: EZH2 is a critical determinant of DOX resistance in breast cancer by sustaining DNA damage tolerance and metabolic homeostasis. Pharmacological targeting of EZH2 in combination with DOX represents a rational strategy to overcome chemoresistance in breast cancer.

overall_design: RNA-seq profiling of DOX-resistant breast cancer cells (231-ADR) treated with EZH2 inhibitors (TAZ or GSK126), doxorubicin (DOX), or their combination to investigate changes in oxidative stress, DNA damage repair, and metabolic pathways.

first: Xiaomin

last: Wang

first: Yunxiao

last: Mai

first: Yuhang

last: Ding

first: Wenlong

last: Chen


title: Transcriptomic profiling of peripheral blood from myasthenia gravis patients before and after efgartigimod treatment

city: Shanghai

first: Sushan

last: Luo

address: 12 Wulumuqi Rd (M), Jing'An, Shanghai

institute: Huashan Hospital

summary: Neonatal Fc receptor (FcRn) blockade with efgartigimod is an effective therapy for myasthenia gravis (MG), yet the molecular changes beyond IgG clearance remain incompletely understood. In this study, paired peripheral blood samples collected at baseline and week 4 after efgartigimod treatment underwent bulk RNA-seq profiling to investigate transcriptomic remodeling associated with FcRn inhibition in MG. Raw sequencing data have been deposited in the National Genomics Data Center (NGDC) under accession subHRA027638.

overall_design:
Peripheral blood samples from patients with myasthenia gravis were collected longitudinally at baseline (pre-treatment) and week 4 after efgartigimod treatment. Bulk RNA-seq was performed in a paired design to characterize treatment-associated transcriptomic changes. Raw sequencing data have been deposited in NGDC under accession subHRA027638.

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Raw files for human/patient samples are being made available in GSA (https://ngdc.cncb.ac.cn/gsa/) for controlled access to the personally identifiable sequence data.
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first: Lei

last: Jin


title: Virus-like particles enable targeted gene engineering and pooled CRISPR screening in primary human myeloid cells [CRISPR KO]

city: San Francisco

first: Pascal

last: Devant

address: 1650 Owens Street

institute: Gladstone Institutes

summary: Primary human myeloid cells are promising candidates for immunotherapy, yet efficient and scalable technologies for genetic engineering and screening in these cells are limited. Here we present a virus-like particle (VLP)-based toolkit that delivers diverse CRISPR genome editing modalities to human monocytes, macrophages, and dendritic cells with high efficiency while preserving viability and innate immune responsiveness. VLP-mediated delivery of ribonucleoprotein payloads supports gene knockout, base editing, and epigenetic silencing. Furthermore, in combination with AAV-mediated donor delivery, this approach enables site-specific integration of large DNA sequences via homology-directed repair. We also developed SLICeVLP, a system combining sgRNA delivery via VPX-lentivirus with Cas9 protein delivery via engineered virus-like particles (eVLPs), and applied it to perform pooled loss-of-function screens and Perturb-seq in human macrophages.  We uncovered regulators of TNF production and CD80 expression in human macrophages, converging on TNFAIP3 as a central regulator of inflammatory polarization. TNFAIP3 ablation promoted a pro-inflammatory cell state that is resistant to suppressive polarization, and augmented cytotoxicity in engineered HER2 CAR-macrophages. Taken together, this platform enables unbiased functional genomics in primary human myeloid cells, with direct implications for myeloid cell therapy design.

overall_design: CRISPR knockout screens in human monocyte-derived macrophages to identify regulators of CD80 cell surface expression or TNF production in response to lipopolysaccaride stimulation.

first: Hyuncheol

last: Jung

first: Alexander

last: Marson

first: Julia

last: Carnevale


title: 53BP1 orchestrates sequence feature of RAG targets to balance DNA repair outcomes during V(D)J recombination [PRO-seq]

first: Xuefei

last: Zhang

first: Sha

first: Hailiang

last: Zha

first: Zifan

last: Yang

first: Zhichen

last: Wan

first: Ruoxi

last: Kong

first: Ruolin

last: Qiao