title: Integrated Spatial Transcriptomics and Single-Cell RNA Sequencing Reveal Lars2-Mediated Spatiotemporal Dynamics of Myocardial Remodeling in a Mouse Model of Transverse Aortic Constriction (TAC)

city: Shanghai

first: Hanwen

last: Ni

state: Shanghai

address: 197th, Ruijin 2nd rd.

department: Department of Cardiology

institute: Ruijin Hostpital, School of Medicine, Shanghai Jiao Tong University

summary: Multi-omics approaches have emerged as a cornerstone in medical biology, offering an integrative perspective on tissue and cellular composition, gene expression patterns, functional states, and metabolic dynamics. In this study, we employed multi-omics methodologies, combining spatial transcriptomics (ST) and single-cell RNA sequencing (scRNA-seq), to perform large-scale bioinformatics analysis on heart samples from Transverse Aortic Constriction (TAC) mouse models at various stages of disease progression. The aim was to investigate the spatial and temporal characteristics of cellular distribution, gene composition, and associated functional changes within the myocardium in response to pressure overload. For the first time, the pathophysiology of myocardial hypertrophy in this model is described through the integrated lens of spatial and single-cell transcriptomics. The spatial transcriptomics analysis revealed a uniform cellular distribution across the heart tissue in TAC mice at different disease stages. However, substantial shifts in cellular composition were observed, with the most significant alterations occurring in cluster 1, which primarily involved changes in fibroblasts and macrophages. Single-cell RNA sequencing further demonstrated that the most notable changes in cellular composition occurred at the TAC-4W stage, characterized by a reduction in fibroblast and macrophage populations and an increase in immune cell subsets, such as neutrophils and T cells. By TAC-6W, the cellular composition returned to a state comparable to that observed at TAC-2W. Further analysis integrating both spatial and single-cell transcriptomes highlighted cluster 1 as the site of the most prominent microenvironmental changes, predominantly involving T cells and macrophages. Notably, the genes Lef1, Ccr7, Sell, and Lars2 were identified as significantly differentially expressed in these cells—an observation not previously reported. In particular, the expression of Lars2 exhibited dynamic modulation throughout disease progression. While its expression at TAC-2W did not differ significantly from controls, Lars2 expression peaked at TAC-4W, only to decline at TAC-6W. This study provides a comprehensive characterization of myocardial hypertrophy in the TAC mouse model, leveraging the power of spatial transcriptomics and single-cell RNA sequencing. The findings offer novel insights into the spatial and temporal dynamics of cellular distribution and gene expression, advancing our understanding of the molecular mechanisms underpinning cardiac remodeling in response to pressure overload.

overall_design: Eight-week-old male C57BL/6J mice (25–27 g) were randomly assigned to sham or transverse aortic constriction (TAC) groups. Hearts were harvested at 2, 4, and 6 weeks after surgery. Cardiac tissues were processed for both spatial transcriptomics (10x Genomics Visium) and single-cell RNA sequencing (10x Genomics Chromium 3’ v3.1). Sequencing was performed on the Illumina NovaSeq 6000 platform. This design enabled the integration of temporal, spatial, and single-cell transcriptomic data to characterize myocardial remodeling under pressure overload.

first: Feng

last: Liang

first: Huanhuan

last: Huo

first: Xuechao

last: Feng

first: Ben

last: He


title: Loss of PIK3CA allows in vitro growth but not in vivo progression of KRAS mutant lung adenocarcinoma in a syngeneic orthotopic implantation model

status: Public on Feb 02 2026

city: Stony Brook

first: Harold

last: Bien

state: NY

address: 100 Nicolls Road

country: USA

institute: Stony Brook University

type: Expression profiling by high throughput sequencing

summary: Constitutively active KRAS mutations are highly prevalent in lung cancers, but the direct role of its downstream phosphatidylinositol 3-kinase (PI3K) pathway in tumor progression remains unclear. A previous study established the requirement for PIK3CA, the alpha catalytic isoform, in lung tumor development in mouse models with an intact Trp53 tumor suppressor. In this study, we further investigated the requirement for PIK3CA for tumor growth both in vitro and in vivo. We first generated a “KPA” cell line by genetically deleting Pik3ca from a murine lung adenocarcinoma “KP” cell line harboring oncogenic KrasG12D and lacking Trp53. We found that Pik3ca is not required for cell survival and growth in vitro, even under anchorage-independent conditions but reduced the growth rate by 20%. We next orthotopically implanted KP and KPA cells into syngeneic mice and found that PIK3CA is absolutely required for tumor progression, even in the absence of Trp53. Implantation of KP cells, or a “KPS” cell line lacking the Stk11 gene, led to rapid tumor growth and death of all host animals. In contrast, mice implanted with KPA cells all survived with no detectable lung tumors. The gene expression profiles from cultured cell lines suggest KPA cells may be vulnerable to oxidative stress. Indeed, we found KPA cells were more sensitive to hydrogen peroxide and diethyl maleate-induced oxidative stress as compared to KP and KPS cells. Together, these results demonstrate that PIK3CA is not required for lung cancer cell growth induced by mutant KRAS in vitro but is critically needed for in vivo progression and growth.

overall_design: Bulk RNA library preparation and sequencing of 3 biological replicates of cultured KP, KPA, and KPS was performed using a commercial supplier (Novogene, Inc.) with the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (New England Biolabs E7770L) with the Poly(A) mRNA Magnetic Isolation Module. Libraries were sequenced at a depth of approximately 33 million paired reads per sample (PE150) on an Illumina NovaSeq XPlus.

first: Abigail

middle: L

last: Booth

first: Giuseppe

last: Caso

first: Barbara

last: Rosati

first: Richard

middle: Z

last: Lin


title: Cryptic redundancy between PAR1b and PAR1a, two members of the PAR1 kinase family, in the survival of PAR1b-knockout mice

city: Sapporo

first: Naoko

last: Murata-Kamiya

state: Hokkaido

address: Kita 15, Nishi 7, Kita-ku

department: Institute for Genetic Medicine

country: Japan

institute: Hokkaido University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The PAR1/MARK family of serine/threonine kinases (Par1a-d) redundantly regulates cell polarity. Furthermore, PAR1b facilitates nuclear translocation of BRCA1 through phosphorylation. Within the nucleus, BRCA1 protects stalled replication forks and repairs DNA double-strand breaks through homologous recombination. Consequently, BRCA1-knockout mice are embryonically lethal. In contrast, conventional PAR1b-knockout mice reach adulthood, suggesting a compensatory mechanism for PAR1b in regulating BRCA1 in these knockout mice. Here we find that while PAR1b knockout leads to the death of wild-type mouse embryonic fibroblasts (MEFs), PAR1b-null MEFs can be readily established from conventional PAR1b-knockout mice. In PAR1b-null MEFs from PAR1b-knockout mice, PAR1a, but not PAR1c or PAR1d, is essential for cell survival. Thus, PAR1a-mediated cryptic redundancy is unleashed only when functional PAR1b is absent from the onset of embryogenesis, which induces epigenetic changes in gene regulation. This study presents the first evidence of cryptic redundancy driven by epigenetic modifications in the regulation of gene expression during early embryogenesis.

overall_design: ATAC-seq of mouse embryonic fibroblasts (MEFs) prepared from wild-type and conventional PAR1b-knockout mice

first: Adriana

middle: A

last: Del Valle Lazarte

first: Ippei

last: Kikuchi

first: Masanori

last: Hatakeyama


title: Functional characterization of BAP1 mutations in genome edited cholangiocarcinoma organoids: role in cell death and drug responses

status: Public on Feb 04 2026

city: Rotterdam

first: Henk

middle: P.

last: Roest

state: Choose State

address: Doctor Molewaterplein 40

department: Surgery

country: Netherlands

institute: Erasmus MC

summary: Cholangiocarcinoma (CCA) is a genetically heterogeneous malignancy of the bile ducts with limited effective treatments and variable chemotherapeutic responses. BRCA1-associated protein 1 (BAP1), a tumor suppressor gene frequently mutated in CCA, encodes a nuclear deubiquitinating enzyme involved in chromatin remodeling and cell death regulation. In this study, we investigated the role of BAP1 mutations in programmed cell death and drug response using patient-derived and prime-edited CCA organoids (CCAOs). BAP1-mutant organoids exhibited impaired activation of apoptosis and necroptosis, as evidenced by reduced cleaved caspase-3 and pMLKL expression. Transcriptomic analysis revealed BAP1-dependent gene expression changes including enrichment of pathways related to stress response, ion transport, and metabolic detoxification. Interesting, BAP1 mutant CCAOs showed enhanced sensitivity to sorafenib, a multikinase inhibitor commonly used in biliary tract cancer. These findings highlight BAP1 as a modulator of cell death and a potential predictive biomarker for sorafenib response in CCA, with implications for personalized therapy design.

overall_design: investigate how BAP1 influences cell death pathways in prime-edited CCAOs. CCAOBAP1-WT was prime edited, FACSorted and clonally expended. Clones were screened by Western blot for BAP1 expression and one clone was selected based on substantial reduction of BAP1 protein level. Three technical replicates of targeted and control were sequenced

first: Wunan

last: Mi

first: Shaojun

last: Shi

first: Imre

middle: F

last: Schene

first: Indi

middle: P

last: Joore

first: Titia

middle: K

last: Sixma

first: Sabine

last: Fuchs

first: Luc

middle: J

last: van der Laan

first: Monique

middle: M

last: Verstegen


title: Hetereogenity of liver Treg in the CDAHFD model of MASH

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Metabolic-dysfunction–associated steatohepatitis (MASH) is a chronic liver disease driven by the confluence of metabolic stress and destructive hepatic inflammation. The immunoregulatory mechanisms that temper this process remain poorly understood. Exploiting a complementary pair of murine models and published single-cell RNA-sequencing (scRNA-seq) datasets from human liver, we uncovered a critical protective role for Foxp3+CD4+ regulatory T cells (Tregs) in MASH. Tregs progressively accumulated in the diseased liver, adopting an activated, nonlymphoid-tissue phenotype marked by the expression of Peroxisome Proliferator-Activated Receptor Gamma (PPARγ) and a reparative transcriptional program. Punctual ablation of Tregs during established MASH unleashed a catastrophic inflammatory cascade, including exaggerated T-helper (Th)1, Th2 and Th17 responses, expansion of a pathogenic CD8+ T cell population, and hepatocellular injury. Concomitantly, Treg deficiency disrupted key metabolic pathways in the liver, accelerating disease progression. These findings establish Tregs as non-redundant custodians of both immunologic and metabolic homeostasis in the liver, highlighting their promise as targets for temporally tuned immunoregulatory therapies in metabolic liver disease.

overall_design: We investigated the transcriptional heterogeneity of liver regulatory T cells (Tregs) 8 days after feeding with CDAHFD or control diet via single-cell RNA sequencing (scRNA-seq). Tregs from livers of Foxp3Gfp mice ere sorted by flow cytometry and encapsulated using the Chromium Single Cell 3′ v2 platform.

first: Bola

last: Hanna

first: Paul

last: Langston

first: Diane

last: Mathis


title: Succinate supplementation ameliorates musculoskeletal defects caused by PLOD3 mutations in a BCARD syndrome model

city: Nashville

first: Ela

last: Knapik

state: TN

address: 2215 Garland Ave.

department: Medicine

institute: Vanderbilt University Medical Center

summary: Background: BCARD syndrome is a rare complex connective tissue disorder associated with variants in the PLOD3 gene, presenting with musculoskeletal, vascular, and sensory deficits. The role of PLOD3 in post-translational modifications of collagens has been established. However, limited treatment options exist to correct connective tissue deficits linked to PLOD3, largely due to sparse knowledge of cellular and molecular mechanisms driving phenotypic changes. Methods: To explain the mechanisms of PLOD3 genotype-phenotype associations, we have used clinical data, molecular assays in patient-derived fibroblasts, perturbation experiments in zebrafish models, cellular and molecular experiments, and unbiased genome- and transcriptome-wide approaches. Results: We show that wild-type human PLOD3 mRNA partially rescued musculoskeletal, vascular, and brain phenotypes in zebrafish plod3 mutants, while clinically identified variants had only a limited effect, validating the pathogenicity of the variants and the high conservation of PLOD3 function across vertebrates.  We found that, at the molecular level, organ systems selectively upregulated the PERK pathway of the Unfolded Protein Response and subsequently activated autophagy as an adaptive response to an extracellular matrix (ECM) protein backlog; however, autophagy inhibitors did not rescue the plod3 mutant phenotypes. Bulk RNA-seq analysis of plod3 mutants revealed downregulation of genes in metabolic pathways, including the electron transport chain and the tricarboxylic acid (TCA) cycle, consistent with structural defects in electron micrographs of mitochondria. Search of Drug Repurposing Data Portals identified a dietary supplement, succinate, to be associated with PLOD3 and 25 additional genes, involved in the TCA cycle and collagen synthetic pathways. We showed that treatment with succinate ameliorated BCARD features, i.e., musculoskeletal defects, and restored reduced expression of TCA cycle genes in the zebrafish model. Conclusions: Our data indicate that the interaction between ECM synthesis and mitochondrial energy metabolism offers an entry point for novel therapies to prevent complex connective tissue decline in BCARD and, potentially, in other rare and common musculoskeletal disorders and conditions such as aging, cancer, or injury. Moreover, the genetic models developed here, and succinate, should be valuable tools in future studies of the underlying mechanisms of the BCARD extensive medical phenome.

overall_design: Bulk RNA-seq of whole larvae AB zebrafish and plod3 KO mgt zebrafish samples at 4 days post fertilization.

first: Dharmendra

last: Choudhary

first: Gokhan

last: Unlu

first: Taylor

last: Nagai

first: David

middle: B

last: Melville

first: Alexandra

last: Scalici

first: Mais

middle: O

last: Hashem

first: Dylan

last: Ritter

first: Georg

last: Schmidt

first: Cory

last: Guthrie

first: Eric

middle: R

last: Gamazon

first: Fowzan

middle: S

last: Alkuraya

first: Nancy

last: Cox

middle: W


title: single cell RNA-seq of mice synovium

city: Bunkyo-ku, Tokyo

first: Hisatoshi

last: Ishikura

state: Japan

department: Orthopaedic

institute: University of Tokyo

summary:
Purpose: Joint function is impaired by disuse. We investigated mice synovium for control and MMS(minimized mechanical stress) model mice.
Method: We developed a MMS model which could represent the disused joint by combining non-weight bearing with tail suspension and knee joint immobilization with a plastic cylinder. We  obtained synovial cells from control and MMS day14 mice.
Conclusion: Specific subsets in MMS synovium expressed many secreted proinflammatory cytokines and are thought to be the tragger of cartilage degeneration..

overall_design: single cell RNA-seq of synovium in control and MMS model mice

first: Taku

last: Saito


title: Single-cell transcriptomic analysis of the AOM/DSS-induced tumor stroma

city: Vari

first: Vasiliki

last: Koliaraki

state: Attiki

address: 34 Fleming street

country: Greece

institute: BSRC "Alexander Fleming"

summary: The aim of this study was to characterise the composition, expression profile, and functions of stromal cells, including fibroblasts, endothelial cells, pericytes, and smooth muscle cells, in the microenvironment of AOM/DSS-induced tumors. This data are expected to provide information on stromal cell functions during carcinogenesis and potentially reveal novel targetable mechanisms of stromal activation at the early stages of tumor development.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed to characterize the transcriptional heterogeneity of the AOM/DSS tumor microenvironment. Tumors were obtained from AOM DSS treated mice. 10X Chromium Next GEM Single Cell 3' Kit v3.1 sequencing was performed at live stromal cells that were isolated by FACS sorting after the exclusion of epithelial and immune cells.

first: Athanasia

last: Stavropoulou

first: Niki

last: Chalkidi


title: mRNAseq profiling of hCoV229E infected A549 cells

city: Braunschweig

first: Fakhar

last: Waqas

address: Inhoffenstr

country: Germany

institute: Helmholtz Zentrum für Infektionsforshcung GmbH

summary: A549 cells are infected with hCoV229E and treated with Bardoxolone, 4-octyl itaconate and Selinexor in order to understand the antiviral mechanism of these treatments

overall_design: A549 cells were infected with hCoV229E for 4 hours and treated with compounds and samples were collected after 24 and 48 h. p.i.

first: Frank

last: Pessler

first: Robert

last: Geffers


title: Effect of ablating DGCR8 expression on steady state RNA levels in embryonic teratocarcinoma PA-1 cells

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The impact of rearing environment on C. elegans: Phenotypic, transcriptomic and intergenerational responses to 3D enriched habitats

status: Public on Feb 01 2026

city: Montreal

first: Michael

last: Hendricks

state: QC

address: 1205 Avenue Docteur Penfield

country: Canada

institute: McGill University

summary: Environmental context profoundly influences organismal biology, yet laboratory studies often rely on simplified conditions that may not fully capture natural phenotypic repertoire. This exploratory study investigated how rearing environment affects various aspects of Caenorhabditis elegans biology by comparing worms cultured in three-dimensional decellularized fruit tissue scaffolds with those raised on standard two-dimensional agar plates. While fat content and feeding rate remained stable across conditions, other life history traits demonstrated varying degrees of plasticity in response to environmental context. We observed that scaffold-grown worms exhibited reduced body size, altered reproductive strategies, and mild enhancements in stress resistance, burrowing ability, swimming kinematics and exploratory behavior. RNA sequencing revealed distinct transcriptional profiles between scaffold-grown and agar-grown worms, with most changes arising within one generation. Some traits showed evidence of intergenerational inheritance. Our findings highlight the sensitivity of C. elegans biology to rearing conditions and underscore the importance of considering environmental context in interpreting laboratory results. This work sets the foundation for future research into the mechanisms underlying environmental adaptation and phenotypic plasticity in model organisms.

overall_design: RNA-seq profiling of WT yound adult C. elegans grown under 2 different rearing habitats (traditional agar habitat or 3D decellularized fruit tissue scaffold) with ancestors (>10 prior generations) also grown on either of these 2 habitats (2x2 factorial design): (1) worms with an agar ancestry and raised on agar (agar:agar); (2) worms with an agar ancestry, but raised on scaffold (agar:scaffold); (3) worms with a scaffold ancestry, but raised on agar (scaffold:agar); and (4) worms with a scaffold ancestry and raised on scaffold (scaffold:scaffold). 3 sequencing replicates per condition. Each sample was pooled from worms collected from at least 3 different plates, on at least 3 different days.

first: Aurélie

last: Guisnet

first: Maxime

last: Rivest


title: Single-cell mitochondrial genotyping of exonuclease-deficient DNA polymerase γ (POLGD274A) knock-in HEK293 cell lines

city: Berlin

first: Leif

last: Ludwig

address: Hannoversche Str. 28

institute: Berlin Institute for Medical Systems Biology

summary: Exonuclease-deficient DNA polymerase γ (POLGD274A) lead to an hypermutated mitochondrial genomes and cause OXPHOS defect. Exonuclease-deficient DNA polymerase γ (POLGD274A) lead to an elevated mutational rate and hypermutated mitochondrial genomes, which cause OXPHOS defect. Here, leverage mitochondrial single-cell ATAC-seq (mtscATAC-seq) to estimate genome-wide mtDNA mutational burden in HEK293 cell lines with POLGD274A knock-in. Our method sensitively detects up to a a median of 472 variants per cell, corresponding to a 50-fold increase comared to control, with a predominance of replication-driven C>T transitions. We further examined how POLGD274A knock-in cells adapt to OXPHOS-enforcing metabolic stress in galactose. After 1 and 3 days in glucose or galactose, CTRL and KI36 were subjected to mtscATAC-seq to examine the mtDNA variants heteroplasmy dynamic. We found that pseudo-bulk heteroplasmy, single-cell VAF distributions, and mtDNA mutational burden were unchanged. Instead, mtDNA copy number rose, and subclone DAGs highlighted stress/inflammatory programs and increasing accessibility at GDF15, suggesting population-wide metabolic rewiring.

overall_design: POLGD274A knock-in HEK293 cell lines, with (Knock-in clone A2, KIA2) or without (Knock-in clone 36, KI36) the introduction of a tetracycline-inducible mitochondrial restriction exonuclease mitoEagI, were previously described (PMID: 29712893). Cryopreserved cells were thawed cultured for a maximum of 2 weeks before single-cell sequencing to limit the accumulation of additional mtDNA mutations. For the Galactose treatment experiment, control and POLGD274A  knock-in clone 36 HEK293 cell lines were cuturled in glucose-free DMEM supplemented with 1 mM sodium pyruvate and with either 10 mM glucose (3 days) or 10 mM galactose (1 day or 3 days). Each cell line–treatment combination was labeled with dedicated TotalSeq-B hashtag antibodies, washed, and pooled at equal ratios. The pooled cells were subsequently processed using the mtscATAC-seq protocol.

first: Yu-Hsin

last: Hsieh

first: Janet

last: Liebold


title: Single-cell transcriptomic analysis of the normal mouse colon and small intestine

summary: The aim of this study was to characterise the composition, expression profile, and functions of stromal cells, including fibroblasts, endothelial cells, pericytes, and smooth muscle cells, in the healthy mouse colon and small intestine. This data are expected to provide information on stromal cell functions in intestinal homeostasis and can be used as control for different murine intestinal disorders, such as inflammation and cancer.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed to characterize the transcriptional heterogeneity of normal colon and small intestinal. 10X Chromium Next GEM Single Cell 3' Kit v3.1 sequencing was performed at live stromal cells that were isolated by FACS sorting after the exclusion of epithelial and immune cells.


title: Effect of ablating DGCR8 expression on steady state RNA levels in embryonic teratocarcinoma PA-1 cells [miRNA-Seq]

summary: Small RNA sequencing analysis to study the effect of DGCR8 absence (knockout) on miRNA levels

overall_design: Comparison between RNA samples from wildtype and DGCR8 KO PA-1 cells (WT samples from small RNA seq were deposited at GSE197470)

first: Lisanne

middle: I

last: Knol

first: Sara

last: Macias


title: RB loss modulates chromatin organization by regulating cohesin-dependent loops and enhancer-promoter interactions [ChIP-seq]

status: Public on Jan 31 2026

first: Hanjun

last: Lee

state: Massachusetts

address: 77, Avenue Louis Pasteur

department: Department of Genetics

summary: The retinoblastoma protein (RB) is a well-characterized repressor of E2F transcriptional activity that controls genes involved in cell proliferation during the G1 phase. Here, we examine the effect of RB on chromatin organization and uncover a non-canonical role for RB in which it promotes the removal of cohesin from insulators and thereby induces the expression of adjacent genes. We identify that RB colocalizes with cohesin across the human genome. During mitosis, RB facilitates the removal of cohesin from CTCF sites, with this effect persisting into early G1, impacting loop formation and extrusion at topologically associating domain (TAD) boundaries. Chromosome conformation capture assays revealed that RB reduces insulation at TAD boundaries and promotes enhancer-promoter interactions marked by histone 3 lysine 27 acetylation. In this way, RB enhances the transcription of hundreds of genes beyond the E2F transcriptional program, a finding that expands our understanding of this key tumor suppressor and cell cycle regulator.

overall_design: ChIP-seq (SMC3, STAG1, STAG2, MED15) for RB WT or RB KO hTERT1-RPE1 cells that are synchronized in G1 or M phase

first: Ioanna-Maria

last: Gkotinakou

last: Lawrence

first: Ioannis

last: Sanidas


title: Baseline tumor features and peripheral blood immune dynamics that underlie efficacy in MSS metastatic colorectal cancer treated with regorafenib, ipilimumab, and nivolumab

city: Duarte

first: Jian

last: Ye

state: CA

address: 1500 E Duarte Rd

department: Department of Medical Oncology and Therapeutics Research

institute: City of Hope National Medical Center

summary: Microsatellite-stable metastatic colorectal cancer (MSS mCRC) remains resistant to conventional immunotherapies, yet in a phase I trial the combination of regorafenib, ipilimumab, and nivolumab (RIN) demonstrated a 27.6% overall response rate and a median overall survival of 20 months, particularly benefiting patients without liver metastases. Correlative studies of tumor biopsies from eight patients and peripheral blood samples from 29 patients revealed that good responders had a more immunogenic tumor microenvironment (TME) at baseline, with enhanced cellular proliferation, active DNA repair pathways, and elevated STING pathway expression, along with a Th1-skewed cytokine profile in peripheral blood. Poor responders exhibited dysregulated inflammation, vascular remodeling, and T cells showing pathogen-response gene signatures indicative of chronic inflammation; in those with liver metastases, T cells showed immune senescence and metabolic hyperactivation. After RIN therapy, good responders displayed increased TME immune cell infiltration, upregulation of immune-related genes, marked expansion of previously low-frequency TCR clones in CD8 T cells, heightened naive T cell proliferation, and activation of immune and metabolic pathways. Poor responders initially showed transient increases in bulk CD8 T cells, NK cells, Th1 cytokine production, and reduced exhaustion markers but did not sustain meaningful TCR repertoire expansion. These findings underscore the potential of RIN to reshape the immunological landscape of MSS mCRC by modulating both TME and systemic immunity, highlighting the importance of predictive biomarkers to guide personalized therapeutic strategies, particularly for overcoming resistance in liver metastases.

overall_design: RNA-seq profiling was performed on snap-frozen tumor biopsies collected at baseline and after 1 cycle of RIN treatment (4 weeks).

first: Chongkai

last: Wang

first: Colt

last: Egelson

first: Weihua

last: Guo

first: Peter

first: Marwan

middle: G

last: Fakih


title: Baseline tumor features and peripheral blood immune dynamics that underlie efficacy in MSS metastatic colorectal cancer treated with regorafenib, ipilimumab, and nivolumab [Blood]

overall_design: RNA-seq profiling was performed on FACS-sorted non-naive CD4 and CD8 T cells from PBMCs collected at baseline and after 1 and 2 cycles of RIN treatment (4 and 8 weeks).


title: Contribution of Gli1+ stem cells to smooth muscle cells in atherosclerosis and vascular injury

first: Jialing

last: Mou

address: NO.320 Yueyang Road

country: China

institute: CEMCS

summary: Adventitial stem cells (ASCs), identified by Gli1 expression, have been proposed as key contributors to the vascular smooth muscle cell (SMC) population during atherosclerosis development. However, their precise role remains a subject of debate. To clarify this, we initially used a Gli1-CreER lineage tracing tool to track these cells in an atherosclerosis model. Our fate-mapping studies revealed that Gli1+ cells contribute to a small subset of SMCs. To definitively differentiate between the true lineage transformation and potential ectopic labeling by Gli1-CreER in SMCs, we developed a dual recombinase-mediated genetic strategy to label Gli1+ ASCs while eliminating ectopic labeling in SMCs. The results from this dual lineage tracing approach demonstrated that Gli1+ ASCs do not contribute to the SMC population in atherosclerotic plaques. Instead, Gli1+ ASCs differentiate into a significant portion of SMCs vascular anastomosis injury, suggesting their role is context-dependent. These findings challenge current paradigms and highlight the need to reconsider cellular targets for therapeutic interventions in atherosclerosis.

overall_design: Two groups of whole cells sorted from the femoral artery Gli1-CreER;R26-tdT mouse(homeostatic, injury) respectively, and subjected to scRNA-seq.


title: RB loss modulates chromatin organization by regulating cohesin-dependent loops and enhancer-promoter interactions [scRNA-seq]

overall_design: Single cell RNA-seq for RB WT or RB KO hTERT1-RPE1 cells that are synchronized in G1 phase

first: Michael


title: RORγt+ APCs require a distinct cis-regulatory element to instruct tolerance to dietary antigens [RNA-seq]

city: Beijing

first: Jie

last: Zhao

state: Beijing

address: No. 1, Qinghuayuan, Haidian District

department: Institute for Immunology

institute: Tsinghua University

summary: RORγt is the linage-specific transcription factor for both ILC3 and T-helper 17 (Th17) counterparts, who take an essential place in regulating intestinal homeostasis. While the biological significance of high RORγt expression and its distinct regulatory mechanisms in ILC3s remains investigation. Through comparing ATAC-seq results on ILC3 and Th17 cells, we identified an open chromatin region (OCR369) which specifically regulates ILC3 RORγt expression and development. Mechanistically, OCR369 is bind by the RORγt activator RUNX3, and is also involved in the chromatin-loop formation between OCR369 and RORγt-promoter. OCR369 depletion also impaired the MHCII+ ILC3s, a group of antigen-presenting cells that regulate RORγt+ Treg cells. And disruption of Th/ Treg balance in the OCR369-deficient mice leads to the spontaneous type 2 inflammation in the small intestine, and impaired generation of oral tolerance. Thus, our study revealed a specific RORγt amplifying mechanism in ILC3 and its important role in maintaining intestinal immune environment and food tolerance.

overall_design: About 0.5 cm length of small intestine was cut at ~10 cm to the cecum from naïve 20 weeks old littermates (n=3), extracted RNA using TRIzol reagent (Invitrogen, 15596026CN).Gene expression profiles were compared btween the  Rorc Δ369 and Rorc WT mice

first: Jiacheng

last: Hao

first: Jincheng

last: Chen

first: Haoyu

last: Liu

last: Li

first: Panwei

last: Song

first: Wenyan

first: Xiaohuan


title: Bulk RNA-seq of mice synovium

first: Hisatoshi

last: Ishikura

summary:
Purpose: Joint function is impaired by disuse. We investigated mice synovium and cartilage for control and MMS (minimized mechanical stress) model mice.
Method: We developed a MMS model which could represent the disused joint by combining non-weight bearing with tail suspension and knee joint immobilization with a plastic cylinder. We followed the time course of MMS model for day 3,7,14 for synovium and day 3,7,14,28 for cartilage. In addition, we used two models to stop the immobilization; in R1, only the joint immobilization was canceled at 2 weeks, but tail suspension was continued; in R2, both the joint motion and weight bearing were allowed at 2 weeks.
Conclusion: MMS synovium expressed many secreted proinflammatory cytokines. MMS cartilage expressed less cartilage anabolic genes.

overall_design: mRNA of synovium and cartilage in control and MMS model mice

first: Taku

last: Saito


title: Single-cell multiomics uncovers an endothelial mechanosensitive PIEZO1-IL-33 axis driving pulmonary fibrosis

status: Public on Jan 30 2026

city: Chengdu

first: Ruijie

last: Hou

address: Renmin South Road

institute: State Key Laboratory of Biotherapy

summary: Pulmonary fibrosis (PF) represents a progressive interstitial lung disease marked by excessive extracellular matrix deposition and architectural distortion. Vascular endothelial cells (ECs) critically contribute to fibrogenesis through paracrine secretion of pro-fibrotic mediators, yet their mechanobiological regulation remains elusive. UsingThrough integrated single-cell multi-omics profiling of human PF specimens and experimental fibrosis models induced by bleomycin or silica (Bleomycin/SiO2-induced), we identify identified mechanosensitive Piezo1 upregulation in ECs as a hallmark of fibrotic progression. Endothelial-specific Piezo1 knockout significantly attenuates attenuated Bleomycin-induced fibrotic remodeling, establishing its pathogenic necessity. Mechanistically, Piezo1 activation promotes promoted PF development by inducing a pro-fibrotic molecule interleukin-33 (IL-33) secretion via CAPN2-mediated STAT3 phosphorylation. These findings suggest that the endothelial PIEZO1-CAPN2-STAT3-IL-33 axis is a promising therapeutic target for PF intervention.

overall_design: Lung tissues of Saline or Silica or Bleomycin induced mice were obtained for sequencing (n=3 per group).

first: Lanlan

last: Zhang


overall_design: Human lung tissues were obtained from five Normal individuals and four IPF patients.


title: Single-cell transcriptomic analysis of KLF15-mediated cardiac protection in heart failure

city: Göttingen

first: Laura

last: Zelarayan

address: Robert-Koch-Str 40

institute: University Medical Center Göttingen

summary: Single-cell RNA sequencing of mouse hearts subjected to transverse aortic constriction (TAC) or sham surgery to characterize the temporal progression of cardiac remodeling from homeostasis through compensated hypertrophy to pathological heart failure. Hearts were harvested at three timepoints (5 days, 8 weeks, and 16 weeks) post-surgery to capture progressive cellular and transcriptional changes during pressure overload-induced heart failure.

overall_design: Mice underwent TAC or sham surgery. Hearts were harvested at 5 days (TAC n=5, Sham n=5), 8 weeks (TAC n=3, Sham n=3), and 16 weeks (TAC n=3, Sham n=3) post-surgery (total 22 animals). Single cells were isolated via Langendorff perfusion. For the 5D and 16W timepoints, cardiomyocyte-enriched (CM) and non-cardiomyocyte-enriched (NCM) fractions were processed separately. Cells were distributed on ICELL8 250v nanowell chips and processed for scRNA-seq. Live cells were selected using Hoechst 33342 and propidium iodide staining. Libraries were prepared using the ICELL8 System and sequenced on Illumina HiSeq 4000.

first: Eric

last: Schoger

first: Rosa

last: Kim

first: Federico

last: Bleckwedel


title: RNA-seq analysis of gene expression regulated by CRAMP1

city: Chicago

first: SHASHANK

last: SRIVASTAVA

state: IL

address: 303 E Superior St, SQE Lab 7-400

institute: Northwestern University

summary: Proper histone gene expression is critical for cell viability and maintenance of genomic integrity. Multiple histone genes are organized into three genomic loci encode replication-coupled core and linker histones. Histone gene expression and transcript processing are orchestrated in the histone locus body (HLB) within the nucleus. We identified human CRAMP1 as a selective regulator of the linker histone H1 expression. CRAMP1 was recruited to the HLB in RPE1hTERT cells. Affinity purification showed that CRAMP1 physically associates with the HLB component GON4L (also known as YARP). We demonstrated that the PAH domains of GON4L interact with CRAMP1. CRAMP1 disruption resulted in a loss of histone H1 expression and a reduction in H1 protein levels. CRAMP1 occupies unmethylated promoters of replication-coupled linker histone genes that reside within the histone locus body and replication-independent histone H1 loci, which reside in a region of the genome without other histone genes. Together, these data identify CRAMP1 as a novel and selective regulator of histone H1 gene expression.

overall_design: To evelaute the gene exprseion changes that occur dependent on CRAMP1 activity we created HEK293T cells thata contain a degraon tag at the endogenous locus.  RNA-seq  was conducted following degradation of CRAMP1 by dTAG addition at defined times.

first: Shashank

last: Srivastava

first: Daniel

last: Foltz


title: Distinct Control of Histone H1 Expression within the Histone Locus Body by CRAMP1

overall_design: To evaluate the acute gene expression changes that occur dependent on CRAMP1 activity we used HEK293T cells that contain a degron tag at the endogenous locus.  TT-seq  was conducted following degradation of CRAMP1 by dTAG addition at defined times.


title: Unravelling WRN helicase: Structural Insights Reveal Conformational States and Opportunities for MSI-H Cancer Drug Discovery

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

institute: The Babraham Institute

summary: Werner syndrome helicase (WRN) is a RecQ-family DNA helicase essential for genome maintenance and is a synthetic lethal target in microsatellite instability-high (MSI-H) cancers. Despite its therapeutic promise, the conformational dynamics that enable WRN to unwind DNA, and how inhibitors disrupt this activity, remains poorly understood. Here, we present crystal structures of apo WRN and WRN bound to single-stranded DNA (ssDNA), capturing key conformations in the helicase catalytic cycle. These structures reveal how WRN engages DNA through conserved polar and aromatic interactions, and how domain rearrangements, including an ordering of the aromatic-rich loop (ARL), drive directional translocation. Biochemical and biophysical data demonstrate how nucleotide and inhibitor binding remodel these conformations and suggest that known clinical inhibitors (HRO761 and VVD-133214) function by locking WRN in inactive, ‘off-DNA’ states. Resistance emerged rapidly in vitro, through acquired point mutations as well as altered WRN expression. Together, our findings provide a structural framework for the WRN structural cycle and support the development of next-generation ‘on-DNA’ inhibitors to overcome resistance

overall_design: Samples were collected to charactersie the changes in gene expression of cell lines after acute or chronic treatment of WRN inhibitors to identify changes. One million cells of 3 biological replicates were washed with PBS and snap-frozen in dry ice. Samples were collected from HCT116, 0.1% DMSO treated HCT116, HRO761 and VVD-133214 chronically treated HCT116 in the early (HRO761: 1uM; VVD-133214: 600nM) and late (HRO761: 13uM; VVD-133214: 3uM) stages of resistance development, and HRO761 and VVD-13321 acute treated HCT116. For acute treatment, the 0.1% DMSO HCT116 cell line was grown in 13uM HRO761 or 3uM VVD-13321 for one passage.

first: Catherine

middle: T

last: Fletcher

first: Abigail

last: Mornement

first: Charlotte

last: Barrett

first: Peter

last: Canning

first: Prakash

last: Rucktooa

first: Sophie

last: Huber

first: Christopher

middle: D

last: Cooper

first: Conor

middle: C

last: Scully

first: Andrew

last: Dore

last: Rohle

first: Geoffrey

last: Smith

first: Sarah

middle: E

last: Skerratt

first: Amanda

last: Kennedy


title: Effect of ablating DGCR8 expression on steady state RNA levels in embryonic teratocarcinoma PA-1 cells [RNA-Seq]

first: Alasdair

last: Ivens

summary: In this dataset we use total RNA-seq to study the effect of DGCR8 absence (knockout) on steady state RNA levels

overall_design: Comparison between RNA samples from wildtype and DGCR8 KO PA-1 cells (WT samples from total RNA-seq were deposited at GSE197472)

first: Lisanne

last: Knol

first: Sara

last: Macias


title: Distinct Control of Histone H1 Expression within the Histone Locus Body by CRAMP1 [ChIP-seq]

first: SHASHANK

last: SRIVASTAVA

overall_design: To determine chromatin binding patterns of CRAMP1, we created RPE-1 PKO hTERT-immortalized cells that express a V5-tagged CRAMP1 construct.  ChIP-seq  was conducted in the above cells using a V5 antibody.

first: Vadlamani

last: Pranathi

first: Daniel

last: Foltz


title: Targeted innate immune inhibition therapy compared to antibiotics for recurrent acute cystitis

city: Lund

first: Ines

last: Ambite

address: Klinikgatan 28

department: Laboratory Medicine

country: Sweden

institute: Lund University

summary: Cystitis is a bacterial infection of the bladder that occurs in about half of women at least once in their lifetime. Antibiotics such as nitrofurantoin are used to treat cystitis but antibiotic resistance is a concern, especially for recurrent infections. Here we report an open label, randomized, single-center, phase 2 study to analyze the acute and long-term safety and efficacy of the IL-1 receptor antagonist anakinra, compared to nitrofurantoin, in recurrent cystitis. Thirty adult female patients with a documented history of recurrent cystitis and a current acute cystitis episode were randomized in a 2:1 ratio to treatment with anakinra (n=20) or nitrofurantoin (n=10) for five days. Primary and secondary efficacy end points were reached, defined as the reduction in typical symptoms, measured by the acute cystitis symptom score (ACSS, day 5), longitudinal symptom scores, recurrence rates, quality of life gene, expression analysis and microbiology at follow-up on days 15, 30 and at six months. Symptom scores were decreased in the anakinra (P<0.001), and nitrofurantoin (P<0.001) arms after five days and remained low after 15, 30 days and 6 months. Recurrences were less frequent after 6 months in both treatment groups compared to the 6-month pre-enrolment history (P<0.001 for anakinra and P=0.004 for nitrofurantoin) and the quality of life was increased, without adverse effects. Immune gene expression was rapidly inhibited in the anakinra treated patients but not in the nitrofurantoin group. Targeted innate immune inhibition therapy shows non-inferiority to nitrofurantoin in patients with recurrent acute cystitis (German Clinical Trials Register, DRKS00025964; EudraCT, 2019-004209-28).

overall_design: Expression data from RNA samples of recurrent cystitis patients. RNA was extracted from blood of patient treated with anakinra or nitrofurantoin. Blood samples were collected longitudinally throughout the clinical study.

first: Catharina

last: Svanborg

first: Florian

last: Wagenlehner


title: Decoding human tRNA modifications and crosstalk by enhanced single-read analysis

first: Mahdi

last: Assari

state: Illinois

address: 1380 E HYDE PARK BLVD APT 806

department: Chemistry

institute: The University of Chicago

summary: tRNA modifications regulate gene expression and protein synthesis. Human tRNAome contains ~40 chemical modification types distributed on average at 13 sites in cytosolic tRNA and 6 sites in mitochondrial tRNA. tRNA modifications display dynamic patterns dependent on cell type and cell state, underscoring the need for advancing methodologies to assess their variations and crosstalks transcriptome-wide. Here, we develop enhanced single-read analysis of tRNA crosstalks (eSLAC), an integrative platform that combines the NGS sequencing method of multiplex small RNA sequencing (MSR-seq), expanded capability to measure pseudouridine (Ψ), 5-formylcytidine (f5C), and N4-acetylcytidine (ac4C), and a single-read analysis pipeline that examines the modification-modification and modification-charging crosstalks. We achieve assessments of over 60% of all human tRNA modification sites and assign Ψ sites to three Ψ writer enzymes. Both Ψ-Ψ and Ψ-charging have strong positive crosstalks. Applying polysome tRNA profiling, we identify differential tRNA isodecoder utilization and tRNA Ψ variations in the E-site versus A and P sites on the polysome. Our approach establishes a foundation for revealing the interconnectedness and the functional complexity of the tRNA modome.

overall_design: Wild-type (WT) cells were analyzed with no treatment (NT), bisulfite treatment (BS), or picoborane treatment (PB) to assess baseline and chemically-induced modification signatures. To dissect the role of specific pseudouridine synthases, bisulfite-treated samples from PUS1, TRUB1, and PUS7 knockout (KO) lines were included. Polysome-associated and input (total) RNA fractions from WT cells were also analyzed with and without bisulfite treatment to evaluate ribosome-associated tRNA modifications. All conditions were performed with biological replicates to ensure robustness in differential modification detection.

first: Brandon

last: Chew

first: Marek

last: Sobczyk

first: Chenyou

last: Zhu

first: Hoang Anh

middle: V

last: Tran

first: Dominika

last: Rudzka

first: Wen

last: Zhang

first: Tao

last: Pan

first: Mohammad Amin

last: Bayat Tork


title: Distinct Control of Histone H1 Expression within the Histone Locus Body by CRAMP1 [BiSulfite-seq]

type: Methylation profiling by high throughput sequencing

overall_design: To evelaute the methyation state of the histone gene promoter, actively proliferating RPE1hTERT cells treated with non-targetting (NT) siRNA were subjected reduced representation bisulfite sequencing.

first: Justin

last: Bodner

first: Qianli

last: Liu

first: Benjamin

last: Singer


title: Plasminogen small RNA cargo promotes immunogenicity and inhibits enzymatic activity [7369-DM]

first: Danielle

middle: L

last: Michell

address: 2220 Pierece Ave

department: Department of Medicine

institute: Vanderbilt Univ. Medical Center

summary: Plasminogen (Plg), the pro-enzyme of the serine-protease plasmin, is a lipoprotein-like particle in biofluids. Plg transports (oxidized) phospholipids and has the ability to accept free cholesterol from macrophages, two processes normally observed with lipoproteins. We have previously reported the biological functions of cell-free small RNA (cf-sRNA) circulating on lipoproteins. We hypothesized that Plg also transports functional cf-sRNAs. Indeed, both human and bovine Plg samples were observed to transport sRNAs (25-60nt in length) in plasma. Small RNA sequencing analyses found that Plg carries both host and non-host (microbial) sRNA. Plg samples were observed to accept sRNAs from donor macrophages in efflux studies and were observed to have moderate affinity (Kd=µM range) towards candidate host and microbial sRNAs, as quantified by microscale thermophoresis. Using PCR and bulk RNA sequencing, we discovered that Plg-sRNAs confer, in large part, Plg’s pro-inflammatory cytokine responses in macrophages. RNase treatments of both human and bovine Plg were found to significantly increase Plg’s enzymatic activity, as observed through both activity assays and clot lysis assays. Collectively, results from this study suggest that Plg is a novel circulating lipoprotein-like ribonucleoprotein and support that sRNA cargo negatively regulate Plg’s enzymatic function and enhance Plg’s immunogenicity. Therefore, Plg-sRNA cargo and its receptors present new therapeutic targets to control fibrinolysis, as well as wound and systemic inflammation.

overall_design: sRNA sequencing of human high density lipoproteins (HDL) and lysine purified plasminogen (PLG) from healthy donors and those with familial hypercholesterolemia

first: Michell

last: Danielle L.

first: Vickers

last: Kasey C.


title: Plasminogen small RNA cargo promotes immunogenicity and inhibits enzymatic activity

overall_design: Total RNA sequencing of bone marrow-derived macrophages treated with PLG exposed to Rnases

first: Danielle L

first: Kasey C

last: Vickers


title: Restoration of endogenous transcription factor activity by nuclease-deficient Cas9VPR prevents cardiac failure upon stress

first: Laura

last: Zelarayan

summary: Cardiac remodeling is linked to maladaptive transcriptional networks, but identifying and targeting key factors with potential to reverse these processes is still a challenge. We employed network-based analysis of single cell heart transcriptomes to compute the transcription factor activities triggering heart failure. We found that the regulation of KLF15 activity is a major driver of cardiomyocyte failure. Through the use of CRISPR/nuclease-deficient (d)Cas9-based transcriptional regulation, we demonstrated that restoration of endogenous Klf15 expression and activity in cardiomyocytes was sufficient to mitigate pathological transcriptional reprogramming and preserve cardiac function in mice and human myocardial models. We also showed that KLF15 is a downstream targetable factor in the broad TGFβ-mediated stress response in human cardiomyocytes, controlling transcriptional embryonalization. Lastly, we engineered a therapeutically applicable mini-dCas9VPR variant suitable for adeno-associated viral delivery, eliciting endogenous KLF15 transcriptional activation in human cardiomyocytes. This case study presents a therapeutic strategy for restoring the stress-induced downregulation of essential genes to prevent heart failure with broader implications for other disease contexts.

overall_design: Double transgenic Myh6-dCas9VPR/Klf15 knockout (KO) mice were generated by crossing Myh6-dCas9VPR mice with Klf15 KO mice. Wild-type C57BL/6N mice were used as controls. Mice (both male and female, 4-6 months old) were injected via the tail vein with either rAAV2/9-TRISPR-Klf15 or rAAV2/9-TRISPR-NT. Following injection, mice underwent transverse aortic constriction (TAC) or sham surgery. Pressure overload was confirmed by measuring the blood flow velocity ratio between the right and left carotid arteries. Echocardiography was conducted at 4 and 8 weeks post-surgery, and hearts were harvested at 12-16 weeks. Ventricular measurements were taken using a VisualSonics Vevo 2100 Imaging System. All procedures were performed in a blinded manner and in accordance with ethical guidelines from the Lower Saxony State Office for Consumer Protection and Food Safety.

first: Eric

last: Schoger

first: Federico

last: Bleckwedel

last: Zelarayán


title: Dnmt1 mediates epigenetic restriction of invasive traits in clonal crayfish [scRNA-seq]

status: Public on Jan 29 2026

city: Heidelberg

first: Jaime

last: Diaz-Larrosa

state: Baden Württemberg

address: INF 580

department: Epigenetics

institute: DKFZ

summary: Marbled crayfish (Procambarus virginalis) are a parthenogenetically reproducing, globally invasive freshwater crayfish species. Previous work has shown that the global population is characterized by a monoclonal genome, which raises important questions about the mechanisms that promote their invasiveness. Dnmt1 is an evolutionarily conserved DNA methyltransferase responsible for maintaining 5-methylcytosine (5mC) patterns across the genome. While its relevance in transcriptional regulation and cell fate specification is well established, its role in ecological adaptation remains poorly understood. Here we show that environmental changes lead to significant downregulation of Dnmt1 in marbled crayfish. When mimicking this effect through a dsRNA-based in vivo knockdown of Dnmt1, we observed that invasiveness-related behavioral traits, such as activity and boldness were enhanced. Using image cytometry and single-cell RNA sequencing, we also detected an increase in the most mature immune cell type, the granular cells and depletion of hemocyte-derived neuronal precursors, which support adult neurogenesis. Further analysis by whole-genome bisulfite sequencing showed that these phenotypic changes are underpinned by a global reduction in gene body DNA methylation and a dysregulation of genes involved in nervous and immune system functions. Additionally, we observed nucleosome destabilization as a key mechanism influencing transcriptional changes after methylation loss. Our findings highlight a role for Dnmt1 in the canalization of cellular and organismal phenotypes, and provide a paradigm for how downregulation of Dnmt1 can enhance invasive traits.

overall_design: 28 days post injection of, 3 control animals (injected with dsGFP) and 3 Dnmt1 KD (injected with dsDNM1) were bled and the hemocytes isolated. 10 X genomics were used for single-cell RNA-sequencing.

first: J. Jaime

first: Vitor

last: Carneiro

first: Katharina

last: Hanna

first: Günter

last: Raddatz

first: Frank

last: Lyko


title: Transcriptomic changes in primary CD4+ T cells upon infection with HIV-1 harboring an intact or defective vpr open-reading frame

city: Tübingen

first: Morgana

last: Barroso Oquendo

address: Otfried-Müller-Straße 37

department: Quantitative Biology Center (QBiC)

institute: University of Tuebingen

summary: We performed unbiased RNA sequencing (RNA-seq) analyses of primary CD4+ T cells infected with HIV-1 harboring an intact or defective Vpr open reading frame and analyzed which genes are deregulated in a Vpr-dependent manner. Our transcriptome analyses showed that NFAT controls 46.5% of 1083 Vpr-deregulated genes in primary CD4+ T cells. Gene set enrichment analyses revealed that Vpr upregulated processes related to T cell signaling, proliferation, and immune function, while downregulating cell cycle progression, ribosome activity, and cytoskeleton organization. qRT-PCR confirmed Vpr-mediated modulation of specific genes, including the upregulation of NEIL1, TNFS4 and CXCL10, and the downmodulation of CCNB1, CDC20, CENPA and PLK1. Hence, a significant portion of Vpr-deregulated genes in primary CD4+ T cells are controlled by NFAT, affecting pathways related to T cell activation, cell cycle progression, cytoskeleton, and chromosome organization.

overall_design: PHA-prestimulated CD4+ T cells were infected with purified and concentrated HIV-1 stocks via spinoculation and analyzed at 48 hours post infection by flow cytometry to assess infection rates. Upon confirmation of similarly high infection rates, CD4+ T cells of three healthy donors were subjected to RNA extraction and RNA-seq. Sequencing yielded 21 to 51 million reads per sample.

first: Darius

last: Anthea

first: Vanegas-Torres

last: Carlos Alberto

first: Schindler

last: Michael

first: Oquendo

last: Morgana Barroso


title: Distinct Control of Histone H1 Expression within the Histone Locus Body by CRAMP1 [ATAC-seq]

first: SHASHANK

last: SRIVASTAVA

first: Vadlamani

last: Pranathi

first: Daniel

last: Foltz


title: Dnmt1 mediates epigenetic restriction of invasive traits in clonal crayfish [RNA-seq]

overall_design: RNA-seq from 2 Control (dsGFP) and 2 Dnmt1-KD (dsDNMT1) animals’ hemocytes 28 days post-injection. These samples were also submitted for WGBS


title: Restoration of endogenous transcription factor activity by nuclease-deficient Cas9VPR prevents cardiac failure upon stress II

first: Laura

last: Zelarayan

summary: Cardiac remodeling is linked to maladaptive transcriptional networks, but identifying and targeting key factors with potential to reverse these processes is still a challenge. We employed network-based analysis of single cell heart transcriptomes to compute the transcription factor activities triggering heart failure. We found that the regulation of KLF15 activity is a major driver of cardiomyocyte failure. Through the use of CRISPR/nuclease-deficient (d)Cas9-based transcriptional regulation, we demonstrated that restoration of endogenous Klf15 expression and activity in cardiomyocytes was sufficient to mitigate pathological transcriptional reprogramming and preserved cardiac function in mice and human myocardial models. We also showed that KLF15 is a downstream targetable factor in the broad TGFβ-mediated stress response in human cardiomyocytes, controlling transcriptional embryonalization. Lastly, we engineered a therapeutically applicable mini-dCas9VPR variant suitable for adeno-associated viral delivery, eliciting endogenous KLF15 transcriptional activation in human cardiomyocytes. This case study presents a therapeutic strategy for restoring the stress-induced downregulation of essential genes to prevent heart failure with broader implications for other disease contexts.

overall_design: Engineered heart muscle (EHM) were generated by combining CRISPRa hiPSC-cardiomyocytes (3.85x10^5) transduced with either non-targeted control gRNAs (NT) or KLF15 gRNAs and with human foreskin fibroblasts (1.65x10^5) in a bovine collagen matrix. These EHM were cast into a 48-well plate (myriamed GmbH) and cultured initially in IMDM (Gibco) supplemented with 4% B27 minus insulin, 100 ng/mL IGF-1, 5 ng/mL VEGF165, 10 ng/mL FGF-2, 100 U/mL penicillin, 100 µg/mL streptomycin, and 5 ng/mL TGF-β1 for 3 days. From day 4 onwards, TGF-β1 was removed. Starting from day 14, the medium was switched to alpha-MEM (Gibco) with 4% B27 minus insulin, 1% MEM non-essential amino acids, 100 ng/mL IGF-1, 5 ng/mL VEGF165, 10 ng/mL FGF-2, 100 U/mL penicillin, and 100 µg/mL streptomycin. On day 28, EHM were either cultured on flexible, silicone poles (control, healthy = Flex) or subjected to mechanical stress by culturing them on rigid metal poles (stressed = Fix) for an additional 7 days. Total RNA was extracted for RNA sequencing to analyze gene expression changes under the different experimental conditions (NT vs. KLF15 gRNA and Flex vs. Fix).


title: Single-cell landscape of piglet lung response with Actinobacillus pleuropneumoniae

city: Changchun

first: Liancheng

last: Lei

state: Jilin

address: 5333, Xi'an Road

institute: Jilin university

summary: Actinobacillus pleuropneumoniae can cause lethal porcine infectious pleuropneumonia, resulting in substantial economic losses for the pig industry. The lung is the main target organ of A. pleuropneumoniae. However, the lung-specific immune responses against the pathogen remain unclear. In this study, single-cell RNA sequencing analysis of the transcriptome of the piglet lung with or without A. pleuropneumoniae infection identified 18 subpopulations with different phenotypes. Monocytes, neutrophils, and plasmacytoid dendritic cells (pDC) were enriched in the lung post-infection and played anti-infection roles by promoting the expression of interferon-induced factors (such as IL-18) and inflammatory response-associated genes. A. pleuropneumoniae reduced the number of macrophages by inhibiting monocyte differentiation into interstitial macrophages (IM) and alveolar macrophages (AM) and triggering AM endogenous apoptosis. Additionally, A. pleuropneumoniae lowered the amount of various T cell subsets and induced CD8A+ γδ T exhaustion and apoptosis. Furthermore, we identified dramatically augmented pathological fibroblast-¬like cells contributing to rapidly developing pulmonary fibrosis, whereas epithelial cells were significantly decreased, and included those with features of epithelial‐mesenchymal transition differentiated into fibroblasts through the signaling of TGFB1 and HIF1A. Cell-to-cell communication analysis further revealed that the interaction between the EMT-epithelial, vascular endothelial, pDC, and fibroblast subsets, except for COL3A1 fibroblasts, were enhanced, mainly via CD74/(COPA or MIF) receptor ligands after infection, whereas COL3A1 fibroblasts interacted via EGFR/MIF and EGFR/TGFB1 pairs. In summary, our study is the first time to systematically analyze the cell response of piglet lung under the status of physiology and A. pleuropneumoniae infection, deepening the understanding of the molecular basis of pathogenesis, and providing a wealth of resources for the prevention and treatment of A. pleuropneumoniae and other fibrotic lung diseases.

overall_design: Single-cell RNA sequencing (10X Genomics) was used to profile the transcriptomes signatures of lung tissue from three Actinobacillus pleuropneumoniae-infected and three healthy pigs.

first: Junhui

last: Zhu

last: Li

first: Xuan

last: Jiang

first: Chuntong

last: Bao

first: Fengyang

first: Rining


title: Dnmt1 mediates epigenetic restriction of invasive traits in clonal crayfish [MNase-seq]

first: Jaime

last: Diaz-Larrosa

overall_design: 28 days post injection with dsGFP and dsDNMT1, 4 control and 6 KD animals were bled. Hemocytes were subject to a Micrococcal Nuclease incubation and sonication to release the Nucleosome-bound DNA, which was sequenced.

first: J. Jaime

first: Vitor

last: Carneiro

first: Katharina

last: Hanna

first: Günter


title: Cruciform-forming AT/TA repeats are acted upon by structure selective endonucleases and Rad51 prior to repositioning to the nuclear periphery for repair

status: Public on Jan 28 2026

city: New York

first: Bertrand

last: Theulot

address: 100 WASHINGTON SQ E, Attn: Duncan Smith

institute: NYU

summary: Structure-forming DNA repeats can pose a barrier to DNA replication and repair and create chromosomal fragile sites. An (AT/TA) 34 DNA repeat, derived from the Flex1 region of human common fragile site FRA16D, can form hairpin and cruciform structures which interfere with DNA replication. When inserted into the S. cerevisiae genome, the Flex1(AT) 34 repeat stimulates chromosome deletions in a manner dependent on the Mus81-Mms4 nuclease and the SLX4 nuclease scaffold. It was previously found that hairpin forming CAG/CTG repeats move to the nuclear periphery to maintain genomic stability. We show that the structure forming AT/TA repeat also relocalizes to the nuclear periphery in late S/G2 phase in a replication and length-dependent manner. In contrast to the CAG repeat, this shift in nuclear positioning is dependent on polySUMOylation and the activity of the Mus81-Mms4 nuclease. Thus, different replication barriers may have differing dependencies for processing and repositioning to the nuclear periphery to protect genome integrity. Processing by the Mre11 nuclease and Rad51 strand exchange occurs prior to repositioning. Replication analysis shows that the replisome likely bypasses the AT structure-induced barrier leaving an under-replicated region that requires resolution. We conclude that AT/TA repeats form post-replicative DNA structures that are targeted for nuclease cleavage and require hairpin processing and repositioning to the nuclear periphery for homologous recombination-dependent repair.

overall_design: OK-seq was performed in Saccharomyces cerevisiae strains carrying either an (AT/TA)_34 DNA repeat or a Flex1 control cassette inserted on chromosome VI or chromosome X, in RAD52+ and rad52Δ genetic backgrounds. UCSC Genome Browser session with strand-specific coverage tracks is available at: https://genome.ucsc.edu/s/bt2459/okseq%2Dboer%2D2026 . Custom analysis scripts used to generate the figures are available here: https://github.com/btheulot/ok-seq-boer-2026

first: Jan L

last: Boer

first: Sara M.

last: Crippen

first: Amelia J.

last: Kim

first: Daphne N.

last: Kramer

last: Dovrat

first: Amir

last: Aharoni

first: Duncan J.

last: Smith

first: Catherine H.

last: Freudenreich


title: Transcriptome changes in trigeminal ganglia in the mouse chronic constriction injury of the infraorbital nerve model - role of TRPM3.

city: Leuven

first: Andrei

last: Segal Stanciu

address: Herestraat 49/801

department: Cellular and Molecular Medicine

country: Belgium

institute: KU Leuven

summary: In this project, we performed bulk RNAseq of mouse trigeminal ganglia at different time points following a constriction of the infraorbital nerve (IoN-CCI model). Samples include both ipsilateral and contralateral samples, as well as samples from sham-operated mice. To evaluate a possible role of TRPM3, trigeminal ganglia were isolated from both wild type and TRPM3-knockout mice. Our data indicate profound and time-dependent transcriptomic changes induced by the IoN-CCI model, but did not reveal IoN-CCI-specific differences between  wild type and TRPM3-knockout mice.

overall_design: Bulk RNAseq of isolated trigeminal ganglia from sham and IoN-CCI wild type and TRPM3 knockout mice, taken at days 0, 3, 11, 18, 25 and 42 after the CCI or sham procedure.

first: Thomas

last: Voets

last: Segal

first: Silvia

last: Pinto

first: Kristof

last: Deseure

first: Nele

last: Van Ranst

first: joris

last: Vriens


title: Cell confinement memory initiates heritable loss of chromosomes and a persistently dysregulated division program

city: Philadelphia

first: Dennis

last: Discher

state: Pennsylvania

address: 129 Towne Bldg

institute: University of Pennsylvania

summary: Heritable genetic changes continually arise in cancer, especially in solid tumors where cells sometimes appear compressed. Rare heritable losses of chromosomes in live cells are quantified here with chromosome reporters (ChReporters) that show similar losses after mild or strong compression. Mild compression (to <40% of interphase height) perturbs mitotic spindles and prolongs pro/metaphase but ruptures few nuclei compared to strong compression. Unexpectedly, chromosome mis-segregation into micronuclei emerges only after release from mild confinement, but arrest and death predominate. All such effects are phenocopied by Nocodazole washout that induces a ‘memory’ of prolonged mitosis. The results differ from transient inhibition of the spindle assembly checkpoint and cell cycle entry with a CDK4/6-inhibitor – both of which quickly generate micronuclei. Single-cell-RNA-sequencing confirms chromosome loss days after confinement and reveals persistent upregulation of chromosome segregation. The results suggest a mitotic memory of confinement, addressing a significant gap in mechanobiology and cancer evolution.

overall_design: Our focus on the very rare cells that are ChReporter-negative (~1-per-500 cells). Therefore we sorted live cells for ChReporter loss after the 48h recovery from confinement or 2D controls, and then we used single-cell RNA-seq (scRNAseq) to quantify transcript changes.  RNA libraries were constructed using the Chromium Single Cell Gene Expression kit (v3.1, single index, Catalog no. PN-1000128; PN-1000127; PN-1000213) from 10X Genomics per the manufacturer's instructions. The libraries were submitted to the University of Pennsylvania's Next Generation Sequencing Core for sequencing using NovaSeq 6000 (100 cycles) from Illumina. Raw base call (BCL) files were analyzed using CellRanger (version 5.0.1) to generate FASTQ files and the ‘count’ command was used to generate raw count matrices aligned to GRCh38 provided by 10X genomics.

first: Mai

last: Wang


title: Mutated fibroblast growth factor receptor 1 is an oncogenic driver and therapeutic target in high-risk neuroblastoma

city: Cologne

first: Matthias

last: Fischer

address: Kerpener Str. 62

department: Department of Experimental Pediatric Oncology

institute: University Children’s Hospital of Cologne

summary: Fibroblast growth factor receptor 1 (FGFR1) is recurrently mutated at p.N546 in neuroblastoma. We here sought to examine whether mutant FGFR1 is an oncogenic driver, a predictive biomarker, and an actionable vulnerability in this malignancy. FGFR1 mutations at p.N546 were associated with high-risk disease and rapid tumor progression, resulting in dismal outcome of neuroblastoma patients bearing this alteration. Ectopic expression of FGFR1N546K induced constitutive down-stream signaling and interleukin-3-independent growth in Ba/F3 cells, indicating oncogene addicted proliferation. In FGFR1N546K;MYCN transgenic mice, neuroblastoma developed within the first days of life with fatal outcome within 3 weeks, reflecting the devastating clinical phenotypes of FGFR1 mutant high-risk neuroblastoma patients. Treatment with FGFR inhibitors impaired proliferation and pathway activation in FGFR1N546K-expressing Ba/F3 and patient-derived FGFR1N546K mutant neuroblastoma cells, and inhibited tumor growth in FGFR1N546K;MYCN transgenic mice and in a chemotherapy-resistant patient-derived xenograft mouse model. In addition, partial regression of FGFR1N546K mutant tumor lesions occurred upon treatment with the FGFR inhibitor futibatinib and low-intensity chemotherapy in a patient with refractory neuroblastoma. Together, our data demonstrate that FGFR1N546K is a strong oncogenic driver in neuroblastoma that is associated with failure of current standard chemotherapy, and suggest potential clinical benefit of FGFR-directed therapies in FGFR1 mutant high-risk patients.

overall_design: RNA-seq and gene expression analysis of 8 FGFR1N546K and 11 FGFR1N546K;MYCN transgenic mice. RNA-seq data of the mice transgenic for ALKF1174L;MYCN were previously published under GSE254751.

first: Lisa

last: Werr


title: Dnmt1 mediates epigenetic restriction of invasive traits in clonal crayfish [BiSulfite-seq]

first: Jaime

last: Diaz-Larrosa

overall_design: 28 days post injection of, 2 control animals (injected with dsGFP) and 2 Dnmt1 KD (injected with dsDNM1) were bled and the hemocytes isolated. After bisulfite-converting the genomic DNA, samples were submitted for sequencing. These samples (before conversion) were split to use for RNA-seq as well

first: J. Jaime

first: Vitor

last: Carneiro

first: Katharina

last: Hanna

first: Günter

last: Raddatz

first: Frank

last: Lyko


title: The integrated stress response promotes immune evasion through Lipocalin 2

first: Yuan

last: Hao

address: Laura and Isaac Perlmutter Cancer Center

institute: NYU Langone Health

summary: ExCITE-Seq immune analysis of sorted CD45+ immune cell clusters from orthotopically transplanted KP LUAD with doxycycline-inducible shLcn2 and shCtr KP tumors 8 days after adding doxycycline

overall_design: Mice were sedated with ketamine and xylazine and then were injected with 2 ug of APC anti-CD45 (2 ug per mouse diluted in 100 uL PBS, Biolegend 30-F11) retro-orbitally 3 minutes prior to lung collection. The lung lobes were minced on a glass slide and then digested (collagenase IV (Sigma Aldrich C5138), DNAse I (Sigma Aldrich, DN25) in RPMI with 10% FBS) for 35 minutes at 37 degrees celsius. Digestion was stopped with EDTA (1 mM). Digested tissue were filtered into a single cell suspension through a 100 micron filter followed by red blood cell lysis (BD Pharm Lyse 555899). Cells were then washed and suspended in a staining buffer. Cells were then stained with live dead staining (Zombie UV fixabable viability dye, Biolegend #423107) and PeCy7 anti-CD45 (see flow cytometry methods section for staining protocol). Approximately 500,000 lung immune cells from each condition (2 mice per condition) were sorted as live+ IV-CD45 - CD45+ and 50,000 tumor cells were sorted as live+ CD45- GFP+. Sorted samples were multiplexed using cell hashing antibodies (Biolegend) and stained with ADTs (see antibody table). Cells from each sample were pooled and loaded into 10X Chromium.

first: Jozef

middle: P

last: Bossowski

first: Thales

last: Papagiannakopoulos


title: A new mouse mutant with a discrete mutation in Pcdhgc5 reveals that the Protocadherin gC5 isoform is not essential for dendrite arborization in the cerebral cortex

city: Bar Harbor

first: Robert

last: Burgess

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: There are ~60 clustered protocadherin (cPcdh) isoforms expressed from three gene clusters (Pcdha, Pcdhb, Pcdhg) arrayed in tandem across nearly 1 Mb in mammals. cPcdhs are homophilic cell adhesion molecules (CAMs) critical for a host of neural developmental functions consistent with a role in cell-cell recognition. Indeed, isoforms make recognition modules in combination to generate recognition diversity far exceeding the ~60 individual CAMs. However, there is also growing evidence for specialized functions for specific isoforms, particularly the C-type isoforms found at the 3’ ends of the Pcdha cluster (aC1 and aC2) and at the 3’ end of the Pcdhg cluster (gC3, gC4, and gC5). We have previously described unique roles for gC3 in dendrite arborization in the cerebral cortex and neural circuit formation in the spinal cord, as well as for gC4 in neuronal survival. Here we report a new mouse mutant specifically targeting the Pcdhgc5 exon encoding gC5. Unlike the rest of the Pcdhg cluster, expression of this isoform does not begin until postnatal stages of mouse development, increasing in the second week of life, suggesting specialized roles. We found significant expression changes in gene pathways involved in synaptic activity, learning and memory, and cognition. Despite this, we saw no major disruption in the cerebral cortex in neuronal organization, survival, dendritic arborization, or synaptic protein expression in these mutants. This new model will be an important tool for future studies delineating specific functions for gC5.

overall_design: Bulk RNAseq was used to examine differential gene expression in the cerebral cortex of mice lacking the Pcdhgc5 isoform of the gamma-protocadherin (Pcdhg) gene cluster.  Six homozygous mutant animals (3 male, 3 female) were compared to 6 wild type littermates (5 male, 1 female).

first: Andrew

last: Garrett

first: Abigail

last: Tadenev


title: Effects of rocking during sleep on the bulk transcriptome of mouse cerebral cortex.

city: Camerino

first: Michele

last: Bellesi

address: Via Gentile III Da Varano

country: Italy

institute: University of Camerino

summary: Transcriptomic studies have revealed that sleep and wake states are associated with widespread changes in gene expression in the brain across multiple species. While these findings have provided important insights into the molecular correlates of sleep, the transcriptional consequences of experimentally enhancing sleep through non-pharmacological interventions remain poorly characterized. In the present study, we investigated the effects of sleep enhancement induced by vestibular stimulation via rocking on the bulk transcriptome of the mouse cerebral cortex. Mice were exposed to repeated rocking sessions during sleep across multiple days, a protocol previously shown to increase sleep duration and consolidation. Cortical tissue was collected following the stimulation protocol, and bulk RNA sequencing was performed to assess global gene expression changes associated with rocking-induced sleep enhancement. Transcriptomic analysis revealed significant modulation of genes involved in synaptic function, neurotransmission, and plasticity-related pathways, consistent with the observed behavioral and synaptic outcomes of the experimental paradigm. These data provide a molecular framework for understanding how sensory-driven sleep enhancement influences cortical gene expression and support a link between improved sleep and transcriptional programs associated with neuroplasticity.

overall_design: Standard RNA sequencing of motor cortex tissue was conducted to compare transcriptomic changes between sleep (S) and sleep-enhanced (SE) C57BL/6 mice. For each animal, primary motor cortex was immediately extracted and snap frozen.

first: Reyila

last: Simayi

first: Letizia

last: Santoni

first: Sabrina

last: Galizia

first: Riccardo

last: Avvisati

first: Ester

last: Biecher

first: Luisa

last: de Vivo


title: Single-cell RNA sequencing for female Schistosoma mansoni to investigate BATT-induced sexual maturation.

city: Shanghai

first: Mengjie

last: Gu

address: 2005, Songhu Rd

institute: Fudan University

summary: Single-cell RNA sequencing (scRNA-seq) was performed on virgin/adult females using 10x Genomics to explore transcriptome change after BATT induction. Egg production by female Schistosoma is central to both the transmission and pathology of schistosomiasis, a neglected tropical disease affecting over 200 million people globally. Female sexual maturation depends on the male-derived pheromone β-alanyl-tryptamine (BATT), yet the molecular mechanisms underlying this process remain largely unknown.

overall_design: Virgins were cultured in A169 medium with either 50 μM BATT or 0.05% DMSO (vehicle control) for 2 days. For each condition, three biological replicates (~200 worms) were processed. In addition, approximately 60 adult females, freshly perfused from mice at 7 weeks post-infection, were processed for single-cell RNA sequencing.

first: Jipeng

last: Wang


title: Selective inhibition of ALDH1A3 impedes breast cancer growth and metastasis by blocking ALDH1A3-driven transcriptional programs

city: Halifax

first: Paola

last: Marcato

state: NS

address: 5850 College street

institute: Dalhousie University

summary: Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer associated with poor survival outcomes. Aldehyde dehydrogenase 1A3 (ALDH1A3) promotes tumor growth, metastasis, and chemoresistance across multiple cancer types including TNBC, glioblastoma, melanoma lung, and colon cancers. Currently, there are no ALDH1A3 inhibitors in clinic and developing targeted ALDH1A3 inhibitors is novel precision medicine approach to treat ALDH1A3+ tumors. For this purpose, we have developed a novel ALDH1A3 specific inhibitor,CLM296

overall_design: MDA-MB-231 breast cancer cells, overpressing ALDH1A3 or vector control, were treated with or without 100nM CLM296 for 24 hours. The RNA was collected and sequencing was performed on Illumina NovaseqX platform. Three replicates per sample were used in this study.

first: Maya

last: MacLean

first: Bianca

last: Bernardoni

first: Wasundara

last: Fernando

first: Giovanni

last: Petrarolo

first: Cheryl

last: Dean

first: Ilaria

last: D’Agostino

first: Christopher

last: Hughes

first: Jaganathan

last: Venkatesh

first: Geetha

last: Marivel

first: Olivia

last: Walker

first: RajPranap

last: Arun

first: Hannah

last: Cahill

first: Kerry

last: Goralski

first: Concettina

last: LaMotta


title: Schisantherin B Alleviates Cisplatin-Induced Hearing Loss via CNPY2 Coordination

status: Public on Jan 27 2026

first: Ziwen

last: Gao

address: Fenyang Road

department: ENT Institute and Department of Otorhinolaryngology

institute: Eye & ENT Hospital, Fudan University

summary: Cisplatin-induced hearing loss (CIHL), is characterized by irreversible hearing impairment and no effective interventions, is a major chemotherapy side effect. Schisantherin B (STB), a natural compound isolated from Schisandra chinensis, have been shown to possess neuroprotective and hepatoprotective properties, whereas research in the auditory field is limited. This study alleviates cisplatin-mediated auditory toxicity in vitro and successfully rescued auditory brainstem response (ABR) thresholds in a CIHL model of adult albino guinea pigs by protecting hair cells, synaptic ribbons and spiral ganglion neurons. The drug affinity responsive target stability (DARTS) assay, the cellular thermal shift assay (CETSA), and the surface plasmon resonance (SPR) assay have determined that the canopy FGF signaling regulator 2 (CNPY2) protein, a key initiator of ER stress, is an important partner of STB, inhibiting downstream signals PERK/CHOP signals and endoplasmic reticulum (ER) stress-induced apoptosis. The collective findings of this study demonstrate that STB is a promising candidate drug for protecting against CIHL. Moreover, the results indicate that CNPY2 primed ER stress is a critical biological process for STB-mediated oto-protection.

overall_design: RNA-seq profiling of cochlears from guinea pigs following treatment with cisplatin, cisplatin plus STB and wildtype.

first: Ping

last: Yang

first: Hui

last: Huang

first: Weida

last: Zhang

first: Yilai

last: Shu


title: Dysregulation of estrogen signaling and HSD17B7 in the prostate stroma of African American men

first: Larisa

last: Nonn

address: 840 S. Wood St, MC847

department: Pathology

institute: University of Illinois at Chicago

summary: African American men experience a higher incidence and severity of prostate cancer relative to European American men, and there is a range of risk factors that may contribute to this disparity. Prostate adenocarcinoma originates from the epithelium, which is significantly influenced by signaling from the surrounding fibromuscular stroma. To identify ancestry-associated differences in the stroma, gene expression profiling was compared between laser-capture microdissected prostate cancer stroma from patients of African descent and those of European descent. Estrogen receptor signaling was the top differential pathway between the groups, with the steroid hormone dehydrogenase HSD17B7 identified as the most differentially expressed gene. In a separate cohort of patients, protein expression of HSD17B7 was higher in African American patients relative to European American patients in a radical prostatectomy tissue microarray, validating the transcriptional findings. African American patients also exhibited significantly increased levels of HSD17B7 protein in the stroma surrounding benign areas compared to the stroma near tumors. These studies provide important evidence of ancestry-associated differences in stromal estrogen signaling.

overall_design: RNA was isoloated from laser-capture micordissected stroma surrounding benign or cancer epithelium

first: Graham

middle: H

last: Read

first: Julian

last: Pacheco

first: Bethany

last: Baumann

first: Zachary

middle: A

last: Richards

first: Ryan

last: Deaton

first: Virgilia

last: Macias

first: Andre

last: Kajdacsy-Balla

first: Rick

last: Kittles

first: Michael

last: Abern


title: Cardiac Radiotherapy-Induced Epigenetic Memory Underlies Electrophysiologic and Metabolic Reprogramming [RNA-seq]

city: Saint Louis

first: Shuhua

last: Fu

state: MO

address: 660 S. Euclid Avenue Campus Box 8103

institute: Washington University in St. Louis

summary: Stereotactic arrhythmia radiotherapy (STAR) is emerging as a highly effective treatment for ventricular tachycardia (VT). Growing evidence indicates that STAR favorably reprograms the electrical substrate via modulating ion channel expression, though the mechanisms whereby single-fraction radiation mediates durable changes in gene expression are incompletely understood. The DNA damage response (DDR) recruits epigenetic regulators during the repair process after irradiation (IR). Here, we demonstrate acute changes in the cardiomyocyte epigenome and transcriptome after IR in vivo and in vitro. A subset of changes persist as late as 6 weeks post-IR in mice, including increased Scn5a expression and chromatin accessibility (encoding the alpha subunit of the sodium channel, NaV1.5), demonstrating a role for epigenetic memory in conduction velocity increases observed after STAR. Transcriptomic and epigenetic sequencing further identify dynamic changes to gene expression and regulatory regions involved in cellular repolarization, calcium handling, and metabolism after IR. Gene expression changes are mirrored by dose-dependent and cell-autonomous changes in repolarization, calcium flux, and mitochondrial respiration after IR, highlighting important cellular processes which may mediate both therapeutic and toxic effects of STAR. Cardiomyocyte-specific knockout of p53 failed to blut conduction velocity changes post-IR, and improved ROS scavenging via SOD2 overexpression had minimal impact on the post-IR transcriptome. Overall, we find that cardiomyocytes exposed to a single fraction of high-dose IR exhibit epigenetic reprogramming that mediates broad and dynamic physiologic responses.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
RNAseq profiliing was performed in control and 25 Gy irradiated hiPSC-cardiomyocytes from two independent sources : (1) commercially available iCell Cardiomyocytes^2 (female) and (2) WTC11-AAV-CAG-GCaMP6 (GCaMP6) differentiated via small-molecule Wnt modulation (male). RNA was prepared at 1 day, 7 days, 14 days, or 28 days (GCaMP6 only) after treatment.  RNAseq profiling was also performed in mice after whole-heart irradiation with 25 Gy or sham treatment. Left ventricle tissue was dissociated, nuclei were isolated, and flow cytometry was used to select PCM1+ cardiomyocyte nuclei prior to sequencing. Samples were collected from sham mice and 6 weeks post-IR.
Myosin Heavy Chain6-Superoxide dismutase (Myh6-SOD) mice overexpresses SOD2 in cardiomyocytes, resulting in enhanced ROS scavenging. After exposuring Myh6-SOD and wild-type FVB mice to 25 Gy whole-heart IR or sham conditions, we performed bulk RNA sequencing at 2 days and 6 weeks post-IR.

first: Samuel

last: Jordan

first: Abigail

last: Fulkerson

first: Khadija

last: Khan

first: Donghua

last: Hu

first: Sherwin

last: Ng

first: David

first: Sneha

last: Manikandan

first: Jeff

last: Szymanski

first: Anish

last: Bedi

first: James

last: Tabor

first: Lauren

last: Boggs

first: Lori

last: Strong

first: Stephanie

last: Hicks

first: Lavanya

last: Aryan

first: Nishanth

last: Gabriel

first: Kuo-Chan

last: Weng

first: Nathaniel

last: Huebsch

first: Julie

middle: K

last: Schwarz

first: Bo

first: Stacey

last: Rentschler


title: Single-cell RNA sequencing analysis of HUVEC in monolayer alone or exposed to (bacterially-infected) macrophage-like U937 cells for 8 h.

first: Effie

last: Bastounis

state: Baden-Württemberg

address: Auf der Morgenstelle 28/E7

department: Interfaculty Institute of Microbiology and Infection Medicine

institute: University of Tübingen

summary: We sought to identify changes in gene expression that occur when endothelial cells (HUVEC) in monolayer interact with either uninfected or Listeria monocytogenes-infected macrophages. To that end we seeded HUVEC in monolayer and either exposed them to nothing, or to uninfected PMA-differentiated macrophage-like U937, or to Listeria monocytogenes-infected PMA-differenitated U937. At 8 hours post U937 exposure (hpe), cells were detached from the wells and cryopreserved for scRNA-seq. scRNa-seq analysis allowed us to distinguish endothelial cells from macrophage like cells and create appropirate clusters. By then analyzing the differentially expressed genes between all conditions for HUVEC and U937 separately, we identified a significant number of differentially regulated genes related to innate immune signaling in both infected U937 exposed HUVEC and to a lesser degree uninfected U937 exposed HUVEC, as compared to control unexposed HUVEC. By perofming pathway enrichment analysis, we also discovered that HUVEC exposed to uninfected U937 showed a higher upregulation in pathways related to mechanotransdcution, like "focal adhesions" and "regulation of the actin cytoskeleton", compared to those exposed to infected U937. This is consistent with the reinforsement of traction and monolayer stresses of HUVEC with uninfected U937 which we observe, a feature that is attenuated significanlty during infection. Finally, when we compare uninfected versus infected U937 cells from co-cultures, we find that the later upregulate cell adhesion molecules, the PI3K signaling pathway and focal adhesions, suggestive of increased cell contractility and adhesion as compared to uninfected U937.

overall_design: Primary endothelial cells HUVEC were seeded in monolayer and exposed to: (1) nothing, (2) uninfected PMA-differentiated U937 macrophage-like cells, or (3) Listeria monocytogenes-infected U937 macrophage-like cells. After 8 hours post-exposure (hpe) to U937, samples were gently washed and detached,  and then cryopreserved for scRNA-seq . For each condition three samples were analysed using 10x Genomics scRNAseq technology. Equipment: 10X Chromium platform with Chromium Next GEM Single Cell 3ʹ Kit v3.1 following the manufacturer’s protocol for library construction. Library sequencing was done with llumina NovaSeq X platform, at 20000 reads per cell per sample. Sequencing read mode applied was: Read 1 28bp; Read 2 90bp; Index Reads 1 and 2 10 bp each.

first: Effie E.

first: Marie

last: Muenkel

first: Julio C.

last: Sanchez-Rendon


title: Detection of mitochondrial DNA mutations in T cells following 5-FU or cisplatin exposure

city: Little Rock

first: Yong-Chen

middle: William

last: Lu

address: 4301 W Markham St

institute: University of Arkansas for Medical Sciences

summary: T cells are pivotal to cancer immunotherapy, yet chemotherapy may erode their fitness. Using a single-cell technique, we show that exposure to two widely used chemotherapeutic agents, 5-FU (5-fluorouracil) and cisplatin, induces non-synonymous mitochondrial DNA mutations (mtDNA) in T cells. Notably, nearly all detected mtDNA mutations are transition mutations. Like the effects observed in genomic DNA mutations, the impacts of mtDNA mutations in T cells appear to be random. Some T cells with mtDNA mutations concentrate in clusters associated with gene markers, while others do not. Additionally, several mtDNA mutations are found in the fraction of treated T cells with low mitochondrial activity, suggesting their potential effect on mitochondrial function. Importantly, mtDNA mutations are detected in tumor-infiltrating T cells from patients with colorectal cancer who received chemotherapy. Our findings uncover an unappreciated consequence of chemotherapy on T cell mitochondria, and these results raise concerns about administering immunotherapy and chemotherapy concurrently.

overall_design: 5-FU-treated and untreated (N) T cells from peripheral blood lymphocytes (PBL) from 3 donors (D1007, D2008, D6053) were studied using scRNAseq/scTCRseq. Single-cell RNA and TCR-seq libraries were prepared using the 10X Genomics 5' immune profing kit (including single-cell 5' mRNA and TCR sequencing). The scRNAseq gene expression (GEX) libraries and scTCRseq libraries were sequenced by an Illumina Novaseq 6000 sequencer. The sequencing data was processed by a Cell Ranger-multi pipeline (v7.1.0; 10X Genomics). The gene expression (GEX) sequencing data was mapped to the standard reference genome database (GRCh38-2020-A, 10X Genomics), and the TCR sequencing data was also mapped to the standard reference genome database (GRCh38-alts-ensembl-7.1.0, 10X Genomics).  For single-cell ATAC-seq, the following samples were studied (1) 5-FU-treated and untreated (N) T cells from 4 donors (2) Cisplatin-treated and untreated (N) T cells from 3 donors, (3) Cisplatin-treated T cells from 3 samples were labeled with mitochondria dyes TMRM or MitoTracker-Green (labeled as MASS). Single-cell sequencing was performed on TMRM or MASS high (Hi) and low T cells. (4) Tumor infiltrating lymphocytes (TILs) and PBL from 3 patients with metastatic colorectal cancer (P1, P2, P3) were subjected to single-cell ATAC-seq sequencing (10X Genomics). The prepared samples were sequenced by an Illumina Novaseq 6000 sequencer. The sequencing data was processed a Cell Ranger-ATAC pipeline (v2.1.0; 10X Genomics) and mapped to reference genome database (GRCh38-r107).

first: Catherine

last: Kirkpatrick

first: Charles

middle: M

last: Quick

first: Steven

last: Post

first: Yuet-Kin

last: Leung

first: Ruud

last: Dings

first: Chrystal

last: Paulos

first: Lyle

last: Burdine


title: Cardiac Radiotherapy-Induced Epigenetic Memory Underlies Electrophysiologic and Metabolic Reprogramming [ATAC-seq]

first: Shuhua

last: Fu

summary: Stereotactic arrhythmia radiotherapy (STAR) is emerging as a highly effective treatment for ventricular tachycardia (VT). Growing evidence indicates that STAR favorably reprograms the electrical substrate via modulating ion channel expression, though the mechanisms whereby single-fraction radiation mediates durable changes in gene expression are incompletely understood. The DNA damage response (DDR) recruits epigenetic regulators during the repair process after irradiation (IR). Here, we demonstrate acute changes in the cardiomyocyte epigenome and transcriptome after IR in vivo and in vitro. A subset of changes persist as late as 6 weeks post-IR in mice, including increased Scn5a expression and chromatin accessibility (encoding the alpha subunit of the sodium channel, NaV1.5), demonstrating a role for epigenetic memory in conduction velocity increases observed after STAR. Transcriptomic and epigenetic sequencing further identify dynamic changes to gene expression and regulatory regions involved in cellular repolarization, calcium handling, and metabolism after IR. Gene expression changes are mirrored by dose-dependent and cell-autonomous changes in repolarization, calcium flux, and mitochondrial respiration after IR, highlighting important cellular processes which may mediate both therapeutic and toxic effects of STAR. Overall, we find that cardiomyocytes exposed to a single fraction of high-dose IR exhibit epigenetic reprogramming that mediates broad and dynamic physiologic responses.

overall_design: ATACseq profiliing was performed in control and 25 Gy irradiated hiPSC-cardiomyocytes from two independent sources : (1) commercially available iCell Cardiomyocytes^2 (FujiFilm, female) and (2) WTC11-AAV-CAG-GCaMP6 (GCaMP6, male) differentiated via small-molecule Wnt modulation. ATACseq was performed at 1 day, 7 days, 14 days, or 28 days (GCaMP6 only) after treatment.  ATACseq profiling was also performed in mice after whole-heart irradiation with 25 Gy or sham treatment. Left ventricle tissue was dissociated, nuclei were isolated, and flow cytometry was used to select PCM1+ cardiomyocyte nuclei prior to sequencing. Samples were collected from sham mice and 2 days or 6 weeks post-IR.

first: Samuel

last: Jordan

first: Abigail

last: Fulkerson

first: Khadija

last: Khan

first: Donghua

last: Hu

first: Sherwin

last: Ng

first: David

last: Zhang

first: Sneha

last: Manikandan

first: Jeff

last: Szymanski

first: Anish

last: Bedi

first: James

last: Tabor

first: Lauren

last: Boggs

first: Lori

last: Strong

first: Stephanie

last: Hicks

first: Lavanya

last: Aryan

first: Nishanth

first: Kuo-Chan


title: MitoPerturb-Seq identifies gene-specific single-cell responses to mitochondrial DNA depletion and heteroplasmy [DamID]

first: Stephen

middle: Peter

last: Burr

address: Mitochondrial Biology Unit, Keith Peters Building, Cambridge Biomedical Campus, Hills Road

department: Clinical Neurosciences

institute: University of Cambridge

summary: Mitochondria contain their own genome, the mitochondrial DNA (mtDNA), which is under strict control of the cell nucleus. mtDNA occurs in many copies in each cell, and mutations often only affect a proportion of them, giving rise to heteroplasmy. mtDNA copy number and heteroplasmy level together shape the cell- and tissue-specific impact of mtDNA mutations, ultimately giving rise to rare mitochondrial and common neurodegenerative diseases. However, little is known about how copy number and heteroplasmy interact within single cells, and how this is regulated by the nuclear genes and pathways that sense and control them. Here we describe MitoPerturb-Seq for CRISPR/Cas9-based high-throughput single-cell interrogation of the impact of nuclear gene perturbation on mtDNA copy number and heteroplasmy. We screened a panel of nuclear mtDNA maintenance genes in cells with heteroplasmic mtDNA mutations. This revealed both common and perturbation-specific aspects of the integrated stress-response to mtDNA depletion, that were only partially mediated by Atf4, and caused cell-cycle stage-independent slowing of cell proliferation. MitoPerturb-Seq thus provides novel experimental insight into disease-relevant mito-nuclear interactions, ultimately informing development of novel therapies targeting cell- and tissue-specific vulnerabilities to mitochondrial dysfunction.

overall_design: DamID-sequencing analysis of Dam-ATF4 (for ATF4 binding) and Dam-only (control), 48 hours after transient transfection in immortalized m.5024C>T mouse embryonic fibroblasts (MEFs)

first: Kathryn

last: Auckland

first: Angelos

last: Glynos

first: Abhilesh

last: Dhawanjewar

first: Wei

last: Wei

first: Cameron

last: Ryall

first: Antony

last: Hynes-Allen

first: Malwina

last: Prater

first: Matylda

last: Sczaniecka-Clift

first: Julien

last: Prudent

first: Patrick

middle: F

last: Chinnery

first: Jelle

last: van den Ameele


title: Cardiac Radiotherapy-Induced Epigenetic Memory Underlies Electrophysiologic and Metabolic Reprogramming [CUT&Tag]

first: Shuhua

last: Fu

overall_design: CUT&Tag profiliing was performed in control and 25 Gy irradiated hiPSC-cardiomyocytes (commercially available iCell Cardiomyocytes^2, FujiFilm, female). CUT&Tag was performed 7-14 days after treatment, probing for H3K27me3, H3K27ac, H3K4me3, H3K4me1, or IgG isotype control.

first: Samuel

last: Jordan

first: Abigail

last: Fulkerson

first: Khadija

last: Khan

first: Donghua

last: Hu

first: Sherwin

last: Ng

first: David

last: Zhang

first: Sneha

last: Manikandan

first: Jeff

last: Szymanski

first: Anish

last: Bedi

first: James

last: Tabor

first: Lauren

first: Lori

last: Gabriel

last: Weng

first: Nathaniel

last: Huebsch

first: Julie

last: Schwarz

first: Bo

first: Stacey

last: Rentschler


title: MitoPerturb-Seq identifies gene-specific single-cell responses to mitochondrial DNA depletion and heteroplasmy [RNA-Seq]

first: Stephen

last: Burr

overall_design: Mouse Embryonic Fibroblasts (MEFs) carrying a heteroplasmic mitochondrial (mt)DNA mutation in mt-Ta (m.5024C>T) and stably expressing Cas9 were transduced in biological duplicate with CRISPR gRNAs to Tfam, Opa1 & a non-targeting gRNA. After six days, cells from each transduced population were flow sorted to select 50,000 transduced cells based on mRFP expression. Total RNA was isolated from each sample using the Quick-RNA Microprep Kit (Zymo Research) and RNAseq libraries were prepared using the NEBNext Single Cell/Low Input RNA Library Prep Kit (NEB).

first: Kathryn

last: Auckland

first: Angelos

last: Glynos

first: Abhilesh

last: Dhawanjewar

first: Wei

last: Wei

first: Cameron

last: Ryall

first: Antony

last: Hynes-Allen

first: Malwina

last: Prater

first: Matylda

last: Sczaniecka-Clift

first: Julien

last: Prudent

first: Patrick

last: Chinnery

first: Jelle

last: van den Ameele