title: Dermal fibroblasts respond to interleukin-4 and 13 and promote T-cell recruitment in atopic dermatitis

city: San Diego

first: Tomofumi

last: Numata

address: 9452 Medical Center Drive, Department of Dermatology

department: Dermatology

institute: university of california, SD

summary: Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by type 2 immune responses. While immune cells and keratinocytes are established contributors to AD pathogenesis, the role of dermal fibroblasts remains less defined. Here, we investigated whether fibroblasts contribute to T cell recruitment by producing chemokines in response to type 2 cytokines. Single-cell RNA sequencing (scRNA-seq) of human AD skin and murine models, including IL-4 receptor-deficient mice, revealed transcriptionally distinct fibroblast clusters, with IL-4Rα-dependent populations expressing high levels of chemokines. In vitro, IL-4/IL-13 synergized with inflammatory cytokines(Inf; TNFa + IL-17A + IL-1b) to induce fibroblast expression of CCR3 ligands, including Ccl8. Conditioned media from stimulated fibroblasts promoted T cell migration in a CCR3-dependent manner. Furthermore, pharmacologic inhibition of CCR3 reduced T cell infiltration and skin inflammation in two AD mouse models. These findings demonstrate that dermal fibroblasts are not passive structural cells but active participants in type 2 inflammation, contributing to the pathogenesis of AD by producing chemokines that facilitate T cell recruitment. Targeting the fibroblast–CCR3 axis may represent a novel therapeutic strategy for AD.

overall_design: Bulk RNA-seq of fibroblasts stimulated in vitro


title: Eos maintains Treg homeostasis and plays a critical role in the function of recirculating thymic Tregs

status: Public on Dec 05 2025

city: Bethesda

first: Tom

last: Hill

state: Maryland

address: NIHBC 10 - CLINICAL CENTER BG RM 11N244A, 10 CENTER DR

country: USA

institute: NIAID

type: Expression profiling by high throughput sequencing

summary: Eos, a member of the Ikaros family of transcription factors, is expressed by T regulatory cells (Tregs) and has been postulated to play a role in Treg suppression and maintenance of Treg stability. We demonstrate that expression of Eos was limited to a subpopulation of thymus-derived, activated Tregs and is undetectable in resting or activated T conventional cells (Tconvs). Eos associates with Helios, Foxp3 and Hdac1 and binds directly to the CD25 locus at a site identical to the Foxp3 binding site resulting in enhancement of CD25 expression. Studies in heterozygous female mice demonstrate that Eos is critical for Treg survival and activation. Eos+ Tregs also represent the major population of recirculating thymic Tregs, in which Eos plays a critical role in regulating their migration and suppression of Treg precursors in the thymus by competing for IL-2 and depleting MHC II from thymic dendritic cells (DCs).

overall_design: sc-RNA seq of thymic Tregs

first: Xuan

last: Xie

first: Angela

middle: M

last: Thornton

first: Shalini

last: Tanwar

first: Patricia

last: Korty

first: Alexandria

middle: C

last: Wells

first: Elisha

last: Segrist

first: Ana

last: Teijeiro

first: Claudia

middle: A

last: Rivera

first: Danping

last: Wei

first: Xi

last: Chen

first: Jinfang

last: Zhu

first: Asya

last: Khleborodova

first: Tovah

middle: E

last: Markowitz

first: Margery

last: Smelkinson

first: Juraj

last: Kubat

first: Tibor

last: Veres

first: Owen

last: Schwartz

first: Francisco

last: Otaizo-Carrasquero

first: Paul

last: Gardina

first: Amirhossein

last: Shamsaddini

first: Craig

last: Martens

first: Kyoungin

last: Cho

first: Cheng-Chao

last: Lin

first: Jaspal

middle: S

last: Khillan

first: Yelena

last: Levin

first: Ying

last: Wu

first: Ethan

last: Shevach


title: Eos maintains Treg homeostasis and plays a critical role in the function of recirculating thymic Tregs [RNA-Seq]

state: MD

address: 10 Center Dr, Building 29B

department: Integrated Data Sciences Section (IDSS)

overall_design: Eos+ Tregs, Eos- Tregs, and Tconvs from thymus, total RNA-seq in quadruplicate

first: Xuan

last: Xie


title: Multiomics profiling of zebrafish embryonic cell line PAC2 across growth phases to assess its relevance for toxicological studies

city: Duebendorf

first: Ksenia

middle: J

last: Groh

address: Ueberlandstrasse 133

department: Environmental Toxicology (Utox)

country: Switzerland

institute: Eawag - Swiss Federal Institute of Aquatic Science and Technology

summary: Permanent fish cell lines offer promising alternatives to traditional animal models for environmental risk assessment of chemicals. However, to facilitate broader uptake into toxicity testing practice, a better understanding of functional capacities and expression of toxicologically relevant molecular targets is needed. Here, we present an extensive molecular profiling of the zebrafish embryonic cell line PAC2, combining global proteomics across cell population growth phases (over 7300 protein groups) with matched transcriptomics at exponential and stationary phases (over 14500 transcripts). Proteome coverage was sufficiently deep to reveal functional insights consistent with those derived from transcriptomics data, despite differences in the total number of measured genes. Major gene expression shifts detected upon transition from exponential to stationary cell population growth phase indicated reduction in DNA replication, translation, metabolism, and cell cycle regulation, along with increased stress and immune system responses, and extracellular matrix remodeling. Functional annotation revealed expression of core cellular processes along with a number of toxicologically relevant pathways, including xenobiotic metabolism, stress signaling, and nuclear receptors responsive to important chemical classes, such as steroids (e.g., estrogens, glucocorticoids) and chemicals known to disrupt lipid metabolism, such as through interaction with peroxisome proliferation activating receptors. These findings reinforce the potential of PAC2 cells to offer a versatile in vitro model for studying fish cell biology and omics-enhanced exploration of chemical toxicity mechanisms, aided by the well-developed molecular annotation in zebrafish. Moreover, the analysis approaches developed in this work offer a blueprint for molecular baseline characterization of other fish cell lines. This work thus strengthens the mechanistic foundation supporting the use of fish cell lines as alternative models in aquatic toxicity testing and risk assessment.

overall_design:
Zebrafish PAC2 were cultured under normal conditions and sampled at day 8 and day 14 post-seeding, corresponding to exponential and stationary cell population growth phases, respectively. These samples were subjected to transcriptomics analysis (RNAseq). Experiment was performed with four biological replicates. One replicate of day 14 (biological replicate 3) was lost during library preparation, so this condition has only 3 biological replicates in the final dataset.
Day 8 (PP) and day 14 (SP).

first: Degeratu

last: Mihai-Ovidiu

first: Bertoli

last: Jessica

first: Huwa

last: Nikolai

first: Lopez-Rodriguez

last: David

first: Revel

last: Marion

first: Schönenberger

last: René

first: vom Berg

last: Colette

first: Schirmer

last: Kristin

first: Groh

last: Ksenia


title: Differential Transcriptome Features of Peripheral Blood Mononuclear Cells in Pulmonary Sarcoidosis with and without Extrapulmonary Lesions

city: Chiba

first: Takeshi

last: Kawasaki

address: 1-8-1, Inohana, Chuoku

department: Respirology

country: Japan

institute: Chiba University

summary: Sarcoidosis is a systemic granulomatous disease of unknown etiology. Pulmonary sarcoidosis with extrapulmonary lesions (EPL), especially in cardiac sarcoidosis, is associated with poor prognosis. The transcriptome features of peripheral blood mononuclear cells (PBMCs) could be crucial in sarcoidosis pathogenesis. However, the gene expression characteristics associated with EPL development in pulmonary sarcoidosis remain unknown. Therefore, we investigated gene expression patterns associated with the development of EPL in pulmonary sarcoidosis. First, we conducted trascriptome analysis between patients with pulmonary sarcoidosis and healthy controls. Principal component analysis (PCA) revealed a clear distinction between them, with 227 differentially expressed genes detected. Enrichment analysis revealed upregulated immunological pathways related to granuloma formation in pulmonary sarcoidosis PBMCs, including T helper 17 and tumor necrosis factor-alpha signaling pathways, inflammatory cytokine production, and response to external stimuli. Furtheremore, PCA differentiated patients with pulmonary sarcoidosis with and without EPL, and 206 differentially expressed genes identified, including interferon-gamma (IFNG) and interferon lambda receptor 1 (IFNLR1). Gene ontology (GO) analysis revealed that interleukin 6 (IL-6) and IL-23 production were upregulated in patients with pulmonary sarcoidosis and EPL. In cardiac sarcoidosis, nitric oxide synthases (NOS), including NOS1 and NOS2, were upregulated in PBMCs. The current study strengthens our understanding of the mechanisms underlying granuloma formation in sarcoidosis and demonstrates the differential transcriptome features of PBMCs in patients with pulmonary sarcoidosis with and without EPL, highlighting IFNG and IFNLR1 upregulation. The upregulation of these genes may be related to EPL development and could serve as potential therapeutic targets for sarcoidosis.

overall_design: To investigate the pathogenesis of pulmonary sarcoidosis in PBMCs, we compared patients with pulmonary sarcoidosis (n=14) and healthy controls (n=26) samples by RNA-seq. Then, to investigate the pathogenesis of pulmonary sarcoidosis with extrapulmonary lesions (EPL), we compared samples between pulmonary sarcoidosis with EPL (n=9) and without EPL (n=5), respectively, by RNA-seq.

first: Yushi

last: Murai

first: Takuro

last: Imamoto

first: Daisuke

last: Ishii

first: Keiichiro

last: Yoshioka

first: Yoshinori

last: Hasegawa

first: Osamu

last: Ohara

first: Koichiro

last: Tastumi

first: Takuji

last: Suzuki


title: Eos maintains Treg homeostasis and plays a critical role in the function of recirculating thymic Tregs [ChIP-Seq]

first: Tovah

last: Markowitz

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Single replicate ChIP-seq of anti-Helios or anti-Eos in WT and EosKO conditions

first: Xuan

last: Xie

first: Ethan

last: Shevach


title: Severe preeclampsia is not associated with significant DNA methylation difference but cell proportion in cord blood

city: Ann Arbor

first: Lana

last: Garmire

state: Michigan

address: 1600 Huron Parkway

institute: University of Michigan

type: Genome binding/occupancy profiling by genome tiling array

summary: Preeclampsia (PE) is a severe pregnancy complication that threatens maternal and neonatal health and well-being. Previous studies on epigenome-wide association analysis (EWAS) of preeclampsia produced inconsistent results, and one possible explanation is their failure to rigorously adjust for confounders. Here, we calculated the DNA methylation change in cord blood from newborns affected by preeclampsia, using a multi-ethnic cohort from Hawaii populations. We comprehensively adjusted confounders from clinical variables such as maternal age, BMI, parity and estimated the cell proportions, in hope of resolving the conflicting results of preeclampsia’s impact on babies epigenetic-wide profile.We showed that after adjusting cell type proportions and patient clinical characteristics, most of the so-called significant CpG methylation changes associated with severe PE disappear. Rather, the major effect of severe PE on cord blood is through the proportion changes in CD8T and natural killer (NK) cell types. We validated such a lack of CpG methylation changes, using multiple previously published cord blood DNA methylation datasets. Moreover, we found that in additional to severe PE,  gestation progression is accompanied by significant proportion changes in several cell types, such as granulocyte, nRBC, CD8T, and B cells. In summary, our study shows that the previously reported significantly differentially methylated patterns are actually artifacts due to confounding of cell type heterogeneity and clinical factors such as gestational age. Severe preeclampsia is not associated with significant DNA methylation changes but cell proportion changes. This finding alerting the scientific rigor needed in EWAS.

overall_design: The umbilical cord whole blood DNA samples were obtained from Hawaii Biorepository (HiBR).  The HiBR collected placenta, maternal, and cord blood samples from deliveries at Kapiolani Women and Children’s Hospital from 2006 to 2013. Severe PE was characterized by OBGYNs at Kapiolani Medical Center as sustained pregnancy-induced hypertension(systolic/diastolic blood pressure >= 140/90) with urine protein and/or organ dysfunction. We originally collected 63 samples. The demographic and clinical information of the patients was collected and analyzed to identify any potential confounding effects.  Data usage was approved by IRB #CHS23976.

first: Xiaotong

last: Yang

first: Wenting

last: Liu

first: Zhixin

last: Mao

first: Yuheng

last: Du

first: Cameron

last: Lassiter

first: Fadhl

last: AlAkwaa

first: Paula

last: Benny

middle: X


title: Scaffolding-dependent CASP1 constrains excessive cell-intrinsic inflammatory signaling in leukemia [MDSL]

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

summary: The inflammatory cytokine Interleukin-1b (IL-1b is implicated in acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS). IL-1b processing is regulated by Caspase-1 (CASP1), a protease that is initially expressed as an inactive zymogen (Pro-CASP1) and can be cleaved into its active form. CASP1 cleaves both pro-IL-1b and Gasdermin-D (GSDMD), which mediates IL-1b secretion and consequently pyroptotic cell death. Despite its known role in inflammation, the contribution of CASP1 to leukemogenesis has not been adequately investigated. To address this, we generated Pro-CASP1 knockout (CASP1KO) MDS/AML cell lines and patient-derived samples. As expected, CASP1KO cells were unable to induce pyroptosis or produce IL-1b. Surprisingly, however, these cells also exhibited impaired leukemic cell expansion, increased myeloid differentiation, and significantly reduced leukemic burden when xenografted into mice. Similarly, Casp1-/- pre-leukemic and AML mouse cells were impaired in their clonogenic potential and leukemia development. Notably, restoring IL-1b expression did not rescue the growth defects, suggesting that IL-1b is not the primary driver of CASP1’s role in MDS/AML. Mutation or inhibition of the CASP1 protease activity did not impact MDS/AML cells, indicating that CASP1’s pro-leukemic function is independent of its proteolytic activity. Transcriptomic and functional analyses of CASP1KO cells revealed excessive NF-kB and inflammatory signaling. Suppression of NF-kB activity restored leukemic cell function and viability, indicating that CASP1 acts as a negative regulator of NF-kB activation. We performed a proximity proteomic and computational prediction analysis and identified RPTOR, a component of the mTORC1 complex, as a key interactor of CASP1. Knockdown of RPTOR in CASP1KO cells reduced excessive NF-kB activity and rescued the leukemic growth defect, suggesting that the CASP1–RPTOR interaction regulates NF-kB signaling in leukemia. To target the scaffolding function of CASP1, we developed a PROTAC degrader (dCASP1-55). dCASP1-55 induced NF-kB activation and reduced the colony-forming potential of MDS/AML cells, supporting its potential as a targeted therapy. CASP1 functions as a critical organizational center regulating NF-kB signaling through mTORC1 in MDS/AML, while IL-1b expression is a secondary contributing event.

overall_design: Bulk RNAseq profiling of WT MDSL or Casp1KO MDSL cells generated by Crispr Cas9 and grown in liquid culture, and validated by PCR and western blot.

first: Emma

last: Uible

first: Kathleen

last: Hueneman

first: Erik

last: Vick

first: William

last: Seibel

first: Kenneth

last: Greis

first: Lynn

last: Lee

first: Timothy

last: Chlon

first: Jorge

last: Henao-Mejia

first: Chandrashekhar

last: Pasare

first: Andrew

last: Volk

first: Daniel

middle: T

last: Starczynowski


title: oHSV-mediated JAG1 blockade induces glioma senescence-associated secretory phenotype to increase macrophage activation and sensitize to cetuximab-mediated senolysis II

city: Augusta

first: Balveen

last: Kaur

state: GA

address: CN-3205, 1410 Laney-Walker Blvd

department: Pathology

institute: Augusta University

summary: Oncolytic HSV-1 (oHSV) treatment induces Notch signaling and myelosuppression in the tumor microenvironment (TME) of preclinical models. In the clinic, upregulation of JAG1 gene expression was observed in recurrent high-grade glioma patients treated with CAN-3110. Since JAG1 is expressed on both glioma cells and tumor-associated macrophages (TAMs), and its expression correlated with a worse prognosis, we engineered a JAG1-antagonizing oHSV (OncoD-0J1) and interrogated its impact on the tumor and myeloid TME. OncoD-0J1 antagonized JAG1-mediated Notch signaling and had a significant therapeutic advantage in vivo, which relied on Notch signature in tumor cells. Kinome profiling revealed that OncoD-0J1 treatment suppressed CDK1, resulting in a G2/M cell cycle checkpoint as seen by cell cycle analysis. Cell cycle arrest led to senescence and correlated with increased reactive oxygen species, p62 accumulation, autophagosome accumulation, and senescence-associated beta-galactosidase activity. This resulted in increased production of inflammatory chemokines and DAMPs such as IL-1β and extracellular ATP. RNA sequencing of murine macrophages co-cultured with infected human tumor cells showed enrichment of chemotactic and pro-inflammatory pathways as well as increased Fc receptor activation following OncoD-0J1 infection. Single-cell RNA sequencing and flow cytometric analysis of F4/80+ cells isolated from infected tumors showed a shift from tumor-supporting TAMs to inflammatory macrophages upon OncoD-0J1 treatment. Senescent cells showed heightened EGFR activation as a mechanism to escape death, which created a unique vulnerability for cetuximab as a senolytic agent. Combination therapy reduced EGFR signaling and induced macrophage-mediated antibody-dependent cellular cytotoxicity, thereby increasing the anti-tumor therapeutic response of OncoD-0J1 as a monotherapy.

overall_design: Primary GBM cells were infected with OncoD or OncoD-0J1 at a multiplicity of infection (MOI) of 0.005 (GBM12) and 0.01 (GBM28) in four replicates. 48 hours post-infection, total RNA was isolated using the Rneasy Plus kit from Qiagen, and samples were submitted for bulk RNA sequencing.

first: Kimberly

last: Rivera-Caraballo

first: Tae Jin

first: Arnoneel

last: Sinha

first: Marco

last: Orecchioni

first: Karina

last: Vazquez-Arreguin

first: Shilpa

last: Sharma

first: Kimya

last: Jones

first: Upasana

last: Sahu

first: Sara

last: Murphy

first: Bangxing

last: Hong

first: Ravindra

last: Kolhe

first: Ashok


title: Anti-CSF-1R therapy with combined immuno- chemotherapy coordinate an adaptive immune response to eliminate macrophage enriched Triple Negative Breast Cancers

city: Houston

first: Diego

last: Pedroza

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Patients diagnosed with metastatic triple negative breast cancer (mTNBC) have limited treatment options, are more prone to develop resistance and are associated with high mortality. A cold tumor immune microenvironment (TIME) characterized by low T cells and high tumor associated macrophages (TAMs) in mTNBC is associated with the failure of standard-of-care chemotherapy and immune checkpoint blockade (ICB) treatment. We demonstrate that the combination of immunostimulatory metronomic Cytoxan (CTX) coupled with anti-CSF-1R antibody targeted therapy (SNDX-ms6352) and anti-PD-1 (ICB), was highly effective against aggressive metastatic syngeneic Trp53 null TNBC genetically engineered mouse models (GEMMs) that present with high macrophage infiltration. Mechanistically, CSF-1R inhibition along with CTX disrupted the M-CSF/CSF-1R axis which upregulated IL-17, IL-15 and type II interferon and elevated B- and T cells. Addition of an anti-PD-1 maintenance dose was necessary to overcome de novo PD-L1 intra-tumoral heterogeneity (ITH) associated recurrence in lung and liver mTNBC.

overall_design: All mice received the final doses 24h prior to euthanasia. Single cell suspensions were processed as previously described and pooled from 3 mice per treatment. Only viable cells were used for single cell analysis as such, isolated single cell suspensions were first stained with Ghost Dye UV 450 (Tonbo Biosciences, 13-0868) for 10 min and sorted via FACS to isolate viable cells. Briefly, primary tumor cells were harvested and resuspended in RBC Lysis Buffer (BioLegend, Inc., 420301) and passed through a 70- µm strainer. Viable single cell suspensions were tagged with 3’ CellPlex barcoding oligos (10X Genomics, PN-1000262) and were quickly subjected for scRNA-seq library preparation by the Single Cell Genomics Core at BCM. Single-cell libraries were prepared following the Chromium Single Cell Gene Expression 3’ v3.1 kit encompassing the multiplex capture CMO barcoding kit (10x Genomics, PN-1000262). Next generation library sequencing was performed using the NovaSeq 6000 (Illumina) following quality control check.


title: Transcriptome analysis of Drosophila melanogaster intestines upon knockdown of Tachykinin (Tk), the GPCR GulpR (CG32547), and bruchpilot (brp)

city: Boston

first: Paula

last: Watnick

state: MA

address: 300 Longwood Avenue

institute: Boston Childrens Hospital

summary: Tk is a peptide hormone mainly expressed in the Drosophila brain and intestine. Gut-derived Tk is known to impact intestinal lipid metabolism and immunity. We used RNA-seq to determine the impact of Tk and the Tk regulators GulpR and brp on intestinal gene expression and further understand their role in metabolism and immunity. We compare the intestinal transcriptome of Tk knockdown, GulpR knockdown, and brp knockdown flies to control driver flies.

overall_design: Tk> (Tk-Gal4) flies were crossed to TRiP control, Tk RNAi, GulpR RNAi, or brp RNAi flies. Progeny was collected and raised at 26°C for 4-7 days. Female intestines were dissected and processed for RNA isolation. RNA sequencing was performed on these samples and the data were analyzed according to 3 different comparisons: 1. Tk>TRiP and Tk>Tk RNAi flies, 2. Tk>TRiP and Tk>GulpR RNAi flies, and 3. Tk>TRiP and Tk>brp RNAi flies.

first: Daniela

last: Barraza

middle: I


title: Complex I deficiency disrupts postnatal neurogenesis in the subventricular zone in a mouse model of Leigh Syndrome

city: Blacksburg

first: Alicia

middle: Mae

last: Pickrell

state: Virginia

address: 970 Washington St SW

department: School of Neuroscience

institute: Virginia Polytechnic Institute and State University

summary: Leigh syndrome (LS) is a complex, genetic mitochondrial disorder defined by neurodegenerative phenotypes with pediatric manifestation. However, recent patient studies suggest behavioral phenotypes more akin to neurodevelopment delays preceding degenerative regression of skills. Reevaluating a mouse model of LS that recapitulates key disease features, we show neurodevelopmental defects occur in the highly neurogenic subventricular zone (SVZ) region postnatally prior to neurodegenerative events. We demonstrate a reduced number of neural stem cells with less regenerative potential and stall in maturation throughout neurodevelopment. We employ single cell RNA sequencing technology to identify shifts in the neural stem cell progenitor lineage in LS mice and identify gene clusters responsible for the dysregulation of neurogenesis. We also demonstrate that cell cycle perturbations are partially responsible for deficits found in the SVZ. Given that LS is purely considered a neurodegenerative disease, we propose that mitochondrial diseases may have neurodevelopmental origins

overall_design: For single-cell RNA sequencing, we isolated cells from the subventricular zone (SVZ) of wild-type and NDUFS4 knockout (KO) mice at postnatal day 14 (P14). A total of four samples were sequenced, including two wild-type and two NDUFS4 KO biological replicates

first: Sahitya Ranjan

last: Biswas

first: Porter

middle: L

last: Tomsick

first: Colin

last: Kelly

first: Brooke

last: Lester

first: Julia

last: Milner

first: Samantha

last: Brindley

first: Nicole

last: DeFoor

middle: N

last: Henry

first: Yairis

last: Soto

first: Paul

middle: D

last: Morton


title: Scaffolding-dependent CASP1 constrains excessive cell-intrinsic inflammatory signaling in leukemia [THP1]

first: Kwangmin

last: Choi

overall_design: Bulk RNAseq profiling of THP1-Cas9 cells  transduced with Lentiviral delivery vectors specific for safe harbor control gene sgAAVS1 (WT), or sgCASP1 (KO), grown in liquid culture, and selected for by cell sorting, and validated by western blot.

first: Emma

last: Uible

first: Kathleen

last: Hueneman

first: Erik

last: Vick

first: William

last: Seibel

first: Kenneth

last: Greis

first: Lynn

last: Lee

first: Timothy

last: Chlon

first: Jorge

last: Henao-Mejia

first: Chandrashekhar

last: Pasare

first: Andrew

last: Volk

first: Daniel

last: Starczynowski


title: Stromal Fibroblast Mutant Trp53 Promotes Mammary Tumor Development via Enhanced Secretion of Paracrine Factors

first: Bin

last: Liu

state: TX

address: 1515 Holcombe BLVD

department: epigenetics and molecular carcinogenesis

institute: University of Texas MD Anderson Cancer Center

summary: Mutations in the tumor suppressor gene TP53 have been identified in breast cancer-associated fibroblasts and are associated with poor patient prognosis. However, the functional impact of fibroblastic mutant p53 on breast cancer development remains unclear. To investigate this, we compared female mice harboring HER2-driven mammary tumors with a fibroblast-specific Trp53 mutation (NP) to those with wild-type fibroblastic Trp53 (N). NP mice exhibited significantly shorter median tumor-free survival than N mice. RNA sequencing of NP and N tumors and mammary glands revealed numerous differentially expressed genes (DEGs) between tumors and the corresponding glands in both genotypes. Notably, the NP tumors showed enrichment of several signaling pathways, including PI3K/AKT/mTOR. Additionally, twenty DEGs encoding secreted proteins were identified between NP and N mammary glands. Among these, Saa1 and Saa2 were also upregulated in human breast tumors with mutant TP53 compared to those with wild type TP53. Previous studies have implicated SAA1, SAA2, and THBS4 in promoting tumor progression via the PI3K/AKT pathway. Consistently, supplementing primary HER2 tumor cultures with recombinant SAA1, SAA2, or THBS4 peptides enhanced tumor cell proliferation and migration. Together, these findings uncover a mechanism by which fibroblastic mutant p53 promotes mammary tumorigenesis—through upregulating secretory proteins such as SAA1, SAA2, and THBS4 in the stroma, thereby enhancing PI3K/AKT signaling and tumor progression.

overall_design: RNA-seq profiling of breast tumors and mammary glands with mutant p53 or wild type p53 in fibroblasts from MMTV-Erbb2 mice (The Jax Lab, Strain #:002376), The mammary glands from wild type mice are usd for normal control

first: Yun

last: Zhang


title: MIF-mediated crosstalk between Thrsp+ hepatocytes and Cd74+ lipid-associated macrophages in hepatic periportal zone drives MASH

city: Shanghai

first: Xu

last: Xu

address: 宜山路600号 科研综合楼13楼

country: China

institute: 上海市第六人民医院

summary: Background & Aims: Spatial location of steatosis is closely related to the progression of metabolic dysfunction-associated steatohepatitis (MASH), and reports suggest lipid-associated macrophages (LAMs) facilitate this progression. However, the underling mechanisms remain elusive. Approach & Results: Spatial transcriptomics (ST) data revealed a significant increase in myeloid cells and MASH-related genes in the hepatic periportal (PP) zone of MASH mice, suggesting a vital role of PP zone in the MASH progression. Thrsp (Spot14), involved in fatty acid synthesis, was markedly elevated in the livers of MASH patients and mice. Notably, CellPhoneDB analysis identified strong interactions between Cd74 and macrophage migration inhibitory factor (MIF) within Thrsp-high zone. Furthermore, Thrsp, Cd74, Mif, Col3a1 and LAMs markers were prominently co-localized in hepatic PP zone of MASH mice, suggesting Thrsp-mediated crosstalk in this region played crucial role in MASH progression. Hepatic Thrsp overexpression/knockout experiments confirmed that Thrsp drove MASH progression by recruiting Cd74+ LAMs mediated by MIF. Mechanistically, Thrsp promoted hepatic palmitic acid (PA) synthesis, mainly by promoting hepatic de novo lipogenesis, and disturbing the binding of FASN-TRIM21, thereby inhibiting FASN’s ubiquitination. Cd74+ LAMs were activated and recruited by chemokine-like MIF secreted from hepatocytes and macrophages stimulated with PA. Additionally, the compound C6 identified as a Thrsp inhibitor, significantly ameliorated MASH in mice. Conclusions: Our study demonstrates that Thrsp drives MASH progression by recruiting Cd74+ LAMs mediated by MIF in hepatic PP zone, providing novel insights into the spatial zonation and crosstalk between lipogenic hepatocytes and LAMs that may result in novel therapies for MASH.

overall_design: Fresh livers from MAFL and MASH mouse livers were embedded in tissue-Tek (OCT) and snap-frozen using dry ice. Tissues were processed for 10 x Visium ST.

first: Huagen

last: Li

first: Hai

last: Lin

first: Qichao


title: Tuneable hydrogel-based micropillar arrays for myelination studies.

city: London

first: Emad

last: Moeendarbary

state: -- Please select --

address: Torrington Place, Roberts Engineering Building,

country: United Kingdom

institute: University College London

summary: Oligodendrocytes (OLs) play a critical role in central nervous system (CNS) function by myelinating axons and enabling rapid signal conduction. To model the key biomechanical parameters that regulate myelination, we developed a tuneable hydrogel-based micropillar array system that mimics the three-dimensional (3D) architecture and mechanical softness of axons. This platform supports a long-term culture of OLs and permits the formation of multilayered compact myelin by both rodent and human iPSC-derived OLs. Using fluorescence confocal imaging and transmission electron microscopy (TEM), we observed a strong linear correlation between immunostained myelin thickness and the number of myelin wraps, enabling fast, high-content quantification of myelination. By systematically varying pillar stiffness, diameter, and surface coatings, we show that both the mechanical and geometric properties of axon-like substrates critically regulate OL differentiation and myelin wrapping. Importantly, we demonstrate that pharmacological agents exhibit stiffness-dependent effects on myelination, suggesting that overly rigid in vitro models may yield false-positive drug hits. This cost-effective and scalable platform offers a physiologically relevant, high-throughput assay to dissect OL biology and accelerate the discovery of remyelinating therapies for demyelinating diseases such as multiple sclerosis.

overall_design: RNA-seq profiling of oligodendrocytes isolated from P7 Sprague Dawley rats, cultured and differentiated on flat or micropillar hydrogels.

first: Claire

last: Vinel

first: Soufian

last: Lasli


title: Distinct Roles of IL-4, IL-13, and IL-22 in Human Skin Barrier Dysfunction and Atopic Dermatitis

city: Davos Wolfgang

first: Yasutaka

last: Mitamura

state: Graubünden

address: Herman-Bruchard-Strasse 9

department: Immunology

institute: Swiss Institute of Allergy and Asthma Research

summary: Atopic dermatitis (AD) is a chronic type-2 inflammatory skin disease characterized by epithelial barrier dysfunction. IL-4, IL-13, and IL-22 represent major cytokines contributing to AD-pathogenesis. Models using reconstructed keratinocytes have been used in previous studies, however, did not represent the real skin situation. Here, we report the distinct effects of IL-4, IL-13, and IL-22 on bio-stabilized human skins with intact barriers and resident immune cells. Spatial transcriptomics on AD-lesions and non-lesional skin of patients, and RNA-sequencing, and proteomics were performed in IL-4-, IL-13- and IL-22-treated native skins. Skin barrier integrity was evaluated using electrical impedance spectroscopy. Spatial transcriptomics demonstrated that CLDN1, FLG, and FLG2 were significantly downregulated in the epidermis of AD lesions. IL-4, IL-13, and IL-22 disrupted the skin barrier in the ex vivo human skin by downregulation of the genes and proteins critical for barrier function and keratinization. IL-4 and IL-13 suppressed, whereas IL-22 upregulated the antimicrobial peptides. Interestingly, IL-4 and IL-13 showed a cross-regulation with IL-22, by downregulation of IL-22Rα1 with IL-4 and IL-13 and upregulation of IL-4Rα with IL-22. Three months of dupilumab treatment in AD patients restored the IL-4 and IL-13-dysregulated genes, whereas genes co-regulated or only regulated by IL-22 remained unaltered. In conclusion, this study comprehensively provides insights into the distinct immune profiles following IL-4, IL-13, and IL-22 stimulation in human skin, highlighting their complex interplay in the pathogenesis of AD modulating keratinocyte and immune responses.

overall_design: RNA-seq profiling of IL-4-, IL-13-, IL-4 + IL-13-, and IL-22-treated (100 ng/mL each) bio-stabilized human skin (NativeSkin®) after 24 hours of stimulation. Controls were treated with PBS with 0.1% BSA.

first: Paolo

last: D’Avino

first: Juno

last: Kim

first: Manru

first: Philipp

last: Gessner

first: Patrick

last: Westermann

first: Yagiz

last: Pat

first: Carina

last: Beha

first: Claudia

last: Traidl-Hoffmann

first: Jeremy

last: Bost

first: Nicolas

last: Gaudenzio

first: Christoph

middle: B

last: Messner

first: Cezmi

last: Akdis


title: Stable isotope tracing in human plasma-like medium reveals metabolic and immune modulation of the glioblastoma microenvironment

city: Dallas

first: Samuel

middle: Kent

last: McBrayer

state: Texas

address: 6000 Harry Hines Boulevard, NL11.110K

department: Children's Research Institute

institute: UT Southwestern Medical Center

summary: Background  In vivo stable isotope tracing is useful for natively surveying glioma metabolism but can be difficult to implement. Stable isotope tracing is tractable using in vitro glioma models, but most models lack nutrient conditions and cell populations relevant to human gliomas. This limits our ability to study glioma metabolism in the presence of an intact tumor microenvironment (TME) and immune-metabolic crosstalk.  Methods  We optimized an in vitro stable isotope tracing approach for human glioma explants and glioma stem-like cell (GSC) lines that integrates human plasma-like medium (HPLM). We performed 15N2-glutamine tracing in GSC monocultures and human IDH-wildtype glioblastoma explants and developed an analytical framework to evaluate microenvironment-dependent metabolic features that distinguish them. We also conducted spatial transcriptomics to assess transcriptional correlates to metabolic activities.  Results  Human plasma-like medium culture preserved glioma explant viability and stemness while unmasking metabolic and immune programs suppressed by conventional culture conditions. Stable isotope tracing in HPLM revealed TME-dependent and TME-independent features of tumor metabolism. Tissue explants recapitulated tumor cell-intrinsic metabolic activities, such as synthesis of immunomodulatory purines. Unlike GSC monocultures, tissue explants captured tumor cell-extrinsic activities associated with stromal cell metabolism, as exemplified by astrocytic guanosine diphosphate mannose production in heterocellular explants. Finally, glioma explants displayed tumor subtype-specific metabolic reprogramming, including robust pyrimidine degradation in mesenchymal cells.  Conclusions  We present a tractable approach to assess glioma metabolism in vitro under physiologic nutrient levels and in the presence of an intact TME. This platform opens new avenues to interrogate glioma metabolism and its interplay with the immune microenvironment.

overall_design:
We performed RNA sequencing on a panel of IDH mutant glioma stem-like cells, IDH WT glioma stem-like cells, and immortalized astrocytes.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Milan

middle: R

last: Savani

first: Mohamad

last: El Shami

first: Bailey

last: Smith

middle: K


title: Divergent immue responses to commensal Clostridia classified based on motility gene arrangement and flagellin diversity

city: Birmingham

first: Craig

last: Maynard

state: AL

address: 1825 University Blvd, SHEL 613

institute: University of Alabama at Birmingham

summary: Flagella-dependent motility is a defining feature of several species of Clostridia that colonize the intestine. The genomes of these bacteria encode varying numbers of flagellins – the basic subunits of flagella - and the machinery necessary for synthesis, assembly, and function of flagella. Although adaptive immune responses to commensal flagellins are hallmarks of Crohn’s disease, it is unclear whether flagellins themselves drive inflammation, or what defines pro-inflammatory flagellated commensals. Here, we show that the arrangement of motility loci and the diversity of encoded flagellins can separate flagellated Clostridia into at least 2 functionally distinct subgroups. Both subgroups induce tolerogenic responses at homeostasis but possess divergent capacities for TLR5 activation and induction of inflammation. We identify a hypervariable region of the flagellin D0 domain that modulates the capacity for TLR5 activation and demonstrate enrichment of bacteria in the pro-inflammatory subgroup in Crohn’s disease biopsies. Collectively, our study identified a subset of colitogenic commensals and revealed one mechanism whereby these organisms can directly initiate intestinal inflammation.

overall_design: Three groups of untreated mice: 1) gnotobiotic with three select G1 bacteria, 2) gnotobiotic with three select G2 bacteria, and 3) germ-free; three replicates of each group for a total of nine samples.

first: Lennard

middle: W

last: Duck

first: Melissa

last: Jennings

first: Jung-Shan

last: Hsu

first: Covenant

middle: F

last: Adeboboye

first: Elizabeth

last: Morgan

first: Kiarra

last: Coger

first: Barbara

last: Klocke

first: Dave

last: Hill

first: Katie

last: Alexander

first: Alexander

last: Rosenberg

first: Goo

last: Lee

first: Qing

last: Zhao

first: Charles

middle: O

last: Elson


title: Single-cell transciptional profiling of thymic hAPCs in perinatal mice

city: Nashville

first: Bryan

middle: Robert

last: Helm

state: Tennessee

address: 2525 West End Avenue, Suite 1100

department: Center for Quantitative Science

institute: Vanderbilt University Medical Center

summary: This study carried out single-cell transcriptional profiling of FACS purified thymic hematopoietic antigen presenting  cells (hAPCs) to determine changes in cellular composition and gene signatures in neonatal to perinatal (P00, P03, P07, P10, and P14)  mice.

overall_design: CD45+ MHC-II lo to + hematopoietic APCs (HAPCs) were FACS-isolated from C57BL6/J (WT) mice at postnatal ages P00, P03, P07, P10, and P14 mice to identify transcriptional heterogeneity of hAPCs throughout perinatal stages of thymus growth.

first: Lauren

last: Ehrlich

first: Jayashree

last: Srinivasan

first: Aparna

last: Calindi

first: Colin

last: Moore

first: Qi

last: Liu

first: Ken

last: Lau


title: Single cell sequncing of Intestinal immune cells from Lamina Propria

city: Mainz

first: Wolfram

last: Ruf

address: Langenbeckstrasse 1

country: Germany

institute: CTH Mainz

summary: A point mutation in GPCR-protease activated receptor-2 (F2RL1) renders PAR2 insensitive to FXa/Matriptase-dependent activation. We characterized the of impact of  the PAR-2 G37I mutation on immune cell populations and gene expression in the gut.

overall_design: Wild type C57BL/6N mice versus PAR2-G37I mutant male mice; Aged 10 to 12 weeks fed with standard chow diet.

first: Jens

last: Posma

first: Dilraj

last: Kaur

first: Thati

last: Madhusudhan


title: High-resolution HIV-1 m6A epitranscriptome reveals splicing-dependent methylation clusters and unique 2-LTR transcript modifications

city: Gif sur Yvette

first: Delphine

last: Naquin

address: avenue de la terrasse

country: France

institute: CNRS

summary: The N6-methyladenosine (m6A) modification of HIV-1 RNAs plays essential roles in regulating viral infection. This modification has been extensively studied but due to a lack of precision of the detection methods, the number and precise positions of m6A sites remain unclear. Here, using the latest Nanopore chemistry and direct m6A base-calling option, we identify 18 m6As among which 14 are located in the 3’ genome extremity and four in central regions. In addition, our data show that these positions are differently methylated among splicing isoforms. Among these sites, eleven are clustered in two short segments (197 nt and 43 nt) presenting peak-shaped methylation profiles. Single molecule analysis reveals a very small number of transcripts which are unmethylated in both clusters (≤ 1.5% of spliced transcripts and ≤ 5.4% of unspliced viral RNA). We also identify a ~732 nt RNA species resulting from the transcription of non-integrated viral DNA circles closed by two long terminal repeats (2-LTR circles). These transcripts start in the first LTR and terminate at the polyA site of the second LTR and harbour six m6A sites. Five of them are shared with the other transcripts and remarkably, they present the highest methylation rates. The sixth site is uniquely methylated in this transcript suggesting that this RNA plays a function in HIV-1 infection. Together, these results reveal a new landscape of HIV m6A transcriptome modifications and open the route to decipher their role in the viral life cycle.

overall_design: CD4+ T and supT1 cells infected by the virus HIV NL4-3 XCS. Cells are harvested 20h, 30h post-infection for SupT1 cells and 48h and 72h for CD4+ T cells. Two independant infections have been done, which were sequenced in duplicate for supT1.

first: Sandra

last: Blanchet

first: Erwin

last: vanDijk

first: Lisa

last: Bertrand

first: Sylvie

last: Grégoire

first: Cécilia

last: Bertha Ramirez

first: Rania

last: Ouazahrou

first: Yan

last: Jaszczyszyn

first: Arnaud

last: Moris

first: Claude

last: Thermes

first: Céline

last: Hernandez

first: Olivier

last: Namy


title: Transcriptome analysis of adult patients with severe Obstructive Sleep Apnea before and after CPAP treatment.

first: Bala S. C.

last: Koritala

address: 3333 Burnet Avenue

department: Division of Pediatric Otolaryngology

summary: Obstructive Sleep Apnea, a sleep related breathing disorder RNA sequencing analysis was conducted to evaluate differentially expressed genes in patients with severe OSA compared to healthy subjects. We further evaluated how these differentially expressed genes and associated pathways altered with short-term (4 months) vs. long-term (24 months) continuous positive airway pressure treatment.

overall_design: RNA profiling of peripheral blood mononuclear cells collected from blood at two different time points, morning and evening, from healthy subjects, patients with OSA, and the same patients following short-term and long-term CPAP treatment.

first: Laetitia

middle: S

last: Gaspar

first: David

last: Smith

first: Ana

last: Álvaro

first: Bala S

middle: C


title: Ralstonia pseudosolanacearum LOV domain protein regulates environmental stress tolerance, iron homeostasis and bacterial wilt virulence

city: Madison

first: Jose

middle: Alberto

last: Sanchez

state: WI

address: 1630 Linden Drive

institute: University of Wisconsin-Madison

summary: Bacteria use diverse sensors to integrate environmental stimuli into physiological responses that ensure fitness and survival. Ralstonia pseudosolanacearum (Rps), a soil-borne plant pathogen that causes bacterial wilt disease, encodes a conserved LOV (light-oxygen-voltage) protein known to mediate photoreception across the tree of life. However, Rps had a minimal LOV-dependent transcriptional response to light. Using clues from functional domains, the lov genomic neighborhood, and in planta transcriptional analyses, we tested the hypothesis that LOV shapes Rps biology in response to stress. We discovered lov modulates Rps stress response and virulence independently of light cues, but in a plant-dependent fashion. A ∆lov mutant had reduced heat tolerance that required a conserved flavin mononucleotide-binding cysteine residue. Deleting lov caused broad metabolic dysregulation, leading to growth defects on several carbon sources. In contrast ∆lov grew better in ex vivo tomato xylem sap and in high-iron medium, a possible consequence of its increased siderophore production. However, LOV is essential for full virulence in the host, mediating attachment to the root surface, stem colonization, and overall symptom development. Together these findings reveal that LOV, which is highly conserved among plant pathogenic Ralstonia, regulates a myriad of functions required for plant fitness independently of light.

overall_design: RNAseq data of Ralstonia pseudosolanacearum strain GMI1000 wild-type compared to ∆lov both in vitro and in planta conditions. In vitro cells were subjected to blue light and dark conditions.

first: Bridget S.

last: O'Banion

first: Mariama D.

last: Carter

first: Jose A.

last: Sanchez-Gallego

first: Hanlei

last: Li

first: Stephanie

last: Hayes

first: Marlee

last: Strysick

first: Ja'Nyla

last: Holcomb

first: Caitilyn

last: Allen


title: Heat Shock Factor 1 Governs Sleep-Wake Cycles Across Species [CUT&RUN]

city: Philadelphia

first: Shintaro

last: Yamazaki

state: PA

address: 10-179/180 Smilow Center, 3400 Civic Center Boulevard, Building 421

department: Department of Systems Pharmacology & Therapeutics

institute: University of Pennsylvania

summary: Sleep represents a fundamental biological necessity, yet the molecular mechanisms controlling this essential process remain largely unknown. Sleep disruption marks numerous pathological states, suggesting undiscovered molecular regulators govern this vital function. While studies have mapped gene expression during sleep, the master regulators that translate sleep pressure into sleep behavior have remained elusive. We demonstrate that Heat Shock Factor 1 (HSF1), previously characterized solely as a stress response transcription factor, serves as a critical molecular switch enabling sleep. HSF1's nuclear levels oscillate with sleep-wake cycles in mouse cortex and increase markedly during sleep deprivation. Systemic and brain-specific Hsf1 knockout mice display sleep disruption due to synaptic dysregulation, even as they accumulate normal sleep pressure. Nuclear HSF1 orchestrates a novel transcriptional program controlling synaptic organization, distinct from its canonical heat shock response. Single-nucleus RNA sequencing reveals that HSF1 deficiency triggers widespread dysregulation of synaptic genes across neuronal and glial populations. This mechanism shows evolutionary conservation, as Drosophila lacking the HSF1 ortholog display similar sleep phenotypes despite elevated sleep pressure. Our findings uncover an unexpected role for this classical stress factor and establish HSF1 as a molecular bridge linking sleep pressure to sleep behavior. These results suggest new therapeutic approaches for sleep disorders.

overall_design: To investigate the alterations of HSF1 binding loci durng sleep deprivation, we performed CUT&RUN (Cleavage Under Targets & Releasing Using Nuclease) using H3k4me3 (positive control), HSF1 and IgG (negative control) antibodies in cerebral cortex tissues of C57B/6 mice.

first: Akhilesh

last: Reddy


title: Heat Shock Factor 1 Governs Sleep-Wake Cycles Across Species [snRNA-Seq]

overall_design: To investigate the functions of HSF1 in sleep regulation, we established conditional Hsf1 knockout mouse model and analyzed the transcriptional alterations in control and the knockout mouse brain under normal sleep and sleep deprived conditions using single nucleus RNA sequencing (snRNA-seq).


title: Irisin improves obesity and glucose intolerance through an IL-33-ST2 pathway

city: BROOKLINE

first: Mu

last: A

address: 77 Pond Ave, Apt 1003

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary: Irisin is secreted by muscle, increased with exercise, and conveys certain physiological benefits. Earlier studies showed that short-term irisin treatment caused browning of subcutaneous adipose tissue (SAT) in mice, with improved glucose tolerance; the effects of more chronic irisin treatment and mechanisms at play have not been explored. We demonstrate here that chronic irisin application improves obesity and dramatically reduces glucose intolerance. This treatment increases an IL-33+ mesenchymal stromal cell (mSC) population in visceral fat tissue while genetic ablation of irisin reduces plasma IL-33 levels and decreases thermogenic gene expression in SAT. Importantly, irisin directly induces IL-33 expression in mSCs and preserves ST2+ regulatory T (Treg) cells. Inhibition of IL-33 blunts these irisin-mediated effects on energy expenditure and glucose homeostasis, largely through IL33-mediated regulation of ST2+ Treg cells. These data indicate that irisin improves obesity and glucose intolerance, with no muscle loss, through a key immunomodulatory pathway in obese mice.

overall_design: RNAseq profiling of iWAT and eWAT tissues from C57BL6 mice administered AAV-irisin or control AAV (AAV-GFP) and fed a high-fat diet or normal chow for 18 weeks.


title: Targeted PDGFRα+ fibroblast ablation exacerbates pathologic features of asthma in house dust mite-induced allergenic asthma model

city: Honolulu

first: Juwon

last: Park

state: HI

address: 651 Ilalo St.

department: Tropical Medicine, Medical Microbiology and Pharmacology

institute: University of Hawaii at Manoa

summary: This study demonstrates the consequence of PDGFRα+ fibroblast ablation in adult lung homeostasis in both steady-state and asthmatic conditions. Our study highlight that the essential roles of PDGFRα+ fibroblast in maintaining immune balance, ECM integrity, and how their loss disrupts these processes, contributing to worsening of asthma.

overall_design: The microarray analysis was performed using lung tissue samples from 12 mice aged over 8 weeks, including both males and females, divided into four groups: three PDGFRα+ fibroblast-ablated mice and three control mice exposed to house dust mite (HDM), and three PDGFRα+ fibroblast-ablated mice and three control mice exposed to PBS. The Affymetrix Clariom S Assay mouse microarray platform (Thermo Fisher Scientific, 902930) was used to evaluate gene expression profiles.

first: Michelle

last: Tallquist

first: Ha

middle: E

last: Shin

first: Sanyeowool

last: An

first: Jack

last: Heckl


title: Heat Shock Factor 1 Governs Sleep-Wake Cycles Across Species [RNA-Seq]

overall_design: To investigate the transcriptional alterations during sleep deprivation, we performed gene expression profiling analysis using data obrained from RNA-seq of cerebral cortex tissues with or without sleep deprivation.


title: Exosomal Prognostic Score (EXPS)-based Prognostic Model in Pancreatic Tumours: Construction and Validation

city: Wuhan

first: Minghe

last: Zhang

state: Hubei

address: Donghu Road

institute: WuHan University

summary: Pancreatic adenocarcinoma (PAAD) is a highly lethal malignancy with limited therapeutic options and poor prognosis. Extracellular vesicles (EVs), essential mediators of intercellular communication, are emerging as non-invasive biomarkers for diagnosis and prognosis. Investigating exosomal gene expression offers a more accurate prognostic tool for PAAD patients.We analyzed four datasets from public databases: PAAD_ExoRbase, TcgaTargetGtex-PAAD, GSE62452_GPL6244, and GSE78229_GPL6244. Differentially expressed exosomal genes were identified, followed by univariate Cox regression to pinpoint prognosis-associated exogenes. Single-cell analysis and single-sample gene set enrichment analysis (ssGSEA) refined the gene selection, assessing their origins and predictive value for immune status. In vitro experiments and RNA-seq validated the regulatory role of the key gene KRT7.LASSO Cox regression identified five prognostic genes: KRT7, KRT19, CXCL5, TNFRSF13C, and GP1BA. The prognostic model accurately predicted overall survival in the TCGA-PAAD, GSE62452, and GSE78229 cohorts. Single-cell analysis revealed the gene signature originated from T-proliferative, malignant, and ductal cells. Immune cell infiltration and immune checkpoint analyses confirmed the model’s predictive strength. In vitro assays and RNA-seq demonstrated that KRT7 promotes PAAD cell proliferation, migration, and invasion.

overall_design: CFPAC1 cells were transfetced with si-Control or si-KRT7, and were  subsequently harvested for RNA sequencing and transcriptome analysis.

first: Tianyin

last: Ma

first: Yufeng

last: Yuan


title: Multiomics analysis of concurrent MASH and atherosclerosis in male and female mice

city: Shreveport

first: Sandeep

last: Das

state: LA

address: 1501 Kings Highway

institute: LSU Health Shreveport

summary: Metabolic dysfunction-associated steatohepatitis (MASH) has reached epidemic proportions with limited therapies available. Surprisingly, the leading cause of death in these patients is atherosclerotic cardiovascular disease. No pharmacological therapy exists to treat MASH and atherosclerosis simultaneously, which is attributed to the lack of translational mouse models, particularly in females. Herein, we have utilized both male and female atheroprone mice, combined with different high-fat diets containing physiologically relevant cholesterol levels, to model concurrent MASH-atherosclerosis. Upon phenotypic characterization using standard histopathology, immunohistochemistry, and biochemical assays on liver, cardiovascular, and plasma samples, we report the first female MASH-atherosclerosis model. Furthermore, we conducted a multi-omics exploration of metabolomic, lipidomic, and transcriptomic profiles altered within these groups, and found metabolic and genomic signatures comparable to the human disease. These models will facilitate future cardiometabolic research to unravel the molecular and metabolic underpinnings at the intersection of MASH and atherosclerosis, which must be pharmacologically targeted.

overall_design: Eight-week-old Ldlr-/- male and female mice were housed under controlled temperature (22±2°C) and humidity conditions (40-60%) on a 12-hour light/dark cycle and fed ad libitum a standard chow diet (LabDiet #5053, 13% of calories from fat). For our dietary model we used established29,42 high-fat and high-cholesterol western diet (WD, Envigo TD.88137, 42 kcal% fat with 0.2% cholesterol), choline deficient with high fat and high cholesterol diet (Research Diets #D22052704, 45 kcal% fat without added choline and 0.2% cholesterol) and modified MASH diet (Research Diets #D22052703, 40 kcal% fat with palmitic acid and trans-fat levels and 0.2% cholesterol) for 24 weeks prior to euthanasia and tissue harvest.

first: Oren

last: Rom

first: Sumit

last: Anand


title: Castration Increases Aggressiveness of Prostatic Luminal Progenitor Cells in Prostate Cancer Through FosL1/AP-1-Mediated Transcriptional Reprogramming

city: Essen

first: Florian

last: Rambow

department: IKIM

institute: University Hospital Essen

summary: In this study, we show that the castration-tolerance potential of prostatic LSCmed (Lin-/Sca-1+/CD49fmed) cells is not intrinsic but rather results from transcriptomic reprogramming that further enhances their aggressiveness. Using scRNAseq specifically applied to Ptenpc-/- LSCmed cells sorted from intact versus castrated mice, we identified three distinct LSCmed cell clusters and we show that castration favors the emergence of a more stem-like LSCmed subpopulation.

overall_design: The transcriptomes of 384 single cells of murine prostate cancer model  were sequenced (scRNAseq) after FACS sorting.


title: Spatiotemporally controlled function of SMARCA5 distinguishes pancreatic malignancy from tissue regeneration

city: BeiJing

first: li

last: yong

address: Hai Dian

department: biomedical

institute: tsinghua university

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

overall_design: Refer to individual Series


title: ILP1 mediates resource allocation for reproduction during the induction of diapause in culex mosquitoes.

city: Arua

first: John Roberts

last: Padde

address: Independence Road

country: Uganda

institute: Muni University

summary: In this study, we demonstrate that ILP1 plays a crucial role in balancing the mosquito's metabolic environment to modulate the reproductive cycle. Exposure of mosquitoes to diapause-inducing conditions led to a significant decrease in ILP1 levels, leading to reduced blood feeding, fat hypertrophy, arrested ovarian development. The inverse expression of ILP1 suggests that this gene regulates mosquito reproduction based on perceived environmental stimuli.  siRNA knockdown of ILP1 resulted in phenotypes similar to those observed in mosquitoes raised under diapause-inducing conditions. Transcriptome analysis revealed that numerous genes related to sucrose, fructose, mannose, linoleic acid glycerophospholipid and negative regulation of protein and amino acid metabolism together with genes involved in negative regulation of endopeptidase activity were significantly up-regulated across the gonotrophic cycle in ILP1-depleted mosquitoes. Metabolomic analysis indicated that many metabolites regulated by these genes in these metabolic pathways were also markedly accumulated when ILP1 is depleted. Consequently, we inferred that linoleic acid of carbohydrate metabolism and the β-oxidation pathway cooperatively generate enough acyl-CoA, which enters the TCA cycle to provide energy for survival at the expense of reproduction during diapause induction. Hence, our study suggests that ILP1 plays an integral role in Culex mosquitoes by directing resource allocation for reproduction.

overall_design:
To investigate the the role of ILP1 in diapause induction, we characterised the expression of ILP1 at different mosquito growth stages, feeding state and under diapause inducing conditions
We then knocked down ILP1 with siRNA primers by microinjection in order to investigate the role of ILP1 in ovarian arrest during diapause induction
We then performed gene expression profiling analysis using the data obtained from RNA-seq of ILP1 depleted mosquitoes (siILP1) and negative control mosquitoes (NC).
Comparative gene expression  profiling analysis was performed using RNA-seq data to identified differentially expressed genes in ILP1 depleted mosquitoes

first: John

first: Yinghui

last: Zhou

first: Yuxiao

last: Zhu

first: Yuxuan

last: Yang

first: Jean

last: Nabusige

first: Min

last: Hou

first: Lu

last: Chen

first: Zhipeng

last: Xu

first: Donghui

first: MinJun

last: Ji

first: Lin


title: Spatiotemporally controlled function of SMARCA5 distinguishes pancreatic malignancy from tissue regeneration [ATAC-Seq]

summary: De-differentiation or trans-differentiation is a common response to injury in many tissues, and the processes predispose cells to cancer. Acute pancreatitis-induced acinar-to-ductal metaplasia (ADM) is similar to pancreatic ductal adenocarcinoma (PDAC) at both the chromatin level and gene expression level. Mutant KRAS induces chromatin remodeling activities required for both regeneration and tumorigenesis at the peak of ADM, and it blocks regeneration. We show that chromatin remodeler SMARCA5 (SNF2H) can promotes the regeneration defects caused by mutant KRAS by maintaining chromatin accessibility at regions specifically required for malignancy. Mechanistically, regeneration-related chromatin remodeling activities are shared between wild-type and mutant KRAS and they occur very early upon pancreatitis, while the malignancy-related chromatin regions become accessible much later. The activity of SMARCA5 is controlled spatiotemporally by transcription factor RUNX1, which is only accumulated at sufficient levels at late ADM lock-in stage. Finally, we show that the malignancy regulation activity of SMARCA5 is different from its general function in CTCF recruitment. In summary, we have identified a specific function of a general chromatin remodeler that is precisely controlled during acinar cell trans-differentiation to separate malignancy from tissue regeneration.

overall_design: Through ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) experiments, we aim to investigate the open chromatin in acinar cells.

first: Yong

last: Li

first: Jing

last: Han

first: Charles

middle: J

last: David

first: Mo


title: Spatiotemporally controlled function of SMARCA5 distinguishes pancreatic malignancy from tissue regeneration [RNA-Seq]

first: li

overall_design: Through RNA-seq, we aim to investigate the gene expression pattern of acinar cells.


title: Renal singel-nuclear transcriptomics identifies novel therapeutic tragets in a preclinical model of chronic kidney disease.

city: Columbia

first: Sathesh

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

summary: Background: The prevalence of chronic kidney disease (CKD) is on the rise, and precision strategies to offset the progression to end-stage kidney disease are needed. We took advantage of a novel pre-clinical translational model of CKD in swine and single nucleus RNA sequencing (snRNA-seq) to identify potential therapeutic targets via characterization of the renal cell-specific transcriptomic landscape. Methods: Normal and CKD pigs were studied in vivo and ex vivo after 14 weeks (n=6/group). In randomly selected pigs (n=3/group), kidneys were harvested, nuclei isolated, libraries prepared, and snRNA-seq performed. Protein expression of candidate differentially expressed genes (DEGs, log2FC>0.25, adjusted p-value<0.05) was determined by immunohistochemistry, and genes were mechanistically modulated (siRNA) in primary normal and CKD renal vascular endothelial cells (RECs). Results: A total of 52,213 nuclei were analyzed. Thirty clusters were identified and filtered by canonical gene markers, revealing 16 unique renal cell types. Endothelial cells were the top category exhibiting the highest number of DEGs; which were subsequently filtered in angiogenic-, inflammatory-, and fibrotic-DEGs (major activated pathways in CKD). Venn diagram analysis identified 5 unique overlapping DEGs among this cluster: VWF, LAMA3, and KDR upregulated, and PTGIS and ICAM1 downregulated. The diagram indicates that VWF, LAMA3, and ICAM1 participate in inflammatory and fibrotic signaling. Renal protein expression of these DEGs matched snRNA-seq findings. Furthermore, in vitro silencing of VWF and LAMA3 ameliorated endothelial cell inflammatory and fibrotic signaling. Conclusions: Our work characterized the single-nuclear renal cell transcriptomic landscape of a translational model of CKD and singled out genes implicated in major renal injury pathways. These genes could serve as potential targets to pave the way for new therapeutic strategies in patients with CKD.

overall_design: Chronic kidney disease (CKD) was induced in juvenile domestic pigs (14 weeks old; n = 6, three males and three females) through bilateral renal artery stenosis combined with a high-cholesterol/high-carbohydrate atherogenic diet, initiated at the time of stenosis induction and maintained for 14 weeks. A control group of age-matched pigs (n = 6, three males and three females) did not undergo CKD induction, were fed a standard chow diet, and served as normal time controls. After 14 weeks, all pigs were anesthetized under sterile conditions for in vivo studies. After completion of the in vivo studies, pigs were euthanized and kidney samples harvested. Isolated tissues from three female pigs from both the CKD and control groups were enzymatically digested into single-nuclei suspensions. Single-nuclei 3’ RNA-Seq libraries were then prepared using the 10x Genomics Chromium Next GEM (V3) platform. Sequencing was performed on a NovaSeq 6000 S4-PE100 flow cell.

first: A

last: Chade

first: S

first: R

last: Sitz

first: E

middle: A

last: McCarthy

last: Eirin


title: TET1-mediated DNA hydroxymethylation controlling ferroptosis resistance in cancer

city: Hangzhou

first: Jun

last: Lu

state: Zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University


title: TET1-mediated DNA hydroxymethylation controlling ferroptosis resistance in cancer [RNA-seq]

summary: Ferroptosis, a non-apoptotic programmed cell death marked by iron-dependent lipid peroxidation, is closely associated with cancer. Despite of intensive investigation about the molecular pathways underlying ferroptosis, the mechanism that determines the disparity of cancer cell vulnerability to ferroptosis remains unclear. Here we show that the expression level of TET1, the founding member of the ten-eleven translocation (TET) family of enzymes that mediate DNA 5-hydroxymethylation, determines the susceptibility of cancer cells to ferroptosis. In ferroptosis resistant cells, the expression level of TET1 was remarkably higher than that of the sensitive cells. Cell response to ferroptosis could be affected by interfering TET1 expression. TET1 promoted DNA 5hmC modification at its target gene GCLM, activated both the canonical glutathione (GSH) synthesis, and the non-cannonical γ-glutamyl-peptide accumulation, and thus, protected cancer cells against ferroptosis. Our results uncover the role of TET1 as a ferroptotic defensor in cancer, and suggest the translational potential of targeting the TET/GCLM axis in cancer therapy.

overall_design: In order to identify the mechanism of TET1 mediated ferroptotic resistance, RNA profiles of ferroptosis-resistant (i.e., Kasumi-1),  –sensitive (i.e., MV4;11), and control and TET1 overexpressed THP1 cells were generated by deep sequencing.

first: Lingling

first: Xi

last: Jiang


title: TET1-mediated DNA hydroxymethylation controlling ferroptosis resistance in cancer [ChIP-seq]

overall_design: Chromatin immunoprecipitation sequencing (ChIP-seq) for TET1 in Kasumi-1 cells transfected with shNC or shTET1 lentivirus.


title: RBM15B Regulates progression of MLL-rearranged leukemia

city: Guangzhou

first: Wen-Tao

last: Wang

state: Guangdong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: sun yat sen university

summary: We identified RBM15B that promotes progression of MLL-r leukemia. In this study, we preformed the m6A RIP-seq, RNA-seq and RBM15B CUT& Tag sequensing to found that RBM15B selectively regulated m6A modified region in the 5′ UTR and in part of the CDS around the start codon (two wings around start codon (TWINS)) of mRNA transcribed from target genes of MLL-fusion proteins, which is guided by histone modification H3K79me2.

overall_design: 1. epz5676  and  DMSO treated MOLM-13 cells used in the   m6A RIP-seq and RBM15B CUT& Tag sequensing.2. Sh-NC and sh-RBM15 MOLM-13 cells used.

first: Yue-Qin

first: Tian-Qi

first: Shun-Xin

last: Zhu


title: RNAseq of 3 and 5 days differentiated C2C12 cells treated with conditioned medium of KPC, 4662, LLC or C26 cells

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

summary: It is well known that tumours can exert direct negative effects on muscle tissue, which can contribute to the development of cancer cachexia. However, the underlying mechanisms and mediators involved in the communication between tumour and skeletal muscle are poorly understood. Cachexia-inducing cancer cell lines are used in both in vivo and in vitro research, they cause cachexia when used in an animal model. In the present study, we investigated the effects of conditioned media (CM) from cachexia-inducing cancer cell lines on differentiating skeletal muscle cells. Muscle-derived C2C12 cells were cultured (3-5 days) under differentiation conditions with CM from KPC, 4662, C26 and LLC cell lines and global gene expression was analysed by RNA sequencing.

overall_design: In vitro experiment

first: Miranda

last: van der Ende

middle: M

first: Mieke

last: Poland

first: Fleur

last: Jansen

first: Jocelijn

last: Meijerink

first: Sander

last: Grefte

first: Jaap

last: Keijer

first: Renger

last: Witkamp

first: Klaske

last: van Norren


title: RNA seq DATA （miR-361-3p mimics transfected Huh7 cells    VS.    mimics-NC  transfected Huh7 cells ）

city: wuhan china

first: haisu

last: tao

address: jiefang street 1095

institute: Wuhan Tongji Hospital.

summary: Studies have shown that miR-361-3p is associated the progression of HCC cells and has potential to be used as a biomarker for cancer therapy. However, the mechanism of how miR-361-3p regulates the progression of HCC cells is not clear. To explore this mechanism, we transfected miR-361-3p mimics into Huh 7 cells , and verified the transfection efficiency with qRT-PCR. Then, we performed transcriptomic analysis using data obtained from RNA-seq of 3 pairs of these transfected cells.

overall_design: Comparative transcriptomic analysis of RNA-seq data for miR-361-3p mimics transfected Huh7 cells and its negative control (miR-361-3p mimics, and NC).

first: Haisu

last: Tao

first: Yuxin

last: Zhang


title: Effect of TPTN on gene expression in doxorubicin-induced dilated cardiomyopathy

city: Chongqing

first: Chen

last: yan

address: 30 Gaotanyan Main Street

institute: Third Military Medical University

summary: To investigate the intrinsic mechanism of TPTN in treating DOX-induced dilated cardiomyopathy, we established DOX-induced dilated cardiomyopathy model mice and TPTN treated mice, using healthy mice as the normal control. We then performed gene expression profiling analysis of the RNA-seq data obtained from the heart tissues of these three groups of mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in normal group, DOX model group and TPTN treated group.

first: Haiyan

last: Chen

first: Houyuan

last: Hu

first: Jianxiang


title: TET1-mediated DNA hydroxymethylation controlling ferroptosis resistance in cancer [5hmC-seq]

first: Jun

last: Lu

overall_design:
Examination of 5hmC modifications in Kasumi-1 and MV4;11 cells.
In order to reveal the regulatory mechanism of TET1 on ferroptosis surveillance, RNA profiles of control and TET1 overexpressed THP1 cells were generated by deep sequencing.

first: Lingling

last: Yang

first: Xi

last: Jiang


title: Decreased endothelial cell retinoic acid signaling accelerates progression of single ventricle pulmonary arteriovenous malformations

status: Public on Dec 04 2025

city: New Orleans

first: Styder

last: Meadows

address: 6400 Freret St, 2000 Stern

department: Cell and Molecular Biology

institute: Tulane University

summary: To investigate transcriptomic changes in the endothelial cells of a mouse model of JP/HHT (Smad4), endothelial cells were isolated from the lungs of P5 Smad4 control (Smad4 conditional floxed mice; Smad4 f/f) and Smad4 HHT mice (Smad4 f/f;Cdh5-CreERT2). Data sets were compared to reveal differentially expressed genes that may provide clues into the molecular changes driving HHT phenotypes.

overall_design: RNA sequencing of isolated lung endothelial cells from Smad4 endothelial cell-specific knock-out mouse mutants and respective floxed controls.

first: Zhou

last: Xingyan

first: Meadows

last: Stryder


title: Comparative RNA-seq analysis of fetal and maternal guinea pig liver transcriptomes reveals widespread transcriptional divergence.

city: Corvallis

first: Daniella

last: Hasan

state: OR

address: Withycombe Hall

department: Animal and Rangeland Sciences

institute: Oregon State University

summary: Background: Maternal Western diet (WD) consumption during pregnancy is linked to adverse gestational and offspring metabolic outcomes. Dimethyl fumarate (DMF), a Nrf2 activator with antioxidant and anti-inflammatory properties, is a proposed therapeutic candidate, but its safety and efficacy during pregnancy remain unexplored. This pilot study aimed to establish a guinea pig model of gestational WD consumption and evaluate the feasibility of DMF treatment on maternal, placental, and fetal outcomes. Methods: Pregnant guinea pigs consuming a modified WD were randomized to receive either DMF or vehicle beginning at gestational day 19. Maternal weight, urinalysis, blood glucose, and ketones were monitored weekly. Dams were sacrificed near-term and placental and fetal biometric measures were recorded. The placenta was evaluated for a panel of antioxidant and angiogenic candidate genes via RT-qPCR, and maternal and fetal livers were assessed for triglyceride content, histopathology, and transcriptomic changes via RNA-sequencing. Results: DMF did not alter maternal weight, blood glucose, urinalysis, nor fetal or placental gross outcomes. Hepatic triglyceride concentrations were unaffected in both dams and fetuses. WD consumption resulted in maternal hepatic glycogen accumulation and mild vacuolar hepatopathy without fibrosis, while fetal livers exhibited microvesicular hepatopathy and abundant extramedullary hematopoiesis without fibrosis, irrespective of treatment. Placental RT-qPCR revealed that exposure to DMF led to a decrease in transcription of Sod1 (p = 0.046) and a tendency to decrease transcription of Hmgcr (p = 0.071) and Nqo1 (p = 0.067) with no changes in other measured genes. RNA-sequencing identified 38 differentially expressed genes (DEG) in maternal livers suggesting some immune suppression and induction of P450 pathway. Fetal hepatic RNA-sequencing identified 51 DEG, distinctly different from maternal DEG, indicating an activation of interleukin 12 production. Distinct differences between fetal and maternal liver transcriptomic profiles were evident, with over 9,000 DEG (65% of annotated transcripts). Dimethyl fumarate conferred no measurable benefit on maternal or fetal hepatopathy and had a paradoxical effect in lowering placental Sod1 gene expression, but, importantly, no overt harm was appreciated. These findings establish the feasibility of a gestational guinea pig WD model and gestational DMF therapy and provide initial insights into maternal-fetal responses to DMF, most notably highlighting divergent hepatic programming between dams and offspring. Future research should assess whether DMF or related Nrf2 activators can be developed as pregnancy therapeutics, explore interactions between antioxidants and placental angiogenesis, and determine long-term offspring outcomes after exposure to WD and DMF during gestational development.

overall_design: This study compares hepatic transcriptomes from fetal and maternal guinea pig (Cavia porcellus) liver to characterize developmental differences and to evaluate the effect of a maternal treatment. A total of 12 biological samples were included: liver tissue from 6 dams fed a Western diet (3 treated with dimethyl fumarate, 3 control) and liver tissue from 6 corresponding fetuses (fetuses of the 3 treated dams are classified as exposed; fetuses of the 3 control dams are unexposed). Thus the design includes two main factors: tissue (maternal vs fetal) and treatment (treated vs control). For the maternal vs fetal comparison, each group has n = 6 biological replicates.

first: Massimo

last: Bionaz


title: PARP1 association with chromatin non-resistant and doxorubicin-resistant MDA-MB-231

city: Lodz

first: Magdalena

middle: Alicja

last: Strachowska

address: Pomorska 141/143

country: Poland

institute: University of Lodz

summary: Despite advances in cancer therapy, drug resistance remains a major obstacle in a range of cancer types, often driven by overexpression of ATP-binding cassette (ABC) transporters that restrict intracellular drug accumulation. Our previous studies identified the BRG1-p300 transcriptional complex at the promoters of specific ABC transporter genes. We used basal and induced doxorubicin-resistant triple-negative breast cancer (TNBC) cell lines to analyze changes in ABC transporter expression and drug accumulation following PARP1 inhibition. Moreover, the effect of commonly used antioxidants on the repressive effect of Veliparib against ABC genes was verified. ChIP-Seq was performed to identify transcription factor mediating PARP1-dependent ABC gene regulation. PARP1 inhibition or silencing of PARP1/HPF1 complex components downregulated ABCC and ABCG2 transporters, leading to increased intracellular accumulation of chemotherapeutic drugs in doxorubicin-resistant cells. Notably, suppression of genotoxic stress via antioxidant treatment reverses the inhibitory effect of Veliparib on ABC transporter expression. We identified SMARCA1 as a key regulator of PARP1-dependent expression of ABCC genes. SMARCA1 is a key effector of PARP1/p300-mediated regulation of ABC transporters and represents a potential therapeutic target in doxorubicin-resistant TNBC. These findings support the development of combinatorial strategies involving PARP1 inhibitors and chromatin remodeling modulators in refractory breast cancers.

overall_design:
To produce resistant lines doxorubicin at a concentration of 1 uM was added to proliferating wild-type MDA-MB-231 cells. The treatment was repeated every 4 weeks or so, each time after the cells returned to their normal proliferation status.For ChIP-Seq involving PARP1 the library for sequencing was constructed using the NEBNext® Ultra™ DNA Library Prep Kit with Sample Purification Beads for Illumina® according to the protocol provided by the manufacturer, and sequenced using the NextSeq 500/550 High Output Kit v2.5 (75 Cycles) at the Department of Clinical Genetics, University of Medical Sciences, Lodz, Poland.

National Science Centre Poland, grant number 2022/45/N/NZ5/01371, Prelude 21 awarded to Magdalena Strachowska.
National Research, Development and Innovation Fund of Hungary, grant number NKFIH-K-142137 and the Thematic Excellence Programme grant number TKP2021-EGA-18 awarded to Lorant Szekvolgyi.

first: Karolina

last: Gronkowska

first: Kinga

last: Kołacz-Milewska

first: Sebastian

last: Skoczylas

first: Éva

last: Nagy

first: Damian

last: Jacenik

first: Lóránt

last: Székvölgyi

first: Agnieszka

last: Robaszkiewicz


title: H3K4me3 and H3K27ac landscape in doxorubicin-resistant MDA-MB-231.

overall_design:
The impact of doxorubicin resistance induction in MDA-MB-231 on H3K4me3 and H3K27ac landscape. To produce resistant lines doxorubicin at a concentration of 1 uM was added to proliferating wild-type MDA-MB-231 cells. The treatment was repeated every 4 weeks or so, each time after the cells returned to their normal proliferation status. Library for sequencing was prepared using MGIEasy Cell-free DNA Library Prep Set and sequenced on MGI DNBSEQ-G400 using DNBSEQ-G400RS High-throughput Sequencing Kit from MGI.

National Science Centre Poland, grant number 2022/45/N/NZ5/01371, Prelude 21 awarded to Magdalena Strachowska.


title: A targetable developmental program co-regulates angiogenesis and immune evasion.

city: New York

first: Pietro

last: Berico

state: NY

address: 550 1st Ave Smilow 305

institute: NYU Langone Health

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Exploring the important role of PRDX proteins in FSGS: Insights from transcriptomic analysis and experimental validation

first: Cao

last: Jiawei

address: No. 1630 Huan Ding Road, Shangcheng District

institute: Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University

summary: To elucidate the mechanistic impact of PRDX family proteins on FSGS, we employed transcriptome sequencing of 6 mice kidney samples. 4358 differentially expressed genes were identified between the FSGS and control groups, with 2414 upregulated and 1944 downregulated.

overall_design: Male Wistar rats in the model group underwent left unilateral nephrectomy during the first week. On postoperative days 7 and 28, adriamycin was administered via tail vein injection at doses of 5 mg/kg and 3 mg/kg, respectively. Control group rats received injections of an equal volume of normal saline. Finally, RNA sequencing analysis was performed on the kidney samples from the rats.

first: Feng

last: Wan

first: Mengdan

last: Lu


title: A specific subset of Mesenchymal Stromal Cells identified in poor prognosis pediatric AML favor leukemic stem cells persistence in the bone marrow [scRNA-seq]

city: Lyon

first: Kevin

last: Geistlich

address: 28 rue Laennec

institute: CRCL

summary: Pediatric Acute Myeloid Leukemia (AML) emerge likely from highly complex, dynamic and multiparametric mechanism. The importance of stromal cells from the hematopoietic bone marrow (BM) microenvironment in early steps of pediatric AML (pAML) was explored in this study, based on samples of patients collected at diagnosis from a multicenter cohort (CONECT-AML). BM-Mesenchymal stem cells (BM-MSC) were isolated and characterized. Flow cytometry analysis revealed in more than a third of patients, the presence of a CD117(c-kit)-expressing sub-population of BM-MSC, rarely observed in healthy donors, associated with a higher LSC-17 score and a poor risk patient’s group. Lastly, single cell RNAseq data from pAML leukemic cells cocultured in a robust 3D-BM physio-pathological system built with CD117+ BM-MSC cells, indicate a high level of cell-cell interaction specific of this MSC. Very importantly, the presence of CD117+ BM-MSC significantly protect leukemic cells from chemotherapy killing trough cell-cell contacts. To summarize, we revealed the existence of a BM-MSC population associated with high risk pAML and that protect leukemic cells from treatments.

overall_design: Mesenchymal stroma cells isolated from bone marrow of either pediatric donors or leukemic patients were categorized according to their phenotypic status for the CD117 / c-Kit / Kit marker. One condition was sent to single cell RNA-seq : a mix of endothelial cells, CD117 positive stromal cells, and hematopoietic cells untreated

first: Sylvain

last: Lefort

first: Sophia

last: Bounaud

first: Véronique

last: Maguer-Satta


title: Spatiotemporal remodeling of chromatin topology architecture and H3K27me3 redistribution underlies vascular pathology in Hutchinson-Gilford progeria syndrome [Hi-C]

city: Ottawa

first: William

middle: L

last: Stanford

state: ON

address: 501 Smyth Rd

country: Canada

institute: Ottawa Hospital Research Institute

summary: Hutchinson-Gilford progeria syndrome (HGPS) is a devastating premature aging disorder driven by the accumulation of progerin, leading to severe vascular pathology. While epigenetic alterations are implicated, the spatiotemporal reorganization of the higher-order chromatin and its functional impact on vascular smooth muscle cell (VSMC) transcription remain poorly defined. Through an integrated multi-omics approach combining in situ high-throughput chromosome conformation capture (Hi-C) and Cleavage Under Targets and Tagmentation (CUT&Tag) profiling of CTCF, SMC1A, H3K27me3, H3K27ac, and H3K36me3 with transcriptomic analyses from control and HGPS iPSC-derived VSMCs, we reveal that global topologically associating domain (TAD) architecture remains largely intact in HGPS. However, the internal chromatin states of TADs undergo dynamic, passage-specific remodeling, characterized by a progressive accumulation of broad H3K27me3-repressed domains. This is accompanied by a loss of A/B compartment segregation, as confirmed by DNA-FISH, indicating a collapse of higher-order chromatin organization in late passage. Crucially, we uncover widespread rewiring of enhancer-promoter (E-P) loops, which is linked to the dysregulation of genes critical for vascular development, extracellular matrix organization, and atherosclerosis. Our study demonstrates that spatiotemporal redistribution of repressive histone marks and reorganization of E-P interactions within a structurally resilient TAD framework underpin widespread transcriptional dysregulation in HGPS vascular pathogenesis. This uncovers a critical dissociation    between higher-order chromatin architecture and epigenetic statehistone modification landscape, providing a mechanistic basis for the failure of vascular homeostasis in progeria.

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) profiling of CTCF, SMC1A, H3K27me3, H3K27ac, and H3K36me3 in vascular smooth muscle cell differentiated from patient-derived induced pluripotent stem cells

first: Mzwanele

last: Ngubo

first: Naveen

last: Ahuja

first: Rana

last: Karimpour

first: Amit

last: Shrestha

first: Michael

last: Hendzel

first: Theodore

last: Perkins


title: Stiffness-related mitochondria transfer promotes tumor progression through metabolic reprogramming

city: Wuhan

first: xinran

last: zhao

address: No. 169, Donghu Road, Wuchang District

department: Department of Stomatology

institute: Zhongnan Hospital of Wuhan University

summary: The physical properties of the tumor microenvironment (TME), particularly extracellular matrix stiffness, are key factors influencing cancer progression. While intercellular mitochondrial transfer is emerging as a vital mechanism for tumor metabolic adaptation, its potential interaction with TME mechanical properties remains unexplored.

overall_design: Here, we demonstrated that matrix stiffness is a crucial negative regulator of mitochondrial transfer from macrophages to tumor cells. Increased mitochondrial uptake by tumor cells compensates for functional limitations in soft niches, thereby promoting metabolic reprogramming to drive proliferation and invasion. Furthermore, downregulating TIAM1 via the DDR2-FAK-TIAM1 signaling axis activates RhoA, enhancing mitochondrial endocytosis and leading to improved energy metabolism. Altogether, this study unveiled a novel mechano-metabolic coupling where physical cues influence organelle-based interplay, revealing a distinct adaptive strategy for tumor cells in soft TME niches and offering new therapeutic targets.

first: Xinran

last: Zhao


title: Effects of Selenium-mediated RUNX2 Overexpression and its Transcriptome Alterations on Chondrocyte Injury in Kashin Beck disease

city: xi'an

first: Di

last: Zhang

state: shaanxi

address: No.76, Yanta West Road, Yanta District, Xi'an City, Shaanxi Province

institute: xi'an jiaotong university

summary: Runt-related transcription factor 2 (RUNX2) is a key regulator of chondrocyte differentiation and apoptosis. To investigate the downstream molecular mechanisms of RUNX2 in chondrocyte injury, we established a RUNX2 overexpression model using lentiviral transfection in human chondrocytes. Total RNA was extracted from RUNX2-overexpressing and control chondrocytes and subjected to RNA sequencing. Differential expression analysis identified 263 upregulated and 216 downregulated genes in RUNX2-overexpressing cells compared with controls. Functional enrichment analysis revealed that these genes were predominantly involved in TNF and MAPK signaling pathways, suggesting that RUNX2 activation promotes inflammatory and apoptotic processes in chondrocytes. These results provide a comprehensive transcriptomic resource for understanding RUNX2-mediated signaling in cartilage degeneration and may contribute to elucidating the molecular pathogenesis of osteoarthropathy such as Kashin-Beck disease.

overall_design: Human chondrocytes were transfected with a lentiviral vector encoding RUNX2 or an empty vector as control. Total RNA was isolated from each group (three biological replicates per condition) and subjected to high-throughput RNA sequencing for differential gene expression and pathway enrichment analysis.

first: Yongmin

last: Xiong

first: Shiquan

last: Sun


title: TBX21 facilitates the progression of prostate cancer by modulating the immunosuppression microenvironment via enhancing the proportion of Treg cells

city: Suzhou

first: Ouyang

last: Jun

address: No.899 Pinghai Road,Gusu District

institute: The First Affiliated Hospital of Soochow University

summary: Abstract Background: Prostate cancer (PCa) remains a major health burden, and identifying target molecules will provide new research ideas for treating PCa. TBX21 is a transcriptional factor with critical functions in tumor development, roles of which in PCa were studied herein. Methods: TBX21 expression was evaluated by RNA-seq, RT-PCR, Western blot, and immunohistochemistry in PCa tissues and cell lines. Functional assays were performed using LNCaP and 22RV1 cells with TBX21 knockdown to assess proliferation and apoptosis. Tumor growth and immune alterations were examined in xenograft and humanized immune cell models, while flow cytometry and Western blot were used to characterize immune cell subsets and effector molecules. Results: TBX21 expression was significantly elevated in PCa tissues and cell lines. TBX21 knockdown was associated with reduced proliferation and increased apoptosis in vitro and suppressed tumor growth in vivo. In humanized xenografts, TBX21 silencing was accompanied by a decrease in regulatory T cells (Treg) and an increase in Th17 and cytotoxic CD8⁺ T cells, together with enhanced expression of effector molecules (TNF-α, GZMB). Co-culture experiments showed that TBX21-deficient tumor cells reduced the induction of CD25⁺Foxp3⁺ Treg cells from activated CD4⁺ T cells. Conclusion: TBX21 is associated with tumor progression and an immunosuppressive microenvironment in PCa, underscoring its potential role in modulating the tumor–immune balance.

overall_design: Samples were sourced from the Department of urology, Lianyungang Affiliated Hospital of Nanjing University of Chinese Medicine, consisting of PCa tissues and corresponding paracancerous tissues from patients who underwent surgical treatment for PCa and were pathologically diagnosed with PCa. For RNA-seq analysis, three pairs of primary prostate cancer tissues and their matched paracancerous tissues were selected

first: Heng

last: Wang

first: Zhaofei

last: Liu

first: Xiangjun

last: Xu

first: Qichao

first: Pingan

last: Chang

first: Lei

last: He


title: Therapeutic Targeting of Epithelial Mesenchymal Cellular Plasticity in Pancreatic Cancer

city: Boston

first: Colin

last: Weekes

address: 55 Fruit Street

institute: Massachusetts General Hospital

summary: Pancreatic ductal adenocarcinoma (PDAC) cells exist on a spectrum of epithelial (E) and quasimesenchymal (QM) transcriptional states with differences in sensitivity to FOLFIRINOX (FFX). GSK-3b is a key regulator PDAC cell epithelial-to-mesenchymal transition (EMT). Here, we performed in vitro analysis of PDAC cell lines combined with multi-omic analysis of data from GSK-3b inhibitor trial (NCT05077800) to evaluate treatment effects on EMT. These data suggested that GSK-3b blockade synergizes with FFX by modulating PDAC plasticity while promoting the development of a tumor suppressive immune microenvironment.

overall_design: We performed single-nucleus RNA sequencing on matched pancreatic cancer patient biopsy specimens over the course of treatment with modified FOLFIRINOX, elraglusib, and losartan.

first: Eric

last: Lin

first: Priyadarshini

last: Pathak

first: Aileen

last: O'Shea

first: Beatrice

last: Awasthi

first: Ildiko

last: Phillips

first: Joshua

last: Kocher

first: Yuhui

last: Song

last: Raabe

first: Katherine

first: Bidish

last: Patel

first: Nicole

last: Lester

first: Jung Woo

last: Bae

first: Lisa

first: Linda

last: Nieman

first: Lawrence

last: Blaszkowsky

first: Elizabeth

last: Walsh

first: Aparna

last: Parikh

first: Andrea

last: Hansen

first: Joanna

last: Caufield

first: Gordon

last: Newbert

first: Akwi

last: Asombang

first: Brenna

last: Casey

first: Jonah

last: Cohen

first: Brian

last: Jacobson

first: Kumar

last: Krishnan

first: Raul

last: Uppot

first: Ralph

last: Weissleder

first: Nora

last: Horick

first: William

last: Hwang

first: Mukesh

last: Harisinghani

first: David

last: Ting


title: DNA methylation mediates transcriptional stability and transposon-driven trans-regulation under drought in wheat

city: York

first: Isaac

middle: Joel

last: Reynolds

state: North Yorkshire

address: Department of Biology, University of York

department: Department of Biology

institute: University of York (York)

type: Methylation profiling by high throughput sequencing

summary: Bread wheat (Triticum aestivum) is a major component of half the global population’s diet, but increasingly frequent  droughts threaten its productivity and food security. While massive transcriptional reprogramming under drought in wheat seedlings is well characterised, DNA methylation’s contribution remains poorly understood. Using paired whole-genome bisulphite sequencing (WGBS) and RNA-seq before and after drought stress in wheat landraces, we probed the nuanced role of DNA methylation in the drought response, uncovering antagonistic trends between cytosine contexts and novel mechanisms, with the ROS1a family potentially playing a key demethylation role under drought. Examination of gene methylation profiles revealed that gene body methylation was strongly positively correlated with gene expression but negatively with stress responsiveness, simultaneously identifying that gene body differentially methylated regions (DMRs) targeted stress-associated genes. Many DMR-associated genes maintained consistent transcription under stress, suggesting a stabilising role for DNA methylation.  Most DMRs localised to intergenic regions and transposable elements (TEs), with the ancient LTR retrotransposon RLX_famc9 emerging as a critical target of differential methylation under drought. We propose a model in which the RLX_famc9 family, enriched in differential methylation and exhibiting substantial sequence similarity to drought-responsive genes, is involved in the trans-regulation of stress-associated genes under control conditions through the generation of regulatory siRNA precursors, a mechanism suppressed by drought-inducible hypermethylation. Our findings suggest an intricate regulatory role of DNA methylation under drought, with genic DNA methylation promoting high, stable expression, ROS1a glycosylases coordinating targeted demethylation, and methylation-controlled TEs modulating the expression of downstream genes in trans.

overall_design:
Fourteen landraces where used to asses the wheat DNA methylation response to drought. The experiment was performed by growing the plant until GS13 (Zadok’s growth scale) and applying the drought stress during 10 days (withhold of water) and three days of recovery (normal watering) after that. DNA from 7 landraces (4 replicates per landrace) was pooled per sample per condition in equimolar concentrations. BD contains pooled DNA from tissue collected before drought treatment; AD is from samples after drought.
DNA samples were sequenced using whole-genome bisulphite sequencing, aligned using Bismark, and analysed using DSS-Single.

last: Harper

first: Liam

last: Barratt


title: Ablation of CD22 Induces a Pro-Inflammatory Transcriptome Shift and Endocytic Deficits in M2-like Macrophages

city: Cleveland

last: Cobb

state: OH

address: 10900 Euclid Avenue, WRB 5132

department: Pathology

institute: Case Western Reserve University School of Medicine

summary: The interactions between environmental glycans and glycan-binding proteins modulate a host of processes across biological systems. The Siglec/sialic acid axis has gained increasing attention as an immunologic checkpoint due to its involvement with reducing inflammatory processes and promoting tumor growth. Siglec-2, or CD22, has been extensively characterized as a co-receptor for the B cell receptor (BCR) and is critical for the prevention of self-reactive B cell responses through its recognition of α2,6-linked sialic acids. More recently, CD22 has emerged as an important receptor for macrophage biology. Here, we investigate the consequences of genetic ablation of CD22 in macrophages (CD22KO). Aged CD22KO mice developed a fatty liver phenotype similar to that seen in aged animals lacking hepatocyte α2,6-sialylation (HcKO). CD22KO bone marrow-derived macrophages (BMDMs) exhibited few differences in canonical markers of M1-like and M2-like polarization, but M2-like CD22KO BMDMs showed a pro-inflammatory shift in transcriptome and a reduction in endocytic and efferocytotic capacity. These data suggest that CD22 in M2-like macrophages is strongly associated with a homeostatic transcriptional profile, and directly participates in immunologically silent housekeeping functions such as clearance of sialylated-self debris through the Siglec-sialic acid axis.

overall_design: Wild type C57Bl/6 mouse bone marrow-derived macrophage mRNA transcriptome versus CD22 knockout mouse bone marrow-derived macrophage mRNA transcriptome after 48 hours of polarization with IL-4.

first: Emily

middle: N

last: Kukan

first: Gabrielle

last: Fabiano

first: Julie

middle: Y

last: Zhou

first: Ava

middle: R

last: Richard

first: Kevin

last: Telfer