title: Spatial Transcriptomic Profiling of the Type 2 Diabetic Coronary Microcirculation Reveals Heterogeneity Varied by Regions of the Heart [scRNA-seq]

city: Columbus

first: Katherine

last: Miller

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

summary: Background: Coronary microvascular disease (CMD) is an early complication of type 2 diabetes (T2D) involving adverse endothelial and smooth muscle dysfunction, vascular remodeling, and alterations in mechanics, which culminate in impaired coronary blood flow. Recent data suggest that vascular layer-specific mechanisms, influenced by the surrounding myocardium, contribute to CMD. To investigate transcriptional differences potentially contributing to CMD, we used spatial and single cell transcriptomic profiling of the coronary microcirculation and surrounding myocardium across distinct heart subregions to identify new pathways to target. Methods: We combined single cell RNA profiling and spatial transcriptomics to examine transcriptional differences and molecular signatures of CMD in T2D mice. Results: Single cell RNA profiling and spatial transcriptomics revealed upregulation of genes linked to adipogenesis, fatty acid metabolism, and oxidative phosphorylation in T2D cell clusters and coronary microvascular-enriched regions. Using spatial transcriptomics, we also examined gene expression in coronary microvessel-enriched areas across different heart subregions. Interestingly, the most pronounced transcriptional differences between T2D and control coronary microvessels were observed in the left ventricular anterior wall, where inflammatory response pathways were downregulated in T2D mice. Genes associated with oxidative phosphorylation and fatty acid oxidation were significantly upregulated in T2D coronary microvessels within the left ventricular anterior wall.Conclusions: These intriguing data support the well-documented concept that cardiac metabolic inflexibility in T2D – characterized by reduced mitochondrial function, increased reliance on fatty acid oxidation, and impaired glucose utilization – contributes to oxidative stress and lipotoxicity, key drivers of heart failure. Furthermore, these data reveal previously unrecognized transcriptomic differences in coronary microvessels across spatially-distinct regions of the T2D heart, suggesting transcriptional heterogeneity in this critical vascular bed.

overall_design: To investigate the transcriptomic changes that occur in the complex cellular landscape of CMD, we isolated hearts from male heterozygous non-diabetic Db/db mice and male homozygous T2D db/db mouse, and we performed paired single cell RNA-sequencing (scRNA-seq) and spatial transcriptomic profiling

first: Patricia

last: McCallinhart

first: Corinne

last: Strawser

first: Elizabeth

last: Garfinkle

first: Jaye

middle: B

last: Navarro

first: Cynthia

last: McAllister

first: Tatyana

last: Vetter

first: Aurora

last: O’Phelan

first: Elaine

middle: R

last: Mardis

first: Louisa

last: Mezache

first: Rengasayee

last: Veeraraghavan

first: Aaron

last: Trask


title: Evaluation of toxicological mechanisms of ochratoxin-A in human primary proximal tubule epithelial cells

status: Public on Dec 10 2025

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

country: USA

institute: University of Washington

type: Expression profiling by high throughput sequencing

summary: Ochratoxin-A (OTA) is a fungal mycotoxin that is one of the most common food contaminants, ubiquitously found in a variety of foodstuffs worldwide. As a known nephrotoxin, hepatotoxin, and class II-b carcinogen, exposure to this compound is a major health concern. Specifically, OTA has been implicated as a potential agent in chronic kidney disease of unknown etiology (CKDu), an endemic form of chronic kidney disease that disproportionally affects rural agricultural communities and is thought to arise from environmental factors rather than diabetes and hypertension. A key pathological difference between CKDu and CKD is the degeneration of the kidney proximal tubule, where OTA has been shown to accumulate. The mechanism of OTA toxicity in the human kidney remains elusive, and this study aims to elucidate OTA-induced molecular toxicological pathways using primary human proximal tubule epithelial cells (PTECs). We demonstrated that the previously reported downregulation of NRF2 target antioxidant response elements is not due to a direct interaction between NRF2 and its cytosolic binder, KEAP1, evidenced by the lack of recovery of mRNA transcripts with co-administration of NRF2 agonists, sulforaphane or tert-butylhydroquinone. Furthermore, exposure to OTA (10 uM) induces 7192 differentially expressed genes, including key regulators of mitochondrial fission and fusion. This was confirmed at the cellular level by confocal microscopy, where a breakdown of the mitochondrial network was observed at 100 nM OTA. Furthermore, OTA was found to significantly induce reactive oxygen species (mROS) and inhibit basal mitochondrial oxidative phosphorylation as well as glycolysis through measurements of oxygen consumption rate and extracellular acidification, corroborating transcriptional findings that OTA induces hypoxic response elements. In conclusion, in this work we demonstrate that OTA causes mitochondrial dysfunction and reduced ATP production, leading to a senescent-like state in PTECs characteristic of renal disease progression. These findings provide insight into early toxicological endpoints induced by OTA which have been established as pathophysiological changes involved in chronic kidney disease.

overall_design: To assess the effects of ochratoxin-A (OTA) on human proximal epithelial cells, we treated with either 10 µM OTA, one of two NRF2 activators (20 µM sulforaphane (SFN),  or 5 µM tert-buthylhydroquinone (tBHQ)), or 10 µM OTA after pre-treating with either 20 µM SFN or 5 µM tBHQ.

first: Anish

last: Mahadeo

first: Theo

middle: K

last: Bammler

first: Angela

last: Zheng

first: Catherine

last: Yeung

first: Honathan

last: Himmelfarb

first: Edward

middle: J

last: Kelly


title: Spatial Transcriptomic Profiling of the Type 2 Diabetic Coronary Microcirculation Reveals Heterogeneity Varied by Regions of the Heart [Visium]

first: Katherine

middle: E

last: Miller

state: OH

first: Patricia

last: McCallinhart

first: Corinne

middle: H

last: Strawser

middle: A


title: Targeted citrullination enables p53 binding to non-canonical sites [CUT&Tag]

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: TP53 encodes for the transcription factor p53, which binds to a diverse set of target genes in response to stress.  Activation of p53 results in highly specific transcriptional responses, but the regulation of promoter selectivity by p53 is poorly understood.  Here we report that sequence-specific binding of p53 is regulated by its target gene and binding partner PADI4.  PADI4 enzymatically converts peptidyl-arginine to peptidyl-citrulline in a process known as citrullination.  We show p53 is citrullinated in vitro at the C-terminus by PADI4, and we confirm two citrullination events in vivo (R306, R363).  ChIP-seq reveals that PADI4 expression causes a redirection of p53 away from canonical binding sites to target genes associated with the ETS transcription factor and the interferon response.  Chromatin profiling using citrullination-specific p53 antibodies supports this conclusion.  These findings link citrullination to p53 function and illustrate how chromatin modifiers like PADI4 can redirect the p53 transcriptional response.

overall_design: CUT&Tag of H3K27me3, IgG, p53, and antibodies against citrullinated p53 (cit 306, cit 342, and cit 363) in H1299 cells transiently transfected with pCMV-p53 or the combination of pCMV-p53 and pCMV-PADI4, or HCT116 cells transfected with a tetracycline-inducible system to induce PADI4 expression. Cells were either treated with vehicle (untreated), nutlin, or the combination of nutlin and doxycyline for 24 hours.

first: Alexandra

last: Indeglia

first: Andrea

last: Valdespino

first: Giulia

last: Pantella

first: Sarah

last: Offley

first: Connor

last: Hill

first: Alessandro

last: Gardini

first: Maureen E.

last: Murphy


title: Aging-associated Increase of GATA4 levels in Articular Cartilage is Linked to Impaired Regenerative Capacity of Chondrocytes and Osteoarthritis

city: Pittsburgh

first: Shuchang

last: Liu

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: Although the causal association between aging and osteoarthritis (OA) has been documented, our understanding of the underlying mechanism remains incomplete. To define the regulatory molecules governing chondrocyte aging, we performed transcriptomic analysis of young and old human chondrocytes from healthy donors. The data predicted that GATA binding protein 4 (GATA4) may play a key role in mediating the difference between young and old chondrocytes. Results from immunostaining and western blot showed significantly higher GATA4 levels in old human or mouse chondrocytes when compared to young cells. Moreover, overexpressing GATA4 in young chondrocytes remarkably reduced their cartilage-forming capacity in vitro and induced the upregulation of proinflammatory cytokines. Conversely, suppressing GATA4 expression in old chondrocytes, through either siRNA or a small-molecule inhibitor NSC140905, increased the production of aggrecan and collagen type II, and also decreased levels of matrix-degrading enzymes. In OA mice, induced by surgical destabilization of the medial meniscus, intraarticular injection of lentiviral vectors carrying mouse Gata4 resulted in a higher OA severity, synovial inflammation, and pain level when compared to control vectors. Mechanistically, we found that overexpressing GATA4 significantly increased the phosphorylation of SMAD1/5. Our work demonstrates that the aging-associated increase of GATA4 in chondrocytes plays a vital role in OA progression, which may also serve as a target to reduce osteoarthritis in the older population.

overall_design: In this study, to understand key regulators that contribute to an “aged” state in chondrocytes prior to OA onset, we first compared the transcriptome of young and old human chondrocytes isolated from healthy donors without known joint diseases and employed unbiased analysis to define the key regulatory molecules that mediate chondrocyte aging. Assessment of the chondrocyte genome demonstrated the upregulation of several factors in aged chondrocytes, and transcription factor GATA binding protein 4 (GATA4) specifically drew our attention since it is associated with DNA damage and cellular senescence. Upregulation of GATA4 in OA chondrocytes was also reported.We thus hypothesized that the increased GATA4 level contributes to chondrocyte aging and accelerated OA progression upon injuries. We first tested the hypothesis by increasing or suppressing GATA4 expression in healthy chondrocytes and examining their cartilage-forming capacity. We also assessed the role of GATA4 in vivo by injecting lentiviral vectors carrying control or mouse Gata4 genes into the knee joints of OA mice induced by surgically created destabilization of the medial meniscus (DMM). Lastly, a mechanistic study was conducted to explore how GATA4 impacts chondrocyte phenotypes and functions.

first: Meagan J

last: Makarczyk

first: Yiqian

last: Zhang

first: Alyssa

last: Aguglia

first: Olivia

last: Bartholomew

first: Sophie

last: Hines

first: Suyash

last: Sinkar

first: Silvia

first: Craig

last: Duvall

first: Hang

last: Lin


title: Reproduction-associated and sex determining genes expressed differently in testes of genotypic and temperature-induced males of gibel carp (Carassius gibelio): the molecular mechanisms underlying the reproductive plasticity and invasiveness

city: Brno

first: Core Facility

last: Bioinformatics

address: Kamenice 5

country: Czech Republic

institute: CEITEC - Masaryk University

summary: Sex in vertebrates is commonly determined by genotype and in some cases by environmental conditions, such as temperature. A few vertebrate species display intermediate conditions of sex determination, combining sex chromosomes with an effect of temperature. This phenomenon is known for the gibel carp (Carassius gibelio), an invasive cyprinid fish species, whose abilities to adapt and colonize new environments is linked with the combination of sexual and asexual reproduction. In this study, the gonad transcriptomes were compared between genotypic males and temperature-induced males of C. gibelio. We specifically focused on the meiosis-related and reproduction-associated genes. Many genes and pathways of cell cycle control and meiosis, male differentiation and spermatogenesis were common to genotypic and temperature-induced males of gibel carp. However, the underrepresentation of several GO terms and KEGG pathways related to reproduction and spermatogenesis in genotypic males suggests lower reproductive abilities of temperature-induced males. Our study highlights the differential transcription regulation of key genes related to male sex differentiation, steroid hormone regulation, meiosis, spermatogenesis and sperm-egg interaction including the genes associated with sperm fertilization, motility and sperm flagellum function. Especially, induced males strongly overexpressed hsd17b2 and slightly overexpressed the meiotic gene mnd1, while genotypic males overexpressed sox8a and cyp19a1a, as well as the crucial fertilization gene izumo. These findings contribute to the understanding of the molecular mechanisms underlying the reproductive plasticity and invasiveness of C. gibelio in Europe. Our study highlighs the role of males, whose appearance was crucial for the transition from asexual to sexual reproduction in this species. Our findings contribute to the understanding of the molecular mechanisms underlying the reproductive plasticity and invasiveness of C. gibelio in Europe.

overall_design: The specimens of cyprinid fish, gibel carp (Carassius gibelio), were obtained from artificial breeding of parental fish sampled in Dyje River (Czech Republic). We performed a set of sexual crossing (diploid females and diploid males) and a set of induced gynogenesis (using sperm of diploid male Carassius gibelio, Cyprinus carpio or Abramis brama for induction of gynogenesis). Fertilized eggs resulting from sexual crossing of diploid (2n) gibel carp were exposed to 22 °C. The eggs resulting from a gynogenesis were activated by the sperm of conspecific or heterospecific males and were exposed to one of the following temperatures 22, 25, 28 or 31 °C. The gibel carp offspring, specifically genotypic diploid males and temperature-induced triploid (3n) males were reared in aquarium conditions until the age of two years (i.e. until reaching maturity) before their testis’s tissues were sampled. For DEGs associated with reproduction, we used the comparison of genotypic diploid males (male 2n) and temperature induced males (male 3n) males. For DEGs associated with sex determination, we used the comparison of genotypic diploid males (male 2n) and three groups of the temperature induced males representing (1) male 3n group 1 – male offspring sampled at 28 and 31 °C and produced by a gynogenetic female for which offspring showed no sex reversal at 22 °C and full sex reversal at 28 and 31 °C, (2) male 3n group 2 – male offspring sampled at 28-31 °C and produced by a gynogenetic female for which offspring showed a high proportion of sex reversal at 22 °C and full sex reversal at 28 and 31 °C, and (3) male 3n group 3 - male offspring sampled at 22 °C and produced by a gynogenetic female for which offspring showed a high proportion of sex reversal  at 22 °C and full sex reversal at 28 and 31 °C.

first: Florian

last: Jaques

first: Lukáš

last: Vetešník

first: Iva

last: Dyková

last: Šimková


title: Distinct Cell-Intrinsic and Extrinsic Consequences of TLR2 Activation Drive Pleiotropic Effects in AML Pathogenesis

first: Ramkrishna

last: Mitra

state: Pennsylvania

address: 233 S 10th street

institute: Thomas Jefferson University

summary: Inflammation can both repress and promote tumor progression depending on the type, frequency, and combination with different therapeutic modalities. In acute myeloid leukemia (AML) generation of effector cells of the innate immune system are attenuated, suggesting that innate immune function has a critical role in leukemogenesis. Using a panel of ligands directed at the Toll-like family of pattern recognition receptors (TLRs) to induce acute inflammation in models of high-risk AML, we uncover that TLR2 ligands exert unique anti-leukemia effects distinct from other TLRs, through cell-type specific autonomous and non-autonomous mechanisms. TLR2 signaling causes non-specific inflammatory-mediated AML cell death, leukemia stem cell (LSC) reprogramming with impaired self-renewal, bi-lineage myeloid maturation, and prolonged survival. Subsequent cytokine signaling both promotes and antagonizes these AML-intrinsic effects, at least in part through G-CSF released from cells in the bone marrow microenvironment. Importantly, TLR2 is the most abundant TLR expressed in human AML regardless of ELN or mutation status, suggesting a key role in human disease. Together, these data indicate functional interplay of innate immune signaling between AML cells and the microenvironment during acute inflammation directly impacts leukemia progression.

overall_design: CITEseq: B6: CD45.1 mice were transplanted with Dnmt3a-/+Flt3ITD/ITD;Mx1-Cre AML. Mice were treated 2 weeks later with either 100µL PBS or 100µg Pam3CSK4. 24 hours after treatment, mice were sacrificed and bone marrow cells were isolated. Cells were FACs sorted for either CD45.2+Lin-CD117+ (HSPC) or CD45.2+CD11b+ (mature) cells

first: Michael

last: Lawler

first: Jennifer

middle: S

last: Romer-Seibert

last: Bowman

first: Christine

middle: M

last: Eischen

first: Robert

middle: L

first: Sara

last: Meyer


title: Ly6G+Nur77+ macrophages initiate the type-2 immune response to allergens in the lung

city: BETHESDA

first: Beatriz

last: León

state: MD

address: 10 CENTER DR

department: Division of Intramural Research (DIR)

institute: National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH)

summary: The mechanisms of allergen sensing and type 2 immune response initiation remain unclear. Using a house dust mite (HDM)-induced allergic airway model, we demonstrated that host detection of protease activity in HDM was crucial for initiating T helper type 2 (Th2) responses. This process was driven by the major allergen Der p 1, a cysteine protease, which was sensed by protease-activated receptor 2 (PAR2) on a novel population of perivascular lung macrophages expressing Ly6G and nuclear receptor Nur77. These macrophages required PAR2 and Nur77 for activation and accumulation and regulated conventional migratory dendritic cell (mDC) migration to draining mediastinal lymph nodes (mLN) via cysteinyl leukotriene (CysLTs) production. CysLTs enhanced CCR7-driven migration of mDCs toward its ligand, CCL21, facilitating arrival to mLNs for T cell priming and expansion. Inhibiting CysLTs biosynthesis reduced mDC migration and dampened Th2 allergic responses, highlighting new therapeutic paths and mechanisms in type 2 immunity.

overall_design: This study aims to characterize the early immune cell populations involved in the response to protease allergens in the lung using single-cell RNA sequencing (scRNA-seq). Eight-week-old C57BL/6J mice (species Mus musculus) were treated intranasally with 10 µg of Alexa Fluor 647-labeled cysteine protease papain in a 100 µL volume. Twenty-four hours later, lungs were processed into a single-cell suspension, and papain⁺ cells were isolated using fluorescence-activated cell sorting (FACS). The sorted cells were then subjected to single-cell RNA sequencing (scRNA-seq) to characterize their transcriptional profiles. This dataset provides insights into early immune interactions in the lung following allergen exposure.

first: Audrey

last: Meloun

first: Holly

last: Bachus

first: Crystal

last: Lewis

first: Brittany

last: Dulek

first: Shivangi

last: Dave

first: Dave

last: Durell Hill

first: Gabriela

last: Pessenda

first: Jose

last: Carlos Gonzalez

first: P’ng

last: Loke

first: Alexander

middle: F

last: Rosenberg


title: Per- and polyfluoroalkyl substances (PFAS) suppress macrophage alternative activation to disrupt hepatic lipid metabolism [RNA-seq I]

city: 北京

first: 丽娟

last: 游

state: 北京Beijing

address: 潘家园南里7号楼

country: China

institute: 国家食品安全风险评估中心

summary: Per- and polyfluoroalkyl substances (PFAS) are pervasive environmental pollutants with diverse toxic effects, including endocrine disruption and hepatotoxicity. As a key class of immune cells, macrophages are critical target for endocrine disrupting chemicals (EDCs); however, their role in PFAS-induced toxicity and the underlying mechanisms remain poorly understood. In this study, we developed a high-content cell model by utilizing the activation and differentiation of human THP-1 monocytes into macrophages, enabling rapid quantitative screening of various PFAS chemicals. Our results identified that PFOA, PFUnDA, and HFPODA suppressed macrophage alternative activation to varying extents by disrupting the PPAR signaling pathway. In vivo, oral exposure to PFOA and PFUnDA in wild-type C57BL/6J mice significantly impaired macrophage alternative activation in the liver, resulting in hepatocyte hypertrophy, liver dysfunction, and systemic lipid metabolism disorders. Furthermore, macrophage-specific PPARγ knockout exacerbated PFAS-induced hepatotoxicity. These findings highlight the immunometabolic regulatory role of macrophage activation in PFAS-induced liver toxicity and provide novel insights into the health risks posed by PFAS exposure in humans.

overall_design: In the study of in vivo toxic effects, wild-type (WT) and macrophage PPARγ knockout (Mac-ko) mice were randomly divided into 4 groups, each receiving an oral gavage of PFOA, PFUnDA, and HFPODA at a dose of 1 mg/kg bw/day, along with 0.1% DMSO, for 35 days (n=6-8). This dose was based on the no observed adverse effect level (NOAEL) for oral administration of PFOA and PFUnDA in mice, which is 1 mg/kg bw/day (ATSDR, 2021). HFPODA was used as a substitute for PFOA, maintaining the same gavage dosage. A 0.1% DMSO group served as the control (CT). Mouse body weight was recorded weekly, and at the end of the experiment, blood samples were collected via retro-orbital venipuncture. Subsequently, cervical dislocation was performed for euthanasia, and the liver was dissected and weighed. The liver was divided into three parts: the first part was fixed in 10% neutral buffered formalin for histopathological examination and immunohistochemical analysis; the second part was quickly frozen in liquid nitrogen and stored at -80°C for liver tissue RNA sequencing; the third part was washed with PBS and used for flow cytometry analysis.In this experiment, PPRE-eGFP THP-1 cells were seeded at a density of 70,000 cells per well in black-walled 96-well plates (model: 960096, n=3) to induce their differentiation into M2 macrophages. During the differentiation induction period, the cells were exposed to perfluorinated compounds. After 48 hours of treatment, they were incubated in the dark at room temperature for 30 minutes with fluorescently conjugated antibodies CD36 (1:100) and CD209 (1:100), along with the nuclear dye Hoechst (1:100). After washing with PBS, FluoroBrite DMEM (Thermo Scientific, A1896701) was added, and fluorescent images of the cells were captured using a high-content high-throughput imaging system (version 6.5, Molecular Devices). The analysis was conducted using CellReporterXpress imaging and analysis software (version 6.5, Molecular Devices). In the analysis, the average stained area and the percentage of positively stained cells were calculated by normalizing the total fluorescent-stained cell area and count to the total cell number in the same image.

first: Lijuan

last: You

first: Jing

last: Yang

first: Hui

first: Xiaohong

last: Wang

first: Yaru

last: Tian

first: Zhisen

last: Zhuang

first: Yi

last: Wan


title: Transcriptomic profiles of liver biopsies in obese patients with metabolic dysfunction-associated steatotic liver disease

city: Singapore

first: Qing

last: Zhao

address: 28 Medical Dr

country: Singapore

institute: NUS

summary: The molecular mechanisms underlying early-stage metabolic dysfunction-associated steatotic liver disease (MASLD) is poorly understood. This study characterized the transcriptomic alterations in obese patients with no pathology or early-stage MASLD.  94 snap-frozen liver biopsies were analyzed through high-throughput RNA sequencing. Distinct features involved in the development of hepatic steatosis and fibrosis were identified. This study also provided novel insights in mechanisms involved in the onset of fibrosis, highlighting potential therapeutic targets.

overall_design: 94 snap-frozen liver biopsies were processe for RNA sequencing on the NoveSeq6000 platform.

first: William

last: De Nardo

first: Hyungwon

last: Choi

first: Matthew

last: Watt

first: Philipp

last: Kaldis


title: CCL5 promotes angiotensin II-induced cardiac remodeling through regulation of platelet-driven M2 macrophage polarization

city: Beijing

first: Mingxuan

last: Zhou

state: China

address: No. 2 Nanwei Road, Tianqiao Street

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences

summary: Aims: Platelet activation plays a critical role in the pathogenesis of cardiovascular disease and inflammation, primarily through interactions with macrophages. CCL5, a chemokine stored in platelet α-granules, is released upon platelet activation. The present study determines the specific role of CCL5 in modulating platelet function, platelet-mediated macrophage polarization, and hypertensive cardiac remodelin. Conclusion: These findings underscore the detrimental role of CCL5-mediated platelet activation in triggering inflammatory responses and promoting M2 macrophage polarization during hypertensive cardiac remodeling, revealing the molecular mechanism by which CCL5 facilitates platelet-derived TGF-β1 signaling via NF-κB activation. These results elucidate the crosstalk between platelets and macrophages that exacerbates cardiac remodeling and highlight CCL5 as a potential therapeutic target for reducing inflammation and cardiac injury.

overall_design: Under Angiotensin II-induced condition, CCL5 is upregulated, which promotes platelet activation and facilitates cardiac inflammatory cascades. CCL5 promotes the infiltration of CD8+ T cell and macrophage in the heart. More importantly, CCL5 facilitates platelet-derived TGF-β1 signaling via NF-κB activation, leading to pro-fibrotic M2 macrophage polarization which in turn promotes myofibroblast differentiation. These results elucidate the regulation of CCL5 in platelet inflammation, the modulation of platelet-derived TGF-β1 by CCL5, and the crosstalk between platelets and macrophages that exacerbates cardiac remodeling and highlight CCL5 as a potential therapeutic target for reducing inflammation and cardiac injury.

first: Silin

last: Lv


title: PHLPP1 Cut&Tag profiling of untreatment (UT) and IL-4 treated alveolar macrophage

city: Shanghai

first: Xingguang

last: Liu

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

institute: Naval medical university

summary: Purpose: To transcriptome widely reveal genes regulation by PHLPP1, we performed Cleavage Under Targets and Tagmentation (CUT&Tag) analysis of wild-type (WT) AMs. Methods: Mouse AMs were generated from bronchoalveolar lavage fluid (BALF). AMs were stained to confirm the surface expression of CD11C and Siglec-F. Cells with purity >97.5% were used for subsequent experiments. WT AMs were stimulated with IL-4 (20ng/ml) for 4 hours. Results: We carried out a CUT&Tag assay using antibodies against PHLPP1,and found the global influence of PHLPP1 in regulating genes for pro-fibrosis macrophage effector function.

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) analysis for PHLPP1-binding DNA  in WT AMs stimulated with IL-4.

first: Yuyu

last: Jiang

first: Yunkai

last: Zhang


title: VGLL1 KO in colon cancer cells primary culture clone E3, clone 22

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

summary: In order to explore the potential role of VGLL1 in metastasis we knocked it out using CRISPR. Here we performed an RNAseq of the mutated cells and the wt cells to have an overview of the transcriptome regulation of cells without VGLL1 protein.

overall_design: Total RNA from each culture (control wt and KO) were extracted using TRIzol Reagent (Ambion) following the manufacturer's protocol. Each condition was independently processed in triplicates and the libraries were prepared using Illimina TruSeq protocols. The samples were sequenced on a HiSeq Illumina 2500 machine with 50bp reads followed by standard analyses.

first: Ariel

last: Ruiz i Altaba

first: Marianna

last: Silvano

first: Luca

last: Dall' Olio

first: Ana

middle: I

last: Borges Grazina


title: Colon cancer low metastatic clone after escape of late apoptosis

summary: In order to explore the potential role of escape of late apoptosis in metastasis, we induced apoptosis and subsequently inhibited the death process in a poorly metastatic clone from a primary culture of colon cancer cells. Here we wanted to explore the transcriptome of such "undead" cells  7 days after apoptosis induction.

overall_design: Primary culture CC14 low metastatic clone C11 was treated with STS and 6h after with DIDS and Q-VD_Oph. 7 days after these treatments , cells were harvested and total RNA extracted using TRIzol Reagent (Ambion) following the manufacturer's protocol. Each condition was independently processed in triplicates and the libraries were prepared using Illimina TruSeq protocols. The samples were sequenced on a HiSeq Illumina 2500 machine with 50bp reads followed by standard analyses.

first: Arwen

last: Conod


title: CEBPB drives endothelial pathological phenotype and promotes atherosclerosis by directly upregulating TGFBR1 expression [scRNA-seq]

city: Hangzhou

first: Cong

last: Qiu

state: Zhejiang

address: No.866 Yuhangtang Road

institute: Zhejiang University

summary: Endothelial cell (EC) dysfunction is crucial in chronic vascular inflammation and diseases like atherosclerosis. An unknown endothelial pathological phenotype potentially driving atherosclerosis was hinted in our previous study. However, the detailed characterizations and underlying molecular mechanisms remain unclear.  Here, we have defined a new endothelial pathological phenotype, characterized by high expression of fibroblast and pro-inflammatory genes with a rapid reduction in EC fate genes by performing single-cell RNA sequencing. Further analysis revealed that increased CEBPB contributes to the fibroblast and inflammatory feature of these atherogenic ECs, which was further confirmed in cultured human aortic ECs. Mechanistically, IL-1β-induced high expression of CEBPB triggers TGF-β signaling and subsequent regulation of downstream genes. This occurs through direct interaction of CEBPB with the promotor region of TGF-β receptor type I (TGFBR1), resulting in its upregulation. Furthermore, exacerbating atherosclerotic plaque area, enhanced vascular inflammation and increased endothelial TGFBR1 expression were confirmed by endothelial overexpression of CEBPB in vivo. These findings suggest endothelial CEBPB functions as a novel regulator of TGFBR1, driving endothelial pathological phenotype, promoting vascular inflammation and atherosclerosis. Targeting endothelial CEBPB may offer new therapeutic avenues for atherosclerotic diseases.

overall_design: We performed scRNA-Seq analysis of ECs from normal aortas (i.e., from C57BL/6 mice fed on a standard diet), mild atherosclerotic aortas (i.e., from Apoe-/- mice fed on a standard diet), and severe atherosclerotic aortas (i.e., from Apoe-/- mice fed on a high fat diet)

first: Linge

last: Fan

first: Yingyi

last: Zhu


title: RNA sequencing of FZD6 knockdown in prostate cancer cells

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: Wnt signaling is a complex pathway consisting of numerous ligands and frizzled (FZD) receptors. These signaling components are widely expressed in human prostate tissues and often undergo upregulation or mutation in advanced prostate cancers. Enhanced Wnt signaling promotes prostate cancer cell proliferation, metastasis, and resistance to therapy. However, targeting pan-Wnt signaling poses challenges due to tissue toxicity. We show that FZD6 is the most highly expressed and frequently amplified Wnt receptor in advanced human prostate cancers. Knockdown of FZD6 suppresses in vitro growth of various prostate cancer cell lines. Additionally, FZD6 knockdown impairs DNA double-strand break (DSB) repair, as determined by both resolution of γH2AX foci and DNA DSB repair reporter assays. Mechanistically, FZD6 knockdown-induced growth suppression is linked to reduced activities of the SRC kinase and STAT3, while DNA damage repair deficiency is mediated through WEE1 downregulation. WEE1 downregulation is mediated through PLK1 but is independent of β-Catenin. Knockdown of FZD6 enhances the therapeutic efficacy of genotoxic agents in preclinical prostate cancer models. Our findings demonstrate that targeting a single FZD receptor highly expressed in prostate cancers can achieve significant therapeutic efficacy.

overall_design: RNA-Seq analysis of DU145 cells expressing scrambled (shSCR) shRNA and two shRNAs against FZD6; two group comparison.

first: Yiqun

first: Li

last: Xin


title: The single-cell transcriptional landscape of the pediatric cystic fibrosis airway from minimally invasive respiratory specimens

city: New York

first: Yifei

last: Sun

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: Cystic fibrosis (CF) is a multisystemic, autosomal recessive disorder caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene with the majority of morbidity and mortality extending from lung disease. In this study, we leveraged single-cell transcriptional analyses to characterize the immune and airway epithelial cell populations in minimally invasive respiratory specimens obtained from pediatric patients with CF and pediatric non-CF controls at the time of clinically indicated flexible bronchoscopy. We focused on the pediatric population in an effort to better understand the early pathophysiology of CF lung disease. Through our approach, we provide insights into the composition of and functional changes within the immune and airway epithelial cell populations in the pediatric CF lung. Understanding the early pathophysiology of CF lung disease, including the changes present in the early cycles of airway infection, inflammation, and tissue damage, may reveal new potential therapeutic targets for CF lung disease.

overall_design: Bronchoalveolar Lavage (BAL), bronchial brush  and tracheal brush samples were collected from CF and non-CF patients. Samples were cleaned and made into  single-cell suspensions, then immediately processed according to manufacturer’s instructions.

first: Alfin

middle: G

last: Vicencio

first: Mary

last: Beasley

first: Martin

last: Walsh

first: Megan

last: Januska


title: CEBPB drives endothelial pathological phenotype and promotes atherosclerosis by directly upregulating TGFBR1 expression [CUT&Tag-Seq]

summary: Endothelial cell (EC) dysfunction is crucial in chronic vascular inflammation and diseases like atherosclerosis. An unknown endothelial pathological phenotype potentially driving atherosclerosis was hinted in our previous study. However, the detailed characterizations and underlying molecular mechanisms remain unclear. In the present study, using single-cell RNA sequencing, the new endothelial pathological phenotype was defined by high expression of fibroblast markers, extracellular matrix, and inflammatory genes, concurrently with a rapid decline in endothelial markers. Further analysis revealed that increased CEBPB contributes to the fibroblast and inflammatory feature of these atherogenic ECs, which was further confirmed in cultured human aortic ECs. Mechanistically, IL-1β-induced high expression of CEBPB triggers TGF-β signaling and subsequent regulation of downstream genes. By performing CUT&Tag analysis, we further investigated  that CEBPB directly regulates TGFBR1 expression in endothelial cells through direct interaction of CEBPB with the promotor region of TGF-β receptor type I (TGFBR1).  These findings suggest endothelial CEBPB functions as a novel regulator of TGFBR1, driving endothelial pathological phenotype, promoting vascular inflammation and atherosclerosis.

overall_design: We performed CUT&Tag-seq for Flag-tag in HAECs which overexpress Flag-CEBPB.


title: Spatial immune landscape of large artery atherosclerotic and cardioembolic thrombus retrieved from mechanical thrombectomy

city: Seoul

first: Sugyeong

last: Jo

address: 50-1, Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University College of Medicine

summary: Cardioembolic (CE) and large artery atherosclerosis (LAA) strokes are two main causes of acute ischemic stroke (AIS), carrying a high risk of recurrence. This study investigated the immune cell-specific role in thrombosis between CE and LAA stroke using NanoString GeoMX Digital Spatial Profiler.

overall_design: Thrombi from AIS patients who underwent mechanical thrombectomy were fixed in 4% paraformaldehyde, embedded in paraffin. The Formalin-fixed paraffin-embedded tissue sections were used for Nanostring's GeoMX Whole Transcriptome Atlas Digital Spatial Profiling.

first: Sugeyong

first: Taedong

last: Ok

first: Kyung-Yul

last: Lee

first: Sungsoon

last: Fang

first: Bo Kyung

last: Yoon


title: Spatiotemporal multi-omics analysis reveals distinct epigenetic and transcriptional signatures in the hippocampal-amygdala circuit during fear memory consolidation

city: Blacksburg

first: Timothy

last: Jarome

address: Mail Stop: 0306,ANIMAL SCIENCES  MC0306,LITTON REEVES   STE 3490

institute: Virginia Tech

summary: The consolidation of contextual fear memories requires the crosstalk among multiple brain regions, including the hippocampus and amygdala. Despite the advance in single cell transcriptomic techniques, tracing the dynamic gene expression across the hippocampal-amygdala circuit remain challenging. Here we integrated high resolution spatial transcriptomics with single nuclei multi-omics techniques to systematically investigate the spatiotemporally transcriptional programs across the hippocampal-amygdala circuit during the encoding and retrieval of contextual fear memory. It reveals highly dynamic gene expression in the subregions of hippocampus and amygdala. Our data provide new insights into the transcriptional programs underlying consolidation of memory.

overall_design: Adult C57BL/6 male mice (12~15 weeks) were subjected to contextual fear conditioning (CFC), mice without foot shock were used as context control (CC), and mice stayed in the home cage until sample harvest were used as home cage control (HC). Mice were harvested 1h or 4h after foot shock on the training day (day 0) and 4h after memory retrieval on day 1 to assess fear memory consolidation and reconsolidation. To profile spatial transcriptome, the mouse brains were freshly isolated to prepare FFPE tissue blocks, then coronally sectioned and placed onto the Visium slides for Visium Spatial Gene Expression library preparation. To simultaneously profile the transcriptome and chromatin accessibility at single cell resolution, hippocampus and amygdala were micro-dissected from the freshly isolated mouse brain tissues for single nuclei suspension preparation and subsequently loaded onto the Chromium iX using the single nucleus multiome kit from 10x genomics. Single nucleus RNA-seq (snRNA-seq) and single nucleus ATAC-seq (snATAC-seq) libraries were simultaneously constructed from the same nucleus following the manufactures' instructions.

first: Xiguang

last: Xu

first: Yu

last: Lin

first: Hehuang

last: Xie


title: Activation of 3, 4-dimethylphenol dimer production from marine Streptomyces sp. FJNU027 under oligotrophic condition

city: Fuzhou

first: Lingjun

last: Yu

address: No. 18 Wulongjiang Middle Avenue, Shangjie Town, Minhou County

institute: Fujian Normal University

summary: Activating the cryptic secondary metabolic gene clusters is a vital research field in Streptomyces. The marine Streptomyces sp. FJNU027 strain which could produce tirandamycins was cultured in the oligotrophic medium. Compared with normal medium, a differential product in oligotrophic culture was found by HPLC assay. After mass fermentation, 2 mg of the differential product was obtained from 30 L fermentation broth by solvent extraction, column chromatography over sephadex LH-20 and reverse phase C18, and other methods. It was identified as 4,4',5,5'-tetramethyl-[1,1'- diphenyl]-2,2'-diol by NMR and MS data. The production of this compound was enhanced with the increment of cultural time. Transcriptome sequencing analysis showed that the highest upregulated genes under oligotrophic condition were glycosidase, TraR/DksA C4-type zinc finger protein and ribonuclease encoding genes, while the expression of a MarR family transcriptional regulator was most significantly decreased under oligotrophic condition. The results indicate that oligotrophic culture is an effective method for altering the secondary metabolism of Streptomyces.

overall_design: To investigate the possible mechanism for the activation of differential product in oligotrophic medium, we performed gene expression profiling analysis using data obtained from RNA-seq of one strain in two different media. Comparative gene expression profiling analysis of RNA-seq data for the strain cultured on oligotrophic medium  and modified Gauze's medium.

first: Yongbiao

last: Zheng

first: Jie

last: Tan

first: Huimin

last: Yuan


title: A hyperactive splice variant of STAT3  promotes colonic inflammation-associated tumorigenesis in mice

city: Wuhan

first: Jingjing

last: Tong

state: Hubei

address: NO.152 Luoyu Road

institute: Central China Normal University

summary: Signal transducer and activator of transcription 3 (STAT3) is essential for cell signaling in response to extracellular stimuli, and its overactivation is a hallmark of inflammation and tumorigenesis. The differential mechanisms underlying the physiological and pathological regulation of STAT3 remain elusive. Here we demonstrate that cryptic splice sites in STAT3 generate heterogeneous isoforms with or without a single amino acid S701 (wS701/ΔS701), with the latter being substantially upregulated in colon cancers. Intrinsic S701 undergoes reversible phosphorylation catalyzed by mTOR complex 1 (mTORC1) and protein phosphatase 2A (PP2A). Upon inflammatory stimulation, precursor phosphorylation at S701 sequesters Y705 phosphorylation by interfering with the access of janus kinase 1/2 (JAK1/2), and restricts STAT3 overactivation. In contrast, the ΔS701 isoform is hyperactive due to absence of this self-restricting mechanism. Deletion of S701 in mice increases susceptibility to colonic inflammation and tumorigenesis. Pharmacological inhibition of PP2A sustains S701 phosphorylation, and alleviates colon inflammation in wild-type but not in ΔS701 mice. Our findings highlight the importance of STAT3 heterogeneity in human diseases.

overall_design: To investigate function of Stat3_ΔS701 isoform in DSS-induced IBD in mice, we established ΔS701 mice. We then treated WT and ΔS701 mice with DSS for 3 days and collected their colons. Total RNA was extracted from the colon of WT and ∆S701 mice after 3-day DSS treatment using TRNzol Universal reagent and then subjected to RNA-seq.

first: Meng

first: Shu

last: Zhong

first: Zhenzhen

last: Lai


title: Per- and polyfluoroalkyl substances (PFAS) suppress macrophage alternative activation to disrupt hepatic lipid metabolism [RNA-seq II]

first: 丽娟

last: 游

institute: 国家食品安全风险评估中心

first: Lijuan

last: You

first: Jing

last: Yang

first: Hui

first: Xiaohong

last: Wang

first: Yaru

last: Tian

first: Zhisen

last: Zhuang

first: Yi

last: Wan


title: Parkinson’s disease-associated shifts between DNA methylation and DNA hydroxymethylation in human brain

city: Piscataway

first: Alison

last: Bernstein

state: NJ

address: 170 Freylinghuysen Rd

department: Pharmacology and Toxicology

institute: Rutgers University

type: Methylation profiling by genome tiling array

summary: The large majority of Parkinson’s disease (PD) cases are due to a complex interaction between aging, genetics, and environmental factors and epigenetic mechanisms are thought to act as critical mediators of the complex interactions between aging, genetics, the environment, and disease. Evidence for a role of epigenetic regulation in PD has been building, particularly for DNA modifications, over the past 10-15 years. 5-methylcytosine (5mC) is one of the most well-studied epigenetic marks. However, there is a growing recognition that 5-hydroxymethylcytosine (5hmC) plays an important role in gene regulation as it has tissue-, cell-, and age-specific patterns across the genome distinct from 5mC. 5hmC occurs at its highest levels in the brain and is now thought to be particularly important in the central nervous system, particularly in the response to neurotoxicants. While multiple studies to date have explored the role of DNA modifications in PD, most studies have relied on bisulfite (BS) conversion, which does not distinguish between 5mC and 5hmC. Only a handful of existing studies focus specifically on 5hmC; these initial studies support a role for 5hmC in regulation of expression of genes important for PD pathogenesis and indicate that additional studies are warranted. Here, to identify changes in 5hmC in PD, we profiled 5hmC and 5-methylcytosine (5mC) simultaneously in an enriched neuronal population from PD post-mortem parietal cortex. This study expands on our previously published epigenome-wide association study (EWAS) performed on DNA isolated from neuron-enriched nuclei from human postmortem parietal cortex from the Banner Sun Health Research Institute Brain Bank. Because we previously used BS conversion and the Illumina MethylationEPIC array, we were unable to differentiation between 5mC and 5hmC. Here, we utilized additional DNA isolated from the samples and performed oxidative BS (oxBS) conversion paired with the EPIC array to specifically measure 5mC and estimate 5hmC from paired BS-oxBS data. From this, we analyzed both 5hmC and 5mC as related measures using our recently proposed mixed effects model for reconciling base-pair resolution 5mC and 5hmC data.

overall_design: This data includes paired BS/oxBS data for 56 male subjects used in the final analyses, including 29 control and 27 PD subjects, and 44 subjects where data did not pass QC and filtering steps and/or sex was female (female subjects were excluded due to small sample size and lack of statistical power after QC and filtering steps).

first: Joseph

last: Kochmanski

first: Juliana

last: Choza

first: Mahek

last: Virani

first: Nathan

middle: C

last: Kuhn

first: Marie

last: Adams


title: CEBPB drives endothelial pathological phenotype and promotes atherosclerosis by directly upregulating TGFBR1 expression [RNA-seq]

first: Cong

last: Qiu

summary: Endothelial cell (EC) dysfunction is crucial in chronic vascular inflammation and diseases like atherosclerosis. An unknown endothelial pathological phenotype potentially driving atherosclerosis was hinted in our previous study. However, the detailed characterizations and underlying molecular mechanisms remain unclear. In the present study, using single-cell RNA sequencing, the new endothelial pathological phenotype was defined by high expression of fibroblast markers, extracellular matrix, and inflammatory genes, concurrently with a rapid decline in endothelial markers. By performing RNA-seq, we found that increased CEBPB contributes to the fibroblast and inflammatory feature of these atherogenic ECs. Further analysis revealed that IL-1β-induced high expression of CEBPB triggers TGF-β signaling and subsequent regulation of downstream genes. This occurs through direct interaction of CEBPB with the promotor region of TGF-β receptor type I (TGFBR1), resulting in its upregulation. Furthermore, exacerbating atherosclerotic plaque area, enhanced vascular inflammation and increased endothelial TGFBR1 expression were confirmed by endothelial overexpression of CEBPB in vivo. These findings suggest endothelial CEBPB functions as a novel regulator of TGFBR1, driving endothelial pathological phenotype, promoting vascular inflammation and atherosclerosis.

overall_design: RNA sequencing was performed on HAECs in 2 groups, each of which contained three biological replicates. Cells were infected by adenovirus overexpressing CEBPB and mock plasmid.

first: Linge

last: Fan

first: Yingyi

last: Zhu


title: Expression data from human mesenchymal stromal cells from osteoarthritis donors treated with the chemokine CCL25

city: Berlin

first: Julia

last: Sonnleitner

address: Charitéplatz 1

country: Germany

institute: Charité - Universitaetsmedizin Berlin

summary:
Osteoarthritis (OA) is a chronic, multifactorial disease of the joint, which involves synovial inflammation, bone remodeling, and cartilage destruction. It poses a serious burden of global disease, with an incidence rate that has increased by 9.3% between 1990 and 2017. In situ tissue engineering represents a strategy that takes advantage of physiological repair mechanisms and seeks to enhance them. A strong focus has been placed on mesenchymal stromal cells (MSCs) as a source for endogenous regeneration, as they have been shown to contribute to tissue recovery in OA and other pathologies like myocardial infarction and injured liver or pancreas tissue. CCL25, also known as TECK, is a chemokine that has been prevsiously shown to recruit MSCs.
We used a microarry analysis to elucidate the broader effect of the chemokine CCL25 on mesenchymal stromal cells derived from patients with osteoarthritis.

overall_design: Mesenchymal stromal cells treated with 1000 nM CCL25 were analyzed in comparison to mesenchymal stromal cells not treated with CCL25. Each group consists of 3 biological replicates.

first: Tilo

last: Dehne

first: Katja

last: Gulich

first: Axel

last: Pruss

first: Carsten

last: Perka

first: Angelika

last: Gursche

first: Daniel

last: Kendoff

first: Michael

last: Sittinger

first: Shabnam

last: Hemmati-Sadeghi


title: The Mechanism by which HIF-2a Promotes MASLD

city: Zhuhai

first: Yang

last: Zhe

address: Kangning Street No.79

institute: Jinan University

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) is characterized by imbalance of lipid metabolism and autoimmune inflammation. The relationship between Hypoxia-inducible Factor 2α (HIF-2α) and the progression of MASLD has been well-documented. However, the mechanistic linkage between HIF-2α and steatohepatitis progression remains largely elusive. Here, hepatocyte-specific HIF-2α knockout mice were used to identify underlying pathophysiological relevance in MASLD. Through multiple gain- and loss-of-function experiments in primary hepatocytes and established human hepatocyte cell lines to investigate the molecular mechanism of HIF-2α in MASLD progression. Compared to their wild-type littermates, hepatocyte-specific HIF-2α knockout mice exhibited a substantial reduction in hepatic steatosis and inflammatory pathway induced by high fat diet (HFD). Furthermore, the HIF-2ɑ deficiency in primary hepatocytes and both L02 and MIHA cell lines markedly inhibited the lipid accumulation, inflammation and endoplasmic reticulum stress in vitro under FFAs challenge. Mechanistically, HIF-2 directly bound to the promoter region of protein kinase RNA-like ER kinase (PERK), leading to the activation of the activating transcription Factor 4 (ATF4) signaling under metabolic stress, thereby aggravating lipogenesis while inhibiting lipid oxidation in hepatocytes.These data indicate that HIF-2α acts as a contributing factor to MASLD progression via ATF4 signaling.

overall_design: To investigate the role of HIF-2α in the progression of MASLD, we performed RNA-seq on liver tissues of HIF-2α-deficient mice subjected to a 16-week HFD

first: Zhe

last: Yang

first: Hongyun

last: Lu


title: Comparison of mesenchymal stromal cells derived from osteoarthritis and non-osteoarthritis patients

summary:
Osteoarthritis (OA) is a chronic, multifactorial disease of the joint, which involves synovial inflammation, bone remodeling, and cartilage destruction. It poses a serious burden of global disease, with an incidence rate that has increased by 9.3% between 1990 and 2017. In situ tissue engineering represents a strategy that takes advantage of physiological repair mechanisms and seeks to enhance them. A strong focus has been placed on mesenchymal stromal cells (MSCs) as a source for endogenous regeneration, as they have been shown to contribute to tissue recovery in OA. A potential senescent phenotype of OA MSCs could impose a major limitation on their regenerative potential.
MSCs derived from the bone marrow of osteoarthritis and non-osteoarthritis patients were analyzed upon their expression of senescence markers using an affymetrix microarray to explore their suitability for an in situ tissue engineering approach.

overall_design: 3 biological replicates from OA and non-OA (ND) donors each were analyzed upon expression of selected senescence markers.


title: Multiomics analysis of differentiating human cholangiocyte organoids

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

summary: We aim to uncover the molecular mechanisms driving liver cellular plasticity in human chronic liver disease. We first derived intrahepatic cholangiocytes organoids (ICOs). The resulting organoid lines were then differentiated into biphenotypic cells expressing hepatocytes markers mimicking a process occurring during chronic injury in vivo. We then utilised multi-omics single nuclei RNA sequencing (snRNAseq) and assased for transcriptomics signatures and transposase-accessible chromatin (ATAC) expression to uncover the molecular pathways and the epigenetic regulations required for the in vitro conversion of cholangiocytes into hepatocytes.These analyses allowed for the identification of transcription factors involved in this process. Our analysis also suggested transdifferentiation could represent the main process by which hepatocytes are produced during liver regeneration.

overall_design: To achieve our aims we used human explant liver  tissue to generate organoids. These organoids were grown under cholangiocyte in vitro conditions and then switched into hepatocyte differentiation media. This process was analysed using snRNAseq and snATACseq. The molecular pathways identified relevant to the transdifferentiation were validated in vitro and in vivo using a corresponding human RNAsequencing database.

first: Galanakis

last: Vasileios

first: Gribben

last: Christopher

first: Munteanu

last: Andi

first: Mohorianu

last: Irina

first: Vallier

last: Ludovic


title: ATP11C Knock down in clone E3 from colon cancer CC14 primary culture

first: Celine

last: Delucinge

summary: In order to explore the role of ATP11C in the metastatic potential of the highly metastatic clone E3 we knocked it down using an shRNA in a lentiviral backbone. Here we aimed to explore the transcriptome of E3 cells on which the expression of ATP11C has been knocked down.

overall_design: E3 clonal cells from primary colon cancer cells (CC14) were infected with pLKO.1 empty backbone as control or with shATP11C, 10 days after infection, cells were harvested and total RNA extracted using TRIzol Reagent (Ambion) following the manufacturer's protocol. Each condition was independently processed in triplicates and the libraries were prepared using Illumina TruSeq protocols. The samples were sequenced on a HiSeq Illumina 4000 machine with 50bp reads followed by standard analyses.

first: Ariel

last: Ruiz i Altaba

first: Yann

last: Tapponnier

first: Céline


title: CSAG1 Knock out in clone E3 from colon cancer CC14 primary culture

summary: In order to explore the role of CSAG1 in the metastatic potential of the highly metastatic clone E3 we knocked it out using CRISPR/Cas9 system . Here we aimed to explore the transcriptome of E3 cells on which the expression of CSAG1 has been supressed.

overall_design: CSAG1 KO mutations were induced using CRISPR/Cas9 system in E3 clonal cells from primary colon cancer cells (CC14). These cells were cloned and mutations analysed by sequencing. One out of frame mutation with  ATG deletion was chosen and functionnaly tested. CSAG1 KO cells were thenharvested and total RNA extracted using TRIzol Reagent (Ambion) following the manufacturer's protocol. Each condition was independently processed in triplicates and the libraries were prepared using Illumina TruSeq protocols. The samples were sequenced on a HiSeq Illumina 4000 machine with 50bp reads followed by standard analyses.


title: Analysis of gene expression patterns tracking increasing metastatic potential of different clones from  colon cancer CC14 primary culture

summary: In order to find genes the expression of which follows the metastatic potential of different clonal cultures from the colon cancer heterogeneous CC14 primary culture. Each of the clonal culture has a different and defined metastatic potential as tested by transfilter assay.

overall_design: Total RNA from each clonal culture extracted using TRIzol Reagent (Ambion) following the manufacturer's protocol. Each condition was independently processed in triplicates and the libraries were prepared using Illimina TruSeq protocols. The samples were sequenced on a HiSeq Illumina 4000 machine with 50bp reads followed by standard analyses.


title: Analysis of gene expression patterns tracking increasing metastatic potential of different clones from  colon cancer CC36 primary culture

summary: In order to find genes the expression of which follows the metastatic potential of different clonal cultures from the colon cancer heterogeneous CC36 primary culture. Each of the clonal culture has a different and defined metastatic potential as tested by transfilter assay.


title: Biomarkers of colorectal precancerous lesions

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

summary: Study of expression profiles of human colorectal adenoma tissue with paired samples of adjacent unaffected mucosa. The aim of the study was to identify novel candidate biomarkers for precancerous stages of colorectal cancer.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for adenoma tissue and adajcent unaffected mucosa.

first: Anna

last: Siskova

first: Kerstin

last: Huebner

first: Chuanpit

last: Hampel

first: Alessio

last: Naccarati

first: Barbara

last: Pardini

first: Carol

last: Geppert

first: Jan

last: Prochazka

first: Jiri

last: Jungwirth

first: Tomas

last: Hucl

last: Kral

first: Ludmila

last: Vodickova

first: Annemarie

last: Gehring

first: Katharina

last: Erlenbach-Wuensch

first: Arndt

last: Hartmann

first: Katerina

last: Honkova

first: Pavel

last: Vodicka

first: Veronika

last: Vymetalkova

first: Regine

last: Schneider-Stock


title: Autoantibody-induced arthritis pain caused by a sustained type I interferon signaling

city: Solna

first: Patrik

last: Ernfors

address: Biomedicum, Solnavägen 9

department: MBB/Molneuro

country: Sweden

institute: Karolinska Institutet

summary: Pain in rheumatoid arthritis is highly debilitating, impacts quality of life and lacks adequate treatment options. Although the presence of pathogenic autoantibodies and systemic and joint inflammation are distinctive features of the disease, the molecular and neuronal basis of pain remains unclear. Here, we identify the molecular mechanism and causative neurons for autoantibody-induced pain in mice. Single-cell RNA sequencing analysis during arthritis pain revealed interferon-stimulated genes, with a persistent nociceptor neuron sensitization, local inflammation and a causative role of interferons acting on polymodal GFRa3-positive C-fiber-nociceptors, as the origin of pain. Consistently, interferon inhibition blocked gene expression alterations and prevented onset as well as reversed established and residual arthritis pain. The discovered pain-causative mechanism may represent a novel therapeutic approach for treatment of pain in rheumatoid arthritis.

overall_design: Mouse dorsal root ganglion cells isolated at different timepoints after induction of experimental arthritis and analyzed using scRNA-seq

first: Jie

last: Su

first: Jussi

last: Kupari

first: Ming-Dong

middle: D

last: Zhang


title: An Investigation of the Anticancer Mechanism of Caesalpinia sappan L. Extract Against Colorectal Cancer by Integrating a Network Pharmacological Analysis and Experimental Validation

status: Public on Dec 09 2025

city: Daejeon

first: Heerim

last: Yeo

address: 99, Daehak-ro, Yuseong-gu

institute: Chungnam National University

summary: Caesalpinia sappan L. has exhibited various pharmacological effects, yet its anticancer activities against colorectal cancer (CRC) and underlying molecular mechanisms remain unclear. This study investigated the anticancer properties of an ethanol extract of C. sappan L. (CSE) against CRC cells, focusing on the identification of bioactive compounds and their mechanisms of action. A network pharmacology analysis was conducted to identify potential CRC targets and bioactive compounds of CSE, using LC-MS for compound identification. The anticancer effects of CSE were then validated through in vitro and in vivo models of CRC. The network pharmacological approach identified 87 overlapping genes between CSE targets and CRC-related genes, with protein–protein interaction analysis highlighting 33 key target genes. CSE inhibited cell proliferation in human CRC cell lines, including HCT 116, KM12SM, HT-29, and COLO 205, and induced apoptosis via caspase 3/7 activation. Western blot analyses confirmed the modulation of critical signaling pathways, including STAT3, AKT, and mitogen-activated protein kinases. Furthermore, CSE significantly suppressed tumor growth in MC38 CRC-bearing mice. These findings suggest that CSE possesses substantial potential as a natural anticancer agent for CRC treatment, highlighting the need for further exploration in therapeutic development.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MC38 tumor tissues by CSE treatment

first: Mibae

last: Jeong

first: Jaemoo

last: Chun

first: Sang-Min

last: Park

first: Se Won

first: In Jin

last: Ha

first: Bonglee

last: Kim

first: Mi-Kyung


title: STING–IFN–CH25H lipid axis links innate immune activation to tau pathology [scRNA-seq]

city: NEW YORK

first: hao

last: chen

state: NY

address: 413 E 69th ST

department: Brain and mind research institute

institute: Weill Cornell Medicine

summary: Genetic risk for Alzheimer’s disease is strongly enriched in pathways governing microglial activation and cholesterol metabolism, yet how these processes converge to drive neurodegeneration remains unclear. Here, we identify the oxysterol 25-hydroxycholesterol (25-HC) as a pathogenic lipid downstream of the cGAS-STING–IFN pathway. In models of tau pathology, interferon signaling induces Cholesterol 25-hydroxylase (CH25H) expression in microglia. Ch25h deletion in female P301S mice suppressed tau aggregation, preserved synapses, prevented brain atrophy, and rescued memory. Mechanistically, loss of CH25H disrupted STING trafficking, attenuated IFN activation, dampened self-perpetuating microglial inflammation. Strikingly, 25HC directly accelerated tau propagation in human iPSC derived neurons. It also disrupted lysosomal and mitochondrial lipid composition, driving cholesteryl ester accumulation and promoting apoptosis under tau-induced stress. These findings define a STING–IFN–CH25H lipid axis that bridges innate immune activation to tau pathology and toxicity, offering a tractable therapeutic pathway for inflammation-driven neurodegenerative conditions.

overall_design: Droplet-based single nuclear RNA sequencing of mouse hippocampus of Ch25h+/+ Tau-, Ch25h-/- Tau-, Ch25h+/+ Tau+ and Ch25h-/- Tau+.

first: Hao

last: Chen

first: Li

last: Fan

first: Manying

last: Wong

first: Yohannes

last: A. Ambaw

first: Jingjie

last: Zhu

first: Kendra

last: Norman

first: Pearly

last: Ye

first: Nessa

last: Foxe

first: Daphne

first: Yuansong

last: Wan

first: Mahalashmi

last: Srinivasan

first: Sue-Ann

last: Mok

first: Laura

last: Beth J McIntire

first: Tobias

last: C. Walther

first: Robert

last: V. Farese Jr.

last: Gan

first: Wenjie

last: Luo


title: STING–IFN–CH25H lipid axis links innate immune activation to tau pathology [RNA-seq]

first: hao

last: chen

overall_design: Bulk RNA sequencing of mouse hippocampus of Ch25h+/+ Tau-, Ch25h-/- Tau-, Ch25h+/+ Tau+ and Ch25h-/- Tau+.


title: Single-nucleus and spatial transcriptomic profiling of human lung tissue in chronic obstructive pulmonary disease (COPD)

city: New Haven

first: Maor

last: Sauler

state: CT

address: 300 Cedar Street

department: Section of Pulmonary, Critical Care, and Sleep Medicine

institute: Yale School of Medicine

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

overall_design: Refer to individual Series


title: Beckwith-Wiedemann syndrome and large offspring syndrome involve alterations in methylome, transcriptome, and chromatin configuration [Hi-C]

city: Columbia

first: Rocío

middle: Melissa

last: Rivera

state: MO

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: University of Missouri, Columbia

summary: Beckwith-Wiedemann Syndrome (BWS) is the most common epigenetic overgrowth syndrome, caused by epigenetic alterations on chromosome 11p15. In ~50% of patients with BWS, the imprinted region KvDMR1 (IC2) is hypomethylated. Nearly all children with BWS develop organ overgrowth and up to 28% develop cancer during childhood. The global epigenetic alterations beyond the 11p15 region in BWS are not currently known. Uncovering these alterations at the methylome, transcriptome, and chromatin architecture levels are necessary steps to improve the diagnosis and understanding of patients with BWS. Here we characterized the complete epigenetic profiles of BWS IC2 individuals together with the animal model of BWS, bovine large offspring syndrome (LOS). A novel finding of this research is the identification of two molecular subgroups of BWS IC2 individuals. Genome-wide alterations were detected for DNA methylation, transcript abundance, alternative splicing events of RNA, chromosome compartments, and topologically associating domains (TADs) in BWS and LOS, with shared alterations identified between species. Altered chromosome compartments and TADs were correlated with differentially expressed genes in BWS and LOS. Together, we highlight genes and genomic regions that have the potential to serve as targets for biomarker development to improve current molecular diagnostic methodologies for BWS.

overall_design: Hi-C sequencing for skin fibroblast primary cells derived from five control and six LOS bovine day 105 fetuses.

first: Yahan

last: Li

first: Ping

last: Xiao

first: Frimpong

last: Boadu

first: Anna

last: Goldkamp

first: Snehal

last: Nirgude

first: Jianlin

last: Cheng

first: Darren

last: Hagen

first: Jennifer

last: Kalish


title: Systems mapping of intra-donor cross-tissue T cell clonal expansion and tissue adaptation in the gut-liver-blood axis

city: St. Petersburg

first: Martin

last: Trapecar

state: FL

address: 600 Fifth Street South

department: Medicine and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

summary: Single-cell RNA sequencing with paired TCR sequencing was performed on CD3+ T cells isolated from matched colon epithelium, colon lamina propria, liver, and peripheral blood samples from three healthy human donors. This study reveals tissue-specific T cell transcriptional programs and cross-tissue clonal relationships, demonstrating that expanded clones adapt their gene expression to local tissue environments while maintaining core identity markers.

overall_design: CD45+CD3+ T cells were FACS-sorted from colon intraepithelial layer (IEL), colon lamina propria (LP), liver, and peripheral blood (PB) from 3 healthy donors. Single-cell RNA-seq and TCR-seq libraries were generated using 10x Genomics Chromium Next GEM Single Cell 5' v2 kit with VDJ enrichment.

first: Ran

last: Ran

first: Merve

last: Uslu

first: Mohda

last: Siddiqui

first: Douglas

last: Brubaker


title: Cardiorenal heart failure with preserved ejection fraction is caused by a reversible rise of mineralocorticoid-induced fibroblast subtypes

city: Freiburg

first: Achim

last: Lother

state: --- Select One ---

address: Albertstr. 25

department: Institute of experimental and clinical Pharmacology and Toxicology,

institute: University of Freiburg

summary: Heart failure with preserved ejection fraction (HFpEF) is driven by co-morbidities. While specific treatments to enable recovery of HFpEF are lacking, recent clinical trials indicate beneficial effects of mineralocorticoid receptor (MR) antagonists. Here, we performed single nucleus RNA sequencing in an aldosterone/salt-induced model of cardiorenal HFpEF in mice and compared it to the high fat diet/L-NAME model of cardiometabolic HFpEF. We found a fibroblast subtype induced that is distinct from the classical myofibroblast observed in heart failure with reduced ejection fraction. Notably, after aldosterone withdrawal the HFpEF-like phenotype fully recovered. This was linked to a restored expression of MR target genes and an upregulation of collagen III, VI, and XV in fibroblasts during recovery. MR deletion from fibroblasts prevented cardiac remodeling and diastolic dysfunction, confirming the central role of fibroblast MR in cardiorenal HFpEF. In summary, our study reveals fibroblast gene expression signatures in heart failure from different causes that may determine the response to pharmacological treatment and potential for recovery.

overall_design: single nucleus RNAseq of mouse left ventricular free-wall tissue after aldosterone infusion with and without recovery and untreated control

first: David

last: Meral

first: Argen

last: Mamazhakypov

first: Duygu

last: Koca

first: Ramona

last: Emig

first: Rémi

last: Peyronnet

first: Sebastian

last: Preissl


title: Microvascular smooth muscle cells exhibit divergent phenotypic switching responses to platelet-derived growth factor and insulin-like growth factor 1

city: Oklahoma City

first: Shannon

middle: M.

last: Conley

state: Oklahoma

address: 940 Stanton L Young Blvd BMSB 100/105

department: Cell Biology

institute: University of Oklahoma Health Campus

summary: Objective: Vascular smooth muscle cell (VSMC) phenotypic switching is critical for normal vessel formation, vascular stability, and healthy brain aging. Phenotypic switching is regulated by mediators including platelet derived growth factor (PDGF)-BB, insulin-like growth factor (IGF-1), as well as transforming growth factor-β (TGF-β) and endothelin-1 (ET-1), but much about the role of these factors in microvascular VSMCs remains unclear. Methods: We used primary rat microvascular VSMCs to explore PDGF-BB- and IGF-1-induced phenotypic switching. Results: PDGF-BB induced an early proliferative response, followed by formation of polarized leader cells and rapid, directionally coordinated migration. In contrast, IGF-1 induced cell hypertrophy, and only a small degree of migration by unpolarized cells. TGF-β and ET-1 selectively inhibit PDGF-BB-induced VSMC migration primarily by repressing migratory polarization and formation of leader cells. Contractile genes were downregulated by both growth factors, while other genes were differentially regulated by PDGF-BB and IGF-1. Conclusions: These studies indicate that PDGF-BB and IGF-1 stimulate different types of microvascular VSMC phenotypic switching characterized by different modes of cell migration. Our studies are consistent with a chronic vasoprotective role for IGF-1 in VSMCs in the microvasculature while PDGF is more involved in VSMC proliferation and migration in response to acute activities such as neovascularization. Better understanding of the nuances of the phenotypic switching induced by these growth factors is important for our understanding of a variety of microvascular diseases.

overall_design: RNAseq profiling of wildtype S31 rat primary vascular smooth muscle cells serum starved and treated with recombinant rat PDGF-BB (25 ng/ml) or with  recombinant human IGF-1 (25 ng/ml). Control cells received fresh serum-free medium lacking any added growth factors. Total RNA was extracted at 24 hours post treatment for (control & IGF-1) and 48 hours post treatment (PDGF-BB).

first: Marisa

last: Bickel

last: Sherry

first: Elizabeth

last: Bullen

first: Michaela

last: Vance

first: Ken

last: Jones

first: Eric

middle: W

last: Howard


title: Single-Cell RNA Sequencing Analysis of Kidney Organoids derived in 2D or 3D from SCTi004-A hiPSC line using the STEMdiff™ Kidney Organoid Kit

city: Vancouver

first: STEMCELL

last: Technologies

state: BC

address: 1618 Station st

department: RND

country: Canada

institute: STEMCELL Technologies

summary: Kidney organoids differentiated from human pluripotent stem cells are complex structures that capture glomerular, tubular and mesenchymal cell types of the developing human kidney. The STEMdiff™ Kidney Organoid Kit is a serum-free cell culture medium system for the efficient and reproducible generation of kidney organoids in 2D using a simple, 18 day, two-stage differentiation protocol. We recently also showed compatibility of this kit for the generation of 3D organoids using single cell dissociation and re-aggregation on Day 7. Here we evaluate kidney organoids derived from the commercially available hiPSC line SCTi004-A with the STEMdiff™ Kidney Organoid Kit for their cellular diversity and transcriptomic profiles. Datasets were created for kidney organoids differentiated in the 2D and 3D format.

overall_design: hiPSC line SCTi004-A, previously maintained in mTeSR™ Plus maintenance medium, was differentiated to kidney organoids at p35 with the STEMdiff™ Kidney Organoid Kit. Organoids were generated in 2D format as described in the manufacturer PIS or as 3D aggregates for 18 days, with the addition of CloneR™2 at the time of seeding. At the end of differentiation, 3D organoids were dissociated with cold 0.05% trypsin and DNase, with multiple rounds of incubations and triturations until a single cell suspension was achieved. For the 2D format, tubules were enriched by a crude removal of the mesenchymal monolayer by a brief incubation with trypsin and forceful trituration. The remaining tubules were dissociated to single cells with fresh trypsin and DNase with multiple rounds of incubations and triturations. Single cell capture and library prep was performed using the Pipseq V T10 3’ Single Cell RNA workflow.

first: Nina

last: Quiskamp

first: Eloi

last: Mercier

first: Ryan

last: Bailey

first: Colleen

last: Umali


title: The protein phosphatase 2C domain contributes to the pathobiological function of adenylyl cyclase in Cryptococcus neoformans

city: Seoul

first: Yong-Sun

last: Bahn

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

department: Department of Biotechnology

institute: Yonsei university

summary: Adenylyl cyclase (AC) is the central regulator of cAMP signalling in fungal pathogens, yet fungal ACs uniquely contain a protein phosphatase 2C (PP2C) domain whose function remains unclear. Here, we characterise the PP2C domain of the AC Cac1 in the human pathogen Cryptococcus neoformans. Structural and biochemical analyses show that Cac1-PP2C adopts a non-canonical scaffold but functions as a Ser/Thr-specific metalloenzyme. Deletion of the PP2C or AC catalytic (ACC) domain demonstrated that PP2C is required for full Cac1 activity, influencing melanin and capsule synthesis, sexual differentiation, titan cell formation, and cell wall integrity. Notably, the PP2C-null mutant induced Th2-biased immunity and extensive pulmonary damage yet failed to cause mortality in mice. Integrated transcriptomic and phosphoproteomic analyses further revealed shared and domain-specific signalling outputs mediated by PP2C and ACC. This study provides the first comprehensive characterisation of a fungal AC-linked PP2C domain and defines its pivotal role in C. neoformans pathobiology

overall_design: RNA extraction was performed from cells grown in the same manner as described for phosphoproteome analysis. Briefly, 10 ml cultures for five strains (wild-type H99, cac1Δ, cac1Δ::CAC1, cac1Δ::CAC1PP2CΔ, cac1Δ::CAC1ACCΔ) were grown in triplicates in two media conditions, YNB and YNB + 2% glucose.

first: Soojin

last: Yu

first: Seong-Ryong

first: Myung Kyung

last: Choi

first: Jae-Hyung

last: Jin

first: Vikas

last: Yadav

first: Hee Seong

first: Eui-Seong

last: Kim

first: Hyun-Woo

first: Jae-Seok

last: Jeong

first: Do-Kyun

first: Joseph

last: Heitman

first: Hyun-Soo

last: Cho

first: Kyung-Tae

last: Lee


title: Spatiotemporal dysregulation of plasma fibrinogen synthesis unveils hepatic initiating role in MS and EAE pathogenesis

city: Xian

first: Jiaji

last: Lin

address: No. 1. XinSi Road

department: Neurology

institute: Forth Military Medicial University

summary: Fibrinogen, Multiple sclerosis, Liver, EAE, Neutrophils

overall_design: Liver transcriptome profiling from RNA-seq data was analyzed using HISAT2, HTSeq, and DESeq2.

first: Xinyan

last: Han

first: Chuanping

last: Zhao

first: Yanan

last: Bai

first: Weitai

last: He

first: Xiaoli

last: Liu

first: Jun

last: Guo


title: To study the expression profile change after treatment of ZN-c5 and 4-OH Tamaxifen in MCF-7 cells

city: SAN DIEGO

first: Jianhui

last: Ma

state: CA

address: 10275 Science center Dr, Suite 200

institute: Zentalis Pharmarceuticals

summary: Endocrine therapy has proven to be beneficial for patients with estrogen receptor (ER) positive, HER2 negative (ER+/HER2-) breast cancer; however, de novo or acquired resistance remains a major clinical challenge. Upon progression, many of the cancers continue to be ER dependent, highlighting the opportunities for novel ER targeting therapies. Fulvestrant, a selective estrogen receptor degrader (SERD) that antagonizes and degrades ER simultaneously, has demonstrated activity in ER+/HER2- breast cancers the ability to overcome endocrine resistance. Fulvestrant has limitations including challenging administration by intramuscular injection and poor bioavailability, resulting in sub-optimal drug exposure, hence several next generation oral SERDs with improved drug properties have been developed and are currently being evaluated in the clinic for their therapeutic benefit. Here, we describe the discovery of ZN-c5, an orally bioavailable SERD with favorable pharmacokinetic properties and potent activities against both wild-type and mutant ER. In vivo studies showed that ZN-c5 treatment resulted in significant tumor growth inhibition in a variety of breast cancer models and patient-derived xenograft models that harbor ESR1 mutations. Combination with CDK4/6 inhibitors or PI3K pathway inhibition enhanced anti-tumor effects compared with single agent alone. ZN-c5 also demonstrated bone protective effect as observed in a mouse osteoporosis model. These data support the clinical utility of ZN-c5 as monotherapy and as a combination therapy for patients with ER+/HER2- breast cancers. While encouraging plasma exposure and tolerability have been observed for ZN-c5 in patients, further studies are needed to optimize its therapeutic efficacy.

overall_design: MCF-7 cells were seeded in phenol red free medium supplemented with 10% charcoal stripped FBS. 48 hours later, the cells were treated with ZN-c5 or 4-OH tamoxifen at 1 µM for 24 hours. RNA was extracted using the methods described above. The Poly (A) tail RNA selection strand-specific cDNA library was prepared by LC Sciences. The aggregated gene counts were used for differential gene expression analyses using StringTie by calculating FPKM. Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

first: Fernando

last: Donate

first: Ahmed

last: Samatar


title: Proteinase 3 Drives Murine Diabetic Kidney Disease by Mediating Caspase-3-dependent Apoptosis of Podocytes

city: Guangzhou

first: DEWEI

last: YE

state: Guangdong

address: 280 Waihuan East Road, Guangzhou Higher Education Mega

institute: Guangdong Pharmaceutical University

summary: Podocytes play a pivotal role in maintaining homeostasis of the glomerular filtration barrier. The underlying mechanism is unclear but podocyte loss represents a critical event that contributes to the development of diabetic kidney disease (DKD). Proteinase 3 (PR3) is a serine protease with selective high abundance in myeloid cells and pleiotropic effects on the regulation of innate immunity. Here, we demonstrate that PR3 abundance in the kidney was markedly increased, predominantly in podocytes, in a mouse model of DKD. Genetic ablation of PR3 significantly attenuated severe proteinuria, mesangial matrix expansion, and podocyte injury in diabetic mice. The present study aimed to investigate the role of PR3 in glomerular podocytes in DKD.

overall_design: Comparative gene expression profiling analysis of RNA-seq data using renal glomeruli from PR3 KO and WT control mice with diabetic kidney disease

first: Dewei

last: Ye

first: Jufei

last: Li

first: Mengjie

last: Kong

first: Fangyu

last: Wan


title: The antibacterial factor APOL3 couples lysosomal damage to mitochondrial DNA efflux and type I IFN induction

city: New York

first: Ryan

last: Gaudet

institute: Columbia Unversity

summary: Lysosomal damage is an endogenous danger signal to the cell, but its significance for innate immunity and how specific signaling pathways are engaged by this stressor remain unclear. Here, we uncover an immune-inducible pathway that connects lysosomal damage to mitochondrial DNA (mtDNA) efflux and type I IFN production. Lysosomal damage elicits mitochondrial outer membrane permeabilization (MOMP) via BAK/BAX macropores; however, the inner mitochondrial membrane (IMM) prevents wholesale mtDNA release in resting cells. Priming with type II IFN (IFN-γ) induced the antibacterial effector apolipoprotein L-3 (APOL3), which upon transient lysosomal damage, targets mitochondria undergoing MOMP and selectively permeabilizes the IMM to enhance mtDNA release and activate cGAS/STING signaling. Biochemical and cellular reconstitution revealed that analogous to its bactericidal detergent-like mechanism, APOL3 solubilizes cardiolipin to permeabilize the IMM. Our findings illustrate how cells use an antibacterial protein to expedite the breakdown of endosymbiosis and facilitate a heightened response to injury and infection.

overall_design: RNA-seq of HeLa NTC and APOL3-/- cells primed with or without IFN-γ, followed by LLOME or DMSO treatment and 8 h recovery.

first: Dominic

last: Ritacco

first: Hamna

last: Shahnawaz

first: Antonia

last: Oduguwa

first: Jacob

last: Hawk

first: Brianna

last: Vizcaino

first: Donna

last: Farber


title: Modeling the chondrocyte-derived osteoblasts formation process reveals its molecular signature and regulation network

city: Muenster

first: Marcos

last: Araúzo-Bravo

address: Rontgenstr. 20

department: Cell and Developmental Biology

institute: Max Planck Institute for Molecular Biomedicine

summary: Endochondral ossification is a physiological process related to the development of long bones, not only on the embryo phase, but also during postnatal development. Mouse cell lineage tracking studies and histology techniques focused on the metaphysis and growth plate area of long bones have described a phenotype transition from chondrocytes to bone cells. However, the molecular events involved in this phenotype transition is still undescribed. Aiming to reproduce this phenotype transition in in vitro cell culture context, primary mesenchymal progenitor cells have been isolated from femur heads, characterized, and cultured following a serial differentiation protocol, first using chondrogenic media and then osteogenic media. RNA samples were obtained at different cell culture time points and processed for RNAseq studies. Time points are: D7 corresponding to 7 days culture in chondrogenic media, D8 corresponding to samples obtained one day after switching to osteogenic media, D10 corresponding to samples obtained three days after switching to osteogenic media, and, D28 corresponding to samples obtained osteogenic terminal end point, compiling 7 days in chondrogenic media and 21 days in osteogenic media.

overall_design: The data D7 (D7), is performed with 3 replicates. The data D8 (D8), is performed with 3 replicates. The data D10 (D10), is performed with 3 replicates. The data D28 (D28), is performed with 3 replicates.

first: Raquel

last: Ruiz-Hernández

first: Amaia

last: Vilas-Zornoza

first: Felipe

last: Prosper

first: María

last: Caffarel

first: Daniela

last: Gerovska

first: Ander

last: Abarrategi


title: mRNA transcription in skeletal muscle drives growth and determines nuclear accretion

city: Cincinnati

first: Douglas

middle: P

last: Millay

state: OH

address: 3333 Burnet Ave Cincinnati, OH 45229

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital and Medical Center

summary: Multinucleation of skeletal muscle cells (myofibers) is a determinant of size and fundamental for function. While it is established that myofibers need to accrue adequate numbers of nuclei for optimal growth, the molecular circuitry linking myonuclei to growth and how myofibers signal the need for additional nuclei remains unknown. We found that growth is still possible after restriction of nuclear content in myofibers and this was associated with increased levels of RNA Polymerase II (Polr2a) leading to elevated mRNA content. Through development of a genetic mouse model where endogenous Polr2a is upregulated in myofibers, we established that increased transcriptional output is sufficient to drive functional growth of myofibers. Notably, we discovered that Polr2a overexpression curtails the need of additional nuclei for myofiber growth. These data highlight a previously neglected mechanism for functional muscle growth through increasing Polr2a-mediated transcription from the vast numbers of nuclei within myofibers, which could be leveraged to combat muscle wasting conditions.

overall_design: scATAC-Seq: Isolated nuclei from wild-type (n=3) and D2W(n=4) mice.

first: Fabian

last: Montecino-Morales

first: Cristofer

last: Calvo

first: Casey

middle: O

last: Swoboda

first: Alena

last: Bruenig

first: Alyssa

last: Cramer

first: Chengyi

last: Sun

first: Xin

last: Lin

first: Jennifer

last: Martin

first: Ramzi

last: Khairallah

first: Yarui

last: Diao

first: Vikram

last: Prasad


title: Large scale mapping of environmental-genetic interactions illustrates the dynamic nature of cell cycle and DNA repair regulation

city: Palo Alto

first: Ben

last: Herken

address: 3181 porter dr.

institute: Arc Institute

summary: Cells integrate exogenous and endogenous signals to grow, repair or die. This is likely achieved through dynamic functional associations between genes but measuring these relationships at scale is non-trivial. Here, we evaluate genetic associations in response to cell cycle interruption, genotoxic perturbation, and nutrient deprivation using conditional genetic interaction mapping in human cells. In five maps measuring ~250,000 genetic interactions or higher order environmental interactions, we discover wide-spread rewiring of relationships between genes, complexes, and ontologies across conditions. Specific bioprocesses drive the rewiring signal in each environmental state as highlighted in our findings that the TIP60 and PP2A complexes radically alter their interaction profiles after inhibition of ATR. This resource reveals numerous genetic relationships for the fields of DNA damage signaling, DNA repair, and cell cycle control and explores their context specificity. Our work advances a framework for using genetic interaction maps to explore environmental rewiring.

overall_design: Genomic sequencing data from single and paired sgRNA CRISPRi screens & Genomic sequencing data from bulk RNAseq experiments

first: Benjamin

first: Garrett

last: Wong

first: Anna

last: Makiniemi

first: Emma

last: Lundberg

first: Thomas

last: Norman

first: Luke

last: Gilbert


title: Environmental Epigenetic Variation During Giraffe Speciation and Evolution

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

type: Methylation profiling by high throughput sequencing

summary: The current study was designed to examine the potential role of environmental epigenetics (DNA methylation) in the phenotypic variation between two species of giraffe and a related species okapi (Okapi johnstoni). The Angolan giraffe (Giraffa giraffa angolensis), subspecies of the southern giraffe (G. giraffa), has a longer neck, and is more muscular and larger in size than the Kordofan giraffe (Giraffa camelopardalis antiquorum), subspecies of the northern giraffe (G. camelopardalis). Epigenetic changes generally have orders of magnitude higher frequency compared to genetic mutations and have been shown to regulate physiological traits in all species examined, from insects to humans. Observations obtained identify differences in the DNA methylation between the two giraffe species. The related okapi (Okapi johnstoni) is also epigenetically distinct from the giraffes. A role for environmental epigenetics in the speciation of giraffes is suggested and supporting data presented. Although genetic mutation change will also have a role, it occurs less frequently than epigenetic change. Genetic single nucleotide polymorphisms (SNPs) were found to have significantly lower frequency than epigenetic differences. Conclusions that environmental induced change in epigenetics will have a significant role in the evolution and speciation of these giraffes is consistent to the observations made in other species such as Darwin’s finches. Observations further support the Unified Theory of Evolution and Extended Evolutionary Synthesis, which integrates neo-Lamarckian and neo-Darwinian concepts.

sample_organism:
Okapia johnstoni
Giraffa giraffa angolensis
Giraffa camelopardalis antiquorum

overall_design: Buccal samples were collected from the Angolan giraffe (Giraffa giraffa angolensis), the Kordofan giraffe (Giraffa camelopardalis antiquorum)  and the related okapi (Okapi johnstoni). Methylated DNA immunoprecipitation (MeDIP) was performed on the buccal cell DNA samples. The MeDIP was followed by DNA sequencing (MeDIP-Seq). Differential DNA methylation regions (DMRs) were identified between the two giraffe species, seperately for males and females. Some Samples are missing processed data for one of two reasons. First, the initial study plan was to collect additional Okapi samples, however that did not end up being feasable. The two samples collected were insufficient to perform a quality DMR analysis. They are included in the submission since they may be useful for other researchers. Other samples without processed data did not have sufficient read depth to include in the analysis.

first: Jessica

last: Riskin

first: Marcus

last: Feldman

first: Julian

last: Fennessy

first: Stephanie

first: Sara

last: Ferguson

first: Floyd

last: Reed

first: Eric

last: Nilsson

first: Alexandra

last: Korolenko


title: Spatial transcriptomic profiling of human lung tissue in chronic obstructive pulmonary disease (COPD) [Xenium]

first: Maor

last: Sauler

summary: To spatially contextualize and extend disease-associated cellular states, we generated Xenium spatial transcriptomics data from FFPE lung tissue of 38 participants spanning the COPD disease spectrum. Four tissue microarrays (TMA1–TMA4) were profiled using a custom 480-gene Xenium panel. These data capture the in situ organization of inflammatory, regenerative, and remodeling cell states and reveal spatially localized niches and patterns of cell–cell communications relevant to COPD pathology. This dataset provides high-resolution spatial context for characterizing microenvironmental structure and cell–cell interactions in COPD lung tissue.

overall_design: FFPE lung tissue from 38 participants across the COPD spectrum was organized into four tissue microarrays (TMA1–TMA4), comprising 99 total cores that sampled parenchymal, airway, and vascular regions. Sections (5 µm) from each TMA were mounted on Xenium slides and processed according to the 10x Genomics FFPE workflow (CG000578, Rev C) using a custom 480-gene probe panel (hLung_480g, design ID EM2BNX, v1.0.0). The workflow included deparaffinization, decrosslinking, RNA release, in situ probe hybridization, signal amplification, and multimodal staining. Each slide was imaged and decoded on the Xenium Analyzer to produce cell-resolved transcript and morphology data.

first: Yuening

last: Zhang

first: Huanhuan

last: Wei

last: Nouws


title: hiv-seq reveals global host gene expression differences between hiv-transcribing cells from viremic and suppressed people with hiv

city: San Francisco

first: Julie

last: Frouard

state: California

address: 1650 Owens street

department: Virology

institute: Gladstone Institutes

summary: In our study, we aimed to improve the identification of active reservoir cells producing HIV in individuals undergoing antiretroviral therapy (ART). We developed a technique called HIV-Seq to enhance the efficiency of capturing HIV transcripts during single-cell RNA sequencing (scRNAseq) analysis. By applying this technique and surface phenotyping using CITE-seq, we compared the transcriptional features of HIV RNA+ cells before and after ART initiation. Our findings highlight distinct transcriptional signatures of active reservoir cells during viremia and suppression, demonstrating the utility of HIV-Seq in elucidating the mechanisms underlying reservoir persistence during ART.

overall_design:
Paired and longitudinal, archived PBMC samples were obtained from different cohort. Samples were collected prior to ART initiation (Week 0) and following ART suppression (week 24 or week 45). PBMCs were thawed, CD4+ T cells were purified by negative selection using the EasySep Human CD4 T cell enrichment kit (StemCell) and then stained with TotalSeq-C antibodiesfollowed by 10X libraries (ADT and GEX) preparation.
-----------------------------------------
ADT     Barcode sequence
TotalSeq™-C0390 anti-human CD127 (IL-7Rα) Antibody     GTGTGTTGTCCTATG
TotalSeq™-C0081 anti-human CD14 Antibody     TCTCAGACCTCCGTA
TotalSeq™-C0050 anti-human CD19 Antibody     CTGGGCAATTACTCG
TotalSeq™-C0148 anti-human CD197 (CCR7) Antibody     AGTTCAGTCAACCGA
TotalSeq™-C0100 anti-human CD20 Antibody     TTCTGGGTCCCTAGA
TotalSeq™-C0088 anti-human CD279 (PD-1) Antibody     ACAGCGCCGTATTTA
TotalSeq™-C0034 anti-human CD3 Antibody     CTCATTGTAACTCCT
TotalSeq™-C0045 anti-human CD4 Antibody     GAGGTTAGTGATGGA
TotalSeq™-C0048 anti-human CD45 Antibody     TCCCTTGCGATTTAC
TotalSeq™-C0063 anti-human CD45RA Antibody     TCAATCCTTCCGCTT
TotalSeq™-C0087 anti-human CD45RO Antibody     CTCCGAATCATGTTG
TotalSeq™-C0046 anti-human CD8 Antibody     GCGCAACTTGATGAT
TotalSeq™-C0154 anti-human CD27 Antibody     GCACTCCTGCATGTA
TotalSeq™-C0576 anti-human CD49d Antibody     CCATTCAACTTCCGG
TotalSeq™-C0147 anti-human CD62L Antibody     GTCCCTGCAACTTGA

first: Sushama

last: Telwatte

first: Xiaoyu

last: Luo

first: Natalie

last: Elphick

first: Reuben

last: Thomas

first: Douglas

last: Arneson

first: Pavitra

last: Roychoudhury

first: Rebecca

last: Hoh

first: Steven

last: Deeks

first: Sulggi

last: Lee

first: Nadia

middle: R

last: Roan

last: Yukl