title: Effect of TOP2B deletion or catalytic inhibition on gene expression in iPSC-derived human cardiomyocytes

first: John

last: Casement

summary: DNA topoisomerase IIB (TOP2B) is required for the correct execution of certain developmental transcription programs. Here, we have compared the transcriptional changes accompanying differentiation of wild type and TOP2B null human iPSC cells to beating cardiomyocytes. In addition we assess the transcriptional effect of short term (3hr) application of two TOP2B catalytic inhibitors in iPSC-derived cardiomyocytes.

overall_design: Human iPSC cells were differentiated to produce beating cardiomyocytes. RNA was prepared from undifferentiated iPSC cells and from induced cardiomyocytes once they  had formed sheets of beating cells. Cardiomyocytes were untreated (control) or exposed to TOP2 inhibitors dexrazoxane (ICRF-187) or topobexin for 3 hours immediately prior to cell lysis and RNA preparation. For all conditions four replica RNA isolations were performed.

first: Ian

last: Cowell

first: Caroline

last: Austin

first: Veronika

last: Keresteš

first: Anna

last: Jirkovská

first: Mushtaq

last: Khazeem

first: Nicola

last: Curtin

first: Adam

last: Creigh

first: Majlinda

last: Lako

first: Lye

last: Armstrong


title: Extracellular vesicles from microglial cells activated by abnormal heparan sulfate oligosaccharides from Sanfilippo patients impair neuronal dendritic arborization

status: Public on Jul 23 2025

city: Toulouse

first: Chloe

last: Dias

address: CHU Purpan

country: France

institute: Infinity

type: Non-coding RNA profiling by high throughput sequencing

summary: Background : In mucopolysaccharidosis type III (MPS III, also known as Sanfilippo syndrome), a pediatric neurodegenerative disorder, accumulation of abnormal glycosaminoglycans (GAGs) induces severe neuroinflammation by triggering the microglial pro-inflammatory cytokines production via a TLR4-dependent pathway. But the extent of the microglia contribution to the MPS III neuropathology remains unclear. Extracellular vesicles (EVs) mediate intercellular communication and are known to participate in the pathogenesis of adult neurodegenerative diseases. However, characterization of the molecular profiles of EVs released by MPS III microglia and their effects on neuronal functions have not been described. Methods : Here, we isolated EVs secreted by the microglial BV-2 cells after treatment with GAGs purified from urines of Sanfilippo patients (MPS-GAGs EVs) or from age-matched healthy subjects (WT-GAGs EVs) to explore the EVs’ proteins and small RNA profiles using LC–MS/MS and RNA sequencing. We next performed a functional assay by immunofluorescence following WT-GAGs- or MPS-GAGs-EVs uptake by WT primary cortical neurons and analyzed their extensions metrics after staining of βIII-tubulin and MAP2 by confocal microscopy. Results : Functional enrichment analysis for both proteomics and RNA sequencing data from MPS-GAGs-EVs revealed a specific content involved in neuroinflammation and neurodevelopment pathways. Treatment of cortical neurons with MPS-GAGs-EVs induced a disease-associated phenotype demonstrated by a lower total neurite surface area, an impaired somatodendritic compartment, and a higher number of immature dendritic spines. Conclusions : This study shows, for the first time, that GAGs from patients with Sanfilippo syndrome can induce microglial secretion of EVs that deliver a specific molecular message to recipient naive neurons, while promoting the neuroinflammation, and depriving neurons of neurodevelopmental factors. This work provides a framework for further studies of biomarkers to evaluate efficiency of emerging therapies.

overall_design: Here, we isolated EVs secreted by the microglial BV-2 cells after treatment with GAGs purified from urines of Sanfilippo patients (MPS-GAGs-EVs) or from age-matched healthy subjects (WT-GAGs-EVs) to explore the EVs’ small RNA profiles using RNA sequencing. EVs were separated by differential ultracentrifugation (dUC) in two different pellets after ultracentrifugation at 12,000g (12K) or 100,000g (100K).

first: Nissrine

last: Ballout

first: Guillaume

last: Morla

first: Katia

last: Alileche

first: Christophe

last: Santiago

first: Ida

middle: C

last: Guerrera

first: Adeline

last: Chaubet

first: Jerome

last: Ausseil

first: Stephanie

last: Trudel


title: Targeting DNA Polymerase Epsilon Leads to Tumor Clearance and Activation of an NF-κB-mediated inflammatory response in Triple Negative Breast Cancer

city: New York

first: Richard

last: Possemato

state: NY

address: 550 First Avenue

department: Pathology

country: USA

institute: NYU School of Medicine

type: Expression profiling by high throughput sequencing

summary: Breast cancer remains the second leading cause of cancer-related mortality among women, with triple-negative breast cancer (TNBC) exhibiting a particularly poor five-year prognosis1. Here, we demonstrate that among genetic and pharmacological perturbations targeting DNA replication, suppression of DNA polymerase epsilon (POLE) in TNBC, induces a potent, TNBC-specific gene expression signature enriched in inflammatory cytokines that are transcriptional targets of NF-κB. TNBC cells exhibit markedly higher levels of DNA damage and canonical NF-κB activation compared to luminal breast cancer cells. Notably, NF-κB activation in this context depends on the canonical component RELA, but not the non-canonical component RELB. Mechanistically, ATM, STING, and RIG-I each contribute to NF-κB activation following POLE suppression. In vivo, POLE suppression in a murine TNBC model leads to cancer cell-intrinsic elimination of tumor burden and increased immune cell infiltration. Together, these findings support a model in which replication stress from POLE inhibition triggers robust NF-κB–mediated inflammation and immune microenvironment remodeling in TNBC and can independently trigger tumor eradication. These results suggest a potential therapeutic avenue for targeting POLE in TNBC.

overall_design: Cancer cell lines MDA-MB-231, Hs578t, or MCF7, each expressing either a control vector or a POLE cDNA, and an shRNA targeting POLE, 6 days after infection. Cancer cell line MDA-MB-231 treated with aphidicolin (APH; 2 µg/mL), which inhibits DNA polymerases α, δ, and ε; hydroxyurea (HU; 2 mM), which depletes nucleotide pools by inhibiting ribonucleotide reductase; paclitaxel (PTX; 4 nM), which induces mitotic stress that indirectly perturbs DNA replication by arresting cells in metaphase; cycloheximide (CHX; 2 µM), which indirectly impairs replication by blocking protein synthesis and depleting essential replication factors; and cisplatin (CP; 12 µM), for 24 hours.

first: Possemato

last: Richard

first: Sher

last: Elizabeth

first: Fujihara

last: Kenji


title: Enhanced Media Optimize Bovine Myogenesis in 2D and 3D Models for Cultivated Meat Applications

status: Public on Jul 24 2025

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

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

overall_design: Refer to individual Series


title: The Contribution of Oestrogen in Muscle Mass, Function, and Molecular Signalling in Females Aged 18-80

city: Geelong

first: Séverine

last: Lamon

state: VIC

address: 1 Gheringhap St

department: School of Exercise and Nutrition Sciences

country: Australia

institute: Deakin University

summary: Whether, and how, the menopausal transition mediates the skeletal muscle response to ageing in females remains to be elucidated. We examined a tightly controlled, cross-sectional cohort of 96 females between 18-80 years to map the trajectory of muscle ageing and determine its relationship with female sex hormones. Across every decade of age, we quantified body composition with dual-energy x-ray absorptiometry, muscle morphology with peripheral quantitative computed tomography, muscle function with leg press and neuromuscular assessment. Vastus lateralis morphology and gene expression was assessed with immunohistochemical staining and RNA sequencing, respectively, and circulating sex hormone concentrations were measured with liquid chromatography mass spectrometry. After adjusting for physical activity and protein intake, age was negatively associated with muscle mass, strength, and overall and type I muscle fibre size, and positively associated with hybrid type I/II fibre prevalence. We found 37 unique patterns of gene expression across individual decades of age. Immune signalling, cellular adhesion, and extracellular matrix organisation pathways were most up-regulated with age, while mitochondrial function pathways were the most down-regulated. Circulating oestradiol and progesterone, but not testosterone, concentrations across the lifespan were positively associated with lean mass and neuromuscular function, and negatively associated with hybrid muscle fibres. Oestrogen receptor binding sites were significantly enriched in genes that are upregulated in pre- versus post-menopausal muscle, suggesting a reduction in the translation of oestrogen target genes after menopause. The effects of sex hormone fluctuations across the female lifespan should therefore be considered in the development of therapies to combat age-related muscle wasting.

overall_design: This study employed a tightly controlled cross-sectional design to examine skeletal muscle ageing and its association with circulating sex hormones across the adult female lifespan. A total of 96 healthy females aged 18 to 80 years were recruited, with each decade of age represented. Vastus lateralis muscle biopsies were collected from a subset of participants for transcriptomic analysis via RNA sequencing (n = 57). Of these, 48 were newly sequenced, and 9 were obtained from a previous study with identical protocols.

first: Annabel

middle: J

last: Critchlow

first: Danielle

last: Hiam

first: Steven

last: O’Bryan

first: Megan

last: Soria

first: Briana

last: Gatto

first: Ross

middle: M

last: Williams

first: Viktor

last: Engman

first: Karel

last: van Belleghem

first: Andrew

last: Garnham

first: Christopher

last: Fry

first: David

last: Scott


title: A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories

city: Bern

first: Irene

last: Paassen

address: Murtenstrasse 28

department: Biomedical Research

institute: Universität Bern

type: Genome binding/occupancy profiling by high throughput sequencing


title: Hypoxia impedes differentiation of cranial neural crest cells into derivatives relevant for palatogenesis

city: Erlangen

first: Matthias

last: Weider

address: Glückstr. 11

department: Department of Orthodontics and Orofacial Orthopedics

country: Germany

institute: Universitätsklinikum Erlangen

summary: Orofacial clefts (OFC) are clefts of the lip and/or palate. They are the second-most prevalent congenital malformation. OFC result from failures in fusion processes of facial structures during embryonic development. Craniofacial structures are derived from ectodermal epithelial cells and cranial neural crest cells (CNCCs). In fact, the ectomesenchymal CNCCs are the source of most midface structures. They proliferate heavily during development and differentiate into a variety of tissues such as bone, cartilage and smooth muscle. Risk factors for OFC are multifactorial and include genetic components but also environmental factors. One environmental factor is hypoxia that can be caused by several reasons during pregnancy, such as tobacco smoking, medication or living at high altitudes. Knowledge about the molecular mechanisms of how hypoxia evokes OFC is at large. We here show that hypoxia has only modest effects on proliferating CNCCs, but dramatically influences their differentiation potential. We detected massive perturbations of differentiation in all of our tested differentiation paradigms, i.e. chondrocytes, osteoblasts and smooth muscle cells. The transcriptional induction of the majority of regulated genes during each of these processes was grossly impaired by hypoxic conditions, as evidenced by genome-wide transcriptomic analyses. Bioinformatic analyses pointed to a central role of cytoskeletal organization and amino acid metabolism being compromised during all three differentiation processes. We could identify several OFC risk genes amongst the genes with constrained induction during hypoxia. Our analyses reveal a drastic influence of hypoxia on the differentiation potential of CNCCs as a possible source for the occurrence of OFC.

overall_design: To assess the differentiation potential of CNCCs under normoxic and hypoxic conditions, we differentiated the cells under 21% and 0.5% O2 into chondrocyte, osteoblast or smooth muscle cell lineages and compared them to proliferating cells. We used four replicates for normoxic and three replicates for hypoxic conditions. We then performed gene expression analysis using RNA sequencing.

first: Theresa

last: Schmid

first: Gabriele

last: Rodrian

first: Elke

last: Bachmann

first: Alexander

last: Kohler

first: Michael

last: Wegner

first: Lina

last: Gölz


title: Profibrotic monocyte-derived alveolar macrophages as a biomarker and therapeutic target in systemic sclerosis-associated interstitial lung disease

city: Chicago

middle: V

last: Misharin

state: Illinois

address: 303 E Superior St

department: Pulmonary and Critical Care

institute: Northwestern University

summary: Interstitial lung disease (ILD) is present in over 60% of patients with systemic sclerosis (SSc) and is the leading cause of SSc-related deaths. Profibrotic monocyte-derived alveolar macrophages (MoAM) play a causal role in the pathogenesis of pulmonary fibrosis in animal models where their persistence in the niche requires signaling through the Colony Stimulating Factor 1 Receptor (CSF1R). We hypothesized that the presence and proportion of MoAM in bronchoalveolar lavage (BAL) fluid from patients with SSc-ILD may be a biomarker of ILD severity. We performed spatial transcriptomics to localize profibrotic MoAM to the alveolar space and identified expansion of interstitial macrophages spilling into the alveolar space. Our findings suggest that the proportion of profibrotic MoAM and interstitial macrophages in BAL fluid may serve as a biomarker of SSc-ILD and credential them as possible targets for therapy.

overall_design: 6 donor and 5 SSc lung tissue sections were obtained. An approximately 10x10x10 mm piece of lung tissue was cut, fixed, and mounted to one of two Xenium slides for each section. Due to the instrument malfunction, the first run (samples with “:1” suffix) was aborted mid-run, and slides were left on the instrument for ~48 hours. The slides were recovered, stored at 4 °C for an additional 24 hours, and then the run was successfully repeated using a new set of reagents. To assess the impact of technical issues on the data quality, we have prepared additional sections from the same tissue blocks (samples with “:2” suffix) and analyzed them using the same gene panel and tissue segmentation kit (replacement reagents were kindly provided by 10x Genomics). The second run completed without technical issues.

first: Nikolay

middle: S

last: Markov

first: Anthony

last: Esposito

first: Maxwell

last: Schleck

first: Radmila

last: Nafikova

first: Zhan

last: Yu

first: Ziyan

last: Lu

first: Monique

middle: E

last: Hinchcliff


title: Single-nucleus RNA sequencing of the cerebral cortex in Gclc knockout mice at 3 and 6 months of age

city: Otsu

first: Shoko

last: Hashimoto

state: Shiga

address: Setatsukinowa-cho

country: Japan

institute: Shiga University of Medical Science

summary: This study investigates the transcriptomic impact of glutamate–cysteine ligase catalytic subunit (Gclc) deficiency in the mouse cortex at 3 and 6 months of age using single-nucleus RNA sequencing.

overall_design: We isolated nuclei from the cerebral cortex of Gclc-KO mice at 3 and 6 months and performed snRNA-seq using the 10x Genomics Chromium system.


title: RNA-seq of oxaliplatin resistant HCT116 and SW480

city: Singapore

first: Mohua

last: Das

country: Singapore

institute: Genome Institute of Singapore

summary: Drug resistance and distant metastases are leading causes of mortality in colorectal cancer (CRC), yet the molecular mechanisms linking these processes remain elusive. In this study, we demonstrate that acquired resistance to oxaliplatin, a first-line chemotherapeutic in CRC, enhances metastatic potential through transcriptional reprogramming. Using a clinically relevant dosing regimen, we generated oxaliplatin-resistant CRC cells that displayed increased metastatic potential. Integrated transcriptomic and phenotypic analyses revealed that dysregulated cholesterol biogenesis amplifies TGF-b signaling, which in turn drives expression of SERPINE1, that serves as a key effector of both oxaliplatin resistance and metastasis. Furthermore, we uncovered a SERPINE1-associated nine-gene expression signature, RESIST-M, that robustly predicts overall and relapse-free survival across distinct patient cohorts. Notably, RESIST-M stratifies a high-risk subtype of CMS4/iCMS3-fibrotic patients that display the poorest prognosis, underscoring its clinical relevance. Targeting of SERPINE1 or cholesterol biosynthesis re-sensitized resistant, pro-metastatic cells to oxaliplatin in mouse xenograft models. Altogether, this study uncovers a mechanistic link between metabolic rewiring and transcriptional plasticity underlying therapy-induced metastasis in primary CRC. Additionally, it also reveals actionable vulnerabilities that offer both prognostic value and therapeutic potential.

overall_design: HCT116 and SW480 cells were treated with 0.5 uM (low dose; LD), 5 uM (mid dose; MD) or 80 uM (high dose; HD) for 72 hours before changing to drug free media. Cells were then subcultured and treated again with the same dose for 72 hours. Cells were treated for 10 cycles. Cells were subsequently cultured in drug free media and used for bulk RNA seq.

first: Stephen

middle: Q

last: Wong

first: Jia Min

last: Loo

first: Tenzin

last: Kenzon

first: Hui Wen

last: Chua

first: Niranjan

last: Shirgaonkar

first: Ramanuj

last: Dasgupta


title: Single cell RNA-seq of oxaliplatin resistant HCT116 cells

summary: Drug resistance and distant metastases are leading causes of mortality in colorectal cancer (CRC), yet the molecular mechanisms linking these processes remain elusive. In this study, we demonstrate that acquired resistance to oxaliplatin, a first-line chemotherapeutic in CRC, enhances metastatic potential through transcriptional reprogramming. Using a clinically relevant dosing regimen, we generated oxaliplatin-resistant CRC cells that displayed increased metastatic potential. Integrated transcriptomic and phenotypic analyses revealed that dysregulated cholesterol biogenesis amplifies TGF-beta signaling, which in turn drives expression of SERPINE1, that serves as a key effector of both oxaliplatin resistance and metastasis. Furthermore, we uncovered a SERPINE1-associated nine-gene expression signature, RESIST-M, that robustly predicts overall and relapse-free survival across distinct patient cohorts. Notably, RESIST-M stratifies a high-risk subtype of CMS4/iCMS3-fibrotic patients that display the poorest prognosis, underscoring its clinical relevance. Targeting of SERPINE1 or cholesterol biosynthesis re-sensitized resistant, pro-metastatic cells to oxaliplatin in mouse xenograft models. Altogether, this study uncovers a mechanistic link between metabolic rewiring and transcriptional plasticity underlying therapy-induced metastasis in primary CRC. Additionally, it also reveals actionable vulnerabilities that offer both prognostic value and therapeutic potential.

overall_design: HCT116 cells were treated with 0.5 uM (low dose; LD), 5 uM (mid dose; MD) or 80 uM (high dose; HD) for 72 hours before changing to drug free media. Cells were then subcultured and treated again with the same dose for 72 hours. Cells were treated for 10 cycles. Cells were subsequently cultured in drug free media and used for single cell RNA seq.


title: Mass generation and long-term expansion of hepatocyte organoids from adult primary hepatocytes

city: Nijmegen

first: Richard

last: Bartfai

state: Gelderland

address: Geert Grooteplein Zuid 28

department: Molecular Biology

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences

summary: Adult primary human hepatocytes (PHHs) are the gold standard in ex vivo toxicological studies and possess the clinical potential to treat patients with liver disease as advanced therapy medicinal products (ATMPs). However, the utility of this valuable cell type has been limited by short-term functionality and limited expansion potential in vitro. While notable advances have been made in the long-term maintenance of primary hepatocytes, there has been limited success in driving the efficient generation and expansion of adult PHH-derived organoids which recapitulate both liver tissue architecture and function, hampering in vitro studies and regenerative medicine applications. Here we describe the mass generation and long-term expansion of hepatocyte organoids with functionally interconnected hepatic and biliary-like structures from adult primary human hepatocytes. Hepatocyte organoids retain the expression of lineage and functional markers, closely resembling PHH, while also acquiring the expression of regeneration, fetal and biliary markers. Organoids perform key hepatocyte functions while proliferating and can be matured to enhance their functionality. As a proof-of-principle, we demonstrate that hepatocyte organoids can recapitulate hallmarks of cholestasis and steatosis in vitro. Moreover, we show that hepatocytes can be transfected, transduced and gene edited in 3D prior to organoid generation, facilitating a wide range of applications. Our novel hepatocyte organoid system bridges the gap between short-term functionality of primary human hepatocytes and the need for scalable, long-term organoid models of the adult liver, offering immense potential for drug testing, disease modeling, and advanced therapeutic applications.

overall_design: Primary adult human hepatocytes were used to form spheroids in hepatocyte spheroid medium, which were then embedded in Matrigel and expanded into hepatocyte organoids (HOs) using a defined hepatocyte expansion medium. These organoids were matured in hepatocyte maturation medium and cultured for several weeks with periodic passaging. Bulk RNA-sequencing was performed on the primary hepatocytes, spheroids and hepato-biliary organoids using the Kapa mRNA HyperPrep Kit, followed by sequencing on Illumina NextSeq2000 and analysis with DESeq2, incorporating donor batch correction and functional annotation of differentially expressed genes.

first: Ary

last: Marsee

first: Arabela

last: Ritchie

first: Adam

last: Myszczyszyn

first: Theo

middle: L

last: Sinnige

first: Abhishek

last: Kanyal

first: Teja

last: Rus

first: Alba

middle: P

last: Moliner

first: Shicheng

last: Ye

first: Arif

middle: I

last: Ardisasmita

first: Indi

last: Joore

first: Jose

last: Castro-Alpízar

first: Sabine

middle: A

last: Fuchs

first: Jung-Chin

last: Chang

first: Kerstin

last: Schneeberger

first: Bart

last: Spee


title: Effect of canonical aryl hydrocarbon receptor pathway inhibitor on human endothelial cells

first: Yang

last: Lin

address: 455 Main Street 06W

institute: Weill Cornell Medicine

summary: To study the effect of blockade of canonical aryl hydrocarbon receptor (AHR) pathway in human endothelial cells, we treated human umbilical vein endothelial cells (HUVECs) and adipose endothelial cells with a canonical AHR inhibitor, Stemreginin 1 (SR1) and performed bulk RNAseq analysis.

overall_design: HUVECs and adipose endothelial cell lines were derived from human donors. Cells from each patient were treated with either 1: 10, 000 DMSO (vehicle), or 0.5uM SR1 in 1: 10, 000 DMSO. At different time points, RNA samples were collected for comparisons.


title: Evaluating CD40 Agonist Alone and in Combination with IL-1R1 Blockade in Pancreatic Cancer

status: Public on Jul 25 2025

city: Tucson

first: Marcas

last: Agostinelli

state: Arizona

address: 2690 W Avenida Azahar

department: Bioinformatics

institute: Novogene

summary: To investigate the immunomodulatory effects of IL-1R1 blockade in pancreatic ductal adenocarcinoma (PDAC), we performed bulk RNA sequencing of tumors subjected to distinct treatment regimens. Tumors were treated with either an anti–IL-1R1 antibody or left untreated, and another cohort received combination therapy with agonistic CD40 and anti–IL-1R1 antibodies versus CD40 agonist monotherapy. Gene ontology enrichment analysis of differentially expressed genes (p ≤ 0.05) revealed that anti–IL-1R1 treatment upregulated genes involved in RNA processing, including spliceosome-associated pathways, compared with untreated controls. Conversely, immune-related pathways—such as response to type II interferon, leukocyte-mediated immunity, and T-cell activation—were significantly downregulated in the anti–IL-1R1 group. In contrast, tumors receiving combination therapy exhibited enhanced innate and adaptive immune signatures compared to CD40 monotherapy, including antigen presentation, lymphocyte-mediated immunity, and regulation of immune effector functions. Metabolic pathways were notably downregulated in the combination group. Gene set enrichment analysis further confirmed the upregulation of key immune pathways, including NOD-like receptor signaling, NF-κB signaling, NK cell–mediated cytotoxicity, and JAK-STAT signaling, in the combination therapy group. These findings highlight the context-dependent effects of IL-1R1 blockade and support its synergistic potential with CD40 agonism in modulating the PDAC tumor microenvironment.

overall_design: To evaluate the impact of IL-1R1 blockade and its combination with CD40 agonist therapy on the tumor microenvironment in pancreatic ductal adenocarcinoma (PDAC), we performed bulk RNA sequencing on murine PDAC tumor (subcutaneous) samples  from four treatment groups: Untreated Control, anti-IL-1R1 antibody, agonistic CD40 antibody, combination of agonistic CD40 and anti-IL-1R1 antibody

first: Akash

last: Boda

first: Irfan N.

last: Bandey

first: Saikat

last: Chowdhury

first: Mekala

last: Venugopala

first: Jason

last: Roszik

first: Manisha

last: Singh


title: Molecular pathology of acute spinal cord injury in middle-aged mice

city: Miami

first: Jae

last: Lee

state: FL

address: 1095 NW 14th Terrace #48

institute: University of Miami

summary: The median age of sustaining a spinal cord injury has steadily increased from 29 to 43 over the last several decades. Although more pre-clinical studies in aged rodents are being done to address this shift in demographics, there have not been comprehensive transcriptomic studies investigating SCI pathobiology in middle-aged mice. To address this gap in knowledge, we compared behavioral, histopathological, and transcriptional outcomes in young (2-4 months-old) and middle-aged (10-12 months-old) mice. In contrast to previous studies, open field tests showed no differences in locomotor recovery between the young and middle-aged mice over a one-month period. The injury site also demonstrated similar histopathology in terms of lesion size, numbers of macrophages and fibroblasts. Acutely after injury, proliferation of macrophages, fibroblasts, and astrocytes were also similar between the two age groups. In addition, spatial transcriptomics showed similar transcriptionally defined regions around the injury site at 3 days post injury. However, single cell RNA-sequencing of the cells at the injury site and surrounding spared tissue showed differences in select cell subpopulations.  Taken together, our results indicate that although young and middle-aged mice display similar locomotor recovery and histopathology after SCI, changes in cell subpopulations may underly a decline in repair mechanisms that are manifested after this age.

overall_design: C57Bl/6J mouse contusive spinal cord injury sites were analyzed with single-cell sequencing (10X Chromium v3.1) at uninjured and 3 days-post injury conditions in middle-aged (10-12 months-old) and young (2-4 months-old) mice. 3dpi injury sites in aged and young mice were analyzed with spatial sequencing (10X Visium v1).

first: Corey

middle: R

last: Fehlberg

first: Danny

last: John

first: Brian

last: Kang

first: James

last: Choi

first: Susana

last: Cerqueira

first: Alexis

last: Brake

middle: K


title: Prognostic microRNA profiling signatures in primary testicular diffuse large B-cell lymphoma

city: Durham

first: Zijun

middle: Yidan

last: Xu-Monette

state: North Carolina

address: 905 S. Lasalle Street

department: Department of Pathology

institute: Duke University

summary: Primary testicular (PT) diffuse large B-cell lymphoma (DLBCL) is a rare and aggressive lymphoma with distinct clinical and molecular characteristics. To further improve the prognosis of PT-DLBCL, not only the common features of PT-DLBCL, but also the molecular heterogeneity within the PT-DLBCL entity, need to be better understood. In this study, 2083 microRNAs and 13 housekeeping genes in RNA samples from 150 patients with PT-DLBCL were sequenced using next-generation sequencing technology. After quality-control, CPM standardization, and normalization, microRNA profiling data were obtained for 113 patients with PT-DLBCL.  Our analysis identified a microRNA signature (comprising 35 microRNAs) that clustered 113 patients with PT-DLBCL into two distinct clusters.  Patients with high expression of 16 microRNAs (miR-514a-3p, miR-202-3p, miR-509-5p, miR-509-3-5p, miR-506-3p, miR-508-3p, miR-514b-5p, miR-513a-5p, miR-510-5p, miR-513b-5p, miR-513c-5p, miR-508-5p, miR-509-3p, miR-202-5p, miR-507, and miR-514b-3p) had significantly better survival.

overall_design:
From microRNAs significantly differentially expressed between PT-DLBCL and systemic DLBCL patients, we selected top microRNAs to perform unsupervised clustering within the PT-DLBCL cohort, and then performed prognostic analysis for resultant clusters.

Please note that the PTL_raw_parsed_data.xlsx contains raw count data for all 150 cases, and the PTL_normalized_data.xlsx contains normalized data for only 113 cases with positive count data after quality control (QC) and normalization. Available survival and clinical data are provided (PTL_OS_clinical_data.xlsx) only for samples passing QC.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Ken

middle: H

last: Young

middle: Y


title: Single-cell RNA sequencing reveals the effects of mental stress on mouse mammary tumors and the tumor microenvironment

city: Shanghai

first: Pengfei

last: Liu

address: 150 Jimo Road

country: China

institute: Shanghai East Hospital, Tongji University School of Medicine

summary: Mental stress has been shown to negatively impact the development and progression of human cancer, including breast cancer. However, its effects on the tumor microenvironment (TME) remain unclear. In this study, we applied single-cell sequencing analysis to tumor tissues from MMTV-PyMT transgenic mice with mammary gland tumors with or without exposure to mental stress. In association with a significant promotion of the cell cycle and tumor growth induced by mental stress, we observed the dedifferentiation of luminal subtype of tumor cells into a subgroup of cancer stem cell-like basal cells, as well as enhanced cell proliferation in epithelial tumor cells, endothelial cells, and fibroblasts. In addition, stress stimulation led to an increase in tumor-associated neutrophils (TANs) and tumor-infiltrating dendritic cells (TIDCs), while suppressing immune cells such as cytotoxic T lymphocytes (CTLs), naïve T cells, B cells, and NK cells within the TME. We also observed a shift in macrophages from the M1 to the M2 phenotype. Furthermore, pathway enrichment analysis of differentially expressed genes, gene signature Uscore analysis, and immunofluorescence staining of the tumor tissue sections were conducted for further validation. The current study not only systematically elucidates the impact of mental stress on mammary gland tumors and the TME in vivo, but also provides insights into the mechanism underlying mental stress-induced tumor growth and progression in breast cancer.

overall_design:
This study includes 4 single-cell RNA sequencing samples, all derived from mammary tumor tissues of 10-week-old female MMTV-PyMT mice, with the following groupings:
Experimental group (n=2): Mammary tumors from MMTV-PyMT mice subjected to two weeks of Chronic Unpredictable Stimulation (CUS) treatment
Control group (n=2): Age-matched mammary tumors from untreated MMTV-PyMT mice

first: Wenjing

last: Ma

first: Tao

last: Wang

first: Jinhui

last: Lü

first: Weizhong

first: Qifan

last: Tang

first: Yixing

first: Jing

last: Di

first: Evelyne

last: Bischof

first: Qian

last: Zhao

first: Zuoren

last: Yu


title: Axonal defasciculation is restricted to specific branching points during regeneration of the lateral line nerve in zebrafish

first: Rohan

middle: Saleem

last: Roy

address: 1230 York Avenue

institute: The Rockefeller University

summary: Peripheral nerve regeneration requires precise selection of the appropriate targets of innervation, often in an environment that differs from the developmental wiring of the neural circuit. Severed axons of the zebrafish posterior lateral line nerve have the capacity to reinnervate mechanosensory neuromast organs positioned at discrete locations along the fish’s trunk. Nerve regeneration is a balance between fasciculated regrowth of the axonal bundle and defasciculation of individual axons into the epidermis where neuromasts reside. The intrinsic and extrinsic factors that guide pathfinding during regeneration of the posterior lateral line nerve are unknown. Here we show that the gene col18a1a, which codes for the secreted heparan sulfate proteoglycan collagen XVIII, biases axon defasciculation to specific choice points along the fish’s trunk that coincide with circumscribed gaps in the extracellular matrix. We found that col18a1a is expressed by the neuromast and by a subset of Schwann cells that are located at the point of axonal defasciculation. Furthermore, we observed aberrant axon branching at inappropriate locations during nerve regeneration in col18a1a mutants, suggesting an auxiliary role for guiding axon growth cones. We propose a model in which a collagen XVIII-axon guidance cue complex attracts defasciculated arbors across the epidermal basement membrane during posterior lateral line nerve regeneration.

overall_design: RNA-seq profiling of isolated hair cells from the posterior lateral line of larval zebrafish either 1 day or 3 days post lateral line nerve lesion and corresponding age-matched, sham-lesioned controls.


title: Effect of external cues on clock-driven protection from Influenza A infection

city: Philadelphia

first: James

last: Garifallou

state: Pennsylvania

address: 3615 Civic Center Boulevard, ARC1014

department: Neonatology

institute: Children's Hospital of Philadelphia

summary: Influenza and other respiratory viral pathogens are leading causes of mortality and morbidity. We previously demonstrated that circadian rhythms confer temporal protection from influenza infection. Here, we investigated whether this protection requires rhythmic function after the initial infection by manipulating environmental cycles. We demonstrate that disrupting environmental lighting cues within a critical window of vulnerability abrogates time-of-day specific protection. This poor outcome is mediated by a dysregulated immune response, evidenced by the accumulation of inflammatory monocytes and CD8+ cells in the lungs and a transcriptomic profile indicative of an exaggerated immune response. Disruption of the light cycle does not affect outcomes in a clock mutant, indicating that it acts by compromising endogenous timekeeping. Importantly, rhythmic meal timing mitigates the adverse effects of disrupted light cycles, suggesting that external cycling cues, which act through different body clocks, can substitute for each other. Our findings highlight the crucial interplay between environmental factors and endogenous clocks in shaping influenza outcomes, offering significant translational potential for improving the care of critically ill patients with respiratory viral infections.

overall_design: Single-nuclei RNA-seq was utilized to assess whole lung gene expression on day 8 post-infection (from IAV).

first: Oindrila

last: Paul

first: Thomas

middle: G

last: Brooks

first: Lora

last: Assi

first: Alisha

last: Shetty

first: Martina

last: Towers

first: Kaitlyn

last: Forrest

first: Alecia

last: Cameron

first: Amita

last: Sehgal

first: Gregory

last: Grant

first: Shaon

last: Sengupta


title: Human induced pluripotent stem cell-derived microglia with a CX3CR1-V249I genetic variant exhibit dysfunctional phenotypes and modulate neuronal growth and function

city: Portland

first: Chi

last: Zhang

state: Oregon

address: 3303 S.W. Bond Avenue

department: Biomedical Engineering

institute: Oregon Health & Science University

summary: The involvement of microglia in neurodegenerative diseases has drawn increasing attention, as many genetic risk factors are preferentially expressed in microglia. Microglial fractalkine receptor (CX3CR1) signaling regulates many key microglial functions, and the CX3CR1-V249I single nucleotide polymorphism (SNP) has been associated with increased risk for multiple neurodegenerative conditions, including Alzheimer’s disease, yet its functional consequences in human microglia remain unexplored. In this study, we generated iPSC-derived human microglia-like cells (hMGLs) and found that the CX3CR1-V249I variant increased susceptibility to starvation-induced cell death, reduced amyloid-beta uptake, altered microglial morphology, and impaired migration, with more pronounced effects in homozygous cells. Co-culture with neurons demonstrated that hMGLs with the CX3CR1-V249I variant misregulated neuronal properties, including abnormal neuronal growth as well as an induction of neuronal hyperexcitability. These findings highlight the critical role of CX3CR1 in regulating microglial function and implicate the V249I variant in driving pathogenic microglial states relevant to neurodegeneration.

overall_design: To assess the transcriptional profiles of human iPSC-derived microglia containing the CX3CR1-V249I variant, iPSCs containing the variant in heterozygous and homozygous states were differentiated alongside isogenic controls for 25 days.

first: Kaylee

last: Tutrow

first: Yue

last: Fang

first: Jason

last: Meyer


title: Effect of resistant secretome on immune cells

city: Oslo

first: Eivind Valen

last: Egeland

address: Ullernchausseen 70

department: Department of Tumor Biology, Institute for Cancer Research

country: Norway

institute: Oslo University Hospital

summary: In order to study how chemoresistance in breast cancer cells influences immune cells, MDA-MB-468 cells resistant to paclitaxel were generated. Bulk RNAseq were used to assess resistant associated changes.

overall_design: MDA-MB-468-PR, was established in-house by exposing MDA-MB-468 cells to paclitaxel (3-4.5nM) for 2 months.

first: Eivind

first: Eleni

last: Skourti

first: Gunhild

last: Mælandsmo

first: Lina

last: Prasmickaite


title: RNA-seq Analysis of Human Lens Capsules from Donors with and without Cataract Surgery History

city: Augusta

first: Xingjun

last: Fan

state: GA

address: 1460 Laney Walker Blvd, Room CB1119

department: Cellular Biology and Anatomy

institute: Augusta University

summary: Cataract surgery is the most commonly performed ophthalmic procedure worldwide, yet the long-term molecular adaptations of lens epithelial cells (LECs) following surgery remain poorly understood. In this study, we conducted bulk RNA sequencing on lens capsules from 34 human donors, including 17 with an average of 7 years post-cataract surgery and 17 non-cataract controls. Differential expression analysis revealed substantial transcriptional changes in post-surgical LECs, including 1,690 upregulated and 579 downregulated genes. Gene Set Enrichment Analysis (GSEA) and Gene Ontology (GO) analyses identified activation of oxidative stress response, cell survival pathways, and immune response signatures. Collectively, our findings reveal that LECs undergo profound and sustained molecular reprogramming following cataract surgery, including inflammatory, fibrotic, migratory, and senescent changes. These adaptations may contribute to posterior capsule opacification (PCO) and highlight potential therapeutic targets for its prevention.

overall_design: 34 lens capsules were used for bulk RNA sequencing (RNAseq), comprising 13 males and 4 females from non-cataract donors and 17 lens capsules from post-surgery cataract donors, consisting of 6 males and 11 females. The post-mortem interval (PMI) for tissue harvest ranged from 2 to 10 hours, with an average PMI of 7.5 hours for non-cataract individuals and 5.4 hours for post-cataract surgery individuals. The average age in the post-cataract group was higher, at 74.1 years, compared to 67.2 years for non-cataract individuals. After stratification by post-cataract surgery status, no significant differences were observed in age or sex. The average time since cataract surgery among donors in the post-cataract group was 7.0 years, with surgeries performed 2 to 14 years before sample collection.

first: Caili

last: Hao

first: Kailin

last: Li

first: Zongbo

last: Wei

first: Kazi

last: R. Radeen

first: Xiang

first: Sharad

last: Purohit


title: Dissection of the immune landscape in Psoriatic Arthritis patients [Mouse scRNA-seq]

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Despite significant advancements in psoriatic arthritis (PsA) treatment modalities, a considerable proportion of patients continue to experience persistent joint inflammation and functional impairment, unresponsive to the armamentarium of biological disease-modifying antirheumatic drugs (bDMARDs) or Janus kinase (JAK) inhibitors. The etiology of resistance in these cases is complex, likely involving intricate immunological and genetic factors which are currently mostly unknown. Identifying novel biomarkers and targets for refractory disease is urgently needed. Here, utilizing single-cell RNA-sequencing of synovial fluid from 41 PsA patients and 9 Osteoarthritis (OA) controls we map the comprehensive immune landscape of PsA. Our analysis reveals major perturbations within the myeloid compartment, identifying distinct cell subsets and altered gene programs in PsA patients. Notably, within the myeloid compartment, refractory patients exhibit elevated expression of interferon- gamma induced gene programs linked to the immunoproteasome and MHC class I antigen presentation, at both the gene and protein level. These results suggest a potential interaction of the immunoproteasome and MHC class I antigen presentation in refractory PsA patients with sustained inflammation. Our research imparts critical insights into PsA pathogenesis, paving the way for both molecular level patient classification and potentially new therapeutic interventions for currently treatment resistant patients.

overall_design: Patients diagnosed with psoriatic arthritis according to the Classification Criteria for Psoriatic Arthritis (CASPAR criteria) (51), who had a personal history of psoriasis and active knee involvement were recruited to the study from the rheumatology departments at Sourasky Medical Center in Israel between June 2018 until April 2023. A control group of nine patients with active knee osteoarthritis was also recruited, either from the rheumatology department or the orthopedics surgery department at Sourasky Medical center. Additionally, seven healthy volunteers were recruited to provide blood samples. The study was approved by the Institutional Review Boards of Weizmann Institution of Science, Rehovot, Israel. All participants provided a written informed consent (in accordance with the Helsinki declaration) prior to sample collection. PsA patients were followed for a minimum of six months from the time of sampling (range) with disease activity assessed using the Disease Activity in Psoriatic Arthritis (DAPSA) score (16) calculated at both the sampling time and during follow up visits. Patients were categorized into four groups based on their clinical response to treatment (assessed using the DAPSA score). (For treatment-naïve patients, we considered the response to the first bDMARD treatment administered following the initial sampling. In case of patients with longitudinal samples (n=6), we included the samples from the last visit. ): Responders, achieved remission during follow up visits (DAPSA ≤ 4); Partial responders, exhibit low disease activity during follow up visits (4 ˂ DAPSA ≤ 14); Non-responders, displayed moderate to high disease during follow up visits (DAPSA ˃14); Refractory, displayed moderate to high disease (DAPSA>14) following three or more sequential bDMARDs/tsDMARD (specifically JAKi) with at least two different mode of action.

first: Reut

last: Tzemach

first: Chamutal

last: Gur

first: Truong-San

last: Phan

first: Eyal

last: David

first: Mor

last: Zada

first: Merav

middle: D

last: Shmueli

first: Kfir

last: Mazuz

first: Fadi

last: Sheban

first: Anna

last: Kurilovich

first: Maya

last: Ben-Yehuda

first: Victoria

last: Furer

first: Arik

last: Polachek

first: Smadar

last: Gertel

first: Nimrod

last: Snir

first: Tali

last: Eviatar

first: Sharon

last: Nevo

first: Yifat

last: Merbl

first: Daphna

last: Paran

first: Shuang-Yin

last: Wang

first: Ori

last: Elkayam


title: Effect of artemisinin derivatives on the expression of genes related to oral tongue squamous cell carcinoma

city: KUNMING City

first: Weixing

last: Zeng

state: Yunnan

address: GuiZhou

institute: Kunming Medical University

summary: To investigate the mechanism of artemisinin derivatives in the treatment of oral tongue squamous carcinoma, we treated Cal-27 oral tongue squamous carcinoma cells with artemisinin derivative (DHA) for 48 hours. The results indicated that DHA effectively inhibited the secretion of PDGF-BB by tumor cells, thereby weakening the tumor cells' reprogramming effects on the tumor microenvironment. This finding provides new theoretical support for the anti-tumor mechanisms of natural product derivatives.

overall_design: Cal-27 cells were exposed to DHA and DMSO for 48 hours, and a comparative gene expression profile analysis of the RNA-seq data was performed.

first: WeiXing

first: YongWen

last: He

first: YaWeng

last: Yang


title: Transcriptomic Profile of Microglia Following Inflammation-Sensitized Hypoxic-Ischemic Brain Injury in Neonatal Rats Reveals Strong Contribution to Neutrophil Chemotaxis and Activation

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Inflammation-sensitized hypoxic brain injury significantly contributes to neonatal mortality as affected neonates will not benefit from standard cooling treatments. To clarify why treatments fail in this special scenario, we aimed to experimentally investigate the immune response of microglia in an inflammation-sensitized neonatal hypoxia-ischemia (HI) model. Transcriptomic analysis of microglia isolated from brains following inflammation-sensitized HI brain injury revealed a strong upregulation of leukocyte recruitment and pro-inflammatory markers. Specifically, markers associated with neutrophil-mediated immune responses and chemotaxis were upregulated in the inflammation-sensitized HI group compared to the non-inflammation-sensitized HI and control groups. Serpine 1 and Selp could be identified as specifically upregulated markers indicating an acute inflammatory condition before HI injury. Our study revealed a microglia population which is primed to recruit peripheral neutrophils to infiltrate the brain and mediate neutrophil immune response. We showed a strong contribution to neutrophil activation in case of inflammation following hypoxia-ischemia in the brain. Targeting microglia-mediated neutrophil recruitment can indicate a possible treatment approach in case of inflammation-sensitized HI brain injury.

overall_design: RNA-seq profiling of mciroglia cells from seven-day-old Wistar rat pubs that underwent hypoxia treatment or sham surgery after LPS- or NaCl-sensitization.

first: Anna-Spohie

last: Bremer

first: Nico

last: Henschel

first: Hannah

last: Burkard

first: Maria Eugenia

last: Bernis

first: Thomas

last: Ulas

first: Hemmen

last: Sabir


title: mESC histone modifications under normoxia and hypoxia

city: Wuhu

first: Xiaopeng

last: Shen

address: 1 East Beijing Rd.

institute: Anhui Normal University

summary: The physiological behavior of mouse embryonic stem cells (mESCs) is intricately regulated by microenvironmental oxygen levels, with normoxia (21% O₂) and hypoxia (1-5% O₂) exhibiting distinct impacts on self-renewal, differentiation, and metabolic adaptation. However, the epigenetic mechanisms underlying oxygen-dependent gene expression remain poorly characterized. This study investigates the dynamic alterations of histone modifications associated with transcriptional regulation—specifically, the active promoter mark H3K4me3 (trimethylation of histone H3 lysine 4) and the enhancer mark H3K27ac (acetylation of histone H3 lysine 27)—in mESCs under normoxic versus hypoxic conditions. Utilizing chromatin immunoprecipitation followed by sequencing (ChIP-seq), we systematically mapped genome-wide occupancy patterns of H3K4me3 and H3K27ac, identifying oxygen-sensitive epigenetic landscapes that correlate with differential gene activity. Comparative analysis revealed hypoxia-induced redistribution of these marks at loci linked to pluripotency maintenance, hypoxia-responsive pathways (e.g., HIF-1α targets), and metabolic reprogramming. These findings highlight the role of oxygen tension in reshaping the epigenetic architecture of mESCs, providing insights into how microenvironmental cues fine-tune stem cell functionality through histone modification dynamics. This work advances our understanding of epigenetic plasticity in stem cells and may inform strategies for optimizing in vitro culture conditions or manipulating cell fate under physiological or pathological oxygen gradients.

overall_design: ChIP-seq of the histone modifications H3K4me3 and H3K27ac in mESCs under normoxia and hypoxia, respectively

first: Meng

last: Li


title: Vascular-type heterogeneity is associated with differential gene expression profiles of endothelial cells under shear stress

city: Aurora

first: Christopher

last: Ng

state: Colorado

address: 12800 East 19th Ave

institute: University of Colorado - Anschutz Medical Campus

summary: Background: Endothelial cell (ECs) heterogeneity is an emerging area of research in EC biology. Veins, arteries, and microvascular endothelial cells, termed “vascular-type” heterogeneity in this report, have been shown to have heterogeneity in gene expression and function. In addition to this innate heterogeneity, we hypothesized that different vascular-type ECs would also demonstrate heterogeneity in their response to shear stress. Objectives: We interrogated whether vascular-type ECs would demonstrate variations in transcriptional expression patterns under shear stress. Methods: Human umbilical vein endothelial cells (HUVECs), human pulmonary arterial endothelial cells (HPAECs), and human microvascular endothelial cells (HMVECs) were commercially purchased and subjected to shear stress conditions of 0, 1, 4, and 10 dynes/cm2 of laminar shear stress. After exposure to shear stress, cells were analyzed for cellular alignment and RNA was extracted and evaluated via bulk RNA-sequencing (RNA-seq). Results: All ECs demonstrated significant changes in alignment under shear stress. Shear stress significantly affected the transcriptomes of ECs resulting in differentially expressed genes and pathways; while several genes were differentially expressed across all three vascular-types (44.2%), most differentially expressed genes were limited to 1 or 2 of the vascular-types. Hemostatic and thrombotic genes were found to have differential expression patterns under conditions of shear stress, and VWF demonstrated a pattern of vascular-type heterogeneity in response to shear stress.  Conclusions: Shear stress causes changes in cellular alignment and transcriptional patterns in ECs that is dependent upon underlying vascular-type. Therefore, endothelial vascular-type heterogeneity can regulate response to shear stress, especially in hemostatic and thrombotic gene expression.

overall_design: Bulk RNA-sequencing of HUVECs, HMVECs, and HPAECs under laminar stress conditions of 0, 1, 4, and 10 dynes/cm^2

first: Allaura

last: Cox

middle: J


title: Identification of transcription factors that regulate placental sFLT1 expression

city: Alphen aan den Rijn

first: Qing

last: Yong

address: Emmalaan

institute: LUMC

summary: Soluble FMS-like tyrosine kinase 1 (sFLT1) is a decoy receptor of vascular endothelial growth factor. Increased sFLT1 levels have been associated with preeclampsia, chronic kidney diseases, and kidney transplant rejection. However, lower levels of sFLT1 also exhibit beneficial properties in various conditions, such as organization of actin cytoskeleton in podocytes, and immune regulation in healthy pregnancy. Therefore, understanding the transcriptional regulation of sFlt-1 and preserving appropriate expression levels are critical for effective treatment of preeclampsia and other diseases. Cytotrophoblasts (CTBs) were isolated from three first trimester placentas and differentiated into extravillous trophoblasts (EVTs) for six days. RNA was extracted at different time points and used for RNA sequencing. Differentially expressed genes (DEGs) and transcription factors (DETFs) were analyzed. TF enrichment analysis and pathway analysis were performed on DEGs screened from EVTs and CTBs. TF inhibitors were added to primary CTBs directly or during CTB to EVT differentiation to confirm the regulatory effect of TFs on sFLT1 expression. In total, 197 transcription factors were differentially expressed between CTBs and EVTs, among which, 15 DETFs (EPAS1, ETS1, TBX3, CEBPB, FLI1, TEAD4, GATA4, TBX2, LMX1B, ARNT, FOXM1, ERF, PRDM1, TFAP2A and NR2F2) that potentially regulate sFLT1 expression were predicted by ChEA3 and KnockTF software. The mRNA levels of 15 DETFs were validated upon CTBs differentiation into both EVTs and syncytiotrophoblast. The regulatory effects of FOXM1 and CEBPB were confirmed in vitro experiments, and their expression patterns were validated during CTBs differentiation into EVTs and in first trimester placentas. Pathway analysis showed that sFLT1 was involved in P13K-Akt, Rap1, MAPK, Ras and HIF-1 signaling pathway, focal adhesion, and cytokine-cytokine receptor interaction. Protein-protein interaction analysis showed FLT4, PDGFB, TGFB1, IL6R, TNFRSF1B, CSF1R, TGFB2 to be interacted with FLT1. The identified transcription factors can serve as therapeutical targets in preeclampsia to keep the sFLT1 levels within appropriate limits.

overall_design: CTBs were isolated from first trimester placentas of three donors and differentiated into EVTs for six days. RNA was collected on day 0, day 3 and day 6 accordingly, and used for RNA sequencing.

first: Hailiang

last: Mei

first: Michael

last: Eikmans

first: Hans

last: Baelde


title: Transcutaneous vagal nerve stimulation improves heart failure with preserved ejection fraction by modulating cardiac resident macrophage function

city: Oklahoma City

first: Kurt

last: Zimmerman

state: Oklahoma

address: 940 Stanton L Young Blvd

department: Internal Medicine

institute: University of Oklahoma Health Sciences Center

summary: Background: We previously showed in a rat model of heart failure with preserved ejection fraction (HFpEF) that transcutaneous vagus nerve stimulation (tVNS) reduced cardiac fibrosis and inflammation. However, macrophage-mediated mechanisms through which tVNS rescues cardiac function remain poorly understood. Methods: We induced HFpEF in 8-week-old mice by a combination of a high-fat diet and L-NAME for 5 weeks followed by 4 weeks of tVNS or sham stimulation. At this time, we analyzed cardiac function by echocardiography and immune cell numbers by single cell RNA sequencing and flow cytometry.  Results: Our data demonstrate that HFpEF mice exhibited diastolic dysfunction, left ventricular hypertrophy and fibrosis, consistent with HFpEF, and that tVNS significantly improved HFpEF severity. Analysis of merged single cell RNA sequencing data from control, HFpEF + sham, and HFpEF + tVNS mice showed that HFpEF was associated with accumulation of Spp1 expressing CCR2+ cardiac resident macrophages (CRM). Further, treatment with tVNS reduced the number of CCR2+ CRM and the expression of Spp1, while also inducing the expression of Igf1 in Timd4+/Lyve1+/Folr2+ (TLF+) and MHC2+ CRM. Global deletion of Spp1 or blockade of CCR2+ CRM recruitment improved HFpEF, whereas TLF+/MHC2+ specific deletion of Igf1 reversed the protective effect of tVNS on HFpEF. The benefits of tVNS were also abolished in the setting of disrupted acetylcholine (ACh)/α7 neuronal ACh receptor (α7nAChR) signaling, either via pharmacological inhibition of α7nAChR or choline acetyltransferase deletion in CD4⁺ T cells. Conclusion: Collectively, our data indicate that tVNS improves HFpEF by reducing Spp1 expressing CCR2+ CRM and inducing expression of pro-reparative Igf1 in TLF+/MHC2+ CRM. These effects are mediated through cholinergic signaling, highlighting a neuroimmune pathway in HFpEF.

overall_design: We performed single cell RNA sequencing (scRNAseq) on heart tissue collected from control, HFpEF, or HFpEF + tVNS treated mice. These samples were collected 9 weeks after beginning the HFpEF diet.

first: Zimmerman

last: Kurt A

first: Stavrakis

last: Stavros


title: HSF1 promotes proliferation and chemoresistance in diffuse large B-cell lymphoma by enhancing cell cycle and DNA repair

city: Guangzhou

first: Yu

last: Fang

state: State...

address: 107th Yanjiangxi Road

institute: Sun Yat-Sen Memorial Hospital

summary: To further elucidate the mechanism of HSF1-mediated transcriptional regulation in diffuse large B-cell lymphoma, we conducted transcriptomic sequencing on SU-DHL-2 and SU-DHL-6 cells treated with or without DTHIB (8 μM).

overall_design: Diffuse large B-cell lymphoma cells SU-DHL-2 or SU-DHL-6 were treated with DMSO or DTHIB (8 μM) for 36 hours. The RNA of the treated cells was extracted and sequenced on Illumina NovaseqTM 6000 platform and 100-bp paired-end reads were generated.

first: Liang

last: Cheng

first: Xu

last: Chen

first: Qingqing

last: Cai


title: RNA sequencing of primary bone marrow-derived macrophages from MAPL KO and control mice.

city: Berkeley

first: Olesia

last: Ignatenko

state: CA

address: Morgan Hall

institute: UC Berkeley

summary: Differential expression analysis

overall_design: untreated, LPS+Ifny 4.5 hours, LPS+Ifny 24 hours

first: Heidi

last: McBride

first: Mai

last: Nguyen

first: Jack

last: Collier


title: Differential Gene Expression Profiles of Pancreatic Ductal Adenocarcinomas Among African American and Caucasian American Patients

city: Birmingham

first: Sooryanarayana

last: Varambally

state: Alabama

address: 1824 6th Avenue S

institute: University of Alabama

summary: PURPOSE: Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer-related deaths. In the United States (US), African Americans (AA) have higher PDAC incidence and mortality than Caucasian Americans (CA). This study aimed to identify distinct gene expression patterns and differentially regulated pathways in AA and CA PDACs. METHODS: Whole transcriptomic analyses were conducted on FFPE sections of PDACs (n=40) from AA (9 PDAC/3 normal) and CA (31 PDAC/5 normal) tissues to evaluate differential expression and signaling pathways within and between racial groups and to identify distinctive and common genes/pathways. RESULTS: We identified uniquely upregulated genes in both racial groups. Among the 25 top upregulated genes in AA PDACs, compared to their normal tissues, were CHST15, PARP15, and NUDT16. Altered pathways in AA PDACs included glycerophospholipid metabolism and regulation of lipolysis in adipocytes. In contrast, a different set of top 25 upregulated genes was found in CA PDACs, including SERPINB3, PADI1, H3C8, and ZNF488. The altered pathways in CA PDACs included cellular senescence and PD−L1/PD−1 checkpoint pathways. Thirteen genes (seven upregulated and six downregulated) were differentially modulated in AA vs. CA PDACs. Using a publicly available database, we analyzed the top 25 upregulated genes (normal vs. tumor) and seven differentially upregulated genes (AA vs. CA) for associations with survival outcomes. Eight genes (CHST15, PARP15, NUDT16, SERPINB3, PADI1, H3C8, ZNF488, and LETM2) correlated with poor survival. CONCLUSION: These findings show distinct gene expression profiles and modulated pathways in AA and CA PDACs, supporting development of race-based therapeutic targets.

first: Prachi

last: Bajpai

first: Ravi

last: Paluri

first: Sameer

last: Al Diffalha

first: Darshan

last: Chandrashekar

first: Upender

last: Manne


title: Exercise-induced microbiota metabolite enhances CD8 T cell antitumor immunity promoting immunotherapy efficacy

city: Pittsburgh

first: Tingting

last: Duan

state: PA

address: 5117 Centre Avenue

institute: University of Pittsburgh

summary: Exercise improves immune checkpoint inhibitor (ICI) efficacy in cancers like melanoma, however, the mechanisms through which exercise mediates this antitumor effect remain obscure. Here we identify the gut microbiota as playing a previously unrecognized, critical role in how exercise improves ICI efficacy in preclinical melanoma. Our study demonstrates that exercise stimulates microbial one-carbon metabolism, increasing levels of the metabolite formate, which subsequently enhances Tc1-mediated ICI efficacy. We further establish that microbiota-derived formate is both sufficient and required to enhance Tc1 cell fate in vitro and promote tumor antigen-specific Tc1 immunity in vivo. Mechanistically, we identified the transcription factor nuclear factor erythroid 2-related factor-2 (Nrf2) as a crucial mediator of formate-driven Tc1 function enhancement in vitro and a key player in the exercise-mediated antitumor effect in vivo. Finally, we identify human microbiota-derived formate as a potential biomarker of enhanced Tc1-mediated antitumor immunity and support its functional role in driving melanoma suppression.

overall_design: Naïve CD8T cells were stimulated with aCD3 + aCD28 along with IL-12  for 18 hrs. After 18 hrs, stimulate with either vehicle contorl or formate for  24 h


title: Microarray profiling of pooled pancreas RNA from control and methionine-deficient mice

city: Tokyo

first: Xuguang

last: Li

address: 1-1-1 Yayoi, Bunkyo-ku

institute: Tokyo University

summary:
Total RNA extracted from pooled pancreas tissue of 10-week-old male offspring of control or methionine-deficient mothers.
Gene expression profiles were generated using Affymetrix Mouse Genome 430 2.0 Arrays. Expression comparison was made between the control and methionine-deficient groups.

overall_design: Pancreatic RNA from control or methionine-deficient mice was pooled per group before microarray analysis. Each pooled sample was analyzed on one chip.

first: Huijuan

last: Jia


title: Pseudouridine Synthesis Targeted Therapy Activates Antiviral Immunity to Boost Cancer Immunotherapy

city: Shanghai

first: Yanfeng

last: Liu

address: No. 160, Pujian Road, Pudong New Area, Shanghai, China

institute: Ren Ji Hospital, School of  Medicine, Shanghai Jiao Tong University

summary: Epigenetic plasticity is critical for tumor transformation, progression, and response to immunotherapy. Although pseudouridine is the first discovered and most abundant epitranscriptomic modification, its cellular functions remain poorly understood. In this study, we identified pseudouridine synthase (PUS) as a key driver of tumor immune evasion. Specifically, we found that PUS was aberrantly overexpressed in tumors and correlated with tumor malignant progression as well as poor patient prognosis, particularly in patients with TP53 mutations. Notably, genetic ablation of PUS effectively suppressed tumor progression, increased T cell infiltration, and boosted T cell function in a de novo MYC/Trp53-/- mouse liver cancer, as well as in chemically induced liver cancer models. Mechanistically, PUS loss induced the expression of retrotransposon sequences, resulting in elevated levels of double-stranded RNA and subsequent activation of innate antiviral immune signaling. We further demonstrated the role of PUS1 in tumor immune evasion was dependent on its enzymatic activity. Importantly, inhibition of PUS1 could sensitize tumors to anti-PD-1 therapy in a MYC/Trp53-/- mouse liver cancer model. Similarly, we revealed that 5-fluorouracil could inhibit pseudouridine synthesis and significantly enhance the efficacy of PD-1 inhibition. Clinically, low PUS level showed a higher response rate and better clinical outcome to immune checkpoint blockade therapies. Overall, our findings demonstrate PUS1 as a critical regulator of immune evasion and targeting pseudouridine synthesis may a novel strategy to enhance immunotherapy efficacy by activating dsRNA-sensing pathways.

overall_design: Given the clinical relevance of PUS enzymes in hepatocellular carcinoma (HCC) development, we further explored their pro-tumorigenic role in liver cancer progression. Using a chemically induced liver cancer model, we compared liver-specific Pus1 knockout mice (Alb-cre; Pus1f/f, hereafter Pus1-cKO) with control mice (Pus1f/f, WT). To determine whether PUS1’s role in tumor progression and immune evasion depends on its pseudouridine synthase activity, we generated a catalytically inactive mutant (PUS1-Mut) by substituting Ala for Asp146 (D146A). The functional impact of wild-type PUS1 (PUS1-WT) and PUS1-Mut was then evaluated in a de novo MYC/Trp53-/- mouse liver tumor model. High-throughput sequencing was performed on both mouse models.

first: Fan

last: Wang

first: Yangfen


title: Targeting the ERα DBD-LBD interface with mitoxantrone disrupts receptor function through proteasomal degradation

city: Cleveland

first: Han

state: Ohio

address: 2109 Adelbert Rd, Wood Building, RT400

institute: Case Western Reserve University

summary: The estrogen receptor (ER or ERα) remains the primary therapeutic target for luminal breast cancer, with current treatments centered on competitive antagonists, receptor down-regulators, and aromatase inhibitors. This therapeutic landscape frames our discovery of an alternative mechanism of ER inhibition that targets the critical interface between the DNA-binding domain (DBD) and ligand-binding domain (LBD) of the receptor. We identified mitoxantrone (MTO), an FDA-approved topoisomerase II inhibitor, as a specific ligand for this previously unexplored DBD-LBD interface. Through integration of computational, biophysical, biochemical, and cellular analyses, we demonstrate that independent of its DNA damage response activity, MTO binding induces ER conformational changes, leading to cytoplasmic redistribution and proteasomal degradation. Notably, MTO also effectively inhibits constitutively active ER mutants (Y537S and D538G) commonly associated with endocrine therapy resistance, suppressing ER/ER-mutant-dependent gene expression and tumor growth more potently than fulvestrant. These findings establish the DBD-LBD interface as a crucial regulatory point for ER function, suggesting a new paradigm for targeting domain interfaces across the nuclear receptor family.

overall_design: Three MCF-7 cell lines (wildtype, Y537S ER knock-in, and D538G ER knock-in) were treated with four different conditions: vehicle control, fulvestrant (1 μM), MTO (1 μM), or combination treatment (fulvestrant + MTO) for 48 hours. Gene expression profiling was performed using RNA sequencing on the Illumina NextSeq 550 platform with 75 bp single-end reads. Two biological replicates were included for each treatment condition across all three cell lines, resulting in a total of 24 samples (3 cell lines × 4 treatments × 2 replicates).

first: Hung-Ying

last: Kao

first: Sichun

last: Yang


title: Application of machine learning (ML) / deep learning (DL) using multiple epigenetic features reveals H3K27Ac as driver of gene expression  prediction across patients with glioblastoma

city: Bronx

first: Jorge

middle: Eduardo

last: Fajardo

state: NY

address: 1301 Morris Park Avenu

department: Computational and Systems Biology

institute: Albert Einstein College of Medicine

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

overall_design: Refer to individual Series


title: The role and mechanism of hypoxia-induced SLC6A8 up-regulation in HCC progression

city: Jinan

first: Rui zhe

address: No.104, Wen hua west Road

institute: Shandong University

summary: Hypoxia is a hallmark of solid tumors and profoundly affects the malignant phenotypes of cancer cells. We find that the creatine transporter solute carrier family 6, member 8 (SLC6A8) is upregulated in hypoxic HCC cells. Hypoxia-induced creatine accumulation drives metabolic reprogramming and antagonizes parthanatos. Pharmacological inhibition of SLC6A8 represents a promising therapeutic strategy for HCC.

overall_design: RNA-seq profiling of control (shNC) and SLC6A8-knockdown (shSLC6A8) HCC cells under hypoxia for 24 hours.


title: Martinostat as a Novel HDAC Inhibitor to Overcome Tyrosine Kinase Inhibitor Resistance in Chronic Myeloid Leukemia

city: Seoul

first: Marc

last: Diederich

address: Gwanak-ro, Gwanak-gu, 1

department: College of Pharmacy

country: South Korea

institute: Seoul National University

summary: Chronic Myeloid Leukemia (CML) remains a therapeutic challenge, particularly in patients who develop resistance to standard tyrosine kinase inhibitors (TKIs) such as imatinib. Here, we present the first demonstration of the potent anti-leukemic activity of the histone deacetylase (HDAC) inhibitor martinostat in both TKI-sensitive and TKI-resistant CML. Structural and biochemical analyses confirmed the efficient and selective binding of martinostat to HDAC isoenzyme ligand-binding pockets, resulting in histone and tubulin hyperacetylation in both imatinib-sensitive and resistant CML cells, outperforming vorinostat, a clinically used HDAC inhibitor (HDACi). It selectively impaired CML cell proliferation and viability and induced apoptosis across various CML models, including resistant cell models and patient blasts, with minimal toxicity to healthy cells and low developmental toxicity in zebrafish. In addition to its single-agent efficacy, martinostat demonstrated enhanced anticancer effects when combined with imatinib, both in vitro and in vivo, significantly reducing tumor growth in resistant CML xenograft models. Mechanistically, mRNA-seq data showed that martinostat disrupted key survival signaling pathways and amplified apoptotic responses, thereby contributing to its anticancer activity. These findings highlight the potential of martinostat as a selective, low-toxicity HDACi that, when combined with TKIs, could provide an effective strategy to overcome drug resistance in CML and improve therapeutic outcomes.

overall_design: K-562 cells were treated with Martinostat (HDAC inhibitor) for 24 h at different concentrations in 3 independent biological replicates.

first: Haeun

first: Vladimir

first: Michael

last: Schnekenburger


title: Unraveling the Development of Cutaneous Neurofibromas in Neurofibromatosis Type 1

city: Créteil

first: Pernelle

last: Pulh

address: 8 rue du général Sarrail

institute: INSERM - IMRB

summary: Neurofibromatosis type 1 (NF1) is a genetic disorder that leads to the formation of cutaneous neurofibromas (cNFs), benign nerve sheath tumors that develop in the skin and significantly impact patients’ quality of life. cNF development begins with bi-allelic NF1 loss in Schwann cell (SC) lineage, followed by the recruitment of a complex tumor microenvironment consisting of fibroblasts, immune cells, blood vessels, axons and a dense extracellular matrix. Despite their high prevalence and clinical impact, the molecular mechanisms underlying cNF formation remain poorly understood. Here, we used an Nf1 knockout (Nf1-KO) mouse model, combined with immuno-histochemistry and single-cell transcriptomics, to explore the mechanisms driving cNF development. Our findings revealed that mutant SCs accumulate in the skin of young mice weeks before cNF onset. However, these cells remain quiescent until triggered by skin trauma, which induces their proliferation and the rapid formation of cNFs. Using a trauma-induced Nf1-KO model with scRNAseq, we conceived a transcriptomic atlas of growing and mature cNFs, as well as adjacent, seemingly healthy skin. This analysis identified a population of non-myelinating Aquaporin1highNestinlow SCs as the likely cells of origin for cNFs. These cells overexpress genes involved in axon growth and guidance, potentially driving the abnormal innervation observed in cNFs from both mice and patients. Additionally, we found that tumor SCs, along with dermal and/or epineurial fibroblasts and pericytes, overexpress collagen-encoding genes, contributing to the extensive fibrosis characteristic of cNFs. Notably, all of these cells exhibit high expression of Periostin and Tenascin C, key extracellular matrix components, highlighting them as novel therapeutic targets for cNF treatment.

overall_design: To elucidate the cellular and molecular landscape driving cNF development in mice, we performed single-cell RNA sequencing (scRNAseq) on cNFs, adjacent healthy-looking skin (HLS), and control healthy skin (HS) at both the growth (P90) and stabilization (P365) periods of cNF development. To optimize cell dissociation while preserving transcriptomic integrity, we compared a 3-hour versus an 18-hour (overnight) dissociation protocol.

first: Fanny

last: Coulpier

first: Audrey

last: Onfroy

first: Layna

last: Oubrou

first: Wanzhen

last: Zhang

first: Léa

last: Toledano

first: Elie

last: Abou Zougheib

first: Laura

last: Fertitta

first: Pierre

last: Wolkenstein

first: Piotr

last: Topilko


title: Age-linked DNA Methylation and Gene Expression in Head and Neck Alveolar Rhabdomyosarcoma

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

type: Methylation profiling by genome tiling array

summary: Alveolar rhabdomyosarcoma (ARMS) primarily affects children in the first decade of life, but it can also occur during adolescence, typically with a more favorable prognosis. This study aimed to explore DNA methylation (DNAm) and gene expression differences that could explain the poorer prognosis in younger patients. Whole-genome DNAm and transcriptome analyses were conducted on 10 head and neck ARMS samples, including 4 from patients under 1 year old and 6 from those over 10 years old. Although DNAm profiles were similar across age groups, significant differences in gene expression were identified. These findings suggest potential age-related molecular mechanisms and highlight candidate genes for further investigation as novel therapeutic targets. Notably, CDK9 emerged as a promising target, warranting further exploration in the context of ARMS treatment.

overall_design: Patients were divided in two age groups. Then we performed differential methylation analysis between patients under one year of age (group A) and over 10 years of age (group B), compared the global methylation profile to other reference sarcoma samples (PMID: 33479225) and used them to compute copy number variations (CNVs) and mitotic age (with epiTOC2).


title: YAP controls cell migration and invasion through a Rho-GTPase switch

city: Jackonsville

first: Alfredo

last: Quinones-Hinojosa

address: 4500 San Pablo Rd

institute: Mayo Clinic

summary:
Delineating the mechanisms controlling the invasive spread of non-diseased and transformed cells is central to understanding diverse processes including cancer progression. Here, we found that Yes-associated protein (YAP), a central transcriptional regulator implicated in controlling organ and body size, modulated a Rho-GTPase switch that drives cellular migration by transactivating the Rac1-GEF protein TRIO through direct modulation of its intronic enhancer. Additionally, YAP and TRIO may promote invasive behavior through putative crosstalk with STAT3 signaling, a potential downstream target. Although we found this YAP-dependent infiltrative program in many cell types, it was particularly enhanced in a patient-specific manner in the most common malignant brain tumor, glioblastoma (GBM), where hyperactivation of the YAP, TRIO, and STAT3 signatures also conferred poor clinical outcome. Our analysis suggests that the YAP-TRIO-Rho-GTPase signaling network identified in this study is a ubiquitous regulator of invasive cell spread in both physiological and pathological contexts.
In this dataset, we knocked down YAP in two patient-derived GBM primary cell lines (JHGB612 and JHGB651) and performed microarray analysis.

overall_design: A total number of 12 samples were analyzed. JHGBM612 and JHGBM651 cells with stable knockdown of YAP (shYAP) and the empty backbone vector as a control (shCtrl), each with 3 replicates. shYAP and shCtrl cells were extracted for microarray analysis.

first: Sagar

last: Shah

first: Nathaniel

last: Tippens


title: Genomic and Behavioral Signatures of Selection for Ethanol Preference from the Heterogeneous Stock Collaborative Cross Mice – The Central Nucleus of the Amygdala II

city: Portland

first: Justin

last: Anderson

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Behavorial Neuroscience

institute: Oregon Health & Science University

summary: Alcohol use disorder (AUD) is a complex disease with heritability of ~0.5, indicating genetic and non-genetic factors contribute to risk. Identifying gene expression networks contributing to risk using post-mortem human brain tissue has the limitation of conflating risk for AUD with consequences of alcohol use. We leveraged mice selectively bred for differential ethanol preference from a highly genetically diverse population to overcome this limitation. Ethanol intake was highly correlated with preference, high-preferring (HP) mice consumed more sweet- but not bitter-tasting solutions compared to low-preferring (LP) mice, and the lines did not differ in rate of ethanol elimination. Adult, ethanol-naïve HP and LP mice contributed tissue from the central nucleus of the amygdala (CeA), a region critical to ethanol preference and intake. Single-nuclei and bulk RNA sequencing data were used to identify cell types and transcriptome changes related to selective breeding for differential risk for ethanol preference. Single nuclei analysis identified populations of inhibitory (~48% of cells) and excitatory (~23%) neurons, and non-neuronal (~29%) cells, but no differences in cell-type composition or gene expression were identified between the lines. Bulk CeA analysis identified differences between the lines for: (1) gene expression (2996 genes), (2) expression variability (426 genes), and (3) wiring (407 significant gene-gene correlations). Overall, lower variance was found in the HP line. Reduced gene-gene correlation, also found in HP mice, suggested that selection for high preference induced changes in transcriptional regulation resulting in reduced connectivity, specific to gene networks enriched in markers for inhibitory neurons expressing Isl1 and Tac1.

overall_design: Mice underwent bidirectional selective breeding for ethanol intake (10% ethanol v/v in water, two bottle choice) for 5 generations starting from the Heteroengeous Stock - Collaborative Cross, a strain which emcompasses ~90% of all genetic diversity known in Mus Musculus. After 5 generations, high and low preference  mouse had ~10fold different prefernce for ethanol and consumed 7fold differently. Ethanol naive mice from generation 5 were sacrificied at adulthood and brain tissue was collected for the central nucleus of the amygdala, a region important for addiction. bulk RNA sequencing (paired-end) was run on 200 samples (n=50/sex/strain) to a mean depth of 20M, and aligned to the GRCm39 using STAR. Raw counts were normalized using the limma+voom method, and differential expression and weighted gene co-expression analysis were carried out to identify risk vs protection markers for ethanol drinking.

first: Priscila

last: Darakjian

first: Robert

last: Hitzemann

first: Rita

last: Cervera-Juanes

first: Kip

last: Zimmerman

first: Cheryl

last: Reed

first: Denesa

last: Lockwood

first: Angela

last: Ozburn

first: Tamara

last: Phillips


title: The role and mechanism of hypoxia in regulating parthanatos in hepatocellular carcinoma

first: Rui zhe

last: Li

summary: Recently, a PARP1-dependent cell-death process termed "parthanatos", driven by DNA damage, has emerged as a crucial regulator of tissue homeostasis and tumorigenesis. Hypoxia is a hallmark of solid tumors and profoundly affects the malignant phenotypes of cancer cells. The crosstalk between parthanatos and hypoxia remains poorly understood. In our study, we find that despite causing DNA damage, hypoxia fails to induce parthanatos in HCC. Transcriptome sequencing upon MNNG stimulation indicated that the creatine transporter solute carrier family 6, member 8 (SLC6A8) was involved in parthanatos antagonism and malignant phenotypes in hypoxic HCC cells.

overall_design: RNA-seq profiling of MNNG (50μM) treated HCC cells under normoxia or hypoxia for 48 hours.


title: Chondrodystrophic Dogs as a Pre-clinical Large Animal Model of Discogenic Back Pain

city: Columbus

first: Maciej

last: Pietrzak

state: OH

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

institute: Ohio State University

summary: Background: Intervertebral disc (IVD) degeneration is a major cause of low back pain (LBP) in humans and canines. IVD degeneration affects the structure and function of both the disc and the innervating dorsal root ganglion (DRG) neurons. Pre-clinical animal models are necessary for elucidating the mechanisms of IVD degeneration (IVDD) and the pain signaling pathways involved in discogenic back pain. The chondrodystrophic (CD) dog exhibits similar characteristics to the clinical population affected by IVDD-associated LBP. However, further investigation of the translational tools to study these conditions and the efficacy of novel treatments is needed in this canine model. The objectives of the present study are to: (1) assess the changes in the structure and function of the IVD and DRG, including pain behaviors, in response to injury using a comprehensive set of outcome measures and (2) evaluate the efficacy of potential therapeutics in mitigating these pathologic changes due to injury in the CD canine model. Methods: Retired female research beagles underwent spinal surgery where T11/T12, T12/T13, and T13/L1 IVDs were identified and punctured with a needle containing either a protease-activated receptor 2 antagonist (PAR2A) and cromolyn sodium (CS) solution (N=3) or phosphate-buffered saline (PBS) (N=3). Pain phenotyping and related outcomes were assessed longitudinally or at the 12-week endpoint via RNA-seq on the DRG, von Frey analysis, FitBark activity, and C-reactive protein (CRP) plasma levels. Changes in the structure/function of the IVD were assessed via MRI, mechanics, Dimethylmethylene Blue Assay (DMMB), histological staining using Picrosirius red/ Alcian Blue (PR/AB) and fluoroscopy, and electrophysiology on the DRG neurons. Results: We evaluated a comprehensive series of outcome measures to determine the effects of IVD injury on the structure/function of the canine IVD and DRG, and pain in the in vivo CD dog model of IVDD and back pain. Specifically, we established methods to obtain high-quality messenger RNA from canine DRGs to perform bulk RNA-seq. We demonstrated that injury to the disc resulted in significant upregulation of inflammatory and pain-signaling genes, and downregulation of developmental genes in the adjacent innervating DRG neurons. Additionally, we isolated and cultured viable neurons from canine DRGs and found through whole-cell patch-clamp that that DRGs innervating the injured disc demonstrated altered voltage-gated sodium channel (VGSCs) activity compared to controls. Using T2 weighted MRI, we demonstrated that relaxation time in punctured discs was reduced in four out of the six dogs compared to internal control discs, indicating potential compositional changes in these injured IVDs. No significant effect of PAR2A and CS treatment was observed in this small cohort.Conclusion: This study evaluated a rigorous series of outcome measures to determine the effects of IVD injury on the disc joint and pain in a CD canine in vivo model of back pain. This was the first study to investigate the effects of disc injury on canine DRG transcriptome and whole-cell patch clamping on canine DRG neurons. Results support the CD dog as a clinically relevant translational model for studying IVDD and LBP, and for evaluating the potential efficacy of novel therapeutics in mitigating the changes associated with these conditions.

overall_design: DRGs from L4/5 (internal control) and T12/L1 (puncture) were dissected and RNA isolated using the TRIzol Plus RNA Purification Kit (Cat#12183555). RNA-seq was performed at The Ohio State University Genomics Core with library generation using a NEBNext rRNA Depletion and Prep Kit. cDNA libraries were sequenced on Novaseq SP system (Illumina, USA).

first: Mary

last: Heimann

first: Brett

last: Klamer

first: Devina

last: Purmessur


title: Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer [normal colon tissue]

first: IlSeok

last: Choi

address: 50, Yonsei-ro, Seodaemun-gu

department: Biotechnology

institute: Yonsei University

summary: Fusobacterium nucleatum (Fn), enriched in human colorectal cancer (CRC), is linked to a worse prognosis. To uncover the cellular and molecular mechanisms behind this Fn-associated prognostic effect, we conducted single-cell transcriptomic analyses on 42 surgically removed colon tissues from newly diagnosed colon cancer patients. Through single-cell and spatial transcriptome data analyses, we found that the development of IgA plasma cells producing functional secretory IgA was impaired due to disrupted communications between IgA plasma cells and macrophages in Fn-positive CRC. Additionally, we identified a dysregulated IgA maturation (IGAM) module in Fn-positive patients, indicating compromised IgA-mediated mucosal immunity. This finding was further supported by observed increases in bacterial infiltration within tumors of Fn-positive patients. Remarkably, we were able to stratify Fn-positive patients based on IGAM activity, which could lead to novel treatment strategies for Fn-positive CRC patients. Our findings indicate that impaired secretory IgA activity by Fn infection increases the bacterial burden within tumors and worsens prognosis through chronic inflammation. Additionally, identifying a novel gene expression biomarker for stratifying Fn-positive patients promises to refine CRC treatment strategies, offering a more tailored approach to patient care.

sample_organism: Fusobacterium nucleatum subsp. nucleatum ATCC 25586

overall_design: To examine the influence of Fn in the colon under monocolonization, we designed an in vivo experiment using germ-free (GF) mice. Six-week-old female GF mice with a C57BL/6 background were used in all experiments. Ten mice were randomly divided into two groups (5 mice per group) including control group and Fn group. GF mice were fasted for 2 hours prior to oral gavage. Fn group received an oral administration of 1 × 10⁹ colony-forming units (CFU) in 200 µL of PBS, while the control group received an equivalent volume of PBS alone, three times per week for 5 weeks. At the end of the experiment, the GF mice were sacrificed, and colon tissues were collected from control (n=5) and Fn (n=5) groups. Dissected colon tissues from PBS control (n=5) and Fn-treated (n=5) GF mice were pooled for each group.

first: Ilseok

first: Kyung-A

last: Kim

first: Sang Cheol

first: Insuk

last: Lee

first: Han Sang

first: Yoon Dae

last: Han


title: Transcriptomics data on muscle atrophy in the state of cancer cachexia, as well as the therapeutic effects of Astragalus membranaceus Decoction

first: tian

last: zhihan

address: No. 16369, Jingshi Road

institute: Affiliated Hospital of Shandong University of Traditional Chinese Medicine

summary: Cancer cachexia (CC) causes severe muscle loss in advanced cancer patients, significantly impacting their quality of life and life expectancy. The autophagy-lysosome system is a key pathway in muscle depletion in CC, yet targeted therapies are limited. This study examines how Astragalus polysaccharides (APS) from Astragalus membranaceus alleviate muscle wasting in CC mice. Mice were divided into control, model, and APS high-dose groups. Transcriptomic analysis identified differentially expressed genes (DEGs) enriched in autophagy and mitochondrial autophagy pathways. Results indicate that APS treatment normalizes the expression levels of some DEGs in cachectic muscle tissue. For instance, autophagy-related genes Gabarapl1, Ggad45b, and Igf1r return to normal levels after APS treatment. KEGG pathway analysis suggests that APS modulates the transcription of autophagy- and mitochondrial autophagy-related genes, reducing over-activated autophagy and mitochondrial autophagy activities. Collectively, our data provide additional insights into the transcriptional profiles of cachectic muscle and muscle treated with APS, highlighting the potential of APS as a therapeutic agent for mitigating muscle depletion in cancer cachexia.

overall_design: Six-week-old male BALB/c nude mice were subjected to subcutaneous injection of CT-26 colon cancer cells (5×10^⁵ cells) into the right flank. At week 28, the entire leg muscles were dissected and homogenized, with three randomly selected samples from each group used for transcriptomic sequencing.

first: Zhihan

last: Tian

first: Yong

last: Wang

first: Xue

last: Liu

first: Xin

last: Xin

first: Shuai

first: Yiwei

last: Qu

first: Ziyuan

first: Xiaoyu

last: Su

first: Dufang

last: Ma


title: Single-stranded DNA binding proteins are essential components of the architectural LDB1 protein complex [4C-seq]

city: Philadelphia

first: Xiaokang

address: 315 A  Abramson Research Center, 3615 Civic Center Blvd.

department: Hematology

institute: Children's hospital of Philadelphia

summary: Transcriptional enhancers are brought into proximity with promoters via chromatin looping. The architectural transcription cofactor LDB1 facilitates spatial connectivity among enhancers and promoters, but whether this occurs through simple dimerization or requires heterotypic protein assemblies is unknown. Here we investigated single-stranded DNA binding proteins (SSBPs) in regulating LDB1-mediated chromatin looping and transcription. SSBP2, SSBP3, and SSBP4 colocalize with LDB1 genome-wide. Among these, only SSBP3 is essential for murine erythroid cell viability, LDB1 function, and transcription. LDB1 but not single-stranded DNA is the predominant genome-wide tether of SSBP3 to chromatin. SSBP3 depletion in SSBP2/4 knockout cells globally weakened LDB1-dependent chromatin loops and lowered nascent transcription without impacting LDB1's chromatin binding. Chromatin tethering experiments revealed SSBP3 and LDB1 mutually depend on each other to form looped contacts. SSBP3 stabilizes LDB1 dimerization in vitro, providing a possible mechanism. SSBPs emerge as key functional components of the architectural LDB1 complex.

overall_design: We performed 4C-seq in G1E cells and G1E cells transfected with ZF-SSBP3-FL or ZF-SSBP3-N; in SSBP3-dTAG cells and SSBP3-dTAG cells transfected with ZF-LDB1-FL or ZF-LDB1-DD under minus or plus dTAGV-1 treatment conditions.

first: Gerd

last: Blobel


title: Single-stranded DNA binding proteins are essential components of the architectural LDB1 protein complex [PRO-seq]

overall_design: We performed PRO-seq using 1-hour DMSO or dTAGV-1 treated SSBP3-dTAG cells (in the SSBP2/4 knockout clone #3 background).


title: Single-stranded DNA binding proteins are essential components of the architectural LDB1 protein complex [Micro-C]

overall_design: We performed Micro-C using 1-hour DMSO or dTAGV-1 treated SSBP3-dTAG cells (in the SSBP2/4 knockout clone #3 background). Two biological replicates generated a total of 1.431 billion and 1.402 billion valid cis contacts for the DMSO and dTAGV-1 treatments.


title: Single-stranded DNA binding proteins are essential components of the architectural LDB1 protein complex [RNA-seq]

overall_design: We performed RNA-seq in WT and SSBP2_4 knockout clones in both uninduced and 24h estradiol induced conditions.


title: Mettl3 regulates lens development by promoting the differentiation processes of secondary fiber cells [RNA-seq]

first: SHUYI

last: CHEN

state: Guangdong

address: 54 S. Xianlie Rd

department: State Key Laboratory of Ophthalmology

institute: Zhongshan Ophthalmic Center, SYSU

summary: Lens development requires tight regulation of cell proliferation and differentiation processes, the disruption of which leads to congenital cataract formation. N6-methyladenosine (m6A) is the most prevalent internal mRNA internal modification and has been shown to play important roles in regulating the development, physiology and pathology of various organs and tissues. However, the function of m6A during lens development remains unknown. In this study, we used lens-specific Mettl3 conditional knockout mice as a model to study the function of Mettl3 during lens development. Our study revealed that Mettl3 plays essential role in lens development by promoting the differentiation processes of secondary fiber cells.

overall_design: Lenses of embryonic day 14.5 pups of different genotype were collected and processed for RNA-Seq sequencing and analyses.

first: Shuyi

last: Chen


title: RNA-seq results of the left ventricle of mice after 5 weeks of sham and transverse aortic coarctation

city: xian

first: Run

middle: jing

last: Li

address: huangchengxi street

institute: xian jiaotong University

summary: Pathological cardiac hypertrophy and heart failure models were established in 6-8 weeks C57 mice after transverse aortic coarctation. Compared with sham-operated mice of the same age, the changes of left ventricular RNA were detected to further study the differential genes

overall_design: RNA-seq profiling of sham mice and mice after 5 weeks TAC surgery


title: Mettl3 regulates lens development by promoting the differentiation processes of secondary fiber cells [m6a-seq]

city: Guangzhou

summary: Lens development requires tight regulation of cell proliferation and differentiation processes, the disruption of which leads to congenital cataract formation. N6-methyladenosine (m6A) is the most prevalent internal mRNA modification and has been shown to play important roles in regulating the development, physiology and pathology of various organs and tissues. However, the function of m6A during lens development remains unknown. In this study, we used lens-specific Mettl3 conditional knockout mice as a model to study the function of Mettl3 during lens development. Our study revealed that Mettl3 plays essential role in lens development by promoting the differentiation processes of secondary fiber cells.

overall_design: Lenses of embryonic day 14.5 pups of wild type mice were used for m6A-Seq sequencing and analyses.


title: Single cell RNA seq of intestinal immune cells and PBMCs in salt-sensitive hypertension

city: Miryang

first: SungYong

last: Joo

address: 1268-50, Samnangjin-ro, Samnangjin-eup

institute: Pusan National University

summary: We perfomred sc RNA seq of intetinal immun cell and PBMCs to figure out the roles of intestine in development of salt-sensitive hypertension. We fed a high salt diet(4% NaCl) or a normal salt diet(0.2% NaCl) to Dahl-salt senstive rats for 4 weeks. We isolated immune cells from small instesinal lamin propria and blood.

overall_design: we feed high salt diet and normal salt diet to dahl salt sensitive rats for 4 weeks and we then islolated immune cells in small intestine lamina propria and PBMCs

first: Myunghoo


title: RNA sequencing of tumor-associated macrophages sorted from OMVs and IN@OMVs-treated mice

city: Tianjin

first: Yu

last: Ren

state: Tianjin

address: No22.Qixiangtai Rd.,Heping Dist

institute: Tianjin Medical University

summary: To investigate the effects of OMVs and IN@OMVs treatments on mouse tumor-associated macrophages, mouse tumors were harvested after treatment, and CD11b+ F4/80+ labeled cells (TAMs) were sorted by FACS for RNA sequencing.

overall_design: 1×10^6 MC38 cells were injected subcutaneously into the right back of 6–8-week-old female C57BL/6 mice. On day 9, mice were randomly divided into three experimental groups: Control, OMVs (625 μg vesicle protein/kg body weight) and IN@OMVs (625 μg vesicle protein/kg body weight). OMVs, IN@OMVs were injected intratumorally, the control mice were injected intratumorally with an equal volume of solvent, and tumors were harvested from mice after treatment. Next, and the CD11b+ F4/80+ -labeled cells (TAMs) were sorted by FACS. Cellular RNA was isolated from TAMs using the TRIzol reagent and then the samples were immediately shipped frozen for transcriptome sequencing.

first: Xuan

last: Zhou

first: Keman

last: Cheng