title: Tumour endothelial cells transcriptomics in response to Doxorubicin treatment.

first: Eleni

last: Maniati

summary: Despite its established role in breast cancer treatment, Doxorubicin remains a challenge in breast cancer treatment as its long-term success is prevented by adaptive resistance mechanisms that extend beyond cancer cell intrinsic alterations. Our study in a MMTV-PyMT-driven mouse breast cancer model reveals that prolonged Doxorubicin exposure triggers a significant reprogramming of the tumour vasculature, substantially altering the angiocrine landscape and shaping treatment outcomes.

overall_design: To elucidate the factors influencing differential responses to Dox, we examined transcriptomic changes in tumour ECs (TECs), which serve as barriers to drug delivery and are implicated in therapeutic resistance. ECs were isolated from tumour cell suspensions using magnetic antibody cell separation (MACS) with a combination of CD31 and ICAM2 antibodies specific for endothelial cells. The unbound fraction of cells was enriched in cancer epithelial cells (non-ECs), as reported previously. Total mRNA from both EC and non-EC preparations was subjected to bulk RNA sequencing (EC-Placebo n = 3; EC-Resistant n = 4; EC-Sensitive n = 4; EC-Stop n = 3; EP-Placebo n = 2; EP-Resistant n = 3; EP-Sensitive n = 5; EP-Stop n =3).

first: Jesus

last: Gomez-Escudero

first: Gabriela

last: D’Amico


title: Plasma-derived miRNAs as fluid biomarkers to differentiate Alzheimer’s and Frontotemporal Dementia

status: Public on Jul 01 2026

city: Pavia

first: Rosalinda

last: Di Gerlando

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

type: Non-coding RNA profiling by high throughput sequencing

summary: Alzheimer’s disease (AD) and Frontotemporal Dementia (FTD) are complex neurodegenerative disorders, often sharing overlapping symptoms. Non-coding RNAs play a central role in both conditions, hence the study of miRNAs isolated from plasma-derived extracellular vesicles (EVs) could increase the understanding of the pathological molecular background and support the identification of new diagnostic tools. The main aim of this work was to identify miRNAs deregulated in both disorders but presenting different expression patterns. A selection of the identified deregulated miRNAs was further studied with the purpose of identifying their mRNA targets and understanding their potential pathological involvement. A total of 340 and 291 differentially expressed miRNAs were found in FTD and AD, respectively. Among the commonly deregulated miRNAs with opposite expression trends between the two conditions, miR-638 emerged as a potentially interesting candidate, showing consistent patterns across our experimental analyses. Although these findings are preliminary and require validation in larger cohorts, miR-638 could represent a SEVs-associated biomarker with potential to distinguish AD from FTD. In addition, the expression of two of its predicted targets in peripheral blood mononuclear cells (PBMCs) appeared to align with miR-638 expression in the same cell type, and may reflect distinct underlying brain pathological states, although their differential expression between the two pathologies should be interpreted cautiously.

overall_design: We performed miRNA-seq profiling of 20 AD patients, 12 FTD patients and 21 HC. We used RNA isolated from small extracellular vesicles derived from plasma.

last: DiGerlando

first: Evelyne

last: Minucchi

first: Francesca

last: Dragoni

first: Maria

last: Garofalo

first: Giulia

last: Perini

first: Alfredo

last: Costa

first: Antonio

last: Pisani

first: Matteo

last: CottaRamusino

first: Stella

last: Gagliardi


title: BMX-001, a selective radioprotector in phase II clinical trials, can reverse radiation-induced fibrosis when given three weeks after radiation [RNA-seq]

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

country: USA

institute: University of Nebraska-Lincoln

type: Expression profiling by high throughput sequencing

summary: Colorectal cancer is a common yet survivable malignancy, partly due to the addition of chemoradiation to treatment regimens. Many patients suffer treatment-related side effects such as pain, diarrhea, and myelosuppression, and increasing toleration of treatment has the potential to improve outcomes. BMX-001, a superoxide dismutase mimetic, is currently in clinical trials as a selective radioprotector for anal and rectal cancer; however, the mechanism by which BMX-001 exerts selective radioprotection of healthy tissue over cancer tissue, particularly when administered at physiologically achievable doses, is not well understood. BMX-001 was given before and during chemoradiation and did not interfere with chemoradiation-induced cancer cell killing in mouse models. In vitro, BMX-001 still induced cancer cell killing in the presence of exogenous catalase, suggesting that BMX-001’s anti-tumor activity is not solely reliant on hydrogen peroxide production. BMX-001 exerted robust acute radioprotection in radiation mouse models five and nine days post-radiation. To assess whether BMX-001’s protection is contingent on Nrf2 expression, we evaluated the effect of BMX-001 on 5-FU treated bone marrow, where Nrf2 is crucial to maintaining hematopoietic stem cell niches. Interestingly, BMX-001 could still exert some chemoprotection in mice without functional Nrf2. To assess whether BMX-001 had any functional effects on protein oxidation status, we performed mass spectrometry on sulfenylated proteins in bone marrow treated with 5-FU in wildtype mice and mice without Nrf2. We found that BMX-001 given before 5-FU treatment resulted in the sulfenylation of CRTC2 and CBP, two proteins involved in CREB signaling and known to enhance Nrf2 activity. We also found that BMX-001 with 5-FU treatment enhanced DPYD sulfenylation, a protein known to detoxify 5-FU, and ALDH7A1 sulfenylation, a protein known to detoxify aldehydes. Together, these results suggest that BMX-001 can protect against oxidative stress in normal tissue via Nrf2 dependent and independent mechanisms.

overall_design: Sixteen total RNA-Seq samples of different treatments in mice: PBS, BMX-001, 5-FU, BMX-001 and 5-FU, with two reps per experimental group for the two genotypes CB57BL/6 and CB57BL/6+Nrf2-/-.

first: Molly

middle: S

last: Myers

first: Elizabeth

middle: A

last: Kosmacek

first: Chia Sin

last: Liew

first: Arpita

last: Chatterjee

first: Melinda

last: Wojkiewicz

first: Pooja

last: Roy

first: R Katherine

last: Hyde

first: Punita

last: Dhawan

first: Ivan

last: Spasojevic

first: Shuo

last: Wang

first: Kyle

middle: J

last: Hewitt

first: Cristina

middle: M

last: Furdui

first: Chi

last: Lin

first: Rebekah

middle: L

last: Gundry

first: Rebecca

last: Oberley-Deegan


title: ATRX inactivation disrupts global chromatin state and topology to dysregulate neurodevelopmental pathways in glioma cells of origin [Hi-C]

city: HOUSTON

first: Ajay

middle: Kumar

last: Saw

state: TX

address: 7900 Cambdrige St

department: Department of Genomic Medicine

institute: University Of Texas MD Anderson Cancer Center, Houston, Texas, USA.

summary: To investigate the 3D genome topology in murine neuroprogenitor model (Tp53-/-, Atrx+; Tp53-/-, Atrx -/-)

overall_design: Hic was performed on murine progenitor models

first: Prit Benny

last: Malgulwar

first: Ajay Kumar

first: Jason T

last: Huse

first: Kunal

last: Rai


title: NUDT21 knockdown RNA-seq in neuroblastoma II

city: suzhou

first: yang

last: yang

address: zhongnan road

country: China

institute: soochow university

summary: Alternative polyadenylation (APA) generates mRNAs with distinct 3′-untranslated regions (3′ UTRs) to regulate post-transcriptional gene expression and is critical in many tumors. However, the role of alternative 3′ UTRs in neurolastoma (NB) remains elusive. Here, we show that NUDT21 knockdown inhibits NB cell proliferation, induces cycle arrest/apoptosis in vitro, and suppresses xenograft growth in nude mice. Mechanistically, NUDT21 silencing triggers global APA dynamics, with ∼85% of APA genes switching to proximal poly(A) sites, shortening 3′ UTRs. Integrative PAS-seq/RNA-seq analyses reveal that NUDT21 regulates E2F targets (e.g., MKI67) via APA. Additionally, NUDT21 occupies gene regulatory regions to directly activate E2F target transcription. Our findings demonstrate NUDT21 sustains NB proliferation through dual APA-dependent and APA-independent mechanisms, highlighting targeting NUDT21 or its downstream pathways as a promising therapeutic strategy.

overall_design: mRNA profiles of SK-N-BE(2) cells treated with short hairpin RNAs (shRNAs) targeting NUDT21 or negative control (shNC) were generated by RNA sequencing, in double, using Illumina NovaSeq X plus.

first: Yang

last: Yang

first: Jian

last: Pan


title: NUDT21 knockdown PAS-seq in neuroblastoma I

overall_design: PAS-seq profiles of SK-N-BE(2) cells treated with short hairpin RNAs (shRNAs) targeting NUDT21 or negative control (shNC) were generated by PAS-seq, in double, using Illumina NovaSeq X plus.


title: Comprehensive analysis of the correlation between circulating biomarkers and tumor-immune microenvironment in advanced or recurrence non-small cell lung cancer in various treatment options, i.e., immunotherapy, EGFR TKI, and chemotherapy

city: Pathumwan

first: Chanida

last: Vinayanuwattikun

state: Bangkok

address: Phayathai Road

department: Department of Medicine

country: Thailand

institute: Chulalongkorn University

summary: The prospective cohort of advanced or recurrence non-small cell lung cancer in 2 academic centers in Bangkok, Thailand. We enrolled participants who received systemic treatment based on biomarker results, for example, EGFR TKI for sensitizing EGFR mutations. Pretreatment specimens and blood were collected and analyzed for circulating biomarkers, including TIME, i.e., CD8, Treg/FOXP3, and PD-L1 (22C3). Advanced omics platforms, such as RNA sequencing and whole-exome sequencing, are also employed to explain biologic meaningful.

overall_design: RNA-Seq profiling of pretreatment tumor specimen

first: Piyada

last: Sitthideatphaiboon

first: Krittiya

last: Korphaisarn


title: Microprotein miP-FERMT3 modulates endothelial cell protein catabolism and induces p53-mediated cell cycle arrest and senescence

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

summary: In this study, the function of a novel 69 amino acid microprotein (miP) encoded by a smORF within the coding sequence of the FERM Domain Containing Kindlin-3 transcript, i.e. miP-FERMT3, was investigated.

overall_design: To identify miP-FERMT3-associated transcriptional changes, human endothelial cells overexpressing FLAG-miRFP670nano (control, n=5 independent cell batches) or FLAG–miP-FERMT3 (miP-100, n=5 independent cell batches) were treated with solvent or interleukin-1β (IL-1β) for 16 h followed by RNA isolation and whole transciptome analysis.

first: Mauro

last: Siragusa

first: Raheja

last: Manav


title: AP-1 mediated chromatin changes govern alveolar type 2 cell transition in lung injury-repair [multiome]

city: Cincinnati

first: Jichao

last: Chen

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Facultative stem cells including alveolar type 2 (AT2) cells in the lung must toggle between unipotent specialization and multipotent plasticity during injury-repair. The underlying molecular switches and epigenetic changes remain unclear yet dictate regeneration versus pathology. Using multiomics and mouse genetics, we show that AP-1 members FOS, FOSB, and JUNB promote an injury-induced transitional AT2 cell state and associated chromatin landscape. Joint transcriptomic-epigenomic profiling and immunostaining distinguish CLDN4+ AT2 cells as a KRT8high subset with open chromatin highly enriched for AP-1 motifs. JUNB and FOSB accumulate in these cells upon viral injury and, along with constitutive FOS, are required for CLDN4 induction, AT2 cell dispersion, and senescence signaling toward fibroblasts, while impacting region-specific alveolar type 1 (AT1) differentiation. AP-1 activation also occurs in mouse AT2 cells expressing oncogenic Kras and transitional cells of human lung adenocarcinoma. Our work refines AT2 transitional states and reveals a gene regulatory logic shared by tissue repair and tumorigenesis.

overall_design: performed single-cell multiome sequencing for RNA and ATAC on 8 week old SftpcCreER/+;RosaSun1GFP/+ and SftpcCreER/+;RosaSun1GFP/+;FosF/F;FosbF/F;JunbF/F mice infected with Sendai virus or mock PBS, harvested 14 days post infection, and sorted for ECAD+ epithelial cells

first: Anne

last: Lynch


title: ATRX inactivation disrupts global chromatin state and topology to dysregulate neurodevelopmental pathways in glioma cells of origin

summary: To investigate the effect of TRIM28 inhibition on global transcriptomics  profile in Atrx + murine NPC

overall_design: Comparative gene expression profiling analysis of RNA-seqdata for murine NPC in controls and Trim28 knockdown

first: Anand

last: Singh


title: Photoperiod perturbations impact perfluorohexane sulfonate (PFHxS) induced developmental toxicity [PFHxS-5day]

city: Clemson

first: Subham

last: Dasgupta

state: South Carolina

address: 142 Long Hall

department: Biological Sciences

institute: Clemson University

summary: Perfluorohexane sulfonate (PFHxS) is a persistent perfluoroalkyl substance with increasing scrutiny due to its widespread occurrence and potential for developmental neurotoxicity. In this study, we investigated how photoperiod - a critical regulator of circadian physiology- modulates PFHxS toxicity in zebrafish embryos. Photoperiods are highly relevant in today’s context, where artificial lighting, shift work, and time-zone travel increasingly disrupt natural light-dark cycles. To evaluate this variable, embryos were raised under either a standard 14-hour light:10-hour dark (14L:10D) cycle,  constant darkness (24D) or constant light (24L) and simultaneously exposed to PFHxS across a concentration range (0.0025–25 µM) from 2 to 120 hours post-fertilization. Since 24L did not elicit any significant phenotypic differences, this photoperiod was excluded from further studies. LC-MS analysis revealed comparable PFHxS uptake across 24D and 14L: 10D photoperiods, ruling out bioaccumulation-induced differences. However, behavioral assays showed photoperiod-specific phenotypes, with hyperactivity during light epochs under 24D. PFHxS elevated melatonin levels under 14L:10D but reduced them under 24D, indicating circadian endocrine disruption. Transcriptomic analysis revealed greater PFHxS-induced dysregulation under 24D, including suppressed DNA replication and cell cycle pathways and increased oxidative stress. These effects coincided with elevated ROS, increased DNA damage, and reduced proliferation. Eye-specific studies revealed reduced retinal proliferating cells and photoreceptor (cone) length under 24D, but not 14L:10D, suggesting that aberrations in eye development may be a driver of phenotypes. Collectively, our findings highlight the critical role of environmental lighting in shaping toxicological outcomes and emphasize the need to incorporate photoperiod context into risk assessments.

overall_design: Zebrafish embryos were exposed to 0, 0.0025 (low) or  25 uM PFHxS (high) under 24D or 14L: 10D light conditions from 0.75 to 120 hpf, followed by sample collection, RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq X plus (Illumina, San Diego, CA) (2x150 bp, ~40m reads/sample).

first: Syed Rubaiyat

last: Ferdous

first: Alfredo

last: Rojas

first: Cole

last: Frank

first: Yasmeen

last: Berry

first: Heidi

last: Sabatini

first: Xixia

last: Luo

first: Sunil

last: Sharma

first: Ryan

last: Thummel

first: Christopher

last: Chouinard


title: The extra-terminal domain drives the role of BET proteins in transcription -- ChEC-seq following 25 min depletion of Bdf1/Bdf2 and expression of Bdf1 variants

city: Oklahoma City

first: John

middle: B

last: Ridenour

state: OK

address: 825 NE 13th St.

department: Cell Cycle and Cancer Biology Research Program

institute: Oklahoma Medical Research Foundation

summary: BET proteins facilitate transcription of most eukaryotic genes, but the specific mechanisms by which BET proteins perform their functions remain poorly understood. As chromatin readers, BET proteins use their tandem bromodomains to interact with acetylated lysine residues on histones and other protein partners. However, recent findings illustrate that bromodomain activity does not fully explain the role of BET proteins in transcription, highlighting the significance of other BET protein domains. We evaluated the importance of all conserved domains of BET proteins and determined that the extra-terminal (ET) domain is essential for cell viability, genome-wide transcription and BET protein chromatin occupancy. Furthermore, we provide evidence that the ET domain performs these functions by serving as a hub for interactions with other factors involved in transcription regulation. Our findings expand current understanding of the complex biology of BET proteins and suggest a potential mechanism by which cells can bypass bromodomain inhibition in pathologic states.

overall_design: Saccharomyces cerevisiae cells were grown in YPD medium. Cultures were treated with 3-indoleacetic acid (IAA) for 25 min to degrade target proteins. Cells were permeabilized and treated with calcium chloride to induce DNA cleavage. DNA libraries were constructed and sequenced on a NovaSeq 6000 (Illumina) at the Oklahoma Medical Research Foundation Clinical Genomics Center. Paired-end 150 bp reads were processed using bbduk, Bowtie 2, and Samtools. A minimum of three biological replicates were collected in all experiments.

first: Iwona

last: Pasionek

first: Agnieszka

last: Machowska

first: Magdalena

last: Donczew

first: Kevin

last: Boyd

first: Michael

middle: T

last: Kinter

first: Rafal


title: AP-1 mediated chromatin changes govern alveolar type 2 cell transition in lung injury-repair

first: Jichao

last: Chen

overall_design:
ATAC-seq of lung AT2 cells from collected from SftpcCreER/+;RosatdT/+ mice 14 days post Sendai viral infection and mock PBS treatment
ATAC-seq of lung AT2 cells from collected from SftpcCreER/+;RosatdT/+ mice 49 days post Sendai viral infection and mock PBS treatment
ATAC-seq of lung AT2 cells from collected from SftpcCreER/+;RosatdT/+;KrasG12D mice and SftpcCreER/+;RosatdT/+ 14 days post tamoxifen induction

first: Anne

last: Lynch


title: Dynamic Resilience: Stress Phenotypes and Their Impact on Opioid-Taking Behavior, Brain Activity, and Gene Expression

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

summary: Stress is a common experience that reveals individual differences in vulnerability. While some individuals succumb to lasting maladaptive behaviors, such as substance use disorders, others demonstrate resilience—a dynamic ability to return to baseline functioning over time. Assessing stress-related behaviors at a single time point may overlook key aspects of resilience. We used chronic social defeat stress (CSDS) to examine phenotypic stability and found mice distributed into the expected susceptible/resilient ratio at both 24 hours and three weeks, with most maintaining their phenotype over the three-week period. We then evaluated intravenous self-administration (IVSA) of remifentanil. One-week post-CSDS, all stressed mice showed increased opioid intake, regardless of phenotype. However, by three weeks, intake in resilient mice returned to baseline levels, while intake in susceptible mice remained elevated. To examine neural correlates of these behavioral shifts, we measured cFOS activity in the basolateral amygdala (BLA) and nucleus accumbens (NAc). In susceptible mice, BLA cFOS remained elevated at both time points. NAc activity was elevated in both groups at one week but normalized in resilient mice by three weeks. This pattern paralleled opioid intake behavior. Additionally, we found distinct gene expression changes that may underlie the adaptive shifts seen in resilient mice. These findings underscore that resilience is a dynamic process characterized by evolving behavioral and neural responses. By evaluating multiple time points, our research provides new insights into how different stress phenotypes influence opioid use trajectories and highlights critical brain regions involved in these processes.

overall_design: In this study, we examined gene expression changes induced by chronic social defeat stress (CSDS) at two post-stress timepoints. Male C57BL/6 (B6) mice were exposed daily to aggressive male CD-1 mice to induce CSDS first, then the mice were classified either stress-susceptible or resilient based on social interaction test. The nucleus accumbens (NAc) of susceptible (SUS) and resilient (RES) mice, along with non-stressed (NS) control mice was collected at 1 week and 3 weeks after CSDS, resulting in six distinct experimental groups: 1wRES, 1wSUS, 1wNS, 3wRES, 3wSUS and 3wNS (n=5-6 per group). Neuronal nuclei were extracted and isolated by FACS, followed by RNA-seq on 8,000 nuclei per library. Illumina NovaSeq X plus with paired-end 150-nt read was used to sequence the RNA-seq libraries, generating ~15 million reads on each library.

first: Xin

last: Zhang


title: PRMT7-specific PROTAC degrader achieves improved adoptive cancer immunotherapy by enhancing CD8+ T effector function through NF-kB activation.

city: Montréal

first: Stéphane

last: Richard

state: Québec

address: 3755 Côte Ste-Catherine Road

department: Departments of Oncology and Medicine

country: Canada

institute: Lady Davis Institute - JGH, McGill University

summary: New therapeutics are required to ameliorate cytotoxic T lymphocytes (CTL) for improved immunotherapy and T cell therapies. Herein we report that deletion of Prmt7 in T cells in mice with CD4-Cre increased CD8+ T effector cell cytokine production, cytolytic activity and anti-tumor activity of CTLs by transcriptional reprogramming. We show that Prmt7-deficiency in CTLs reprograms the CD8+ T cells with many transcription factors allowing them to exhibit increased proliferation, and express effector molecules. To translate these findings into a potential clinically applicable treatment, we generated a PRMT7 PROTAC degrader (MS54). We show that CTLs treated with the MS54 had similar reprogramming as the Prmt7 cKO CTLs. Adoptive cell transfer of MS54-treated CTLs from OT-I mice significantly enhanced their anti-tumor activity in a syngeneic melanoma murine cancer model. Human CTLs treated with the MS54 had increased proliferation, and enhanced activation markers. Our findings show that the MS54 has potential therapeutic utility for immunotherapy and adoptive cell therapy by reprogramming CTLs.

overall_design: CD8⁺ T cells were isolated from spleens of PRMT7F/F and PRMT7cKO mice and activated with anti-CD3 and anti-CD28 antibodies for 72 hours.

first: Nivine

last: Srour

first: Zhenbao

last: Yu

first: Oscar

middle: D

last: Villarreal


title: Targeting Bruton tyrosine kinase with acalabrutinib attenuates murine sclerodermatous chronic graft versus host disease

city: Huntington

first: Mohit

last: Verma

state: WV

address: 1676 3rd Ave, 4th Floor, Suite #4109

department: Department of Biomedical Sciences

institute: Marshall University

summary: Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is considered the only curative option for certain malignant hematopoietic disorders, yet its benefits are limited by the developmentof graft-versus-host disease (GVHD). Chronic GVHD (cGVHD) is often characterized by chronic inflammation and fibrosis, propagated by alloreactive donor B- and T-cell involvement. Bruton tyrosine kinase (BTK) is the downstream effector in the B-cell receptor signaling pathway and further has a crucial role in mast cell activation, both of which are critical in the pathogenesis of cGVHD. Selective inhibition of BTK may be beneficial in ameliorating cGVHD pathogenesis. In this study, we evaluated the efficiency of acalabrutinib, a highly selective Bruton tyrosine kinase inhibitor using a murine sclerodermatous cGVHD model. Recipient BALB/c mice received total body irradiation (800cGy), followed by infusion of bone marrow and splenocytes of either syngeneic (BALB/c) or allogeneic (B10.D2) mice and were subsequently treated with acalabrutinib or control from starting three weeks after HSCT until end of week 8. Mice were monitored for clinical signs of GVHD, survival, organ pathology of skin and other organs, and inflammatory mediator expression in serum and skin. Acalabrutinib treatment showed better survival, improved clinical cGVHD scores, and reduced skin pathology. Significant reductions in dermal thickness and skin fibrosis, and mast cell numbers in the acalabrutinib-treated group. In vitro, experiments on mast cell activation show increased pro-inflammatory chemokines CCL2, CCL3, and CCL4 were effectively inhibited by acalabrutinib in a dose-dependent manner. Chemokine analysis from serum samples revealed significant differences in CXCL10, CXCL13, and CCL22 levels compared to the allogeneic control group. Furthermore, the acalabrutinib treatment showed decreased B220+ cells and CD3 infiltration in the skin. RNA-seq analysis of skin identified genes associated with keratinization were downregulated with acalabrutinib treatment. Our results demonstrate that specific inhibition of BTK with acalabrutinib has a potentially beneficial role in ameliorating cGVHD and warrants further investigation in patients with cGVHD.

overall_design: RNA-seq samples were obtained from skin of BALB/cJ mice (n=3-5/cohort) following treated orally using oral gavage with acalabrutinib 25 mg/kg or placebo from week 3 to week 8. Mice were monitored for survival, scored weekly for clinical symptomology of GVHD, and euthanized on week 8 for collection of skin and other organs and stored in RNA later for further analysis.

first: Vasantharaja

last: Raguraman

first: Miranda

last: Mysinger

first: Shanid

last: Mohiyuddin

first: Nashwan

last: Jabbour

first: Melissa

last: Kesler

first: Trupti

last: Joshi

first: Senthilnathan

last: Palaniyandi

first: Gerhard

middle: C

last: Hildebrandt


title: Bulk RNA sequencing of murine pancreatic ductal adenocarcinoma cell lines with and without C1galt1c1 knockout

city: Philadelphia

first: Avery

last: Posey

state: PA

address: 3400 Civic Center Blvd SPE 8-106

institute: University of Pennsylvania

summary: Pancreatic ductal adenocarcinoma (PDAC) frequently displays aberrant O-glycosylation that contributes to tumor progression and immune evasion. To investigate the transcriptional consequences of altered O-glycosylation, we performed bulk RNA sequencing of murine PDAC (mPDAC) cell lines derived from the KPC model (Kras^LSL-G12D/+; Trp53^LSL-R172H/+; Pdx1-Cre) and their isogenic C1galt1c1 knockout (KO) counterparts. C1galt1c1 encodes Cosmc, an essential chaperone for core 1 O-glycan synthesis, and its loss leads to expression of the Tn antigen. Cells were harvested under standard culture conditions, RNA was extracted, and libraries were prepared and sequenced on an Illumina HiSeq platform (20–30 million reads per sample). Reads were processed and mapped to the mouse reference genome (mm39), and gene-level counts were generated. This dataset provides a resource for understanding how truncated O-glycosylation reshapes the transcriptome of PDAC cells and may influence tumor biology and immune interactions.

overall_design: This study profiles transcriptome changes caused by loss of core 1 O-glycan synthesis in murine pancreatic ductal adenocarcinoma (mPDAC) cells. Isogenic wild-type (WT) and C1galt1c1-knockout (KO; Cosmc-deficient, Tn-antigen–positive) mPDAC lines were cultured under identical conditions and harvested at matched confluence. Four biological replicates per genotype were collected to capture biological variability. Total RNA was extracted, poly(A)-selected, and used to generate stranded RNA-seq libraries. Libraries were sequenced on an Illumina HiSeq to a depth of ~20–30 million paired-end reads per sample. Cleaned reads were aligned to the mouse reference genome (mm39), and gene-level counts were generated for differential expression analysis (WT vs. C1galt1c1-KO). The dataset enables discovery of transcriptional programs associated with truncated O-glycosylation in PDAC.

last: Posey Jr


title: Adenosine - a regulator of human testicular peritubular cells

city: Planegg-Martinsried

first: Artur

last: Mayerhofer

address: Großhadernerstr. 9

department: Biomedical Center

institute: LMU Munich

summary: Extracellular purines, particularly ATP and adenosine, are key regulators of physiological and pathophysiological processes throughout the human body. Despite their systemic importance, the specific roles of purinergic signaling in the human testis and their potential relevance for male fertility, are not well studied. As these processes cannot be readily studied in vivo, human testicular peritubular cells (HTPCs), which form the wall of seminiferous tubules, provide a unique and accessible in vitro model. HTPCs were isolated from testicular samples and cultured. Transcriptional profiles of adenosine-treated cells were analyzed using scRNA-seq, revealing strong upregulation of IL33, STAR, HIF1A, and others. Pathways linked to cell communication, migration and inflammation were enriched in HTPCs following adenosine treatment.

overall_design: Single-cell RNA-seq of in vitro cultured human testicular peritubular cells (HTPCs).

first: Lina

last: Scholz

first: Annika

last: Liebich

first: Youli

last: Stepanov

first: Mirko

last: Peitzsch

first: Michaela

last: Schneider

first: Julia

first: Matthias

last: Trottmann

first: Frank-Michael

last: Köhn

first: Jovica

last: Ninkovic

first: Thomas

last: Fröhlich


title: Blood-Based Gene Signatures Associated with Therapeutic Response to Anti-TNF Therapy in Rheumatoid Arthritis: A Combined Meta-Analytical and Machine Learning Approach

city: Daejeon

first: Yoonjung

last: Choi

address: 7-12, Daehak-ro 179beon-gil, Yuseong-gu

country: South Korea

institute: Yoonjung

summary:
Objective Tumor necrosis factor alpha (TNF-α) inhibitors have significantly improved outcomes in rheumatoid arthritis (RA); however, up to 30–40% of patients show inadequate response. This highlights the need for predictive biomarkers to guide personalized therapy. Blood transcriptome profiling is a promising strategy for identifying gene signatures linked to treatment response, though prior studies have shown inconsistent results due to technical and biological heterogeneity.
Methods We performed a comprehensive meta-analysis of baseline blood transcriptome datasets from eight independent RA cohorts to identify genes consistently upregulated in patients who responded to TNF-α inhibitors. This analysis identified a core set of 39 recurrent genes (the Recurrent gene set). To evaluate its predictive relevance, we trained machine learning models using four gene subsets: the Recurrent set, the Patent gene set derived from a biomarker patent, the Top-ranked gene set based on Cohen’s d effect size, and the full gene set. External validation was performed using an independent dataset.
Results The Recurrent gene set showed strong and consistent predictive performance across machine learning models. Notably, several genes overlapping with the Patent and Top-ranked sets were among the top contributors, supporting their potential value for future diagnostic applications.
Conclusion Our study demonstrates the feasibility of transcriptome-guided prediction of response to TNF-α inhibitors in RA. The integration of meta-analysis and machine learning provides a strong foundation for the development of precision diagnostic tools to support personalized treatment strategies in clinical practice.

overall_design: RNA-seq profiling of blood samples from Korean patients with rheumatoid arthritis (RA) prior to anti-TNF-α inhibitor treatment

first: Taeseong

last: Kim

first: Hyun Jeong

first: Daeyoup

last: Lee

first: Kyung Eun


title: ATRX inactivation disrupts global chromatin state and topology to dysregulate neurodevelopmental pathways in glioma cells of origin [CTCF CUT&TAG]

first: Ajay

last: Saw

summary: Our analysis reports increase in CTCF occpancy in Atrx- murine NPCs as compared to Atrx+ cells

overall_design: CTCF CUT&TAG was performed on murine NPCs

first: Prit Benny

last: Malgulwar

first: Anand

last: Singh

first: Ajay Kumar

first: Jason T

last: Huse

first: Kunal

last: Rai


title: Elevated Serum IL-10 in the Setting of Relapsed B-ALL in Patients Previously Treated with CART

first: Rawan

last: Shraim

address: 3501 Civic Center Blvd

department: Oncology

institute: Children's Hospital of Philadelphia

summary: Cytokine release syndrome (CRS) is a life-threatening toxicity of chimeric antigen receptor T-cell therapy (CART) for B-cell acute lymphoblastic leukemia (B-ALL). Lower rates of severe CRS are reported in patients treated with CD22-directed CART (CART22) compared to those treated with CD19-directed CART (CART19). Here, we identify interleukin-10 (IL-10) as a critical endogenous modulator of CRS and demonstrate that previous treatment with CART is associated with increased serum IL-10 in the setting of subsequent relapse. Mechanistically, IL-10 induced higher interferon gamma (IFNγ) expression and SOCS3 upregulation in both CART19 and CART22 cells. IL-10 differentially impacted the CART immune synapse, prolonging the CART19 but shortening the CART22 immune synapse. Using single cell RNA sequencing (scRNAseq) we demonstrate upregulation of SOCS3 in CART22 patient CD4 T-cells, potentially suppressing gp130-mediated IL-6 signaling. These findings reveal IL-10 as a potent CRS‐mitigating factor and support IL-10 enhancement strategies to improve the safety of CART.

overall_design: scRNA-sequencing data from B-cell acute lymphoblastic leukemia (B-ALL) patients treated with CART19 or CART22. Samples are from peripheral blood and bone marrow. CART22 Peripheral blood n=4, CART19 Peripheral blood n=3, CART22 bone marrow n=4, CART19 bone marrow n=5. Bulk RNA-sequencing from B-ALL cell lines NALM6 and UOCB with the addition of IL10.

first: Caroline

last: Diorio

first: Apoorva

last: Babu


title: Beneficial Effects of Tanimilast and Formoterol on Mouse Lung Epithelial Progenitors In Vitro

city: Groningen

first: Reinoud

last: Gosens

address: Antonius Deusinglaan 1

department: Molecular Pharmacology

country: Netherlands

institute: University of Groningen

summary: Background: The progressive decline of lung function in chronic obstructive pulmonary disease (COPD) is driven by exacerbations, during which inflammation leads to impaired lung regeneration. Dysfunctional lung epithelial cells contribute to defective repair and tissue remodelling. This study explored regeneration and differentiation mechanisms, focusing on the cAMP pathway, and whether targeting this pathway with the phosphodiesterase 4 (PDE4) inhibitor Tanimilast and the β2 adrenoceptor agonist Formoterol could promote lung repair in vitro. Methods: A mouse lung organoid model and precision-cut lung slices (PCLS) were used to assess the regenerative potential of Tanimilast and Formoterol. In lung organoid studies, injury was induced by cigarette smoke extract (CSE) exposure. In PCLS, injury was induced by treatment with elastase. RNA-sequencing (RNA-seq) was used to identify transcriptional changes. Results: CSE exposure resulted in reduced organoid formation efficiency compared to air-exposed controls. Both combined and single treatments with Tanimilast and Formoterol increased organoid numbers compared to controls, with the most pronounced effect observed in CSE-exposed lung organoids. In PCLS, Tanimilast and Formoterol inhibited negative effects of elastase on alveolar airspace size. Under combined treatment with Tanimilast and Formoterol, RNA-seq analysis revealed positive enrichment of genes involved in epithelial cell differentiation and positive enrichment of genes encoding secreted factors involved in epithelial-mesenchymal signalling in lung fibroblasts, which was strongest in cultures exposed to CSE. Conclusion: Our findings indicate that the combination of Tanimilast and Formoterol, likely through a cAMP mechanism, reverses both the negative effects of CSE on lung organoid formation and the negative effects of elastase on alveolar airspace enlargement in vitro implying beneficial effects in lung regeneration.

overall_design: An extended organoid culture was used to model the effect of initial cigarette smoke exposure on the subsequent Tanimilast and Formoterol treatment. In the first window, primary mouse epithelial cells isolated from naïve mouse lungs were co-cultured with CCL206 fibroblasts and maintained in culture for 14 days. From day 0 to 14, organoids were exposed to either 5% cigarette smoke extract (CSE) or vehicle. On day 14, organoids were disrupted and dissociated into single cells again to re-initiate lung organoid growth. Equal numbers of epithelial cells with fresh CCL206 were then replated and treated with Tanimilast (100 nM) and/or Formoterol (100 nM). On day 28, the organoids were harvested for RNA isolation.

first: Rocío

last: Fuentes-Mateos

first: Valentina

last: Violi

first: Ka Yu

last: Wang

first: Pratama

last: Saputra

first: Barbro

middle: N

last: Melgert

first: Fabrizio

last: Facchinetti

first: Gino

last: Villetti


title: Disruption of broad H3K9me3 domains and chromatin folding regulates oncogenic transcriptional milieu in ATRX-deficient gliomas [ChIP-seq]

first: Ajay

summary: To further understand the downstream epigenomic dysfunction induced by ATRX deficiency, we compared genome-wide chromatin-state maps of Atrx+ and Atrx- primary murine neuroepithelial progenitors (mNPCs). This ChIP–seq analysis revealed major differences in the localization of heterochromatin repressive marks H3K9me3 and H3K27me3. Specifically, we identified peculiar locations in the genome displaying H3K9me3 depletion and gain of H3K27me3 upon Atrx inactivation.

overall_design: ChIP-seq Libraries were sequenced using Illumina NextSeq 500 system to obtain single end reads per sample. Histone modifications ChIPed are A-H3K4Me1, B-H3K9Me3, C- H3K27Ac, D-H3K79Me2, E-H3K4Me3, F-H3K27me3, G-Input

first: Carla

last: Danussi

first: Jason


title: Ischemic stroke accelerates atherosclerosis progression via FTO-mediated epigenetic modification [RNA-Seq]

city: Shanghai

first: Jian

address: Pujian Load 160th, Pudong New Aera

institute: Shanghai Jiao Tong University School of Medicine

summary: Residual risk of stroke recurrence persists despite the administration of the prevention measures. The recurrent risk is particularly high in patients with atherosclerosis. However, the underlying mechanisms leading to atherosclerosis progression and recurrent stroke have not been fully understood. We found that stroke accelerated atherosclerosis progression.

overall_design: Human umbilical vein endothelial cells (HUVEC) were subjected to control or stroke plasma collected from controls or patients with ischemic stroke at 1 day, respectively.

first: Qi

last: Chen

first: Jianfeng

last: Shi

first: Lingqun

last: Mao

first: Zhencang

last: Zheng

first: Xinwei

last: He


title: Human bladder Visium spatial gene expression

city: Houston

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: In this study, we present an atlas of gene and isoform expression across major cell types of the healthy human bladder using a combination of single nuclei RNA sequencing, Xenium In Situ, and Visium spatial gene expression assays.

overall_design: The dome region of a human bladder from deceased organ donor was preserved by OCT embedding and sectioned onto a Visium slide. The resulting library was sequenced at 151 bases paired-end on Illumina NovaSeq.

first: Alexandra

last: Krylova

first: Briana

last: Santo


title: Deletion of CEACAM 1 does not affect retinal and choroidal morphology or transcriptome

city: Hamburg

first: Andreas

last: Neueder

address: Falkenried 94

department: Center for Molecular Neurobiology (ZMNH)

institute: University Medical Center Hamburg-Eppendorf

summary: CEACAM1 (CC1) is an important mediator of cell proliferation and adhesion and serves as an angiogenic factor through interaction with VEGF. Although the role of CC1 has been extensively studied in organs such as the heart, liver and lung in which CC1 is considered as important regulator of various pathological conditions, little is known about the function of CEACAM1 in the eye. In this study, we investigated the expression and function of CC1 in the retina and choroid of healthy adult mice using immunohistochemistry, fluorescence activated cell sorting (FACS) and RNA sequencing. We found a strong expression of CC1 in endothelial and myeloid cells of the retina and the choroid. However, deletion of CC1 did not result in vascular abnormalities of the retina and choroid or changes in retinal myeloid cell morphology and number. Furthermore, the retinal architecture was not affected and morphometric measurements of the thickness of the inner and outer retinal layers were not altered by deletion of CC1. Accordingly, we did not observe structural or transcriptomic changes in the choroid. Our data suggest that the role of CC1 in the adult eye during steady state is attenuated or can be compensated by other molecular mediators. However, one could speculate that CC1 may become functionally relevant during pathological conditions, such as in neovascular eye diseases such as proliferative diabetic retinopathy or neovascular age-related macular degeneration.

overall_design: RNAseq of choroidal tissue from wildtype and Ceacam1-/- mice

first: Barbara

last: Braunger

first: Nikolai

last: Kleefeldt

first: Lea

last: Cagol

first: Jonathan

last: Müller

first: Laura

last: Hannig

first: Bianka

last: Brunne

first: Hamza

last: Ahmad

first: Mario

last: Vallon

first: Süleyman

last: Ergün

first: Jost

last: Hillenkamp

first: Anja

last: Schlecht


title: Spatial chromatin architecture and accessibility co-profiling of mammalian tissues

city: CHICACO

first: Feng

last: Yue

state: ILLINOIS

address: 303 E. Superior Simpson Querrey

institute: Northwestern University Feinberg School of Medicine

summary: Recent advancements of spatial omics techniques have enabled the profiling of different molecular features with spatial information. We developed Spatial-ATAC-Hi-C, which can provide spatially resolved, genome-wide joint-profiling of 3D genome organization and chromatin accessibility on tissue slides. Applying Spatial-ATAC-Hi-C in mouse and human brains, we revealed distinct chromatin architecture features and gene regulatory programs of different types of neuron and non-neuron cells in their original tissue locations.

overall_design:
Two mouse brain sections (R6 and R8), two human brain sections and 3 brain tumor samples were analyzed with Spatial-ATAC-Hi-C

[UPDATE on July 1, 2026]
The second round of raw sequencing data has been added to each sample and the processed data files have been replaced with the merged version.

first: Ping

last: Wang

first: Juan

first: Qixuan


title: Ischemic stroke accelerates atherosclerosis progression via FTO-mediated epigenetic modification

first: Jian

summary: Residual risk of stroke recurrence persists despite the administration of the prevention measures. The recurrent risk is particularly high in patients with atherosclerosis. However, the underlying mechanisms leading to atherosclerosis progression and recurrent stroke have not been fully understood. We found that stroke accelerated atherosclerosis progression.FTO overexpression suppressed atheroprogression after stroke via inhibiting autophagy-dependent ferroptosis.

overall_design: HUVEC were transfected with the FTO overexpression or vector plasmid.

first: Qi

last: Chen

first: Jianfeng

last: Shi

first: Lingqun

last: Mao

first: Zhencang

last: Zheng

first: Xinwei

last: He


title: Single-cell, multi-region profiling of the macaque brain across the lifespan

city: Tempe

first: Noah

last: Snyder-Mackler

state: Arizona

address: 214 Life Sciences C

department: School of Life Sciences

institute: Arizona State University

summary: Brain aging is a complex process with profound health and societal consequences. However, the molecular and cellular pathways that govern its temporal progression—along with cell type-, region-, and sex-specific heterogeneity—remain poorly defined. Here, we present a transcriptomic atlas of 5.3 million cells from 582 samples spanning 11 brain regions of 55 rhesus macaques (29 female, 26 male), aged 5 months (early life) to 21 years (late adulthood). We annotate 12 major cell classes and 226 subclusters, including region-specific subtypes of excitatory and inhibitory neurons, astrocytes, and ependymal cells. We identify a vulnerable excitatory neuron population in the superficial cortical lamina that is less abundant later in life, along with subtle, region-specific, age-associated compositional differences in subpopulations of microglia and oligodendrocytes, whose detection required single cell resolution. Finally, we chart convergent and divergent age-associated molecular signatures—some sex-specific—across brain regions and cell types. This work provides a temporal, regional, and sex-stratified atlas of the aging primate brain, offering insights into cell type-specific vulnerabilities and regional heterogeneity with translational human relevance.

overall_design: In brief, we performed snRNA-seq on 5.3 million nuclei from 582 brain samples from 55 rhesus macaques (29 female, aged 5 months-21 years) derived from a free-ranging, provisioned island population living on Cayo Santiago. From each animal, we dissected up to 11 distinct regions (48-55 individuals profiled per brain region; mean 10.6 brain regions profiled per individual): anterior cingulate cortex (ACC), dorsolateral prefrontal cortex (dlPFC), inferior posterior parietal (IPP), primary motor cortex (M1), entorhinal cortex (EC), hippocampus (HIP), nucleus accumbens (NAc), caudate nucleus (CN), mediodorsal thalamic nucleus (mdTN), midbrain (MB), and lateral cerebellum (lCb). We specifically targeted individuals to uniformly cover the lifespan of healthy wild macaques and balanced representation of males and females.

first: Wei

last: Yang

first: Kelsi

last: Watkins

first: Alex

middle: R

last: DeCasien

first: Mary

last: O’Neill

first: Martin

middle: O

last: Bohlen

first: Diana

last: O’Day

first: Madeleine

last: Duran

first: Chengxiang

last: Qiu

first: Anastasia

last: Meleshko

first: Anh

last: Vo

first: Melia

last: Menke

first: Diego

last: Calderon

first: Cayo Biobank Research

last: Unit

first: Jérôme

last: Sallet

first: James

middle: P

last: Higham

first: Melween

middle: I

last: Martínez

first: Cole

last: Trapnell

first: Lea

last: Starita

first: Michael

last: Montague

last: Platt

first: Kenneth

last: Chiou

first: Jay

last: Shendure


title: Ischemic stroke accelerates atherosclerosis progression via FTO-mediated epigenetic modification [Ribo-Seq]

first: Jian

last: Wang

first: Qi

last: Chen

first: Jianfeng

last: Shi

first: Lingqun

last: Mao

first: Zhencang

last: Zheng

first: Xinwei

last: He


title: Ischemic stroke accelerates atherosclerosis progression via FTO-mediated epigenetic modification [MeRIP-Seq]


title: Ischemic stroke accelerates atherosclerosis progression via FTO-mediated epigenetic modification [CUT&Tag]


title: Systematic Mapping of Protein Interactions Underlying IL-2 Secretion in Human T Cells

city: La Jolla

first: Nathan

middle: E

last: Lewis

state: California

address: 9500 GILMAN DR

institute: University of California San Diego

summary: Protein secretion plays a crucial role in maintaining immune homeostasis, yet the molecular interactions governing this process remain incompletely understood. While transcriptional and post-transcriptional regulation of protein expression is well characterized, the subcellular interactions between secreted proteins and trafficking machinery are less explored. To address this, we systematically mapped protein–protein interactions (PPIs) involved in the secretion of interleukin-2 (IL-2) from human T cells using proximity-based labeling coupled with mass spectrometry. Our analysis revealed significant enrichment of proteins associated with conventional secretory pathways, including ER-to-Golgi transport, protein folding, and vesicle-mediated trafficking. Functional validation confirmed that several of these proteins are critical for IL-2 secretion, underscoring their direct roles in cytokine processing. In addition, time-resolved profiling of PPIs and transcriptomic changes following T cell stimulation revealed dynamic remodeling of the cytokine secretion machinery, reflecting multilayered regulation at both the protein and gene expression levels. These findings offer a systems-level understanding of IL-2 secretion and identify new molecular components that can be targeted to modulate immune responses. This work provides a framework for dissecting complex secretory processes and has broad implications for therapeutic strategies in immune-related diseases.

overall_design: RNA-seq profiling of Jurkat T cells under unstimulated conditions and after stimulation for 4, 6, and 8 hours.

first: Seunghyeon

last: Shin

first: Frances

last: Rocamora


title: Milk osteopontin protects against infant bronchiolitis by enhancing microbiome-mediated extramedullary DC hematopoiesis

city: New York

first: Chrysothemis

last: Brown

state: New York

department: Immuno-Oncology Program

institute: Memorial Sloan Kettering Cancer Center

summary: Breastfeeding reduces the risk of severe lower respiratory infections (sLRI), a leading cause of infant mortality however, the protective mechanisms remain elusive. Here we demonstrated that the absence of milk-derived osteopontin (OPN), highly expressed in colostrum, predisposes neonate mice to viral and bacterial sLRI, consequent to disrupted dendritic cell (DC) hematopoiesis in the liver and lung. Oral supplementation with bovine milk-derived OPN to neonates reared by OPN-deficient dams ameliorated disease susceptibility. This protection was associated with increased enteric Lactobacillales abundance and an altered metabolome, most notably elevated levels of 3-phenyllactic acid (PLA). OPN or PLA supplementation restored DC hematopoiesis and disease tolerance via the induction of hepatic stem cell factor (SCF) and airway Flt3L. These beneficial effects were attenuated by plasmacytoid DC depletion, immunoneutralization of SCF, or genetic deletion of airway epithelial Flt3L. Our findings identify a novel microbiome-host interaction by which milk OPN confers protection against sLRI.

overall_design: Stem-like progenitors, pre-DCs and differentiated-DCs were sorted via FACS from the lung and mediastinal lymph node of neonatal mice at post-natal day 10 (naive) and 5 days post-infection with PVM. Wild-type C57Bl/6J neonates were fostered to OPN-sufficient (OPN+/+) or OPN-deficient (OPN-/-) dams, and supplemented orally with vehicle or D-3-phenyllactic acid. Six biological replicates were pooled for each sample.

first: Daniel

last: Howard

first: Anushka

last: Yadav

first: Simon

last: Phipps


title: Primary murine cardiac endothelial cells exhibit Lcn2 up-regulation under uremic conditions.

city: Aachen

first: Dickson

last: Wong

address: Pauwelsstr. 30

institute: University Hospital Aachen

summary: Cardiovascular diseases, including uremic cardiomyopathy, remain the leading cause of mortality in patients with chronic kidney disease (CKD). Myocardial capillary rarefaction and microvascular dysfunction were proposed as potential mechanisms of uremic cardiomyopathy, but the understanding was hampered by the lack of in vitro models and primary myocardial endothelial cells (ECs). Methods & Results: We developed an in vitro model for studying uremic endothelial dysfunction using primary murine cardiac endothelial cells (pmCECs). We describe the isolation and culture protocol for pmCECs in parallel to the isolation of primary cardiomyocytes  . We validated the cell lineage of pmCECs using flow cytometry (CD146⁺, CD31⁺) and isolating cells from transgenic mice with EC-specific reporter (Cdh5-Cre::tdTomato). pmCEC exhibited similar endothelial responses as Human umbilical vein endothelial cells (HUVECs) to hypoxia, including Hif1-α upregulation and enhanced angiogenesis. Exposure to hemodialysate from CKD patients significantly impaired pmCEC proliferation and angiogenic capacity. Bulk RNA sequencing revealed enrichment of oxidative stress pathways, including the up-regulation of lipocalin-2, a key component of these pathways. Increased lipocalin-2 expression in myocardial ECs was confirmed in vivo in Col4a3⁻/⁻ mice, a model of progressive CKD. In the Alport mice, lipocalin-2 correlated with diastolic dysfunction, reduced ejection fraction, and increased cardiac injury markers (pro-ANP, BNP). Conclusion: Primary murine cardiac ECs represent a useful in vitro model, facilitating studies of uremic cardiomyopathy and identification of potential molecular mediators, such as endothelial-derived lipocalin-2.

overall_design: pmCECs were treated with or without human hemodialysate extract

first: Li

last: Zhang

first: Jessica

last: Pritchard

first: Burcu

last: Yesilyurt Öztürk

first: Julia

last: Möllmann

first: Ertjola

last: Koroni

last: Große

first: Patrick

last: Droste

first: Sylvina

middle: S

last: Fernandes

first: Nikolaus

last: Marx

first: Vera

last: Jankowski

first: Rebekka

middle: K

last: Schneider

middle: W

first: Peter

last: Boor


title: Therapeutic targeting of lipidated amino acid deficiency ameliorates MASH via a PPARα/CCL2 axis

city: Shreveport

first: SUMIT KUMAR

last: ANAND

state: Louisiana

institute: LSU Health, Shreveport, LA, USA

summary: Metabolic dysfunction-associated steatohepatitis (MASH), affects nearly one-third of the global population with limited pharmacotherapy approved, underscoring the urgent need for new therapeutic strategies. N-acyl amino acids (NAAs), comprising amino acids linked to long-chain fatty acid acyl groups, are gaining interest, yet their metabolic regulation in MASH remains elusive. Metabolomic profiling in mice and humans with MASH revealed a marked depletion of NAAs, particularly C18:1-Leu, which inversely correlated with disease severity. The bidirectional PM20D1 expression was suppressed in the livers of human and mice with MASH, as well as in lipid-loaded primary mouse hepatocytes and hepatic cell lines. Stable isotope tracing studies in mice with and without MASH confirmed reduced biosynthesis of C18:1-Leu. Genetically, hepatocyte-specific overexpression of PM20D1 or pharmacological treatment with exogenous C18:1-Leu significantly attenuated or reversed established MASH. Mechanistically, C18:1-Leu bound and activated peroxisome proliferator-activated receptor alpha (PPARα), enhancing fatty acid β-oxidation and suppressing the NF-κB/CCL2 axis, thereby reducing hepatic macrophage infiltration, inflammation, and fibrosis. These therapeutic effects were abolished in hepatocyte-specific PPARα- and CCL2-deficient mice, identifying C18:1-Leu as a promising metabolic therapy for MASH.

overall_design: Eight-week-old C57BL6/J male  mice were housed under controlled temperature (22±2°C) and humidity conditions (40-60%) on a 12-hour light/dark cycle and fed ad libitum a standard chow diet (LabDiet #5053) and MASH diet (Research Diets #D17010103) for 16 weeks. Mice were further treated with Vehicle C18:1, C18:1-Leucine for 6 more weeks on MASH diet prior to euthanasia and tissue harvest.

first: Oren

last: Rom

first: Sumit

last: Anand

first: Sandeep

last: Das


title: DNA methylation profiling identifies long-range epigenetic silencing of clustered protocadherins as a key determinant of meningioma progression [cell line]

city: Tübingen

first: Daniel

middle: J.

last: Merk

address: Otfried-Müller-Str. 27

institute: Hertie-Institute for Clinical Brain Research

type: Methylation profiling by genome tiling array

summary: Meningioma is the most common primary brain tumor in adults, but molecular drivers of progression occurring in a subset of meningiomas are poorly understood. We hypothesized that epigenomic variations are causal for the clinical heterogeneity of meningiomas and may be functionally relevant for disease progression. To test this hypothesis, we performed global DNA methylation profiling of a large cross-sectional cohort and a longitudinal cohort of human meningiomas. Our analysis identifies a DNA hypermethylation signature that is correlated with clinical outcomes and enables more accurate prognostication in intermediate-risk meningiomas than previous classification systems. Analyses of longitudinal high-grade meningioma samples in comparison to clinically benign meningiomas and normal meningeal tissue show convergent contributions, but differing plasticity of copy number variations and DNA hypermethylation along the trajectory of meningioma progression. Systematic analysis of DNA hypermethylation in high-grade meningiomas unravel a tumor suppressive role of clustered protocadherins by regulating b-catenin signaling. Together, our study provides fundamental insights into the molecular mechanisms underlying the heterogeneity of clinically benign and aggressive meningiomas and the microevolutionary adaptation during disease progression.

overall_design: DNA methylation profiling was peformed on 5 human meningioma cell lines, two generated from benign meningiomas, three generated from malignant meningiomas.

middle: J

first: Ghazaleh

last: Tabatabai


title: Fluoxetine disrupts cholesterol metabolism in endothelial cells via SREBP2 activation

city: Leipzig

first: Bilal

last: Sheikh

state: Sachsen

address: Philipp-Rosenthal-Str. 27

department: HI-MAG

institute: Helmholtz Zentrum München

summary: Fluoxetine is a selective serotonin reuptake inhibitor (SSRI) widely prescribed for the treatment of depressive disorders. However, its long-term cardiovascular safety remains unknown. Here, we report an association between fluoxetine intake and an increased risk of cardiovascular diseases in the UK biobank cohort . In PCSK9-overexpression mouse model of atherosclerosis and primary human endothelial cells (ECs), we uncover that fluoxetine deregulates lipid and cholesterol metabolism. Fluoxetine triggered an upregulation of cholesterol metabolism genes in ECs, leading to accumulation of lipid droplets, with higher levels of cholesterol esters, ceramides, sphingolipids and fatty acids. The disruption of lipid homeostasis was associated with increased cholesterol biosynthesis, and low-density lipoprotein (LDL) uptake in ECs via the LDL receptor. Mechanistically, fluoxetine activates the SREBP2 transcription factor, and SREPB2 inhibition attenuates lipid accumulation in ECs. Our findings reveal a mechanism through which fluoxetine-induced reprogramming of lipid metabolism in ECs can contribute to cardiovascular diseases.

overall_design: Single nuclei RNA-sequencing of abdominal aortas of AAV-PCSK9 induced female mice treated with fluoxetine in the drinking water ad libitum at 160 mg/ml  for 10 weeks. Mice were kept on a high fat diet. n = 4 mice per group.

first: Fabiana

last: Oliveira

first: Muhammad

middle: A

last: Farhan

first: Anne

last: Hoffmann

first: Jesús

last: Rodríguez-Aguilera

first: Saira

last: Ambreen

first: He

last: Yao

first: Florian

last: Geier

first: Hugo

last: Martin

first: Nora

last: Klöting

first: Matthias

last: Blüher


title: DNA methylation profiling identifies long-range epigenetic silencing of clustered protocadherins as a key determinant of meningioma progression [longitudinal]

overall_design: DNA methylation profiling was peformed on a total of 42 meningioma samples from 18 individual patients. All patients contributed one primary and the first reccurence each, with a total of 6 patients contributing a second recurrence as well.


title: Oxidation Polyethylene Microplastics Disrupt Lipid Transport in Aquatic Models: A Comparative Study Using Planktonic Crustacean and Zebrafish Embryo

city: Yangsan-si

first: Hyerin

last: Lee

address: 49, Busandaehak-ro

institute: Pusan National University

summary: Environmental aging processes, such as oxidation, can significantly alter the physicochemical properties and toxicity profiles of microplastics (MPs). Here, we investigated the toxicological impact of pristine polyethylene (PE) and oxidized polyethylene (OPE) microplastics using a dual-species aquatic model comprising Daphnia magna and zebrafish embryos. Characterization confirmed OPE particles exhibited increased surface roughness, higher surface charge, and broader size distribution compared to PE. Exposure to OPE induced pronounced lipid accumulation and reduced heart rate in both models. Transcriptomic analysis revealed that OPE suppressed key lipid transport and metabolism genes, including mttp, apoea, and apobb. These effects were validated through qPCR and lipid staining techniques. Notably, zebrafish embryos exposed to OPE showed significant developmental impairment even with intact chorions, suggesting enhanced bioavailability of oxidized particles. This study highlights the amplified toxicity of aged microplastics and underscores the importance of evaluating environmentally relevant forms when assessing the ecological risk of MPs.

overall_design:
These are the results from the bulk RNA sequencing of zebrafish embryos treated with polyethylene (PE) and oxidized polyethylene (OPE) particles larger than the chorion pores.

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

last: Kim

first: Yun Hak

first: Chang-kyu

last: Oh


title: RNA-seq and MeRIP-seq comparison of Mettl3 knockout basal cell derived organoids

city: Guangzhou

first: Kechen

last: Chen

state: Guangdong

address: Shatai South Road

institute: Southern Medical University

summary: Airway basal stem cells are critical for maintaining epithelial homeostasis and repairing tissue damage, yet the epitranscriptomic mechanisms governing their stemness remain poorly understood. We show that METTL3 deficiency in murine airway basal cells leads to aberrant differentiation, loss of stemness, and impaired organoid formation. RNAseq and MeRIP-seq reveal that METTL3 directly targets the mRNA of Ninj1 for m6A modification, promoting its degradation. Loss of METTL3 leads to Ninj1 upregulation.

overall_design: For MeRIP-Seq, Basal cells isolated from M3CKO and control (Ctrl) mice were cultured for 14 days to generate tracheal epithelial organoids. Total RNA was extracted using Trizol reagent.  purified mRNAs were fragmented using an RNA fragmentation kit. A portion of the fragmented mRNA (~4%) was reserved as input control, while the remaining fragmented RNA was incubated with an anti-m6A antibody and subjected to m6A immunoprecipitation (IP) using the EpiMark N6-Methyladenosine Enrichment Kit according to the manufacturer’s protocol. Both the IP-purified fragmented mRNA and input RNA were used to construct libraries with the SMARTer Stranded Total RNA-seq Kit v2-Pico Input Mammalian, following the manufacturer’s instructions. For RNA-Seq, Total RNA was isolated from cells using TRIzol reagent (Invitrogen), and mRNA was subsequently purified, fragmented, and employed as the template for cDNA synthesis and library construction. The resulting libraries were subjection to sequencing using the Illumina HiSeq instrument with a 150bp paired-end module.

first: Xinlong

last: Wang

first: Zhili

last: Rong


title: RNA sequencing analysis of photon irradiated 5-, 7- and 11-day old thyroid gland organoids

first: Rufina

last: Maturi

department: Radiotherapy

institute: University Medical Center Groningen

summary: The specific effects of radiotherapy treatment on thyroid physiology remain poorly understood. In our previous work, we characterized thyroid gland organoids grown from isolated mice thyroid cells. Herein, we used this model to investigate the events occurring at 2 days post-irradiation (corresponding to 7-day-old organoids) and at 6 days post-irradiation (corresponding to 11-day-old organoids) using bulk RNA sequencing. To compare the expression profile to an healthy standard sample, 5-day-old organoids (day of irradiation) were used as controls. This analysis outlined key dysregulated pathways activated in thyroid cells with photon exposure.

overall_design: Organoids derived from 4 different mice were grown for 5 days and then exposed to photon irradiation (2,4 and 7 Gray). Organoids were collected at day 5, day 7 and day 11, and processed for RNA-seq analysis.

first: Davide

last: Cinat

first: Rob

last: Coppes


title: DNA methylation profiling identifies long-range epigenetic silencing of clustered protocadherins as a key determinant of meningioma progression [RNA-seq]

first: Daniel

last: Merk

overall_design: We performed mRNAseq on human meningiomas categorized as METHlow or METHhigh methylation cluster samples (n=5 each)

first: Ghazaleh

last: Tabatabai


title: Hexanucleotide element of miR-29b interacts with IPO5 and mediates the protection of miR-29b against herpes simplex encephalitis in mice

city: Suzhou

first: Xingchen

state: Jiangsu

address: No 100 Chongwen Road Suzhou Industrial Park, Suzhou

institute: Suzhou Institute of Systems Medicine   Chinese Academy of Medical Sciences

summary: Viruses have evolved sophisticated immune evasion strategies to establish persistent and latent infections. While type I interferon (IFN-I) signaling through the IFNAR–JAK–STAT axis constitutes a major antiviral defense, IFNAR-independent mechanisms also play complementary roles in restricting viral replication. Herpes simplex virus type 1 (HSV-1), a widespread DNA virus capable of lifelong latency, can exploit the host nuclear transport machinery to facilitate its replication. Here, we identify a distinct IFNAR-independent antiviral mechanism mediated by the nuclear-enriched microRNA miR-29b. We show that miR-29b, but not its closely related family member miR-29a, restricts HSV-1 replication by targeting the nuclear transport receptor Importin-5 (IPO5). Proteomic, imaging, and biochemical analyses reveal that miR-29b binds to IPO5 and disrupts IPO5-mediated nuclear import of the HSV-1 protein UL47, a key regulator of viral genome packaging. Notably, mutation of the hexanucleotide element “AGUGUU” in miR-29b by using Prime editing technology, which governs its nuclear localization, abolishes both its interaction with IPO5 and its antiviral activity in vitro and in vivo, exacerbating the progression of herpes simplex encephalitis. Our findings uncover a previously unrecognized miRNA–protein regulatory axis, in which miR-29b interferes with viral hijacking of host nuclear import pathways to selectively block viral protein trafficking, highlighting miR-29b and IPO5 as promising targets for antiviral intervention.

overall_design: To identify RNA molecules associated with IPO5, we performed RIP-seq (RNA immunoprecipitation followed by sequencing) using HeLa cell lysates. Two experimental groups were established: one incubated with a mouse IgG antibody as the negative control, and the other with an IPO5-specific mouse monoclonal antibody. After immunoprecipitation, RNA bound to the antibodies was isolated and subjected to library preparation and high-throughput sequencing. Biological replicates were included for each group to ensure data reliability. The resulting sequencing data were used to characterize IPO5-associated RNA profiles.

first: Dapei

last: Li

first: Tianbin

last: Cheng

first: Youming

last: Wu

first: Zigang

last: Qiao

first: Ruihan

last: Cao

first: Yuanqing

last: He

first: Shengtao

last: Yuan

first: Xiaohui

last: Zhang

first: Feng

last: Ma


title: Histological and transcriptomic analyses of lignin biosynthesis in stenospermocarpic seedless and seeded grape ovules

city: Zhengzhou

first: Yongzhou

address: No. 28, Gangwan Road, Guancheng District

institute: Chinese Academy of Agricultural Sciences Zhengzhou Fruit Research Institute

summary: Seedlessness is a highly desirable trait in table and processing grape cultivars. However, the molecular mechanisms underlying stenospermocarpic seedless in grapes remain largely unclear.In this study, the stenospermocarpic seedless cultivar ‘Zhongpu No.18’ (ZP) and the seeded cultivar ‘Muscat Hamburg’ (MH) grapes were chosen for comprehensive histological and transcriptomic analyses to screen the related key genes regulating lignin biosynthesis in grape ovules and explore the relationship between lignin biosynthesis and embryo abortion. we observed that 55-58 days after flowering (DAF) marked a critical transition stage for embryo abortion in ‘ZP’ . From 35 to 61 DAF, the lignin content in ‘ZP’ ovules was significantly lower than in ‘MH’. Histological analysis showed that in ‘MH’, the endotesta connected with vascular bundles by 25 DAF, followed by extensive lignin deposition in the endotesta at 35 DAF. In contrast, in ‘ZP’ , the connection between endotesta and vascular bundles occurred via the mesotesta from 15 to 64 DAF, with little lignin deposition observed in the mesotesta. This insufficient lignification may impair nutrient transport, leading to embryo abortion in ‘ZP’. Transcriptome profiling revealed that differentially expressed genes (DEGs) between the two cultivars were significantly enriched in lignin biosynthesis-related pathways. Meanwhile, twelve potential related genes may involved in grape lignin biosynthesis were identified, Among which MYB (LOC100246160), PAL (LOC100233012) and 4CL (LOC100245991) were selected as key candidate genes. Overall, the findings provide valuable insights into the molecular basis of lignin biosynthesis and its role in embryo abortion, offering potential targets for improving seedlessness traits in grape breeding.

overall_design: The mRNA of the ovule of ‘Muscat Hamburg’ and ‘Zhongpu No. 18’ at 35, 45, 55, and 61 days after flowering.

first: Zhaoxian

last: Liu

first: Sanjun


title: Biomarkers for Predicting Therapeutic Response to Preoperative Chemoradiotherapy in Rectal Cancer

city: Seoul

first: Chungyeop

last: Lee

address: Songpagu Olympicro 43gil

institute: Asan Medical Center

summary: This study analyzed 102 rectal cancer patients treated with PCRT and surgery to identify molecular subtypes predicting treatment response. Using transcriptomic data and pathway-based clustering, an immunogenic cluster was identified, showing high immune activity and a 90.3% favorable response rate. The findings were validated in external datasets, and a 16-gene predictive model demonstrated high accuracy. These results suggest that immune-related gene expression can guide personalized treatment in rectal cancer.

overall_design: The study included 102 patients with locally advanced rectal cancer who underwent preoperative chemoradiotherapy (PCRT) followed by surgical resection. Surgical procedures, including local excision and radical resection, were performed 6–8 weeks after completion of PCRT according to total mesorectal excision principles. Gene expression profiling was conducted using the nCounter PanCancer Pathway Panel (NanoString Technologies, Seattle, WA), which measures 770 cancer-related genes, including 40 internal controls. Transcriptomic data from pretreatment FFPE biopsy samples were analyzed using single-sample gene set enrichment analysis (ssGSEA), followed by unsupervised clustering with non-negative matrix factorization to identify molecular subtypes predictive of treatment response.

first: In ja

last: Park

first: Sung Hwan

first: Woo Young

last: Kwon


title: Synergistic Multiple Effects of Resveratrol Combatting Salmonella Infection

city: changchun

first: Jiayang

last: liu

state: 柳加洋

address: xian road

institute: jlu

summary: This study investigates the host-directed therapeutic mechanism of resveratrol against Salmonella infection, a response to the escalating threat of antimicrobial resistance. The primary objective was to elucidate the global transcriptomic changes in host cells that underpin resveratrol's anti-pathogen efficacy. To achieve this, we performed RNA sequencing (RNA-seq) on murine macrophage-like RAW264.7 cells under four conditions: untreated control, resveratrol treatment alone, S. Typhimurium infection, and S. Typhimurium infection with concurrent resveratrol treatment. The goal of this transcriptomic analysis was to identify key host genes and cellular pathways that are manipulated by the pathogen during infection and subsequently modulated by resveratrol to clear the infection.

overall_design: The experiment consisted of four treatment groups: Control(B), RV-treated (Y), S. Typhimurium-infected (X), and S. Typhimurium-infected with RV treatment (D).

first: Xueyu

first: Hongtao

first: Jiazhang

last: Qiu


title: Mechanism of maintenance and establishment of repression by the Mtg16 tumor suppressor [CUT&RUN, ChIP-Seq]

city: Nashville

first: Scott

last: Hiebert

state: TN

address: 2220 Pierce Ave.

institute: Vanderbilt University

summary: The MTG family of transcriptional corepressors are frequent targets of chromosomal translocations and deletions in cancer, yet the mechanisms underlying tumor suppression are unclear. We employed a chemical-genetic approach to investigate the molecular mechanism of Mtg16-mediated repression. Analysis of nascent transcription revealed that Mtg16 is required to repress hundreds of genes and enhancers, including the oncogenes Myb and Gfi1b. Because Mtg16 tightly regulated its own transcription, this model yielded a rapid “on/off/on” switch for Mtg16, providing a unique opportunity to study maintenance and establishment of repression within the same system. Mtg16 directly opposed histone acetylation at regulated loci, but analysis of H3K27ac revealed that changes in this mark correlated better with Mtg16 itself than with transcriptional activity. Importantly, both the relationship between Mtg16 and Class I HDAC activity and Mtg16-mediated re-establishment of repression were dependent target transcription. We propose that Mtg16 acts as a transcription-sensitive damper at highly accessible loci.

overall_design: Mtg16-FKBP-2XHA was degraded for 0-2hrs and recovered for 0-2hrs. CUT&RUN and/or ChIP-Seq was performed to assay changes in histone marks and transcription cofactor association across this timecourse.

first: Anna

last: Gilbert

first: Monica

middle: L

last: Bomber

first: Jacob

last: Ellis

first: Luke

last: Bartlett

first: Joyeeta

last: Chakraborty

first: Andrew

last: Folkmann

first: Kristy

last: Stengel


title: Mechanism of maintenance and establishment of repression by the Mtg16 tumor suppressor

overall_design:
Mtg16-FKBP-2XHA was degraded for 0-2hrs and recovered for 0-2hrs, with and without co-treatment with A485 or LBH589. Nascent transcription was assessed along these timecourses using PRO-Seq.
WO" refers to samples that were treated with dTAGV1 for 2hrs, then washed for the indicated time and returned to complete growth media-hence, "washout.


title: Pharmacological inhibition of CXCR4 increases the anti-tumor activity of conventional and targeted therapies in B-cell lymphoma models

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Bioinformatics Core Unit

country: Switzerland

institute: IOR

summary: CXCR4 is a chemokine receptor frequently implicated in the pathogenesis and treatment resistance of B-cell lymphomas and other tumor types. Thus, CXCR4 targeting is explored using various approaches, including small molecules, antibodies, and short peptides Here, we investigated the antitumor effects of the CXCR4 pharmacological inhibition with the synthetic peptides SPX5551 and balixafortide, as single agents and in combination, in various B-cell lymphoma models.

overall_design: REC1 B-Cell lymphoma cell lines has been exposed to DMSO, SPX551 or ibrutinib and a combination of them

first: Alberto

last: Arribas

first: Laura

last: Barnabei

first: Francesco

last: Bertoni


title: Mechanism of PGAM5 regulating lactate production through pyruvate metabolism pathway to promote the progression of non-small cell lung cancer

city: Dalian

first: Jianxin

last: Wang

state: Liaoning

address: West Lushun South Road

institute: Dalian Medical University

summary: Study on the regulation of pyruvate and its metabolites by knocking down PGAM5 through transcriptome analysis

overall_design: lung cancer H358 cells with stable knockdown of PGAM5 and shCON as a negative control.  shCON and shPGAM5 cells were extracted for RNA sequencing

first: Guodong

last: Hu


title: Nuclear PTK7 Interacts with DNA-PK Drives DNA Repair and Immune Evasion in Triple-negative Breast Cancer

city: Hangzhou

first: Xueying

last: Liu

address: No. 150 Dongfang Road, Qiantang District

institute: Hangzhou lnstitute of Medicine Chinese Academy of Sciences

summary: Membrane proteins with nuclear localization often exert context-dependent functions, yet the mechanistic understanding of this phenomenon remains limited. PTK7, an evolutionarily conserved pseudokinase and a clinically relevant diagnostic and therapeutic target, has been detected in both membrane and nuclear compartments, but its nuclear function has not been elucidated. Here, we identify a critical role of nuclear PTK7 in coordinating DNA damage repair and regulating tumor immunogenicity in triple-negative breast cancer (TNBC). Mechanistically, PTK7 interacts with DNA-PKcs to promote its activation and facilitate non-homologous end-joining (NHEJ). Loss of PTK7 impairs DNA repair and activates type I interferon signaling via cytosolic DNA accumulation, enhancing tumor immunogenicity. These effects are consistent across cellular and mouse tumors, and further validated in patient samples. Clinically, PTK7 expression inversely correlates with tumor-intrinsic immune activation across multiple TNBC cohorts. Collectively, our findings uncover a previously unrecognized nuclear function of PTK7 in modulating DNA repair and immune evasion, and nominate PTK7 as a potential therapeutic target for precision immuno-oncology in TNBC.

overall_design: To validate the biological function after PTK7 knockout (KO) at the transcription level, we utilized PTK7 KO and PTK7 NC SUM159PT cells with two different sgRNA and negative sgRNA pretreated in the Lentivirus packaging system for RNA sequencing. Analysis of the RNA-seq data revealed significant alterations in the transcriptome of SUM159PT cells upon PTK7 absence.

first: Yong

last: Wei

first: Qin

last: Wu


title: A Panel of Differentially Methylated Putative Imprinting Control Regions Associated with Hepatocellular Carcinoma [Bisulfite-seq]

city: RALEIGH

first: Dereje

last: Jima

state: NC

address: 850 Main Campus Drive

department: CHHE

institute: NCSU

type: Methylation profiling by high throughput sequencing

summary: Site-specific 5-methylcytosine levels measured in mixed blood leukocytes have been used as surrogate for inaccessible tissues and associated with hepatocellular carcinoma (HCC) risk. However, findings are difficult to replicate as methylation patterns at many of these sites do not always correlate with those in liver tissue. An exception is methylation at imprinting control regions (ICRs), which regulate the monoallelic expression of imprinted genes, a developmentally critical process requiring parental allele-specific DNA methylation that is consistent across cell types. Aberrant methylation of several ICRs have been linked to advanced liver disease or HCC. We aim to create a DNA methylation-based risk stratification panel to improve early detection and triaging of patients before the onset of HCC in those at increased risk. From whole genome bisulfite sequencing (WGBS) of mixed leukocyte-derived DNA of HCC cases and controls, 1,519 regions were significantly differentially methylated. This list was augmented with a compendium of 3,275 HCC-, cirrhosis-, and fibrosis-associated differentially methylated regions (DMRs) identified from primary literature on PubMed, for a total of 4794 unique DMRs. Filtering these DMRs with a published list of ICRs revealed 97 ICRs within these liver disease-associated DMRs, 21 of them previously characterized and 76 novel. Of these ICRs, 46 replicated in an independent case-control comparison using the novel Illumina custom Imprintome Methylation array. Limited sample sizes notwithstanding, this comprehensive analysis supports the use of altered DNA methylation of ICRs for HCC risk stratification from readily accessible tissue, blood.

overall_design: Differential methylation analysis was performed using WGBS data in peripheral blood of participants with histologically confirmed HCC who underwent tumor resection surgery (N=10) and otherwise healthy individuals (N=51). WGBS was performed on an Illumina NovaSeq 6000 Sequencing System using S2 flow cells with 150bp PE reads.

first: Annie

last: DiFrank

first: Bruce

last: Corliss

first: James JH

last: Park

first: David A

last: Skaar

first: Dereje D

first: Michael

last: Cowley

first: Susan K

last: Murphy

last: Lui

first: Cynthia A

last: Moylan

first: Cathrine

last: Hoyo


title: Phosphorylated ubiquitin is a secondary messenger and an epigenetic mark mediating mitochondria-nucleus crosstalk

city: South San Francisco

first: Daniel

last: Le

state: CA

address: 1 DNA Way

institute: Genentech

summary: Parkinson’s disease (PD) is commonly associated with dysfunctional mitochondrial homeostasis. PINK1, a S/T kinase mutated in early-onset PD, generates phosphoserine 65 ubiquitin (pS65Ub) on damaged mitochondria facilitating their removal. Here, we show that pS65Ub translocates into the nucleus after generation at damaged mitochondria and is directly attached to substrates by resident E3 ligases. Histone H2A is a major substrate and is modified at lysine 119 (H2AK119) by the polycomb silencer, E3 ligase RING1B. At nucleosomes, pS65Ub simultaneously suppresses RING1B and potentiates H2A deubiquitinases USP16 and USP21. Epigenetic profiling and RNA sequencing reveal that pS65Ub is enriched at the promoters of poorly expressed yet dynamically regulated genes, typically implicated in neurodevelopmental programs. Our data suggest that pS65Ub drives gene expression by relieving H2AK119ub-dependent repression. Importantly, post-mortem PD brains exhibit elevated nuclear pS65Ub, potentially linking nuclear pS65Ub accumulation with disease pathogenesis. Together, these data indicate that pS65Ub generated at damaged mitochondria regulates fundamental cellular processes at distant sites.

overall_design: ChIP Seq (pS65Ub, H2AK119ub), CUT&RUN (pS65Ub, Nonspecific IgG, H3K4Me3, H3K27Me3) libraries from HeLa or NGN2-derived iNeurons (ChIP only) treated with oligomycin + antimycin (24hrs, 1µM) or DMSO.

first: Bence

last: Daniel

first: Mercer

last: Thomas


title: Transcriptional and functional architecture of the whole neutrophil compartment [Multiome_ATAC_GEX]

city: New Haven

first: Andrés

last: Hidalgo

address: 10 Amistad Street

institute: Yale University

summary: In this study, we present NeuMAP, a comprehensive single-cell analysis of neutrophils spanning over 40 anatomical, physiological, and pathological contexts in mice. NeuMAP confirms and expands previous models of neutrophil diversity, revealing the organization of neutrophils into distinct functional hubs under both normal and pathological conditions. Furthermore, we delineate prototypical trajectories as key organizers of granulopoiesis and examine neutrophil dynamics along these trajectories during acute inflammation and cancer. Integrating insights from fate mapping, mutant mouse models, and in vitro experiments, we identified immunological signals guiding neutrophil through these typical trajectories of granulopoiesis, that balance immune protection, tissue homeostasis and repair. Specifically, we identified IFNB, GMCSF, and TGFB as drivers of pro-inflammatory, cancer-associated, and mature neutrophil states, respectively and found that the transcription factor JUNB drives the angiogenic and immunosuppressive function of neutrophils. Additionally, we uncover conserved transcriptional signatures for human neutrophil states, validate their prognostic significance in cancer patients, and introduce a proof-of-concept strategy for exploring the diagnostic potential of neutrophil functional diversity across various diseases using single-cell transcriptomics of blood neutrophils. Our study provides a model that delineates the global architecture of the neutrophil compartment in mammals, and stablishes a robust framework for further exploration of neutrophil biology.

overall_design: 8 weeks old Male C57Bl6 mice were sacrificed via CO2, and blood, spleen, bone marrow, and lung were collected. 1ml of blood was collected in BD Microtainer tubes containing EDTA (365974, BD), and red blood cell were lysed in 10ml of 1X ACK buffer for 10min on ice. The spleen and lung  cell suspensions were washed, resuspended in 1ml of 1X ACK buffer and incubated for 5min on ice to get rid of the red blood cells. The cell suspension was washed, resuspended in cold staining buffer, and kept on ice. The bone marrow was harvested by flushing the femur’s shaft with cold staining buffer and filtered to obtain a single cell suspension. The cells were washed and red blood cell were lysed using 1ml of 1X ACK buffer (5min on ice). After lysis, the cells were further washed, resuspended in cold staining buffer, and kept on ice. Cell suspensions  were incubated with Fc block (TruStain FcX PLUS – 156603 – Biolegend) for 10min on ice, and for another 30min with an antibody cocktail containing: anti-Ly6G_PE (127608 - Biolegend), anti-CD11b_APC (101211 - Biolegend), TotalSeq_A Hashtag antibodies cocktail (Biolegend). The hashtag antibodies used were: TotalSeq_A0301 (155801, Biolegend – spleen), TotalSeq_A0302 (155803, Biolegend – bone marrow), TotalSeq_A0303 (155805, Biolegend – blood), TotalSeq_A0310 (155819, Biolegend – lung). Before acquisition and sorting, single cell suspensions were incubated for 15min with Dapi (NBP2311561, Novus Biologicals). Live-CD11b+-Ly6G+ neutrophils were sorted out. After sorting, the 4 neutrophil suspensions were enumerated and pooled in equal proportion. After that, we proceded with the library preparation.

first: Daniela

last: Cerezo-Wallis

first: Andrea

last: Rubio-Ponce

first: Ivan

last: Ballesteros


title: Evaluation of KDAC6 (HDAC6) inhibitor selectivity in HT1080 cells

city: New Orleans

first: Terry

last: Watt

state: LA

address: 1 Drexel Dr.

department: Chemistry

institute: Xavier University of Louisiana

summary: To investigate the specificity and biological impacts of KDAC-selective inhibitors, we treated wild-type HT1080 cells with KDAC6 selective inhibitors SW-113 and SE-138. Expression profiling analysis was then performed on the treated cells vs. untreated wild-type HT1080 cells.  Comparable wild-type data is available in GSE302260.

overall_design: Gene expression profiling analysis of RNA-seq data for HT1080 cells treated with 1 micromolar inhibitors for 2 days, with 3 replicates.

first: Tasha

middle: B

last: Toro


title: RNA Sequencing of primary mouse hepatocytes treated with manganese (Mn) or insulin

city: New York

first: Jennifer

last: Gamarra

address: 1150 St Nicholas Ave, Russ Berrie Building, Floor 6-613

institute: Columbia University

summary: Kinases require divalent cations for enzymatic activity. In vivo manganese shows glucose lowering properties in mice and humans. Here, we used RNA-Seq to investigate the effects of increasing cellular Mn content on gene expression in primary mouse hepatocytes compared to insulin treatment.

overall_design: Primary mouse hepatocytes were treated with or without 6 micromolar Mn overnight (16 hours) in serum-free conditions. Cells were pre-treated with 100 nanomolar of insulin for 1 hour, then treated with forskolin (10 micromolar) and dexamethasone (1 micomolar) 5 hours prior to cell lysis. The groups are: Mock, forskolin/dexamethasone (FD), FD + Mn (FDMn), FD + Insulin (FDI). 3 samples from each treatment group were submitted for RNA sequencing.

first: Rebecca

last: Haeusler


title: An Atypical Class C G-Protein Coupled Receptor (GPCR) Homolog Regulates Movement and Phagocytosis in the Protozoan Parasite Entamoeba histolytica

city: Bunkyo-ku

first: Rivo

middle: Yudhinata Brian

last: Nugraha

state: Tokyo

address: 7-3-1 Hongo

department: Biomedical Chemistry

country: Japan

institute: The University of Tokyo

summary: Amebiasis is a parasitic infection of the human intestines, primarily caused by Entamoeba histolytica. Its pathogenesis relies on the environmental sensing-induced cytoskeletal remodeling as the basic mechanism for motility and tissue invasion. We identified and characterized a G protein-coupled receptor-like protein, EhGPCR (CL6EHI_096680), predicted to contain a Venus Fly-Trap (VFT) extracellular domain with an Atrial Natriuretic Factor (ANF) receptor domain, as commonly found in the class C GPCR family protein. This protein is uniquely lacking a transmembrane domain. Instead, the glycosylphosphatidylinositol (GPI) anchor is responsible for its cell membrane localization. Removal of the GPI signal led to unexpected mitosomal localization, highlighting the importance of GPI modification in subcellular targeting. Functional studies revealed that EhGPCR knockdown reduced parasite motility and phagocytosis following the reduction of expression of actin cytoskeleton-related genes, including myosin II, villidin, and gelsolin. Our findings suggest that EhGPCR (CL6EHI_096680) plays a role in regulating downstream signaling linked to Entamoeba motility and phagocytosis. This study provides novel insights into GPCR-like signaling in E. histolytica, an area previously understudied.

overall_design: RNAseq profilling of E. histolytica harboring psAP2-EhGPCR (CL6EHI_096680) silencing plasmid and psAP2-mock plasmid as control strain

first: Ghulam

last: Jeelani

first: Herbert

last: Santos

first: Tomoyoshi

last: Nozaki


title: Analysis of gene expression after CRISPR-mediated activation of TEDAR (LINC00302) lncRNA in primary human keratinocytes

city: Uppsala

first: Andor

last: Pivarcsi

address: BMC B11:3

department: Department of Medical Biochemistry and Microbiology

country: Sweden

institute: Uppsala Univesrity

summary: Long non-coding RNAs (lncRNAs) are emerging as key regulators of epidermal differentiation. To investigate the function of the skin-enriched lncRNA TEDAR (LINC00302), we performed CRISPR-mediated activation in primary human keratinocytes and profiled global gene expression using the Affymetrix Clariom D Human microarray platform. Differential expression analysis demonstrated that TEDAR regulated genes involved in late epidermal differentiation and barrier formation.

overall_design: Primary adult human keratinocytes were transfected with CRISPR activation constructs targeting TEDAR lncRNA or with non-targeting control sgRNA. After induction of differentiation, total RNA was extracted and hybridized to Affymetrix Clariom D Human microarrays. The experiment included 4 biological replicates per condition (TEDAR activation and control). Differential gene expression analysis was performed to identify TEDAR-regulated transcripts in differentiated keratinocytes.

first: Kunal

last: Das Mahapatra


title: Interferons promote autophagy via the STAT1/STAT5B-SOCS1 axis

city: Ulm

first: Konstantin

middle: MJ

last: Sparrer

address: Meyerhofstr. 1

department: Institute of Molecular Virology

institute: Ulm University Medical Center

summary: Concerted activation of the interferon (IFN) system and autophagy upon viral infection is paramount for efficient immune defences. Here, we show that IFN activates autophagy via STAT1/5B heterodimer-mediated upregulation of SOCS1 and contributes to virus-induced autophagy. Our data demonstrate that autophagic flux activation by type I and II IFNs peaks at 24 h post treatment, whereas type III IFNs induce autophagy with slower kinetics. Mechanistically, IFN-mediated autophagy induction is dependent on JAK1-3 and both STAT1 as well as STAT5B. We show that STAT1 and STAT5B form heterodimers and co-localize following IFN treatment. Transcriptome analyses revealed that SOCS1 is induced in a STAT5B-dependent manner, and depletion of SOCS1 prevented IFN-induced autophagy. Finally, pharmacological inhibition of STAT5B or scavenging of IFN diminishes autophagosome levels upon infection with Sendai, respiratory syncytial, measles and influenza A viruses. Taken together, our data indicate that the IFN system and autophagy are connected via the STAT1/STAT5B-SOCS1 axis and that this axis is required for concerted activation of both systems during viral infections. Targeting of this signalling axis may allow to boost autophagy against viral infections.

overall_design: RNA-seq profiling of HeLa autophagy reporter cells expressing eGFP-tagged LC3B treated with either STAT5 Inhibitor, Interferon beta or both or left untreated 16 hours after Interferon treatment and if applicable 17h after STAT5 Inhibitor treatment.

first: Victoria

last: Hunszinger

first: Jana-Romana

last: Fischer

first: Alexander

last: Graf

first: Stefan

last: Krebs

first: Helmut

last: Blum


title: Analysis of gene expression after RNAi (siPool)-mediated knockdown of TEDAR (LINC00302) lncRNA in primary human keratinocytes

summary: Long non-coding RNAs (lncRNAs) are emerging as key regulators of epidermal differentiation. To investigate the function of the skin-enriched lncRNA TEDAR (LINC00302), we performed RNAi (siPool)-mediated knockdown in 3D organotypic skin models and analyzed changes in gene expression using the GeneChip™ Human Transcriptome Array 2.0 microarray platform. Differential expression analysis demosntrated that TEDAR regulated genes involved in late epidermal differentiation and barrier formation.

first: Lorenzo

last: Pasquali


title: SFB-Driven Remodeling of Peyer’s Patches Enhances IgA and IgG2b Class Switching and Atypical Memory B Cell Generation [scRNA-Seq]

city: Bethesda

first: Byunghyun

last: Kang

state: Maryland

address: 9000 Rockville Pike

institute: NIAID

summary: The intestinal microbiota plays a central role in shaping host mucosal immunity, but the mechanisms by which specific commensals influence B cell responses remain incompletely defined. Segmented filamentous bacteria (SFB), potent inducers of Th17 cells, have been implicated in both protective and pathogenic immune outcomes. Here, we show that SFB colonization in specific pathogen-free (SPF) mice induces a profound remodeling of Peyer’s patches (PPs), characterized by increased cellularity, germinal center (GC) formation, and robust class switching to IgA and IgG2b, but not IgG1. Using flow cytometry, bone marrow chimeras, and single-cell RNA sequencing coupled with BCR repertoire analysis, we demonstrate that SFB enhances recruitment of naïve B cells through the CXCR5-CXCL13 axis and promotes T cell-dependent expansion of both GC and memory B cells. These memory B cells exhibit hallmark features of atypical B cells (ABCs), including CD11c expression and somatic hypermutation, and arise via a GC-dependent pathway. SFB increases the number of activated CD11c+SIRPa+BST2-CD11b+ DCs in the the PP subepithelial dome (SED), and T helper 17 (Th17) and T follicular helper (Tfh) cells. Surprisingly, unlike previous reports, neither Th17 effector function (IL-17R-/-) nor Th17-to-Tfh conversion (CD4CRE-RORgtfl/fl) was essential for the observed B cell changes. Finally, we show that SFB colonization enhances clonal diversity and somatic hypermutation in IgA⁺ and IgG2b⁺ B cells qualitatively as well as quantitatively. These findings establish a mechanistic link between microbiota composition and mucosal B cell immunity, with implications for vaccine responses, mucosal homeostasis, and autoimmune susceptibility.

overall_design: To examine how SFB colonization alters the cellular landscape, Peyer’s patches were isolated from the small intestines of five SFB(−) and five SFB(+) Taconic WT mice, then pooled and processed into single-cell suspensions, respectively.

first: Eun-Do

last: Kim

first: Brian

last: Kelsall


title: SFB-Driven Remodeling of Peyer’s Patches Enhances IgA and IgG2b Class Switching and Atypical Memory B Cell Generation II

overall_design: To examine how SFB colonization alters the class-switched B cell repertoire, B cells expressing the three major isotypes (IgA, IgG1, and IgG2b) were FACS-sorted from the Peyer’s patches (PPs) of SFB(−) and SFB(+) Taconic WT mice, pooled from five individual mice per group. To increase the total number of cells collected, each pooled sample was loaded into two separate wells on the same 10x Genomics chip for GEM formation. As a result, a total of four individual libraries were generated, representing two groups: SFB(−) and SFB(+).