title: The Pseudogene RPS27AP5 Reveals Novel Ubiquitin and Ribosomal Protein Variants Involved in Specialised Ribosomal Functions.

city: Sherbrooke

first: Michelle

last: Scott

state: QC

address: 3201 Jean-Mignault

institute: Université de Sherbrooke

summary: Pseudogenes, traditionally considered non-functional gene copies resulting from evolutionary mutations, have garnered attention due to recent transcriptomics and proteomics revealing their unexpected expressions and consequential cellular functions. Ubiquitin, transcribed from UBA52 and RPS27A genes, fused to ribosomal proteins eL40 and eS31, and polyubiquitin precursors encoded by UBB and UBC genes, has additional pseudogenes labeled as non-functional. However, recent evidence challenges this notion, demonstrating that these pseudogenes produce ubiquitin variants with minimal differences from the canonical sequence, suggesting a new regulatory dimension in ubiquitin-mediated cellular processes. To systematically catalogue possible Ubiquitin (Ub) and Ubiquitin-like (Ubl) variants from pseudogenes, expression data was compiled, identifying potential functional variants. Among these pseudogenes, RPS27AP5 expresses both Ubiquitin variant (UbP5) and ribosomal protein variant (S27aP5), with precursor proteins maturing through cleavage and exhibiting behavior similar to their counterparts post-translation. Notably, S27aP5 integrates into translating ribosomes, increasing the 80S monosomal ribosomal fraction and indirectly influencing p16INK4A transcriptional activation. The discovery of a functional S27a pseudogene supports the concept that a subset of ribosomes may incorporate diverse subunits for specific translational functions.

overall_design: Translating ribosome bound RNA pulldown (TRAP) assay: HeLa cells were transfected with HA-RPS27A-Myc or HA-RPS27AP5-Myc constructs, immunoprecipitated with MycTrap beads, and the RNA was extracted prior to RNAseq.

first: Anna

last: Meller

first: Dominique

last: Lévesque

first: Jennifer

last: Raisch

first: Étienne

last: Fafard-Couture

first: Xavier

last: Roucou

first: Francois-Michel

last: Boisvert


title: Depletion of the TRF1 telomere-binding protein leads to leaner mice with improved metabolism

status: Public on Sep 22 2025

city: Madrid

first: Ruth

last: Álvarez-Díaz

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology

country: Spain

institute: Spanish National Cancer Research Center (CNIO)

type: Expression profiling by high throughput sequencing

summary: TRF1, a component of the telomere shelterin complex, plays crucial roles in telomere protection, telomere length regulation, and stemness. Here, we describe a previously unknown connection between TRF1 and metabolism. Telomere attrition has been linked to obesity. Our study reveals that Trf1-deficient mice exhibit a leaner phenotype, reduced adiposity, and improved glucose tolerance, even when subjected to a high-fat diet, independently of telomere shortening. These findings uncover a previously unknown role of TRF1 in regulating metabolism. Our research not only contributes to the understanding of obesity onset but also positions TRF1 as a potential therapeutic target for combating metabolic syndrome.

overall_design: Tamoxifen (TMX) (Sigma Aldrich, T-5648-1G) was intraperitoneally (i.p.) injected to fifeteen-week-old  female Trf1+/+  Cre+/t and Trf1lox/lox  Cre+/t mice for three times a week for 5 weeks until the sacrifice.

first: Jessica

last: Louzame Ruano

first: Leire

last: Bejarano Bosque

first: Rosa

last: Serrano

first: Juana

middle: M

last: Flores

last: Álvarez Díaz

first: Ana

last: Cayuela López

first: María

last: Blasco


title: Persistent injury-induced mtDNA mutations compromise organ fitness by suppressing nucleotide biosynthesis

status: Public on Sep 20 2025

city: Dallas

first: Samir

last: Parikh

state: Texas

address: 5901 Forest Park Rd. ND9.300B

country: USA

institute: UT Southwestern Medical Center

summary: The mitochondrial genome is present at thousands of copies/cell in metabolically active tissues. In organs such as the kidney that are exposed to frequent sublethal insults, the impact on mitochondrial DNA (mtDNA) quality is unknown. Here we show that acute kidney injury induces a burst of persistent random mtDNA mutations (mtDNA) that impair mitochondrial function, induce fibrosis, and increase subsequent injury risk in cells, mice, and humans, implicating a feed-forward loop of accumulating mtDNA mutations driving chronic disease. Multi-omic interrogation of mtDNA settings implicates marked reduction of energy-intensive nucleotide biosynthesis. Strikingly, repletion of adenosine, but not other nucleosides, restores ATP and ameliorates injury risk via the purine biosynthetic enzyme adenylate kinase 4. mtDNA may therefore be a durable remnant of acute injuries that compromise future health and both a genetic and tissue-based indicator of organ fitness. Augmented purine biosynthesis may protect vulnerable organs from acute insults.

overall_design: To inverstigate how mtDNA mutations contribute to injury following ischemia reperfusion injury, we applied RNA sequencing to IRI kidneys from Polg+/+ and PolgD257A littermates


title: Programmable targeted RNA degradation via dCas13d-directed chaperone-mediated autophagy (dCasCMA)

city: Tianjin

first: Shu-Lin

last: Liu

address: No.94 of Weijin Road

country: China

institute: Nankai University

summary: RNA-targeted degradation technologies offer significant promise for treating diseases by selectively disrupting gene expression. However, a robust method to specifically, efficiently, and programmability degrade targeted RNAs in mammalian cells is still in demand. Here, we present a versatile platform, dCas13d-directed chaperone-mediated autophagy (dCasCMA), which integrates the precise targeting capabilities of dCas13/CRISPR with the degradation efficiency of chaperone-mediated autophagy (CMA) to achieve efficient degradation of specific RNAs. By combining dCas13d with a CMA-targeting motif and customizable guide RNA (gRNA), the platform allows for accurate targeting of both exogenous and endogenous RNAs in cells. Moreover, the incorporation of multiplexed gRNA expression arrays enables the simultaneous degradation of multiple RNA targets during viral pathogenesis in live cells and in vivo. Our findings emphasize the platform’s modular design, which enables flexible combinations of dCCTM components with user-defined gRNA sequences. This versatility positions it as a promising tool for developing innovative therapies for various diseases.

overall_design: 293T cells were transfected with constructs expressing either WT Cas13d or dCCTM, each paired with EGFP-targeting gRNAs or non-targeting (NT) gRNA, followed by RNA-Seq analysis.

first: Hui

middle: P

last: Wen

first: Shu

middle: L


title: Optimal CXCR5 Expression during Tfh Maturation Involves Bhlhe40-Pou2af1 Axis

status: Public on Sep 21 2025

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Bcl6/Blimp1 are well-known for Tfh cell determination, but they are dispensable in regulating the expression of CXCR5, which is critical for Tfh migration into germinal center (GC). In this study, we uncovered a novel pair of transcription factors, Bhlhe40/Pou2af1, that regulate Tfh maturation through regulation of CXCR5. Pou2af1 promotes Tfh generation by upregulating CXCR5, while Bhlhe40 represses Tfh differentiation by inhibiting Pou2af1. Pou2af1 was further verified being essential for GC Tfh cell localization, whereas Bhlhe40 inhibits pre-Tfh cells import into GC. Such migration behavior change can be explained by an alteration in the MFI of CXCR5. RNA-Seq analysis confirmed Bhlhe40 inhibiting Pou2af1 and the requirement of Pou2af1 upregulation in optimal CXCR5 expression. Thus, our study filled a long-standing gap in the regulation of optimal CXCR5 expression by revealing a key transcriptional regulatory circuit involving Bhlhe40/Pou2af1, which operates downstream of the Bcl6/Blimp-1 circuit that determines Tfh cell fate. RNA-Seq analysis of gene expression in T cell subsets (Th1, Th2, Th17 and iTreg), which are primed and differentiated in vitro from WT mice or Bhlhe40f/f-CD4Cre mice. RNA-Seq analysis of gene expression in antigen-specific Tfh cells and non-Tfh cells, which were sorted from the indicated bone marrow chimera mice (WT, Pou2af1-/-, Bhlhe40-/-). ChIP-Seq analysis of binding sites by Bhlhe40  in Th1, Th2, Th17 and iTreg. ChIP-Seq analysis of binding sites by Pou2af1 in splenic B cells.

overall_design: RNA-Seq analysis of gene expression in T cell subsets (Th1, Th2, Th17 and iTreg), which are primed and differentiated in vitro from WT mice or Bhlhe40f/f-CD4Cre mice. RNA-Seq analysis of gene expression in antigen-specific Tfh cells and non-Tfh cells, which were sorted from the indicated bone marrow chimera mice (WT, Pou2af1-/-, Bhlhe40-/-). ChIP-Seq analysis of binding sites by Bhlhe40  in Th1, Th2, Th17 and iTreg, which are primed and differentiated in vitro from Bhlhe40-V5 tagged mice . ChIP-Seq analysis of binding sites by Pou2af1 in splenic B cells from WT or Pou2af1-HA-TG mice. AS15-specific cells from draining lymph nodes of two weeks AS15/CFA-immunized mice were identified by tetramer staining. All the cell subsets were harvested by cell sorting after staining.

first: Xiaoliang

last: Zhu

first: Xi

last: Chen

first: Chengyu

last: liu

first: Zoey

middle: J

last: Kline

first: Gangqing

last: Hu

first: Sundar

last: Ganesan

first: Tibor

middle: Z

last: Veres

first: Difeng

last: Fang

first: Shuai

first: Danping

last: Wei

first: Hirofumi

last: Shibata

first: Dominic

last: Golec

first: Hyunwoo

last: Chung

first: Ronald

middle: N

last: Germain

first: Pamela

last: Schwartzberg

first: Keji

last: Zhao

first: Jinfang


title: Differential chromatin landscape in myxoid liposarcoma and Ewing sarcoma

city: Gothenburg

first: Anders

last: Ståhlberg

address: Medicinaregatan 1F

department: Department of Laboratory Medicine

country: Sweden

institute: University of Gothenburg

summary: A subgroup of sarcomas and leukemias is defined by characteristic FET (FUS, EWSR1, TAF15) fusion oncogenes. Myxoid liposarcoma (MLS) and Ewing sarcoma (EWS) are the most common entities characterized by the fusion oncogenes FUS-DDIT3 and EWSR1-FLI1, respectively. Here, we performed ATAC-Seq on the cell lines MLS 1765-92 and EWS TC-71 to characterize and compare their chromatin landscape.

overall_design: ATAC-Seq was performed on the myxoid liposarcoma cell line MLS 1765-91 and the Ewing sarcoma cell line EWS TC-71 (n=3) to compare chromatin accessibility patterns.

first: Lisa

last: Andersson


title: Genetic landscape of non-UV-induced cutaneous squamous cell carcinomas

status: Public on Sep 19 2025

city: Paris

first: Carmen

last: AL YOUSSEF

state: Paris

address: 24 rue du faubourg saint jacques

department: Institut Cochin

country: France

institute: Inserm, U1016

summary: Skin squamous cell carcinoma (cSCC) is the second most common skin cancer and is most often caused by cumulative UV exposure. However, cSCC may also arise independently of UV exposure, on sites of sustained skin damage like chronic ulcers, scars, Recessive Dystrophic Epidermolysis Bullosa (RDEB), and inflammatory skin diseases such as hidradenitis suppurativa (HS). Little is known about non-UV-induced skin carcinomas. We aimed to describe the clinical, pathological, and genetic features, of non-UV-induced cSCC. We collected clinical and pathologic data corresponding to 31 patients with non-UV-induced cSCC, including 5 cSCC on HS, 4 on chronic leg ulcers and 8 on RDEB. DNA was extracted from FFPE samples and analysed using a NGS assay targeting 523 cancer genes. A comparison was performed with published genetic data obtained in non-UV-induced and UV-induced cSCC. We found that The Tumour Mutational Burden (TMB) of non-UV-induced cSCC was 6-times lower than the published TMB of UV-induced cSCC. The predominant mutational signature was a clock-wise signature. By comparing the frequency of driver mutations, we found TP53 and NOTCH1 to be significantly less frequently mutated than in UV-mutated cSCC. Interestingly, KMT2B (a histone methyl transferase) was mutated in 11/31 non-UV-induced cSCC and this proportion was significantly higher than in UV-mutated cSCC. These mutations were high impact loss-of-function mutations. We found that knocking down KMT2B expression using siRNA did not affect cell proliferation of SCC-13 and A-431 cell lines, however, it significantly increased cell migration in vitro. Taken together, this study provides a comprehensive description of non-UV-induced cSCC and identifies that KMT2B is mutated and involved in non-UV-induced cSCC carcinogenesis.

overall_design: We performed mutational screening of 31 cSCCs and one pre-cancerous lesion from 31 patients by sequencing an exhaustive panel of 523 cancer genes using Illumina TruSight Oncology 500 (TSO500) kit, with mean depth of 919X and 98.9% of target sequences covered ≥100X (supplementary material, Table S1). Our data was compared with UV-induced cSCC data selected from 3 representative studies

last: Al Youssef

first: Mansour

last: Alkobtawi

first: Bénédicte

last: Oulès

first: Selim

last: Aractingi

first: Dany

last: Nassar


title: Low-input unstranded RNA sequencing on bulk tumor or FACS isolated tumor cells from  known rhabdomyosarcoma models [Low-input_BulkRNAseq]

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

summary:
Comparision of aP2-Cre, Myog-Cre and Cdh5-Cre SmoM2 driven tumors shows that Cdh5-Cre tumors express muscle markers but have unique gene expression profiles
Comparision of aP2-Cre SmoM2/tdTomato tumor cells and Cdh5-Cre SmoM2/tdTomato tumor cells isolated by FACS for CD31-/tdTomato+ cells reveals that Cdh5-Cre tumors are not rhabdomyosarcoma

overall_design: We performed RNA sequencing on bulk tumor or FACS isolated tumor cells from  known rhabdomyosarcoma models to compare to our novel tumor.

first: Katherine

middle: E

last: Gadek

first: Mark

last: Hatley


title: Total stranded RNA sequencing on bulk tumor or FACS isolated tumor cells from  known rhabdomyosarcoma models [Total-Stranded_RNAseq]

overall_design: We performed RNA sequencing on bulk tumor from known rhabdomyosarcoma models to compare to our novel tumor.


title: Exosomal miR-122-5p from tubular cells ameliorates renal interstitial fibrosis by regulating fibroblasts via HIF-1α

city: Baoding

first: Haisong

last: Zhang

address: 212 Yuhua East Road, Lianchi District

institute: Hebei University

type: Non-coding RNA profiling by high throughput sequencing

summary: Renal interstitial fibrosis (RIF) is a common pathological feature and final manifestation of chronic progressive kidney disease. Although exosome-mediated intercellular communication is known to play a crucial role in RIF, the mechanism by which injured tubular epithelial cells (TECs) contribute to fibrogenesis remains incompletely understood. In this study, we investigated the role of exosomal miR-122-5p derived from TECs in modulating fibroblast activation and renal fibrosis. Exosomes were isolated from kidneys of unilateral ureteral obstruction (UUO) mice and from TGF-β1-stimulated HK-2 cells. These exosomes were either co-cultured with fibroblasts (NRK-49F cells) or injected into UUO mice via the tail vein. High-throughput miRNA profiling was used to identify differentially expressed miRNAs in exosomes derived from HK-2 cells, and miR-122-5p was selected for further investigation based on expression level and bioinformatic prediction. Functional analyses were performed using miRNA mimics, inhibitors, and target validation assays. The results showed that exosomal miR-122-5p was significantly downregulated in both fibrotic kidneys and TGF-β1-induced HK-2 cells. In vivo and in vitro, restoration of miR-122-5p levels markedly attenuated renal fibrosis, as evidenced by the reduction of fibrotic markers including α-smooth muscle actin, fibronectin, and collagen I. Mechanistically, miR-122-5p was found to directly target hypoxia-inducible factor 1-alpha (HIF-1α), thereby inhibiting activation of the TGF-β1/Smad signaling pathway. These findings suggest that decreased expression of miR-122-5p in TEC-derived exosomes promotes renal fibrosis through the HIF-1α/TGF-β1/Smad axis, while reintroduction of miR-122-5p can effectively reverse these effects. Taken together, our study provides new insights into the intercellular communication between TECs and fibroblasts via exosomal miRNAs, and identifies miR-122-5p as a potential therapeutic target for the treatment of renal interstitial fibrosis.

overall_design: In this study, high-throughput sequencing was performed to profile the microRNA (miRNA) expression of exosomes derived from renal tubular epithelial cells (HK-2) with or without TGF-β1 stimulation, and miR-122-5p was identified through literature review and bioinformatics analysis as the focus for further investigation. HK-2 cells were divided into six groups—untreated control, TGF-β1, TGF-β1 plus miR-122-5p mimic, TGF-β1 plus mimic negative control, TGF-β1 plus miR-122-5p inhibitor, and TGF-β1 plus inhibitor negative control—and exosomes were isolated from each group. These exosomes were co-incubated with TGF-β1-pretreated rat fibroblasts (NRK-49F), and the expression of fibrosis markers (α-SMA, collagen I, fibronectin) was assessed by immunofluorescence and Western blot to evaluate fibroblast activation. In vivo, a unilateral ureteral obstruction (UUO) mouse model was established, and exosomes from different HK-2 treatment groups were administered via tail vein injection; renal miR-122-5p levels, serum creatinine, blood urea nitrogen, and histological fibrosis (HE, Masson’s trichrome, Sirius Red staining, and immunofluorescence) were evaluated. Potential miR-122-5p target genes were predicted using PITA, miRanda, and RNAhybrid, identifying HIF-1α as a key candidate, which was validated by wild-type/mutant 3′UTR luciferase reporter assays. Finally, Western blot was used to analyze HIF-1α and TGF-β1/Smad pathway proteins (Smad2, p-Smad2, Smad3, p-Smad3, Smad7, E-cadherin), and HIF-1α overexpression experiments were conducted to confirm that miR-122-5p exerts anti-fibrotic effects by regulating the HIF-1α/TGF-β1-Smad signaling axis.

first: Jifeng

last: Yang

first: Fengxia

last: Bai

first: Yao

last: Li

first: Qian

last: Gao

first: Linqian

first: Zhaomu

last: Zeng

first: Juan

last: Jia

first: Yuhao

first: Yan


title: Patient-Specific Pharmacogenomics demonstrates xCT as Predictive Therapeutic Target in Colon Cancer with Possible Implications in Tumor Connectivity

city: Jerusalem

first: Keren

last: Zohar

address: Safra Campus, Givat Ram

country: Israel

institute: Hebrew University of Jerusalem

summary: Colorectal cancer (CRC) represents the third-leading cause of cancer-related deaths. Knowledge covering diverse cellular and molecular data from individual patients has become valuable for diagnosis, prognosis, and treatment selection. Here, we present an in-depth comparative mRNA-seq analysis of tissue samples from 32 CRC patients, pairing tumors with adjacent healthy tissues. The differential expression gene (DEG) analysis revealed apparently dysregulated metabolic programs,in what we focused on the impact of overexpressed SLC7A11 (xCT) and SLC3A2 genes which compose the cystine/glutamate transporter (Xc-) system. To assess the oncogenic potency of the Xc- system in a cellular setting, we applied a knowledge-based approach for analyzing gene perturbations from CRISPR screens across various cell types as well as using a variety of functional assays in five primary patient-derived organoid cell models to functionally verify our hypothesis. We identified a previously undescribed cell surface protein signature predicting chemotherapy resistance and further highlighted the causality and potential of pharmacological blockage of ferroptosis as promising avenue for cancer therapy. Biological processes such as redox homeostasis, ion/amino acid transporters and regulators of neuronal survival and differentiation were associated with these co-dependent genes in patient specimens. This study highlights a number of potential clinical targets for CRC and promotes patient-individual in vitro model systems as functionally validate in silico predictions.

overall_design: The mRNA expression levels of all genes (coding and non-coding) were determined by pairwise analysis of cancerous and healthy tissues obtained from the same patient. Healthy tissue samples were harvested from the aboral margin of the colectomy specimen, at least 5–7 cm distal to the primary tumor, in accordance with national and international guidelines for oncologic resection safety. These normal adjacent tissue samples were macroscopically examined, approved by the pathologist and underwent extensive washing procedures prior to sequencing to ensure the absence of tumor cell contamination. Total of 32 patients were analyzed with 73 deep sequencing results. Altogether, there were 36 samples marked as tumor (T) and 37 samples marked as healthy (H). Each participant provided at least one sample for T and H. For four participants the number of samples was higher. Each sample was studied by partition total RNA by size to support mRNA and miRNA transcriptomics.

first: Ethical approval to conduct this study was granted by the ethics committee of the medical faculty of Magdeburg (33/01

last: amendment 43/14). Transcriptomic data from Magdeburg patients can be shared upon sending reasonable a request to the corresponding author UDK.

first: Marco

last: Strecker

first: Martin

last: Böttcher

first: Thomas

last: Wartmann

first: Henry

last: Freudenstein

first: Maximilian

last: Doelling

first: Mihailo

last: Andric

first: Wenjie

last: Shi

first: Or

last: Kakhlon

first: Katrin

last: Hippe

first: Beatrix

last: Jahnke

first: Dimitrios

last: Mougiakakos

first: Franziska

last: Baenke

first: Daniel

last: Stange

first: Roland

middle: S

last: Croner

first: Michal

last: Linial

first: Ulf

middle: D

last: Kahlert


title: Humanization of CD47 enables development of functional human neutrophils via post-irradiation remodeling of the bone marrow.

city: New Haven

first: Richard

last: Flavell

state: CT

address: 300 Cedar Street

institute: Yale University

summary: A major limitation of current models is suboptimal myelopoiesis, particularly lack of functional human neutrophils, hampering the modeling of human immune responses and chronic diseases. Here, we describe a novel humanized mouse model, named MaGIC for genes replaced, in the C57Bl/6N strain, which improves human myelopoiesis and enables development of functional human neutrophils. In MaGIC mice, human cytokines M-CSF/CSF1(M), GM-CSF/CSF2(G)  and IL-6(I) are knocked-in replacing mouse genes and murine IL2rg  and Rag1(a) are deleted.  Human THPO in these mice supports human hematopoiesis. More importantly, insertion of human CD47 (C) under the control of endogenous mouse CD47 promoter enables xenotransplantation and human neutrophil development.  We characterized the transcriptome of human neutrophils from MaGIC mice using 10x Genomics. MaGIC mice support all human neutrophil subsets found in human bone marrow and blood, a major improvement.

overall_design: Blood, bone marrow, and spleen from MaGIC mice were hashed and sequenced using 10x single cell 3' v3.1 RNA-sequencing.

first: Esen

last: Sefik

first: Fengrui

last: Zhang

first: Kriti

last: Agrawal


title: From gene expression to pregnancy prediction: towards precision ART through systems biology and Bayesian modeling

city: Milano

first: Michela

last: Riba

address: via Olgettina 60

department: COSR, Center for Omics Sciences

country: Italy

institute: IRCCS, Ospdale San Raffaele

summary: Purpose: This study investigates molecular differences between receptive and non-receptive endometrium by analyzing RNA cargo of uterine fluid-derived extracellular vesicles (UF-EVs). A total of 82 women who underwent blastocyst transfer with confirmed euploid embryos via Pre-implantation Genetic Testing (PGT-A) were included and followed to assess clinical pregnancy outcomes. The aim is to identify the transcriptomic profile of the endometrium during the window of implantation (WOI) by comparing gene expression between patients who achieved pregnancy and those who did not, and to use the WOI gene expression profile to predict pregnancy outcomes through a Bayesian logistic model. Methods: UF samples were collected on day 7 after the urinary LH surge (LH+7) in the cycle preceding the scheduled blastocyst transfer. In the subsequent natural cycle (LH+7), an ultrasound-guided transfer of the euploid blastocyst was performed, and clinical outcomes were recorded. A Differential Gene Expression (DGE) analysis (pregnant vs. not pregnant) was conducted, followed by a gene co-expression network analysis (WGCNA), which identified modules of co-expressed genes. These gene modules were integrated with clinical data to develop a Bayesian logistic regression model. Results: UF-EVs collected from 82 women were analyzed. Among the patients, 37 achieved pregnancy, while 45 did not. Differential gene expression analysis identified 966 significant genes (nominal p < 0.05), with a predominant upregulation in the pregnant group. Applying SEQC thresholds (nominal p < 0.01, |log₂FC| > 1) refined the list to 262 differentially expressed genes, the majority of which were overexpressed in patients who conceived. Four genes,RPL10P9, LINC00621, MTND6P4, and LINC00205, remained significant after multiple testing correction. Gene Set Enrichment Analysis (GSEA) revealed enriched biological processes such as adaptive immune response, lymphocyte-mediated immunity, and ion homeostasis. Weighted Gene Co-expression Network Analysis (WGCNA) grouped differentially expressed genes into four modules, with the grey and brown modules showing the strongest positive correlation with pregnancy. Functional enrichment of these modules highlighted immune regulation, transcriptional activity, and extracellular matrix remodeling. A Bayesian logistic regression model integrating gene expression modules with clinical variables accurately predicted pregnancy outcomes with 82.9% accuracy, an F1-score of 0.80, and an AUC of 0.88. Positive associations were observed for the grey module and co-expression patterns in the brown and turquoise modules, while increased EVs size and a history of miscarriages were negatively associated with pregnancy. Conclusions: This study demonstrates that UF-EV transcriptomic profiling can non-invasively capture endometrial receptivity signatures during the WOI. The integration of molecular and clinical data enables accurate pregnancy prediction, offering a promising approach to personalize embryo transfer timing and improve outcomes in ART.

overall_design:
This study analyzed uterine fluid-derived extracellular vesicles (UF-EVs) collected during the window of implantation (WOI) from 82 women undergoing ART with single euploid blastocyst transfer. RNA sequencing was performed to identify transcriptomic differences between patients who achieved pregnancy (N=37) and those who did not (N=45). Differential gene expression and weighted gene co-expression network analyses (WGCNA) were conducted to uncover biological processes associated with endometrial receptivity. A Bayesian logistic regression model was then developed, integrating gene expression data with clinical variables to predict pregnancy outcomes. The study aimed to establish a non-invasive, molecular-based tool to assess endometrial receptivity in ART. This work represents a further development of a previously published study (DOI: 10.1093/humrep/deab123) and also incorporates UF-EVs transcriptomic data from that study, including 42 samples available in the GEO repository under accession number GSE158958.

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

last: Marzanati

first: Francesco

last: Ranucci

first: Luca

last: Pagliardini

first: Valeria Stella

last: Vanni

first: Nicoletta

last: Barberis

first: Enrico

last: Papaleo

first: Massimo

last: Candiani

first: Giulia Maria

last: Scotti

first: Dejan

last: Lazarevic

first: Paolo

last: Giardina

first: Laura

last: Privitera

first: Paola

last: Viganò

first: Davide

last: Gentilini

first: Elisa

last: Giacomini


title: Host cell Z-RNAs activate ZBP1 during virus infections [MEF]

city: Oxford

first: Aleksandr

last: Fedorov

address: John Radcliffe Hospital/Headley Way

department: Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

summary: Herpes simplex virus 1 (HSV-1) and Influenza A viruses (IAV) trigger Z-form nucleic acid Binding Protein 1 (ZBP1)-initiated cell death. ZBP1 is activated by Z-RNA, and the Z-RNAs which activate ZBP1 during HSV-1 and IAV infections were assumed to be of viral origin. However, we show here that host cell-encoded Z-RNAs are major and sufficient ZBP1 activating ligands following infection by these two human pathogens. The majority of cellular Z-RNAs mapped to intergenic endogenous retroelements (EREs) embedded within abnormally long 3’ extensions of host cell mRNAs. These aberrant host cell transcripts arose as a consequence of Disruption of Transcription Termination (DoTT), a virus-driven phenomenon which disables Cleavage and Polyadenylation Specificity Factor (CPSF)-mediated 3’ processing of nascent pre-mRNAs. Mutant viruses lacking ICP27 or NS1, the virus-encoded proteins responsible for inhibiting CPSF and triggering DoTT, failed to induce host cell Z-RNA accrual and were attenuated in their ability to stimulate ZBP1. Ectopic expression of HSV-1 ICP27 or IAV NS1, or pharmacological blockade of CPSF activity, induced accumulation of host cell Z-RNAs and activated ZBP1. These results demonstrate that DoTT-generated cellular Z-RNAs are bona fide ZBP1 ligands, and position ZBP1-activated cell death as a host response to counter viral disruption of the cellular transcriptional machinery.

overall_design: Directional total RNA-seq of input and immunoprecipitated RNAs from FLAG-ZBP1-expressing MEF (ZBP1 -/-) cells. Cells were either mock-infected or infected with HSV-1 or IAV; immunoprecipitation was performed using Z22, IgG, or anti-FLAG antibodies.

first: Chaoran

last: Yin

first: Hongyan

last: Guo

first: Jeremy

middle: C

last: Crawford

first: Claire

last: Rousseau

first: Xiao

last: Zhong

first: Riley

last: Williams

first: Avishekh

last: Gautam

first: Heather

last: Koehler

first: Adam

middle: W

last: Whisnant

first: Thomas

last: Hennig

first: Anna

last: Rozina

first: Yuhan

first: Shuangjuan

last: Lv

first: Valter

last: Bergant

first: Shuqi

last: Wang

first: Peter

last: Dröge

first: Sven

last: Miller

first: Maria

last: Poptsova

first: Jan

last: Rehwinkel

first: Andreas

last: Pichlmair

first: Edward

last: Mocarski

first: Paul

middle: G

last: Thomas

first: Lars

last: Dölken

first: Ting

last: Zhang

first: Alan

last: Herbert

first: Siddharth

last: Balachandran


title: Methylome of grape berry reveal tissue specific features associated with metabolic processes [RNA-seq]

city: Shenzhen

first: Yu

last: Ma

address: 1088 Xueyuan Bivd, Nanshan District

institute: Southern University of Science and Technology

summary: DNA methylation is a conserved epigenetic mark that is involved in many biological processes including the ripening process of various crop species bearing fleshy fruit, such as tomato, strawberry, and orange. The dynamics and importance of DNA methylation during grapefruit ripening, has however not yet been characterized. In this study, we observed an increase in DNA methylation level during grape berry ripening. The application of a DNA methylation inhibitor delayed ripening, consistent with an important role for DNA methylation in grape berries.  In addition, we characterized the methylomes of the flesh and the skin the two main tissues of grape berry pericarp, as they present very distinct metabolic features. Results indicate that grape berry skin has a lower DNA methylation level than the flesh. Whereas in both tissues ripening is associated with an increase in DNA methylation, methylation patterns are clearly distinct between these two tissues as are the metabolic and transcriptomic profiles. Results indicated that the DNA methylation changes are associated with tissue specific metabolic modifications that occur during ripening, and involved in the synthesis of secondary metabolites.

overall_design: mRNA sequencing (mRNA-Seq) data of grape fruit pulp and berry extracted in F+6W and V+3W

first: P

last: Gallusci

first: Zhaobo

last: Lang


title: Methylome of grape berry reveal tissue specific features associated with metabolic processes [Bisulfite-seq]

type: Methylation profiling by high throughput sequencing

overall_design: Bisulfite sequencing (BS-Seq) data of grape berry and grape pulp and berry extracted in F+6W and V+3W


title: Host cell Z-RNAs activate ZBP1 during virus infections [HT-29]

first: Aleksandr

last: Fedorov

overall_design: Directional total RNA-seq of input and immunoprecipitated RNAs from FLAG-ZBP1-expressing HT-29 cells. Cells were either mock-infected or infected with HSV-1 or IAV; immunoprecipitation was performed using Z22 or anti-FLAG antibodies.

first: Chaoran

last: Yin

first: Hongyan

last: Guo

first: Jeremy

last: Crawford

first: Claire

last: Rousseau

first: Xiao

last: Zhong

first: Riley

last: Williams

first: Avishekh

last: Gautam

first: Heather

last: Koehler

first: Adam

last: Whisnant

first: Thomas

last: Hennig

first: Anna

last: Rozina

first: Yuhan

first: Shuangjuan

last: Lv


title: In-situ glial cell-surface proteomics identifies pro-longevity factors in Drosophila

city: Houston

first: Hongjie

last: Li

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Much focus has shifted towards understanding how glial dysfunction contributes to age-related neurodegeneration due to the crucial roles glial cells play in maintaining healthy brain function. Cell-cell interactions, which are largely mediated by cell-surface proteins, control many critical aspects of development and physiology; as such, dysregulation of glial cell-surface proteins in particular is hypothesized to play an important role in age-related neurodegeneration. However, it remains technically difficult to profile glial cell-surface proteins in intact brains. Here, we applied a cell-surface proteomic profiling method to glial cells from intact brains in Drosophila. Importantly, this enabled us to fully profile cell-surface proteomes in-situ, preserving native cell-cell interactions that would be omitted using more traditional proteomics methods. Applying this platform to young and old flies, we investigated how glial cell-surface proteomes change during aging. We identified candidate genes predicted to be involved in normal brain aging, including several associated with neural development and synapse wiring molecules not previously thought to be particularly active in glia. Through a functional genetic screen, we identified one surface protein, DIP-β, which is down-regulated in old flies and can increase fly lifespan when overexpressed in adult glial cells. We further performed whole-head single-nucleus RNA-seq, and revealed that DIP-β overexpression mainly impacts glial and fat cells. We also found that glial DIP-β overexpression was associated with improved cell-cell communication, which may contribute to the observed lifespan extension. Our study is the first to apply in-situ cell-surface proteomics to glial cells in Drosophila, and to identify DIP-β as a potential glial regulator of brain aging.

overall_design: Single-nucleus RNA-sequencing

first: Madeline

last: Marques

first: Bo

last: Sun

first: Ye-Jin

last: Park

first: Tyler

last: Jackson

first: Tzu-Chiao

last: Lu

first: Yanyan

last: Qi

first: Erin

last: Harrison

first: Kartik

last: Venkatachalam

first: Omar

last: Pasha

first: Amogh

last: Varanasi

first: Namrata

last: Udeshi

first: Dominique

last: Kiki Carey

first: D

middle: R

last: Mani

first: Steven

middle: A

last: Carr

first: Jonathan

last: Zirin

first: Mujeeb

last: Qadiri

first: Yanhui

last: Hu

first: Norbert

last: Perrimon

first: Liqun

last: Luo

first: Jiefu


title: Yamanaka factors-induced rejuvenation and immortalization of SIX2-positive renal progenitor cells from urine obtained from a male of African origin

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

country: Germany

institute: Universitätsklinikum Düsseldorf

summary: Recent demographic studies indicate that renal diseases are the leading cause of mortality globally. In the United States alone, approximately 37 million individuals are unaware that they suffer from chronic kidney disease (CKD). Podocytes, a primary cell type in the kidneys, play critical roles in blood filtration. These cells are terminally differentiated and incapable of division in vivo, making the establishment of primary cultures particularly challenging. The ability of cells to proliferate and avoid senescence is closely linked to telomere length, which shortens with each cell division. When telomere length becomes critically reduced, cells enter a state of proliferative arrest, triggering DNA damage responses and cellular senescence.  In this study, we present the successful immortalization of a human nephron progenitor cell line derived from the urine of a 30-year-old African male (UM30-OSN). These cells demonstrate stable morphology and proliferation for over one year in culture (~100 passages). To achieve partial reprogramming, plasmids encoding the reprogramming factors OCT4, SOX2, NANOG, cMyc, and KLF4 were employed, resulting in successful reprogramming over multiple passages.  Similar to the primary urine-derived renal progenitor cells (UdRPC) UM30, UM30-OSN expresses the pluripotency-associated marker SSEA4, as well as renal stem cell markers such as SIX2, CD133, CD24 and Vimentin, as determined by immunofluorescence, FACS and qPCR analyses. To verify the immortalization and rejuvenation potential of this cell line, the expression of key cell cycle regulators was analyzed by qPCR. We observed a downregulation of p21 and p53, alongside an upregulation of PCNA, KI67, and TERT, which supports the successful immortalization of UM30-OSN.  Furthermore, we demonstrate the efficient differentiation of UM30-OSN into human podocytes, a process that was compared to the widely used immortalized human podocyte line (AB 8/13) (Moin Saleem et al.). UM30-OSN podocytes express specific podocyte markers, including NPHS2, NPHS1, CD2AP and SYNPO. In contrast, podocytes (AB 8/13) express NPHS1, NPHS2, CD2AP and SYNPO, which was further validated by immunofluorescence qPCR and Western blot.  Given their robust proliferation capacity and ease of handling, UM30-OSN cells represent a valuable model for investigating nephrogenesis, kidney-related diseases, and drug screening. It is noteworthy that, in addition to the commonly used immortal podocyte (AB 8/13) cells, the UM30-OSN cells may serve as a potential alternative, exhibiting mature podocyte markers expression and a more stable karyotype.

overall_design: comparison of primary Urine derived SIX2-positive UdRPCs (UM30), immortalized UM30-OSN and a pluripotent stem cell line UM51-iPSC

first: Chantelle

last: Thimm

first: James

last: Adjaye


title: Targeting the PDGFRa-SHP2 Signaling Enhances Therapeutic Effect of Radiotherapy on Treating IDH1 Mutant Glioma

city: Chicago

first: Shi-yuan

last: Cheng

state: Illinois

address: 303 E. Superior Street, The Robert H. Lurie Cancer Center

institute: Northwestern Univeristy

summary: Background: Isocitrate dehydrogenase mutant (IDH-mut) glioma represents a distinct subtype of adult glioma. Although IDH-mut glioma displays slightly better prognosis among adult gliomas, these tumors are still incurable largely due to the lack of effective treatments. Targeting SHP2 has been shown to be a promising therapeutic approach in various types of malignancies, and our previous research demonstrated its efficacy against IDH wildtype (WT) glioblastoma (GBM). However, whether IDH-mutant gliomas are responsive to SHP2 inhibition remains unknown. Methods: Bioinformatic and biological analyses revealed increased expression and activation of PDGFRα-SHP2-ERK pathway in clinical IDH-mutant gliomas and patient-derived IDH-mut glioma stem-like cells (GSCs). Therapeutic effects of a SHP2 inhibitor on inhibition of the PDGFRα-SHP2-ERK signaling and tumorigenicity of IDH-mut GSCs, individually or in combination with radiation therapy (RT) were assessed by cell growth, glioma sphere formation, cell differentiation, flow cytometry, immunoblotting, orthotopic brain tumor xenograft, bioluminescent tracking, and immunohistochemistry. Results: We found a marked increase in PDGFRα expression in clinical IDH-mutant gliomas and IDH-mut GSCs, leading to the activation of the downstream SHP2-ERK pathway. Treatment with a blood-brain barrier-penetrable SHP2 inhibitor, SHP099 significantly inhibited GSC tumorigenic properties in vitro and in vivo by impeding SHP2-ERK axis and inducing cellular differentiation. Additionally, SHP099 treatment synergistically enhanced cytotoxicity of RT on IDH-mut GSCs in vitro and in orthotopic glioma xenografts, the standard treatment for IDH-mut glioma. Mechanistically, the PDGFRα -SHP2-ERK axis is activated in IDH-mut gliomas while radiation activates the SHP2-ERK pathway. Targeting SHP2 suppressed the activated ERK signaling thereby enhancing cytotoxicity of RT against IDH-mut gliomas. Conclusion: Targeting SHP2 in combination with RT for treating IDH-mut glioma displays promising therapeutic efficacy through suppressing a preferentially activated SHP2-ERK axis in IDH-mut gliomas.

overall_design: SF10602 cells are treated with SHP099 (15 μM) or DMSO for 7 days. Samples are duplicates in each group.

first: Xiaozhou

last: Yu

first: Xiao

last: Song

first: Deanna

last: Tiek

first: Runxin

last: Wu

first: Maya

last: Walker

first: Craig

last: Horbinski

first: Bo

first: Shi-Yuan


title: Single Cell RNA Sequencing of C57BL6 mouse whole aortas after 8 weeks of L-NAME treatment

first: Alireza

last: Khoddam

state: IL

address: 303 E Superior St 8-400

department: Cardiology

institute: Northwestern University

summary: Humans with a heterozygous loss-of-function SERPINE1 variant exhibit protection against biological aging and cardiometabolic dysfunction. Here, we reverse engineered a mouse model mimicking the human mutation (Serpine1TA700/+) and compared cardiovascular responses with wild-type littermates. Under L-NG-Nitro-arginine methyl ester (L-NAME)-induced vascular stress, Serpine1TA700/+ mice exhibited protection from systolic hypertension (SBP), preserved left ventricular diastolic function, and diminished aortic pulse wave velocity (PWV) compared to controls. Single cell transcriptomic analyses of Serpine1TA700/+ aortas, revealed a vascular-protective mechanism that involves the downregulation of extracellular matrix regulators Ccn1 and Itgb1.

overall_design: We crossed WT and heterozygous mice to have littermate controls with the correct genotypes. When the littermates reached 12 weeks old, they recieved 1 g/L of L-NAME in their drinking water for 8 weeks. At the end of their treatment, their whole aortas were extracted, and either (1) subjected to bulk RNA sequencing, or (2) single cell suspension was created, and subjected to 10x genomics single cell workflow. Our bulk RNA-seq experimental group had 6 biological replicates: Serpine1TA700/+ (3 males and 3 females). Our control group had biological replicates 6 Serpine1+/+ aortas (3 males and 3 females) Our scRNA-seq experimental group had 4 biological replicates: Serpine1TA700/+ (2 males and 2 females). Our control group had biological replicates 6 Serpine1+/+ aortas (3 males and 3 females)

first: Lisa

last: Wilsbacher

first: Douglas

last: Vaughan


title: Effects of a Probiotic Formulation Based on SF68, Phytosterols, and 6S-5-Methyltetrahydrofolic Acid on Body Composition, Biochemical Parameters, Gut Microbiota, and Gastrointestinal and General Symptoms of Overweight/Obese Subjects: The PrObesity Study

city: Florence

first: Sara

last: Bertorello

address: Viale Gaetano Pieraccini 6

institute: University of Florence

summary: Obesity and dyslipidemia are increasingly widespread. Considering gut microbiota's (GM) role in energy balance, probiotics represent a promising non-pharmacological approach. This study assessed a probiotic formulation (SF68 + phytosterols + (6S)-5-methyltetrahydrofolic acid) on anthropometric, biochemical, and GM parameters, as well as gastrointestinal and general symptoms, in overweight/obese individuals with low-to-moderate cardiovascular risk. Forty participants (30F, mean age 51.5 ± 11 years) were randomized to receive either the probiotic or placebo daily for 12 weeks. Anthropometric data, questionnaires, and biological samples were collected pre- and post-intervention. While both groups showed significant (p < 0.05) improvements, the probiotic group showed greater reductions in waist circumference (−1.8 cm), fat mass (−1.8 kg; −1.7%), total cholesterol (−11 mg/dL), and LDL-cholesterol (−10.3 mg/dL), along with an increased HDL/LDL ratio (+0.1). Both probiotic and placebo resulted in a significant reduction in HbA1c (−1.7 mmol/mol and −1.5 mmol/mol, respectively). The probiotic formulation also reduced erythrocyte ROS (−29.7%), granulocyte ROS (−28.4%), and plasma nitrite/nitrate (49.5%) and significantly increased erythrocyte glutathione (GSH; +81.9%). Gastrointestinal symptoms improved, and GM analysis showed an increased Evenness index and reduced Lachnospirales abundance after probiotic treatment. These findings suggest the multi-component probiotic formulation may support metabolic and gut health in overweight or obese individuals, although further research is warranted

overall_design: Patients were divided into two groups, each assigned to consume the probiotic formulation based on SF68® + Phytosterols + (6S)-5-methyltetrahydrofolic or placebo for 12 weeks. Total DNA was extracted from stools, amplified to collect amplicons of variable V3–V4 region of the bacterial 16S rRNA gene and sequenced in paired-end mode (2 × 300 cycles) on the AVITI™ System.

first: Giuditta

last: Pagliai

first: Simone

last: Baldi

first: Marta

middle: T

last: Asensi

first: Ilaria

last: Giangrandi

first: Sofia

last: Lotti

first: Alessia

last: Bertelli

first: Francesco

last: Cei

first: Gianluca

last: Bartolucci

first: Serena

last: Borghi

first: Amedeo

last: Amedei

first: Matteo

last: Becatti

first: Claudia

last: Fiorillo

first: Anna

last: Gori

first: Rossella

last: Marcucci

first: Barbara

last: Colombini

last: Sofi


title: (6-4)PP and CPD Damage-seq data for L1 stage wildtype, csb-1 and xpc-1 C.elegans

city: Chapel Hill

first: Cansu

last: Kose

state: NC

address: 120 Mason Farm Rd.

department: Biochemistry and Biophysics

institute: UNC-Chapel Hill

summary: Caenorhabditis elegans is widely used to study DNA repair and related processes such as aging, yet genome-wide nucleotide excision repair remains largely unexplored. Here, we present a comprehensive whole-organism map of UV-induced DNA damage and repair in L1 larvae. Of the two repair pathways - global repair and transcription-coupled repair - global repair predominates, accounting for over 80% of lesion removal; and notably, (6-4) photoproducts are removed by transcription-coupled repair at an extent comparable to CPD, a feature not previously observed in animals. Integration of damage and repair profiles with chromatin features reveals that despite non-uniform damage formation, repair efficiency is the stronger determinant of residual damage. Finally, repair around accessible regions exhibit periodicity, reflecting underlying nucleosome architecture. Together, these findings establish Caenorhabditis elegans as a valuable model organism for interrogating excision repair within a chromatin context and reveal species-specific features that broaden our understanding of DNA repair mechanisms across metazoans.

overall_design: Damage-seq was performed on naked DNA and 0 hour, 8 hours, 24 hours and 48 hours after UVB 4 kj/m2, no UV treatment or in L1 stage wild-type. Either anti (6-4)PP or anti CPD antibodies used to purified  sonicated genomic fragments.


title: Loss of macroH2A1.1 causes kidney abnormalities secondary to a change in nutrient metabolization

city: Badalona

first: David

last: Corujo

address: Ctra de Can Ruti, Camí de les Escoles

institute: Josep Carreras Leukaemia Research Institute

summary: Histone variants with metabolite-binding macrodomains provide a poorly understood link between chromatin composition and metabolism. To address their contribution to physiological health, we have generated and analyzed mice exclusively lacking the histone variants macroH2A1.1, macroH2A1.2, or macroH2A2. We identify several histopathological changes in the kidney as a novel isoform-specific phenotype of complete macroH2A1.1 loss. Kidney alterations, such as increased cast formation or the presence of interstitial inflammatory infiltrates, were not associated with organ-intrinsic changes in gene expression but strongly correlated with a shift in nutrient metabolization. Reduced lipid oxidation and increased glycolysis were found in both male and female mice with isoform-specific macroH2A1.1 loss. However, male macroH2A1.1 knock-out mice had a better glucose tolerance accompanied by changes in the expression of metabolic genes in the liver. Forcing mice to metabolize fat by replacing chow diet with a ketogenic diet overrode the macroH2A1.1-dependent metabolic phenotype and prevented the appearance of kidney abnormalities. Taken together, our results indicate that macroH2A1.1 controls nutrient metabolization and links macroH2A1.1 levels to secondary changes in the kidney.

overall_design: RNA sequencing of homogenized liver and kidney tissue from male WT or macroH2A1.1 KO mice

first: Winkler

last: René

first: Armangué-Comas

last: Gemma

first: Corujo

last: David

first: Shubhra

last: Bhattacharya

first: Teperino

last: Raffaele

first: Buschbeck

last: Marcus


title: The Ashkenazi-centric G334R variant of TP53 is severely impaired for transactivation but retains tumor suppressor function in a mouse model [RNA-seq]

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Mutations in the TP53 tumor suppressor gene are the most abundant genetic occurrences in cancer.  Some of these mutations lead to loss of function of p53 protein, some are gain of function, and some variants are hypomorphic (partially-functional).  Currently, there is no clinical distinction between different p53 mutations and cancer therapy or prognosis.  Mutations in the oligomerization domain of p53 appear to be quite distinct in function, compared to mutations in the DNA binding domain.  Here we show that, like other p53 oligomerization domain mutants, the Ashkenazi-specific G334R mutant accumulates to very high levels in cells and is significantly impaired for the transactivation of canonical p53 target genes.  Surprisingly, we find that this mutant retains the ability to bind to consensus p53 target sites.  A mouse model reveals that mice containing the G334R variant show increased predisposition to cancer, but only a fraction of these mice develop cancer at late onset.  We show that the G334R variant retains the ability to interact with the SP1 transcription factor and contributes to the transactivation of joint SP1-p53 target genes.  The combined evidence indicates that G334R is a unique oligomerization domain mutant that retains some tumor suppressor function.

overall_design: RNA sequencing (RNA-seq)  in HCT116 cells with either WT p53 or G334R before and after exposure to nutlin-3a treatment to determine differences in transcription.

last: Stieg

first: Katilyn

last: Casey

first: Bhanu

last: Karisetty

first: Julia

middle: I

last: Leu

first: Fiona

last: Larkin

first: Peter

last: Vogel

first: Jozef

last: Madzo

first: Maureen

last: Murphy


title: RNA sequencing of murine ovarian follicles +/- NTY

city: Aarhus N

first: Morten

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

summary: NOT PROVIDED; REQUESTED

overall_design: Differential gene expression comparison

first: Mahboobeh

last: Amoushahi

first: Karin

last: Lykke-Hartmann


title: Epigenetic regulation of Treg specific genes by BATF in lymphoid tissues

first: Weiguo

last: Cui

address: 303 E Chicago Ave

department: Pathology

summary: In the absence of BATF in Treg accessibility at the enhancer regions of Treg specific genes involved in different aspects of Treg biology including suppressive function, homeostasis, tissue adaptation and stability was reduced.

overall_design: Spleenocytes from two mice, wild-type Treg (WLT) and BATF knock-out Treg (TBKLT), were prepared for ATAC seq (Assay for transposase accessible chromatin with sequencing) between 5-7 weeks of age.

first: Achia

last: Khatun


title: Targeting of HIF2-driven cachexia in kidney cancer

city: Boston

first: Qinqin

last: Jiang

state: Ma

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Kidney cancer frequently causes paraneoplastic syndromes, including hypercalcemia and cachexia, but the underlying mechanisms are incompletely understood. The most common form of kidney cancer, clear cell renal cell carcinoma (ccRCC), is frequently caused by loss of the pVHL tumor suppressor protein and the resulting upregulation of the HIF2 transcription factor. We show that PTHLH, which resides on a ccRCC amplicon on chromosome 12p, is a direct HIF2 transcriptional target in ccRCC. Further, we show that the increased PTHLH expression is both necessary and sufficient for the induction of hypercalcemia and cachexia in preclinical orthotopic cell line tumor models. Consistent with these observations, two different allosteric HIF2 inhibitors, belzutifan and NKT2152, rapidly ameliorated hypercalcemia and cachexia in patients with ccRCC, including in some who did not exhibit objective tumor shrinkage. Our findings support prospective clinical studies to determine whether HIF2 inhibitors can be leveraged not only for tumor control, but also for the treatment of cancer-associated cachexia in renal cell carcinoma.

overall_design: We aim to systematically identify HIF-responsive genes by RNA-Seq in OS-RC-2 cells. We generated two isogenic comparisons to create HIF2 high and low status, for which cells 1) were treated with 2 uM PT2399 (PT) or vehicle (Veh) for 72 hours, 2) underwent CRISPR-based gene editing with a HIF2a sgRNA or a contrl sgRNA (sgCtrl). We then performed RNA-Seq experiments to quantify gene expression for each condition in triplicates.

first: Muhannad

last: Abu-Remaileh

first: Zachary

last: Herbert

first: William

last: Kaelin Jr


title: TH17 cells converted into exTH17 cells sustain rheumatoid-like IL-17–independent inflammatory arthritis

city: La Jolla

first: Ferhat

last: Ay

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

summary: T helper 17 (TH17) cells are found in the periphery and synovium of patients with rheumatoid arthritis (RA); however, IL-17–targeted interventions have limited efficacy in established RA. Inflammation can induce TH17 cell transdifferentiation into IL-17–negative exTH17 cells, but the role of exTH17 cells in arthritis is unknown. We performed TH17 cell lineage tracing in the SKG mouse model of RA. In arthritic mice, synovial TH17 cells transdifferentiate into CD44+ exTH17 cells, which are more arthritogenic and sustain inflammation that is IL-17 independent. The exTH17 cell gene signature includes up-regulation of CD44 and sphingosine-1-phosphate receptor 4 (S1PR4) and correlates with the profile of human RA synovial CD4+ T cells. We demonstrate that cross-talk between TH17 cells and fibroblast-like synoviocytes (FLSs) via S1P promotes TH17-exTH17 cell conversion. CD44 is necessary for exTH17 cell–mediated arthritis. Our study suggests that FLS expansion during RA progression promotes TH17-exTH17 cell conversion. These results could potentially enable RA precision therapy.

overall_design: Perfroming a 10X multiome experiment we wanted characterize the potential heterogeneity within joint exTh17 cells and identify potential transcriptional regulatory mechanisms responsible for upregulation of their signature genes.

first: M

last: Zoccheddu

last: Svensson

first: P

last: Dutta

last: Ro

first: Y

last: Wang

first: H

last: Kim

first: Z

last: Mikulski

first: K

last: Dobaczewska

first: F

last: Ingegnoli

first: A

last: Denn

first: R

last: Caporali

last: Randelli

first: D

last: McBride

first: N

last: Shah

first: W

last: Zhipin

first: J

last: Moore

last: Won

last: Bottini


title: Fidelity in lineage determination and stimulus-inducible gene expression requires ISWI chromatin remodeling activity [ChIP-seq 2]

status: Public on Sep 18 2025

city: Milan

first: Francesco

last: Gualdrini

address: Via Adamello, 16

department: Department of Experimental Oncology

institute: European Institute of Oncology

summary: Control over the accessibility of the genomic cis-regulatory information is key for the accurate deployment of gene expression programs. Such control is exerted by the combined action of pioneer transcription factors and chromatin remodelers with different ability to alter nucleosome positioning and occupancy. Here we show that SMARCA5 ( SNF2H), a chromatin remodeler enforcing linker DNA length, controls spacing of nucleosomes adjacent to sites where the myeloid lineage determining and pioneer TF PU.1 is constitutively bound, without however affecting PU.1 binding. Loss of SMARCA5 caused a widespread increase in the accessibility of sites for stimulus-regulated TFs, causing not only macrophage hyper-activation in response to inflammatory stimulation but also the induction of stimulus-inappropriate genes. SMARCA5 deficiency also determined the extensive increase in binding of C/EBPb to cognate sites normally not accessible in macrophages but instead exposed in white or brown adipogenesis. Overall, enforcement of nucleosome phasing by ISWI controls fidelity in both lineage specification and response to stimulation.

overall_design: Chip-seq in primary BMDM derived from wildtype or Smarca5 deleted cells for C/EBPb (Chip) in untreated or LPS stimulated condition.

first: Sara

last: Polletti

first: Júlia

last: Melià Alomà

last: Pileri

first: Chiara Anna

last: Di Lena

first: Viviana

last: Piccolo

first: Alessandro

last: Cuomo

first: Tomas

last: Stopka

first: Gioacchino

last: Natoli


title: Fidelity in lineage determination and stimulus-inducible gene expression requires ISWI chromatin remodeling activity [RNA-Seq 2]

overall_design: RNA-seq in mouse primary BMDMs derived from wild-type or Smarca5-deficient cells, pre-treated for 1 hour with either DMSO or the TBK1 inhibitor MRT67307 (5 µM), followed by either no stimulation or 2-hour LPS treatment.

first: Stefano

last: Rizzieri

first: Mattia

last: Marenda


title: Investigation of a global mouse methylome atlas reveals subtype-specific copy number alterations in pediatric cancer models

city: Hamburg

first: Melanie

last: Schoof

address: Martinistr. 52

institute: Research Institute Childrens Cancer Center Hamburg

type: Methylation profiling by genome tiling array

summary:
Mouse models represent the gold standard for cancer-related preclinical in vivo trials. However, their molecular characterization has often been limited and lacks global DNA methylation profiling, which has emerged as a crucial classification tool for various human tumor entities. Therefore, the epigenetic tumor cell identity, proximity to respective human counterparts, and their underlying CNVs have mostly remained elusive.
Here, we generate a comprehensive DNA methylation atlas of globally available mouse models for pediatric solid tumors, including an extensive, novel cohort of high-grade glioma models. We show that tumors cluster within dedicated tumor entities and exhibit previously suggested connections to putative cells of origin. Using tailor-made cross-species analysis, we highlight the epigenetic resemblance of analyzed models to the human disease and demonstrate entity-specific immune infiltration by custom deconvolution. Strikingly, we identified that specific mouse models harbor highly recurrent CNV signatures that are unique to the respective tumor subtype. We further show that these CNVs share syntenic regions with their respective human counterparts and occur reliably during multi-passage tumor evolution.
Our results reveal epigenetic insights into a global conglomerate of mouse models for pediatric solid cancers and seminally showcase recurrent CNVs in murine tumors, granting long-awaited access to CNV research."

overall_design: Mouse sample were dissected and fresh frozen,cryoconserved or FFPE tissue was used for DNA extraction. The DNA was extracted and analyzed by the MM285 mouse methylation array (Illumina).

first: Marc

last: Zuckermann

first: Tuyu

last: Zheng

first: Ulrich

last: Schüller


title: Fidelity in lineage determination and stimulus-inducible gene expression requires ISWI chromatin remodeling activity [ChIP-seq]

overall_design: Chip- and Mnase Chip-seq in primary BMDM derived from wildtype or Smarca5 deleted cells for H3K27ac (Chip), C/EBPb (Chip), PU.1 (Chip), CTCF (Chip) and Smarca5 (Mnase Chip) in untreated, LPS or IFNb stimulated conditions (see individual sample).


title: Fidelity in lineage determination and stimulus-inducible gene expression requires ISWI chromatin remodeling activity [ATAC-seq]

overall_design: ATACseq in Mouse primary BMDM derived from wildtype or Smarca5 deleted cells in untreated, LPS stimulated or IFNb stimulated conditions for 1 and 2 hours.


title: Totipotent-Like Cell-Based Embryo Model Recapitulating Mouse Embryogenesis from Pre-Implantation to Gastrulation [RNA-Seq]

city: Beijing

first: Ruoqi

last: Cheng

state: Beijing

address: NO.5, Yiheyuan Road, Haidian District

department: School of Life Sciences

institute: Peking University

summary: The development of stem-cell-derived models of mammalian embryogenesis has provided invaluable tools for investigating embryo development. However, constructing embryo models that can continuously recapitulate the full developmental trajectory, from zygotic genome activation (ZGA) to gastrulation, remains a major challenge. Here, we developed a new chemical cocktail to induce totipotent-like cells with robust proliferation ability, and leveraged these cells to establish a stepwise protocol to generate a continuous embryo model. This model sequentially mimics mouse embryogenesis from embryonic day 1.5 to 7.5. It recapitulates key developmental milestones, including ZGA in 2-cell embryos, the diversification of embryonic and extraembryonic lineages from 4-cell to 64-cell stages, the formation of blastocysts, and the subsequent development into post-implantation egg cylinders. Notably, these structures can undergo gastrulation, as evidenced by primitive streak formation and the subsequent emergence of several hallmarks of early organogenesis. Our study opens new avenues for modeling mammalian embryogenesis in vitro.

overall_design: A series of bulk RNA-seq data were analyzed, including EPSCs under 6 conditions: E (EPSC), C (EPSC + CHIR-99021), CE (EPSC + CHIR-99021 + Elvitegravir), CP (EPSC + CHIR-99021 + PD0325901), CCD2 (EPSC + CHIR-99021 + CD1530), and "all" (EPSC + all small molecules); long-term passaged S1 samples (P25, P38); S2, S3, S5, and their corresponding samples treated with drug combinations minus one agent; as well as mESCs, mESC-derived S1.

first: Yixuan

last: Ren

first: Xuyang

last: Wang

first: Haiyin

last: Liu

first: Yaxing

last: Xu

first: Cheng

last: Li

first: Hongkui

last: Deng

first: Jun


title: Signal pathway-based culture condition improves differentiation potential of canine induced pluripotent stem cells

city: Stanford

first: Kyomi

last: Igarashi

address: 265 Campus Drive

department: Genetics

institute: Stanford University

summary: Naturally occurring diseases in companion dogs such as cancer, immune-mediated and neuro-degenerative diseases are increasingly being recognized as valuable translational disease models. While induced pluripotent stem cell (iPSC) technology had revolutionized the field of human bio-medical research, canine iPSC technology is still in its infancy and robust canine specific iPSC media formulations and differentiation protocols are lacking. Here, we have established NANOG-reporter canine iPSC (ciPSC) lines and found that FGF, activin/TGF beta, and WNT signals were critical for the robust maintenance of ciPSCs. Manipulating these signaling pathways stabilized the culture of ciPSC regardless of the cell line, basal medium, or extracellular matrix. These conditions allowed ciPSC lines to form a teratoma, including one line that could not form with the previous medium lacking these factors. Canine iPSCs cultured in the optimized medium showed the suppression of lineage-specific genes and homogenized global gene expression pattern. Furthermore, the ciPSCs cultured in this medium successfully differentiated into cardiomyocytes displaying homogenous contraction as well as sarcomere alignment. This universal and robust culture condition provides a valuable resource to facilitate the utilization of ciPSCs for various studies, including the generation of canine translational models for human disease.

overall_design: RNA-seq profiling of canine induced pluripotent stem cells cultured in either StemFit (control) or AR medium.

first: Toshiya

last: Nishimura


title: Methyl jasmonate seed treatment mitigates the defense-growth trade-off and tailors plant response to specific pests

city: Madrid

first: Lucia

last: Talavera

address: Parque Científico y Tecnológico, UPM Campus de Montegancedo, Ctra, M-40, km 38

institute: CBGP

summary: Seed defence priming is emerging as a novel, cost-efficient and environmentally safe tool for pest management. Previous reports suggest that this strategy could potentially uncouple the defence-growth trade-off in plants, but this role and the mechanisms underlying it remain elusive. Here, we investigated the ability of seed priming with four phytohormones and two plant vitamins to uncouple the growth-defence trade-off in Arabidopsis thaliana upon pest infestation, focusing on its molecular dynamics. To broaden our scope, two phytophagous species from different feeding guilds were used: the generalist cell-content sucker Tetranychus urticae, and the specialist chewer Pieris brassicae. A combined -omics approach revealed distinct and interactive effects of seed priming and herbivory. Specifically, seed priming with 0.1 mM methyl jasmonate induced a state of readiness characterized by reduced stomatal aperture, high transcriptomic variation, increased sugar content and enhanced translational rate. Upon pest infestation, primed plants exhibited herbivore-specific responses. Interaction of seed priming and T. urticae infestation increased amino acid levels, hydroxycinnamic acid amide production, and reallocated resources from arabidopsides and anthocyanin biosynthetic pathways. In contrast, P. brassicae infestation in primed plants led to enhanced anthocyanin biosynthesis, alterations in lignin metabolic intermediates, and sustained carbon and nitrogen sources. These findings demonstrate that seed priming can enhance pest-specific defences in plants without incurring a fitness penalty, effectively managing infestations while maintaining growth.

overall_design: RNA-seq profiling of methyl jasmonate-primed and non-primed plants under three infestation conditions (control, 24 hpi Tetranychus urticae and 24 hpi Pieris brassicae)

last: Talavera Mateo

first: Alejandro

last: Garcia

first: Estrella

last: Santamaria


first: Ferhat

last: Ay

overall_design: Analyze differences between Th17 and exTh17 and explore the pathogenic mechanism of exTh17 in SKG arthritis

first: M

last: Zoccheddu

last: Svensson

first: P

last: Dutta

last: Ro

first: Y

first: H

last: Kim

first: Z

last: Mikulski

first: K

last: Dobaczewska

first: F

last: Ingegnoli

first: A

last: Denn

first: R

last: Caporali

last: Randelli

first: D

last: McBride

first: N

last: Shah

first: W

last: Zhipin

first: J

last: Moore

last: Won

last: Bottini


last: Ay

overall_design: Refer to individual Series


title: Mechanistic models position ceritinib as a nuclear integrity disrupting therapy in pediatric liver tumors

city: München

first: Salih

last: Demir

address: Lindwurmstr. 2a

institute: LMU kinderchirurgie

summary: Pediatric liver tumors with high-risk features pose therapeutic challenges, necessitating the development of more targeted and effective treatment strategies. Computational modeling of virtual patients and in silico drug response simulations, based on properly trained mechanistic models, is a powerful strategy to predict new treatment options. We aimed to leverage patient-specific mechanistic cell models to identify therapeutic alternatives for pediatric patients with high-risk liver tumors. We generated digital twins of high-risk pediatric liver tumor patients by integrating clinical, genetic, and transcriptomic data and performed computational drug response simulations using mechanistic models. We validated the therapeutic potential of ceritinib in patient-derived xenograft models both in vitro and in vivo and used fluorescence microscopy-based imaging for functional analyses. Mechanistic models trained with digital twins of high-risk pediatric liver tumor patients identified ceritinib as the most effective treatment option through iterated in silico drug response simulations. Validation on a comprehensive drug-testing platform demonstrated that ceritinib, unlike other ALK receptor tyrosine kinase inhibitors with lower prediction scores, inhibited tumor growth by targeting non-canonical kinases. Mechanistically, ceritinib suppressed expression of nucleoporins, essential components of the nuclear pore complex overexpressed in pediatric liver tumors, consequently leading to the disruption of nuclear membrane integrity, perinuclear accumulation of mitochondria, production of reactive oxygen species, and induction of apoptosis. In patient-derived xenograft mouse models, ceritinib reduced tumor burden and extended survival by promoting cell death. This study demonstrates the successful application of mechanistic models on virtual patients to position ceritinib as a promising therapeutic agent for high-risk pediatric liver tumors, highlighting its impact on key kinases implicated in tumor aggressiveness and its ability to compromise nuclear integrity.

overall_design: mRNA profiles of pediatric liver tumor patients

first: Roland

last: Kappler


title: Fidelity in lineage determination and stimulus-inducible gene expression requires ISWI chromatin remodeling activity [RNA-Seq]

first: Francesco

last: Gualdrini

overall_design: RNA-seq in Mouse primary BMDM derived from wildtype or Smarca5 deleted cells in untreated, LPS stimulated or IFNb stimulated conditions for 1 and 2 hours.

first: Sara

last: Polletti

first: Júlia

last: Melià Alomà

last: Pileri

first: Gioacchino

last: Natoli


title: Single cell profiling reveals three endothelial to hematopoietic transitions with divergent isoform expression landscapes [scRNA-Seq]

city: Manchester

first: Georges

last: Lacaud

state: England

address: Wilmslow Raod

department: Stem Cell Biology

institute: Cancer Research UK Manchester Institute

summary: Hemogenic endothelium (HE) is recognized as the origin of all definitive blood cells including hematopoietic stem cells (HSC). However, the mechanisms governing the hematopoietic progenitor versus HSC fate choice within the HE remains unknown. To explore this, we combined differentiation assays with full-length single-cell transcriptome data for extra-embryonic yolk sac (YS) and intra-embryonic aorta–gonad–mesonephros (AGM) region HE populations. We identified and localized three differentiation trajectories, each containing a distinct HE subset and potential: erythro-myeloid progenitor-primed HE in the YS plexus, lympho-myeloid progenitor-primed HE in large YS arteries, and HSC-primed HE in the AGM. Chromatin modifiers and spliceosome components were enriched AGM HE. Nanopore long-read sequencing identified AGM specific, functionally unique, splice variants of stemness-associated factors Runx1, Mecom, and Dnmt3b. Our data indicate that isoform expression changes are associated with HSC generation and provide a unique resource for studying cell fate decisions in HE.

overall_design: Single cell RNA-seq of cells undergoing hemogenic to endothelial transition in AGM at E9.5 and E10.5 and Yolk Sac (YS) at E9, E9.5, E10.5.  To study the HE populations present at different anatomical locations and time points during the mouse development, we used transgenic reporter mouse lines GFI1-GFP and RUNX1B-RFP and performed Smart-seq2 (single cell RNA seq) on FACS isolated E9.5 and E10.5 AGM HE cells (RUNX1+,KIT-, CDH5+, GFI1+/-, CD41-, CD45-), and E9, E9.5, E10.5 YS HE cells (RUNX1+, KIT+, GFI1+/-, CD31+, CD41-, CD45-). Total 1494 cells used.

first: Wen

middle: H

last: Neo

first: Muhammad

last: Zaki Hidayatullah Fadlullah

first: Harshangda

last: Bhatnagar

first: Cristiana

last: Barone

first: Giulia

last: Quattrini

first: Filipa

last: Timóteo-Ferreira

first: Joana

last: Carrelha

first: Gianluca

last: Sala

first: John

last: Weightman

first: Wolfgang

last: Breitwieser

first: Natalia

last: Moncaut

first: Roshana

last: Thambyrajah

first: Sten

last: Jacobsen

first: Mudassar

last: Iqbal

first: Syed

last: Murtuza Baker

first: Emanuele

last: Azzoni

first: Michael

last: Lie-A-Ling


title: Totipotent-Like Cell-Based Embryo Model Recapitulating Mouse Embryogenesis from Pre-Implantation to Gastrulation [scRNA-Seq]

first: Ruoqi

last: Cheng

overall_design: Total of 8 scRNAseq samples were analyzed, which include s1, s2, s3, s4, s4-2 (a new batch of s4), s5, s7 and s8.

first: Yixuan

last: Ren

first: Xuyang

last: Wang

first: Haiyin

last: Liu

first: Yaxing

last: Xu

first: Cheng

last: Li

first: Hongkui

last: Deng

first: Jun


title: Fidelity in lineage determination and stimulus-inducible gene expression requires ISWI chromatin remodeling activity [scRNA-seq]

first: Francesco

last: Gualdrini

overall_design: scRNA-seq was performed on mouse primary BMDMs derived from wild-type or Smarca5-deficient cells, either unstimulated or treated with LPS for 2 hours, using the 10x Genomics 3’ Gene Expression assay with CellPlex multiplexing.

first: Sara

last: Polletti

first: Júlia

last: Melià Alomà

last: Pileri

first: Stefano

last: Rizzieri

first: Mattia

last: Marenda

first: Gioacchino

last: Natoli


title: Single cell transcriptomic profiling of trunk tissue isolated from spinal cord-lesioned control zebrafish larvae or following depletion of pdgfrb+ cells

city: Erlangen

first: Daniel

last: Wehner

address: Staudtsraße 2

department: Division Biological Optomechanics

institute: Max Planck Institut for the Science of Light

summary: The goal of this study was to map the transcriptional changes with or without depletion of pdgfrb+ cells after spinal cord lesion in zebrafish larvae at single cell level.

overall_design: RNA profiles of single cells isolated from trunk tissue of spinal cord-lesioned Tg(BAC(pdgfrb:Gal4ff))ncv24;Tg(UAS-E1b:Eco.NfsB-mCherry)c264 (referred to as pdgfrb:NTR-mCherry) transgenic zebrafish larvae, treated with Metronidazole or DMSO control, were generated by scRNA-seq, in duplicates, using Illumina NovaSeq 6000


title: Host cell Z-RNAs activate ZBP1 during virus infections.

city: Oxford

first: Aleksandr

last: Fedorov

address: John Radcliffe Hospital/Headley Way

institute: University of Oxford

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: snRNAseq of mouse kidney stromal cells

city: Los Angeles

first: Jonathan

middle: William

last: Nelson

address: 1333 San Pablo St.

department: Medicine

institute: University of Southern California

summary: Kidney stromal cells display a remarkable amount of regional and functional heterogeneity. We applied single-nucleus RNA-seq to map the molecular heterogeneity of enriched mouse stromal cells.

overall_design: Kidney stromal cells from Pdgfrb-CreERT2-INTACT mice were isolated by Fluorescence-activated nuclei sorting (FANS) according to the presence or absence of GFP signal and analyzed using snRNAseq.


title: Transgenerational Adaptation to Hypoxia

city: St. Louis

first: Eric

middle: Lieberman

last: Greer

state: MO

address: 660 S Euclid Ave

institute: Washington University School of Medicine

summary: Adaptation to environmental stresses is crucial for survival. Transgenerational epigenetic inheritance allows organisms to respond to irregular conditions, alert their naïve descendants that stresses could still be present, and for distant descendants to eventually return to a basal state after several generations without the stress. However, it is still unclear whether organisms adapt on a transgenerational scale after repeated generational exposures to the same environmental stress. We recently found that C. elegans exposed to hypoxia in the parental (P0) generation: increased longevity in the P0 generation, caused an intergenerational reduction in lipids, and elicited a transgenerational reduction in fertility (P0-F2) that was dependent on small RNAs that were transmitted from parents to their naïve children. Here, we find that exposure of subsequent generations of C. elegans to hypoxia caused a transgenerational adaptation such that C. elegans that had repeated generational exposure to hypoxia failed to display hypoxia induced phenotypes. We show that upon two repeated generational exposures to hypoxia, C. elegans no longer display an increase in lifespan, and after four repeated generational exposures to hypoxia, C. elegans no longer display a decrease in reproduction. Transgenerational adaptation of the reproduction phenotype is dependent on the putative H3K27 trimethytransferase PRC2 complex and we identified critical genes that adapted on a transgenerational timeframe to repeated hypoxia exposure. Our findings reveal that transgenerational adaptation occurs and suggest that H3K27me3 is a critical modification for adapting to repeated generational stresses.

overall_design:
To investigate potential genes and mechanisms involved in transgenerational adapatation to hypoxia in C. Elegans, worms and their progeny were exposed to normoxia or hypoxia conditions for 4 generations.
Differential gene analysis was performed using data obtained from RNA-seq of C. Elegans after each generation of exposure

first: Kathleen

last: Kim

first: Ariel

last: Telger

first: Gautam

last: Sarkar

first: Sharan

last: Surya

first: Mohd Hafiz

last: Rothi

first: Michael

middle: P

last: Meers

first: Simon

middle: Y


title: Fidelity in lineage determination and stimulus-inducible gene expression requires ISWI chromatin remodeling activity [MNase-seq]

first: Francesco

last: Gualdrini

overall_design: Mnase-seq in primary cBMDM derived from wildtype or Smarca5 deleted cells in untreated or LPS stimulated conditions


title: Dicer is essential for proper maturation, composition, and function in the postnatal retina.

city: New York

first: Stefanie

last: Wohl

state: NY

address: 33w 42nd Street

department: Biological and Vision Sciences

institute: SUNY Optometry

summary: microRNAs (miRNAs) play a pivotal role during the early phases of retinal development, but their impact on late-phase retinogenesis is unknown. We depleted miRNAs in late retinal progenitor/precursor cells (RPCs/PCs) via a conditional Dicer knock-out. Optical coherence tomography (OCT), electroretinography (ERG), histological, and transcriptional analyses were conducted in young and adult mice. Alterations in gene expression of late-born cells were observed as early as postnatal day 7 (P7), resulting in impaired rod function, a significantly reduced number of rod bipolar cells and their associated function, and a decreased Müller glia population at adult age. These defects appear to be caused by a delay in differentiation/ incomplete maturation, as indicated by an enlarged progenitor/precursor population at young ages that persists into adulthood. Notably, an increased population of HuC/D+ amacrine cells was found. Luciferase assays led us to speculate that this increase may be due to the absence of Elavl3 suppression via RPC-miRNAs. This suggests that Dicer/miRNAs in late RPC/PCs are essential for the proper formation and maturation of late RPC progenies and may also play a role in regulating cell state.

overall_design: single cell RNA-Seq, bulk RNA-Seq for long RNAs (mRNA) and small RNA (miRNA) from FACS_purified P7 Ascl1:CreERT:tdTomato wildtype cells and P7 Ascl1:CreERT:Dicer-cKO:tdTomato cells

first: Seoyoung

last: Kang

last: Larbi

first: Eik

last: Bruns

first: Konstantin

last: Hahne

first: Mariana

last: Lima-Carneiro

first: Alireza

last: Khodadadi-Jamayran

first: Chaitra

last: Sreenivasaiah

first: Monica

last: Andrade

first: Khulan

last: Batsuuri

first: Shaoheng

last: Chen

first: Julia

last: Jager

first: Suresh

last: Viswanathan

first: Brian

last: Clark


title: The distinct roles of TGF-β signaling in retinal development

city: Pittsburgh

first: Kun-Che

last: Chang

address: 1622 Locust St

department: Department of Ophthalmology

institute: University of Pittsburgh School of Medicine

summary: Glaucoma is primarily caused by the loss or degeneration of retinal ganglion cells (RGCs), leading to permanent blindness. Cell replacement is a feasible therapeutic approach since RGCs do not regenerate after injury. Understanding what regulates RGC development provides new recipes for RGC formation. Using double knockout animals, we found that GDF-15 is the stronger regulator than GDF-11 and Smad2 in RGC differentiation. Deletion of TGFβR2 promotes RGC differentiation but attenuates photoreceptor differentiation. Single-cell RNA sequencing analysis showed that TGFβR2 knockout promotes RGC formation by upregulating genes associated with cell proliferation, axon guidance, and RGC subtype specification. TGFβR2 knockout reduces photoreceptor differentiation and delays its maturation by promoting the expression of apoptotic genes and decreasing the photoreceptor developmental genes. The roles of GDF-11/TGFβR2 signaling in photoreceptor differentiation were further confirmed in human retinal organoids. These findings provide insight into the mechanisms of retinal cell development and potential recipes for RGC differentiation.

overall_design:
P0 retinas from Tgfβr2 control (Cre-) and Tgfβr2 knockout (Cre+) mice were isolated and analyzed using scRNA-seq.

Sample Multiplexing: 3' v3 CellPlex

P5_S1: Tgfβr2 control
P5_S2: Tgfβr2 control
P7_S3: Tgfβr2 knockout
P7_S4: Tgfβr2 knockout

first: Chi-Yu

first: Chia-Chun

last: Liu


title: Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription [RNA-seq]

city: Seattle

first: Chia-Lin

last: Wei

state: WA

address: 3720 15th Ave NE

department: The Northwest Genomics Center (NWGC)

institute: University of Washington

summary: Extrachromosomal, circular DNA (ecDNA) is a prevalent and significant oncogenic alteration in cancer genomes. Its frequency is associated with aggressive tumor behavior and poor patient outcome. To understand how ecDNA promotes oncogenesis, we map ecDNA-associated chromatin complexes at single-molecule resolution in three well-characterized ecDNA+ cancer models that harbor different oncogenes. Using a suite of 3D genome mapping and imaging analyses, we determined ecDNA nuclear organization and uncovered that ecDNA hubs are part of MED1-mediated condensates that can be rapidly disrupted by agents perturbing liquid-liquid phase separation (LLPS). The functional relevance of ecDNA condensates was demonstrated by inhibition of LLPS which led to hub dispersal, the reduction of MED1 co-activator binding, inhibition of oncogenic transcription and selectively increase cell death of ecDNA-containing cells across a broad range of cancer models. Robust epigenetically silencing of the regulatory modules within ecDNAs effectively disrupts ecDNA’s mode of actions and demonstrates the causality between ecDNA enhancer function, chromosomal contacts, transcription and cellular proliferation, which directly corroborate ecDNA’s trans-activator activity. Our findings reveal that ecDNA drives tumor promotion activity through nuclear condensate and suggests that exploiting these nuclear structures may serve as a universal strategy against malignant tumors. Our work elucidates the structures, functions and regulation of ecDNA which is expected to transform the paradigm for studying cancer genomes and expand the current views of how oncogenes are regulated, from which new clinical strategies can be realized.

overall_design: Perform chromatin interaction assays including WGS, ChIA-Drop, ChIA-PET, ChIATAC, ChIP-seq, CUT&Tag, and RNA-seq to define genome-wide ecDNA-mediated chromatin interactomes and characterize their functional impact on transcription programs following 1,6-HD treatment and CRISPR-based epigenomic perturbations in cancers.

first: Harianto

last: Tjong

first: Chia-Hao

last: Tung

first: Aziz

last: Taghbalout

first: Ping

last: Wang


title: Temporal single-cell transcriptome profiling of zebrafish spinal cord regeneration

first: Daniel

last: Wehner

summary: The goal of this study was to map transcriptional changes at the single cell level at different time points after spinal cord injury in zebrafish larvae.

overall_design: RNA profiles of single cells isolated from trunk tissue of spinal cord-lesioned Tg(BAC(pdgfrb:Gal4ff))ncv24;Tg(UAS:EGFP)zf82 (referred to as pdgfrb:EGFP) transgenic zebrafish larvae (uninjured, 6, 12, 24, 48 hours after injury), were generated by scRNA-seq, in duplicates, using Illumina NovaSeq 6000


title: Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription [ChIA-PET]


title: Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription [CUT&TAG]


title: Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription [ChIATAC]


title: Mesenchymal Stem Cell Extracellular Vesicles Ameliorate Radiation-caused Dry Mouth

city: College Station

first: Fei

address: 206 Olsen Blvd

institute: Texas A&M University Health Science Center

summary: Locally injected extracellular vesicles from iPS cell derived mesenchymal stem cells (iEVs) ameliorated long-term dry mouth, a common side effect of radiation therapy for head and neck cancer.

overall_design: 8-10 weeks old male C57BL/6 mice received no treatment (NT) or 15 Gy irradiation (IR) at submandibular gland (SMG) region. Since day 1 after IR, some mice received weekly intra-SMG treatment of iEVs. SMGs were collected at 4 or 30 days after IR for RNA sequencing.

first: Jaiswal

last: Juhi

first: Zhao

last: Qingguo

first: Shahsavari

last: Arash

first: Liu

last: Fei


title: Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription [ChIA-Drop]


title: Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription [WGS]

overall_design:
Perform chromatin interaction assays including WGS, ChIA-Drop, ChIA-PET, ChIATAC, ChIP-seq, CUT&Tag, and RNA-seq to define genome-wide ecDNA-mediated chromatin interactomes and characterize their functional impact on transcription programs following 1,6-HD treatment and CRISPR-based epigenomic perturbations in cancers.

>>>Submitter states that raw data are not available for the GM171DM sample due to patient privacy concerns.<<<


title: Mast cell tryptase induces nuclear remodeling in breast cancer cells and has a negative impact on breast cancer cell growth

status: Public on Sep 17 2025

city: Uppsala

first: Débora

last: Parrine

state: Uppsala

address: Husargatan 3,

department: NBIS

institute: Scilifelab

summary: Mast cells are known to accumulate in breast cancer, but there is only limited knowledge of how they may impact on breast cancer growth. Tryptase is one of the major compounds stored in the mast cell secretory granules, and here we investigated whether tryptase can have an influence on breast cancer cells. Our findings reveal that tryptase has profound effects on breast cancer cell morphology and that tryptase has a negative impact on the growth of breast cancer cells, the latter by a combination of anti-proliferative and pro-apoptotic effects. Mechanistically, we show that tryptase is taken up by breast cancer cells, and enters their nuclei. Further, tryptase was shown to cause major effects on chromatin organization, and to induce truncation of core histone 3 (H3). H3 truncation was accompanied by reduced levels of epigenetic marks associated with H3. In vivo, tryptase-positive mast cells were found in PyMT breast cancer tumors in mice, and a proliferation clearance zone was seen in the vicinity of tryptase-positive mast cells. Similarly, a proliferation clearance zone was observed in the vicinity of tryptase-positive mast cells in human triple negative breast cancer. It was also observed that mast cells were activated to a higher extent in breast cancer tumors than in healthy breast tissue. In agreement with an anti-proliferative impact of tryptase on breast cancer, ATAC-seq analysis revealed that tryptase affected chromatin accessibility at several regions of the genome associated with genes known to influence breast cancer growth. Altogether, the present study introduces a mechanism for how mast cell tryptase can regulate breast cancer cell growth.

overall_design: Hs578T, a triple breast cancer cellline, was either treated (sample name: trypstase) or not treated (control) with tryptase for 48h.

first: Filip

last: Panos

first: Laura

last: Bub

first: Aida

last: Paivandy

first: Anna-Karin

last: Olsson

first: Gunnar

last: Pejler

first: Fabio

last: Rabelo Melo


title: Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription [RNA-seq II]

first: Chia-Lin

last: Wei

first: Harianto


title: Fidelity in lineage determination and stimulus-inducible gene expression requires ISWI chromatin remodeling activity

first: Francesco

last: Gualdrini

overall_design: Refer to individual Series


title: Self-assembly of hybrid 3D cultures by integrating living and synthetic cells

city: Saarbruecken

first: Nils

last: Piernitzki

state: Saarland

address: Campus D2 2

institute: INM - Leibniz Institute for New Materials

summary: Self-assembly is a fundamental property of living matter that drives the three-dimensional (3D) organization of cell collectives such as tissues and organs. Here, the co-assembly of synthetic and natural cells is leveraged to create hybrid living 3D cancer cultures. We demonstrate that synthetic cells based on droplet-supported lipid bilayers can establish artificial tumor immune microenvironments (ART-TIMEs), mimicking immunogenic signals within tumoroids formed by the cell line PANC-1 and eliminating the need to integrate complex living immune cells. Using the ART-TIME approach, we identify a co-signaling mechanism between PD-1 and other T cell-derived surface receptors as a driver in immune evasion of pancreatic ductal adenocarcinoma.

overall_design: RNA-Seq profiling of WT PANC-1 tumoroids or hybrid tumoroids with integrated synthetic cells carrying various combinations of PD-1 and other surface receptors.

first: Gilles

last: Gasparoni

first: Oskar

last: Staufer


title: IFNgamma-driven skewing towards Th1 over Th17 differentiation underlies CRS and neutropenia in CAR-T therapy

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: CAR-T (Chimeric antigen receptor T cell) therapy has led to significant improvements in patient survival. However, a subset of patients experience high-grade toxicities, including cytokine release syndrome (CRS) and immune cell-associated hematological toxicity (ICAHT). We utilized IL-2Ralpha knockout mice to model toxicities with elevated levels of IL-6, IFNgamma, and TNFalpha and increased M1-like macrophages. Onset of CRS was accompanied by a reduction in peripheral blood neutrophils due to disruption of bone marrow neutrophil homeostasis characterized by an increase in apoptotic neutrophils and a decrease in proliferative and mature neutrophils. Both non-tumor-bearing and Emu-ALL tumor-bearing mice recapitulated the co-occurrence of CRS and neutropenia. IFNgamma-blockade alleviated CRS and neutropenia without affecting CAR-T efficacy. Mechanistically, a Th1-Th17 imbalance was observed to drive co-occurrence of CRS and neutropenia in an IFNgamma-dependent manner leading to decreased IL-17A and G-CSF, neutrophil production, and neutrophil survival. In patients, we observed an increase in the IFNgamma-to-IL-17A ratio in the peripheral blood during high-grade CRS and neutropenia. We have uncovered a biological basis for ICAHT and provide support for the use of IFNgamma-blockade to reduce both CRS and neutropenia.

overall_design: We performed single cell sequencing to compare differences in Neutrophils and Macrophages from Bone marrow derived mononuclear cells isolated at week 4 from IL-2Ralpha knockout mice treated with wild type CD1928zeta CAR-T(Group 1, n=2), IFNgamma knockout CAR-T(Group 2, n=2) and wild type CAR-T+Th17(Group 4, n=2).

first: Payal

last: Goala

last: Cortes Gomez

first: Jianmin

last: Wang

first: Prashant

last: Singh

first: Marco

last: Davila


title: The Gain-of-Function TREM2-T96K Mutation Increases Risk for Alzheimer’s Disease by Impairing Microglial Function

city: Charlestown

first: Ana

last: Griciuc

state: MA

address: 114 16th Street

department: Neurology

institute: Massachusetts General Hospital

summary: The aim of this study is to characterize the underlying molecular mechanisms of the gain-of-function Trem2T96K mutation in Alzheimer’s disease (AD) pathogenesis by using the constitutive Trem2T96K knock-in mouse crossed to the 5xFAD mouse model of AD. Gene expression analyses were performed on microglial cells isolated from male and female Trem2+/+ (WT), 5xFAD;Trem2+/+, 5xFAD;Trem2T96K/+, and 5xFAD;Trem2T96K/T96K mice at 8 months of age to analyze the impact of the Trem2T96K mutation on the transcriptome of microglia in the setting of neuroinflammation (i.e. in the 5xFAD brain). The results revealed that Trem2T96K reprogrammed microglial gene expression and downregulated signaling pathways related to microglial function, specifically, in female 5xFAD mice.

overall_design: Microglia were isolated from brains of both male and female Trem2+/+, 5xFAD;Trem2+/+, 5xFAD;Trem2T96K/+, and 5xFAD;Trem2T96K/T96K mice at 8 months of age, using FACS sorting for CD11b and CD45. Libraries were prepared using the Nextera XT DNA Sample Prep Kit (Illumina) and sequenced on an Illumina NextSeq 2000 sequencing system. Reads were aligned to mouse genome mm9 using the STAR aligner.

first: Dominika

last: Pilat

first: Hoang

last: Le

first: Dmitry

last: Prokopenko

first: Chih-Chung Jerry

last: Lin

first: William

last: Eimer

first: Luisa

last: Quinti

first: Evan

last: Gavrilles

first: Sheyla

last: Garcia

first: Sara

last: Heitman

first: Alzheimer’s Disease Neuroimaging Initiative

last: ADNI

first: Danielle

last: McGinty

first: Murat

last: Centibas

first: Ruslan

last: Sadreyev

first: Rudolph

last: Tanzi


title: The Gain-of-Function TREM2-T96K Mutation Increases Risk for Alzheimer’s Disease by Impairing Microglial Function [scRNA-Seq]

summary: The aim of this study is to characterize the underlying molecular mechanisms of the gain-of-function Trem2T96K mutation in Alzheimer’s disease (AD) pathogenesis by using the constitutive Trem2T96K knock-in mouse crossed to the 5xFAD mouse model of AD. By transcriptional single cell sorting, we comprehensively mapped all microglial populations in 8-month-old female 5xFAD;Trem2+/+, 5xFAD;Trem2T96K/+, and 5xFAD;Trem2T96K/T96K mice. Single-cell RNA-seq analysis revealed that Trem2T96K leads to concomitant suppression of the disease-associated microglia (DAM) gene signature and activation of homeostatic (HOM) genes and impairs the transition of HOM microglia into DAM in female 5xFAD mice. Collectively, these results suggest that Trem2T96K leads to reduced microglial immune activation in female 5xFAD mice.

overall_design: Transcriptional profiling of single cells from CD11b+CD45Low-to-Intermediate microglial populations of 8-month-old female Trem2+/+, Trem2T96K/+, 5xFAD;Trem2+/+, 5xFAD;Trem2T96K/+, and 5xFAD;Trem2T96K/T96K mice, generated from deep sequencing of tens of thousands of cells, sequenced on Illumina NextSeq 2000 sequencing platform.


title: Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription

first: Chia-Lin

last: Wei