title: Effects of OGT-ISS deletion on gene expression in NK92 cells

city: Daejeon

first: In-Hwan

last: Jang

address: 125, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea

department: Immunotherapy Research Center

institute: Korea Research Institute of Bioscience and Biotechnology

summary: O-GlcNAcylation, a type of post-translational modification, is known to regulate the functions of various immune cells. In this study, we report that increasing O-GlcNAcylation enhances the tumor-killing efficacy of NK cells. By removing the ISS (intronic splicing silencer) of OGT in NK92 cells, we achieved stabilized O-GlcNAcylation even under tumor microenvironment (TME)-mimicking conditions, which led to a heightened killing effect against tumors. To investigate how OGT-ISS deletion impacts gene expression profiles associated with NK cell activity, we performed RNA sequencing (RNA-seq) to compare the global transcriptomes of wild-type (WT) and ΔOGT-ISS_NK92 cells. This comparative transcriptome analysis aims to identify gene expression profiles that influence NK cell cytotoxicity and functional responses in the context of tumor immunity.

overall_design: To investigate the function of O-GlcNAc in NK cell immune responses, we generated a ΔOGT-ISS NK92 cell line with enhanced O-GlcNAc levels by deleting the intronic splicing silencer (ISS) of the OGT gene using the CRISPR-Cas9 system to enable sustained expression of OGT. RNA-seq was performed on both the WT NK92 cells and the ΔOGT-ISS NK92 cells to compare gene expression profiles.

first: Se-Chan

last: Oh

first: Bong Chan

last: Jeon

first: Sung-Kyun

last: Park

first: Tae-Don

last: Kim


title: MBNL1 hijacks a structured single-stranded distal DNA element to sustain FLT3 expression in KMT2A-rearranged leukemias

status: Public on Jun 10 2026

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

country: USA

institute: St Jude Children's Research Hosipital

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary: The molecular mechanisms by which KMT2A-rearranged (KMT2A-r) leukemias maintains the oncogenic FLT3 expression remain largely unclear, limiting therapeutic opportunities. Here, we identify the RNA-binding protein MBNL1 as a novel positive regulator of FLT3 by DepMap dataset exploration and combinatorial CRISPR screens. MBNL1 promotes leukemia cell survival by sustaining FLT3 expression in a KMT2A-r context-dependent manner. Mechanistically, we discover that MBNL1 recognizes a structured single-stranded DNA (ssDNA) element containing five consecutive guanines within the FLT3 enhancer, through MBNL1?s zinc finger domains and the C-terminal unstructured region.

overall_design:
We used antibody to immunoprecipitate the endogenous RNA-binding protein MBNL1 or tagged exogenous MBNL1, followed by high-throughput sequencing to reveal the genome-wide chromatin binding peaks.

MOML13-Cas9 expressing cells were infected with Lenti-puromycin-U6-sgRNA against coding regions of MBNL1. Total RNAs were collected from puromycin-selected as at day 3 and day 5. Total RNA was extracted from replicate samples using TRIzol (Thermo Fisher Scientific, #15596026). About 200?ng of total RNA was treated using Kapa rRNA depletion reagents to remove ribosomal RNA, followed by conversion into cDNA libraries using Kapa RNA HyperPrep Kit with RiboErase (HMR).

first: Meixia

last: Che

first: Shaela

last: Fields

first: Siqi

last: Yi

first: Judith

last: Hyle

first: Yong

last: Cheng

first: Chunliang

last: Li


title: BMAL1 regulates tubular epithelial-derived exosomal miR-27a-3p to inhibits macrophage-myofibroblast transition thus alleviating ischemia/reperfusion induced renal fibrosis

city: wuhan

first: wu

last: chen

address: jiefang road

department: urology

country: China

institute: Renmin Hospital of Wuhan University

type: Non-coding RNA profiling by high throughput sequencing

summary: Exosomal microRNAs are closely related to the progression of renal fibrosis. The circadian rhythm gene BMAL1 is thought to be involved in a variety of diseases. However, how BMAL1 regulates renal fibrosis induced by ischemia-reperfusion injury (IRI) has not been determined. We first examined BMAL1 expression, exosomal expression, the macrophage-to-myofibroblast transition (MMT) ratio, and renal fibrosis levels in mice with renal IRI. The results showed that renal IRI induced a decrease in BMAL1 expression, along with an increase in exosome secretion, MMT formation and renal fibrosis. Next, we overexpressed BMAL1 in mouse kidneys and found that BMAL1 inhibited IRI-induced MMT and fibrosis. We confirmed that exosome-mediated MMT directly aggravated renal fibrosis and that this process was directly regulated by BMAL1 through in vivo and in vitro exosome uptake experiments and Rab27a knockout mouse construction. High-throughput miRNA sequencing of exosomes derived from TCMK-1 cells and ChIP assays were used to confirm that exosomal miR-27a-3p was downregulated after hypoxia-reoxygenation (H/R) treatment and that BMAL1 directly promoted the transcription of miR-27a-3p. We identified TGFBR1 as the target gene of miR-27a-3p by transfecting cells with miR-27a-3p mimics and miR-27a-3p inhibitors and performing dual luciferase assays. Finally, we transfected cells with si-TGFBR1 and identified the TGFBR1/smad3 pathway as a key pathway for regulating MMT and renal fibrosis regulated by tubular epithelium-derived exosomal miR-27a-3p. Our findings indicated that BMAL1 was suppressed in renal IRI, which promoted MMT and renal fibrosis by upregulating the level of miR-27a-3p in tubular epithelial-derived exosomes.

overall_design: To investigate the regulatory effects of Bmal1 on exosomal miRNAs derived from renal tubular epithelium, we constructed a TCMK-1 cell line overexpressing Bmal1 using lentiviruses.We then collected exosomes secreted by the three groups of cells with or without H/R modeling.

first: Wu

last: Chen

first: Sheng

last: Zhao

first: Fan

first: Wei


title: Glycan adjuvantation expands the breadth and duration of protection of a mRNA-based vaccine

city: Los Angeles

first: Roberto

last: Spreafico

state: CA

address: UCLA

department: Institute for Quantitative and Computational Biosciences

institute: University of Califonia Los Angeles

summary: Inflammation initiated in response to microbial encounter, or deliberately induced upon vaccination, is central for the activation of adaptive lymphocytes. The stimulation of pattern recognition receptors (PRRs) orchestrates the inflammatory programs that regulate adaptive immunity. Nevertheless, only few PRRs have been tested for their capacity to potentiate the efficacy of vaccines. Here, we took advantage of a mRNA-based vaccine generated against the ancestral Spike protein of SARS-CoV-2 to test whether tuning inflammation enhances the efficacy of the vaccine. We combined a mRNA-based vaccine with the mannadjuvant, a formulation of fungal mannan and alum hydroxide that targets a class of PRRs known as C-type lectin receptors. The mannadjuvant increased the magnitude and durability of the response elicited by the mRNA-based vaccine, and it also led to the induction of neutralizing antibodies directed against variants of concern with a high escape capacity. Overall, our data demonstrate that inflammation can be harnessed to create more potent and durable mRNA-based vaccines.

overall_design: Mice were immunized with Comirnaty only, mannadjuvant+Comirnaty, alum+Comirnaty and draining lymph nodes were collected after 1, 3, and 7 days for bulk RNA seq.

first: Kautilya

middle: K

last: Jena

first: Daniel

last: Boehmer

first: Ivan

last: Zanoni


title: RNA sequencing of Mmrn1-high LT-HSCs and Mmrn1-low LT-HSCs from murine bone marrow

city: Chongqing

first: Naicheng

state: Chongqing

address: Gaotanyan Street 30

department: College of Preventive Medicine

institute: Third Military Medical University

summary: Mmrn1-high and Mmrn1-low LT-HSCs (lineage- Sca-1+ c-kit+ CD34- Flk2- cells) from murine bone marrow were isolated to explore the differentially expressed genes by RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Mmrn1-high and Mmrn1-low LT-HSCs isolated from murine bone marrow.

first: Mengjia

last: Hu


title: Neuronal-class specific molecular cues drive differential myelination in the cortex

city: Cambridge

first: Paola

last: Arlotta

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: Myelination represents a unique milestone in vertebrate brain evolution that has enabled the  expansion of the brain and emergence of complex neurological functions. Oligodendrocytes are  a heterogeneous population of cells that differentially myelinate specific neuronal subtypes,  resulting in characteristic amounts and patterns of axonal myelination for each neuronal class  across the cortical layers. The molecular mechanisms by which neurons communicate with  oligodendrocytes to direct subtype-specific myelination remain to be understood. Here, we  generated a single-cell molecular map of cortical oligodendrocyte-lineage cells across the  different cortical layers, over a time course spanning the process of myelination. We find that  mature, myelinating oligodendrocytes are transcriptionally heterogenous, and that more mature  subtypes are enriched in the deep layers. We applied differential gene expression analysis of  myelinating oligodendrocytes and weakly-myelinated upper-layer projection neurons vs heavily-  myelinated deep-layer projection neurons to identify candidate genes that mediate neuronal  subtype-specific myelination. We show that deep-layer-specific candidate genes drive an  increase in myelination when misexpressed in the upper cortical layers, which is synergistically  increased when these candidate factors are co-expressed. Our results demonstrate that gene-  expression signatures are essential for neuronal cell-type specific myelin targeting. Identifying  these molecular players may offer new therapeutic opportunities for treating demyelinating  disorders.

overall_design: Examination of oligodendrocytes from different layers of the cerebral cortex.

first: Nuria

last: Dominguez-Iturza

first: Vahbiz

last: Jokhi

first: Kwanho

first: Ashwin

middle: S

last: Shetty

first: Daniela

middle: J

last: Di Bella

first: Milagros

last: Pereira Luppi

first: Wen

last: Yuan

first: Catherine

last: Abbate

first: Paul

last: Oyler-Castrillo

first: Nalini

middle: A

last: Oliver

first: Vaishnavi

last: Venkat

first: Xin

last: Jin

first: Sean

last: Simmons

first: Joshua

middle: Z

last: Levin

first: Juliana

last: Brown


title: Molecular mechanisms underlying the determination of axillary bud fate and outgrowth into branch crown in strawberry.

city: Villenave d'Ornon

first: Amèlia

last: GASTON

address: av. E. Bourlaux

department: UMR1332 - BFP

country: France

institute: INRAE

summary: In strawberry, axillary bud (AXB) can either produce an elongated stem called stolon giving a daughter-plant (asexual reproduction) or an inflorescence-bearing branch (sexual reproduction). AXB fate depends on position on the axis, as well as genetic and environmental factors. Here, in Fragaria vesca, we addressed the largely unanswered question of how genetic factors determine  AXB fate. - To get insights into the mechanisms occuring in undifferentiated AXB with different subsequent developmental trajectories, we combined (1) phenotypic characterization of AXB fate throughout plant development with (2) molecular characterization using RNA-seq analysis of morphologically undifferentiated AXB, in three different genotypes producing either branch crowns or stolons (fvetfl1 and fvega20ox mutants, FveFT3 overexpressor). - Results shed light on the molecular mechanisms involved in the determination of AXB fate and outgrowth. Among the genes was FveBRC1. Analysis of FveBRC1 expression in genotypes combining various traits (perpetual/seasonal flowering; runnering/runneless) and the generation of CRISPR/Cas9 brc1 mutants allowed us to show a new function of FveBRC1 in strawberry in addition to the well-known function in AXB outgrowth into branch crown. These original results introduce new hypotheses regarding the control of AXB fate determination and, consequently, the control of fruit yield in strawberry.

overall_design: mRNA profiles of undifferentiated AXB collected at the fourth node of 4-leaf stage plants on the newly non-expanded leaf on H4, FT3OE and RdV strawberry genotypes using a stereomicroscope, on an Illumina NovaSeq instrument in triplicates

last: Gaston

first: Marie

last: Alonso

first: Béatrice

last: Denoyes

first: Christophe

last: Rothan

first: Pascal

middle: G

last: Martin


title: Distinct Impact of Neuronal and Astrocytic IFNAR1 Loss in Parkinson-like Dementia

city: Copenhagen

first: Shohreh

last: Issazadeh-Navikas

address: Ole Maaløes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: University of Copenhagen

summary: Interferon-alpha/beta-receptor (IFNAR) signal defects were recently identified to contribute to sporadic Parkinson’s disease (PD) with dementia (PDD). Mice lacking interferon-beta (IFNβ) develop PDD-like disease; however, the phenotypic, cellular, and molecular impacts of IFNAR1 loss in vivo have not been explored. Studying cell-specific pathology in Ifnar1-/- mice may reveal potential disease-modifying therapeutic targets for PDD. Here, we present that Ifnar1-/- mice exhibit PDD-like pathogenesis, including dopaminergic neurodegeneration in the substantia nigra, Lewy-body-like alpha-synuclein+ inclusions, gliosis-associated phosphorylated-tau and amyloid-beta proteinopathy, and progressive PDD-like behavior deficits. Hallmark neuropathology and motor and cognitive behavior deficits were specifically recapitulated in mice lacking neuronal IFNAR1. Ifnar1-/- mice also exhibited early-onset nociceptive pain and neuropsychiatric abnormalities, recapitulated in mice lacking astrocytic IFNAR1. Neuron/astrocyte-specific transcriptomic and proteomic alterations in early-manifest Ifnar1-/- mice implicate synergistic dysfunctional excitatory neurotransmission upon IFNAR1 loss, leading to glucose hypermetabolism prior to cognitive decline. Targeted restoration of dysfunctional neuronal and astrocytic IFNAR1 could therefore potentially mitigate PDD progression through concerted regulation of excitatory neurotransmission.

overall_design: Comparison of cell-specific transcriptomes from cortical brain tissue of 6-week-old Ifnar1-/- and wild-type mice

first: Erika

middle: B

last: Villanueva

first: Jon

last: Lundstrom

first: Niels

middle: H

last: Skotte

first: Jens

middle: V

last: Andersen

first: Filippa

middle: L

last: Qvist

first: Emil

middle: W

last: Westi

first: Andrea

last: Marin

first: Lluís

last: Riera-Ponsati

first: Emilie

last: Tresse

first: Oliver

last: Kretz

first: Desiree

last: Loreth

first: Tobias

last: Goldmann

first: Thomas

last: Blank

first: Marco

last: Prinz

first: Blanca

middle: I

last: Aldana

first: Matthias

last: Mann

first: Zala

last: Zebec

first: Gisela

last: Jimenez-Duran


title: Neural stem cells epigenomes and fate bias are temporally coordinated during corticogenesis [MPRA]

city: Neuherberg

first: Boyan

last: Bonev

state: Deutschland

address: Ingolstädter Landstr. 1

country: Germany

institute: Helmholtz Zentrum München

summary: The cerebral cortex orchestrates complex cognitive functions, yet how its distinct temporal lineages are molecularly patterned during development remains unresolved. Here, we integrate single-cell transcriptomics and chromatin accessibility, together with genome-wide profiling of DNA methylation and 3D chromosomal contact across mouse corticogenesis (E13–E18) to elucidate cell fate transitions. We reveal using metacell flow analysis that neural stem cells (NSC) progressively shift from an intermediate progenitor–biased state toward an astrocytic lineage and that his process is accompanied with DNA methylation programming and chromosomal insulation changes. A model integrating transcription factor motif affinities with epigenetic features, identifies key regulators of cis-regulatory element (CRE) activation. In vivo reporter assays further decouple the intrinsic regulatory potential of CREs from context-dependent synergistic activation. Collectively, our findings uncover temporal epigenomic reprogramming that underlies the evolving differentiation potential of NSC, providing insights into the intrinsic and extrinsic mechanisms that pattern cortical lineages.

overall_design: scRNA-seq and scATAC-seq were performed on the somatosensory cortex of mouse embryos at E13, E15, E16, E17 and E18. Methyl-Hi-C was carried out on neural stem cells (NSC) (Pax6+ cells) isolated from the somatosensory cortex at E13, E15, E16 and E17. Additionally, in utero electroporation for massively parallel reporter assay (MPRA) was performed in the somatosensory cortex at E12, E13, E14, E15 and E16 and MPRA was subsequently conducted on NSC (Pax6+ cells) and intermediate progenitors (IPC) (Tbr2+ cells) isolated 24 hours after each respective time point.

first: Yonatan

last: Shapira

first: Florian

last: Noack

first: Silvia

last: Vangelisti

first: Faye

last: Chong

first: Aviezer

last: Lifshitz

first: Amos

last: Tanay


title: Transcriptome analysis of circSmad5 knockdown in immortalized hair follicle stem cells (iHFSC2)

status: Public on Jun 09 2026

first: Yuhong

last: Li

address: Gaotanyan Street No.30 Shapingba

department: Cell Biology

institute: Army Medical University

summary: To investigate the role ofcircSmad5 in hair follicle stem cells (HFSCs), we performed RNA-seq on iHFSC2 cells with circSmad5 knockdown (shcircSmad5) versus empty vector control. Knockdown of circSmad5 increased hair count in a hair reconstitution model and activated Wnt/β-catenin and Mrs/Erk signaling pathways. This study provides transcriptomic insights into how circSmad5 regulates HFSC stemness and differentiation.

overall_design: To reveal the regulatory function of circSmad5 in HFSCs, iHFSC2 cells were infected with lentivirus carrying circSmad5 knockdown (pwslv-shcircSmad5) or empty vector control. After puromycin selection for 15 days, stable cell lines were established. Total RNA was extracted and subjected to RNA sequencing.

first: Haiying

last: Guo

first: Jin

last: Chen

first: Fei

last: Xiang

first: Hao

last: Gong

first: Jia

last: Tang

first: Yizhan

last: Xing


title: Dock2 Deficiency Exacerbates Colitis by Impairing Akkermansia muciniphila Colonization via the IL-22–Reg3 Antimicrobial Axis Suppressed by Type 1 T Cell Responses

city: Guangzhou

first: Shaoting

last: Xu

state: Outside of the US

address: 58 ZhongShan Second Road

institute: SYSU

summary: Dedicator of cytokinesis 2 (Dock2), a guanine nucleotide exchange factor that activates the small GTPase Rac1, plays a crucial role in host defense and cytoskeletal regulation. While Dock2 is predominantly expressed in intestinal T cells and is significantly upregulated in patients with inflammatory bowel diseases (IBD), its precise role in intestinal inflammation remains obscure. In this study, we demonstrate that systemic Dock2-deficient mice and T cell-specific Dock2 conditional knockout (Dock2-cKO) mice exhibit exacerbated chemically induced colitis compared to wild-type (WT) controls. Dock2 deficiency led to a substantial reduction in both total and IFN-γ-producing CD8+ T cells, accompanied by elevated colonic IL-22 levels, increased expression of Reg3γ and Reg3β antimicrobial peptides (AMPs), and diminished colonization by Verrucomicrobia, particularly Akkermansia muciniphila (A. muciniphila), at steady state. The expression of Reg3γ&β was suppressed in IL-22- and RORγt-deficient mice, and these AMPs exhibited antimicrobial activity against the expansion and intestinal colonization of A. muciniphila. Co-housing Dock2-cKO mice with WT mice or reintroducing A. muciniphila restored colitis severity to levels comparable to WT mice. The inhibitor against Dock2-Rac1 signaling significantly impaired IFN-γ production in both murine and human T cells. Furthermore, IFN-γ suppressed IL-22 expression induced by IL-1, likely via aryl hydrocarbon receptor (Ahr)-dependent but RORγt-independent mechanisms. Collectively, these findings reveal a critical Dock2-mediated axis linking T cell type 1 responses, IL-22–Reg3 AMPs, and commensal microbiota, particularly A. muciniphila. Targeting Dock2 and its downstream pathways may offer novel therapeutic strategies for IBD and other mucosal-associated immune disorders.

overall_design: DNA was extracted from fecal pellets of 8-week-old Dock2fl/fl and CD4-cre;Dock2fl/fl mice. The bacterial 16S rRNA gene V3-V4 region was amplified using universal primers and sequenced on the Illumina NovaSeq platform (NovaSeq 6000 SP Reagent Kit). Raw sequence data processing was conducted in QIIME2 and Dada2 following official tutorials.

first: Ce

first: Min

last: Lu

first: Ying

last: Tan

first: Shaowei

last: Dong

first: Rui

last: Feng


title: Nephrotoxicity modelled ex vivo in the founder strains of the BXD mouse consortium

city: Bern

first: Matthias

middle: B.

last: Moor

address: Freiburgstrasse

country: Switzerland

institute: University Hospital Bern

summary: To investigate genetically determined susceptibility, we used precision-cut kidney slices (PCKS) from the two parental founder strains of the BXD mouse consortium, C57BL/6J and DBADBA/2J/2J. PCKS preserves tissue architecture and cell-cell interaction, allowing close experimental control while maintaining the renal microenvironment. Slices were exposed to cyclosporine A (80 nM for 6h, 20nM for 24h and 48h) and Tunicamycin (1 µM for 6h and for 24h) as well as normoxia (4°C for 20h) and hyperoxia (4°C for 20h and 4h in incubator). Slices were then analysed using histopathological scoring, TUNEL staining, ATP quantification and bulk RNA sequencing. We found that the main source of variation was experimental duration. Nevertheless, a subtle difference between the strains could be observed for both cyclosporine A and Tunicamycin, with DBADBA/2J showing a stronger response to nephrotoxic stress, including lower ATP levels, higher proportion of apoptotic cells and a more pronounced transcriptomic response. For both strains, normoxia was the least harmful condition. These findings support the hypothesis that the BXD parental founder strains differ in their susceptibility to nephrotoxic kidney injury and support the use of PCKS as a relevant ex vivo model for studying early renal stress response. This provides the foundation to extend this approach to a broader spectrum of the BXD population to identify genetic loci and candidate genes involved in genetic susceptibility to nephrotoxins.

overall_design: To investigate renal effects of nephrotoxins and perturbations, we assessed bulk transcriptomes in kidney slices of mice that underwent ex vivo treatment with tunicamycin, cyclosporin A, normoxia, or normoxia-hyperoxia.

first: Jana

last: Andres

first: Nichakorn

last: Phengpol

first: Mikhail

last: Burmakin

first: Jaakko

last: Patrakka

first: Hannes

last: Olauson


title: roX1 and roX2 lncRNAs promote heterochromatinization in intestinal stem cells and impair longevity.

city: Shanghai

first: Yonghao

last: Li

address: Siping Road No.1239

department: School of Life Sciences and Technology

institute: Tongji University

summary: Maintenance of the genome and epigenome stability is vital for animal longevity. Long noncoding RNAs (LncRNAs), roX1 and roX2, are only known to be important in the male X chromosome dosage complex to double the expression levels of the genes on the X chromosome in Drosophila males. However, their functions in Drosophila females have never been explored. This study demonstrates the surprising role of roX1 and roX2 in acquiring heterochromatin in intestinal stem cells (ISCs) and progenitor enteroblasts (EBs) of Drosophila females under pathogen infection or aging. Increased heterochromatin formation in ISCs/EBs is associated with decreased active epigenetic modifications and global gene repression.

overall_design: To assess the chromatin landscape, we conducted ATAC-seq on Kc167 cells with ectopic expression of roX2, using GFP overexpression as a control.

first: Kaile

first: Chen

last: Wang

first: Jianquan

last: Ni

first: Fanglin

last: Sun


title: Robust mammalian RNA localization elements are large and multipartite

city: Aurora

first: Matthew

last: Taliaferro

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado Anschutz Medical Campus

summary: The subcellular localization patterns of RNAs are controlled by regulatory elements contained within them. However, for most localized RNAs, the identities of these elements are unknown. We had previously identified several localization elements that are necessary and sufficient for robust, kinesin-dependent RNA targeting to microtubule plus ends in a variety of cell types. Yet the characteristics of these elements that are critical for function remained unclear. To address this, we systematically created tens of thousands of mutant localization elements and quantified their ability to regulate subcellular RNA localization in neuronal cells. We found that the minimally active size of these localization elements is large, approximately 200 nt. These elements contain multiple important subsequences, with some being completely intolerant of any changes and others being tolerant to a shuffling of nucleotide order but not to changes in nucleotide composition. Using single molecule microscopy, we verified these findings in primary rat neurons. These results demonstrate that highly active mammalian RNA localization elements are large, complex, and multipartite and lay a foundation for further mechanistic studies of their function.

overall_design: The abilities of tens of thousands of discrete RNA sequences to drive RNA localization to neurites were tested using a massively parallel reporter assay. Reported results are the counts of each sequence, as determined through targeted RNA-seq in soma and neurite fractions.


title: Analysis of chromatin accessibility changes by ATAC-seq to determine how sustained exposure to physiologically relevant Tryptophan metabolites in HNSCC cells remodels chromatin.

city: State College

first: Gary

last: Perdew

state: PA

address: 101 Huck Life Sciences Building, Suite 315

department: Veterinary and Biomedical Sciences

institute: Pennsylvania State University

summary: The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor implicated in inflammation, immune modulation, and tumor progression. While environmental AHR ligands have been extensively studied, the impact of sustained exposure to physiologically relevant endogenous AHR agonists on tumor-intrinsic behavior remains poorly defined. Circulating tryptophan (Tryp) metabolites—including kynurenine and indole derivatives—are continuously present in human serum and collectively contribute to basal AHR activity. This study is designed to determine if prolonged exposure to these metabolites promotes aggressive tumor phenotypes in head and neck squamous cell carcinoma (HNSCC). Using a defined mixture of six serum-derived Tryp metabolites and a custom dish-in-dish culture system to model sustained exposure, we demonstrate persistent AHR activation in HN30 and OSC19 cells, evidenced by induction of canonical target genes and nuclear translocation of AHR. Transcriptomic profiling revealed upregulation of inflammatory and tumor-associated gene programs, including CSF3, MMP1, and AP-1–associated targets. ATAC-seq analysis in OSC19 cells showed ligand-dependent chromatin remodeling and enrichment of inflammatory transcription factor motifs, supporting epigenetic reprogramming under prolonged AHR signaling.

overall_design: ATAC-seq analysis on OSC19 cell that are treated with vehicle, tryptophan metabolites (Tryp pool), or tryptophan metabolites along with AHR inhibitor CH223191 (Tryp+CH) for 72h, to determine changes in chormatin accessibility.

first: Dhwani

last: Patel

first: Iain

last: Murray


title: TROP2/claudin program mediates immune exclusion to impede checkpoint blockade in breast cancer

city: Phoenix

first: Bogang

last: Wu

state: AZ

address: 5777 E. Mayo Blvd.

department: Immunology

institute: Mayo Clinic Arizona

summary: To investigate TROP2-dependent transcriptomic changes in breast cancer, we performed RNA-seq on frozen tumor sections from 4T1 Trop2 wild-type and Trop2 knockout tumors. This dataset was generated to define transcriptional programs regulated by TROP2 in the tumor microenvironment and to determine how TROP2 contributes to immune exclusion and resistance to immune checkpoint blockade. Analysis of these tumors identified TROP2-associated enrichment of cell-cell contact and tight-junction pathways, while inflammatory, antitumor immune response, and T-cell cytotoxicity programs were relatively increased in Trop2 knockout tumors. These findings supported the conclusion that TROP2 promotes a claudin/tight-junction-mediated barrier that limits T-cell infiltration and impairs response to anti-PD-1 therapy in triple-negative breast cancer.

overall_design: Trop2 wild-type and knockout 4T1 tumors were implanted into BALB/c mice and allowed to grow for 3 weeks. Tumors were then harvested, sectioned as frozen tissue, and processed for RNA isolation and sequencing.

first: Leif

last: Ellisen


title: Psychotropic-drug and neurotransmitter perturbation RNA-seq of human iPSC-derived cardiac and retinal organoids (ToxiPred)

city: Trondheim

first: Aleksandr

last: Ianevski

address: Høgskoleringen 1

country: Norway

institute: NTNU

summary: Bulk 3'-barcoded RNA-sequencing (Drop-seq-style digital gene expression) of human iPSC-derived cardiac and retinal organoids treated for 24 h at 5 uM with psychotropic drugs (aripiprazole, loxapine, sertraline, quetiapine, xanomeline) versus a No_drug reference, each crossed with neurotransmitter / co-treatment conditions (adrenaline, dopamine, histamine, retinoic acid, serotonin) plus vehicle/chemical controls. Generated for the ToxiPred study to test predicted tissue-resolved drug liability and recover lipid/sterol pathway mechanisms.

overall_design: Two iPSC-derived organoid systems (cardiac, retinal) were each arranged on a 96-well plate as a drug x neurotransmitter factorial with vehicle/chemical controls. Wells were barcoded with a 12 bp cell barcode + 8 bp UMI on read 1, pooled per organoid (Pool-1 cardiac, Pool-2 retinal), sequenced paired-end on Element AVITI (run B + a depth re-run), and demultiplexed by cell barcode. Raw FASTQs here are demultiplexed so each well/sample has its own R1+R2. A forebrain organoid arm described in the manuscript is not contained in this dataset and is not part of this series.

first: Erlend

last: Ravlo

first: Jorn-Ove

last: Schjolberg

first: Rakel

last: Saether

first: Maria

last: Camara-Quilez

first: Ine

last: Nordli

first: Hilde

last: Lysvand

first: Synnove

last: Fjeldstad

first: Marte

last: Skjelle

first: Emil

last: Wiik

first: Anna

last: Lademo

first: Maja

last: Dahle

first: Evgeny

last: Kulesskiy

first: Jani

last: Saarela

first: Juho

last: Vaananen

first: Niklas

last: Andersen

first: Vidar

last: Saasen

first: Anne

last: Makela

first: Anni

last: Nieminen

first: Kenneth

last: Nazir

first: Jing

last: Ye

first: James

last: Booth

first: Emily

last: Helgesen

first: Magnar

last: Bjoras

first: Denis

last: Kainov


title: CONCR lncRNA organizes a 3´-end structural domain that engages DDX11 for DNA replication and sister chromatid cohesion

city: Montpellier

first: Isabel

last: Chillón

address: 1919 Route de Mende

department: Institut de Génétique Moléculaire de Montpellier (IGMM)

institute: Centre National de la Recherche Scientifique (CNRS)

summary: CONCR is a long noncoding RNA (lncRNA) necessary for the establishment of sister chromatid cohesion. Despite its activity, it remains unknown whether it contains structural elements essential for its function. To address this gap, we determined CONCR structural organization and its functional relevance, by integrating SHAPE-MaP, AFM, evolutionary analyses, cryo-EM, and cellular genetic studies. CONCR molecular topology is modular, with highly structured domains connected by flexible linkers. The longest and the most complex is the 3’-end domain, which comprises two helical arms connecting two multiway junctions with structural motifs conserved among all primate groups. This domain is responsible for binding to DDX11 helicase in vitro and in vivo, can trigger DDX11 ATPase activity, and is essential for proper DNA replication and sister chromatid cohesion. Our results highlight the critical role of RNA structure in CONCR function, providing further evidence of the importance of RNA structural studies in determining lncRNA activity.

overall_design: SHAPE-MaP analysis of the human CONCR lncRNA produced by in vitro synthesis. The chemical probe 1M7 (1-methyl-7-nitroisatoic anhydride) was used to a final concentration of 10 mM. DMSO was used as a control.

first: Andrés

last: López-Perrote

first: Eva María

last: Martín-Cuevas

first: José Antonio

last: Mérida-Cerro

first: Clara

last: Aicart-Ramos

first: Ana

last: González-Corpas

first: Jovanna

last: González

first: Johanne

last: Le Coq

first: Jasminka

last: Boskovic

first: Oscar

last: Llorca

first: Fernando

last: Moreno-Herrero

first: Maite

last: Huarte


title: Integrin beta 4 promotes colorectal cancer progression by upregulating Ezrin and activating the Wnt/β-catenin signaling pathway

city: Shijiazhuang

first: Yi

last: Si

state: Hebei

address: No. 89 Donggang Road

institute: The First Hospital of Hebei Medical University

summary: Colorectal cancer (CRC) is a major cause of cancer-related mortality worldwide. Integrin beta 4 (ITGB4) has been previously identified as being overexpressed in CRC; however, its precise oncogenic mechanism remains unclear. The present study aimed to elucidate the functional role of ITGB4 in CRC progression and identify its downstream molecular effectors to provide new insights for targeted therapy.The biological functions of ITGB4 were investigated in CRC cell lines (SW480 and HCT116) using a series of in vitro assays, including CCK-8, colony formation, Transwell migration and invasion, and flow cytometry for apoptosis following ITGB4 knockdown. An in vivo xenograft mouse model was used to evaluate the effect of ITGB4 on tumor growth. Downstream targets were screened using RNA sequencing (RNA-seq) and validated by co-immunoprecipitation and co-immunofluorescence. The underlying signaling pathway was investigated by Western blotting and functional rescue experiments.Knockdown of ITGB4 significantly suppressed CRC cell proliferation, migration, and invasion, while promoting apoptosis in vitro. Similarly, silencing ITGB4 markedly inhibited tumor growth in the in vivo xenograft model. RNA-seq analysis identified Ezrin (EZR) as a key downstream target of ITGB4, and a direct protein-protein interaction was confirmed between them. Mechanistically, ITGB4 knockdown decreased the expression of EZR at both the mRNA and protein levels. ITGB4 was demonstrated to exert its pro-tumorigenic effects through the regulation of EZR, which subsequently activated the Wnt/β-catenin signaling pathway. Interestingly, EZR overexpression partially restored ITGB4 levels, suggesting a potential positive feedback loop via Wnt/β-catenin signaling that further amplifies this oncogenic axis. Notably, the malignant phenotypes suppressed by ITGB4 silencing were significantly rescued by the overexpression of EZR.The present study identified a novel ITGB4/EZR/Wnt/β-catenin signaling axis in colorectal cancer. ITGB4 promotes CRC progression by modulating EZR expression and subsequently activating the Wnt/β-catenin pathway. These findings highlight ITGB4 as a potential prognostic biomarker and a promising therapeutic target for CRC.

overall_design: SW480 cells transfected with siRNA-negative control or siRNA-ITGB4 (three biological replicates per group)

first: Jing

last: Wang

first: Mingda

last: Xuan

first: Shuangshuang

last: Han

first: Kunyi

last: Liu

first: Jiao

last: Jiao

first: Xiaoyan

last: Men

first: Hongfei

last: Li

first: Jia

first: Ting

first: Weifang

last: Yu


title: Exercise-induced renal tubular Cdo1 protects against diabetic nephropathy

first: Linjing

last: Yan

address: No. 650 Hengren Road, Yangpu District, Shanghai, China

institute: Shanghai University of Sports

summary: Exercise is an effective intervention for diabetic nephropathy (DN), but its molecular mechanisms remain incompletely understood. Here, we identify cysteine dioxygenase type 1 (Cdo1) as a mediator of exercise-induced renal protection. Exercise upregulates renal tubular Cdo1 expression via the α-ketoglutarate-TET-DNA demethylation pathway. Tubular epithelial cell-specific deletion of Cdo1 exacerbates DN and attenuates exercise-mediated alleviation of DN, whereas Cdo1 overexpression improves renal function and synergizes with exercise in ameliorating DN. Mechanistically, tubular Cdo1 promotes taurine production, which suppresses macrophage glycolysis and inflammatory activation by disrupting PKM2-HIF-1α interaction. Taurine supplementation rescues kidney injury in Cdo1-deficient mice, and alleviates DN in synergy with exercise. Thus, exercise ameliorates DN through Cdo1-mediated metabolic crosstalk between renal tubules and macrophages via the taurine-PKM2-HIF-1α axis.

overall_design: To further clarify the key signaling pathways affected by renal tubular Cdo1, RNA sequencing (RNA-seq) was performed to explore differentially expressed genes (DEGs) in the kidneys of WT/Sed and Cdo1KKO/Sed mice with type 1 diabetes-induced DN.

first: Ruoying

first: Kaichun

first: Sijie

last: Gu

first: Wanqiu

last: Peng

first: Wanli

last: Zhang

first: Shan

first: Jieying

last: Zhu

first: Wangjing

last: Mu

first: Yang

first: Mengting

last: Yin

first: Humin

last: Chen

first: Xin

first: Yalan

last: Yang

first: Quan

first: Le


title: Cardiotoxin from Naja atra Activates the NLRP3/Caspase-1/GSDMD Pyroptosis Pathway to Induce Skin Tissue Injury

city: Guilin

first: Nianying

last: Qin

address: No. 2 Lingui Road, Xiangshan District, Guilin, Guangxi Zhuang Autonomous Region

department: Department of Emergency

institute: Guilin Municipal Hospital of Traditional Chinese Medicine

summary: Cardiotoxin (CTX) from Naja atra venom is a principal virulence factor responsible for progressive local tissue necrosis and systemic inflammation following snakebite. Despite its clinical importance, the molecular mechanisms underlying CTX-induced skin injury remain poorly defined.

overall_design: We employed a two-arm strategy combining transcriptome-guided discovery with mechanistic functional validation. In the transcriptomic arm, C57BL/6 mice received intradermal CTX injection (120 μg/50 μL), and skin tissues were harvested at 6, 12, and 24 h post-injection for RNA-seq analysis. Differentially expressed genes (DEGs) were screened and subjected to KEGG/GO enrichment and ssGSEA-based cell death mode scoring. In the functional validation arm, a separate cohort of mice was assessed at 72 h post-injection, with gross necrosis area quantified, followed by H&E staining, immunohistochemistry (IHC), and Western blot.  In vitro validation was performed in human HaCaT keratinocytes using CCK-8 cytotoxicity assay, optical microscopy, transmission electron microscopy (TEM), propidium iodide/DAPI (PI/DAPI) dual staining, ROS detection, ELISA for IL-1β, LDH release assay, and pharmacological inhibition with MCC950 (NLRP3 inhibitor), VX-765 (caspase-1 inhibitor), and N-acetylcysteine (NAC, ROS scavenger).


title: Super-enhancer formation in scirrhous gastric cancer-associated fibroblasts, and its presence in fibroblasts in non-cancerous tissues (2)

city: Maebashi

first: Naoko

last: Hattori

state: Gunma

address: 3-39-15 Showa-mach

department: Institute for Molecular and Cellular Regulation

country: Japan

institute: Gunma University

summary: Scirrhous gastric cancer has aggressive clinical courses and is characterized by dominating cancer-associated fibroblasts (CAFs).  We here aimed to explore the molecular basis for scirrhous CAFs and their origin.  Scirrhous CAFs had heavily acetylated super-enhancers, and therapeutic targeting of super-enhancers by a BET bromodomain inhibitor, mivebresib, markedly decreased their migration-promoting activity.

overall_design: ChIP-seq for H3K4me1 and H3K4me3 of cancer-associated fibroblasts from scirrhous gastric cancer and non-scirrhous gastric cancer

first: Yu-Yu

first: Yoshimi

last: Yasukawa

first: Toshikazu

last: Ushijima


title: Immune Re-sensitization in Checkpoint Inhibitor Refractory and Relapsed Cancers with Plinabulin, Radiation and Immune Checkpoint Blockade

city: Houston

first: Ziyi

state: TX

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

summary: Plinabulin exerts immunomodulatory activity through guanine-nucleotide-exchange-factor (GEF)-H1 activation, particularly in antigen-presenting cells. Here we demonstrate that radiation (RT) potentiates plinabulin-induced dendritic cell (DC) maturation, and when combined with immune-checkpoint-inhibitors (ICI), triggers an abscopal antitumor response via increased tumor-infiltrating CD86+ DCs and CD8+ T-cells. Nonclinical findings were translated in a phase 1 basket study (ClinicalTrial.org: NCT04902040) in patients with ICI-relapsed/refractory cancers. Plinabulin treatment after RT initiation plus ICI was safe and achieved an encouraging disease-control-rate (DCR) of 54% (3/13 partial response [PR] and 4/13 stable disease [SD]) in out-of-field unirradiated lesions; Enduring and 2/2 PR responses were seen in Hodgkin's lymphoma patients who had progressed after 12- or 16-prior lines of therapy. Responding PR+SD subjects had significant increases in peripheral blood proinflammatory monocytes, and activated DCs, and GEF-H1 induction in immune cells, T-cell clonal expansion, and intratumoral immune activation and GEF-H1 induction in DC subsetsactivation . These promising preliminary results provide the rationale for using this triple combination approach (RT/plinabulin/ICIdefine therapies?) in post-ICI-failure settings in future confirmatory trials.

overall_design: Tumor biopsies and PBMC samples were obtained from patients. scRNA-seq and scTCR-seq experiments were performed.

first: Ye-Lin

last: Son

first: Yue

last: Lyu


title: The Transcriptomic landscape of Kaposi Sarcoma Herpes Virus

city: New Haven

first: Jeffrey

last: Ishizuka

state: CT

address: 300 George Street

institute: Yale University

summary: Kaposi sarcoma (KS) is a tumor caused by Kaposi sarcoma herpesvirus (KSHV), also known as human herpesvirus 8 (HHV-8). Unlike other virus-associated tumors, where disease progression often continues even after viral eradication, KS requires the persistent presence of KSHV for disease progression. This unique dependency underscores the potential of strategies targeting the virus to also target the tumor. This study aims to characterize the expression of KSHV viral proteins and identify factors associated with differences in viral gene expression, ultimately formulating treatment targets.

overall_design: RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue blocks and subjected to bulk RNA sequencing.

first: Yuewei

last: Fei

first: Philippos

last: Costa

first: Muhammad

last: Junejo

first: Emily

last: Chang

first: Michelle

last: Li

first: Curtis

last: Perry

first: Alisson

last: Didduchi

first: William

last: Damsky


city: Seattle

first: Stephen

last: Tapscott

state: Washington

address: 1100 Fairview Ave N, Room C3-123

institute: Fred Hutchinson Cancer Research Center

summary: DUX4 initiates the first wave of zygotic genome activation (ZGA) in the human embryo and its misexpression in skeletal muscle causes facioscapulohumeral muscular dystrophy (FSHD). However, other factors that help regulate ZGA-like transcription in human development and disease are still not fully understood. Here we identify Krüppel-like factor 18 (KLF18) as a component of a DUX4 feed-forward network that is necessary for expression of KLF17 and a subset of the DUX4-regulated totipotency-associated genes. We mapped the genome-wide binding profile of KLF18 downstream of DUX4 and showed that its activity is influenced by DUX4 and chromatin accessibility. We find that in contrast to the rodent ortholog, human KLF18 has a predicted beta-solenoid structure composed of a variable number of tandem repeats (VNTRs) with multiple different structural variants in the human population. Expression of different KLF18 variants in combination with DUX4 showed similar transcriptional activity, whereas assessment of KLF18 structural variants in individuals with FSHD1 showed inconsistent association with disease severity that requires further study as a modifier locus. Together these findings establish the polymorphic transcription factor KLF18 as a critical component of a DUX4-initiated feed-forward network and a candidate locus for human diversity.

overall_design: Differential RNA-seq analysis of MB135iDUX4 with CRISPR/Cas9-mediated KLF18 knockouts after 18 hours of doxycycline induction of DUX4

first: Danielle

middle: C

last: Hamm

first: Aidan

last: O’Donnell

first: Sean

middle: R

last: Bennett

first: Richard

last: Lemmers

first: Patrick

last: van der Vliet

first: Silvère

middle: M

last: van der Maarel


title: Gene expression profile of 31 RAS/RAF-wild-type colorectal cancer (CRC) stem-cell (SC)  spheroids and 7 FGFR-inhibitor resistant CSC-SC spheroids

city: Kyoto city

first: Makoto

middle: Mark

last: Taketo

state: Kyoto prefecture

address: 53 Shogoin-Kawahara-cho Sakyo-ku

institute: Kyoto University

summary: This study investigated mechanisms of acquired resistance to FGFR inhibitor therapy in RAS/RAF–wild-type colorectal cancer (CRC). RNA sequencing (RNA-seq) data from 47 RAS/RAF-wild-type colorectal cancer stem-cell (CRC-SC) spheroid lines previously deposited under GSE205787 were integrated with newly generated RNA-seq data from 31 additional RAS/RAF-wild-type CRC-SC spheroid lines and seven FGFR inhibitor-resistant CRC-SC derivatives. The resistant derivatives were established from parental CRC-SC spheroid lines by continuous exposure to erdafitinib or futibatinib. Comparative transcriptomic analysis between matched parental and resistant lines revealed consistent upregulation of EGFR and downregulation of PTPROt, a truncated isoform of PTPRO, in resistant derivatives. Gene set enrichment analysis further indicated activation of EGFR-related signaling pathways in FGFR inhibitor-resistant spheroids. In addition, the integrated RNA-seq dataset comprising 78 RAS/RAF-wild-type CRC-SC lines was used to validate the inverse correlation between EGFR and PTPRO mRNA expression, supporting the involvement of PTPROt downregulation and EGFR pathway activation in acquired resistance to FGFR inhibition.

overall_design:
RNA-seq data from 47 RAS/RAF-wild-type CRC-SC spheroid lines previously deposited under GSE205787 were combined with newly generated RNA-seq data from 31 additional RAS/RAF-wild-type CRC-SC spheroid lines, resulting in an integrated dataset of 78 RAS/RAF-wild-type CRC-SC lines. In addition, seven FGFR inhibitor-resistant CRC-SC derivatives were newly generated from four parental CRC-SC spheroid lines by continuous exposure to erdafitinib or futibatinib. Matched comparisons between parental and resistant lines were performed to identify genes and pathways associated with acquired resistance to FGFR inhibitors. The integrated dataset of 78 RAS/RAF-wild-type CRC-SC lines was further analyzed to evaluate the correlation between EGFR and PTPRO mRNA expression.

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

first: Shoichi

last: Kitano

first: Hiroyuki

last: Miyoshi

first: Takehito

last: Yamamoto

last: Matsubara

first: Tomonori

last: Morimoto

first: Fumihiko

last: Kakizaki


title: Globally enhanced ATF4 occupation on genomic loci under mitochondrial stress

city: Ottawa

first: Ruth

last: Slack

state: Ontario

address: 451 Smyth Road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

summary: ATF4 is a stress-responsive gene which is critical for cell survival under stress conditions. ATF4 expression is upregulated under mitochondrial stress. Global ATF4-bound targets were mapped using chromatin Immunoprecipitation followed by high-throughput sequencing on differentiated neurons after lentiviral shOpa1-knockdown or shScrambled control. ATF4 antibody is from Cell Signaling (#11815S).

overall_design:
To investigate genomic ATF4-binding sites under mitochondrial stress, ChIP-seq was performed using ATF4-specific antibody on cortical neurons.
ATF4-binding peaks were mapped using MACS2.

first: Imane

last: Chakroun

first: Maria

last: Bilen


title: Differential RNA-seq analyses in MB135iDUX4_KLF18 KO_i3xFLAG-KLF18_AAVSI short and long cell lines

last: Tapscott


title: NEMO lysine mutant mice reveal ROS-RelA signaling required for optimal CD40-induced humoral immunity

city: Madison

first: Huy

last: Dinh

state: WI

address: 1111 Highland Avenue

institute: University of Wisconsin-Madison

summary: Oxidative and genotoxic stresses activate NF-κB signaling through intracellular pathways distinct from those initiated by membrane receptors, but their physiological roles remain incompletely defined. We created the NEMODK mouse model with germline arginine substitutions at NEMO (NF-κB essential modulator) lysines 270 and 302, key sites for post-translational modifications selectively induced by these intracellular stresses to enable NF-κB signaling in vitro. NEMODK mice exhibited B cell-intrinsic defects in the generation of germinal center B cells and humoral responses. Mechanistically, NEMODK B cells displayed a CD40-specific NF-κB signaling defect, unrelated to acute canonical and delayed noncanonical NF-κB activity, which was accompanied by the lack of sustained NEMO monoubiquitination downstream of mitochondrial reactive oxygen species generation without relying on nuclear DNA damage. This specifically reduced persistent RelA activity and a failure to mount transcriptomic and epigenetic changes critical for homotypic B cell aggregation, cell proliferation, class switch recombination and antibody secreting cell generation. Thus, CD40 induces a uniquely sustained NEMO modification and persistent RelA transcriptional activity to efficiently generate class-switched antibodies.

overall_design: Splenic B cells were isolated from WT and NEMODK mice, either left unstimulated or stimulated with anti-CD40 and IL-4 for three days.  On day three, cells were collected and subjected to density gradient centrifugation using LymphoprepTM (18061, Stemcell Technologies) to remove dead cells and debris. 40,000 cells were used to make single-cell RNA-seq libraries using the PIPseq T20 3′ Single Cell RNA Kit (Fluent BioSciences, FBS-SCR-T20-4-V3) according to the manufacturer’s instructions. Libraries were sequenced by Novogene using lane-based sequencing on a NovaSeq X Plus platform (25B flow cell, paired-end 150 bp configuration).

first: Donna

last: Li

first: Shelly

last: Davis

first: Parth

last: Khatri

first: Shigeki

last: Myiamoto


title: Epigenetic Subtypes of High-Grade T1 Bladder Cancer Reveal Intra-Tumor Heterogeneity and Distinct Interactions with Tumor Microenvironment [scATAC-Seq]

city: Boston

first: Yingtian

last: Xie

address: 450 BROOKLINE AVE

institute: DANA FARBER CANCER INSTITUTE INC

summary: High-Grade T1 (HGT1) Non-Muscle Invasive Bladder Cancer (NMIBC) is a clinically heterogeneous disease, characterized by unpredictable treatment responses and limited tools for recurrence prediction. Although molecular classification efforts have been made, patient stratification still primarily relies on clinicopathological features, which offer limited clinical precision. In this study, we integrated chromatin profiling in bulk with single-nuclei(sn) RNA-seq, immunohistochemistry and spatial transcriptomics to define epigenetic subtypes of HGT1, characterize their heterogeneity, and investigate tumor–microenvironment interactions. Our findings reveal distinct chromatin profiles differentiating urothelial (URO) and micropapillary (MP) histological variants of high-risk HGT1. We identified three epigenetic states: two within the URO group, luminal-like inflammatory (LLI) and basal-like (BL), and a separate signature unique to MP tumors. Single-cell and spatial resolution approaches validated intratumoral heterogeneity and provided insight into subtype-specific microenvironmental contexts. Notably, ∼40% of URO tumors exhibited spatially distinct coexisting LLI and BL components. BL regions showed enrichment for angiogenesis and hypoxia pathways and were preferentially located near vascular stroma, while LLI regions showed to be located at the core of the tumor. MP tumors featured a markedly different microenvironment, characterized by diverse populations of cancer-associated fibroblasts (CAFs) and M2-polarized macrophages intermingled with tumor cells, suggesting a more immunosuppressive niche which could account for their worse clinical outcome. URO tumors, by comparison, showed a more immune-excluded phenotype. These findings provide a detailed molecular and spatial map of bladder cancer heterogeneity, highlighting how distinct epigenetic subtypes and histological variants are associated with tumor architecture and microenvironmental interactions. Our data underscore the need for subtype-specific therapeutic strategies to more effectively address the complexity already existing at HGT1 bladder cancer.

overall_design: For each of the two HGT1 cases, a 40 μm section was obtained and nuclei isolation was performed as previously described (Font-Tello et al. 2020; Cejas and Long 2022). In brief, the section was suspended in 300 μl of cold buffer comprising 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. The homogenate tissue was then transferred to a pre-chilled 1.5 ml microfuge tube and incubated on ice for 10 min. Lysates were then filtered through a 40 μm cell strainer, and nuclei were centrifuged for 10 min at 1500 relative centrifugal force (RCF) in a pre-chilled (4°C) fixed-angle centrifuge. Nuclei were resuspended in 300 μl of buffer containing 0.1% Tween-20 and enumerated using a hemocytometer with Trypan blue stain. Approximately 7000 cells were targeted per sample and processed following the 10× Genomics scATAC-seq sample preparation protocol (Chromium Single Cell ATAC Library & Gel Bead Kit, 10× Genomics). 150 bp paired end reads were sequenced in a NovaSeq XP.


title: CD40-induced humoral immunity

address: 1111 Highland Ave

department: Biostatistics and Medical Informatics

institute: University of Wisconsin - Madison

summary: CD40CD40 induces a uniquely sustained NEMO modification and persistent RelA transcriptional activity to efficiently generate class-switched antibodies.

overall_design: CD40+IL-4 or LPS+IL-4 for 48 hours with untreated controls to analyze the role of NEMO K270/K302 in T-dependent B cell responses.

last: Wuerzberger-Davis

first: Avtar

last: Roopra

last: Miyamoto


title: RNA transcriptom under mitochondrial stress (shOpa1) in terminal differentiated cortical neurons

summary: RNA was extracted from differentiated neurons after shOpa1 knock-down or scrambled control. cDNA library was established and sequenced in National Research Council Canada on Illumina NextSeq 550 platform.

overall_design:
To investigate gene expression changes under mitochondrial stress, we knocked-down Opa1, a mitochondria fusion protein, in cultured cortical neurons.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 biological replicates.
Comparative gene expression profiling analysis of RNA-seq data was performed for shOpa1-neurons and shControl-neurons.

first: Ziying

last: Liu

first: Youlian

last: Pan


title: let-7 and lin-46 are the essential targets of the LIN28 RNA-binding protein in temporal patterning [smallRNA-seq TC2]

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

department: Computational Biology

institute: Friedrich Miescher Institute for Biomedical Research

summary: We examined the levels of small RNAs in wild-type and lin-28(xe192) animals throughout postembryonic development (0-44 h) with hourly resolution. The first time points (0h to 23h) of this experiment were published previously and are accessible under the accession GSE245900 (Nahar et al. 2024). In that previous submission, all samples were sequenced twice to increase coverage (two fastq files per sample on SRA). The new samples published here (24h-44h) were only sequenced once and are thus compatible with the first sequencing round of GSE245900. While in this submission only the raw data of the new samples (24h-44h) are published, we included the time points 0h to 23h (considering only the first sequencing run, see above) in the processed data files. Due to the differences in sequencing depths between the two submissions, the intensity values for time points 0h to 23h are not identical even though they originate from the same biological samples.

overall_design: Wild-type and lin-28(xe192) animals were grown at 25°C and collected hourly at 0 to 44 hours after resumption of feeding.

first: Jana

last: Brunner

first: Chiara

last: Azzi

first: Helge

last: Grosshans


title: Gut microbiota-derived indole-3-acetic acid induces granulosa cell dysfunction under metabolic stress in PCOS_RNAseq

city: Lanzhou

first: yan

last: wang

address: No. 199 Donggang West Road Chengguan District

department: The First School of Clinical Medicine

institute: Lanzhou University

summary: Polycystic ovary syndrome (PCOS) is a multifactorial disorder closely associated with metabolic dysfunction, yet the contribution of gut microbiota–derived metabolites remains incompletely understood.

overall_design: In this study, we integrated clinical multi-omics analysis with in vivo and in vitro functional experiments to investigate the role of microbiota-associated metabolites in PCOS. Metagenomic and metabolomic profiling in obese women with PCOS identified coordinated alterations in gut microbiota and indole-related metabolites, among which Bacteroides fragilis and indole-3-acetic acid (IAA) were selectively enriched and positively correlated. Functional analyses revealed that neither Bacteroides fragilis nor IAA alone was sufficient to induce PCOS-like phenotypes under basal conditions, whereas both promoted ovarian dysfunction under high-fat diet–induced metabolic stress. At the cellular level, IAA suppressed granulosa cell proliferation by inhibiting G1/S cell cycle progression, accompanied by activation of aryl hydrocarbon receptor (AHR) signaling, which was partially reversed by AHR inhibition. Mechanistically, high-fat conditions enhanced cellular sensitivity to IAA, potentially through induction of oxidative stress. Collectively, these findings support a context-dependent role of a Bacteroides fragilis–IAA–AHR axis in linking gut microbiota to ovarian dysfunction under metabolic stress, providing insight into the gut–ovary interaction in PCOS.

first: Yan

last: Wang


title: Human Myometrial Cell Fate under Chronic Oxidative Stress for Leiomyomagenesis

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

institute: Northwestern University

summary: Uterine Leiomyoma are the most common benign tumors in women of reproductive age. Studies show that both leiomyoma and surrounding myometrium exist in a state of high oxidative stress, characterized by reactive oxygen species (ROS) production and impaired antioxidant defenses including defects of manganese superoxide dismutase (MnSOD). Oxidative stress has been proposed as a driver of leiomyoma initiation by promoting oxidative DNA damage leading to mutations in MED12 and leiomyoma growth. We hypothesize that chronic oxidative stress in human myometrial cells induces cellular remodeling and genomic alterations that promote adaptation and contribute to early events in leiomyoma development. To test this hypothesis, we generated stable human myometrial cell lines (Myo-hTERT) of wild type, MnSOD68K and mutant MnSOD68Q that impairs MnSOD antioxidant activity thereby imposing sustained oxidative stress.  Experiments were performed both in vitro using three-dimensional spheroid cultures and in vivo using xenograft models in immunocompromised mice, with some studies extending up to 10 months to model chronic oxidative stress. Cells were exposed to the oxidative inducer paraquat (PQ) and analyzed using cellular and molecular approaches including spatial transcriptomics and MED12 mutational analysis. Cells expressing MnSOD68Q exhibited increased intracellular ROS and oxidative DNA damage, as indicated by accumulation of 8-hydroxy-deoxyguanosine (8-OHdG). Transcriptomic analysis revealed activation of pathways associated with oxidative stress responses including collagen/extracellular matrix, cellular senescence and IGF/AKT signaling. Xenografts of primary myometrial cells subjected to prolonged oxidative stress demonstrated similar molecular responses and showed an increased frequency of MED12 mutations. These changes were accompanied by modest increases in cell proliferation with minimal induction of cell death.  Together, these findings provide mechanistic evidence that sustained oxidative stress can drive molecular and genomic changes in myometrial cells and support a causal role for chronic redox imbalance in the initiation of uterine leiomyomas.

overall_design: Stable human myometrial cell lines (Myo-hTERT) of wild type, MnSOD68K and mutant MnSOD68Q that impairs MnSOD antioxidant activity thereby imposing sustained oxidative stress were generated.  Experiments were performed using these mutant cell lines both in vitro using three-dimensional spheroid cultures and in vivo using xenograft models in immunocompromised mice, with some studies extending up to 10 months to model chronic oxidative stress. Cells were exposed to the oxidative inducer paraquat and analyzed using cellular and molecular approaches including spatial transcriptomics and MED12 mutational analysis.

first: Jian-Jun

last: Wei

first: Yue

last: Feng

first: Wenan

last: Qiang

first: David

last: Gius

first: Julie

last: Kim


title: NEMO lysine mutant mice reveal ROS-RelA signaling required for optimal CD40-induced humoral immunity [NEMODK_ATACSeq]

city: Milwaukee

first: Demin

address: 8727 W Watertown Plank Rd

institute: 1Versiti Blood Research Institute

overall_design: ATAC-seq was performed as previously described (Buenrostro et al, 2013). Briefly, 50,000 splenic B cells were isolated from WT and NEMODK mice and stimulated with anti-CD40 and IL-4 for two days. Cells were washed once with cold PBS, lysed in cold lysis buffer, and immediately centrifuged to collect nuclei. The nuclei pellet was resuspended in a transposition reaction mix (Illumina) and incubated at 37°C for 30 minutes. Following transposition, DNA was purified using the MinElute Kit (Qiagen) and amplified with NEBNext PCR Master Mix (New England Biolabs). Libraries were sequenced on an Illumina NovaSeq platform to generate paired-end 150 bp reads.


title: Spatial transcriptomics reveals molecular mechanisms underlying neuroinflammatory and neurodegenerative sequelae of immune checkpoint inhibition [RNA-Seq]

city: IRVINE

first: Devyani

last: swami

state: CA

address: 811 Health Sciences Road

department: Anatomy & Neurobiology

institute: UNIVERSITY OF CALIFORNIA IRVINE

summary: Immune checkpoint inhibitors (ICIs) that block cytotoxic T-lymphocyte–associated protein 4 (CTLA-4) and programmed cell death protein 1 (PD-1) signaling are among the most promising therapeutic approaches in tumor immunotherapy. We demonstrated that ICI disrupts synaptic integrity and neuronal plasticity by adversely altering microglial and neuro-immune homeostasis. However, the cell type–specific molecular mechanisms underlying ICI-induced neuroinflammation and neuronal dysfunction remain poorly defined. To address this gap, we performed spatial transcriptomic profiling in a syngeneic melanoma mouse model using multiplexed error-robust fluorescence in situ hybridization (MERFISH) to map gene expression at single-cell resolution. By integrating spatial single-cell data with bulk RNA-seq from the hippocampus, we characterized the distribution of microglia, astrocytes, synaptic, and neuroinflammatory markers and determined how ICI reshapes hippocampal cellular composition in cancer-bearing and non-cancer mice brains. MERFISH revealed upregulation of microglial, astrocytic, oligodendrocytic and T cell markers post-ICI treatment, implicating pathways involved in neuroinflammation, synaptic function, and cellular signaling. Immunofluorescence analysis corroborated these findings in postmortem brains from patients treated with ICIs and demonstrated elevated microglial activation and astrogliosis, along with reduced expression of myelin sheath stability markers. Mechanistically, conditional T cell depletion in a transgenic mouse model revealed that ICI-mediated microglial activation is contingent on the presence of T cells, thus establishing a causal T cell-microglia crosstalk axis driving neuroinflammation. Collectively, this work provides a high-resolution framework for understanding ICI treatment-associated neurotoxicity and establishing a significant link with neuroinflammation-associated cognitive decline, while also revealing potential molecular targets for therapeutic intervention.

overall_design: Bulk RNA seq data from hippocampus of Control, melanoma, Melanoma ICI treated samples,

last: Swami

first: Suhas

last: Sureshchandra

first: Shivashankar

last: Othy

first: Munjal

last: Acharya


title: Spatial transcriptomics reveals molecular mechanisms underlying neuroinflammatory and neurodegenerative sequelae of immune checkpoint inhibition [MERFISH]

overall_design: MERFISH analysis in Hippocampus from Control, Melanoma and Melanoma ICI treated mouse samples


title: Effect of ablation of Etv4 and Etv5 from nephron progenitor cells (NPCs) and derivatives

city: Cincinnati

first: Cristina

last: Cebrian

state: Ohio

address: 240 Albert Sabin Way

department: Division of Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

summary: During kidney development, Etv4 and Etv5 are essential for ureteric bud branching. They are also expressed in NPCs and developing nephrons. Here we ablated Etv4 and Etv5 from NPCs and compared the gene expression profile of mutant and control mice at embryonic day 14.5.

overall_design: We have compared the RNA expression profile of mutant (Six2-GFPcre tg/+; Etv4-/-; Etv5fl/fl) and control (Six2-GFPcre tg/+; Etv4+/-; Etv5fl/fl) kidneys from E14.5 embryos.

first: Kaitlin

last: Day

first: Konrad

last: Thorner


title: Dipeptidyl peptidase 3 sets the threshold for immune activation and survival during experimental bacterial infection

city: Pieve Emanuele (MI)

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

country: Italy

institute: IRCCS Humanitas Research Hospital

summary: Effective host defense against infection relies on the tight coordination of immune activation, metabolic adaptation, and redox control, yet how these processes are integrated remains incompletely understood. Here, we identify dipeptidyl peptidase 3 (Dpp3) as a negative regulator of antimicrobial immunity. Dpp3-/- mice exhibit enhanced resistance to Klebsiella pneumoniae infection, with reduced bacterial burden, preserved tissue integrity, and attenuated systemic inflammation. This response is associated with increased phagocytic activity, expansion of germinal centres and plasma cells, and elevated interferon-γ production by T cells. Mechanistically, Dpp3 deficiency leads to reduced Nrf2 protein levels upon stimulation, resulting in heightened ROS accumulation and amplified NF-κB signaling. Integrated metabolomic and transcriptomic analyses of Dpp3-/- immune cells reveal mitochondrial dysfunction and a shift toward biosynthetic and antioxidant-supportive metabolic programs. Collectively, our findings identify Dpp3 as a molecular brake on host defense and uncover a regulatory axis linking redox balance, immunometabolism, and inflammation during infection.

overall_design: To investigate the molecular basis underlying the altered immune response observed in Dpp3-deficient mice, we conducted whole-transcriptome analysis by RNA-seq on sorted CD3⁺ T cells, CD19⁺ B cells, and CD11b⁺ innate immune cells isolated from the lungs of naïve WT and Dpp3-/- mice


title: PTEN, a biomarker and a master mediator of non-healing venous leg ulcers, suppresses immune response, angiogenesis and lymphangiogenesis

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary: Venous leg ulcers (VLUs) are the most common cause of leg ulcers, yet only 44% heal with standard of care, highlighting the critical need for better understanding of their cellular pathology. We used a combination of single-cell RNA-Sequencing (scRNA-Seq) and bulk RNA-Seq to identify molecular mechanisms and cellular functions contributing to VLU pathophysiology. scRNA-Seq of chronic VLUs revealed impairments in immune, lymph-endothelial, and endothelial cells, along with the underlying signaling pathways. Next, RNA-Seq was performed to asses clinical outcomes in patients receiving standard of care, with wound healing rate monitored for at least 4 weeks. Transcriptomes of healing and non-healing VLUs were compared to those of human acute wounds (AW), revealing a robust suppression of inflammatory response, lymphangiogenesis and angiogenesis in non-healing VLUs. In contrast,  healing VLUs resembled gene expression signature of physiological, acute wound healing. Reduced inflammatory response resulting from impaired leukocyte transmigration and egression, with suppression of kinases’ activity, including AKT, ERK, JNK1/2, SRC, and PDGFR, underlines the non-healing VLU signature. Bioinformatic analyses pinpointed PTEN as a master regulator of these processes and signaling pathways. Indeed, increased PTEN was confirmed in non-healing compared to healing VLUs, both on scRNA-Seq and protein levels. Functional in vivo murine studies confirmed that pharmacological PTEN inhibition enhanced immune response and proinflammatory signals, angiogenesis and lymphangiogenesis which resulted in accelerated wound closure. We identified PTEN as a master regulator of non-healing phenotype controlling multiple key processes responsible for impaired healing, underscoring its potential use as diagnostic and therapeutic target to promote wound closure in VLUs.

overall_design: We utilized C57 black mice at 8wks of age, whereby 5mm wounds were induced on the dorsal-cranial aspect of the animal and sutured with a 10mm silicone split prior to administration of vehicle or pten inhibitor. Animals were covered with Tegaderm and wrapped in Coban for the duration of the experiment and wounds collected at D3 post wounding.

first: Jelena

last: Marjanovic

first: Irena

last: Pastar

first: Marjana

last: Tomic-Canic


title: Intestinal FXR deficiency uncouples steatosis protection from liver inflammation and fibrosis in MASH-diet fed mice [scRNA-seq]

city: Lille

first: Simon

last: Peschard

address: 1, rue du professeur Calmette BP245

institute: INSERM UMR 1011

summary: The bile-acid receptor FXR is known to be expressed in both intestine and liver, and FXR agonists are currently Under clinical evaluation for Metabolic Associated SteatoHepatitis (MASH) treatment. However, the specific question about activate or de-activate FXR specifically in the intestine in MASH is still unlear, protective results being available for both case.

overall_design: Mouse CD45+ cells were isolated from livers of intestinal-FXR knock-out mice and their control floxed littermate after 20 weeks of high-fat sucrose and cholesterol diet. After CMO labelling, cells were processed through 10x Genomics process to capture, amplify and construct library prior to RNA sequencing.

first: Margaux

last: Nawrot

first: Morgane

last: Thibaut

first: Kévin

last: Ory

first: Emmanuelle

last: Vallez

first: Emilie

last: Dorchies

first: Véronique

last: Touche

first: Amandine

last: Descats

last: Dubois-Chevalier

first: Céline

last: Gheeraert

first: Sandrine

last: Caron

first: Kadiombo

last: Bantubungi

first: Philippe

last: Lefebvre

first: Anne

last: Tailleux

first: Joel

middle: T

last: Haas

first: Laure

last: Bindels

first: Isabelle

last: Leclercq

last: Dombrowicz

first: Sophie

last: Lestavel

first: Bart

last: Staels


title: CDK10 suppression sensitizes cells to CDK12/13 blockade

city: Kyoto

first: Kosuke

last: Yusa

state: Kyoto

address: 53 Shogoin Kawaharacho, Sakyo-ku

department: Institue for Life and Medical Sciences

summary: A CRISPR screen with a CDK12/13 inhibitor identified CDK10 as a modulator of CDK12/13 blockade. CDK10 KO cells in OVCA and BRCA showed higher sensitivity to CDK12/13 inhibitors and increased apoptosis, compared to wild type cells. To investigate the effects on transcription, CDK10 KO cells with or without CDK12/13 inhibitor treatment were analyzed by RNA-sequencing.

overall_design: The ovarian cancer cell line OVCAR8 was cultured in RPMI1640 supplemented with 10% FBS. In the first set of the experiments, CDK10 wildtype and knockout cells were treated with the CDK12/13 inhibitor CTX-439 at 0, 10, 30 and 90 nM for 6 hours and total RNA was extracted. In the second set of the experiments, cells were treated with CTX-439 at 90nM for 6, 24 and 48 hours or DMSO for 6 hours and total RNA was extracted. The breast cancer cell line MDA-MB-231 was cultured in DMEM/F12 supplemented with 10% FBS. CDK10 wildtype and knockout cells were treated with CTX-439 at 90 nM for 0, 6, 24 and 48 hours and total RNA was extracted.  Total RNA extreaction was performed using the RNeasy Mini kit (Qiagen) according to the manufacturer’s protocol. RNA-seq library was generated using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions. Resulting libraries were sequenced using DNBSEQ-G400RS by 100-bp paired-end sequencing.

first: Yusuke

last: Tarumoto


title: ALKBH5 fuels angiogenesis and collagen deposition via m6A-YTHDF2-Dependent NLRP3 mRNA stabilization aggravating scarring after glaucoma surgery [scRNA-seq]

city: Shanghai

first: Ning

last: Li

address: 160 Pujian Road

department: Department of Ophthalmology, Renji Hospital

institute: Shanghai Jiao Tong University School of Medicine

summary: Glaucoma is a leading cause of irreversible blindness. For patients unresponsive to medical therapy, glaucoma filtration surgery (GFS) is the primary intervention to lower intraocular pressure (IOP). However, postoperative scarring often causes surgical failure, and the mechanisms remain poorly defined. Here, we identify the RNA demethylase alkB homolog 5 (ALKBH5) as a regulator of fibrotic remodeling after GFS via an epitranscriptomic mechanism involving N6-methyladenosine (m6A) modification. In both patients and rabbit models, increased vascular perfusion and decreased bleb height—quantified by anterior segment optical coherence tomography angiography (AS-OCTA) and ultrasound biomicroscopy (UBM)—were associated with elevated IOP. Immunohistochemistry and single-cell RNA sequencing revealed ALKBH5 upregulation in vascular endothelial cells (VECs) within scar tissue. Functional assays, rabbit GFS models, and Alkbh5-deficient mice revealed that ALKBH5 promotes angiogenesis and collagen deposition, accelerating postoperative fibrosis. Methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and RNA sequencing (RNA-Seq) identified NLR family pyrin domain containing 3 (NLRP3) as a downstream target of ALKBH5. Mechanistically, ALKBH5 removes m6A modifications from NLRP3 mRNA, preventing YTH N6-methyladenosine RNA binding protein 2 (YTHDF2)-mediated degradation and stabilizing its expression. These findings uncover a role of ALKBH5–YTHDF2–NLRP3 axis in GFS-induced fibrosis and suggest targeting this epitranscriptomic pathway in VECs may improve outcomes.

overall_design: We performed single-cell RNA sequencing (scRNA-seq) on four human ocular conjunctival tissue samples, including two from the scar group and two from the control group. Following stringent quality control, a total of 35,334 cells were retained for subsequent analysis. This analysis revealed an increased abundance of VECs in scar tissue relative to control tissue. Notably, the expression of ALKBH5 was also significantly elevated within the VECs of scar tissue. Collectively, these findings suggest that the upregulation of ALKBH5 in VECs plays a critical role in GFS-induced scarring.

first: Ting

last: Yu

first: Fan

last: Yang

first: Jijingru

first: Chang

last: Shu

first: Xitai

last: Zhang

first: Qin

last: Liu

first: Yajie

first: Xin

last: Liang

first: Min

first: Wenjun

last: Hu

first: Bilian

last: Ke

first: Xiaojun

last: Zha


title: Reversion of T cell exhaustion enables cancer vaccine efficacy in BRCA1-deficient ovarian cancer

city: Lausanne

first: Aspram

last: Minasyan

address: Bugnon 25A

institute: Ludwig Institute for Cancer Research / CHUV

summary:
Background:
BRCA mutations in ovarian cancer (OC) are associated with increased tumor-infiltrating lymphocytes and inflammatory features, yet immunotherapy for OC has failed to meet expectations. This study hypothesizes that BRCA1 or BRCA2 deficiency differently influences the response to cancer vaccine.
Methods:
We used the syngeneic orthotopic ID8 mouse ovarian tumor models deficient for Trp53, Trp53 and Brca1, or Trp53 and Brca2. Tumor-implanted mice were vaccinated with a dendritic cell-based whole tumor lysate vaccine (termed OCDC) alone or in combination with anti-VEGF therapy, PARP inhibitor, and/or anti-PD-1 immune checkpoint inhibitor. Tumor burden, mice survival and monitoring of T cell responses were evaluated by bioluminescence imaging, flow cytometry and interferon gamma (IFNg)-ELISpot assay. Transcriptomic profiling of tumor cell and immune cell-compartments was performed using NanoString GeoMx digital spatial profiling.
Results:
Brca1 deficiency—but not Brca2— impairs effectiveness of OCDC vaccine. OCDC vaccine reduced tumor growth rates and improved survival of mice implanted with Trp53-/- and Trp53-/-Brca2-/-ID8 tumors, but was ineffective in mice implanted Trp53-/-Brca1-/- tumor model. Transcriptomic analysis revealed that tumors responsive to OCDC (Brca wild-type or Brca2-/-) underwent metabolic and immunologic reprogramming post-vaccination, unlike Brca1-/- tumors. Inefficacy of the cancer vaccine was driven by a tumor microenvironment that was already inflamed, characterized by a high level of activated yet exhausted T cells, which hinder additional immune activation by vaccination. Combining OCDC with anti-VEGF and PARP inhibitors partially overcame vaccine resistance in Brca1-/- tumors, while adding anti-PD-1 further improved vaccine effectiveness by boosting T cell activity and promoting long-term survival.
Conclusion:
These findings highlight BRCA1’s role in cancer vaccine sensitivity and support using rational combinations to overcome vaccine inefficacy in BRCA1-mutated OC.

overall_design: Nanostring GeoMx DSP using the whole trancriptome atlas (WTA) panel was used to profile ID8 mouse ovarian tumors

first: Laurent

last: Beziaud

first: Cheryl

last: Chiang

first: Rania

last: Soukarieh

first: Mathilde

last: Coppi

first: Raphaël

last: Rovelli

first: Jonathan

last: Thevenet

first: Stéphanie

last: Tissot

first: Denarda

last: Dangaj-Laniti

first: Lana

middle: E

last: Kandalaft


title: ALKBH5 fuels angiogenesis and collagen deposition via m6A-YTHDF2-Dependent NLRP3 mRNA stabilization aggravating scarring after glaucoma surgery [MeRIP-seq]

first: Ning

last: Li

overall_design: To further investigate the mechanism of ALKBH5 in vascular endothelial cells, we combined methylated RNA immunoprecipitation sequencing (MeRIP-Seq) combined with RNA-Seq to predict a potential target of ALKBH5-mediated regulation. MeRIP-Seq, performed with three independent biological replicates, was used to identify m6A-modified targets in HUVECs.

first: Ting

last: Yu

first: Fan

last: Yang

first: Jijingru

first: Chang

last: Shu

first: Xitai

first: Qin


title: let-7 and lin-46 are the essential targets of the LIN28 RNA-binding protein in temporal patterning

first: Dimos

last: Gaidatzis

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

overall_design: Refer to individual Series


title: RNA-seq and acRIP-seq in NAT10 overexpression HaCaT cells [RIP-seq]

city: hangzhou

first: zhiqi

last: xie

address: huzhou street 51

institute: Hangzhou city university

summary: To elucidate the function of the RNA acetyltransferase NAT10 in keratinocytes and its regulatory impact on atopic dermatitis pathogenesis, we conducted RNA-seq and acRIP-seq of HaCaT cells overexpressing NAT10 versus empty-vector controls.

overall_design: NAT10 overexpression or vector control HaCaT cells were used to investigate the different expression genes which were correlated to NAT10.

first: Zhiqi

last: Xie

first: Jinjin

last: Shao


title: S100A8/A9 Priming Alters Translational Related Proteins and Upregulates Pro‑Regenerative Factors in Mesenchymal Stromal Cells

city: Ulm

first: Pallab

last: Maity

address: Meyerhofstrasse/James Franck Ring

department: Dermatology

institute: University of Ulm

summary: Background: Non-healing wounds cause profound suffering of patients and a huge economic burden on society. Current research attempts to refine MSC-based therapies for this type of difficult-to-treat wounds. We earlier reported that injection of S100A8/A9 primed MSCs into the wound edge in mice accelerates wound healing compared to non-primed MSCs. We here describe a protective response of differentially expressed isoforms of genes, proteins and their potential role in the reported beneficial effects of S100A8/A9 primed MSCs on tissue repair.  Methods: Adipose‐derived MSCs were characterized for specific cell surface markers using flow cytometry and assessed for their ability to differentiate into different lineages. To further investigate the mechanisms underlying the beneficial effects of S100A8/A9 primed MSCs, we employed a multi‐omics strategy that combined transcriptome, secretome, and proteome analyses. Global translational activity and a potential metabolic shift were examined using fluorescent labeling alongside seahorse‐based metabolic assays. Additionally, in silico analysis was conducted to assess the presence of the DRACH motif in mRNAs encoding these proteins, thereby evaluating their potential for cap-independent, m6A‐mediated translation. Results: Enhanced protein translation was observed in MSCs primed with S100A8/A9. Priming significantly increased the levels of the cap-independent translation initiation factor EIF3I, while reducing the cap-dependent factor EIF4A1, suggesting a shift in the mode of translation. In addition, the secretome of S100A8/A9-primed MSCs exhibited upregulation of cystatin C, a tissue protective protease inhibitor, and angiopoietin-1, an inducer of angiogenesis. Furthermore, various collagens, which serve as MSC niche-protecting proteins, were expressed at higher levels in the S100A8/A9 primed MSCs. Notably, the mRNAs corresponding to these factors contained DRACH motifs. Conclusion: We uncovered a protective response in S100A8/A9 primed MSCs that alters translation processes and increases the secretion of protective proteins, whose functions warrant further exploration. In the long term, S100A8/A9 priming holds promise for developing more effective MSC‐based therapies to enhance wound healing.

overall_design: 1 µg of total RNA from total skin was first rRNA depleted using either Ribominus Eukaryotic system v2 kit (ThermoFisher Scientific). rRNA depleted RNA was subjected to preparation of Illumina compatible RNA-seq libraries using NEBNext Ultra II Directional RNA Library Preparation kit (NEB). RNA-seq libraries were quality controlled through Qiaxcel advanced system (Qiagen) and Bioanalyzer (Agilent) and finally measured by Qubit fluorimeter (ThermoFisher Scientific). Validated libraries were sequenced on Illumia NOVASEQ 6000 system.

first: Maity

last: Pallab

first: Wang

last: Yongfang


title: Exploring the inhibitory mechanism of DSS-induced ulcerative colitis by Banxia Xiexin Decoctionthrough the combination of serumpharmacochemistry, networkpharmacology, and transcriptomics.

city: Fuzhou

first: xiuli

last: Zhang

address: No. 1 Qiuyang Road, Minhou Street, Fuzhou City, Fujian Province

institute: Fujian University of Chinese Medicine

summary: The aim of this study was to identify differentially expressed genes (DEGs) in colonic tissue samples from mice treated in the Control, DSS, BXD low dosage (BXD-L), and BXD high dose (BXD-H) groups (n = 3 per group). The DEGs between different treatment groups (such as BXD-H vs. DSS) were analyzed.

overall_design: The colonic tissue samples from mice were divided into four groups: Control, DSS, BXD low dosage (BXD-L), and BXD high dose (BXD-H) groups, and RNA sequencing was performed to identify differentially expressed genes (DEGs) and their related pathways.

first: Xiu

first: Qing

middle: S

last: Wwang

first: Cheng

last: Wu

first: Yao

last: Lin


title: Multi-omics of chorionic villus samples reveals early pregnancy placental dysfunction associated with preeclampsia

city: Melbourne

first: Ellen

last: Menkhorst

state: Victoria

address: Royal Women's Hospital

department: Obstetrics, Gynecology and Newborn Health

country: Australia

institute: The University of Melbourne

summary: Preeclampsia is a serious pregnancy-induced disorder unique to humans affecting 4.6% of pregnancies worldwide. Advances in the detection, prevention and treatment of preeclampsia have been poor due to our inadequate understanding of its pathogenesis. Here, we perform a multiomics study on early pregnancy placental biopsies (chorionic villus samples) from pregnancies that developed preterm and term preeclampsia compared to normotensive controls. Using an integrative multivariate approach, we uncovered distinct molecular signatures: preterm preeclampsia was strongly associated with dysregulated lipoprotein metabolism, while term preeclampsia exhibited alterations in inflammatory pathways, notch signaling and ribosome assembly. These results challenge the prevailing notion that term preeclampsia is unrelated to early placental pregnancy dysfunction. Our study provides critical insights into the early pregnancy aberrations underlying both preterm and term preeclampsia, paving the way for novel predictive biomarker and targeted preventative treatments. This work represents a significant step towards unravelling the complex etiology of preeclampsia and improving maternal and perinatal health outcomes.

overall_design: Chorionic villous samples (CVS, n=14) taken from women undergoing screening for fetal chromosomal abnormalities were snap frozen immediately after collection. CVS were collected from pregnancies that were normotensive (n=6), preterm preeclamptic (preeclampsia onset <37 weeks gestation, n=4) or term preeclamptic (preeclampsia onset >37 weeks gestation, n=4). RNA was extracted from snap-frozen tissue and cells using the RNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions. Genomic DNA was digested using the on column (RNase-free DNase set, #79256, QIAGEN) according to the manufacturer’s instructions. The Illumina NovaSeq RNA-seq sequence production of a 150bp paired-end run and the primary bioinformatics analysis was performed by the Australian Genome Research Facility (Project code: CAGRF20062989). After the RNA libraries were prepared using Illumina’s Ribo-zero Gold protocol, they were sequenced on an Illumina NovaSeq platform in two flowcells. Following primary bioinformatics analysis (demultiplexing and quality control) the data was processed through RNA-seq expression analysis workflow, including alignment, transcript assembly, quantification and normalization.

first: Guannan

first: Leilani

last: Santos

first: Wei

last: Zhou

first: Argyro

last: Syngelaki

first: Kypros

last: Nicolaides

first: Kim-Anh

last: Le Cao

first: Evdokia

last: Dimitriadis


title: Leveraging dynamic cell responses to design new protocols for pluripotency maintenance

city: Bristol

first: Lucia

last: Marucci

state: UK

address: University Walk

department: Engineering Mathematics and School of cellular and molecular biology.

country: United Kingdom

institute: University of Bristol

summary: Pluripotent stem cells have a high potential for research and development applications in biomedicine. They are unspecialized cells that can be indefinitely expanded retaining pluripotency or pushed into specific differentiated states by proper stimuli. Various protocols have been proposed to maintain mouse embryonic stem cells (mESCs) in the pluripotent state; state of the art cell culture protocols are based on serum-free media, and continuous provision of drugs inhibiting pathways associated to differentiation. We explore here the possibility to avoid continuous drug exposure. First, we employ an external feedback control microfluidics/microscopy platform to steer the expression of a pluripotency reporter. Control experiments show a significant delay in cell response to drugs; these dynamics are confirmed by flow-cytometry open-loop experiments. We then harness such delays to design novel culture protocols with limited cell exposure to small-molecule inhibitors; in so doing, we reduce cell exposure to drug, but we maintain pluripotency. Our results suggest new approaches to design cell culture protocols based on the quantitative analysis and control of cellular dynamics.

overall_design: RNA-seq of  E14Tg2a are male ESCs of 129 background containing a monoallelic protein GFPd2 knockin at the REX1 locus. They were analyzed at zero passage, one month culture and two months culture in different media.

first: Antonella

last: La Regina

first: Elisa

last: Pedone


title: Transcriptome-wide mapping of m6A in bovine oocytes and preimplantation embryos by SAC-seq

city: Gainesville

first: Zongliang

last: Jiang

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

summary: RNA N6-methyladenosine (m6A) plays a crucial role in regulating gene expression and early embryonic development. However, the m6A dynamics at single-nucleotide resolution during preimplantation development has not been characterized, and the function of m6A marks in specific transcripts remain largely unexplored. Here, by using SAC-seq, we overcome the limitation of antibody-based m6A profiling and define m6A landscapes in bovine oocytes and pre-implantation embryos at unprecedented level. Notably, we identify a specific m6A site on RPL12 (m6A-RPL12), which was highly methylated at the 8-cell stage. m6A-RPL12 deficient leads to reduced protein synthesis, disrupted expression of translation-related genes, and impaired zygotic genome activation and blastocyst formation. Supplementation with wild-type RPL12 mRNA failed to rescue the developmental arrest, indicating that m6A regulation extends beyond transcript abundance. This study provides invaluable m6A single-nucleotide resolution recourse in early embryogenesis and demonstrates that precise regulation of m6A at selected transcripts can shape early developmental outcomes in mammals.

overall_design: RNA-seq profiling was performed on bovine 4-cell and 8-cell stage embryos. Control and RPL12A148G-edited embryos were collected at both stages. Five embryos per stage per replicate per group were used as starting material for the RNA-seq protocol.

first: Rajan

last: Iyyappan


title: Single nucleus (sn) RNA sequencing analysis of murine liver cells after 12 weeks of weekly treatment with either PBS, 50nm polystyrene or 500nm polystyrene

city: Bonn

first: Lisa

middle: Maria

last: Steinheuer

state: NRW

address: Venusberg Campus 1

department: Institute of Experimental Oncology

institute: University Hospital Bonn

summary: Plastic pollution poses a universal yet understudied environmental risk to the immune system. Once ingested, nano- and microplastic particles (MNPs) can translocate from the gut into internal organs, likely via circulation. In humans, MNPs have been detected in macrophages within carotid artery plaques, suggesting that these highly phagocytic cells, may also serve as key targets for MNPs under homeostatic conditions. Kupffer cells (KCs), the liver-resident macrophages, play a crucial role in liver homeostasis by regulating metabolism, clearing opsonized target cells, and serving as the first line of defence against bacteria. Residing within the liver sinusoids, they continuously monitor the bloodstream, efficiently capturing and eliminating pathogens and circulating particles to maintain immune and metabolic balance5. It remains unknown whether KCs efficiently capture and store MNPs and how this might affect liver function. Here, we utilize a mouse model of chronic plastic exposure to assess how ingested MNP influence KC core functions, and thereby also liver function. We show that KCs are the primary hepatic target of MNPs and that 12 weeks of exposure alters their transcriptome and impairs phagocytic capacity, leading to dysregulated liver metabolism. Microplastics, but not nanoplastics, exposure reduces KC-mediated clearance of circulating cells and bacteria and exacerbates diet-induced obesity. These findings suggest that chronic MNP exposure disrupts tissue-specific macrophage functions in a size-dependent manner, with distinct long-term consequences for liver function and overall health.

overall_design: 8-10 week old male C57Bl6/J mice received weekly oral gavages of either PBS, 100mg/kg 50nm polysterene particles or 500nm polysterene particles. After 12 weeks, mice were euthanised and the liver was collected and immediately snap-frozen for nuclei isolation.

first: Nikola

last: Makdissi

first: Maria Francesca

last: Viola

first: Lisa Maria

first: Nelli

last: Blank-Stein

first: Eliana

last: Franco Taveras

first: Katharina

last: Sieckmann

first: Ronja

last: Cardinal

first: Frederike

last: Graelmann

last: Mauel

first: Nele

last: Kronau

first: Jake

last: Thomas

first: David

last: Bejarano

first: Sandra

last: Högler

first: Joachim

last: L. Schultze

first: Christoph

last: Thiele

first: Lukas

last: Kenner

first: Andreas

last: Schlitzer

first: Falk

last: Nimmerjahn

first: Dagmar

last: Wachten

first: Martin

last: Fuhrmann

first: Kevin

last: Thurley

first: Elvira

last: Mass


title: Conserved principles of spatial biology define tumor heterogeneity and immunotherapy sensitivity

city: Chicago

first: Arjun

last: Raman

address: 900 E. 57th Street, KCBD rm. 4126

department: Department of Pathology and Duchossois Family Institute

institute: University of Chicago

summary: Spatial transcriptomics experiments were performed on human patient pre-treatment biopsies for patients with either NSCLC or DLBCL. This was part of a larger study on pan-tumor spatial biology organization.

overall_design:
18 tissue sections representing 16 pre-treatment NSCLC tumors and 2 pre-treatment DLBCL tumors were subject to spatial transcriptomics using the 10x Genomics Visium platform, followed by high throughput sequencing. Raw data not submitted due to patient privacy concerns.

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

first: Vivek

last: Behera

first: Marina

last: Garassino

first: Justin

middle: P

last: Kline


title: Stem-like precursors of helper T cells dependent on Eomes and Myb sustain CD4+ T cell responses during chronic infection

first: Nikita

last: Potemkin

state: Vic

address: 792 Elizabeth St

department: The Peter Doherty Institute for Infection and Immunity

institute: University of Melbourne

summary: CD4+ T helper cells are critical for sustaining adaptive immunity against infection. However, the factors that regulate their maintenance and function in response to protracted infections remain poorly understood. Here, using the Lymphocytic Choriomeningitis Virus (LCMV) model, we identify a transcriptionally defined population of CD4+ helper T cells, which manifest in chronic but not acute infection, to be essential to sustain chronic CD4+ T cell immunity. These cells, which are distinct from memory-like CD4+ T cells, express markers typically associated with exhausted T cells, including PD-1 and TOX, and can self-renewal and give rise to both type 1 T helper (Th1) and follicular T helper (Tfh) cells, thus acting as precursors of T helper (pTh) cells. These cells also mediate the Th1-biased differentiation and expansion in response to PD-1-targeted immune checkpoint blockade (ICB). Molecularly, we show that the development, function and maintenance of pTh cells depend on the transcription factors EOMES and MYB, respectively. While EOMES instructs the overall pTh transcriptional program and the subsequent progression into mature T helper cells, MYB preserves pTh cells by limiting their downstream differentiation. Consequently, the maintenance of both Th1 and Tfh responses is severely compromised in CD4+ T cells lacking either EOMES or MYB. Thus, our findings reveal a precursor-progeny hierarchy in CD4+ T cells and its molecular underpinnings that sustain long-term helper response specifically in chronic infection and during immunotherapy.

overall_design: Single cell RNA-sequencing of PD1+ CD4+T cells were sorted from spleens and LNs of wildtype mice infected with either LCMV Armstrong or LCMV Docile at 28 dpi. And single cell RNA-sequencing of PD1+ CD4+T cells were obtained from spleens of control, Eomesfl/flCd4cre and Mybfl/flCd4cre mixed bone-marrow mice infected with LCMV Docile at 28 dpi.

first: Lifen

last: Wen

first: Chun-Hsi

last: Su

first: Lachlan

last: Dryburgh

first: Lei

last: Qin

first: Sining

last: Li

first: Jan

last: Schroder

first: Carlson

last: Tsui

first: Axel

last: Kallies