title: BCL6B suppresses acute myeloid leukemia progression by transcriptionally repressing GGT5 and modulating MAPK signaling

city: Kunming,Yunnan,CHina

first: Pan

last: Yuqing

address: 295 Xichang Road, Wuhua District, Kunming City, Yunnan Province, China

institute: the First Affiliated Hospital of Kunming Medical University

summary: Acute myeloid leukemia (AML) is a genetically heterogeneous hematologic malignancy with poor prognosis. In this study, we investigated the role of B-cell lymphoma 6 member B (BCL6B) in AML progression. Integrated analyses of TCGA-LAML, GTEx, and GEO datasets revealed that BCL6B was significantly downregulated in AML and associated with adverse clinical features and shorter overall survival. Functional assays demonstrated that BCL6B overexpression suppressed AML cell proliferation, induced apoptosis, and caused G0/G1 cell cycle arrest, whereas BCL6B knockdown exerted opposite effects. Mechanistically, transcriptome analysis and promoter-binding assays identified gamma-glutamyltransferase 5 (GGT5) as a direct transcriptional target of BCL6B. BCL6B bound to the GGT5 promoter and repressed its expression, thereby modulating MAPK signaling by inhibiting ERK phosphorylation and activating p38 and JNK pathways. Rescue experiments confirmed that GGT5 partially mediated the biological effects of BCL6B. In vivo, BCL6B overexpression significantly inhibited leukemic growth, migration, angiogenesis, and improved survival in zebrafish and mouse xenograft models. These findings identify the BCL6B–GGT5–MAPK axis as a key regulatory pathway in AML and a potential therapeutic target.

overall_design: This study employed an integrated experimental framework combining bioinformatics, in vitro functional assays, and in vivo validation. Public transcriptomic datasets (TCGA-LAML, GTEx, GEO) were analyzed to evaluate BCL6B and GGT5 expression patterns, clinical associations, and prognostic relevance. Clinical bone marrow samples from AML patients and healthy donors were used for expression validation by RT-qPCR. Gain- and loss-of-function experiments were performed in multiple AML cell lines using lentiviral-mediated BCL6B overexpression or shRNA knockdown. Cell proliferation, apoptosis, and cell cycle distribution were assessed by CCK-8 assays and flow cytometry. Epigenetic regulation of BCL6B was examined using methylation-specific PCR and decitabine treatment. RNA sequencing was conducted to identify BCL6B-regulated genes, followed by GO and KEGG pathway enrichment analyses. Direct transcriptional regulation of GGT5 by BCL6B was validated using dual-luciferase reporter assays and electrophoretic mobility shift assays. MAPK pathway activation was analyzed by Western blotting. Functional rescue experiments were performed by co-overexpression of GGT5 and BCL6B. In vivo effects were evaluated using zebrafish and nude mouse xenograft models to assess tumor growth, migration, angiogenesis, and survival.

first: Yuqing

last: Pan

first: Kun

last: Wu

first: Chong

last: Guo

first: Yixun

last: Li

first: Zhengjie

first: Shenju

last: Cheng

first: Yan

last: Du


title: TRIMs in the placental tissue of HIV-1 infection

status: Public on Mar 01 2026

city: São Paulo

first: Maria

middle: Notomi

last: Sato

state: São Paulo

address: Av. Dr. Eneas de Carvalho Aguia, 470

department: Dermatology

country: Brazil

institute: University of São Paulo

type: Expression profiling by high throughput sequencing

summary: Innate immunity is a crucial mechanism for protecting the maternal-fetal interface, whereas little is known about the placenta in chronic HIV-1 infection in mothers treated with antiretroviral therapy (ART). The maternal-fetal interface, we previously observed an enrichment of antiviral factors and inflammatory components in HIV-1 infection. TRIM family proteins are potent antagonists of viral replication; however, others can promote viral replication by ubiquitinating and degrading specific innate immune signalling proteins. We verified the expression of genes involved in innate immunity focusing on the TRIM gene profile in placental tissue (villus and decidua) from HIV-1-infected mothers. We conducted RNA sequencing of placental tissue (villus and decidua) from HIV-1 infected and control mothers.  DEGs validation performed by the RT-qPCR method confirms  the upregulation of TRIM21 and TRIM39 in both the decidua and the villus of HIV-1-infected samples.

overall_design: Pregnant women living with HIV-1, as well as placentas from control pregnant women, were submitted to the same for histopathological analysis, total RNA sequencing, real-time PCR and immunohistochemistry.

first: Beatriz

middle: N

last: Campo

first: Emanuella

middle: S

last: Souza

first: Nátalli

middle: Z

last: Pereira

first: Anna Julia

last: Pietrobon

first: Helaine Maria

middle: B

last: Milanez

first: Mirian

last: Sotto

first: Gabriel

last: Simões

first: Gabriela

middle: D

last: Mattos

first: Dennyson

last: Fonseca

first: Frederico

middle: M

last: Ferreira

first: Yasmim

middle: A

last: Ramos


title: Blood-brain barrier disruption in sports-related traumatic encephalopathy syndrome

city: Dublin 2

first: Jeffrey

last: O'Callaghan

state: Dublin

address: Smurfit Institute

country: Ireland

institute: Trinity College, Dublin

summary: Cerebrovascular disruption has been implicated in the pathophysiology of head trauma and chronic traumatic encephalopathy (CTE).  However, the long-term consequences of repetitive head trauma on blood–brain barrier (BBB) integrity and its link to cognitive function remains unknown. Here, using dynamic contrast enhanced MRI (DCE-MRI), we show that BBB disruption can be detected years after combat and collision sports athletes (n = 47) have retired from their respective sports. A subgroup of individuals (n = 17) with extensive BBB disruption displayed worse cognitive decline compared to those with less extensive disruption. While commonly used systemic biomarkers of central nervous system injury and neurodegeneration were of limited utility, we did observe a greater systemic inflammatory burden with a higher proportion of circulating monocytes that was significantly associated with cognitive decline in retired athletes. Transcriptomic analysis of these peripheral immune cells revealed dysregulation of the complement system and vascular developmental pathways. Altered expression of complement receptors including C5AR1, ITGAM, ITGB2 and CD59, a potent inhibitor of the membrane attack complex (MAC), was associated with BBB disruption and cognitive decline. Post-mortem tissue from confirmed cases of CTE showed MAC deposition around cerebral blood vessels. Finally, bioinformatic analysis of single nucleus RNA sequencing data from post-mortem CTE cases revealed microglia-endothelial crosstalk which may mediate complement dysregulation. Together, our data suggest that sustained systemic inflammation and persistent BBB disruption is associated with the long-term outcome of repetitive head trauma.

overall_design: RNA-seq profiling of peripheral blood mononuclear cells from retired athletes with a history of repetitive head trauma as well as controls from a non-contact sporting background

first: Chris

last: Greene

first: Declan

last: Brennan

first: Sheida

last: Mirloo

first: Ruairi

last: Connolly

first: Avril

last: Reddy

first: Jeff

last: Henderson

first: Gergő

last: Porkoláb

first: Adam

last: McGlinchey

first: Nicole

last: Hanley

first: Siobhan

last: Hutchinson

first: James

middle: F

last: Meaney

first: Michael

last: Farrell

first: Sarah

middle: L

last: Doyle

first: Alon

last: Friedman

first: Colin

middle: P

last: Doherty

first: Matthew

last: Campbell


title: Interspecies Organoids Reveal Human-Specific Molecular Features of Dopaminergic Neuron Development and Vulnerability

status: Public on Mar 02 2026

city: San Francisco

first: Alex

last: Pollen

address: 651 4th Street

country: USA

institute: UCSF

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The disproportionate expansion of telencephalic structures during human evolution involved tradeoffs that imposed greater connectivity and metabolic demands on midbrain dopaminergic neurons. Despite the central role of dopaminergic neurons in human-enriched disorders, molecular specializations associated with human-specific features and vulnerabilities of the dopaminergic system remain unexplored. Here, we establish a phylogeny-in-a-dish approach to examine gene regulatory evolution by differentiating pools of human, chimpanzee, orangutan, and macaque pluripotent stem cells into ventral midbrain organoids capable of forming long-range projections, spontaneous activity, and dopamine release. We identify human-specific gene expression changes related to axonal transport of mitochondria and reactive oxygen species buffering and candidate cis- and trans-regulatory mechanisms underlying gene expression divergence. Our findings are consistent with a model of evolved neuroprotection in response to tradeoffs related to brain expansion and could contribute to the discovery of therapeutic targets and strategies for treating disorders involving the dopaminergic system.

sample_organism:
Macaca mulatta
Pan troglodytes
Pongo abelii
Homo sapiens

overall_design: Pluripotent stem cells from human, chimpanzee, macaque and orangutan were pooled and differentiated into ventral midbrain progenitors for 16 days. For neuronal maturation, D16 progenitors were assembled to organoids and maintained in culture until D40, 80 or 100. For organoids at D80, a subset of the interspecies-organoids were subjected to 500nM rotenone for 24 or 72 hours, while a control subset was cultured in parallell without rotenone. Samples from all timepoints and conditions were used for combined single nucleus (sn)RNA sequencing and ATAC sequencing (using the 10x Single Cell Multiome ATAC + Gene Expression kit). In the first two sequencing rounds, nuclei were labeled with MULTIseq barcodes to enable pooling of samples.

first: Sara

last: Nolbrant

first: Jenelle

last: Wallace

first: Nathan

middle: K

last: Schaefer

first: Ding

last: Jingwen


title: IL-17–Driven Tumor Cell–Intrinsic Inflammatory Programming Creates an Immunotherapy-Permissive Microenvironment in Ovarian Clear Cell Carcinoma [scRNA-Seq]

city: Sakai

first: Kosuke

last: Murakami

state: Osaka

address: 1-14-1, Miharadai, Minami-ku

country: Japan

institute: Kindai University

summary: Ovarian clear cell carcinoma (OCCC) is a chemoresistant subtype of ovarian cancer with limited effective therapeutic options. Although immune checkpoint inhibitors (ICIs) have shown little benefit in unselected ovarian cancer populations, clinical activity observed in a subset of OCCC patients suggests the presence of a histotype-specific immune vulnerability that remains poorly defined. To elucidate this biology, we integrated transcriptomic analyses from multiple independent human OCCC cohorts with immunohistochemical profiling and mechanistic studies using an immunocompetent syngeneic OCCC mouse model. Tumor cell–intrinsic and microenvironmental responses to IL-17 were investigated through in vitro stimulation assays, in vivo IL-17 administration, single-cell RNA sequencing of tumor-infiltrating T cells, and immune checkpoint blockade in a Th17-biased partial chimera model. OCCC was characterized as an IL-6–high tumor entity with a globally immune-sparse but CD4⁺ T-cell–skewed tumor immune microenvironment. Transcriptomic analyses identified a Th17-associated program marked by elevated RORC expression in a subset of tumors. Across large clinical cohorts, an IL17A^high subset demonstrated a T cell–inflamed gene expression profile independent of microsatellite instability and tumor mutational burden; however, this phenotype was not associated with survival in untreated disease. Mechanistically, IL-17 directly activated NF-κB–dependent inflammatory programs in OCCC tumor cells, inducing cytokines involved in T-cell recruitment and activation. In vivo, IL-17 remodeled the immune microenvironment, increasing infiltration and activation of both CD4⁺ and CD8⁺ T cells. Single-cell profiling further revealed expansion of Th17/Tfh-like CD4⁺ T cells and cytotoxic, non-terminally exhausted CD8⁺ T cells. Consistent with these findings, anti–PD-L1 therapy significantly improved survival exclusively in Th17-biased partial chimera mice. Collectively, these results demonstrate that a Th17-biased, IL-17–responsive immune contexture in OCCC engages tumor cell–intrinsic NF-κB inflammatory signaling to prime antitumor T-cell states and enable checkpoint blockade efficacy. This immune biology is predictive rather than prognostic, supporting a biomarker-driven immunotherapy strategy for OCCC within otherwise ICI-refractory ovarian cancer.

overall_design: Tumor tissues were collected from syngeneic murine ovarian clear cell carcinoma models established in immunocompetent mice. In selected experiments, tumors were generated under IL-17 or control conditions. Single-cell suspensions were prepared from excised tumors and processed for single-cell RNA sequencing using the BD platform. The study aimed to determine how an IL-17–enriched tumor microenvironment shapes immune cell infiltration, activation states, and immune checkpoint expression. Comparative analyses were performed between IL-17–exposed and control tumors.

first: Shiki

last: Takamura

first: Chiho

last: Miyagawa

first: Kazuhiro

last: Kakimi

first: Noriomi

last: Matsumura


title: Metformin-induced longevity is associated with retrotransposon dynamics in yeast chronological aging

city: Irapuato

first: Jimena

middle: Meneses

last: Plascencia

state: Guanajuato

address: Libramiento Norte Km 9.6, 36821 Irapuato, Gto.

department: UGA-LANGEBIO

country: Mexico

institute: CINVESTAV

summary: The widely used antidiabetic drug metformin extends lifespan across diverse model organisms,  from yeast to primates. However, the cellular mechanisms underlying its anti-aging effects remain only partially understood. Here, we combined large-scale genetic screening and high-resolution  lifespan phenotyping with transcriptomic and proteomic analyses to provide a systems view of  metformin’s impact on the chronological lifespan of Saccharomyces cerevisiae. Unexpectedly, we  uncovered pronounced gene-drug interactions between metformin and chromatin-modifying factors. Specifically, deletions of Set3C histone deacetylation complex subunits phenocopied the longevity effect of metformin, with no additive benefit when combined, suggesting convergence 10 on shared pathways. Transcriptome profiling further revealed that metformin reprogrammed stationary-phase gene expression, with Ty1-copia retrotransposons emerging as a consistently induced signature, thereby suggesting a possible mechanism for the observed interactions with Set3C regulation.

overall_design: We performed RNAseq analysis comparing populations of WT cells in mid exponential and late stationary phase with or without metformin.

first: Meneses-Plascencia

last: Jimena

first: Moreno-Méndez

last: Ericka

first: DeLuna

last: Alexander


title: Reprogramming the Tumor Microenvironment with a Membrane-Proximal AXL Antibody to Overcome Immune Checkpoint Blockade Resistance [scRNA-seq]

city: Beijing

first: Zuming

last: Yang

address: No. 30 Shuangqing Road Haidian District

country: China

institute: Tsinghua University

summary: Immune-cold tumors failed to respond to immunotherapy due to insufficient lymphocytes infiltration within tumor tissue. How to increase the objective response rate is an urgent challenge. Here, we report the development of a monoclonal antibody (6C5) that specifically targets the membrane-proximal epitope of receptor tyrosine kinase AXL, which modulates the anti-tumor immunity. Unlike traditional membrane-distal AXL antibodies, 6C5 significantly enhanced innate immune sensing by promoting macrophage-mediated antigen uptake and type I interferon production via the MyD88 pathway. This reshaped the tumor microenvironment , further boosting CD8+ T cell infiltration and effector function. However, AXL antibody treatment concurrently induced a suppressive subset of PD-1hiFoxp3-CD4+ T cell, attenuating antitumor responses. The combination of AXL Ab with dual immune checkpoint blockade (anti-PD-1 plus anti-CTLA-4) or PD-1-targeted IL-2 fusion protein therapy mitigated this immunosuppression, achieving potent tumor regression and durable immune memory. Our findings demonstrate that membrane-proximal AXL targeting antibody effectively converts immune-cold tumor microenvironment, overcoming resistance to both conventional and next-generation immune checkpoint inhibitors.

overall_design: Mice were inoculated with B16-hAXL cells and treated with either PBS or 200 µg of 6C5 Ab by intraperitoneal injection . Tumor tissues were collected and digested , CD45+ cells were sorted by flow cytometer and analyzed using scRNA-seq.


title: Effect of miR-15b and miR-16-2 overexpression on gene expression profiles in the human T-cell acute lymphoblastic leukemia (T-ALL) cell line CUTLL1.

city: Madrid

first: María

last: Toribio

state: Madrid

address: Calle Nicolás Cabrera, 1. Campus Cantoblanco

department: Interactions with the environment

country: Spain

institute: Centro de Biología Molecular Severo Ochoa (CSIC-UAM)

summary: T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy arising from the neoplastic transformation of immature T cells during their development in the thymus. Deciphering the developmental programs whose dysregulation leads to T-ALL pathogenesis is critical for the development of novel targeted therapies, which remain an urgent unmet need for the treatment of this disease. MicroRNAs (miRNAs) have emerged as key post-transcriptional regulators of numerous physiological processes and cancer. However, the specific role of miRNAs in human T- cell development and T-ALL pathogenesis remains largely unexplored. In this study, we comprehensively evaluated miRNA expression profiles across human T-cell development by microarray analysis and identified a dynamic expression pattern of miR-16-2, which is upregulated across early pre-T cell proliferative stages up to the resting stage of immature thymocytes immediately preceding TCRab expression, and decreased thereafter. We confirmed the coordinated regulation of miR-15b expression, consistent with the reported clustered genomic location of both miRNAs. Notably, functional studies identified the miR-15b/16-2 cluster as a negative regulator of early thymocyte proliferation, and showed that overexpression of miR-15b/16-2 in T-ALL cells impaired leukemic growth in vitro and tumor progression in patient-derived xenotransplantation assays. Mechanistically, miR-15b/16-2 expression represses the genes encoding BCL-2 and CYCLIN D3, leading to T-ALL apoptosis and cell cycle dysregulation, with an accumulation of G0-phase cells and a defective transition to the G2/M phase. Moreover, RNA-seq analysis revealed that miR-15b/16-2 expression in the human T-ALL cell line CUTLL1 represses cell cycle-associated pathways (i.e. G1-to-S transition, G2-to-M transition), upregulates apoptotic and programmed cell death pathways, and modulates genes associated to DNA replication and DNA damage repair. Overall, these findings support a novel function for miR-15b/16-2 as tumor suppressors in T-ALL, highlighting their role as promising targets for T-ALL therapy.

overall_design: RNA-seq profiling of human T-ALL cell line CUTLL1 transduced with lentiviral vectors encoding either GFP alone (mock control vector, GFP) or the miR-15b/16-2 genomic cluster together with GFP (MIRS). GFP-positive transduced cells were enriched by flow cytometry sorting 4 days after transduction. The experiment was performed in triplicate.

first: S

last: González-García


title: SiYSL1 may Paticipate in Iron Absorption, Transportation, and Grain Accumulation in Foxtail Millet

city: Wuhan

first: Shuo

last: Zhang

address: No. 3, Nanhu Avenue

institute: Food Crops Institute, Hubei Academy of Agricultural Sciences

summary: Iron  (Fe) deficiency is a globally widespread condition in which the body lacks sufficient Fe to produce hemoglobin. However, major food crops generally have low grain Fe contents. Consequently, enhancing grain Fe concentrations is important for improving the health of populations that rely on grains as staple foods. Here, we isolated a yellow stripe leaf mutant of foxtail millet (Setaria italica), designated yellow stripe-like 1 (ysl1). This mutant exhibited typical Fe deficiency symptoms that were alleviated when grown under Fe-sufficient conditions. Compared with the wild-type, Siysl1 showed lower Fe concentrations in seedling roots, shoots, stems, elongation-stage leaves, panicles, and seeds, but a higher Fe concentration in heading-stage leaves. Using MutMap+, we identified and cloned SiYSL1 and validated its function through CRISPR/Cas9-mediated knockout experiments. SiYSL1 encodes an Fe-phytosiderophore transporter and is highly induced under Fe deficiency conditions. Histochemical staining revealed that SiYSL1 is specifically expressed in vascular bundles of roots and leaves of plants grown under Fe deficiency conditions, and in spikelets, expanding ovaries, basal endosperm, and embryo-surrounding tissues. Thus, SiYSL1 appears to regulate Fe uptake and homeostasis, and plays an essential role in Fe translocation to seeds. The overexpression of SiYSL1 in rice and foxtail millet significantly increased seed Fe contents, suggesting its value in crop breeding. Predicted transcription factor binding sites in the SiYSL1 promoter and a spikelet transcriptome analysis indicated that transcription factors regulate SiYSL1 expression. Our study provides new genetic resources for the Fe bio-enhancement of food crops and insights into the mechanisms responsible for seed Fe accumulation.

overall_design: The spikelets of Yugu1 and Siysl1 were harvested on the 3rd day after flowering for the RNA-seq analysis. For each sample, spikelets from three individuals were collected as three biological replicates.

first: Hui

last: Zhi

first: Sha

last: Tang

first: Guanqing

last: Jia

first: Chanjuan

first: Hailong

last: Wang

first: Mingzhao

last: Luo

first: Chunhai

last: Jiao

first: Haiya

last: Cai

first: Yanhao

last: Xu

first: Xianmin

last: Diao


title: FGF12-overexpression HEL cell line

city: Wenzhou

first: Xiulan

last: Lou

address: Chashan

institute: Wenzhou Medical University

summary: Fibroblast Growth Factor 12 (FGF12), a non-secretory member of the FGF homologous factor family, plays a pivotal role in modulating intracellular signaling and cellular homeostasis. In this study, we successfully established stable FGF12-overexpression cell lines using HEL cell line via lentiviral transduction. To rigorously evaluate the phenotypic and molecular shifts, an empty vector Negative Control (NC) group was simultaneously generated. By integrating high-throughput transcriptomic analysis and biochemical assays, we aimed to explore the molecular landscape altered by FGF12 upregulation. Our preliminary findings indicate significant perturbations in p53 signaling ,providing new insights into the regulatory network of FGF12 and its potential as a therapeutic target in AML.

overall_design: Establishment of FGF12-overexpression cell lines and NC to explore the molecular landscape


title: scATAC sequencing data of subdural, dural CAMs and MG 8 weeks after repopulation

city: Freiburg

first: Maximilian

last: Fliegauf

address: Breisacherstraße 113

department: Institute for Neuropathology

country: Germany

institute: Uniklinikum Freiburg

summary: Perivascular and leptomeningeal macrophages are non-parenchymal macrophages summarized as central nervous system (CNS)-associated macrophages (CAMs) that mediate immune responses at brain boundaries. Both, CAMs and juxtaneuronal microglia are derived from prenatal yolk sac (YS) precursors, long-living and maintain their populations by homeostatic self-renewal without input from the periphery. Whereas microglia have been shown to be repopulated by CNS endogenous remnants of the same lineage following depletion, the renewal biology of CAMs is still poorly understood. Here, by combining multilineage myeloid fate mapping, bulk and single-cell profiling and high resolution confocal imaging, we show that the repopulation is strikingly different between CAMs and microglia. In contrast to microglia, CAMs do not renew exclusively cell-autonomously, but transiently utilize CCR2+Ly-6C+ monocytes after niche induction in an integrin-dependent manner. Remarkably and unlike repopulated microglia, replenished monocyte-derived CAMs remain transcriptionally and functionally distinct from their YS-derived counterparts. Finally, we established a protocol that allows to selectively exchange CAMs modulating disease response without functionally affecting parenchymal microglia. These new insights into the biology of the CNS immune system offer completely new therapeutic avenues for diverse neuroinflammatory and neurodegenerative diseases.

overall_design: Two male and two/one female Mrc1CreERT2 R26tdT mice per group were treated with CTL or BLZ945 for seven consecutive days. Eight weeks after the treatment, CD45int-hi CD11b+ and CD206+/- cells were isolated from the brains of these mice, CD11b+CD206+CD64+ cells were isolated from dura mater and Ly6ChiCD115+ monocytes were isolated from blood. Dural and Brain macrophages were additionally split into tdT+ and tdT- gates and sorted. Cells from the same treatment group and of the same cell type were pooled (4 samples for BLZ945 and 3 samples for CTL) and additonally, microglia and monocytes from same condition were pooled and used for the generation of in total 8 single-cell ATAC-sequencing libraries.

first: Lukas

last: Amann

first: Francesco

last: Cardamone

first: Mohit

last: Navander

first: Nicola

last: Iovino

first: Marco

last: Prinz


title: A CRISPR screen in human iPSC-derived neurons reveals convergent transcriptomic effects of neurodevelopmental disorder genes

city: Las Vegas

first: Huanyao

last: Gao

state: Nevada

address: 11845 Ampucia Ct

department: Department of Psychiatry

institute: Yale University

summary: Diverse risk genes have been identified for neurodevelopmental disorders (NDDs), but how these genes converge on similar biological pathways in neurons, and thus give rise to similar phenotypes, is unclear. Here, we apply a pooled CRISPR approach to target 23 (out of 29) NDD loss-of-function genes and examine convergent effects on gene expression across human induced pluripotent stem cell (hiPSC)-derived neural progenitor cells, glutamatergic neurons, and GABAergic neurons. Points of convergence vary between these cell-types and are greatest in mature glutamatergic neurons, where they broadly regulate synaptic, epigenetic, and, unexpectedly, mitochondrial pathways. The strongest convergent networks were observed between NDD genes with shared biological annotations, clinical associations, and co-expression patterns in human post-mortem brain.  Drugs that were predicted to reverse convergent transcriptomic signatures and/or arousal and sensory processing behaviors ameliorated behavioral phenotypes in NDD model zebrafish. These results suggest that convergent effects of NDD risk genes could provide clinically useful insights. Code and secondary analysis data can be found on Synapse ( ID=syn72039767, link=https://www.synapse.org/Synapse:syn72039767/wiki/636167)

overall_design: Transient transcription factor overexpression from stable clonal hiPSCs was used to induce control hiPSCs to iNPCs (here SNaPs), Lentiviral Cas9v2-HygroR and pooled LentiArray-gRNA-PuroR CRISPR-KO library including 29 genes (ARID1B, ASH1L, CHD2, MED13L, NRXN1, PHF21A, SETD5, SIN3A, SMARCC2, BCL11A, CHD8, KDM5B, KDM6B, KMT2C, MBD5, PHF12, SKI, WAC, CREBBP, ASXL3, ANK3, POGZ, SCN2A, SHANK3, SLC6A1, PPP2R5D, FOXP2, DPYSL2) as well as scrambled gRNA were packaged as high-titer lentiviruses were transduced via spinfection three days prior to harvest (e.g., d4 for D7 iGLUTs, d18 for D21 iGLUTs, d33 for d36 iGABA) (MOI 0.3-0.5). The entire cell were then submitted for single cell RNAseq (10X single cell 5' v2 HT with CRISPR barcode kit) in four lanes per cell type, targeting 20,000 cells per lane for a total of ~80,000 targeted cells per cell type, at Yale Genomics Core.

first: Meilin

last: Garcia

first: Kayla

last: Retallick-Townsley

first: April

last: Pruitt

first: Elizabeth

last: Davidson

first: Novin

last: Balafkan

first: Jonathan

last: Warrell

first: Tzu-Chieh

last: Huang

first: Alfred

last: Kibowen

first: Zhiyuan

last: Chu

first: Yi

last: Dai

first: Sarah

middle: E

last: Fitzpatrick

first: Ran

last: Meng

first: Annabel

last: Sen

first: Sophie

last: Cohen

first: Olivia

last: Livoti

first: Suha

last: Khan

first: Charlotte

last: Becker

first: Andre

last: Silva

first: Jenny

last: Liu

first: Grace

last: Dossou

first: Jen

last: Cheung

first: Susanna

first: Sadaf

last: Ghorbani

first: Peter

last: Deans

first: Marisa

last: DeCiucis

first: Prashant

last: Emani

first: Hongying

last: Shen

first: Mark

last: Gerstein

first: Zuoheng

first: Laura

last: Huckins

first: Ellen

middle: J

last: Hoffman

first: Kristen

last: Brennand


title: RNA sequencing data of dural CAMs 8 weeks after repopulation stimulated with LPS

first: Maximilian

last: Fliegauf

overall_design: tdTpos and tdTneg dural CNS-associated macrophages (CAMs) were isolated from 5 individual Ccr2CreERT2 R26tdT mice per treatment group (LPS vs CTL) and used for the generation of bulk transcriptomics data. RNA expression levels between the different groups were compared.

first: Lukas

last: Amann

first: Marco

last: Prinz


title: scRNA sequencing data of cells from leptomeninges, cortex and dura mater from CTL, 5d and 8 weeks after macrophage deletion

overall_design: WT mice were treated with BLZ945 or Vehicle (CTL) and cells were isolated from cerebral cortex, dura mater and leptomeninges 8 weeks, 5 days post 7 days BLZ945-mediated macrophage depletion or CTL. After isolating whole brain and removing choroid plexuses under a stereomicroscope in ice cold PBS, cortex and leptomeningeal and dural immune and niche cells were sorted by gating DAPI- cells and then for CD11b+CD45+ (immune), CD31+ (endothelial), PDPN+ (fibroblasts) and marker negative (other cell types) cells as described in the flow cytometry section and as seen in the gating strategies (Supplementary Fig. 1).

first: Jovana

last: Cupovic

first: Roman

last: Sankowski


title: Activity-dependent ribosome profiling reveals the landscape of canonical and non-canonical translation in brain tissue

city: Wako

first: Nayan

last: Suryawanshi

state: Saitama

address: Hirosawa 2-1

department: Center for Brain Science

institute: RIKEN

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

overall_design: Refer to individual Series


title: Bone marrow RNA sequencing profiles from AML patients and healthy donors

first: Xiulan

last: Lou

summary: Acute Myeloid Leukemia (AML) is a complex hematological malignancy characterized by the clonal expansion of undifferentiated myeloid precursors. Despite advances in treatment, intra-tumoral heterogeneity and the remodeling of the bone marrow (BM) microenvironment remain significant hurdles to durable remission. This study aims to characterize the distinct cellular landscapes of AML compared to healthy hematopoiesis to identify key drivers of leukemogenesis and immune evasion.

overall_design: RNA sequencing data were generated from bone marrow samples of acute myeloid leukemia (AML) patients and healthy donors to characterize cellular heterogeneity in AML.


title: Transcriptional programs associated with migratory capacity and 5-ALA–induced PpIX fluorescence in glioblastoma

city: Bunkyo-ku

first: Kouichi

last: Tabu

state: Tokyo

address: 1-5-45, Yushima

institute: Institute of Science Tokyo

summary:
Glioblastoma (GBM) cells were fractionated by a two-dimensional Transwell migration assay (no extracellular matrix coating) into migratory and non-migratory populations, followed by subdivision based on 5-aminolevulinic acid (5-ALA)–induced protoporphyrin IX (PpIX) fluorescence (high vs low).
Gene expression profiling was performed using Agilent one-color microarrays. One biological sample per condition was analyzed (no biological replicates).

overall_design: A patient-derived GBM line was subjected to chemotactic migration-based fractionation using a non-coated Transwell assay to separate migratory and non-migratory fractions. Each fraction was further separated into PpIX-high and PpIX-low populations after 5-ALA exposure, yielding four conditions (Non-migratory/PpIX-low, Non-migratory/PpIX-high, Migratory/PpIX-low, Migratory/PpIX-high). Total RNA from each condition was analyzed on an Agilent one-color microarray platform (Agilent-072363). Processed data represent normalized signal intensities used for downstream transcriptomic analyses.


title: RNA sequencing data of fate-mapped leptomeningeal/perivascular CAMs 8 weeks after repopulation and 1 day after MCAo

overall_design: tdTpos and tdTneg subdural CNS-associated macrophages (sdCAMs) were isolated from Ccr2CreERT2 R26tdT from MCAo model mice 1 day after stroke induction and used for the generation of bulk transcriptomics data. RNA expression levels between the different groups were compared.


title: Activity-dependent ribosome profiling reveals the landscape of canonical and non-canonical translation in brain tissue [Ribo-Seq]

summary: Neural activity-dependent translation is essential for synaptic plasticity and diverse brain functions. Translation involves not only canonical main open reading frames (mORFs) but also upstream ORFs (uORFs), which may regulate mORF expression. However, due to technical limitations, systematic in-vestigation of activity-dependent uORFs and mORFs in brain tissues remains challenging. Here, we developed a ribosome tagging and purification strategy that bypasses the prolonged turnover of ribo-somal proteins, enabling ribosome profiling with one-hour temporal resolution after neural stimulation. Applying this strategy to mouse hippocampal slices undergoing long-term potentiation, we identified hundreds of activity-induced mORFs and uORFs, a subset of which served as robust markers for ac-tivity status. Notably, ~22% of the upregulated uORFs overlapped with those induced by the integrated stress response, suggesting potential crosstalk between these signaling pathways. This study provides a useful technique and resources for deciphering molecular mechanisms underlying activity- and trans-lation-dependent brain functions in health and disease.

overall_design: Ribo-seq, Postnatal day 5 mice Organotypic hippocampus slice culture

first: Yi-Kai

last: Chen


title: A Phase II Trial of Pembrolizumab plus Granulocyte Macrophage Colony Stimulating Factor in Advanced Biliary Cancer [Spatial Transcriptomics]

first: Bridget

last: Keenan

state: CA

address: 505 PARNASSUS AVE

institute: University of California San Francisco

summary: Immune checkpoint inhibitors have limited activity as monotherapy in biliary cancers. Granulocyte-macrophage colony-stimulating factor (GM-CSF) is a pleiotropic immune cell growth factor which resulted in prolonged survival when combined with ipilimumab in melanoma. We conducted a single-center, phase II trial to evaluate the efficacy and safety of combining GM-CSF with pembrolizumab in patients with advanced biliary cancers after prior standard chemotherapy but no prior immune checkpoint inhibitor. Pembrolizumab 200 mg was administered intravenously in 21-day cycles, along with two cycles of GM-CSF 250 µg subcutaneously days 1 through 14. The primary endpoint was objective response rate. Among 42 patients enrolled, the median age was 61 years, 67% had intrahepatic cholangiocarcinoma, 90% had stage IV disease, and 24% had underlying viral hepatitis. The confirmed objective response rate was 12% (95% confidence interval: 4, 26), including two patients with complete response, and 26% of patients had progression-free survival ongoing at 6 months. Treatment was well-tolerated with treatment-related grade 3-4 events in 7% and treatment-related serious adverse events in 10%. Tumor PD-L1 expression was present in 46% and was associated with a higher rate of 6-month progression-free survival. Paired tumor biopsies showed upregulation of CD8+ T cell populations and antigen processing pathways after the addition of GM-CSF. In conclusion, the addition of GM-CSF to pembrolizumab was well-tolerated but did not meet the pre-specified response rate for efficacy.  A subset of patients experienced deep responses and prolonged stable disease. GM-CSF elicited changes in the tumor immune microenvironment that could guide future combination approaches.

overall_design: FFPE tissues from patients with biliary tract cancer, collected pre-GM-CSF and post-pembrolizumab ("pre" biopsy) and post-combined GM-CSF and pembrolizumab ("post" biopsy).

first: Robin

last: Kelley

first: Paige

last: Bracci

first: John

last: Gordan

first: Spencer

middle: C

last: Behr

first: Zoe

last: Quandt

first: Chloe

last: Atreya

first: Wesley

last: Kidder

first: Andrew

middle: H

last: Ko

first: Huat

last: Lim

first: Katherine

last: Van Loon

first: Nia

last: Adeniji

first: Alan

last: Venook

first: Lawrence

last: Fong


title: Aortic Stenosis is associated with reduced serotonin transporter expression and mitigated by pharmacological inhibition of serotonin receptor 2B

city: Philadelphia

first: Ting

last: Peng

state: PA

address: CTRB 6200

department: Pathology and Laboratory Medicine

institute: Children's hospital of Philadelphia

summary:
Background: Aortic Stenosis (AS) is a highly prevalent disease involving physiological and structural remodeling of aortic valve, yet lacks effective medical therapy to halt its progression. Serotonin (5HT) signaling has been implicated in valvular disease. We hypothesized that AS is associated with impaired 5HT clearance due to reduced serotonin receptor (SERT) expression and increased 5HT receptor (HTR) activity.
Methods: Sixty-six patients with severe AS undergoing aortic valve (AV) replacement were enrolled in the study, and samples from their explanted AV were harvested. Anatomically normal control AVs were obtained from transplant donors. Explanted AVs were collected for gene expression analysis and 5-HTTLPR genotyping. Gene expression was assessed by RT2-profiler gene array. In vivo, 8-week-old mice received 28-day Angiotensin-II (AngII) infusions ± HTR2B antagonist (LY272015) through subcutaneous Alzet osmotic-pump implants. AV structure and function were assessed via echocardiography, histology, and RNA sequencing. Human aortic valve interstitial cells (AVICs) were treated with either H2O2 or AngII ± SERT siRNAs to assess 5HT signaling and fibrotic/osteogenic markers.
Results: AS patients exhibited reduced SERT and increased HTR expression. Oxidative stress in cultured human AVICs suppressed SERT and induced HTR2B expression. AngII ± SERT siRNA promoted VIC osteogenic marker expression. In mice, AngII caused AV thickening, increased velocities and gradients, and activation of fibrosis and calcification-related gene sets, including serotonin, TGFβ, Wnt/β-catenin, PI3K/Akt, and Notch pathways. Pharmacological inhibition of HTR2B preserved AV structure, normalized transvalvular velocities and pressure gradients, and reversed AngII-induced transcriptional changes.
Conclusions: In human and mouse AVs, reduced SERT and elevated HTR2B signaling contribute to early-onset fibro-calcific remodeling. HTR2B inhibition by LY272015 reverses these effects, suggesting it as a potential therapeutic strategy for AS.

overall_design: 8-week-old wild type male mice, Jackson Lab, (C57BL/6J) were fed a hypercholesterolemic diet (Breslow Western Diet, Fisher and Son Inc. Cat#: TD1810724) and infused with AngII (1000 ng/kg/min) using osmotic pumps (Alzet 2004) for 28 days, as previously described. Osmotic pumps were implanted subcutaneously on the back, posterior to scapulae, through a small skin incision. LY272015 treatment (3 mg/kg in sterile PBS) was given twice/week over the 28-day AngII infusion by intraperitoneal injection, as previously described. After 28 days, mice in the AngII and AngII + LY groups had their pumps removed and survived for an additional 48 hours. They were then anesthetized with isoflurane, followed by heart perfusion with PBS and sample collection. Hearts were collected and aortic valves were extracted under dissection microscope. RNA was extracted and purified for bulk RNAseq experiment. Group sizes were 4 mice per group (Control, LY272015, AngII, and AngII+LY).

first: Dov

last: Levine

first: Chiara

last: Camillo

first: Estibaliz

last: Castillero

first: Emre

last: Bektik

first: Yaagnik

last: Kosuri

first: Anthony

last: Campbell

first: Cary

last: Karcher

first: Abba

last: Krieger

first: Liming

last: Pei

first: Nicole

last: Zeak

first: Erfan

last: Faridmoayer

first: Mark

last: Oyama

first: Juan

last: Grau

first: Robert

last: Levy

first: Giovanni

last: Ferrari


title: A Phase II Trial of Pembrolizumab plus Granulocyte Macrophage Colony Stimulating Factor in Advanced Biliary Cancer [CITE-Seq]

first: Bridget

last: Keenan

overall_design: Peripheral blood mononuclear cells (PBMC) were obtained from patients with biliary tract cancer as part of a Phase II trial of pembrolizumab and GM-CSF. Blood samples were processed using ficoll; after centrifugation, the PBMC layer was isolated and cryopreserved in cell media with human serum and DMSO. Previously frozen PBMCs were thawed using media containing RPMI, heat-inactivated sterile filtered human serum, penicillin-streptomycin, non-essential amino acids, sodium pyruvate, and L-glutamine. Samples were then incubated for DNAse I before washing and counting. 1 x10>6 cells from 16 unique samples were combined and stained with one pooled cocktail containing 99 AbSeq antibody-oligonucleotide conjugates (BD Biosciences) per standard protocols (Olvera JG et al., 2018), following pre-incubation with TruStain FcX (Fc Receptor Blocking Solution). Samples from different individuals and timepoints were randomly mixed across experiments to minimize batch and confounding effects. Droplet-based single cell RNA sequencing (scRNAseq) was performed using the 10x Genomics Chromium Single Cell 3ʹ Reagent Kits v3, according to manufacturer instructions.

first: Robin

last: Kelley

first: Paige

last: Bracci

first: John

last: Gordan

first: Spencer

last: Behr

first: Zoe

last: Quandt

first: Chloe

last: Atreya

first: Wesley

last: Kidder

first: Andrew

last: Ko

first: Huat

last: Lim

first: Katherine

last: Van Loon

first: Nia

last: Adeniji

first: Alan

last: Venook

first: Lawrence

last: Fong


title: circASCOR enhances platinum resistance  in ovarian cancer

city: Hefei

first: Hanyuan

last: Liu

address: 443 Huangshan Road Hefei, Anhui Province

institute: University of Science and Technology of China

summary: We have employed a snRNA-seq to study circRNA ASCOR in ovarian cancer cisplatin resistance.

overall_design: The expression level of circASCOR was detected by RT-qPCR, and samples were divided into high-expression and low-expression groups according to the expression level and analyzed using snRNA-seq.

first: Ying

last: Zhou


title: Single cell LARRY state-fate analysis of Npm1cA/Flt3-ITD acute myeloid leukemia stem cells

city: Barcelona

first: Alejo

last: Rodriguez-Fraticelli

state: Barcelona

address: Carrer Baldiri Reixac 10

department: Aging and Metabolism

institute: IRB Barcelona and ICREA

summary: AML leukemia stem cells are principal drivers of leukemia disease. Leveraging novel leukemia stem cell cultures (PLSTCs) we performed state-fate analysis to understand the trajectories of distinct AML LSC clones in vivo and ex vivo using a LARRY expressed barcoding strategy. The results indicate that self-renewing LSCs show clonally-heritable programs that predict in vivo engraftment, fitness and therapy response. Targeting those programs using a CROPseq perturbation and single-cell sequencing approach, we identify a novel mechanism regulating the LSC state.

overall_design: We first developed PLSTC cultures of AML cells and compared them with standard Stemspan based cultures (experiment 1). Then, we performed multi-indexed LARRY-EGFP(v3) barcoding of inducible Npm1cA/Flt3-ITD hematopoietic stem cells (multiple donors), followed by oncogene activation by Flpo recombinase (experiments 2-5). These origin-barcoded cells were subsequently barcoded using an additional LARRY-Tsapphire barcoding lenti library at day 20. AML cells were processed at day 20 ex vivo (PLSTC cultures, experiment 2), at day 40 in vivo (d20 split-transplant, experiment 3), at day 40 ex vivo (PLSTC cultures, experiment 4), and at day 70 in vivo with and without standard induction chemotherapy (experiment 5). In all these experiments, cells from multiple wells/recipients/donors are multiplexed using TotalSeq cell-hashing (leveraging feature barcoding). In a final experiment, we performed targeted CROPseq to test potential regulators of LSC state-fates (experiment 6).

first: Indranil

last: Singh

first: Andrea

last: Polazzi

first: Celine

last: Bauer

first: Alex

last: Maya Pombo

first: Pedro

last: Sánchez Sánchez

first: Daniel

last: Fernández Perez


title: Effect of cisplatin and neomycin damage on the HEI-OC1 cell line

city: nanjing

first: Wenli

last: Hao

address: No. 22 Hankou Road, Gulou District, Nanjing City, Jiangsu Province

institute: Nanjing University

summary: In order to explore the effects of ototoxic drugs on the HEI-OC1 type of hair cell-like cells in vitro, we here examined the changes in gene regulation expression caused by the damage of cisplatin and neomycin on HEI-OC1.

overall_design: RNA sequencing analysis was conducted on HEI-OC1 cells after they were treated with PBS, cisplatin, and neomycin for 24 hours respectively.


title: Ep300 Cuttag for WT and DKO  (Rara and Rxra deletion) of mESC RA-induced differentiation

city: Tianjin

first: Bohan

last: Chen

address: NO.94 Weijin Road

institute: Nankai University

summary: To investigate the effect of Ep300 binding in Rara and Rxra deletion for mESC differetiation and development

overall_design: WT and DKO cells was performed for RA-induced differentiation

first: Bohan Chen

last: Wange Lu


title: Activity-dependent ribosome profiling reveals the landscape of canonical and non-canonical translation in brain tissue [RIP-Seq]

first: Nayan

last: Suryawanshi

overall_design: RNA-seq, P5 mice Organotypic hippocampus slice culture, EGFP-L10a, Ha-GFPnanobody-HALO-PEST

first: Yi-Kai


title: Cryo-thermal therapy reprograms myeloid cells into CCL5+ mature phenotype to increase T cell infiltration and potentiates anti-PD-1 therapy

city: Shanghai

first: Yuankai

address: No. 1954, Huashan Road

institute: Shanghai Jiao Tong University

summary: Although immune checkpoint blockade (ICB) represented by anti-PD-1 therapy has demonstrated significant clinical benefits, its efficacy remains limited by the immunosuppressive tumour microenvironment (TME). Cryo-thermal therapy (CTT) not only completely ablates local solid tumours by pre-freezing before radiofrequency heating, but also reverses immunosuppression and triggers strong systemic anti-tumour immunity to inhibit tumour recurrence and metastasis. Our present study reveals that combining CTT with anti-PD-1 treatment potently enhances myeloid cell maturation and simultaneously promotes the infiltration and functional activation of T cells in distal tumours, resulting in superior suppression of distal tumour growth compared to either cryoablation or radiofrequency ablation combined with anti-PD-1. Mechanistically, CTT specifically induces TNF-α production in mature myeloid cells, triggering autocrine CCL5 secretion that recruits peripheral IFN-γ+ T cells induced by CTT in distal tumours, creating a cytokine loop where IFN-γ derived from T cells and TNF-α derived from myeloid cells collectively promote CCL5 secretion in myeloid cells to enhance effector T cell recruitment in distal tumours. Subsequently, after CTT, anti-PD-1 treatment amplifies this cascade by enhancing TNF-α production in T cells, and high levels of IFN-γ and TNF-α in distal tumours promotes higher secretion of CCL5 in myeloid cells, resulting in robust infiltration of T cells. The parallel activation of STAT1 by IFN-γ and NF-κB by TNF-α in myeloid cells converges to drive IRF7-dependent CCL5 upregulation to create a local immune enhancing environment via CCL5-mediated recruitment of T cells. Our study demonstrates that CTT establishes an immunologically favorable TME by reprogramming immunosuppressive myeloid cells into mature myeloid cells with high CCL5 production, thereby facilitating effector T cell recruitment, providing an efficient therapeutic strategy to promote the response to anti-PD-1 therapy.

overall_design: RNA-seq profiling of untreated side tumours from mice after cryoablation, combined cryoablation and anti-PD-1 therapy, radiofrequency ablation, combined radiofrequency ablationand anti-PD-1 therapy, cryo-thermal therapy, combined cryo-thermal or anti-PD-1 therapy

first: Zelu

last: Zhang

first: Ke

last: Wang

first: Shicheng

first: Junjun

first: Yichen

last: Yao

first: Xiaohui

first: Ping


title: A Phase II Trial of Pembrolizumab plus Granulocyte Macrophage Colony Stimulating Factor in Advanced Biliary Cancer

city: San Francisco

first: Bridget

last: Keenan


title: Spatial transcriptomic profiling of human heart tissue obtained from mRNA vaccine-associated myocarditis cases using GeoMx DSP

city: Tsukuba

first: Atsushi

last: Kawaguchi

address: 1-1-1 Tennodai

institute: University of Tsukuba

summary: Spatial transcriptomic analysis was performed using the NanoString GeoMx Digital Spatial Profiler to characterize region-specific gene expression patterns in heart tissue sample obtained from mRNA vaccine-associated myocarditis cases.

overall_design: Spatial transcriptome profiling was performed to compare gene expression patterns in myocardial regions between mRNA vaccine-associated myocarditis cases and control samples.


title: DDX18 enhances platinum resistance  in ovarian cancer

first: Hanyuan

last: Liu

summary: To investigate functional mRNAs regelated by DDX18, we performed high-throughput RNA sequencing (RNA-seq) of WT and DDX18 knockdown SKOV3 cells

overall_design: We performed ribosomal RNA (rRNA) depleted RNA sequencing (RNA-seq) of WT and DDX18 knockdown SKOV3 cells

first: Ying

last: Zhou


title: A Programmable Liquid Ultrasound Transduer

city: Los Angeles

first: Jun

address: 420 Westwood Plaza 5121 Engineering V

department: Bioengineering

institute: University of California, Los Angeles

summary: Conventional ultrasound energy harvesters are solid with an acoustic impedance up to ~37 MRayl, which is about 20 times higher than that of biological tissues (1.63 MRayl). This impedance mismatch largely undermines the energy conversion efficiency and the spatial-access freedom for in vivo ultrasound energy harvester implantation. Here, to the best of our knowledge, we for the first time report a liquid ultrasound energy harvester with an ultralow acoustic impedance of ~1.66 MRayl, which shows near-zero impedance mismatch with biological tissues. Based on a coupling of magneto-viscoelasticity and magnetic induction, the liquid ultrasound energy harvester can deliver an unprecedentedly high-power density of ~21.63 mW cm-2 at a lower incident spatial peak temporal peak ultrasound intensity of ~1.36 W cm-2. Furthermore, it is programmable, deformable and can be adaptive to the dynamically evolving biological tissue surfaces via arbitrary dimensional architecture design. The liquid ultrasound energy harvester provides a seamless interface with biological tissues and is expected to revolutionize the current ultrasound technology.

overall_design: Bulk RNA-seq of rat tissue collected from the implantation/surgery site in dorsal (back) and leg region. Samples include no treatment/sham surgery controls (NT) and magnetic fluid injection treatment (MFIT), collected at 7 days and 14 days post-surgery (n=3 biological replicates per timepoint per condition). Paired-end sequencing was performed; reads were aligned with STAR and gene-level counts were analyzed with DESeq2 and GO/GSEA to assess immune/inflammatory/fibrotic responses.

first: Xiao

last: Wan

first: Chen

last: Gong

first: Ziyuan

last: Che

first: Jing

last: Xu

first: Songyue

first: Liupeng

last: Zhao

first: Trinny

last: Tat

first: Runze

last: Li

first: Jie

last: Ji

first: Bo

first: Yihao

first: Yushun

last: Zeng

first: Song

first: Qifa


title: Loss of epigenetic adaptation to a high-fat diet in alpha-synuclein transgenic mice

city: Saarbrücken

first: Julia

middle: Maria

last: Schulze-Hentrich

address: Campus, Building A2.4

department: Genetics and Epigenetics

institute: Saarland University

type: Methylation profiling by genome tiling array

summary: In humans, a high-fat diet and obesity are associated with a higher risk and accelerated progression of Parkinson’s disease (PD). Similarly, in animal models a high-fat diet exacerbates PD-related phenotypes, including dopaminergic neurodegeneration, and alpha-synuclein aggregation. We previously demonstrated that transgenic mice overexpressing human, mutated A30P alpha-synuclein failed to transcriptionally adapt to metabolic stress which could be a potential explanation for the high-fat diet-dependent aggravation of PD pathology. However, the underlying epigenetic mechanisms that might regulate this impaired response remained unknown. Here, we profiled genome-wide DNA methylation and hydroxymethylation in brainstem and hippocampus of wild type and transgenic mice exposed to a long-term standard or high-fat diet. Wild type mice displayed pronounced diet-dependent adaptions that were largely missing in transgenic mice. In the brainstem, a high-fat diet increased the epigenetic age and induced a loss of DNA methylation of neuronal genes involved in protein degradation and mitochondrial metabolism—changes that were largely driven by DNA hydroxymethylation and absent in transgenic mice. Integration of methylation and gene expression data further revealed shared and brain region-specific interaction networks implicated in metabolism, proteostatis, and neuronal pathways showing molecular adaption specifically in wild type mice upon high-fat diet. Together, these findings point to failure of high-fat diet-induced epigenetic adaptability under alpha-synuclein overexpression, suggesting that altered DNA methylation and DNA hydroxymethylation might contribute to diet-dependent acceleration of PD pathology.

overall_design: We aimed to profile DNA methylation and DNA hydroxymethylation changes in brainstem and hippocampus of wild type (WT) and trangenic (TG) mice overexpressing human A30P SNCA fed a standard diet (SD) or high-fat diet (HFD) until the age of 12 months with three to four animals per experimental group.

first: Vivien

last: Hoof

first: Thomas

last: Hentrich


title: Sensory nerve-derived CGRP controls osteoclastogenesis by limiting macrophage bioenergetics in bone repair

city: Gold coast

first: Jiaying

address: G40, parkland drive

country: Australia

institute: Griffith university

summary: Bone healing is a tightly orchestrated, multiphase process that requires coordinated interactions between immune cells and skeletal cells. Sensory nerves act as intrinsic effectors of the inflammatory response, whose role in osteoimmunology during healing remains poorly defined. Using a bone healing model with sensory denervation, it’s shown that sensory nerves protect bone repair by suppressing excessive osteoclastogenesis. During the acute inflammatory phase, sensory nerves are upstream regulators of macrophage activation. At the molecular level, calcitonin gene-related peptide (CGRP), a sensory neuron–derived neuropeptide, is identified to modulate macrophage activation by restricting key functions such as migration, phagocytosis, and pro-inflammatory cytokine production. Importantly, CGRP rapidly constrains adenosine triphosphate (ATP) synthesis with limited mitochondrial respiration in activating macrophages, accompanied by downregulating genes associated with oxidative phosphorylation and mitochondrial complex components. Following the metabolic checkpoint, macrophages exposed to CGRP show attenuated osteoclastogenic capacity, with decreased secretion of multiple key factors that support osteoclast differentiation and survival. Together, these findings indicate the neuro–immune–metabolic axis in bone healing, where sensory nerve–derived CGRP influences macrophage bioenergetics and thereby contributes to osteoimmunological regulation. It emphasizes the potential of incorporating sensory signals into therapeutic strategies, particularly those targeting immunometabolism in bone regeneration.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design:
For in vivo samples, healing tissue within the bone defect in different groups at different time points was collected. Samples were tested using the DNBSEQ platform. Reads of low quality, adapter contamination, and high content of unknown bases (N) were removed. After obtaining clean reads, we used HISAT to align the clean reads to the reference genome sequence (Rattus_norvegicus_10116.NCBI.GCF_015227675.2_mRatBN7.2.v2201). Bioinformatic analysis was performed using Dr. Tom platform and RStudio (GSVA).

For in vitro samples, RAW 264.7 were then treated with LPS alone or in combination with CGRP (10 nm) for 6 h. RNA was extracted by PureLink RNA Mini Kit (Thermo Fisher Scientific). Samples were tested using the Illumina NextSeq 2000 platform. Reads of low quality, adapter contamination, and high content of unknown bases (N) were removed using the Cutadapt tool. After obtaining clean reads, we used STAR to align the clean reads to the reference genome sequence (Mus_musculus_mm10/GCF_000001635.20). Bioinformatic analysis was conducted with RStudio (key package info e.g. FeatureCounts, DESeq2, FactoMineR, etc.). Samples that failed quality control were not included in the analysis.

first: Ting

last: Zhang

first: Lili

first: Kevin

last: Dudley

first: Fuhua

last: Yan

first: Lan

last: Xiao

first: Yin


title: A FOXA1/SPDEF Co-regulatory Axis Maintains Luminal Identity in HER2-Positive Breast Cancer by Driving ERBB2 Expression and Suppressing a TEAD/YAP-Driven EMT Program [RNA-Seq]

city: Seoul

first: Jungmin

last: Choi

address: 73, Goryeodae-ro, Seongbuk-gu

country: South Korea

institute: Korea University College of Medicine

summary: The function of the pioneer factor forkhead box A1 (FOXA1) in estrogen receptor (ER)-negative, human epidermal growth factor receptor 2 (HER2, encoded by the ERBB2 gene)-positive breast cancer represents a critical gap in our understanding of lineage identity in tumorigenesis. Here, we solve this enigma by addressing this question through the identification of an indispensable, co-dependent regulatory circuit formed between FOXA1 and the SAM pointed domain containing ETS-family transcription factor (SPDEF). Using integrative multi-omics analyses of patient tumors and experimental models, we demonstrate that this circuit functions as the master guardian of the HER2-positive luminal state. It executes this role via two distinct, essential mechanisms: it directly binds regulatory elements to drive high-level expression of the ERBB2 oncogene, and it simultaneously preserves epithelial identity by suppressing a latent program of epithelial-to-mesenchymal transition (EMT). Mechanistically, the FOXA1/SPDEF circuit promotes the expression of the transcriptional repressor TRPS1, which in turn antagonizes the pro-mesenchymal activity of the TEAD/YAP complex. Our findings define a central regulatory node that couples lineage fidelity to oncogenic output in HER2-positive cancer, revealing the FOXA1/SPDEF–TRPS1 axis as a critical determinant of tumor plasticity and a potential therapeutic target for overcoming resistance in HER2-positive breast cancer.

overall_design: To investigate the effect of SPDEF on HER2-related pathways, a stable cell line expressing shRNA directed against SPDEF was generated by transducing cells with commercially prepared lentiviruses containing three individual shRNA directed against SPDEF mRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells. Comparateive gene expression profiling analysis of RNA-seq data for MCF7 and SKBR3 cells and its KD derivates (SPDEFKD).

first: Jongwon

last: Lee

first: Jaekwang

last: Jeong

first: Wysolmerski

last: John


title: A FOXA1/SPDEF Co-regulatory Axis Maintains Luminal Identity in HER2-Positive Breast Cancer by Driving ERBB2 Expression and Suppressing a TEAD/YAP-Driven EMT Program [ATAC-seq]

overall_design: To investigate the effect of SPDEF on chromosomal accessibility, several cell lines were assessed.Comparateive chromosomal accessibility profiling analysis for MCF7 and SKBR3 cells and its SPDEF KD derivates (SKBR3_SPDEFKD).


title: Reduced Representation Bisulfite Sequencing (RRBS) of hippocampus from Mtr-cKO and wild-type mice

city: Strasbourg

first: Karim

last: Matmat

address: 1 Rue Eugène Boeckel

department: Faculty of Medicine

country: France

institute: University of Strasbourg

type: Methylation profiling by high throughput sequencing

summary: This dataset reports Reduced Representation Bisulfite Sequencing (RRBS) of hippocampal tissue from 21-day-old Mtr-cKO and wild-type mice. Genomic DNA was extracted from hippocampus, quantified, and quality-checked prior to RRBS library preparation using the Diagenode Premium RRBS kit. Bisulfite conversion efficiency was evaluated using methylated and unmethylated spike-in controls. Single-end 75 bp sequencing was performed on an Illumina NextSeq 550 system. Raw FASTQ files and processed CpG methylation tables are provided. Differential methylation analysis was performed using methylKit (R), including filtering, normalization, CpG calling, DMR identification, and genome annotation.

overall_design: Twelve hippocampal samples (6 Mtr-cKO and 6 wild-type controls) collected from 21-day-old mice were processed for RRBS. Genomic DNA was extracted and prepared following the Diagenode Premium RRBS kit protocol, bisulfite-converted, and amplified. Sequencing was carried out in single-end mode (75 bp) on an Illumina NextSeq 550. FASTQ files were trimmed, aligned, and used for CpG methylation quantification. Differentially methylated CpG sites and DMRs were detected using methylKit with FDR correction.


title: Transcriptomic Profiling of the Hypothalamic PVN in a Rat Model of Hypertension

city: São Paulo

first: Victor

middle: Jardim

last: Duque

state: SP

address: Rua da Contagem, 273, Porta Madeira

institute: Federal University of Sao Paulo

summary: In this study, we investigated the transcriptomic profile of the Paraventricular Nucleus (PVN) in hypertensive strains and across sexes, aiming to identify novel sex-specific molecular pathways involved in the regulation of blood pressure.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from the Paraventricular Nucleus (PVN) across sexes in Wistar rats and Spontaneously Hypertensive Rats (SHR)

first: David

last: Murphy

first: Nina

last: Japundžić

first: Andre

last: Mecawi


title: Kinetics-seq enables comprehensive profiling of single-cell RNA kinetics in vivo to reveal dynamic tumor heterogeneity

first: Rui

last: Cheng

state: Shanghai

address: No. 1630 East Road, Pudong New Area

summary: Tumor tissue is a dynamic system governed by complex transcriptional kinetics. Although scRNA-seq has revolutionized cellular profiling, it captures static expression snapshots, lacking direct access to transcriptional dynamics. Here, we present Kinetics-seq, a time-resolved single-cell method that integrates in vivo metabolic labeling strategy with scRNA-seq to construct a comprehensive transcriptional kinetic landscape within tissues. This approach enables transcriptome-wide quantification of RNA abundance, turnover, synthesis, and degradation rates at single-cell resolution. By incorporating RNA kinetic parameters, Kinetic-seq introduces a dynamic dimension to cellular profiling, revealing heterogeneities not only across cell types but also within individual populations. Through joint modeling of RNA synthesis and degradation rates, Kinetics-seq uncovers gene-specific regulatory strategies and pronounced kinetic diversity among tumor cells. Moreover, RNA kinetics serves as a screen tool to identify transcriptionally active gene subsets, revealing pathways such as cholesterol homeostasis, myogenesis, and complement that display stronger temporal associations with tumor progression than abundance-based analyses. Collectively, KineMap-seq provides a powerful tool for refining cellular taxonomy, elucidating RNA regulatory strategies, and identifying actively regulated genes that affect tumor ecosystem, while also offering new opportunities for mechanistic investigation, biomarker discovery, and therapeutic intervention.

overall_design: Expression profiling by high throughput sequencing

first: Yiling

last: Xu

first: Zhong

last: Zheng

first: Jia

last: Song

first: Kun

last: Yin

first: Chaoyong

last: Yang


title: A SINGLE NUCLEOTIDE DELETION DISRUPTS THE TRANSCRIPTIONAL RESPONSE OF THE HAIRLESS GENE TO THYROID HORMONE AND THYROID HORMONE SIGNALLING IN MICE.

city: Lyon

first: Frédéric

last: Flamant

state: France

address: 46 allée d'Italie

department: IGFL

institute: ENSL

summary: The transcription of the Hairless gene, which encodes a histone demethylase, is strongly induced by thyroid hormone in many cell types. To address the significance of this regulation, we identified a DNA response element in the regulatory sequences of the Hairless gene, which plays a key role in this regulation. A single mutation in this response element proves to be sufficient to alter thyroid hormone signaling in mice. RNA-seq analysis in the heart and striatum of mice homozygous for this mutation highlights the influence of the Hairless cofactor in thyroid hormone signaling.

overall_design: RNA-seq analysis was performed on 3 groups of mutant mice (HrDR5/DR5 genotype) and 3 groups of wild-type mice, for two tissues: heart and striatum. The 3 groups correspond to 3 conditions: euthyroid/hypothyroid/hypothyroid treated with thyroid hormone (24h) to quickly restore hormonal levels.

first: Denise

last: Aubert

first: Shijia

last: Wu

first: Karine

last: Gauthier

first: Suzy

last: Markossian

first: Romain

last: Guyot


title: Camellia oleifera meal peptides alleviates atherosclerosis by regulating lipid metabolism through AMPK/ACC/CPT-1 pathway

first: Wenjun

last: Wang

address: No.130, Dong'an Road, Xuhui District

institute: FDU

summary: Background: The potential of Camellia oleifera meal peptides（PP) in the treatment of atherosclerosis and its potential mechanism need to be further clarified. Objective: the aim of this study was to clarify the effect of PP in the treatment of atherosclerosis and its potential mechanism. Methods: After cell modeling, it was used to detect the antioxidant, anti-inflammatory and lipid-lowering effects of PP in vitro. As mouse model was used to evaluate the anti atherosclerotic effect of PP in vivo. The changes of protein and metabolites after the treatment of atherosclerosis by PP were studied by liver proteomics, metabonomics and transcriptomics, and the possible mechanism of its regulation of lipid metabolism was clarified. Results:Using cell inflammation model, oxidative damage model and high-fat model, CCK8 test and qPCR detection showed that PP had antioxidant, anti-inflammatory and lipid-lowering effects. The animal results showed that the lipid deposition in the root of aortic valve and liver tissue was reduced, and the PP had the effect of alleviating atherosclerosis. Metabonomics and proteomics analysis showed that the activities of various enzymes related to lipid metabolism were changed after PP treatment, and the lipid metabolism pathway was changed. Transcriptomics analysis showed that AMPK pathway was changed. The experimental results showed that AMPK regulated lipid oxidation pathway to alleviate atherosclerosis in mice through acetyl CoA carboxylase (ACC) - CPT-1 pathway.

overall_design: AML12 cells in logarithmic growth phase and in good condition were seeded into 6-well and 96-well plates, with a seeding density of 1×106 cells/ml for the 6-well plate. AML12 cells were treated with PP and modeling reagent (PA/OA,400 nM/800 nM)24 hours. The experiment was divided into 3 groups: a blank group (control group, cultured in regular complete medium), a model group, and groups treated with PP (final concentrations of 250 μg/ml in PP-containing medium).

first: Tao

last: wang

last: Gan

first: Juan

last: Zhou

first: Ruiyun

last: Hong

first: Lu

last: Liang

first: Jiajia

first: Guilin

last: Ye

first: Xiaohua

last: Liu

first: Huiting

last: Ning

first: Bin

last: Zeng

first: Huaping

first: Hongen

last: Qu

first: Minjuan

first: Minen

first: Liefeng


title: AID Orchestrates MYC/E2F Target Gene Activation and Cell-of-Origin Transcriptional Programs in Diffuse Large B-cell Lymphoma [ABC_AID-ER_RNA-seq]

city: Amsterdam

first: Linda

last: Gijsbers

address: Meibergdreef 9

department: Pathology

country: Netherlands

institute: Amsterdam UMC - location AMC

summary: Activation-induced cytidine deaminase (AID), which is essential for antibody diversification, exhibits elevated expression in the activated B-cell-like (ABC) subtype of diffuse large B-cell lymphoma (DLBCL). Here, we demonstrate that AID modulates transcriptional programs linked to cell cycle progression, proliferation, and DLBCL subtype identity. AID loss in ABC-type DLBCL cell lines impairs MYC and E2F pathway activity, while AID re-expression restores activity, establishing a causal link. Furthermore, AID expression correlates with ABC-type stratification gene expression.

overall_design: RNA-seq profiling was performed on three AID-deficient and three non-targeting (NT) guide RNA-expressing clones of the cell lines HBL1, TMD8 and OCI-LY10.

first: Tijmen

last: van Dam

first: Martin

last: de Rooij

first: Guus

last: de Wilde

first: Richard

last: Bende

first: Ad

last: van Gorp

first: Carel

last: van Noesel

first: Jeroen

last: Guikema


title: AID Orchestrates MYC/E2F Target Gene Activation and Cell-of-Origin Transcriptional Programs in Diffuse Large B-cell Lymphoma [GCB_AID-ER_RNA-seq]


title: Nucleolar Protein Nop2 Promotes Neural Differentiation by Regulating Ribosome Biogenesis-related Processes

city: Zhan Jiang

first: Xiaoyu

last: Li

state: Guangdong

address: 57 People's Avenue

institute: Affiliated Hospital of Guangdong Medical University

summary: The NOP2 nucleolar protein (NOP2) serves pivotal functions in ribosome biogenesis, cell cycle regulation and embryonic development, yet its spatiotemporal dynamics and mechanistic contributions to neural development remain elusive. Through CRISPR/Cas9-mediated knockout modeling in zebrafish, we demonstrated that NOP2 nucleolar protein homolog (yeast) (nop2) deficiency induced embryonic lethality within 3-5 days post-fertilization (dpf), accompanied by pathognomonic microcephaly and cerebral edema. Mechanistic analysis suggested that nop2 ablation triggered differentiation impairment in neural progenitors, which accumulated extensively in brain tissue and led to impaired generation of neurons and glial cells. In addition, nop2 deficiency activated p53-dependent apoptosis in neural cells. Biochemical characterization revealed compromised pre-ribosomal particle processing in mutants, establishing defective ribosome biogenesis as the primary molecular lesion. Ribosome profiling (Ribo-seq) uncovered aberrant regulation of nervous system processes and activation of p53-mediated apoptosis in neural cells. Genetic epistasis experiments demonstrated that tp53 mutation partially rescued neurogenic defects and reduced cerebral edema, but failed to rescue microcephaly. These findings provide evidence supporting the role of Nop2 as a significant regulator in neural development. Our results demonstrate that Nop2 promotes neural differentiation by regulating ribosome biogenesis-related processes, thereby extending our previous research on rRNA metabolism-related genes in neurodevelopment. Moreover, our study provides critical insights into developing early interventions against neurodevelopmental disorders associated with ribosomopathies.

overall_design:
For Ribo-seq:
Brain tissues of siblilng and nop2 mutant zebrafish at 48 hpf were isolated in  1xPBS at 4°C, rapidly froze in liquid nitrogen, and sent to Gene Denovo for ribosome sequencing. Ribosomes were separated, and sequencing libraries were prepared.
For RNA-BS-seq:
We collected brain tissues of these two zebrafish groups mention above at 48 hpf in pre-cooling 1xPBS, rapidly frozen them in liquid nitrogen, and sent E-GENE for RNA bisulfite sequencing. mRNA was isolated, bisulfite-converted, and purified. Libraries were generated through cDNA synthesis and PCR amplification.


title: Plasma proteomics improves thrombosis prediction in cancer and implicates a targetable IL-17-driven endothelial activation pathway

city: Boston

first: Marisa

last: Brake

state: MA

address: 3 Blackfan Cir

institute: Beth Israel Deaconess Medical Center

summary: Thrombosis remains a major cause of morbidity and mortality in cancer patients. Existing risk models fail to reliably predict venous thromboembolism (VTE), underscoring the need for more accurate predictive models. In this study, we conducted a high-throughput proteomic analysis of 1,105 plasma proteins from newly diagnosed lung and gastric cancer patients prospectively monitored for VTE development. Utilizing a Bayesian probabilistic machine learning approach, we developed a predictive model incorporating 11 protein biomarkers and five clinical parameters (age, sex, history of VTE, body mass index, and hemoglobin), which significantly outperformed the Khorana prediction model. Orthogonal validation in an external placebo cohort from a phase III trial confirmed the model’s predictive power. Further investigation into the mechanistic role of CD200R1, a checkpoint receptor limiting leukocyte inflammatory response that contributed strongly to the model, showed that reduced levels in plasma correlated with higher D-dimer and thrombosis risk. In CD200R1-deficient mice, elevated thrombin-antithrombin complexes confirmed a prothrombotic state characterized by increased IL-17A and endothelial inflammation. Administration of anti-IL-17A antibodies to CD200R1 deficient mice normalized thrombin generation in vivo, and a meta-analysis of human clinical IL-17A inhibitory antibody studies confirmed antithrombotic activity. These findings improve the prediction of thrombosis in cancer and highlight the utility of plasma proteomics to identify unanticipated mechanistic insights and therapeutic targets in thrombo-inflammatory disease.

overall_design: To investigate transcriptional difference in gene expression in whole liver between wildtype and Cd200r1 knockout mice.

first: Brake

last: Marisa

first: Schulman

last: Sol

first: Zwicker

last: Jeff


title: Characterizing the Impact of MLL Fusion Variants and Fusion Partners on Leukemia Plasticity Using a Human CRISPR-Engineered MLL-Rearranged Leukemia Model

first: Julia

last: Schulze-Hentrich

summary: Acute leukemias involving MLL (KMT2A) rearrangements are aggressive hematologic malignancies associated with poor prognosis. MLL fusions typically involve MLL exons 8-14, with AF4 (AFF1) and AF9 (MLLT3) being frequent partners. To investigate how fusion partners and breakpoint locations influence the disease, we developed a CRISPR/Cas9 model by introducing MLL-AF4 or MLL-AF9 fusions with MLL breakpoints in intron 9 or 11 into cord blood CD34+ cells. The MLL-rearranged cells showed increased proliferation and stemness, as well as an altered immunophenotype involving the upregulation of AML markers. Transcriptomic profiling revealed breakpoint- and partner-specific gene expression patterns that influence the characteristics of the disease. MLL(intron 9)-AF9 cells engrafted robustly in NSG mice and showed high lineage plasticity, switching from a myeloid to a B-lymphoid identity in vivo. Our model enables mechanistic studies across MLL fusion variants and may guide the development of targeted therapies for MLL-rearranged leukemias.

overall_design: MLL-AF4 (t(4;11)) or MLL-AF9 (t(9;11)) fusions with MLL breakpoints in intron 9 or 11 into cord blood CD34+ cells. MLL-rearranged cells were compared to healthy control cells (wildtype, wt) from the same donors.

first: Corina

last: Schneidawind

first: Rahel

last: Fitzel

first: Pia

last: Radszuweit

first: Thomas

last: Hentrich


title: Dysregulated ClpP Activation Depletes AML Cells and Restores T-cell Function via Metabolic Competition

city: Chengdu

first: Lei

last: Zhao

state: Sichuan

address: Guoxue Alley 37

department: Department of Hematology

institute: West China Hospital, Sichuan Universtiy

summary: We employed single-cell RNA sequencing (scRNA-seq) to investigate immune responses in a syngeneic acute myeloid leukemia (AML) model generated by transplantation of murine WEHI-3-luc cells into BALB/c mice. Treatment with the novel CLPP inhibitor IMP125 (5 mg/kg) demonstrated superior therapeutic effects compared with ONC201, lower-dose IMP125, and conventional chemotherapy agents, including reductions in leukemic burden, prolonged survival, and enhanced immune activation. Spleen, bone marrow, and liver tissues were profiled to provide insights into the immune mechanisms underlying IMP125 efficacy.

overall_design:
single-cell RNA-seq was performed on splenocytes from four groups: healthy control (H,n=1), AML xenograft control (CON,n=3), AML with doxorubicin treatment (DOX,n=3), and AML with IMP125 treatment (T125,n=3).

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first: Xinrong

last: Xiang

first: Yu

last: Wu


title: The Neuronal Primary Cilium is a Key Regulator of Homeostatic Plasticity

city: Nijmegen

first: Sofia

last: Puvogel

address: Geert Grooteplein Zuid 10

institute: RadboudUMC

summary: The capacity of neurons to maintain stable activity levels through homeostatic plasticity is essential for proper brain function. Primary cilia, which are non-motile, antenna-like organelles projecting from the surface of most vertebrate cells, serve as key hubs for signal transduction, playing crucial roles in tissue development and cellular homeostasis. In this study, we identify a previously unrecognised role for primary cilia in mediating neuronal homeostatic plasticity using human induced pluripotent stem cell-derived neurons. We show that neuronal cilia exhibit dynamic, bidirectional changes in volume in response to alterations in network activity: elongating during chronic activity suppression and shortening after increased activity. To assess the functional relevance of this ciliary plasticity, we modelled ciliary dysfunction in neurons carrying homozygous loss-of-function mutations in genes associated with neuronal ciliopathies, including NPHP1 and CEP290. Mutations affecting ciliary function either increased ciliary length or led to ciliary loss, and these mutant neurons exhibited severe impairments in homeostatic regulation across multiple domains—morphological, functional, and transcriptional. Specifically, NPHP1 and CEP290 deficient neurons failed to adapt synaptic strength, intrinsic excitability, and ciliary morphology in response to prolonged activity suppression. They also displayed dysregulated baseline network activity, and exhibited blunted gene expression changes. Together, these findings establish the primary cilium as a critical regulator of homeostatic plasticity in human neurons and provide a new framework through which to examine neurodevelopmental and neuropsychiatric disorders linked to ciliary dysfunction.

overall_design: Neurons derived from human iPSCs were grown together with rat astrocytes in culture plates. Three replicates were prepared for each condition: control (WT iPSC-neurons), NPHP1⁻/⁻ iPSC-neurons, and CEP290⁻/⁻ iPSC-neurons. For each genotype, cells were treated either with vehicle or with TTX for 24 hours (three replicates per condition). For quality checks, additional cells from the same batches were grown on microelectrode arrays and coverslips for imaging. After treatment, cells were collected, and RNA was isolated. RNA quality was high (RIN 9.4–9.8). Libraries were prepared using a standard RNA-seq kit and sequenced with paired-end reads on an Illumina NovaSeq 6000 platform.

first: Emma

last: Dyke

first: Astrid

last: Oudakker

first: Ronald

last: Roepman

first: Brooke

last: Latour

first: Nael

last: Nadif Kasri


title: scRNA-seq analysis of liver nonparenchymal cells from the mouse model of CCl4-induced liver fibrosis

city: Suita

first: Seiya

last: Kato

address: 2-2, Yamadaoka

department: Gastroenterology and Hepatology

institute: Osaka University

summary: We performed scRNA-seq analysis on livers from the mouse model of CCl4-induced liver fibrosis. The scRNA-seq analysis showed that CTGF expression was increased only in zone 2 LSECs, and that YAP was not activated in any cluster of LSECs.

overall_design: After liver perfusion with pronase and collagenase, hepatocytes were removed via low-speed centrifugation, and dead cells and erythrocytes were removed via density gradient centrifugation.

first: Hayato

last: Hikita

first: Tetsuo

last: Takehara


title: Differential Expression Analysis of the SLIT Family in Different Brain Regions

first: Arthur

middle: Barbarini

last: Yoshida

address: Dr. Arnaldo, 455 – 4º andar – sala 4110 - Cerqueira César

department: Neurology

institute: Faculdade de Medicina da Universidade de São Paulo

summary: The ageing human brain undergoes extensive remodelling of its extracellular matrix (ECM), yet the regional specificity and molecular drivers remain poorly defined. Here we combine bulk RNA-sequencing of post-mortem tissue (n = 63 across eight regions) with independent validation in the Genotype-Tissue Expression (GTEx) cohort (n = 962) to chart the expression landscape of the 239-member core matrisome. Hippocampus emerged as a major ECM outlier, with 114 matrisome genes—dominated by glycoproteins—up-regulated compared to the other seven regions (Fisher’s combined test, FDR < 0.05). Genes coding the axon-guidance ligands SLIT1, SLIT2 and SLIT3 ranked among the top hippocampal signatures and displayed strong co-expression with ROBO2 (r > 0.70). Age-stratified analysis in GTEx revealed a concerted decline of the SLIT-ROBO2 axis after 60y, aligning with hallmarks of cognitive ageing. Immunohistochemistry and western blotting (n = 3 per region) supported regional and subcellular patterns of SLITs ROBO2. These findings identify the SLIT-ROBO2 module as a hippocampus-centric, age-labile component of the human matrisome. We propose that sustained SLIT-ROBO signalling supports hippocampal synaptic plasticity, whereas its late-life attenuation may diminish structural resilience and heighten vulnerability to neurodegeneration. Our resource provides a framework for targeting ECM pathways to preserve brain connectivity during ageing.

overall_design: This study employed a comparative bulk RNA-sequencing analysis of human post-mortem brain tissue focused on the core matrisome (comprising ECM glycoproteins, collagens, and proteoglycans). Samples: The submission includes sixty-three autopsy specimens (n=63) derived from a local research group’s biorepository. Inclusion criteria required death from natural causes, while cases of neurodegenerative disease, stroke, or infectious conditions were excluded. Experimental Conditions and Variables: The primary variable under investigation was the anatomical brain region. Samples were collected from eight distinct regions: Cerebellum (CER, n=8); Hippocampus (HCP, n=8); Hypothalamus (HTL, n=8); Substantia Nigra (SN, n=5); Temporal Cortex (TEMP, n=5); Occipital Cortex (OCC, n=5); Frontal Cortex (FRO, n=8); Parietal Cortex (PAR, n=16). Replicates and Controls: The design utilized paired samples for differential expression analysis across regions, meaning multiple samples (regions) were obtained from the same subject. This pairing was controlled for statistically by including the Subject Identifier as a covariate in the model, controlling for inter-individual variability. Reference/Comparison Samples: The Hippocampus (HCP) served as the critical comparison site, as the study aimed to evaluate differential expression in the matrisome genes in HCP relative to each of the other seven brain regions. HCP was determined to be a major ECM outlier site. Statistical comparisons were performed gene-wise, with the alternative hypothesis that the median expression in HCP exceeds that of the comparison site.

first: Sueli

last: Oba-Shinjo

first: Adriana

last: Nakahata

first: Paula

last: Sola

first: Adaliana

last: Mousessian

first: Stella

last: Cavalcante

first: Christiane

last: Ozaki

first: Antonio

last: Lerario

first: Suely

last: Marie


title: Spatial transcriptomics of human FALD and normal livers

summary: Spatial transcriptomic analysis was performed on Fontan-associated liver disease (FALD) and normal livers using CosMx Spatial Molecular Imager.

overall_design: CosMx technology, a high-plex spatial molecular imager (SMI), was used to analyze 2 FALD liver samples that were histologically diagnosed with cirrhosis and 1 donor liver sample. FFPE samples were sectioned (5 μm), mounted on VWR Superfrost Plus microscope slides. Anti-B2M/CD298, anti-PanCK, anti-CD45, and anti-CK8/18 antibodies and DAPI were used as morphological markers. The CosMx Human Universal Cell Characterization RNA Panel (1000-plex) + 9 custom genes, including CCN2, was used for the CosMx assay. The samples were prepared according to the manufacturer’s instructions. Cell segmentation was performed by combining image preprocessing and CellPose neural network models. Serial thin sections prepared from FFPE samples were stained with H&E and Sirius red for field of view (FOV) determination. Each FOV was 0.5 × 0.5 mm in size. The data were analyzed by the CosMx SMI instrument, followed by quality control, normalization, principal component analysis and clustering using the count matrix and subpopulation assignments of the reference scRNA-seq dataset on the AtoMx platform.


title: Alternative splicing diversifies HSF1 function to enable desiccation tolerance of P. vanderplanki cells

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

institute: Juntendo University

summary: Heat shock factor 1 (HSF1) is a transcription factor that contributes to induction of desiccation tolerance and allow larvae of Polypedilum vanderplanki successfully enter anhydrobiosis state. Here we report the identification of five alternative splicing isoforms of P. vanderplanki HSF1 (PvHSF1) and their distinct functional roles during anhydrobiosis cycle and heat shock in Pv11 cells, derived from P. vanderplanki. All five PvHSF1 isoforms induced desiccation tolerance, but with varible efficiency followed by distinct gene expression patterns. We revealed that PvHSF1 isoform 2 is the most abundant isoform in the anhydrobiosis state. It directly regulates gene esxpression resulting in both activation and suppression. Other two PvHSF1 isoforms (1 and 3) were responsible for cell adaptation to severe heat shock by modulating expression of genes. Importantly, none of Drosophila melanogaster HSF1 (DmHSF1) splicing isoforms were able to induce the desiccation tolerance tolerance, while one DmHSF1 isoform (a) resulted in Pv11 cells survival after heat shock. Our results demonstrate that PvHSF1 splicing isoforms possess distinct regulatory roles in anhydrobiosis and heat shock to cope with different stress conditions.

overall_design: mRNA-seq profiles for WT, HSF1-KO and PvHSF1- and DmHSF1- isoforms expressing Pv11 cells with trehalose treatment for 48h, rehydration for 24h and heat shock for 6h.

first: Shoko

last: Tokumoto


title: AID Orchestrates MYC/E2F Target Gene Activation and Cell-of-Origin Transcriptional Programs in Diffuse Large B-cell Lymphoma [ABC_AID_KO_RNA-seq]

first: Linda

last: Gijsbers

first: Tijmen

last: van Dam

first: Martin

last: de Rooij

first: Guus

last: de Wilde

first: Richard

last: Bende

first: Ad

last: van Gorp

first: Carel

last: van Noesel

first: Jeroen

last: Guikema


title: scRNA-seq analysis of the livers from the mice treated with a pan-integrin αV inhibitor after pIVCL

first: Seiya

last: Kato

summary: We performed scRNA-seq analysis on the livers from the mice treated with a pan-integrin αV inhibitor, CWHM-12, after partial inferior vena cava ligation (pIVCL), a mouse model of congestive hepatopathy. The scRNA-seq analysis showed that integrin αV inhibition decreased the expression of YAP/TAZ target genes in pericentral LSECs and collagen expression in HSCs, caused by hepatic congestion.

first: Hayato

last: Hikita

first: Tetsuo

last: Takehara


title: Viral transcriptional regulators extensively rewire host pathways through diverse mechanisms

city: Callao

first: George

middle: Dereck

last: Muñoz

state: Callao

address: Ca. Dalias 204-A, Bellavista - Callao

country: Peru

institute: Rockefeller University

summary: Viral transcriptional regulators (vTRs) reprogram host gene regulatory networks to promote replication, persistence, and immune evasion. Despite the identification of hundreds of vTRs in human viruses, how they rewire host pathways remains unclear. Here, we systematically profiled 95 vTRs from diverse human viruses across multiple functional assays. vTRs perturb immune, cell proliferation/death, and signaling pathways through various mechanisms; some bind DNA directly, others cooperate or antagonize human transcription factors (hTFs), and some remodel chromatin. vTRs can act as activators or repressors and recruit similar but not identical repertoires of proteins as hTFs. These findings reveal vTRs as versatile transcriptional modulators that converge on conserved host “pressure points” while diversifying across pathways to promote viral replication and persistence. Notably, many vTR dysregulate genes within autoimmune, neurological, and cardiovascular risk loci, revealing mechanistic links to disease. Together, we provide a comprehensive resource for understanding and targeting viral control of human transcription.

overall_design: To determine the transcriptomic effects of vTRs in human cells, we performed bulk RNA barcoding and sequencing (BRB-seq) in HEK293T cells expressing individual vTRs. Expression vTR clones were generated via Gateway LR cloning into the pEZY3 constitutive expression vector (Addgene plasmid #18672). Following transformation, plasmids were extracted, and insertion was confirmed via PCR and gel electrophoresis. The full list of vTRs tested by BRB-seq is provided in Data S2. For BRB-seq experiments, HEK293T cells were cultured in DMEM media supplemented with 10% FBS and seeded in two 96-well plates at a density of 18,000 cells/well. The following day, cells were transfected in quadruplicate using Lipofectamine 3000 (Thermo Fisher Scientific) with 80 ng of the pEZY3-vTR plasmids, as well as empty pEZY3 vector controls. After 24 hours, cells were either infected with 4.0 × 10⁶ CEID₅₀/mL Sendai virus (VR-907, ATCC), or left uninfected. RNAs were harvested 2 days post transfection, a time point that we showed has minimal interferon pathway activation due to transfection. Sequencing libraries were prepared using the MERCURIUS DRUG-seq kit (Alithea Genomics) according to manufacturer’s instructions and as described previously.24 Briefly, HEK293T cells were permeabilized using a cell lysis buffer on ice 15 min with periodic agitation, followed by centrifugation to clear cellular debris. Individual RNA-containing lysates were then reverse-transcribed using barcoded oligo-dT primers such that the resulting cDNA from each individual sample was uniquely barcode-labeled. cDNA from all samples in a single plate were then pooled and purified using the column-based Zymo Clean & Concentration Kit according to manufacturer’s instructions (Zymo, D4014). The pooled cDNA was then cleared of non-incorporated primers via exonuclease digestion, followed by second strand synthesis and quantification of ds-cDNA via Qubit HS-DNA kit (Thermo Fisher). Tagmentation was then performed on 20 ng cDNA, followed by library indexing and amplification using standard Illumina NGS adapter sequences. Indexed libraries were sequenced at a depth of 5 million raw reads per sample on an Illumina Novaseq platform. Scripts to process sequencing data are deposited in https://github.com/FuxmanBass-lab/vTRs.

first: Jaice

middle: T

last: Rottenberg

first: Xing

last: Liu

first: Anna

last: Berenson

first: Luis

last: Soto-Ugaldi

first: Mohamed

middle: Y

last: ElSadec

first: James

last: Corban

first: Phillip

last: Dexheimer

first: Berkay

last: Engin

first: Ryan

last: Lane

first: Sakshi

last: Shah

first: Kerstin

last: Spirohn-Fitzgerald

first: Shubham

last: Khetan

first: Cheng-Che

last: Lee

last: Munoz-Esquivel

first: Zhaorong

last: Li

first: Lucia

last: Martinez-Cuesta

first: Yunwei

last: Lu

first: Philipp

last: Trollmann

first: Tong

last: Hao

first: S

middle: S

last: Yi

first: Nidhi

last: Sahni

first: Martha

last: Bulyk

first: Michael

last: Calderwood

first: Mattthew

last: Weirauch

first: Marc

last: Vidal

first: Jsrivatsan

last: Raman

first: Juan

middle: I

last: Fuxman


title: Tumour-associated high endothelial venules drive portal-specific immune evasion in lymph nodes via ALOX12 [Metastatic lymph node]

city: Guangzhou

first: Qidong

last: Xia

address: No.107, Yangjiangxi Road, Guangzhou

department: Breast Tumor Center

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

summary: High-endothelial-venules (HEVs) offer another entry point for tumor metastasis in mice. To investigate whether HEVs and non-specialized blood vessels exert different effects on disseminating tumor cells, we enriched EO771 derivatives HEVM3 (preferentially metastasize through HEVs) cells and BVM3 (preferentially metastasize through blood vessels) cells. To further explore potential factor(s) that influence tumor cells, we isolated blood vessel endothelial cells (BECs) in metastatic lymph nodes from six C57BL/6J mice and analyzed them with single-cell RNA sequencing.

overall_design: BECs in metastatic lymph nodes from six C57BL/6J mice were analyzed with single-cell RNA sequencing.

first: Shicheng

last: Su


title: Characterizing the Impact of MLL Fusion Variants and Fusion Partners on Leukemia Plasticity Using a Human CRISPR-Engineered MLL-Rearranged Leukemia Model [RNA-Seq Classical]

first: Julia

last: Schulze-Hentrich

address: Campus, Building A2.4

institute: Saarland University

summary: Acute leukemias involving MLL (KMT2A) rearrangements are aggressive hematologic malignancies associated with poor prognosis. MLL fusions typically involve MLL exons 8-14, with AF4 (AFF1) and AF9 (MLLT3) being frequent partners. To investigate how fusion partners and breakpoint locations influence the disease, we developed a CRISPR/Cas9 model by introducing MLL-AF4 (t(4;11)) or MLL-AF9 (t(9;11)) fusions with MLL breakpoints in intron 9 or 11 into cord blood CD34+ cells. The MLL-rearranged cells showed increased proliferation and stemness, as well as an altered immunophenotype involving the upregulation of AML markers. MLL(intron 9)-AF9 cells engrafted robustly in NSG mice and showed high lineage plasticity, switching from a myeloid to a B-lymphoid identity in vivo. Transcriptomic profiling confirmed the lineage switch and the transcriptomic signature revealed progressive stages of B-cell lineage commitment in individual mice. Our model enables mechanistic studies across MLL fusion variants and may guide the development of targeted therapies for MLL-rearranged leukemias.

overall_design: RNA-seq profiling of human cord blood-derived t(9;11) cells generated by CRISPR/Cas9. We compared in vitro cultured cells with ex vivo cells from the same human cord blood donors that have been transplanted into NOD scid gamma (NSG) mice and engrafted in the bone marrrow.

first: Corina

last: Schneidawind

first: Pia

last: Radszuweit

first: Thomas

last: Hentrich

middle: M


title: scRNA-seq analysis of the livers from the endothelial cell-specific CTGF KO mice after pIVCL

first: Seiya

last: Kato

summary: We performed scRNA-seq analysis on the livers from the endothelial cell-specific CTGF knockout (KO) mouse or control wild-type (WT) littermate after partial inferior vena cava ligation (pIVCL), a mouse model of congestive hepatopathy. The scRNA-seq analysis showed that CTGF knockout in LSECs suppressed the expression of YAP/TAZ target genes and basement membrane-related genes in LSECs caused by hepatic congestion.

first: Hayato

last: Hikita

first: Tetsuo

last: Takehara