title: Compromised lipid metabolism, mitochondria respiration and neuroprotective effects in iPSC-derived astrocytes from a Smith-Lemli-Opitz syndrome patient

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

summary: Smith-Lemli-Opitz syndrome (SLOS) is a rare, autosomal recessive disorder characterized by congenital malformations, intellectual disability, and behavioral abnormalities. SLOS results from mutations in the DHCR7 gene, leading to impaired cholesterol biosynthesis due to dysregulation of 7-dehydrocholesterol reductase. Cholesterol plays crucial roles in neurophysiology, including synaptic formation and neurotransmitter receptor regulation, which likely contribute to neurological manifestations in SLOS patients. While astrocytes are the main cholesterol producing cells in the brain, their specific role in SLOS pathogenesis remains unclear. In this study, we utilized induced pluripotent stem cell (iPSC)-derived astrocytes from a SLOS patient with DHCR7 c.C278T mutation and the isogenic control. We found decreased lipid droplet formation in SLOS iPSC astrocytes compared to controls, accompanied with diminished efflux of cholesterol and apolipoprotein E. Lipidomics revealed reduced cholesterol and cholesterol esters, as well as altered profiles of other lipids in SLOS iPSC astrocytes. While RNA-sequencing identified various genes and pathways affected by the disease status, those related to mitochondria functions were top-ranked. Mitochondrial electron transport chain oxidative phosphorylation gene expression decreased in SLOS iPSC astrocytes, alongside impaired mitochondrial respiration. Furthermore, SLOS iPSC astrocytes less effectively mediated neuroprotection on iPSC neurons than control astrocytes in serum-starvation conditions. SLOS iPSC astrocytes also poorly contributed to synaptic networks when co-cultured with iPSC neurons. Overall, our findings provide mechanistic insights into how DHCR7 disruption impacts astrocyte function, contributing to SLOS neuropathology by dysregulating lipid metabolism, mitochondrial respiration, and impaired neuroprotection.

overall_design: We performed bulk RNA sequencing of induced pluripotent stem cell (iPSC)-derived astrocytes from a SLOS patient with DHCR7 c.C278T mutation and the isogenic control to investigate genes and pathways affected by the disease status.

first: Keiji

last: Kawatani

first: Takahisa

last: Kanekiyo


title: Comprehensive gene expression analysis of Huntington disease model mouse brains using Transcriptome Tomography

status: Public on Dec 05 2025

city: Wako-shi

first: Yuko

last: Okamura-Oho

state: Saitama

address: 2-1, Hirosawa

country: Japan

institute: RIKEN

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

overall_design: Refer to individual Series


title: Astrocyte Transcriptomics in a Three-Dimensional Tissue-Engineered Rostral Migratory Stream

status: Public on Dec 04 2025

city: Philadelphia

first: D Kacy

last: Cullen

state: PA

address: 3320 Smith Walk, 105E Hayden Hall

department: Neurosurgery/Bioengineering

country: USA

institute: University of Pennsylvania

type: Expression profiling by high throughput sequencing

summary: The glial tube is a longitudinal structure predominantly composed of densely bundled, aligned astrocytes that projects from subventricular zone (SVZ) to olfactory bulb. Neural precursor cells (NPCs) generated in the SVZ migrate through this glial tube – referred to as the rostral migratory stream (RMS) – to replace olfactory bulb interneurons in the mammalian brain.  RMS astrocytes have distinct morphological and functional characteristics. These characteristics facilitate the unique purpose of the RMS as an endogenous living scaffold directing NPC migration and maturation. However, the transcriptomic factors underlying these unique structure-function attributes versus standard stellate astrocytes have not been examined. We previously developed biofabrication techniques to create the first tissue-engineered rostral migratory stream (TE-RMS) that replicates key features of the glial tube in vivo. We have shown that TE-RMS astrocytes exhibit elongated nuclei, longitudinally aligned intermediate filaments, and enrichment of key functional proteins – cytoarchitectural and surface features characteristic of native RMS astrocytes. In the current study, we performed RNAseq on TE-RMS astrocytes in comparison to planar astrocyte cultures to identify gene expression patterns that may underlie their profound morphological and functional differences. Remarkably, we found 4008 differentially expressed genes in TE-RMS astrocytes, with 2076 downregulated (e.g. LOC690251, ccn5) and 1932 upregulated (e.g. lrrc45, cntn1) compared to planar astrocytes. Moreover, there were 256 downregulated and 91 upregulated genes with >3-fold change. We also conducted analyses of gene sets related to cytoskeleton and nuclear structure, revealing greatest enrichment of actin-related components. Overall, the TE-RMS offers a platform to study interplay between transcriptomic and cytoarchitectural dynamics in a unique astrocyte population.

overall_design: RNAseq profiling of rat astrocytes in a planar 2D culture (2Dastro) vs rat astrocytes in a 3D tissue engineered Rostral Migratory Stream (TE-RMS)

first: Michael

middle: R

last: Grovola

first: Erin

middle: M

last: Purvis

first: Andres

middle: D

last: Garcia-Epelboim

first: Elizabeth

middle: N

last: Krizman

first: John

middle: C

last: O'Donnell


title: Spatial and functional dissection of cancer-associated fibroblasts-mediated immune modulation in H. pylori-associated gastric cancer [LACE-seq]

city: Zhuhai

first: Hongzhen

last: Tang

state: Guangdong

address: Cuijing Road, Qianshan, Xiangzhou District

country: China

institute: BioMega Spatiotemporal Pathology Research Center

summary: We identify four transcriptionally and spatially distinct CAF subtypes with differential immune associations across histological and infection-defined subtypes of GC. Notably, in H. pylori-positive tumors, THBS1+ CAFs exhibit a strong spatial association with regulatory T cells and are linked to local immunosuppression via WNT-FZD interactions. In parallel, the RNA-binding protein ZFP36 post-transcriptionally represses FN1 expression, thereby attenuating FN1+ CAF-mediated cytotoxic T cell engagement.

overall_design: LACE-seq was performed in the human gastric cancer cell line HGC-27 to map endogenous ZFP36–RNA interactions using four independent biological immunoprecipitation (IP-only) replicates processed in parallel (no IgG/Input controls). Cells were cultured under standard conditions (RPMI-1640 + 10% FBS, 37 °C, 5% CO₂) and harvested at ~70–80% confluence, then subjected to laser-assisted UV crosslinking on ice to covalently fix RNA–protein complexes. Crosslinked lysates were prepared under RNase-controlled conditions and incubated with a ZFP36-specific antibody immobilized on protein A/G magnetic beads; after stringent high-salt and detergent washes to reduce nonspecific binding, complexes were eluted, digested with proteinase K to release crosslinked RNA fragments, and purified by silica-membrane columns. RNA fragments underwent 3′/5′ adaptor ligation, reverse transcription, and limited-cycle PCR amplification with unique sample indices, followed by size selection (enriching ~50–150-nt inserts) and library QC (Bioanalyzer profile and qPCR quantification). Indexed libraries were pooled equimolarly and sequenced on an Illumina platform using paired-end reads, with replicate processing steps randomized where feasible to mitigate batch effects.

first: Bonan

last: Chen


title: Methionine deficiency causes spermatogonial apoptosis via oxidative stress and DNA damage response pathway

city: guangzhou

first: Weiyong Wang

last: Wang

address: 382 Outer Ring East Road, Guangzhou Higher Education Mega Center

institute: south china university of technology

summary: Methionine serves as an essential amino acid regulating de novo protein synthesis and redox homeostasis. Previous studies have established adverse impacts of methionine restriction and deprivation on semen quality, but effects on early spermatogenesis remain poorly characterized. In this study, methionine dietary model (0.86%, 0.17%, 0%) was used to investigate the role of methionine in early spermatogenesis. The results indicated that methionine deprivation caused spermatogenesis defects by inhibiting spermatogonial proliferation and increasing apoptosis. Further studies showed that methionine deprivation downregulated mitochondrial function-related genes (Gpx4, Fis1 and Gstm1), but upregulated ISR- (Atf4, Chac1 and Ddit3) and DNA damage response-related genes (Cdkn1a, Chek2 and Atm). Meanwhile, methionine deprivation caused mitochondrial dysfunction characterized by mitochondrial membrane potential depolarization, ROS accumulation, and MitoSOX accumulation. Methionine deprivation also caused an obvious increase in DNA damage response proteins (γH2AX, p-CHK2 and p-p53) and pro-apoptotic proteins (PUMA, BAX and c-PARP1), but suppressed anti-apoptotic protein BCL2. Furthermore, NAC effectively reversed the proliferation deficiency of GC-1 cells caused by methionine deprivation. Collectively, these findings suggest that methionine deprivation triggers ISR activation, which subsequently induces spermatogonial apoptosis via oxidative stress and the CHK2-p53/p21 signaling cascade. This study highlights the critical role of methionine in early spermatogenesis, provides mechanistic insights for optimizing dietary interventions and addresses related reproductive disorders.

overall_design: Methionine restriction or deprivation was performed in mice and GC-1 cells. Proliferation, apoptosis, and blood-testis barrier integrity in the testes were examined. Finally, mechanisms were investigated through transcriptome analysis, immunofluorescence staining, and Western blotting.

first: Weiyong

first: Yong

last: Ruan

first: Ting

last: Gong


title: Phosphatidylserine and RhoB connect phosphatidylinositol 4-phosphate and phosphatidic acid metabolism at the plasma membrane

city: Ithaca

first: Saori

last: Uematsu

state: New York

address: 526 Campus Road, Cornell University

institute: Cornell University

summary: Cells tightly control the homeostatic levels and subcellular localizations of membrane phospholipids through the regulation of the activities of numerous lipid-metabolizing enzymes and lipid transfer proteins. Yet, the mechanisms by which lipid imbalances are sensed and corrected to establish and maintain homeostasis are, in many cases, unknown. Here we present an expanded view of plasma membrane phosphoinositide metabolism by revealing an unexpected metabolic connection between two key anionic lipids in this membrane, phosphatidylinositol 4-phosphate (PI4P) and phosphatidic acid (PA). Plasma membrane pools of PI4P are generated by PI 4-kinase Type IIIα (PI4KIIIα/PI4KA), an essential enzyme whose partial dysfunction leads to numerous hereditary human diseases. We find that depletion of PI4P by pharmacological inhibition of PI4KA increases the activity of phospholipase Ds (PLDs) and the levels of their lipid product, PA. Guided by RNA-seq analysis and proximity labeling proteomics, we elucidate how cells connect this PI4P decrease to a compensatory increase in PA levels. Loss of plasma membrane PI4P induces a concomitant decrease of phosphatidylserine (PS) levels, and this metabolic rewiring activates a reciprocal relationship between PS synthesis and PLD-mediated PA generation. These metabolic changes lead to transcriptional and translational upregulation of the small GTPase RhoB, which enhances PLD-mediated PA synthesis and subsequent actin cytoskeletal remodeling. Our study reveals how disease-relevant perturbation of phosphoinositide synthesis induces an integrated response that ultimately boosts levels of a key anionic lipid and metabolic intermediate in phosphoinositide resynthesis.

overall_design: Ribo-seq and mRNA-seq from HEK293T cells treated with GSK-A1 at different timepoints (0, 60, and 360 min).


title: Extraskeletal Osteosarcoma Harboring ETV6:NTRK3 Fusion Treated Successfully with Larotrectinib: A Case study [Archer Fusion Plex Pan Solid Tumor v2 panel]

city: Graz

first: Kristijan

last: Skok

address: Neue Stiftingtalstraße 6

department: Diagnostic and Research Institute of Pathology

country: Austria

institute: Medical University of Graz

summary:
Background: Extraskeletal osteosarcoma (ESOS) is a rare, aggressive mesenchymal tumor with limited therapeutic options and a poor prognosis due to frequent metastases. Identifying targetable genetic alterations could improve treatment outcomes. The objective is to report the first worldwide case of ESOS harboring an ETV6::NTRK3 fusion and describe the clinical response to larotrectinib, a selective TRK inhibitor.
Methods: Case report of a 74-year-old man with a rapidly enlarging, inoperable neck tumor measuring 7.9 x 7.1 x 6.6 cm. The case underwent histopathological, immunohistochemical, and molecular analyses, including targeted RNA sequencing using the Archer Fusion Plex Pan Solid Tumor v2 panel and DNA-based targeted analysis with the Ion Torrent Oncomine Comprehensive Assay Plus. The clinical course was monitored over an 8-month treatment period.
Results: Molecular analysis revealed an actionable, in ESOS previously not described, ETV6::NTRK3 fusion. Treatment with larotrectinib (100 mg twice daily) led to a rapid clinical response within 3 weeks. MRI demonstrated partial remission after 2 months (4.7 x 3.9 x 2.8 cm), with further tumor shrinkage at 8 months (4.4 x 3.7 x 2.4 cm). Despite complications, including urothelial carcinoma recurrence requiring chemotherapy and surgery, larotrectinib was resumed with dose adjustments. No significant adverse effects related to TRK inhibition were observed.
Conclusions: This case represents the first reported instance of ESOS with an NTRK fusion. The rapid and sustained response to larotrectinib highlights the potential of precision medicine in managing rare and aggressive tumors, emphasizing the importance of molecular profiling to identify actionable targets.

first: Florian

last: Ochsenhofer

first: Raphael

last: Gassner

first: Andreas

last: Leithner

first: Joanna

last: Szkandera

first: Christian

last: Viertler

first: Sonja

last: Hasenschwandtner

last: Reichinger

first: Bernadette

last: Liegl-Atzwanger


title: Identification of Differentially Expressed Genes and Associated Immune Cell Types In South African Gallbladder Cancer Patients

city: Parktown, Johannesburg

first: Ekene

last: Nweke

state: Gauteng

address: 7 York Road

department: Surgery

country: South Africa

institute: University of the Witwatersrand

summary: Introduction: Gallbladder cancer (GBC) is a highly aggressive malignancy with limited therapeutic options, particularly in underrepresented populations, including South Africa. Understanding the molecular landscape of GBC may provide novel insights into its pathogenesis and potential therapeutic targets. Molecular changes are known to be associated with GBC, however, there is a paucity of this information especially in African populations. Furthermore, within the tumour microenvironment, different immune cells contribute to GBC progression. We investigated gene expression patterns in GBC tumours and their association with different immune cells in a cohort of South African patients. Methods: RNA sequencing was conducted on 2 normal and 8 gallbladder cancer tissues from South African patients (Ethics: M160640) to identify differentially expressed genes. Bioinformatics tools were used for pathway analysis, while immune cell quantification was performed using the quanTIseq software and presented as median [IQR]. Verification studies were further carried out using real-time PCR on an independent cohort comprising 7 gallstone samples and 26 gallbladder tumour samples. Results: A total of 65 genes were found to be significantly differentially expressed between the gallbladder tumours and gallstone controls.  We also identified 37 upregulated and 28 downregulated genes in this cohort. Among the most upregulated genes, MUC16 was confirmed to be significantly overexpressed in tumours. Normal tissues exhibited a significantly higher proportion of dysregulated genes associated with B cells (17.132 [14.866–18.483], p<0.0001) and M1 macrophages (18.943 [1.097–36.790], p<0.0001) compared to tumours. In contrast, tumours showed a greater association with dysregulated genes linked to regulatory T cells (Tregs) (14.373 [9.696–20.162]) relative to normal tissues. Pathway analysis further revealed the upregulation of defective GALNT12, defective GALNT3, defective C1GALT1C1 and termination of O-glycan biosynthesis, highlighting key mechanisms potentially involved in tumour progression. Conclusion: The study has shown the dysregulation of key genes in South African gallbladder cancer patients. Specifically, MUC16 was verified to be significantly elevated in tumour samples. Furthermore, the association of these dysregulated genes with key immune cells in this patient group may further highlight their roles in dysfunctional immune processes linked with tumourigenesis.

overall_design: RNA-seq profiling of Gallbladder tumours (8) and normal gallbladder tissues (2)

last: Devar

first: Pavan

last: Baichan

first: Phelelani

middle: T

last: Mpangase

first: Nnenna

last: Elebo

first: Geoffrey

last: Candy

first: Martin

last: Smith

first: Ekene Emmanuel


title: Extraskeletal Osteosarcoma Harboring ETV6:NTRK3 Fusion Treated Successfully with Larotrectinib: A Case study [Ion Torrent Oncomine Comprehensive Assay Plus]

overall_design: The case underwent histopathological, immunohistochemical, and molecular analyses, including targeted RNA sequencing using the Archer Fusion Plex Pan Solid Tumor v2 panel and DNA-based targeted analysis with the Ion Torrent Oncomine Comprehensive Assay Plus.


title: Ramulus Mori (Sangzhi) Alkaloids Attenuate Diet-Induced Obesity by Promoting White Adipose Browning and Enhancing Brown Fat Thermogenesis

city: Chengdu

first: nanwei

last: tong

address: No. 37, Guoxue Alley, Wuhou District

department: Department of Endocrinology and Metabolism

institute: West China Hospital of Sichuan University

summary: Obesity is a chronic metabolic disorder characterized by excessive adipose accumulation and is closely associated with type 2 diabetes mellitus (T2DM), cardiovascular diseases, and metabolic dysfunction associated steatotic liver disease. Enhancing adipose thermogenic capacity has emerged as a promising strategy to counteract obesity. Ramulus Mori (Sangzhi) alkaloids (SZ-A), a natural alkaloid complex clinically approved for T2DM, exhibit multiple metabolic benefits, but their anti-obesity mechanisms remain unclear.

overall_design: In this study, male C57BL/6 mice were fed a high-fat diet (HFD) for 14 weeks and subsequently treated with SZ-A (200 or 600 mg/kg) for 6 weeks. SZ-A markedly reduced HFD-induced weight gain independent of food intake, improved glucose tolerance and insulin sensitivity, and alleviated dyslipidemia and hepatic steatosis. SZ-A also decreased adipose tissue mass and upregulated key thermogenic regulators and beige adipocyte markers in white adipose tissue (WAT). In brown adipose tissue (BAT), SZ-A restored thermogenic activity by enhancing uncoupling protein 1 (UCP1) expression and improving tissue morphology. In vitro, SZ-A increased the expression of thermogenic and mitochondrial biogenesis–related genes in 3T3-L1 adipocytes, promoting a beige-like phenotype. Transcriptomic profiling further revealed activation of fatty acid catabolism, oxidation pathways, and enrichment of brown adipocyte differentiation signatures. Collectively, these findings demonstrate that SZ-A exerts potent anti-obesity effects through dual actions on WAT browning and BAT thermogenesis. Given its established clinical safety, SZ-A represents a promising therapeutic candidate for adipose-based obesity and metabolic disorders.

first: Nanwei

last: Tong


title: Spatiotemporal remodeling of chromatin topology architecture and H3K27me3 redistribution underlies vascular pathology in Hutchinson-Gilford progeria syndrome [CUT&Tag]

city: Ottawa

first: William

middle: L

last: Stanford

state: ON

address: 501 Smyth Rd

country: Canada

institute: Ottawa Hospital Research Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Hutchinson-Gilford progeria syndrome (HGPS) is a devastating premature aging disorder driven by the accumulation of progerin, leading to severe vascular pathology. While epigenetic alterations are implicated, the spatiotemporal reorganization of the higher-order chromatin and its functional impact on vascular smooth muscle cell (VSMC) transcription remain poorly defined. Through an integrated multi-omics approach combining in situ high-throughput chromosome conformation capture (Hi-C) and Cleavage Under Targets and Tagmentation (CUT&Tag) profiling of CTCF, SMC1A, H3K27me3, H3K27ac, and H3K36me3 with transcriptomic analyses from control and HGPS iPSC-derived VSMCs, we reveal that global topologically associating domain (TAD) architecture remains largely intact in HGPS. However, the internal chromatin states of TADs undergo dynamic, passage-specific remodeling, characterized by a progressive accumulation of broad H3K27me3-repressed domains. This is accompanied by a loss of A/B compartment segregation, as confirmed by DNA-FISH, indicating a collapse of higher-order chromatin organization in late passage. Crucially, we uncover widespread rewiring of enhancer-promoter (E-P) loops, which is linked to the dysregulation of genes critical for vascular development, extracellular matrix organization, and atherosclerosis. Our study demonstrates that spatiotemporal redistribution of repressive histone marks and reorganization of E-P interactions within a structurally resilient TAD framework underpin widespread transcriptional dysregulation in HGPS vascular pathogenesis. This uncovers a critical dissociation    between higher-order chromatin architecture and epigenetic statehistone modification landscape, providing a mechanistic basis for the failure of vascular homeostasis in progeria.

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) profiling of CTCF, SMC1A, H3K27me3, H3K27ac, and H3K36me3 in vascular smooth muscle cell differentiated from patient-derived induced pluripotent stem cells

first: Mzwanele

last: Ngubo

first: Naveen

last: Ahuja

first: Rana

last: Karimpour

first: Amit

last: Shrestha

first: Michael

middle: J

last: Hendzel

first: Theodore

last: Perkins


title: Single-cell multi-omic and multi-region atlas of the Human Alzheimer's Disease Brain

city: La Jolla

first: Joseph

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Alzheimer’s disease (AD) is the leading cause of dementia, driven by complex molecular alterations that disrupt neural and glial cell function. However, the precise epigenomic and chromatin regulatory changes underlying AD pathogenesis across different brain regions remain incompletely understood. To address this, we generated a comprehensive single-cell multi-omic atlas of the human AD brain. We profiled 11 AD donors and 9 age-matched healthy donors, spanning three key brain regions implicated in AD pathology: the visual cortex (VC), temporal cortex (TC), and prefrontal cortex (PFC). Using single-nucleus methylome sequencing (snmC-seq3) and joint profiling of chromatin conformation and DNA methylation (snm3C-seq), we obtained extensive datasets enabling integrated analysis of transcriptional regulation, epigenetic remodeling, and 3D genome architecture. This resource allowed us to characterize AD-associated alterations in DNA methylation at promoters, enhancers, and transposable elements, as well as their consequences on transcription factor motif accessibility. At the chromatin level, we identified disease-related changes in higher-order genome organization, including compartments, topologically associating domains (TADs), and loops. By comparing multiple cortical regions, we also uncovered regional heterogeneity within matched cell types, highlighting both shared and region-specific epigenetic signatures of AD. Together, this atlas provides a systematic, multi-region view of single-cell epigenomic landscapes in AD and offers insights into regulatory mechanisms underlying disease progression.

overall_design:
We analyzed postmortem brain tissue from 20 human donors (11 clinically and neuropathologically confirmed AD cases, 9 healthy controls), with balanced representation of males and females. For each donor, the visual cortex (VC), temporal cortex (TC), and prefrontal cortex (PFC) were dissected. Frozen tissue samples were processed for nuclei isolation using established protocols. Single-nucleus methylome sequencing (snmC-seq3) and joint methylome–chromatin conformation profiling (snm3C-seq) were performed, yielding multiple technical and biological replicates per donor and brain region. No statistical methods were used to predetermine sample size; rather, the cohort size was determined by tissue availability and designed to capture both inter-individual and inter-regional heterogeneity. Randomization and blinding were not performed during tissue handling. All samples were processed in a standardized pipeline to minimize technical variability.

Samples are included in:
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE308668
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE308906

first: Wenliang

last: Wang

first: Anna

last: Bartlett

last: Nery

first: Rosa

last: Gomez Castanon

first: Chumo

last: Chen

first: Jordan

last: Altshul

first: Cynthia

last: Valadon


title: Sibling Cell size contributes to cell cycle progression and cell fate decisions in asymmetrically dividing Drosophila neural stem cells

city: Seattle

first: J.

middle: Ian

last: Hertzler

state: WA

address: 3745 W Stevens Wy NE

department: Biology

institute: University of Washington

summary: We used 10x single cell RNAseq technology to explore the differences in cell types generated by aberrant division of neuroblasts. Drosophila neuroblasts, neuronal stem cells, divide asymmetrically such that the apical, large cell renews as a neuroblast and the basal, small cell is destined to become either a neuron or a glial cell. We use two manipulations that result in symmetric or inverted asymmetric divisions of neuroblasts. We used single cell RNA sequencing to learn more about the effects that symmetric and inverted divisions have on both neuroblast and neuronal identity.

overall_design: Drosophila larvae were allowed to grow from 72-96hr after egg laying. Larval brains were dissected and type 1 neuroblasts and their lineages expressing our two genetic manipulations, as well as type 1 lineages in control brains, were captured with FACS sorting.

first: Clemens

last: Cabernard

first: J. Ian

first: Chang

last: Yin


title: DNA methylation alterations in acute lymphoblastic leukemia survivors with late neurocognitive deficits: NPG cohort

city: Toronto

first: Sarah

middle: J.

last: Goodman

address: PGCRL, 686 Bay St.

department: Genetics and Genome Biology

institute: Hospital for Sick Children

type: Methylation profiling by genome tiling array

summary: Many survivors of acute lymphoblastic leukemia (ALL) develop late effects that include lifelong impairments in cognitive function. We examined DNA methylation (DNAm) patterns in healthy blood from two independent cohorts of ALL survivor to 1) identify distinct genome-wide DNAm alterations (signatures) in survivors, and establish long-term epigenetic dysregulation as a common outcome of ALL treatment, and 2) elucidate the role of epigenetics as a biomarker and potential mechanism of neurocognitive deficits in ALL survivors. We identified a signature of 452 CpG sites in the blood of ALL survivors vs. controls, that demonstrated ~99% sensitivity and 85% specificity, irrespective of time elapsed from the end of treatment. Using St. Jude LIFE as a validation cohort, we found that survivors of non-ALL childhood cancers carried a different DNAm signature. Finally, we found 43 distinct CpGs associated with neurocognitive deficits as defined by the neuropsychological test, DIVERGT, that replicated across our two cohorts of ALL survivors. We propose DNAm as a potential biomarker that could predict patients most likely to experience neurocognitive deficits following ALL treatment and inform early interventions.

overall_design: Venous blood samples were collected from ALL survivors participating in the NPG study, at least two after the completion of chemotherapy treatment for ALL. Genomic DNA was extracted, bisulfite converted and DNA methylation was assayed on the Infinium MethylationEPIC Bead Chip array (GPL21145). Healthy controls described in the associated publication are not included here due to lack of consent for public deposition of data. There are no replications in this submission.

first: Darci

last: Butcher

first: Sharon

last: Guger

first: Eric

last: Diehl

first: Jack

last: Brzezinski

first: Brenda

last: Spiegler

first: Brian

last: Nieman

first: Prajkta

last: Kallurkar

first: Aubrée

middle: B

last: Craig

first: Maja

last: Krajinovic

first: Julie

last: Laniel

first: Caroline

last: Laverdière

first: Daniel

last: Sinnett

last: Lippé

first: Andrei

last: Turinsky

first: Mary

last: Shago

first: Lisa

last: Strug

first: Shinya

last: Ito

first: Johann

middle: K

last: Hitzler

first: Russell

last: Schachar

first: Rosanna

last: Weksberg


title: Hierarchical regulation of cerebellar neurogenesis by Sin3A-mediated gene repression (ChIP-seq)

city: Nashville

first: Lei

last: Chen

state: TN

address: 465 21st Ave. South

department: Department of Cell and Developmental Biology

institute: Vanderbilt University

summary: Cerebellar granule cells (GCs) are critical for motor and cognitive functions. Lineage tracing studies have identified a hierarchical developmental progression of GC neurogenesis, transitioning from Sox2+ stem-like quiescent cells to Atoh1+ rapidly proliferating granule cell precursors (GCPs), and ultimately to NeuN+ mature GCs. However, the molecular mechanisms governing these transitions remain poorly understood. Here, we demonstrate that Sin3A, a core component of the histone deacetylase (Hdac) complex, plays a sequentially essential role in driving GC lineage progression across distinct precursor stages. In Sox2+ cells, Sin3A facilitates their transition to GCPs by repressing Sox2 expression. In GCPs, Sin3A suppresses Atoh1 transcriptional activity by recruiting Neurod1 as a co-repressor, thereby promoting GCP differentiation. Additionally, Sin3A ensures the survival and specification of GCPs by repressing non-lineage-specific gene expression. Our findings highlight the central role of the Sin3A complex in orchestrating distinct stages of cerebellar GC lineage development.

overall_design: ChIP-seq of Cerebellar granule cell precursors of control and Sin3A CKO mice.

first: Chin

last: Chiang


title: Efficacy and potential mechanisms of Yi-Ping Lin Circum-knee acupuncture in the treatment of knee osteoarthritis

city: kunming

first: Xingyou

last: Deng

state: --- Select One ---

address: 120 Guanghua Street, Kunming City, Yunnan Province

institute: Yunnan Provincial Hospital of Traditional Chinese Medicine

summary:
Background: Degenerative knee osteoarthritis (KOA) may lead to disability in adults. Current treatment modalities for KOA often involve significant side effects and high costs. Yi-Ping Lin Circum-knee Acupuncture (CKA-L) emerged as a cost-effective and nearly side-effect-free alternative. However, its efficacy and the underlying mechanisms remain unclear, which raised our concern.
Methods: Female SD rats were randomly divided into 4 groups: Sham, Model, CKA-L treatment (Treatment), and positive control (Piroxicam). The Arthritis Index (AI) and body weights were recorded. ELISA was used to quantify levels of IL-1β and TNF-α. X-ray, HE, and Toluidine blue staining were employed to assess cartilage regeneration. Transcriptome sequencing was performed on Sham, Model, and Treatment groups. Functional enrichment analysis alongside PPI. RT-qPCR and western blot were utilized to determine the hub genes.
Results: Both CKA-L and piroxicam effectively alleviated KOA, albeit with slower response times for CKA-L. ELISA results demonstrated significant reductions in pro-inflammatory cytokines, with a pronounced decline in TNF-α in the Treatment group. CKA-L markedly increased chondrocyte populations and narrowed the knee joint gap. Transcriptome analysis identified 3,363 DEGs. Functional enrichment analyses highlighted significant associations with DNA repair, inhibition of cysteine-type endopeptidases, and cell-cycle regulation. The PPI analysis of DEGs designated five hub genes: Bgn, Ctsb, Lum, Serpine1, and Tnfaip6, which demonstrated consistent transcriptional and translational expression levels.
Conclusion: CKA-L promotes chondrocyte proliferation and provides effective treatment for KOA, with the advantages of low price, low side effects, and convenient operation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for sham, model and treatment.

first: Lijun

last: Huang


title: Integrated Transcriptomics and Physio-Biochemical Revealed Key Genes of Seed Hulls Affecting Seed Germination of Leymus chinensis

city: Hohhot

first: yumei

last: Feng

address: No. 120, Ulanqab East Road, Saihan District

institute: Institute of Grassland Research, Chinese Academy of Agricultural Sciences

summary: In this study, RNA-seq analysis of seeds at different developmental stages was carried out to explore the potential regulatory factors of seed hulls affecting seed germination of L. chinensis.

overall_design: de-hulled and hulled seeds were soaked in sterile water for 12h and for normal germination. Subsequently, samples were collected at 0 day, 2 days and 7 days after germination, respectively. These samples were defined as DH_CK_0, DH_CK_2, DH_CK_7, H_CK_0, H_CK_2, and H_CK_7, respectively. Transcriptomic analyses were performed by Shanghai OE Biotech Co., Ltd (Shanghai, China). All of the experiments contained three replicates. (The original data name of DH_CK_0 is H_CK_0；DH_CK_2 is H_CK_2；DH_CK_7 is H_CK_7；H_CK_0 is HP_CK_0；H_CK_2 is HP_CK_2；H_CK_7 is HP_CK_7)

first: Yumei

first: Wenlong

last: Gong

first: Lemeng

last: Liu

first: Chunyu

last: Tian

first: Yanting

last: Yang

first: Zinian

last: Wu


title: Integrative multi-omics deciphers the potential mechanism and microbial biomarkers for lymph node metastasis in colorectal cancer

city: Seoul

first: Min Seob

last: Kwak

address: 892, Dongnam-ro, Gangdong-gu

country: South Korea

institute: Kyung Hee university

summary: Understanding and accurate diagnosis of lymph node metastasis (LNM) for patients with colorectal cancer (CRC) is essential to determine treatment and follow-up strategies. Therefore, in this study, we aimed to elucidate the biological process and identify the potential biomarker for LNM in CRC.  In total, 12 significant DEGs between the patients with and without LNM were identified, consisting of significantly upregulated S100A8 gene, a proinflammatory gene. The GSEA revealed that gene sets involving “MULTI CANCER INVASIVENESS” in terms related to epithelial-mesenchymal transition was significantly upregulated in the patients with LNM. Integrated functional analysis of DNA methylation with transcriptome profile shows that significantly hypomethylated promoters of the genes are enriched for LNM. The phylum Proteobacteria, unassigned (p_PU) presented significantly higher proportions in cancer tissues from the adjacent normal tissues. Notably, when compared to the patients without LNM, the gut microbiota of those with LNM appears to exhibit a significantly lower abundance of the p_PU, indicating its potential as promising biomarker for LNM in CRC. We explained the mechanism of tumor spreading using multi-omics analysis and identified the relevant metagenomic biomarker to predict the LNM in CRC by the recognition of host-microbial interaction, thereby can make the cancer surveillance of the patients more individualized and convincing.

overall_design: A total of 33 patients who received a histologically confirmed diagnosis of CRC with Stage I to III and a curative surgery between November 2020 and July 2021 at Kyung Hee university hospital at Gangdong were included. We performed multi-omics approach integrating the data on somatic mutation, transcriptomic expression, DNA methylation, and microbiome with tumor and adjacent matched normal tissues of each patient.

first: Jae Myung

last: Cha

first: Chang Woo

last: Kim

first: Kyu Yeoun

last: Won

first: Chang-Il

last: Hwang


title: Virally encoded interleukin-6 (vIL-6) coordinates with human IL-6 to modulate cytokine expression during KSHV infection

city: Springfield

first: Yahaira

last: Bermudez

state: MA

address: 15 Oakhurst street

department: Microbiology

institute: University of Massachusetts, Amherst

summary: Kaposi Sarcoma-Associated Herpesvirus (KSHV) is characterized by its ability to establish lifelong infections that can lead to disease in immunocompromised individuals. Understanding the complex interactions between KSHV, the host cellular machinery, and the immune response is essential for unraveling the mechanisms underlying viral persistence and pathogenesis. KSHV extensively remodels the host gene expression landscape by inducing widespread RNA decay via the viral endoribonuclease SOX. While the vast majority of cellular mRNAs are degraded by SOX, select transcripts including Interleukin 6 (IL-6) escape degradation. Interestingly, KSHV encodes a viral homolog of the IL-6 transcript, known as viral interleukin-6 (vIL-6). Given the importance of IL-6 for KSHV biology and its ability to escape SOX-mediated decay, we explored how vIL-6 expression is regulated upon KSHV infection. Our data demonstrate that unlike IL-6, vIL-6 3’UTR does not provide protection from SOX degradation, yet vIL-6 mRNA steady state levels remain high throughout KSHV lytic cycle, suggesting a distinct transcriptional regulation. To assess the contributions of vIL-6 and IL-6 in modulating host genes expression, inflammatory signaling and KSHV-driven pathogenesis, we used a vIL-6 null viral mutant combined with an IL-6 knock down to perform transcriptomic analyses. This analysis revealed that depletion of IL-6, vIL-6 or both results in distinct alterations of the host gene expression environment, with differential effects on chemokine signaling and related pathways as well as a synergetic effect when both IL-6 and vIL-6 are present. Furthermore, functional assays confirmed vIL-6 alone is sufficient to activate key signaling pathways and pro-inflammatory responses, including the JAK/STAT pathway. Collectively, our findings suggest a mechanistic synergy between vIL-6 and IL-6 that may enhance KSHV-mediated immune modulation and contribute to viral persistence and tumorigenesis.

overall_design: RNA-seq profiling of iSLK.BAC16 vIL-6-STOP ( Delta vIL-6, null) and vIL-6-ReV (revertant, WT) cells, with or without IL-6 knockdown, during KSHV latency and lytic reactivation at 48 hours

first: Bermudez

last: Yahaira

first: Schultz

last: Samantha

first: Miles

last: Jacob

first: Dwyer

last: Will

first: Muller

last: Mandy


title: Nicotinamide counteracts endothelin-1’s detrimental effect on uterine decidualization during early pregnancy by influencing EDNRB

city: chapel Hill

first: Feng

last: Li

state: NC

address: 101 medical drive

department: Pathology

institute: UNC at CH

summary: Endothelin-1 is involved in pathogenesis of preeclampsia. Mice (Edn1H/+) having excess endothelin-1developed preeclampsia-like phenotypes during pregnancy in a maternal genotype-dependent manner. Here, we investigate whether decidualization is impaired in Edn1H/+ dams, and whether nicotinamide (a potent inhibitor of endothelin-1) executes any beneficial effect. We compared implantation sites between wild type (WT) and Edn1H/+ dams with or without nicotinamide treatment. Implantation sites of Edn1H/+ dams exhibited abnormal ectoplacental cone and sinusoids with reduced vascular density in mesometrial regions of deciduae. There was more VEGF expression in decidua of Edn1H/+ dams than WT dams. The markers of decidualization were decreased in Edn1H/+ dams. Nicotinamide corrected the abnormality in Edn1H/+ dams. During differentiation (decidualization) of cultured human endometrial stomal cells, endothelin-1 halved the upregulated expression of markers of decidualization.  Nicotinamide normalizes their expression. Nicotinamide counteracts ET-1’s detrimental effects on endometrial decidualization. It has potential to improve embryo implantation and subsequent pregnancy outcomes.

overall_design: a unilateral renal IRI model was established in wild-type (WT) and ELMO1-overexpressing (Elmo1 H/H) mice.

first: Yuye

last: Wang


title: Genetic profiling of first-trimester chorionic villus samples using Affymetrix CytoScan 750K arrays

city: Hefei

first: Qi

last: Zhang

state: Anhui

address: No. 15, Yimin Street, Shushan District, Hefei City, Anhui Province

institute: Anhui Women and Children's medical center

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: While chromosomal microarray analysis (CMA) is increasingly utilized in prenatal diagnosis, most research focuses on mid-to-late pregnancy amniotic fluid samples. Chorionic villus samples (CVS) from the first trimester possess distinct biological characteristics. To evaluate the efficacy of CMA in early pregnancy prenatal diagnosis, we performed a genomic analysis of CVS from high-risk pregnancies.We conducted a single-center cohort study of singleton pregnancies that underwent CVS between 11⁺⁰ and 13⁺⁶ weeks of gestation. Indications for testing included advanced maternal age, ultrasound-detected soft markers or structural anomalies, abnormal first-trimester serum screening, or adverse obstetric history. All villus samples were analyzed using CMA (Affymetrix CytoScan 750K arrays). Among the samples analyzed by CMA, 16.6% showed chromosomal abnormalities, with CNVs accounting for 58.9% of these cases. Compared with other indicators, the detection rate was significantly higher in the group with ultrasound abnormalities. Complex ultrasound abnormalities, in particular, hold greater clinical significance. This study demonstrates the utility of CMA for detecting chromosomal abnormalities in first-trimester CVS. Our findings support the integration of CMA into early prenatal diagnostic protocols.

overall_design: This dataset includes 28 chorionic villus samples obtained from pregnancies between 11-14 weeks of gestation. Genomic DNA was extracted from each sample and hybridized to Affymetrix CytoScan 750K arrays according to the manufacturer's protocols. Copy number variation and SNP genotype analyses were performed.

first: Junxiang

last: Tang


title: Medroxyprogesterone acetate inhibits tumorigenesis in mouse models of oviductal high-grade serous carcinoma

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

institute: University of Michigan

summary: Background/Objectives: Tubo-ovarian high-grade serous carcinoma (HGSC) is a highly lethal malignancy, usually diagnosed at an advanced stage due to the lack of early symptoms and biomarkers. Contraceptive hormone use is associated with reduced risk of HGSC, but the relative contributions of natural versus synthetic progestins, and their interaction with estrogens, are poorly characterized. Methods: We evaluated the chemopreventive efficacy of a synthetic progestin medroxyprogesterone acetate (MPA), progesterone (P4), and combined 17β-estradiol-progesterone (E2+P4) in a well-characterized genetically engineered mouse model (GEMM) of oviductal HGSC based on conditional inactivation of one or both alleles of the Brca1, Trp53, Rb1, and Nf1 tumor suppressor genes (BPRN-het and BPRN-homo mice, respectively). Mice received hormones or placebo via slow-release pellets implanted subcutaneously, and after induction of tumor formation, mice were monitored for tumor development, progression, and survival. Tumor incidence was assessed histologically, and hormone effects were further explored via RNA-seq analysis of oviductal tissues. Results: MPA significantly reduced HGSC incidence and delayed tumor progression compared to placebo, P4, and P4 + E2, in both BPRN-homo and BPRN-het mice, with up to 78% tumor-free survival in the MPA-treated BPRN-het cohort. P4 monotherapy did not provide significant protection vs. placebo, while the E2+P4 combination accelerated tumorigenesis and reduced survival (p < 0.0001 in BPRN-homo and p = 0.0004 in BPRN-het mice). MPA did not affect tumorigenesis in a colon cancer GEMM, or the growth of mouse HGSC-derived cells in vivo, suggesting a role for MPA in the early stages of HGSC development. Gene expression analyses showed that P4 and MPA downregulated cholesterol homeostasis, early and late estrogen response, and epithelial-mesenchymal transition pathways, though only MPA translated this into substantial tumor protection. Conclusions: These findings demonstrate that a synthetic progestin, specifically MPA, confers robust protection against HGSC development, while P4 is not effective and a combination including E2 increases risk. This work also illustrates how HGSC GEMMs can be used to compare the chemopreventive effects of various synthetic progestins on HGSC development in order to prioritize the most effective ones for use in preventing HGSC in high-risk populations.

overall_design: To identify genes in mouse oviductal epithelial tissue that are regulated by different hormones in the earliest phases of tumor development, RNA-Seq analysis was used to compare gene expression in the oviducts of Ovgp1-iCreERT2; Brca1flox/+, Trp53 flox/+, Rb1 flox/+,  and Nf1 flox/+,  (BPRN-het) mice treated with placebo, MPA, P4, or E2+P4. Mouse oviductal tissues were obtained from six groups: (1) No treatment (no pellets, no TAM, n=4), (2) TAM only (no pellets, n=4), (3) Placebo pellets + TAM (n=3), (4) P4 pellets + TAM (n=3), (5) MPA pellets + TAM (n=3), (6) E2+P4 pellets + TAM (n=3). Slow-release pellets containing steroid hormones (MPA, P4, or E2+P4) or placebo controls were implanted subcutaneously into 6–8-week-old female BPRN-het mice. Three days later, mice received intraperitoneal (i.p) Tamoxifin (TAM) injection to induce Cre expression. Mice were euthanized 14 days post TAM, and the distal portion of the oviducts were collected for RNA isolation. Paired comparisons of gene expression profiles (e.g., placebo versus P4, placebo versus MPA, and placebo versus E2+P4) were performed using the RNA-seq data obtained from these RNA samples.

first: Yali

last: Zhai

first: Rong

first: Ying

last: Feng

first: Maranne

last: Green

first: Celeste

last: Pearce

first: Malcolm

last: Pike

first: Eric

last: Fearon

first: Kathleen

last: Cho


title: Effect of depletion of  NEAT1 on gene expression of A549 cells during influenza virus infection.

city: 福州市

first: 二英

last: 徐

state: 福建省

address: 福建农林大学金山校区

department: 福建省畜禽病原感染与免疫学重点实验室

institute: 动物科学学院

summary: To investigate the function of NEAT1 in the regulation of influenza virus replication, we established A549 cell lines in which each target gene was regulated by depletion of NEAT1.

overall_design: We established a stable sh-NEAT1 cell line using A549 cells, with three replicate samples as the control group sh-LUC and three replicate experimental groups as sh-NEAT1.

first: Rongrong

last: Gu

first: Erying

last: Xu

first: Jingjie

last: Hong

first: Shasha

last: Liu

first: Jilong

last: Chen


title: Ribo-TRAPseq identifies spacially distinct roles for the anterior and posterior intestine for metabolic regulation in C. elegans

city: Davis

first: Nicolas

last: Seban

address: 1544 Newton Court

institute: UC Davis

summary: Animals must couplefood-relatedcuesin the intestinetotheirphysiology, yetit is unclearwhether discrete intestinal segments specialize in this sensing.Here, we generatecelltype-resolved translatomes of the anterior intestinal ring (INT1) and the remaining intestine (INT2-9)inCaenorhabditis elegansusing celltype-specific TRAP-seq under acute and chronicfasting/refeedingconditions. Across states, INT1 shows adistinct identity enriched for immuneand stress-response programs, including C-type lectinsand ShKT-domain families. INT1-targeted perturbations alter bacterial avoidance and survival, indicating specialized immunefunctions. Fasting/refeeding elicit divergent regulatory dynamics; modulating INT1 undulatinggeneschangesthesecretiondynamicsof an INT1-derived enteroendocrine peptide, INS-7.Mechanosensation or bacterial supernatant fails to resetthesecretionof INS-7after fasting,whereasbacteria or pyruvate restore basal levels. Pyruvate requires mitochondrial import andmetabolism;anacute blockade of pyruvate processing prevents refeeding normalization.Thus,we identify INT1 as sentinel enteroendocrine sensors that couple pyruvate-dependentmitochondrial metabolism toenteroendocrine output, providing a resource for segment-specificintestinal biology.

overall_design: Ribo-TRAPseq profiling of C. elegans intestinal cells (INT1 vs INT2-9) under fasting (acute/30min vs chronic/90min) and refeeding (acute/30min vs chronic/90min) conditions.

first: Chung-Chih

first: Supriya

last: Srinivasan


title: DNA methylation signature from acute lymphoblastic leukemia pediatric Mexican patients

city: XOCHIMILCO

first: ALAN

middle: ALBERTO

last: FONG LÓPEZ

state: CDMX

address: CALLE PRIVADA SAN LORENZO #45

country: Mexico

institute: INMEGEN

summary: Acute lymphoblastic leukemia (ALL) is the most common childhood cancer worldwide, with higher incidence and lower survival rates observed in the Mexican population. This study aimed to characterize the genome-wide DNA methylation landscape in a cohort of Mexican pediatric ALL patients. Bone marrow (BM) or peripheral blood (PB) samples were collected at diagnosis from 53 children under 17 years old with B-cell ALL, alongside BM samples from 5 pediatric non-ALL controls. DNA methylation profiling was performed using the Illumina Infinium MethylationEPIC v2.0 array. Data processing and identification of differentially methylated positions (DMPs) were conducted using the ChAMP package in R. This dataset provides a comprehensive epigenomic resource for investigating methylation-based biomarkers and dysregulated pathways in this understudied population.

overall_design: This study is based on a prospective cohort of 58 pediatric subjects from Mexico: 53 patients with newly diagnosed B-cell acute lymphoblastic leukemia (B-ALL) and 5 non-leukemia control patients. Genomic DNA was isolated from either bone marrow aspirates or peripheral blood samples collected at diagnosis using the QIAGEN Puregene Blood Core Kit. Bisulfite conversion of 500 ng of DNA was performed using the Zymo Research EZ DNA Methylation Kit. Genome-wide DNA methylation profiling was conducted using the Illumina Infinium MethylationEPIC BeadChip (v2.0). The study design is case-control. Clinical outcomes, including relapse status and overall survival, were recorded for association analysis.

first: Alan Alberto

last: Fong López

first: Juan Carlos

last: Núñez Enríquez

first: Juan Manuel

last: Mejía-Aranguré

first: Silvia

last: Jiménez-Morales


title: A Tonic Signaling Code Governs CAR-T Cell Efficacy in Diffuse Midline Glioma

city: Cincinnati

first: Richard

last: Lu

state: Ohio

institute: CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER

summary: Diffuse midline glioma (DIPG/DMG) is a uniformly fatal pediatric brain tumor. While CAR T-cell therapy holds promise, clinical responses remain inconsistent, largely due to limited CAR-T persistence and premature exhaustion. Reliable biomarkers to predict therapeutic efficacy are lacking, and proposed T-cell exhaustion or stemness markers offer limited predictive value. Here, we systematically evaluate CAR-T cells against the clinically relevant tumor antigen B7-H3 and identify tonic signaling, antigen-independent CAR activation, as a key determinant of therapeutic performance. B7-H3 CAR-T cells with minimal tonic signaling show superior tumor killing, persistence, and resistance to exhaustion in patient-derived DIPG models. Integrative single-cell and multi-omic profiling identifies a tonic signaling–associated gene signature that consistently outperforms conventional exhaustion or stemness markers in predicting CAR-T efficacy across multiple independent clinical trial datasets, including DIPG/DMG and other tumor types. Thus, our findings establish a mechanistic and predictive framework to guide CAR design and improve clinical outcomes.

overall_design: Single-cell RNA sequencing was performed using the sorted 376.96, MGA271, and Hu8H9 CAR-T cells and control T cells on day 12 of culture.

first: Bing

last: Deng

first: Dazhuan

last: Xin


title: Gcm1 ChIP-seq of C57BL/6 mouse embryonic stem cells with folate deficiency

city: Taiyuan

first: Yuan

last: Fu

state: Shanxi

address: No. 56, Xinjian South Road, Yingze District

department: Department of Biochemistry and Molecular Biology, School of Basic Medicine

institute: Shanxi Medical University

summary: In order to investigate whether folate deficiency affects Gcm1 enrichment and then affecting the activity of Wnt signaling pathway, we performed ChIP-seq of Gcm1 on  folate-free embryonic stem cells  and normal embryonic stem cells, respectively. Our sequencing data provides a new theoretical basis for the effect of folate on histone modification.

overall_design: C57BL/6 mouse embryonic stem cells were cultured in normal C57BL/6 mESC and folate-deficient C57BL/6 mESC for six generations.  Folate-deficient culture medium were purchased from Sigma with lot No D2429, and normal cell  medium were added with folate(Sigma:F7876) with 4mg/L. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Gcm1 in control C57BL/6 mouse embryonic stem cells  and folate-deficient C57BL/6 mouse embryonic stem cells  separately.

first: jianting

last: Li

first: Lu

first: Xiaolong

first: Qi

last: Xie

first: Xuefen

last: Wu

first: Zengli


title: Intercellular signaling and synaptic deconstruction uncovered by single-cell and spatial transcriptomics in an AD tauopathy model

city: New Orleans

first: Surjyadipta

last: Bhattacharjee

state: Louisiana

address: 2020 Gravier Street, Suite D, 8th floor

department: Neuroscience Center of Excellence

institute: LSU Health, New Orleans

summary: Alzheimer’s disease (AD) is the leading cause of dementia in elderly individuals worldwide; however, all the mechanisms leading to its onset and progression are not fully understood. Here, we report single-cell multiome and spatial transcriptomics analysis of the brain in a transgenic rat model of human-like tauopathy. In this advanced transgenic model, we have identified new markers of a tau-driven AD pathology and provided single-cell evidence for previously known genes implicated in AD. Our findings reveal how tau pathological hyperphosphorylation and aging alter ligand-receptor communication, transcription factor regulatory networks, and specific cellular networks. Notably, we found intriguing changes in cell communication involving glutamatergic transmission and netrin signaling as a consequence of the tauopathy. Overall, this study reinforces the concept of synaptic dysfunction as a hallmark of AD and highlights potential targets for future mechanistic investigations or novel therapeutic strategies.

overall_design: Multiome-seq: Joint snRNA-seq and scATAC-seq performed using 10x Genomics platform. Spatial-seq: performed using 10x Genomics Visium platform. Both consist of AD model rat hippocampal or cortex tissues from 10 month and 20 months old samples and wild-type counterparts.

first: Jeff

middle: X

last: Ji

first: Brian

last: Giles

first: Marie-Audrey

middle: I

last: Kautzmann

first: Alisdair

middle: P

last: Masson

first: Sonia

last: Do Carmo

first: Claudio

last: Cuello

first: Nicolas

middle: G

last: Bazan


title: Effect of Has3 deficiency on gene expression in the aorta of a mouse model of abdominal aortic aneurysms

city: Düsseldorf

first: Patrick

last: Petzsch

state: NRW

address: Universitätsstrasse 1

department: BMFZ

country: Germany

institute: UKD

summary: HAS3-derived hyaluronan (HA) is implicated in inflammatory processes of multiple human diseases. Employing a model of Angiotensin II -induced abdominal aortic aneuryms (AAA), we here examine the gene expression profiles of the aorta from Has3-deficient (Apoe/Has3-DKO) and Has3-competent (Apoe-KO) mice. We find a set of 53 differentially regulated genes involved in inflammation and leukocyte cell migration. Specifically, CXCL3 was profoundly upregulated in the aorta of Apoe/Has3-DKO, together with the pathways 'Agranulocyte adhesion and diapedesis' and 'Granulocyte adhesion and diapedesis`. Our data highlight the role of HAS3 as regulator of inflammation and immune cell recruitment in the devlopment of AAA.

overall_design: RNA seq profiling of aortic tissue from Apoe/Has3-DKO Apoe-KO mice 3 days post Angiotensin II treatment.

first: Christian

middle: O

last: Hundhausen

first: Fedor

last: Brack

first: Maria

last: Grandoch


title: BM-MSC-Derived Migrasomes Reverse Stroke-Induced Thymic Atrophy and Immunosuppression via Pin1 Delivery to Thymic Epithelial Cells

city: Guangzhou

first: Haotong

last: Yi

state: Guangdong Province

address: 600 TIANHE ROAD

department: Department of Neurology

institute: the Third Affiliated Hospital of Sun Yat-sen University

summary: This dataset comprises bulk RNA-seq and scRNA-seq data derived from thymic tissues of stroke-induced murine models. The data investigate the therapeutic effects of bone marrow-derived mesenchymal stem cell (BM-MSC)-originated migrasomes on stroke-induced thymic atrophy and immunosuppression. The results highlight the mechanistic role of BM-MSC migrasomes in reversing thymic involution and the immunosuppressive state through the specific delivery of the Peptidylprolyl Cis/Trans Isomerase (Pin1) to thymic epithelial cells (TECs). This dataset serves as a valuable resource for understanding post-stroke immunosuppression and the molecular basis of BM-MSC/migrasome-mediated therapy.

overall_design: BulkRNA-seq and scRNAseq of C57 mice on the 7th day after thymus stroke (treated with Veh, BM-MSC and Migrasome)


title: Comprehensive Funtional Mapping of ADPRylation sites on Gene Regulatory Targets of PARP1 [RNA-Seq]

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: Breast cancer molecular subtypes are based on distinct gene expression patterns. Recently, we described how subtype-specific transcription factors and their cognate enhancers drive the distinct gene expression patterns observed across breast cancer subtypes. As an extension of these studies, we employed a mass spectrometry-based proteomic approach to screen gene regulatory proteins for ADP-ribosylation (ADPRylation) across six breast cancer cell lines representing the luminal and triple-negative subtypes. Using an analog-sensitive PARP1- coupled with mass spectrometry approach, we have identified and catalogued the PARP1 ADPRylated proteome. We find that ADPRylation varies dramatically across the different subtypes of breast cancers.  We hypothesize that ADPRylation of subtype-specific gene regulatory proteins dictates their function and may influence the response of breast cancer cells to PARP inhibitors. Using RNA-seq (T-47D and MDA-MB-468) and ChIP-seq (T-47D) with or without PARP inhibitor (Olaparib) we sought to understand how the ADPRylated proteome drives gene regulation and gene expression in breast cancer. We find that Olaparib treatment modulates the binding activity of certain transcription factors in a subtype-specific manner, thereby regulating the downstream gene expression.

overall_design: Breast cancer cell lines (T-47D and MDA-MB-468) treated with DMSO (control) or Olaparib (PARP1 inhibitor).

first: Minjung

last: Kwon

first: Poulami

last: Tapadar

first: Yangyang

last: Dai

first: Sneh

last: Koul

first: Tulip

last: Nandu

first: Dan

last: Huang

first: Cristel

middle: V

last: Camacho

first: Kraus

last: W Lee


title: Spatial and functional dissection of cancer-associated fibroblasts-mediated immune modulation in H. pylori-associated gastric cancer

city: Zhuhai

first: Hongzhen

last: Tang

state: Guangdong

address: Cuijing Road, Qianshan, Xiangzhou District

institute: BioMega Spatiotemporal Pathology Research Center

summary: We performed high-plex spatial molecular imaging (NanoString CosMx SMI) on 200,182 cells collected from 71 gastric cancer samples.

overall_design: All spatial single-cell mRNA profiles were generated with NanoString CosMx SMI from 71 tumour tissue sections , yielding  200,182 spatially resolved single-cell transcriptomes for downstream analysis.

first: Bonan

last: Chen

first: Xiaohong

last: Zheng

first: Fuda

last: Xie

first: Peiyao

last: Yu

first: Yang

last: Lyu

first: Tiejun

last: Feng

first: Jialin

last: Wu

first: Jingya

last: Liu

first: Yi

last: Xu

first: Alvin

middle: H

last: Cheung

first: Canbin

last: Fang

first: Zhangding

last: Wang

first: Shouyu

first: Justin

first: Yujuan

last: Dong

first: Chi

last: Wong

first: Jun

first: William

first: Wei

last: Kang

first: Kam

last: Leung

first: Ka

middle: F

last: To


title: Comparative transcriptomic signatures of virulent and attenuated Mycobacterium bovis growing in vitro and in mice

city: Seattle

first: Hazem

last: Abdelaal

address: 1900 9th street

institute: Seattle Children's Researcch Institute

summary: Bovine tuberculosis (bTB), caused by Mycobacterium bovis (M. bovis), poses a signi!cant global health and economic burden. Despite extensive research, a comprehensive understanding of M. bovis pathogenesis, particularly its transcriptional adaptation across different growth phases and within the host environment, remains incomplete. Here, we performed a comprehensive transcriptomic analysis of virulent M. bovis and the attenuated M. bovis BCG strain (BCG) across early-log, mid-log, and stationary growth phases to elucidate the molecular underpinnings of their phenotypic distinctions. RNA sequencing revealed distinct gene expression pro!les, highlighting signi!cant differences in pathways related to cell wall biosynthesis, lipid metabolism, transcriptional regulation, protein secretion, and the PE/PPE protein family. Notably, the virulent M. bovis exhibited an upregulation of virulence-associated genes, especially those involved in lipid metabolism and secretion systems, during the transition from early- and mid-log phases to the stationary phase. In contrast, BCG demonstrated an enrichment in stress response and metabolic adaptation pathways during the similar transition. Gene network analysis of differentially expressed genes (DEGs) provided a systems-level view of the transcriptional programs governing M. bovis and M. bovis BCG physiology, identifying !ve key modules of co-expressed genes that regulate small molecules transport, amino acid biosynthesis and immune evasion in M. bovis. Furthermore, we analyzed M. bovis transcriptional responses during murine lung infection, identifying a core set of DEGs linked to host-pathogen interactions and mechanisms of persistence. These !ndings offer novel insights into M. bovis adaptation strategies during survival under de!ned, in vitro growth conditions and highlight potential targets for improved vaccine design and therapeutic interventions following further analyses during host infection.

overall_design: Cultures of Mycobacterium bovis AF2122/97 and M. bovis BCG Russia were grown in Middlebrook 7H9 with albumin dextrose catalase, pyruvate, and Tween 80 at thirty seven Celsius and harvested at three optical density points that represent early log, mid log, and stationary phases, specifically OD six hundred equal zero point five, one point zero, and two point zero. Two biological replicates were sequenced per condition. This design profiles growth phase dependent transcriptional programs and between strain differences

first: Hazem F

middle: M


title: KDM8 is a master regulator for hypoxia-induced metastatic heterogeneity in pancreatic cancer

city: New Brunswick

first: Shin-Heng

last: Chiou

state: NJ

address: 195 Little Albany St, Room 3001

department: Medicine

institute: Rutgers Cancer Institute of New Jersey

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

overall_design: Refer to individual Series


title: KDM8 is a master regulator for hypoxia-induced metastatic heterogeneity in pancreatic cancer [ChIP_Seq_K27ac]

summary: This study aims to elucidate how hypoxia promotes pancreatic cancer metastasis by suppressing the JmjC-containing histone lysine demethylase KDM8. In solid tumors, hypoxia is a key factor that reprograms cancer cells into a highly metastatic state. Hypoxia is a well-established inducer of epithelial-to-mesenchymal transition, which is associated with treatment resistance and metastasis. In addition, hypoxia promotes chromosomal instability - a hallmark of cancer and a key contributor to metastasis. Despite this, the mechanisms by which cancer cells simultaneously hijack these elements of hypoxic adaptation to promote metastasis remains unknown. We found that CRISPR-mediated targeting of Kdm8 in a genetically engineered mouse model of pancreatic ductal adenocarcinoma rewires the cancer cell transcriptomic programs, leading to a profound loss of the differentiated morphology and widespread metastatic disease. Importantly, Kdm8 suppression in normoxia recapitulates major aspects of the global epigenetic changes and the transcriptomic rewiring induced by hypoxia. Further, Kdm8 deficiency leads to mitotic defects, increased micronuclei formation, Kras copy number gains, and enhanced chromosomal instability. Notably, disruption of the demethylase function of KDM8 phenocopies the effects of KDM8 loss, whereas expression of hypermorphic KDM8 variants that are resistant to hypoxic suppression reduces metastasis beyond that achieved by the wildtype Kdm8. Through the suppression of Kdm8 demethylase activity, hypoxia unleashes a potent metastatic program by simultaneously advancing cellular plasticity and chromosomal instability.

overall_design: Bulk Histone 3 lysine 27 acetylation (H3K27ac) ChIP-Seq profiling of control (shGFP) and Kdm8 knockdown (shKdm8_1 & shKdm8_2) 688M pancreatic cell line (derived from a Kras-LSL-G12D;Trp53-LSL-R172H;Pdx1-Cre mouse) cultured in either normoxia or hypoxia in duplicates.

first: Pradeep Moon

last: Gunasekaran


title: KDM8 is a master regulator for hypoxia-induced metastatic heterogeneity in pancreatic cancer [RNA-Seq]

overall_design: Bulk RNA-Seq profiling of control (shGFP) and Kdm8 knockdown (shKdm8) 688M pancreatic cell line (derived from a Kras-LSL-G12D;Trp53-LSL-R172H;Pdx1-Cre mouse) cultured in either normoxia or hypoxia in duplicates.


title: KDM8 is a master regulator for hypoxia-induced metastatic heterogeneity in pancreatic cancer [WGS]

overall_design: Bulk WGS profiling of control (shGFP) and Kdm8 knockdown (shKdm8) 688M pancreatic cell line (derived from a Kras-LSL-G12D;Trp53-LSL-R172H;Pdx1-Cre mouse) cultured in normoxia in duplicates.


title: KDM8 is a master regulator for hypoxia-induced metastatic heterogeneity in pancreatic cancer [ATAC-Seq]

overall_design: Bulk ATAC-Seq profiling of control (shGFP) and Kdm8 knockdown (shKdm8) 688M pancreatic cell line (derived from a Kras-LSL-G12D;Trp53-LSL-R172H;Pdx1-Cre mouse) cultured in either normoxia or hypoxia in duplicates.


title: KDM8 is a master regulator for hypoxia-induced metastatic heterogeneity in pancreatic cancer [ChIP-Seq]

overall_design: Bulk H3K36me2 & H3K27me3 ChIP-Seq profiling of control (shGFP) and Kdm8 knockdown (shKdm8_1 & shKdm8_2) 688M pancreatic cell line (derived from a Kras-LSL-G12D;Trp53-LSL-R172H;Pdx1-Cre mouse) cultured in either normoxia or hypoxia in duplicates.


title: KDM8 is a master regulator for hypoxia-induced metastatic heterogeneity in pancreatic cancer [scRNA-Seq]

overall_design: Single-cell RNA-Seq (scRNA-Seq) profiling of ex vivo isolated cells from 11 samples of the Trp53-flox/flox;R26-LSL-Tomato;H11-LSL-Cas9 (PTC) mice induced to develop spontaneous PDA with CRISPR-mediated Kdm8 depletion.


title: ALS-Associated TDP-43 Dysfunction Compromises UPF1-Dependent mRNA Metabolism Pathways Including Alternative Polyadenylation and 3’UTR Length [IPS_RNASeq]

city: Chicago

first: Evangelos

last: Kiskinis

state: IL

address: 303 E. Superior Street

department: Neurology

institute: Northwestern University Feinberg School of Medicine

summary: UPF1-mediated decay entails several mRNA surveillance pathways that play a crucial role in cellular homeostasis. However, the precise role of UPF1 in postmitotic neurons remains unresolved, as does its activity in amyotrophic lateral sclerosis (ALS), a devastating neurodegenerative disease characterized by TDP-43 pathology and disrupted mRNA metabolism. Here, we used human iPSC-derived spinal motor neurons (MNs) to identify mRNAs subject to UPF1 degradation by integrating RNA-seq before and after UPF1 knockdown with RIP-seq to identify RNAs that co-immunoprecipitate with the active form of phosphorylated UPF1. We define a stringent set of bona fide UPF1 targets in MNs that are functionally enriched for autophagy and structurally enriched for GC-rich and long 3' UTRs but not for premature termination codon (PTC)-containing transcripts. TDP-43 depletion in iPSC-derived MNs reduces UPF1 phosphorylation and consequently post-transcriptional upregulation of UPF1 targets, suggesting that TDP-43 dysfunction compromises UPF1-mediated mRNA surveillance. Intriguingly, our datasets reveal that UPF1 and TDP-43 regulate alternative polyadenylation and 3'UTR length of mRNAs associated with synaptic and axonal function, a process that we find to be compromised in ALS models in vitro and ALS patient tissue. Our study provides a comprehensive description of UPF1-mediated mRNA decay activity in neurons, reveals overlapping roles between UPF1 and TDP-43 in regulating 3'UTR length, and offers novel insight into the intricate interplay between RNA metabolism and neurodegeneration in ALS.

overall_design: RNA sequencing of iPSCs, treated with either a scrambled siRNA (control), or an siRNA to induce knockdown of UPF1

first: Francesco

last: Alessandrini

first: Matthew

last: Wright

first: Tatsuaki

last: Kurosaki

first: Lynne

middle: E

last: Maquat


title: ALS-Associated TDP-43 Dysfunction Compromises UPF1-Dependent mRNA Metabolism Pathways Including Alternative Polyadenylation and 3’UTR Length [RIP-Seq]

overall_design: Sequencing of immunoprecipitated RNA from iPSC-derived spinal motor neurons. RNA was pulled down against either phosphorylated-UPF1 (pUPF1) or rIgG for non-specific binding. Input RNA was also sequenced and is included for background.


title: Transcriptomic and metabolic profiles of apple peels in different colors

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

summary: Apple is a woody tree in the Rosaceae family, genus Apple. It has been widely reported that MYBs are critical regulators for red color of apple peel by activating the expression of anthocyanin biogenesis genes. However, it is still not clear what is the molecular mechanism for the yellow color of apple peel. In order to investigate key genes and metabolites responsible for yellow coloration of apple peel, three strains of apples, "Venus Gold (Ype)" with yellow peel, "Yanfu8 (Mpe)" with medium red peel, and "Red love" with dark red peel, were selected in this study. Transcriptomic and metabolomic profiles were obtained for the peels of the three apple strains, respectively. After analyzing the transcriptomic profiles, our results suggest that DFR and LAR1 are two critical genes for the yellow color of Ype peel. Analysis of metabolomic profiles revealed that the abundances of Catechin and Epicatechin in Ype peel was higher than that of Rpe, indicating an important reason for the yellow color of Ype peel. Furthermore, when comparing volatile metabolites from Ype, Mpe and Rpe, hundreds of volatile metabolites show significantly differently abundances, suggesting that apples with different peel colors have different odors. In summary, our results provide new insights into the yellow coloration for the peels of some apple cultivars.

overall_design:
This study investigated the molecular mechanisms underlying apple peel coloration by analyzing transcriptomic and metabolomic profiles of three apple cultivars: "Venus Gold (Ype)" (yellow peel), "Yanfu8 (Mpe)" (medium red peel), and "Red Love (Rpe)" (dark red peel). Fruits were harvested 205 days after flowering, and peels were immediately frozen in liquid nitrogen for analysis. Three biological replicates per cultivar were used. Transcriptomic profiling involved RNA extraction, library preparation, and sequencing on an Illumina Novaseq 6000 platform, followed by alignment to the apple genome (Golden Delicious) and differential gene expression analysis using edgeR.

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

last: Ao


title: ALS-Associated TDP-43 Dysfunction Compromises UPF1-Dependent mRNA Metabolism Pathways Including Alternative Polyadenylation and 3’UTR Length

overall_design: RNA sequencing of iPSC-derived spinal motor neurons, treated with either a scrambled siRNA (control), or siRNAs to induce knockdown of TDP43, UPF1, or both


title: Chimeric hemagglutinin-based universal influenza mRNA vaccine induces protective immunity and bone marrow plasma cells in rhesus macaques

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: A universal influenza vaccine that elicits a strong and lasting stalk-specific antibody response is advantageous. We utilize nucleoside-modified mRNA in lipid nanoparticles (mRNA-LNP) and unmodified self-amplifying mRNA in modified dendritic nanoparticles (sam-MDNP), expressing chimeric hemagglutinin (cHA) antigens to induce stalk-specific humoral immunity in non-human primates (NHPs) with preexisting influenza virus immunity. mRNA-LNP immunization induces strong stalk-specific binding antibodies, protecting mice from lethal heterologous influenza virus challenges, along with bone marrow plasma cells (BMPC) that persist for up to 8 months. sam-MDNP vaccine induces lower humoral immunity, despite showing strong innate activation. Transcriptomic and cytokine analyses reveal a more persistent induction of interferon responses, IL-1β signaling, and IL-6 production in the mRNA-LNP group, correlating with the induction of serum antibody responses and BMPC. We identify a transcriptional signature associated with induction of BMPC following mRNA vaccination and highlight the utility of cHA-based mRNA-LNP vaccines in inducing persistent stalk-directed protective antibody responses.

overall_design: Ten male RMs were immunized intramuscularly (IM) with the 2020/2021 quadrivalent influenza vaccine (QIV) at weeks 0 and 6 to induce influenza specific immunity (Fig. 1A). Eighteen weeks post QIV booster, RMs were divided into two groups based on their binding antibody response to influenza stalk and immunized IM with 100g of cH8/1 LNP-mRNA or 30g of cH8/1 samRNA vaccine. Twelve weeks later, RMs were again immunized IM with 100g of cH5/1 LNP-mRNA or 30g of cH5/1 samRNA. Animals were followed for up to 40 weeks after the final vaccination.

first: Tiffany

last: Styles

first: Akil

last: Akhtar

first: Chunyang

last: Gu

first: Gabriele

last: Neumann

first: Hiromi

last: Muramatsu

first: Justine

middle: S

last: McPartlan

first: Poulami

last: Talukder

first: Derrik

last: Gratz

first: Kasey

last: Stokdyk

first: Hannah

middle: L

last: Turner

first: James

middle: A

last: Ferguson

first: Alesandra

last: Rodriguez

first: Madhumathi

last: Loganathan

first: Benjamin

last: Francis

first: Anass

last: Abbad

first: Ghania

last: Chikh

first: Ying

last: Tam

first: Zhaohui

last: Qin

first: Julianna

last: Han

first: Juan

last: Carreño

first: Andrew

last: Ward

first: Jasdave

last: Chahal

first: Christian

middle: W

last: Mandl

first: Norbert

last: Pardi

first: Yoshihiro

last: Kawaoka

first: Florian

last: Krammer

first: Rafi

last: Ahmed

first: Rama

middle: R

last: Amara


title: A comprehensive analysis of supermere, exomere, and extracellular vesicle isolation and cargo in colorectal cancer

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Biofluids contain a heterogeneous mixture of extracellular vesicles and non-vesicular nanoparticles (including exomeres and supermeres) that transport a diverse array of proteins, RNA, and lipids. Our previous efforts to characterize the contents of these carriers in colorectal cancer relied on 2D culture systems requiring large-scale setups and time-consuming ultracentrifugation-based isolation. To streamline this process, we have combined 3D hollow-fiber bioreactor production and fast-protein liquid chromatography-based size-exclusion chromatography. Here, we compare the impact of culture methods and purification strategies on small extracellular vesicle, exomere and supermere cargo. Proteomic analyses show distinct profiles for extracellular vesicles, exomeres, and supermeres consistent regardless of culture conditions or isolation method. In contrast, these two variables influence small RNAs, their base modifications, and lipidomic profiles. We present an online tool to query these and future secretome datasets (https:/superomics.shinyapps.io/browse).

overall_design:
small RNAseq of the extracellular vesicles, exomeres, and supermeres from 2D or 3D cell culturing conditions isolated by either ultracentrifugation-based method, straight cushion-density gradient ultracentrifugation or FPLC-SEC
Gradient samples:  They represent two classes of extracellular vesicles, heavy (hEV in our paper) and light (EV in our paper), as well as non-vesicular material (NV in our paper); NV is a mixture of different entities, mostly dense material that may include histones and other non-lipid containing protein complexes and some exomeres. All the EVs are small as we prepare the media by gravity filtering through a 0.22um filter.

first: Oleg

last: Tutanov

first: Clark

last: Massick

first: James

middle: N

last: Higginbotham

first: Lizandra

last: Jimenez

first: Mark

last: Castleberry

first: Zheng

last: Cao

first: Eliana

last: John

first: Maxwell

last: Hamilton

first: Qin

last: Zhang

first: Dennis

middle: K

last: Jeppesen

first: Danielle

last: Michell

first: Sarah

last: Glass

first: Purvi

last: Patel

first: Kristie

last: Lindsey Rose

first: Evan

last: Krystofiak

first: Huachang

last: Chen

first: Quanhu

last: Sheng

first: Qi

last: Liu

last: Patton

first: Alissa

last: Weaver

first: Jeffrey

last: Franklin

first: Kasey

middle: C

last: Vickers

first: Robert

middle: J

last: Coffey


title: Effects on gene expression of lapatinib and/or GSK126 treatment in SKBR3 cells

city: Boston

first: Naiara

last: Perurena

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine/Genetics

institute: Brigham and Women's Hospital

summary: SKBR3 cells were treated with DMSO (as control), lapatinib, GSK126 or lapatinib + GSK126 for 24 h to identify genes and pathways differentially upregulated/downregulated by these treatments.

overall_design: SKBR3 cells were treated with DMSO or 5 µM GSK126 starting at day -6. At day -3, cells were split and continued to be treated with DMSO or GSK126. At day -1, cells were seeded at 350,000 cells per 6-cm plate in DMSO or GSK126. At day 0, cells pre-treated with DMSO were treated with DMSO or 100 nM lapatinib, while cells pre-treated with GSK126 were treated with 5 µM GSK126 or 5 µM GSK126 + 100 nM lapatinib. 24 h later (day 1), RNA was extracted using a RNeasy Plus Mini kit (Qiagen) and sequenced in an Illumina NextSeq500 run with single-end 75 bp reads.


title: KAT2A-driven succinylation of SRSF11 enforces spliceosome-mediated RAD52 splicing to promote homologous recombination and radioresistance in hepatocellular carcinoma [RIP-seq]

city: Chengdu

first: Jun

last: Wu

address: Guoxue street

institute: West   32 China Hospital, Sichuan University

summary: Posttranslational modification succinylation plays a pivotal role in tumorigenesis across malignancies, yet its mechanistic contributions to hepatocellular carcinoma (HCC) pathogenesis and therapeutic resistance remain poorly characterized. In this study, we systematically demonstrated that the splicing factor SRSF11 undergoes functional consequential succinylation in HCC progression. Mechanistically, lysine acetyltransferase 2A (KAT2A) directly interacts with SRSF11 to catalyze its succinylation at lysine 419 (K419), thereby enhancing DNA damage repair capacity in both in vitro and in vivo HCC models. Structural and functional analyses revealed that K419 succinylation stabilizes SRSF11-spliceosome interactions, which promote the inclusion of exon 10 of RAD52 through enhanced pre-mRNAs binding. This exon-specific splicing event preserves the RAD51-binding domain essential for homologous recombination (HR) repair, ultimately facilitating RAD52-RAD51 dimer assembly and HR-mediated genomic stabilization. Clinically, elevated SRSF11 expression is correlated with increased HR activity, radioresistance, and reduced survival in HCC patients. Notably, genetic disruption of the KAT2A-SRSF11 axis sensitizes HCC cells to radiation-induced apoptosis. Our findings establish succinylation as a novel regulatory mechanism linking alternative splicing to DNA repair fidelity in HCC, while proposing therapeutic targeting of this pathway to overcome radioresistance in advanced HCC.

overall_design: RIP-seq for identifying the binding RNA of SRSF11

first: Jingsheng

last: Yuan

first: Jiayin

last: Yang


title: Specific Intratumoral Microbiome Signatures in Human Glioblastoma and Meningioma: Evidence for a Gut–Brain Microbial Axis

city: Florence

first: Sara

last: Bertorello

address: Viale Gaetano Pieraccini 6

country: Italy

institute: University of Florence

summary: Brain tumors (BTs), including glioblastoma (GBM) and meningioma (MGM), contribute significantly to the global cancer burden. The microbiome has been implicated in carcinogenesis, yet its role in BTs remains underexplored. We performed 16S rRNA gene sequencing of the gut microbiota (GM) and intratumoral microbiome (ItM) from fresh tissue samples of 9 patients with GBM and 18 with MGM. 12 age- and sex-matched healthy controls (HCs) were also enrolled. GM profiling revealed reduced alpha diversity and distinct microbial communities in BT patients versus HCs. Notably, Verrucomicrobiota and Synergistaceae were enriched, while Lachnospiraceae, Peptostreptococcaceae, and Muribacter spp. were depleted. GBM patients showed reductions in Peptostreptococcaceae and the Eubacterium hallii group, while MGM patients had increased Synergistia and Erysipelatoclostridium. Compared with MGM, GBM patients were enriched in Peptostreptococcales–Tissierellales, Coprobacillus, and Peptoniphilus but depleted in Weissella. Venn analysis revealed 176 genera shared across groups with unique taxa distinguishing tumor patients and HCs. ItM profiling revealed enrichment of Proteobacteria, Actinomycetota, and Campylobacterota in GBM, while MGM contained higher levels of Bacillota and Bacteroidota. GBM tissues harbored Burkholderia-Caballeronia-Paraburkholderia, Helicobacter, and Leifsonia, whereas MGM tissues were dominated by Bacteroides and Blautia. Notably, stool and tumor samples shared 91 genera in GBM and 105 in MGM. This study provides novel insights by (i) characterizing ItM from fresh samples, (ii) comparing ItM profiles of GBM and MGM, (iii) linking GM and ItM within the same patients, and (iv) suggesting potential clinical implications for BT management.

overall_design: Brain tumors (BT), including glioblastoma (GBM) and meningioma (MGM), contribute significantly to the global cancer burden. While genetic, environmental, and lifestyle factors are well-recognized contributors to tumorigenesis, emerging evidence suggests a role for the microbiome, both gut and tumor-associated, in cancer development and progression. We performed 16S rRNA gene sequencing to characterize the gut microbiota (GM) and intratumoral microbiome (ItM) from fresh tissue samples in 9 patients with GBM and 18 with MGM. Additional 12 age- and sex-matched healthy controls (HC) were enrolled.

first: Dalila

last: Mehelleb

first: Abderezak

last: Ghidouche

first: Simone

last: Baldi

first: Ferhat

last: Djoudi

first: Leandro

last: Di Gloria

first: Matteo

last: Ramazzotti

first: Elena

last: Niccolai

first: Menad

last: Madaoui

first: Idir

last: Takbou

first: Souhil

last: Tliba

first: Amedeo

last: Amedei


title: Inactivation of phosphatidylinositol 4-kinase IIIalpha (PI4KA) by GSK-A1 inhibitor in HEK293 cells

city: Bethesda

first: Tamas

last: Balla

email: matthew.menold@nih.gov, ryan.dale@nih.gov, ballat@mail.nih.gov, kimyj@mail.nih.gov

state: MD

address: 6 Center Dr

institute: National Institute of Child Health and Human Development

summary: Phosphatidylinositol 4-kinases (PI4Ks) are lipid kinase enzymes that play important roles in cellular signaling, membrane trafficking, viral replication and lipid metabolism. They catalyze the phosphorylation of phosphatidylinositol (PI) to produce phosphatidylinositol 4-phosphate (PI4P) at various organelle membranes. Among the four isoforms of PI4Ks, PI4KA is localized at the plasma membrane where it generates the lipid, PI4P. GSK-A1 is a well-characterized and specific inhibitor of PI4KA. In this study, we investigated transcriptional changes that occur following prolonged (24 h) treatment with GSK-A1. This RNA-seq analysis revealed significant changes in the mRNA levels of a distinct set of proteins, including transcription factors and small GTP-binding proteins. These changes were analyzed in the context of overall lipid level alterations induced by GSK-A1 treatment, as determined by lipidomic analyses.

overall_design: RNA-seq profiling of HEK293 cells treated with dimethyl sulfoxide (DMSO) or GSK-A1 for 24 hours.

first: Yeun Ju

last: Kim

first: Matthew

middle: T

last: Menold

first: Ryan

last: Dale


title: ATAC-seq in SKBR3 cells treated with lapatinib + tazemetostat

first: Naiara

last: Perurena

summary: SKBR3 cells were treated with lapatinib + tazemetostat for 24 h. ATAC-seq was performed to identify accessible chromatin regions.

overall_design: SKBR3 cells were treated with 5 µM tazemetostat starting at day -6. At day -3, cells were split and continued to be treated with tazemetostat. At day -1, cells were seeded at 3.5 million cells per 15-cm plate. At day 0, cells were treated with 100 nM lapatinib and 5 µM tazemetostat. 24 h later (day 1), cells were collected by trypsinization and frozen cells were submitted to the AGCT Core at Cedars-Sinai for ATAC-seq.


title: Parental age selection in C. elegans influences progeny stress resistance capacity

city: Los Angeles

first: Sean

middle: P

last: Curran

state: CA

address: University of Southern California

institute: University of Southern California

summary: With parental age rising around the globe, an increased understanding of the impact on health and longevity is needed.  Here, we report how the continuous selection of the last progeny during the Caenorhabditis elegans reproductive span results in a diminishment of multiple age-related health measures.  After more than fifty generations of late selection, progeny displayed diminished resistance to acute oxidative stress, disrupted partitioning of stored lipids, reduced movement capacity, and an overall shortening of lifespan (36.84% reduction). In contrast, starvation resistance was improved and late selection had negligible effects on developmental timing and total reproductive output that suggests a reduction in lifespan health to preserve reproductive capacity. The phenotypes of late selection are reminiscent of animals with activation of the cytoprotective transcription factor SKN-1 but are unlikely the result of a spontaneous genetic mutation. While none of the accumulated mutations recapitulated the WT Late phenotypes, transcription factor enrichment analysis revealed significant changes in the targets of SEX-1 and ELT-3.    These findings suggest the existence of a homeostatic mechanism for bookmarking the temporal boundaries of the parental reproductive span that reshapes the way we think about parental age influencing offspring fitness.

overall_design: RNAseq profiling of WT and WT Late selected Caenorhabditis elegans samples at L4 stage

first: Bennett

last: Van Camp


title: Dual Impact of Interleukin-17A Blockade on Inflammatory and Stromal Pathways in Peripheral Spondyloarthritis

city: Amsterdam

first: Nataliya

last: Yeremenko

state: North Holland

address: Meibergdreef 9

department: Department of Rheumatology and Clinical Immunology

country: Netherlands

institute: Amsterdam University Medical Centers

summary: Background: IL-17A plays a role in the pathology of spondyloarthritis (SpA), as evidenced by the clinical efficacy of IL-17A inhibitors (IL-17Ai). Nevertheless, the exact role of IL-17A in driving synovial inflammation and pathological remodeling remains unknown. In this study, we investigated the molecular pathways affected by IL-17Ai in SpA synovitis to determine whether this response is tissue- and/or treatment-specific. Methods: Synovial biopsies from 12 peripheral SpA (pSpA) patients before and after 12 weeks of IL-17Ai treatment were analyzed by RNA-sequencing and qPCRs. The synovial tissue response to IL-17Ai in 7 psoriatic arthritis (PsA) patients was compared to: open-source gene expression data of skin biopsies from 15 psoriasis (PsO) patients treated with IL-17Ai; and synovial biopsies from 7 PsA patients receiving IL-12p40/IL-23p40 blockade. Results: Compared to baseline, IL-17Ai significantly modulated the expression of 1255 genes (549 upregulated and 706 downregulated, FDR < 0.1) in the synovium at week 12. The downregulated genes were predominantly associated with inflammatory processes and stromal functions. Comprehensive analysis revealed that IL-17Ai-mediated suppression of bone remodeling is independent of its inhibition of inflammatory pathways. While IL-17Ai consistently attenuated inflammation-related pathways in both psoriatic joints and skin, its effect on bone remodeling pathways was specific to the synovium. This distinguishes IL-17Ai from IL-12p40/IL-23p40 inhibitors, which, while mitigating synovial inflammation, did not affect tissue remodeling. Conclusions: Our findings provide new insights into the molecular mechanisms of IL-17A blockade in pSpA, underscoring its unique role in selectively targeting bone-remodeling processes specific to the joints of individuals with SpA.

overall_design: RNAseq profiling of synovial biopsies from 12 peripheral SpA (pSpA) patients before and after 12 weeks of IL-17Ai treatment

first: Ihsan

last: Hammoura

first: Renée

last: Fiechter

first: Leonieke

last: van Mens

first: Henriëtte

last: de Jong

first: Inka

last: Fluri

first: Sander

last: Tas

first: Dominique

last: Baeten

first: Marleen

last: van de Sande


title: Tonic Signaling Shaped by Epitope Targeting Governs CAR-T Cell Fitness and Antitumor Activity in Diffuse Midline Glioma [CUT&Tag]

city: Cincinnati

first: Richard

last: Lu

institute: CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER

summary: We systematically evaluated B7-H3–targeting CAR-T cells derived from three monoclonal antibodies (376.96, MGA271, and Hu8H9) in diffuse midline glioma (DMG or DIPG), a fatal pediatric brain tumor. Among these, 376.96 CAR-T cells had markedly lower tonic signaling, diminished expression of exhaustion markers, and enhanced tumor killing, cytokine production, and persistence. Transcriptomic and epigenomic profiling revealed a restrained activation state with reduced tonic signaling pathways and elevated stemness properties, oxidative metabolism, and innate immune sensing in these cells. In patient-derived spheroids and orthotopic DIPG xenografts, mRNA-based 376.96 CAR-T cells achieved robust tumor control and extended survival. By leveraging epitope selection, we reveal a mechanistic link between tonic signaling and CAR-T cell exhaustion, and provide a rational framework for optimizing CAR-T cell design to achieve improved efficacy and durability in pediatric brain tumor therapy.

overall_design: To further investigate the epigenetic enhancer landscape, we performed CUT&Tag profiling of H3K27ac, a marker of active regulatory enhancer regions, in control T cells and B7-H3 CAR-T cells .

first: Bing

last: Deng

first: Dazhuan

last: Xin


title: fMyBP-C is a vital regulator in young and aged fast skeletal muscle homeostasis [5-6 months old]

city: Tucson

first: Sakthivel

last: Sadayappan

state: AZ

address: 1656 E Mabel Street, Medical Research Building, Rm 315, Cellular and Molecular Medicine

department: Cellular and Molecular Medicine

institute: University of Arizona College of Medicine

summary: Skeletal Myosin binding protein-C (MyBP-C) paralogs, slow (sMyBP-C) and fast (fMyBP-C) interacts with myosin and actin filaments within sarcomeres, modulating the force development during contraction. These display differential expression in muscle fibres, with fMyBP-C higher in fast twitch fibres. However, our knowledge about the changes in the fMyBP-C expression in diseased conditions and its role in skeletal muscle aging is lacking. In this study we use mice model lacking fMyBP-C to understand its significance in skeletal muscle physiology. Skeletal muscle samples from wild type and Mybpc2 knockout (C2-/-)old male mice (22 months) were used to define the role of fMyBP-C in aging. Western immunoblotting was employed to analyze the expression of fMyBP-C and sMyBP-C, and phosphorylation status of sMyBP-C. The impact of C2-/- and aging on the fiber type, size, and number as well as general muscle structure was assessed by immunohistochemistry and electron microscopy. The functional effect of C2-/- and aging was measured in terms of in vivo and ex vivo muscle force generation. Lastly, RNA sequencing was performed to identify the molecular pathways dysregulated in the C2-/- mediated muscle dysfunction in young and old mice. The aged male C2-/- mice compared to their wildtype counterparts, display significant deficits in muscle strength and endurance, accompanied by changes in muscle fiber size and molecular signaling pathways critical for muscle homeostasis.Thus, fMyBP-C is an important regulator of muscle function and homeostasis in the young and aged fast-twitch muscle fibers. The absence of fMyBP-C aggravates the effect of aging on muscle structure and function. fMyBP-C has the potential to be a therapeutic target to modulate muscle wasting caused by aging and disease.

overall_design: Mybpc2 KO mouse model (C2-/-) was generated by the targeted replacement of Mybpc2 exon 2 to 22 with a Neo cassette flanked by two LoxP sites. The Tibialis anterior muscle dissected from 5-6 months old male Wildtype and C2-/- (n=4 in each group). RNA extracted from TA muscles are subjected to RNA Sequencing to determine the altered molecular signatures.

first: Akhil

last: Baby

first: Kalyani

last: Ananthamohan

first: Brenn

last: McIntyre

first: Taejeong

last: Song


title: WTAP Regulates NCOA4-Mediated Ferroptosis via a YTHDF2-Dependent Mechanism in Preeclampsia

city: Qing Dao

first: Chan

last: Li

address: Jiangsu Road No. 16, Shinan District, Qingdao

department: Department of Obstetrics and Gynecology

institute: The Affiliated Hospital of Qingdao University

summary: WTAP knockdown alters gene expression in trophoblasts, notably downregulating YTHDF2 and upregulating NCOA4. These changes are linked to disrupted pathways in proliferation, migration, and oxidative stress, and are consistent with abnormal expression patterns observed in preeclampsia placental tissues.

overall_design: HTR-8/SVneo trophoblast cells were transfected with siRNAs against WTAP, YTHDF2, and NCOA4 to assess changes in proliferation, migration, and ferroptosis. WTAP expression in PE placentas was evaluated via qRT-PCR and immunohistochemistry. MeRIP-qPCR assessed m6A methylation of NCOA4 mRNA. Ferroptosis markers were analyzed. A PE mouse model was established to examine in vivo effects of YTHDF2 knockdown and NCOA4 overexpression, with or without Ferrostatin-1 treatment, to evaluate therapeutic relevance.


title: Tonic Signaling Shaped by Epitope Targeting Governs CAR-T Cell Fitness and Antitumor Activity in Diffuse Midline Glioma [RNA-Seq]

state: Ohio

overall_design: To investigate potential mechanism underlying the enhanced antitumor efficacy of 376.96 CAR-T cells, we performed RNA sequencing and epigenomic profiling of 376.96, MGA271, and Hu8H9 CAR-T cells and control T cells transduced with empty vector as well as untransduced T cells.