title: Cisplatin resistance in an ovarian cancer model is mediated by the microtubule dynamics regulator TPPP3 which synergizes with tubulin code rewiring

city: East Lansing

first: Sachi

last: Horibata

address: 766 Service Rd, Room 2014

institute: Michigan State University

summary: Cisplatin is a mainstay in cancer treatment, but toxicity and resistance limit its potential. Using RNA-seq, we show that ovarian cancer cells undergo broad changes in the microtubule cytoskeleton that correlate with resistance.  Consistent with this, we find that cisplatin directly impacts microtubule dynamics in vitro and in cells. Paclitaxel counteracts cisplatin and increases resistance. By purifying tubulin from cisplatin sensitive resistant and re-sensitized ovarian cancer cells, we demonstrate that resistance acquisition rewires the tubulin code leading to microtubule stabilization. Furthermore, tubulin polymerization promoting protein 3 (TPPP3) contributes to resistance. In vitro, TPPP3 synergizes with tubulin isotypes from resistant cells to yield maximal microtubule stabilization in response to cisplatin. Database analysis shows that patients with low TPPP3 levels have improved therapeutic outcome. Our findings implicate TPPP3 and microtubule dysregulation in cisplatin resistance, independent of effects through DNA damage, and have bearing on the etiology of cisplatin-associated neuropathies and ototoxicity.

overall_design: RNA-seq were performed on cisplatin sensitive (1A9), resistant (1A9CP80), and resensitized (1A9CP80R or 1A9CP80rev) cells.

first: Kishore

middle: K

last: Mahalingan

first: Ruchi

last: Patel

first: Yu

last: Fan

first: Jordan

middle: M

last: Hotz

first: Adriana

last: Ponton-Almodovar

first: Keith

last: MacRenaris

first: Yan

last: Li

first: Daoud

last: Meerzaman

first: Michael

last: Gottesman

first: Antonina

last: Roll-Mecak


title: Engrailed-1 Potentiates Mitochondrial Transplant Neuroprotection in Spinal Cord Ischemia-Reperfusion Injury [RNA-Seq]

status: Public on Apr 17 2026

city: shenyang

first: Wei

last: Wang

address: No. 155 Nanjing North Street

country: China

institute: China Medical University Affiliated First Hospital

type: Expression profiling by high throughput sequencing

summary: Spinal cord ischemia-reperfusion injury (SCI/RI) is characterized by severe mitochondrial dysfunction and neuronal apoptosis. The transcription factor Engrailed-1 (En-1) has been identified as a potential regulator of mitochondrial homeostasis and neuroprotection. In this study, we utilized an integrated multi-omics approach to elucidate the molecular mechanisms by which En-1 protects cells from ischemia-like injury. We performed RNA-sequencing (RNA-seq) on PC12 cells with stable En-1 overexpression and their respective controls under both normoxic and oxygen-glucose deprivation/reoxygenation (OGD/R) conditions. To identify direct genomic targets of En-1, Cleavage Under Targets and Tagmentation (CUT&Tag) analysis was conducted. Integration of transcriptomic and DNA-binding profiles revealed a distinct regulatory network through which En-1 modulates mitochondrial function and cell survival. These data provide a comprehensive resource for understanding the transcriptional landscape governed by En-1 and identify potential therapeutic targets for mitigating mitochondrial damage in ischemic neural injuries.

overall_design: CUT&Tag analysis was performed on stable En-1-overexpressing PC12 cells using an En-1-specific antibody, with IgG as a negative control.

first: Rui

last: Tang

first: Shilun

last: Gao

first: Xiaotian

last: Han

first: Teng

last: Shi

first: Tianxiang

last: Gu

first: Enyi


title: Engrailed-1 Potentiates Mitochondrial Transplant Neuroprotection in Spinal Cord Ischemia-Reperfusion Injury

overall_design: Comparison of PC12 control cells and stable En-1-overexpressing cells under normoxic culture conditions (n = 3 per group).


title: Mast cells interact directly with colorectal cancer cells to promote epithelial-to-mesenchymal transition

city: Bloomington

first: Heather

last: O'Hagan

state: IN

address: 1001 E 3RD ST

department: School of Medicine

country: USA

institute: Indiana University

summary: Mast cells (MCs), a type of granulocytic immune cell, can be both pro- and anti-tumorigenic in colorectal cancer (CRC). We hypothesized that these contrasting findings may be in part due to differential interactions of MCs with CRC subtypes. BRAF mutant CRC uniquely contains intestinal secretory cell types. In this study, we demonstrated that MCs are enriched in BRAF mutant CRC, likely because they are recruited by factors released from cancer secretory cells. To investigate the functional consequences of MC-CRC cell interactions, we performed direct coculture experiments. We demonstrated that MCs promote epithelial-to-mesenchymal transition (EMT) in CRC cells in a calcium- and contact-dependent fashion. Furthermore, inhibiting LFA-1 and ICAM1 integrin binding reduced the coculture-induced EMT-related marker expression in CRC cells. The MC-CRC cell interaction facilitates the transfer of biological materials, including mRNA molecules, from MCs to CRC cells. This study is the first to report a contact-dependent, pro-tumorigenic role of MCs in CRC, as well as the transfer of molecules encoded by MCs to CRC cells. These findings enhance our comprehension of cell-cell communication between immune and cancer cells. Furthermore, this work suggests that targeting MC-CRC interactions, particularly through modulating integrin pathways, could offer new therapeutic strategies for aggressive CRC subtypes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HT-29 cells incubated alone or in coculture with LAD2 cells and for LAD2 cells incubated alone or in coculture with HT-29 cells for 12 hours.

first: Rosie

last: Lanzloth


title: KIAA1199 aggravates sepsis-induced lung injury by promoting complement activation

city: Wenzhou

first: Xinyu

last: Yang

state: Not applicable

address: Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, China.

department: School of Pharmaceutical Sciences

institute: Wenzhou Medical University

summary: Sepsis-induced acute lung injury (ALI) is a life-threatening condition associated with high mortality rates. While emerging evidence suggests that KIAA1199 (also known as cell migration-inducing protein, CEMIP) contributes to the pathogenesis of bacterial infections, its specific role in sepsis-induced ALI remains largely unexplored. This study aimed to investigate the role of KIAA1199 in sepsis-induced ALI. Our findings revealed that serum levels of KIAA1199 were significantly elevated in sepsis patients compared to healthy individuals, demonstrating a positive correlation with the sequential organ failure assessment (SOFA) scores. Additionally, we observed the expression of KIAA1199 increased in the lung tissue of septic mice, particularly in alveolar epithelial Type II (AT2) cells. To further elucidate its function, we generated AT2-specific KIAA1199 knockout mice and established an LPS-induced ALI model. The results indicated that KIAA1199-deficient mice exhibited improved survival rates, reduced lung injury, and decreased levels of proinflammatory cytokines. To further explore the specific downstream target of KIAA1199, RNA sequencing of AT2 cells was conducted in this study.

overall_design: To identified the downstream target gene of KIAA1199, we performed RNA sequencing (RNA-seq) on AT2 cells isolated from LPS-induced KIAA1199 knockout mice and control mice (KO= KIAA1199 knockout group, FL=control mice group, n=3 per group.)

first: Yang

last: Qin

first: Jiani

last: Zhang

first: Yanwen

first: Sunwang

last: Ling

first: Weikang

last: Ren

first: Li

last: Liu


title: Ustekinumab Resistance in Individuals with Ulcerative Colitis is Associated with an Alteration of a Subset of Pro-inflammatory Mucosal Regulatory T cells

city: Bethesda

first: Kristi

last: Briggs

address: 10 Center Drive

institute: NIDDK

summary: Background & Aims: Ustekinumab is a monoclonal antibody therapy targeting interleukin 12 and 23 for the treatment of inflammatory bowel diseases, including ulcerative colitis (UC).  While these pathways remain quite attractive for UC therapy, response to ustekinumab can be variable.  There is an urgent need to better understand the underlying mucosal immune alterations associated with treatment to guide therapy decisions.   This study aims to examine the mucosal immune signatures in individuals with UC with variable treatment response to ustekinumab. Methods: Sigmoid colon tissue from individuals treated with ustekinumab were analyzed using a multi-modal approach.  Single-cell RNA and T cell receptor sequencing was performed on mucosal biopsies.  In a subset of these patents, multiparameter flow cytometry and spatial transcriptomics was also completed on matched pre- and post-treatment tissue samples.  Key findings were also validated on a larger cohort using immunohistochemistry. Results: Ustekinumab significantly altered the frequency and phenotype of mucosal regulatory T cells (Tregs).  Non-responders to ustekinumab had a higher frequency of Tregs that expressed OX40 and GITR, which is associated with decreased suppressive abilities.  In contrast, responders had Tregs with elevated GPR15 and reduced expression of the kinase PIM2, which can alter Treg stability and function.  Additionally, Th17 cells in non-responders demonstrated an enhanced pro-inflammatory gene expression profile. Conclusion: Non-response to ustekinumab in UC is linked to a mucosal immune environment enriched with pro-inflammatory T cell phenotypes and impaired regulatory T cell function. These findings suggest that Tregs are both targets and potential biomarkers of ustekinumab response, with their phenotypic and transcriptional features providing insight into mechanisms of therapeutic resistance.

overall_design: sigmoid colon biopsy tissue analysis of patients with ulcerative colitis on IL12/23 inhibitor


title: Endothelial FGF13 impairs angiogenesis by accelerating oxygen-independent HIF-1α degradation

first: Zhaohang

last: Wu

address: Chashan

summary: Angiogenesis is a tightly regulated process essential for both development and disease, yet the role of fibroblast growth factor 13 (FGF13) in vascular remodeling has remained unclear. Here, we identify FGF13 as a key negative regulator of physiological and pathological angiogenesis. Using endothelial cell–specific knockout and overexpression mouse models, combined with retinal vascularization assays, hindlimb ischemia and myocardial infarction models, and in vitro endothelial cell functional assays, we demonstrate that loss of FGF13 enhances, whereas its overexpression impairs, neovascularization. Mechanistically, FGF13 binds to the PAS domain of HIF-1α and facilitates its interaction with RACK1, leading to oxygen-independent degradation of HIF-1α and suppression of downstream angiogenic signaling. Importantly, adenoviral overexpression of HIF-1α reversed the inhibitory effects of FGF13, confirming its essential role in mediating FGF13-driven angiogenic regulation. These findings reveal FGF13 as a critical endothelial-intrinsic brake on angiogenesis and suggest its potential as a therapeutic target in ischemic vascular disease.

overall_design: Total RNA from the cells was collected using RNAiso Plus and subjected to genome-wide transcriptomic analysis using Gene Denovo Biotechnology Co. (Guangzhou, China).

first: Weitao

last: Cong


title: Mytho/Phaf1 is required to prevent DNA damage and tissue degeneration in Danio rerio

city: Padova

first: Marco

last: Sandri

state: Padova

address: Via Orus 2

department: Biomedical Sciences

country: Italy

institute: University of Padova

summary: Mytho (Macroautophagy and YouTH Optimizer) is a novel FoxO-dependent gene that has been recently identified to control health- and life-span in C. elegans via autophagy regulation. However, the role of this gene in tissue development and function in vertebrates has not yet been established. To address these issues, we generated a zebrafish mytho KO model and observed that mutants exhibited a higher mortality rate than wild-type (WT) siblings during the first month of life and a lower resistance to oxidative stress. Mytho silencing resulted in a decrease of larval locomotor activity and muscle birefringence and caused alteration of adult muscle structure. Autophagy impairment was confirmed in tissues with the highest mytho expression such as brain, muscle and testis. Finally, mutants showed tissue degeneration in pancreas, retina, muscle and a reduction of reproductive capabilities of males and morphological alterations in gonads of both sexes. Importantly, males presented a higher incidence of seminomas, a testicular cancer. The increased susceptibility to cancer is associated with an enhanced DNA fragmentation in sperm cells.  In conclusion, this study highlights the key role of Mytho in maintaining proper tissue function and DNA integrity.

overall_design: RNA was isolated from frozen testicles collected from male zebrafish aged 15 mpf (4 WT and 4 KO, two of which had developed a seminoma), using TRIzol (ThermoFisher Scientific) according to the manufacturer's instruction. RNA quality was assessed using an Agilent 2200 TapeStation System (Agilent Technologies). Sample RIN (RNA integrity number) values ranged from 9.3 to 9.9. Total RNA samples (1 µg) were used for library preparation (Illumina’s TruSeq Stranded mRNA LT Sample Prep Kit with poly A selection). Sequencing was performed using an Illumina NovaSeq 6000 System (150 length, paired-end) platform (Illumina, Inc., San Diego, CA).

first: Tommaso

last: Pagliarusco

first: Anais

last: Franco-Romero

first: Francesca

last: Terrin

first: Filippo

last: Citton

first: Ludovica

last: Carducci

first: Nicola

last: Facchinello

first: Camilla

last: Fontana

first: Marta

last: Giacomazzo

first: Ranieri

last: Verin

first: Maria

middle: B

last: Rasotto

first: Lisa

last: Locatello

first: Luisa

last: Dalla Valle


title: Altered Nephron Progenitor Cell Dynamics Drive Long-Term Kidney Abnormalities Following Preterm Birth in Mice.

city: Melbourne

first: Mehran

last: Piran

state: VIC

address: 19 Innovation Walk

department: Anatomy and Developmental Biology

country: Australia

institute: Monash University

summary: Preterm birth-affecting ~10% of live births globally-is associated with a markedly increased lifetime risk of chronic kidney disease (CKD), reportedly up to fivefold higher than in term births. Yet, the mechanisms linking prematurity to impaired renal development remain incompletely understood. Here, we investigated how preterm birth influences nephron endowment, kidney function, and the trajectory of kidney injury in a mifepristone-induced mouse model. We compared renal structure and function between preterm and term-born mice at postnatal day (P) 30 and P180, quantifying nephron number, glomerular morphology, and injury markers. We also performed bulk RNA sequencing on sorted nephron progenitor cells (NPCs) and non-NPC fractions from post-conception (PC) days 19.5–21.5, spanning the final window of nephrogenesis. Preterm mice exhibited up to 17% fewer nephrons at P30 (p < 0.01) and a ~25% lower kidney-to-body-weight ratio at P30 and P180 (both p < 0.05), despite a ~40% increase in body weight by P180. Injury biomarkers were elevated at P30 and P180, with serum creatinine increased by ~50%, NGAL by ~35%, urinary albumin excretion approximately doubled (p < 0.001), and KIM-1 elevated in preterm versus term controls. Glomerular density at P180 was reduced by ~30% in preterm mice; glomeruli were disproportionately localized in the medulla, and increased Bowman’s space area and capsule ratios suggested filtration defects. Transcriptomic profiling around the time of preterm birth revealed acute induction of cellular stress pathways and transiently impaired NPC differentiation that resolved within 24 hours. Concomitantly, we observed a short-lived increase in NPC proliferation and an approximate 24-hour extension of nephrogenesis, consistent with a compensatory response to bolster nephron formation and indicating a potential therapeutic window. In summary, preterm birth perturbs NPC developmental timing and stress responses, leading to reduced nephron endowment and persistent susceptibility to kidney injury.

overall_design: Sixteen pregnant CD1 wild-type females were mated with Six2-Cre males and randomly assigned (1:1) to preterm (n = 8) or term-control (n = 8) groups. Preterm dams received a single subcutaneous dose of mifepristone at post-conception (PC) day 17.5, inducing delivery at PC18.5; term controls received the same dose at PC18.5, delivering at PC19.5. From each group, kidneys from four entire litters were designated for collection at PC19.5 and the remaining four litters at PC20.5. Nephron progenitor cells (GFP⁺) and non-nephron progenitor cells (GFP⁻) were fluorescence-sorted, pooled per litter, and processed for RNA extraction and sequencing. Each RNA-seq sample therefore represents one litter.

first: Athar

last: Amleh

first: Morris

last: Nechama

first: Julie

last: Moreau

first: Oded

last: Volovelsky

first: Alex

last: Combes


title: scRNA-seq of immune and structural cells in hypercholesterolemic mice

city: Münster

first: Oliver

last: Soehnlein

address: Von-Esmarch-Str. 56

department: Institute of Experimental Pathology

country: Germany

institute: University Hospital Münster

summary: We performed scRNA-seq analysis using the 10X genomics platform of ApoE-/- mice fed for 16 weeks with high-fat diet (HFD). In these mice, we isolated brachiocephalic artery (BCA, digested), blood, bone marrow, spleen as well as perfusates of lung and liver at two times of the day (ZT1 and ZT13). For BCA cells, not-enriched cells and enriched cells (neutrophils, B- and T-cells, F4/80+ macrophages, CD31+ endothelial cells and CD31- stromal cells) were isolated and loaded for processing. For blood, bone marrow, spleen and the lung and liver perfusates,  Lineage- Gr1+ were sorted together with enriched cKit+ cells.

overall_design: ApoE-/- (C57BL6/J background) mice fed for 16 weeks with HFD. Single cells suspensions from brachiocephalic artery (BCA), blood, bone marrow, spleen as well as lung and liver perfusates were obtained and FACS-sorted using the following gating strategies: DAPI- Gr1+ Lineage- (Ter119, B220, CD3, FcRe, NK1.1) and DAPI-Gr1-cKIT+ was used for blood, bone marrow, lung and liver samples. For aortic cells, cell sorting was used to obtain enrich for Ly6G+, CD31+, B220+, CD3+, CD11b+F4/80+ and CD11b-F4/40-CD31-B220-CD3- cells. In addition, non-enriched DAPI- cells were included in the analysis. Cells were sorted using BD FACS Aria III Cell Sorter with the purity >95%. A total 6 10x Genomic samples were loaded with around 16000 cells each. All cells were hashtaged by mouse, organ and enrichment strategy. Sequencing was performed to aim 40k reads per cell.

first: Alexander

last: Bender

first: Celia

last: Borja Almarcha

first: Raphael

last: Chevre

first: Carlos

last: Silvestre-Roig


title: EBNA1 inhibitors reveal CDC7 and POU2F1 as direct functional targets in EBV epithelial cancers [ChIP-Seq]

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Epstein-Barr virus (EBV) latent infection is ubiquitously associated with nasopharyngeal carcinoma and gastric cancer, expressing very few viral protein components (EBNA1 and LMP1/2A). We previously showed that EBNA1 inhibitor VK1727 blocked cell cycle progression and growth of EBV+ tumors in vivo. However, the underlying molecular mechanism requires more evidence. In this study, we employed VK1727 to remove EBNA1 binding to viral and cellular genomes in three EBV+ epithelial tumors (PDX C15, C666-1 and SNU719). Then we integrated EBNA1 ChIP-seq and transcriptomic analysis to identify direct gene targets of VK1727, which involve in cell cycle progression and cell proliferation. Our analysis characterized a cell cycle dependent kinase CDC7 and a stem cell transcription factor POU2F1. Further analysis illustrated that EBNA1 binding to CDC7 promoter and POU2F1 intron promotes RNA Pol II-pS5 to initiate transcription of these two genes. Moreover, our results revealed CDC7 inhibitor Simurosertib is epistatic with VK1727 in reduction of EBV copy number, induction of cell cycle arrest, and inhibition of cell proliferation in EBV+ epithelial cancer. While POU2F1 knockdown reduced copy number of EBV, decreased expression of viral genes and inhibited proliferation of SNU719 cells. Our study revealed two functional gene targets of VK1727 in EBV+ epithelial cancers, which provides two potential biomarkers for following therapeutical research.

overall_design: 20 million C666-1 cells were collected for  chromatin precipitation sequencing to characterize EBNA1-bound gene targets in EBV+ epithelial cancers, which were performed using antibody against EBNA1

first: Songtao

last: HE

first: Niseno

last: Terhuja

first: Bhanu Chandra

last: Karisetty

first: Paul

last: Lieberman


title: scRNA-seq of bone marrow and splenic emergency granulopoiesis

last: Silvestre Roig

address: Von Esmarch Str. 56

institute: University of Münster

summary: We performed scRNA-seq analysis using the 10X genomics platform of mice following a model of extramedullary hematopoiesis or control. Here, we isolated bone marrow, spleen and blood Gr1+and cKit+-enriched cells to investigate the dynamics of production across both sites of origin. In addition, we performed the following treatments and blood cells were sorted following similar strategy: (1) Splenectomy: a group of mice was subjected to splenectomy before CPM/AMD treatment; (2) partial irradiation with a shield protecting the abdominal region of the mouse followed by CPM/AMD treatment; (3) Mice treated with CPM/AMD were administered with anti-CXCR2 depleting antibody.

overall_design: C57BL6/J female mice were administered with cyclophosphamide (CPM), followed by daily administration of 5 mg/kg of AMD3100 (AMD). Single cells suspensions from blood, bone marrow, spleen and organ_01 from CPM/AMD-treated mice were obtained and FACS-sorted using the following gating strategy: DAPI- Gr1+ Lineage- (NK1.1, FcRe, Ter119, B220, CD3) and DAPI-Gr1-cKit+. Cells were sorted using BD FACS Aria III Cell Sorter with the purity >95%. A total 10 10x Genomic samples were loaded with around 16000 cells each. All cells were hashtaged by mouse, organ and treatment. Sequencing was performed at 40mio reads per cell.


title: Whole Blood Transcriptomics Differentiates Circulating Gene Expression Between Coronary Artery Disease and Peripheral Artery Disease

city: New York City

first: Matthew

last: Muller

state: NY

address: 550 First Avenue

department: Department of Medicine

institute: New York University

summary: Coronary artery disease (CAD) and peripheral artery disease (PAD) are prevalent atherosclerotic disorders that exhibit distinct clinical and pathological presentations. We used whole-blood RNA sequencing to investigate circulating transcriptomic differences between PAD and CAD. Whole-blood RNA sequencing was performed in 71 subjects 40-65 years of age with symptomatic PAD (n=20) or CAD (n=51). Patients with concomitant PAD and CAD were excluded. Differential expression analysis was performed to compare circulating gene expression in patients with PAD and patients with CAD. We identified 106 genes differentially expressed between PAD and CAD (p adj. < 0.1). Pathway analysis identified upregulation of interferon signaling pathways in CAD and upregulation of neutrophil degranulation and toll-like receptor signaling pathways in PAD. Cell type deconvolution revealed greater fractional abundance of T cell subsets in CAD compared to PAD. Patients with PAD had higher neutrophil-lymphocyte ratio that patients with CAD (3.4 vs. 2.3, p=0.01). In conclusion, PAD and CAD have unique circulating transcriptomes characterized by differences in inflammatory gene expression.

overall_design: Whole blood RNA-seq comparison of patients with  PAD and patients with CAD adjusted for demographic variables

first: Richard

last: Ni

first: Kelly

middle: V

last: Ruggles

first: Tessa

last: Barrett

first: Jeffrey

middle: S

last: Berger


title: TET2-mutant clonal hematopoiesis prevents T-cell exhaustion and suppresses cancer metastasis [scRNA-seq]

city: Tsukuba

first: AI NHAN THI

last: LE

state: Ibaraki Prefecture

address: 2-1-1 Amakubo, University of Tsukuba Global Village, 305-8575

department: Department of Hematology

country: Japan

institute: Graduate School of Comprehensive Human Sciences, University of Tsukuba

summary: TET2-mutant clonal hematopoiesis (CH) is associated with reduced cancer metastasis in human cohorts. Using mouse models of colorectal cancer liver metastasis, we demonstrate that Tet2-deficient hematopoietic cells suppress metastatic tumor burden by preventing CD8+ T-cell exhaustion. Single-cell RNA-seq with paired V(D)J T-cell receptor (TCR) sequencing of CD45+ tumor-infiltrating leukocytes from Vav1CreTet2KO and Tet2fl/fl mice was performed to characterize transcriptional and clonotypic changes associated with TET2 loss in tumor-infiltrating immune cells.

overall_design: CD45+ live tumor-infiltrating leukocytes were sorted by flow cytometry (BD FACSAria III) from liver metastatic tumors of Vav1CreTet2KO (KO_04, KO_05) and Tet2fl/fl control (WT_75, WT_89) mice at day 30 post-intrasplenic injection of Venus-AKTPM/LOH colorectal cancer cells. Sorted cells were processed to generate barcoded 5' gene expression (GEX) libraries and TCR-enriched libraries using the Chromium Next GEM Single Cell 5' Kit v1.1 (10x Genomics, Cat#1000165) and GEM Single Cell V(D)J Reagent Kits v1.1 (10x Genomics, Cat#1000181), targeting 10,000 cells per library. Libraries were sequenced on the Illumina NovaSeq X Plus platform (Macrogen, RRID: SCR_016387) and mapped to the mouse genome (GRCm39) using Cell Ranger v8.0.1 (10x Genomics, RRID: SCR_017344).

first: Tran

last: Nguyen

first: Ai-Nhan

middle: T

last: Le

first: Mamiko

last: Sakata-Yanagimoto

first: Robert

last: Vanner


title: Heat shock factor 5 is indispensable for pachynema progression and LINE1 silencing during spermatogenesis in mice [smallRNA-Seq]

city: Wuhan

first: shen

last: jin

state: Hubei

address: No. 299, Bayi Road, Wuchang District, Wuhan City

institute: Wuhan university

type: Non-coding RNA profiling by high throughput sequencing

summary: Testes were collected from 16-day-old wild-type and Hsf5 knockout  mice; small RNA libraries were constructed and sequenced on the Illumina NovaSeq 6000 platform, with adapter trimming, extraction of 18–32 nt reads for piRNA analysis, alignment to miRBase, non-coding RNAs, piRNA clusters, and transposable elements (RepeatMasker, mm39), categorization of aligned 25–32 nt piRNAs, and ping-pong analysis using LINE1 and IAP consensus sequences from Repbase, to determine whether HSF5 deficiency affects piRNA biogenesis and transposon silencing during mouse spermatogenesis by assessing piRNA abundance, length distribution, annotation profile, and ping-pong amplification in Hsf5-/- testes

overall_design: This study aims to perform small RNA-seq profiling of testes from 16-day-old wild-type mice and their knockdown counterparts, thereby investigating piRNA expression changes during spermatogenesis.

first: Qi

last: Sun

first: Yuming

last: Cao

first: Zhiyi

last: Chen

first: Jin

last: Shen

first: Zejia

last: Li

first: Binyi

last: Wang

first: Muyang

last: Cheng

first: Jiemin

first: Weihao

last: Gong

first: Mengcheng

last: Luo

first: Yuanzhen

last: Zhang

first: Rong

last: Liu


title: The C16orf87 protein is a subunit of the MIER corepressor complex controlling embryonic development and cell migration

city: Uppsala

first: Débora

last: Parrine

state: Uppsala

address: Husargatan 3,

department: NBIS

country: Sweden

institute: Scilifelab

summary: Histone modifications by histone deacetylases (HDACs) are essential for controlling chromatin structure and regulating gene expression. Functionally, HDACs act as enzymatic subunits within diverse multisubunit corepressor complexes, thereby targeting distinct sets of genes. Here, we identify C16orf87 as a previously uncharacterized functional subunit of the MIER corepressor complex that mediates HDAC1 and MIER1 protein interactions. Using CRISPR/Cas9 genome editing, we demonstrate that loss of C16orf87 in human cells alters chromatin accessibility, reduces cell migration, and impairs healthy embryonic development of zebrafish. Based on these findings, we propose renaming C16orf87 as HDAC Interacting Protein (HDIP), to reflect its newly revealed function.

overall_design: Approximately 2 x 106 Panc-01WT or Panc-01KO cells were crosslinked in triplicate with 1% paraformaldehyde in PBS buffer for 15 min and stopped by the addition of 1.25 M glycine for 5 minutes at room temperature. Cells were lysed and sonicated using Bioruptor Plus (Diagenode) for 10 min with 5s on and 5s off pulses in low power output at 4ºC. Optimal chromatin fragmentation of 400-300 bp was verified in reversed cross-linked samples on a TapeStation 2200 system (Agilent Technologies). Library preparation was performed with the Omni-ATAC method. Once the final library was obtained, a purification step using AMPure XP beads was done before concentration and fragment size assessment. A quality control step consistent of size distribution and yield estimation is applied before the library sequencing. The libraries were pooled and sequenced on the NextSeq 2000 sequencer on one P2-100 flowcell (2x50 bp set-up) and resulted in approximately 60 - 100 M read pairs at the individual sample level across the six samples. The sequencing results from the ATAC-seq analysis performed by the NGI platform were analysed by the Nextflow pipeline NF-core/atacseq version 2.1.2 (https://nf-co.re/atacseq) 37. Briefly, sequence adapters are trimmed by Trim Galore! and aligned by the BWA software. The Picard package marks duplicates and merges alignments from multiple libraries into a single sample. It then filters mitochondrial DNA, duplicates, unmapped regions, and other unwanted sequences using SAMtools, Pysam, and BAMTools. Normalized bigWig files were generated by BEDTools, and bedGraphToBigWig. Genome-wide enrichment was done by deepTools and peaks were called using MACS2. Differential accessibility analysis was performed by DESeq2 and Homer was used to annotate gene features. Data was visualized with the Integrative Genome viewer (IGV) and additional tracks for HDAC1, HDAC2, MIER1, MIER2, MIER3 and H3K27ac markers were obtained from ChIP-Atlas.

first: Tanel

last: Punga

first: Mårten

last: Larsson

first: Endrina

last: Mujica

first: Fabio

last: Rabelo Melo

first: Dandan

first: Marcel

last: den Hoed

first: Leif

last: Andersson


title: Semaglutide Slows Epigenetic Aging in a Randomized Trial of HIV-Associated Lipohypertrophy

city: La Jolla

first: Michael

last: Corley

state: CA

address: 9575 Gilman Drive

department: Department of Medicine, Division of Geriatrics, Gerontology and Palliative Care The Sam and Rose Stein Institute for Research on Aging and Center for Healthy Aging

institute: University of California San Diego

type: Methylation profiling by genome tiling array

summary:
Genome-wide DNA methylation profiling of PBMC samples from people living with HIV
HIV-1 infection impacts biological aging, and epigenetic clocks highlight epigenetic age acceleration in people with HIV. Despite evidence indicating Glucagon-like peptide-1 receptor agonist in beneficial HIV-associated cardiometabolic outcomes, effects on aging biomarkers in HIV epigenetic studies is a major gap in knowledge. Hence, we generated a  representative epigenetic dataset to examine Glucagon-like peptide-1 receptor agonist  in epigenetic ageing and relationships to clinical phenotypes.

overall_design: Bisulfite converted DNA from whole blood were hybridized to the Illumina MethylationEPIC v2.0 Beadchip


title: Changes in tRNA wobble modifications under a norepinephrine gradient coincide with codon-biased translation and induction of virulence in EHEC O157:H7

city: Cambridge

first: Abigail

last: McShane

state: MA

address: 77 Massachusetts Ave

department: Biological Engineering

institute: Massachusetts Institute of Technology

summary: The goal of this study was to investigate how Enterohemorrhagic Escherichia coli O157:H7 (EHEC) strain EDL933 remodels its tRNA pool in response to the catecholamine hormone norepinephrine, a host-derived cue that stimulates virulence in this pathogen. Here, we performed Absolute Quantitative RNA-sequencing (AQRNA-seq) to measure levels of tRNA isoacceptors in EHEC samples exposed to 0, 25, and 50 micromolar norepinephrine.

overall_design: An overnight culture of EHEC O157:H7 EDL933 was diluted 1:100 in DMEM low glucose (supplemented with HEPES and pyruvate, no serum) with 0, 25, and 50 micromolar norepinephrine. cDNA libraries were constructed from purified small RNA using a variation of the Absolute Quantitative RNA Sequencing (AQRNA-seq) library preparation protocol (PMCID: PMC8355021), described in the library construction protocol. Constructed libraries were subjected to quality assessment using Fragment Analyzer and qPCR, followed by paired-end sequencing (PE75) on a Illumina MiSeq platform.

first: Peter

last: Dedon


title: ATP2B1 expression identifies human hematopoietic stem cells across ontogeny with superior repopulation and self-renewal capacity

city: Toronto

first: Angelica

last: Varesi

state: ON

address: 101 College Street

country: Canada

institute: University of Toronto

summary: Long-term hematopoietic stem cells (LT-HSC) maintain lifelong hematopoiesis while preserving the stem cell compartment through self-renewal. The human LT-HSC compartment is molecularly and functionally heterogeneous and also varies across ontogeny.  Dissecting the molecular basis for this variation is impeded by the absence of immunophenotypic markers to resolve LT-HSC heterogeneity. Here, we identified ATPase plasma membrane Ca2+transporting 1 (ATP2B1/PMCA1) as a novel cell surface marker that is heterogeneously expressed by CD49f+ LT-HSC across ontogeny. ATP2B1 immunophenotypic expression stratified human CD49f+ LT-HSC from fetal liver (FL), neonatal cord blood (CB) and adult mobilized peripheral blood (mPB) sources into functionally distinct subpopulations in single-cell (sc) clonogenic assays. CD49f+ATP2B1+ LT-HSC exhibited superior long-term repopulation and self-renewal capacities in vivo compared to CD49f+ATP2B1– LT-HSC. Molecular profiling by scMultiome and immunofluorescence microscopy point to enrichment of an HSC self-renewal program that includes the TFEB-endolysosomal axis in CD49f+ATP2B1+ LT-HSC. Our study provides a new tool to dissect the heterogeneous molecular programs in LT-HSC across ontogeny.

overall_design:
scMultiomics: CD49f+ATP2B1+, CD49f+ATP2B1- and CD49f-ATP2B1- were sorted from a pool of CD34+-enriched cord blood samples and sequenced.

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

first: Murtaza

last: Nagree

first: Isabella

last: Di Biasio

first: Andy

middle: G

last: Zeng

first: Sayyam

last: Shah

first: Hyerin

last: Kim

first: Alex

last: Murison

first: John

middle: E

last: Dick

first: Stephanie

middle: Z

last: Xie


title: Engrailed-1 Potentiates Mitochondrial Transplant Neuroprotection in Spinal Cord Ischemia-Reperfusion Injury [OE]

first: Wei

last: Wang

address: No. 155 Nanjing North Street

summary: Spinal cord ischemia-reperfusion injury (SCI/RI) is characterized by severe mitochondrial dysfunction and neuronal apoptosis. The transcription factor Engrailed-1 (En-1) has been identified as a potential regulator of mitochondrial homeostasis and neuroprotection. In this study, we utilized an integrated multi-omics approach to elucidate the molecular mechanisms by which En-1 protects cells from ischemia-like injury. We performed RNA-sequencing (RNA-seq) on PC12 cells with stable En-1 overexpression and their respective controls under both normoxic and oxygen-glucose deprivation/reoxygenation (OGD/R) conditions. To identify direct genomic targets of En-1, Cleavage Under Targets and Tagmentation (CUT&Tag) analysis was conducted. Integration of transcriptomic and DNA-binding profiles revealed a distinct regulatory network through which En-1 modulates mitochondrial function and cell survival. These data provide a comprehensive resource for understanding the transcriptional landscape governed by En-1 and identify potential therapeutic targets for mitigating mitochondrial damage in ischemic neural injuries.

overall_design: Comparison of PC12 control cells and stable En-1-overexpressing cells subjected to oxygen-glucose deprivation/reoxygenation (OGD/R) injury (n = 3 per group).

first: Rui

last: Tang

first: Shilun

last: Gao

first: Xiaotian

last: Han

first: Teng

last: Shi

first: Tianxiang

last: Gu

first: Enyi


title: ATAC-seq of the granulopoiesis lineage from different organs

first: Carlos

last: Silvestre Roig

summary: We performed ATAC-seq of 7,000-50,000 ex-vivo flow-sorted cells from the granulopoietic tree in mice.  For this we sorted Granulocyte-Macrophage Progenitors (GMP) from bone marrow (BM) and spleen (SP), Pre-Neutrophils (PreN) from BM and SP as well as Immature Neutrophils (imNeu) and Mature neutrophils (Neutro) from BM, SP and Blood (Bld). After sorting, cells were immediately processed using the OmniATAC protocol (Corces, Nat Methods 2014) and sequenced on a Novaseq-6000.

overall_design: C57BL6/J female mice were administered with cyclophosphamide (CPM), followed by daily administration of 5 mg/kg of AMD3100 (AMD). Single cells suspensions from blood, bone marrow, and spleen from CPM/AMD-treated mice were obtained and FACS-sorted using the following gating strategy: GMPs: DAPI- cKIT+, Sca1-, CD16/32high, CD34+, Lineage- (CD19-biot, F4/80-biot, Ter119-biot, B220-biot, CD3-biot, CD11b-biot, NK1.1-biot), PreN: DAPI- CD11b+ Gr1+ cKIT+ CXCR4+ Lineage- (CD19-biot, F4/80-biot, Ter119-biot, B220-biot, CD3-biot, NK1.1-biot), Neutrophils: DAPI- CD11b+ Gr1+ cKIT- CXCR4med Ly6G+ CXCR2low (imNeu) or CXCR2high (Neutro), Lineage- (CD19-biot, F4/80-biot, Ter119-biot, B220-biot, CD3-biot, NK1.1-biot).

last: Silvestre-Roig

first: Alexander

last: Bender

first: Raphael

last: Chevre

first: Oliver

last: Soehnlein


title: scRNA-seq of murine oropharyngeal carcinoma

summary: We performed scRNA-seq analysis using the 10X genomics platform of mice following injection of mouse oropharyngeal carcinoma cell line MOPC in the flank of C57BL6/J to generate a model of murine oropharyngeal carcinoma. Here, we isolated bone marrow, spleen, blood and tumor from Gr1+and cKit+-enriched cells to investigate the dynamics of production across both sites of origin.

overall_design: The MOPC cells were injected subcutaneously (s.c. 1 x 106 in 100 µl PBS) into the flank of C57BL6/J female mice. Single cells suspensions from blood, bone marrow, spleen and tumor were obtained and FACS-sorted using the following gating strategy: DAPI- Gr1+ Lineage- (NK1.1, FcRe, Ter119, B220, CD3) and DAPI-Gr1-cKit+. Cells were sorted using  FACS Aria III (BD) and  SH800S (Sony) cell sorter with the purity >95%. A total 4 10x Genomic samples were loaded with around 16000 cells each. All cells were hashtaged by mouse, organ and treatment. Sequencing was performed at 40mio reads per cell.

first: Jadwiga

last: Jablonska


title: Analysis of a pfap2-g reporter line provides insight into the epigenetic mechanisms regulating sexual commitment in the malaria parasite Plasmodium falciparum [RNA-seq]

city: Nijmegen

first: Martijn

middle: van den

last: Broek

address: Geert Grooteplein 24, route 846

department: Molecular Biology

country: Netherlands

institute: Radboud university - RIMLS Science

summary: This study aimed to investigate the changes occuring in parasites that are commited to express the sexual commitment transcription factor: ap2g.

overall_design: ChIP-seq of an adapted P.falciparum 3D7 strain. The pfap2-g locus was replaced by an hDHFR-GFP cassette, which allows to select for parasites that have an active pfap2-g locus using WR. The ChIP-seq was performed on parasites under WR-, WR+ and WR+/- conditions to visualize epigenetic differences. WR- indicates non-selected parasites, WR+ parasites selected for an active pfap2-g locus and WR+/- parasites selected for an active pfap2-g locus that have been placed off selection for >42 generations. This submission also includes RNA-seq samples using the same parasite strain. Parasites were selected for by an active pfap2-g locus (using WR- or WR+) and RNA-seq samples were taken at several time points after invasion of the RBC (time points: TP1, 8-16h; TP2, 16-24h; TP3, 24-32h; TP4, 32-40h; TP5, 40- 48h).

first: Elvira

last: Carrió

last: van den Broek

first: Beatriz

last: Graça

first: Jonas

last: Gockel

first: Sylwia

middle: D

last: boltryk

first: Richárd

last: Bártfai

first: Till

last: Voss


title: bulkRNA-seq LSKs CMPs MEPs GMPs from bone marrow and spleen

summary: Comparison of bone marrow or splenic originated stem cell populations (LSKs, CMPs, MEPs, and GMPs) in a mouse model of emergency granulopoieis.

overall_design: C57BL6/J female mice were administered with cyclophosphamide (CPM), followed by daily administration of 5 mg/kg of AMD3100 (AMD). Single cells suspensions from bone marrow and spleen from CPM/AMD-treated mice were obtained and FACS-sorted using the following gating strategy: DAPI- cKIT-Pe-Cy7, Sca1-PerCP-Cy5.5, CD16/32-FITC, CD34-PE, Lineage- (CD19-biot, F4/80-biot, Ter119-biot, B220-biot, CD3-biot, CD11B-biot). Cells were sorted using BD FACS Aria III Cell Sorter with the purity >95%. A total between 25000 and 350000 cells were sorted from each organ into lysis buffer from PicoPure RNA isolation kit (Thermofisher). RNA was extracted following manufacturer’s protocol and sequenced at 40mio paired end reads.


title: High-resolution spatial transcriptomics of human liver with VisiumHD

first: Rachel

last: Edgar

department: Ajmera Transplant Centre

institute: University Health Network

summary: The liver plays a critical role in metabolism and immune function. These crucial functions are diminished in chronic liver diseases, leading to over two million deaths annually worldwide due to liver failure. Single-cell transcriptomics has provided insights into the cellular composition of the liver in health and disease, but is inherently biased due to cell type-specific enrichment and destruction during the single-cell dissociation process. Previous work has highlighted difficulties in capturing specific populations such as cholangiocytes and hepatocytes. Spatial transcriptomics is a promising approach that does not have inherent bias for cell populations and adds important spatial context. Until recently, spatial transcriptomics technologies have only been at a multi-cellular resolution leading to mixed signals from different cell types. The latest spatial transcriptomic technology from 10X Genomics, VisiumHD, enables high-resolution spatial mapping of gene expression in tissue samples, offering a sophisticated platform for exploring the cellular composition of the liver. With a bin width of 2um, it can quantify transcripts at a sub-cellular resolution. Samples from three healthy human liver donors were sequenced and cells were clustered into cell types by integrating spatial transcriptomic data with existing single-cell reference maps. Spatially distinct cell signatures were identified through differential expression analyses and a high-resolution map of the liver was created. This resource provides cell-level and spatially-resolved insights into the cellular and geographical heterogeneity of the liver to serve as a resource for researchers to identify disease-specific spatial signatures and novel therapeutic targets.

overall_design: We applied 10x Genomics Visium HD to liver tissue from three healthy human donors to generate subcellular-resolution spatial transcriptomic profiles. Adjacent sections were imaged and sequenced to identify spatially distinct cell signatures and map the organization of the healthy liver.

first: Faizan

last: Hasan

first: Gary

last: Bader

first: Sonya

middle: A

last: MacParland


title: Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response

first: Brian

last: Yee

address: 9500 Gilman Dr

department: Health

institute: UCSD

summary: RNA binding proteins (RBPs) shape cellular function in health and disease. However, the function of RBPs expressed specifically in the central nervous system (CNS) remain uncharacterized. Within the CNS, we identify ARID5A as a microglial-specific RBP and integrate multi-omics analyses of ARID5A's RNA, DNA, and protein interactions to uncover its RNA-mediated regulation of microglial functions. We show ARID5A regulates the splicing and translation of its RNA targets, many of which are integral to microglial functions. We find ARID5A modulates cytokine secretion, lysosome activity, and iron accumulation, as well as ferroptosis sensitivity in microglia and co-cultured neurons. We illustrate the neuroprotective potential of ARID5A modulation, in which knockdown restored dysregulated functions in TREM2 mutant microglia. Our results highlight the potential of leveraging ARID5A-RNA interactions to restore dysregulated pathways in neurodegeneration.

overall_design: The following are sequencing data for RNA sequencing experiment performed on ipsc-derived microglia comparing crispri-mediated knockdown of ARID5A to a nontargeting control. Total RNA sequencing was used in splicing analysis and for input comparison controls to ribosome-protected RNA footprints in ribosome profiling.

first: Danielle

last: Schafer

first: Steven

last: Blue

first: Shuhao

last: Xu

first: Orel

last: Mizrahi

first: Maya

middle: L

last: Gosztyla

first: Katherine

last: Rothamel

first: Gene

middle: W

last: Yeo


title: Platelet lncRNA LUCAT1 Associates with Risk of Major Adverse Cardiovascular Events

first: Matthew

last: Muller

summary: CD34+ cell–derived megakaryocytes from four independent donors following treatment with PBS control, IFNα (1000 U/mL), or IFNγ (100 ng/mL). These data define donor-resolved interferon-responsive gene programs in human megakaryocytes under type I versus type II interferon stimulation.

overall_design: Human CD34+-derived megakaryocytes from 4 donors were infected stimulated with IFNα, IFNγ or PBS (vehicle control) for 24 hours.

first: Coen

last: van Solingen

first: Marcin

last: Sowa

first: Tessa

last: Barrett


title: Progesterone receptor (PGR)-mediated transcriptional networks in human ovulatory follicles: Identification of SOX9 as a novel PGR-downstream mediator [ChIP-seq]

city: Lexington

first: Hayce

last: Jeon

state: KENTUCKY

address: 800 Rose Street

department: Dept. of OB/GYN

institute: University of Kentucky

summary: Progesterone receptor (PGR) is an essential transcription factor for successful ovulation. Clinically, PGR inhibitors have been used as emergency contraceptives due to their ability to delay or block ovulation. While much of the current understanding of PGR’s function has been derived from animal models, the specific downstream target genes and pathways PGR regulates in human ovulatory follicles remain largely unexplored. In the present study, we utilized a human granulosa cell (hGLC) model that mimics preovulatory hCG-induced increases in PGR expression and progesterone production, combined with a PGR inhibitor (RU486), to identify hCG-induced, PGR-regulated genes in human ovulatory follicles. RNA-Seq and ChIP-Seq analyses revealed numerous genes regulated by PGR in response to human chorionic gonadotropin (hCG) treatment for 12 h, which are involved in diverse biological processes, including metabolism, steroidogenesis, signaling activation, cell cycle regulation, and transcriptional control. By comparing these findings with the existing data from PgrKO mouse models, we also identified both conserved and species-specific PGR-regulated genes. Notably, SOX9 was identified as a human-specific, hCG-induced PGR-target gene in hGLCs. A further characterization study using dominant follicle samples collected before and at different times after ovulatory hCG administration from regularly cycling women demonstrated that SOX9 expression is predominantly induced in the granulosa cells of ovulatory follicles and persists in the developing corpus luteum. Functional studies showed that SOX9 knockdown by siRNA reduced progesterone production and the expression of steroidogenesis-related genes (CYP11A1 and STAR) in hGLCs. In summary, the present finding provides the first comprehensive list of preovulatory PGR-downstream genes in human granulosa cells and unveils SOX9 as a novel human-specific ovulatory transcription factor with potential roles in steroidogenesis. This foundational information not only enhances our understanding of the PGR-regulated ovulatory pathway but also provides a critical resource for developing improved strategies to manage women’s fertility.

overall_design: ChIP-Seq of PGR in cultured human granulosa/lutein cells treated wth or without hCG for 12 h.

first: Yohan

last: Choi

first: Mats

last: Brännström

first: James

last: Akin

first: Thomas

last: Curry Jr

first: Misung

last: Jo


title: Progesterone receptor (PGR)-mediated transcriptional networks in human ovulatory follicles: Identification of SOX9 as a novel PGR-downstream mediator [RNA-seq]

overall_design: RNA-Seq profiling of cultured human granulosa/lutein cells treated wthout (Control) or treated with hCG ± RU486 for 12 h.


title: Cysteine availability tunes ubiquitin signaling via inverse stability of LRRC58 E3 ligase and its substrate CDO1

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

institute: Max-Planck-Institute for biochemistry

summary: Regulation of metabolic enzymes through degradation by the ubiquitin-proteosome system regulation is essential towards maintenance of cellular homeostasis. Our approach directly addresses a problem in the field; linking metabolic signal to an E3 ligase response. We employ active E3 ligase profiling coupled with broad MS-based screening, to reveal the changes in the proteome and E3 ligase-ome in response to the starvation or excess of a specific metabolite. We then use computationally driven strategies to connect these responses before in vitro and in cellulo reconstitution. The application of this strategy on cysteine metabolism led to our finding of LRRC58 mediated control of CDO1 degradation. Through reconstitution of this system, we also reveal that endogenous CDO1 degradation by LRRC58 is distinct from degradation induced by a molecular glue. Additionally, we have visualized CDO1 ubiquitylation by an LRRC58 CRL through cryo-EM, demonstrating the structural basis for CDO1 targeting by LRRC58.

overall_design: RNA-Seq was performed for HEK293T cells grown for 24hr in either normal media or Cys-free media


title: Developing Midbrain-like Organoid of Gaucher Disease as A Platform for Drug Assessment

city: Cincinnati

first: Stuart

last: Adler

state: OH

address: 3333 Burnet Ave

department: Human Genetics

institute: Cincinnati Children's Hospital Medical Center

summary: Gaucher disease (GD) is a lysosomal storage disorder caused by GBA1 mutations, leading to defective acid β-glucosidase (GCase) and accumulation of glucosylsphingolipids, causing inflammation and neurodegeneration. We developed midbrain-like organoids (MLOs) from induced pluripotent stem cells (iPSCs) of nGD patients with GBA1L444P/P415R and GBA1L444P/RecNcil mutations to model nGD brain pathogenesis. These nGD MLOs exhibited GCase deficiencies, reduced enzyme activities, lipids accumulation, transcriptomic alterations, and impaired dopaminergic neuron differentiation, mirroring nGD pathology. GBA1 correction mediated by CRISPR/Cas9 restored GCase activity, normalized lipids levels, and rescued dopaminergic neuron function, confirming the causal role of GBA1 mutations during early brain development. Using this novel platform, we further evaluated therapeutic strategies, including SapC-DOPS nanovesicles delivering GCase, AAV9-GBA1 gene therapy, and substrate reduction therapy (SRT) with GZ452, a glucosylceramide synthase (GCS) inhibitor currently under clinical investigation. These treatments either restored GCase activity, and/or reduced lipid accumulation, improved lysosomal function, and partially corrected dysregulated neural development and lysosomal pathways identified by transcriptomic analysis. These findings highlight MLOs as a physiologically relevant platform for studying nGD mechanisms and testing novel therapies, offering insights into potential treatments for this devastating disorder.

overall_design: Midbrain-like organoid (MLO) generated from WT-75.1 (WT) and GD2-1260 (nGD) iPSC cells at week 8 were collected for bulk RNA sequencing. Tree MLOs were pooled as one biological sample and three biological replicates were included for each genotype group.

first: Yi

last: Lin

first: Ying

last: Sun


title: Porphyromonas gingivalis inhibits Respiratory Syncytial Virus infection while suppressing anti-viral immunity

city: Columbus

first: Juhi

last: Bagaitkar

address: 700 Children’s Drive

department: Department of Pediatrics

institute: The Ohio State University

summary: Colonizing microbiota can differentially impact the outcomes of viral infections. While synergistic interactions between invading viruses and specific bacterial colonizers can enhance viral infectivity, resulting in severe disease, other bacteria can play a more antagonistic role by destabilizing viral particles, thus protecting against infection.  Here, we explored whether Porphyromonas gingivalis (Pg), a periodontal bacterial pathogen that can translocate to the airways, increases susceptibility to infection with the respiratory syncytial virus (RSV) and Sendai virus (SeV). Using a model of primary human bronchial epithelial (HBE) air-liquid interface cultures, we found that Pg co-infection significantly reduced RSV infection by rapidly inactivating RSV particles. This protection was conferred by the proteolysis of RSV fusion and attachment proteins by Pg proteases (gingipains), thus limiting viral entry. Despite this initial bottleneck, RSV replication within Pg co-infected cells was higher, indicating Pg created an intracellular environment favorable for viral replication. RNA-seq studies revealed that Pg infection led to the broad suppression of interferons (IFNs), particularly IFN-λ, and downstream interferon-stimulated genes (ISGs). Thus, our data show that P. gingivalis initially restricts RSV infection by inactivating the virus but later facilitates viral replication by suppressing IFNs. Our findings are clinically relevant as RSV infections are significant health concerns in both pediatric populations and older adults, who have a higher prevalence of periodontitis.

overall_design: A549 cells were primed with IFN-λ for 24h or left untreated. Following treatment, cells were infected with P. gingivalis (MOI100) for 4h, after wich the cells were washed with PBS and incubate for 24 hours. After incubation, cells were harvested and RNA extracted. We profiled gene expression to determine the effect the bacteria has on the antiviral immune response of airway epithelium.

first: Carlos

last: Rodriguez-Hernandez

first: Phylip

last: Chen

first: Marina

last: Terekhova

first: John

last: Perpich

first: Barbara

last: Potempa

first: Mark

last: Peeples

first: Mitchell

middle: H

last: Grayson

first: Jan

first: Maxim

middle: N

last: Artyomov

first: Richard

last: Lamont


title: The role of miR-10b-5p/Brain-derived Neurotrophic Factor Axis Deregulation in Poststroke Epileptogenesis

city: Linz

first: Anna

middle: Regina

last: Tröscher

address: Krankenhausstraße 5

department: Center for Medical Research

country: Austria

institute: Johannes Kepler University Linz

summary: Objective: Poststroke epilepsy (PSE) is a common complication following stroke, associated with increased mortality, poorer functional outcomes, greater disability, and heightened dementia risk. Currently, no standardized guidelines exist for the primary prevention of PSE, and prophylactic antiseizure medications (ASMs) are not routinely recommended. Management typically begins with ASM initiation after the first unprovoked seizure. Identifying predictive biomarkers is critical for improving post-stroke care and preventing PSE. Materials&Methods: We retrospectively analyzed 25 patients with PSE, ischemic stroke without epilepsy, and epilepsy. Serum-derived miRNA sequencing was conducted to identify differentially expressed miRNAs across the groups. Selected miRNAs were validated by quantitative PCR (qPCR), and target prediction was performed in silico. Brain-derived neurotrophic factor (BDNF), a key regulator of post-stroke recovery and epileptogenesis, was identified as a primary target of miR-10b-5p. BDNF levels were measured using ELISA and correlated with clinical parameters. Results: miRNA profiling revealed significant differences among the groups, with miR-10b-5p expression markedly reduced in PSE patients compared to those with stroke alone. qPCR validation confirmed miR-10b-5p as a potential biomarker distinguishing PSE from stroke. In PSE patients, BDNF concentration correlated with disease duration and latency to first seizure, whereas no such association was observed in stroke or epilepsy groups. Conclusion: Our findings suggest a novel pathophysiological mechanism involving the miR-10b-5p/BDNF axis in PSE development. miR-10b-5p may serve as a promising biomarker for early identification and targeted follow-up of stroke patients at high risk for developing epilepsy.

overall_design: total of 24 samples: 9 epilepsy, 8 PSE, 7 stroke

middle: R

first: Rainer

last: Dormann

first: Joachim

last: Gruber

first: Mariia

last: Ragozina

first: David

last: Demmel

first: Daniel

last: Wallinger

first: Franziska

last: Ammer-Pickhardt

first: Raimund

last: Helbok

first: Tim

last: von Örtzen


title: Gestational and Postnatal Age Define Airway Epithelial Maturation and RSV Responses During the First Year of Life: Results of an ex-vivo/in-vitro Airway Epithelial Cell Study

city: Belfast

first: Guillermo

last: López-Campos

state: Northern Ireland

address: 97 Lisburn road

department: Welcome-Wolfson Institute for Experimental Medicine

country: United Kingdom

institute: Queen's University of Belfast

summary: Respiratory syncytial virus (RSV) is the leading cause of severe lower respiratory tract infection in infants globally.  Newborns, especially those born prematurely, are at increased risk of severe RSV-related illness, yet the influence of age on early-life airway epithelium innate immune responses remains relatively understudied.  We established ex-vivo/in-vitro well-differentiated paediatric nasal epithelial cell (WD-PNEC) cultures derived from preterm and term infants at birth and again at one-year-old.  Infection characteristics and innate immune responses were determined following in vitro RSV infection.  RSV growth kinetics and cytopathology were similar irrespective of gestation or age.  Secretion of interferon lambda-1 (IFN-λ1), CXCL10, CCL5, and CXCL8 were comparable between RSV-infected preterm- and term-newborn WD-PNECs.  Importantly, following RSV infection, secretion of RSV-induced IFN-λ1 (p<0.05) and CCL5 (p<0.01) and expression of the IFN-stimulated gene, IFI6 (p<0.05) were significantly higher in one-year- compared to newborn-derived WD-PNECs. Interestingly, secretion of the cell signalling cytokine pleiotrophin increased significantly with longer gestation (p<0.01) and older age (p<0.001). Differential gene expression analysis demonstrated 156 differentially expressed genes (DEGs) with age and revealed transcriptomic changes linked to gestation in newborns that persisted at 1-year. These findings indicate two major conclusions.  Firstly, we report transcriptomic differences in airway epithelial cell (AEC) development between term and preterm infants across the first year of life.  Secondly, we demonstrate that RSV infection responses of AECs become more robust with age in early-life.  Further investigation of identified DEGs and differentially expressed chemokines/cytokines is warranted to clarify their role in increased susceptibility of very young infants to severe RSV disease, as well as the significance of these factors in the emergence of wheezing phenotypes and long-term respiratory outcomes.

overall_design: Well-differentiated primary nasal epithelial cells from newborn and 1 year old infants were mock-infected and infected with RSV BT2a and gene expression was measured at 96 hpi.

first: Helen

last: Groves

first: Mary

last: McCabe

first: Jonathon

last: Coey

first: Lindsay

last: Broadbent

first: Hong

last: Guo-Parke

last: Lopez Campos

first: Michael

last: Shields

first: Ultan

middle: F

last: Power


title: Spatial Transcriptomics Reveals a Molecular Tumor Budding Signature in Head and Neck Cancer

city: Heidelberg

first: Jan

last: Budczies

address: Im Neuenheimer Feld 224

department: Institute of Pathology

institute: University Hospital Heidelberg

summary: Tumor budding is a histopathological feature associated with poor prognosis across multiple cancer types, including head and neck squamous cell carcinoma (HNSCC). Tumor buds represent the earliest traceable local invasion and are considered the origin of minimal residual disease, local recurrence, and metastasis. However, the molecular features underlying this phenomenon in HNSCC remain only partially characterized due to challenges in isolating tumor buds while preserving spatial context. Here, we employed high-plex spatial transcriptomics to specifically isolate and characterize tumor buds, complemented by single-cell RNA sequencing and pharmacogenomic analyses to comprehensively characterize the transcriptional landscape of tumor budding in human papillomavirus (HPV)-negative HNSCC. Our unprecedented spatial resolution revealed that tumor buds exhibited distinct gene expression profiles compared to tumor bulk, with significant upregulation of epithelial-mesenchymal transition (EMT) markers, extracellular matrix remodeling genes (including fibronectin and laminin-332 subunits), and coagulation pathway components. Unlike previous bulk tissue analyses, our approach enabled differential correlation analysis that uncovered extensive gene network rewiring both within tumor cells and between tumor and stromal compartments, highlighting dynamic molecular reprogramming during the budding process. We developed a novel 28-gene tumor budding signature (TBS) that effectively distinguished tumor buds from other compartments (AUC=0.97) and demonstrated independent prognostic value in the TCGA-HNSC cohort (HR=1.54, p=0.02), representing the first molecularly defined biomarker for tumor budding applicable to conventional transcriptomic data in HNSCC. Analyses of single-cell RNA-seq datasets confirmed the tumor-specific expression of the TBS, its association with a hybrid epithelial-mesenchymal state, its expression predominantly at the leading edges of tumors, and its induction via subtypes of epidermal growth factor receptor activities. Uniquely, our pharmacogenomic analysis revealed that SCC cell lines with high TBS scores showed increased sensitivity to Raf-MEK inhibitors, suggesting clinically actionable therapeutic vulnerabilities, which was confirmed in a 3D model of early local invasion. This integrated spatial-molecular approach provides novel insights into tumor budding in HNSCC and establishes a foundation for a better understanding of the molecular mechanisms of tumor budding, as well as improved risk stratification and targeted therapeutic interventions for this aggressive tumor phenotype.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Formalin-fixed, paraffin-embedded (FFPE) primary tumor sections from 43 immunohistochemically p16-negative (HPV-negative) HNSCC patients (24 exhibiting tumor budding, 19 non-budding) were used for the analysis using the Nanostring GeoMx Digital Spatial Profiler Whole Transcriptome Atlas. For sampling, distinct regions of interest (ROIs) were selected, corresponding to tumor buds, tumor bulk from budding tumors, and tumor bulk from non-budding tumors, along with their adjacent stromal compartments. Two to three ROIs were selected per patient and per tissue type (tumor buds, bulk from budding tumors, bulk from non-budding tumors). Patient samples were unique in the cohort. These ROIs were then segmented into distinct areas of illumination (AOIs) based on immunofluorescence morphology markers: PanCK was used for epithelial cells (tumor AOI), CD45 for immune cells (immune AOI), and cells negative for both PanCK and CD45 were assigned to the stromal AOI. Transcript quantification was performed via UV-cleavage and next-generation sequencing (NGS) of the released oligonucleotide barcodes

first: Iordanis

last: Ourailidis


title: The effect of carnitine treatment on palmitic acid-treated C2C12 myotubes

city: Lishui

first: Yahong

last: Lu

state: Zhejiang

address: No.289, Kuocang Road, Liandu District, Lishui City, Zhejiang Province, China

institute: The Fifth Affiliated Hospital of Wenzhou Medical University

summary: Skeletal muscle fatty infiltration has been shown to be strongly associated with sarcopenia. In this study, we used palmitic acid to treat C2C12 myotubes to cause fatty acid overload, along with carnitine, and analyzed gene expression in different groups of C2C12 myoblasts by RNA sequencing.

overall_design: The C2C12 cell line differentiated into myotubes was divided into a control group, a palmitic acid group, and a palmitic acid + carnitine group, with three replicates in each group.

first: Yu

last: Bai

first: Weiqing

last: Li

first: Zhiguo

last: Zhou

first: Heihuan

last: Lai

first: Xingyu

last: Hu

first: Tao

last: Yang

first: Chendi

last: Wang

first: Yitao

last: Chen

first: Keping

last: Gan

first: Kechi

first: Haiwei

last: Ma

first: Lin

last: Shen

first: Dengwei

last: He


title: Analysis of a pfap2-g reporter line provides insight into the epigenetic mechanisms regulating sexual commitment in the malaria parasite Plasmodium falciparum [ChIP-seq]

first: Martijn

last: Broek

first: Elvira

last: Carrió

last: van den Broek

first: Beatriz

last: Graça

first: Jonas

last: Gockel

first: Sylwia

last: boltryk

first: Richárd

last: Bártfai

first: Till

last: Voss


title: Pattern separation memory requires Cerebellin 4-Neogenin 1 signaling at dentate gyrus synapses

city: Palo Alto

first: Xiao

last: Han

state: California

address: 265 Campus Drive

institute: Stanford University

summary: The ability to avoid confusion between similar episodic memories enables organismal survival and fitness. This evolutionarily conserved differentiation process of memories as distinct representations is known as pattern separation. A central role for the entorhinal cortex->dentate gyrus (EC->DG) circuit in pattern separation is well established, but the molecular mechanisms that enable this circuit to mediate pattern separation memory is not known. Here we show the involvement in murine pattern separation memory of a unique transsynaptic protein complex formed by Cerebellin-4, Neogenin-1, and neurexins that is known to be selectively required for long-term plasticity in the EC->DG circuit. In vivo deletion of either presynaptic Cerebellin-4 in the entorhinal cortex or of postsynaptic Neogenin-1 in the dentate gyrus impairs acquisition of pattern separation memory. Thus, we describe a specific memory function for a defined molecular complex at an identified synapse, providing direct support for the hypothesis that synaptic plasticity contributes to the encoding of memory.

overall_design: WT mice (BL/6 background) were divided into three groups: home cage, context exposure, and foot shock. After 90 minutes of behavioural paradigm, each mouse was sacrificed, and the medial entorhinal cortex (MEC), lateral entorhinal cortex (LEC), and hippocampal subregions CA1 and  CA3  were dissected and RNAs were extreacted using TRIzol method. The RNA-seq was performed on IlluminaTruSeq platform.

first: Kif

last: Liakath-Ali

first: Dong

middle: I

last: Choi

first: Thomas

middle: C

last: Südhof


title: Early Intervention of the PKC-Hippo Signaling Alleviates Post-Traumatic Osteoarthritis

city: Miami

first: xiaomin

last: cai

state: Florida

address: Rosenstiel Medical Science Building 1600 NW, 10th Ave.

institute: University of Miami

summary: Post-traumatic osteoarthritis (PTOA) is a progressive joint disease triggered by mechanical injury and characterized by inflammation and cartilage degradation. The Hippo signaling pathway and its upstream regulator PKCζ have emerged as key modulators of mechano-inflammatory responses in chondrocytes. This study aimed to investigate the dynamic regulation of the PKC-Hippo signaling axis following joint injury and to evaluate the therapeutic potential of targeting this pathway in early PTOA.

overall_design: This study investigates the early gene expression changes in post-traumatic osteoarthritis (PTOA) and the therapeutic impact of PKC inhibition on PTOA progression.  A mouse model of PTOA was established through anterior cruciate ligament (ACL) injury. Mice were randomly assigned into three experimental groups:  Sham control group: Mice without ACL injury, tissues harvested at 24 hours post-procedure.  PTOA model (vehicle control): Mice subjected to ACL injury and treated with 0.9% saline as a control, tissues harvested at 24 hours post-injury.  PKC inhibitor treated group: Mice subjected to ACL injury and treated with a PKC inhibitor, tissues harvested at 24 hours post-injury.


title: Single-Cell RNA Sequencing Reveals Yiqi Huayu Jiedu Formula Alleviates Acute Respiratory Distress Syndrome Through Regulation of Macrophage Chemotaxis

status: Public on Apr 16 2026

city: Beijing

first: Boyue

last: Wang

address: No.11 BeiSanHuanDongLu, ChaoYang District

institute: Dongzhimen Hospital

summary: Integrated network pharmacology, single-cell RNA sequencing, and experimental analyses revealed that Yiqi Huayu Jiedu Formula (YQHYJDF) protects lung tissue by inhibiting macrophage chemotaxis and neutrophil recruitment through suppression of proinflammatory cytokines IL-6, IL-1β, and TNF-α, PI3K/AKT, MAPK, and NF-κB signaling, and downregulation of chemokines CCL2, CCL7, and CCL12.

overall_design:
An ARDS rat model was established by tail vein injection of LPS, after pre-prepared intervention with the intragastric administration of YQHYJDF. 3 rats in each Groups: Blank Control Group, ARDS Model Group, YQHYJDF Group. Single-cell RNA sequencing was performed with lung tissues of all groups of rats to explore differentially expressed genes between groups.

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raw files were not provided by the submitter
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title: Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [cutnrun]

first: Brian

last: Yee

overall_design: The following are sequencing data for Cut & Run of ARID5A and Epicypher controls prepared from nuclei isolated from THP-1 macrophages

first: Danielle

middle: M

last: Schafer

first: Steven

last: Blue

first: Shuhao

last: Xu

first: Orel

last: Mizrahi

first: Maya

last: Gosztyla

first: Katherine

last: Rothamel

first: Gene

last: Yeo


title: LHX2 drives neuroendocrine transformation in TP53/RB1-deficient prostate cancer

city: shenyang

first: Shouyi

last: Zhang

state: Liaoning

address: No. 44 Xiaoheyan Road, Dadong District

institute: Liaoning Cancer Institute and Hospital

summary: Neuroendocrine prostate cancer (NEPC) is an aggressive subtype that progresses after androgen deprivation therapy (ADT) resistance and has extremely poor prognosis. Its underlying regulatory mechanisms remain incompletely understood. Through analyses of cell lines, organoids, transgenic mouse models, and clinical samples, this study systematically revealed the core role and regulatory network of LIM homeobox transcription factor 2 (LHX2) in NEPC occurrence and development. In the genetic context of TP53/RB1 deficiency, LHX2 is activated and induces prostate cancer cell transdifferentiation into a neuroendocrine (NE) phenotype. LHX2 and FOXA2 exhibit a mutually exclusive expression pattern, forming two NEPC subpopulations (FOXA2high and LHX2high) that synergistically maintain NE features. Analysis of clinical samples demonstrated that LHX2 expression was closely associated with NEPC progression and ADT resistance. The LHX2-001 transcript containing the LIM domain was found to be the key subtype driving NE transformation, and was found to functionally depend on the transcriptional coactivator CEBPB and to collectively regulate the expression of NE genes. ACTIVIN, identified as a signal specific to the LHX2high subpopulation, played a major role in enhancing tumor stemness, and its key receptor ACVR2B was transcriptionally regulated by LHX2. Targeted blocking of Activin A (garetosmab) effectively inhibited the progression of LHX2-overexpressing tumors. Our findings clarified the molecular mechanism through which specific LHX2 transcripts drive NEPC, revealed the subtype heterogeneity of NEPC, and may provide a new theoretical basis and potential targets for NEPC diagnosis and targeted therapy.

overall_design: This study mainly detected the chromatin accessibility of PC-3 cells after knockdown of RB1, overexpression of LHX2-001, and overexpression of LHX2-003 through ATAC-seq, and observed the binding differences of LHX2-001 and LHX2-003 in the genome by CUT&TAG.

first: Yu

last: Zeng

first: Guangyi

last: Shan

first: Chang

last: Liu

first: Yuyan

last: Zhu


title: Cultured ex vivo human brain tissue maintains cell-type transcriptional identities

city: Houston

first: JP

last: McGinnis

state: TX

address: 5306 Creekbend Dr

department: Neurosurgery

institute: Baylor College of Medicine

summary: There is growing recognition of the need for human-based models of the nervous system and its diseases. We used single-nucleus RNA sequencing of six patient samples to determine how well various cell types maintain their transcriptional identities over two weeks in organotypic slice culture. Patient samples included two pediatric temporal lobectomies, one adult frontal cortex, two glioblastomas, and one medulloblastoma. For each patient sample, we compared day 0 (flash-frozen at collection) to day 14 (organotypic slice culture) tissue. We found generally high correlations between day 0 and day 14 transcriptional profiles across cell types, especially in tumour cells, microglia, oligodendrocytes, and endothelial cells. This holds significant promise for the use of ex vivo human brain tissue in mechanistic studies and therapeutic screens.

overall_design:
Single-nucleus RNA sequencing (10x Genomics Chromium Single Cell Gene Expression 3' v3.1) of six human brain tissue samples at two time points each: day 0 (flash-frozen immediately after surgical resection) and day 14 (after 14 days in organotypic slice culture). 12 libraries total, one per tissue per time point. Each library is named TissueA–F with d0 or d14U suffixes. Donor mapping and pathology details are in the corresponding sample characteristics field.
**Submitters state "Raw FASTQs are not included due to patient privacy considerations — raw reads contain potentially identifying genotype information. Patients consented to broad data sharing but we are submitting processed counts only as an additional privacy safeguard"

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

middle: P

first: Sai

last: Mallannagari

first: Daniel

last: Curry

first: Benjamin

last: Arenkiel


title: Rapid evolution of mouse saliva through regulatory rewiring and gene expansions

city: Buffalo

first: Omer

last: Gokcumen

address: 135 Founders Promenade

department: Biological Sciences

institute: University at Buffalo

summary: Mammalian saliva plays essential roles in digestion, immunity, and host-microbiome interactions, yet its protein composition varies widely across species and sexes. This diversity makes saliva a powerful model to study evolution of gene expression. Here, we compared mouse and human salivary glands at the genomic, transcriptomic, and proteomic levels to understand how saliva composition evolves. We found that evolution of gene expression in mouse salivary glands is driven by rapid gene turnover and sexual dimorphism. In the submandibular and sublingual glands, 68% and 73% of expression from genes encoding secreted proteins derives from lineage-specific genes that lack one-to-one human orthologs. This contrasts the prevailing view that gene expression is largely conserved across tissues and highlights saliva as an unusually dynamic system of molecular evolution. Mouse submandibular gland shows striking sexual dimorphism, with 1537 tissue specific sex-biased genes, five times higher than in the liver, a classic model of sex-biased expression. These genes cluster in regions shaped by recent gene duplication, such as the kallikrein gene cluster, a mouse-specific expansion that accounts for ~16.4% of male-biased submandibular gland expression. Our analyses suggest that this bias arises through regulatory changes that are expanded by gene duplication, including the spread of a testosterone-associated regulatory motif and the expansion of a shared chromatin domain that promotes coordinated gene regulation. Our results describe a novel mechanism through which lineage-specific gene duplication and regulatory rewiring drive rapid, sex-specific evolution of the mammalian saliva.

overall_design: Bulk RNA-seq was performed on salivary glands (parotid, submandibular, and sublingual), pancreas, and liver from male and female mice of two strains. Each strain included 3 males and 3 females, for a total of 12 individuals.

first: Luane

middle: B

last: Landau

first: Shika

last: Jain

first: Nathan

last: Griffin

first: Achisha

last: Saikia

first: Jill

last: Kramer

first: Sarah

last: Knox

first: Stefan

last: Ruhl


title: Prolonged duration induces divergent transcriptomic responses to manganese, distinct from concentration effects, in an SH-SY5Y neurotoxicity model

city: West Lafayette

first: Priyanka

last: Baloni

state: IN

address: 207 S. Martin Jischke Dr, DLR 342

department: School of Health Sciences

institute: Purdue University

summary: Understanding manganese (Mn) neurotoxicity requires experimental models that realistically reflect human exposure scenarios. A key limitation of current in vitro paradigms is the reliance on acute, high-concentration exposures, which may not accurately capture the molecular consequences of long-term Mn accumulation. To address this, this study compared transcriptomic responses to acute (6-hour) and chronic (40-day) Mn exposures in SH-SY5Y cells, using Mn concentrations spanning near-physiological to sub-cytotoxic ranges. The 6-hour exposure design replicates a widely applied acute duration in the literature, while the 40-day duration was selected to mimic prolonged, low-level Mn burden reported in epidemiological and occupational studies. Bulk RNA sequencing revealed that chronic Mn exposure induced distinct and more extensive transcriptional alterations compared to acute exposure, independent of concentration. Pathway enrichment analyses indicated that cellular functions selectively perturbed under chronic conditions are highly relevant to neurodegenerative risks and aligns with independent Parkinson’s disease transcriptomic datasets. These pathways include axonal guidance signaling, amyloid fiber formation, extracellular matrix organization, and synaptic functioning. In contrast, acute exposures primarily disturbed intracellular ion homeostasis maintenance mechanisms. Protein kinase A signaling and metallothionein-mediated metal-binding pathway were the only two pathways that were shared between both applied durations exposed at Mn concentrations with reported adverse outcomes. Transcriptomic alterations in this study highlighted the contribution of mechanisms related to normal Mn-dependent cellular functions in the development of its neurotoxicity. Furthermore, these results emphasized that exposure duration is a critical determinant to be considered when evaluating long-term Mn overload-induced neurodegeneration via in vitro platforms.

overall_design: Bulk RNA-seq profiling of differentiated SH-SY5Y neuroblastoma line following 40-day or 6-hour manganese exposures.

first: Xueqi

last: Tang

first: Michael

last: Aschner

first: Aaron

last: Bowman


title: miR-151-5p Regulates Neural Stem Cell Fate by Targeting Aph1a to Modulate Notch Signaling Gradients

first: Xinrun

last: Wang

address: Dongdan

institute: PUMC

summary: To investigate the role of miR-151-5p in regulating neural stem cell (NSC) fate during neocortical development, we performed RNA-seq profiling of NSCs isolated from the developing mouse cerebral cortex. Conditional knockout of miR-151-5p led to increased Sox2 expression and enhanced NSC proliferation. Mechanistically, Aph1a, a core subunit of the γ-secretase complex, was identified as a direct target of miR-151-5p. Overexpression of Aph1a phenocopied the knockout phenotype, promoting NSC proliferation via elevated NICD levels. Our results demonstrate that miR-151-5p biases NSC fate specification by targeting Aph1a to modulate Notch signaling, thereby fine-tuning the balance between NSC maintenance and differentiation. This study reveals a novel miR-151-5p/Aph1a/Notch signaling axis governing NSC fate, providing a critical post-transcriptional regulatory layer in mammalian neocortical development.

overall_design: RNA-seq profiling of wildtype NSCs and miR-151-5p knockout cells from E14.5 mice cortex.


title: Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [eclip]

city: La Jolla

first: Brian

last: Yee

address: 9500 Gilman Dr

institute: UCSD

summary: RNA binding proteins (RBPs) shape cellular function in health and disease. However, the function of RBPs expressed specifically in the central nervous system (CNS) remain uncharacterized. Within the CNS, we identify ARID5A as a microglial-specific RBP and integrate multi-omics analyses of ARID5A's RNA, DNA, and protein interactions to uncover its RNA-mediated regulation of microglial functions. We show ARID5A regulates the splicing and translation of its RNA targets, many of which are integral to microglial functions. We find ARID5A modulates cytokine secretion, lysosome activity, and iron accumulation, as well as ferroptosis sensitivity in microglia and co-cultured neurons. We illustrate the neuroprotective potential of ARID5A modulation, in which knockdown restored dysregulated functions in TREM2 mutant microglia. Our results highlight the potential of leveraging ARID5A-RNA interactions to restore dysregulated pathways in neurodegeneration.

overall_design: The following are sequencing data for an enhanced crosslinking immunoprecipitation-seq experiments. The sets contain the RNAs directly crosslinked to ARID5A with a size-matched control used as an input.

first: Danielle

last: Schafer

first: Steven

last: Blue

first: Shuhao

last: Xu

first: Orel

last: Mizrahi

first: Maya

last: Gosztyla

first: Katherine

last: Rothamel

first: Gene

last: Yeo


title: RNAseq analysis of blood specimens from ART-suppressed people with HIV prior to analytical treatment interruption

city: San Francisco

first: Tongcui

last: Ma

address: 1650 Owens street

institute: UCSF

summary: Blood from ART-suppressed people with HIV (PWH) were characterized by bulk RNAseq analysis of total PBMCs, or of purified CD4+ T cells from PBMCs. Specimens were obtained from four cohorts: CLEAR, TEACH, REDUC, and ACTG A5345. All participants enrolled in these cohorts underwent analytical treatment interruption (ATI) and were monitored for time-to-rebound of HIV viremia.

overall_design: Included are seequencing files generated from clinical trial specimens of people with HIV (PWH) who underwent analytical treatment interruption (ATI). All specimens were obtained before analytical treatment interruption, and the primary association of the study was the time it took for viral rebound during the ATI. Specimens from four trials are included. Three trials were interventional trials performed in Denmark: CLEAR wherein participants orally received the latency reversal agent (LRA) panobinostat for 8 weeks (n=9 participants), REDUC wherein participants received therapeutic vaccination followed by intravenous administration of romidepsin as an LRA (n=16 participants), and TEACH wherein participants received the TLR9 agonist lefitolimod as both an LRA and an immune-boosting agent (n=9 participants). The fourth trial was the AIDS Clinical Trials Group (ACTG) trial A5345, a prospective study wherein individuals underwent ATI in the absence of any therapeutic intervention (n=41 participants). Bulk RNAseq was performed on either total PBMCs (CLEAR, REDUC, TEACH), or purified CD4+ T cells (A5345).

first: Mauricio

last: Montano

first: Yusuke

last: Matsui

first: Reuben

last: Thomas

first: Warner

last: Greene

first: Nadia

last: Roan


title: Soy Isoflavone Improves Reproductive Performance and Antioxidant Capacity of Sows and Reshapes Colostrum-Derived Exosomal microRNA Profiles

city: Chengdu

first: Qiming

last: Duan

state: Sichuan

address: No.211, Huimin Road, Wenjiang District

department: Animal Nutrition Institute

institute: Sichuan Agriculture University

summary: Background: This study investigated the effects of dietary soy isoflavone supplementation on reproductive performance, antioxidant capacity, and colostrum-derived exosomal microRNA profiles in sows, with the aim of exploring the molecular basis of maternal–offspring integrated regulation. A total of 120 Landrace × Yorkshire sows were assigned to either a control diet or a diet supplemented with 200 mg/kg soy isoflavone from gestation day 106 to lactation day 28. Reproductive performance and serum antioxidant indices were evaluated, and colostrum-derived exosomes were isolated for small RNA sequencing and bioinformatic analysis. Results: Dietary soy isoflavone supplementation significantly increased the total number of piglets born, the number of live-born piglets, litter weight at birth, and litter weight at weaning, while shortening farrowing duration (P < 0.05). In addition, soy isoflavone significantly elevated serum total antioxidant capacity and catalase activity on lactation day 21 (P < 0.05). Transmission electron microscopy, nanoparticle tracking analysis, and flow cytometry confirmed the successful isolation of colostrum-derived exosomes. Small RNA sequencing showed that most microRNAs ranged from 18 to 26 nucleotides, with a predominant peak at 22–23 nucleotides. Principal component analysis and differential expression analysis revealed that soy isoflavone markedly reshaped the microRNA cargo of colostrum-derived exosomes. Functional enrichment analysis indicated that the predicted target genes of differentially expressed microRNAs were mainly involved in transcriptional regulation, kinase-mediated signaling, inflammatory responses, and metabolic pathways, including mitogen-activated protein kinase, Ras, Rap1, endocytosis, autophagy, and adherens junction pathways. Integrated network analyses further suggested coordinated regulation of inflammatory signaling and metabolic homeostasis. Conclusions: Dietary soy isoflavone supplementation improved sow reproductive performance and antioxidant capacity, while reshaping colostrum-derived exosomal microRNA profiles and their associated regulatory networks. These findings provide a potential molecular basis for maternal–offspring integrated regulation.

overall_design: A total of 8 colostrum-derived exosomal small RNA libraries were analyzed in this study, including 4 biological replicates from the control group (CON) and 4 biological replicates from the soy isoflavone-supplemented group (SIF, 200 mg/kg). Samples were collected from healthy sows within 1 h postpartum. The CON group served as the control, and no separate reference sample was included. Biological replicates were used for sequencing analysis.

first: Jun

last: He


title: Limosilactobacillus reuteri-derived exopolysaccharides facilitate the repair of intestinal epithelium barrier compromised by chemotherapy exposure

city: Stockholm

first: Gintare

last: Lasaviciute

address: Svante Arrhenius väg 20C

department: Department of Molecular Biosciences

institute: Stockholm University

summary: A majority of patients undergoing chemotherapy treatment develop side effects that delay further cancer treatment. Antimetabolites, like 5 Fluorouracil (5 FU), are known to induce gut and oral inflammation, highlighting the importance of chemotherapy toxicity management. Here, we aimed to study whether probiotic bacterium Limosilactobacillus reuteri DSM 17938 (LR)-secreted components, including cell-free supernatant (CFS), exopolysaccharides (EPS), and extracellular membrane vesicles (MV), can improve gut barrier integrity following 5 FU exposure. Collectively, 5 FU altered the viability, metabolic activity, barrier integrity, and functional response of Caco-2 cells. EPS stimulation after 5 FU removal significantly improved the integrity and permeability of intestinal barrier through modulation of the transcriptional program associated with extracellular matrix and structure organization. Further, we found that CFS, MV and EPS differentially influenced monocyte polarization pathways, when monocytes were cultured with the supernatant from 5 FU exposed Caco-2 cells. Together, our findings suggest that the incorporation of bacterial metabolites, such as EPS, during chemotherapy could accelerate intestinal barrier recovery without suppressing the immune system, potentially allowing for a more effective scheduling of therapy in cancer patients.

overall_design: Total RNA was extracted from differentiated Caco-2 cells which were exposed to 50 microg/ml of 5 FU on the apical and basolateral sides or were left unexposed as a control. RNA-seq profiling was prepared from these samples.

first: Marta

last: López Plana

first: Sofia

last: Sundberg Örtegren

first: Sevasteia

last: Telli

first: Symeon

last: Kourmoulakis

first: Ludwig

last: Ermann Lundberg

first: Kenny

last: Lidberg

first: Oshadi

last: Peiris

first: Markus

last: Hiding

first: Indranil

last: Sinha

first: Ann-Beth

last: Jonsson

first: Stefan

last: Roos

first: Anna

last: Nilsson

first: Manuel

last: Mata Forsberg

first: Eva

last: Sverremark-Ekström


title: Deciphering molecular responses to radiofrequency microneedling in a 3D human skin model: New insights and modulation by aftercare treatment

city: Aachen

first: Sebastian

last: Huth

address: Pauwelsstraße 30

institute: Uniklinik RWTH Aachen

summary: Radiofrequency microneedling (RFMN) is an emerging therapeutic approach that enhances skin rejuvenation by delivering targeted thermal injury to the dermal and subdermal layers while sparing the epidermis. However, the molecular mechanisms underlying its biological effects especially in comparison to medical microneedling remain poorly understood. In this study, we aimed to investigate, for the first time, the molecular and histological responses to RFMN using a standardized three-dimensional (3D) human skin model. As a secondary objective, we assessed the modulatory effects of RFMN aftercare treatment with a dexpanthenol-containing ointment.Histological analysis of RFMN-treated 3D skin models showed dermal coagulation zones that disappeared after post-treatment with a dexpanthenol-containing ointment. Transcriptomic profiling 48 hours after RFMN showed an early pro-inflammatory response with upregulated chemokines and cytokines (e.g., CCL7, CXCL2, IL24) and downregulated matrix metalloproteinases and barrier genes, indicating controlled inflammation and skin renewal initiation. Aftercare with the dexpanthenol-containing ointment elicited distinct gene expression changes at 120 hours post-RFMN, including increased expression of cytokines (IL37), matrix metalloproteinases (MMP3, MMP8), and epidermal regeneration markers (LCE1B, VEGFA), consistent with accelerated wound healing, re-epithelialization, and inflammation modulation.In conclusion, this study elucidates the molecular and histological effects of RFMN and highlights the benefits of dexpanthenol-containing topical post-treatment, which may further shorten the already brief downtime. These findings support the optimization of clinical protocols for safer and more effective skin rejuvenation.

overall_design: We investigated the molecular and histological responses to RFMN utilizing a previously established standardized  human 3D skin model composed of primary dermal fibroblasts and epidermal keratinocytes. Histological assessments and transcriptomic analyses employing next-generation sequencing were conducted 48 and 120 hours after RFMN treatment. In addition, the effects of a topical dexpanthenol-containing ointment administered immediately following RFMN on wound healing and gene regulation were evaluated.

first: Yvonne

last: Marquardt

first: Laura

first: Sina

last: Djahed

first: Jens

last: Baron


title: Transcriptome analysis of ureter tissues from wild-type and COL17 knockout mice.

city: Sapporo

first: Takashi

last: Namba

state: Hokkaido

address: Kita 18-Nishi 9, Kita-ku

department: Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine

institute: Hokkaido University

summary: Type XVII collagen (COL17A1) is well-characterized as a critical structural component of the epidermal basement membrane in the skin; however, its presence and function in the urinary tract remain poorly described. We discovered that COL17A1 is also expressed in the urothelium under urological condition. To elucidate the molecular mechanisms underlying early urothelial abnormalities caused by COL17A1 deficiency, we performed transcriptomic profiling (bulk RNA-seq) of ureter tissues from 2-week-old wild-type and Col17a1 knockout mice.

overall_design: To elucidate the molecular mechanisms underlying COL17A1-mediated urothelial homeostasis, bulk RNA-sequencing was performed on ureter tissues isolated from 2-week-old Col17a1 knockout (KO) mice with C57BL/6N background and its wild-type (WT; n = 3 per group) .

first: Amy

last: Suzui

first: Osamu

last: Ichii


title: mRNA sequencing analysis of diquat herbicide-exposed (1/5 LC50) Aedes albopictus mosquito larvae at 72hours

city: CALICUT UNIVERSITY

first: ANUSRUTHI

last: RAMAKRISHNAN

address: THENHIPALAM

department: ZOOLOGY

country: India

institute: UNIVERSITY OF CALICUT

summary: Diquat, a bipyridinium aquatic herbicide, targets freshwater weeds but may also affect non-target species, such as the mosquito Aedes albopictus, in shared habitats. These results provide the first molecular insights into the effects of herbicides on aquatic dipterans, with implications for vector ecology, insecticide cross-resistance, and environmental risk assessment.

overall_design: Aedes albopictus fourth instar larvae were exposed to a sublethal concentration ( 1/5 LC₅₀) for transcriptomic profiling. One control and one treated ( 1/5 LC₅₀) samples and their duplicates were subjected to mRNA sequence analysis

first: Anusruthi

last: Ramakrishnan


title: Small Non-Coding RNAs in the Regulatory Network of Wheat Dwarf Virus-Infected Wheat

city: České Budějovice

first: Abdoallah

last: Sharaf

address: Branišovská 31

country: Czech Republic

institute: Biology Centre ASCR, v.v.i.

summary: Wheat dwarf virus (WDV) is a major constraint to global wheat production, causing severe yield losses and economic disruption. Understanding the molecular basis of wheat–WDV interactions is essential for developing resistant cultivars. Non-coding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), are key regulators of gene expression and defence. This study identified ncRNAs involved in wheat responses to WDV, including host lncRNAs, miRNAs, and viral small interfering RNAs (siRNAs) targeting WDV genomic regions. High-throughput sequencing revealed extensive ncRNA reprogramming under WDV infection. A total of 437 differentially expressed lncRNAs (DElncRNAs) and 58 miRNAs (DEmiRNAs) were detected. Resistant genotypes displayed more DElncRNAs (204 in Svitava; 163 in Fengyou 3) than the susceptible Akteur (141). In Akteur, 66.7% of DElncRNAs were downregulated, whereas in Svitava, 56.9% were upregulated. Akteur also exhibited more DEmiRNAs (28) than resistant genotypes (15), with predominant downregulation. A co-expression network analysis revealed 391 significant DElncRNA–mRNA interactions mediated by 16 miRNAs. The lncRNA XLOC_058282 was linked to 298 transcripts in resistant genotypes, suggesting a central role in the host defence. Functional annotation showed enrichment in signalling, metabolic, and defence-related pathways. Small RNA profiling identified 1166 differentially expressed sRNAs targeting WDV, including conserved hotspots and 408 genotype-specific sites in Akteur versus Fengyou 3. Infected plants displayed longer sRNAs, a sense-strand bias, and a 5′ uridine preference, but lacked typical 21–24 nt phasing. These findings highlight the central roles of ncRNAs in orchestrating wheat antiviral defence and provide a molecular framework for breeding virus-resistant wheat.

overall_design: Triticum aestivum miRNA profiles of genotypes associated with resistance against the Wheat dwarf virus were generated

first: Nuc

last: Przemyslaw

first: Jan

last: Ripl

first: Glenda

last: Alquicer

first: Emad

last: Ibrahim

first: Xifeng

last: Wang

first: Midatharahally

last: Maruthi

first: Jiban

last: Kumar