title: Cell quality attributes, clinical features and biomarker levels influence osteoarthritis patient responses to mesenchymal stromal cells

city: Toronto

first: Sowmya

last: Viswanathan

address: 60 Leonard Avenue

institute: University Health Network

summary: Bone marrow-derived mesenchymal stromal cells (MSC(M)) are promising immunomodulatory therapeutics for osteoarthritis (OA); however, mixed clinical efficacy has been reported. We present new 24-month follow-up data from our previous clinical trial investigating single intra-articular injection of autologous MSC(M) in knee OA, with analysis of responders and non-responders to probe differential baseline disease features and MSC(M) basal fitness. Analysis of patient-reported outcome measures (PROMs) showed responders had greater OA severity at baseline. Lower baseline levels of angiogenic/inflammatory synovial fluid biomarkers correlated to improved PROMs. A gene panel of putative immunomodulatory critical quality attributes (CQAs) distinguished MSC(M) donors classified as responders versus non-responders. Furthermore, an algorithm was developed to rank MSC(M) donors based on in vitro monocyte/macrophage polarization readouts and clinical efficacy. Lastly, microRNA-sequencing of MSC(M) revealed 69 microRNAs associated with responder status. Our data provide evidence for specific clinical phenotype features and biomarkers to stratify OA patients, as well as CQAs for quantifying basal immunomodulatory fitness of MSC(M) in knee OA.

overall_design: Biobanked MSC(M) were thawed and plated on 24-well plates at 50,000 cells/well and cultured for 72 h in proliferation medium. Cells were then washed with phosphate-buffered saline (PBS) and treated with low-glucose DMEM (Sigma) supplemented with or without synovial fluid. To treat cells with synovial fluid, samples were collected from unrelated late-stage OA patients (KL 3-4) outside of the clinical trial cohort (REB #14–7483), pooled from eight patients, and stored at ‑80°C until use, as previously described (82). For treated wells, DMEM was supplemented with 30% (v/v) synovial fluid. After 24 h, RNA extraction was performed on cell samples using a miRNeasy Mini Kit (Qiagen, Hilden, Germany) and stored at -30°C until analysis.

first: Kevin

last: Robb

first: Razieh

last: Rabani

first: Moaath

last: Saggaf

first: Shabana

last: Vohra

first: Antonietta

last: Fazio

first: Jaskarndip

last: Chahal

first: Anthony

last: Perruccio

first: Rajiv

last: Gandhi


title: Wenshen Xiaozheng Tang ameliorates endometriosis by interrupting the lactate/H3K9la-mediated crosstalk between ectopic endometrial stromal cells and macrophages

status: Public on Aug 05 2026

city: Nanjing

first: xiaohong

last: dong

address: Qixia District, Hongshan Road, Shizi Street 100

department: technical support

country: China

institute: Affiliated Hospital of Integrated Traditional Chinese and Western Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: WXT significantly reduced ectopic lesion volume, alleviated peritoneal adhesions, and decreased the proportion of M2 macrophages in both lesion tissues and peritoneal fluid, along with reduced lactate accumulation and suppressed M2-associated cytokine secretion. Single-cell transcriptomic analysis revealed enhanced glycolytic activity in eESCs and a positive correlation between M2 macrophage polarization and lactate-sensing gene signatures. WXT-containing serum inhibited eESC-derived lactate production, reduced H3K9la levels in macrophages, and blocked lactate-induced M2 polarization. Through UPLC-Q-TOF-MS/MS and molecular docking screening, we identified tormentic acid as a key absorbed component with strong predicted binding to both GLUT1 (a key glycolytic transporter) and p300 (a key regulator of histone lactylation). Tormentic acid reproduced the effects of WXT-containing serum, suppressing lactate production, reducing H3K9la levels, and attenuating M2 polarization. CUT&Tag and ChIP-qPCR further revealed that tormentic acid reduced H3K9la enrichment at the WNT2B promoter and suppressed its expression, defining a lactate-H3K9la-WNT2B axis through which tormentic acid ameliorates endometriosis.

overall_design: To identify potential downstream target loci of H3K9la, we mapped genome-wide H3K9la binding by CUT&Tag, comparing lactate-treated macrophages with those co-treated with lactate and tormentic acid.

first: Xiaohong

last: Dong

first: Shihan

last: Xu

first: Xiao

last: Wei

first: Xiajie

last: Zheng

first: Qiao

last: Wang

first: Kun

last: Gao

first: Wenjuan

last: Zhou


title: Increasing TET expression and 5-hydroxymethylcytosine formation by a carbocyclic 5-aza-2’-deoxy-cytidine antimetabolite

status: Public on Aug 06 2026

city: Saarbruecken

first: Gilles

last: Gasparoni

state: Saarland

address: Campus

department: Genetics Department

country: Germany

institute: Saarland University

type: Methylation profiling by genome tiling array

type: Expression profiling by high throughput sequencing

summary: Ten-eleven translocation (TET) enzymes are critical epigenetic regulators, which oxidize the methylated cytosine nucleobase 5-methyl-dC (5mdC) in the genome to 5-hydroxymethyl-dC (5hmdC) in an α-ketoglutarate-dependent manner. Because the presence of 5mdC in the promoter region of a given gene silences its expression, this oxidation goes in hand with the reactivation of such silenced genes. In different highly aggressive cancers such as acute myeloid leukemia (AML) and glioblastoma, loss of TET enzyme function and therefore reduced 5hmdC levels pave the way for tumor development. Impairment of TET activity can occur through metabolic inhibition, through loss-of-function mutations in TET genes themselves, and finally through suppression of TET-expression via epigenetic silencing. Reactivation of TET enzyme expression represents a major aim of epigenetic cancer therapy. Here we show that the carbocyclic antimetabolite 5-aza-2’deoxycytidine (cAzadC), which is supposed to suppress the methylation of DNA during replication, leads to a substantial increase of TET2 expression and strongly increasing 5hmdC levels. We show that the treatment with cAzadC goes in hand with the broad reactivation of the cellular anti-tumor responses. With patient-derived xenograft AML-mouse models, we show that this translates into a strongly improved anti-cancer effect in vivo.

overall_design: Refer to individual Series


title: Transcriptomic effects of combined AZD4573 and SMAP-2 treatment in resting and anti-CD3/CD28-activated primary human CD4+ T cells

city: San Francisco

first: Zichong

last: Li

state: CA

address: 1650 Owens Street

department: Gladstone Infectious Disease Institute

country: USA

institute: The J. David Gladstone Institutes

summary: This study characterized the effects of combined CDK9 inhibition and PP2A activation on host gene expression in primary human CD4+ T cells. In the broader study, the CDK9 inhibitor AZD4573 and the PP2A activator SMAP-2 cooperatively suppressed HIV transcription and promoted durable transcriptional silencing. The RNA-seq experiment was performed to determine whether this drug combination caused broad or selective host-transcriptome changes in uninfected primary CD4+ T cells under resting and T-cell receptor-activated conditions.  Primary CD4+ T cells from three independent HIV-negative donors were either maintained without stimulation or activated for 48 h with plate-bound anti-CD3 and anti-CD28 antibodies. Resting and activated cells were subsequently treated for 24 h with either 0.1% DMSO or a combination of 5 nM AZD4573 and 5 μM SMAP-2. Within each activation state, drug-treated samples were compared with donor-matched DMSO controls.  The transcriptional response to AZD4573 plus SMAP-2 was dependent on T-cell activation state. Resting CD4+ T cells exhibited a larger number of differentially expressed transcripts, many corresponding to unannotated protein-coding loci or long non-coding RNAs, with the P-TEFb-responsive gene MYC among the annotated downregulated genes. Activated CD4+ T cells exhibited fewer transcriptional changes; among these, HEXIM1 was downregulated and the transcriptional corepressor SLFN5 was upregulated. These data define the host-transcriptome effects of combined AZD4573 and SMAP-2 treatment in resting and activated primary human CD4+ T cells.

overall_design: A paired 2 × 2 factorial experimental design was used, with primary CD4+ T cells from three independent HIV-negative donors serving as biological replicates. For each donor, cells were divided into two activation conditions: resting cells maintained without stimulation and activated cells cultured for 48 h with plate-bound anti-CD3 and anti-CD28 antibodies. Each activation group was then divided into two treatment conditions: 0.1% DMSO vehicle control or 5 nM AZD4573 plus 5 μM SMAP-2 for 24 h. The study therefore comprised 12 RNA-seq samples in total: three donors × two activation states × two treatment conditions. Drug-treated samples were compared with donor-matched DMSO controls separately within the resting and activated cell states.

first: Francisco

middle: J

last: Zapatero-Belinchón

first: Patrik

last: Geleziunas

first: Melanie

last: Ott


title: Symbiosis with Penicillium sp. D7 Rewires Molecular Modules to Boost Plant Growth and As(III) Stress Tolerance

city: Pozuelo de Alarcón

first: Stephan

last: Pollmann

state: Madrid

address: Campus de Montegancedo, Autovia M-40 (km 38)

country: Spain

institute: CBGP (UPM-INIA/CSIC)

summary: Numerous non-mycorrhizal fungi have been reported to form close symbiotic relationships with plants. These tight mutual relationships can provide physiological benefits to the interacting organisms, including the improvement of nutrient assimilation or enhanced stress tolerance. The root-colonizing fungus Penicillium sp. strain D7 has been isolated from roots of Digitalis thapsi L. that were grown on the As-rich tailings of the Mónica mine in Bustaviejo, Spain. Here, we report the promotion of plant biomass production and stress tolerance of Arabidopsis thaliana L. plants inoculated with D7. The comparative analysis of the effect of mock- and D7-inoclulated wild-type Arabidopsis plants (Col-0) in the absence and presence of arsenite As(III) stress conditions (15 µM NaAsO2). Our data provide evidence for a profound effect of D7 on As(III) detoxification through the activation of a regulatory network that includes several plant hormones. In addition, fungus inoculation resulted in a significant induction of As sequestration in the root, which allowed for an enhanced shoot growth under As(III) stress conditions.

overall_design: To investigate differential gene expression in mock- and Penicillium sp. strain D7-inoculated (F) Arabidopsis wild-type plants (Col-0) under control (C) and arsenite stress (A) conditions (15 µM NaAsO2) in shoots (S) and roots (R).

first: Jesús

last: Vicente-Carbajosa


title: Transcriptomic Profiling of Mitochondrial RNA in HepG2 Cells Exposed to GenX, a Short-Chain PFAS

city: Winston-Salem

first: Sarah

last: Adjei-Fremah

state: North Carolina

address: 601 S Martin Luther King Jr Dr

department: Biological Sciences

institute: Winston-Salem State University

summary: This study investigated the transcriptomic effects of GenX on the mitochondria of human liver HepG2 cells. Cells were exposed to GenX at 10 µM and 100 µM concentrations for 48 hours. Mitochondria were isolated and mitochondrial RNA was extracted using TRIzol. High-quality RNA samples were sequenced using ribosomal-RNA-depleted libraries on the Illumina NovaSeq platform.  Per and polyfluoroalkyl substances (PFAS) such as hexafluoropropylene oxide dimer acid (GenX) are emerging environmental contaminants with increasing concern regarding their potential mitochondrial toxicity. This BioProject investigated the effects of GenX exposure on mitochondrial gene expression in human hepatic HepG2 cells. Cells were treated with GenX at 10 µM and 100 µM concentrations for 48 hours, followed by mitochondrial isolation and RNA sequencing of mitochondrial transcripts. Mitochondrial transcriptomic analysis revealed regulation of genes involved in oxidative phosphorylation, redox homeostasis, and apoptotic signaling. This dataset provides a resource for understanding PFAS induced mitochondrial dysfunction and hepatotoxicity mechanisms.

overall_design: RNASeq profile of mitochondria RNA in HepG2 exposed to GenX. HepG2 cells were treated with 0 µM (control), 10 µM, or 100 µM GenX for 48 hours. Mitochondria were isolated, and total mitochondrial RNA was extracted. High-quality RNA (RIN > 7) was sequenced to assess mitochondrial gene expression profiles across dose groups.

first: Michael

last: McNeil


title: scRNAseq of Hoxa10+ and Hoxa10-Lineage cells in uninjured and injured tibia

city: New York

first: Philipp

last: Leucht

state: New York

address: 540 1st Avenue, RB 4-530

department: Orthopedic Surgery

institute: NYU Langone Health

summary: We have employed PIPseq to probe the transcriptomes of Hoxa10+ skeletal stem and progenitor cells and their downstream lieneage in both control and HoxA mutant mice to explore a stemness role for Hox in this cell population.

overall_design: Single cell RNA sequencing was performed on cells isolated from iHoxa10 and iHoxa10ΔHoxA 1) uninjured tibiae with the proximal and distal epiphysis cut off, leaving only the diaphysis for further analysis, and 2) fracture calluses from 5 and 14 days post-injury tibiae with the rest of bones discarded (2♀, 2♂ per genotype/per timepoint and resulting in 6 pooled samples). Skeletal elements were crushed once using a mortar and pestle, then cut into small pieces with scissors. Half of each sample was subjected to two rounds of enzymatic digestions with 0.25% Trypsin (powder; Millipore Sigma, T4799) and 0.8% collagenase type II (ThermoFisher Scientific, 17101015) at 37 °C under agitation for 20 minutes each.  The other half of each sample was subjected to 1 round of enzymatic digestion with 0.1% collagenase type I (Sigma, C3867) and 0.1% collagenase type IV (ThermoFisher Scientific, 17104019) followed by two rounds of digestion with 0.2% collagenase type II, at 37 °C under agitation for 20 minutes each. The resulting cell suspensions were filtered through a 70 μm strainer and centrifuged at 1500 rpm for 5 minutes at 4 °C. Red blood cells were lysed with NH4Cl (StemCell Technologies) for 10 minutes on ice, washed with staining medium (HBSS containing 2% fetal bovine serum (Life Technologies, 10437-028), 1% HEPES (10 mmol·L−1; Thermo Fisher Scientific) and 1% penicillin–streptomycin (Thermo Fisher Scientific)), and resuspended in HBSS. Samples were stained for CD45 (hematopoietic), TIE2 (endothelial), and TER-119 (erythroid). The six samples were then multiplexed using MULTI-seq (Sigma, LMO001-30RXN) according to the manufacturer’s instructions and then pooled. Nonhematopoietic/non-endothelial (CD45-Ter119-TIE2-) Hoxa10+ (GFP+Tomatovariable), Hoxa10 Lineage (GFP-Tomato+), and other stromal (GFP-Tomato-) cells were then separately isolated by flow cytometry from each of the 6 groups. The 3 sorted cell populations were then submitted to NYU Langone’s Genome Technology Center for 3 separate PIP-seq preparations (with each preparation containing a combination of the 6 multiplexed mouse groups).

first: Kevin

last: Leclerc


title: Cysteine and Glycine Rich Protein 3 (Csrp3) modulates cardiomyocyte mitotic cell cycle entry through Ring Finger Protein 5 (Rnf5)/p38 MAPK dependent pathway

city: Houston

first: Riham

middle: Raafat Elgharib

last: Abouleisa

state: Texas

address: 6519 Fannin Street

department: surgery

institute: Baylor College of Medicine

summary: Adult cardiomyocyte (CM) has limited proliferative capacity, which is correlated with rigid sarcomere structures. Our previous studies showed that overexpression of Cdk1, Cdk4, Ccnb, and Ccnd (collectively 4F) induces adult CM proliferation with observed sarcomere disassembly during mitosis. However, it is unclear how the sacrcomeres disassemble during mitosis and whether sarcomere disassembly alone could enhance mitotic cell cycle entry in CMs. In this study  we identified CSRP3 that is highly expressed in adult CM, as a structural checkpoint that links sarcomere integrity to ubiquitination-dependent regulation of CM cell cycle progression. Temporal proteomics and ubiquitin linked proteomics in CMs transduced with control or 4F adenovirus for 24h (early cell cycle entery), 48h (mitosis dominant), and 72h ( end of cell cycle) revealed that CSRP3, a Z-disk–associated protein interacting with T-Cap and α-actinin, was the most downregulated sarcomeric protein during mitosis, returning to baseline at the end of the cell cycle. Csrp3 Knockdown (KD) results in sarcomere disassembly and promotes CM mitotic entry in adult human heart slices, evidenced by a significant increase in PHH3-positive nuclei, a marker for G2/M phase, with no major impact on DNA synthesis. In MADM mice, Csrp3 KD results in a significant increase in single coloured cells which indicates complete CM cell division confirming the role of Csrp3 in modulating mitosis in CMs. In vivo, 21 day old (P21) Csrp3KO mice hearts showed a significant increase in mononucleation, proliferation markers and cell cycle gene expression. Mechanistically, RNAseq from P21 Csrp3KO mice hearts demonstrated increased expression of Rnf5, an E3 ubiquitin ligase. The upregulated Rnf5 resulted in significant reduction in p38 MAPK protein expression, hence promotes mitotic entry. Moreover, Rnf5 overexpression in human heart slices results in activation of CM cell cycle while Rnf5 KD in naturally proliferating neonatal P1 CM reduced cell cycle activity. In conclusion, our findings identify CSRP3 as a structural checkpoint that couples sarcomere integrity to Ring Finger Protein 5 (RNF5)-mediated ubiquitination of p38 MAPK, thereby controlling CM mitotic entery and uncovering a previously unrecognized mechanism governing cardiac regenerative potential.

overall_design: RNA sequencing profiling in postnatal P1 and P21 wt mice heart and Csrp3 KO mice heart

first: Tamer

last: Mohamed


title: Time-series RNA-seq of U2OS cells following CCCP-induced mitochondrial damage and recovery upon drug washout

city: Hangzhou

first: Nuo

last: Chen

state: Zhejiang

address: 866 Yuhangtang Rd, Hangzhou 310058, P.R. China

institute: Zhejiang University

summary: Mitochondria are continuously exposed to damage that contributes to aging and disease. While prolonged mitochondrial damage triggers mitophagy, how cells respond to transient damage remains unclear. To investigate the transcriptional programs underlying transient mitochondrial damage and subsequent recovery, we performed time-series RNA-seq analysis in human U2OS cells treated with the mitochondrial uncoupler CCCP. Four groups were analyzed: untreated control (WT), 50 μM CCCP for 30 min (CCCP), 50 μM CCCP for 30 min followed by 1 h washout (W1H), 50 μM CCCP for 30 min followed by 6 h washout (W6H). Each condition was analyzed in triplicate. This dataset reveals the dynamic transcriptional landscape during mitochondrial damage and recovery, highlighting the activation of stress-responsive transcription factors and antioxidant defense pathways that facilitate mitochondrial repair.

overall_design: RNA-seq profiling of human U2OS cells treated with 50 μM CCCP for 30 minutes, followed by washout for 0, 1, or 6 hours. Four groups: untreated control (WT), 50 μM CCCP for 30 min (CCCP), 50 μM CCCP for 30 min followed by 1 h washout (W1H), 50 μM CCCP for 30 min followed by 6 h washout (W6H). Three biological replicates per group. Total RNA was extracted using TRIzol, and sequencing libraries were prepared using standard protocols.

first: Chao

last: Tong


title: Cytoplasmic ATM restricts oncolytic VSVΔ51 replication by sustaining TBK1-IRF3 signaling in glioblastoma cells

city: Guangzhou

first: xiaohui

last: chen

address: No.106 Zhongshan 2nd Road,Yuexiu District

institute: Guangdong Provincial People's Hospital

summary: ATM is a nuclear DNA damage response kinase with tumor-suppressive functions, but its cytoplasmic function during virus infection remains poorly understood. Here, we identify cytoplasmic ATM as an antiviral factor that restricts oncolytic virus (OVs) replication. Infection with oncolytic VSVΔ51 triggered CRM1-dependent nuclear export of ATM, generating cytoplasmic ATM that associated with viral dsRNA-containing complexes. Blocking ATM nuclear export or inhibiting ATM attenuated type I interferon induction, thereby licensing viral replication. Mechanistically, cytoplasmic ATM interacted with the ubiquitin-like domain of TBK1 and sustained TBK1-IRF3 signaling. ATM inhibition potentiated oncolytic cytotoxicity and promoted immunogenic cell death in cancer cells. In multiple tumor models, pharmacological inhibition or genetic loss of ATM cooperated with VSVΔ51 to suppress tumor growth, prolong survival of mice, and promote durable antitumor immunity. These findings reveal the cytoplasmic function of ATM in antiviral innate immunity and identify it as a therapeutic vulnerability for improving oncolytic virotherapy.

overall_design: To elucidate the mechanism by which ATM loss facilitates oncolytic VSVΔ51 replication, RNA sequencing was performed on LN-18 human glioblastoma cells. Wild-type (sgNC) and ATM-knockout (sgATM) LN-18 cells were either mock-infected or infected with oncolytic VSVΔ51 (MOI = 5) for 10 hours. Total 12 samples with 3 biological replicates per group were analyzed. Differential gene expression analysis was conducted to identify the transcriptional programme commonly regulated by both ATM loss and VSVΔ51 infection, with a focus on antiviral pathways including type I interferon signaling, interferon-gamma response, and TNF-mediated signaling.

first: Xiaohui

first: Fan

last: Xing

first: Xiao

last: Xiao


title: Urocortin 1 promotes trigeminal neuropathic pain by enhancing HSPB1-mediated interactions between neurons and non-neuronal cells in the trigeminal ganglion

city: Nantong

first: Ling-Jie

last: Ma

state: Jiangsu

address: Seyuan Road 9

institute: Nantong University

summary: Trigeminal neuropathic pain (TNP) is one of the most debilitating forms of neuropathic pain, with its underlying mechanisms not yet fully understood. Urocortins (UCNs), a family of peptides within the corticotropin-releasing factor (CRF) family, have been implicated in various functions, including stress, anxiety, and social behaviors. In this study, we demonstrate that UCN1 in the trigeminal ganglion (TG) plays a pivotal role in partial infraorbital nerve transection (pIONT)-induced TNP in mice. pIONT induced UCN1 upregulation in large-diameter TG neurons, and silencing Ucn1 using siRNA or adeno-associated virus (AAV)-mediated shRNA effectively attenuated pIONT-induced orofacial mechanical allodynia. Furthermore, the transcription factor BTB-and-CNC homology 1 (BACH1) was identified as a direct regulator of Ucn1 expression, and knockdown of Bach1 reduced Ucn1 expression and alleviated pIONT-induced TNP. Mechanistically, pIONT increased the expression of corticotropin-releasing hormone receptor 1 (CRHR1), and intra-TG injection of UCN1 induced CRHR1-dependent mechanical allodynia, accompanied by activation of extracellular signal-regulated kinase (ERK) and cyclic-AMP responsive element binding protein (CREB), as well as upregulation of heat shock protein-1 (HSPB1). Finally, HSPB1, released from neurons via extracellular vesicles, activated satellite glial cells and macrophages through TLR2/TLR4 signaling, thereby promoting neuroinflammation. Collectively, our results suggest that BACH1-regulated UCN1 contributes to TNP by activating CRHR1/ERK/CREB/HSPB1 signaling pathway in the TG, and targeting this signaling axis may present a promising therapeutic strategy for TNP.

overall_design: RNA-seq profiling of TG from mice at 10 days after pIONT or sham, and TG from mice at 6 hours after intra-TG injection of UCN1 or PBS.

first: Hao

last: Wu

first: Lin-Peng

last: Zhu

first: Fei-Fei

last: Xu

first: Zuo-Hao

last: Yao

first: Qiong

first: Yong-Jing

last: Gao


title: The Small Protein cS24 Encoded by Gene ssr3189 is an RNA-Binding Ribosomal Protein Specific for Cyanobacteria that Is Involved in Metabolic Regulation

city: Freiburg

first: Wolfgang

middle: R.

last: Hess

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

institute: University of Freiburg

summary:
Cyanobacteria are oxygenic phototrophs that are regularly exposed to fluctuating environmental conditions. Particularly the availability of CO2 and combined nitrogen sources vary in many aquatic habitats. In the present study we characterized the phenotype of an ssr3189 deletion mutant. Gene ssr3189 encodes a recently discovered small protein of the ribosomal small subunit, here called cS24. This gene and its homologs are specific for cyanobacteria.
We demonstrate that cS24, the protein encoded by ssr3189 is an RNA-binding protein. Deletion of ssr3189 resulted in lower pigmentation, delayed growth, and alterations in the expression of genes encoding transporters for nitrogen and Ci, and metabolic enzymes. Metabolomic analysis revealed a substantial overaccumulation of glutamine and tricarboxylic acid (TCA) cycle intermediates in the deletion mutant, and further differences in the amino acid and organic acid pools compared to the wild type. Co-immunoprecipitation with a strain expressing C-terminally tagged cS24 yielded ribosomal protein S21, enolase and the Cas6-1 endoribonuclease as the most strongly co-enriched proteins, consistent with the involvement with ribosomes and pointing at further functions.

overall_design: Total RNA (5 µg) was extracted from the WT and ∆ssr3189 mutant grown at 50 μmol photons m-2 s-1 in BG11 medium and after a shift to nitrogen-free BG11-N medium for 3 h and for 24 h. Total RNA was DNase-treated using TURBO DNase (Thermo Fisher Scientific). 2 µg DNase-treated RNA were labeled with Cy3 using the ULS Fluorescent Labeling Kit for Agilent arrays (Kreatech). A high-resolution microarray manufactured by Agilent (Design ID 075764, format 8 × 60 K, slide Layout = IS-62976-8-V2) was used. 600 ng labeled RNA were used per array for hybridization for 17 h at 65 °C.

first: Nouha

last: Abdelaziz

first: Alexander

last: Kraus

first: Viktoria

last: Reimann

first: Marc

last: Broghammer

first: Manuel

last: Brenes-Alvarez

first: Martin

last: Hagemann

middle: R


title: A germline-encoded lncRNA-mitochondrial axis rewires oxidative phosphorylation and therapeutic susceptibility in clear cell renal cell carcinoma

city: Shanghai

first: Wenjie

address: Dongan road

institute: Fudan University

summary: Clear cell renal cell carcinoma (ccRCC) exhibits profound metabolic reprogramming and substantial inherited susceptibility, yet how genetic determinants mechanistically shape tumor metabolism and therapeutic vulnerability remains poorly defined. Here, we integrate whole-genome sequencing and transcriptomic profiling of matched tumor and normal kidney tissues from a large ccRCC cohort with cross-ancestry genome-wide association, cis-expression quantitative trait locus, and transcriptome-wide association analyses to systematically define the germline regulatory landscape of renal cancer. We identify the long noncoding RNA LINC02068 as a genetically-regulated tumor suppressor whose repression mediates inherited ccRCC risk. The risk variant rs234043 functions as an allele-specific silencer by preferentially recruiting the transcription factor HOXC8, leading to transcriptional repression of LINC02068. Loss of LINC02068 promotes aggressive tumor phenotypes and is associated with adverse clinical outcomes. Mechanistically, LINC02068 localizes to mitochondria and directly interacts with the co-chaperone DNAJA3, accelerating its destabilization and thereby constraining mitochondrial oxidative phosphorylation. Allele-specific genome editing, genetic rescue, and metabolic profiling support a functionalrs234043-HOXC8-LINC02068-DNAJA3 regulatory axis that links inherited genetic variation tomitochondrial activity and tumor progression. Pharmacologic inhibition of mitochondrial complex I by MitoTam suppresses ccRCC cell migration and proliferative growth, further supporting complex I-linked mitochondrial respiration as a functional metabolic dependency in ccRCC. Collectively, these findings uncover a germline-encoded metabolic checkpoint linking noncoding genetic variation to mitochondrial regulation, tumor aggressiveness in ccRCC, providing a mechanistic rationale for exploring mitochondria-targeted therapeutic strategies.

overall_design: We performed gene expression profilling analysis using data obtained from RNA-seq of 786-O cells.

first: Gong-Hong

last: Wei

first: GuoWen

last: Duan


title: Microfluidic Co-Encapsulation of Exosomal miRNAs and Antioxidant Enzymes Ameliorates Hepatic Steatosis by Driving M2 Polarization and Reparative Neutrophil Recruitment

city: Qingdao

first: Liangxiu

last: Xing

state: Shandong

address: Laoshan

institute: Qingdao University

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a prevalent chronic liver disorder lacking universally effective pharmacotherapies due to its complex pathogenesis involving lipotoxicity, oxidative stress, and inflammation. While natural mesenchymal stem cell-derived exosomes present promising therapeutic potential, their clinical translation is hindered by low manufacturing yields, batch-to-batch heterogeneity, and rapid systemic clearance. To overcome these limitations, we report LSCR, an innovative exosome-mimetic nanotherapeutic fabricated via a single-step microfluidic assembly. By systematically decoding natural exosomes, we identified and co-encapsulated a core therapeutic payload—comprising three pivotal miRNAs (hsa-miR-29a-3p, hsa-miR-27a-3p, and hsa-miR-20a-5p) and two potent antioxidant enzymes (superoxide dismutase and catalase)—into liver-targeting lipid nanoparticles. The engineered LSCR exhibits exceptional colloidal stability, robust resistance to physical stress, and prolonged preservation of enzyme catalytic activity for over 30 days. In vivo evaluations in a high-fat diet-induced murine model demonstrate that LSCR selectively accumulates in the liver, effectively ameliorating hepatic steatosis, normalizing lipid profiles, and restoring liver function with an excellent biosafety profile. Mechanistically, LSCR synergistically reverses the pathological transcriptomic network by suppressing inflammatory and fibrotic signaling cascades, such as the AGE-RAGE, MAPK, and PI3K-Akt pathways. Furthermore, LSCR actively remodels the hepatic immune microenvironment by driving pro-resolving M2 macrophage polarization and recruiting indispensable tissue-reparative (N2-like) neutrophils. Ultimately, this highly translational nanomedicine platform offers a scalable and effective strategy for MASLD treatment and prevention.

overall_design: Male C57BL/6 mice were fed a high-fat, high-cholesterol (HFHC) diet starting at 4 weeks of age for 18 weeks to establish hepatic steatosis. Bulk RNA-sequencing was performed on liver tissues from three groups: (1) untreated HFHC-fed mice (Control, n=9); (2) HFHC-fed mice treated with natural UCMSC-derived exosomes (Exosome, n=9); and (3) HFHC-fed mice treated with the dual-payload LSCR nanotherapeutic (LSCR, n=9). Treatments were administered via tail-vein injection every 72 hours for 8 weeks at a dose of 5×108 particles/g body weight. At endpoint, liver tissues were collected, and total RNA was extracted for bulk RNA-seq library preparation.

first: Ruidong

last: Ding

first: Shunjie

first: Haonan

last: Zhang

first: Yingying

last: Liu

first: Guojie

first: Kun

last: yu

first: Xinwei

last: Li

first: Feng

last: Wang


title: WTAP overexpression in M2-polarized human THP-1 macrophages: transcriptome profiling

city: Shenyang

first: Ming

state: China

address: Department of Pharmacology, School of Pharmacy

institute: China Medical University

summary: N6-methyladenosine (m6A) RNA modification has been studied extensively in tumour cells, but its contribution to the tumour microenvironment is far less well defined. We found that the m6A writer WTAP is preferentially expressed in M1 rather than M2 macrophages and that its level influences macrophage polarization. To define the WTAP-dependent transcriptional program in macrophages, we performed bulk mRNA sequencing of IL-4-polarized M2 macrophages derived from the human monocytic cell line THP-1 after transient transfection with a WTAP-overexpressing plasmid (pcDNA3.1-WTAP, OE group) or the corresponding empty vector (pcDNA3.1, NC group), with three biological replicates per group. Intersecting the differentially expressed genes with immune-related gene sets identified MYO1G as a WTAP-responsive candidate. WTAP was subsequently shown to increase the m6A level and the stability of MYO1G mRNA, thereby driving an M1-like phenotype and suppressing the proliferation, migration and epithelial-mesenchymal transition of ovarian cancer cells in vitro and in vivo. This series contains the bulk RNA-seq data underlying that analysis.

overall_design: Human THP-1 monocytes were differentiated into macrophages with PMA and polarized towards the M2 phenotype with IL-4, then transiently transfected with pcDNA3.1 empty vector (NC) or pcDNA3.1-WTAP (OE). Poly(A)-selected RNA from three independent biological replicates per group (6 libraries in total) was sequenced as 150 bp paired-end reads. Differential expression was assessed between the OE and NC groups (OE_vs_NC).

first: Feihong

last: Dong

first: Hang

last: Yin

first: Yueyue

first: Guanyu

first: Yumin

last: Xie

first: Ke

last: Wu

first: Huiyi

last: Lv


title: Site-Specific Inhibition of Translation Initiation via 2'-O-methylation

city: Chicago

first: Daniel

last: Arango

state: IL

address: 303 E Superior St, Office 7-119

institute: Northwestern University

summary: Translation initiation involves a concerted set of intermolecular interactions that efficiently recognize optimal AUG start codons. However, translation initiation complexes often start at upstream non-optimal AUGs or near-cognate codons, leading to the expression of upstream Open Reading Frames (uORFs). Using retrospective analyses of translation preinitiation cryo-EM structures, we identified putative hydrogen bonds between the 2'-OH groups of mRNA start codons with 18S rRNA. Disruption of these interactions using a chemical modification of mRNA, 2'-O-methylation (Nm), repressed translation initiation by preventing the preinitiation complex from recognizing start codons. Notably, 2'-O-methylation in upstream AUG and near-cognate codons inhibits upstream translation initiation while enhancing the expression of canonical ORFs. These findings revealed a transcript- and site-specific inhibitory role for 2'-O-methylation in translation initiation, providing novel insights into the mechanisms of start codon selection in human transcriptomes.

overall_design: Total RNA-seq in wild-type HeLa cell grown under normal physiological conditions

first: Adan

last: Suh


title: Genome-wide H3K4me3 profiling of circulating immune cells reveals dynamic epigenetic reprogramming during acute critical COVID-19

city: Heidelberg

first: Dominik

last: Schaack

address: Im Neuenheimer Feld 420

institute: Heidelberg University Hospital

summary: Severe COVID-19 is associated with innate immune dysregulation resembling sepsis-induced immunoparalysis. Epigenetic mechanisms, particularly changes in H3K4me3 enrichment at gene promoters, have been observed in immune tolerance and monocyte dysfunction in sepsis. Whether comparable H3K4me3 alterations occur during acute critical COVID-19 illness has not been investigated. Among 706 differentially bound consensus peaks with promoter association between ICU and non-ICU groups, 704 showed increased H3K4me3 occupancy in ICU patients, predominantly at neutrophil effector gene loci, supported by pathway enrichment of neutrophil degranulation and innate immune activation. Monocyte HLA-DR expression and ex vivo TLR-stimulated IL-6 secretion were persistently reduced throughout the first week of ICU treatment. Longitudinal profiling in the ICU group revealed a shift from an interferon-driven chromatin signature at admission toward sustained innate immune activation and ECM remodelling at day seven. This study provides the first genome-wide H3K4me3 characterization of circulating immune cells during acute critical COVID-19, demonstrating that epigenetic reprogramming is an active and dynamic process that mirrors the functional immune dysregulation observed in these patients.

overall_design: In this prospective single-centre study, 46 hospitalized COVID-19 patients were enrolled, of whom 27 were treated in the intensive care unit (ICU group) and 19 on the normal ward (non-ICU group). Genome-wide H3K4me3 ChIP-seq was performed on PBMCs at hospital admission (T1) in the total cohort and after seven days (T2) in the ICU group.

first: Benedikt

middle: H

last: Siegler

first: Jan Niklas

last: Thon

first: Markus

middle: A

last: Weigand


title: Hepatocyte angiotensinogen deletion protects against Western diet-induced adiposity and hepatic steatosis under thermoneutral housing

city: Lexington

first: Liyuan

last: Zhu

state: KY

address: 741 South Limestone Street

institute: University of Kentucky

summary: Room-temperature housing imposes adaptive cold stress in mice and can alter brown adipose tissue activity and systemic energy expenditure. This study tested whether hepatocyte-specific Agt deletion protects against Western diet-induced metabolic dysfunction under thermoneutral housing. Male hepAGT-/- and hepAGT+/+ littermate mice were housed at room temperature or thermoneutrality and fed a Western diet for 12 weeks. Liver, brown adipose tissue, and epididymal white adipose tissue were collected for bulk RNA-seq to define tissue-specific transcriptional programs associated with hepatocyte angiotensinogen deletion and thermal environment.

overall_design: Bulk RNA-seq was performed on liver, brown adipose tissue, and epididymal white adipose tissue from male hepAGT+/+ and hepAGT-/- mice housed at room temperature (20-22 degrees C) or thermoneutrality (30 degrees C) during 12 weeks of Western diet feeding. The design includes biological replicates across genotype, housing temperature, and tissue.

first: Alan

last: Daugherty

first: Hong

middle: S

last: Lu


title: Identification of miR-708-5p in peripheral blood monocytes: Potential marker for postmenopausal osteoporosis in Mexican-Mestizo population

city: México city

first: Rogelio Frank

last: Jiménez-Ortega

state: Alcaldía Tlalpan

address: Calzada México-Xochimilco No. 289

department: Subdirección de investigación Biomédica

country: Mexico

institute: Instituto Nacional de Rehabilitación

type: Non-coding RNA profiling by high throughput sequencing

summary: This is the first study in which hsa-miR-708-5p has been identified in peripheral blood monocytes (osteoclast precursors) and associated with postmenopausal osteoporosis through small RNA-Sequencing, in an Admixed Mexican Mestizo population. By conducting in silico and bioinformatic analyzes, we identified target genes and important signaling pathways involved in bone metabolism pointing hsa-miR-708-5p as a candidate marker for osteoporosis in Mexican population. These approaches provide a landscape of the post-transcriptional regulation, which can be useful for the management of postmenopausal osteoporosis along with the potential use of microRNAs as markers for its early detection.

overall_design: Fourteen unrelated postmenopausal Mexican-Mestizo women were included, comprising seven non-osteoporotic controls and seven women with osteoporosis. Peripheral blood was collected, mononuclear cells were isolated, and CD14-positive peripheral blood monocytes were enriched before RNA isolation. Small RNA/miRNA sequencing libraries were generated and sequenced to compare miRNA expression profiles between osteoporotic and non-osteoporotic groups. Processed expression matrices were generated for downstream differential expression and pathway analyses.

first: Aldo

last: De-la-Cruz-Montoya

first: Eric

middle: G

last: Ramirez-Salazar

first: Mayeli

middle: M

last: Martínez-Aguilar

first: Rafael

last: Velázquez-Cruz


title: The Oncogenic Role of Prostate Stem Cell Antigen (PSCA) in Colorectal Cancer: Implications for Targeted Therapy

city: Changchun

first: Jinyue

last: Duan

state: Jilin

address: 1266 Fujin Street

department: Department of Regenerative Medicine

institute: Jilin University

summary: Prostate stem cell antigen (PSCA), a pivotal member of the lymphocyte antigen-6 (Ly6) protein family, has been implicated in the tumorigenesis and neoplastic progression of diverse cancer types. In this study, we conducted a thorough investigation into the role of PSCA in the development of colorectal cancer (CRC). Survival analysis based on The Cancer Genome Atlas (TCGA) dataset demonstrated that elevated expression of PSCA was tightly correlated with unfavorable overall survival, inferior relapse-free survival and worse post-progression survival among CRC patients.Additionally, PSCA exhibited significantly higher expression levels in colorectal cancer stem cell (CRC-SCs) rel-ative to CRC cell lines.Loss-of-function assaysusing small interfering RNA (siRNA)-mediated silencing were performed to evaluate the effects of PSCA downregula-tion on the stemness properties of CRC-SCs, including proliferative capacity, invasive potential and apoptotic rate, which were assessed by MTS assay, transwell invasion assay and flow cytometry analysis, respectively. The results showed that silencing PSCA markedly suppressed the proliferation and invasion of CRC-SCs, while significantly promoting cellular apoptosis. RNA sequencing was performed to identify differentially expressed genes (DEGs) in the PSCA knockdown group compared to the negative control group.

overall_design: RNA-seq of HCT116 stem cells transfected with PSCA siRNA or negative control siRNA

first: Yi

last: Wang

first: Qisen

last: Li

first: Yujue

first: Jinrui

last: Liu

last: Qi

first: Yichi

last: Zhang

first: Changhao

last: Fu

first: Zhongyi

last: Cong

first: Can

first: Manman

last: Su


title: Integrated transcriptomic and proteomic analysis reveals Runx2b-associated molecular regulation of intermuscular bone development in Culter alburnus

city: Jiaxing

first: Jianbo

last: Zheng

address: No. 705 Yatai Road

institute: Yangtze Delta Region Institute of Tsinghua University Zhejiang

summary: This study investigated transcriptomic changes associated with runx2b-mediated regulation of intermuscular bone development in Culter alburnus. Bulk RNA-seq was performed on muscle/myoseptal region samples from wild-type, runx2b heterozygous mutant, and runx2b homozygous mutant juveniles. The dataset supports integrated transcriptomic and proteomic analysis of molecular changes related to intermuscular bone reduction and loss.

overall_design: Wild-type, runx2b heterozygous mutant, and runx2b homozygous mutant Culter alburnus were analyzed. Three biological replicates were collected for each genotype group, resulting in nine RNA-seq libraries: WT1-WT3, He1-He3, and Ho1-Ho3.

first: Xu

last: Yi

last: Xiaohui

first: Li

last: Fei

last: Caiyan

first: Huang

last: Cancan

first: Zheng

last: Jianbo


title: Obesity Promotes Lung Carcinogenesis Through Airway Immune Dysfunction

city: Boston

first: Minyi

last: Lee

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University Chobanian & Avedisian School of Medicine

summary: Rationale: Despite clear links between obesity and dysfunctional anti-tumor immunity, a high Body Mass Index has been associated with decreased lung cancer risk, leading to an “Obesity Paradox”. Objective: We sought to clarify this relationship and gain mechanistic insights using both clinical and preclinical modeling. Methods & Measurements: A case control study of early-stage lung cancer risk was conducted in 1170 high-risk individuals (594 with cancer) stratified by total abdominal fat area (TFA) determined using CT scans. Airway gene expression data from 278 additional patients was analyzed as a function of TFA, and obesity’s impact on chemical- and mutation-driven lung carcinogenesis models was examined. Effects on the immune contexture of murine lungs and patient broncho-alveolar lavage (n=109) were profiled using flow cytometry. Results: Lung cancer was linked to higher TFA in univariate and multivariable models. Gene expression in high-TFA airways suggested suppressed immune activity. Compared to lean controls, the lungs of obese mice displayed abundant potentially suppressive myeloid cells, activated Regulatory T cells, and effector T cell deficits at baseline and during carcinogenesis, which was significantly exacerbated by obesity. Functional assays and depletion studies suggested obesity-enhanced Tregs can potentiate rapid tumor growth, and flow analysis of patients airway leukocytes further suggest compromised lung immune surveillance in patients of high TFA. Conclusions: Obesity is associated with enhanced lung carcinogenesis. Mechanisms of immune suppression upregulated with excess adiposity, including activated, functional Tregs, are evident in clinical and preclinical systems. These results refute the concept of an obesity paradox for lung cancer risk.

overall_design:
183 Samples

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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: Ehab

last: Billatos

first: Jennifer

last: Beane

first: Marc

middle: E

last: Lenburg


title: Neuroprotective function of dietary lycopene in Parkinson’s disease mice: targeting the dopamine transporter DAT/SLC6A3 to restore dopaminergic homeostasis

city: Jiamusi

first: Jun

last: Xia

address: No. 258 Xuefu Street, Xiangyang District

department: School of Basic Medical Sciences

institute: Jiamusi University

summary: Currently, there are still many limitations in the prevention and treatment of Parkinson's disease (PD), and the development of effective preventive and therapeutic drugs remains a top priority. The aim of this study is to investigate whether lycopene (LYC) can exert neuroprotective effects by regulating solute carrier family 6 member 3 (DAT/SLC6A3).

overall_design: In the study, PD mouse model was established, and a series of methods including molecular docking, untargeted metabolomics, behavioral tests and histopathological analysis were used.


title: LPC 18:2-Driven Apoptosis In Neutrophils Is Non-Inflammatory and Lipid Raft Dependent.

city: La Jolla

first: Sonia

last: Sharma

address: 9420 Athena Cir

department: Center for Autoimmunity and Inflammation

institute: La Jolla Institute of Immunology

summary: Lysophosphatidylcholines (LPCs) are potent bioactive lipids whose fatty acid composition dictates their immunomodulatory effects. Here, we delineate how unsaturated LPC 18:2 and saturated LPC 16:0 differentially regulate neutrophil survival and inflammatory programs. LPC 18:2 markedly increased reactive oxygen species (ROS) generation and caspase-3/7 activation, accompanied by Annexin V positivity, mitochondrial membrane depolarization, and cytochrome C release, f. Features consistent with intrinsic apoptosis. In contrast, LPC 16:0 induced robust LDH and HMGB-1 release, indicating membrane rupture and pyroptosis-like death. Bulk RNA sequencing revealed that LPC 16:0 strongly upregulated inflammatory and cytokine genes. Disruption of lipid-raft integrity abolished LPC 18:2–induced ROS and apoptosis, underscoring the dependence of these effects on membrane organization. Collectively, these results identify LPC 18:2 as a non-inflammatory, mitochondria-dependent inducer of neutrophil apoptosis, whereas LPC 16:0 promotes inflammatory, lytic death programs. These findings highlight how lipid saturation determines neutrophil fate and immune tone, providing mechanistic insight into how distinct LPC species shape inflammation and tissue injury.

overall_design: The experiment was conducted using Homo sapiens primary peripheral blood neutrophils. Cells were subjected to two treatment conditions: unstimulated (vehicle control) and LPC 18:2 at 10 µM for 2 hours. A single time point of 2 hours post-treatment was analyzed. Each condition included three independent biological replicates derived from distinct healthy donors, resulting in a total of six RNA-seq libraries. Each donor served as a unique biological replicate, and within a given donor, only one treatment was applied per sample without any technical pooling.

first: Priyanka

last: Saminathan

first: Alicia

last: Gibbons

first: Ian

last: Mathews

first: Maija

last: Corey

first: Ashmitaa

last: Logandha Ramamoorthy Premlal

first: Mahati

last: Rayadurgam

first: Namratha

last: Nadig

first: Camille

last: Fang

first: Mousa

last: Vatanmakanian

first: Carolina

last: Altbaum


title: IGF2BP2 promotes esophageal squamous cell carcinoma progression through the PI3K/AKT signaling pathway

first: XIAOHANG

last: GAO

state: Guangdong

address: the south of Xianlie Road

institute: Sun Yat-sen University Cancer Center

summary: This study investigated the role of IGF2BP2 in esophageal squamous cell carcinoma. Bulk RNA-seq was performed in ECA109 cells stably transfected with negative-control shRNA or IGF2BP2 shRNA to identify transcriptomic changes associated with IGF2BP2 knockdown.

overall_design: Bulk RNA-seq was performed in ECA109 cells stably transfected with negative-control shRNA (n = 3) or IGF2BP2 shRNA (n = 3). Differential expression and pathway enrichment analyses were used to identify downstream pathways associated with IGF2BP2 knockdown.

first: Xiaohang

last: Gao

first: Minghui

last: Yang

first: Jing

first: Chao

last: Ma

first: Guoliang

last: Xu

first: Lin

last: Zhang

first: Rong


title: The hsa_circ_0031607 Restricts Dengue Virus Replication in Association with PARP1 and Ferroptosis

city: Kunming

first: Ruixia

last: Tang

address: Jiaoling Road 935

institute: Chinese  Academy  of Medical Sciences & Peking Union Medical College

summary: Dengue virus (DENV) infection remains a global health threat without specific antiviral therapy. Although circular RNAs (circRNAs) are increasingly recognized in antiviral immunity, their roles during DENV infection are largely undefined. Here, we performed transcriptome sequencing of PBMCs from dengue patients stratified by disease phase and severity, identifying differentially expressed circRNAs across severity groups and clinical phases. Cross-stage intersection identified 15 circRNAs dysregulated across all phases, enriched in ferroptosis, glutathione metabolism, and endocytosis. Among these, hsa_circ_0031607 (circSNX6) was the only one associated with all three pathways and was significantly upregulated in both dengue patients and DENV2-infected HUVECs. circSNX6 overexpression suppressed DENV2 replication, whereas its knockdown enhanced viral propagation. circSNX6 localized to the cytoplasm and physically interacted with PARP1. DENV infection was accompanied by partial redistribution of PARP1 from the nucleus to the cytoplasm. circSNX6 suppressed PARP1 expression, and its knockdown was accompanied by altered global PARylation, including increased NRF2 PARylation and changes in TFR1 and GPX4 expression. In mice, pharmacological PARP1/2 inhibition with olaparib attenuated DENV pathology, accompanied by ferroptosis suppression. Pharmacological ferroptosis inhibition reduced DENV2 replication, whereas ferroptosis induction enhanced it, suggesting that the cellular ferroptotic state correlates with DENV2 replication. Collectively, these findings provide a circRNA expression profile across dengue disease progression and suggest that circSNX6 restricts DENV2 replication, an effect associated with PARP1 interaction and ferroptosis modulation.

overall_design: Transcriptome sequencing of PBMCs from DENV-2-infected patients stratified by disease phase (early/late) and severity (mild/severe) versus healthy controls to profile circRNA expression. Cross-stage comparison identified 15 consistently dysregulated circRNAs enriched in ferroptosis, glutathione metabolism, and endocytosis pathways. hsa_circ_0031607 (circSNX6) was selected for functional validation in DENV2-infected HUVECs via overexpression and knockdown. Mechanistic studies included RNA pull-down, mass spectrometry, RIP, and FISH to identify circSNX6-PARP1 interaction. In vivo efficacy of PARP1 inhibitor olaparib was evaluated in A129 mice. This study delineates the circRNA landscape during dengue progression and identifies circSNX6 as an antiviral regulator that restricts DENV replication via the PARP1/NRF2/ferroptosis axis.

first: Jianyu

first: Haiting

last: Long

first: Jiahong

first: Junying

last: Chen

first: Yue

last: Pan

first: Zhengcun

last: Wu

first: Qiangming

last: Sun


title: Transcriptome profiling of miR-206-transfected lung adenocarcinoma cell lines

city: Kaghosima City

first: Takuya

last: Tokunaga

address: 8-35-1 Sakuragaoka

country: Japan

institute: Kagoshima University

summary: This study investigated transcriptomic changes induced by miR-206 transfection in lung adenocarcinoma cell lines. PC9 and A549 cells were transfected with miR-206 mimic or negative control, followed by mRNA sequencing analysis.

overall_design: PC9 and A549 lung adenocarcinoma cells were transfected with miR-206 mimic or negative control. Total RNA was extracted and subjected to mRNA sequencing for differential gene expression analysis.

first: Aya

last: Takeda

first: Masaya

last: Aoki

first: Kauhiro

last: Ueda

first: Naohiko

last: Seki


title: A Versatile Distance-Based Approach for Gene Expression Selection Across Diverse Biological Systems

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary:
Differential gene expression analysis is essential for characterizing immune cell phenotypes, yet conventional approaches—typically based on log₂ fold‑change (log₂FC) and False Discovery Rate (FDR) thresholds—often struggle to capture the complexity and continuum of transcriptional states. To address this limitation, we developed a new computational method for gene selection from mRNA‑seq data: the Cartesian Distance‑Based Gene Expression (CDBGE) selector. This algorithm identifies differentially expressed genes by leveraging multidimensional expression distances rather than relying on traditional univariate statistical cutoffs, enabling a more refined and biologically coherent gene‑marker selection. We applied the CDBGE selector to construct a gene‑based framework for distinguishing macrophage polarization states. The model was trained using publicly available macrophage transcriptomic datasets and subsequently validated with in vitro human macrophages stimulated with IFN‑γ/LPS, conditioned medium from HepG2 liver cancer cells, or IL10. To evaluate its generalizability beyond macrophage biology, we further tested the method on human embryonic stem cell differentiation datasets. Compared with standard differential expression pipelines, the CDBGE selector more effectively identified subtype‑specific markers and revealed dynamic transcriptional transitions over time. These findings demonstrate that distance‑based gene classification provides an improved strategy for analyzing complex mRNA‑seq datasets. Overall, the CDBGE selector offers a robust, scalable, and broadly applicable tool for differential gene expression analysis and phenotype characterization.
Overall design	Transcriptomic RNA-seq from Human macrophages stimulated with IFN‑gamma/LPS, conditioned medium from HepG2 liver cancer cells, or IL10 at different times.

overall_design: Transcriptomic RNA-seq from Human macrophages stimulated with IFN‑gamma/LPS, IL4, or IL10 at different times

first: Sarrias

last: Maria-Rosa

first: Ye

last: Qiaoling


title: Spp1 Mediates Antimony Trioxide-Induced Male Reproductive Toxicity via Regulating Inflammatory Response and Blood-Testis Barrier Integrity

city: xuzhou

first: zhao

middle: yi

last: wei

state: jiangsu

address: No. 209, Tongshan Road, Xuzhou City, Jiangsu Province

institute: Xuzhou Medical University

summary: This study investigated the male reproductive toxicity of antimony trioxide (Sb₂O₃) using in vivo male mice and in vitro TM4 Sertoli cell models. Sb₂O₃ exposure impaired spermatogenesis, triggered inflammatory responses, and disrupted blood-testis barrier integrity by upregulating Spp1, whereas Spp1 knockdown effectively alleviated Sb₂O₃-induced inflammation, cell migration dysfunction and tight junction protein loss, identifying Spp1 as a crucial regulator of Sb₂O₃-mediated male reproductive injury.

overall_design: This study established an in vivo male mouse exposure model and an in vitro TM4 Sertoli cell experimental system to explore the reproductive toxicity of Sb₂O₃. Combined with transcriptome sequencing, qPCR, Western blot, CCK-8, scratch assay and siRNA-mediated Spp1 knockdown, we systematically observed testicular pathological changes, sperm quality alterations, cell biological behaviors and the expression of inflammation and blood-testis barrier-related molecules.

first: Weiyi

last: Zhao


title: Small RNA sequencing of primary EGFR-mutated lung adenocarcinoma tissues from patients with postoperative recurrence

summary: Small RNA sequencing was performed to identify dysregulated microRNAs associated with postoperative recurrence of EGFR-mutated lung adenocarcinoma. Five primary EGFR-mutated lung adenocarcinoma tissues from patients who later developed recurrence and five normal lung tissues were analyzed.

overall_design: Total RNA was extracted from five primary EGFR-mutated lung adenocarcinoma tissues obtained at the time of initial surgery from patients who later developed postoperative recurrence and five normal lung tissues. Small RNA libraries were prepared using the QIAseq miRNA Library Kit and sequenced on the Illumina NextSeq platform using single-end 75 bp reads.

first: Nohiko

first: Yuka

last: Ishihara

first: Kazuhiro


title: Transcriptomic response to dexamethasone after chronic social defeat stress in dorsal raphe nucleus

city: Novosibirsk

first: Natalya

last: Bondar

address: 10, Ac. Lavrentieva ave.

country: Russia

institute: Institute of Cytology and Genetics SB RAS

summary: Chronic stress often leads to the development of various psychopathologies and is usually associated with a change in the function of the HPA axis. An elevated level of glucocorticoid (GC) hormones in the blood initially causes an acute reaction of the body, which subsequently fades, even with continued stimulation with glucocorticoids. It is known that the degree of resistance to elevated hormone levels can affect the effectiveness of therapy in the treatment of stress-induced psychopathologies. In order to identify the molecular basis for the formation of GC resistance, we analyzed the effect of chronic social stress on the transcriptome of the dorsal raphe nuclei in an experimental model of depression. We assessed the level of gene expression in the dorsal raphe nuclei of the control C57BL/6 mice and mice with stress experience for 30 days, both in the basal state and with additional stimulation with dexamethasone. The introduction of dexamethasone made it possible to simulate the situation of an increase in the level of glucocorticoids and activation of the glucocorticoid receptor.

overall_design: RNA-seq of the dorsal raphe nuclei was performed in control C57BL/6 male mice and mice subjected to chronic social stress for 30 days. Using behavioral profiling in the agonistic confrontation test followed by clustering of responses during non-aggressive contact, we identified two subgroups of stressed mice that differed in coping strategy: dep1 (passive coping strategy) and dep2 (active coping strategy). Transcriptomic responses were analyzed in basal conditions (saline injection) and 6h following dexamethasone stimulation (2 mg/kg).

first: Polina

last: Ritter

first: Anastasia

last: Shulyupova


title: A sncRNA profile of semen extracellular vesicles as non-invasive biomarker to discriminate benign from malignant prostate disease in the PSA grey zone

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

summary: Prostate‑specific antigen (PSA) testing plays an important role in the diagnostic work‑up of prostate cancer; although the low cancer specificity is a well‑recognized limitation. This fact contributes to potential overdiagnosis and overtreatment on one hand, and delayed or missed diagnoses on the other. Consequently, there is a growing need for more reliable, non-invasive diagnostic tools capable of improving specificity while maintaining sensitivity, thereby enabling better risk stratification, personalized patient management, and reduction of unnecessary invasive procedures. In this study, we characterized the small RNA profile—including miRNAs and tsRNAs—in seminal small extracellular vesicles (sEVs) using high‑throughput sequencing to improve biomarker discovery for distinguishing benign from malignant prostate conditions, particularly in patients with moderately elevated PSA levels. Our analysis confirms minimal differences in sncRNA content of seminal sEVs between benign and malignant prostate disease, consistent with prior RT‑qPCR array data. This result suggests that shared underlying molecular mechanisms are likely to occur especially in this group of patients with moderate PSA levels. Given the complexity of the underlying pathophysiological process and the heterogeneity of clinical phenotypes, multivariate approaches (including isomiRs or tRFs) are proposed as prostate cancer biomarkers, offering improved accuracy and enhancing the negative predictive value of PSA used in clinical settings.

overall_design: Four seminal exosomal vesicle total RNA samples per group (16 in total) were used as input for small RNA sequencing. Differential expression analysis between the groups under study was perfomed at several levesl including miRNA, miRNA isoforms and tRNA. derived fragments

first: Sara

last: Larriba

first: Adriana

last: Ferre-Giraldo

first: Dave

last: Rojas-Calderón

first: Helena

last: Raurell

first: Manel

last: Castells

first: Clara

last: Mayayo

first: Esther

last: Prat

first: Olga

last: López-Rodrigo

first: Maurizio

last: de Rocco-Ponce

first: Lluís

last: Bassas

first: Francesc

last: Vigués


title: Lamins gate nuclear and chromatin structures for cardiomyocyte maturation genes. (Hi-C)

city: Baltimore

first: Yixian

last: Zheng

state: MD

address: 3520 San Martin Dr

institute: Carnegie Institution of Washington

summary: The nuclear lamina contains intermediate filaments, called lamins, which function to maintain nuclear integrity and organize the Lamina-Associated chromatin Domains (LADs). Despite near ubiquitous expression, lamins show cell-type-specific functions. In the heart, they support epicardial cell migration, cardiomyocyte nuclear integrity and maturation. How these functions are integrated with different gene expression programs in these cells during heart development is unknown. We show that cardiomyocytes require lamin-A and -B1 for perinatal mouse survival. Importantly, lamin-B1 facilitates timely cardiomyocyte maturation by maintaining LADs and chromosome territories. By examining changes in cardiomyocyte gene expression and 3D genome organization upon lamin-B1 deletion, we show lamin-B1 maintains chromatin neighborhoods, which can in turn support transcription factors that regulate genes involved in cardiomyocyte structural maturation and gradual cessation of cell division. We propose a genomic logic by which the widely expressed lamins collaborate with transcription factors to specifically promote cardiomyocyte maturation and cell cycle exit during development.

overall_design: Cardiomyocytes were isolated and purified from Nkx2-5Cre;Lmnb1F/+ and Nkx2-5Cre;Lmnb1F/-P0.5 hearts and used for Hi-C profiling.

first: Katherine

last: Bossone

first: Xiaobin

first: Lidya

last: Kristiani

first: Reni

last: Marsela

first: Youngjo

last: Kim


title: Lamins gate nuclear and chromatin structures for cardiomyocyte maturation genes. (CUT&RUN)

overall_design: Cardiomyocytes were isolated and purified from Nkx2-5Cre;Lmnb1F/+ and Nkx2-5Cre;Lmnb1F/-P0.5 hearts and used for CUT&RUN mapping of histone markers and LADs.


title: Prophylactic and therapeutic itaconate treatment alleviates COVID-19-associated lung injury

city: XIAMEN

first: Peida

last: Yang

state: 福建

address: XIAMEN UNIVERSITY

institute: XIAMEN UNIVERSITY

summary: Itaconate (ITA), an immunomodulatory metabolite with known anti-inflammatory properties, has underexplored therapeutic and prophylactic potential against coronavirus disease 2019 (COVID-19). Metabolomic analyses revealed that intranasal administration of a dNS1-RBD vaccine (a live-attenuated, cold-adapted influenza virus-based vaccine deficient in nonstructural protein 1 [NS1] and expressing the SARS-CoV-2 receptor binding domain (RBD)) upregulated ITA levels, prompting further exploration of its immunomodulatory role. This multiomics study investigates the therapeutic and prophylactic potential of ITA against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-induced acute lung injury (ALI) using an interanimal transmission hamster model that mimics the predominant natural route of SARS-CoV-2 infection. Both prophylactic and therapeutic ITA treatments significantly mitigated weight loss and improved lung pathology in infected hamsters. Transcriptional profiling demonstrated that ITA downregulated immune activation pathways while enhancing fatty acid β-oxidation (FAO)-related genes, correlating with reduced pro-inflammatory cytokine/chemokine release.

overall_design: This transcriptomics study analyzes 35 Syrian hamster lung tissue samples (all sequenced on Illumina NovaSeq 6000, GPL28997) utilizing an RNA-Seq approach. The design systematically compares the effect of itaconate (ITA) administered via different routes (intraperitoneal/IP vs. intranasal/IN) and at different timings relative to infection (pre-exposure prophylaxis vs. post-infection therapy), against PBS controls, at two key post-infection timepoints (3 and 5 days post-infection, dpi). Biological replicates are included for each condition/timepoint combination, ranging from 4 to 5 replicates per group.

first: Yao

last: JIANG

last: YANG


title: Lamins gate nuclear and chromatin structures for cardiomyocyte maturation genes. (P0.5 scRNA-seq)

overall_design: P0.5 hearts of Nkx2-5Cre;Lmnb1F/+ and Nkx2-5Cre;Lmnb1F/- pups were dissociated and used for scRNA-seq.


title: Lamins gate nuclear and chromatin structures for cardiomyocyte maturation genes. (P0.5 ATAC-seq)

overall_design: P0.5 hearts of Nkx2-5Cre;Lmnb1F/+ and Nkx2-5Cre;Lmnb1F/- pups were dissociated and purified for ATAC-seq.


title: Lamins gate nuclear and chromatin structures for cardiomyocyte maturation genes. (P7.5 Bulk RNA-seq)

overall_design: P7.5 hearts of Nkx2-5Cre;Lmnb1F/+ and Nkx2-5Cre;Lmnb1F/- pups were pulverized for bulk RNA-seq.


title: HHO5 orchestrates feedback regulation between organic and inorganic N-dose dependent signaling in Arabidopsis; DoubleTARGET

city: New York

first: Will

last: Hinckley

state: New York

address: 12 Waverly Pl

department: Biology

institute: New York University

summary: A major goal in agriculture is to engineer crops that can maintain yield with less nitrogen (N) fertilizer input. Important regulators of plant N-responses include the HRS1 HOMOLOG (HHO) transcription factors (TFs), yet their redundant repressive mode of action has hindered functional analyses. Here, we highlight HHO5 as a unique HHO TF based on its phylogenetic position, phloem specific expression, and its dual role in orchestrating responses to both inorganic and organic N-dose signals. Moreover, single hho5 T-DNA mutants show reduced N-dose dependent growth, and decreased seed N content, indicating phenotypic defects in systemic N-dose responses. Our meta-analysis revealed that HHO5 expression is repressed by nitrate but induced by organic N treatments. To uncover its mode of action, we derived a validated HHO5 gene regulatory network path in which the direct and indirect targets of HHO5 encompass ~12% of all N-dose response genes in planta. We show that HHO5 acts as a direct repressor of genes functionally enriched for nitrate responses. By contrast, HHO5 indirectly induces expression of organic N-response genes functionally enriched in nutrient level versus defense response genes. We propose that WRKY21 may act as a partner TF that aids HHO5 in the induction of defense related gene expression using the new DoubleTARGET TF co-perturbation assay. Physiological experiments of hho5 mutants support the hypothesis that HHO5 plays a dual regulatory in balancing inorganic vs organic N-dose signals. Overall, these results support a model of energy conservation, whereby HHO5 pivots feedback repression of inorganic nitrate sensing/transport under organic N satiety.

overall_design: DoubleTARGET allows for the co-overexpression of two transcription factors (TFs) in the same plant protoplasts, using PEG mediated plasmid co-transfection in combination with FACS sorting. Transcriptomes from these co-transfected cells are analyzed with RNA-seq and compared to single TF or empty vector (EV) controls to measure combinatorial TF effects in vivo. DoubleTARGET was carried out similarly to the standard TARGET approach (Bargmann et al. 2013). 3-4 million root protoplasts were transfected with 120 micrograms of plasmid DNA, which was prepped using the ZymoPure II Plasmid Maxi-prep kit. For single transfections (empty vector GFP (AKA EV), HHO5 alone as GFP, or WRKY21 alone as RFP, 120 µg of DNA was provided. For co-transfection samples, 60 µg of HHO5-GFP and 60 µg of WRKY21-RFP vectors were mixed and transfected in parallel with single transfection samples. After overnight incubation to allow for protein expression, cells were treated with 35 µM cycloheximide (CHX) for 20 minutes, followed by 2 hours of 10 µM dexamethasone (DEX). Cells were suspended in 200 µL of W5 buffer supplemented with 0.01% BSA and successfully transfected cells were collected using a BD FACSDiscoveryS8. 10 to 20,000 transfected cells were collected per sample and moved to dry ice. Cells were collected and frozen in RLT lysis buffer for later processing with the Qiagen RNeasy RNA micro prep kit with on-column DNAse digestion, and quality checked using Agilent Tapestation HSRNA Kit. mRNA was isolated using the NEB mRNA purification module. RNA was processed for sequencing using the NEB Ultra II library prep kit. Libraries were pooled and sequenced using an Illumina Novaseq 6000 S1 1x100 run. The reads were basecalled using Picard IlluminaBasecallsToFastq version 2.23.81, with APPLY_EAMSS_FILTER set to false. Following basecalling, the reads were demultiplexed using Pheniqs version 2.1.02. The entire process was executed using a custom nextflow pipeline, GENEFLOW3. Reads were trimmed using CutAdapt to remove the standard illumina universal adapters. Trimmed reads were aligned to the Tair10 genome using STAR. FeatureCounts from SubRead  was used to generate a count matrix that was used in DESEq2 for downstream analysis. References "Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/; Broad Institute. Galanti, L., Shasha, D. & Gunsalus, K.C. Pheniqs 2.0: accurate, high-performance Bayesian decoding and confidence estimation for combinatorial barcode indexing. BMC Bioinformatics 22, 359 (2021). https://doi.org/10.1186/s12859-021-04267-5. "GENEFLOW." 2023. New York University Center for Genomics and System Biology Genomics Core, GitHub Repository. https://github.com/gencorefacility/GENEFLOW; New York University.

first: Joseph

last: Swift

first: Francisco

last: Romei

first: Jorge

middle: P

last: Muschietti

first: Samantha

last: Frangos

first: Shao-shan

middle: C

last: Huang

first: Gloria

last: Coruzzi

first: Mariana

last: Obertello


title: Dihydrotestosterone Supplementation in P301S Female Mice Exacerbates Tauopathy and Microgliosis via the TR4-Trem2 axis

first: Leigh-Ana

last: Rossitto

state: CA

address: 9500 Gilman Drive

department: Neurosciences

institute: UC San Diego

summary: Alzheimer's disease (AD) disproportionately affects women, who exhibit greater vulnerability to Tau pathology and neuroinflammation. While estrogen and progesterone have been extensively studied in this context, the effects of androgens on female AD pathophysiology are largely unexplored. Here, we report that supplementation with the non-aromatizable androgen dihydrotestosterone (DHT) exacerbates Tau pathology in female tauopathy models, with microglia as a main driver of this effect. DHT treatment upregulates proinflammatory gene expression in microglia and promotes the disease-associated microglia (DAM) phenotype. Genetic deletion of Trem2 prevented DHT-driven neuroinflammation and Tau pathology exacerbation. Surprisingly, canonical androgen receptor (AR) signaling is dispensable for these DHT-induced effects in microglia. We identified an orphan nuclear receptor, TR4, as a mediator of DHT-driven effects through its transcriptional regulation of Trem2 in microglia. Moreover, TR4 protein levels are elevated in postmortem brain tissue from Braak stage 6 female AD patients and correlate with p-Tau levels. Together, our findings identify a non-canonical DHT–TR4–Trem2 signaling axis in microglia and position TR4 as a previously unrecognized regulator of neuroinflammation in female neurodegeneration, providing mechanistic insights into sex-specific vulnerabilities in AD. This GEO record is for the hippocampal bulk RNA sequencing data generated for our hormonal treatment paradigm.

overall_design: To determine the effects of elevated androgen on tau pathogenesis in females, we supplemented adult female P301S human Tau transgenic mice (P301S) with DHT, a non-aromatizable androgen. Unlike testosterone, which can be converted into estrogen by the enzyme aromatase, DHT cannot be aromatized into estrogen. We treated P301S female mice at 6 months of age, coinciding with the onset of pathological changes, with a subcutaneous implant of SILASTIC tubing containing 10 mm of DHT powder. Females were supplemented with DHT for a total of 12 weeks At this time, mice were perfused with cold PBS, and hippocampi were dissected on ice, flash frozen, and stored at -80C until RNA extraction. Five mice per group were included in this sequencing experiment for a total of 10 samples.

first: Daniel

last: Muñoz-Mayorga

first: Xinchen

last: Lyu

first: Suborno

last: Jati

first: Jibin

last: Zhang

first: Yuren

last: Tao

first: Shanshan

last: Zhao

first: Enfu

last: Hui

first: Alexander

last: Kauffman

first: Bokai

last: Zhu

first: Xu

last: Chen


title: Programmable synthetic cytokine receptors polarize macrophages to user-defined functional states

city: Stanford

first: Judith

last: Lunger

address: 240 Pasteur Drive

department: Genetics

institute: Stanford University

summary: Macrophage-based immunotherapies hold promise for cancer and other diseases, but lack of methods to precisely control macrophage polarization limits both mechanistic understanding and therapeutic applications. Here, we use a programmable synthetic cytokine receptor (SCR) platform to control primary human macrophage polarization. SCRs containing signaling motifs from the interferon-gamma (IFN-γ) or Interleukin-10 (IL-10) receptors are sufficient to mimic pro-inflammatory or anti-inflammatory polarization, respectively. Combinatorial assembly of nine distinct signaling motifs within the SCR signaling domain generates a diverse landscape of synthetic macrophage states with varied expression of inflammatory markers (CD80, CD40, PDL1), anti-inflammatory markers (CD163, CD206) and phagocytic capacity. SCRs programmed with multiple YxxQ motifs drive macrophage phagocytosis of E. coli and chimeric antigen receptor (CAR)-macrophage phagocytosis of cancer cells in mice, reducing tumor burden by 30-fold. Quantitative analysis reveals that motif-dependent polarization follows a two-state equilibrium model, enabling rational prediction of macrophage polarization state from SCR composition. Leveraging this framework, we design SCRs that simultaneously enhance phagocytosis and maintain pro-inflammatory function. Together, these findings establish a framework to synthetically program macrophage polarization states with potential applications in cancer immunotherapy and other disease contexts.

overall_design: RNAseq profiling of human primary monocytes transduced with SCR0, SCR(S1-S1), SCR(S2-S2), SCR(S3-S3), and/or treated with IFNg (50ngs/mL) or IL-10 (50ngs/mL) for 48 hours

first: Lucas

last: Sant'Anna

first: Antonio

last: Salcido-Alcántar

first: Rebeca

last: Hornero

first: Wansang

last: Cho

first: Alun

last: Vaughan-Jackson

first: Mingxin

last: Gu

first: Jenny

middle: Y

last: Liu

first: Joaquin

last: Parrilla-Garcia

first: Michael

last: Bassik

first: Sneha

last: Ramakrishna

first: Kyle

last: Daniels


title: Genetic suppression of myeloid receptor Clec7a attenuates microglia neuroinflammation and promotes microglial phagocytosis to delay disease progression in ALS models

city: Houston

first: haichao

last: wei

state: TX

address: 1825 Pressler St., SRB 637.C, 1825 Pressler St., SRB 637.C

institute: UTHealth

summary: Microglial activation has been closely associated with accelerated ALS disease progression. However, specific microglial pathways that regulate microglial activation and ALS disease progression remain limitedly understood. Here, we determined the role of Clec7a (or Dectin-1), a core signature gene of disease-associated microglia (DAM) in ALS, in regulating microglial activation and ALS disease progression. Our spinal cord scRNA-Seq results found that Clec7a deficiency specifically attenuated microglial neuroimmune gene expression in SOD1G93A mice and human ALS. In addition, in vivo two-photon imaging of human (h) TDP43 phagocytosis by microglia in the cortex showed that Clec7a deficiency promotes microglial phagocytosis of pathological hTDP43 by enhancing microglial process dynamics. Subsequent survival analysis further showed that selective deletion of Clec7a in microglia mitigates motor neuron degeneration and delays disease progression in SOD1G93A ALS mice. Together, our results establish that Clec7a is a key regulator in shaping disease microglial functions and promotes disease progression in ALS.

overall_design: To investigate the role of myeloid cell receptor Clec7a in regulating microglial immune responses in the context of ALS disease, we performed single cell RNA sequencing of spinal cord tissues from WT, Clec7aKO, SOD1G93A and SOD1G93A/Clec7aKO mice at mid-disease stage.

first: Xuan

first: Huilan

last: Yan

first: Sanaz

last: Sajadi

first: Haichao

last: Wei

first: Jingwen

last: Hu

first: Vinicius

last: Vasconcellos

first: Ashley

last: Kim

first: Tarun

last: Shriram

first: Huizhong

last: Tan

first: Kyoeun

last: Keum

first: Jiaqian

last: Wu

first: Martin

last: Paukert

first: Yongjie

last: Yang


title: Cholesterol-mediated Lysosomal Dysfunction in APOE4 Astrocytes Promotes α-Synuclein Pathology in miBrains, a Human iPSC-derived Brain Tissue

first: Joel

middle: W.

last: Blanchard

state: NY

address: 619 W54th Street, 8th Floor

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: The pathological hallmark of neurodegenerative disease is the aberrant post-translational modification and aggregation of proteins, leading to the formation of insoluble protein inclusions. Genetic factors like APOE4 are known to increase the prevalence and severity of tau, amyloid, and α-synuclein inclusions. However, the human brain is largely inaccessible during this process, limiting our mechanistic understanding. Here, we developed an iPSC-based 3D model that integrates neurons, glia, myelin, and cerebrovascular cells into a functional human brain tissue (“miBrain”). Single-nucleus RNA sequencing of miBrains confirmed the presence of diverse cell populations and revealed cell-type-specific transcriptional responses to synuclein pathology. Like the human brain, we found that pathogenic phosphorylation and aggregation of α-synuclein are increased in the APOE4 miBrain. Combinatorial experiments revealed that endolysosomal dysfunction caused by cholesterol accumulation in APOE4 astrocytes impairs the degradation of α-synuclein and leads to a pathogenic transformation that seeds neuronal inclusions of α-synuclein. Collectively, this study establishes a robust model for investigating protein inclusions in human iPSC-derived brain tissue and highlights the role of astrocytes and cholesterol in APOE4-mediated pathologies, opening therapeutic opportunities.

overall_design: miBrains were cultured in standard conditions for 18 days, rinsed with PBS and frozen without media. Fresh frozen miBrains were processed using the Chromium Nuclei Isolation Kit (10x Genomics), with RNase inhibitors. Nuclei were quantified via DAPI staining using a Countess II FL automated cell counter (Life Technologies). 20,000 nuclei per sample were processed using 3’ GemX v4 reagents (10x Genomics), and libraries prepared according to the manufacturer’s instructions. All libraries were sequenced at Azenta using the NovaSeq X platform (Illumina).


title: Transcriptome analysis of lung derived from LPS-induced ARDS model mice treated with EVs or SPLEVs.

city: Saga

first: Ryo

last: Yanagiya

state: Saga

address: 5-1-1 Nabeshima

department: Department of Internal Medicine

institute: Saga University

summary: To investigate the molecular mechanism of SPREDs-induced anti-inflammatory response, differentially-expressed genes between SPREDs teated- or EVs (control)-treated lungs of ARDS model mice were performed. As a result, PI3K-Akt signaling pathway was annotated as a key regulatory pathway of SPREDs-induced anti-inflammatory response by KEGG pathway analysis.

overall_design: LPS-induced ARDS model mices were treated with EVs or SPREDs intravenously, and transcriptome of treated lungs were compared to figure out the molecular pathways of SPREDs-derived anti-inflammatory response.

first: Shunya

last: Nakayama

first: Kosuke

last: Kamiya

first: Ai

last: Kotani


title: Dietary Poricoic acid A alleviates depressive-like behaviors by targeting the gut microbiota-immune axis

city: Hangzhou

first: Jiangwei

address: No.234,Gucui Road, Xihu District

department: Mental health centerof Zhejiang Province

institute: Tongde Hospital of Zhejiang Province

summary: This study investigated whether dietary poricoic acid A (PAA) alleviates chronic unpredictable stress (CUS)-induced depressive-like behaviors in mice by modulating the gut microbiota-immune axis. Male C57BL/6J mice were subjected to CUS and treated with PAA. Results showed that PAA alleviated depressive- and anxiety-like behaviors, reduced hippocampal neuronal damage, and restored gut microbiota composition by suppressing harmful bacteria like Ligilactobacillus murinus while promoting beneficial taxa such as Akkermansia muciniphila and Lactobacillus reuteri. Hippocampal transcriptomics revealed that PAA modulated immune cell infiltration by reducing M1 and restoring M2 macrophages, with significant correlations between gut microbial taxa and hippocampal immune gene expression. Functional analyses indicated that PAA regulated pathways related to synaptic plasticity and neuroinflammation, which was confirmed by qPCR and Western blot showing restored expression of HSP90B1, RPS6KB2, IGF2BP2, and COL4A5. In conclusion, dietary PAA alleviates depressive-like behaviors in CUS mice by remodeling the gut microbiota and modulating the hippocampal M1/M2 macrophage balance via the gut-brain axis, supporting its potential as a prebiotic-like nutritional agent for major depressive disorder.

overall_design: Hippocampal tissues were collected from mice in the control group (Control), depression model group (Model), and model group treated with a high dose of poricoic acid A (Treatment) for transcriptome sequencing

first: Yun

last: Ma

first: Zixin

last: Liang

first: Shuihong

last: Wang

first: Heqiu


title: Cerebrovascular Single-Nucleus RNA-Seq Reveals Heat Shock Activation and Vascular Remodeling in Alzheimer’s Disease and Primary Tauopathies

city: Cambridge

first: Sudeshna

last: Das

state: Massachusetts

address: 65 Landsdowne St

institute: MGH

summary: Cerebrovascular dysfunction contributes to disease progression in Alzheimer’s disease (AD) and primary tauopathies, yet molecular alterations within vascular cell populations remain poorly understood. We performed single-nucleus RNA sequencing of postmortem human inferior temporal gyrus to characterize transcriptomic changes across cerebrovascular cell types in AD and primary tauopathies, including corticobasal degeneration, Pick’s disease, and progressive supranuclear palsy. Differential expression analyses revealed predominantly disease-specific transcriptional programs across vascular cell populations. However, genes involved in the heat-shock response were consistently upregulated across all diseases, suggesting a conserved cerebrovascular stress response during neurodegeneration. We also report extensive cerebrovascular remodeling taking place in AD compared with primary tauopathies and identified a dysregulation of genes within AD genome-wide association study (GWAS) loci in cerebrovascular-associated cells. Transcriptomic findings were validated using tissue clearing, light-sheet microscopy, and immunofluorescence quantification of vascular markers. We highlight shared and disease-specific vascular mechanisms in neurodegeneration with potential for newly redefined targeted therapies.

overall_design:
Following postmortem tissue collection, vascular cells from the inferior temporal gyrus (BA20) of human donors were isolated by fluorescence-activated cell sorting (FACS) using NeuN and OLIG2 markers and analyzed using snRNA-seq. Donors included individuals diagnosed with Alzheimer’s disease (AD), Corticobasal Degeneration (CBD), Pick’s Disease (PiD), Progressive Supranuclear Palsy (PSP), and neurologically normal controls.

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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: Luis Daniel

last: Estrella

first: Swarnali

last: Dasgupta

first: Akhila

last: Gundavelli

first: Huan

last: Li

first: Stanley

first: Maya

last: Woodbury

first: Lin

last: Gen

first: Knut

last: Biber

first: Kiran

last: Yanamandra

first: Nandini

last: Romanul

first: Sarah

last: Chancellor

first: Timothy

last: Pastika

first: Aicha

last: Abdourahman

first: Ergina

last: Agastra

first: Astrid

last: Doering

first: Janina

last: Ried

first: Bradley

middle: T

last: Hyman

first: Alberto

last: Serrano-Pozo

first: Theodore

last: Zwang

first: Rachel

last: Bennett


title: Shared and distinct gain-of-function consequences from pathologic cytoplasmic versus nuclear TDP-43

city: Seattle

first: Nicole

last: Liachko

state: WA

address: 1660 Columbian Way S.

department: GRECC

institute: VA Puget Sound Health Care System

summary: While predominantly nuclear localized in healthy cells, TDP-43 can transport between the nucleus and cytoplasm. In frontotemporal lobar degeneration (FTLD-TDP) and Amyotrophic Lateral Sclerosis (ALS), TDP-43 accumulates in hyperphosphorylated cytoplasmic aggregates. However, a subset of patients develop nuclear aggregates. Expression of wild-type TDP-43 in C. elegans neurons results in nuclear protein accumulation and gain of function neuronal dysfunction. To enable comparative study of nuclear and cytoplasmic TDP-43 phenotypes, we generated new models with inactivating mutations in the nuclear localization sequence (NLS) of TDP-43. When compared to nuclear TDP-43 strains, similar protein levels of cytoplasmic TDP-43 caused less neuronal dysfunction in C. elegans. Using RNA sequencing, we found innate immune pathway increases in response to cytoplasmic but not nuclear TDP-43. We also found that overexpression of the unfolded protein response (UPR) transcription factor XBP-1s worsened outcomes for wild-type TDP-43 animals but improved TDP-43deltaNLS, suggesting different pathways controlling toxicity and clearance of nuclear versus cytoplasmic TDP-43. Taken together, this comparative approach supports a better understanding of human disease by allowing the study of cytoplasmic TDP-43 alongside nuclear TDP-43 models.

overall_design: RNA sequencing of cytoplasmic and nuclear models of TDP-43 proteinopathy in C. elegans.

first: Aaron

last: Long

first: Heather

last: Currey

first: Matvey

last: Goldberg

first: Randall

last: Eck

first: Marina

last: Han

first: Rebecca

last: Kow

first: Brian

last: Kraemer


title: Fucoxanthin ameliorates metabolic dysfunction-associated steatohepatitis via suppression of CD36-driven fatty acid uptake

city: Shenzhen

first: Chen

last: Yang

address: 1068 Xueyuan Avenue, Nanshan District, Shenzhen,China

institute: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences

summary: Metabolic dysfunction-associated steatohepatitis (MASH) is a progressive liver disease with limited treatment options. Here, we demonstrate that fucoxanthin (FUCO), a natural marine carotenoid, ameliorates MASH by targeting the EGR2-CD36 axis. In FFA-induced hepatocyte models (HepG2, Hep3B, and AML12), FUCO significantly reduced lipid accumulation and inflammatory markers without cytotoxicity. Mechanistic studies revealed that FUCO specifically inhibited fatty acid uptake and transport by downregulating CD36, while TG degradation remained unaffected. RNA sequencing identified EGR2 as a master regulator induced by FFA and suppressed by FUCO. Functional validation showed that EGR2 overexpression completely blocked FUCO's lipid-lowering effects and restored CD36 expression, confirming that FUCO acts through EGR2-dependent CD36 inhibition. Bioinformatic analysis further supported EGR2-mediated regulation of CD36 via TNF and SREBF pathways. Collectively, our findings establish EGR2 as a critical molecular target for FUCO and provide mechanistic insights supporting its clinical development for MASH therapy.

overall_design: RNA seq profiling of fucoxanthin-treated Hep3B steatosis model


title: Human myeloid ontogeny drives differentiation potential in the brain environment [LPS_RNA-seq]

city: Austin

first: Anna

last: Warden

address: 2500 Speedway

institute: University of Texas at Austin

summary: Microglia, the brain-resident macrophages, play key roles in neurodevelopment and aging, including neurogenesis, synaptic pruning, and myelination. Dysregulated microglia are implicated in various central nervous system (CNS) disorders. Developing safe microglia replacements and eliminating toxic microglia are promising but challenging approaches for treating CNS diseases. Microglia uniquely originate from primitive yolk-sac hematopoiesis, unlike other tissue-resident macrophages that arise from the postnatal bone marrow. Previous studies show that peripheral macrophages fail to adopt microglial characteristics after transplantation. We aim to understand the transcriptional networks underlying the ontological and environmental differences between microglia and peripheral macrophages, which may guide therapeutic strategies. Using human stem cell-derived hematopoietic progenitors (iHPCs) in a humanized mouse model deficient in resident microglia, we demonstrate that iHPCs can replicate the yolk-sac-derived fate of human microglia. We transplanted iHPCs, CD34+ hematopoietic progenitor cells, and umbilical cord blood (UCB)-derived monocytes into murine brains and livers, comparing their differentiation into microglia/macrophages. We found that iHPCs generated more microglia-like cells in the brain compared to CD34+ cells and UCB-derived monocytes, with significant differences in migration and differentiation based on the tissue environment. These findings reveal transcriptional network differences influenced by ontogeny and environment, providing insights for developing microglial-based therapies for CNS disorders.

overall_design:
To investigate  the transcriptional networks underlying ontological and evironmental differences between transplanted microglia and peripheral macrophages, we transplanted iHPCs, CD34+ hematopoietic progenitor cells and umbilical cord blood monocytes into murine brains and livers.
We then performed gene expression profiling of these celltypes across engrraftment sites to determine the effect of both ontology and transplantation site, LPS was also used to determine differing effects of immune activation between celltypes. We leveraged comparitive gene expression methods (DESeq2) to determine differential expression, gene patterns (DEGreport) and upstream regulators (IPA).

first: Jing

last: Wang

first: Bing

last: Xia

first: Katie

last: Mostoller

first: Benjamin

last: Brandon

first: Michelle

last: Du

first: Nathan

last: Spann

first: Rick

middle: Z

last: Li

first: Karen

last: Mestan

first: Fatir

last: Qureshi

first: Olivia

last: Corradin

first: Christopher

middle: K

last: Glass

last: Coufal


title: Metabolic and Skeletal Muscle Dysfunctions Correlate with Fatigue-Like Behavior in an Animal Model of Multiple Sclerosis

city: Morgantown

first: Lei

state: West Virginia

address: 64 Medical Center Drive

department: Department of Microbiology, Immunology and Cell Biology

institute: west virginia university

summary: Multiple sclerosis associated fatigue (MS fatigue) is one of the most common and troubling symptoms experienced by people with MS, but the cause of MS fatigue remains unknown. The nature of cognitive and physical exhaustion suggests that MS fatigue can be a metabolic disease that impacts energy demanding processes such as neuronal activity and skeletal muscle contraction. In this study, we investigated how autoimmune-mediated inflammation causes skeletal muscle atrophy and metabolic dysfunctions, which may contribute to MS fatigue. Using a relapsing-remitting model experimental autoimmune encephalomyelitis (EAE), we found that disease manifestations substantially altered the metabolic activities of the mice over time. EAE decreased muscle mass and force input in both fast-twitch extensor digitorum longus (EDL) and slow-twitch soleus muscles but only increased the rate of fatigue in EDL muscle. Gene expression analysis of EDL muscle shows that genes related to cellular respiration and mitochondrial functions were significantly down regulated during when EAE manifestations were the most severe, but this genotype was reversed during disease remission. In addition, EAE-induced mice showed fatigue-like behavior during treadmill test. Surprisingly, this fatigue-like behavior was also observed with mice immunized with a CNS non-specific antigen, suggesting the contributions of the central nervous system-independent immune activation. To our knowledge, this is the first report to characterize skeletal muscle properties and fatigue-like behavior in mice following EAE induction.

overall_design: Female SJL/J mice were immunized subcutaneously with 100 mg [Ser140]-PLP139-151 emulsified in 200 ml complete Freund’s adjuvant (CFA) (Hooke Laboratories EK-0120) into the upper and lower flank. Control groups included mice that were not immunized or immunized with 200 mg ovalbumin (OVA) emulsified in 200 l CFA (Hooke Laboratories EK-0301). Gene expression in EDL muscles was determined 14 and 40 days following EAE induction.

first: Gangqing

last: Hu

first: Edwin

last: Wan


title: Gene expression profiling of the adult male mouse brain after experimental ischemic stroke in C57BL/6 and TNF knockout mice

city: Milano

first: Stefano

last: Raffaele

state: -- Please Select (only U.S. / Can / Aus)

address: Via Balzaretti 9

department: Department of Pharmaceutical Sciences

country: Italy

institute: Università degli Studi di Milano

summary: Tumor necrosis factor (TNF) is a pleiotropic immunomodulatory cytokine rapidly induced after ischemic stroke, but its effects on lesion evolution and tissue remodeling remain unclear. Here we investigated the transcriptional changes induced in the brain by experimental stroke in C57BL/6 and TNF knockout adult male mice compared to naive genotype-matched controls.

overall_design: Male C57BL/6 and TNF knockout mice of 8 weeks of age were kept in naive conditions or subjected to experimental stroke by permanent middle cerebral artery occlusion (pMCAO). After 24 h, whole brain tissue was dissected and processed for transcriptomics profiling using Affymetrix GeneChip Mouse Gene 1.0 ST Arrays.

first: Kate

last: Lykke Lambertsen