title: IRF1 rs2057656 Polymorphism Regulates IRF1-AS1 Transcription and Immune Dysfunction in ARDS via Allele-Specific Epigenetic Repression

city: jinan

first: yuanyuan

last: Zhang

address: jinan

institute: Shandong Second Medical University

summary: Acute respiratory distress syndrome (ARDS) is a severe and life-threatening variant of respiratory failure. Effective targeted therapies are lacking, and patient heterogeneity is substantial. Interferon regulatory factor 1, a key inflammatory transcription factor implicated in ARDS pathogenesis, has poorly defined genetic regulation. By integrating clinical cohorts with genome-wide association studies, we identified a functional single-nucleotide polymorphism, rs2057656, in the antisense promoter of IRF1. The C allele significantly increased ARDS risk (odds ratio = 3.39). This variant modulates local DNA methylation, thereby regulating the expression of the antisense transcript IRF1-AS1, mediating histone deacetylation at the IRF1 promoter and establishing an epigenetic cascade, DNA methylation, antisense RNA, and histone modification that controls IRF1 transcription and pulmonary inflammation. Exogenous IRF1-AS1 delivery alleviated ARDS in C-allele mice. Our study systematically elucidates an epigenetic mechanism governing IRF1 expression and ARDS susceptibility, identifying a genotype-informed therapeutic target.

overall_design: Peripheral blood mononuclear cells (PBMCs) were collected from ARDS patients and healthy controls. Chromatin immunoprecipitation (ChIP) was performed using antibodies against (H3K4me1 / H3K4me3 / DNMT3a). Immunoprecipitated DNA and corresponding input controls were subjected to high-throughput sequencing. Samples were grouped according to rs2057656 genotype. Biological replicates were included for each condition.

first: Shi

first: Yuanyuan


title: Parkinson’s Disease-Associated Pink1 Loss Disrupts Ensheathing Glia And Causes Dopaminergic Neuron Synapse Loss

status: Public on Mar 05 2026

city: Leuven

first: Kristofer

middle: James

last: Davie

address: Herestraat 49

department: Center for Brain and Disease Research

country: Belgium

institute: Vlaams Instituut voor Biotechnologie

type: Expression profiling by high throughput sequencing

summary: Parkinson’s disease (PD) is commonly associated with the loss of dopaminergic neurons in the substantia nigra, but many other cell types are affected even before neuron loss occurs. Recent studies have linked oligodendrocytes to early stages of PD, though their precise role is still unclear. PINK1 is mutated in familial PD, and through unbiased single-cell sequencing of the entire brain of Drosophila Pink1 models, we observed significant gene deregulation in ensheathing glia (EG); cells that share functional similarities with oligodendrocytes. We found that the loss of Pink1 leads to abnormalities in EG, similar to the reactive response of EG seen upon nerve injury. Using cell-type-specific transcriptomics, we identified deregulated genes in EG as potential functional modifiers. Specifically downregulating two trafficking factors in EG, Vps35 and Vps13, also mutated in PD, was sufficient to rescue neuronal function and protect against dopaminergic synapse loss. Our findings demonstrate that Pink1 loss in neurons triggers an injury-like response in EG, and that Pink1 loss in EG in turn disrupts neuronal function. Vesicle trafficking components, which may regulate membrane interactions between organelles in EG, seem to play a role in maintaining neuronal health and ultimately preventing dopaminergic synapse loss. Our work highlights the essential role of glial support cells in the pathogenesis of PD and identifies vesicle trafficking within these cells in disease progression.

overall_design: Bulk RNA-seq of sorted Ensheathing Glia in both WT and Pink1 KO samples. 300 cells were sorted per sample and processed with SMART-seq2

first: Lorenzo

last: Ghezzi

first: Sabine

last: Kuenen

first: Ulrike

last: Pech

first: Nils

last: Schoovaerts

first: Ayse

last: Kilic

first: Suresh

last: Poovathingal

first: Jochen

last: Lamote

first: Roman

last: Praschberger

first: Patrik

last: Verstreken


title: 9-PAHSA orchestrates TCR-T cell fate to boost anti-tumor immunity [KPC]

city: Hangzhou

first: xiaozhen

last: zhang

state: Zhejiang

address: 79 Qingchun Road

country: China

institute: The first affiliated hospital, zhejiang university school of medicine

summary: We identify the endogenous lipid 9-PAHSA as a potent enhancer of T cell anti-tumor function and stemness, validated in murine models and a clinical trial. Mechanistically, we identify ICAM2 as a direct surface sensor for 9-PAHSA and delineate a downstream signaling axis whereby the ICAM2-Ezrin-mTORC2 cascade drives FOXO1 O-GlcNAcylation at S318, facilitating its nuclear translocation to enact a stem-like transcriptional program. Translating this discovery, we engineered armored human TCR-T cells with potentiated ICAM2 expression, which achieve superior tumor control through their enhanced intrinsic efficacy and a remarkable ability to ignite a coordinated and durable host anti-tumor immune response. Our work establishes a new paradigm of metabolite-sensing in T cell biology and provides a compelling therapeutic strategy to potentiate cellular immunotherapy for intractable cancers.

overall_design: Single-cell RNA sequencing of the tumor microenvironment from a KPC mouse model of pancreatic ductal adenocarcinoma (PDAC). Following tumor harvest, cells from dissociated whole tumors were isolated and analyzed using scRNA-seq. Three independent biological samples (individual tumors) were processed.

first: Xiaozhen


title: Transcriptionally permissive heterochromatin domains emerge from fast-evolving genetic elements

city: Cambridge

first: Juan

middle: Carlos

last: Rueda Silva

address: 80 Tennis Ct Rd

department: Biochemistry

country: United Kingdom

institute: University of Cambridge

type: Non-coding RNA profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Histone posttranslational modifications are a main driver for gene regulation, nevertheless, several questions remain unanswered regarding their heritability. The replisome recycles parental histones through the cell cycle, but how this is accomplished in vivo and impacts epigenetic inheritance remains unknown. Here, we show that Caenorhabditis elegans mutants with disrupted replisome-mediated histone recycling display transgenerational defects in RNAi inheritance and fertility. These strains uncovered a particular kind of heterochromatic domain that we called Corrie domains, which are located at the borders of relatively high and low H3K9me3-rich regions and contain gene and AT-rich transposable-element (TE) clusters poised for activation upon deficient H3K9me3 maintenance. Corrie domains are conserved in Mus musculus highlighting an evolutionarily conserved heterochromatic architecture that operates as a hub for regulatory diversity.

overall_design: ChIP-Seq for histne H3, H3K9me3 and H3K27me3 and RNA-Seq for N2, mcm-2(mj632), pola-1(mj635), pole-3(mj630);pole-4(mj636) C. elegans strains.

middle: C

last: Rueda-Silva

first: Miguel

last: V. Almeida

first: Giulia

last: Furlan

first: Lisa

last: Lampersberger

first: Helena

last: Santos-Rosa

first: Chenming

last: Zeng

first: Enric

last: Cata Socias

first: Eric

middle: A

last: Miska


title: Differential expression pattern of venous versus aortic endothelial cells from adult mice

status: Public on Mar 06 2026

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

institute: VIB

summary:
Vena cava and thoracic aorta fragments were dissected out from 12 to 20 Tie2-GFP donor mice and GFP+ endothelial cells were isolatred by FACsorting and collected in RNA lysis buffer for subsequent total RNA isolation.
Total RNA was loaded on a chip for microarray.

overall_design: A differential expression analysis between arterial and venous endothelial cell samples was performed.

first: Aernout

last: Luttun

first: Manu

last: Beerens


title: A noncanonical function of SCIMP restricts JAK1 activity to counteract immune evasion in bladder cancer

city: Wuhan

first: You

last: yongqiang

address: 1277, Jiefang road

institute: Wuhan union hospital

summary: Despite the fact that immunotherapy is reshaping the therapeutic landscape of bladder cancer, immune evasion remains a major obstacle to durable clinical benefit. In this study, we performed a genome-wide CRISPR-Cas9 screen in bladder cancer cells co-cultured with CD8⁺ T cells and identified SCIMP as a key gene that enhances CD8⁺ T cell antitumor immunity. SCIMP serves as a favorable prognostic biomarker in bladder cancer patients treated with immunotherapy. Mechanistically, SCIMP inhibits JAK1 phosphorylation in an adaptor-independent manner, suppressing IFN-γ/JAK1/STAT5A/PD-L1 signaling axis. Meanwhile, YTHDF2 destabilizes the m6A tagged SCIMP transcripts. Remarkably, SCIMP synergizes with PD-1 blockade in suppressing tumor growth. Collectively, these findings reveal a previously unexplored noncanonical role of SCIMP in preventing immune evasion and provide a potential therapeutic target for bladder cancer.

overall_design: We perform CRISPR screen on T24 cells co-cultured with CD8+ T cells to explore essential genes regulating bladder cancer immune evasion. To determine the target genes and downstream signaling pathways of SCIMP in bladder cancer cells, transcriptome analysis was performed in Vector and SCIMP-overexpressing cells upon co-culture with CD8+ T cells.

first: Yongqiang

last: You

first: Hui

last: Zhang

first: Jiayin

last: Sun

first: Liang

last: Wang

first: Chao

last: Huang

first: Guosong

last: Jiang


title: Dysregulated NK-cell gene expression defines the enduring symptoms of long COVID-19

city: Tubingen

first: Yogesh

last: Singh

address: Calwerstrasse 7

department: Institute of Medical Genetics and Applied Genomics

country: Germany

institute: Tubingen University

summary: Long-term COVID-19 syndrome (LTCS) or “long COVID” is a debilitating post-viral condition affecting approximately 2%–8% of individuals after SARS-CoV-2 infection. It manifests typically ≥3 months post-infection with symptoms persisting for at least 2 months, including fatigue, pulmonary dysfunction, and cognitive impairment, in the absence of alternative diagnoses. The biological mechanisms underlying LTCS remain poorly defined, yet emerging evidence implicates immune dysregulation.  We profiled plasma antibodies and cytokines from healthy controls (HC, N = 66), convalescents (CONV, N = 24), and LTCS patients (N = 94), followed by multiparametric 14-color flow cytometry of PBMCs from HC (N = 9), CONV (N = 6), and LTCS (N = 23) participants. To gain mechanistic insight, we performed single-cell transcriptomic profiling (scRNA-seq) on PBMCs from HC (N = 8), CONV (N = 6), and LTCS (N = 32) individuals. LTCS patients exhibited elevated anti-SARS-CoV-2 IgG (spike S1/RBD/N) titers compared to HC, but displayed significantly reduced systemic cytokine levels, including IFN-g, TNF-a, IL-6, and IL-10. Flow cytometry revealed marked depletion of CD56+CD16+ NK cells and CD56+CD3+ NKT cells, accompanied by altered T-cell activation states. scRNA-seq confirmed NK type I cell loss and uncovered broad transcriptional reprogramming with upregulation of PDCD4, CHD1, CXCR4, and SLC7A5 and downregulation of TGFBR3, RIPOR2, and MBNL1. Gene set enrichment analyses indicated activation of circadian and translational programs and suppression of olfactory receptor, neurotransmitter receptor, and GABA-gated ion-channel pathways. Functional assays validated reduced NK-cell inflammatory capacity in LTCS participants. LTCS is characterized by systemic cytokine attenuation and a quantitative and functional NK-cell deficit coupled to neurosensory pathway suppression. These findings identify NK cells as key sentinels of LTCS pathophysiology and highlight an NK-centric neuroimmune axis as a promising target for biomarker discovery and therapeutic intervention.

overall_design: The study design comprised a cross-sectional comparison of three participant groups: healthy controls with no history of SARS-CoV-2 infection or COVID-19 vaccination (HC; n=66), individuals who had recovered from mild–severe SARS-CoV-2 infection (convalescent, CONV; n=35), and participants with long-term COVID-19 syndrome (LTCS; n=114). Blood/PBMC samples were collected and profiled using complementary immune assays. Humoral immunity was assessed using a 3-plex SARS-CoV-2 antibody panel (HC n=66; CONV n=24; LTCS n=94), systemic inflammation was quantified using a 13-plex inflammation panel (HC n=66; CONV n=24; LTCS n=86), and cellular immune composition was characterized by 14-color immunophenotyping (HC n=9; CONV n=6; LTCS n=23). In a subset of participants, PBMCs were additionally analyzed by single-cell RNA sequencing using the Parse Biosciences Evercode combinatorial barcoding platform (HC n=8; CONV n=6; LTCS n=32) to resolve cell-type–specific transcriptional programs associated with convalescence and long-term COVID-19.

first: Urvi

last: Ray

first: Antje

last: Schulze Selting

first: Roshan

last: Priyarangana Perera

first: Zhiqi

last: Yang

first: Vladislav

last: Lysenkov

first: Siri

last: Göpel

first: Michael

last: Bitzer

first: Madhuri

middle: S

last: Salker

first: Stephan

last: Ossowski

first: Olaf

last: Riess

first: Nicolas

last: Casadei


title: Epigenetic alterations of the imprinted SLC22A18 gene contributed to congenital "Allergy-Short-stature-fatty liver" syndrome by via β-catenin-Ascl2 axis

city: Shanghai

first: Jing

last: Li

address: No.1678 Dongfang Road

institute: Shanghai Children's Medical Center

summary: Epigenetic syndrome is a multisystem, eternal, and devastating disease associated with imprinted gene variants. Our previous study showed a strong correlation between the SLC22A18 and the "Allergy-Short stature-fatty liver" (ASFL) syndrome in children. However, the mechanisms by which SLC22A18 influences ASFL syndrome remain unknown.SLC22A18 deficiency also induced higher lipid accumulation in liver in the mouse model. Whether SLC22A18 deletion promotes hepatic steatosis deserves further investigation.

overall_design: the liver tissues from SLC22A18-/- or SLC22A18+/+ mice were collected and analysed using single-cell RNA sequencing (scRNA-seq)

last: Qiao

first: Zhiyan

last: Zhan


title: Single cell and spatial sequencing analysis of cancer associated fibroblasts in the brain metastasis tumor microenvironment

city: Los Angeles

first: Bodour

last: Salhia

state: CA

address: 1450 Biggy Street

department: Department of Cancer Biology

country: USA

institute: University of Southern California

summary: Brain metastasis (BM) remains largely incurable. Cancer-associated fibroblasts (CAFs) can either support or inhibit tumor growth in the tumor microenvironment (TME), yet their roles in BM remain under-described. Here we report a single-cell and spatial sequencing analysis of human BM tissues and define four transcriptionally distinct CAF subpopulations. BM CAF subpopulations are characterized by either extracellular matrix (ECM), immune, contractile, or neural features, and show distinct spatial distributions within the BM TME. Further analyses reveal that BM CAFs engage extensively in cell-cell communication and adopt distinct cell states, including an ECM CAF cell state marked by high levels of immunoglobulin superfamily containing leucine rich repeat expression (ISLR-CAFs). Functionally, ISLR-CAFs reduce BM tumor cell viability in vitro, consistent with a tumor-inhibitory role. These findings highlight the heterogeneity and plasticity of CAFs in BM, emphasizing the importance of precision in defining stromal contributions to disease progression and therapeutic response.

overall_design: The spatial organization of BM TME cell types was investigated through spatial transcriptomic profiling of four BM tissue samples (BBM-USC-5-1, LBM-RIH-2, LBM-RIH-3, and LBM-USC-2-1). Three samples were from lung-to-brain metastases (LBM) and one from a breast-to-brain metastasis (BBM).

first: Thomas

last: Simon

first: David

middle: N

last: Buckley

first: Zeyi

first: Chikako

last: Matsuba

first: Ben

middle: Y

last: Tew

first: Gerald

last: Gooden

first: Kyle

last: Hurth

first: Steven

last: Toms

middle: D

last: Tran

first: Gabriel

last: Zada

first: Matthew

middle: P

last: Salomon


title: Innate Imprinting of Transcriptional Trajectories Governs Respiratory TRM Fate and Persistence

city: Madison

first: Hongtae

last: Park

state: Wisconsin

address: 2015 Linden Drive

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

summary: Respiratory T cell immunity wanes rapidly, and inducing durable mucosal memory remains a major challenge. We demonstrate that precision adjuvancy, using distinct PRR agonists to shape innate inflammation, imprints transcriptional trajectories that govern CD8 T cell fate. Using a nano-emulsion platform, TLR4 signaling induces neutrophilic inflammation and a C/EBP–NF-κB–HIF program that promotes durable, stem-like Type 3 CD127⁺ TRMs. Conversely, STING drives DC–monocytic inflammation and activates an IRF–STAT–T-bet axis that programs attrition-prone Type 1 TRMs. We reconcile systemic and tissue divergence models by identifying distinct TRM precursors. During influenza, Ly6CloPD-1hiLAG-3hiCD69hi precursors differentiate via local reprogramming (tissue divergence). In contrast, vaccination generates Ly6CloLAG-3loCD103hi precursors in lymph nodes and lungs that bypass inhibitory stages (systemic divergence). Mechanistically, T-bet limits TRM precursor formation and differentiation into long-lived Type 3 TRMs. Thus, selecting precision adjuvants that limit T-bet activity is critical for durable mucosal T cell immunity.

overall_design: The study contains two sequencing arms. 1) Bulk RNA-seq of whole mouse lung homogenates collected 48 hours after primary or secondary intranasal vaccination with adjuvants (ADJ+GLA, ADJ+CDN, ADJ+CpG) or unvaccinated controls (n=3 biological replicates per group). 2) Single-cell RNA-seq (10x Genomics) of sorted NP366-specific CD8 T cells from mouse lungs at peak effector, memory, and recall phases following vaccination (ADJ+GLA, ADJ+CDN) or IAV-PR8 infection.

first: Brock

last: Kingstad-Bakke

first: M

last: Suresh


title: Perk is dispensable for smooth muscle cell phenotype switching in atherosclerosis

city: New York

first: Chenyi

last: Xue

state: NY

institute: Columbia University

summary: Smooth muscle cell (SMC) derived cells (SDCs) form the bulk of cells in atherosclerotic lesions and modulate lesion stability and cardiovascular disease outcomes. Unfolded protein response (UPR) markers, thin fibrous caps, and inflammation correlate with human lesion instability and rupture. In mice, UPR drives macrophage and endothelial apoptosis and inflammation, but its impact on lesion stability through SMC modulation is debated. The UPR protein Perk was recently shown to drive SMC modulation in vivo, suggesting that depletion of SMC Perk may regulate lesion stability. We sought to determine if inducible SMC-specific Perk deletion in adult mice improves characterizations of lesion stability during development and progression of disease.

overall_design: Perk was depleted from the SMCs of adult Ldlr-/- hypercholesterolemic mice via tamoxifen-induced Cre under a Myh11 promotor, which also activated the expression of ZsGreen lineage tracing marker in these cells. Mice were assayed at 0, 4, 8, 12, and 16 weeks of western diet feeding. Aortic tissue from the ascending aorta (root to the distal arch) were isolated from three age-matched male mice of each genotype at each timepoint, hashed with 10X Cell Multiplexing Oligos, sorted for viable ZsGreen1+ and ZsGreen1- populations, pooled by Perk genotype, and subject to scRNA-seq.

first: Lucie

last: Zhu


title: Rectal RNA-seq of mice treated with a multistrain Lactobacillus/Bifidobacterium-derived postbiotic (IBM)

city: Akabanedai

first: Takumi

last: Iwasawa

state: KIta

department: Institute of Life Innovation Studies

country: Japan

institute: Toyo University

summary: This dataset provides rectal transcriptomic profiles of mice after 7-day oral IBM administration, enabling pathway-level analyses of epithelial and mucosal responses to a multistrain postbiotic preparation.

overall_design: Male C57BL/6NJ mice (8 weeks old) were randomly assigned to receive oral IBM or vehicle twice daily for 7 consecutive days. IBM is a cell-free fermented soybean extract produced by co-culturing 31 Lactobacillus/Bifidobacterium-related strains. At day 7, rectal tissues were collected and total RNA was extracted for bulk RNA sequencing. The primary objective of this experiment was to identify DSS-independent transcriptional programs associated with IBM administration, with emphasis on epithelial barrier- and circadian-related pathways.


title: Targeting USP14 Enhances Immunotherapy Response by Reprogramming Tumor-Associated Macrophages in Colon Cancer

first: Lisen

last: Lu

address: Hongshan District, Wuhan City, Hubei Province, No. 1 Shizishan Street

institute: Huazhong agriculture university

summary: Combining immunotherapy with other treatments improves survival in colorectal cancer, yet some patients remain unresponsive. Tumor-associated macrophages (TAMs) are a key immune cell population driving this immunotherapy resistance and fostering an immunosuppressive microenvironment. To overcome this, we screened a deubiquitinating enzyme (DUB) library targeting TAMs and identified USP14 as specifically upregulated in TAMs. Inhibiting USP14 reversed their pro-tumor functions, promoted M1 polarization, enhanced tumor cell killing, and activated effector T cells. USP14 inhibition also increased PD-L1 expression on tumor cells, alleviating T-cell suppression. In vivo, combining a USP14 inhibitor with an anti-PD-1 antibody synergistically enhanced immunotherapy efficacy, suppressed tumor progression, and improved survival in a mouse colon cancer model. Thus, USP14 is a promising target to overcome immunotherapy resistance in colorectal cancer.

overall_design: For transcriptomic profiling, total RNA was extracted from FACS-sorted TAMs (CD45+CD11b+F4/80+) pooled from 3-4 tumors per group (PBS vs. IU1-treated) using the MicroElute Total RNA Kit.


title: A Translocation within an Ogataea Clade Species Alters Local Subtelomeric Chromatin while Maintaining Global Genome Organization [Hi-C]

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

institute: University of Colorado Colorado Springs

summary: Eukaryotic genomic DNA is packaged in the nucleus as chromatin – a DNA-protein aggregate regulating genome function, including transcription. Chromatin is classified as either active euchromatin or silent heterochromatin, with each marked by distinct histone post-translational modifications (PTMs). Chromatin composition also mediates genome organization, including how heterochromatin aggregates at the nuclear periphery while euchromatin localizes to the nucleus center. In fungi, heterochromatic loci cluster, including independent centromere and telomere clusters that form the Rabl chromosome conformation. However, it is unknown if chromatin composition and genome organization are conserved in closely related fungi, including some yeast species. Here, we examined differences in histone PTM deposition, gene expression, and genome organization in two yeast species from the order Pichiales, which diverged from a common ancestor with Saccharomyces cerevisiae more than 200 million years ago. We focused on Ogataea polymorpha, which is used for industrial protein production, and Ogataea haglerorum, an isolate of which harbors a translocation between chromosomes 1 and 6. We show that the enrichment of three activating PTMs – the trimethylation of lysine 4 of histone H3 (H3K4me3) and the acetylation of lysine 9 of histone H3 (H3K9ac) or lysine 16 of histone H4 (H4K16ac) – are similar genome-wide yet individual gene orthologs have distinct chromatin and expression patterns. While both Ogataea genomes organize into a Rabl conformation, the O. haglerorum translocation alters subtelomeric chromatin composition and expression of genes affected by the translocation. Our work highlights the genome function differences that occur on a microevolutionary scale.

sample_organism:
Ogataea polymorpha
Ogataea haglerorum

platform_organism:
Ogataea polymorpha
Ogataea haglerorum

overall_design: Chromosome conformation capture coupled with high-throughput sequencing of two closely related species within the Ogataea clade, Ogataea polymorpha and Ogataea haglerorum, to assess whether changes in three dimensional genome organization occur following speciation

first: Tiffany

middle: J

last: Lundberg

first: Nickolas

middle: M

last: Lande

first: Daniel

last: Turevski

first: Riley

last: Figueroa

first: Mai

last: Nguyen

first: Collin

last: Ralston

first: Sara

last: Hanson


title: A Translocation within an Ogataea Clade Species Alters Local Subtelomeric Chromatin while Maintaining Global Genome Organization

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

overall_design: Refer to individual Series


title: A Translocation within an Ogataea Clade Species Alters Local Subtelomeric Chromatin while Maintaining Global Genome Organization [ChIP-Seq]

overall_design: Chromatin Immunoprecipitation-sequencing (ChIP-seq) of either the trimethylation of lysine 4 on histone H3, or the acetylation of either lysine 9 on histone H3 (H3K9ac) or lysine 16 on histone H4 (H4K16ac) in two closely related species of the Ogataea clade, Ogataea polymorpha or Ogataea haglerorum, to assess the changes in chromatin composition that could occur following speciation.


title: Lung fibroblasts contribute to release of Serum Amyloid A as potential biomarker of exacerbation of lung fibrosis in mice [RNA-seq]

city: Hannover

first: Svenja

last: Gaedcke

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

summary: Fibroblasts are important contributors to collagen deposition in interstitial lung diseases (ILD), but their inflammatory role in acute exacerbation of ILD including idiopathic pulmonary fibrosis (IPF) is currently undefined. Using a well described model of S. pneumoniae (Spn) induced exacerbation of lung fibrosis in mice, we found that platelet-derived growth factor receptor A (PDGFRα) positive lung fibroblasts developed an early inflammatory phenotype upon infection including increased production of Serum Amyloid A (SAA) proteins, as determined by RNA sequencing, single-cell RNA sequencing and secretome profiling of sorted lung fibroblasts. Moreover, lung fibroblasts responded to pneumococcal challenge with increased SAA mRNA and protein levels in vitro. SAA levels were significantly elevated in BAL and plasma of mice with Spn-induced exacerbation of AdTGF-β1- or bleomycin-induced lung fibrosis. Antibiotic therapy caused a significant drop in SAA levels in BAL and plasma of mice with infection-driven fibrosis exacerbation. Finally, levels of SAA protein were dramatically increased in plasma of patients with acute exacerbation of interstitial lung disease (AE-ILD) but not in patients without exacerbation. We conclude that analysis of plasma levels of SAA protein may aid in the identification of underlying inflammation in patients with ILD who are more likely to deteriorate towards a critical clinical stage during acute exacerbation.

overall_design: We established a FACS-based protocol for subsequent flow-sorting of PDGFRαpos lung fibroblasts from  AdTGF-β1+mock (mice with established fibrosis) versus AdTGF-β1+Spn treated mice (acute exacerbation of fibrosis) at days 15 or 21 post-treatment

first: Lara-Kristin

last: Steinmetz

first: Benjamin

last: Seeliger

first: Jonas

last: Schupp

first: Tina

last: Röpke

first: Franziska

last: Aschenbrenner

first: Regina

last: Maus

first: David S.

last: DeLuca

first: Andreas

last: Pich

first: Lars

last: Knudsen

first: Lavinia

last: Neubert

first: Fabio

last: Ius

first: Antje

last: Prass

first: Martin

last: Kolb

first: Ulrich A.


title: RNA-seq of human NK cells that were co-cultured with DU-145 cells, which were pre-treated with hIgG1 isotype, 7C6-hIgG1, or 7C6-GAALIE

first: Lucas

last: Ferrari de Andrade

address: 1425 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

summary: 7C6 is a monoclonal antibody that inhibits the shedding of MICA and MICB, which are stress-induced ligands often expressed by tumor cells. We developed a new version of 7C6, 7C6-GAALIE, which better binds Fc gamma-activating receptors, and analyzed how it reprograms human NK cell gene expression in vitro after co-culture with a target cell line, DU-145.

overall_design: Human NK cells were isolated from volunteer donors and co-cultured for four hours with DU-145 cells, which represent human prostate cancer. Such target cells were pre-treated overnight with hIgG1 isotype, 7C6-hIgG1, or 7C6-GAALIE. After the co-culture, NK cells were collected, and NK cell mRNA was isolated with genomic DNA removal and analyzed by RNA-seq.

first: Ferrari de Andrade

last: Lucas

first: Pimenta

last: Ruan


title: A Translocation within an Ogataea Clade Species Alters Local Subtelomeric Chromatin while Maintaining Global Genome Organization [RNA-Seq]

first: Andrew

last: Klocko

overall_design: polyadenylated messenger RNA-sequencing (RNA-seq) of log phase growth cultures of the strain Ogataea haglerorum to assess the gene expression within this species (and for comparison with another closely related species in the Ogataea clade, Ogataea polymorpha)

first: Tiffany

last: Lundberg

first: Nickolas

last: Lande

first: Daniel

last: Turevski

first: Riley

last: Figueroa

first: Mai

last: Nguyen

first: Collin

last: Ralston

first: Sara

last: Hanson


title: Spatial Transcriptomics Data from Human Choroid Plexus

city: New Haven

first: Marcello

last: DiStasio

state: CT

address: 300 George St. Rm. 353D Rm. 353D

department: Pathology

institute: Yale School of Medicine

summary: This study presents spatial transcriptomic data generated from postmortem human choroid plexus tissue. Spatially resolved gene expression profiles were obtained using the Curio Bioscience Seeker v1.1 platform, enabling in situ transcript capture across intact tissue sections. This dataset provides a resource for investigating spatial organization, cellular heterogeneity, and regional transcriptional programs within the human choroid plexus.

overall_design: OCT-embedded snap frozen tissues  were cryosectioned at 10 µm thickness and applied to barcoded Curio Bioscience Seeker v1.1 3x3mm slide-seq tiles according to the manufacturer’s protocol. Sections were fixed, permeabilized, and processed for spatially resolved cDNA synthesis using Slide-seq reagents. Libraries were prepared and sequenced using an Illumina NovaSeq 6000, achieving a mean spatial resolution of ~10 µm per bead. Raw sequencing data were processed using the Curio computational pipeline implements in Nextflow.

first: DiStasio

last: Marcello


title: Cross-organ multi-omics profiling of microbiome and metabolome along the gut–liver axis in MASH model mice induced by Western diet and MC4R knockout

city: Fujisawa

first: Akira

last: Mitsui

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-chome

department: DMPK & Safety Business Unit

institute: Axcelead Drug Discovery Partners, Inc.

summary: Background: Western diet (WD) fed Melanocortin 4 receptor-knockout (MC4R-KO) mice develop a phenotype resembling human metabolic dysfunction-associated steatohepatitis (MASH). Despite its clinical relevance, the role of the gut–liver axis in MASH pathogenesis remains unclear. This study investigated the gut-liver axis through microbiomic and metabolomic analyses of WD-fed MC4R-KO mice, and examined their association with MASH pathology. Methods: We performed an integrated microbiome and metabolome analysis of the liver, small intestinal contents, large intestinal contents, and plasma of wild-type (WT) and MC4R-KO mice fed either a normal diet or WD. Markers of hepatic inflammation, fibrosis, and steatosis measured in this study were used to assess MASH severity and to correlate microbiome and metabolite alterations. Results: WD-fed MC4R-KO mice exhibited significant hepatic steatosis, inflammation, and fibrosis. The abundance of certain microbiota, including Muribaculaceae and Allobaculum, negatively correlated with MASH severity, whereas increased levels of Desulfovibrionaceae and Bacteroides positively correlated with hepatic lipid accumulation, steatosis, and inflammation. Metabolomic profiling revealed increased triglyceride and diglyceride levels in the liver and a concomitant decrease in free fatty acids and monoglycerides in the intestines. Additionally, plasma taurine-conjugated bile acids were elevated in WD-fed MC4R-KO mice, which correlated with the reduced hepatic transport of bile salts from pathway enrichment analysis. These findings highlight substantial alterations in the gut microbiota and lipid and bile acid metabolism, indicating a mechanistic dysregulation of the gut–liver axis that may contribute to MASH progression. Conclusions: The observed gut microbial and metabolic alterations, particularly bile acid and lipid metabolism dysregulation, offer insights into potential therapeutic targets aimed at modulating the gut–liver axis to treat or prevent MASH.

overall_design: Approximately 100-200 mg of small intestine or large intestine contents from WD-fed or ND-fed MC4RKO and WT mice were freeze-dried using a VD-250R Freeze Dryer (TAITEC). The freeze-dried samples were homogenized at 1,500 rpm for 2 min using a multi-bead shocker (Yasui Kikai, Osaka, Japan). The DNA was extracted as follows: Lysis Solution F (Nippon Gene, Tokyo, Japan) was added to the crushed samples and incubated at 65 °C for 10 min. The samples were then centrifuged at 12,000 × g for 2 min, and the supernatant was collected. DNA was purified from the collected solution using the MPure-12 system and MPure Bacterial DNA Extraction Kit (MP Biomedicals, Tokyo, Japan). The concentration of the purified DNA was measured using Synergy LX (BioTek, Winooski, Vermont, USA) and QuantiFluor dsDNA System (Promega, Madison, WI, USA). The sequencing library was prepared using a 2-step tailed PCR method. In the first PCR, 16S region-specific primers were used to amplify the V3-V4 region: 341f_MIX:5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNCCTACGGGNGGCWGCAG-3' 805r_MIX:5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNGACTACHVGGGTATCTAATCC-3' Each 10 μL reaction contained 0.05 U/μL of RxTaq HS (Takara Bio, Shiga, Japan), 0.5 μM of each primer, and 1 ng of template DNA. The PCR conditions were as follows: initial denaturation at 94°C for 2 min; 30 cycles of 94°C for 30 s, 55°C for 30 s, and 72°C for 30 s; followed by a final extension at 72°C for 5 min. PCR products were cleaned using AMPure XP beads (Beckman Coulter, CA, USA) following the manufacturer’s protocol. A second PCR was performed using the following indexed primers: F:5’-AATGATACGGCGACCACCGAGATCTACAC-Index2 ACACTCTTTCCCTACACGACGC-3' R:5’-CAAGCAGAAGACGGCATACGAGAT-Index1 GTGACTGGAGTTCAGACGTGTG-3' In this step, cleaned amplicons from the first PCR served as templates in 10 μL reactions with 0.05 U/μL of RxTaq HS (Takara Bio) and 0.5 μM of each indexed primer. Amplification was conducted for 10 cycles under the same cycling conditions as the first PCR. The concentration of the library was measured using Synergy H1 (BioTek) and QuantiFluor dsDNA System. Library quality was assessed using a Fragment Analyzer and a dsDNA 915 Reagent Kit (Advanced Analytical Technologies, Orangeburg, NY, USA). DNA sequencing was performed on MiSeq system using MiSeq Reagent Kit v3 (Illumina, San Diego, CA, USA), generating 2 x 300 bp paired-end reads.  Read sequences (39,000 – 60,000 paired-end reads) whose starting sequences perfectly matched the primer sequences used were extracted using the fastx_barcode_splitter tool from FASTX-Toolkit (ver. 0.0.14). When the primer sequences contained N-mix, this process was repeated, considering the number of Ns (six types on the forward side × six types on the reverse side = 36 types). The extracted reads were trimmed to remove primer sequences using fastx_trimmer from the FASTX-Toolkit. Sequences with a quality score <20 were removed using Sickle (ver. 1.33), and sequences shorter than 130 bases along with their paired sequences were discarded. Paired-end read merging was performed using FLASH script (ver. 1.2.11). After removing chimeric and noisy sequences using the DADA2 plugin in Qiime2 (ver. 2021.4), 23,000 – 35,000 amplicon sequence variants (ASVs) and their feature table were generated. Taxonomic classification was performed by assigning the ASV sequences against Greengenes database (ver. 13_8) using a feature classifier plugin.

first: Mitsuharu

last: Matsumoto

first: Osamu

last: Miura

first: Takeo

last: Moriya

first: Hitomi

last: Ogino

first: Megumi

last: Hirayama

first: Takaharu

first: Yukihiko

last: Ebisuno

first: Manami

last: Kaneko

first: Yoshinori

last: Satomi

first: Yasunori

last: Nio


title: Transcriptional profiling of GFP-Cre–expressing mesenchymal nephron progenitors

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

overall_design: This study examines the transcriptional effects of GFP-Cre expression in mesenchymal nephron progenitors during mouse kidney development. Both the BAC transgenic Six2TGC line and the knock-in Six2-T2A-GFP-Cre (Six2Cre) line express Cre recombinase fused to GFP. GFP-positive mesenchymal nephron progenitors were isolated by FACS and analyzed by bulk RNA-seq.

first: Azadeh

last: Haghighitalab

first: Zeinab

last: Dehghani-Ghobadi

first: Eunah

last: Chung

first: Joo-Seop

last: Park


title: scRNA-seq of endothelial cells from PyMT murine mammary tumors

city: Houston

first: Luis

last: Becerra Dominguez

state: TX

address: 1 Baylor Plz

department: Breast Cancer

institute: Baylor College of Medicine

summary: The goal of this study is to characterize and compare endothelial cell populations within PyMT mammary tumors exhibiting distinct tumor immune microenvironments. Using single-cell RNA sequencing of endothelial-enriched tumor samples, this dataset enables systematic comparison of endothelial transcriptional states between PyMT-M and PyMT-N tumors. The study is designed to provide a resource for investigating tumor-associated vascular heterogeneity and endothelial remodeling in the PyMT mouse model.

overall_design: This project contains single-cell RNA sequencing data from mammary tumors derived from the PyMT mouse model that were enriched and sorted for endothelial cells. Tumor cells from three independent PyMT-M or three independent PyMT-N mammary tumors were mechanically and enzymatically dissociated separately, subjected to endothelial magnetic enrichment, and endothelial cells were subsequently isolated by sorting prior to pooling and single-cell library preparation. Single-cell transcriptomic profiling was performed to enable comparative analysis of endothelial cell populations between PyMT-M and PyMT-N tumors.

last: Becerra-Dominguez

first: L

last: Yu

first: CH

last: Rivas

first: Sergio

last: Aguirre

first: David

last: Edwards

first: I

last: Hu

last: Wu

first: T

last: Lee

first: X

last: Hao

first: F

last: Liu

first: Xiang H.-F.

last: Zhang


title: Human Choroid Plexus Single Nucleus RNA Sequencing Data [snRNA-Seq]

first: Marcello

last: DiStasio

summary: This study presents single-nucleus RNA sequencing data generated from postmortem human choroid plexus tissue. Isolated nuclei were profiled using the 10x Genomics Chromium platform to characterize gene expression across diverse cell populations of the choroid plexus. The resulting dataset provides a resource for investigating cell-type-specific transcriptional programs and cellular heterogeneity within the human choroid plexus in health and disease.

overall_design: Single-nucleus RNA sequencing was performed on postmortem human choroid plexus tissue from donors in defined study groups (e.g., disease and unaffected controls). Nuclei from each donor were processed as independent samples using the 10x Genomics Chromium Single Cell 3′ workflow. Libraries were sequenced and processed to generate gene–barcode UMI count matrices, enabling comparison of cell-type composition and cell-type–specific gene expression between groups.

first: DiStasio

last: Marcello


title: Cell type diversification and phenotype convergence underlying white fin-ornamentation of cyprinid fishes

city: Charlottesville

first: Delai

last: Huang

state: VA

address: 2071 Winterfield Circle

institute: University of Virginia

summary: White fin ornamentation in teleosts provides a striking model to study pigment cell diversity, differentiation, and patterning. In zebrafish (Danio rerio), white melanoleucophores (ML) and xantholeucophores (XL) produce white and yellowish-white fin patterns, respectively, arising from melanophore and xanthophore lineages. Here, we investigated white fin-pattern cells in zebrafish and a closely related cyprinid, the white cloud minnow (Tanichthys albonubes), which diverged 32–52 million years ago. We identified three distinct leucophore phenotypes in cyprinids: ML, XL, and Tanichthys leucophores, the latter containing white material but lacking substantial carotenoid pigmentation. Transmission electron microscopy revealed that XL and Tanichthys leucophores contain large pterinosome-like organelles, distinct from melanoleucophores and iridophores, suggesting different physicochemical bases for these white phenotypes. Fate-mapping in zebrafish demonstrated that XL arise directly from xanthophore-like progenitors, a process dependent on gap-junction-mediated communication via Gja5b and Cx39.4. Bulk mRNA sequencing of XL versus progenitor cells revealed upregulation of pteridine biosynthesis genes, notably sepiapterin reductase (spra), whose disruption via CRISPR/Cas9 abrogated white pigment formation in both zebrafish XL and Tanichthys leucophores. Chemical analyses confirmed enrichment of colorless pteridines, including biopterin and pterin, in tissues containing these cells. Together, our findings demonstrate that convergent white fin patterns in zebrafish and white cloud minnow rely on pteridine-based leucophores, arising via lineage-specific differentiation programs, and underscore the diversity of cellular and molecular strategies underlying white pigmentation in cyprinids.

overall_design: We collected tissue from yellow and white regions of the anal fins of Tg(aox5:palmEGFP) zebrafish at ~14 mm standard length. For each of five biological replicates, tissue from 20 fish was dissociated into a single-cell suspension, and healthy EGFP⁺ cells were isolated by fluorescence-activated cell sorting. Total mRNA was then extracted and used to generate sequencing libraries.

first: Tiffany

first: Yipeng

last: Liang

first: Pietro

last: H. de Mello

first: Leah

last: P. Shriverb

first: Gary

last: J. Patti

last: M. Parichy


title: Hypatia: a statistical framework for single-cell RNA isoform data analysis

city: Evanston

first: Timothy

last: Pan

state: IL

address: 633 Clark St

institute: Northwestern University

summary: Cells express distinct splicing isoforms in normal physiology and disease. Long-read single-cell RNA-sequencing (LR-scRNAseq) enables isoform quantification at single-cell resolution. However, methods to assess isoform complexity between cell populations are lacking. To address this, we present Hypatia, a toolkit for analyzing isoform usage shifts, diversity, and expression. Using simulated data, we establish a framework for comparative analysis. Using three LR-scRNAseq data sets, we identify widespread transcript-level heterogeneities across cells.

overall_design: Single-nuclear Nanopore RNA-sequencing of a glioblastoma sample.

first: Ruli

last: Gao


title: Fusion gene discovery in single cells with LongFUSE from high throughput long read single cell transcriptomes

city: Chicago

address: Simpson Querrey, 7th Floor

department: Department of Biochemistry and Molecular Genetics

summary: High-throughput long-read single cell RNA sequencing enables full-length transcript discovery of thousands of genes in thousands of cells. Robust computational tools for detecting fusion genes in individual cells remain missing. Here, we report LongFUSE, a new computational tool that employs XOR logic gate for fast and accurate detection of cell-specific fusion genes and their splicing isoforms. LongFUSE outperformed existing tools in simulation and real data, demonstrating high accuracy and robustness.

overall_design: Single cell suspension of all samples were loaded onto 10X Genomics Chromium instrucment for barcoding with scNanoRNAseq protocol. Full-length cDNAs were sequenced with PromethION Oxford Nanopore sequencer.

first: Cheng-Kai

last: Shiau

first: Hsiao-Yun

last: Lin

first: Xiao-Dong

last: Lu

first: Minhua

last: Wang

first: Yueying

last: He

first: Lina

first: Jindan

last: Yu


title: Lung fibroblasts contribute to release of Serum Amyloid A as potential biomarker of exacerbation of lung fibrosis in mice [scRNA-seq]

first: Svenja

last: Gaedcke

first: Lara-Kristin

last: Steinmetz

first: Benjamin

last: Seeliger

first: Jonas

last: Schupp

first: Tina

last: Röpke

first: Franziska

last: Aschenbrenner

first: Regina

last: Maus

first: David S.

last: DeLuca

first: Andreas

last: Pich

first: Lars

last: Knudsen

first: Lavinia

last: Neubert

first: Fabio

last: Ius

first: Antje

last: Prass

first: Martin

last: Kolb

first: Ulrich A.


title: Allergen-Induced Epithelial Senescence Drives Airway Inflammation via the AhR-c-Myc Axis

city: Baltimore

first: Wenjing

last: Gu

state: Maryland

address: 5501 Hopkins Bayview Circle, Asthma Allergy Center,FL 3A,RM4

institute: Johns Hopkins University

summary: Background: Environmental allergens can induce epithelial cellular senescence, which contributes to airway inflammation. The aryl hydrocarbon receptor (AhR), a ligand-activated transcription factor responsive to environmental stimuli, may regulate this process. Objectives: We sought to determine whether epithelial AhR controls cellular senescence and to define its underlying mechanisms in allergic airway inflammation. Methods: Club cell-specific p16 conditional knockout mice (p16ΔScgb1a1) were used to assess the role of epithelial senescence and allergic airway inflammation. AhR regulation of senescence was examined using AhR agonist, antagonist, and Club cell-specific AhR-deficient mice (AhRΔScgb1a1) in both in vitro and in vivo models. Bulk RNA-seq was performed to identify AhR-regulated, senescence-associated genes, and immunoprecipitation (IP) along with ChIP-PCR was employed to validate AhR-target gene interactions. Results: Single-cell transcriptomics revealed epithelial senescence as a key feature of allergen-induced asthma. p16ΔScgb1a1 mice exhibited reduced cockroach allergen–induced airway inflammation and decreased Th2/Th17 cytokines in bronchoalveolar lavage fluids (BALFs). AhR signaling was enhanced in airway epithelial cells of allergen-treated asthmatics and regulated senescence, as indicated by SA-β-gal activity and expression of Cdkn2a, Cdkn1a, and γH2AX. The AhR agonist VAF347 suppressed, whereas AhRΔScgb1a1 deficiency exacerbated, airway inflammation. RNA-seq identified senescence as a major AhR-regulated pathway, highlighting c-Myc, TGF-β2, IGFBP3, and SERPINE1 as key targets. AhR binding to the c-Myc promoter was validated, and c-Myc inhibition with EN4 reduced allergen-induced senescence and inflammation. Conclusions: Epithelial AhR suppresses allergen-induced senescence and airway inflammation through direct regulation of c-Myc. These findings establish the AhR–c-Myc axis as a potential therapeutic target in allergic asthma.

overall_design: RNA-seq profiling was performed on HBE cells after 24 - hour treatment with CRE alone, VAF347 alone, or the combination of CRE and VAF347.

first: Zhifeng

last: Chen

first: Rongjun

last: Wan

first: Yixiang

last: Zeng

first: Xudong

last: Xiang

first: Ruoyun

last: Ouyang

first: Peisong

last: Gao


title: Transcriptomic and proteomic insights into progressive myoclonus epilepsy, EPM1

city: Helsinki

first: Tarja

middle: Hannele

last: Joensuu

address: P.O. Box 63 (Haartmaninkatu 8)

country: Finland

institute: Folkhälsan Research Center/Medicum

summary: Progressive myoclonus epilepsy EPM1 is a rare neurodegenerative disease caused by partial loss of function of cystatin B (CSTB), a cysteine protease inhibitor with known neuroprotective roles. The disease mechanisms remain largely unsolved, and no treatments are available to control the debilitating myoclonus in EPM1. We investigated the impact of CSTB loss on transcriptome in three regions of CSTB-deficient (Cstb-/-) mouse brain — the cerebellum, cerebral cortex, and hippocampus — during disease progression, providing comprehensive insights into the molecular changes and disease mechanisms.

overall_design: RNA-seq analysis of the cerebellum, cortex, and hippocampus in Cstb⁻/⁻ and wild-type mice across four time points: P14 (14 days, pre-symptomatic, early microglial activation), 1 month (disease onset with myoclonic seizures and glial activation in cerebellum and cortex), 3 months (progressive neuronal loss and brain atrophy), and 6 months (widespread brain atrophy).

first: Alina

last: Malyutina

first: Carina

last: Lund

first: Saara

last: Tegelberg

first: Paula

last: Hakala

first: Tuula

last: Nyman

first: Anna-Elina

last: Lehesjoki


title: BRD9 Reads Lactate-Induced H3K18 Lactylation to Drive Oncogenic Chromatin Remodeling in Hepatocellular Carcinoma

city: Changchun

first: enwei

last: Wei

address: Xinjiang Street

institute: the first hospital of Jilin University

summary: Histone lactylation bridges glycolytic metabolism to oncogenic transcription, but its mechanistic readers remain poorly defined. Here, we identify bromodomain-containing protein 9 (BRD9) as a lactyl-lysine reader that links lactate-driven H3K18 lactylation (H3K18la) to chromatin remodeling in hepatocellular carcinoma (HCC). Clinically, elevated H3K18la levels correlate with poor HCC prognosis. Structural (NMR) and biophysical analyses demonstrate BRD9’s bromodomain engages H3K18la through its acetyl-lysine pocket with weak, transient affinity, distinct from stable H3K18ac binding, enabling lactate-dependent chromatin interactions. Multi-omics profiling reveals H3K18la recruits BRD9 and the non-canonical BRG1-associated factor (ncBAF) complex to active enhancers and promoters, promoting chromatin accessibility and oncogenic transcription (SPARC, TMEM64, ANGEL1, SCARB1). Glycolytic inhibition or BRD9 targeting displaces BRD9 from chromatin, suppresses oncogenes, and impairs HCC proliferation. p300 or HDAC inhibition attenuates H3K18la-driven oncogenic transcription and tumor viability. Our findings establish BRD9 as a metabolic-epigenetic mediator that translates glycolytic flux into chromatin remodeling, offering actionable therapeutic targets for HCC.

overall_design: This study aims to investigate the transcriptional and epigenetic alterations in HepG2 cells induced by metabolite stress. The overall design encompasses three distinct sequencing assays. RNA-seq: HepG2 cells were treated under three conditions: negative control (NC), Nala (40 mM, 24h), and 2-DG (40 mM, 48h). Each treatment group had three biological replicates (n=3). ChIP-seq: HepG2 cells treated with NC or 2-DG (40 mM, 48h) were subjected to chromatin immunoprecipitation using antibodies against H3K18la and BRD9 (n=1). ATAC-seq: HepG2 cells were treated with NC or 2-DG (40 mM, 48h) to assess changes in chromatin accessibility (n=1).

first: Enwei

first: Donglei

last: Ji

first: Yanjie

last: Jia

first: Ze

last: Sun

first: Chunfeng

first: Caroline

first: Chunyu

last: Wang

first: Miaomiao

last: Yu

first: Guanglei

last: Shang

first: Linying

last: Xie

first: Wenju

last: Zhang

first: Yameng

last: Li

first: Yingying

last: Liang

first: Bai

first: Yanzhu

last: Yue

first: Yahui

last: Liu

first: Ming-Ming

last: Zhou

first: Lei


title: Gene expression in HCV-infected Huh-7.5 cells treated with or without tyrosine kinase inhibitors

city: Yoshida-gun

first: Kiyonao

last: Sada

state: Fukui

address: 23-3 Matsuoka-Shimoaizuki, Eiheiji

department: Genome Science and Microbiology

institute: University of Fukui

summary:
HCV hijacks host tyrosine kinases to support its life cycle. Non-receptor kinases such as Abl can interact with viral proteins including NS5A, thereby modulating viral assembly. These findings highlight tyrosine kinases as promising therapeutic targets for antiviral intervention.
We used microarrays to profile the global gene expression changes in HCV-infected Huh-7.5 cells treated with bosutinib or entospletinib compared with control, and identified distinct sets of differentially expressed genes associated with viral regulation.

overall_design: Huh-7.5 cells were seeded in 24-well plates one day prior to infection and subsequently infected with HCVcc at an MOI of 5 (TCID₅₀/cell) in the presence of optimized concentrations of bosutinib or entospletinib. After 24 hours, the medium was replaced with fresh medium containing the same concentrations of inhibitors, and the cultures were maintained for an additional 48 hours. Total RNA was then extracted, and only samples with an RNA integrity number (RIN) ≥ 9.0 were used for microarray analysis.

first: Leihua

last: Fu

first: Kenji

last: Takeuchi

first: Kazuyasu

last: Chihara


title: Unconventional Control of Fetal Hematopoiesis by Ribosomal Subunits RPS19 and RPL5

city: Manhasset

first: Lionel

last: Blanc

state: New York

address: 350 Community Drive

department: Pediatric Hematology/Oncology

institute: Feinstein Institutes for Medical Research

summary: Ribosomopathies are associated with anemia; yet, the precise control of ribosomal protein (RP) stoichiometry and activity during erythroid development remains elusive. Using Diamond-Blackfan anemia (DBA) as a model, we generated novel in vivo models of RP haploinsufficiency to define the roles of small and large RP subunits in fetal hematopoiesis. Rpl5 haploinsufficiency caused prenatal lethality due to a reduction in erythroid translation. Conversely, Rps19 haploinsufficiency led to neonatal stem cell exhaustion and impaired erythroid progenitor expansion, resulting from combined translational and transcriptional defects. The stem cell factor RUNX1 is upregulated in RPS19-haploinsufficient DBA patients and its deletion partially rescued hematopoiesis in Rps19 mutant mice. Our findings reveal distinct, subunit-specific roles for RPs in fetal hematopoiesis and demonstrate that imbalanced RP stoichiometry disrupts developmental programs, providing key insights into DBA pathogenesis and patient heterogeneity while underscoring the importance of balanced RP expression in stem cell and erythroid progenitor development.

overall_design: Sequencing of free cytoplasmic and polysome-bound mRNA in the c-Kit+ and Ter119+ cells collected from fetal livers of mice, with and without riboprotein gene mutations targeted to the hematopoietic compartment


title: A patient derived xenograft repository capturing clinical and molecular heterogeneity of large B-cell lymphoma

first: Haopeng

last: Yang

address: 7455 Fannin ST

department: Lymphoma and Myeloma

institute: The University of Texas MD Anderson Cancer Center

summary: Large B-cell lymphomas (LBCLs) are a clinically and molecularly diverse group of malignancies with a rapidly evolving therapeutic landscape that has introduced new areas of clinical need such as post-CD19 chimeric antigen receptor T (CART19) progression. Patient derived xenograft (PDX) models are an important tool for mechanistic studied and preclinical evaluation of new therapies and can be generated from a variety of clinical contexts that capture tumor-intrinsic resistance mechanisms. We therefore undertook a comprehensive effort to generate PDX models that encompass the molecular landscape of LBCLs and include important clinical scenarios for new drug development. Here we describe the first 48 models within this publicly available repository, capturing the transcriptional and genetic subsets of LBCL. These models also include 30 generated from post-CART progression biopsies which reproduce patterns of progression driven by CD19 mutation or expression loss, as well as tumor cell-intrinsic CART19 resistance that we validate in vivo.

overall_design: We perform ATAC-seq and RNA-seq to profile PDX samples to understand their molecuar and epigenetic basis.

first: Michael

last: Green


title: The long noncoding RNA Malat1 contains an internal ribosome entry site mediating micropeptide translation

first: Tanja

last: Hann

address: 260 Whitney Avenue, YSB 308

department: Molecular Biophysics & Biochemistry

institute: Yale University

summary: To determine the structure of the Malat1 IRES, fbDMS-MaP structure probing experiments were performed in BV2 cells for endogenous mouse Malat1 probing, and N2a cells for probing of reporter constructs pDual-GFP-(1-739) IRES-RFP and pDual-GFP-(558-695) IRES-RFP. Two biological replicates were collected for each probing target. For each replicate, fbDMS-MaP includes a sample treated with dimethyl sulfate (modified), and one sample treated with ethanol (unmodified). DMS reacts with the Watson-Crick face of unpaired bases in RNA, covalently modifying them with a methyl adduct. These modifications are encoded as mutations during reverse transcription with MarathonRT. Amplicons are then PCR amplified, next-generation sequencing libraries are prepared, and sequenced using an Illumina NextSeq 2000 platform. The sequencing data are aligned to the reference sequence, and a reactivity profile of 'modified' and 'unmodified' samples is used to calculate the DMS reactivity values of each base. These data can subsequently be used for RNA secondary structure modelling.

overall_design: fbDMS-MaP probing of endogenous Malat1 in BV2 cells and Malat1 IRES reporter constructs (pDual-GFP-(1-739) IRES-RFP and pDual-GFP-(558-695) IRES-RFP) in N2a cells.

first: Wen

last: Xiao

first: Zion

last: Perry

first: Vijaya

last: Pandey

first: Jeffrey

last: Cheng

first: James

last: Wohlschlegel

first: Anna

last: Pyle

first: Douglas

middle: L

last: Black


title: Transcriptomic and Epigenomic profiles analysis during human adaptation to simulated High-Altitude Hypoxia

city: Padova

first: Giulio

last: Ceolotto

address: Via Orus 2B

department: Medicine

country: Italy

institute: University of Padova

summary: Hypobaric hypoxia (HH) is characterized by reduced oxygen availability resulting from the decreased barometric pressure at high altitudes. This condition imposes substantial physiological challenges not only on populations permanently residing in high-altitude regions but also on individuals who intermittently ascend to such environments for occupational, recreational, or other purposes.

overall_design: RNA-Seq and microRNA-seq from PBMCs of subjects exposed to acute hyperbaric hypoxia by terraXcube facility

first: Alessandra

last: Giannella

first: Simona

last: Mrakic-Sposta

last: Vezzoli

first: Arianna

last: Magrini

first: Narjis

last: Khatoon

first: Giacomo

last: Strapazzon

first: Hannes

last: Gatterer

first: Christoph

last: Siebenmann

first: Maja

last: Schlittler

first: Sandro

last: Malacrida


title: Loss-of-function mutants of timP toxin

city: Bordeaux

first: Nicolas

middle: J.

last: Tourasse

address: 146 rue Leo Saignat

department: INSERM U1212, CNRS UMR5320

country: France

institute: University of Bordeaux

summary: FASTBAC-Seq of the timP toxin mRNA to identify loss-of-function mutations. We selected and deep-sequenced surviving transformants expressing mutagenized timP under the J23106 promoter and performed differential expression analysis (compared to a strain not expressing timP = NP) to identify enriched single-nucleotide substitutions. The timP locus originates from S. enterica Typhimurium strain SL1344 (TA07144 from T1TAdb database).

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Amplicon DNA sequencing of bacterial strains transformed with mutated PCR libraries of the TimP mRNA of the TimP/TimR toxin-antitoxin system, either with a full promoter or no promoter. The PCR products were generated using the DreamTaq and Mutazyme II polymerases, and after recombination into the chromosome of E.coli, the DNA was extracted and amplified using the KAPA and Phusion polymerases. Three biological replicates were sequenced for each PCR library and polymerase combination (24 samples in total).

first: Anaïs

last: Le Rhun


title: Methylomic Analysis of Nasal Brushings Reveals Two Subgroups in Pediatric Acute Respiratory Distress Syndrome

city: Little Rock

first: Akhilesh

last: Kaushal

state: Arkansas

address: One Children’s Way, Slot 512-43

department: Hematology/Oncology

institute: University of Arkansas for Medical Sciences

type: Methylation profiling by genome tiling array

summary: Pediatric acute respiratory distress syndrome (PARDS) is a significant cause of mortality in the pediatric intensive care unit (PICU), and supportive care remains the mainstay of treatment. The biological heterogeneity of PARDS hampers the development of new therapies. One source of heterogeneity is the epigenetic regulation of gene expression via methylation. We hypothesized that PARDS patients could be classified into at least two subgroups defined by differential methylation of immune-related genes.

overall_design: We conducted a prospective, single-center cohort study of PARDS and control patients under 18 years of age admitted to the PICU. Nasal brushings were obtained on day 1 for methylomic analysis, and clinical information and outcomes were recorded until discharge.

middle: G

last: Williams

first: Nirmeen

last: Elmadany

first: Rashika

last: Joshi

first: Rhonda

last: Jones

first: Nathan

last: Gregor

first: Patrick

last: Lahni

first: Steven

last: Standage

first: Brian

last: Varisco


title: Mixed-lineage leukemia cells undergo unique adaptations in the CNS niche

city: Edinburgh

first: Alasdair

last: Duguid

address: 5 Little France Drive

department: Institute for Regeneration and Repair

institute: University of Edinburgh

summary: KMT2A-rearranged (KMT2A-r) infant leukaemia can present as a lymphoid, myeloid or mixed lineage leukaemia and frequently involves the central nervous system (CNS), yet the impact of this lineage diversity and plasticity on CNS involvement remains poorly understood. Using a fully murine model of KMT2A-AFF1+ mixed lineage infant leukaemia, we investigated how the CNS niche influences the phenotype and function of leukaemia propagating cells (LPC). Previously defined bone marrow (BM)-derived LPCs were transplanted and shown to engraft the CNS, although not equally; LK/CLP cells were consistently underrepresented in the niche. Transplants of CNS-derived LPCs, modelling relapse, demonstrated reduced systemic repopulation capacity, with many recipients exhibiting stable long-term engraftment without developing overt leukaemia, a phenomenon not observed in BM-derived transplants. Transcriptomic profiling of matched CNS- and BM-derived LPCs revealed enrichment of pathways involved in hypoxia, lipid and cholesterol homeostasis, and inflammatory signalling. Notably, LPC subsets that successfully adapted to the CNS niche upregulated lipid and fatty acid metabolic programmes. CNS-derived LPCs showed increased expression of genes involved in T cell immune modulation, suggesting a skew to a more immunosuppressive environment. These findings indicate that the CNS niche imposes lasting metabolic, functional, and immunological constraints on leukemic cells, impairing their ability to reestablish systemic disease. We show that the CNS niche imposes selective pressures and causes functional reprogramming of mixed lineage LPCs, affecting their systemic repopulation capacity and, we hypothesise, immune cell interactions. We further believe this study has relevance to primary mixed lineage infant leukaemia and, increasingly important, lineage-switched infant leukaemia.

overall_design: BM and CNS cells were harvested from the miR-130a overexpression Kmt2a-AFF1+ mouse model of infant mixed lineage leukaemia, as described in Malouf et al. (2021), and from the BM of a miR-scramble Kmt2a-AFF1+ mouse (non-leukaemic control). These cells were FACS-sorted into distinct leukaemia-propagating or haematopoietic stem and progenitor populations (HSC/MPP: Lin⁻ c-Kit⁺ Sca-1⁺ Flt3⁻; LMPP: Lin⁻ c-Kit⁺ Sca-1⁺ Flt3⁺; LK/CLP: Lin⁻ c-Kit⁺ Sca-1⁻) for RNA extraction and bulk sequencing. Transcriptomic comparisons were performed by cell type and by niche.

first: Camille

last: Malouf

first: Katrin

last: Ottersbach


title: Change in miRNA levels in SH-SY5Y cells after electroporation of peptide nucleic acid (PNA) targeting precursor micro RNA

city: Kobe

first: Tamai

last: Endoh

address: 7-1-20, Minatojima-minamimachi, Chuo-ku

department: FIRST/FIBER

institute: Konan University

summary: Peptide nucleic acid (PNA) is a neutral DNA analog uniquely suited for triple helical recognition of nucleic acids. However, the practical applications of triplex-forming PNAs have been limited by sequence restrictions, as stable base triples are formed only with purines. Hoogsteen recognition of pyrimidines has been a long-standing challenge. Here, a new approach to improve pyrimidine recognition by enhancing nucleobase stacking in the PNA strand is demonstrated by targeting procursor micro RNA (pre-miRNA).  Placing 5-triazolyl uridine adjacent to the modified nucleobases designed for Hoogsteen recognition of pyrimidines in double helical RNA increased the binding affinity while maintaining sequence specificity.  The increased binding affinity improved the biological activity of triplex-forming PNAs. RNA-seq analysis targeting mature microRNAs showed that a PNA recognizing a mixed sequence of three nucleobases (G, A, and U) had higher specificity than a similar PNA featuring a uniform purine recognition tract. These results demonstrate a novel strategy to address the issue of pyrimidine recognition, which has been the critical bottleneck for triple helical targeting of nucleic acids.

overall_design:
Triplicate of miRNA profiling using MCF7 cell lines with or without electroporation of PNA, which targets miRNA-155 or miR-197, after 66-incubation by using QIAseq miRNA Library Kit for Thermo Fisher Scientific NGS Systems and Ion GeneStudio S5 system.
PNA21: targets miR-155
PNA22: does not have exact target miRNA (scrambled control of PNA21)
PNA23: targets miR-197
PNA24: targets miR-197
PNA25: does not have exact target miRNA (scrambled control of PNA24)

first: Sara Farshineh

last: Saei

first: Tamaki

first: Vladislavs

last: Baskevics

first: Ilze

last: Kumpina

first: Martins

last: Katkevics

first: Naoki

last: Sugimoto

first: Eriks

last: Rozners


title: Deep profiling of multiple mouse tumor microenvironments using scRNAseq

city: San Francisco

first: Tristan

last: Courau

address: 513 Parnassu Ave

institute: UCSF

summary: The HuMu dataset (https://www.biorxiv.org/content/10.1101/2025.07.01.661217v1) contains single-cell sequencing data from 9 mouse tumor models that we use to dissect gene expression profiles across populations and tumor models. The data can be readily queried here https://quipi.org/app/quipi_humu

overall_design: Tumors were grown in mice before harvesting at day 14 or ~500mm3, enzymatic dissociation, hashing using TotalSeq A, FACS-based denrichment of lymphoid and myeloid populations, and scRNAseq processing using 10X V3 3' chemistry


title: Transcriptional Response of pe/ppe Knockout Mutants in Mycobacterium tuberculosis

city: Seattle

first: Christoph

last: Grundner

state: WA

address: 1900 9th Ave

department: Center for Global Infectious Disease Research

institute: Seattle Children's Research Institute

summary: To investigate the impact of ppe51, pe25/ppe41 and ppe42 deletion on global transcriptional changes in Mycobacterium tuberculosis, we compared gene expression profiles of the knockout strains with wild-type H37Rv.

overall_design: Wild-type (WT) H37Rv and the ppe51, pe25/ppe41 and ppe42 deletion strains were cultured in 7H9 medium supplemented with 10% OADC, 0.5% glycerol, 0.05% Tyloxapol, and 100 μM sodium propionate until an OD600 of 0.8 was reached. Cells were then pelleted, resuspended in buffered water, and incubated for an additional 5 hours. Bacterial pellets were collected, RNA was isolated and gene expression quantified by sequencing.

first: Vishant

last: Boradia

first: Andrew

last: Frando


title: Multi-tissue, multi-time-point transcriptomic atlas of aging in mice and rats [rat]

city: Tarrytown

first: Kun

last: Xiong

address: 777 Old Saw Mill River Road

department: Molecular Profiling and Data Science

institute: Regeneron Pharmaceuticals

summary: In order to get a greater understanding as to the genes and signaling pathways which are up- or down-regulated in a consistent manner throughout the rodent lifespan, we generated a high N age-related gene expression atlas in mice and rats, by profiling 28 tissues in male and female C57BL/6J mice, and 32 tissues in male Sprague Dawley rats (> 5000 samples) over multiple time points. We identified age-related genes and pathways that change either early in life, at mid-age, late in life, or linearly. Linear genes dominated many but not all tissues, and certain tissues (e.g. gut tissues) were relatively spared from age-related changes. We identified tissues that showed a strong sex bias or species bias. Given the expanse of our transcriptomic dataset, we hope this study will serve as a useful resource for understanding the timing, the tissue-specificity, the gender-specificity, and the species-specificity of age-related gene and pathway changes in male and female mice and male rats.

overall_design: Bulk RNAseq of 32 tissues of male rats at 7 age groups. Samples of diaphragm, soleus, gastrocnemius, and tibialis anterior were previously submitted to GEO under GSE226118, and were reprocessed here by using the same pipeline as other tissues.

first: Tea

last: Shavlakadze

first: Romain

last: Donne

first: Corissa

last: McEwen

first: Abhilash

last: Gadi

first: Matthew

last: Wakai

first: Hunter

last: Salmon

first: Jacob

last: Treinish

first: Elias

last: Pavlopoulos

first: Larry

last: Proctor

first: Shuo

last: Li

first: Nicole

last: Negron

first: Min

last: Ni

first: Yi

last: Wei

first: Yu

last: Bai

first: David

last: Glass


title: USP8-mediated mitochondrial regulation in osteoclasts is essential for skeletal development

city: SHREWSBURY

first: SACHIN

middle: RAMDAS

last: CHAUGULE

state: MA

address: 44 SHREWSBURY GREEN DRIVE

department: Genetic and Cellular Medicine

institute: UMass Chan Medical School

summary: Aberrant protein regulatory pathways disrupt bone homeostasis and contribute to skeletal diseases. Many of cysteine protease family of deubiquitinating enzymes (DUBs) are critical for regulation of bone-resorbing osteoclasts and bone-forming osteoblasts. Here, we demonstrate that the DUB ubiquitin-specific protease 8 (USP8) is highly expressed in osteoclasts and its deletion impairs osteoclast development and bone resorption activity. Deletion of USP8 in osteoclasts (Usp8Ctsk) results in low bone mass due to defective endochondral ossification and short stature resulting from abnormal growth plate structure. Mechanistically, USP8 deficiency in osteoclasts dampens mitochondrial number, activity, oxidative phosphorylation, and mitophagy, while reactive oxygen species (ROS) inflammatory responses are increased in these cells. Moreover, USP8-deficient osteoclasts in metaphysis produce secretory factors that hinder both cartilage formation in the growth plate and trabecular bone formation. Collectively, these findings identify USP8 as a key regulator of osteoclast development and secretory factor production, shaping the microenvironment essential for skeletal development.

overall_design: RNAseq profilling of shCtrl- or shUSP8-treated Raw264.7 cells at day 4 under osteoclast differentiation conditions.

first: Sachin

last: Chaugule

first: Yeon-Suk

last: Yang

first: Sato

last: Toshi

first: Emma

last: Mayer

first: Jae-Hyuck

last: Shim


title: scRNA-seq of wildtype and MZwnt11/slb zebrafish embryos

city: Heidelberg

first: Nicoletta

last: Petridou

state: BW

address: Meyerhofstrasse 1

department: DB

institute: EMBL

summary: Transcriptomics dataset for the study of developmental differences between wildtype and MZwnt11/slb mutants at shield stage

overall_design: scRNA-seq using ACME dissociation fixation of zebrafish wildtype and MZwnt11/slb embryos at shield stage

first: Camilla

last: Autorino

first: Cristina

last: Pallares Cartes

first: Louise

last: Harari

first: Michael

last: Dorrity


title: Cellular Reprogramming of H3K27M Pediatric High-Grade Glioma to Neuron-like State

city: Montréal

first: Jacek

last: Majewski

state: QC

address: 740 Av. du Docteur-Penfield

department: Human Genetics

country: Canada

institute: McGill University

summary: This study explores the cell fate reprogrammability of H3K27M-mutant pediatric high-grade gliomas (pHGG) using neuronal transdifferentiation as a potential targeted therapy. We treated the BT245 patient-derived glioma cell line with pharmacological combinations targeting neuronal differentiation pathways and performed bulk RNA sequencing to characterize gene expression patterns driving cell fate transitions. Our findings reveal that the drug combinations induce transcriptomic changes consistent with differentiation towards mature neuronal phenotypes, including the upregulation of synaptic and dendritic signaling genes and the downregulation of malignant signatures. In comparison, astrocytic differentiation media (DM) and H3K27M knockout (KO) promote residual astrocytic or stem-like phenotypes, suggesting neuronal transdifferentiation as a more effective strategy for mitigating tumor aggressiveness and progression. Differentially expressed genes such as GRIK1, GRIN1, NRXN3, NRXN1, CALB2, SCGN, SLC32A1, SLC1A2, KCNC3, and neurodevelopmental regulators including WNT7A, DLX6, ERBB4, ARX, BCL11B, SEMA3C, and FGFBP3 were identified as key markers regulating the neuron-like lineage transition. This study demonstrates that pHGGs can be phenotypically redirected toward stable, less invasive neuronal identities through modulating cell fate differentiation programs. These findings advance the concept of 'transition therapy' as a promising intervention to reduce phenotypic plasticity and malignancy in pHGG ecosystems. While these are early in vitro findings, the ability to steer and control glioma cells toward stable, less malignant fates offers promising translational potential for patient-centered targeted therapies.

overall_design: This study aimed to reprogram H3K27M-mutant pediatric glioma cells (BT245) into less malignant neuron-like states using pharmacological differentiation therapies. Two drug combinations—FID (Forskolin, ISX9, DAPT, Laduviglusib, IBET151) and FTT (Fasudil, Tranilast, Temozolomide)—were used to induce neuronal trans-differentiation. Controls included BT245 cells in standard stem cell media or media with diluted BrainPhys, with equivalent volumes of DMSO administered across all conditions. RNA sequencing was performed to assess transcriptomic changes and infer cell identity transitions via bioinformatic analyses.

first: Abicumaran

last: Uthamacumaran

first: Cynthia

last: Horth

first: Eric

last: Bareke


city: Memphis

first: Te

last: Ling

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children's Research Hospital

overall_design: Fetal liver cells from E13.5 embryos were used for scRNA-seq or scMultiome-seq and 2 individual fetal livers from the same genotype group were utilized.

first: Yuefeng

last: Tang

first: Rashid

last: Mehmood

first: John

last: Crispino

first: Lionel

last: Blanc


title: Multi-tissue, multi-time-point transcriptomic atlas of aging in mice and rats [mouse]

first: Kun

last: Xiong

state: NY

overall_design: Bulk RNAseq of 28 tissues of male and female mice at 6 age groups. Samples of diaphragm, soleus, gastrocnemius, and tibialis anterior were previously submitted to GEO under GSE226117, and were reprocessed by using the same pipeline as other tissues.

first: Tea

last: Shavlakadze

first: Romain

last: Donne

first: Corissa

last: McEwen

first: Abhilash

last: Gadi

first: Matthew

last: Wakai

first: Hunter

last: Salmon

first: Jacob

last: Treinish

first: Elias

last: Pavlopoulos

first: Larry

last: Proctor

first: Shuo

last: Li

first: Nicole

last: Negron

first: Min

last: Ni

first: Yi

last: Wei

first: Yu

last: Bai

first: David

last: Glass


title: Brucella tRNA-derived fragment tRF-Leu-CAG reprograms macrophage polarization for intracellular survival via up-regulation of IL13RA1 expression

city: wuhan

first: hongrong

last: hong

state: hubei province

address: Huazhong Agricultural University, Lion Street, Hongshan District

department: preventive veterinary medicine

institute: Huazhong Agricultural University

summary: Outer membrane vehicles (OMVs) are secreted from gram-negative bacterium to enable bacterial survival and regulate microbial interactions within bacterial communities. The components of OMVs comprise RNA, but the generation as well as the function of OMVs RNA needs to be elucidated. Here, we report that a small non-coding RNA fragment tRF-Leu-CAG, detected in Brucella OMVs, regulates interleukin 13 receptor subunit alpha 1 (IL13RA1) to activate the phosphorylation of Signal Transducer and activator of Transcription 6 (STAT6) via the JAK-STAT6 pathway to reprogram macrophage M2 polarization. We identified the presence of tRF-Leu-CAG in Brucella OMVs by sRNA sequencing and tRF sequencing from bacterial lysate. tRF-Leu-CAG interacts with argonaute 2 (AGO2) protein to exert its function. Meanwhile, the interleukin 13 receptor subunit alpha 1 (IL13RA1) was proved to be the target genes of tRF-Leu-CAG. Overexpression of phosphorylated STAT6 by western blot further substantiated that tRF-Leu-CAG promotes macrophage M2 polarization via the JAK-STAT6 pathway. Finally, tRF-Leu-CAG and small interfering IL13RA1 facilitates the survival of Brucella in macrophage. Thus, our results highlight the function of tRF-Leu-CAG in Brucella OMVs by reprogramming macrophage M2 polarization to improve the survival of extracellular Brucella. The study unravels a new mechanism of intracellular parasitism and immune escape in Brucella, providing strategy for the mechanisms of other intracellular parasitic bacteria.

overall_design: High-throughput sequencing was provided by Shanghai Cloud Sequencing Biotechnology Co. The total RNA of each sample was used to prepare tRF&tiRNA(41). Sequencing libraries were prepared, denatured into single-stranded DNA molecules, captured on an Illumina flow cell, amplified in situ into clusters and 50 cycles of sequencing on Illumina Novaseq 6000 sequencer according to the vendor's instructions. After sequencing on Illumina sequencer, image analysis, and base identification, the raw reads were harvested after QC. Q30 was first used for QC. The original reads were de-joined using cutadapt software (v1.9.3), which removes low-quality reads and retains reads >=16 nt in length, resulting in trimmed reads. Then, tDRmapper software(42) was used to identify tRFs and tiRNAs and the corresponding count numbers in each sample, and then edgeR(43) software (v3.16.5) was used for normalization, and P-value and Fold Change were calculated between the two groups of samples (with replicates), and screened for differentially expressed tRFs & tiRNAs.

first: Guan Yin

last: Zhang

first: Hong Rong

last: Hong

first: Chang Xian

last: Wu

first: Feng Dong

last: Zhu

first: Yu Peng

last: Fang

first: Shuang Yan

last: Xiao

first: Zheng Fei

last: Liu


title: Decitabine-Primed CAR T-Cell Therapy for Relapsed/Refractory Non-Hodgkin's Lymphoma: A Phase 1/2 Clinical Study Demonstrating Enhanced Efficacy and Prolonged Survival

city: Beijing

first: Yipeng

address: Fuxing Road 22

institute: Chinese PLA gerneral hospital

type: Methylation profiling by high throughput sequencing

summary: Relapsed/refractory Non-Hodgkin's lymphoma (R/R NHL) remains a therapeutic challenge despite advances in immune checkpoint inhibitors (ICIs). While chimeric antigen receptor (CAR) T-cell therapy has shown promise in hematologic malignancies, its efficacy in NHL is limited by T-cell exhaustion and tumor microenvironment (TME) immunosuppression. Preclinical studies suggest that low-dose decitabine, a DNA hypomethylating agent, can epigenetically reprogram T cells to enhance cytotoxicity and persistence. This open-label phase 1/2 trial (NCT04697940) enrolled 33 R/R NHL patients (aged 16–73 years) to evaluate the safety and efficacy of decitabine-primed CAR T cells targeting CD19/CD20 (CART19/20). Patients received lymphodepletion followed by escalating doses (0.5–5×10^6 cells/kg) of decitabine-activated CAR T cells. Primary endpoints included dose-limiting toxicities (DLTs) and objective response rate (ORR); secondary endpoints encompassed progression-free survival (PFS) and mechanistic analyses of T-cell dynamics.In the phase 1 cohort (n=18), no severe cytokine release syndrome (CRS) or neurotoxicity was observed, establishing 5×10^6 cells/kg as the recommended phase 2 dose (RP2D). Among 15 evaluable patients in phase 2, the ORR reached 86.7% (13/15), with a complete remission (CR) rate of 60% (9/15). Median PFS was 22.1 months, significantly surpassing historical controls of PD-1 monotherapy (median PFS: 12–15 months). Mechanistic studies revealed that decitabine pretreatment upregulated AP-1 transcription factor JunD in CAR T cells, promoting clonal expansion of progenitor-exhausted CD8+ T cells and enhancing tumor infiltration.

overall_design: CAR T cells were exposed to low-dose decitabine (0.1 μM, 72 hours) prior to harvest.At 24 hours after decitabine priming (immediately prior to infusion), 1×10^6 cells per patient were aliquoted and cryopreserved in freezing medium (90% FBS + 10% DMSO) for subsequent single-cell RNA sequencing (scRNA-seq)  analysis.

first: Yao

last: Wang

first: Weidong

last: Han


title: Genomic characterization of sub-populations in human pluripotent stem cell-derived retinal progenitor cells that drive retinal layer structure

first: YASUAKI

last: IWAMA

address: 2-1-8, Minatojimaminamimachi, Chuo-ku

department: Research Center

institute: Kobe City Eye Hospital

summary: The mechanisms of layer formation of retinal spheroids were investigated using Rax::GFP-positive retinal progenitor cells (RPCs) obtained from human embryonic stem cell-derived retinal organoids. Single-cell RNA sequencing revealed that well-layered spheroids exhibited a transient activation of canonical WNT2B–FZD7 signaling followed by a temporary expression of non-canonical WNT5A, processes associated with the formation of organized retinal layers. Despite structural differences in vitro, both non-layered and well-layered retinal spheroids of differentiation day 60 successfully developed into each cone and rod subtypes of photoreceptors and established synaptic connections with host bipolar cells after transplantation in retinal degeneration model rats, resulting in light-evoked functional recovery.　Additionally, part of the presumable RPCs differentiated into non-retinal lineages, including ciliary marginal zone-like, retinal pigment epithelium-, and spinal cord-like tissues in vitro, reflecting the developmental plasticity of RAX-positive cells. These findings suggest that canonical and non-canonical WNT signaling pathways sequentially orchestrate early retinal morphogenesis, while environmental factors within the host retina strongly drive the alignment and functional integration of graft photoreceptors.

overall_design: Human retinal spheroids were dissociated into a single cell suspension and run on the 10x Genomics Chromium Single Cell System platform using ver3.1 chemistry. Libraries were sequenced on Illumina HiSeq X and processed through the Cell Ranger pipeline using the GRCh38 reference genome.

first: Yasusaki

last: Iwama

first: Tomohiro

last: Masuda

first: Mika

last: Yoshimura

first: Masayo

last: Takahashi

first: Itoshi

last: Nikaido

first: Michiko

last: Mandai


title: Transcriptomic and Epigenomic profiles analysis during human adaptation to simulated High-Altitude Hypoxia [miRNA-Seq]

first: Giulio

last: Ceolotto

first: Alessandra

last: Giannella

first: Simona

last: Mrakic-Sposta

last: Vezzoli

first: Arianna

last: Magrini

first: Narjis

last: Khatoon

first: Giacomo

last: Strapazzon

first: Hannes

last: Gatterer

first: Christoph

last: Siebenmann

first: Maja

last: Schlittler

first: Sandro

last: Malacrida


title: Functional characterization of immune-related cells in a cnidarian

city: Barcelona

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

summary: We performed single-cell transcriptome analysis of a Nematostella vectensis transgenic line expressing RLRb::mCherry. We sampled gastrula stage embryo, including a control group of non-injected embryos, a control group injected with NaCl, and a group injected with poly(I:C)

overall_design: Adult specimens were fixed, dissociated and pooled before sorting single-cells for scRNAseq. Some samples were mixed (cross-species or cross-treatments) and processed together. Instructions for demultiplexing cells are provided.

first: Shani

last: Levy

first: Yehu

last: Moran

first: Itamar

last: Kozlovski


title: Kupffer Cell Calibration of T Cell Responses via VSIG4-CD5 Interaction Promotes Tumor Evasion

city: Hefei

first: xia

last: zhou

address: huang shan Road 443

institute: university of science and technology of china

summary: Liver metastasis often resists T cell-based immunotherapy, indicating an adaptation of metastatic tumors towards reduced immunogenicity in the liver. Here we demonstrate that VSIG4, an immune checkpoint molecule predominantly expressed on Kupffer cells, plays an opposing role in determining the growth of liver metastases with varying antigenicity by modulating cognate TCR signaling through its interaction with CD5. Mechanistically, VSIG4-CD5 engagement impedes activation of low-affinity CD8+ T cells while enhancing responses of high-affinity CD8+ T cells by rescuing them from activation-induced cell death. This bi-directional regulation promotes selective outgrowth of metastatic tumor clones with low antigenicity, thereby fostering an T cell-unfavorable immune landscape as metastatic liver cancer progresses. Blockade of VSIG4-CD5 interaction with a newly generated anti-VSIG4 nanoantibody sensitizes liver metastases to anti-PDL1 therapy, achieving remarkably synergistic efficacy in mice. Our findings provide mechanistic insights into cancer immunoediting in liver metastasis and propose a promising approach for treating immunologically cold tumors.

overall_design: DAPI-CD45+ singlets were sorted by FACS from liver tissues enriched for metastatic B16F10 melanomas of WT or Vsig4-/- mice.These cells were further processed for scRNA-seq.

first: Xia

last: Zhou

first: Wei

last: Liu

first: Jing

last: Hu

first: Qi

last: Yao


title: An AAV variant enables human T cell engineering in vivo

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake university

summary: Autologous chimeric antigen receptor T (CAR-T) cell therapy has exhibited prominent therapeutic effectiveness in hematologic malignancy and autoimmune disease, but the manufacturing complexity and the required lymphodepletion hindered its wide clinical application. Engineering human T cells in vivo holds promise to conquer these limitations but requires effective T cell-targeted CAR delivery with demonstrated safety. Recombinant adeno-associated virus (rAAV) emerged as a promising vehicle in eight FDA-approved gene therapy drugs and shows attractive potential in tropism redirection via capsid engineering. Here, we showcased that T-cell-tropic rAAV variants successfully enabled CAR expression in human T cells and de-targeted from the liver down to 1% of the parental serotypes. In a humanized mouse model, systematic injection of rAAV-CAR turned up to 8.3% of human T cells into CAR-T cells, which successfully eliminated the number of B cells and controlled tumor progression. Moreover, we identified and verified three cell surface receptors corresponding to the superior transduction efficiencies of the rAAV variants to T cells. This study demonstrated the effectiveness and safety of AAV-based in vivo generation of CAR-T cells in a humanized mouse model, which illustrated a route of in vivo CAR-T therapy via a delivery vector proved in clinics. Furthermore, the identified receptors provide mechanistic insights into the translational potential and guidance to receptor-based capsid engineering.

overall_design: Cas9-expressing Jurkat cells were transduced with the lentiviral library at MOI=0.3 by spinfection and incubated overnight. Then, the transduced Jurkat-Cas9 cells were selected and expanded in culture medium with puromycin. When mKate2+% achieved above 95%, 2.3×10^7 cells per replicate were transduced with rAAV-WT-EGFP or rAAV-M-EGFP at indicated MOI. At 72 h after rAAV transduction, cells were collected for top 20% and bottom 20%. Then, specific PCR amplification was performed based on genomic DNA extracted from sorted cells.


title: GSK3β-Mediated Phosphorylation of SOX4 and Its Interaction with STAT6 to Regulate MTHFD2 Expression, NADPH Production, Cancer Stemness, and Prognosis in Hepatocellular Carcinoma [ChIP-Seq]

city: Taoyuan

first: Jang-Hau

last: Lian

address: No. 5, Fuxing Street

country: Taiwan

institute: Chang Gung Memorial Hospital

summary: SOX4 is associated with poor prognosis in various cancers, including hepatocellular carcinoma (HCC). SOX4 plays a crucial role in angiogenesis, cellular differentiation, and cell growth through interactions with transcription factors in response to stimuli. Despite its overexpression and link to poor prognosis, SOX4 remains an undruggable target. Therefore, targeting its interacting or regulatory proteins might disclose a therapeutic strategy in HCC. Our aim was to elucidate SOX4 regulation and interactions in HCC cells to provide further insights into its role in tumorigenesis. GSK3β phosphorylated SOX4 at serine residues 379, 383, 387, 391, and 395, as revealed by in vitro kinase assays, which stabilized SOX4 protein. Interactions between SOX4, STAT6, and GSK3β in HCC cells were confirmed by co-immunoprecipitation, immunofluorescence, and proximal-ligation assay. Knockout SOX4 or inhibition of STAT6 repressed cell growth, sphere formation, and NADPH production through modulating MTHFD2 expression, which in turn repressed expression of PD-L1 in HCC cells. The significant elevated NADPH was found in SOX4high HCC tumor specimen as compared with the SOX4low tumors. Positive correlations of GSK3β & SOX4, STAT6 & SOX4, and SOX4 & MTHFD2 proteins were observed in liver cancer specimens through western blot analysis. Furthermore, tumor lesion with elevated of SOX4, MTHFD2, or both SOX4 and MTHFD2 transcripts tend to have poor prognosis in patients with HCC using TCGA-LIHC database. Treatment with inhibitors targeting STAT6 or MTHFD2 reduced cell proliferation in vitro and attenuated tumor growth in an HCC patient-derived xenograft (PDX) mice model in vivo. The GSK3β/SOX4/STAT6/MTHFD2 regulatory axis played a critical role in modulating NADPH production and maintaining cancer stemness, associated with poor prognosis in HCC that might be a potential therapeutic target.

overall_design: Chromatin immunoprecipitation DNA sequence (ChIP seq) for SOX4 and STAT6 in Hep3B cells

first: Chia-Lung

last: Tsai

first: Ming-Chin

last: Yu

first: Chi-Neu


title: Transcriptional changes in the guts of Drosophila malanogaster upon tyramine treatment

city: London

first: Nazif

last: Alic

address: Gower St

institute: UCL

summary: Adrenergic signalling is heavily implicated in human age-related disease and yet the potential for this neuroendocrine signalling pathway to modulate ageing has received little attention. Here, we use Drosophila melanogaster to test if adrenergic-like signalling can promote longevity by manipulating tyramine (TA) or octopamine (OA), the invertebrate equivalents of adrenergic hormones. Increased neuronal synthesis of TA boosts health and longevity in both sexes, whereas OA is marginally beneficial in males. Orally administered TA or OA extend female or male lifespan, respectively. Increased activation of the ß-adrenergic-like signalling in the gut, by manipulating a ß-adrenergic-like receptor, PKA or CrebB, is sufficient to delay female ageing. Transcriptional profiling reveals that CrebB links the ß-adrenergic pathway to longevity-promoting processes in the gut where its function is required for the beneficial effects of TA feeding in females. Here we show that localised activation of ß-adrenergic signalling has the potential to counter animal ageing.

overall_design: For RNA extraction, eight mid-guts from Tyramine (TA: 100 µg/ml) or control food-fed flies were dissected at indicated times in ice-cold PBS and placed into ice-cold TRIzol (Thermo Fisher Scientific, 15596026). Five experimental replicates were performed and RNA samples were preserved in -80oC freezer prior to extraction by TRIzol/choloroform method as per manufacturer’s instructions and quantified by NanoDrop 2000c spectrophotometer. For RNA sequencing, library preparation (Illumina, strand-specific RNA-seq with PolyA selection) and sequencing (Illumina NovaSeq 2 x 150 bp sequencing) were performed by Azenta Life Sciences (GENEWIZ UK Ltd., Essex, UK). Read quality was assessed with FastQC and transcript abundance was estimated with Salmon against the fasta file containing all Drosophila transcripts (Flybase, r6.55). Data was imported into R with RStudio, using tximport package and differential expression assessed with DESeq2 and ihw packages.

first: Ahmed

last: Sumit

first: Shajahan

last: Anver


title: GSK3β-Mediated Phosphorylation of SOX4 and Its Interaction with STAT6 to Regulate MTHFD2 Expression, NADPH Production, Cancer Stemness, and Prognosis in Hepatocellular Carcinoma

overall_design: Comparative gene expression profiling analysis of RNA seq data for Hep3B cells and its knockdown derivaties (SOX4 KO and STAT6si)


title: Transcriptional changes in the guts of Drosophila melanogaster upon gut specific CrebB induction

overall_design: For RNA extraction, eight mid-guts were dissected from gut-induced CrebB (TIGS>CrebB- plusRU486) flies, non-induced CrebB (TIGS>CrebB- minusRU486) flies, driver alone (TIGS only- plusRU486) and driver alone (TIGS only- minus RU486) flies at indicated times in ice-cold PBS and placed into ice-cold TRIzol (Thermo Fisher Scientific, 15596026). Five experimental replicates were performed and RNA samples were preserved in -80oC freezer prior to extraction by TRIzol/choloroform method as per manufacturer’s instructions and quantified by NanoDrop 2000c spectrophotometer. For RNA sequencing, library preparation (Illumina, strand-specific RNA-seq with PolyA selection) and sequencing (Illumina NovaSeq 2 x 150 bp sequencing) were performed by Azenta Life Sciences (GENEWIZ UK Ltd., Essex, UK). Read quality was assessed with FastQC and transcript abundance was estimated with Salmon against the fasta file containing all Drosophila transcripts (Flybase, r6.55). Data was imported into R with RStudio, using tximport package and differential expression assessed with DESeq2 and ihw packages.


title: Plasmodesmal closure triggers stress responses

first: Hannah

middle: Rae

last: Thomas

address: 866 Yuhangtang Road

department: Horticulture

institute: Zhejiang University

summary: Plant cells function cell autonomously, but are connected to their cellular neighbors via plasmodesmata. Changes in cellular connectivity is required for cell signaling, with elicitor-induced plasmodesmal closure and consequent cellular isolation required for a full immune response. To understand what occurs when plasmodesmal closure is initiated, we generated two inducible transgenic lines (LexA::PD-Plug and LexA::icals3m). Inducing these genetic tools results in callose deposition at plasmodesmata, leading to plasmodesmal closure and cellular isolation, independent of a stimulus. We found that prolonged cellular isolation led to the upregulation of stress responsive genes and accumulation of salicylic acid, in addition to increased resistance to Pseudomonas syringae DC3000. We observed a more homogenous cellular isolation in LexA::icals3m lines in comparison to a heterogenous cellular isolation in LexA::PD-Plug, the latter which reflects more biological relevant observations in response stress elicitors. Interestingly, the LexA::icals3m displayed detrimental phenotypes with prolonged plasmodesmal closure in the form of hypersensitivity to Botrytis cinerea, perturbations of photoassimilate distribution with the accumulation of starch and sugars, and decrease in size of leaves and increased leaf senescence. These findings of what happens when a cell is isolated from its neighbors indicates we need to consider these factors in any context which plasmodesmata close, and also defines why cell-to-cell connectivity is regulated during key biological processes.

overall_design:
To investigate the downstream effects of plasmodesmal closure, we utilized two estradiol-inducible lines, LexA::PD-Plug (PD-plug) and LexA::icals3m (icals3m), which close plasmodesma in response to estadiol. These lines along with Col-0 wildtype were grown on plates and treated with esradiol or DMSO (mock).
2 leaves from four plants were collected for each samples, with 3 biological replicates. Samples were collected 12, 24, 48, and 72 hours after estradiol treatment. RNA was extracted and sequenced
Differential gene expression analysis was conducted on total RNA.

first: Estee

middle: E

last: Tee

first: Andrew

last: Breakspear

first: Diana

last: Papp

middle: R

first: Catherine

last: Walker

first: Annalisa

last: Bellandi

first: Christine

last: Faulkner