title: Performance evaluation of Arabidopsis scRNA-seq sample processing strategies

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

summary: Plant cells display significant heterogeneity, complicating the isolation and profiling of diverse cell populations from complex tissues. Optimizing methodologies for cell enrichment and single-cell transcriptomics is therefore critical for accurately capturing cellular diversity. Here, we systematically compared protoplast enrichment technologies (including conventional and image-based flow cytometry, as well as magnetic cell sorting) and single-cell RNA sequencing (scRNA-seq) platforms (10X Genomics Chromium, BD Rhapsody) using Arabidopsis roots. Image-based flow cytometry offered greater precision due to customizable gating strategies, while magnetic sorting provided faster processing and better representation of cell size heterogeneity. Both scRNA-seq platforms captured root cell heterogeneity and yielded reproducible gene expression profiles, but we observed platform-specific biases in cell type composition. Notably, single nucleotide polymorphism analysis of a mixed ecotype sample revealed that computational doublet detection algorithms misclassified two-thirds of the cells as doublets. Since the Arabidopsis root contains a wide range of cell types and developmental stages, our findings have broad implications. In summary, these insights can guide the end user to optimise their scRNA-seq workflows and improve data quality across plant species.

overall_design: Root meristems from Col-0 and Ler-0 plants were protoplasted, protoplasts were mixed in equal proportions and loaded on 10X Chromium and BD Rhapsody in two independent experiments

first: Eekhout

last: Thomas

first: Lindsy

last: De Veirman

first: Jolien

last: De Block

first: Freya

last: Persyn

first: Vera

last: Goossens

first: Dominique

last: Audenaert

first: Gert

last: Van Isterdael

first: Carolin

last: Grones


title: SIRT3 regulation of hematopoietic stem cell aging

status: Public on Jun 24 2026

city: BERKELEY

first: DANICA

last: CHEN

state: CA

address: 119 Morgan Hall

department: NST

country: USA

institute: UC BERKELEY

type: Genome binding/occupancy profiling by high throughput sequencing

summary: SIRT3 is a mitochondrial NAD+-dependent deacetylase. To investigate the role of SIRT3 in hematopoietic stem cell aging, we generated and characterized mouse models overexpressing SIRT3.

overall_design: single-nuclei ATAC-sequencing of lineage-negative bone marrow cells from 2-year-old Mx1-Cre and Mx1-T3 mice

first: Wei-Chieh

last: Mu

first: Danica

last: Chen

first: Jie

last: Li


title: ZMAT3 drives metabolic adaptation in Fanconi anemia, creating a preleukemic niche through sphingolipid reprogramming.

city: VILLEJUIF

last: Bluteau

address: Gustave Roussy, PR2, 114, rue Edouard Vaillant

country: France

institute: EPHE, PSL Research university

type: Expression profiling by high throughput sequencing

summary: ZMAT3 alleviates cell death cells in Fanconi anemia via adaptation of sphingolipid metabolism.

overall_design: LSK cells from Fancg KO and WT mice were sorted, subsequently lysed, total RNA extracted and RNA-sequencing libraries were prepared using CATS RNA-seq Kit v2  mRNA  Sample Prep Kit. Sequencing librarie were sequenced on Illumina Nextseq 500 sequencer.

first: Samuel

last: Quentin

first: Jean

last: Soulier


title: BoNT/A Modulates Microglial Phagocytic Activity in the Hippocampus Revealed by Single-Cell RNA Sequencing

city: Suzhou

first: QIEI

last: CONG

state: Jiangsu

address: No 199. Ren-ai Road

country: China

institute: Soochow University

summary: To investigate the impact of Botulinum Neurotoxin A (BoNT/A) on hippocampal cellular landscapes, we performed single-cell RNA sequencing (scRNA-seq) on tissues from Saline-, MPTP-, and MPTP+BoNT/A-treated mice. We identified and annotated 10 major cell types through canonical marker gene expression. A focused sub-clustering analysis of microglia revealed 11 distinct subpopulations. Notably, KEGG pathway enrichment analysis identified three subclusters (1, 3, and 5) as phagocytosis-related microglia, enriched in pathways such as lysosome, phagosome, and FcγR-mediated phagocytosis. Our findings demonstrate that BoNT/A plays a definitive role in modulating microglial phagocytic activity in the hippocampus.

overall_design:
Objective: To delineate the impact of BoNT/A on hippocampal cell-type composition and microglial functional heterogeneity.
Subjects: Mice divided into three treatment groups:
Saline-treated (Saline-HIP)
MPTP-treated (MPTP-HIP)
MPTP + BoNT/A-treated (MPTP-BONT-A-HIP)
Methodology:
Tissue Processing: Hippocampal tissues were dissected from mice in each treatment group.
Single-Cell RNA Sequencing: Single-cell suspensions were prepared and subjected to scRNA-seq using a standard platform (e.g., 10x Genomics).
Data Processing: Raw sequencing data underwent stringent quality control and filtering.
Cell Clustering and Annotation: Filtered cells were clustered using UMAP. Major cell types (microglia, astrocytes, neurons, etc.) were identified and annotated based on the expression of established canonical marker genes.
Microglial Sub-clustering: Microglial cells were isolated and re-clustered to identify subpopulations.
Functional Analysis: Differential gene expression and KEGG pathway enrichment analyses were performed on the microglial subclusters to infer their functional states.

first: Qifei

last: Cong

first: Yuan

last: Qin


title: DNA-PKcs inhibitor KU-57788 synergizes with ferroptosis in anaplastic thyroid cancer cells

city: Hangzhou

first: Lingling

last: Ding

address: Shangtang street

institute: Zhejiang Provincial People’s Hospital

summary: Next Generation Sequencing Facilitates Quantitative Analysis of 8505C cells treated with KU-57788 and DMSO

overall_design: mRNA profiles of 8505C cells were generated by deep sequencing, in duplicate, using Illumina Navoseq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using  SYBR Green assays.

first: Guowan

last: Zheng

first: Chuanming


title: SEMA6A inhibits tumor progression and boosts anti-tumor immunity via blocking the ISG15/TGFβ axis in colorectal cancer

city: Beijing

first: Fang

last: Zhang

address: No. 2 Nanwei Road

institute: Chinese Academy of Medical Sciences

summary: Semaphorin is an axon-guiding factor regulating nervous system development. A growing body of evidence shows that semaphorin could regulate tumor progress and immune responses. The research found that Semaphorin 6A (SEMA6A) may play a dual role in the occurrence and development of tumors. Nevertheless, the regulatory role of SEMA6A in colorectal cancer (CRC) remains unclear. This study aimed to investigate the prognostic value, expression pattern, clinical significance, and immune effects of SEMA6A in CRC. Through multi-database analyses and validation with clinical specimens and tissue microarray, we identified reduced SEMA6A expression in CRC tissues, establishing it as an independent prognostic factor. Functional enrichment and immune infiltration analyses revealed SEMA6A's protective role through tumor immune microenvironment modulation, with elevated expression correlating with enhanced immune cell infiltration. Cellular experiments including CCK8, Transwell, and immunofluorescence assay demonstrated SEMA6A can suppress the proliferation, migration, and invasion ability of CRC. Integrated RNA-seq and proteomic analyses, we identified ISG15 as a downstream effector of SEMA6A. Functional validation confirmed that ISG15 promotes malignant progression and counteracts SEMA6A-mediated tumor suppression. Coculture experiments revealed that SEMA6A can activate the CD8+ T cells and inhibit the expression of TGF-β1 by reducing the expression level of ISG15. Moreover, SEMA6A could induce the response of CRC to PD-1 monoclonal antibody by up-regulating immunostimulatory factors, thus playing an anti-tumor role in a subcutaneous CRC model. Our findings indicate that SEMA6A can stratify the risk of CRC patients and serve as a novel biomarker to predict response to immunotherapy, providing novel insights into precision medicine and immunotherapeutic strategies for CRC.

overall_design: Transfection of SEMA6A lentivirus in mouse colorectal cancer cells SL4 yielded SL4 cells stably overexpressing SEMA6A and RNA-seq was performed on them and control cells.

first: Rixin

first: Min

last: Yang


title: Diabetes mellitus is associated with a shared hyper-inflammatory immune response in melioidosis and tuberculosis patients: an observational case-control study

city: London

first: PATPONG

last: RONGKARD

address: Du Cane Rd

department: National Heart and Lung Institute

country: United Kingdom

institute: Imperial College London

summary: Melioidosis is a serious infection caused by the bacterium Burkholderia pseudomallei (Bp) with a case fatality rate of up to 40% in Northeast Thailand. Diabetes increases the risk of developing melioidosis by 12-fold. A similar, but less marked, relationship with diabetes is seen in tuberculosis (TB) patients, with a 3-fold increased risk of developing TB in people with diabetes. However, the mechanisms underlying increased susceptibility are not fully understood. Whole blood samples of 81 acute melioidosis patients from Northeast Thailand and 151 TB patients from South Africa, Indonesia, Romania and Peru alongside uninfected control cohorts were studied by whole blood RNA sequencing. We identified that having diabetes is associated with a hyper-inflammatory response to both melioidosis and TB, with increased neutrophil and platelet degranulation, and exaggerated activation of coagulation and scavenger activation pathways. The impact is more subtle in melioidosis but pronounced in tuberculosis with stunted interferon responses

overall_design: Total RNA sequencing was performed on RNA isolated from whole blood samples of culture confirmed melioidosis patients along with outpatients with diabetes and healthy donors.

first: Patpong

last: Rongkard

first: Barbara

last: Kronsteiner

first: Clare

last: Eckold

first: Direk

last: Limmathurotsakul

first: Narisara

last: Chantratita

first: Eoin

last: West

first: Sina

last: Gharib

first: Jacqueline

last: Cliff

first: Nicholas

last: Day

first: Paul

last: Klenerman

first: Susanna

last: Dunachie


title: Gene expression profile of tibialis anterior from  Gaa-/- mice compared to wild type mice

city: Nantes

first: Candice

last: BABARIT

address: 101 route de Gachet

department: Santé Animale

institute: INRAE

summary: Pompe disease is an autosomal recessive metabolic disorder caused by acid alpha-glucosidase deficiency, characterized by progressive skeletal muscle weakness and respiratory insufficiency. Affected muscles exhibit glycogen-filled lysosomes, autophagic build-up, and mitochondrial abnormalities. Despite global myofibrillar disorganization, satellite cells (SCs) fail to activate, due to mechanisms that remain unclear. This study aimed to further characterize the muscle phenotype in Pompe disease, with particular attention to proteins associated with membrane repair processes, as membrane damage is a primary trigger for SC activation. Longitudinal transcriptomic analysis of skeletal muscle from a Pompe disease mouse model, combined with immunohistochemical and biochemical approaches, showed early and sustained overexpression of dysferlin (DYSF), annexin A2 (ANXA2), and AHNAK2. These membrane repair-associated proteins displayed abnormal localization during disease progression, with sarcoplasmic accumulation associated with T-tubules, lysosomes and autophagosomes, respectively. Analysis of muscle biopsies from some patients with late-onset Pompe disease (LOPD) identified similar expression patterns in moderately affected cases, whereas these patterns were less evident or absent in the most severe samples, suggesting stage-dependent redistribution associated with advanced myoarchitectural disorganization. Furthermore, in the mouse model, we observed persistent post-transcriptional accumulation of mature myostatin (MSTN), a key negative regulator of muscle growth, alongside a decrease in the phospho-SMAD3/SMAD3 ratio and reduced SMAD7 expression, which point toward a more complex modulation of its canonical bioactivity rather than a simple increase. Altogether, these findings identify modified distribution proteins linked to membrane repair and dysregulation of MSTN as features of muscle remodeling in Pompe disease.

overall_design: Gene expression profiling was performed on the tibialis anterior of Gaa-/- and wild type mice aged of 1.5, 4, 6 and 9 month-old ( n = 4 animals per group).

last: Babarit

first: Sabrina

last: Jagot

first: Karl

last: Rouger

first: Marie-Anne

last: Colle


title: LINC01857 regulates antigen-presenting cell viability and antimicrobial defense in humans

city: Marburg

first: Leon

middle: Nicolas

last: Schulte

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

country: Germany

institute: Philipps-Universität Marburg

summary: Macrophages are essential for balancing pathogen clearance with tissue homeostasis, yet the molecular regulators of this equilibrium remain incompletely defined. Here, we identify LINC01857, a primate-specific lincRNA, as a critical modulator of macrophage survival and antimicrobial defense. LINC01857 is induced during monocyte-to-macrophage differentiation but rapidly downregulated upon bacterial challenge via NFκB. Under homeostatic conditions, it dampens adhesion, phagocytosis and invasion factors, including SIGLEC1 and MMP7, and suppresses apoptosis. Loss of LINC01857 during infection creates a 'dead-end' niche that limits Salmonella Typhimurium intracellular replication, whereas enforced expression promotes pathogen propagation. Mechanistically, LINC01857 interacts with the adaptor protein 14-3-3β to support macrophage survival. Notably, downregulation of LINC01857 is mirrored in circulating immune cells from patients with severe COVID-19 and sepsis. Together, our findings position LINC01857 as a central regulator linking macrophage survival to host-pathogen interactions and disease pathophysiology.

overall_design: The long noncoding RNA LINC01857, identified as immune-responsive lncRNA in human myeloid cells, was silenced by RNAi in blood-derived macrophages (BDM) differentiated with GM-CSF. In parallel, LINC01857 was exctopically expressed in THP1 from a lentiviral vector. Both LINC01857 silenced and overexpressing cells and the corresponding controls, challenged with bacterial lipopolysaccharide or Salmonella enterica serivar Typhimurium, were subjected to RNA-seq analysis.

middle: N

first: Jörg

last: Vogel


title: SIRT3 regulation of hematopoietic stem cell aging [RNA-Seq, Gastrocnemius muscle]

first: DANICA

last: CHEN

overall_design: RNA-seq profiling of muscles from aged mice transplanted with control or SIRT3 overexpressing HSCs.

first: Wei-Chieh

last: Mu

first: Chih Ling

last: Wang

first: Danica

last: Chen


title: Characterization of the effects of ISX9 treatment on RBPJ target genes.

city: Philadelphia

first: Tobias

last: Friedrich

state: Pennsylvania

address: 421 Curie Boulevard

institute: University of Pennsylvania

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

overall_design: Refer to individual Series


title: Characterization of the effects of ISX9 treatment on RBPJ target genes. [ATAC-Seq]

summary: The Notch signaling pathway regulates several processes including development and differentiation and its aberrant regulation leads to several diseases. The transciption factor RBPJ is the main mediator of the Notch signaling pathway, regulating both repression and activation of Notch target gens. Here, we first identified RBPJ target genes by analyzing the transcriptional effects of RBPJ depletion and the binding of RBPJ by ChIP-Seq in H1299 cells. Subsequently, we analyzed the gene expression profile upon 12 or 24 hours ISX9 treatment in H1299 cells focusing on the identified RBPJ target genes. Finally, we analyzed the effects of 12 hours ISX9 treatment on the chromatin in H1299 cells by performing ChIP-Seq versus H3K4me1, H3K4me3 and H3K27ac.

overall_design: Human H1299 cells were treated with ISX9 or with DMSO as a control for 12 hours. Cells were analyzed by ATAC-Seq.

first: Subhamita

first: Friedrich

last: Tobias

first: Giaimo

last: Benedetto Daniele


title: Longitudinal monitoring of cytoplasmic RBP-RNA interactions and transcriptome in living cells by engineered protein nanocages

first: Yangming

address: No.5 Yiheyuan Road, Haidian District

department: Institute of Molecular Medicine, College of Future Technology

institute: Peking University

type: Non-coding RNA profiling by high throughput sequencing

summary: Most existing RNA sequencing methods rely on cell lysis or fixation, limiting their use in longitudinal studies of the same cell population. Here, we introduce POND-seq (Protein nanocage-empOwered Non-Destructive sequencing), a strategy that employs secretory protein nanocages fused to RNA-binding proteins (RBPs) to recover RBP-associated RNAs from living cells. POND-seq robustly identifies RNA targets of cytoplasmic RBPs across multiple cell types and enables longitudinal tracking of dynamic changes in RBP-associated RNA profiles under stress conditions. Fusion to PABPC1 further allows monitoring of transcriptomic responses and selectively profile cell-type-specific transcriptomes from mixed populations without cell dissociation and sorting. Additionally, POND-seq supports functional interrogation of RBP domains and residues involved in RNA association and enables scalable analysis of RBP variants, as demonstrated by a systematic assessment of disease-associated FMR1 mutations. Together, POND-seq provides a versatile and scalable platform for non-destructive and longitudinal analysis of cytoplasmic transcriptome and RBP-associated RNAs.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
To overcome the destructive nature of existing RNA profiling approaches, we sought to engineer a genetically encoded system capable of exporting RNA information from living cells without requiring cell lysis. The core design principle was to redirect cytoplasmic RBP-associated or transcriptome-wide RNA cargo into secreted particles that could be collected non-invasively from culture supernatants.
Viral capsid–based virus-like particles (VLPs) were a potential starting point given their natural RNA packaging capacity. However, intrinsic RNA-binding activity and large internal volumes may promote non-specific encapsulation and elevate background signal. Therefore, we explored whether a fully engineered, non-viral scaffold could provide improved modularity and specificity. POND-seq (Protein nanOcage–empowered Non-Destructive sequencing) is built on fusion of RNA-binding proteins to EPN24, a computationally designed nanocage protomer that self-assembles and is efficiently secreted from mammalian cells. In this architecture, RNA selectivity is conferred by the fused RBP, while EPN24 serves as a secretion-competent carrier. This modular framework enables interchangeable RBPs for interactome profiling and, through fusion with PABPC1, transcriptome-wide capture of polyadenylated RNAs. Because RNA recovery relies solely on supernatant collection, POND-seq is inherently compatible with longitudinal sampling and parallelized experimental designs, and can be combined with cell type–specific promoters to enable selective transcriptome recovery in mixed cellular environments.

first: Lu-Feng

last: Hu

first: Gang

last: Xie


title: Characterization of the effects of ISX9 treatment on RBPJ target genes. [ChIP-Seq]

overall_design: Human H1299 cells were treated with ISX9 for 12 hours. Alternatively, H1299 cells were transfected with plasmids delivering sgRNAs targeting the human RBPJ gene together with a CAS9-encoding gene. As control, empty vector plamid was used.Cells were analyzed by ChIP-Seq using antibody directed against RBPJ, H3K4me1, H3K4me3 or H3K27ac.

last: Day


title: Characterization of the effects of ISX9 treatment on RBPJ target genes. [RNA-Seq]

summary: The Notch signaling pathway regulates several processes including development and differentiation and its aberrant regulation leads to several diseases. The transciption factor RBPJ is the main mediator of the Notch signaling pathway, regulating both repression and activation of Notch target gens. Here, we first identified RBPJ target genes by analyzing the transcriptional effects of RBPJ depletion and the binding of RBPJ by ChIP-Seq in H1299 cells. Subsequently, we analyzed the gene expression profile upon 12 or 24 hours ISX9 treatment in H1299 cells focusing on the identified RBPJ target genes.

overall_design: Human H1299 cells were treated with ISX9 for 12 or 24 hours. Alternatively, H1299 cells were transfected with plasmids delivering sgRNAs targeting the human RBPJ gene together with a CAS9-encoding gene. As control, empty vector plamid was used. RNA was purified and the gene expression profile was analyzed by RNA-seq


title: MDM4 overexpression alleviates developmental and hematopoietic defects in Fancg deficient mice.

first: Dominique

last: Bluteau

summary: Fanconi anemia (FA) is the most frequent inherited cause of bone marrow failure (BMF). Most FA patients experience hematopoietic stem cell attrition and cytopenia during childhood, which along with intrinsic chromosomal instability, favor clonal evolution and the frequent emergence of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) in their teens or young adulthood. In the present study, we have developed a joint molecular and cellular approach to get further insights into the mechanisms that set this "pre-leukemic" state up. For this purpose, we developed a mouse model of MDM4 overexpression by introducing a wide genomic region surrounding the gene that includes its proximal regulatory sequences. Finally, we evaluated the consequences of alteration of the FA pathway in HSPCs in KO or in KOTg mice at steady state and under Poly-IC (pIC) stress.

overall_design: LSK cells from Fancg KO mice  treated with Poly (IC) or VEHICLE were sorted, subsequently lysed, total RNA extracted and RNA-sequencing libraries were prepared using CATS RNA-seq Kit v2  mRNA  Sample Prep Kit. Sequencing librarie were sequenced on Illumina Nextseq 500 sequencer.

first: Samuel

last: Quentin

first: Jean

last: Soulier


title: SIRT3 regulation of hematopoietic stem cell aging [Cut & Tag]

overall_design: Cleavage Under Targets and Tagmentation sequencing (Cut&Tag-sequencing) of HSCs isolated from 2-year-old Mx1-T3 and Mx1-Cre control mice using an antibody against H3K18la


title: SGLT2 inhibitor ameliorates podocyte hypertrophic stress and progression by suppressing the mTOR/p70S6K/cyclin D1 signaling pathway in a model of obesity-related nephropathy

city: Yufu City

first: Miho

last: Suzuki

address: 1-1 Idaigaoka, Hasama-Machi

department: Department of Endocrinology, Metabolism, Rheumatology and Nephrology, Faculty of Medicine

country: Japan

institute: Oita university

summary: Obesity-related nephropathy (ORN) has been a risk factor for chronic kidney disease, end-stage of kidney disease and increased mortality. However, the underlying mechanism and treatment remain unclear. In this study, using Zucker fatty (ZF) rats with non-diabetic obesity model, we revealed that podocyte hypertrophic stress through the activation of the mammalian target of rapamycin (mTOR)/ 70 kDa ribosomal protein S6 kinase (p70S6K)/cyclin D1 signaling pathway leads to the development of ORN, which is suppressed by sodium-glucose co-transporter 2 inhibitor (SGLT2i). Compared with Zucker lean (ZL) rats as control, ZF rats showed marked increases in body weight, urinary protein, urinary sediment podocin (U-sed pod) mRNA excretion, glomerular and podocyte hypertrophy with increasing weeks of age, suggesting that podocyte hypertrophic stress is related to the development of nephropathy. In addition, ZF rats treated with SGLT2i showed decreased body weight, urinary protein, U-sed pod mRNA excretion, glomerular and podocyte hypertrophy, leading to reduced progression of nephropathy. RNA sequencing was performed for the renal cortex and a significant increase in expression of cyclin D1, which is involved in the cell cycle and has a crucial role for cell hypertrophy and proliferation, was observed in ZF rats. Furthermore, increased insulin-like growth factor-1(IGF-1) expression in the renal cortex and increased phosphor S6 expression in podocytes by immunofluorescence staining were also observed, suggesting that the activation of the mTOR/p70S6K/cyclin D1 signaling pathway by obesity-induced IGF-1 elevation may be related to the development of nephropathy. And these changes were suppressed by SGLT2i treatment. Restriction of calories equivalent to those lost by SGLT2i administration did not show as much podocyte protective effect as observed by SGLT2i administration. These findings suggest that SGLT2i may have a podocyte protective effect beyond calorie restriction. Therefore, SGLT2i may represent a new strategy for the treatment of ORN by inhibiting the mTOR/p70S6K/cyclin D1 signaling pathway.

overall_design: To investigate the mechanism of obesity-related nephropathy progression, we used male leptin-deficient Zucker fatty rats as an obesity model and Zucker lean rats as the control model. Total RNA was isolated from the renal cortex in Zucker Lean rats, Zucker Fatty rats and SGLT2 inhibitor-treated Zucker Fatty rats.

first: Akihiro

last: Fukuda

first: Ryo

last: Kurimoto

first: Hirotaka

last: Shibata


title: Microwave therapy for the treatment of cutaneous melanoma metastases

city: Southampton

first: Andres

middle: Felipe

last: Vallejo Pulido

address: University of Southampton

department: Medicine

institute: University of Southampton

summary: The management of recurrent skin melanoma is often challenging due to acquired or primary resistance to immunotherapy; for many patients additionally, surgical excision of recurrence is unsuitable. This study evaluated a potential efficacy of microwave treatment for cutaneous melanoma metastases by comparing pre- and post-treatment changes over three weeks. RNA sequencing of tissue with HTG EdgeSeq system’s Precision Immuno-Oncology Panel (PIP) was undertaken from all samples. All treated metastases reduced in size following microwave therapy. Twenty five percent of participants showed an improvement in Dermatology Life Quality Index scores. RNA sequencing data revealed downregulated cancer-related markers in complete responders compared to partial responders. These findings provide evidence supporting the efficacy of microwave ablation for the treatment of advanced cutaneous melanoma.

overall_design: Twelve adult patients with skin metastases from malignant cutaneous melanoma, not resolving on standard of care treatment were recruited. Microwave energy was applied using the Swift S800 Microwave Device programmed to deliver 50 J or 15±5 J. Size, morphological and histological changes, VAS pain scores and DLQI scores were assessed. Tissue RNA sequencing was utilized to examine the transcriptomic changes.

first: Purevsuren

last: Losol


title: Pharmacodynamic evaluation of MgIG in animal models of acute and chronic alcoholic fatty liver

city: guangzhou

first: Lu

last: Xiao

state: Please Select

address: No. 601 Huangpu Avenue West

institute: The First Affiliated Hospital of Jinan University

summary: Objective: To assess gene expression differences in liver tissues of National Institute on Alcohol Abuse and Alcoholism (NIAAA) mouse models induced by alcohol-containing liquid diets, with or without magnesium isoglycyrrhizinate (MgIG) treatment.Methods: The NIAAA mouse model was established through dietary intervention and divided into three groups: control + saline (n=3), NIAAA + saline (n=3), and NIAAA + MgIG (n=3). After 16 days of modeling, mice were sacrificed, and liver tissues were collected for RNA sequencing analysis. Comparative analysis of gene expression among the three groups was conducted to identify potential therapeutic targets of MgIG.Results: The findings suggest that genes such as Idi1, Acot2, Gstm1, and Ugt1a5 may play a role in mediating the protective effects of MgIG in the NIAAA model.

overall_design: Using RNA-seq analysis to evaluate gene expression differences in liver tissues of NIAAA models induced by alcohol-containing liquid diets, with or without magnesium isoglycyrrhizinate (MgIG) treatment.

first: Jia


title: Pioneer transcription factor TAL1 reshapes chromatin architecture to direct erythroid cell fate commitment [ATAC-Seq]

city: zhengzhou

first: Hengchao

last: Zhang

state: Henan

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

institute: zzu

summary: Pioneer transcription factors critically regulate chromatin organization and hematopoietic cell lineage commitment. During erythropoiesis, hematopoietic stem cells undergo dynamic transcriptional and chromatin remodeling to differentiate into erythrocytes. Functionally validated pioneer factors capable of orchestrating erythropoiesis through dynamic chromatin remodeling remain limited, leaving their regulatory mechanisms incompletely resolved. Here, we identify T-cell acute lymphocytic leukemia 1(TAL1) as a pioneer factor that remodels chromatin to drive transcriptional reprogramming during erythropoiesis. By recruiting SWI/SNF complex, TAL1 drives erythroid fate specification while suppressing alternative lineages through lineage-restricted chromatin compartment reorganization. As a pioneer factor, TAL1 recruits chromatin remodelers BPTF and KMT2A to establish erythroid-specific genomic architecture. These complexes collectively execute TAL1 directed differentiation programs by transcriptionally activating erythroid regulators while repressing non-erythroid determinants. Our work establishes a generalizable chromatin accessibility-directed pioneer factor screening strategy, we identify TAL1 as a master pioneer factor and resolve its mechanism in driving erythroid commitment through 3D epigenome restructuring.

overall_design: Primary human CD34+ cells from cord blood were isolated from mononuclear cells (MNC) obtained by human peripheral blood lymphocyte isolation fluid and followed by positive selection using CD34+ magnetic selective beads system (Miltenyi Biotechnology, Germany) according to the manufacturer’s protocol. Then we explored the the roles of TAL1 during early stage of erythropoiesis using an in vitro 3 phases erythroid-inducing cell culture system employing CD34+ cells from core blood. Cells were transfected with lentivirus containing shTAL1 at day 2, compared with the scramble control. Next,we performed a TAL1 and BRG1 CUT&Tag sequencing at day 7.

first: Lixiang

last: Chen

first: Ying

last: Cheng

first: Lei

last: Sun

first: Xiuyun

last: Wu


title: SIRT3 regulation of hematopoietic stem cell aging [RNA-Seq]

first: DANICA

last: CHEN

summary: SIRT3 is a mitochondrial NAD+-dependent deacetylase. To investigate the role of SIRT3 in hematopoietic stem cell aging, we generated and characterized mouse models overexpressing SIRT3.

overall_design: RNA-sequencing analysis of HSCs from control and SIRT3 overexpressing mice

first: Wei-Chieh

last: Mu

first: Danica


title: Pioneer transcription factor TAL1 reshapes chromatin architecture to direct erythroid cell fate commitment

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: CXCR4 influences PUFA desaturation and oxidative stress injury in experimental prostatitis mice by activating Fads2 via PPARγ

city: Hefei

first: Yi

address: Jixi Road 218, Shushan District, Hefei City 230022, Anhui Province, People’s Republic of China.

institute: the First Affiliated Hospital of Anhui Medical University

summary: The aim of this study was to further understand the changes in mRNA expression in the prostate tissue of EAP mice after using LIT-927. After constructing the EAP mouse model, the experimental group received intraperitoneal injection of LIT927, while the control group received an equal amount of the solvent methyl-β-cyclodextrin. After continuous injections for 14 days, mRNA expression in the mouse prostate was sequenced and analyzed. Using RNA-Seq technology, a large number of differentially expressed genes were identified at the whole-genome level. Our study indicates that compared to the control group, under the action of LIT927, CXCR4 can affect unsaturated fatty acid metabolism to alleviate oxidative stress damage in prostate tissue.

overall_design: After dividing the mice used to establish the EAP model into two groups, the experimental group received intraperitoneal injections of LIT-927 (25 mg/kg/d/mouse), while the control group received an equal amount of methyl-β-cyclodextrin as the solvent. After continuous intraperitoneal injections for 14 days, the mice were sacrificed to collect prostate tissues for RNA-Seq analysis of mRNA expression levels.

first: Rui

last: Feng

first: Haolin

last: Li

first: Weikang

first: Wenming

last: Ma

first: Xianguo

first: Jing

first: Chaozhao

last: Liang


title: Temporal transcriptome analysis of transplanted human cells and chicken neighboring cells

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: To analyze gene expression dynamics of human NECs after transplantation, we isolated these cells and the surrounding chicken cells at 3, 6, 9, 12, 15 and 17 days post transplantation and investigated their gene expression using RNA-seq.

sample_organism:
Gallus gallus
Homo sapiens

platform_organism:
Gallus gallus
Homo sapiens

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Day3, Day6, Day9, Day12, Day15 and Day17 in transplanted human cells and surrounding chicken cells.

first: Yeganeh

last: Meghdad

first: Guenther

last: Stefan


title: Spatiotemporal Single-Cell Profiling Reveals T Cell Clonal Dynamics and Phenotypic Plasticity in Human Graft-versus-Host Disease

city: New York

first: Lingting

last: Shi

address: 500 West 120th Street ET351

institute: Columbia University

summary: Allogeneic hematopoietic cell transplantation (alloHCT) cures hematologic disease but is limited by acute graft‑versus‑host disease (GVHD). How human T‑cell clones evolve across blood and gut to injure epithelium remains unclear. We prospectively fingerprinted T cell clones pre‑transplant and tracked them longitudinally in 20 recipients, integrating TCR repertoire profiling with scRNA/TCR‑seq and high‑resolution spatial transcriptomics (Visium HD). We developed DecompTCR to resolve temporal expansion programs in blood and adapted computational tools to map clonotype phenotypes and niches in gut tissue. Severe GVHD was marked by persistent expansion and diversification of alloreactive clones and by shared CD8⁺ clonotypes that acquired Hobit (ZNF683)⁺ tissue‑resident memory (TRM) programs migrating from lamina propria to epithelium. Spatial deconvolution identified CD8⁺ effector/Hobit+ TRM hubs that localized near intestinal stem‑cell (ISC)–rich crypt bases and concentrated in crypt‑loss regions. Post‑transplant cyclophosphamide selectively depletes alloreactive clones, whereas incomplete depletion and early expansion are associated with severe disease. This clonotype‑resolved framework links tissue‑instructed TRM remodeling to ISC‑proximal cytotoxic hubs, nominating early repertoire scores and spatial hub burden as biomarker candidates.

overall_design: A multimodal, longitudinal study integrating pre-transplant MLR-based alloreactive T cell fingerprinting, time-series bulk TCR sequencing in peripheral blood, and single-cell RNA/TCR-seq and high-resolution spatial transcriptomics of gut biopsies to resolve the clonal, phenotypic, and spatial dynamics of T cells in human GVHD from patients following allogeneic hematopoietic cell transplantation (alloHCT).

first: Ajna

last: Uzuni

first: Ximi K.

last: Wang

first: Michael

last: Pressler

first: David W.

last: Harle

first: Shami

last: Chakrabarti

first: Rodney

last: Macedo

first: Kirubel

last: Belay

first: Christian A.

last: Gordillo

first: Thomas

last: McMahon-Skates

first: Erik

last: Raps

first: Jia Yi (Ady)

first: Achille

last: Nazaret

first: Joy L.

last: Fan

first: Yinuo

last: Jin

first: Xumin

last: Shen

first: Joshua S.

last: Fuller

first: Tamjeed

last: Azad

first: Jessie

last: Huang

first: Pranik

last: Chainani

first: Jose

last: Pomarino Nima

first: Julian A.

last: Abrams

first: Armando

last: Del Portillo

first: Markus Y.

last: Mapara

first: Mohamed

last: Alhamar

first: Megan

last: Sykes

first: José L.

last: McFaline-Figueroa

first: Elham

last: Azizi

first: Ran

last: Reshef


title: Pioneer transcription factor TAL1 reshapes chromatin architecture to direct erythroid cell fate commitment [RNAseq]

first: Hengchao

last: Zhang

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

overall_design: Primary human CD34+ cells from cord blood were isolated from mononuclear cells (MNC) obtained by human peripheral blood lymphocyte isolation fluid and followed by positive selection using CD34+ magnetic selective beads system (Miltenyi Biotechnology, Germany) according to the manufacturer’s protocol. Then we explored the the roles of TAL1 during early stage of erythropoiesis using an in vitro 3 phases erythroid-inducing cell culture system employing CD34+ cells from core blood. Cells were transfected with lentivirus containing shTAL1 at day 2, compared with the scramble control. BZ1 was purchased from MCE and adding in cell culture at a final concentration of 1μM, WDR5-0103 was purchased from MCE and adding in cell culture at a final concentration of 0.1μM at day 2. Experiment procedure before sequencing: 2 million cells(shLuciferase and shTAL1 erythroblasts, BZ1 and WDR5-0103 treated erythroblasts) were collected and washed twice with PBS. RNA was extracted and used as cDNA input, cDNA library was prepared by Illumina Truseq DNA library kit, and sequenced on Illumina NovaSeq 6000.

first: Lixiang

last: Chen

first: Ying

last: Cheng

first: Lei

last: Sun

first: Xiuyun

last: Wu


title: Transcriptome analysis of NECs derived from different hPSCs with different protocols

first: Stefan

last: Günther

summary:
To obtain neuroepithelial cells (NECs) for transplantation, we differentiated human embryonic stem cells (hESCs) using a 3-day or 12-day protocol and also human induced pluripotent stem cells (hiPSCs) using a 3-day protocol.
Then, using RNA-seq, we studied the dynamics of gene expression in each differentiation and compared them with each other.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NEC_3d_hESC and NEC_12d_hESC vs hESC and NEC_3d_hiPSC vs hiPSC

first: Yeganeh

last: Meghdad

first: Guenther

last: Stefan


title: Spatial transcriptomic analysis of tumor heterogeneity in HPV+ and HPV- Head and Neck Squamous Cell Carcinoma

city: St Louis

first: Thomas

middle: F

last: Barrett

state: MO

address: 660 Euclid Ave

department: Otolaryngology

institute: Washington University

summary: Head and neck squamous cell carcinoma is the 6th most common malignancy worldwide. We performed spatial transcriptomics to profile intra- and inter-tumor heterogeneity. We identified recurring patterns of spatial gene expression that co-localize in subsets of tumors.

overall_design:
Human tumor samples were collected from patients undergoing surgery for head and neck squamous cell carcinoma. Samples were frozen in OCT, sectioned to 10 microns, and processed according to the 10X Visium Spatial Gene Expression protocol.
Human tumor samples were collected from patients undergoing surgery for head and neck squamous cell carcinoma. Samples were were dissociated using the Miltenyi Human Tumor Dissociation Kit, cleaned with ACK RBC lysis, and sorted with CD45+ beads. Cells were loaded onto the 10X chip with a ratio of 70% CD45- and 30% CD45+ cells. cDNA libraries were prepared according to the 10X Chromium Next GEM Single Cell 3' Reagent Kits v3.1 protocol.
Human tumor FFPE samples from patients who underwent surgery for head and neck squamous cell carcinoma were reviewed for tumor purity. Samples with DV200 values >30% were cut to 5 micron sections on slides according to the 10X Demonstrated Protocol. Regions of interest were placed in the tissue slide cassette, probe hybridization and ligation were performed and then slides were loaded onto the CytAssist instrument, per protocol. Samples were aligned to grch38 reference genome and 16 micron bin sizes were used for each sample.

first: Dor

last: Simkin

first: Itay

last: Tirosh

first: Sid

last: Puram


title: Human pluripotent stem cell-derived neuroepithelial cells develop into an organizer for optic tectum formation in the chicken telencephalon

overall_design: Refer to individual Series


title: Transcriptome analysis of iTeO, TeO and NCC

summary: To investigate the identity of the ectopic structure induced by transplantation of hPSC-derived NECs into chicken telencephalon, we performed RNA-sequencing on this ectopic structure (iTeO_ES and iTeO_iPS), natural optic tectum (TeO) and normal chicken cerebral cortex (NCC).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for iTeO, TeO and NCC.


title: From enrichment to inference: a multi-target framework for scalable aptamer discovery

status: Public on Jun 23 2026

first: Han

last: Guo

state: Zhejiang

address: Xiasha

department: Aptamer Selection Center

institute: Hangzhou Institute of Medicine, Chinese Academy of Sciences

summary: SELEX has greatly advanced aptamer discovery; however, traditional workflows face considerable challenges in scaling due to the labor-intensive screening and validation processes. More critically, in conventional SELEX, sequencing abundance does not always correlate directly with binding properties due to amplification bias, matrix adsorption, and initial copy-number advantages. We establish an automated framework that converts enrichment readouts into affinity- and specificity-informed candidate prioritization. The framework integrates two key innovations: a distribution-reset secondary screening and a relative abundance ratio for candidate selection. Furthermore, the 96-target workflow generates a systematically organized sequence-target dataset that can be utilized as a valuable resource for analyzing SELEX mechanisms and facilitating AI-assisted ap-tamer discovery. Here, we release the sequencing data of the enriched libraries. Within each sequence-protein matrix, the dataset integrates raw read counts,  relative abundance ratios, sequence ranks, and target identities into a unified format. This structure preserves both successful and unsuccessful screening results, which are crucial for com-prehending target screenability and distinguishing genuine target-specific enrichment from general back-ground retention.

overall_design: Sequencing data were obtained from high-throughput automated SELEX for aptamer screening against 96 protein targets. Four random ssDNA libraries (lib10, lib13, lib18, lib25) were each applied to 24 targets. After 5 rounds of preliminary screening, the Round 5 library was sequenced. The top 3000 enriched sequences served as the starting material for 2 rounds of secondary screening. The Round 2 library of the secondary selection was then sequenced.

first: Shaokang

last: Lv

first: Zhaofeng

last: Luo


title: Cellular and immunometabolic mechanisms of inflammation in depression: Preliminary findings from single cell RNA sequencing

city: Atlanta

first: Mandakh

last: Bekhbat

state: GA

address: 1365 Clifton Rd NE, Room 5204

department: Psychiatry and Behavioral Sciences

institute: Emory University

summary: Inﬂammation is associated with symptoms of anhedonia, a core feature of major depression (MD). We have shown that MD patients with high inﬂammation as measured by plasma C-reactive protein (CRP) and anhedonia display gene signatures of metabolic reprograming (e.g., shift to glycolysis) necessary to sustain cellular immune activation. To gain preliminary insight into the immune cell subsets and transcriptomic signatures that underlie increased inﬂammation and its relationship with behavior in MD at the single-cell (sc) level, herein we conducted scRNA-Seq on peripheral blood mononuclear cells from a subset of medically-stable, unmedicated MD out-patients. Three MD patients with high CRP (>3 mg/L) before and two weeks after anti-inﬂammatory challenge with the tumor necrosis factor antagonist inﬂiximab and three patients with low CRP (≤3 mg/L) were studied. Cell clusters were identiﬁed using a Single Cell Wizard pipeline, followed by pathway analysis. CD14+ and CD16+ monocytes were more abundant in MD patients with high CRP and were reduced by 29% and 55% respectively after inﬂiximab treatment. Within CD14+ and CD16+ monocytes, genes upregulated in high CRP patients were enriched for inﬂammatory (phagocytosis, complement, leukocyte migration) and immunometa-bolic (hypoxia-inducible factor [HIF]-1, aerobic glycolysis) pathways. Shifts in CD4+ T cell subsets included ~30% and ~10% lower abundance of CD4+ central memory (TCM) and naïve cells and ~50% increase in effector memory-like (TEM-like) cells in high versus low CRP patients. TCM cells of high CRP patients displayed down-regulation of the oxidative phosphorylation (OXPHOS) pathway, a main energy source in this cell type. Following inﬂiximab, changes in the number of CD14+ monocytes and CD4+ TEM-like cells predicted improve-ments in anhedonia scores (r = 1.0, p < 0.001). In sum, monocytes and CD4+ T cells from MD patients with increased inﬂammation exhibited immunometabolic reprograming in association with symptoms of anhedonia. These ﬁndings are the ﬁrst step toward determining the cellular and molecular immune pathways associated with inﬂammatory phenotypes in MD, which may lead to novel immunomodulatory treatments of psychiatric illnesses with increased inﬂammation.

overall_design: Samples were analyzed from six patients with major depression. All patients were female and non-Hispanic African Americans to limit demographic differences. Patients were stratified into high plasma C-reactive protein [CRP] (>3 mg/L; n = 3) and low plasma CRP (≤3 mg/L; n = 3) groups. Samples from patients with high CRP were obtained both before and 2 weeks after a single infusion of infliximab (5 mg/kg) for a total of 9 samples.  Fasting whole blood samples were collected between 8 and 10 a.m. after 30 min of rest (to avoid circadian influences and effects of stress) in chilled EDTA tubes. Peripheral blood mononuclear cells (PBMCs) were isolated from EDTA whole blood on Histopaque-1077. After washing, cells were counted, and 3-5 million cells were resuspended in sterile freezing media (90% FBS and 10% DMSO). Cells were slowly frozen in an isopropanol-containing cryopreservation vessel at -80C for 24 h then stored in liquid nitrogen.  Upon thawing for sequencing, cells were washed and resuspended in PBS+ 0.04%BSA. The quantity and quality of the cells were accessed by Acridine Orange and Propidium iodide dye on a Cellometer Auto 2000 (Nexcelom). Dead cell removal was performed per manufacturer’s recommendation using Miltenyi Biotec Dead Cell Removal (Miltenyi Biotec, Bergisch Gladbach, Germany). 7000 cells with the viability higher than 70% were loaded on a 10x Chromium Controller using 10X Genomics 3’ GEX v3.1 Platform (10x Genomics). After cell partitioning and GEM generation, reverse transcription was performed, and cDNA was pooled and cleaned up by beads. cDNA was further amplified for 13 cycles and cleaned up by SPRI beads (Beckman). Final library was constructed using 10X Genomics 3’ GEX v3.1 (10x Genomics) based on manufacturer’s manual. The quality of FL was assessed by High Sensitivity D5000 Tapestation (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 DNA HS assay (ThermoFisher, Massachusetts, USA). The average final library size is 400bp with an insert size of about 250bp. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® Hiseq X (Illumina, California, USA) with a read length configuration of 150 PE targeting for 100M total reads per sample (50M in each direction).

first: Gulay

middle: B

last: Bengü

first: Manoj

middle: K

last: Bhasin

first: Jennifer

middle: C

last: Felger

first: Andrew

middle: H

last: Miller


title: Loss of YY1 in Purkinje Cells Triggers Cerebellar Ataxia via Wnt10b-Mediated Impairment of Dendrite Development

city: Hong Kong

first: Kin Ming

last: Kwan

address: Room EG03, Science Center East Block, The Chinese University of Hong Kong

department: School of Life Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: The cerebellum relies on Purkinje cells (PCs) to coordinate motor functions and maintain neural circuitry. Impaired PC dendritogenesis is linked to neurological disorders, yet intrinsic molecular mechanisms remain unclear. We demonstrate that postnatal deletion of Yin Yang 1 (Yy1) in PCs disrupts dendrite and spine formation, impairs synaptic plasticity, and alters Protein kinase C gamma (PKCγ) expression, leading to cerebellar ataxia and progressive atrophy. Mechanistically, YY1 transcriptionally activates wingless-type MMTV integration site family, member 10B (Wnt10b), which signals through Frizzled-4 (Fzd4) in PCs. Wnt10b downregulation mimics the dendritic defects seen in Yy1 mutants, indicating its crucial role in dendrite growth and synaptic environment regulation. These changes result in defective synapse innervation. Our findings reveal that YY1 governs PC dendritogenesis and synaptogenesis via Wnt10b, while also modulating PKCγ and β-catenin signaling. The YY1-Wnt10b axis emerges as a critical pathway underlying YY1-associated cerebellar dysfunction.

overall_design: Bulk RNA-seq profilling of cerebella from Postnatal day 14 Pcp2 Cre/+; Yy1 fx/fx (Yy1 cKO, n=3)  and littermate Pcp2 Cre/+; Yy1 fx/+ (Controls, n=2) (mixed sex). Paired-end 150 bp sequencing.

first: Ying Lam

last: Lui

first: Xiaonan

last: Dong

first: Tsz Ho

last: Li

first: Ting Fung

last: Chan


title: Transcriptomics of hypothalamic core areas suprachiasmatic nucleus and paraventricular nucleus of the short photoperiod adapted Djungarian Hamster during spontaneous daily torpor entry and normothermia using a de novo assembly of transcriptomes

city: Ulm

first: Annika

last: Herwig

address: Albert-Einstein-Allee 11

department: Institute of Neurobiology

institute: Ulm University

summary: Transcriptome analyses were performed to further disentangle hypothalamic control of spontaneous daily torpor and seasonal adaptation, concentrating on the most extreme metabolic and seasonal states of the Djungarian hamster (Phodopus sungorus). The data must be interpreted with respect to the metabolic and seasonal context, as described in the manuscript of the original research.

overall_design: comparison between torpor entry and normothermia for SCN as well as PVN samples

first: Elena

last: Haugg


title: Transcriptomics of hypothalamic core areas suprachiasmatic nucleus and paraventricular nucleus during spontanous daily torpor arousal in the Djungarian hamster (Phodopus sungorus).

summary: Transcriptome analyses were performed to further disentangle hypothalamic control of spontaneous daily torpor in the Djungarian Hamster (Phodopus sungorus) acclimated to winter-like short photoperiod (SP). Samples of hypothalamic core areas suprachiasmatic nucleus (SCN) and paraventricular nucleus (PVN) were taken about seven hours after lights on (ZT07). After a de novo assembly of transcriptomes and a mapping against RefSeq of the house mouse (Mus musculus), data from hamsters sampled with hypothermic (HT) core body temperature during torpor arousal on a torpor-day (TD) were compared with data from hamsters sampled with normothermic (NT) core body temperature on a torpor-free day (TFD). The data must be interpreted with respect to the metabolic and seasonal context, as described in the manuscript of the original research.

overall_design: For each SCN an PVN, data were compared between TD and TFD. For the de novo assembly and in the manuscript, not only samples gained about seven hours after lights on (ZT07) were used, but also samples gained about one hour after lights on (ZT01) during torpor entry (TD) and on a torpor-free day. Latter are accessible through GEO Series accession number GSE181298  (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?&acc=GSE181298).


title: Zanidatamab in Patients with Early Stage HER2-positive Breast Cancer: The NeoZanHER Phase 2 Single-Arm Open-Label Trial

city: Houston

first: Xiaofeng

last: Zheng

state: TX

address: 7007 Bertner Ave

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

summary: Strategies are needed to avoid chemotherapy in early stage HER2-positive (HER2+) breast cancer (BC). We conducted a neoadjuvant therapy trial with zanidatamab, a dual HER2-directed bispecific antibody, in patients with 1-3 cm, node-negative HER2+ BC. Primary endpoint was pathologic complete response (pCR). Secondary endpoints were radiographic response by ultrasound and magnetic resonance imaging. US and MRI, pathologic response by residual cancer burden (RCB), rate of adverse events, feasibility of accrual and biomarkers of response. Fifteen patients with HER2 IHC 3+, and 5 with HER2 IHC 2+/ISH+ BC were enrolled. Patients received zanidatamab 20 mg/kg every 2 weeks for 6 (n=11) or 10 doses (n=9). Fourteen patients also received endocrine therapy. At 6 weeks, there was a significant decrease in tumor size and volume. At surgery, six patients (30%) had pCR, meeting the prespecified pCR target, and four had limited RCB (RCB-1; 20%). Treatment was well tolerated. All patients with pCR had HER2 IHC 3+ tumors, ERBB2 amplification on WES, PAM50 HER2-high subtype, and a trend towards higher HER2 mRNA expression (p=0.06). In conclusion, de-escalation to HER2-targeted therapy alone may be feasible. Further research is needed to refine patient selection.

overall_design:
The gene expression profiles of fresh-frozen tumor samples of primary HER2-positive breast cancer patients were analyzed by bulk RNA sequencing.
Submitters state "Given the small study size, we would like to make clinical data only available through request from  PI".


title: 16S rRNA Datasets of Gut Microbiota in Stent-Based Diverting Technique and Ileostomy from A Prospective, Open-Label, Multicenter Randomized Controlled Trial

city: Hangzhou

first: Zhongyu

last: Wu

state: Zhejiang Province

address: 3 East Qingchun Road

department: Sir RunRun Shaw Hospital,School of Medicine

institute: Zhejiang University

summary: This study performed gut microbiota 16s rDNA sequencing on patients receiving stent-based diversion technique (SDT) and temporary ileostomy surgery, with fecal samples collected at preoperative baseline and postoperative follow-up time points. This study aims to characterize perioperative gut microbial signatures, assess alterations in microbial alpha/beta diversity and differential taxa abundance, identify core microbial biomarkers affected by fecal diversion and surgical intervention, and map dynamic gut flora variation induced by SDT and ileostomy. Both ileostomy and minimally invasive SDT alter intestinal luminal conditions and fecal flow, thereby disrupting intestinal microecology and increasing risks of postoperative inflammation, stoma complications and gastrointestinal disorders; however, few studies have illustrated their effects on perioperative gut microbiota. This dataset fills the relevant microecological research gap, helps reveal microbial mechanisms of postoperative gastrointestinal complications, and provides evidence for targeted perioperative microecological intervention to optimize intestinal rehabilitation and reduce stoma-related adverse outcomes in this patient cohort.

overall_design:
eighty patients with rectal cancer were randomized to the SDT group (n=37) and the ileostomy group (n=43). Two patients initially assigned to the SDT group were converted to ileostomy, and 35 patients in the SDT group and 45 patients in the ileostomy (ILE) group was included in the as-treated analysis. A total of 113 fecal samples were collected, comprising 77 preoperative and 33 postoperative specimens. In the present study, fecal samples (prior to surgery and postoperative 90-day) were collected from patients in this trial, via sterile cotton swabs, with sampling performed at the deep rectal site. Following quality control, unqualified samples were excluded (n=3), leaving 34 preoperative and 11 postoperative samples from the SDT group, and 43 preoperative and 22 postoperative samples from the ILE group for subsequent analyses.Eligible patients were assigned to receive either ileostomy or SDT procedures following low anterior resection[9]. After low anterior resection, patients were randomly allocated to two groups (SDT group and ileostomy group) using a computer-generated random number sequence for randomization. SDT Group: (1) A median incision was made in the lower abdomen to expose the segment of small intestine located 20 cm from the ileocecal junction. (2) A longitudinal incision was created on the mesenteric margin of this intestinal segment; a degradable stent was implanted, and the intestine was sutured closed. The stent was secured in place with an external tie around the bowel. (3) A 28 Fr mushroom-shaped tube was inserted into the intestinal segment 5-10 cm proximal to the implanted stent. (4) After closing the intestinal incision, this segment was fixed to the abdominal wall using absorbable sutures. The other end of the mushroom-shaped tube was passed through the right lower abdominal wall and connected to a drainage bag. (5) Before closing the abdominal cavity and the lower abdominal incision, an abdominal drainage tube or anal tube was placed at the appropriate site if clinically necessary. (6) Abdominal X-rays were performed weekly to monitor stent degradation. After 3-4 weeks, the 28 Fr mushroom-shaped tube was removed 2 days after complete stent degradation. Ileostomy Group: (1) A 2 cm-diameter incision was made in the right lower abdomen, and the tissue layers were dissected sequentially to access the abdominal cavity. (2) Under laparoscopic visualization, the segment of small intestine 20 cm from the ileocecal junction was exteriorized out of the abdominal cavity. (3) The anterior sheath of the rectus abdominis and the serous layer of the exteriorized intestine were sutured together using absorbable sutures. (4) The mesenteric margin of the intestine was transected at its midpoint, and the intestinal segment was fixed to the skin surface. (5) Laparoscopic inspection was performed to confirm the absence of intestinal volvulus or angulation.16S rRNA genes of distinct regions (16SV3-V4) were amplified used specific primer with the barcode. All PCR reactions were carried out with 15 µL of Phusion® High-Fidelity PCR Master Mix (New England Biolabs); 0.2µM of forward and reverse primers, and about 10 ng template DNA. Thermal cycling consisted of initial denaturation at 98℃ for 1 min, followed by 30 cycles of denaturation at 98℃ for 10s, annealing at 50℃ for 30 s, and elongation at 72℃ for 30s and 72℃ for 5 min. The PCR products were purified using magnetic bead purification. Samples were mixed in equidensity ratios based on the concentration of PCR products. After thorough mixing, the PCR products were detected and target bands were recovered. Sequencing libraries were generated and indexes were added. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required.

[UPDATE] The following files have been added on Aug 17, 2026:
sample_codebook.xlsx
Supplementary_File.1_Supplementary_data.xls


title: Ythdf3 Knockdown Protects Against Hypoxic-Ischemic Cortical Neuron Injury by Wwtr1

city: nantong

first: Xia

last: Jin

address: No. 399, Shiji Avenue, Chongchuan District, Nantong, Jiangsu, China

institute: Affiliated Maternity and Child Health Care Hospital of Nantong University

summary: To identify potential target genes regulated by ythdf3 knockdown protects against hypoxic-ischemic cortical neuron injury, we performed RNA-sequencing (RNA-seq) analysis on  Ythdf3-knockdown cells

overall_design: RNA-seq profiling of negative control and Ythdf3-knockdown cells derived from sicontrol or siYthdf3.


title: In Vivo CRISPR Screens Identify SLC1A5 as a Metabolic Checkpoint for Cancer Immunotherapy [ATAC]

city: Wuhan

first: Wenlong

last: Jia

address: 1095 Jiefang Avenue

institute: Tongji Hospital

summary: Tumor cells often evade immune pressure via metabolic reprogramming, yet the key metabolic regulators orchestrating this process remain poorly defined. Here, using in vivo metabolic CRISPR screening under distinct immune pressures, we identified tumor cell–derived solute carrier family 1 member 5 (SLC1A5) as a critical metabolic node that sustains an immunosuppressive tumor microenvironment (TME). SLC1A5-mediated glutamine metabolism in tumor cells modulates CD8 T cell infiltration and effector function, reshaping tumor response to immune checkpoint blockade therapy. Mechanistically, glucose deprivation up-regulated SLC1A5 isoforms in tumor cells, enhancing glutamine uptake and metabolic flux remodeling to reset intracellular metabolic homeostasis. This program suppressed inflammatory tumor cell differentiation characterized by cyclic GMP-AMP synthase–stimulator of interferon genes (cGAS–STING) pathway activation, reducing interferon-β secretion and impairing CD8 immunity. These findings define a glutamine-fueled metabolic program as a critical barrier to tumor immunogenicity, positioning SLC1A5 as a metabolic immune checkpoint with therapeutic relevance.

overall_design: This bulk ATAC-seq study was designed to determine how glucose availability and caloric restriction regulate chromatin accessibility in tumor cells. Tumor cells were analyzed after culture under plasma-level or tumor-relevant low-glucose conditions and after isolation from tumors collected from wild-type mice maintained on a control diet or subjected to caloric restriction (CR). For the in vivo experiments, GFP-labeled tumor cells were isolated by fluorescence-activated cell sorting before ATAC-seq library preparation. Biological replicates were included for each experimental condition. The data were used to compare genome-wide chromatin accessibility and identify regulatory regions associated with nutrient stress, MYC activity, and SLC1A5 transcription.

first: Guanxing

last: Yu

first: Shenqi

last: Han

first: Zhao

last: Huang

first: Bixiang

last: Zhang


title: Gene Expression of SlanMo migrating on Immune Complexes

city: Heidelberg

first: Micahel

last: Hertwig

institute: Universitätsklinikum Heidelberg

type: Methylation profiling by genome tiling array

summary: Immune complexes (ICs) play a central role in autoimmune diseases, where they accumulate in tissues, activate Fc gamma receptor-expressing cells, and promote chronic inflammation. However, the role of ICs as directional migratory cues for human eukocytes remains poorly defined. Here, we identify pro-inflammatory Slan+ non-classical monocytes (SlanMo), a CD14dim CD16++ monocyte subset, as the onlyblood leukocyte population that migrates directionally toward ICs. Using in vitro transmigration assays, we demonstrate that SlanMo respond to ICs in a concentration-dependent, gradient-dependent, and CD16-mediated manner. Strikingly, SlanMo follow IC gradients with high specificity, enabling their active and directed migration towards high concentrations of ICs. This migration is independent of G protein-coupled receptor signaling, and is, therefore, not dependent on chemokines. Guided by our phosphoproteomic analysis of migrating SlanMo, we identified ROCK, Lyn, crk, FAK, and moesin as relevant signaling proteins. Our transcriptomic profiling of SlanMo after migration on immobilized ICs versus uncoated surfaces revealed enrichment of pathways linked to SLE as well as an upregulation of genes associated with antigen processing, endocytosis, and protein digestion. These findings suggest that ICs can act as directional cues for selective leukocyte recruitment of pro- inflammatory SlanMo which may be of relevance in IC-rich environments such as in SLE.

overall_design: Cells from 4 different donors were analyzed. Slan+ non-classical monocytes (SlanMo) and Classical monocytes (CD14) were isolated from donors and left untreated, treated with immobilized immune complexes (ICs) or treated with LPS. This results in biological replicates or 6 different samples (SlanMo, SlanMo+IC, SlanMo+LPS, CD14, CD14+IC, CD14+LPS).

first: Michael

first: Stephanie

last: Oehrl

first: Thomas

last: Döbel

first: Hao

first: Stefan

last: Meisel

first: Amelie

last: List

first: Knut

last: Schäkel


title: A Phase 1/1b Study of the All-Oral Regimen CC-486 and Venetoclax in Acute Myeloid Leukemia

city: Aurora

first: Austin

middle: E

last: Gillen

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

summary: Venetoclax with azacitidine is the standard of care for newly diagnosed AML patients who are unfit for intensive induction chemotherapy. CC-486 is the oral formulation of azacitidine that is currently approved for post-induction chemotherapy maintenance in AML. In this single center open label, Phase 1/1b study, we investigated CC-486 and venetoclax in relapsed and refractory AML and newly diagnosed patients. In the dose escalation phase, patients received CC-486 at one of two cohorts (200 mg PO days 1-14 and 300 mg PO days 1-14). Venetoclax was given at the 400 mg/day PO regimen, for 28 days, after an initial intra-patient dose escalation per the standard of care. Using a 3+3 study design for these two cohorts, we determined the recommended dose of CC-486 to be 300mg daily on days 1-14.  Most common adverse events included nausea, diarrhea, fatigue and cytopenias. The incidence of grade 3 or greater neutropenia or thrombocytopenia was 97% and 66%, respectively. There were no dose limiting toxicities in either cohort. The expansion phase of the study consisted of 10 additional relapsed and refractory patients and 16 patients with newly diagnosed AML. Responses were seen in all phases of the study, and six patients were successfully bridged to hematopoietic stem cell transplant. Correlative analyses including sequencing and metabolomics performed on patient samples suggested this regimen had a similar effect on leukemia stem cells compared with conventional (intravenous) azacitidine and venetoclax.

overall_design: Bone marrow samples from AML patients treated with venetoclax (28 days) and oral azacitidine (14 days) were collected at baseline (prior to treatment) and after 4 and 28 days of treatment. Mononuclear cells were isolated from these samples and analyzed using single-cell RNA-seq.

first: Maria

middle: L

last: Amaya

first: Craig

middle: T

last: Jordan

first: Daniel

middle: A

last: Pollyea


title: Carotid Body Dysfunction Contributes to Respiratory Dysfunction in Rett Syndrome

city: Storrs

last: Mulkey

state: Connecticut

address: 69 North Eagleville Road

department: Physiology and Neurobiology

institute: University of Connecticut

summary: Rett syndrome (RTT) is a neurodevelopmental disorder caused by mutations in MECP2.  Disordered breathing is a hallmark feature of RTT that negatively impacts quality of life and can be life-threatening. Despite this, mechanisms underlying disordered breathing in RTT are poorly understood. Although RTT is primarily considered a central nervous system disorder, we found that increased drive from peripheral respiratory chemoreceptors may contribute to unstable breathing in MeCP2 deficient mice. Consistent with this, breathing pure oxygen to limit output of peripheral chemoreceptors stabilized breathing in MeCP2 deficient mice. Also, knockdown of MeCP2 within the carotid body recapitulates RTT-like unstable breathing. We also found that MeCP2 deficiency alters the carotid body transcriptome, including disruption of genes involved in dopaminergic signaling; and treatment with a dopamine receptor agonist stabilized breathing in MeCP2 deficient mice. These results identify the peripheral chemoreceptors as high priority therapeutic targets for disordered breathing in RTT.

overall_design: Bulk RNA-sequencing was performed on carotid body bifurcations isolated from male MeCP2 knockout (Mecp2-/y) mice and wild-type littermate controls (Mecp2+/y) at postnatal day 42 (P42)

first: Monica

last: Strain

first: Eliandra

last: da Silva

first: Michelle

last: Olsen


title: In Vivo CRISPR Screens Identify SLC1A5 as a Metabolic Checkpoint for Cancer Immunotherapy [CUT&Tag]

first: Wenlong

last: Jia

overall_design: This bulk CUT&Tag study was designed to determine how glucose availability and MYC expression regulate MYC chromatin occupancy in human hepatocellular carcinoma cells. Cells were cultured under plasma-level high-glucose, tumor-relevant low-glucose, or tumor-relevant low-glucose conditions with MYC overexpression. CUT&Tag was performed using an antibody against MYC. The data were used to compare genome-wide MYC occupancy across conditions and to identify glucose- and MYC-dependent changes in chromatin binding, with particular emphasis on MYC-binding sites within the promoter and transcription start site regions of SLC1A5.

first: Guanxing

last: Yu

first: Shenqi

last: Han

first: Zhao


title: Multi-omics profiling supports the diagnosis of histiocytic sarcoma and mesenchymal mimics

city: Basel

first: Baptiste

last: Ameline

address: Schoenbeinstrasse 40

department: Pathology

country: Switzerland

institute: University hospital basel

summary: The differential diagnosis between histiocytic sarcoma (HS) and undifferentiated pleomorphic sarcoma (UPS) remains an underexplored area of histopathological and oncological relevance. Both entities are rare, high-grade neoplasms that may arise in soft tissue, skin, the nervous system, and the gastrointestinal tract, among other sites, predominantly in adult patients. Their clinical and morphological overlap may be underrecognized, partly due to the subspecialized structure of contemporary surgical pathology practice. Comparative data on their natural history, treatment, and prognosis remain limited. Furthermore, while UPS is managed according to established international guidelines, no standardized treatment approach exists for HS.  In this study, we compared the clinical, histopathological, and genetic features of three patient groups diagnosed with HS, UPS, and dedifferentiated liposarcoma (DLS) – control group. In a “real-life” diagnostic setting, we explore their diagnostic relevance, applying a comprehensive, multi-platform approach, including immunophenotyping, high-throughput sequencing, gene expression profiling, and methylome analysis.  We demonstrated a substantial morphophenotypic overlap among the three neoplasms, while also identifying distinct features within each group. Histiocytic sarcoma samples were enriched for mutations in the MAPK pathway, along with other recurrent mutations characteristic of myeloid neoplasms, and exhibited a functional genetic signature consistent with derivation from mononuclear phagocytes. In contrast, soft tissue sarcomas showed a markedly higher tumor mutational burden and evidence of Hippo pathway activation, as well as FGF/FGFR signaling.  Our work represents an initial step toward establishing a comprehensive diagnostic framework for malignant histiocytosis, facilitating the identification of relevant therapeutic and prognostic factors, and ultimately improving the clinical management of these rare patients.

overall_design: 10 specimens were analyzed using the MethylationEPIC v1.0 and v2.0 BeadChips

first: Alexander

last: Tzankov

last: Baumhoer


title: Assessment of differences in immune responses to albumin compared with crystalloids for resuscitation in sepsis

city: Edinburgh

first: John

last: Cafferkey

address: Queens Medical Research Institute, Little France Campus

institute: University of Edinburgh

summary: Crystalloid fluid is central to the management of sepsis, but 5% human albumin solution may offer advantageous immune and intravascular filling properties. We explored whether the choice of first line fluid for resuscitation in sepsis affects the immunological response.

overall_design: We sampled adult patients presenting to the Emergency Department with suspected sepsis and needed fluid resuscitation who had undergone randomisation to either treatment with balanced crystalloid or 5% human albumin solution for the first 6 hours. We collected blood samples at baseline (T1), 12 hours (T2) and 24 hours (T3) after randomisation. We compared the difference in leucocyte subsets, cytokine expression and the pan-leucocyte transcriptome.

first: Jennifer

last: Rynne

first: Andrew

last: Ferguson

first: Julia

last: Grahamslaw

first: Peter

last: Smith

first: Ewan

last: Pow

first: Katherine

last: Oatey

last: Horner

first: Alasdair

middle: R

last: Corfield

last: Gray

first: Manu

last: Shankar-Hari


title: Tumor-derived exosomal METTL3 reprograms macrophages through the m6A–IGF2BP2–ATG2A axis to promote lung adenocarcinoma stemness and brain metastasis

city: Hohhot

first: jiemin

last: wang

address: State Key Laboratory of Reproductive  Regulation and Breeding of Grassland  Livestock

institute: inner Mongolia university

summary: Lung adenocarcinoma (LUAD) brain metastasis remains a major clinical challenge, yet how tumor-derived exosomes remodel macrophage states to support metastatic colonization is incompletely understood.

overall_design: Here, integrative analyses of publicly available single-cell RNA-seq, spatial transcriptomic, transcriptomic, and proteomic datasets, combined with clinical and experimental validation, identified METTL3 as a stemness-associated N6-methyladenosine (m6A) regulator in LUAD and revealed METTL3 enrichment within macrophage-centered signaling networks and M2-like macrophage niches. Exosomes isolated from METTL3-overexpressing LUAD cells were efficiently transferred to macrophages, promoted M2-like macrophage reprogramming, enhanced tumor stemness, and accelerated LUAD growth and brain metastatic colonization. Macrophage depletion markedly attenuated exosome-driven brain metastatic progression, and ATG2A silencing in reconstituted macrophages suppressed exosome-driven brain metastatic growth. Integrated analysis of macrophage RNA-seq and METTL3-associated MeRIP-seq data, combined with LASSO and random forest feature selection, identified ATG2A as a key exosomal METTL3-regulated target in macrophages. Mechanistically, exosomal METTL3 increased m6A modification of ATG2A transcripts, which facilitated the recognition of ATG2A mRNA by the m6A reader IGF2BP2 and enhanced IGF2BP2-dependent stabilization of ATG2A mRNA, ultimately leading to ATG2A upregulation in macrophages. Exosomal METTL3-induced ATG2A further restrained NF-κB/NLRP3 inflammatory signaling, thereby promoting M2-like macrophage reprogramming. Furthermore, the exosomal METTL3/IGF2BP2-m6A/ATG2A interaction promoted macrophage autophagic flux. Collectively, this study highlights tumor-derived exosomal m6A signaling as a regulator of macrophage homeostasis and identifies exosomal METTL3-driven ATG2A regulation as a potential therapeutic target for limiting LUAD stemness and brain metastasis.

first: Jiemin

last: Wang


title: Involvement of Tumor Suppressor Candidate 3 in Mouse Survival, Craniofacial, and Cortical Development

city: Columbus

first: Rolf

last: Stottmann

state: OHIO

address: 575 Children's Crossroads

department: Pediatrics

institute: Nationwide Children's Hospital

summary: Tumor Suppressor Candidate 3 (TUSC3) is an integral component of the oligosaccharyltransferase complex and is required for the N-glycosylation of proteins. While TUSC3 has been implicated in cancer and autosomal recessive non-syndromic intellectual disability, some patients also exhibit distinct facial features. However, the role of Tusc3 in craniofacial development is unknown. Here, we report a patient presenting with cleft lip and palate who was found to carry a homozygous variant in the TUSC3 promoter region in addition to a maternally inherited chromosomal duplication. In order to evaluate a potential role for TUSC3 in craniofacial development, we analyzed Tusc3 deletion mouse mutants from the International Mouse Phenotyping Consortium (IMPC). Initial IMPC phenotyping data suggested that a subset of Tusc3 deletion mice could develop cleft palate, micrognathia, and aglossia. We further identified that Tusc3 is expressed in the craniofacial and brain regions during embryonic development. Upon characterizing the Tusc3 deletion line, we observed that most homozygous mutants exhibit preweaning lethality. While craniofacial defects occur at a very low frequency in the deletion mutants, we identified a consistent reduction in cortical area. Furthermore, RNA-seq analysis surprisingly revealed that no other genes in the developing brain or face were significantly affected upon loss of Tusc3. These findings suggest that Tusc3 can contribute to congenital malformations in both craniofacial and cortical development.

overall_design: RNA-seq profiling of E14.5 brain and craniofacial tissues from wildtype and Tusc3 homozygous deletion embryos.

first: Paul P

last: Iyyanar

last: Vontell

first: Ammar

last: Husami

first: Ethan

last: Sperry

first: K

last: Weaver

middle: W


title: DMAP1 promotes lung cancer progression by maintaining replication fork stability and suppressing IFN signaling-mediated anti-tumor immunity [CUT&Tag]

city: Shanghai

first: Kan

last: Huang

address: 130, Dongan Road

institute: Fudan University

summary: Despite substantial progress in targeted and immune therapies, lung cancer remains the leading cause of cancer-related mortality, highlighting the urgent need for novel therapeutic strategies. Through a CRISPR-based knock-out screen, we identified the DNA methyltransferase 1-associated protein 1 (DMAP1) as a critical regulator of tumor progression. Functional studies showed that loss of DMAP1 exerts its anti-tumor effects through attenuating tumor cell proliferation and activating T cell-mediated adaptive anti-tumor effects. Mechanistically, loss of DMAP1 causes replication fork retardance, disturbs genome stability, and induces endogenous DNA damage, thereby activating tumor-intrinsic immune signaling and enhancing anti-tumor immune response during cancer cell growth. Clinical data analyses revealed that high DMAP1 expression is associated with reduced immune infiltration, a “cold” tumor microenvironment, and poorer overall survival in lung cancer. These findings significantly advance our knowledge of DMAP1's function in lung cancer development and offer a scientific basis for designing novel treatment approaches.

overall_design: CUT&Tag of HA-tagged Dmap1 in mouse KP lung adenocarcinoma cellline with or without shRNA-induced silencing of Dmap1.

first: Xi

last: Dai

first: Shuaihu

last: Li

first: Yingxue

last: Chen

first: Yaxin

last: Yu

first: Lin

first: Kun

last: Liu

first: Chongyang

first: Yihua

last: Sun

first: Fei


title: CD4⁺ T Cell Dysregulation in Long COVID: Insights from an Unvaccinated Cohort

city: Santiago

first: Adolfo

middle: Alexis

last: Rojas-Hidalgo

address: OLIVOS 1007

country: Chile

institute: Universidad de Chile

summary: Objective: The pathogenesis of Long COVID (LC) remains poorly understood, with the analysis of immune responses often obscured by variables such as vaccination and reinfection. This study aimed to determine the primary immunological footprint of LC by examining a specific cohort that minimizes these confounding factors. Methods: We analyzed a Brazilian cohort of patients recruited between September 2020 and February 2021, during the first wave of the pandemic (Wuhan-Hu-1 variant), comprising mostly unvaccinated individuals. We assessed humoral responses to SARS-CoV-2 and latent viruses in 104 patients. Additionally, we investigated the immune signatures of CD4+ T cells in a subset of 6 LC and 4 recovered control (RC) unvaccinated patients, recruited 1 to 2 months after symptom onset, utilizing a combination of flow cytometry and single-cell RNA sequencing. Results: Systemic humoral responses to SARS-CoV-2 and reactivated latent viruses were comparable between the LC and RC groups, as were the overall distributions of CD4+ T cell subsets. However, single-cell RNA sequencing revealed distinct immune signatures. Antigen-responsive CD4+ T cells in LC patients demonstrated a signature of acute activation, characterized by the upregulation of genes such as CD38 and interferon-stimulated genes, including IFITM1. Furthermore, gene set enrichment analysis indicated that LC patients exhibit increased expression of interferon-alpha/gamma signatures compared to RC. Analysis of the T cell receptor repertoire presented no evidence of clonal expansion. Discussion: Our findings imply that LC immunopathology is driven by a qualitative T cell dysfunction characterized by CD4+ non-proliferative activation more than one month after symptom onset. This pattern is consistent with persistent antigen stimuli, though the underlying mechanism and its therapeutic implications require further investigation

overall_design: Immune signatures of CD4+ T cells in a subset of 6 LC and 4 recovered control (RC) unvaccinated patients, recruited 1 to 2 months after symptom onset, utilizing a combination of flow cytometry and single-cell RNA sequencing

first: Thiago

last: Cerqueira-Silva

first: Benjamin

last: Goodwin

first: Vinicius

last: Maracaja-Coutinho

first: Ricardo

last: Khouri

first: Viviane

middle: S

last: Boaventura


title: The ‘Metabolic Trap’: Candida parapsilosis Inhibits Staphylococcus aureus Biofilm Maturation by Disrupting pH Homeostasis and Inducing Premature Exodus

city: Dublin

first: Linda

last: Holland

address: Glasnevin

country: Ireland

institute: Dublin City University

summary: Biofilms are surface-attached communities of microorganisms surrounded by an extracellular matrix. The biofilm matrix plays an integral role in protecting the microorganisms within. Biofilm infections are incredibly difficult to treat. Staphylococcus aureus is a major human pathogen and can produce robust biofilm. Candida parapsilosis is an emerging fungal pathogen that is frequently isolated as the cause of infection. Its interaction with S. aureus has yet to be explored. The aim of this experiment was to characterise the transcriptional effects that occur in S. aureus during co-culture with C. parapsilosis cells or C. parapsilosis cell-free supernatant. RNA sequencing identified global changes in transcription that occur in S. aureus in the presence of C. parapsilosis cells or cell-free supernatant.

overall_design: Two different conditions were tested: (1) S. aureus (DSM799) was grown as a single speices biofilm, in a mixed bioiflm with C. parapsilosis CLIB214 cells OR in the presence of 50% C. parapsilosis CLIB214 cell free supernatant in TSB 0.2% glucose. Biofilms were grown in triplicate in 6-well nunclon plates (Thermo Fisher)  for 24 hrs under static conditions at 37°C. Following 24 hrs of growth, biofilm cells were pelleted at 4°C and total bacterial RNA was extracted. We then performed differential gene expression analysis using data obtained from RNA-sequencing. (2) S. aureus (DSM799) was grown as a single speices biofilm or in the presence of 50% C. parapsilosis CLIB214 cell free supernatant in TSB 1% glucose. Biofilms were grown in triplicate in 6-well nunclon plates (Thermo Fisher)  for 24 hrs under static conditions at 37°C. Following 24 hrs of growth, biofilm cells were pelleted at 4°C and total bacterial RNA was extracted. We then performed differential gene expression analysis using data obtained from RNA-sequencing.

first: Ciara

last: Furlong

first: Salini

last: Mohapatra

first: Denise

last: Harold

first: Emma

last: Finlay


title: In Vivo CRISPR Screens Identify SLC1A5 as a Metabolic Checkpoint for Cancer Immunotherapy

first: Wenlong

last: Jia

overall_design: This single-cell RNA-seq study was designed to characterize how hepatocyte-specific Slc1a5 deficiency remodels tumor-cell states and the tumor immune microenvironment. Liver tumors were collected from DEN/CCl₄-induced hepatocellular carcinoma models in control Slc1a5f/f and Slc1a5Hep mice. For each sample, live CD45+ immune cells and unsorted tumor cell suspensions were processed for single-cell 3′ RNA-seq. Biological replicates were included for each genotype, and the data were used to compare tumor-cell inflammatory programs, immune-cell composition, and immune functional states associated with Slc1a5 deficiency.

first: Guanxing

first: Shenqi

last: Han

first: Zhao

last: Huang

first: Bixiang

last: Zhang


title: PLA2G2D in tumour-draining lymph nodes regulates anti-tumour immunity

city: Rotterdam

first: Anneloes

last: van Krimpen

state: Zuid-Holland

address: Doctor Molewaterplein 40

department: Pulmonary Medicine

country: Netherlands

institute: Erasmus MC

summary: Current cancer immunotherapies can induce tumour regression, although responses are often not durable. Recent studies have highlighted the importance of enforcing a systemic immune response from tumour-draining lymph nodes (TDLNs). However, mechanisms driving immune suppression in TDLNs remain poorly studied. We applied spatial proteogenomics on melanoma TDLNs and identified regional differences in immune cell composition in lymph nodes from patients with long-term (>5 years) disease control compared to those with early (<2 years) disease recurrence. TDLNs from patients with a poor prognosis were characterized by the expansion of regulatory T cells (Tregs), dendritic cells (DCs), and macrophages interacting with cytotoxic CD8+ T cells. Targeted transcriptomics of cell types within this spatial neighbourhood revealed immunoregulatory myeloid cell phenotypes engaging with CD8+ T cells poised for exhaustion. Besides known immune-suppressive molecules such as IDO and PD-L1, paracortex macrophages and DCs in patients with recurrent disease expressed high levels of the secreted phospholipase PLA2G2D across different cancer types. Additionally, PLA2G2D was upregulated in non-small cell lung cancer patients who developed acquired resistance to anti-PD-1 immunotherapy. Importantly, PLA2G2D loss-of-function or therapeutic inhibition markedly improved survival in tumour-bearing mice and increased the efficacy of anti-PD-1 immunotherapy. Collectively, we show that in-depth spatial profiling of cancer patient TDLNs offers novel insights into systemic anti-tumour immunity and identifies PLA2G2D as a target for cancer immunotherapy.

overall_design: scRNAseq of B10F16-induced mice, untreated or treated with αPD-1, αPLA2G2D or IFNy

first: Mike

last: Eterman

first: Menno

last: van Nimwegen

first: Ralph

last: Stadhouders

first: Floris

last: Dammeijer


title: BMAL1 and YAP cooperate to hijack enhancers and promote inflammation in the aged epidermis [ChIP-Seq]

city: Barcelona

first: Sandra

last: Garcia Mulero

address: Baldiri Reixac 10

country: Spain

institute: IRB Barcelona

summary: Ageing is characterised by persistent low-grade inflammation that is linked to impaired tissue homeostasis and functionality. However, the molecular mechanisms driving age-associated inflammation remain poorly understood. The mammalian skin is a clinically relevant site of ageing-driven inflammation associated with compromised barrier function, inefficient wound healing, elevated oxidative stress, and DNA damage accumulation. Here, we show that during ageing a previously uncharacterised BMAL1–YAP transcriptional complex displays enhanced binding at inflammation-related enhancers, amplifying the transcription of their target genes. Independent of its known role as a core circadian clock component, we report that BMAL1 partners with the mechanosensitive transcriptional cofactor YAP at enhancer regions to regulate epidermal identity genes. However, in aged skin, this BMAL1–YAP cooperative binding undergoes a functional shift, enhancing the activity of enhancers of inflammation-related genes, co-regulated by NF-κB. Interestingly, aged pro-inflammatory signals from the IL-17 pathway activate YAP in a Hippo-independent manner. These findings unveil a transcriptional mechanism underlying epidermal ageing, linking chromatin dynamics to inflammatory transcriptional programs through BMAL1–YAP-bound enhancer rewiring. By elucidating how ageing reprograms transcriptional networks, our work highlights potential strategies to counteract chronic inflammation and restore tissue homeostasis across age-related loss of functionality.

overall_design: ChIP-seq of YAP of adult (18-25 weeks old) BMAL1 KO and BMAL1 WT mouse epidermis, at Zeitgeber time 4 (ZT4).

first: Camile

last: Stephan Otto Attolini

first: Guiomar

last: Solanas

first: Júlia

last: Bonjoch


title: Establishment and validation of the NEX-RiboTag system for profiling the excitatory neuronal translatome in the postnatal mouse forebrain

city: Beijing

first: Jue

last: Wang

address: No.10, Xi Tou Tiao, Youanmen wai, Fengtai District

department: School of Basic Medical Sciences

institute: Capital Medical University

summary: Excitatory neurons are the principal neurons of the mammalian cortex and hippocampus and are essential for postnatal circuit maturation. Although single-cell RNA sequencing has refined their molecular taxonomy, dissociation-induced stress artifacts and the disconnect between transcript abundance and translational output can limit functional interpretation. Bulk proteomics lacks cell-type specificity, while single-cell proteomics remains constrained by limited sensitivity and throughput. These limitations leave a gap between transcriptional identity and cell-type-resolved translational output. Because translation directly governs the selective recruitment of mRNAs for protein synthesis, defining excitatory neuron-specific translatome in vivo is valuable to bridge this gap. Here, we established and validated a NEX-RiboTag mouse line for targeted profiling of ribosome-associated mRNAs in cortical and hippocampal excitatory neurons. By crossing Neurod6 (NEX)-Cre mice with RiboTag reporter mice, we achieved Cre-dependent ribosomal tagging in excitatory neurons of the cortex and the hippocampus. RNA sequencing analysis at the 1-week postnatal stage demonstrated enrichment of excitatory neuronal markers and depletion of inhibitory neuronal and glial transcripts. Comparative analysis revealed a clear separation between the whole-tissue transcriptome and the ribosome-associated fractions, with enrichment of synaptic and metabolic pathways characteristic of excitatory neurons. Together, these datasets provide a valuable resource for investigating translational regulation in postnatal excitatory neurons and for studying molecular programs underlying neuronal maturation and synapse formation.

overall_design: A total of 11 RNA-seq samples from NEX-RiboTag mice were analyzed, including two P7(1w) Input-RNA samples and three TRAP-enriched IP-RNA samples at each developmental stage: P7, P14(2w), and P21(3w). NEX-RiboTag mice were generated by crossing Neurod6 (NEX)-Cre mice with Cre-dependent eGFP-Rpl10a reporter mice. Cortex and hippocampus tissues were collected at the indicated postnatal stages and processed together for TRAP. Ribosome-associated mRNAs from excitatory neurons were isolated using anti-GFP magnetic beads, while Input-RNA samples represented whole-tissue lysates. The purified RNA was subjected to RNA sequencing for downstream translatome analysis.

first: Kangnan

last: Zheng

first: Mengna

last: Liu

first: Bingxue

last: Jin

first: Guoliang

last: Chai

first: Changqing

last: Lu

first: Xiannian

first: Chen


title: BMAL1 and YAP cooperate to hijack enhancers and promote inflammation in the aged epidermis [RNA-Seq]

overall_design: Bulk RNA-seq profiling of K14-Cre;Bmal1flox/flox and K14-Cre;Bmal1wt/wt adult (18-25 weeks old) mouse epidermis at Zeitgeber time ZT4


title: DNA Methylation Signatures Distinguish Extranodal NK/T-cell Lymphoma and EBV-Positive Nodal T/NK-Cell Lymphoma and Identify Prognostic Subgroups

city: Singapore

first: Siok-Bian

last: Ng

address: National University Hospital, 5 Lower Kent Ridge Road, Main Building, level  3

department: Department of Pathology

country: Singapore

institute: National University Health System, Singapore

type: Methylation profiling by high throughput sequencing

summary: Extranodal NK/T-cell lymphoma (ENKTL) and primary Epstein–Barr virus (EBV)-positive nodal T/NK-cell lymphoma (nodal-TNKL) are aggressive lymphomas with overlapping clinicopathologic features but distinct underlying biology. While their genomic landscapes have been increasingly defined, comparative epigenetic characterization remains limited. We performed methylated DNA immunoprecipitation sequencing (MeDIP-seq) on formalin-fixed paraffin-embedded samples from ENKTL, nodal-TNKL, ENKTL cell lines, and control tissues. ENKTL displayed extensive promoter hypermethylation associated with repression of tumor suppressor genes, lineage regulators, and lymphoid signaling genes, including LEF1 and BANK1, together with focal hypomethylation of immune- and interferon-responsive genes such as IFITM1. In contrast, nodal-TNKL showed global hypomethylation, particularly affecting cytotoxicity, immune-response, and antigen-presentation pathways; TET2-mutated cases exhibited locus-specific methylation changes consistent with impaired active demethylation. Across all samples, global DNA methylation levels correlated with genomic instability. Unsupervised clustering identified two epigenetically distinct ENKTL subgroups, one characterized by higher global methylation, TP53 loss, increased copy number alterations and loss of heterozygosity, and significantly poorer overall survival. Together, this study defines fundamental epigenetic differences between ENKTL and nodal-TNKL and links DNA methylation dynamics to genomic instability and clinical outcome, highlighting the value of methylation profiling for refined classification, risk stratification and therapeutic guidance.

overall_design: MeDIP-seq profiling was performed on formalin-fixed paraffin-embedded (FFPE) samples from patients with Extranodal NK/T-cell Lymphoma (43 samples from 39 patients), EBV-Positive Nodal T/NK-Cell Lymphoma (12 samples), and Extranodal NK/T-cell Lymphoma-derived cell lines (5 samples).The 28 control samples comprised reactive tonsils (n = 10), lymph nodes (n = 2), nasal mucosa (n = 6), primary T cells (n = 5), and primary NK cells (n = 5).  All samples, including cell lines, purified primary peripheral blood T cells, purified primary peripheral blood NK cells, and tissue controls, were analyzed in FFPE format.

first: Ling-Wen

last: Ding

first: The

last: Phyu

first: Shangying

last: Chen

first: Sai Mun

last: Leong


title: Transcriptomic profiling reveals AVP-responsive molecular changes in GT1-7 GnRH neurons

city: Dallas

first: Ran

last: Tao

address: 3302 Gaston Avenue

department: Biomedical Sciences

institute: Texas A&M University College of dentistry

summary: Arginine vasopressin (AVP) has been implicated in the regulation of gonadotropin-releasing hormone (GnRH) neurons, but the transcriptomic mechanisms underlying this effect remain unclear. In this study, GT1-7 GnRH neuronal cells were treated with AVP and analyzed by bulk RNA sequencing. Compared with control cells, AVP treatment induced broad transcriptional changes, with 1,094 differentially expressed genes identified, including 549 up-regulated and 545 down-regulated genes. Functional enrichment analysis highlighted AVP-associated changes in signaling pathways related to TNF signaling, PI3K-Akt signaling, MAPK signaling, cAMP signaling, axon guidance, and Wnt signaling. These data provide a transcriptomic resource for understanding AVP-responsive molecular programs in GT1-7 GnRH neurons.

overall_design: GT1-7 cells were divided into control and AVP-treated groups, with three independent biological replicates per group. Cells were serum-starved for 12 h and then treated with 200 pg/mL AVP or vehicle control for 6 h. Total RNA was extracted from each sample and subjected to RNA sequencing using the Illumina HiSeq X Ten platform. Differential gene expression analysis was performed between AVP-treated and control cells.

first: Tao

last: Ran