title: Erythroid ACKR1 deficiency aggravates immune-mediated kidney disease

city: Graz

first: Katharina

last: Artinger

address: Auenbruggerplatz 27

department: Division of Nephrology, Department of Internal Medicine

country: Austria

institute: Medical University of Graz

summary: Single nucleotide polymorphisms (SNP) of atypical chemokine receptor 1 (ACKR1) gene encode human Duffy Antigen blood groups. The majority of individuals of West African ancestry carry a SNP in the promoter region of the ACKR1 that disrupts its transcription in erythroid cells only, but not in venular endothelial cells, leading to an “erythroid silent”, FyBES Duffy phenotype.Irradiation bone marrow ACKR1 chimeric mice lacking erythroid ACKR1 (KO->WT) showed increased disease activity and fibrosis after induction of nephrotoxic serum nephritis (NTSN), as compared to their respective controls (WT->WT).

overall_design: Renal tissue from irradiation bone marrow ACKR1 chimeric mice  (WT->WT and KO->WT) after NTSN induction was analyzed using snRNAseq.


title: Gpnmb is required for immune and fibrotic responses during zebrafish heart regeneration

status: Public on Apr 15 2026

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

type: Expression profiling by high throughput sequencing

summary: Myocardial infarction occurs when coronary supply of oxygen and nutrients to a part of the heart is interrupted.  In contrast to adult humans, adult zebrafish have a unique ability to regenerate their heart after cardiac injury.  To identify potential regulators of the regenerative response, we performed transcriptomic profiling of regenerating coronary endothelial cells (cECs) at 7 days post cryoinjury, when revascularization is vigorous, and identified gpnmb to be upregulated.  Gpnmb (glycoprotein non-metastatic melanoma protein B) is a transmembrane glycoprotein implicated in inflammation resolution and tissue regeneration.  Expression analyses at earlier time points revealed gpnmb specific expression in infiltrating macrophages post cryoinjury in zebrafish ventricles.  Using newly generated gpnmb mutants, we analyze its role during heart regeneration and find that animals lacking gpnmb exhibit neutrophil retention and decreased macrophage recruitment as well as reduced myofibroblasts numbers.  Moreover, loss of gpnmb impairs coronary endothelial cell regeneration and cardiomyocyte dedifferentiation.  Transcriptomic analyses identified enhanced collagen production and extracellular matrix (ECM) related pathway activated in cryoinjured gpnmb mutant hearts.  Furthermore, gpnmb mutant hearts exhibit larger fibrotic scars revealing defects in cardiac regeneration.  Overall, these data suggest that gpnmb expressing macrophages modulate inflammation and ECM deposition after cardiac cryoinjury and highlight the importance of this subset of immune cells to support a regenerative response.

overall_design: Transcriptomic profiling of regenerating and non-regenerating coronary endothelial cells

first: Ruben

middle: M

last: Juez

last: Guenther


title: ITGB1 is a TNBC tumor microenvironment-dependent immune modulator

city: LOS ANGELES

first: NUOZI

last: SONG

state: CALIFORNIA

address: City of Hope 1500 E Duarte Rd INTL Stud

country: USA

institute: city of hope

summary: Tumorigenesis and metastasis, as well as insufficient response and the emergence of resistance to immunotherapy, are frequently attributed to the intricate interplay between cancer cells and tumor microenvironment (TME). Cancer cells significantly contribute to the recruitment of tumor-infiltrating leukocytes, which, in turn, directly regulate cancer cell proliferation and viability. Comprehending the mechanism and key regulators of the crosstalk between cancer cells and immune components in the TME is imperative for developing efficacious immunotherapeutic interventions. Here, through an in vivo CRISPR screen targeting cell surface genes, we identify ITGB1 as a central arbiter dictating the tumorigenicity of triple-negative breast cancer (TNBC). ITGB1 mediates the establishment of pro-tumorigenic TME by orchestrating tumor-associated myeloid populations and impeding T cell infiltration, while transducing pro-survival signaling from the tumor-favorable milieu into TNBC cells, to bolster tumor development.

overall_design: we seek to interrogate whether ITGB1 is directly involved in transducing tumor-favorable signaling from the TME into the malignant cells for their survival and growth. Bulk RNA-seq of MDA-MB-231A tumor cells directly from in vitro cell culture or isolated from mouse tumor tissues, respectively, were conducted.

first: Nuozi

last: Song

first: Siqi

last: Chen

first: Mingye

last: Feng


title: Single-cell RNA-sequencing of calli harvested 7 and 12 days after incubation on callus-inducing medium

city: Seoul

first: Soon Hyung

last: Bae

state: South Korea

address: Gwanak-ro 1, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: Plant somatic cells can be reprogrammed to form a pluripotent cell mass, known as callus, which can be used to regenerate organs or an entire plant via de novo organogenesis. Exogenous treatment of tissue explants with a high auxin-to-cytokinin ratio stimulates callus formation. Here, we found that the pluripotency acquisition in the callus is transient during callus formation, independent of explant origin. Using single-cell transcriptome analysis of pluripotent and nonpluripotent calli, obtained at 7 and 12 days after incubation on callus-inducing medium (CIM), respectively, we found that root stem cell activity conferred by the WUSCHEL-RELATED HOMEOBOX5 (WOX5)-TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 (TAA1) module is diminished by the prolonged incubation of callus on CIM. The reduced root stem cell activity led to the differentiation mainly into mature lateral root cap (LRC)-like cells in callus. Concomitant with differentiation into LRC-like cells, epidermis-like cells accumulating very long chain fatty acids (VLCFAs) that promote cellular pluripotency are sloughed off. Additionally, stress responses that induce the loss of pluripotency are activated in the mature LRC-like cells and a sub-cluster of xylem pole pericycle cells. Taken together, our data indicate that callus formation is likely a continuous developmental program, in which stem cell activity is acquired then lost, resulting in the transient nature of cellular pluripotency in callus.

overall_design: Leaves of 2-week-old Arabidopsis thaliana seedlings were excised and incubated on callus-inducing medium. After 7 and 12 days of incubation, calli were collected to perform single-cell RNA-sequencing.

first: Soon

middle: H

first: Ok-Sun

last: Park

first: Hun-Young

last: Lee

first: Kyounghee

first: Sangrea

last: Shim

first: Yoo-Sun

last: Noh

first: Pil

middle: J

last: Seo


title: RNA-seq analysis in progeny leaves on rice seed treatd with heat

city: Fukuoka

first: Yushi

last: Ishibashi

address: 744 Motooka

country: Japan

institute: Kyushu university

summary: We report the relationship between transgenerational growth and  transcriptome in progeny leaves on rice seeds treated with heat.

overall_design: Examination of RNA-seq in progeny leaves on rice seeds treated with heat.

first: Ishibashi

last: Yushi

first: Suriyasak

last: Chetphilin


title: RNA sequencing of naïve, activated and HIV-1 infected CD4+ T cells

status: Public on Apr 14 2026

city: Boca Raton

first: Sean

last: Paz

state: Florida

address: 777 Glades Road

department: Biomedical Sciences

institute: Florida Atlantic University

summary: CD4+ T cells play a major role in immune function regulation. Naive CD4+ T cells undergo major transcriptional changes upon activation through simultaneous engagement of the T-cell receptor and co-stimulatory molecules (anti-CD3/anti-CD28). Activated CD4+ T cells are the preferential target of HIV-1. Both T cell activation and HIV-1 infection modulate the expression and splicing of multiple genes. This study characterizes the transcriptome of naive, activated, and activated-HIV-1 infected CD4+ T cells from 3 healthy donors using bulk RNA-Seq, with validation of gene expression and alternative splicing by RT-qPCR and RT-PCR respectively.

overall_design: Comparison of the transcriptome in naive, activated, and activated-infected CD4+ T cells from 3 healthy donors. CD4+ T cells were isolated by negative selection from 3 healthy donors. Naive CD4+ T cells from each donor were split into two batches: one batch was used directly for RNA extraction; the second batch was activated for 5 days using anti-CD3, anti-CD28 antibodies and soluble IL-2. Following activation, cells from each donor were divided: one batch was infected at high MOI (MOI>1000) with HIV-1 NL4-3 isolate, while the other was mock infected. RNA was extracted 5 days post-infection from the activated and activated-infected cell populations.

first: Massimo

last: Caputi


title: Bulk RNA-sequencing of calli harvested 7 and 12 days after incubation on callus-inducing medium

overall_design: Leaves of 2-week-old Arabidopsis thaliana seedlings were excised and incubated on callus-inducing medium. After 7 and 12 days of incubation, calli were collected to perform bulk RNA-sequencing. Three biological replicates for each time point were generated.


title: Defined cell culture medium contributes to transcriptional reprogramming to enhance membrane-associated mucin expression in human corneal epithelial cells

city: Taipei

first: CHO-YI

last: CHEN

address: No.155, Sec.2, Linong St.

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: This study investigates the transcriptional mechanisms by which a defined culture condition enhances membrane-associated mucin expression in human corneal epithelial cells (HCECs). RNA sequencing was performed on HCECs cultured in keratinocyte serum-free medium (KSFM) or a defined special medium. Transcriptomic analysis revealed coordinated activation of epithelial maintenance and mucin biosynthesis pathways. These findings provide insight into epithelial homeostasis and suggest potential therapeutic strategies for dry eye disease.

overall_design: Human corneal epithelial cells (HCECs) were cultured in either keratinocyte serum-free medium (KSFM) or a defined special medium. RNA sequencing was performed with pooled three independent biological replicates per condition to compare transcriptomic differences between conditions.

first: Hsieh

last: Hsiu-Hui

first: Lin

last: Chen-Hua

first: Hung

last: Kai-Feng

first: Sun

last: Yi-Chen


title: T cell lymphoma associated STAT3 variants impose a type 1 regulatory phenotype

city: Maimi

first: Alejandro

last: Villarino

address: 1600 NW 10th Ave, Rosenstiel Medical Science Building (RMSB), Room 3152A

institute: University of Miami

summary: STAT3 signaling is fundamental to T cells, where it underlies basic cellular processes like metabolism and apoptosis, and specialized processes like differentiation and cytokine production. However, mutations of STAT3 are strikingly prevalent in T cell cancers and aberrant or excessive STAT3 signaling is thought to mobilize cellular pathways that encourage malignancy. To better understand how STAT3 mutations drive T cell cancers, we compared two frequent cancer-associated variants, Y640F and N647I, at cellular and molecular levels. Using a retrogenic system, we demonstrate that they are qualitatively similar yet quantitatively distinct; each bears a gain-of-function phenotype but Y640F has greater transcriptome-wide effects. We also discovered that these and other common STAT3 mutants invoke a T regulatory 1 (Tr1) gene program characterized by expression of IL-10 and other factors that dampen T cell responses, most notably LAG3 and CD39. Importantly, Tr1 ’skewing’ is evident in both mouse T cells expressing cancer-associated STAT3 variants and humans afflicted with T cell malignancies. These studies advance current understanding of how cancer-associated mutations impact STAT3 function and reveal anti-inflammatory properties that may help transformed T cells persist, expand and/or avoid eradication.

overall_design: bulk' RNA-seq and scRNA-seq analysis of transduced CD4+ and CD8+ T cells sourced from WT mice or mice lacking STAT3

first: Aaron

last: Schultz

first: Molly

last: Dalzell

first: Luis

last: Nivelo

first: Sarah

last: Henrickson

middle: V


title: Modulating alternative splicing of MECP2: A potential therapeutic strategy for Rett syndrome

city: Houston

first: Hu

last: Chen

state: TX

address: 1250 Moursund St,

department: Pediatrics

institute: Baylor College of Medicine

summary: Rett syndrome (RTT) is a neurological disorder caused by loss-of-function mutations in methyl CpG binding protein 2 (MECP2), a transcriptional regulator essential for maintenance of normal neuronal function. The current FDA-approved treatment for RTT, Trofinetide, mildly alleviates some symptoms. In contrast, re-introducing MeCP2 or upregulating it through transgenesis in mouse RTT models improves most neurological phenotypes and enhances survival. Here, we devised a therapeutic strategy to moderately increase MeCP2 protein by modulating the alternative splicing of MECP2 to switch the less efficiently translated e2 to the more efficiently translated e1 isoform. We deleted Mecp2 exon 2 (unique to e2), leading to production of only e1 mRNA, and show this upregulates MeCP2 by 50-60% in mice. Next, using two independent RTT induced pluripotent stem cell (iPSC)-derived neuron models harboring mutations that reduce both MeCP2 expression and function, we show that exon 2 deletion upregulates MeCP2 and ameliorates morphological and electrophysiological deficits in these neurons. Isoform switching also significantly corrects the dysregulated transcriptome in RTT neurons. Lastly, an exon 2-skipping Morpholino upregulates MeCP2-E1 in vivo. These data set the stage for a promising therapeutic strategy using antisense oligonucleotides to promote isoform switching in patients with RTT who carry partially functioning alleles of MECP2.

overall_design: To determine the transcriptomic signature in the RTT neurons and to determine how upregulating mutant MeCP2 protein by exon 2 deletion in the RTT-G118E neurons altered this transcriptomic signature, we performed bulk RNA-sequencing on NGN2-driven iPSC-derived neurons at two timepoints (4 weeks and 8 weeks), and NPC-derived iPSC-derived neurons at one timepoint using total RNA. Additionally to examine the effect of exon 2 deletion on transcriptomic signature in the context of another RTT mutation, T158M, we performed bulk RNA-sequencing on NG2-derived iPSC-derived neurons at one timepoint (8-weeks) using total RNA.

first: Harini

last: Tirumala

first: Alex

last: Trostle

first: Yan

last: Li

first: Sameer

last: Bajikar

first: Huda

last: Zoghbi


title: JMJD1C-mediated epigenetic control of autoimmunity and HIT antibody production [RNA-seq]

city: Milwaukee

first: Demin

last: Wang

state: WI

address: 8727 W Watertown Plank Rd

institute: 1Versiti Blood Research Institute

summary: Heparin-induced thrombocytopenia (HIT) is a common drug-induced immune disorder occurring in a subset of heparin-treated patients. Immune complexes comprising heparin, platelet factor 4 (PF4), and PF4/heparin-reactive antibodies are central to its pathogenesis. However, the role of epigenetic modification in HIT remains unexplored. Our study identified JMJD1C, a member of the lysine-specific histone demethylase 3 subfamily, as an essential regulator of PF4/heparin-specific antibody production. While JMJD1C was expressed throughout B-cell development and was dispensable for normal B-cell development, its deficiency disrupted immune tolerance and promoted production of self-reactive antibodies in systemic autoimmune diseases, including PF4/heparin-specific platelet-activating antibodies, a hallmark of pathogenic HIT antibodies. JMJD1C-deficient B cells were hyperresponsive, characterized by enhanced B-cell receptor (BCR)-induced proliferation. Transcriptomic analysis (RNA-Seq) revealed upregulation of pathways associated with BCR signaling, NF-kB activation, the cell cycle, and systemic lupus erythematosus (SLE). CUT&Tag profiling demonstrated that JMJD1C deficiency increased H3K36me1 modification at gene start sites in these pathways, indicating that epigenetic dysregulation drives B-cell hyperactivation. Importantly, transcriptional profiling and regulon analysis of B cells from HIT patients showed enrichment of BCR signaling, cell-cycle, NF-κB, and SLE-associated pathways, closely mirroring those in JMJD1C-deficient B cells. Epigenetic analyses further revealed enhanced promoter chromatin accessibility and elevated H3K36me1 deposition at promoter-TSS regions in HIT B cells. Together, these findings establish a strong molecular overlap between JMJD1C deficiency and human HIT B cells and reveal a previously unrecognized epigenetic mechanism underlying HIT pathogenesis. Our study provides the first evidence linking epigenetic regulation to HIT, offering new insights into its pathophysiology.

overall_design: Splenic FO B cells were sorted and stimulated with anti-IgM for 2 hours, then lysed in TRIzol for RNA extraction. mRNA was isolated (10 to 50 ng) using the NEBNext poly(A) mRNA Magnetic Isolate Module and converted into libraries with the NEBNext Ultra RNA Library Prep kit (New England Biolabs). Libraries were quantified using Qubit-Fluorometer and the Kapa Library Quantification Kit. Library size (150–900 bp) was determined with the D1000 ScreenTape system (Agilent).


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

city: Wuhan

first: shen

last: jin

state: Hubei

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

country: China

institute: Wuhan university

summary: Pachytene spermatocytes were isolated from adult wild-type and Hsf5 knockout mouse testes using STA-PUT velocity sedimentation. Single-cell suspensions were prepared by enzymatic digestion of seminiferous tubules with collagenase and trypsin. Cells were loaded onto a 4%–2%–0.5% BSA gradient and allowed to sediment for 1 hour and 45 minutes at 4°C. Fractions were collected, and pachytene spermatocytes were identified by SYCP3, γH2AX, and DAPI staining under microscopy. Enriched pachytene cells were pooled and processed for RNA-Seq.

overall_design: This study aims to perform RNA-seq profiling to compare purified pachytene spermatocytes from wild-type mice and their knockdown counterparts, thereby exploring gene expression changes during the pachytene stage of meiosis and spermatogenesis.

first: Qi

last: Sun

first: Yuming

last: Cao

first: Zhiyi

first: Jin

last: Shen

first: Zejia

first: Binyi

first: Muyang

last: Cheng

first: Jiemin

first: Weihao

last: Gong

first: Mengcheng

last: Luo

first: Yuanzhen

last: Zhang

first: Rong

last: Liu


title: Inhibition of endoplasmic reticulum stress prevents renal pathology in hindlimb unloaded mice

city: Mangalore

first: animikh

last: ray

state: Karnataka

address: Indoor Stadium Complex, Father Muller Campus, Kankanady,

country: India

institute: Father Muller Research center

summary: The hindlimb unloaded (HU) mouse, an animal model of prolonged bedrest and spaceflight, exhibits detriment of several body organs. However, relevant effects on renal tissues are unknown. We investigated the effects of protein dysregulation by endoplasmic reticulum (ER), termed ER stress to renal histology and molecular phenotype in HU mice. We categorized c57BL/6j mice into ground-based controls, (GC), and HU mice treated with vehicle (HU) or 4-phenyl butyrate (4PBA), an ER stress inhibitor for three weeks. We found an HU-induced glomerular widening and an obliteration of Bowman’s space, which were partly reversed by 4PBA (all p<0.05).  The GO enrichment analysis validated the heightened ER stress in HU kidneys and its reversal with 4PBA treatment. The transcriptome analysis, including the differentially expressed genes analysis revealed a significant reversal of genetic perturbation by 4PBA and mitigation of microgravity-induced renal decline. These findings were supported by KEGG-based and Reactome-based pathway analysis. 4PBA treatment upregulated the PPAR signaling pathway, which provides protection against ER stress. Enrichment analysis based on Reactome database also reveals that 4PBA activated the detoxification of reactive oxygen species. Collectively, our novel findings show a role for elevated ER stress in HU-induced renal injury. We also propose 4PBA as a potential therapeutic to restore renal structure and function in microgravity conditions.

overall_design: In this study we have investigated the interface of ER stress and renal pathology in HU mice. We hypothesized that HU causes elevated ER stress and disruption of renal microarchitecture, while treatment with 4-PBA partly prevents these pathological changes. We also performed a detailed transcriptomic analysis of renal tissues to unravel the novel molecular pathways connecting elevated ER stress with renal decline

first: Anu

last: Ranade

first: Animikh

last: Ray

first: Amir

middle: A

last: Khan

first: Muhammad

middle: T

last: Gul

first: Josemin

last: Jose

first: Gopika

last: Ramachandran

first: Asima

last: Karim

first: Firdos

last: Ahmad

first: Suni

last: Ebby

first: Rizwan

last: Qaisar


title: Transcriptomic and Metabolic Basis of Volatile Compound Dynamics in Apricot Fermentation

city: Zhengzhou

first: Zhifei

last: Chen

state: Hunan

address: No. 16, Yulin South Road

institute: Technology Center for China Tobacco Henan Industrial Limited Company

summary: Aroma is one of the most important qualities that defines the appeal and value of the fermented fruit products. This study provides the first integrative analysis of volatile compound dynamics and transcriptomic regulations during apricot fermentation by Wickerhamomyces anomalus Using GC-MS, we tracked the temporal evolution of key aroma-active metabolites including s 3-hydroxy-2-butanone, 2,3-butanediol, benzaldehyde, isoamyl alcohol, and phenethyl alcohol across 0, 16, 32 ,48, and 64 h. these aromatic compounds exhibited  a distinct accumulation pattern, peaking at 48h with concentrations of 11.14 μg/g, 1.28 μg/g, 6.13 μg/g, 29.12 μg/g, and 13.59 μg/g respectively. Metatranscriptomicprofiling revealed extensive differential gene expression at different time points of fermentation. KEGG pathway analysis revealed  the mechanisms to produce 3-hydroxy-2-butanone and 2,3-butanediol, as well as the phenylalanine-dervided aromatic compounds.  Gene annotation establish direct link between transcriptional regulation and volatile  production, uncovering mechanistic connections between yeast metabolism and aroma development.  The findings highlight W. anomalus  as a promising non-conventional yeast for natural aroma enhancement, offering new biotechnological strategies to optimize flavor quality in fruit-based fermentations and functional foods.

overall_design: RNA-seq of Volatile Compound Dynamics in Apricot Fermentation (Wickerhamomyces anomalus) in 0h,16h, 32h,48h,64h


title: In planta transcriptome analysis of Pseudomonas syringae pv. tomato DC3000 two component regulator mutant cvsR during early infection and early exposure to pattern-triggered immunity in Arabidopsis thaliana

city: Athens

first: Brian

middle: Howard

last: Kvitko

state: GA

address: 120 Carlton St.

department: Plant Pathology

institute: University of Georgia

summary: We extracted P. syringae transcriptome from infected A. thaliana tissue under naive or PTI preactivated tissue by flg22 treatment, through physical separation by low speed centrifugation at 5 hours post inoculation. We compared the transcriptome of wildtype strain and mutant strain of cvsR, a previous identified two component regulator. This study aim to understand bacterial response to PTI and the role of cvsR regulon in plant.

sample_organism: Pseudomonas syringae pv. tomato str. DC3000

overall_design: Bacteria extracted from naïve mock-treated leaves and immune activated leaves (flg22)  at 5 hours post inoculation. Bacterial initial inoculum as in vitro media-based sample (KB). Samples collected in triplicate on different days for each strain and treatment.

first: Hsiao-Chun

first: Brian Howard


title: Targeting UBE2F induces a resilience program enhancing CD8 T cell immunity

city: Beijing

first: Xiaonan

last: Ma

address: NO.30 Shuangqing Road

institute: Tsinghua University

summary: CD8 memory T cells (TMEM) and exhausted T cells (TEX) are essential for host defense against infection and cancer, yet their therapeutic potential is often limited by insufficient persistence and sustained functional capacity. Strategies to enhance the longevity of both populations remain scarce. Here, we demonstrate that ablation of UBE2F, a neddylation E2 enzyme, induces a resilience program in CD8 T cells that operates across both TMEM and TEX compartments, resulting in improved viral and tumor control. This resilience state is characterized by enhanced self-renewal and survival without perturbing the conventional CD8 T cell differentiation trajectories. Mechanistically, UBE2F deficiency inhibited neddylation of CUL5, leading to accumulation of JUNB and upregulation of IL-2Rβ. The increased IL-2Rβ expression hypersensitizes CD8 T cells to physiological IL-15, thereby conferring the resilience features. Together, these findings identify the UBE2F-CUL5-JUNB-IL-2Rβ axis as a conserved post-translational mechanism regulating CD8 T cell longevity across memory and exhausted states, providing a novel strategy for enhancing antiviral and antitumor immunity.

overall_design: Naive wildtype (WT) or UBE2F KO (CKO) P14 cells were transferred into recipient mice infected with LCMV Armstrong. 15 days or 75 days post-infection, donor P14 cells from spleens were sorted by FACS for single-cell RNA-seq analysis.


title: Faecalibacterium prausnitzii EXL01 for the Maintenance of Steroid-induced Clinical Response or Remission in Patients with Crohn’s Disease: a first in human trial

city: Saint-Malo

first: Phuong

middle: Hang

last: PHAM

address: 7 allée Métis

department: Data science

country: France

institute: Parean Biotechnologies

summary: A marked decrease in Faecalibacterium prausnitzii is a hallmark of Crohn’s disease (CD)-associated dysbiosis and predicts disease relapse. Here, we present the development and first-in-human evaluation of F. prausnitzii strain EXL01 for CD treatment. The EXL01-strain demonstrated anti-inflammatory effects in four models of colitis in rodents. A first-in-human, open-label, single-arm study of oral EXL01 was conducted in eight adult participants with mild to moderate CD, following corticosteroids-induced clinical response or remission. The primary endpoint was safety, and secondary endpoints included clinical, endoscopic, histological, molecular, and microbiome assessments. EXL01 was well-tolerated with no treatment-related adverse events. Six participants completed the study; two discontinued treatment due to disease flare. While gut microbiota composition remained largely stable, transcriptomic analyses revealed distinct changes in ileal gene expression following EXL01 treatment, notably modulation of immune-related genes and upregulation of energy metabolism pathways. Compared to participants who remained in remission, those who flared showed higher baseline systemic inflammation markers and innate immunity gene expression. These findings demonstrate that oral administration of EXL01 is feasible and well tolerated, and establishes proof-of-concept for F. prausnitzii as a first-in-class live biotherapeutic for CD. ClinicalTrials.gov registration: NCT05542355.

overall_design: MAINTAIN was a Phase 1, 2-parts, randomised, parallel arm, placebo controlled, partially double-blind, multicentre study evaluating the safety and target engagement of EXL01 in adults with mild to moderate CD (Crohn Disease Activity Index (CDAI) 180-350) with ileal involvement who achieved corticosteroid (CS)-induced clinical response (CDAI decrease ≥70) or remission (CDAI <150).

first: Perle

last: Guarino-Vignon

first: Edouard

last: Louis

first: Hang-Phuong

last: Pham

first: Giovanna

last: Orianne

first: Emma

last: Tkacz

first: Loic

last: Brot

first: Eolia

last: Mazzetti

first: Delphine

last: Sedda

first: Pauline

last: Ruffié

first: Nathalie

last: Rolhion

first: Geert

last: D’Haens

first: Benjamin

last: Hadida

first: Philippe

last: Langella

first: Harry

last: Sokol


title: Targeting STAT3-Mediated Lipid Metabolism Reprogramming Overcomes Chemoresistance in Acute Myeloid Leukemia

city: Guangzhou

first: Keren

last: Peng

address: Guangzhou University Town, Panyu District

institute: Sun Yat-sen University

summary: Chemotherapy resistance and intolerance pose significant challenges in the effective treatment of leukemia. Among the distinctive features associated with chemoresistance, metabolic reprogramming emerges as a key factor. In this study, we unveil a novel mechanism contributing to chemoresistance in leukemia, specifically highlighting the pivotal role of altered lipid homeostasis.We found that multiple lipid metabolism processes are aberrantly activated in Ara-C resistant AML cells, with upregulation of JAK-STAT3 signaling pathways and multiple enzymes in the process of fatty acid metabolism. A potent, and highly selective STAT3 inhibitor, W1307, was designed, and exhibited significant anti-tumor activities in vitro and in vivo. Genetic and pharmacological inhibition of STAT3 leads to inhibition of lipid synthesis and catabolism, resulting lipids metabolic disorder. Mechanistically, STAT3 binds to consensus DNA response elements in the promoters of the lipid metabolism associated genes (SREBP1, CPT2) and regulates their expression. Furthermore, inhibition of STAT3 enhances the anti-tumor effect of Ara-C and sensitizes resistant AML cell line to Ara-C through disrupting lipid homeostasis and triggering lipotoxicity. Collectively, our work illuminates the pivotal role of lipid metabolism adaptation driven by STAT3 in chemoresistance. The identification of W1307 as a promising candidate compound underscores its potential as a therapeutic intervention in leukemia treatment and overcoming chemoresistance.

overall_design: Conparative gene expression profiling analysis of RNA-seq data for MOLM-13 and MOLM-13/AR (Ara-C resistant) cells.

first: Jianshan

last: Mo

first: Zhenjiao

last: Yang

first: Wen

last: Ding


title: Single-cell transcriptomic analysis of synovial tissues from aged mice

first: Tao

last: Gui

address: Huangpu Ave

institute: Jinan University

summary: We employed a single‑cell RNA sequencing approach using the 10x Genomics platform to profile synovial tissues from aged (24‑month‑old) wilt-typt mice. This study aims to delineate cell‑type‑specific transcriptional changes in the synovium associated with aging, thereby providing insights into how aging reshapes the synovial cellular landscape and may contribute to the increased susceptibility to joint pathologies, such as osteoarthritis, in the elderly.

overall_design: This study employed a single‑cell RNA sequencing (scRNA‑seq) approach using the 10x Genomics platform to investigate age‑related transcriptional changes in synovial tissues. Synovial tissues were collected from aged (24‑month‑old, N=12) mice, and processed to obtain viable single synovial tissue cells for scRNA‑seq.

first: Rui

first: Bo

last: Yu

first: Lutian

last: Yao

first: Lei

last: Zhang


title: High-throughout sequencing of ovarian cancer cells treated with YY-15

city: Wenzhou

first: Yeying

last: He

address: Chashan

institute: Wenzhou Medical University

summary: After treating human ovarian cancer cells A2780 and ES2 with YY-15, high-throughput sequencing technology was employed. The transcriptome analysis revealed that YY-15 does not exert its anti-tumor effect solely through telomere dysfunction, but instead simultaneously regulates cell cycle, senescence, apoptosis, and metabolic-related signaling pathways, thereby synergistically inducing the death of ovarian cancer cells.

overall_design: SKOV3 and ES2 cells (3×10^5 cells per well, placed in 6-well plates) were treated with YY-15 for 48 hours. After the treatment, the cells were collected and total RNA was extracted from each group using TRIzol (TaKaRa Company, Japan). Finally, paired-end sequencing was performed on the Illumina HiSeq 4000 platform at LC-BIO Technology Company (Hangzhou, China).

first: Jiaying

last: TONG

first: Xiaohui

last: Zheng


title: Gene expression profile at single cell level of Lamina propria mononuclear cells from intestinal biopsies from IBD patients.

city: Erlangen

first: Christian

last: Büttner

address: Schwabachanlage 10

department: Institut of Human Genetics

institute: University Hospital Erlangen

summary: Inhibition of NLRP3 causes significantly reduced proliferation of intestinal fibroblasts in IBD patients.

overall_design: Lamina propria mononuclear cells (LPMCs) from IBD patients were isolated from human intestinal biopsies taken during endoscopy or from resected gut specimen. Cells were isolated using the lamina propria dissociation kit (Miltenyi Biotec) and analyzed using scRNAseq. Single-Cell gene expression sequencing was performed to compare NLRP3 inhibitor treatment responders and non-resonders.

first: Simone

last: Weber

first: Anna-Lena

last: Vögele

first: Selina

last: Sitte

first: Arif

middle: B

last: Ekici

first: Philipp

last: Kirchner

first: Raja

last: Atreya


title: Human Chondrocyte Dedifferentiation Bulk RNA-Seq

city: Philadelphia

first: Ellen

state: PA

address: 36th Street and Hamilton Walk

department: Orthopaedic Surgery

institute: University of Pennsylvania

summary: Chondrocyte-based cartilage repair strategies such as autologous chondrocyte implantation (ACI) require extensive in vitro expansion to obtain clinically relevant cell numbers. However, monolayer expansion drives chondrocyte dedifferentiation, reducing matrix-forming capacity and contributing to variable repair outcomes, a long-standing problem in cell-based cartilage repair.

overall_design: RNA-seq was performed on primary human articular chondrocytes from 4 independent donors (D1-D4) at three in vitro passage numbers (P0, P3, P6), yielding 12 samples total (4 donors x 3 passages). Paired-end 2×150bp sequencing was performed on an Illumina HiSeq X.

first: Su Chin

last: Heo


title: Canavanine-based assay for gross chromosomal rearrangements reveals hotspots and genome instability modulating genes in fission yeast

city: Atlanta

first: Kirill

middle: S

last: Lobachev

address: 315 Ferst Drive

department: School of Biological Sciences

institute: Georgia Institute of Technology

summary: Gross chromosomal rearrangements are a hallmark of many diseases and cancers. The study of their biogenesis and the mechanisms underlying their formation is greatly facilitated by the availability of genetic reporter assays in model organisms. We present here a novel GCR assay developed in fission yeast, a highly relevant model for understanding genome instability related to human biology. The reporter employs canavanine counter-selection to detect GCRs within a chromosomal context. Using this assay, we identified natural hotspots for GCRs, including inverted long terminal repeats (IR-LTRs). Structural analysis of GCR events showed that IR-LTR–induced GCRs mainly result in either terminal deletions with adjacent inverted duplications or repair via long-range break-induced replication (BIR). Deleting IR-LTRs reduces the GCR rate and reveals another hotspot driven by BIR between homeologous aldo/keto reductase genes on opposite arms of chromosome I. This is the first evidence that BIR can occur in S. pombe on long tracks reaching up to 600 kb. Besides highlighting genome rearrangement hotspots, the assay also identifies regulators of genome instability in fission yeast. Loss of Nup132, a component of the nuclear pore complex, increases IR-LTRs-induced GCRs, while the budding yeast homolog Nup133 has no effect on the stability of a structurally similar IR. In contrast, disrupting djc9, which encodes a conserved histone H3–H4 binding protein, decreases GCR rates. Overall, this sensitive GCR assay enables the identification of factors that control spontaneous and fragile motif–induced chromosomal instability, including those conserved in humans but lost through evolution in other organisms.

overall_design: NGS profiling of S. pombe isolates carrying gross chromosomal rearrangements

first: Anissia

last: Ait Saada

first: Cassandre

last: Ollivie

first: Alex

last: Costa

first: Kevin

last: Moreau

first: Sarah

last: Lambert


title: RNA-seq analysis of soleus muscle from control and StarD7 mKO mice

city: Tochigi

first: Yasuhiro

last: Horibata

address: 880 Kitakobayashi

institute: Dokkyo Medical University

summary: RNA sequencing was performed on soleus muscle from control and StarD7 mKO mice to investigate transcriptional changes associated with mitochondrial lipid dysregulation.

overall_design: RNA-seq analysis was performed on soleus muscle from control and StarD7 mKO mice (n = 3 per group). Total RNA was extracted and poly(A)-selected libraries were prepared and sequenced using the Illumina NovaSeq 6000 platform with paired-end 50 bp reads. Differential gene expression between control and mKO mice was analyzed.


title: The hepatoprotective benefits of semaglutide in MASH require the intrahepatic endothelial GLP-1 receptor

city: Toronto

first: Daniel

middle: J.

last: Drucker

address: 25 Orde Street, Rm 5-1034

country: Canada

institute: Mt. Sinai Hospital, Lunenfeld Tanenbaum Research Institute, University of Toronto

summary: GLP-1 receptor agonists such as semaglutide improve metabolic dysfunction-associated liver disease (MASLD), yet the hepatic cell types mediating these effects remain unclear. GLP-1R expression in the liver is restricted to non-parenchymal cells, but its detection by conventional single-cell RNA sequencing is limited due to low transcript abundance. We performed GEM-X Flex-seq (10x Genomics) single-cell RNA sequencing on liver single-cell suspensions from wild-type C57BL/6J mice fed a standard chow diet, a choline-deficient high-fat diet (CDHFD), or CDHFD with semaglutide treatment. This dataset enables cell type-resolved mapping of Glp1r expression across the hepatic niche and characterization of transcriptomic changes associated with semaglutide treatment, revealing pericentral liver sinusoidal endothelial cells (LSECs) as direct targets mediating weight loss-independent improvements in hepatic inflammation, fibrosis, and immune remodeling.

overall_design: Four samples were generated from wild-type C57BL/6J mice (Jackson Laboratory, Strain #000664): STD (n=4 mice pooled), CDHFD (n=3 pooled), and two semaglutide-treated CDHFD groups (SEMA1, n=4 pooled; SEMA2, n=2 pooled). Semaglutide was administered by daily subcutaneous injection at escalating doses (10–40 µg/kg/day). Cells were fixed using the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit prior to library preparation and sequencing.

first: María

last: González Rellán

first: Cristina

last: Riobello

first: Susanna

last: Fang

first: Eloisa

last: Martins da Silva

first: Jacqueline

last: Koehler

first: Rui

last: Shang

first: Rola

last: Hammoud

first: Xiemin

last: Cao

first: Marta

last: Varela Rey


title: Wnt-dependent ontogeny of acellular cementum-forming cementoblasts on the tooth root surface

first: Taishi

last: Komori

address: 7500 Cambridge St #1210

institute: The University of Texas Health School of Dentistry

summary: Cementum is a specialized mineralized tissue that covers the tooth root surface and anchors the tooth to the surrounding periodontal ligament. The coronal acellular cementum (AC) is indispensable for periodontal attachment and represents a key target for periodontal regenerative therapies. However, the developmental origin and molecular identity of AC-forming cementoblasts remain poorly understood. Here, through an integrated spatial and single-cell transcriptomic analysis, we identify AC-forming cementoblasts as a distinct population of noncanonical mineralizing cells enriched for cell-matrix organization and Wnt signaling signatures, distinguishing them from cellular cementum-forming cementoblasts localized in the apical portion. Lineage tracing using a Wnt inhibitory factor 1 (Wif1-creER) demonstrates that AC-forming cementoblasts originate exclusively from peri-epithelial apical Wif1+ cells of the elongating tooth root via canonical Wnt signaling activation. Collectively, our findings uncover the unique ontogeny and molecular signature of acellular cementum, providing insights into the formation and maintenance of the periodontal attachment apparatus.

overall_design: We generated a cellular-resolution spatial transcriptomic map of the murine mandible at P25 to comprehensively define the transcriptomic landscape of cementoblasts.

first: Noriaki

last: Ono


title: Expression profile characteristics and clinical significance of plasma  extracellular RNA(exRNA) in patients with rheumatoid arthritis

first: Huan

last: Dong

state: Guangdong

address: No. 58, Zhongshan Road, Yuexiu District, Guangzhou

institute: Sun Yat-sen University First Affiliated Hospital

summary: Plasma from rheumatoid arthritis(RA) patients and healthy controls underwent Heber sequencing to profile exRNA in RA and assess their association with disease activity.

overall_design: Heber sequencing of plasma in patients with rheumatoid arthritis and healthy individuals

first: Ting

last: Liu

first: Huijuan

last: Hu

first: Kai

last: Sun

first: Chenxi

last: Peng

first: Hao

last: Li

first: Youjun

last: Xiao

first: Liuqin

last: Liang


title: Association of serum uric acid with cardiovascular risk and exploratory analysis of circulating tsRNA biomarkers in gout patients

type: Non-coding RNA profiling by high throughput sequencing

summary: Sreum from gout patients and healthy controls underwent high-throughput small-RNA sequencing to profile tRNA-derived small RNAs(tsRNAs) in gout.

overall_design: High-throughput sequencing was conducted on serum samples from 10 gout patients and 10 matched healthy controls to identify differentially expressed tsRNAs.

first: Shaofan

last: Zhang

first: Hanshi

last: Xu

first: Qian

last: Qiu


title: Stem cell activity is linked to a transient acquisition of pluripotency during callus proliferation

city: Seoul

first: Soon Hyung

last: Bae

address: Gwanak-ro 1, Gwanak-gu

institute: Seoul National University

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

overall_design: Refer to individual Series


title: Mutual interaction between Schwann cells and CD4+T cells promotes the progression of perineural invasion in colorectal cancer [RNA-seq]

first: Huayuan

state: Beijing

address: New Student Apartment Building, No. 17, South Panjiayuan, Chaoyang District, Beijing

institute: Chinese Academy of Medical Sciences Cancer Hospital

summary: Background: Perineural invasion (PNI) is a common pathological feature associated with poor prognosis of colorectal cancer (CRC). However, the mechanisms underlying PNI formation and its relationship with CD4+T cells within the tumor immune microenvironment remain unclear. Aims: This study investigated the role of CD4+T cells in the development and progression of PNI in CRC by examining the interactions between Schwann cells (SCs), primary glial cells in peripheral nerves, and CD4+T cells. Methods: Single-cell RNA sequencing, spatial transcriptomics, and multiplex immunohistochemistry were used to profile the characteristics and spatial relationship between SCs and CD4+T cells in PNI CRC tissues. This study established an SCs-CD4⁺T-cells co-culture system and used flow cytometry, transcriptomic sequencing, proteomics, and ATAC-seq to investigate the mechanisms of their interaction. The key findings were validated in mouse models of sciatic nerve invasion and subcutaneous tumor formation. Finally, the origin of PNI was explored by co-culturing SCs with CRC cells. Results: The results revealed the presence of a distinct heat shock protein family A member 6 (HSPA6)+CD4+T cell subset—CD4+Tstr cells—in CRC PNI tissues. These cells are induced by SCs, further enhancing SCs' migration and tumor-promoting capabilities while contributing to an immunosuppressive microenvironment. Moreover, SCs in contact with tumor cells possess the ability to recruit CD4+T cells, potentially representing a key mechanism underlying PNI formation. Conclusion: This study suggests that SCs near CRC tissues recruit CD4+T cells, promote their conversion to CD4+Tstr cells, establish an immunosuppressive microenvironment, and simultaneously enhance SCs' migration and tumor-promoting capabilities, thereby accelerating PNI development.

overall_design: Transcriptome sequencing to identify differentially expressed genes and enriched pathways between the SCs group and the SCs+CD4+T co-culture group


title: PD-1 Deficiency Exacerbates Mycobacterium abscessus Lung Infection via Metabolic Rewiring and Dysregulated Neutrophil  Responses

city: Chongqing

first: Xiaowen

last: Yu

address: No. 6, Panxi 7th Branch Road, Jiangbei District

department: Basic Research Laboratory of Traditional Chinese Medicine

institute: Chongqing Traditional Chinese Medicine Hospital

summary: A PD-1-deficient MAB-infected mouse model was established. The impact of PD-1on bacterial clearance, immune cell activity, and metabolism was evaluated via colony counting, histopathology, flow cytometry, multiplex immunofluorescence, transcriptomics, and metabolic profiling. PD-1−/− mice exhibited increased susceptibility to MAB. Late infection featured further Th1 decline, neutrophil rise, and enhanced glycolysis. Peripheral blood displayed lower CXCL9 but elevated IL-6, IL-21, IL-27, CXCL2, CXCL10, and S100A8 production.

overall_design: Transcriptomic Analysis of Immune Cell Recruitment and Functional Alterations in Pulmonary Tissues of Wild-Type and PD-1-Deficient Mice Following MAB Infection at 21 Days Post-Infection

first: Lu

last: Huang


title: Miniaturisation of duckweeds occurred through compression of the angiosperm body plan

city: Sutton Bonington

first: Alexander

middle: George

last: Ware

state: Leicestershire

address: Sutton Bonington Campus

country: United Kingdom

institute: University of Nottingham

summary: We performed RNA-seq on microdissected regions of Lemna minor (clone 8263) and Spirodela polyrhiza (clone 9509) fronds, alongside the related aroid Colocasia esculenta (taro), to define region-specific transcriptomes and compare organ-identity programmes across species. Transcript abundance was quantified with Salmon v1.10.0 and cross-species comparisons were performed on 7,480 one-to-one orthologues identified by OrthoFinder v3.0.1b1.

sample_organism:
Colocasia esculenta
Lemna minor
Spirodela polyrhiza

overall_design: RNA-seq of microdissected frond regions (Apical, Basal, LowerWall, NodeTract for duckweeds; plus Stipe for Spirodela; Apical, Basal, Petiole, Sheath for taro) with 2-6 biological replicates per region per species. 51 samples total (14 Lemna, 20 Spirodela, 17 Taro).

first: Ware

last: Alexander

first: Bishopp

last: Anthony

first: Bhosale

last: Rahul

first: Chan

last: Emily


title: Impact of urban air ultrafine particles on embryonic development and their association to transport emissions

city: Barcelona

first: Benjamin

last: Piña

address: Jordi Girona, 18

department: Environmental Chemistry

country: Spain

institute: IDAEA-CSIC

summary: Airborne ultrafine particles (UFP) constitute a potential risk factor for human health, being transport one of the most relevant sources, particularly in urban environments. We collected UFP from outdoor sites in Barcelona and Valencia (Spain) selected to distinguish between the contributions of road traffic, trains, ships, and planes.  Zebrafish embryos were exposed to organic extracts from the collection filters, and their transcriptomes were analysed by RNA deep sequencing. Functional analysis of 2,941 significantly affected transcripts revealed a strong enrichment in functions related to general embryotoxicity, like induction of degradation pathways (endocytosis, necroptosis), and inhibition of development- and cell division-related genes. This embryotoxicity-related transcriptional response was linked to elevated  concentrations of UFP, sulfur, and other inorganic species in the air samples, and it was particularly strong in UFP-rich airport samples. In addition,  the functional analysis also identified a relatively small subset of genes configuring a typical  dioxin-like response, traditionally associated with exposure to airborne combustion particles, and that was linked to PAH-rich emissions from harbour and traffic samples. Consistently, relative abundance of the implicated genes showed  a strong correlation with high concentrations of polycyclic aromatic hydrocarbons (PAHs) in the extracts. Our findings indicate that the parameters currently used to assess air quality overlook the role of UFP in total airborne toxicity and, consequently, they do not adequately protect human populations.

overall_design: Zebrafish embryos (96 hpf) were exposed for 24 hours to extracts from air particle filters collected at different places in Barcelona and Valencia (Spain). Embryos were collected and RNA extracted and sequenced a the Spanish National Center for Genomic Analysis (CNAG, Barcelona, Spain)


title: Rat knee joint scRNA-seq data with meniscus injury treated by 4PPBP

city: New York

first: Chang

middle: Hun

last: Lee

state: NY

institute: Columbia University

summary: Avascular meniscus tears are a major contributor to mechanical joint locking, compromised gait and function, and the initiation and progression of post-traumatic osteoarthritis. Unfortunately, the avascular meniscus tears hardly heal. Here, we report a novel small molecule, 4-PPBP, a sigma-1 receptor (σ1R) agonist, exhibiting significant potential to promote avascular meniscus healing by activating synovial mesenchymal stem cells (syMSCs) and modulating macrophage-regulated inflammation via multi-tissue crosstalk. In vivo, a single injection of 4-PPBP-loaded bioglue minimized meniscal gapping, with improved meniscus healing and gait performance. In contrast to the degenerative changes in the untreated control, 4-PPBP/bioglue application resulted in integrated fibrocartilaginous tissues. scRNA-seq and CellChat analyses revealed 4-PPBP-activated cell-cell communications leading to inflammatory regulation and cell differentiation. Macrophages showed a robust reduction in pro-inflammatory genes, and fibroblasts, chondrocytes, and fibrochondrocytes increased genes associated with differentiation and matrix synthesis in response to 4-PPBP. Anti-inflammatory cell-cell communication signals were significantly elevated between adipocytes and macrophages.

overall_design: Sprague-Dawley rats (250 to 275g, Charles River, Boston) were used approximately 1 week before the procedure to allow adequate animal acclimation. For surgeries, animals were placed in an induction chamber with isoflurane  administration at 4% for induction of anesthesia before placement on a surgical table. Sustained-release buprenorphine was administered before surgery. Continuous isoflurane administration at 1.5-2% was used for maintenance of anesthesia. The anesthetic state was assessed using a hind-limb toe pinch and respiratory observation. The state of anesthesia was continuously monitored (pinch reflex) throughout the procedure. The surgical site was shaved, prepped with povidone-iodine/ethanol, and draped in a sterile surgical manner. Each rat was positioned in the supine position to expose the meniscus after hair removal and 3 surgical disinfections. The right knee was shaved and prepped with povidone-iodine/ethanol and draped in a sterile surgical manner. Rats were placed on a warm water-flowing heating pad to maintain body temperature. A 1.5 cm vertical incision was made and then the medial joint capsule was sectioned. Before the defects were created, all menisci were confirmed to have a sufficient size for creating the planned defects. A 2 mm complete meniscus injury was performed in the inner two-thirds of the anterior portion of the medial meniscus. 20 μl bioglue was injected between the injury sites. The skin was sutured continuously with absorbable sutures. 2 rats per cage were housed under pathogen-free conditions. They were fed standard laboratory rodent and water ad libitum. Animals were maintained at a constant temperature of 25°C and kept on a 12-h light/dark cycle. Finally, rats were euthanized by carbon dioxide inhalation at each time point. At 2 weeks post-op, cells were isolated from whole knee joint tissues, including synovium, ligament, infrapatellar fat pad, cartilage, and medial meniscus. The harvested tissues were minced, followed by 5 mg/ml collagenase I and IV in serum-free DMEM for 2.5 h at 37°. After enzymatic digestion, an equal volume of 10% FBS in DMEM was added to neutralize the enzymes. Suspended cells were transferred to a 100 µm strainer, centrifuged at 1,600 rpm, and rinsed 3 three times using PBS with 10% FBS. All cells from three animals per group were combined for scRNA-seq analysis.

first: Meng

last: Feng

first: David

middle: D

last: Pellei

first: Ming

last: Wang

first: Angelyn

last: Nguyen

first: Sarah

last: Ginsberg

first: Hun Jin

last: Jeong


title: JMJD1C-mediated epigenetic control of autoimmunity and HIT antibody production

city: Milwaukee

first: Demin

address: 8727 W Watertown Plank Rd

institute: 1Versiti Blood Research Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Heparin-induced thrombocytopenia (HIT) is a common drug-induced immune disorder occurring in a subset of heparin-treated patients. Immune complexes comprising heparin, platelet factor 4 (PF4), and PF4/heparin-reactive antibodies are central to its pathogenesis. However, the role of epigenetic modification in HIT remains unexplored. Our study identified JMJD1C, a member of the lysine-specific histone demethylase 3 subfamily, as an essential regulator of PF4/heparin-specific antibody production. While JMJD1C was expressed throughout B-cell development and was dispensable for normal B-cell development, its deficiency disrupted immune tolerance and promoted production of self-reactive antibodies in systemic autoimmune diseases, including PF4/heparin-specific platelet-activating antibodies, a hallmark of pathogenic HIT antibodies. JMJD1C-deficient B cells were hyperresponsive, characterized by enhanced B-cell receptor (BCR)-induced proliferation. Transcriptomic analysis (RNA-Seq) revealed upregulation of pathways associated with BCR signaling, NF-kB activation, the cell cycle, and systemic lupus erythematosus (SLE). CUT&Tag profiling demonstrated that JMJD1C deficiency increased H3K36me1 modification at gene start sites in these pathways, indicating that epigenetic dysregulation drives B-cell hyperactivation. Importantly, transcriptional profiling and regulon analysis of B cells from HIT patients showed enrichment of BCR signaling, cell-cycle, NF-κB, and SLE-associated pathways, closely mirroring those in JMJD1C-deficient B cells. Epigenetic analyses further revealed enhanced promoter chromatin accessibility and elevated H3K36me1 deposition at promoter-TSS regions in HIT B cells. Together, these findings establish a strong molecular overlap between JMJD1C deficiency and human HIT B cells and reveal a previously unrecognized epigenetic mechanism underlying HIT pathogenesis. Our study provides the first evidence linking epigenetic regulation to HIT, offering new insights into its pathophysiology.

overall_design: CUT&Tag was performed as described68. Sorted FO B cells were stimulated with anti-IgM for 2 h, washed, bound to ConA-coated beads (Bangs Laboratories), and incubated overnight with anti-H3K36me1 (Abcam), followed by anti-rabbit IgG secondary antibodies (Antibodies Online). Samples were incubated with the pA-Tn5 adapter complex (Epicypher) for 1 h at room temperature and subjected to tagmentation at 37°C. DNA was extracted, PCR-amplified, and sequenced on an Illumina NextSeq 500 using the NextSeq 500/550 v2 kit.


title: PD-1 Deficiency Exacerbates Mycobacterium abscessus Lung Infection via Dysregulated T Cell Responses

summary: A PD-1-deficient Mycobacterium abscessus -infected mouse model was established. The impact of PD-1 on bacterial clearance, immune cell activity, and metabolism was evaluated via colony counting, histopathology, flow cytometry, multiplex immunofluorescence and transcriptomics. We fonud that PD-1−/− mice exhibited increased susceptibility to MAB. Early infection showed elevated lung CD4⁺ T cells, reduced neutrophils, and higher blood cytokines (IFN-γ, IL-21, IL-6, IL-27).

overall_design: Transcriptomic Analysis of Immune Cell Recruitment and Functional Alterations in Pulmonary Tissues of Wild-Type and PD-1-Deficient Mice Following MAB Infection at 3, 7, and 14 Days Post-Infection


title: Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates [Bisulfite-Seq 2]

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

type: Methylation profiling by high throughput sequencing

summary: Recent breakthroughs in single-cell genomics allow probing molecular states of cells with unprecedented detail along the sequence of the DNA. Biological function relies, however, on emergent processes in the three-dimensional space of the nucleus, such as droplet formation through phase separation. Here, we use single-cell multi-omics sequencing to develop a theoretical framework to rigorously map epigenome profiling along the DNA sequence onto a description of the emergent spatial dynamics in the nucleus. Drawing on scNMT-seq multi-omics sequencing in vitro and in vivo we exemplify our approach in the context of exit from pluripotency and global de novo methylation of the genome. We show how DNA methylation patterns of the embryonic genome are established through the interplay between spatially correlated DNA methylation and topological changes to the DNA. This feedback leads to the predicted formation of 30-40nm sized condensates of methylated DNA and determines genome-scale DNA methylation rates. We verify these findings with orthogonal single cell multi-omics data that combine the methylome with HiC measurements. Notably, this scale of chromatin organization has recently been described by super-resolution microscopy. Using this framework, we identify local methylation correlations in gene bodies that precede transcriptional changes at the exit from pluripotency. Our work provides a general framework of how mechanistic insights into emergent processes underlying cell fate decisions can be gained by the combination of single-cell multi-omics and methods from theoretical physics that have not been applied in the context of genomics before.

overall_design: E14 mESC were cultured in 2i+LIF media. For induction for 2i-relase experiment, the cells were rinsed with PBS before the culture media was changed to serum + LIF medium. Each each collection time point cells were lysed and processed for BS-seq

first: Fabrizio

last: Olmeda

first: Tim

last: Lohoff

first: Ioannis

last: Kafetzopoulos

first: Stephen

last: J Clark

last: Benson

first: Fatima

last: Santos

first: Felix

last: Krueger

first: Simon

last: Walker

first: Wolf

last: Reik

first: Steffen

last: Rulands


title: GelMa/TPGS@Tea Polyphenols hydrogel slows down NLRP3/CASP1-mediated chondrocyte scorch death after growth plate Injury

city: Fuzhou

first: tianpeng

last: dai

address: No. 1 Qiuyang Road, Shangjie Town, Minhou County

department: College of Orthopedics and Traumatology

institute: Fujian University of Traditional Chinese Medicine

summary: In this paper, a GelMA/TPGS@Tea Polyphenols (TP) bioactive hydrogel system was successfully prepared. The system utilizes the injectability and mechanical support of GelMA hydrogel, combined with the temperature-sensitive gel-forming property of TPGS and the specific inhibitory effect of tea polyphenols (TP) on NLRP3 inflammatory vesicles, with the aim of solving the problem of induced bridge formation and deformity after growth plate injury in pediatric orthopaedic clinics. In vitro and in vivo experiments showed that the hydrogel system could rapidly gel and fill the defects at physiological temperature (37°C), and the TP component significantly slowed down CASP1-mediated chondrocyte pyroptosis by inhibiting the activation of NLRP3 inflammasome, thus preventing the occurrence of bone bridges. Our study provides a bioactive, injectable, and NLRP3-targeted filler material for growth plate injury repair in pediatric orthopedics, which has great potential for preventing bone bridge formation!.

overall_design:
Sham group (intact rat femur, 7D post sham surgery)
GPI group (intact rat femur, 7D post distal femoral growth plate injury modeling)
GMTT group (intact rat femur with growth plate, 7D post distal femoral growth plate injury modeling + GMTT hydrogel treatment)
Sampled at: Orthopaedic Research Institute, Fuzhou Second General Hospital, Fujian Province | Time: 2026.3.1 17:00 | Specimens: Intact femurs from male rats, n=3 per group

first: Tianpeng

last: Dai


title: Transcriptional profiling of L4-L6 DRGs in Twik-1 knockout mice following chronic constriction injury

city: Daegu

first: Myungin

last: Baek

address: Techno jungang Daero 333

department: Department of Brain Sciences

institute: DGIST (Daegu Gyeongbuk Institute of Science and Technology)

summary: To identify the molecular mechanisms of reduced pain response in Twik-1 knockout mice, we performed bulk RNA-sequencing on lumbar DRGs from WT and Twik-1 knockout mice. Thirty days after sciatic nerve injury, the ipsilateral L4-L6 DRGs were manually sectioned into ~150 µm slices using a razor blade. RNAs were extracted from the sliced DRGs using PicoPure™ RNA Isolation Kit. RNA libraries were constructed using the SMART-Seq v4 Ultra Low Input RNA Kit. High-quality libraries were pooled and sequenced on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads. Image analysis was performed using the NovaSeq 6000 Control Software (v1.8.2), and base calling data were demultiplexed using bcl2fastq (v2.20.0.422), generating FASTQ files. Raw sequencing reads were aligned to the Mus musculus reference genome (GRCm39) using STAR aligner (version 2.7.11a). The genome index was built from the primary assembly FASTA file (Mus_musculus.GRCm39.dna.primary_assembly.fa.gz) and the corresponding gene annotation file (Mus_musculus.GRCm39.113.gtf.gz), ensuring accurate mapping across exon–intron boundaries. Resulting SAM/BAM files were then processed, sorted, and indexed with Samtools (version 1.18). Gene-level counts were generated using htseq-count (version 2.0.3) with the corresponding GTF annotation file.

overall_design: Transcript profiles of lumbar (L4-L6) DRGs were generated using bulk RNA sequencing. The study utilized two variables: genotype (WT vs. Twik1-KO) and injury model (Sham vs. CCI). The data set comprises 17 samples divided into four groups: Sham-WT (n=5), CCI-WT (n=5), Sham-Twik1-KO (n=4), and CCI-Twik1-KO (n=3).

first: Seo Young

last: Yang

first: Tery

last: Yun

first: Junhee

last: Park

first: Hyosang

last: Lee


title: Gene expression profile on a single-cell level of monocytes isolated from dura mater of mice infected with group B streptococci

city: Freiburg

first: Vitka

last: Gres

address: Breisacherstraße 115b

department: Institute for Infection Prevention and Control

institute: University of Freiburg

summary: Monocytes in dura change their ontogenic source in streptococcal infection, from GMP-dominated to a mixed lineage of GMP and MDP-derived monocytes. We utilized Ms4a3Cre;R26Tomato mice to understand transcriptomical differences between monocytes sourced from different ontogenic sources.

overall_design:
Prior FACS, single-cell suspension of each individual mouse was labelled using the 10X 3' CellPlex Kit Set A (PN-1000261) following manufacturer’s recommendations. In total, around 7500 MDP-monocytes and 59400 GMP-monocytes were sorted from dura mater of 4 mice infected with GBS for 2 days. Sorted samples were processed using the 10X Chromium Next GEM Single Cell 3’ Kit v3.1 (PN-1000269) and 3' Feature Barcode Kit (PN-1000262). Single cell droplets were generated using Chromium Next GEM Chip G Single Cell Kit (PN-1000127) and Chromium Controller for 3’ gene expression and cell multiplexing libraries were generated according to the manufacturer’s specifications. Library quality was assessed using Agilent High Sensitivity DNA Kit (cat. no. 5067-4626). The single cell libraries were sequenced using Ilumina NovaSeq X Plus, with a minimum targeted sequencing depth of 20,000 reads per cell. Fastq files were aligned to prebuilt CellRanger reference refdata-gex-GRCm39-2024-A using the CellRanger version 9.0.1.
Please note that processed data files are generated from both GEX and Cellplex raw files, and are linked to the corresponding GEX sample records.

first: Sagar

last: Sagar

first: Florens

last: Lohrmann

first: David

last: Obwegs

first: Philipp

last: Henneke


title: Regulation of BCL11A DNA binding and expression in human erythrocyte precursor HUDEP-2 cells

city: Houston

first: Yue

last: Lu

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: BCL11A is a transcription factor crucial for neurodevelopment and hematopoiesis. It regulates the developmental switch from fetal hemoglobin (HbF) to adult hemoglobin and is a major therapeutic target for sickle cell disease and b-thalassemia. We investigated BCL11A functions in human erythrocyte precursor HUDEP-2 cells. We treated HUDEP-2 cells (which normally express adult hemoglobin) with inhibitors targeting epigenetic silencing marks - DNA methylation and histone H3 lysine 27 methylation. All treatments, individually or in combination, increased HbF expression to varying degrees.

overall_design: Four samples were prepared for whole genome bisulfite sequencing (WGBS) analysis: non-differentiated HUDEP-2 cells and differentiated cells after treatment with vehicle (DMSO), DNMT1-inhibitor and EED-inhibitor. Genomic DNA of HUDEP-2 cells was extracted and subjected to bisulfite conversion. Bisulfite-converted DNA was used to prepare sequencing libraries and sequenced on an Illumina NovaSeq X plus 25B (2 x 150 bp) in paired-end 150/8/8/150 configuration. Approximately 80% pairs of sequence reads were uniquely mapped to the human genome hg38.

first: Puspa

last: Das

first: Tingting

last: Hong

first: Marcos

middle: R

last: Estecio

first: Yun

last: Huang

first: Xing

last: Zhang

first: Xiaodong

last: Cheng


title: Wnt-dependent ontogeny of acellular cementum-forming cementoblasts on the tooth root surface [scRNA-seq]

first: Taishi

last: Komori

overall_design: Building on the spatial transcriptomic findings, we next investigated the ontogeny and hierarchy of the cementoblast lineage using single-cell transcriptomics. Pthrp-mCherry+ cells were isolated by fluorescent-activated cell sorting (FACS) at P15 (completion of AC formation), P25 (onset of CC formation), and 8 weeks (maturation), followed by single-cell RNA-sequencing (scRNA-seq). We then computationally integrated these datasets with a previously published Pthrp-mCherry dataset from P6.

first: Noriaki

last: Ono


title: Gastrointestinal CAR T-cell Lymphoma after ciltacabtagene autoleucel

city: Los Angeles

first: Hitomi

last: Hosoya

state: CA

address: 116 N Robertson Blvd

institute: Cedars-Sinai Medical Center

summary: We employed a single cell sequencing approach using 10x Genomics to study CAR T-cell lymphomagenesis. This study provides new insights into mechanisms of homing and malignant transformation of CAR T cells.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed on 1 PBMC sample and 3 gastrointestinal biopsies (stomach, duodenum, ileum). Dead cells were removed using the Dead Cell Removal Kit (Miltenyi Biotec). Gene expression and TCR libraries were generated according to the Chromium Next GEM Single Cell 5’ v2 chemistry protocol (10x Genomics).

first: Michael

last: Khodadoust


title: Therapeutic Efficacy, Biomarker Signatures and Translatability of Semaglutide in the Liver Biopsy-Confirmed GAN DIO-MASH Mouse Model (study 6)

city: Hørsholm

first: Henrik

last: Hansen

address: Hørsholm Kongevej 11

department: Histology & NGS

country: Denmark

institute: Gubra

summary: 12-week semaglutide treatment was characterized in the GAN-DIO MASH mice. Endpoints included body weight, plasma biochemistry and proteomics as well as liver histological and transcriptome assessments.

overall_design: GAN DIO-MASH mice with liver-biopsy confirmed MASH and fibrosis were administered semaglutide (30 nmol/kg, s.c.) or vehicle once daily for 12 weeks. Liver samples were collected for RNA sequencing and transcriptome data were compared to plasma proteome data

first: Jens B

last: Kristensen

first: Maja W

last: Andersen

first: Henrik H

last: Feigh


title: Massively multiplex multi-modal chemical screens at single-cell resolution with DOGMA-plex

city: San Francisco

first: Romain

last: Lopez

state: California

address: 1396 Sanchez St

institute: New York University

summary: We present DOGMA-plex, a novel cellular barcoding systems that enable multiplexed analysis of multiple independent samples within a single experiment through a combination of viral barcodes and antibody-based plate-barcodes. Using this platform, we successfully profiled around 1,200 drug-dose responses across 475 surface proteins, chromatin accessibility, and the whole transcriptome in human treated with around 300 different chromatin inhibitors, demonstrating the method's ability to capture multi-modal cellular responses to chemical perturbations.

overall_design: DOGMA-plex

first: Kelvin

last: Chen

first: Basak

last: Eraslan

first: Aviv

last: Regev

first: Shimon

last: Sakaguchi


title: Transcriptome-based classification of resected pancreatic ductal adenocarcinoma enhances prognostic modelling accuracy of overall survival following adjuvant treatment

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

summary: In pancreatic ductal adenocarcinoma, patient outcomes after resection remain highly variable. Prognostic models are often inaccurate. Our study aimed to improve survival prediction by adding transcriptome-based classification to a validated prognostic model and applying it on a multicenter real-world cohort. Fresh-frozen tumor resection materials were obtained from the Dutch Pancreas Parel biobank. RNA was sequenced if tumor cellularity was >30%. The samples were classified using transcriptome-based classification. Survival differences between transcriptome-based subtypes were studied in patients treated with and without adjuvant chemotherapy. Both patients receiving neoadjuvant treatment (NAT) and patients undergoing immediate surgery were included. Samples of 461 patients were collected, of which 118 samples underwent RNA sequencing. Of those, 39.0% were of the basal-like subtype and 61.0% were of the classical subtype. The basal-like subtype became dominant after NAT (63.3%, p = 0.004). Adjuvant gemcitabine-treated patients with a classical tumor survived longer than those with a basal-like tumor (median overall survival (OS): 22.8 vs. 11.4 months; p < 0.001). In multivariable Cox regression, the classical subtype significantly associated with increased survival (hazard ratio = 0.38; p = 0.002) and adding transcriptome-based subtyping significantly improved the prognostic model (p = 0.002). Subtype and adjuvant treatment independently statistically significantly associated with OS. Transcriptome-based subtyping significantly adds to clinical variables in survival prediction after surgery. The independent associations for subtype and adjuvant treatment with OS indicate that subtypes are prognostic, but not predictive for OS with adjuvant treatment. The provided prognostic information could potentially support treatment decisions and serve as stratification factor.

overall_design:
Retrospective cohort study: Resection specimen of PDAC patients were collected, and selected for sufficient tumor cell percentage. Subsequently, RNA was isolated and submitted for RNA sequencing.

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

first: Marjolein

middle: F

last: Lansbergen

first: Vincent

last: Lanting

first: Paul

last: Manoukian

first: Marc

middle: G

last: Besselink

first: Geert

last: Kazemier

first: Ignace

last: de Hingh

first: Mike

last: Liem

first: Casper

last: van Eijck

first: Erwin

last: van der Harst

middle: E

last: de Meijer

first: Ronald

last: van Dam

first: Martijn

middle: W

last: Stommel

first: Jan

last: Koster

last: Tanck

first: Arantza

last: Fariña

first: Joanne

last: Verheij

first: Frederike

last: Dijk

first: Johanna

last: Wilmink

first: Maarten

last: Bijlsma

first: Hanneke

last: van Laarhoven


title: HNRNPH controls alternative splicing cooperatively on a transcriptome-wide scale [in vitro iCLIP]

city: Würzburg

first: Julian

last: Konig

address: Am Hubland

institute: Würzburg University

summary: The in vitro binding potential of HNRNPH1 to RNA is not available. Hence, we performed an high-throughput in vitro binding assay for recombinant MBP-HNRNPH1 using an RNA oligo library consisting of 2000 individual sequences. We used this in vitro binding assay to map binding of  recombinant HNRNPH1 protein to RNA in individual nucleotide resolution. To understand the impact of RNA G-quadruplex structures for HNRNPH1 binding, we compared the binding of HNRNPH1 to GTP RNA and 7-deaza-GTP RNA.

overall_design: The 2000 chosen HNRNPH binding sites were ordered as a DNA oligo library (Twist Bioscience). The DNA oligo library was in vitro transcribed to RNA using either GTP or 7-deaza-GTP for the in vitro transcription. Then, the GTP and 7-deaza-GTP RNA libraries were radioactively labelled and afterwards UV-crosslinked (at 254 nm with 250 mJ/cm2) with recombinant MBP-HNRNPH1 protein in four technical replicates each. The protein-RNA complexes were separated using a Tris-Acetate gel and transferred to a nitrocellulose membrane. The RNA was isolated from the nitrocellulose membrane following the iCLIP2 protocol (PMID: 31610236). Then, the isolated RNA was reversely transcribed for library preparation for the high-throughput sequencing (PMID: 31610236).

first: Kerstin

last: Tretow

first: Mario

last: Keller

first: Mirko

last: Brüggemann

first: Anke

last: Busch

first: Kathi

last: Zarnack

last: König


title: HNRNPH controls alternative splicing cooperatively on a transcriptome-wide scale [RTstop profiling]

summary: High-throughput experimental validation of G-quadruplex formation for RNAs with HNRNPH binding sites is not available. Hence, we performed an in vitro Reverse Transcriptase Stop-Profiling (RT-Stop profiling) in high-throughput to map G-quadruplex structure formation of 2000 individual RNAs that have been identified to be bound by HNRNPH.

overall_design: The 2000 chosen HNRNPH binding sites were ordered as a DNA oligo library (Twist Bioscience). The DNA oligo library was in vitro transcribed to RNA using either GTP or 7-deaza-GTP for the in vitro transcription. Then, the GTP and 7-deaza-GTP RNA libraries were reversely transcribed in KCl or NaCl reverese transcription buffer in three technical replicates each. The cDNAs were used for library preparation for the high-throughput sequencing.


title: Altered plasma tRNA-derived small RNA profiles and their clinical relevance in rheumatoid arthritis

city: Guangzhou

first: Huan

last: Dong

address: No. 58, Zhongshan Road, Yuexiu District, Guangzhou

institute: Sun Yat-sen University First Affiliated Hospital

summary: Plasma from rheumatoid arthritis(RA) patients and healthy controls underwent high-throughput small-RNA sequencing to profile tRNA-derived small RNAs(tsRNAs) in RA and assess their association with disease activity.

overall_design: PANDORA sequencing of plasma in patients with rheumatoid arthritis and healthy individuals

first: Ting

last: Liu

first: Qian

last: Qiu

first: Dubo

last: Chen

first: Liuqin

last: Liang

first: Shiyao

last: Wu

first: Youjun

last: Xiao


title: Research on the Pathogenesis of Systemic Sclerosis

city: Hefei City

first: jing

last: wang

address: No. 81 Meishan Road

institute: Anhui Medical University

summary: By analyzing differentially expressed genes, a preliminary CeRNA network related to the pathogenesis of SSc was established. Further studies will be conducted to determine the impact of genes in this network on the development of SSc.

overall_design: RNA-seq and miRNA-seq were performed on five samples each from the systemic sclerosis case group and the healthy control group.

first: Jing

last: Wang


title: Systems-level investigation of mucopolysaccharidosis IIIA identifies deficient synaptic activity as a key driver of disease progression

city: Melbourne

first: Jan

last: Kaslin

state: Victoria

address: 15 Innovation Walk

department: Australian Regenerative Medicine Institute

country: Australia

institute: Monash University

summary: Mucopolysaccharidoses are lysosomal storage diseases that collectively represent a major cause of lethal, treatment-refractory childhood dementias. Clinically-useful interventions are hampered by an incomplete understanding of their neuropathological origins. Using the zebrafish sgshΔex5-6 model of mucopolysaccharidosis IIIA (MPS IIIA, Sanfilippo syndrome A), we conducted several ‘omics-based analyses to define important features in the progression of neurological disease. We find that the massive endolysosomal burden resulting from increased lysosomal storage of heparan sulfate and other secondarily accumulating substrates induces abnormal microtubule organisation and vesicle trafficking in neurons. This results in a gradual impairment of synaptic vesicle localisation at the presynaptic terminal and consequently impaired neuronal activity. Importantly, the endolysosomal phenotype in MPS IIIA zebrafish precedes the onset of molecular hallmarks of overt synaptic dysfunction, though the larval MPS IIIA brain was found to be more susceptible to perturbation than wild type siblings. Ubiquitous transgenic overexpression of sgsh in sgshΔex5-6 zebrafish corrected neuropathological features at the cellular and molecular level, but was associated with low but elevated rates of developmental malformation. Our findings provide mechanistic evidence linking the well-described lysosomal storage basis for MPS IIIA to its disproportionately neurological manifestations, facilitating development and refinement of future therapeutic interventions for this currently untreatable disorder.

overall_design: RNA-seq profiling of zebrafish of the following genotypes at the indicated stages/tissues: 1) wild type; 24 hpf whole embryos (n = 50 pooled), 5 dpf larval heads (n = 50 pooled), 2-month-old brain (n = 3 pooled), 3-month-old brain (n = 3 pooled), 18-month-old brain (n = 3 pooled). 2) sgshΔex5-6; 24 hpf whole embryos (n = 50 pooled), 5 dpf larval heads (n = 50 pooled), 2-month-old brain (n = 3 pooled), 3-month-old brain (n = 3 pooled), 18-month-old brain (n = 3 pooled). 3) wild type ubiquitously overexpressing wild type sgsh; 2-month-old brain (n = 3 pooled). 4) sgshΔex5-6 ubiquitously overexpressing wild type sgsh; 2-month-old brain (n = 3 pooled).

first: Alon

middle: M

last: Douek

first: Abbas

last: Salavaty

first: Mirana

last: Ramialison

first: Peter

last: Currie


title: HNRNPH controls alternative splicing cooperatively on a transcriptome-wide scale [iCLIP]

first: Julian

last: Konig

summary: To investigate the RNA binding landscape of HNRNPH, we performed an individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) experiment for HNRNPH in MCF7 cells

overall_design: iCLIP2 experiments were performed in MCF7 cells in seven replicates.

first: Kerstin

last: Tretow

first: Mario

last: Keller

first: Mirko

last: Brüggemann

first: Heike

last: Hänel

last: Busch


title: Arid3b suppresses CD8+ T cell infiltration and function in microsatellite stable colorectal cancer via Runx3 [RNA-seq]

city: Beijing

first: Zhidong

last: Gao

address: No.11 Xizhimen South Street

institute: Peking University People’s Hospital

summary: Microsatellite stable/proficient mismatch repair (MSS/pMMR) colorectal cancer (CRC) is characterized by a cold tumor microenvironment, marked by sparse CD8⁺ T cell infiltration and resistance to immune checkpoint inhibitors (ICIs). To uncover regulators that limit CD8⁺ T cell infiltration in MSS CRC, we conducted an in vivo CRISPR/Cas9 screen targeting genes in CD8⁺ T cells using a CMT93 cell-derived tumor model. This screen identified Arid3b as a key negative regulator of CD8⁺ T cell tumor infiltration and antitumor activity. Genetic ablation of Arid3b in CD8⁺ T cells significantly enhanced their intratumoral accumulation and mediated robust tumor control. Mechanistically, Arid3b deficiency upregulated Runx3, promoting a tissue-resident memory phenotype and effector function. Notably, the benefits conferred by Arid3b knockout were abrogated by Runx3 deletion, indicating a Runx3-dependent mechanism. In summary, targeting ARID3B could offer a promising strategy to reshape the tumor microenvironment and sensitize MSS CRC to immunotherapy.

overall_design: RNA-seq profiling of Arid3b-KO or Control OT1 CD8+ T cells co-cultured with or without CMT93-OVA cells for 4 hours

first: Shuo

first: Sen

last: Hou

first: Ce

last: Luo

first: Yingjiang

last: Ye

first: Zexian

last: Zeng


title: Arid3b suppresses CD8+ T cell infiltration and function in microsatellite stable colorectal cancer via Runx3

overall_design: ChIP-seq of HA or IgG in HA-tagged Arid3b-overexpressing CD8+ T cells

last: Wang

first: Yiteng

last: Jin


title: HNRNPH controls alternative splicing cooperatively on a transcriptome-wide scale

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

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Ryder: Epigenome Normalization and Variable Feature Identification

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

summary: Sequencing-based epigenomic profiling significantly advances our understanding of chromatin regulation, yet inherent technical variability complicates accurate cross-sample comparisons. We introduce Ryder, a flexible Python package leveraging stable internal reference regions to perform robust genome-wide normalization. Ryder effectively reduces technical artifacts, distinguishes biological signals, and identifies variable genomic regions across diverse assays, including DNase-seq, ATAC-seq, MNase-seq, and ChIP-seq, with or without spike-in controls.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: DNase-seq with spike-in controls (GSM9065800-GSM9065803) or without spike-in controls (GSM9065796-GSM9065799) were generate to study normalization mehtods for cross-sample comparsions.

first: Guangzhe

last: Ge

first: Keji

last: Zhao


title: Soluble uric acid suppresses neutrophil-mediated host defense in sepsis

city: Munich

first: Qiubo

last: Li

institute: LMU Klinikum

summary: Neutrophils play a critical role in host defense and sterile inflammation. However, neutrophil dysfunction is a hallmark of the acquired immunodeficiency in kidney disease, contributing to an increased susceptibility to infections such as peritonitis, sepsis, and pneumonia. We speculated that the impaired renal clearance of the metabolite soluble uric acid (sUA) may account for neutrophil dysfunction. Indeed, hyperuricemia (HU, serum UA of 9-14 mg/dL) related or unrelated to kidney disease significantly exacerbated the inflammatory immune response to infection by impairing neutrophil dynamics and functions in mice with mono- and polybacterial sepsis. This aggravated inflammatory response was partially reversible by lowering UA levels with febuxostat. We validated these findings in vitro using either neutrophils or serum from healthy individuals or hyperuricemic patients with chronic kidney disease. Depleting UA partially restored neutrophil dysfunction. Mechanistically, sUA impaired the phagocytic capability, bacterial clearance, and oxidative burst in neutrophils by modulating cytoskeletal dynamics and promoting degranulation, processes essential for host defense. In contrast, sUA had no impact on neutrophil extracellular trap formation in neutrophils from healthy subjects exposed to LPS or E.coli. Our findings identify HU related or unrelated to kidney disease as immune regulator in exacerbating the inflammatory response during sepsis, primarily by impairing neutrophil-mediated phagocytosis, pathogen clearance, and oxidative burst. Targeting UA may help to overcome the acquired immunodeficiency during infection, while aggravating sterile forms of inflammation.

overall_design: Human peripheral blood neutrophils were isolated and subjected to different stimulations, including LPS, soluble uric acid (sUA), and fMLP, either individually or in combination. RNA sequencing was performed to investigate the transcriptional responses of neutrophils under these conditions.

first: Juliane

last: Anders

first: Kailey

last: Flora

first: Fengjun

last: Zhang

first: Oliver

last: Soehnlein

first: Stefanie

last: Steiger


title: HNRNPH controls alternative splicing cooperatively on a transcriptome-wide scale [RNA-seq]

first: Julian

last: Konig

summary: To investigate alternative splicing regulation mediated by HNRNPH, we gradually decreased and increased HNRNPH protein concentration in MCF7 cells. Then, we performed splicing analysis using the data from the RNA-Seq.

overall_design: Comparative splicing analysis of RNA-Seq data for MCF7 cells and the derivates with gradual decreased and increased HNRNPH protein levels

first: Kerstin

last: Tretow

first: Mario

last: Keller

first: Mirko

last: Brüggemann

first: Simon

last: Braun

first: Anke

last: Busch

first: Kathi

last: Zarnack

last: König


title: The bone derived from scl-progenitors micromass forms bone marrow [scRNAseq]

city: Chengdu

first: Zhonghan

state: Sichuan

address: 29 Wangjiang Road

department: College of Life Sciences

institute: Sichuan University

summary: Sclerotomal progenitors derived from pluripotent stem cells hold promises for modeling skeletal development and recreating embryonic bone microenvironment to restore hematopoiesis and immunity in ageing. Current strategy to derive mouse sclerotomal progenitors suffered from low differentiation efficiency and heterogenous cell progenies. Here, we developed a fast and efficient strategy to generate sclerotomal progenitors from murine embryonic stem cells (mESCs). Naïve mESCs were differentiated through epiblast-like cells (EpiLCs) and primitive streak, and the sclerotomal fate was directly induced from primitive streak by modulating BMP and SHH signaling, achiving an 85.8% differentiation efficiency. Moreover, the resulting progenitors showed similar global gene expression profiles as primary sclerotome, possessed strong osteochondral bipotential and could recapitulate key features of endochondral ossification upon micromass-mediated osteogenic induction, including bone marrow niche regeneration.  To investigate the cellular component of the bone marrow derived from scl-progenitors micromass , we performed droplet-based scRNAseq (10X Genomics) of the differentiated bone tissue.

overall_design: Single cell RNA sequencing of the cellular component of the bone marrow derived from scl-progenitors micromass

first: Yanhui

last: Deng

first: Jingfei

last: Xiong


title: Therapeutic Efficacy, Biomarker Signatures and Translatability of Semaglutide in the Liver Biopsy-Confirmed GAN DIO-MASH Mouse Model (study 7/9)

first: Henrik

last: Hansen

summary: To investigate the effect of treatment duration on therapeutic efficacy, semaglutide was administered in the GAN-DIO MASH mice. Endpoints included body weight, plasma biochemistry as well as liver histological and transcriptome assessments.

overall_design: GAN DIO-MASH mice with liver-biopsy confirmed MASH and fibrosis were administered semaglutide (30 nmol/kg, s.c.) or vehicle once daily for 12 weeks or 20-24 weeks. Liver samples were collected for RNA sequencing.

first: Jens

last: Kristensen

first: Maja

last: Andersen

middle: H

first: Michael

last: Feigh


title: Effect of hepatic FPN ablation on the liver transcriptome in mice

city: Jeonju

first: Chang Yeob

last: Han

address: 20, Geonji-ro, Deokjin-gu

department: School of Pharmacy

institute: Jeonbuk National University

summary: Iron overload has emerged as a key risk factor for MASLD and metabolic disorders. We explored the effects of hepatocyte-specific knockout of ferroportin (FPN), the only known iron exporter, on the pathogenesis of MASLD and the associated metabolic dysfunction. To investigate the molecular basis, we carried out RNA-sequencing analysis using liver samples from littermate control and hepatocyte-specific Fpn KO mice.

overall_design: RNA-seq profiling of the liver from littermate control and hepatocyte-specific FPN KO mice fed a high-fat diet

first: Hye Jin

last: Jo

first: Ayoung

last: Kim


city: Rosario

first: Tomás

middle: José

last: Steeman

state: Santa Fe

address: Ocampo y Esmeralda

country: Argentina

institute: IBR

summary: Neural crest cells are a transient, multipotent population that gives rise to diverse structures during vertebrate embryonic development, including craniofacial cartilage and pigment cells. Although the transcriptional regulation of neural crest development is well characterized, the role of microRNAs remains less understood. Using a double-transgenic zebrafish model expressing fluorescent reporters under the sox10 promoter, combined with fluorescence-activated cell sorting and RNA sequencing, we identified microRNAs enriched in neural crest cells. We focused on miR-133a-3p and miR-338-3p, previously linked to tumor suppression, to explore their developmental roles. The overexpression of either microRNA led to craniofacial cartilage malformations and reduced melanophore number, accompanied by decreased expression of key regulators including sox9b, sox10, and runx3. Reporter assays confirmed direct targeting of the sox9b 3′untranslated region. In addition, miR-338-3p overexpression increased neural crest cell numbers, suggesting a role in proliferation. These findings uncover novel functions for miR-133a-3p and miR-338-3p in vertebrate craniofacial and pigment cell development, highlighting shared regulatory features between embryogenesis and tumorigenesis.

overall_design: Small RNA-seq profiling of neural crest, non-neural crest, and whole-embryo samples from Tg(sox10:eGFP,mRFP) zebrafish at 16 and 28 hpf.

middle: J

first: Mercedes

last: Torres

first: Andrea

last: Weiner

first: Juan

middle: A

last: Rubiolo

first: Laura

last: Sánchez

first: Gabriela

last: Coux

first: Nora

last: Calcaterra


title: Condensin and topoisomerases cooperate to relieve topological stress at stalled replication forks

city: Montpellier

first: Mégane

last: Da Mota

address: 141 rue de la cardonille

institute: CNRS

summary: Resolving complex topological structures at replication forks is essential for faithful DNA replication, yet the underlying mechanisms remain poorly understood. Evidence from diverse eukaryotes suggests that condensin – best known for driving chromosome condensation in mitosis – may also operate during S phase to alleviate torsional stress in cooperation with topoisomerases. Here, we show in budding yeast and human cells that condensin binds stressed replication forks, where it cooperates with topoisomerases I and II to promote nascent DNA resection and restart replication. Our data indicate that condensin acts together with topoisomerase I at reversed forks to convert positive supercoils into topological DNA structures that are relaxed by topoisomerase II, enabling fork restart. These findings reveal an evolutionarily conserved role for condensin in resolving topological constraints at arrested forks, reminiscent of its function in chromosome segregation, and suggest that this activity helps prevent the formation of toxic chromosome structures during fork arrest and reversal.

overall_design: DNA Copy Number analysis and Chromatin immunoprecipitation DNA sequencing (ChiP-seq) for Brn1-PK9

first: Axel

last: Delamarre

first: Antoine

last: Barthe

first: Jessica

last: Jackson

first: Nail

last: Bouzalmad

first: Alba

last: Torán-Vilarrubias

first: Yea-Lih

last: Lin

first: Cyril

last: Ribeyre

first: Alessandro

last: Vindigni

first: Philippe

last: Pasero

first: Armelle

last: Lengronne


title: Massively multiplex multi-modal chemical screens at single-cell resolution with icCITE-plex

first: Romain

last: Lopez

summary: We present icCITE-plex, a novel cellular barcoding systems that enable multiplexed analysis of multiple independent samples within a single experiment through a combination of viral barcodes and antibody-based plate-barcodes. Using this platform, we successfully profiled 360 drug-dose responses across 475 surface proteins, 64 intracellular epitopes, and the whole transcriptome in human and mouse T cells treated with 56 different kinase inhibitors, demonstrating the method's ability to capture multi-modal cellular responses to chemical perturbations.

overall_design: icCITE-seq of human CD4+ T cells with drug treatments. Naïve CD4+ T cells were isolated from healthy donor PBMCs, transduced with CellTag barcodes, and treated with compounds for 72 hours before single-cell analysis.

first: Kelvin

last: Chen

first: Basak

last: Eraslan

first: Aviv

last: Regev

first: Sakaguchi

last: Shimon


title: Mitochondrial metabolism regulates the immunogenic responsiveness of dendritic cells

city: MADRID

first: Ignacio

last: Heras-Murillo

state: MADRID

address: c/Melchor Fernandez Almagro, 3

institute: CNIC

summary: Activation of dendritic cells (DCs) is linked to increased glycolysis. However, the role of the mitochondrial electron transport chain (ETC) in conventional DC subset function is poorly defined. Here, we revealed that immunogenic activation elevates late oxygen consumption in cDC1s, but not cDC2s. To investigate the relevance of the ETC in DC immunogenicity, we generated mice with impaired ETC complex III function in DCs. ETC complex III impairment attenuated poised or adjuvant-triggered cDC1 activation, migration and capability to prime T cells for anti-cancer immunity, while it had a mild effect on cDC2s. Mechanistically, loss of complex III in cDC1s led to a deregulated redox and metabolite balance causing DNA hypermethylation of PU.1-binding regions. This DNA hypermethylation diminished early stimulus-induced gene expression linked to immunogenic responsiveness of cDC1s, which was rescued via ectopic expression of alternative oxidase. Our findings show how the ETC differentially regulates the immunogenic function of cDC subsets.

overall_design: cDC1s from Uqcrqf/f,  Itgax-Uqcrqf/f, Uqcrqf/f AOX-Rosa26 and Itgax-Uqcrqf/f AOX-Rosa26 mice were FACS sorted and used for WGBS.

first: Josep

last: Calafell-Segura

first: Diego

last: Mañanes

first: Esteban

last: Ballestar

first: Stefanie

last: K. Wculek

first: David

last: Sancho