title: Dysfunctional Mesenchymal Stem Cell-derived Extracellular Vesicles in Chronic Kidney Disease: A Role in Vascular Calcification

city: Beijing

first: Fu

last: Chen

state: Changping District

address: No. 68 North Huinan Street

department: Department of Nephrology

institute: Beijing Jishuitan Hospital

summary:
Background: Vascular calcification (VC) is a severe complication of chronic kidney disease (CKD) and increases cardiovascular morbidity and mortality. Extracellular vesicles (EVs) from bone mesenchymal stem cells (BMSCs) may influence vascular health through intercellular communication. This study investigated how CKD alters the anti-calcific function of BMSC-derived EVs, focusing on microRNA content, particularly miR-29a-3p.
Methods: EVs were isolated from healthy and CKD-affected BMSCs and assessed for size, uptake by vascular smooth muscle cells (VSMCs), and miRNA content. High-phosphate-treated VSMCs and CKD rat models of vascular calcification were used to evaluate the effects of EVs on VC. Circulating miR-29a-3p was measured in hemodialysis patients and correlated with VC severity.
Results: EVs from both groups showed comparable size and VSMC uptake. However, CKD-derived EVs had an altered miRNA profile, including markedly reduced miR-29a-3p, and showed diminished ability to inhibit phosphate-induced calcification. Restoration of miR-29a-3p suppressed calcification in vitro and in vivo. In hemodialysis patients, circulating miR-29a-3p was inversely associated with calcification severity.
Conclusions: CKD impairs the anti-calcific function of BMSC-derived EVs partly through downregulation of EV-associated miR-29a-3p. Restoring miR-29a-3p may help mitigate VC in CKD, and circulating miR-29a-3p may serve as a clinical biomarker.

overall_design: RNA samples extracted from primary bone marrow mesenchymal stem cells (BMSCs) isolated from both chronic kidney disease (CKD) model rats and healthy controls. The experimental design includes three biological replicates for each condition. The study compares gene expression profiles between CKD-affected and normal BMSCs to investigate the molecular alterations associated with CKD.

first: Chen

last: Fu

first: Qiaojing

last: Liang

first: Wenhu

last: Liu

first: Yingjie

first: Weikang

last: Guo


title: Smoothened-mediated signaling contributes to immune and non-immune functions of microglia

status: Public on Jul 01 2026

city: Le Kremlin-Bicêtre

first: Elisabeth

last: TRAIFFORT

address: 80 Rue du Général Leclerc

country: France

institute: Inserm

type: Expression profiling by high throughput sequencing

summary: As the brain resident macrophages, microglia are endowed with functions ranging from key roles in cerebral development to mediation of innate immune responses. Diversity in microglia actions is consistent with the wide repertoire of their context-dependent states. However, mechanisms involved in the control of those states are still poorly understood. Here, we studied a small population of microglia expressing Smoothened, the well-known key transducer of the Hedgehog signaling. Our loss- and gain-of-function approaches uncover the so far unsuspected role of Smoothened intrinsic activity in triggering suitable innate immune responses to pathogens via the control of proper inflammatory and phagocytic states. This observation corelates with the detection of Smoothened upregulation in human fetal brains with congenital cytomegalovirus infection. Moreover, Smoothened contributes to the emergence of transient neonatal microglia by controlling its molecular signature. Altogether, our results shed new insight on improper microglial states related to impaired Smoothened activity and open therapeutic perspectives based on exogenous and non-canonical activation of this receptor.

overall_design: RNA-Seq profiling of microglial cells isolated from conditional Smo inducible KO (SmoiKO) and Smo wild-type (SmoWT) animals analyzed at the early postnatal day 7 (P7) and in adulthood (P90).

last: Traiffort

first: Carlos

last: Parras


title: Transcriptomic analysis of the human macrophage response to 13 polymeric materials.

city: Bilthoven

first: Els

last: Alsema

address: Antonie van Leeuwenhoeklaan 9

department: Centre for Health Protection

country: Netherlands

institute: RIVM

summary: Fibrosis around implanted medical devices is a common complication that affects their functionality and long-term success. However, reliable in vitro assays to predict this fibrotic response are currently lacking, limiting the ability to generate human-relevant preclinical data. In this study, we used THP-1-derived human macrophages to evaluate cellular responses relevant for in vitro prediction of fibrosis across six groups of polymeric materials with varying surface texture, chemical composition, stiffness, or porosity. Cell death, metabolism, cytokine secretion, and transcriptomic profiles were assessed and compared to previously characterised in vivo fibrosis outcomes. All assays were able to distinguish between high and low fibrosis-inducing materials within one or more material groups. Importantly, different biomaterials differentially modulated the various readouts, with some assays showing greater sensitivity to specific material properties than others. Conditional logistic regression modelling identified increased secretion of TNF-α at the 24 hour timepoint and IL-1RA at the 72 hour timepoint as being associated with higher fibrosis levels. Transcriptomic profiling revealed distinct, material-specific gene expression changes, alongside shared responses for certain material subsets, indicating convergent macrophage activation pathways. Notably, several high fibrosis materials showed differential regulation of genes involved in oxidative stress pathways. Additionally, gene set enrichment analysis revealed an upregulation of lipid and cholesterol metabolism pathways in several high fibrosis materials. Altogether, these findings demonstrate the potential of multi-assay macrophage profiling for in vitro biomaterial screening and suggest candidate markers for future assay development.

overall_design: mRNA profiles of human THP-1 derived macrophages that were cultured on 13  polymeric materials. THP-1 cells were differentiated to macrophages on the polymer surfaces by 16h treatment with 50ng/ml phorbol 12-myristate 13-acetate (PMA). RNA samples were collected after a 24h rest period without PMA. N=1 and n=3 replicates for all experimental conditions.

middle: C

first: Jeroen

middle: L

last: Pennings

first: Hennie

middle: M

last: Hodemaekers

first: Juul

last: Verbakel

first: Leanne

middle: E

last: Fisher

first: Matthew

middle: J

last: Price

first: Derek

last: Irvine

first: Morgan

middle: R

last: Alexander

first: Amir

last: Ghaemmaghami

first: Nick

last: Beijer

first: Jan

last: de Boer


title: In vivo circadian transcritpome of human enobronchial tissue

city: St Louis

first: Jeffery

last: Haspel

state: MO

address: 660 S Euclid Avenue

country: USA

institute: Washington University, St Louis

summary: The goal of this experiment was to identify genes exhibting biological rhythms in gene expression in human endobornchial tissue.

overall_design: We performed serial bronchoscopies on organ transplant donors awaiting organ procurement at a regional organ procurement center in our area.  Bronchoscopies were performed every 4 hours for 24-28 hours, obtaing endobronchial brush samples from 2-4 sub-semental airways with each instance.  The samples were processed to obtain bulk mRNA and analyzed by bulk sequencing using standard protocols.

first: Huram

last: Mok

first: Carrie

last: Gierasch

first: Jeff


title: SFB-Driven Remodeling of Peyer’s Patches Enhances IgA and IgG2b Class Switching and Atypical Memory B Cell Generation

city: Bethesda

first: Byunghyun

last: Kang

state: Maryland

address: 9000 Rockville Pike

institute: NIAID

summary: The intestinal microbiota plays a central role in shaping host mucosal immunity, but the mechanisms by which specific commensals influence B cell responses remain incompletely defined. Segmented filamentous bacteria (SFB), potent inducers of Th17 cells, have been implicated in both protective and pathogenic immune outcomes. Here, we show that SFB colonization in specific pathogen-free (SPF) mice induces a profound remodeling of Peyer’s patches (PPs), characterized by increased cellularity, germinal center (GC) formation, and robust class switching to IgA and IgG2b, but not IgG1. Using flow cytometry, bone marrow chimeras, and single-cell RNA sequencing coupled with BCR repertoire analysis, we demonstrate that SFB enhances recruitment of naïve B cells through the CXCR5-CXCL13 axis and promotes T cell-dependent expansion of both GC and memory B cells. These memory B cells exhibit hallmark features of atypical B cells (ABCs), including CD11c expression and somatic hypermutation, and arise via a GC-dependent pathway. SFB increases the number of activated CD11c+SIRPa+BST2-CD11b+ DCs in the the PP subepithelial dome (SED), and T helper 17 (Th17) and T follicular helper (Tfh) cells. Surprisingly, unlike previous reports, neither Th17 effector function (IL-17R-/-) nor Th17-to-Tfh conversion (CD4CRE-RORgtfl/fl) was essential for the observed B cell changes. Finally, we show that SFB colonization enhances clonal diversity and somatic hypermutation in IgA⁺ and IgG2b⁺ B cells qualitatively as well as quantitatively. These findings establish a mechanistic link between microbiota composition and mucosal B cell immunity, with implications for vaccine responses, mucosal homeostasis, and autoimmune susceptibility.

overall_design: SFB-containing fecal material from SFB(+) Taconic C57BL/6J wild-type (WT) mice was transferred to SFB(-) JAX C57BL/6J WT mice via oral gavage. Two weeks post-transfer, ileal Peyer’s patches were harvested from both SFB(-) (control) and SFB-colonized JAX WT mice.  Libraries were then normalized, pooled, and subjected to high-throughput sequencing on the Illumina HiSeq X platform.

first: Eun-Do

last: Kim

first: Brian

last: Kelsall


title: Mitochondrial double-stranded RNA triggers chronic stress in aged neurons

city: Tucson

first: Kevin

last: Rhine

state: AZ

address: 1703 E Mabel St

department: Pharmacology & Toxicology

institute: University of Arizona

summary: Neurodegenerative diseases are linked with dysregulation of the integrated stress response (ISR), which coordinates cellular homeostasis during and after stress events. We previously showed that aged neurons suffer from chronic stress that compromises cellular resiliency to new stress events; however, the cause of aging-linked chronic stress was unclear. Here, we leverage directed transdifferentiation of human fibroblasts into aged neurons to determine the source of ISR activation. We demonstrate that increased accumulation of cytoplasmic double-stranded RNA (dsRNA) activates the eIF2α kinase PKR, which in turn triggers the ISR in aged neurons and leads to sequestration of dsRNA in stress granules. Aged neurons accumulate endogenous mitochondria-derived dsRNA that directly binds to PKR. This mitochondrial dsRNA leaks through damaged mitochondrial membranes and forms cytoplasmic foci in aged neurons. Finally, we demonstrate that PKR inhibition leads to the cessation of stress, resumption of cellular translation, and restoration of RNA-binding protein expression. Together, our results identify a source of RNA stress that destabilizes aged neurons and may contribute to neurodegeneration.

overall_design: This accession code contains four types of RNA-seq: (1) bulk RNA-seq, (2) dsRNA-seq relying on a J2 immunoprecipitation following RNA isolation; (3) eCLIP-seq relying on RNA purified from an immunoprecipitated protein; and (4) Riboseq relying RNA shielded from digestion by ribosomal footprints.

first: Elle

last: Epstein

first: Orel

last: Mizrahi

first: Gene

middle: W

last: Yeo


title: Single-cell RNA sequencing of kidney tissue from a conditional Vhlh knockout mouse model. [sc-RNA_Seq]

city: Taichung

first: Hieu-Huy

last: Nguyen-Tran

state: Taichung

address: Xueshi

department: Graduate Institute of Biomedical Sciences

country: Taiwan

institute: China Medical University

summary: Clear cell renal cell carcinoma (ccRCC) is the most common and aggressive subtype of renal cancer, accounting for approximately 75% of cases. A well-established early oncogenic event in ccRCC tumorigenesis is the loss of the tumor suppressor gene von Hippel-Lindau (VHL), which occurs in roughly 80% of cases. However, deletion of Vhlh— the mouse VHL locus —alone is insufficient to drive malignant ccRCC development in mouse models. Previously, we generated a conditional Vhlh knockout model targeting a subset of kidney epithelial cells using Hoxb7 promoter-driven Cre recombinase (Hoxb7-Cre-GFP; VhlhloxP/loxP, henceforth Vhlh-KO). This model recapitulates several features of premalignant ccRCC, including immune cell infiltration, fibrosis, epithelial hyperplasia in cortical and medullary tubules, pseudohypoxic responses (e.g., metabolic reprogramming and increased angiogenesis), and the presence of clear-cell clusters. As such, this strain represents a rare example of an autochthonous model of early-stage ccRCC. To further investigate the early oncogenic and microenvironmental changes that contribute to ccRCC initiation, we performed single-cell RNA sequencing (scRNA-seq) on whole kidney tissues from Vhlh-KO mice and their wild-type (WT) counterparts.

overall_design: We performed single-cell RNA-Seq of whole kidney tissue from three-month-old of Hoxb7-Cre-GFP; VhlhloxP/loxP (Cre-Vhlh-KO) or Hoxb7-Cre-GFP (wild-type; Cre-WT) mice. Mice were anesthetized and perfused with 30 mL Hank's Balanced Salt Solution (HBSS; Gibco, 14170112) to remove serum and red blood cells. Kidney tissues were collected and homogenized using gentleMACS C Tubes (Miltenyi Biotec) in 10 mL of HBSS digestion buffer containing 0.2% collagenase II (Sigma #6885), 0.04% Dispase (Sigma #D4693), 1 mg/mL DNase I (Sigma #10104159001), 1% BSA, and 1.5 mM CaCl₂. The homogenates were incubated at 37 °C for 30 minutes with intermittent shaking. Cell suspensions were passed through 40 µm cell strainers, and the resulting pellet was collected by centrifugation at 300 × g for 10 minutes at 4 °C. Cells were then stained with 7-AAD (BioLegend #420403) to assess viability. After staining, the cell suspensions were washed and subjected to flow cytometric sorting using a FACSAria III Cell Sorter (BD Biosciences) to isolate live, single cells (singlets, 7-AAD-negative). The sorted cells were submitted to Genomics BioSci & Tech Co. (New Taipei City, Taiwan) for single-cell RNA sequencing, performed using the Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3 (#CG000183, 10x Genomics, Pleasanton, CA, USA) according to the manufacturer’s instructions. Single-cell RNA-seq analysis was performed using the Seurat package (v5) in R. Briefly, a Seurat object was created from the input files: “barcodes.tsv,” “genes.tsv,” and “matrix.mtx.” Low-quality cells were filtered by excluding those with fewer than 200 or more than 2,500 unique feature counts, as well as those with >10% mitochondrial gene content. Data normalization, scaling, and dimensionality reduction were performed following the standard Seurat pipeline. Cell type annotation was conducted using canonical markers with the SingleR package.

first: Thi-Ngoc

last: Nguyen

first: Tuong-Vi

first: Dinh-Xuan

last: Pham

first: Tien

last: Hsu


title: Genetic diagnosis of 5 patients in a consanguineous family

city: Istanbul

first: Elif

last: ÖNEL

address: Buyukdere Street

country: Turkey

institute: Istanbul Technicial University

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Rare disease loci is searched via linkage mapping using these SNP markers.

overall_design: 7 individuals from a consanguineous Pakistani family is genotyped using many different bead chips. GT files are merged and common SNPs are used for linkage mapping to detect rare disease loci.

first: Aslı

last: TOLUN


title: The airway transcriptome in type2 cytokine biomarker-high and -low severe asthma

city: Oxford

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

country: United Kingdom

institute: University of  Oxford

summary: Type-2 (T2) cytokine-driven eosinophilic exacerbations in severe asthma respond to targeted biological therapies, but the mechanisms of residual disease expression when T2-cytokine biology is suppressed are poorly understood. Pathological studies indicate that ongoing mast cell activation and persistent airway remodelling are important factors contributing to symptoms, reduced lung function, and non T2 disease. The molecular mechanisms driving these features of asthma in the absence of T2 biology are ill-defined. To explore the molecular pathways that are dysregulated in T2 biomarker-high and -low severe asthma. T2 biomarker-high severe asthma (T2-high, n=18) was compared to biomarker-intermediate (T2-intermediate, n=23) and biomarker-low (T2-low, n=11) severe asthma, and healthy controls (n=20). Bronchoscopy samples were analysed by bulk RNAseq. Treatment-optimised asthma, independent of confounding by therapeutic corticosteroids, was characterised by upregulation of the mucins MUC5AC, MUC2, lysozyme, CEACAM5, SYNCRIP, typical T2-genes POSTN and IL33, the transcription factor FOS; and ITGB8 which regulates TGF-β activation and airway remodelling. When comparing between phenotypes steroid-resistant T2-high severe asthma was characterised by upregulation of expected T2 high genes, epithelial barrier genes and keratins. T2-low asthma was characterised rather by Th1 and Th17 associated genes, including IDO1, CXCL10, GBP1, the T cell checkpoint receptor LAG3, neuroimmune genes SGC2 and CALCA, and by enrichment of mast cells. Steroid-responsive T2-intermediate asthma was distinctly characterised by expression of the antimicrobial peptide BPFIA1, virus activated signatures, enrichment for  mast and NK cells, and distinct transcription factors NFKB1, TBX21, IRF1, IRF2, BATF and STAT2 associated with pathogen defence. We have characterised three major asthma phenotypes, independent of confounding by therapeutic corticosteroids, identifying gene sets and pathways distinct to each.

overall_design:
Adults aged 18–70 with asthma were recruited, all of whom were non-smokers with less than 15 pack-years of smoking history. Participants were confirmed adherent to treatment through prescription checks, biomarker assessments, and FeNO suppression testing. Current biologic use was an exclusion criterion. Participants underwent comprehensive baseline assessments including clinical history, lung function, methacholine challenge (when appropriate), and induced sputum sampling. Severe asthma patients were prospectively classified into T2 biomarker-defined groups: T2-high FeNO-non suppressors, T2-low, and T2-intermediate, based on FeNO, blood eosinophils, and previous participation in the RASP biomarker-guided treatment optimisation study.

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

first: Jiashu

last: Shen

first: Rekha

last: Chaudhuri

first: Steve

last: Bicknell

first: Adel

middle: H

last: Mansur

first: Rahul

last: Shrimanker

first: Ian

middle: D

last: Pavord

first: Stephen

last: Fowler

first: Vanessa

last: Brown

first: Lorcan

middle: P

last: McGarvey

first: Peter

last: Howarth

first: Joseph

last: Arron

first: Liam

middle: G

last: Heaney

first: David

middle: F

last: Choy

middle: S

first: Emanuele

last: Marchi

last: Bradding


title: RNA-seq analysis of BRD4 knockdown in U937 cells

city: Hefei

first: Mengqing

last: Gao

state: Anhui

department: Department of Hematology

country: China

institute: The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China

summary: Succinyl-CoA synthetase was reported to sustain mitochondrial respiration and enhance leukemia proliferation. However, the biological mechanisms of mitochondrial metabolism and leukemia pathogenesis, beyond energy production, remains underexplored. Here we report that depletion of SUCLG1 causes hypersuccinylation in leukemia cell lines, which impairs cell proliferation and leukemia progression. We hypothesize that increased histone H3 succinylation attenuates bromodomain interaction with chromatin, hence disrupting BRD4-mediated leukemogenic genes transcription. To confirm the hypothesis, we performed RNA-seq analysis in SUCLG1 knockout cell lines, JQ1-treated cells, Ksuc high and low primary AML patients.

overall_design: To characterize BRD4-mediated gene transcription, we generated control and two BRD4 knockdown (KD) U937 cells with lentiviral shRNAs and performed RNA-seq analysis.

first: Domenico

last: Iuso

first: Xiaoyu

last: Zhu


title: Molecular characterization of flower bud dormancy under constrained temperatures

city: Villenave d Ornon

first: mathieu

last: fouché

state: Gironde

address: 71 avenue Edouard Bourlaux

department: UMR BFP

institute: INRAE

summary: Temperate perennial plants have to adapt their growth in order to survive over winter conditions and protect their tissues by entering into dormancy.  The dormancy phenomenon is a complex process regulated by many factors, externals (photoperiod and temperature) or internals through the transport towards the buds. In order to better understand the molecular mechanisms involved in the regulation of dormancy, we conducted a transcriptomic analysis of flower buds from the late flowering sweet cherry cultivar 'Regina' in controlled condition with a cold deprivation treatment and in field conditions from July 2018 to June 2019. Moreover, to complement this experiment in order to explore the response to temperature in this opposite way, we performed a cold exposure from July 2023 and March 2024.

overall_design: Flower buds of sweet cherry cultivar 'Regina' were sampled from July 2018 to May 2019 at 11 dates: July 30th, August 30th, October 1st, October 31th, December 3th, January 2nd, January 15th, February 1st, February 28th, March 28th, April 30th, May 31th with three biological replicates, corresponding to independent buds. Cold exposure sampling was preformed during 2023-2024 season at 11 dates July 21th, August 22nd, September 21th, October 24th, November 23th, December 15th, January 5th, January 26th, February 16th and March 16th.

first: Bénédicte

last: Wenden

first: Mathieu

last: Fouché

first: Hélène

last: Bonnet


title: Subclinical Neonatal HSV-1 Infection Triggers Immune Responses and Modulates Neurological Pathways Leading to Long-Term Sequelae [Visium]

city: Lebanon

last: Leib

state: NH

address: 1 Medical Center Drive

department: Dept. of Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth

summary: Subclinical neonatal infections represent a poorly understood but potentially critical determinant of long-term neurodevelopmental outcomes. Here, we show that neonatal exposure to herpes simplex virus type 1 (HSV-1), even in the absence of overt symptoms, induces persistent transcriptional and cellular changes in the brain that correlate with anxiety-like behavior later in life. Neonatal mice were subclinically infected intranasally with HSV-1 and assessed at acute (3 days post-infection) and chronic (5–6 weeks post-infection) stages using cytokine profiling, bulk RNA sequencing, and spatial transcriptomics. We observed sustained elevation of immune mediators, including CXCL10, IL-6, and IL-10, at both acute and chronic stages. Bulk RNA-seq analysis identified over 490 differentially expressed genes, with distinct expression modules that diverged significantly between early and late infection phases. Notably, several modules exhibited minimal acute changes but showed pronounced dysregulation chronically, highlighting a temporal evolution in gene expression extending beyond the initial immune response. Spatial transcriptomic analysis at the acute phase demonstrated region-specific dysregulation in pathways involving MAPK signaling, chemokine signaling, axon guidance, and long-term depression. These changes were localized to brain regions critical for affective regulation, including the midbrain, hypothalamus, and alar thalamus. Cell-type deconvolution of bulk RNA-seq data further revealed an increased abundance of astrocytes and microglia, underscoring the early involvement of glia in neuroimmune responses. Collectively, our findings illustrate that clinically silent neonatal HSV-1 infection induces spatially and temporally distinct transcriptional alterations in the developing brain. This study provides mechanistic insights into the relationship between early-life viral exposure and long-term modifications in neural circuitry and behavior, highlighting the developmental vulnerability of the neonatal brain to subclinical immune perturbations.

overall_design: Visium spatial transcriptomics of brain sample, mock infection and 100 PFU subclinical HSV-1

first: R

last: Alers-Velazquez

first: A

last: Dutton

first: C

last: Garland

first: J

last: Mehrbach

first: M

last: Martinez

first: OM

last: Wilkins


title: Combination with oxaliplatin improves abscopal effect of oncolytic virotherapy through reorganization of intratumoral macrophages [scRNA-seq]

city: Ibaraki

first: Kentaro

last: Ikegami

address: 21 Miyukigaoka, Tsukuba

country: Japan

institute: Astellas Pharma Inc.

summary: Oncolytic virotherapy is a unique and promising immunotherapy. In our prior study, a recombinant oncolytic vaccinia virus carrying IL-7 and IL-12 (hIL-7/mIL-12-VV) showed robust antitumor efficacy in both immunogenic CT26.WT and poorly immunogenic Lewis lung carcinoma (LLC) within the treated tumors. However, the efficacy was limited in virus non-treated (distant) LLC tumors. Here we identified oxaliplatin as a powerful combination partner for an oncolytic vaccinia virus to achieve strong efficacy in the virus-injected tumors and the distant tumors. To understand the molecular and cellular mechanisms underlying the improved abscopal effect of the combination treatment, distant LLC tumors were assessed via single cell RNA-sequencing.

overall_design: scRNA-seq profiling of oxaliplatin and recombinant vaccinia virus carrying IL-7 and IL-12 treated LLC tumor (distant tumor) on seven days after each treatment.

first: Kyoko

last: Tomita

first: Midori

last: Yamashita

first: Yoshiko

last: Shimizu

first: Nobuaki

last: Amino

first: Shinsuke

last: Nakao


title: Combination with oxaliplatin improves abscopal effect of oncolytic virotherapy through reorganization of intratumoral macrophages II

summary: Oncolytic virotherapy is a unique and promising immunotherapy. In our prior study, a recombinant oncolytic vaccinia virus carrying IL-7 and IL-12 (hIL-7/mIL-12-VV) showed robust antitumor efficacy in both immunogenic CT26.WT and poorly immunogenic Lewis lung carcinoma (LLC) within the treated tumors. However, the efficacy was limited in virus non-treated (distant) LLC tumors. Here we identified oxaliplatin as a powerful combination partner for an oncolytic vaccinia virus to achieve strong efficacy in the virus-injected tumors and the distant tumors. To understand the molecular mechanism of abscopal effect of hIL-7/mIL-12-VV in combination with oxaliplatin, we evaluated RNA-sequencing signatures of LLC tumors on the virus non-treated side.

overall_design: RNA-seq profiling of oxaliplatin and recombinant vaccinia virus carrying IL-7 and IL-12 treated LLC tumor (distant tumor) on three and seven days after each treatment.


title: Combination with oxaliplatin improves abscopal effect of oncolytic virotherapy through reorganization of intratumoral macrophages III

summary: Oncolytic virotherapy is a unique and promising immunotherapy. In our prior study, a recombinant oncolytic vaccinia virus carrying IL-7 and IL-12 (hIL-7/mIL-12-VV) showed robust antitumor efficacy in both immunogenic CT26.WT and poorly immunogenic Lewis lung carcinoma (LLC) within the treated tumors. However, the efficacy was limited in virus non-treated (distant) LLC tumors. Here we identified oxaliplatin as a powerful combination partner for an oncolytic vaccinia virus to achieve strong efficacy in the virus-injected tumors and the distant tumors. To understand the molecular mechanism of abscopal effect of hIL-7/mIL-12-VV in combination with oxaliplatin, we evaluated RNA-sequencing signatures in LLC tumors inoculated in immuno-comprobised mice.

overall_design: RNA-seq profiling of oxaliplatin and recombinant vaccinia virus carrying IL-7 and IL-12 treated LLC tumor in NOD SCID mice on three days after each treatment.


title: Combination with oxaliplatin improves abscopal effect of oncolytic virotherapy through reorganization of intratumoral macrophages

summary: Oncolytic virotherapy is a unique and promising immunotherapy. In our prior study, a recombinant oncolytic vaccinia virus carrying IL-7 and IL-12 (hIL-7/mIL-12-VV) showed robust antitumor efficacy in both immunogenic CT26.WT and poorly immunogenic Lewis lung carcinoma (LLC) within the treated tumors. However, the efficacy was limited in virus non-treated (distant) LLC tumors. Here we identified oxaliplatin as a powerful combination partner for an oncolytic vaccinia virus to achieve strong efficacy in the virus-injected tumors and the distant tumors. To understand the molecular mechanism of enhanced antitumor efficacy, we evaluated RNA-sequencing signatures in LLC tumors treated with oxaliplatin alone, hIL-7/mIL-12-VV alone and their combination.

overall_design: RNA-seq profiling of oxaliplatin and recombinant vaccinia virus carrying IL-7 and IL-12 treated LLC tumor


title: Subclinical Neonatal HSV-1 Infection Triggers Immune Responses and Modulates Neurological Pathways Leading to Long-Term Sequelae

first: David

overall_design: Data iare whole-brain bulk RNASeq samples from mice that were infected with either mockulum (cell debris) or 100 PFU HSV-1 at two timepoints, 7 days-post-infection and 5 weeks-post-infection. For the 7DPI group, 7 samples are HSV-1 infected, 5 are mockulum infected. For the 5WPI group, 4 samples are HSV-1 infected and 4 are mockulum infected.


title: Spatial transcriptomics and scRNA-sequencing on gastrocnemius muscle form B6-mdx and D2-mdx mice

city: Lyon

first: Benedicte

last: Chazaud

address: 8 Avenue Rockefeller

department: Institut NeuroMyoGène

institute: Université Claude Bernard Lyon 1

summary: We investigated the cell-type composition of muscle domains that associate with muscle degeneration severity in two mouse models of human DMD, namely the B6.mdx and D2.mdx. We first combined immunofluorescence-based histological analysis and spatial transcriptomics to highlight specific muscle tissue clusters that display dystrophic features with necrotic fibers, inflammatory cell infiltration and increased fibrosis. Using single-cell RNA-sequencing reference and spatial deconvolution, we profiled cell types and states within each dystrophic domain, thereby identifying the enrichment for specific cell subpopulations in these spatial clusters.

overall_design: For spatial transcriptomics, gastrocnemius muscles from 10-week-old C57BL/6J and D2.B10 (DBA/2-congenic) mice were either isolated, embedded in OCT and flash-frozen in liquid nitrogen-cooled isopentane. Embedded muscle was transversely sectioned at 10µm thickness and processed for 10X Genomics Visium analysis. For single-cell RNA-sequencing, FACS-isolated cells of gastrocnemius muscles from 10-week-old C57BL/6J and D2.B10 mice were captured using the 10X Genomics Chromium Platform and sequenced using an Illumina NextSeq 50.

first: Caroline

last: Brun

first: Fabien

last: Le Grand


title: Maternal Helminths Rewire the Microbiota to Promote Offspring Antiviral Immunity via Indole-3-Propionic Acid

city: Princeton

first: Krist

last: Antunes Fernandes

state: NJ

address: 215 Ewig St

department: MOLBIO

institute: Princeton University

summary: Maternal environmental exposures are critical in shaping offspring immunity. Yet, the role of helminths, mammals’ symbiotic evolutionary partners that have been eliminated from modern societies, remains poorly understood. Here, we show that maternal helminth infection enhances type I interferon (IFN-I) signaling in the offspring’s lung epithelium, conferring broad and lasting protection against respiratory viruses. Using cross-fostering, antibiotics, and gnotobiotic systems, we demonstrate that this antiviral immunity is mediated by helminth-altered maternal microbiota. Mechanistically, we identify the microbial tryptophan metabolite indole-3-propionic acid (IPA) as a key driver of IFN-I responses in lung epithelium. Furthermore, the tryptophan metabolic pathway is enriched in the microbiome of helminth-infected human populations, and IPA alone is sufficient to enhance IFN-I signaling in human bronchial epithelial cells. We uncover a conserved trans-kingdom mechanism by which maternal helminths imprint offspring antiviral immunity and propose that microbial metabolites could be harnessed to restore early-life antiviral defenses in helminth-depleted societies.

overall_design: Epithelial cells in barrier tissues form the primary interface between the host and the environment. Building on prior studies that have shown epithelial cells can retain memory of environmental insults, including maternal exposures, we profiled epithelial transcriptomes in the lung, small intestine, and skin of adult offspring of control or Heligmosomoides polygyrus bakeri (Hpb) infected mothers.


title: Single-cell transcriptomic analysis of endometrium pre-receptivity and receptivity stages in porcine

city: Qingda

first: yadan

last: Jin

state: 山东Shandong

address: Qingdao

institute: Qingdao Agricultural University

summary: The reproductive efficiency of pigs directly affects the economic benefits of the industry. Endometrial receptivity, as a key factor affecting embryo implantation and development, is of great significance for its research. We constructed the single-cell transcriptome maps of the pre-receptivity and receptivity phases of porcine endometrium and identified epithelial cells and stromal cells as the main types of endometrial cells. There are significant differences in the composition of epithelial cell subsets between the two tissues. We also studied the functional characteristics of epithelial cells and stromal cells in the endometrium during the pre-receptivity and receptivity phases, as well as the gene expression levels and cell differentiation pathways related to endometrial receptivity in these two types of cells. Intercellular communication analysis indicated that luminal epithelial cells exhibited high activity in the endometrium before receptivity. In the endometrium during the receptivity period, glandular epithelial cells and ciliated epithelial cells are more active. Furthermore, the BMP, VEGF and TGF-β signaling networks related to endometrial receptivity also exhibited different characteristics in the two periods. We also compared the functional differences of immune cells and the expression levels of genes related to the inflammatory microenvironment between the two tissue types. This study analyzed the transcriptional characteristics of porcine endometrial cells during the receptivity phase and revealed its unique molecular regulatory mechanism. It provides an important theoretical basis and a new perspective for understanding the abnormalities of the endometrial microenvironment in reproductive disorders.

overall_design: All experimental animals were three years old with a similar genetic background. We selected two Yorkshire sows with successful artificial insemination. The one at 7 days of gestation was the Pre endometrial receptive period (Pre-ER) sample, and the one at 13 days of gestation was the Endometrial receptive period (ER) sample. We defined the day of artificial insemination as day 0 of pregnancy and endometrial samples were collected from each uterine horn; animals requiring slaughter were humanely euthanized as necessary to relieve suffering.


title: Characterising Interferon-beta responses in human stem-cell derived glia

city: Dublin

first: Michael John

last: Dolan

state: Dublin 2

address: Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin

country: Ireland

institute: Trinity College Dublin

summary: This repository contains data characterizing the transcriptomic response of human stem-cell derived glia to Interferon-Beta or Control. This consists of two experiments. First, human embryonic stem cell-derived microglia were differenciated and exposed to both conditions, then subjected to single-cell RNA sequencing. Second, induced astrocytes were derived from the same line, exposed to interferon-beta and underwent bulk RNA sequencing.

first: Michael-John

first: Raphael

last: Rakosi-Schmidt

first: Naeem

last: Nadaf

first: Yuesang

last: Lin

first: Beth

last: Stevens

first: Evan

middle: Z

last: Macosko


title: ARP-1 wild-type and ARP-1 carfilzomib-resistant cells RNA-seq analysis

city: houston

first: chuanchao

last: zhang

address: 6550 fanin st

institute: houston methodist

summary: Proteasome inhibitors (PIs) such as carfilzomib (Cfz) are highly efficacious for patients with Multiple myeloma (MM). However, relapses and acquired resistance to PI treatment emerges in most patients. Here, we established Cfz-resistant MM cells. RNA-seq analysis revealed significant alterations in cholesterol- and lipid-related metabolic pathways in the resistant cells.

first: Chuanchao

last: Zhang


title: Large-scale and high-resolution mass spectrometry-based proteomics profiling defines molecular subtypes of nasopharyngeal carcinoma for therapeutic targeting

city: Fuzhou

first: Guosheng

last: Hu

state: Fujian

address: Fujian Normal University, Cangshan Campus, No.8 Shangsan Road, Cangshan District, Fuzhou, Fujian, China

department: College of Life Sciences

institute: Fujian normal university

summary: Challenges in the precision diagnosis and treatment of nasopharyngeal carcinoma (NPC) persist, primarily due to the lack of a multi-omics-based molecular typing system and effective targeted therapeutic strategies. In this study, we integrated proteomic and phosphoproteomic analyses of NPC tissues and normal nasopharyngeal tissues to systematically identify key dysregulated protein networks, which are enriched in genes associated with cell cycle, cilium function, immune response, metabolism, mTOR signaling, and responses to virus infection. Based on these proteomic characteristics, we classified NPC into two molecular subtypes, subtype 1 and 2, which exhibit significant clinical heterogeneity. Moreover, we identify protein signatures for both normal and cancerous tissues, as well as for the two molecular subtypes, and developed diagnostic and prognostic models. Through computational drug repurposing and experimental validation, we identified the pan-histone deacetylase inhibitor Panobinostat as a potent anti-tumor agent for NPC in both in vitro and in vivo models. Our findings revealed that Panobinostat inhibits MYC signaling, thereby disrupting the transcriptional activation of the ATR-CHK1 axis. This reduction in ATR-CHK1 activity leads to impaired homologous recombination repair efficiency, ultimately leading to DNA damage accumulation. Notably, we demonstrated a synergistic therapeutic effect when Panobinostat was combined with radiotherapy, resulting in enhanced cytotoxicity against NPC cells. In summary, we established a multi-omics molecular typing system for NPC, developed diagnostic and prognostic marker panels, and highlighted the therapeutic potential of Panobinostat in combination with radiotherapy. These findings lay a solid foundation for precision diagnosis, prognostic stratification, and personalized treatment strategies in NPC.

overall_design: The RNA-seq sequencing performed in this study was designed to reveal the gene changes regulated by the treatment of Panobinostat.

first: Yiping

last: Wu

first: Yaohui

last: He

first: Zhiqin

last: Li

first: Qingwen

first: Wen

last: Liu

first: Qin


title: Circadian Rhythm in Coronavirus Pneumonia Severity

first: Jeffery

last: Haspel

summary: The goal of this experiment is to examine how circadian rhythms affect coronavirus pneumonia severity. To this end, we infected mice at different times of day with mouse hepatitis virus-1 (MHV-1), which is a beta-coronavirus native to rodents that produces similar histological features as SARS, MERS, and COVID-19. Bulk RNAseq was used to generate a list of differentially expressed genes (DEGs) based on the circadian time of MHV-1 exposure. mice The cells were synchronized with 100nM dexmethosone to produce coherent circadian gene expression patterns in the cultures.  Cells were then longitudinally harvested every 4 hours for 48 hours starting 12 hours after dexamethasone treatment.  To obtain basic spatial information, we also analyzed lung parenchyma and BAL cells separately, representing the lung parenchyma and luminal airspace compartment that is largely composed of AMs and other luminal macrophages. In both the lung parenchyma and BAL, the number of time-sensitive DEGs also peaked at 2 DPI. DEGs overexpressed with ZT6 infection proved functionally enriched for  inflammatory pathways, interferon signaling, and circadian rhythms.

overall_design:
To examine how the time of day affects coronavirus pneumonia severity in mice, A/J mice were infected with mouse hepatitis virus-1 (MHV-1) at different times of day
We then collected bronchoalveolar lavage fluids and whole lungs from these mice and performed gene expression profiling analysis with RNA-seq

first: Huram

last: Mok

first: Carrie

last: Gierasch

first: Brielle

last: Patlin

first: Janice

last: Huss

first: Manoj

last: Arra

first: Elaine

last: Ostendorf

first: Avi

last: Adler

first: Alexander

last: Ganninger

first: Andrew

first: Carolyn

last: Fox

first: Krzysztof

last: Hyrc

first: Aryaman

last: Jaiswal

first: Prisha

last: Kumar

first: Jeffrey

middle: A


title: MASH Mouse Model Transcriptomic Characteristics

city: Guangzhou

first: Yongjian

last: zhou

address: No.1, Pan Fu Road, Yuexiu District

institute: Guangzhou First People’s Hospital

summary: Metabolic dysfunction-associated fatty liver disease (MAFLD) is currently the most common liver disease worldwide, characterized primarily by liver fat accumulation. The progression of MAFLD occurs in a series of stages, from simple steatosis to metabolic dysfunction-associated steatohepatitis (MASH), and eventually to cirrhosis.The MASH mouse model developed pathological fat deposition and inflammatory infiltration after being subjected to a methionine/choline-deficient (MCD) diet for 6 weeks. Transcriptome sequencing was then conducted to analyze differentially expressed genes.

overall_design: Wild-type C57BL6J mice were randomly divided into two groups: one group was fed a methionine/choline-deficient (MCD) diet, and the other group was fed a methionine/choline-sufficient (MCS) diet. Body weight changes were monitored weekly, and after 6 weeks, liver tissues were collected under anesthesia for transcriptomic analysis.

last: Zhou

first: Chen

last: Huang

first: Jiawei

last: Chen

first: Siqi

last: Yang

first: Diwen

last: Shou


title: Interferon-induced immune signatures are associated with suppression of HEV infection in porcine cell culture models

city: Bochum

first: André

last: Gömer

address: University Street 150

department: MMV

country: Germany

institute: Ruhr University Bochum

summary: Hepatitis E virus genotype 3 (HEV-3) is a zoonotic pathogen with pigs representing the natural host. Although HEV-3 infections in humans are often self-limiting, severe or chronic cases can occur. In contrast, HEV-3 infections in pigs, the primary reservoir, remain asymptomatic. To assess the initial transcriptional response in porcine cells during HEV-3 infection and pave the way for mechanistic studies of species-specific virus-host interactions, we aimed to establish porcine cell culture models, including primary porcine hepatocytes (PPHs) and porcine cell lines. PPHs supported the full HEV-3 replication cycle while intrinsic immunity, driven by the interferon-stimulated gene (ISG) system, played a central role in restricting viral replication. JAK-inhibition enhanced viral replication and suppressed ISG expression, highlighting the importance of IFN signaling in antiviral defense. Transcriptional profiling revealed a global modulation of host responses upon HEV infection, including pathways linked to immunity, inflammation, and metabolism. Porcine cell lines were permissive to HEV infection and treatment with recombinant porcine IFN-α subtypes induced a robust ISG response and effectively inhibited HEV replication in a dose-dependent manner. These findings establish porcine hepatocytes and cell lines as valuable tools to study HEV-host interactions, demonstrating the critical role of IFN-mediated intrinsic immunity in HEV restriction and highlighting subtype-specific antiviral effects of porcine IFN-α.

overall_design: RNA-seq profiling of primary porcine hepatocytes mock-infected or infected with hepatitis E virus, mock-treated or treated with 1 µM baricitinib, after 4 hours or 72 hours.

first: Sarah

last: Schlienkamp

first: Olinda

last: Pinto Veiga

last: Goemer

first: Luca

last: Noerthemann

first: Leyla

last: Sirkinti

first: Kathrin

last: Sutter

first: Florian W. R.

last: Vondran

first: Axel

last: Hamprecht

first: Daniel

last: Todt

first: Eike

last: Steinmann

first: Volker

last: Kinast


title: ALDH1A1+ cells are endometrial progenitors contributing to regeneration and endometriosis

city: Houston

first: Peixin

last: Jiang

state: TX

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Transcriptional analysis of direct NSD2 target genes in t(4;14) multiple myeloma reveals H3K36me2-dependent regulation and H3K27me3 antagonism [CUT&TAG]

city: Miami

first: sanxiong

last: liu

state: FL

address: 1501 NW 10th Avenue

department: Human Genetics

institute: University of Miami Miller School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This study aimed to identify the direct transcriptional targets of the H3K36me2 methyltransferase NSD2 in t(4;14) multiple myeloma (MM), where its aberrant expression drives oncogenesis, and to elucidate the molecular mechanisms underlying its regulatory role. To achieve this with precise temporal control and minimize cellular adaptation artifacts, we established an inducible dTAG-mediated acute NSD2 degradation system in the KMS-11 t(4;14) MM cell line. Using this model, we performed time-resolved SLAM-seq to measure newly synthesized mRNA levels at 7, 14, and 21 days post-NSD2 degradation, enabling the identification of primary transcriptional targets. Further SLAM-seq datasets were generated under conditions of NSD2 depletion followed by reconstitution with either wild-type NSD2 (NSD2WT) or a catalytically inactive mutant (NSD2Y1179A) to evaluate the requirement for SET domain activity. The contribution of H3K27me3 antagonism to NSD2-mediated gene regulation was investigated by performing SLAM-seq on NSD2-depleted cells treated with distinct PRC2 inhibitors (EPZ-6438 and MAK-658). Complementing the transcriptomic data, we performed CUTTAG to map the genomic distribution of the H3K27me3 histone mark following NSD2 depletion relative to control conditions. Analysis of these datasets revealed 308 primary NSD2 transcriptional targets, predominantly downregulated upon NSD2 loss and enriched for functionally relevant transcription factors. Reconstitution experiments demonstrated that NSD2's transcriptional effects are almost entirely dependent on its SET domain catalytic activity. Furthermore, PRC2 inhibition partially rescued the downregulation of approximately half of the NSD2 target genes, highlighting a significant role for H3K27me3 antagonism. Importantly, CUTTAG analysis showed that the compensatory increase in H3K27me3 upon NSD2 loss occurred primarily across genome-wide intergenic regions, rather than directly at the promoters or gene bodies of NSD2 target genes. Collectively, these deposited transcriptomic (SLAM-seq) and epigenomic (H3K27me3 CUTTAG) data support a model where NSD2 regulates target gene transcription via H3K36me2 deposition, which, in part, functions by antagonizing H3K27me3 deposition at distal regulatory elements to foster a permissive chromatin environment, providing a valuable resource for understanding NSD2 function in t(4;14) MM and Wolf-Hirschhorn syndrome.

overall_design: CUTTAG profiling for the H3K27me3, H3K27ac and H3K4me3 histone modifications was performed to assess its genomic distribution changes upon NSD2 loss in human t(4;14) multiple myeloma KMS-11 cells. The dataset includes: 1) Parental wild-type (WT) KMS-11 cells compared to two independent NSD2 knockout (KO) clones derived from WT KMS-11. 2) The parental KMS-11 cell line used for dTAG engineering compared to two independent NSD2dTAG clones derived from it. These NSD2dTAG clones were assessed following treatment with dTAGV-1 for 0 days (untreated control), 7 days, 14 days, and 21 days to investigate the temporal dynamics of H3K27me3 following acute NSD2 depletion. Biological replicates are provided for both the NSD2 KO clones and the NSD2dTAG clones across all conditions and time points.

first: Yubao

last: Wang

first: Sanxiong

last: Liu

first: Gareth

last: Morgan


title: ALDH1A1+ cells are endometrial progenitors contributing to regeneration and endometriosis [mouse scRNA-seq]

summary: Endometrial stem cells and their regenerative properties are implicated in the pathogenesis of endometriosis. Using single-cell RNA sequencing of the adult mouse endometrial epithelium, we identified a sub-population of aldehyde dehydrogenase 1a1+ (Aldh1a1+) stem-like cells that co-expresses stemness genes (Lgr5, Axin2) and lack proliferative markers (Top2a, Mki67). Using an Aldh1a1cre/ERT2;ROSA26tdTomato reporter mouse, we found that Aldh1a1+ cells give rise to long-lived endometrial cells and contribute to post-partum endometrial repair. Selective ablation of ALDH1A1+ cells with diphtheria toxin (DT) in Aldh1a1cre/ERT2; ROSA26-DTRflox/flox mice decreased glands and FOXA2 expression in vivo. Mouse and human ALDHHI endometrial cells had higher organoid formation capacity and stem-like gene signatures than ALDHLO cells. Ectopic lesion-derived organoids showed higher ALDH activity than patient-matched eutopic cells and displayed enriched pro-inflammatory, stemness, and ciliated cell transcriptomes. Here we provide evidence that ALDH1A1+ cells display progenitor/stem cell characteristics in the endometrium and contribute to the pathology of endometriosis.

overall_design: WT mouse endometrial epithelium was isolated from 5-6 mice during the estrus or diestrus phases. The epithelium was enzymatically isolated to single cells and viable cells were sorted using FACS.

first: Diana

last: Monsivais

first: Suni

last: Tang


title: ALDH1A1+ cells are endometrial progenitors contributing to regeneration and endometriosis [mouse]

overall_design: Mouse endometrial epithelial organoids were established from 6-8-week old mice and separated into ALDH_HI or ALDH_LO cells, as determined by the ALDEFLUOR activity assay. The ALDH_HI or ALDH_LO organoids were then collected, RNA was extracted, and subjected to bulk RNA sequencing.


title: ALDH1A1+ cells are endometrial progenitors contributing to regeneration and endometriosis [Human]

overall_design: Eutopic (EuE) or ectopic (deep infiltrating endometriosis, DIE) epithelial organoids were established from patients with endometriosis. After expanding, the organoids were enzymatically separated and sorted into ALDH_HI or ALDH_LO cells based on the ALDEFLOUR assay. The transcriptomes of ALDH_HI and ALDH_LO organoids were then obtained using Illumina sequencing.


title: ORCA-mediated Polycomb Repressive Complex stabilization maintains 3D-genome architecture and controls replication timing [TSA-seq]

city: Urbana

first: Supriya

last: Prasanth

state: IL

address: 601 S Goodwin Avenue

department: Cell and Developmental Biology

institute: University of Illinois Urbana Champaign

summary: Polycomb bodies, also called Polycomb group (PcG) protein complexes, are implicated in gene regulation, especially during development, differentiation, and during the maintenance of tissue-specific functions in multicellular organisms. Predominantly, in transformed cells, PcG bodies  form distinct nuclear foci, within which PcG-bound DNA is localized. These structures likely represent misregulated gene expression due to the loss of normal regulatory mechanisms, yet the molecular function of these bodies in cellular homeostasis remains unknown. Using TSA-Seq (Tyramide signal amplification), we provide the first-of-a-kind comprehensive view of the genomic regions, including specific centromeric and telomeric sites that are in proximity to the PcG bodies. Further, these regions are enriched for the repressive histone marks, H3K27me3, H3K9me3 and depleted for active marks, H3K4me3 consistent with a lack of accessible chromatin. We find high density of replication origins around PcG bodies, consistent with the replication factor, ORCA/LRWD1 localizing at these sites. ORCA interacts with the PRC complex, stabilizes the H3K27 methyltransferase, and facilitates the deposition of this histone mark at specific chromatin sites. Loss of ORCA impacts the chromatin organization around the PcG bodies, leading to decompaction of the repeat regions, and enhanced initiation from replication origins. Our results indicate that ORCA interacts with the PcG complex-bound chromatin and maintains a repressed heterochromatin environment to control the timing of replication origin firing.

overall_design: TSA-Seq was performed in control and siORCA cells using antibody against RNF2. Cells were labelled with Tyramide conjugated to streptavidin based on free radical diffussion.  Genomic DNA  was extracted and sonicated

first: Neha

last: Chetlangia

first: Bhushan

last: Thakur

first: Christophe

last: redon

first: Oraya

last: Zinder

first: Lorinc

last: Pongor

first: YouJin

last: Song

first: Darya

last: Asoudegi

first: Dazhen

first: Chris

last: Fields

first: Kannanganattu

middle: V

first: Mirit

middle: I

last: Aladjem


title: scRNAseq of MC38 mouse tumors reveals diverse functions of LMO7 in regulating tumor microenvironment

city: Shanghai

first: Mengkai

middle: MK

last: Li

address: Dongchuan street 800

department: School of pharmacy

institute: Shanghai Jiaotong University

summary: We have employed a single cell sequening approach using 10x Genomics scRNAseq to study the function of LIM domain only 7 (LMO7) in tumor microenvironment. LMO7 has been widely reported in recent years as an E3 ubiquitin ligase with a wide range of regulatory effects on macrophages and fibroblasts. Based on this characteristic, we used scRNA-seq of tumor tissues from wild-type and LMO7 knockout mice to further explore its regulatory effects on the tumor microenvironment. The results showed that LMO7 could significantly inhibit the pro-inflammatory polarization phenotype and phagocytic potential of macrophages, as well as inhibit the killing effect of CD8+ T cells.

overall_design: MC38 tumors from wild-type and LMO7 knockout mice were isolated, prepared into single-cell suspensions, and analyzed using scRNA-seq.

first: Zhiming

first: Yuwen

last: Zhong

first: Lei

last: Sun

first: Feng

last: Qian


title: C57BL6 Substrain Differences in Hippocampal-Dependent Learning and Transcriptome

city: Boston

first: Lisa

last: Goldberg

state: Massachusetts

address: 72 E Concord St, R604

institute: Boston University School of Medicine

summary: Here, we evaluated B6J and B6NJ substrains in a fear conditioning paradigm with varied conditioned stimulus-unconditioned stimulus pairings to assess if the strength of learning varies between substrains. For all number of pairings, B6NJ showed enhanced contextual freezing compared to B6J. To investigate baseline and learning-induced changes in hippocampal transcriptome that may underlie the observed behavioral differences between B6J and B6NJ, dorsal and ventral hippocampi were analyzed for RNAsequencing from B6J and B6NJ male mice from three groups: direct from home cage, 30 minutes after 2-pairings of shock and cue, 30 minutes after 2 exposures to cue alone. RNASeq pathway and network analysis identified several genes related to BDNF signaling that could contribute to the differences in levels contextual fear learning observed. Together, these behavioral and transcriptomic findings confirm differences in conditioned fear between the commonly used B6 substrains B6J and B6NJ and suggest that hippocampal transcriptome differences related to BDNF may contribute to differences in learning

overall_design: Examination of RNASeq in both ventral and dorsal hippocampi from male mice from two strains (C57BL/6J, C57BL/6NJ) either directly from home cage or 30 mins after either fear conditioning or cue alone.

first: Goldberg

last: Lisa Ruth

first: Sebastian

last: Aswathy


title: KSHV-infected endothelial cells expand and up-regulate angiogenic pathways and CXCR4 in patient-derived Kaposi sarcoma models

city: Bethesda

first: Laurie

middle: T

last: Krug

address: 10 Center Drive

institute: National Cancer Institute

summary: Here, we characterize eight KS tumors and four patient-derived KS xenografts (PDXs) in immunodeficient NOD/SCID/gamma (NSG) mice.Digital spatial profiling transcriptome analysis revealed increased expression of CXCR4 in the LANA+ endothelial cells of tumor regions compared to the levels in uninfected vessel regions.

overall_design: Here, we characterize 8 patient KS biopsy samples and, for a subset of biopsies, four corresponding patient-derived KS xenografts (PDXs) in immunodeficient NOD/SCID/gamma (NSG) mice.

first: Krug

last: T. Laurie

first: Afsari

last: Bahman

first: Cauley

last: Ned

first: Ramaswami

last: Ramya


title: Deciphering the single-cell atlas of fetal donkey (Equus asinus) gonad development in early pregnancy

first: yadan

last: Jin

summary: (1) Introduction: The ovaries are the reproductive organs of female animals and play a key role in fertility and maintaining endocrine balance. Gonadal development is a complex process that involves sex determination and subsequent maturation into the ovaries or testes. At present, the understanding of the mechanisms of donkey gonad development is still limited. (2) Objectives: This study explores the comprehensive single-cell transcriptomics of donkey gonads, providing insights into the cellular and molecular events behind sex norms and gonad differentiation. (3) Methods: We used single-cell sequencing technology to construct a high-resolution map of fetal donkey gonad development, analyze the diversity and complexity of the cell composition of donkey gonads at different developmental stages, and reveal the characteristics of key cell types and gene expression patterns. (4) Results: The different cell states and active molecular pathways during the development of donkey gonadal tissue were revealed, and the gonadal ridge developed into ovary at 4-8 weeks. (5) Conclusions: This study provides a foundational resource for understanding the complex biology of donkey gonadal development and may have implications for donkey reproductive health and fertility.

overall_design: The tissue samples used in this study were collected from the gonads and mesonephric tissues of four week gestation (FG) fetal donkey and the ovarian tissue of the eight week gestation (EG) fetal donkey, which were freshly slaughtered in Dong 'e Ejiao Co., LTD., Shandong Province. In order to reduce the influence of other factors, the excess fat and connective tissue around the ovary collection should be removed as much as possible.


title: Granzyme K CD8⁺ T cells with tissue-resident features promote intestinal inflammation in patients with Crohn’s disease

city: Seoul

first: Yoonho

last: Lee

address: 88, Olympic-ro 43-gil, Songpa-gu, Seoul, Republic of Korea

department: Department of Biochemistry and Molecular Biology

country: South Korea

institute: University of Ulsan College of Medicine

summary: The role of CD8+ T cells in Crohn's disease (CD) pathogenesis remains incompletely understood. This study aimed to characterize CD8+ T cells in CD and elucidate their potential contribution to intestinal inflammation.

overall_design:
T cells were isolated from blood, inflamed, and uninflamed intestinal tissues of 15 patients with CD. Various combinations of single-cell RNA sequencing were performed on subsets of these samples to comprehensively analyze the cellular landscape.

An inflamed intestinal tissue obtained from a patient with CD was processed for 10x visium spatial transcriptomic analysis.

An inflamed intestinal tissue obtained from a patient with CD was processed for 10x xenium spatial transcriptomic analysis.

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We cannot provide raw files for hospital policy reasons.
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first: Jiwon

last: Baek

first: Yongjae

last: Kim

first: Hwan

last: Park

first: Sung Wook

last: Hwang

first: Jong Lyul

first: Sang Hyoung

first: Jihun

first: Suk-Kyun

last: Yang

first: Buhm

last: Han

first: Mi-Na

last: Kweon

first: Kyuyoung

last: Song

first: Yong Sik

last: Yoon

first: Byong Duk

last: Ye

first: Ho-Su


title: Blocking a Lipid Messenger from Osteocytes: A Novel Strategy for Prevention and Treatment of Metabolic Associated Fatty Liver Disease

city: changsha

first: yi

middle: yi

last: wang

address: xiangya road

institute: central south university

summary: The increasing prevalence of metabolic-associated fatty liver disease (MAFLD) represents a significant public health challenge, largely attributed to the excessive consumption of sugars and lipids in modern society. The liver serves as the central regulator of systemic energy homeostasis, while the bones, as high-energy-consuming organs, are now recognized for their active role in metabolic regulation. In this study, osteocyte-derived extracellular vesicles (OCY-EV) are identified as critical mediators in the crosstalk between bone and hepatic lipid metabolism. OCY-EV are found to facilitate hepatic lipid accumulation through miR-483-5p, which activates lipid metabolism-related pathways, thereby promoting fatty acid uptake and lipogenesis in hepatocytes. Genetic ablation of OCY-EV secretion or antagonism of miR-483-5p markedly attenuated hepatic steatosis in high-fat diet-induced MAFLD models. Moreover, treatment with bone resorption inhibitors, such as denosumab and zoledronic acid, reduced the release of OCY-EV from bone matrix, leading to decreased circulating OCY-EV/miR-483-5p levels and amelioration of MAFLD progression. Clinical data further indicated a positive correlation between circulating OCY-EV/miR-483-5p levels and MAFLD severity. These findings uncover a novel "bone-liver axis" that regulates hepatic lipid homeostasis and provide promising therapeutic targets for the prevention and treatment of MAFLD, as well as broader implications for metabolic syndrome and related diseases.

overall_design: Hepatocytes were treated with aged OCY-EV pre-incubated with either antagomiR-483-5p (OCY-EV + ANTA) or a control of antagomiR-NC (OCY-EV + ANTA-NC). After treatment of free fatty acid (FFA) induced hepatocytes, RNA sequencing was performed on the solvent control, OCYA-EV + ANTA, and OCYA-EV + ANTA-NC groups.

first: Yi-Yi

last: Wang


title: LUAD spatial transcriptomics

city: Singapore

first: Damien

last: Chua

address: 11 Mandalay Road

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University, Singapore

summary: In this study, we performed spatial transcriptomics and bulk transcriptomics to profile LUAD patient samples. Next we constructed lung tumoroid from the patient and performed bulk transcriptome profiling to demonstrate its relevancy, and drug sensitivity assays

overall_design: Spatial CosMx Molecular Imager

first: Shumin

last: Liao

first: Liang

last: Li


title: LUAD tumor, normal adjacent and tumoroid bulk transcriptomics

overall_design: Bulk RNAsequencing of biopsies and tumoroid.


title: Multi-Omics Insights into Postharvest Deterioration in Artichoke for Enhanced Shelf Life and Health Benefits

city: GAINESVILLE

first: FAHONG

last: YU

address: 2033 Morway RD

department: ICBR

institute: UNIVERSITY OF FLORIDA

summary: Artichokes provide a wide range of health-promoting nutrients and produce ornamental flowers with pleasant sensory appeal. However, their high photosynthetic activity, respiration rate, and sensitivity to mechanical injuries makes them highly perishable. Using the high-throughput RNA-seq and metabolomics analysis, we identified significant variations in the expression levels of differentially expressed genes (DEGs) and metabolites between ‘Green Queen’ (GQ) and ‘Imperial Star’ (IS) cultivars, relating to their shelf-life. The DEGs were categorized into pathways involved in hormone signaling, cell wall metabolism, stress response, organ development, and health beneficial compounds with expression varying across storage intervals. Notably, genes and transcription factors (TFs) involved in plant hormone signaling pathways and senescence were primarily upregulated in IS, explicating its shorter shelf life. Genes such as b -carotene 3-hydroxylase (BHY) and 11-beta-hydroxysteroid dehydrogenase-like 4A (HSD4), upregulated in both cultivars during storage, facilitate the production of metabolites with reported anti-aging, anti-inflammatory, diabetic resistance, and cardiovascular benefits. Metabolomics analysis unveils an accumulation of phenols, flavonoids, vitamins and breakdown of inulin, which remain stable in GQ and occur in a time-dependent manner in IS during storage. These findings elucidate the genotypic effect on the shelf-life of artichoke stored under same conditions and provide valuable insights for improving postharvest shelf life and nutritional quality through gene editing techniques.

overall_design: To extend the shelf life benefitting the producer and consumer, our aim was to investigate the genes involved in produce rapid ageing and quality degradation using high throughput omics technology

first: Avninder

last: Kaur

first: Gabriela M

last: Olmedo

first: Weining

first: Chiawah

last: Tseung

first: Fahong

last: Yu

first: Jinhe

last: Bai

first: Shinsuke

last: Agahara

first: Tie

last: Liu


title: Molecular subtypes of autism spectrum disorder: Convergent genetic pathways and environmental modulation

city: Kodaira

first: Satoshi

last: Watanabe

state: Tokyo

address: 4-1-1 Ogawa Higashi

institute: National Center of Neurology and Psychiatry

summary:
Gene expression in the cerebral cortex of VPA-exposed (VPA) and unexposed (UE) marmosets at five age points (neonates, 2 months, 3 months, 6 months, and adults) was analyzed using microarrays.
VPA marmosets recapitulated the molecular signature of human ASD, with glial gene expression alterations emerging in the neonatal period, preceding neuronal gene expression alterations.

overall_design: Tissues from two cortical areas (area 12 and TE) of UE and VPA marmosets at 5 age points (2-4 animals per condition) were isolated. RNA was extracted and hybridized on custom microarrays.

first: Tomofumi

last: Oga

first: Tetsuya

last: Sasaki

first: Kayo

last: Sumida

first: Kohei

last: Hoshino

first: Koichi

last: Saito

first: Izuru

last: Miyawaki

first: Keiko

last: Nakagaki

first: Jun

last: Noguchi

first: Noritaka

last: Ichinohe


title: Overcoming intrinsic mechanisms of cell cycle inhibitor resistance in estrogen receptor-positive (ER+) breast cancer

city: Duarte

first: Aritro

last: Nath

state: California

address: 1500 E Duarte Rd

department: Medical Oncology & Therapeutics Research

institute: City of Hope

summary: Estrogen receptor-positive breast cancer (ER+BC) represent about 70% of all breast cancer cases. Approximately 30-50% of ER+BCs eventually develop resistance to primary endocrine therapy and progress to metastatic disease. The addition of cyclin-dependent kinases 4 and 6 inhibitors (CDK4/6i) to endocrine therapy has improved disease control in advanced and metastatic ER+BC. However, progression on CDK4/6i is common and further research is required to fully understand and overcome the mechanisms of CDK4/6i resistance in ER+BC. We performed single-cell RNA sequencing (scRNA-seq) of temporal tumor samples from the FELINE clinical trial (NCT02712723) to uncover emergent resistance phenotypes in ER+BC patients receiving a combination of ribociclib with letrozole or letrozole alone in a neoadjuvant setting. In the majority of patient tumors, resistant cancer cells activated ErbB growth factor signaling during treatment, with an upregulation in ERBB2 and ERBB4 in post-treatment cells, as well as increased activity of transcription factors downstream of ErbB signaling. This indicates that endocrine therapy plus CDK4/6i activated compensatory ErbB growth factor signaling in resistant cells, supporting an established estrogen-independent state of proliferation. To further understand this shift in cell state, we used afatinib, an ErbB family blocker, in combination with ribociclib to target this resistance mechanism. We developed multiple in vitro three-dimensional ER+BC cell culture models that are sensitive or resistant to ribociclib. Samples were collected regularly during monotherapy or combination of ribociclib and afatinib treatment and bulk RNA-sequencing measured the dynamical changes in the cell state over short and long timescales. Generalized additive models quantitatively evaluated cancer cell plasticity and synergy of combination therapy using the RNA-seq data. Our models revealed how activity of signaling pathways drive transcriptional changes in cell cycle regulators that promote or inhibit cell cycle progression. We found that ribociclib plus afatinib synergize to promote early and sustained cell cycle arrest, and later apoptosis, in both sensitive and resistant cells. Combination therapy simultaneously restored G1/S phase regulation by inhibiting the cyclin E/CDK2 complex and enforced G2/M phase control by inhibiting the cyclin B/CDK1 complex, thereby blocking entry into mitosis. This dual inhibition strategy not only controlled cancer proliferation, but also induced caspase-dependent apoptosis. Overall, our study revealed a key CDK4/6i resistance mechanism, and demonstrated that a combination of ribociclib plus afatinib overcomes intrinsic mechanisms of resistance in ER+BC.

overall_design: The samples are CAMA-1 and MCF-7 ER+ breast cancer cell lines treated with DMSO (control), ribociclib, afatinib, and combination of ribociclib and afatinib.

first: Kimya

middle: L

last: Karimi

first: Jason

last: Griffiths

first: Eric

last: Medina

first: Elena

last: Farmaki

first: Andrea

last: Bild


title: Blood-circulating memory-phenotype CD4+ T cells rapidly accumulate in ischemic organs to exacerbate tissue injury in an innate manner

city: Sendai

first: Kosuke

last: Sato

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

institute: Tohoku University

summary: Memory-phenotype (MP) CD4+ T lymphocytes develop from peripheral naïve precursors via self-recognition at homeostasis. While previous studies revealed their innate immune function in infectious and autoimmune contexts, functional significance of MP cells in ischemia remains unclear. Ischemia-reperfusion injury (IRI) is induced by acute occlusion of organ-feeding arteries and subsequent reperfusion where innate immunity plays an important role. Here we show that blood-circulating MP lymphocytes rapidly infiltrate to the gut in the absence of antigen recognition during intestinal IRI. This MP migration is directed by α4β7 that binds to vascular MAdCAM-1, with the latter expression immediately upregulated by ischemia-induced TNF-α. Moreover, gut-accumulating MP cells respond to IL-12 to produce IFN-γ in an innate manner to orchestrate neutrophils, thereby exacerbating tissue injury. Furthermore, such innate MP responses are operative in hepatic IRI as well. Together our results reveal an essential innate function of blood-circulating MP CD4+ T lymphocytes that rapidly accumulate in ischemic organs to contribute to pathogenesis of IRI.

overall_design: Ischemia was induced in the small intestine of C57BL/6 mice by clamping the superior mesenteric artery (SMA) for 45 minutes with a microvascular clamp, followed by removal of the clamp to allow reperfusion (IRI-"reperfusion time"). Small intestinal lamina propria cells were obtained at 0 and 6 h post reperfusion. The cells were enriched for live CD4+ cells using Dead Cell Removal Kit and CD4 Microbeads (all from Miltenyi Biotec), fixed for 19 hours at 4 °C with Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10x Genomics), and analyzed by single-cell RNA sequencing.Live CD4+ cells were pooled from 20 IRI-0h and 26 IRI-6h mice. Data of purified CD11b- cells are available in GSE325534.

first: Takeshi

last: Kawabe


title: Regulation of CD45 isoforms during human effector and memory CD8 T cell differentiation: Implications for T cell nomenclature

city: Atlanta

first: Donald

last: McGuire

state: GA

address: 1462 Clifton Road room 412

institute: Emory University School of Medicine

summary: This study shows a detailed analysis of the expression of CD45 isoforms on virus specific CD8 T cells after YFV vaccination (YFV-17D) longitudinally starting at two weeks after infection going out to over 10 years. As expected, effector CD8 T cells at day 14 express CD45RO but interestingly within 4-6 weeks all of the virus specific CD8 T cells become CD45RA and then remain CD45 RA for > 10yrs. The journey for these YFV specific CD8 T cells goes from naïve (CD45RA+ CCR7+) to effector/EM (CD45RO+ CCR7-) to TEMRA (CD45RA+ CCR7-) to TSCM (CD45RA+ CCR7+).  These YFV specific CD8 T cells rarely acquire the canonical Tcm phenotype (CD45RO+ CCR7+).  The few CM cell found in the YFV CD8 T cell response are effector cells in the first 11 days of the infection and their numbers become almost undetectable in subsequent samples.  We found that CD8 T cells returned to expressing a mixture of CD45 isoforms similar but not identical to those found in naive T cells.  CD45RA expression correlated closely with reduced expression of the splicing mediator hnRNP LL.  This CD45RO to RA switch happens around one month post-infection and coincides with clearance of YFV, so we hypothesized that antigen may be playing a role in which CD45 isoform is expressed by the virus specific CD8 T cells. We addressed this issue by ex vivo analysis and provide evidence that this switch is indeed regulated by antigen.  Sorted CD45RO positive YFV specific effector CD8 T cells re-express CD45RA when cultured ex vivo in the absence of antigen. We then show that SARS-CoV-2 spike specific CD8 T cells undergo the same CD45RA to RO to RA transition in vivo in a longitudinal analysis of a cohort of COVID-19 patients receiving the SARS-CoV-2 mRNA vaccine. These studies have important implications for T cell nomenclature and in particular for defining human memory CD8 T cell subsets. The re-expression of CD45RA in CD8 T cells likely explains the large number of TEMRA and absence of CM CD8 T cells.  However, comparison to CD4 populations suggests that these findings are only applicable to CD8 T cells.

overall_design: Comparison of transcription of bulk CD4 and CD8 memory subset populations from three healthy donors

middle: J

first: Rama

last: Akondy

first: Shu

last: Yang

first: Srilatha

last: Edupuganti

first: Shashi

last: Nagar

first: Garett

last: Michael

first: Stephen

middle: C

last: De Rosa

first: Evan

last: Newell

first: Haydn

last: Kissick

first: Juliana

last: McElrath

first: Rafi

last: Ahmed

first: Donna

last: Farber


title: Integration and annotation of spatial multi-omic data with DIRAC highlights spatial organization of lymphoid organs

first: Shibo

last: Liu

address: 12 Science Drive 2

institute: National University of Singapore

summary: Spatial multi-omics technologies enable simultaneous measurements of multiple omics modalities. Integration across spatial omics modalities followed by multi-omic spatial domain and cell-type annotation are two fundamental tasks for downstream analysis. We present Domain Invariant Representation through Adversarial Calibration (DIRAC), a geometric deep learning model that unifies both tasks by treating horizontal integration (different cells/spots, same omic modality) and vertical integration (same cells/spots, different omics modalities) under a generalized domain adaptation framework. DIRAC uses an adversarial domain discriminator to integrate multiple spatial omics modalities into a unified domain-invariant embedding space and to automate cell-type annotation by transferring labels from reference multi-omic data. DIRAC delineated more biologically meaningful spatial domains and improved clustering and cell-type annotation performance across omics modalities (histone marks, chromatin accessibility, RNA, and protein) and technology platforms (sequencing and imaging-based). We used DIRAC to build cellularly resolved spatial multi-omics atlases of mouse spleen and thymus, revealing the spatial migratory patterns of T cells in the thymus and the spatial organization of finely-resolved immune cell types in the spleen. DIRAC is substantially faster than existing multi-omic integration methods and scales to millions of cells.

overall_design: Prior to the experiment, all solutions were freshly prepared and maintained on ice. Blocking Buffer (50 µl per sample) was composed of 3x SSC, 0.1% Triton-X-100, 10% serum, 1 µg/µl sheared salmon sperm DNA, 2.5 µl TruStain FcX PLUS (anti-mouse CD16/32) antibody (BioLegend, Cat. No. 156604), 5% RNase inhibitor (RI), and 5 µM 32-nt Poly A. The Wash Buffer consisted of 3x SSC with 5% RI. Cryosectioned OCT-embedded tissue, cut to 10 µm thick, was carefully transferred onto the Stereo-seq chip. These chips, now bearing tissue sections, were immediately warmed to 37℃ for 1 minute using a thermocycler adaptor. Tissues were then fixed by 4% PFA at room temperature for 5 minutes. The tissue sections on chips were then washed two times with Wash Buffer, each for 1 min. After washing, blocking was performed by incubating the tissue with Blocking Buffer for 20 minutes, after which the sections were exposed to the TotalSeqTM-A antibody mix in Blocking Buffer for 45 minutes at room temperature. The tissue sections on chips were then washed three times with Wash Buffer, each for 30 seconds. After DAPI staining, the tissue sections were mounted with glycerol and imaged. Subsequent processing followed the Stereo-seq Transcriptomics T Kit protocol with minor adjustments. Briefly, the sections were permeabilized with Permeabilization Mix for an optimized duration, as recommended in the Stereo-seq Permeabilization Kit instructions. After reverse transcription, cDNA and antibody-derived tag (ADT) products were released from the chips using cDNA Release Mix and collected. Separation of the cDNA fraction from the ADT library was achieved via a 0.8X bead selection, followed by preparation of the cDNA sequencing library in accordance with the Stereo-seq Transcriptomics T Kit. The ADT product in the supernatant was purified using a 2.0X (0.8X + 1.2X) bead selection, then amplified with Protein PCR Primer Mix. Finally, both ADT and cDNA libraries were sequenced using MGI DNBSEQ-T7 or DNBSEQ-G400 sequencing platforms.

first: Chang

last: Xu

first: Yang

last: Heng

first: Yuan

last: Cao

first: Junbin

last: Gao

first: Dongmei

last: Jia

first: Diyan

last: Liang

first: Chen

first: Yong

last: Ma

first: Siok-Bian

last: Ng

first: Ao

last: Chen

first: Xun

first: Sha

last: Liao

first: Qinghua

last: Jiang

first: Boxiang


title: In vivo single-cell ribosome profiling reveals cell-type-specific translational programs during aging [scRNA-Seq]

city: Zurich-Schlieren

first: Ataman

last: Sendoel

address: Wagistrasse 12

country: Switzerland

institute: University of Zurich

summary: Somatic stem cells are characterized by their low overall protein synthesis rates, a feature implicated in driving their stemness. Yet, how aging reshapes the translational landscape of stem cells and how these changes impact their regenerative capacity remains poorly understood.  Here, we present an in vivo single-cell ribosome profiling strategy to monitor tissue-wide translational landscapes of the young and aged mouse skin. By implementing efficient in vivo cell isolation and switching to RNAse I-based ribonuclease for generating ribosomal footprints, we enhance the accessibility of single-cell ribosome profiling and facilitate the evaluation of triplet periodicity, a hallmark of high-quality data. Leveraging this strategy and integrating single-cell RNA sequencing with ribosome profiling, we document the translational landscapes of the major epidermal cell types, outline cell-type-specific translational efficiencies and capture heterogeneity in differentiation commitment among stem cell populations. Notably, we identify a pronounced translational reprogramming of AP-1 subunits specifically in aged epidermal stem cells. Our proof-of-concept study illustrates the power of in vivo single-cell ribosome profiling to map cell-type-specific translational landscapes and offers a scalable strategy for tissue-wide interrogation of translational landscapes at single-cell resolution.

overall_design: To disentangle transcriptional and translational control of gene expression in these samples, we performed single-cell RNA-sequencing to calculate translation effiencies (TE). We performed single-cell RNA-sequencing on in vivo epidermal cells isolated from the backskin of one young (60 days old) and one aged female (24 months old) wildtype C57BL/6 mice were used. The single-cell libraries were generated using the BD Rhapsody Single-Cell Analysis System using BD Rhapsody Cartridge Kit (633733). The cell suspension were barcoded using BD Single-Cell Multiplexing Set (Rat anti-mouse MHC-H2 Class I, BD Biosciences, 626545). The cartridge was loaded with 40,958 cells. Reverse transcription from beads and sequencing library production was carried out according to the manufacturer’s instructions (BD Biosciences, doc ID: 210967 rev. 1.0). RNA single-cell sequencing was performed using 1 lane SP Flowcell of the Illumina Novaseq 6000 #1. Read configuration used was, read1 60 cycles I1, 8. Read 2, 62 cycles. 1.8nM of the ready-made library was loaded with 20% PhiX.

first: Clara

last: Duré

first: Umesh

last: Ghoshdastider

first: Ramona

last: Weber

first: Peter

last: Renz

first: Fabiola

last: Valdivia-Francia

first: Ameya

last: Khandekar

first: Federica

last: Sella

first: Katie

last: Hyams

first: Yigit

last: Merve

first: Mark

last: Ormiston

first: Homare

last: Yamahachi

first: Mitchell

last: Levesque

first: Stephanie

last: Ellis


title: In vivo single-cell ribosome profiling reveals cell-type-specific translational programs during aging

overall_design: To investigate the translational landscape of the young and aged mouse epidermis, we blocked protein synthesis via cycloheximide administration by a tail vain injection of the mice prior to the cell isolation process. In this sutdy, three young female C57BL/6 mice ( 56-60 days old) and three old female C57BL/6 mice (22-26 months old) were used. We enzymatically and mechanically isolated the epidermal cells from the backskin of the young and aged animals, sorted them into 384-well plates and generated single-cell sequencing libraries using the Mosquito liquid handler. The libaries were sequencenced on the Illumina NovaSeq 6000 or NovaSeq X Plus with 75 cycles for read 1, 6 cycles for the i7 index read (plate index), and 10 cycles for the i5 index read (cell index) with 10% PhiX. This study includes three biological replicates per age group and several technical replicates represented as individual plates, indicated by different numbers (barcodes).  We included one 384-well plate of young and old skin samples, sorted for Sca-1-negative cells using the Ly-6A/E (Sca-1) Monoclonal Antibody (Therma eBioscience, 11-5981-82) to enrich for other cell types than stem cells. The upper half of the plate were old cells (row A-H), the lower half were young cells (row I-P).

first: Merve

last: Yigit


title: The effect of the high-peak power electromagnetic pulse (HPEM, 1 MV/m) on gene expression in normal human bone marrow derived mesenchymal stem cells (hMSC)

city: Warsaw

first: Alicja

last: Trebinska-Stryjewska

address: gen. S. Kaliskiego 2

department: Institute of Optoelectronics

country: Poland

institute: Military University of Technology

summary: The aim of the study was to analyze the cell response to a single high-peak power electromagnetic pulse (HPEM) at the gene expression level. Normal human bone marrow-derived mesenchymal stem cells (hMSC) from two donors were used as a model. Cells were exposed to HPEM with a peak field of 1 MV/m, rise time 3 ns, pulse width 30 ns and center frequency 50 MHz. Transcriptomic analysis was carried out immediately after exposure (0 h), 4 or 24 h after treatment.

overall_design: Normal human bone marrow-derived mesenchymal stem cells (hMSC) from two different donors were exposed to a single high-peak power electromagnetic pulse (HPEM). Gene expression in HPEM-exposed, sham-exposed or untreated (control) hMSC was measured immediately (0 h), 4 h and 24 h after exposure. Two independent experiments were performed for each cell line with three biological replicates (HPEM-exposed, sham-exposed) or two replicates (control) for each time point and treatment.

first: Elzbieta

last: Trafny


first: Laurie

last: Krug

state: Maryland

summary: Kaposi sarcoma (KS) is defined by hyperangiogenesis driven by Kaposi sarcoma herpesvirus (KSHV) infected endothelial cells. The exploration of novel therapies is hampered by the lack of a patient-derived preclinical animal model. Here, we characterize patient-derived KS xenografts (PDXs) in immunodeficient NOD/SCID/gamma (NSG) mice. Thirteen cutaneous KS biopsies were subcutaneously implanted into NSG or NOG mice transgenic for human IL-6. Immunohistochemistry staining for KSHV LANA revealed that infected endothelial cells were maintained for long periods in recipient NSG. LANA+ human endothelial cells increased by a mean 4.3-fold in fifteen PDX compared to respective input biopsies, regardless of numerous implantation variables and clinical history of patient volunteers. The Ki-67 proliferation marker overlapped with LANA+ cells, consistent with virus-driven cell expansion. Spatial transcriptome analysis revealed increased expression of viral transcripts from latent and lytic gene classes in the PDX. In addition, the expanded KSHV+ regions of the PDX maintained signature gene expression of KS tumors, with a notable enrichment in pathways associated with angiogenesis, development of endothelium, lipid transport and cell growth. Spatial analysis revealed that fibroblasts in the KS tumor microenvironment may be one source of CXCL12 signaling to CXCR4 that was upregulated in KS tumor regions. Taken together, the reproducible expansion of KSHV-infected endothelial cells across PDX from multiple donors and the recapitulation of a KS tumor gene signature, discovers new biology and supports the application of patient-derived cutaneous KS xenografts as a pre-clinical model to test novel therapies.

overall_design: Here, we characterize patient-derived two KS Biopsy Samples and two corresponding xenografts (PDXs) in immunodeficient NOD/SCID/gamma (NSG) mice.

first: Bahman

last: Afsari

first: Xiaofan

last: Li

first: Anna

last: Grosskopf


title: Silicon Nitride Induces Osteoconduction Via Activated Mitochondrial Oxidative Phosphorylation and Neovascularization

city: Los Angeles

first: Karolina Elzbieta

middle: Kaczor

last: Urbanowcz

state: CA

address: 10833 Le Conte Avenue

institute: UCLA

summary: Silicon Nitride (Si3N4: SiN) is a thermodynamically stable ceramic material with excellent mechanical properties and wear/corrosion resistance for industrial applications. SiN is also proposed for orthopedic and dental implant applications because of its enhanced osteoconduction. However, the biological mechanism of SiN-induced bone formation has not been fully elucidated. In this study, SiN significantly increased in vitro mineralization of human bone marrow mesenchymal stromal cells (BM-MSC) and in vivo peri-implant bone volume in mouse femurs over conventionally used titanium (Ti) implants. RNA sequencing of BM-MSC cultured on SiN disc revealed that the functional gene clusters associated with mitochondrial oxidative phosphorylation were significantly elevated over the Ti disc groups. SiN in aqueous solution releases ammonium/ammonia, which may provide a source for glutamine-dependent energy production. It was confirmed that BM-MSC upregulated the glutamate-ammonia ligase (GLUL) expression with osteogenic condition. In addition, SiN increased the expression of functional gene clusters involving vascular formation. The upregulation of HIF1a in vitro and the increased VEGFR3-positive blanching vascular structures in vivo supported that SiN-induced neovascularization. This study has uncovered an important mechanism that SiN stimulates osteoconduction through unique glutamine-driven mitochondrial oxidative phosphorylation and establishes oxygen and nutrient supply by neovascularization, leading to stable osseointegration.

overall_design: To investigate the mechanism of SiN-induced osteoconduction, human bone marrow stromal cell (BM-MSC) was cultured on SiN disc and the effect was determined by RNA sequencing that was compared to BM-MSC cultured on control Titanium (Ti) discs.

first: Taro

last: Inagaki

first: Satomi

last: Arimoto

first: Karolina

middle: E

last: Kaczor-Urbanowicz

first: Ichiro

last: Nishimura


title: Effect of SPP1 stimulation on gene expression of human skin fibroblast cell line (HSF)

first: Xin

last: Huang

state: China

address: zhizaoju Road 639

institute: Ninth People's Hospital affiliated to Shanghai Jiao Tong University School of Medicine

summary: To investigate the function of exogenous SPP1 in the regulation of fibroblast cellular function. The concentration of SPP1 for treatment is 10nM and the duration of treatment is 24h. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 independent experimental replicates.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for fibroblast with or without SPP1 stimulation (10nM for 24h).

first: Tao

last: Zan

first: Qingfeng


title: Glucose-Chi3l1 interaction tunes metabolic imbalance in Kupffer cells and ameliorates metabolic dysfunction-associated fatty liver

city: Kunming

first: Bo

last: Chen

address: East Outer Ring South Road

institute: YunnanUniversity

summary: Kupffer cell (KCs) death has been observed in metabolic dysfunction-associated fatty liver disease (MAFLD). However, the metabolic alterations triggering KCs death in MAFLD remain elusive. This study aims to elucidate the glucose metabolic changes during KCs death and explore potential regulatory mechanisms.We confirmed KCs death in various MAFLD mouse models and deciphered the correlation between KCs death and glucose metabolic changes via single-cell RNA sequencing (scRNA-seq) and experimental approaches. Notably, we identified a key regulatory molecule, Chi3l1, which interacts with glucose and inhibits glucose uptake in KCs, thereby delaying KCs death during the early stages of MAFLD. This mechanism ultimately alleviates KCs death and the consequent lipid accumulation in the liver.Our findings highlight the intricate interplay between glucose metabolism and KCs death in MAFLD and provide novel insights into the underlying mechanisms driving this complex disease.

overall_design: We explained the correlation between KCs death and glucose metabolism by single cell RNA sequencing (scRNA-seq).

first: Jia

last: He

first: Zhao

last: Shan


title: Biomimetic design of inhalable self-assembled polypeptide nanozymes for cascade intervention in pulmonary fibrosis progression

city: Beijing

first: Qizhi

last: Wang

address: Chaoyang District

institute: Chinese Academy of Sciences

summary: Pulmonary fibrosis is a chronic, progressive disease characterized by heightened oxidative stress and irreversible inflammatory damage in lung tissue, with limited therapeutic options and insufficient clinical efficacy. Here, we design an inhalable, self-assembled polypeptide nanozyme (PepNzyme) that mimics the natural enzyme active centers. This nanozyme demonstrates enhanced superoxide dismutase-like activity (10,000 U/mg) and catalase-like activity (70,000 U/mg), optimized through activity screening of the PepNzymes library biomineralized from a polypeptide library and molecular dynamics simulations. This design incorporates a lung epithelial cell-targeting peptide, along with a pH-sensitive and mitochondria-targeted peptide sequence, achieving high-efficiency localized inhalation delivery of PepNzyme. It enables lysosomal escape and mitochondrial accumulation, significantly enhancing therapeutic efficacy and minimizing side effects. The inhaled PepNzyme effectively scavenged free radicals in pulmonary lesions, thereby reversing the inflammatory immune environment, downregulating the TGF-β/SMAD signaling pathway, and inhibiting fibrosis progression. This groundbreaking antioxidant strategy offers promising implications for the treatment of pulmonary fibrosis.

overall_design: To investigate the underlying therapeutic mechanism of PepNzymeSOD-CAT in pulmonary fibrosis, mouse lung tissues of PepNzymeSOD-CAT, pulmonary fibrosis model and normal groups were collected for transcript detection.

first: Zhuoran

first: Yaxin

last: Hou


title: Role of IL-13 receptor signal in T cells.

city: Yokohama City

first: Masato

last: Kubo

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Research Center for Integrative Medical Science (IMS)

institute: RIKEN Yokohama Institute

summary: Skin barrier dysfunction in the setting of atopic dermatitis (AD) leads to cutaneous allergen sensitization (CAS).1 The atopic march hypothesis proposes that CAS leads to the subsequent development of other allergic disorders such as asthma and food allergy.2-5 The latter is associated with IgE-mediated anaphylaxis6. However, the precise mechanisms by which CAS promotes IgE-mediated allergic responses remain unclear. We thus established a CAS model of anaphylaxis and identified a unique role of the Interleukin (IL)-13 signal in DCs to generate anaphylactic IgE responses. Single-cell RNA-seq revealed the emergence of IL-13 receptor alpha 1 chain (IL-13Rα1)-expressing type 2 conventional dendritic cells (cDC2s) in CAS. Similar DC populations were identified in allergic rhinitis humans with cedar pollan-specific IgE antibodies. Lineage-specific disruption of IL-13 signaling resulted in a marked reduction in cDC2s that highly expressed MHC class II: these cells controlled the germinal center entry of TFH cells required for IgE responses. These data reveal a unique role for IL-13 in controlling the expansion of MHCIIhi cDC2s and associated TFH cell responses in the setting of allergy.

overall_design: T cell sample: We investigated how the IL-13 signal contributes to the development of TFH cells, which help the antibody response. We employed the OTII transfer system to track the transcriptional changes during TH differentiation. OTII T cells were transferred into control or IL-13RΔDC mice, then at D7 after CAS and second priming, we sorted the OTII T cells and examined their gene expression by scRNAseq.

first: Yasuyo

last: Harada

first: Takanori

last: Sasaki

first: Takashi

last: Watanabe

first: Sewon

last: Ki

first: Yoshie

last: Suzuki


title: Transcriptomic profiling reveals the effect of Napabucasin (BBI608) on liver microenvironment in mice

city: Guangzhou

first: Li

last: Lin

address: No.1838, Guangzhou Avenue North

institute: Southern Medical University

summary: To investigate the effect of Napabucasin (BBI608) on liver microenvironment, mice were pretreated with Napabucasin  or vehicle control (1% NaCMC) via daily gavage for one week.

overall_design: Mice were randomly divided into two groups: 1) Control group: Mice received 1% NaCMC by daily gavage for one week. 2) Treatment group: Mice received Napabucasin (BBI608) at 20mg/kg by daily gavage for one week. At the end of the treatment, liver tissues were harvested from both groups. Total RNA was extracted and used for RNA-seq analysis to compare the gene expression profiles between the Napabucasin-treated and control groups. The study aimed to identify genes and pathways that are affected by Napabucasin treatment in the liver microenvironment.