title: The function of Toll-like receptor 2 in control of transcriptome responses to the microbiome and microbiome composition

city: LEIDEN

first: Li

last: Liu

address: Verbeekstraat 29D

institute: Leiden University

summary: Background: Toll-like receptor 2 (TLR2) plays a pivotal role in innate immunity and has recently emerged as a criti-cal regulator of host-microbiome interactions. However, how TLR2 influences host transcriptional responses to colonized microbiome and microbial community dynamics remains largely unclear. Germ free (GF) and conven-tionalized zebrafish (Danio rerio) model provides a valuable system to study microbiome functions. Results: RNAseq analysis revealed that transcriptomic alterations resulted from tlr2 mutation were more extensive in the presence of the microbiome than under the GF condition, indicating that tlr2 mutation has a more pro-nounced impact on host transcriptional responses when microbial signals are present. KEGG enrichment analyses showed an enhanced host response to the energy metabolism in the presence of microbial stimuli resulting from tlr2 deficiency. In addition, microbiome colonization elicited a broader transcriptional response in tlr2 wild-type larvae than in the mutants, highlighting the essential role of tlr2 in regulating host transcriptomic programs in re-sponse to microbial signals. In terms of how tlr2 influences microbial composition, 16S rRNA gene sequencing showed that tlr2 mutants exhibited higher microbial diversity during early development, whereas adult microbial diversity was highest in wild-type males, indicating a developmental stage- and sex-specific restructuring of the gut microbiome. For larvae at the genus level, tlr2 mutant larvae showed increased Chryseobacterium and Flecto-bacillus but reduced Gracilibacteria abundance relative to wild-type controls. For adult gut samples, the relative abundance of Cetobacterium was lower, while genera such as Romboutsia, Aeromonas and Pseudarthrobacter were more abundant in tlr2 wild-type male group compared to other groups. Predicted functional analyses revealed that tlr2 deficiency induced complex alterations in microbial metabolic pathways, with distinct pathway enrichments observed between larval and adult stages. Conclusions: TLR2 not only modulates host transcriptional responses to microbial colonization but also shapes gut microbial diversity, composition, and metabolic potential. Our findings highlight the critical role of TLR2 in orchestrating immunometabolic homeostasis and provide new insights into its broader function in maintaining host-microbiota symbiosis across developmental stages.

overall_design: Germ free (GF) and conventionalized (CONVD) zebrafish larvae at 5 dpf from line tlr2 mutant and wild-type control were collected for RNAseq.

first: Herman

middle: P

last: Spaink


title: Impacts of Amylose Synthesis Knockout on Sorghum Seed Development and Grain Quality

status: Public on Jul 31 2025

city: Lubbock

first: Pallavi

last: Dhiman

address: 1006 Canton Avenue

country: USA

institute: Texas Tech University

type: Expression profiling by high throughput sequencing

summary: Waxy sorghum seeds, defined by reduced amylose content in starch, offer the potential for improving grain quality in food and industrial applications. While waxy endosperms arising from non-functional waxy (wx) allele leading to the absence of Granule-bound starch synthase (GBSS) enzyme have been identified in sorghum, their broader effects on seed development and grain quality remain inadequately understood. To address this gap, we identified a novel wx loss-of-function allele, "wxe" in the mutant population of the sorghum reference genome line BTx623. Beyond reduced amylose content, wxe exhibited increased kernel hardness, elevated protein content, reduced endosperm-to-germ ratio, and decreased kernel weight compared to the wild-type. Integrating transcriptomic, metabolomic, and seed chemistry analyses revealed coordinated regulatory changes during seed development due to disrupted amylose synthesis. This included altered starch granule structure, enhanced lipid profiles, and reduced carbohydrate content. Differentially expressed genes and transcription factors related to starch metabolism provided insights into the regulatory mechanisms. Furthermore, metabolic profiling showed significant changes in the accumulation of compounds influencing flavor and nutritional properties. This study enhances our understanding of the molecular coordination of sorghum seed development and provides new insights into regulating seed development.

overall_design: Transcriptome profiling of endosperm was performed in Wily type Btx623 (samples designated as WT) and waxy mutant (samples designated as M) at 6, 11, 16, and 21 days post-anthesis to investigate the effects of GBSS1 gene knockout on seed development.

first: Shejal

last: Soumen

first: Deepti

last: Nigam

first: Scott R.

last: Bean

first: Xiaorong

last: Wu

first: Gunvant B.

last: Patil

first: Zhanguo

last: Xin

first: Yinping

last: Jiao


title: The genes involved in histone deacetylation regulates lipid metabolism through H4K5 and H4K8

city: Kunming

first: Qinyi

state: Yunnan

address: No.1076 Yuhua Road

country: China

institute: Yunnan University of  Chinese Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To identify genes which were involved in histone deacetylation regulates lipid through H4K5 and H4K8. ChIP-seq and motif analysis of C. elegans which were fed with E. coli OP50 until reach to adult. After washing by M9 buffer for three times, worms were re-suspended in PBS, frozen immediately in liquid nitrogen for ChIP-seq which were carried out by Wuhan SeqHealth Tech Co.,Ltd (Wuhan, China). The chromatin was sheared into 0.2 to 1kb fragments then subjected to immunoprecipitation using antibodies for H4K5ac (Abcam, ab51997) or H4K8ac (Abcam ab45166). Indexed ChIP-seq libraries were prepared using the NEB Next Ultra DNA library prep kit (New England Biolabs) and pair-end sequences on iIIumina NovaSeq 6000. HOMER was used in motif analysis of deferentially enriched peaks 31.

overall_design: The worms which fed on E. coli OP50 were collected after reaching to adult stage. The chromatin was sheared into 0.2- to 1-kb fragments. The soluble chromatin fraction was immunoprecipitated using antibodies specific for H4K5ac (Abcam, ab51997) or H4K8ac (Abcam, ab45166). ChIP-seq libraries were prepared using the NEBNext UltraDNA library prep kit (New England Biolabs) followed with paired-end sequencing on an Illumina NovaSeq6000.

first: Qin-Yi

first: Yi-Cheng

last: Ma

first: Meng

last: Zhou

first: Rui

last: Zhu

first: Cheng-Gang

last: Zou


title: Cancer cells subvert ZNF93 to escape surveillance by L1 epigenetic sentinels and control APOBEC3B

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

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

overall_design: Refer to individual Series


title: OXPHOS driven by glycolysis through the malate aspartate shuttle is required for cardiomyocyte re-differentiation and long-term fish heart regeneration [scRNA-seq]

city: Oxford

first: Mathilda

last: Mommersteeg

address: | Institute of Developmental and Regenerative Medicine (IDRM) | IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Drive

department: Department off Physiology, Anatomy and Genetics

country: United Kingdom

institute: University of Oxford

summary: In contrast to humans after myocardial infarction, fish can fully regenerate their hearts. However, not all fish are equally able to regenerate, allowing comparative inter- and intra-species analysis to identify novel mechanisms controlling successful heart regeneration. Here, we report a differential regenerative response to cardiac cryo-injury between seven different wild-type zebrafish strains. Correlating this data to single cell and bulk RNAseq data, we identify oxidative phosphorylation (OXPHOS) as a positive regulator of long-term regenerative outcome. OXPHOS levels, driven by Glycolysis through the Malate aspartate shuttle (MAS), increase as soon as cardiomyocyte proliferation decreases, and this increase is required for cardiomyocyte re-differentiation and successful long-term regeneration. We confirm these findings in Astyanax mexicanus and link it to a dynamic temporal sarcomere gene expression programme during cardiomyocyte re-differentiation. These findings challenge the current stance that OXPHOS inhibits regeneration and provide new targetable pathways to enhance heart repair in humans after myocardial infarction.

overall_design: scRNA-seq data on FAC-sorted nppa-positive border zone cardiomyocytes at 1. 3 and 7dpci. Zebrafish underwent cryo-injury of the cardiac ventricle.

first: Jeroen

last: Bakkers

first: Phong

last: Nguyen

first: Hessel

last: Honkoop


title: Profibrotic monocyte-derived alveolar macrophages as a biomarker and therapeutic target in systemic sclerosis-associated interstitial lung disease [Duke]

city: Chicago

first: Alexander

middle: V

last: Misharin

state: Illinois

address: 303 E Superior St

department: Pulmonary and Critical Care

institute: Northwestern University

summary: Interstitial lung disease (ILD) is present in over 60% of patients with systemic sclerosis (SSc) and is the leading cause of SSc-related deaths. Profibrotic monocyte-derived alveolar macrophages (MoAM) play a causal role in the pathogenesis of pulmonary fibrosis in animal models where their persistence in the niche requires signaling through the Colony Stimulating Factor 1 Receptor (CSF1R). We hypothesized that the presence and proportion of MoAM in bronchoalveolar lavage (BAL) fluid from patients with SSc-ILD may be a biomarker of ILD severity. To test this hypothesis, we performed BAL in 9 prospectively enrolled patients with SSc-ILD on imaging and 13 healthy controls and analyzed the cellular fraction using flow cytometry and single-cell RNA sequencing. Compared to healthy controls, patients with SSc-ILD showed increased abundance of MoAM and interstitial macrophages in BAL fluid that was associated with worse lung function and lung disease on imaging. We identified changes in the MoAM transcriptome as a function of treatment with mycophenolate, an effective therapy for SSc-ILD.

overall_design:
Bronchoalveolar lavage (BAL) fluid from 8 heathy volunteers was obtained at the bronchoscopy suite of Duke University Hospital. Single cell RNA-seq libraries were prepared with 10x 3' gene expression kit. Libraries were sequenced on Illumina NovaSeq 6000. Gene expression matrices were generated with 10x Cell Ranger v3.1.0 (exon-only mode) software and reads were mapped to GRCh38.84 reference genome (10x Genomics Cell Ranger Human 1.2.0 GRCh38 reference).

***************************************************************
Protected Health Information: fastq files have been omitted.
***************************************************************

first: Nikolay

middle: S

last: Markov

first: Anthony

middle: J

last: Esposito

first: Maxwell

last: Schleck

first: Radmila

last: Nafikova

first: Zhan

last: Yu

first: Ziyan

last: Lu

first: Robert

middle: M

last: Tighe

first: Monique

middle: E

last: Hinchcliff


title: OXPHOS driven by glycolysis through the malate aspartate shuttle is required for cardiomyocyte re-differentiation and long-term fish heart regeneration [Astyanax_mexicanus_RNAseq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the Astyanax mexicanus surface fish and Pachon cavefish populations.  The fish underwent cryo-injury of the cardiac ventricle and hearts were isolated at 6 hours, 1, 3, 7, 14 and 30 days post cryo-injury as well as 6 hours, 1 and 3 days post sham and uninjured controls.

first: Zhilian

last: Hu


title: Cytotoxic CX3CR1+ Vδ1 T cells clonally expand in an interplay of CMV, microbiota, and HIV-1 persistence in people on antiretroviral therapy

status: Public on Jul 30 2025

city: Toulouse

first: Pierre

last: Delobel

address: CHU Purpan – BP 3028

country: France

institute: Infinity

summary: We performed a comprehensive characterization of Vδ1 T cells in blood of people with HIV-1 on antiretroviral therapy and HIV-seronegative controls, in a substudy of the ANRS EP61 GALT study (NCT02906137). We deciphered the single-cell transcriptome of Vδ1 cells. Vδ1 T cells were mainly terminally differentiated effectors that expanded in the blood with some trafficking with the gut of people with HIV-1. Most expressed CX3CR1 and displayed a highly cytotoxic profile, but low cytokine production, supported by a transcriptomic shift towards enhanced effector lymphocytes. The increase in Vδ1 T cells observed in people with HIV-1 has multiple triggers, particularly CMV and microbiota, and may in turn contribute to the control of the HIV-1 reservoir.

overall_design:
For Vδ1 single-cell RNA sequencing, Vδ1 T cells were sorted after a stainingn step with TotalSeq-B anti-human hashtags (LNH-94; 2M2/BioLegend) directed against CD298 and β2-microglobulin. Sorted Vδ1 T cells were stored on ice and immediately processed for single-cell library generation. Vδ1 cells were sorted from PBMC of 6 PLWH and 6 controls, all CMV seropositive. Single-cell libraries were generated using the Chromium iX Single-Cell Instrument and Chromium Next GEM Single Cell 3′ Kit v3.1, Chip G Single Cell kit, Dual Index kit TT Set A and NT set A, and 3’ Feature Barcode kit (10x Genomics). Sequencing was then performed on a full SP flow cell 100 cycles (2 lanes) on the Illumina NovaSeq 6000 instrument (Illumina, San Diego, USA).

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

first: N

last: Collercandy

first: C

last: Vellas

first: M

last: Requena

last: Zahm

first: P


title: Dnmt3a2 expression during embryonic development is required for phenotypic stability

city: Grand Rapids

first: Peter

middle: A

last: Jones

state: MI

address: 333 Bostwick Ave NE

department: Center of Epigenetics

institute: Van Andel Research Institute

type: Methylation profiling by genome tiling array

summary: Proper function and switching of regulatory elements is essential for the development of vertebrates and is known to be controlled by DNA cytosine methylation. We used isoform-specific knockouts of the two known DNA methyltransferase variants, Dnmt3a1 and Dnmt3a2 to probe their roles in regulatory element methylation in embryogenesis and in postnatal development. Mouse embryos lacking Dnmt3a1 showed minimal loss of genomic methylation confirming that this isoform may not be directly involved in embryonic development. However, they were smaller than their littermates and died about 4 weeks after birth with considerable postnatal demethylation as has been previously reported. On the other hand, embryos lacking Dnmt3a2 showed widespread genomic hypomethylation which was particularly prevalent at enhancers, CTCF sites and imprinted  genes. Interestingly these methylation deficits were largely repaired after birth, presumably by the remaining Dnmt3a1 isoform. The mice lacking Dnmt3a2 were viable; however, they showed an increased prevalence of sporadic abnormalities as previously observed at a low frequency in laboratory mice, including anophthalmia, hydrocephalus, hydronephrosis and male infertility phenotypes. Interestingly, hypomethylation of several imprinted genes  was also observed in sperm which might explain the infertility phenotype.  Therefore, the interaction between the two isoforms is developmentally regulated, with Dnmt3a2 playing a key role in ensuring the methylation states of enhancers, CTCF sites and imprinted genes, thereby reducing the likelihood of stochastic phenotypes emerging after birth.

overall_design: We investigated the DNA methylation changes that might be associated with the stochastic developmental defects observed in Dnmt3a2-/- mice compared to their WT litter mates, focusing on two critical developmental windows: E15.5, and 21 days postnatal (PD 21). These time points were selected to capture methylation dynamics during peak embryonic DNA methylation establishment (E15.5) and during postnatal tissue maturation (PD 21). We also determined DNA methylation changes in Dnmt3a1-/- mice compared to their WT litter mates at these time points. To examine tissue-specific DNA methylation patterns, we isolated brain and liver tissues and used the Illumina MM285 Infinium Methylation EPIC array to perform genome-wide methylation analysis.

first: Minnin

last: Liu

first: Guillermo

last: Urrutia


title: The mechanism of FSTL3 in the progression of colon cancer

city: Nanjing

first: Leqian

last: Ying

state: Jiangsu

address: Ding Jiaqiao street

department: Oncology

institute: Southeast University

summary: FSTL3 is a multifunctional protein, and its role in cancer has attracted considerable attention. Firstly, overexpression of FSTL3 has been found to be closely associated with the occurrence and development of various tumors. The expression levels of FSTL3 are significantly elevated, which is linked to its role in promoting tumor cell proliferation, migration, and invasion. Additionally, the expression levels of FSTL3 are associated with the grading and prognosis of tumors, where high expression of FSTL3 is often correlated with the malignancy and adverse prognosis of tumors. Therefore, this study primarily explores the mechanisms by which FSTL3, acting as an exosomal cytokine, promotes the progression of colon cancer.

overall_design: In order to investigate the mechanistic role of FSTL3 in the progression of colon cancer, the study involved the exogenous addition of humanized FSTL3 protein to the culture medium of HCT116 cells. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells after 24 hours. This aimed to explore its impact on the biological functions of colon cancer cells and underlying mechanisms.


title: FRA1 drives melanoma metastasis through an actionable transcriptional network

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

summary: Transcriptional dysregulation has emerged as a critical driver of melanoma progression, yet the molecular mechanisms governing this process and their potential as therapeutic targets remain inadequately characterized. Here, we identify FRA1 as a potent and actionable driver of melanoma metastasis. FRA1 enhanced both the initial seeding and subsequent outgrowth of metastatic lesions. Comprehensive multi-omics integration revealed transcriptional target genes of FRA1, with AXL, CDK6, and FSCN1 exhibiting increased expression in melanoma metastasis and a significant correlation with poor patient outcomes. Silencing AXL, CDK6, or FSCN1 abrogated FRA1-mediated invasion in vitro and reduced metastatic colonization. Furthermore, pharmacological inhibition of CDK6 and FSCN1, and to a lesser extent AXL, suppressed melanoma metastasis and prolonged overall survival. The expression of FRA1 and its target genes correlates with shortened survival across multiple cancer types, highlighting the broader clinical relevance of this pathway. This study unveils an actionable FRA1-mediated transcriptional network that drives cancer progression and metastasis, offering potential avenues for therapeutic interventions.

overall_design: RNAseq and Cut&Run profiling of A375 and 1205Lu cells treated with siRNAs targeting human FRA1.

first: Xiaonan

last: Xu

first: Manon

last: Chadourne

first: Zulaida

last: Soto-Vargas

first: Vinesh

last: Jarajapu

first: Jiqiang

last: Yao

first: Xiaoqing

first: Florian

last: Karreth


title: OXPHOS driven by glycolysis through the malate aspartate shuttle is required for cardiomyocyte re-differentiation and long-term fish heart regeneration

first: Mathilda

last: Mommersteeg

sample_organism:
Danio rerio
Astyanax mexicanus

platform_organism:
Danio rerio
Astyanax mexicanus


title: Cell-type-specific contributions to impaired blood-brain barrier and altered cerebral metabolism in prodromal 5XFAD mice

city: Cambridge

last: Sun

state: MA

address: 455 Main St

department: EECS

institute: Whitehead Institute

summary: Single-nucleus RNA sequencing (snRNA-Seq) further revealed cell type-specific transcriptomic changes in the hippocampus of prodromal 5XFAD mice, including downregulation of synaptogenesis and synaptic transmission genes in the CA1 and dentate gyrus excitatory neurons, impaired endothelia gene expression linked to brain barrier function and angiogenesis, altered innate immune response genes in astrocytes, as well as upregulation of cholesterol biosynthesis and metabolism genes in the CA1 excitatory neurons.

overall_design: We performed snRNA-seq in mouse hipppcampus from 3 months old 5xFAD and wild type mice with and without blood vessel enrichment.

first: Wenzhen

last: Duan


title: Single-Cell RNA Sequencing Reveals Shenbai Granule Retards Colorectal Tumorigenesis by Modulating Cholesterol-Induced Ccl22+ DCs and Tregs Crosstalk

first: yang

last: sun

address: Nanjing University Academy of Sciences, No. 163 Xianlin Avenue, Qixia District, Nanjing City, Jiangsu Province

department: Life Sciences

institute: Nanjing University

summary: Colorectal tumorigenesis generally follows a progressive sequence from adenoma to adenocarcinoma, accompanied by dynamic changes in the tumor microenvironment (TME). Randomized controlled trials have confirmed that Shenbai Granule (SBG), a traditional Chinese medicine formula, is safe and effective for the prevention of recurrent colorectal adenoma. However, the effects and mechanisms of SBG on colorectal tumorigenesis and the TME remain unclear. To investigate this, single-cell RNA sequencing (scRNA-seq) was conducted to reveal the dynamic evolution of the TME. Primary cells were isolated for in vitro validation experiments. The findings demonstrated that SBG reduces both the number and volume of tumors. There was a marked accumulation of Ccl22+ dendritic cells (DCs) and an enhanced interaction between Ccl22+ DCs and CD4+ regulatory T cells (Tregs), which were reversed by the treatment of SBG and its active compound, berberine. Combined treatment with cholesterol and lipopolysaccharide induced characteristic gene expression in Ccl22+ DCs, which may represent a type of “exhausted DCs”. Intraperitoneal injection of the Ccl22+ DCs after SBG treatment eliminated its therapeutic effects. These findings highlight critical crosstalk between Ccl22+ DCs and CD4+ Tregs in colorectal cancer. The multi-component properties of natural products may restore TME homeostasis and offer novel cancer therapy.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: scRNA-seq analysis of single-cell suspensions from colorectal adenoma patient tissues and APCmin/+ mice

first: Yuquan

last: Tao

first: Yinuo

last: Ma

first: Lisha

last: Zhou

first: Yang

first: Haibo

last: Cheng


title: OXPHOS driven by glycolysis through the malate aspartate shuttle is required for cardiomyocyte re-differentiation and long-term fish heart regeneration [WT_ZF_strain_RNAseq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 7 different wild-type zebrafish strains (AB, KCL, NA, SAT, TL, TU and WIK). Zebrafish underwent cryo-injury of the cardiac ventricle and hearts were isolated at 1 and 7 days post cryo-injury as well as uninjured control.

middle: T

first: Konstantinos

last: Lekkos


title: Local growth hormone facilitates aging of the colon epithelial microenvironment

city: Los Angeles

first: Richard

last: Ainsworth

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

summary: We elucidate mechanisms underlying loca non-pituitary GH (npGH) action in the non-tumorous colon tissue microenvironment. We demonstrate autocrine npGH action in normal human colon cells (hNCC) infected with lentivirus-expressing hGH (lentiGH), as well as paracrine npGH action in hNCC co-cultured with lentiGH hNCC and in intact human 3-dimensional intestinal organoids co-cultured with organoids infected with lentiGH. Enriched gene ontology and pathway analysis of intact organoids exposed to paracrine npGH identified distorted extracellular matrix (ECM) and focal adhesion pathways concurrent with altered expression of ECM and cytoskeletal proteins. Significant phosphoprotein changes associated with cytoskeleton and cell migration pathway occurred in GH-exposed hNCC. Paracrine npGH triggers these changes by activating epithelial-mesenchymal transition, as shown by suppression of E-cadherin and induction of Twist2 in cellular models, as well as in the colon of nude mice inoculated with GH-secreting xenografts. These changes are consistent with observed increased migration of hNCC overexpressing lentiGH, or in those co-cultured with GH-secreting hNCC or with GH-secreting normal colon fibroblasts. Furthermore, whole exome sequencing detected increased structural variation in intact organoids co-cultured with lentiGH-infected organoids, likely as a consequence of GH-mediated suppressed DNA damage repair, thereby favoring cell transformation.

overall_design: human colon entestinal organoids were infected with lentivirus expressing GH or lentivirus expressing vector  and cultured for 2 month. Organoid cells growing in a presence of lentiGH or lenti V were selected and compared.

first: Shlomo

last: Melmed

first: Vera

last: Chesnokova

first: Richard I.


title: H3K4 methylation-promoted transcriptional memory supports faithful zygotic genome activation and development

status: Public on Jul 29 2025

city: Munich

first: Eva

last: Hoermanseder

state: Bavaria

address: Feodor-Lynen-Str. 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Center Munich

summary: Accurately established transcriptional programs are paramount for successful embryonic development. At zygotic genome activation, gene expression is initiated for the first time in the life of an embryo. Pioneer transcription factors present in the embryo are essential for this process, however, the role of active chromatin modifications is less clear. It is unknown if active chromatin modifications established in the gamete are propagated in the embryo as epigenetic memory to support zygotic genome activation and development. Here, we provide evidence that in Xenopus laevis, H3K4 methylation contributes to epigenetic memory of active chromatin states, which is required for faithful zygotic genome activation and successful embryonic development. We find that chromatin configurations of promoters displaying high H3K4me3 intensity and breadth, alongside DNA hypomethylation and increased GC content, are maintained from the gametes to the embryo across multiple cell divisions and a transcriptionally quiescent phase in early development. We show that this maintenance of H3K4 methylation is essential for precise zygotic genome activation. Finally, we demonstrate that Kmt2b and Cxxc1 facilitate transcription-independent maintenance of H3K4me3 and proper zygotic gene expression. In summary, our study establishes a role for H3K4 methylation for memory of active chromatin states in embryos and reveals its importance for successful embryonic development.

overall_design: Profiling of H3K4me3 occupancy using CUT&RUN of H4K4me3-depleted Xenopus laevis embryos via Kdm5b-wt and H3.3-K4M mRNA mutant overexpression  at mid-ZGA stage (6.5hpf). Kdm5b-ci (catalytically inactive) plus H3.3-wt were overexpressed as the respective control conditions. Treatments were performed either in a developmental "window" from zygote to ZGA, or "persistently" from zygote onwards.

first: Meghana

last: Oak

first: Marco

last: Stock

first: Matthias

last: Mezes

first: Tobias

last: Straub

first: Antony

last: Hynes-Allen

first: Jelle

last: van den Ameele

first: Ignasi

last: Forne

first: Andreas

last: Ettinger

first: Axel

last: Imhof

first: Antonio

last: Scialdone

last: Hörmanseder


title: The transitional cerebellar progenitor is a technical artifact driven by low-quality cells [re-analysis]

city: Memphis

first: Paul

middle: A.

last: Northcott

address: 262 Danny Thomas Place

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

summary: We reprocessed the raw FASTQ files from the published single-cell RNA-seq atlas of the developing human cerebellum (accession GSE198565) and, following rigorous quality control, removed low-quality cells and refined the cell-type annotations.

overall_design: Both raw scRNA-seq FASTQs and cellranger mapping outputs from the fetal human cerebellar atlas (accession GSE198565, sample GSM5952337), were obtained and reprocessed using the same parameters described in the publication. FASTQ files for GSM5952337 were provided by the submitter. FASTQ files were mapped with CellRanger (V3.2, the same as the cellranger outputs provided) and cell type annotations were adopted from the original publication (GSE198565). The dataset was composed of 95,542 cells collected from fetal cerebella of eight individual donors. Additional QC metrics were calculated for each sample utilizing CELLBENDE and DropletQC. UMAP coordinates were all calculated using cosine distance between the top 100 nearest neighbors based on the first 50 principal components. Unsupervised clustered were determined using leiden clustering at a resolution of 0.8 as implemented in scanpy.

first: Kyle

last: Smith

first: Yiran

last: Li

first: Brian

middle: L

last: Gudenas


title: Nox1 and Npy1r mark regional colon stem cell populations that serve as cancer origins in vivo [scRNA_seq]

first: Bernett

last: Lee

address: 8A Biomedical Grove #03-06 Immunos

country: Singapore

institute: Singapore Immunology Network

summary: Current colorectal cancer (CRC) mouse models lack either colon specificity, limiting progression towards more advanced disease, or preclude evaluation of resident stem cells as cancer origins. Here, we report identification of Nox1 and Npy1r as cell-surface markers enriched in Lgr5+ stem cells predominantly within the caecum and exclusively within the mid-distal colorectum respectively. Selective dysregulation of Wnt signalling in Nox1+ or Npy1r+ stem cells using new CreERT2 mouse lines drives colon cancer initiation, predominantly within the caecum and the rectum respectively, establishing these stem cell populations as important sources of colon cancer. Selective conditional activation of Wnt signalling and oncogenic K-RAS in combination with loss of Trp53 in these stem cell compartments resulted in development of advanced, invasive cancers. This study establishes the new CreERT2 drivers as valuable tools for studying stem cell contributions to colon cancer.

overall_design: Crypts from individual regions of the colon and small intestine were isolated and dissociated into single cells. The single cell transcriptomics were analyzed using scRNA-Seq.

first: Maxime

last: Gasnier

first: Tanysha

middle: C

last: Chen

first: Swathi

last: Yada

first: Sowmya

last: Sagiraju

first: Yusuke

last: Yoshikawa

first: Stefano

last: Perna

first: Grace

middle: H

last: Lim

first: Nick

last: Barker


title: Nox1 and Npy1r mark regional colon stem cell populations that serve as cancer origins in vivo [RNA_seq]

overall_design: RNA-seq profiling of GFP-sorted epithelial cell from small intestine and colon Lgr5-2A-eGFP mice.


title: Nox1 and Npy1r mark regional colon stem cell populations that serve as cancer origins in vivo [RNA-seq2]

overall_design: RNA-seq profiling of GFP-sorted epithelial cell from small intestine and colon Lgr5-2A-eGFP mice. Small intestine is separated in 3 equal parts (proximal, middle and distal). Colon is separated in 2 parts (proximal and distal).


title: Single-Cell Transcriptional Analysis of Murine Mesenteric Lymph Nodes Following Oral Lyso-phosphatidylserine Nanoparticle Administration Reveals Cellular Heterogeneity in Tolerance Features

city: Buffalo

first: Jonathan

last: Bard

state: New York

address: 701 Ellicott Street

department: Genomics and Bioinformatics Core

institute: University at Buffalo

summary: Unwanted immune responses against self-proteins or exogenous therapeutic proteins can trigger autoimmune diseases or compromise the safety and efficacy of life-saving therapeutic biologics. To address this issue, we utilized the ability of phosphatidylserine (PS) to convert an immunogen into a tolerogen and rationally developed a LysoPS-containing tolerogenic nanoparticle platform to prevent and mitigate unwanted immune responses. We demonstrated that prophylactic oral treatment with LysoPS-containing proteins prevents unwanted immune responses by inducing tolerance. However, the biological processes and cellular communication involved in LysoPS-mediated oral tolerance remain unclear. Therefore, this study aimed to characterize immune cell interactions and the potential tolerogenic mechanism in mice treated with LysoPS using Single-cell RNA sequencing (scRNA-seq). Our data showed that LysoPS nanoparticles increased the expression of RNAs associated with tolerogenic features in B cells, T cells, and NK cells, primarily through TGF-β responses.

overall_design: Animals were continuously fed Buffer, Free OVA, and LysoPS-OVA for four weeks via oral administration. Mesenteric lymph nodes (MLNs) were collected, enzymatically digested, and purified into a single live cell suspension before scRNA-seq. Six animal per group were used in this study and animal from the same group were pooled together for scRNA

first: Vincent

last: Chak

first: Edwin

last: Ovalle

first: Elizabeth

last: Wohlfert

first: Jason

middle: G

last: Kay

first: Sathy

last: Balu-Iyer


title: The epigenomic landscape of single vascular cells reflects developmental origin and identifies disease risk loci

city: Stanford

first: Chad

last: Weldy

state: CA

address: 870 Quarry Road, CVRC Falk

department: Medicine, Cardiovascular Medicine

institute: Stanford University

summary: Vascular sites have distinct susceptibility to atherosclerosis and aneurysm, yet the biological underpinning of vascular site-specific disease risk is largely unknown. Vascular tissues have different developmental origins that may influence global chromatin accessibility, and understanding differential chromatin accessibility, gene expression profiles, and gene regulatory networks (GRN) on single cell resolution may give key insight into vascular site-specific disease risk. Here, we performed single cell chromatin accessibility (scATACseq) and gene expression profiling (scRNAseq) of healthy adult mouse vascular tissue from three vascular sites, 1) aortic root and ascending aorta, 2) brachiocephalic and carotid artery, and 3) descending thoracic aorta. Through a comprehensive analysis at single cell resolution, we discovered key regulatory enhancers to not only be cell type, but vascular site specific in vascular smooth muscle (SMC), fibroblasts, and endothelial cells. We revealed an epigenetic ‘memory’ of embryonic origin with differential chromatin accessibility of key developmental transcription factors such as Tbx20, Hand2, Gata4, and Hoxb family members and discovered transcription factor motif accessibility to be cell type and vascular site specific. Notably, we identify ascending fibroblasts to have distinct epigenomic patterns, highlighting SMAD2/3 function to suggest a differential susceptibility to TGF, a finding we confirmed through in vitro culture of primary adventitial fibroblasts. Finally, to understand how vascular site-specific enhancers may regulate human genetic risk to disease, we integrated genome wide association study (GWAS) data for ascending and descending aortic dimension, and through using a novel technique, we employed ChromBPNet, a distinct base resolution deep learning model to predict variant effect on chromatin accessibility We trained nine ChromBPNet models to predict variant effect in SMC, Fibroblasts, and Endothelial cells within ascending aorta, carotid, and descending aorta sites of origin. We reveal that although cell type remains a primary influence on variant effect, vascular site modifies effect within cell type and highlights genomic regions that are enriched for specific TF motif footprints — including MEF2A, SMAD3, and HAND2. This work supports a paradigm that the epigenomic and transcriptional landscapes of vascular cells are cell type and vascular site-specific and that these vascular site-specific enhancers govern complex genetic drivers of vascular site-specific disease risk.

overall_design: Tissues were collected and dissociated for single cell capture as previously described. Briefly, vascular tissue was washed three times in PBS, tissues were then placed into an enzymatic dissociation cocktail (2 U ml−1 Liberase (5401127001; Sigma–Aldrich) and 2 U ml−1 elastase (LS002279; Worthington) in Hank’s Balanced Salt Solution (HBSS)), and minced. After incubation at 37 °C for 1 h, the cell suspension was strained and then pelleted by centrifugation at 500g for 5 min. The enzyme solution was then discarded, and cells were resuspended in fresh HBSS. To increase biological replication, 16 mice were used to obtain single-cell suspensions for each vascular tissue (aortic root/ascending aorta, brachiocephalic/carotid, and descending thoracic aorta) with two captures per vascular site. Cells were FACS sorted and live cells were identified as previously described. Briefly, cells were sorted on a BD Aria II instrument, where cells were gated on forward/side scatter parameters to exclude small debris and then gated on forward scatter height versus forward scatter area to exclude obvious doublet events. Approximately 100-150,000 live cells were sorted for each vascular site, where a portion of cells were taken directly to scRNAseq capture. For single cell ATAC, cells were collected in BSA-coated tubes, and nuclei isolated per 10X recommended protocol, and captured on the 10X scATAC platform.  All single-cell capture and library preparation was performed in the Quertermous lab and sequencing was performed at MedGenome (Foster City, CA). Cells were loaded into a 10x Genomics microfluidics chip and encapsulated with barcoded oligo-dT-containing gel beads using the 10x Genomics Chromium controller according to the manufacturer’s instructions. Single-cell libraries were then constructed according to the manufacturer’s instructions (Illumina). Libraries from individual samples were multiplexed into one lane before sequencing on an Illumina platform with targeted depth of 50,000 reads per cell for RNA and 75,000 reads/cell for ATAC. Post filtering for non-cells, mean number of reads within peaks per cell in scATAC data was 18,000-20,000 as was seen in our prior report.


title: Effect of conditional SMC specific deletion of ADAR1 with constitutive deletion of RNA sensor MDA5 on mouse aortic single cell transcriptomic profile and effect on atherosclerosis

summary: Mapping the genomic architecture of complex disease has been predicated on the understanding that genetic variants influence disease risk through modifying gene expression. However, recent discoveries have revealed that a significant burden of disease heritability in common autoinflammatory disorders and coronary artery disease is mediated through genetic variation modifying post-transcriptional modification of RNA through adenosine-to-inosine (A-to-I) RNA editing. This common RNA modification is catalyzed by ADAR enzymes, where ADAR1 edits specific immunogenic double stranded RNA (dsRNA) to prevent activation of the double strand RNA (dsRNA) sensor MDA5 (IFIH1) and stimulation of an interferon stimulated gene (ISG) response. Multiple lines of human genetic data indicate impaired RNA editing and increased dsRNA sensing by MDA5 to be an important mechanism of coronary artery disease (CAD) risk. Here, we provide a crucial link between observations in human genetics and mechanistic cell biology leading to progression of CAD. Through analysis of human atherosclerotic plaque, we implicate the vascular smooth muscle cell (SMC) to have a unique requirement for RNA editing, and that ISG induction occurs in SMC phenotypic modulation, implicating MDA5 activation. Through culture of human coronary artery SMCs, generation of a conditional SMC specific Adar1 deletion mouse model on a pro-atherosclerosis background with additional constitutive deletion of MDA5 (Ifih1), and with incorporation of single cell RNA sequencing cellular profiling, we further show that Adar1 controls SMC phenotypic state by regulating Mda5 activation, is required to maintain vascular integrity, and controls progression of atherosclerosis and vascular calcification. Through this work, we describe a fundamental mechanism of CAD, where cell type and context specific RNA editing and sensing of dsRNA mediates disease progression, bridging our understanding of human genetics and disease causality.

overall_design: To investigate the role of SMC specific ADAR1 and RNA sensor MDA5 on vascular function and progression of atherosclerosis, we used the Adar1 flox mouse crossed onto an Myh11 CreERT2 background, with additional constitutive either homozygous or heterozygous deletion of Mda5 (Ifih1), that has additional hyperlipidemia with ApoE-/- and SMC lineage tracing with ROSA tdTomato alleles. In our prior experiments, we performed homozygous deletion of Adar1 by treating 8 week old male mice with tamoxifen (Adar1 fl/fl, Myh11CreERT2, ApoE-/-,  tdTomato+/+). These mice develop severe disease and single cell RNAseq was performed of the ascending aorta and aortic root at 2 weeks post tamoxifen. In the submitted data, SMC Adar1 deletion was performed with additional constitutive homozygous deletion of MDA5 (Adar1 fl/fl, Ifih1-/-, Myh11CreERT2, ApoE-/-,  tdTomato+/+). Control mice were wild type for the Adar1 fl/fl allele and Ifih1 allele ( Myh11CreERT2, ApoE-/-,  tdTomato+/+) and were similarly treated with tamoxifen at 8 weeks of age. To then evaluate the effect of SMC Adar1 haploinsufficiency in atherosclerosis, in our prior experiments we treated mice that were heterozygous for the Adar1 flox allele (Adar1 fl/WT, Myh11CreERT2, ApoE-/-,  tdTomato+/+) with tamoxifen at 8 weeks of age, and then put on a high fat diet for 16 weeks to induce atherosclerosis. In the submitted dataset, these SMC Adar1 het mice where then crossed onto the Mda5 het background where scRNAseq was performed at the same 16 week timepoint.


title: Primary adventitial fibroblast response to TGFb is dependent on vascular site and implicates functional developmental epigenomic memory

summary: We have shown that vascular SMCs, fibroblasts, and endothelial cells have transcriptional and epigenomic features that are distinct to vascular site. Further, TF motif accessibility analysis in fibroblasts reveals an increased accessibility of AP1, and SMAD2:3:4, and TCF21 motifs in the ascending fibroblast population compared to carotid and descending fibroblasts, with further gene regulatory network analysis suggesting distinct regulatory TF module activity in ascending fibroblasts highlighting master regulator of fibroblast activation Meox1. This differential chromatin accessibility would suggest the potential for heightened biological response to TGFb in ascending fibroblasts. To evaluate the functional effect of this differential chromatin accessibility and to identify if differential gene expression is retained following removal from vascular site flow conditions, we isolated and cultured primary adventitial fibroblasts from healthy 14 week old C57BL/6 mice from the ascending and descending aorta and stimulated them with control or TGFb (10ng/mL, 48hrs) and performed bulk RNA sequencing (n = 3 per condition).

overall_design: We isolated and cultured primary adventitial fibroblasts from healthy 14 week old C57BL/6 mice from the ascending and descending aorta and stimulated them with control or TGFb (10ng/mL, 48hrs) and performed bulk RNA sequencing (n = 3 per condition)


title: Single-cell characterization of enterovirus infection of spinal cord organoids

city: Bethesda

first: Philip

last: Murphy

state: MD

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

summary: The mechanisms by which enteroviruses, particularly enterovirus D-68 (EV-D68) and enterovirus A-71 (EV-A71), contribute to acute flaccid myelitis (AFM), a severe neurological condition characterized by sudden muscle weakness and paralysis, remain poorly understood. To investigate the cellular tropism and infection dynamics of these enteroviruses, we utilized human spinal cord organoids (hSCOs) derived from induced pluripotent stem cells (iPSCs). We performed single-cell RNA sequencing (scRNA-seq) to profile the cellular composition of hSCOs and identify infected cell types post-infection. We found that hSCOs exhibit a diverse cellular landscape, including neurons, astrocytes, oligodendrocyte progenitor cells (OPCs), and multipotent glial progenitor cells (mGPCs), with astrocytes predominant in earlier developmental stages and neurons more abundant in later stages. Upon infection with two EV-D68 strains (US/IL/14-18952 and US/CO/18-23089) and one EVA71 strain (Tainan/4643/1998), we observed distinct viral tropism. EV-D68-18952 showed a significant increase in infected neurons, while EV-D68-23089 exhibited higher infection rates in cycling astrocytes and OPCs. In contrast, EVA71 demonstrated a broader tropism, with a statistically significant increase in infected mGPCs, suggesting enhanced infection efficiency across multiple cell types. These findings provide novel insights into the cell-type specificity of EV-D68 and EVA71 in the spinal cord, offering a deeper understanding of potential mechanisms underlying AFM pathogenesis. Understanding the dynamics of infection at single-cell resolution will inform future therapeutic strategies aimed at mitigating the neurological impact of enteroviral infections.

overall_design: Human spinal cord organoids (hSCOs) were infected in pools of 12 organoids each and inoculated with virus at 105 PFU/pool. After 1 hour of incubation at room temperature, hSCOs were washed 3X with PBS and moved to new wells before incubation with fresh medium. No further media changes were performed for the rest of the experiment. The EV-D68 infected pool was incubated at 33oC and EV-A71 at 37oC for 48 hours post infection (hpi). After 48hpi, the pools were dissociated to a single-cell suspension with Accumax (Invitrogen). They were incubated for 15 minutes in the water bath at 37℃, gently mixed, and then proceeded with the proposed 10X Genomics protocol (Cell Preparation Guide - CG00053 Rev C). Once the cell's concentration is achieved the cells are moved to analyze using scRNA-seq.

first: Nathânia

last: Dábilla

first: Sarah

last: Maya

first: Colton

last: McNinch

first: Taylor

last: Eddens

first: Patrick

last: Dolan

first: Megan

last: Freeman


title: Senataxin regulates cisplatin resistance through an R-loop mediated mechanism in HPV-associated Head and Neck Cancer

city: Sheffield

first: Hannah

last: Crane

address: Western Bank

institute: University of Sheffield

summary: Resistance to cisplatin is a key clinical concern in HPV-independent (HPV-) and HPV-associated (HPV+) head and neck cancer. Upregulation of DNA repair is known to contribute to cisplatin resistance and a major source of endogenous DNA damage are DNA/RNA hybrids, known as R-loops. Following creation of HPV+ and HPV- cisplatin resistant cell lines, RNA-Sequencing revealed alterations in the expression of known R-loop regulators. Resistant cells had elevated global R-loop levels and in HPV+ resistant cells there was a corresponding upregulation of the R-loop resolving protein, senataxin. Depletion of senataxin led to increased sensitivity to cisplatin, an increase in DNA damage and elevated R-loops at specific genomic loci. In summary, using an in vitro model of cisplatin resistance, we identified that senataxin modulates sensitivity to cisplatin through an R-loop mediated mechanism in HPV+ cells. R-loops may represent a potential therapeutic target and warrant further investigation.

overall_design: To investigate cisplatin resistance in HPV+ and HPV- cells, cisplatin resistance clones were developed and RNA-Sequencing was carried out on the parental clones and their resistant counterparts.

first: Ian

last: Carr

first: Keith

last: Hunter

first: Sherif

last: El-Khamisy


title: BRD9 Dictates Oncolytic Virus Resistance in Glioblastoma

city: Hangzhou

first: Zhilin

last: Long

address: No. 600 Dunyu Road Sandun Town

institute: Westlake University

summary: Glioblastoma multiforme (GBM) treatment is a persistent challenge for oncologists, and this challenge has motivated the exploration of novel therapeutic strategies such as oncolytic virus therapy. Despite recent advancements in oncolytic virus therapy clinical trials for glioblastoma, a substantial number of patients have shown limited responses to this treatment. Here, we performed CRISPR‒Cas9 knockout screening and identified non-canonical BRG1/BRM-associated factor (ncBAF) complex as a pivotal determinant of oncolytic virus resistance. Knockout of the ncBAF-specific subunit Bromodomain-containing protein 9 (BRD9) markedly augmented the antitumor efficacy of oncolytic herpes simplex virus type 1 (oHSV1), as evidenced by our in vitro and in vivo studies. Mechanistically, BRD9 bound to RELA, a key transcription factor in the nuclear factor-κB (NF-κB) signaling pathway, to potentiate the expression of downstream antiviral genes. The application of a small molecule inhibitor targeting BRD9 (IBRD9) significantly enhanced oHSV1 activity against GBM across various models, including cell lines, patient-derived organoids, ex vivo cultured primary tumor slices, and mouse models. Moreover, reduced BRD9 levels correlated with improved patient outcomes in oHSV1 clinical trials. These findings highlight BRD9 as a prospective target for augmenting the effectiveness of oncolytic virus therapy against glioblastoma, providing insights for the development of novel combination treatments.

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for BRD9 in human glioblastoma stem cell line MGG4.

first: Chen

last: Guo

first: Qi

last: Xie


title: Effect of conditional SMC specific deletion of ADAR1 on mouse aortic single cell transcriptomic profile and effect on atherosclerosis

summary: Mapping the genomic architecture of complex disease has been predicated on the understanding that genetic variants influence disease risk through modifying gene expression1. However, recent discoveries have revealed that a significant burden of disease heritability in common autoinflammatory disorders and coronary artery disease is mediated through genetic variation modifying post-transcriptional modification of RNA through adenosine-to-inosine (A-to-I) RNA editing2. This common RNA modification is catalyzed by ADAR enzymes, where ADAR1 edits specific immunogenic double stranded RNA (dsRNA) to prevent activation of the double strand RNA (dsRNA) sensor MDA5 (IFIH1)3,4. Multiple lines of human genetic data indicate impaired RNA editing and increased dsRNA sensing to be an important mechanism of coronary artery disease (CAD) risk2,5. Here, we provide a crucial link between observations in human genetics and the mechanistic cell biology leading to progression of CAD. Through analysis of human atherosclerotic plaque, we implicate the vascular smooth muscle cell (SMC) to have a unique requirement for RNA editing, and that MDA5 activation occurs in SMC phenotypic modulation — demonstrating a cell type and context specific role of RNA editing. We further show Adar1 controls SMC phenotypic state, is required to maintain vascular integrity, and controls progression of vascular calcification. Through this work, we describe a fundamental mechanism of CAD, where cell type and context specific RNA editing and sensing of dsRNA mediates disease progression, bridging our understanding of human genetics and disease causality.

overall_design: To investigate the role of SMC specific ADAR1 on vascular function and progression of atherosclerosis, we used the Adar1 flox mouse crossed onto an Myh11 CreERT2 background, that has additional hyperlipidemia with ApoE-/- and SMC lineage tracing with ROSA tdTomato alleles. First, we performed homozygous deletion of Adar1 by treating 8 week old male mice with tamoxifen (Adar1 fl/fl, Myh11CreERT2, ApoE-/-,  tdTomato+/+). These mice develop severe disease and single cell RNAseq was performed of the ascending aorta and aortic root at 2 weeks post tamoxifen. Control mice were wild type for the Adar1 fl/fl allele ( Myh11CreERT2, ApoE-/-,  tdTomato+/+) and were similarly treated with tamoxifen at 8 weeks of age. To then evaluate the effect of SMC Adar1 haploinsufficiency in atherosclerosis, we treated mice that were heterozygous for the Adar1 flox allele (Adar1 fl/WT, Myh11CreERT2, ApoE-/-,  tdTomato+/+) with tamoxifen at 8 weeks of age, and then put on a high fat diet for 16 weeks to induce atherosclerosis. We then performed single cell RNAseq of the ascending aorta/aortic root for these Adar1 het mice along with controls to evaluate how Adar1 haploinsufficiency modifies atherosclerosis


title: Effect of ADAR1 and MDA5 knock down by siRNA on human SMC phenotypic modulation and calcification in vitro

overall_design: To investigate the role of ADAR1 and IFIH1 (MDA5) in regulating SMC phenotype in vitro, first we performed an in vitro assay using primary human coronary artery smooth muscle cells (HCASMC) and performed a phenotypic modulation assay with siRNA KD of ADAR1 or ADAR1 and IFIH1 and performed bulk RNA sequencing in both mature SMC phenotype (serum starved) and modulated SMC phenotype (serum stimulated). Second, we performed an in vitro assay of SMC calcification by culturing immortalized HCASMC cells in control or pro-calcification media for 7 days following siRNA KD of ADAR1, ADAR1 and IFIH1, or IFIH1 alone and performed bulk RNA sequencing.


title: Intrauterine hyperglycemia impairs primordial germ cell development and fertility by sex-specific epigenetic reprogramming interference in mice offspring [RNA-seq]

status: Public on Jul 28 2025

city: Shanghai

first: Jiangshan

last: Cong

address: No.130,Dongan Road

institute: Fudan University

summary: Adverse intrauterine environments, such as hyperglycemia, impair the sexual reproduction and species continuous, yet the underlying mechanisms remain poorly understood. In this study, we demonstrated that intrauterine hyperglycemia significantly disrupted primordial germ cell (PGC) development, especially in female offspring and thus reduced fertility. Using Oct4-EGFP transgenic mice with intrauterine hyperglycemia exposure, we revealed that hyperglycemia compromised sexually specific chromatin accessibility and DNA methylation reprogramming during PGC development. Particularly, in female PGCs, hyperglycemia leads to the aberrant retention of chromatin accessibility at pluripotency gene promoters such as Nanog and Tfap2c, inhibiting proper gene silencing and blocking the initiation of meiosis, which ultimately hinders oocyte maturation. Conversely, male PGCs exhibit less severe changes in chromatin accessibility and gene transcription. Intriguingly, the global DNA methylation reconstruction is impaired in male PGCs, particularly in key imprinted gene regions, suggesting potential developmental ramifications for later stages and even subsequent generations. Particularly, our findings indicate that intrauterine hyperglycemia adversely affects sex differentiation in PGCs by disrupting the expression of critical sex-determining transcription factors. Collectively, these findings highlight how intrauterine hyperglycemia interferes with sex-specific epigenetic reprogramming during PGC development, leading to abnormal germ cell development, reduced fertility, and adverse intergenerational effects.

overall_design: RNA-seq profiling of control group and  IUHG (intrauterine hyperglycemia) group gonads (E13.5 female) and PGCs (E12.5, E13.5 female, E13.5 male, E16.5 female, and E16.5 male) at development stage.

first: Hefeng

last: Huang

first: Yu

last: Zhang

first: Yangyang

last: Li


title: Intrauterine hyperglycemia impairs primordial germ cell development and fertility by sex-specific epigenetic reprogramming interference in mice offspring [ATAC-seq]


title: Understanding molecular response of Arabidopsis to salt, heat and highlight stress combinations.

city: Columbia

first: Ron

last: Mittler

state: Missouri

address: University of Missouri,1201 Rollins St

department: Division of Plant Science and Technology

institute: University of Missouri - Columbia

summary: Plants in nature are exposed to combinations of abiotic and biotic stresses. Climate change driven increase in frequency of abiotic stress combinations is being detrimental to the plant survival and growth. Previously we found that Arabidopsis plants when exposed to combination of abiotic stresses termed as multifactorial stress combination (MFSC), the accumulation of multiple mild abiotic stresses becomes damaging to plants causing severe reduction in plant survival which otherwise not detrimental when exposed as single stresses. Here in this study, we investigated the role of a transcription factors Basic helix loop helix (bHLH35) in MFSC tolerance in Arabidopsis seedlings.

overall_design: In this study, Arabidopsis thaliana wild-type (Col0), and mutants of bHLH35 gene plants were subjected to salt stress (S; 50mM), high light stress (HL; 700 µE), heat stress (HS; 33 °C) and different combinations of these three stresses (S+HL, S+HS, HL+HS, S+HL+HS). Sterilized seeds of above-mentioned genotypes were germinated on ½ MS (murashige and Skoog media) with or without salt, at 21°C temperature and 150 µE light intensity. 7 days old seedling were subjected to HL and HS for 3 days (in combinations mentioned above) to determine the impact of stresses on survival. Seedlings for control were grown on ½ MS media without salt at 21°C temperature and 150 µE light intensity. To understand the transcriptomic response of Arabidopsis genotypes, 7 days old seedling growing on ½ MS with or without salt were exposed to HS and HL stress (in combinations mentioned above) for 1.5 hrs and seedlings from all the stress treatments and control were snap frozen in liquid nitrogen. Total RNA from the seedlings were isolated using Qiagen RNeasy® Plant Mini Kit. The RNAseq analysis was performed by Novogene Co. RNA libraries were prepared using standard Illumina protocols and RNA-Seq was performed using a NovaSeq 6000 PE150 platform by Novogene Co. Ltd. (https://en.novogene.com/; Sacramento, CA, USA). Read quality control was performed using Trim Galore v0.6.4 and FastQC v0.11.9.

first: Ranjita

last: Sinha

first: Abdul

last: Ghani

first: Sai Preethi

last: Induri

first: Trupti

last: Joshi

first: Felix

middle: B

last: Fritschi

first: Sara

middle: I

last: Zandalinas


title: Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets

first: Jasmine

last: Plummer

state: TN

address: 262 Danny Thomas Pl

summary: Spatial transcriptomics is a rapidly advancing field, yet it lacks standardized metrics for evaluating imaging-based in situ hybridization technologies. In this study, we emphasize the importance of rigorous experimental design and standardized operating procedures (SOPs) in defining performance metrics across multiple modalities—from single-cell to spatial transcriptomics to spatial proteomics. Our Spatial Touchstone (ST) dataset, generated from six tissue types across three global sites (n=76 assays), provides a comprehensive evaluation of reproducibility, sensitivity, dynamic ranges, signal-to-noise ratio, false discovery rates, cell type annotation, and congruence with single-cell profiling. Using single-nucleus RNA sequencing (snRNA-seq) on the same formalin-fixed paraffin-embedded tissues, we created a reference for transcriptional profiles to assess cellular organization and biomarker localization. In the absence of an independent 'gold standard’ in the field, this study provides an objective assessment of technical performance through standardized protocols, Spatial Touchstone Protocols (STSOP). Our open-source software, SpatialQC, allows users to evaluate samples across all technical metrics and directly impute cell annotations from single-cell datasets. This study features the largest imaging-based spatial transcriptomics data repository available, with a total of 203 spatial profiles. It incorporates both public (n=127) and ST datasets (n=76) through the Spatial Touchstone Portal (STP), available at www.spatialtouchstone.org. This resource offers users easy access to analyze and compare their own data against an extensive collection of imaging-based datasets. We show that the ST datasets demonstrate high reproducibility (r=0.93 to 1.0) and set a new benchmark for the field. Finally, we establish metrics to evaluate and integrate imaging based multi omics data from single cell into spatial transcriptomics to spatial proteomics. The ST project provides a comprehensive, reproducible assessment across platforms and sites, establishing essential standards for imaging-based spatial multi omics (transcriptomics and proteomics) and paving the way for future research and technological advancements.

overall_design: The study utilized two leading spatial technologies, Xenium and CosMx SMI, as representative examples of cutting-edge commercial platforms for evaluating technical performance. These platforms were evaluated across six tissue types in both normal (appendix/AP, colon/CO, pancreas/PA, ileum/IL) and cancerous (breast/BR and prostate/PR) conditions, focusing on accuracy, precision, reproducibility, sensitivity, and specificity. It used commercially available panels for both RNA (CosMx Human Universal Cell Characterization RNA Panel targeting 950 human genes and a 50-target add-on panel set; Xenium Human Multi-Tissue and Cancer Panel targeting 377 human genes; Xenium Human Breast Panel targeting 380 human genes) and protein (NanoString 64-plex human protein panel). All samples were analyzed on both imaging-based platforms (full scan of the entire section) generating 76 profiles, subjected to snRNA-seq (snPATHO-seq, n=6) and hematoxylin and eosin (H&E) staining (n=44) (n=126 total).

first: Felipe

last: Segato Dezem

first: David

last: Cook

first: Jiwoon

last: Park

first: Luke

first: Yutian

last: Liu

first: Maycon

last: Marcao

first: Hannah

last: DuBose

first: Arjumand

last: Wani

first: Kellie

last: Wise

first: Natalia

last: Morosini

first: Kirk

last: Jensen

first: Michael

last: Roach

first: Kate

last: Harvey

first: Taopeng

last: Wang

first: Roberto

last: De Gregorio

first: Alicia

last: Alonso

first: Shauna Lee

last: Houlihan

first: Robert

last: Schwartz

first: Erika

last: Hissong

first: Catherine

last: Snopkowski

first: Jeffrey

last: Wrana

first: Natalie

last: Ryan

first: Lisa

last: Butler

first: George

last: Church

first: Alex

last: Swarbrick

first: Christopher

last: Mason

first: Luciano

last: Martelotto


title: Harnessing proximal T cell signaling molecules for enhanced CAR T cell activity

status: Public on Jul 25 2025

city: New York

first: Caleb

last: Lareau

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: Chimeric antigen receptor (CAR) T cells mediate durable complete responses in patients with certain hematologic malignancies, but antigen downregulation is a common mechanism of resistance. While the native TCR can respond to very low levels of peptide presented in MHC, engineered CARs are incapable of responding to antigen-low targets, likely due to a disorganized immune synapse and poor recruitment of proximal signaling molecules. We developed a platform that endows CARs with the ability to kill antigen-low cancer cells, consisting of a membrane tethered version of the signaling molecule SLP-76 (MT-SLP-76). MT-SLP-76 can be expressed alongside any CAR to lower its threshold for activation and overcomes antigen low escape in multiple xenograft models. While SLP-76 is natively in the cytosol, only the engineered membrane tethered version can adequately amplify CAR signaling, a process that is mediated through recruitment of ITK and PLC1. MT-SLP-76 was designed based on biologic principles to render CAR T cell therapies less susceptible to antigen downregulation and is poised for clinical development to overcome this common mechanism of resistance.

overall_design: Human CAR T cells were co-cultured with and without MTSLP76 engineering. CAR T cells were either left or restimulated and compared against other CARs. Two donors were mixed per run. A CD22-targeted CAR was used for each Experiment

first: Maria

last: Rotiroti

first: Robbie

last: Majzner


title: Regulatory T cells epigenetically reprogrammed from autoreactive effector T cells mitigate established autoimmunity

city: Boston

first: Xudong

last: Li

address: 150 Harrison Avenue, Jaharis 523a, M&V 702 Building

department: Immunology

institute: Tufts University

summary: Reprogramming autoreactive CD4⁺ effector T (Teff) cells into immunosuppressive regulatory T (Treg) cells represents a promising strategy for treating established autoimmune diseases. However, the stability and function of such reprogrammed Tregs under inflammatory conditions remain unclear. Here, we show that demethylation of core Treg identity genes in Teff cells yields lineage-stable Effector T cell Reprogrammed Tregs (ER-Tregs). A single adoptive transfer of ER-Tregs not only prevents autoimmune neuroinflammation in mice when given before disease onset but also arrests its progression when administered after onset. Compared to Foxp3‑overexpressing Teff cells, induced Tregs from naïve precursors, and endogenous Tregs, ER‑Tregs provide superior protection against autoimmune neuroinflammation. This enhanced efficacy stems from their inherited autoantigen specificity and selectively preserved effector‑cell transcriptional programs, which together bolster their fitness in inflammatory environments and enhance their suppressive capacity. Our results establish epigenetic reprogramming of autoreactive Teff cells as an effective approach to generate potent, stable Tregs for the treatment of refractory autoimmune conditions.

overall_design: Ex vivo RNA-seq profiling of ER-Tregs and nTreg at day 7 after CFA/MOG immunization of recipient mice.

first: Tyler R

last: Colson

first: James J

last: Cameron

first: Hayley I

last: Muendlein

first: Mei-An

last: Nolan

first: Jamie L

last: Leiriao

first: James H

last: Kim

first: Alexander N

last: Poltorak


title: Single-cell analysis of testicular bacterial microbiome changes during aging and effect on reproductive capacity in mice

city: xuzhou

first: Jianteng

last: zhou

state: JiangSu

address: Tongshan road 209, Xuzhou Medical University, Xuzhou, China

department: College of Life Sciences

institute: Xuzhou Medical University

summary: The testis supports spermatogenesis through a tightly regulated microenvironment, and the bacterial microbiome (BM) may influence host cells through immune and metabolic pathways, thereby impacting reproductive capacity. Here, we applied invasion-adhesion-directed expression sequencing (INVADE-seq), a single-cell RNA sequencing approach that simultaneously captures host and bacterial transcripts, to examine how bacterial signals shape testicular cell states. We detected a sparse but widespread bacterial presence across multiple cell types, with somatic and early germ cells outside the blood-testis barrier (BTB) showing relatively higher bacterial abundance. Bacterial load increased with age, coinciding with transcriptional signatures of reduced BTB function. At the cellular level, bacterial-positive Leydig cells exhibited activation of steroidogenic genes, whereas macrophages upregulated pathways related to autophagy and immune modulation. These findings not only deepen our understanding of testicular microbiome biology but also hold promise for the discovery of novel diagnostic biomarkers and therapeutic targets for BM-related and age-associated male subfertility.

overall_design: C57BL/6 male mice at 5 months (young) and 20 months (older) were used, with 3 biological replicates per group.

last: Zhou

first: Ying

first: Tao

last: Zhu

first: Conghui

last: Han

first: Zuobin


title: Profibrotic monocyte-derived alveolar macrophages as a biomarker and therapeutic target in systemic sclerosis-associated interstitial lung disease

status: Public on Jul 23 2025

city: Chicago

first: Alexander

last: Misharin

address: 303 E Superior St

institute: Northwestern University

summary: Interstitial lung disease (ILD) is present in over 60% of patients with systemic sclerosis (SSc) and is the leading cause of SSc-related deaths. Profibrotic monocyte-derived alveolar macrophages (MoAM) play a causal role in the pathogenesis of pulmonary fibrosis in animal models where their persistence in the niche requires signaling through the Colony Stimulating Factor 1 Receptor (CSF1R). We hypothesized that the presence and proportion of MoAM in bronchoalveolar lavage (BAL) fluid from patients with SSc-ILD may be a biomarker of ILD severity. We performed spatial transcriptomics to localize profibrotic MoAM to the alveolar space and identified expansion of interstitial macrophages spilling into the alveolar space. Our findings suggest that the proportion of profibrotic MoAM and interstitial macrophages in BAL fluid may serve as a biomarker of SSc-ILD and credential them as possible targets for therapy.

overall_design: 6 donor and 5 SSc lung tissue sections were obtained. An approximately 10x10x10 mm piece of lung tissue was cut, fixed, and mounted to one of two Xenium slides for each section. Due to the instrument malfunction, the first run (samples with “:1” suffix) was aborted mid-run, and slides were left on the instrument for ~48 hours. The slides were recovered, stored at 4 °C for an additional 24 hours, and then the run was successfully repeated using a new set of reagents. To assess the impact of technical issues on the data quality, we have prepared additional sections from the same tissue blocks (samples with “:2” suffix) and analyzed them using the same gene panel and tissue segmentation kit (replacement reagents were kindly provided by 10x Genomics). The second run completed without technical issues.

first: Nikolay

last: Markov

first: Anthony

last: Esposito

first: Maxwell

last: Schleck

first: Radmila

last: Nafikova

first: Zhan

last: Yu

first: Ziyan

last: Lu

first: Monique

last: Hinchcliff


title: Allosteric and energetic remodeling of a PDZ domain by protein domain extensions

city: Barcelona

first: cristina

last: Hidalgo-Carcedo

address: Dr. Aiguader 88

country: Spain

institute: CRG

summary: Many functions of proteins are performed by independently folding structural units called domains. These domains are structurally conserved but not identical in different proteins. Here, to understand the consequences for regulation and evolvability of domain extensions, we quantify the energetic effects of two extensions in a model protein domain. Quantifying abundance and ligand binding for >190,000 protein variants allows us to measure the free energy changes for mutations throughout a PDZ domain and ~7000 energetic couplings between these mutations and two domain extensions. Both a structured extension and a more dynamic extension substantially but specifically re-shape the energy landscape. In particular, deleting an ɑ-helix alters the energetic consequences of >400 mutations in >50 sites on fold stability or binding energy, and the effects of >300 allosteric mutations, including at solvent-accessible surface sites. Extending or pruning the domain therefore reshapes its energetic and allosteric landscape, adding and removing opportunities for the allosteric control of protein function.

overall_design: DNA-seq of PCR amplicon; 3 biological replicates from Saccharmocyes cerevisiae

first: Cristina

first: Andre

last: Faure

first: Aina

last: Martí-Aranda

first: Taraneh

last: Zarin

first: Ben

last: Lehner


title: Histone deacetylase HDA-5 regulates lipid metabolism through H4K5 and H4K8 acetylation in Caenorhabditis elegans

status: Public on Jul 24 2025

city: kunming

first: meng

last: zhou

state: yunnan

address: tuanjiexiang

institute: Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China;

summary: To identify genes were involved in hda-5 regulation. The C. elegans N2 were subjected to hda-5 RNAi and empty vector RNAi until reach to adult. Then the worms were collected and washed by M9 buffer for three times following re-suspended in PBS, and frozen immediately in liquid nitrogen for RNA sequencing. RNA sequencing was carried out by Biomarker Technologies (BMK) GmbH (Beijing, China). Total RNA of worms were extracted by using RNeasy Plus Mini Kit (Qiagen) and assessed for quality by NanoDrop, Qubit 2.0 and Agilent 2100. mRNA was enriched via Oligo(dT) magnetic beads, fragmented, and reverse-transcribed to cDNA with random hexamers. After end repair, A-tailing, adapter ligation and PCR amplification, libraries were qualified by Qubit 2.0, Agilent 2100 and Q-PCR, then sequenced on Illumina NovaSeq 6000 (PE150).

overall_design: The C. elegans N2 were subjected to hda-5RNAi and empty vector RNAi until reach to adult. Total RNA from C. elegans was extracted with RNeasy Plus Mini Kit (Qiagen), assessed for quality by NanoDrop, Qubit 2.0 and Agilent 2100. mRNA was enriched via Oligo(dT) magnetic beads, fragmented, and reverse-transcribed to cDNA with random hexamers. After end repair, A-tailing, adapter ligation and PCR amplification, libraries were qualified by Qubit 2.0, Agilent 2100 and Q-PCR, then sequenced on Illumina NovaSeq 6000 (PE150). Raw reads were trimmed with trim_galore, mapped to hg38 using HISAT 2.2.1, and counted in genes by featureCounts. Normalized to CPM, differential expression was analyzed with DESeq2 (≥10 reads in at least one condition; adjusted P<0.01, |log2FC|≥1)

first: Qin-Yi

last: Wu

first: Yi-Cheng

last: Ma

first: Meng

first: Rui

first: Cheng-Gang

last: Zou


title: Axonal defasciculation is restricted to specific branching points during regeneration of the lateral line nerve in zebrafish

first: Rohan

middle: Saleem

last: Roy

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

summary: Peripheral nerve regeneration requires precise selection of the appropriate targets of innervation, often in an environment that differs from that during the developmental wiring of the neural circuit. Severed axons of the zebrafish posterior lateral line nerve have the capacity to reinnervate mechanosensory hair cells clustered in neuromast organs. Regeneration represents a balance between fasciculated regrowth of the axonal bundle and defasciculation of individual axons into the epidermis where neuromasts reside. The cues that guide pathfinding during regeneration of the posterior lateral line nerve are unknown. Here, we show that regenerating axons selectively defasciculate through distinct gaps in the epidermal boundary layer. We found that the gene col18a1a, which encodes the secreted heparan sulfate proteoglycan collagen XVIII, is expressed by the neuromast and by a subset of Schwann cells that are located at the points of axonal defasciculation. Furthermore, we observed aberrant axonal branching at inappropriate locations during nerve regeneration in col18a1a mutants. We propose a model in which collagen XVIII patterns the basement membrane to affect the precision of axonal navigation.

overall_design: RNA-seq profiling of isolated hair cells from the posterior lateral line of larval zebrafish either 1 day or 3 days post lateral line nerve lesion and corresponding age-matched, sham-lesioned controls.


title: Intrauterine hyperglycemia impairs primordial germ cell development and fertility by sex-specific epigenetic reprogramming interference in mice offspring [Bisulfite-Seq]

first: Jiangshan

last: Cong

type: Methylation profiling by high throughput sequencing

first: Hefeng

last: Huang

first: Yu

last: Zhang

first: Yangyang

last: Li


title: Effect of external cues on clock-driven protection from Influenza A infection

city: Philadelphia

first: James

last: Garifallou

state: Pennsylvania

address: 3615 Civic Center Boulevard, ARC1014

department: Neonatology

institute: Children's Hospital of Philadelphia

summary: Influenza and other respiratory viral pathogens are leading causes of mortality and morbidity. We previously demonstrated that circadian rhythms confer temporal protection from influenza infection. Here, we investigated whether this protection requires rhythmic function after the initial infection by manipulating environmental cycles. We demonstrate that disrupting environmental lighting cues within a critical window of vulnerability abrogates time-of-day specific protection. This poor outcome is mediated by a dysregulated immune response, evidenced by the accumulation of inflammatory monocytes and CD8+ cells in the lungs and a transcriptomic profile indicative of an exaggerated immune response. Disruption of the light cycle does not affect outcomes in a clock mutant, indicating that it acts by compromising endogenous timekeeping. Importantly, rhythmic meal timing mitigates the adverse effects of disrupted light cycles, suggesting that external cycling cues, which act through different body clocks, can substitute for each other. Our findings highlight the crucial interplay between environmental factors and endogenous clocks in shaping influenza outcomes, offering significant translational potential for improving the care of critically ill patients with respiratory viral infections.

overall_design: Single-nuclei RNA-seq was utilized to assess whole lung gene expression on day 8 post-infection (from IAV).

first: Oindrila

last: Paul

first: Thomas

last: Brooks

first: Lora

last: Assi

first: Alisha

last: Shetty

first: Martina

last: Towers

first: Kaitlyn

last: Forrest

first: Alecia

last: Cameron

first: Amita

last: Sehgal

first: Gregory

middle: R

last: Grant

first: Shaon

last: Sengupta


title: Effect of ablation of PRDM1 on gene expression in human regulatory T cells

city: Miami

first: Ying

last: Ding

address: 1600 NW 14th st

department: Microbiology and Immunology

institute: University of Miami

summary: To gain an insight into the contribution of BLIMP-1 in human Tregs, we ablated PRDM1 in ex-vivo expaned human Tregs by Crispr/Cas9. Tregs transfected with scramble gRNAs were used as controls. 7 days after transfection, Tregs were rested overnight in media, and were re-stimulated through the TCR and IL2R for 16 hr prior to isolation of RNA for genome-wide RNA-seq. Gene expression profiling analysis was performed using data obtained from RNA-seq of four replicates of PRDM1KO and control cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PRDM1KO and control cells.

first: Luis

last: Nivelo

first: Alejandro

last: Villarino

last: Malek


title: Targeting c-Jun orchestrates heat stroke induced myocardial injury and reveals its biomarker potential

status: Public on Jul 26 2025

city: chongqing

first: Fating

last: Zhou

state: chongqing

address: No. 1 Jiankang Road, Yuzhong District

department: Department of Emergency Medicine, Chongqing Emergency Medical Center

institute: Chongqing University Central Hospital

summary: These experiments aim to detect changes in the transcript (mRNA) of cardiac tissue when animals are exposed to high temperatures and heat stroke occurs due to the increase in environmental temperature. The research objectives include: 1) detecting changes in transcripts (mRNA) of heart tissue during heat stroke caused by elevated environmental temperatures; 2) Detecting transcripts that can serve as biomarkers for heat stroke induced myocardial injury.

overall_design: This study used 6–8 weeks C57BL/6N male mice (body weight: 20–25 g). All mice were acclimated for 1 week under standard housing conditions: 22–25°C with a 12-hour light/dark cycle, and free access to food and water.The sham group was maintained in a normal environment (22–25°C, 60–65% humidity) with fasting and water deprivation. The HS group was exposed to high temperature intervention in a climate controlled chamber, with the temperature set to 40±0.5°C and humidity maintained at 60–65%. During this period, the mice were fasted and water-deprived. Rectal temperature was measured every 30 minutes using a rectal thermometer until the core body temperature reached 42°C, at which point the mice were immediately transferred to a recovery environment (22–25°C, 60–65% humidity).After confirming the successful modeling, we collected mouse heart tissue for further experiments.


title: SOX2 Drives Esophageal Squamous Carcinoma by Reprogramming Lipid Metabolism and Histone Acetylation Landscape

status: Public on Jul 21 2025

first: ruofei

last: dai

address: dong'an road 130

summary: SOX2 is not only a pioneer transcription factor with critical roles in stem cell function and cell reprogramming but also a potent initiating oncodriver for a multitude of squamous cancers. How SOX2 exerts a potent oncogenic activity in squamous lineage is largely unknown. Here we uncovered a unique role of SOX2 in driving up global histone acetylation in various esophageal squamous cancer cells (ESCCs). Chromatin immunoprecipitation sequencing (ChIP-seq) analyses demonstrated that knockdown of SOX2 in ESCC cells resulted in a global down-regulation of histone acetylation and impaired about half of the super-enhancers. We engineered an ESCC SOX2-dTAG cell line that allowed rapid degradation of SOX2, and subsequent ChIP-seq confirmed a role of SOX2 in promoting global histone acetylation, beside its role in promoting local histone acetylation at SOX2 binding regions. Combined metabolic and transcriptional analyses revealed two mechanisms by which SOX2 drives up global histone acetylation in ESCCs: promoting the expression of a panel of histone acetyltransferases and reducing long chain fatty acid synthesis/elongation at least in part by repressing the expression of long-chain acyl-CoA synthase 5 (ACSL5), which in turn channels acetyl-CoA to histone acetylation. We demonstrated that ACSL5 knockdown downregulated fatty acid synthesis/elongation and enhanced histone acetylation, whereas overexpression of ACSL5 resulted in lipid accumulation, histone hypoacetylation, and tumor growth inhibition. Finally, we showed that SOX2 expression correlates negatively with ACSL5 and positively with histone acetylation in clinical esophageal squamous tumors. Altogether, our study uncovers a role of SOX2 in reprogramming lipid metabolism and driving histone hyperacetylation and super-enhancer function, providing new mechanistic insights of SOX2 acting as a potent oncodriver.

overall_design: ChIP-seq of the histone modification H4ac in KYSE-450 cell with dTAG induced SOX2 rapidly regradation in 3 or 24 hours. And use drosophila S2 cells as spike-in.

first: Zhen

last: Wang

first: Ruofei

last: Dai

first: Li

last: Kang

first: Huan

last: Yang

first: Zhaosu

last: Chen

first: Jianzhong

last: He

first: Lei

last: Shu

first: Yiting

last: Zhong

first: Yunfeng

last: Zhang

first: Zhengyi

last: Hua

first: Yuanyong

last: Huang

first: Yunhan

last: Jiang

first: Jiwen

last: Li

first: Liyan

last: Xu

first: Fei

last: Lan

first: Shu-Hai

last: Lin

first: Jiemin

last: Wong


title: Effect of ablation of CEACAM1 on gene expression in human regulatory T cells

first: Ying

last: Ding

summary: To study the contribution of CEACAM1 in human Tregs, CEACAM1 was knocked out in ex-vivo expanded human Tregs by Crispr/Cas9. Tregs transfected with scramble gRNAs were used as controls. After electroporation, scramble or CEACAM1KO Tregs were subcultured with IL-2 for 7 days and RNA was isolated for genome-wide RNA-seq. Gene expression profiling analysis was performed using data obtained from RNA-seq of two replicates of CEACAM1KO and control cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CEACAM1KO and scramble control human Tregs.

first: Molly

last: Dalzell

first: Alejandro

last: Villarino

first: Thomas

last: Malek


title: Effect of Lactobacillus crispatus on E. coli gene expression profiles in the gut of mice with inflammatory bowel disease.

status: Public on Jul 22 2025

city: Suwon-si, Gyeonggi-do

first: kim

last: jungtak

state: suwon

address: Yeongtong-gu, 206, World cup-ro, songjaegwan 711

country: South Korea

institute: Microbiology part/ajou University

summary: Gut microbiota modulation has emerged as a potential therapeutic and diagnostic approach for inflammatory bowel disease (IBD). We generated transcriptomic data by Record-seq, a method based on CRISPR-Cas system, that enables recording of gene expression in reporter bacteria within the mouse gut.

overall_design: IBD was induced in male C57BL/6 mice by DSS or DNBS administration. Additionally, feed containing Lactobacillus crispatus was provided to the mice to modulate the gut microbiota. For record sequencing, we utilized Escherichia coli BL21(de3) transformed with pFS_0453 plasmid containing a CRISPR array. Plasmid-derived spacer libraries were constructed according to original Record-seq protocol and sequenced on a Illumina NovaSeq X Plus platform.

first: Jungtak

last: Kim

first: Karolina

last: Prazanowska

first: Su Bin

last: Lim

first: Sun

last: Park


title: ZFTA fusion oncoproteins drive tumorigenesis through transcriptional condensates

city: Memphis

first: Stephen

last: Mack

state: Tennessee

address: 262 Danny Thomas Place

institute: St. Jude Children’s Research Hospital

summary: Over 95% of ependymomas (EPNs) that arise in the cortex are driven by a gene fusion involving the zinc finger translocation associated (ZFTA) protein. Using super-resolution and lattice light sheet microscopy, we demonstrate that the most frequent fusion variant, ZFTA-RELA (ZR), forms dynamic nuclear condensates that are required for oncogene expression and tumorigenesis. Mutagenesis of ZR reveals a key intrinsically disordered region (IDR) that governs condensate formation. Condensate-modulating ZR IDR mutations impaired genomic occupancy at oncogenic loci, and inhibited the recruitment of transcriptional effector proteins, such as MED1, BRD4 and RNA polymerase II. Using nuclear magnetic resonance spectroscopy, we examined the protein structure of the critical zinc finger found in ZR, and characterized its significance for condensate formation, genomic binding, and oncogene activation. Our data leverages microscopy, genomics, cell biology, animal modeling, structural biology, and machine learning approaches to provide mechanistic insights into the processes that govern oncogene expression in ZFTA FO-driven tumors.

overall_design: RNAseq exepriments to decipher molecular mechanisms driving ZFTA-RELA target gene expression.

first: Srinidhi

last: Varadharajan

first: Amir

last: Arabzade


title: Targeting the ERα DBD-LBD interface with mitoxantrone disrupts receptor function through proteasomal degradation

city: Cleveland

first: Han

last: Wang

state: Ohio

address: 2109 Adelbert Rd, Wood Building, RT400

institute: Case Western Reserve University

summary: The estrogen receptor (ER or ERα) remains the primary therapeutic target for luminal breast cancer, with current treatments centered on competitive antagonists, receptor down-regulators, and aromatase inhibitors. This therapeutic landscape frames our discovery of an alternative mechanism of ER inhibition that targets the critical interface between the DNA-binding domain (DBD) and ligand-binding domain (LBD) of the receptor. We identified mitoxantrone (MTO), an FDA-approved topoisomerase II inhibitor, as a specific ligand for this previously unexplored DBD-LBD interface. Through integration of computational, biophysical, biochemical, and cellular analyses, we demonstrate that independent of its DNA damage response activity, MTO binding induces ER conformational changes, leading to cytoplasmic redistribution and proteasomal degradation. Notably, MTO also effectively inhibits constitutively active ER mutants (Y537S and D538G) commonly associated with endocrine therapy resistance, suppressing ER/ER-mutant-dependent gene expression and tumor growth more potently than fulvestrant. These findings establish the DBD-LBD interface as a crucial regulatory point for ER function, suggesting a new paradigm for targeting domain interfaces across the nuclear receptor family.

overall_design: Three MCF-7 cell lines (wildtype, Y537S ER knock-in, and D538G ER knock-in) were treated with four different conditions: vehicle control, fulvestrant (1 μM), MTO (1 μM), or combination treatment (fulvestrant + MTO) for 48 hours. Gene expression profiling was performed using RNA sequencing on the Illumina NextSeq 550 platform with 75 bp single-end reads. Two biological replicates were included for each treatment condition across all three cell lines, resulting in a total of 24 samples (3 cell lines × 4 treatments × 2 replicates).

first: Hung-Ying

last: Kao

first: Sichun

last: Yang


title: Single-cell analysis defines heterogenous differentiation pathways of human innate T cells

city: Seoul

first: Suyeong

address: 1, Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea

department: College of Pharmacy

institute: Seoul National University

summary: MAIT, NKT and γδ T cells are innnate-like T cells developed from thymic tissue. We used single cell RNA sequencing (scRNA-seq) to profile transcriptomic landscape of innate-like T cells in human thymus.

overall_design: Innate T cells from human thymic tissue were isolated by combination of Magentic-activated cell sorting (MACS) and Fluorescence-activated cell sorting (FACS) according to the presence or absence of tetramer binding affinity and analyzed using scRNAseq.


title: Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [PS_CUTnRUN]

first: Ly-sha

last: Ee

address: 413 E 69th Street

institute: Weill Cornell Medicine

summary: We discovered a role for the transcription factor OTX2 in formation of mouse definitive endoderm (DE). We used CUT&RUN to map OTX2-bound genomic regions and identify OTX2-regulated genes during directed differentiation of EpiSCs to DE

overall_design: EpiSCs were converted to DE and live cells isolated by flow cytometry. OTX2 binding sites were mapped in mouse EpiSCs, Primitive Streak (PS), and definitive endoderm using CUT&RUN for HA in OTX2-HA tagged cell lines.

first: Matthias

last: Stadtfeld

first: Daniel

last: Medina-Cano

first: Alexander

last: Polyzos


title: SOX2 Drives Esophageal Squamous Carcinoma by Reprogramming Lipid Metabolism and Histone Acetylation Landscape (RNA-seq)

first: Yiting

last: Zhong

address: 130 Dong'an Road

institute: Fudan University

summary: SOX2 is not only a pioneer transcription factor with critical roles in stem cell function and cell reprogramming but also a potent initiating oncodriver for a multitude of squamous cancers. How SOX2 exerts a potent oncogenic activity in squamous lineage is largely unknown. Here we uncovered a unique role of SOX2 in driving global histone acetylation and demonstrated that SOX2 is required for the formation of about half of the super-enhancers in esophageal squamous cancer cells (ESCCs). Combined metabolic, chromatin and transcriptional analysis revealed at least two mechanisms by which SOX2 drives histone acetylation in ESCCs: promoting the expression of a panel of histone acetyltransferases and program fatty acid metabolism, which channels acetyl-CoA to histone acetylation by promoting the expression of multiple genes in fatty acid -oxidation and by repressing the expression of long-chain acyl-CoA synthase 5 (ACSL5) involved in fatty acid synthesis. We demonstrated that ACSL5 knockdown  downregulated fatty acid synthesis and enhanced histone acetylation, whereas overexpression of ACSL5 resulted in lipid accumulation, histone hypoacetylation, and tumor growth inhibition. Finally, we showed that SOX2 expression correlates negatively with ACSL5 and positively with histone acetylation in clinical esophageal squamous tumors. Altogether, our study uncovers a role of SOX2 in reprogramming lipid metabolism and driving histone hyperacetylation and super-enhancer function, providing new mechanistic insights of SOX2 acting as a potent oncodriver.

overall_design: RNA-Seq profiles of control and SOX2 knockdown KYSE450 cells were generated by deep sequencing, in triplicate, using Illumina Novaseq 6000

first: Zhen

first: Ruofei

last: Dai

first: Li

last: Kang

first: Huan

first: Yunpeng

last: Zhang

first: Jiwen

last: Li

first: Liyan

last: Xu

first: Fei

last: Lan

first: Shu-Hai

last: Lin

first: Jiemin

last: Wong


title: SOX2 Drives Esophageal Squamous Carcinoma by Reprogramming Lipid Metabolism and Histone Acetylation Landscape (ChIP-seq)

overall_design: ChIP-seq for SOX2, H4ac, H3K27ac and H3K4me3  in control and SOX2 knockdown KYSE450 cells.


title: Gene expression profiles of E. coli in the gut of inflammatory bowel disease models.

first: kim

last: jungtak

first: Jungtak

last: Kim

first: Karolina

last: Prazanowska

first: Su Bin

last: Lim

first: Sun

last: Park


title: The Neurolipid Atlas: a lipidomics resource for neurodegenerative diseases

status: Public on Jul 18 2025

city: Irvine

first: Ricardo

last: Miramontes

address: 845 Health Sciences Rd

institute: UC Irvine

summary: Lipid alterations in the brain have been implicated in many neurodegenerative diseases. To facilitate comparative lipidomic research across brain diseases here we establish a data common named the Neurolipid Atlas, that we have pre-populated with isogenic induced pluripotent stem cell (iPSC)-derived lipidomics data for different brain diseases. Additionally, the resource contains lipidomics data of human and mouse brain tissue. Leveraging multiple datasets, we demonstrate that iPSC-derived neurons, microglia, and astrocytes exhibit distinct lipid profiles that recapitulate in vivo lipotypes. Notably, the AD risk gene ApoE4 drives cholesterol ester (CE) accumulation specifically in human astrocytes, and we also observe CE accumulation in whole human AD brain lipidomics. Multi-omics interrogation of iPSC-derived astrocytes revealed that altered cholesterol metabolism plays a major role in astrocyte interferon-dependent pathways such as the immunoproteasome and major histocompatibility complex class I antigen presentation. Our data commons, available at neurolipidatlas.com, and allows for data deposition by the community and provides a user-friendly tool and knowledge base for a better understanding of lipid dyshomeostasis in neurodegenerative diseases.

overall_design: We performed bulk RNA sequencing on an isogenic pair of iPSC-derived ApoE3/3 and ApoE4/4 astrocytes.

first: Femke

last: Feringa

first: Sascha

last: J. Koppes-den Hertog

first: Lian

last: Wang

first: Rico

last: Derks

first: Iris

last: Kruijff

first: Lena

last: Erlebach

first: Jorin

last: Heijneman

first: Nadine

last: Pömpner

first: Niek

last: Blomberg

first: Damien

last: Olivier-Jimenez

first: Lill Eva

last: Johansen

first: Alexander

last: Cammack

first: Ashling

last: Giblin

first: Christina

last: Toomey

first: Indigo

last: Rose

first: Hebao

last: Yuan

first: Michael

last: Ward

first: Adrian

last: Isaacs

first: Martin

last: Kampmann

first: Deborah

last: Kronenberg-Versteeg

first: Tammaryn

last: Lashley

first: Leslie

last: Thompson

first: Alessandro

last: Ori

first: Yassene

last: Mohammed

last: Giera

first: Rik

last: van der Kant


title: Synergistic Effects of Red Light and Direct Current Electric Fields on Neurite Growth in 3D Neural Cell Cultures

status: Public on Jul 19 2025

city: Taipei

first: Yu Chiu

last: Kao

address: Academia Road

country: Taiwan

institute: Academia Sinica

summary: Both red-light illumination and direct-current electric fields (dcEFs) have independently been shown to promote neurite outgrowth in two-dimensional (2D) neural cell cultures. However, their combined effects in a three-dimensional (3D) culture environment remain unexplored. In this study, we examined the synergistic effects of red light and dcEFs on neurite extension in human neuroblastoma (SH-SY5Y) and mouse neuroblastoma (N2a) cells embedded within a 3D collagen gel matrix. Our results demonstrated that optimized dcEF stimulation and red-light exposure significantly enhanced neurite elongation and directional alignment. RNA sequencing further identified Neuropeptide Y (NPY) and its receptors as key mediators of these effects. Moreover, electrophysiological assessments revealed that neurons subjected to the combined stimulation exhibited enhanced functional maturation. These findings provide compelling evidence supporting the potential applications of red light and dcEFs in neural regeneration and repair.

overall_design: This study investigates the combined effects of direct current electric field (175 mV/mm, 3 hours) and red light (620 nm, 2 mW/cm², 45 hours) stimulation on neurite growth in 3D SH-SY5Y neural cell cultures. Cells were embedded in 3D collagen scaffolds at a concentration of 1 mg/mL, with a seeding density of 1×10⁶ cells/mL. Four experimental groups were included: (1) Control (no treatment), (2) dcEF only, (3) Red light only, and (4) Combined dcEF and red light. Total RNA was extracted after treatment. Two independent batches of RNA-seq libraries were generated using the same experimental design and were jointly analyzed to assess reproducibility and treatment effects. Each group included biological triplicates. Sequencing was performed using the Illumina NovaSeq X Plus platform with paired-end reads.

first: Yu-Chiu

first: Her-Bang

last: Huang

first: Chau-Hwang

last: Lee


city: Shanghai

first: Yiting

last: Zhong

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

overall_design: Refer to individual Series