title: Effect of fructose on human colon DNA methylation: implication for racial disparities in colorectal cancer risk

status: Public on Mar 15 2025

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

summary: Background: An increasing body of evidence has linked fructose intake to colorectal cancer (CRC). African Americans (AAs) consume greater quantities of fructose and are more likely to develop right-side colon cancer than European Americans. Objective: We examined the hypothesis that fructose consumption leads to genomic differences associated with CRC tumor biology.  Methods: DNA methylation data from this study was obtained using the Illumina Infinium MethylationEPIC kit (GSE151732). Right and left colon differentially methylated regions (DMRs) were identified using DMRcate through analysis of fructose consumption in normal AA colon biopsies (n=79) undergoing screening colonoscopy. Secondary analysis of CRC tumors was carried out using data derived from TCGA-COAD, GSE101764 and GSE193535. Right colon organoids derived from AA normal colon tissues were exposed to 4.4mM of fructose for 72 hours. Fructose-associated differentially expressed genes (DEGs) were identified using DESeq2. This package was also used to identify DEGs in CRC tumors from TCGA-COAD.  Results: We identified 4,263 right colon fructose-associated DMRs (FDR<0.05). In contrast, only 24 DMRs survived multiple testing corrections (FDR<0.05) in matched, left colon. Almost 50% of right colon fructose-associated DMRs overlapped regions implicated in CRC in at least one of three datasets. A highly significant enrichment was also observed between genes corresponding to right colon fructose-associated DMRs and DEGs associated with fructose exposure in AA right colon organoids (P=3.28E-30). Further, overlapping and significant enrichments for a number of fatty acid metabolism, glycolysis and cell proliferation pathways were also found. By further examining the overlap of genes within these pathways that were also differentially expressed in TCGA-COAD, our analysis reveals potential role for PFKP and ANKRD23 in fructose-mediated CRC risk.  Conclusions: Our data support that dietary fructose exerts a greater CRC risk-related effect in right than left colon among AAs, alluding to its potential role in contributing to racial disparities in CRC.

overall_design: To investigate the effects of fructose on normal colon epithelial cells we exposed 5 colon organoid lines to 4.4mM fructose for 72 hours.

first: Graham

last: Casey

first: Li


title: Dipeptidase-1 knockout mice develop invasive tumors with features of microsatellite unstable colorectal cancer

city: Nashville

first: guoqiang

last: Gu

state: Tennessee

address: 9415D Medical Research Building IV

department: Department of Cell and Developmental Biology

country: USA

institute: Vanderbilt University Medical Center

type: Expression profiling by high throughput sequencing

summary: The goal of this study was to employ a single cell RNA sequencing approach to determine cell population differences between wildtype and DPEP1 KO mice that were induced to form distal colonic tumors by an AOM/DSS regimen.  This study represents the first scRNA-seq assessment of tumors formed in DPEP1 KO mice

overall_design: Following an AOM/DSS regimen of treatment for mice and waiting for 105 days, resulting tumors were removed and analyzed by scRNA-seq

first: Sarah

middle: E

last: Glass

first: Chelsie

middle: K

last: Sievers

first: Robert

middle: J

last: Coffey

first: Alan

last: Simmons

first: Yanwen

last: Xu

first: Yu

last: Wang

first: Qi

last: Liu


title: Fragile X Syndrome Patient-Derived Neurons Developing in the Mouse Brain Show FMR1-Dependent Phenotypes

status: Public on Mar 16 2025

city: Leeds

first: Marine

last: Krzisch

state: West Yorkshire

address: Woodhouse Lane

department: School of Biomedical Sciences

country: United Kingdom

institute: University of Leeds

summary: Fragile X syndrome (FXS) is the most commonly inherited form of developmental and intellectual disability. Here, we used a new approach, i.e. neurons derived from FXS patients and transplanted in the mouse brain, to study this disease. It provided new insights into the development of FXS neurons, by facilitating their development in a 3D context: we found that FXS neurons had an altered maturation process, and our data suggest that their synapses might be hyperactive.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for FXS cells and their isogenic controls..

first: Bingbing

last: Yuan


title: EZH1/EZH2 Inhibition Enhances Adoptive T-cell Immunotherapy Against Multiple Cancer Models

city: Philadelphia

first: Patrizia

last: Porazzi

state: PA

address: 3400 Civic Center Blvd

department: Center for Cellular Immunotherapies

institute: University of Pennsylvania

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Tumor resistance to chimeric antigen receptor T-cell (CART) therapy is a major challenge. Epigenetic modulation, which rewires cancer cells to a more immunogenic phenotype, could improve adoptive T cell (ACT) efficacy. This study hypothesized that inhibiting EZH2 would enhance ACT. In Germinal Center-derived B-cell human lymphoma models, EZH2 inhibition with tazemetostat improved anti-CD19 CART (CART19) tumor control. The goal of this experiment is to test is tazemetostat-treated tumors showed chromatin opening at genes related to cell-cell adhesion, B-cell activation, and inflammatory responses.

overall_design: To understand the role of EZH2 in shaping the chromatin accessibility of tumor cells in response to CART19 treatment, a diffuse large B-cell Lymphoma derived cell line (SUDHL4-GFP+) was pre-treated with the EZH2 inhibitor tazemetostat or a vehicle control. The cell lines were subsequently exposed to either untransduced (UTD) T cells or CART19. The tumor cells were then sorted from the T cells and processed for assay for transposase-accessible chromatin (ATAC-seq).

first: Siena

last: Nason

first: Melody

middle: C

last: Tan

first: Linhui

last: Chen

first: Puneeth

last: Guruprasad

first: Anushka

middle: A

last: Padmanabhan

first: Marco

last: Ruella


title: Effects of chronic heat exposure on gene expression in abdominal fat of growing broiler chickens.

city: Minamiminowa, Kamiina

first: Yukako

last: Tokutake

state: Nagano

country: Japan

institute: Shinshu University

summary: Exposure to chronic heat stress not only reduces body weight gain in growing broilers, but also enhances fat deposition in the abdomen, subcutaneous, and intramuscular. To elucidate this phenomenon, numerous studies have examined changes in the transcripts, protein, and metabolic levels in the liver, the primary site of de novo fat synthesis in birds. On the other hand, changes in adipose tissue, the direct site of fat deposition, have not been unclear. To elucidate the changes in adipose tissue of chickens heat-exposure, we demonstrated the experiments rearing chickens in a heat environment (32°C) for 14 days, and then compared with the control group that reared in thermoneutral condition (22°C), and a pair-fed groups that reared in thermoneutral condition but feed intake was limited to the same levels as that in the heat-exposed group. Despite the feed intake was equal to that of the pair-fed group, the ratio of abdominal fat to body weight in the heat-exposed group was maintained at the same level as that in the control group. In addition, the heat-exposed group showed a significant decrease in the concentration of free fatty acids in plasma compared with the other 2 groups. Transcriptome analysis of abdominal fat between the heat-exposed and control groups revealed 459 differentially expressed genes were indicated. Notably, in heat-exposed group, the expression of genes related to lipid synthesis increased in adipose tissue compared with control group. Taken together, these results indicate that chronic heat has a lipid-deposition-promoting effect on growing broiler chicken adipose tissue

overall_design:
Male broiler chicks were allocated to two treatments with 12 chickens at 21 days of age. Control and heat-stressed group chickens were exposed to thermoneutral condition (22.0 °C ± 0.5, humidity 50% ± 0.5) or heat stress condition (32.0 °C ± 0.5, humidity 50% ± 0.5) until 35 days of age.

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Submitter states that missing raw files are due to file loss.
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first: Kan

last: Sato


title: Chromatin Landscape of Macrophages Following Helminth Enzyme Exposure Targeting Prostaglandin Synthesis

city: Epalinges

first: Julia

last: Esser-von Bieren

state: non

address: Chemin des Boveresses 155

country: Switzerland

institute: UNIL

summary: The molecular mechanisms by which worm parasites evade host immunity are incompletely understood. In a mouse model of chronic intestinal helminth infection, we identify helminthic glutamate dehydrogenase (heGDH) as an essential factor for parasite chronicity by using antibody mediated neutralization or treatment with exogenous recombinant heGDH. Macrophages efficiently internalize heGDH and represent a major target of the enzyme in vivo. Combining RNA-seq, ChIP-seq, targeted lipidomics and inhibitor studies, we identify prostaglandin E2 (PGE2) as a major immune regulatory mechanism of heGDH. The induction of PGE2 and further immune regulatory factors (IL-12 family cytokines, IDO1) by heGDH depended on the p300-mediated acetylation of histones. While the enzyme’s catalytic activity was dispensable for key immune regulatory functions, an N-terminal handle-like structure distinct from mammalian GDHs may confer interaction of heGDH with its targets (CD64, GPNMB), identified via proteomics. Thus, helminths employ a ubiquitous metabolic enzyme to epigenetically target macrophages and establish chronicity.

overall_design: Chromatin immunoprecipitation DNA-Seq sequencing (ChIP-seq) for histone modification H3K4

first: Sina

last: Bohnacker

first: Christiane

last: Boeckel

first: Minhaz

last: Ud-Dean


title: Gene expression profile of Macrophages Following Helminth Enzyme Exposure Targeting Prostaglandin Synthesis

overall_design: RNA-Seq of human monocyte derived macrophages treated with helminthic glutamate dehydrogenase (heGDH) or LPS

first: Arie

last: Geerlof


title: Two eIF4E paralogs occupy separate germ granule mRNPs that mediate mRNA repression and translational activation

status: Public on Mar 14 2025

city: Greenville

first: Brett

middle: D

last: Keiper

state: NC

address: 600 Moye Blvd

department: Biochem and Mol Biol

institute: Brody School of Med at ECU

summary: We studied translation factor eIF4E paralogs that regulate germline mRNAs. Translational control of mRNAs is essential for germ cell differentiation and embryogenesis. Messenger ribonucleoprotein (mRNP) complexes assemble on mRNAs in the nucleus, as they exit via perinuclear germ granules, and in the cytoplasm. Bound mRNP proteins including eIF4Es exert both positive and negative post-transcriptional regulation. In C. elegans, germ granules are surprisingly dynamic mRNP condensates that remodel during development. Two eIF4E paralogs (IFE-1 and IFE-3), their cognate eIF4E-Interacting Proteins (4EIPs), and polyadenylated mRNAs are present in germ granules. Affinity purification of IFE-1 and IFE-3 mRNPs allowed mass spectrometry and mRNA-Seq to identify other proteins and the mRNAs that populate stable eIF4E complexes. We find translationally repressed mRNAs (e.g. pos-1, mex-3, spn-4, etc.) enriched with IFE-3, but excluded from IFE-1. Identified mRNAs overlap substantially with mRNAs previously described to be IFE-1-dependent for translation. The findings suggest that oocytes and embryos utilize the two eIF4Es for opposite purposes on critically regulated germline mRNAs. Biochemical composition of isolated mRNPs indicates opposing yet cooperative roles for the two eIF4Es. We propose that the IFEs accompany controlled mRNAs in the repressed or activated state during transit to the cytoplasm. Copurification of IFE-1 with IFE-3 suggests they may interact to move repressed mRNAs to ribosomes.

overall_design: RNA-Seq analysis of mRNA population precipitated with each of two eIF4E paralogs from C elegans. The eIF4Es (IFE-1 and IFE-3) were individually tagged by CRISPR and co-expressed in the same worm strain. Each was purified from extracts by Trap (IP) using unique N-terminal tags. RNA-IP enrichment was compared to total mRNA-Seq from the same strain. RIP-Seq from strains expressing tags alone were also included but not used in the analysis because of poor mRNA representation.

first: Hayden

middle: P

last: Huggins

first: Dustin

last: Updike

first: Weihua

last: Huang


title: Glycolytic activity instructs germ layer proportions through regulation of Nodal and Wnt signaling

city: BARCELONA

first: Patryk

last: Polinski

state: BARCELONA

address: C/ del Dr. Aiguader, 88

country: Spain

institute: EMBL Barcelona

summary: Metabolic pathways can influence cell fate decisions, but their regulative role during embryonic development remains poorly understood. Here, we demonstrate a crucial role of glycolytic activity in regulating signalling pathways involved in mesoderm and endoderm specification. Using an mESC-based in vitro model for gastrulation, we found that glycolysis inhibition increases ectodermal cell fates at the expense of mesodermal and endodermal lineages. We used single cell RNA sequencing (scRNA-seq) to analyze the  mechanistic insight into the nutritional regulation of cell fate decision making.

overall_design: Control gastruloids at 96hpa or treated with indicated chemicals were desegregated and analyzed using scRNAseq.

first: Kristina

last: S. Stapornwongkul

first: Elisa

last: Hahn

last: Poliński

first: Laura

last: Salamó Palau

first: Krisztina

last: Arató

first: LiAng

last: Yao

first: Kate

last: Williamson

first: Nicola

last: Gritti

first: Kerim

last: Anlas

first: Mireia

last: Osuna Lopez

first: Kiran

last: Patil

first: Idse

last: Heemskerk

first: Miki

last: Ebisuya

first: Vikas

last: Trivedi


title: Clear-Cell Renal Cell Carcinoma Molecular Subtypes Differ by African and European Genetic Similarity

city: Baltimore

first: Roy

last: Elias

state: Maryland

address: 201 N Broadway

institute: Johns Hopkins University

summary: Self-reported Black (B) individuals remain underrepresented in molecular studies of clear cell renal cell carcinoma (ccRCC) relative to White (W) individuals. We performed whole-exome and transcriptome sequencing on paired tumor and normal samples from 59 matched B and W patients undergoing nephrectomy for localized ccRCC, comparing molecular differences by estimated genetic similarity to African (AFR) and European (EUR) 1000 Genomes groups. We validated our findings with a propensity-matched subset of TCGA, yielding a final cohort of 254 patients (79 AFR, 175 EUR) with similar baseline clinical variables. Significant differences emerged in VHL mutation frequency (AFR: 23.4%, EUR: 57.5%; FDR = 0.0029) and chromosome 3p deletions (AFR: 59.2%, EUR: 82.6%; FDR = 0.086). Transcriptomic analyses identified 34 genes associated with genetic similarity, and gene set enrichment revealed inflammatory (interferon gamma/alpha, allograft rejection), proliferative (E2F targets, G2M checkpoint), and metabolic (bile acid, fatty acid, glycolysis, MTORC1, peroxisome) pathway enrichment in EUR. We also observed differences in ccRCC molecular subtype distribution, with “Proliferative” and “Angio/Stromal” subtypes more common in AFR (p = 0.018). Importantly, differential subtype membership explained most group-level differences. These results link EUR and AFR genetic similarity to distinct ccRCC molecular subtypes, underscoring the importance of molecular classifiers in disease stratification and the need to include diverse populations in molecular studies to improve our understanding and treatment of ccRCC.

overall_design:
RNAseq of patient nephrectomy samples. Both tumor (clear cell renal cell carcinoma) and benign kidney were submitted

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

last: Nirschl

first: Michael

last: Rezaee

first: Anirudg

last: Yerrapragada

first: Shirley

last: Wang

first: Joseph

last: Cheaib

first: Ridwan

last: Alam

first: Sunil

last: Patel

first: Yuezhou

last: Jing

first: Mohamad

last: Allaf

first: David

last: McKean

first: Alison

last: Klein

first: Elana

last: Fertig

first: Ezra

last: Baraban

first: Yasser

last: Ged

first: Srinibasa

last: Yegnasubramanian

first: Nirmish

last: Singla


title: Characterization of a gene expression biomarker predictive of hypoxia-inducible factor-1 modulation

city: Durham

first: Chris

last: Corton

email: corton.chris@epa.gov, cortonchris@gmail.com, jie@liuonline.com, prpfeiffer@gmail.com, treasure.bailley@gmail.com

address: 109 TW Alexander Dr

institute: EPA

summary: We describe here a gene expression biomarker that can accurately identify chemicals and genetic conditions that perturb hypoxia-inducible factor-1 (HIF-1), a transcription factor critical for the cellular response to hypoxia involved in the pathophysiology of cancer, inflammation, and ischemia. The HIF-1 biomarker genes were identified from transcript profiles in a variety of human cell lines after hypoxia as well as genetic knockdown of the HIF1A gene. The HIF-1 biomarker of 122 genes was found to be enriched for: genes bound by HIF-1 using ChIP-Seq, metabolic pathways regulated by HIF-1 (e.g., gluconeogenesis). Using Ingenuity Pathway Analysis, HIF-1 was the top predicted regulator of the genes. The biomarker could identify activation of HIF-1 by overexpression of the HIF1A gene or suppression of the negative regulator, von-Hipple Lindau (VHL) gene; suppression of HIF-1 occurred by inhibition of the expression of HIF1A or the heterodimer partner aryl hydrocarbon receptor nuclear translocator (ARNT). The biomarker was specific for HIF-1 activation, as activation or suppression of the HIF-2 gene was not detected by the biomarker. Using a reference chemical set with 180 positives and 45 negatives, the balanced accuracy of the HIF-1 biomarker to identify activation was 94.1%. An in-silico screen of a gene expression compendium identified hundreds of potential activators. Eleven of these were selected for verification and all were found to activate HIF-1 biomarker genes in wild-type but not HIF1A-null cells. The HIF-1 biomarker will be a useful tool to identify environmentally relevant chemicals that affect HIF-1 in high-throughput transcriptomics screening studies.

overall_design: Wild-type and HIF1A-null cells were purchased from Synthego, Inc. The HIF1A-null cells were a knockout pool that contained at least 90% HIF1A-null cells. Gene expression changes were evaluated in wild-type and HIF1A-null cells after 6hr exposure to ciclopirox, CoCl2, and wortmannin using the whole genome RNA-Seq platform (BioSpyder, Inc, Carlsbad, CA). Total RNA samples were processed by BioSpyder, Inc. (Carlsbad, CA) for analysis using the human full genome TempO-Seq platform. There are 24 samples in this submission.

first: J

first: Jie

last: Liu


title: Multiomic profiling of glioblastoma metabolic lesions reveals complex intratumoral genomic evolution and dipeptidase-1-driven vascular proliferation

city: Copenhagen N

first: Bjarne

middle: Winther

last: Kristensen

state: Denmark

address: Ole Maaløes Vej 5, building 2, 3 floor

department: Bartholin Institute

country: Denmark

institute: Rigshospitalet, University of Copenhagen

summary: Glioblastoma undergoes a complex and dynamic evolution involving genetic and epigenetic changes. Understanding the mechanisms behind this evolution is vital for effective therapies. While treatment resistance is associated with glioblastoma's intratumoral heterogeneity, it remains uncertain if hypometabolic and hypermetabolic lesions observed through PET imaging are influenced by spatial intratumoral genomic evolution. In this study, we precisely isolated autologous hypometabolic and hypermetabolic lesions from glioblastoma using advanced neurosurgical and brain imaging technologies, followed by comprehensive whole-genome/exome and transcriptome analysis. Our findings reveal that hypermetabolic lesions evolve from hypometabolic lesions, harbor shrewd focal amplifications and deletions, and exhibit a higher frequency of critical genomic alterations linked to increased aggressiveness. We also found gene signatures in hypermetabolic lesions, including upregulated APOBEC3, hypoxic genes, and downregulated putative tumor suppressors. This study highlights a spatial genomic evolution with diagnostic implications and unveils obstacles and possibilities that should be considered in the development of novel therapeutic strategies.

overall_design: We embark on making a comprehensive analysis of genomic alterations in glioblastoma of kryo, zesto, and akri samples by performing exome and genome sequencing of tissue and blood samples to identify critical copy number variations, single nucleotide variants, gene fusions, somatic variants as well as RNA sequencing for functional analysis. By conducting these multi-omics analyses on multisectoral paired biopsies from the same patients with glioblastoma, allowing us to investigate intratumoral alterations, we identified a set of molecular alterations that may influence the regulation of glioblastoma biology and contribute to its heterogeneity and therapeutic resistance. This is the first study to perform a thorough genomic analysis on predetermined multi-regional metabolic tumor lesions from patients with glioblastoma, with an ideal experimental control setup.

first: Atul

last: Anand

first: Jeanette

last: Krogh Petersen

first: Lars

last: van Brakel Andersen

first: Mark

last: Burton

first: Martin

last: Jakob Larsen

first: Christian

last: Bonde Pedersen

first: Frantz

last: Rom Poulsen

first: Peter

last: Grupe

first: Torben

last: Kruse

first: Mads

last: Thomassen

last: Winther Kristensen

first: Clara

last: Oudenaarden


title: The mitochondrial-targeted peptide therapeutic elamipretide improves cardiac and skeletal muscle function during aging without detectable changes in tissue epigenetic or transcriptomic age [RNA-seq]

city: Boston

first: Wayne

last: Mitchell

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

summary: Aging-related decreases in cardiac and skeletal muscle function are strongly associated with various comorbidities. Elamipretide (ELAM), a novel mitochondrial-targeted peptide, has demonstrated broad therapeutic efficacy in ameliorating disease conditions associated with mitochondrial dysfunction across both clinical and pre-clinical models. ELAM is proposed to restore mitochondrial bioenergetic function by stabilizing inner membrane structure and increasing oxidative phosphorylation coupling and efficiency. Although ELAM treatment effectively attenuates physiological declines in multiple tissues in rodent aging models, it remains unclear whether these functional improvements correlate with favorable changes in molecular biomarkers of aging. Herein, we investigated the impact of 8-week ELAM treatment on pre- and post- measures of C57BL/6J mice frailty, skeletal muscle, and cardiac muscle function, coupled with post-treatment assessments of biological age and affected molecular pathways. We found that health status, as measured by frailty index, cardiac strain, diastolic function, and skeletal muscle force are significantly diminished with age, with skeletal muscle force changing in a sex-dependent manner. Conversely, ELAM mitigated frailty accumulation and was able to partially reverse these declines, as evidenced by treatment-induced increases in cardiac strain and muscle fatigue resistance. However, at the level of gene expression and DNA methylation, ELAM did not produce statistically significant changes in molecular organization and biological age in most treatment groups. Pathway analyses indicated that ELAM treatment showed pro-longevity shifts in gene expression such as upregulation of genes involved in fatty acid metabolism, mitochondrial translation and oxidative phosphorylation, and downregulation of inflammation. Together, these results indicate that ELAM treatment is effective at mitigating signs of sarcopenia and heart failure in an aging mouse model, but that these functional improvements occur independently of changes in epigenetic and transcriptomic age. Thus, age-related changes in function may be uncoupled from changes in molecular biological age.

overall_design: Young (5-month-old) and old (24-month-old) male and female C57BL/6J mice were treated with saline or elamipretide (3 mg/kg/day) for 8 weeks using subcutaneously implanted osmotic minipumps

first: Gavin

last: Pharaoh

first: Alexander

last: Tyshkovskiy

first: Matthew

last: Campbell

first: David

last: Marcinek

first: Vadim

middle: N

last: Gladyshev


title: Shaking culture attenuates circadian rhythms in induced pluripotent stem cells during osteogenic differentiation through the YAP-TEAD axis

city: Sendai

first: Yunyu

last: Fu

address: 4-1, Seiryouchou, Aoba-ku

institute: Tohoku University

summary: Circadian rhythms synchronize cellular activities with the Earth’s 24-hour cycle, primarily regulated by clock genes that influence metabolism, physiology, and osteogenesis. While genetic regulation of circadian rhythms is well characterized, how extracellular mechanical forces modulate these rhythms during iPSC osteogenic differentiation remains unclear. Here, we show that shaking culture, which promotes three-dimensional iPSC-EB formation, disrupts clock gene oscillations by activating YAP-TEAD signaling. Inhibition of YAP-TEAD with verteporfin restores circadian oscillations and enhances osteogenesis, highlighting a biomechanical-circadian interplay with implications for regenerative medicine.

overall_design: Total RNA was extracted from adherent and shaking cultures two days after osteogenic induction, with two biological replicates per group. To analyze transcriptome profiles, RNA sequencing reads were mapped to the mm10 reference genome.

first: Hiroko

last: Okawa

first: Hiroshi

last: Egusa


title: PBAF associates with repressed chromatin to enable REST occupancy [ATAC-Seq]

city: New York

first: Elena

last: Grossi

state: NY

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Multimeric SWI/SNF chromatin remodelers assemble in distinct conformations, with individual functions difficult to dissect. Importantly, mutations in specific SWI/SNF genes are enriched in distinct cancers, as the PBAF-specific component ARID2 in melanoma. Through comprehensive epigenomic profiling of SWI/SNF complexes and their associated chromatin states in melanoma and melanocytes, we found that a subset of PBAF-exclusive regions unexpectedly coexists with PRC2 and repressed chromatin. Time-resolved approaches revealed that PBAF regions are generally less sensitive to ATPase-mediated remodeling compared to BAF sites. Notably, PBAF/PRC2-bound loci are enriched for REST, a transcription factor that represses neuronal genes. In turn, absence of ARID2 and consequent PBAF loss hinders REST ability to bind and inactivate its targets, leading to upregulation of neuronal and synaptic transcripts, a gene signature also associated with ARID2 mutations in melanoma patients. In sum, we demonstrate a unique role for PBAF in generating accessibility for a silencing transcription factor at repressed chromatin.

overall_design: Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) in melanoma 113/6-4L cells (4L) and normal human epithelial melanocytes (NHEM), in normal conditions or upon BRM014 treatment

first: Emily

last: Bernstein


title: Single amino acid mutations in histone H3.3 illuminate the functional significance of H3K4 methylation in plants [ChIP-seq_GFP]

city: beijing

first: Danhua

last: Jiang

address: No. 1 West Beichen Road, Chaoyang District

country: China

institute: Chinese Academy of Sciences

summary: Although numerous data have revealed correlations of histone modifications with chromatin activities such as transcription, proofs of their causal importance in gene expression regulation remain limited. Sequence variants within each histone family expand chromatin diversity and may carry specific modifications, further raising the question of how histone modifications coordinate with different variants. Here, we investigate the regulatory role of lysine 4 (K4) of Arabidopsis histone H3 by point mutating K4 in two major H3 variants, H3.1 and H3.3. K4 is essential for the function of H3.3 but not H3.1 in plant development. H3K4 methylation levels decreased drastically upon K4 mutation in H3.3, and the associated transcriptome changes are similar to those observed in a mutant lacking SDG2, a major enzyme responsible for depositing H3K4 trimethylation (H3K4me3). Moreover, H3.3K4 and SDG2 are required for de novo gene activation and RNA Pol II elongation. H3K4 methylation is preferentially accumulated on H3.3 compared to H3.1, likely due to the close association of the H3.3 deposition and H3K4 methylation machineries. Furthermore, we reveal the diverse impacts of K4 nearby residue mutations on H3K4 methylation and H3.3 function. Collectively, these findings suggest that H3.3 serves as a critical substrate for H3K4 methylation, which is important for gene expression regulation.

overall_design: HTR5 genome occupancy were examinated in  in HTR5-GFP and HTR5 K4A-GFP seedlings

first: Mande

last: Xue

first: Lijun

last: Ma


title: SUMOylated Etv1 establishes tumor-initiating cells during mammary oncogenesis [scRNA-seq]

city: Iowa City

first: Zhijie

last: Li

state: IA

address: 285 Newton Road

institute: University of Iowa

summary: scRNA-seq was used to compare the cell populations and transcriptiome in 6-week-old and 10-week-old FVB, MMTV-NIC, MMTV-NIC-Ube2ifl/fl mice

overall_design: Mammary glands were harvested from 6-week-old MMTV-NIC and MMTV-NIC/Ube2ifl/fl mice, and 10-week-old FVB, MMTV-NIC and MMTV-NIC/Ube2ifl/fl mice (all in FVB background).Freshly sorted basal and luminal epithelial cells were mixed at a 1:1 ratio for sequencing and analyzed using scRNA-seq

first: Kelsey

last: Koch

first: Dakota

middle: T

last: Thompson

first: Jeremy

last: Chang

first: Christopher

middle: M

last: Franke

first: Jeffrey

middle: R

last: White

first: Mikhail

middle: V

last: Kulak

first: Colin

last: Kenny

first: Ronald

last: Weigel


title: The mitochondrial-targeted peptide therapeutic elamipretide improves cardiac and skeletal muscle function during aging without detectable changes in tissue epigenetic or transcriptomic age.

first: Wayne

last: Mitchell

type: Methylation profiling by genome tiling array

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

platform_organism:
Macaca mulatta
Homo sapiens
Mus musculus
Rattus

overall_design: Refer to individual Series


title: Single amino acid mutations in histone H3.3 illuminate the functional significance of H3K4 methylation in plants [ChIP-seq_H3K4me3]

overall_design: Examination of H3K4me3 enrichment in Col, h3.3ko;HTR5, h3.3ko;HTR5 K4A and sdg2 mutant seedlings


title: Single amino acid mutations in histone H3.3 illuminate the functional significance of H3K4 methylation in plants [BS-seq]

type: Methylation profiling by high throughput sequencing

overall_design: Examination of DNA methylation in Col, h3.3ko;HTR5, h3.3ko;HTR5 K4A and sdg2 mutant seedlings


title: The mitochondrial-targeted peptide therapeutic elamipretide improves cardiac and skeletal muscle function during aging without detectable changes in tissue epigenetic or transcriptomic age [methylation array]

first: Gavin

last: Pharaoh

first: Alexander

last: Tyshkovskiy

first: Matthew

last: Campbell

first: David

last: Marcinek

first: Vadim

last: Gladyshev


title: Single amino acid mutations in histone H3.3 illuminate the functional significance of H3K4 methylation in plants [ChIP-seq_Pol II Ser5p & Pol II Ser2p]

first: Danhua

last: Jiang

overall_design: Examination of Pol II Ser5p and Pol II Ser2p enrichment in Col, h3.3ko;HTR5, h3.3ko;HTR5 K4A and sdg2 mutant seedlings

first: Mande

last: Xue


title: Single amino acid mutations in histone H3.3 illuminate the functional significance of H3K4 methylation in plants [RNA-seq]

overall_design: Transcriptome profiles were examined by RNA-seq in WT (Col), h3.3ko;HTR5, h3.3ko;HTR5 K4A and sdg2

first: Lijun

last: Ma

first: Huiren

last: Zhang


title: Single amino acid mutations in histone H3.3 illuminate the functional significance of H3K4 methylation in plants [ATAC-seq]

overall_design: Examination of chromatin accessibility in Col, h3.3ko;HTR5, h3.3ko;HTR5 K4A and sdg2 mutant seedlings


title: Memory-like natural killer cell and CD19-antibody based immunotherapy in combination with tyrosine-kinase inhibition of Ph(-like) acute lymphoblastic leukemia (MethylationEPIC)

city: Hamburg

first: Michael

last: Spohn

address: Martinistr. 52

department: Bioinformatics Core

country: Germany

institute: UKE Hamburg

summary: Epigenetic re-programming has been proposed to prime NK cells for an adaptive immune response. Additionally, priming NK cells with IL-12, IL-15, and IL-18 induces a memory-like condition marked by improved immune response capabilities when encountering target cells later on. In order to obtain a more thorough understanding of the memory-like state of NK cells induced by cytokines, we examined the impact of activating cytokines on the DNA methylation across the entire genome of NK cells derived from peripheral blood (referred to as PBNK cells). This investigation conducted after isolating the PBNK cells using antibody-bead isolation or after expanding them in a 7-day co-culture with irradiated K562 cells that expressed membrane-bound IL-21 and co-stimulatory 4-1BB ligand. The memory-like state was by stimulating either PBNK sample group with IL-12, IL-15, and IL-18 for 16 hours and compared with non-preactivated magnetically isolated or mbIL-21/4-1BB K562 co-cultured and expanded NK cells. We observed that Magnetic bead-isolated NK cells clearly separated into preactivated and non-preactivated clusters in contrast to IL21/4-1BB K562 expanded NK cells which exhibited methylation patterns mailnly mimicking epigenetic features of preactivated magnetic bead-isolated PBNK cells. Thus, The pre-activation along with IL21/4-1BB K562 co-culture led to the hypomethylation of CpG regions across various gene loci, suggesting a strong and extensive epigenetic reaction that promotes a transcriptionally permissive chromatin state.

overall_design: We aim to compare the methylation profile of memory-like Nk cells by comparing the pre-activated magnetically isolated PBNKcells and IL21/4-1BB K562 expanded one with the none preactivated magnetically isolated NK cells. Breifely, FACS sorted NK cells underwent genome-wide DNA methylation analyses using Infinium Methylation arrays (850k) (Illumina)  and the results demonstrated in a demonstrated by unsupervised hierarchical clustering.

first: Martin

last: Horstmann

first: Ulrich

last: Schüller

first: Zoya

last: Eskandarian


title: Memory-like natural killer cell and CD19-antibody based immunotherapy in combination with tyrosine-kinase inhibition of Ph(-like) acute lymphoblastic leukemia


title: Memory-like natural killer cell and CD19-antibody based immunotherapy in combination with tyrosine-kinase inhibition of Ph(-like) acute lymphoblastic leukemia (RNA-Seq)

summary: Epigenetic reprogramming determines transcriptional output of preactivated NK cells. We conducted RNA-sequencing on individually sorted NKC cells to analyze the transcriptional pattern of preactivated and canonical NK cells when exposed to K562 target cells.Gene set enrichment analysis (GSEA) of DEG analysis results showed a positive enrichment of the following Gene Ontology (GO) terms among others: Ribosome and mitochondrial function, immune system process, cell adhesion and motility. In general, the pre-activation of bead-isolated NK cells induced by IL12/15/18 and mbIL-21/4-1BB K562 expansion results in significant epigenetic reprogramming and enhanced transcriptional output. The epigenetic and transcriptional characteristics of IL12/15/18 pre-activated bead-isolated NK cells closely resemble those of mbIL-21/4-1BB K562 cell co-culture expanded NK cells, suggesting that a memory-like state can be induced in NK cells solely through IL21 4-1BB K562 co-culture conditions.

overall_design: We performed RNA-sequencing of single cell FACS-sorted NKC to determine the transcriptional activities of preactivated vs none preactivated NK cells upon K562 target cell exposure in a co-culture system. RNA sequencing was performed with a SMART-Seq mRNA kit from Takara for cDNA synthesis, and the library preparation was carried out using the Nextera XT kit from Illumina. The quality-controlled libraries were then sequenced on an Illumina NextSeq2000 in paired-end mode.


title: Memory-like natural killer cell and CD19-antibody based immunotherapy in combination with tyrosine-kinase inhibition of Ph(-like) acute lymphoblastic leukemia (scRNA-Seq)

summary: The transcriptional profile of NK cells changes upon interaction with their target cells. Our in vitro experiments involving co-culturing NK cells with K562 cells to induce memory formation showed an altered transcriptional pattern. We hypothesized that leukemia-infiltrating NK (LINK) cells would exhibit a distinct transcriptional profile due to their encounter with malignant target cells. To investigate this, single cell RNA sequencing was conducted on Facs-sorted NK cells obtained from patients diagnosed with B-cell precursor ALL. The analysis of LINK cells' transcriptome revealed a significant decrease in ribosomal biogenesis transcripts, indicating that IL-mediated pre-activation of NK cells might compensate for the translational deficiency observed in LINK cells.

overall_design: Anonymous bone marrow samples from a healthy individual and patients with B precursor ALL were obtained from the biobank of the Dept. of Pediatric Oncology at the University Medical Center Hamburg-Eppendorf and sorted based on NK cells markers to isolate LINK cells, prior to being subjected to single cell RNA sequencing by an Illumina NextSeq 500 machine.


title: Coordinated transcription factor and chromatin dynamics enable innate immune memory in single macrophages

city: Los Angeles

first: Aleksandr

last: Gorin

state: CA

address: 570 Boyer Hall

department: Medicine

institute: UCLA

summary: Cells of the innate immune system need to interpret dynamic microenvironments and rapidly respond to sequential signals to control inflammation and infection. It is unclear how complex immune signals are encoded and decoded through a small number of transcription factors and ultimately coordinate cellular decision-making. Here, we use single live cell analysis and ATAC sequencing to show that sequential inflammatory signals via the NFκB network induce memory through reprogramming of signaling network state and chromatin accessibility in primary macrophages. We use transcriptomic profiling and deep learning to show that these regulatory modes combine to explain macrophage decision-making in response to new inflammatory signals. Macrophage response to prior stimulus predicts memory state and transcriptional response to subsequent stimulus. Surprisingly, we find that innate immune memory is mediated via intracellular individual-cell factors and not via paracrine signaling between macrophages. This work comprehensively profiles the dynamic regulation of signaling networks and chromatin accessibility and their role in tuning macrophage responses to evolving inflammatory signals.

overall_design: Murine BMDMs were treated with media along (M), CpG (C), PolyI:C (P) for 4 hours at which point the media was replaced with fresh media containing media alone (M), LPS (L), PolyI:C (P), CpG (C), or TNF (T). Treated BMDM were lifted from plates and ATACseq was performed as described in the methods. High throughput sequencing was performed with 50bp bi-directional reads.

first: Andrew

middle: G

last: Wang

first: Minjun

last: Son

first: Emma

last: Kenna

first: Abinash

last: Padhi

first: Bijentimala

last: Keisham

last: Hoffmann

first: Savas

last: Tay


title: Impaired T cell and neoantigen retention in time serial analysis of metastatic non-small cell lung cancer in patients unresponsive to TIL cell therapy

status: Public on Mar 12 2025

city: Tampa

first: Chao

address: 12902 USF Magnolia Dr

department: Immunology

institute: H Lee Moffitt Cancer Center & Research Institute

summary: Cell therapy with tumor-infiltrating lymphocytes (TIL) has yielded durable responses for multiple cancer types, but the causes of therapeutic resistance remain largely unknown. Here multi-dimensional analysis was performed on time serial tumor and blood in a lung cancer TIL therapy trial. Using T-cell receptor sequencing on both functionally expanded T cells and neoantigen-loaded tetramer-sorted T cells, we identified tumor antigen specific TCRs. We then mapped clones into individual transcriptomes and found that tumor-reactive clonotypes expressed a dysfunctional program and lacked stem-like features among patients who lacked clinical benefit. Tracking tumor-reactive clonotypes over time, decay of antigen-reactive peripheral T-cell clonotypes was associated with the emergence of progressive disease. Further, subclonal neoantigens previously targeted by infused T cells were subsequently absent within tumors at progression, suggesting potential adaptive resistance. Our findings suggest that targeting clonal antigens and circumventing dysfunctional states may be important for conferring clinical responses to TIL therapy.

overall_design:
We collected time serial peripheral blood, tumors and TIL infusion for TCRB sequencing before and after TIL therapy.

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Adaptive Biotechnologies does not provide raw data.
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first: Ben

last: Creelan

first: Sean

last: Yoder

first: Chaomei


title: Nanostring gene expression of tissues from MC4R WT and KO mice

status: Public on Mar 13 2025

city: Nashville

first: Jamey

middle: Dale

last: Young

address: 2414 Highland Ave

department: Chemical and Biomolecular Engineering

institute: Vanderbilt University

summary: We present an isotope-based metabolic flux analysis (MFA) approach to simultaneously quantify metabolic fluxes in the liver, heart, and skeletal muscle of individual mice. The platform was scaled to examine metabolic flux adaptations in age-matched cohorts of mice exhibiting varying levels of chronic obesity. We found that severe obesity increases hepatic gluconeogenesis and citric acid cycle flux, accompanied by elevated glucose oxidation in the heart that compensates for impaired fatty acid oxidation. In contrast, skeletal muscle fluxes exhibit an overall reduction in substrate oxidation. These findings demonstrate the dichotomy in fuel utilization between cardiac and skeletal muscle during worsening metabolic disease and demonstrate the divergent effects of obesity on metabolic fluxes in different organs. This multi-tissue MFA technology can be extended to address important questions about in vivo regulation of metabolism and its dysregulation in disease, which cannot be fully answered through studies of single organs or isolated cells/tissues

overall_design: Heart, Gastrocnemius, and Vastus samples were analyzed in 16 week old MC4R WT Chow (n=4), KO Chow (n=5), and KO Western Diet (n=6) mice. Nanostring gene expression data is presented here.

first: Mohsin

last: Rahim


title: ArcAB two-component system is associated with susceptibility of Aggregatibacter actinomycetemcomitas to superoxide and hydrogen peroxide

city: Kagoshima

first: Yuichi

last: Oogai

address: sakuragaoka 8-35-1

institute: Kagoshima univ.

summary: Aggregatibacter actinomycetemcomitans is a Gram-negative facultative anaerobe and is associated with periodontal disease. A two-component system ArcAB plays a crucial role in adaptation to several conditions, but its function in A. actinomycetemcomitans remains unclear. To identify the genes regulated by the ArcA response regulator in A. actinomycetemcomitans, differentially expressed genes were analyzed using the wild-type strain NUM4039 and its isogenic mutant of arcA. The obtained data indicated that 68 genes were differentially expressed with 40 genes upregulated more than 2-fold and 28 genes downregulated more than 2-fold.

overall_design: RNA-seq profiling of A. actinomycetemcomitans wild type and its inactivated mutant of arcA grown in A. actinomycetemcomitans growth medium (AAGM) broth at 37˚C under ambient air supplemented with 5% CO2.

first: Masanobu

last: Nakata


title: CREM is a regulatory checkpoint of CAR and IL-15 signaling in NK cells

city: Houston

first: Katy

last: Rezvani

address: Zayed Building, 5th floor 6565 MD Anderson Blvd. Unit 1061 Houston, TX 77030

department: Stem Cell Transplantation & Cellular Therapy department

institute: MD Anderson Cancer Center

summary: This is a preclinical study investigating the role of CREM transcription factor in CAR NK cells. We found thata CREM is a regulatory checkpoint induced by CAR CD3z signaling and IL-15 stimulation that leads to suppression of NK cell function. CREM KO enhances the anti-tumor efficacy of CAR NK cells.

overall_design: Multiple in vitro and in vivo experiments were conducted to establish the role of CREM in CAR NK cells. Mechanistic assays such as with phosphorylation studies, and transcriptomic (bulk RNA seq) and epigenetic (bulk ATAC and ChIP seq) analyses were conducted.

first: Katayoun


title: Cxcr3 promotes protection from colorectal cancer liver metastasis by driving NK infiltration and plasticity

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

summary: The anti-metastatic activity of NK cells is well established in several cancer types, but the mechanisms underlying NK cell metastasis infiltration and acquisition of anti-tumor characteristics remain unclear.  Herein, we investigate the cellular and molecular factors required to facilitate the generation of an ILC1-like CD49a+NK cell population within the liver metastasis environment in orthotopic mouse models of colorectal cancer (CRC). We show that CD49a+NK cells have the highest cytotoxic capacity among metastasis-infiltrating NK cells in the MC38 mouse model. Furthermore, the chemokine receptor CXCR3 promotes CD49a+NK cell accumulation and persistence in metastasis where NK cells co-localize with macrophages in CXCL9 and CXCL10 rich areas. We confirmed the accumulation of CXCR3+ NK cells in metastatic samples mined from a published sc-RNAseq dataset of a cohort of treatment-naïve CRC patients. Conditional deletion of Cxcr3 in NKp46+ cells and antibody-mediated depletion of metastasis-associated macrophages markedly impair CD49a+NK cell development, indicating that CXCR3 and macrophages contribute to efficient NK cell localization and polarization in liver metastasis. Conversely, CXCR3neg NK cells maintain a CD49a- phenotype in metastasis with reduced parenchymal infiltration and tumor killing capacity. Furthermore, CD49a+NK cell accumulation is impaired in an independent SL4-induced CRC metastasis model, which fails to accumulate CXCL9+ macrophages. Together, our results highlight a role for CXCR3/ligand axis in promoting macrophage-dependent NK cell accumulation and functional sustenance in liver metastasis from colorectal cancer.

overall_design: We performed MC38 cell intrasplenic injection in C57BL6/J  mice to induce liver metastasis. For bulk RNA-seq cells from 6 to 8 pooled samples of metastasis-free liver or metastasis were sorted with FACS Aria III (BD Bioscience) as following: NK cells (live lin- CD45+ NKp46+ CD49a- CD49b+), ILC1 (live lin- CD45+ NKp46+ CD49a+ CD49b-) and CD49+ NK cells cells (live lin- CD45+ NKp46+ CD49a+ CD49b+).

first: Eleonora

last: Russo

first: Chiara

last: D'Aquino

first: Giovanna

last: Peruzzi

first: Mattia

last: Laffranchi

first: Giovanni

last: Bernardini


title: Effects of electrical pulse stimulation and hydrogen peroxide as its byproduct on in vitro contractile skeletal muscle tissue.

city: Shinjuku-ku

first: Kanae

last: Otsutomo

state: Tokyo

address: 8-1 Kawada-cho

department: Institute of Advanced Biomedical Engineering and Science

institute: Tokyo Women's Medical　University

summary: The in vitro human skeletal muscle model is a valuable tool for studying muscle physiology and the mechanisms underlying muscle diseases. Tissue engineering approach could produce contractile human muscle tissue, with electrical pulse stimulation (EPS) enhancing its contractile ability.  We evaluated transcriptomic changes induced by EPS, two different patterns of EPS were applied to differentiated human myofiber sheets with cultured fibrin-gel. After 3 days of EPS-induced exercise, RNA was extracted from these two differently stimulated samples and non-stimulated control sample and analyzed by RNA-sequencing. For the samples with an excess EPS pattern, catalase was supplemented in the media to degrade hydrogen peroxide generated by EPS, and RNA  was extracted from the stress-mitigated sample and also analyzed by RNA-sequencing.

overall_design: RNA-sequencing profiling of two different patterns of EPS and catalase supplementation for mitigating the hydrogen peroxide stress in an excess EPS conditions.

first: Hironobu

last: Takahashi

first: Tatsuya

last: Shimizu


title: Clinically translatable mitochondrial gene therapy in muscle using tandem zinc finger nuclease architecture

city: Cambridge

first: Lindsey

last: Van Haute

address: Hills Road

department: MRC Mitochondrial Biology Unit

institute: University of Cambridge

summary: We studied the use of tandem zinc finger nucelase arrangements delivered by AAV in a mouse model of mitochondrial genetic disease.

overall_design: Assessments of nuclear DNA off-targets was analysed by Illumina NGS

first: Pavel

last: Nash


title: Changing dynamics of the fibroblast differentiation hierarchy during mammary gland morphogenesis and tumorigenesis

city: Parkville

first: Yunshun

last: Chen

state: VIC

address: 1G Royal Parade

department: ACRF Cancer Biology and Stem Cells

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

overall_design: Refer to individual Series


title: LMX1B missense-perturbation of regulatory element footprints disrupt postnatal serotonergic forebrain axon arborization [ChIP-seq]

city: Cleveland

first: Evan

last: Deneris

state: Ohio

address: 2210 Circle Dr., Robbins E640

department: Neurosciences

institute: Case Western Reserve University

summary: Pathogenic coding mutations are prevalent in human neuronal transcription factors (TFs) but how they disrupt development is poorly understood. Lmx1b is a master transcriptional regulator of postmitotic serotonin (5-HT) neuron development; over two hundred pathogenic heterozygous mutations have been discovered in human LMX1B, yet their impact on brain development has not been investigated. Here, we developed mouse models with different LMX1B DNA-binding missense mutations. Missense heterozygosity effected highly specific deficits in the postnatal maturation of forebrain serotonin axon arbors, primarily in the hippocampus and motor cortex, which was associated with spatial memory defects. Digital Genomic Footprinting (DGF) revealed that missense heterozygosity caused complete loss of Lmx1b motif protection and chromatin accessibility at sites enriched for a distal active enhancer/active promoter histone signature and homeodomain binding motifs; at other bound Lmx1b motifs, varying levels of losses, gains or unchanged accessibility were found. The spectrum of footprint changes was strongly associated with synapse and axon genes. Lmx1b missense heterozygosity further caused wide disruption of Lmx1b-dependent regulatory networks comprising diverse TFs. These findings suggest Lmx1b missense heterozygosity forces complex dominant negative-like and hypomorphic perturbations on serotonergic regulatory element TF binding and accessibility. Our work illustrates the power of DGF for gaining insight into how TF missense mutations disrupt regulatory networks within neuronal epigenomes.

overall_design: ChIPmentation for CTCF was deep sequenced using an Illumina HiSeq 550.

first: Brent

last: Eastman

first: Nobuko

last: Tabuchi

first: Xinrui

middle: L

last: Zhang

first: William

last: Spencer

middle: S


title: GIPR agonism and antagonism decrease body weight and food intake via different mechanisms in male mice

city: Neuherberg

first: Robert

middle: Michael

last: Gutgesell

state: Bavaria

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

institute: Helmholtz Center Munich

summary: Agonists and antagonists of the glucose-dependent insulinotropic polypeptide receptor (GIPR) enhance body weight loss induced by glucagon-like peptide-1 receptor (GLP-1R) agonism. However, while GIPR agonism decreases body weight and food intake in a GLP-1R-independent manner via GABAergic GIPR+ neurons, it remains unclear whether GIPR antagonism affects energy metabolism via a similar mechanism. Here we show that the body weight and food intake effects of GIPR antagonism are eliminated in mice with global loss of either Gipr or Glp-1r but are preserved in mice with loss of Gipr in either GABAergic neurons of the central nervous system or peripherin-expressing neurons of the peripheral nervous system. Single-nucleus RNA-sequencing shows opposing effects of GIPR agonism and antagonism in the dorsal vagal complex, with antagonism, but not agonism, closely resembling GLP-1R signalling. Additionally, GIPR antagonism and GLP-1R agonism both regulate genes implicated in synaptic plasticity. Collectively, we show that GIPR agonism and antagonism decrease body weight via different mechanisms, with GIPR antagonism, unlike agonism, depending on functional GLP-1R signalling.

overall_design:
35 week-old DIO mice were treated 2 h prior to the end of the light phase with a single s.c. injection of either vehicle (PBS), acyl-GIP (150 nmol/kg)11-13, acyl-GLP-1 (50 nmol/kg)11-13, the GIPR:GLP1R co-agonist MAR709 (50 nmol/kg)11-13, or an acylated peptide GIPR antagonist (1,500 nmol/kg)20. Hypothalamus and hindbrain were harvested 8 h after drug administration and stored in liquid nitrogen. Nuclei were isolated using the 10X Genomics Chromium Nuclei Isolation Kit including RNase Inhibitor (10X Genomics; Pleasanton, CA, USA; #PN-1000494), and using the 10X Genomics protocol for Single Cell Multiome ATAC + Gene Expression (10X Genomics; Pleasanton, CA, USA; #CG000505 Rev A).
Only the GEX data are included in this submission.

first: Ahmed

last: Khalil

first: Arkadiusz

last: Liskiewicz

first: Gandhari

last: Maity-Kumar

first: Aaron

last: Novikoff

first: Gerald

last: Grandl

first: Daniela

first: Callum

last: Coupland

first: Ezgi

last: Karaoglu

first: Seun

last: Akindehin

first: Russel

last: Castelino

first: Fabiola

last: Curion

first: Xue

last: Liu

first: Cristina

last: Garcia-Caceres

first: Alberto

last: Cebrian Cerrano

first: Jonathan

last: Douros

first: Patrick

last: Knerr

first: Brian

last: Finan

first: Richard

last: DiMarchi

first: Kyle

last: Sloop

first: Ricardo

last: Samms

first: Fabian

last: Theis

first: Matthias

middle: H

last: Tschöp

first: Timo

last: Müller


title: LMX1B missense-perturbation of regulatory element footprints disrupt postnatal serotonergic forebrain axon arborization

first: Evan

last: Deneris

overall_design: RNA-seq for control, Lmx1bN246K/+, and  Lmx1bR200Q/+ Pet1-neurons, in triplicate, at E17.5 were deep sequenced using an Illumina HiSeq 550.

first: Brent

last: Eastman

first: Nobuko

last: Tabuchi

first: Xinrui

last: Zhang

first: William

last: Spencer


title: ChIP-seq profiling of estrogen receptor binding in MCF-7 cells exposed to 5α-DTT, Flutamide, Estradiol, and Bisphenol B

city: Busan

first: BuHyun

last: Youn

address: Busandaehak-ro 63beon-gil, Geumjeong-gu

department: Biological Sciences

country: South Korea

institute: Pusan National University

summary: Endocrine-disrupting chemicals (EDCs) can modulate estrogen receptor (ER) signaling by altering its transcriptional activity. To investigate these effects, we performed chromatin immunoprecipitation sequencing (ChIP-seq) on cells treated with 5α-Dihydrotestosterone (5α-DTT), Flutamide, Estradiol, and Bisphenol B. This dataset includes raw sequencing reads, processed peak files, and metadata, enabling the identification of ER binding sites influenced by each EDC. Gene ontology (GO) analysis of ChIP-enriched regions revealed that these compounds affect key pathways, including antibody-dependent cytotoxicity, BMP signaling in cardiac induction, and hepatocyte growth factor receptor signaling. This dataset provides insights into EDC-induced transcriptional regulation and contributes to the understanding of their role in endocrine disruption.

overall_design: This study analyzes the effects of endocrine-disrupting chemicals (EDCs) binding to the estrogen receptor (ER) in MCF-7 cells and how this binding influences subsequent ER-DNA interactions using ChIP-seq. Cells were treated with four different EDCs: 5α-Dihydrotestosterone (5α-DTT), Flutamide, Estradiol, and Bisphenol B. ChIP was performed using an anti-ER antibody to capture ER-bound chromatin, followed by high-throughput sequencing. This dataset provides insights into EDC-induced transcriptional regulation and ER-DNA interactions.

first: HyeSook

first: Soomin

last: Yum

first: Haksoo

last: Lee


title: LMX1B missense-perturbation of regulatory element footprints disrupt postnatal serotonergic forebrain axon arborization [ATAC-seq]

overall_design: 5-HT neuron ATAC-seq profiles of control (CON), Lmx1bN246K/+, and  Lmx1bR200Q/+ at E14.5 mice were generated by deep sequencing using Illumina HiSeq 550. The sequence reads that passed quality filters were processed using the ENCODE ATAC-seq pipeline and replicates merged and downsampled to 100M reads per sample.


title: Implication of bone marrow adipose tissue in bone homeostasis during osteoarthritis

city: PAMPLONA

first: Juan R

last: Rodriguez-Madoz

address: AV PIO XII 53

institute: CIMA

summary: Objective: To explore the role of bone marrow adipocytes (BMAds) in osteoarthritis (OA). Methods: Male and female C57BL/6 mice (n=4/group) underwent meniscectomy (MNX) or SHAM surgery. OA was determined using OARSI score and the number of perilipin+ adipocytes was quantified. Mesenchymal Stromal Cells (MSCs) from MNX and SHAM mice were differentiated into osteoblasts and adipocytes. Human adipocytes and MSCs (n=8) were enzymatically isolated from epiphyseal and metaphyseal marrow, and from subcutaneous adipose tissue (SCAT) of hip OA patients. Human OA MSCs were differentiated into osteoblasts and adipocytes (OA-Diff-hAdipo). Gene expression patterns of epiphyseal and metaphyseal BMAds, SCAT adipocytes and OA-Diff-hAdipo were evaluated by RNAseq (n=4). The effect conditioned media from OA epiphyseal bone (n=5) on the alkaline phosphatase (ALP) activity and mineralization kinetics was assessed in vitro. Results: Increase in BMAd density was positively correlated with cartilage degradation in MNX mice. OA modified the differentiation capacity of MSCs, accelerating adipocyte differentiation and failing to produce osteoblasts in both human and mice. Human epiphyseal, metaphyseal and SCAT adipocytes from the same OA patients each displayed a specific transcriptome, suggesting different functions. Enrichment analysis defined metaphyseal OA-BMAds as cells implicated in hematopoietic stem cell differentiation. On the other hand, epiphyseal OA-BMAds were considered as osteogenic cells showing an up-regulation of genes related to bone mineralization and remodeling. Specifically, OA epiphysis-secreted molecules decreased ALP activity and altered in vitro the mineralization process. Conclusion: All these results support the emergence of BMAds as new cell partners in OA, opening new venues for therapeutic approaches.

overall_design: RNA-seq profiling of primary bone marrow adipocytes and  differentiatied adipocytes from mesenchymal stromal cells from the same OA patients.

first: Natalia

last: ZAPATA-LINARES

first: Maria E.

last: CALLEJA-CERVANTES

first: Juan R.

last: RODRIGUEZ-MADOZ

first: Stéphanie

last: LUCAS

first: Xavier

last: HOUARD


title: Targeting the chromatin remodeler BAZ2B mitigates liver aging and fibrosis

city: shanghai

first: shi-qing

last: cai

address: number 320 yueyang road

institute: CAS Center for Excellence in Brain Science and Intelligence Technology

summary: Increasing age enhances the liver's vulnerability to nonalcoholic steatohepatitis (NASH) with fibrosis. Unraveling the intricate molecular relationship among aging, cellular senescence, and NASH is critical for developing effective treatments, yet it remains a daunting challenge. Here we report a vital epigenetic mechanism that links liver aging to NASH fibrosis. We find that up-regulation of a chromatin remodeler BAZ2B in a subpopulation of hepatocytes contributes to the pathological progression of NASH in patients. Genetic ablation or hepatocyte-specific knockdown of Baz2b rejuvenates hepatic cells and limits diet-induced steatohepatitis and liver fibrosis via preserving the peroxisome proliferator-activated receptor α (PPARα)-mediated lipid metabolism, which was impaired in both naturally aging and NASH mouse livers. Mechanistically, Baz2b down-regulates the expression of genes related to the PPARα signaling pathway by directly binding their promoter regions and reducing chromatin accessibility. Our study thus unravels the BAZ2B-PPARα-lipid-metabolism signal axis as a key pathway linking liver aging to NASH fibrosis, suggesting that BAZ2B is a potential therapeutic target for hepatic fibrosis.

overall_design:
For ChIP assays, chromatin immunoprecipitation was performed as described with some modifications 46. Briefly, for liver tissue, frozen samples were chopped into small pieces, immediately incubated in freshly prepared disuccinimidyl glutarate solution (2 mM in PBS), and rotated for 30 min at room temperature; for cell lines, samples were collected from 10 cm cultured dishes using cell scrapers. Then samples were washed in PBS buffer twice, crosslinked by 1% formaldehyde (in PBS with proteinase-inhibitor cocktail), and fixed on a nutator shaker for 10 min at room temperature. Fixed samples were quenched with 0.125 M glycine and washed with cold PBS buffer with protease inhibitors three times. Ground the liver tissues with a dounce homogenizer on ice, passed the homogenized tissue suspension through a 70 μM cell strainer to remove the connective tissue, and then washed samples with cold PBS buffer with protease inhibitors three times. Samples were then lysed by ice-cold lysis buffer (50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% Triton X-100, 1 mM PMSF and protease inhibitor cocktail) with 0.1% SDS. Lysates were digested using 0.5 μl micrococcal nuclease (MNase) (10011S, CST) in reaction buffer (50 mM Tris, 5mM CaCl2, pH 8.0) for 3 min at 37 °C, and then were stopped with 25 mM EDTA. About 10 μg of the digested chromatin was used for immunoprecipitation. Primary antibodies including anti-H3K4me3 (Abcam ab8580), anti-H3K27ac (Abcam ab4729), and anti-Flag (F1804, Sigma-Aldrich) were incubated with chromatin overnight at 4 C with rotation. The next day, 1.5 mg Dynabeas® Protein A beads (Invitrogen, 10001D) were added to each immunoprecipitated sample, and incubated at 4 C for 2 hours with rotation to collect chromatin/antibodies. DNAs were eluted from washed magnetic beads with incubation of SDS elution buffer (1% SDS,10 mM EDTA, 50 mM Tris-HCl) overnight at 65 °C. The remaining RNA and protein residues were removed by incubating with 3 mL of 0.5 mg/mL RNaseA at 37 °C for 15 min and then 3 mL of 20 mg/mL Proteinase K at 65 °C for 30 min. The ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England BioLabs) and NEBNext Multiplex Oligos for Illumina (New England BioLabs). Sequencing was performed on an Illumina NovaSeq 6000.  ATAC-seq Briefly, frozen liver samples were chopped into small pieces, and immediately incubated in homogenization buffer (10mM Tris, 0.25mM sucrose, 25mM KCl, 5mM MgCl2, 0.1 mM DTT, 1% BSA, 0.1% NP 40 with RNase inhibitor). Ground the liver tissue pieces with a dounce homogenizer on ice, passed the homogenized tissue suspension through a 70 μM and 40 μM cell strainer, washed once in cold Nuclei Wash Buffer (20% iodixanol in HB solution), and then resuspended samples in Blocking Buffer (10% BSA in PBS with RNase inhibitor). The segmentation reaction was performed using transposases (Vazyme, TD501) for 30 min at 37 °C. Segmented DNAs were purified and amplified using the TruePrepTM Index Kit (Vazyme, TD202). DNA sequencing was performed using an Illumina NovaSeq 6000.

Total RNAs of livers were isolated and purified by using TRIzol (Invitrogen) and the RNeasy Mini kit (Qiagen), respectively. Then these RNA samples were subjected to library preparation and sequencing. The RNA-seq library was prepared by TruSeq Stranded Total RNA Sample Preparation kit (Illumina) for 150-bp paired-end sequencing. Poly-A-containing mRNAs were purified, fragmented to 300 bp nucleotides, and used for the synthesis of single-stranded cDNAs by random hexamer priming. Then the constructed single-stranded cDNAs were used as templates to synthesize the second-strand cDNA, leading to the generation of double-stranded cDNAs which were then amplified by polymerase chain reaction (PCR). Subsequently, qualified cDNA libraries were sequenced on an Illumina NextSeq500 platform. The HISAT aligner with –rna-strandness F 44 was used to map sequencing reads to the mouse reference genome GRCm38 (mm10) and mapped reads were counted using HTSeq to obtain raw read counts for each gene 45. The R package DESeq2 46 was used to identify the differentially expressed genes (DEGs) between groups. Genes with a P < 0.05 were designated as DEGs between groups.


title: Embryological cellular origins and hypoxia-mediated mechanisms in PIK3CA-driven refractory vascular malformations

city: Tsu

first: Sota

last: Torii

state: Mie

address: 2-174 Edobashi

department: Graduate School of Medicine

institute: Mie University

summary: Congenital vascular malformations, affecting 0.5% of the population, frequently occur in the head and neck, complicating treatment due to their vital functions. Our previous research identified distinct developmental origins for blood and lymphatic vessels in these regions in both mouse and human embryos. In this study, we expressed Pik3caH1047R in the cardiopharyngeal mesoderm (CPM) to investigate the pathogenesis of these malformations. Mice expressing Pik3caH1047R in the CPM developed abnormal vasculature restricted to the head and neck. Single-cell RNA sequencing revealed that Pik3caH1047R promotes Vegf-a expression in endothelial cells via Hif-driven hypoxia signaling. Human samples corroborated these findings, showing elevated HIF-1α and VEGF-A in malformed vessels. Notably, treatment with Hif-1α and Vegf-a inhibitors significantly reduced abnormal vasculature in the mouse model. Our findings highlight the role of developmental origins and hypoxia-driven mechanisms in vascular malformations, providing a basis for developing targeted therapies for these refractory conditions.

overall_design: Cardiopharyngeal mesoderm (CPM) cells were isolated from the pharyngeal arch of Isl1-Cre;R26R-eYFP (control) or Isl1-Cre;R26R-eYFP;Pik3caH1047R mice using Fluorescence-activated cell sorting (FACS) and analyzed using scRNA-seq.

first: Keiki

last: Nagaharu

first: Kazuaki

last: Maruyama


title: Changing dynamics of the fibroblast differentiation hierarchy during mammary gland morphogenesis and tumorigenesis [scRNA-Seq II]

first: Yunshun

last: Chen

summary: Fibroblasts form a major component of the stroma in normal mammary tissue and breast tumors. Here we have applied single-cell transcriptome profiling to characterize fibroblasts in the mouse mammary gland across five different developmental stages and during mammary oncogenesis. In the normal gland, diverse stromal populations were resolved, including lobular-like fibroblasts, committed preadipocytes and adipogenesis-regulatory, as well as cycling fibroblasts in puberty and pregnancy. These specialized cell types appear to emerge from CD34high mesenchymal progenitor cells, accompanied by elevated Hedgehog pathway activity. During late tumorigenesis, diverse cancer-associated fibroblasts were identified in different models of breast cancer, including a population of CD34– myCAFs that were transcriptionally and phenotypically similar to senescent CAFs. Moreover, Wnt9a was demonstrated to be a regulator of senescence in CD34– myCAFs. These findings reflect a diverse and hierarchically organized stromal compartment in the normal mammary gland that provides a framework to better understand fibroblasts in normal and cancerous states.

overall_design: Single-cell RNA-seq profiling on normal developmental fibroblasts.

first: Jinming

last: Cheng

first: Gordon

middle: K

last: Smyth

first: Rosa

last: Pascual

first: Jane

middle: E

last: Visvader

first: Geoffrey

middle: J

last: Lindeman


title: Changing dynamics of the fibroblast differentiation hierarchy during mammary gland morphogenesis and tumorigenesis [scRNA-Seq I]

overall_design: Single-cell RNA-seq profiling on normal developmental, hormone-treated, hyperplasia- and cancer-associated fibroblasts.


title: Placental Malaria Induces a Unique Methylation Profile Associated with Fetal Growth Restriction

city: San Francisco

first: Stephanie

middle: L.

last: Gaw

address: 513 Parnassus Avenue, Health Sciences East 1622

department: Obstetrics, Gynecology and Reproductive Sciences

institute: University of California, San Francisco

summary: Fetal growth restriction (FGR) is associated with perinatal death and adverse birth outcomes, as well as long-term complications, including increased childhood morbidity, abnormal neurodevelopment, and cardio-metabolic diseases in adulthood. Placental epigenetic reprogramming associated with FGR may mediate these long-term outcomes. Placental malaria (PM), characterized by sequestration of Plasmodium falciparum-infected erythrocytes in placental intervillous space, is the leading global cause of FGR, but its impact on placental epigenetics is unknown. We hypothesized that placental methylomic profiling would reveal common and distinct mechanistic pathways of non-malarial and PM-associated FGR. We analyzed placentas from a US cohort with no malaria exposure (n = 12) and a cohort from eastern Uganda, a region with a high prevalence of malaria (n = 12). From each site, 8 cases of FGR  and 4 healthy controls were analyzed. PM was diagnosed by placental histopathology. We compared the methylation levels of over 850K CpGs of the placentas using Infinium MethylationEPIC v1 microarray. Non-malarial FGR was associated with 65 differentially methylated CpGs (DMCs), whereas PM-FGR was associated with 133 DMCs, compared to their corresponding controls without FGR. One DMC (cg16389901, located in the promoter region of BMP4) was commonly hypomethylated in both groups. We identified 522 DMCs between non-malarial FGR vs. PM-FGR placentas, independent of differing geographic location or cellular composition. Placentas with PM-associated FGR have distinct methylation profiles compared to placentas with non-malarial FGR, suggesting novel epigenetic reprogramming in response to malaria. Larger cohort studies are needed to determine the distinct long-term health outcomes in PM-associated FGR pregnancies.

overall_design: In this study, we compared methylation profiles in placentas of non-malarial and PM-associated pregnancies, with or without FGR. Samples were divided into four groups: 1) FGR (no malarial FGR, n=8), 2) C-FGR (healthy controls from the US, n=4), 3) PM-FGR (placental malaria associated FGR, n=8), and 4) C-PM-FGR (healthy controls from Uganda, n=4). Bisulphite converted DNA from the 24 placental samples were hybridised to the Illumina Infinium MethylationEPIC v1 microarray. Differential methylation analysis was performed by first computing M values, i.e., the log ratios of methylated vs. unmethylated signal intensities for each probe and limma (version 3.54.2) implemented in the R-package minfi package. Secondly, β-values were calculated, representing the total % methylation level of each CpG site.

first: Nida

last: Ozarslan

first: Corina

last: Mong

first: John

last: Ategeka

first: Lin

last: Li

first: Sirirak

last: Buarpung

first: Joshua

middle: F

last: Robinson

first: Jimmy

last: Kizza

first: Abel

last: Kakuru

first: Moses

last: Kamya

first: Grant

last: Dorsey

first: Philip

last: Rosenthal


title: Age-Related  Transcriptomic Profiling of Human Granulosa Cells Reveals mRNA-microRNA Regulatory Network Associated with Key Ovulation Dynamics [miRNA-Seq]

city: Lone Tree

first: Ye

last: Yuan

state: Colorado

address: 10290 RidgeGate Circle

department: Research

institute: Colorado Center for Reproductive Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Advanced maternal age (AMA) patients experience decreased success from assisted reproductive technologies (ART), attributed to quantity and quality of oocytes, which is significantly influenced by the health of surrounding granulosa cells (GCs). In this study, we compared mRNA and microRNA (miRNA) transcriptomes between young (<32 y.o.) and AMA (>38 y.o.) patients' GCs to identify ovarian aging molecular signatures. Granulosa cells were isolated from 18 patients’ follicular fluid, and RNA was isolated for sequencing and subsequent bioinformatics analysis. We identified 293 and 21 differentially expressed genes (DEGs) and miRNAs (DE miRNA), respectively, between young and AMA GCs (P value < 0.05, FDR < 0.25, Fold Change > 1.5). Highly expressed mitochondrial-encoded genes, MT-ND3, MT-ND6, and MT-CYB are upregulated in young GCs. Pathway analysis indicates DEGs play a role in inflammation, cytokine signaling, extracellular matrix (ECM) remodeling, and angiogenesis. Some key DEGs include CXCL8, IL1B, NLRP3, SIGIRR, ANGPT2, ADAM8, and ADAMTS14. Additionally, target gene prediction and pathway analysis of DE miRNA indicates both up- and downregulated miRNA in young GCs are likely targeting genes associated with cell signaling, mitochondrial function, oxidative stress, apoptosis, and senescence pathways in addition to cytokine signaling, angiogenesis, and ECM remodeling. To further investigate regulatory mechanisms, we looked at the convergence of DEGs with predicted target genes of DE miRNA and identified miR-483-3p, miR-1268a, miR-4497, miR-7704, miR-135a-5p, miR-1261, and miR-4791 as key regulators of pathways involved with inflammation, ECM, and angiogenesis. The gene expression data suggests aged GCs have an impaired ability to elicit the same pro-inflammatory response combined with a dysregulation of angiogenesis and ECM remodeling when compared to young GCs, and miRNA may be playing a key role in the regulation of these key ovulatory events.

overall_design: Human granulosa cells were isolated from patients' follicular fluid collected during hormone-stimulated oocyte retrieval cycles. Patients were split into two groups: young and aged. The young group consisted of patients under 32 years old, and the aged group consisted of patients over 38 years old. Patients with a BMI greater than 25, endometriosis, or polycystic ovarian syndrome were excluded from the study. RNA was isolated from a minimum of 1 million cells from each patient. Patient RNA samples were pooled into groups of three to limit individual variation. Each group contained nine patients pooled into three biological replicates.

first: Heather

last: Rogers

first: Ahmed

last: Gad

first: Gentry

last: Cork

first: Nico

last: Menjivar

first: Dawit

last: Tesfaye


title: Impact of Mfn1 and H3.3 on DNA methylome in early mouse embryos

city: Wuhan

first: Li-quan

last: Zhou

state: Hubei

address: 13 Hangkong road

department: Tongji Medical College

institute: Huazhong University of Science and Technology

summary: In this study, we knocked down Mfn1/H3.3 in mouse early embryos and examined their impact on DNA methylome in mouse 8-cell embryos.

overall_design: Generally, siRNA against Mfn1/H3.3 was injected into mouse zygotes, and cultured to 8-cell stage for DNA methylome analysis by WGBS.

first: Yin

last: Ying

first: Zhou

last: Liquan


title: Molecular characterization of pancreatic neuroendocrine tumor tissue: characterization of altered pathways and potential non-invasive biomarkers

city: Riga

first: Helvijs

last: Niedra

address: Ratsupites 1

country: Latvia

institute: Latvian Biomedical Research and Study centre

summary: The study aimed to identify potential non-invasive biomarkers for pancreatic neuroendocrine tumours (PanNETs) through transcriptomic profiling of various tissue samples. The analysis encompassed samples from non-functional PanNETs (NF-PanNETs), insulinomas, and adjacent tumour tissues. In tumor vs. tumors adjacent pancreatic tissues differential expression analysis we identified 1210 differentially expressed genes (DEGs). Further pathway enrichment analysis revealed a multitude of overrepresented signaling pathways related to cell proliferation, survival and tumorigenesis. Notable findings were Beta-catenin independent and TCF dependent WNT signaling pathways, MAPK1/MAPK3 signaling and PIP3 activates AKT signaling. Amongst the list of DEGs we also identified 28 upregulated genes encoding for cell surface proteins and 24 upregulated genes encoding for cancer associated secretome proteins. Since the products of these genes are found in the bloodstream, there is a potential for further testing of these markers as biomarkers for liquid biopsy assay. Overall, the findings have underscored the promise of transcriptomic landscape analysis in identifying PanNET-specific non-invasive biomarkers and uncovering potential therapeutic targets.

overall_design: To investigate changes in PanNET transcriptome compared to adjacent pancreatic tissues we performed whole transcriptome-based RNA-sequencing analysis for 30 tumor samples (17 grade I, 10 grade I, and three grade III tumors) and six tumor adjacent pancreatic tissue samples. The samples used were formalin-fixed paraffin-embedded tissue samples.

first: Olesja

last: Rogoza

first: Rihards

last: Saksis

first: Raitis

last: Peculis

first: Anzela

last: Halilova

first: Aija

last: Gerina-Berzina

first: Sofija

last: Vilisova

first: Natalja

last: Shenterjakova

first: Aldis

last: Pukitis

first: Ignacio

last: Ruz-Caracuel

first: Julie

last: Earl

first: Georgina

last: Kolnikova

first: Peter

last: Dubovan

first: Miroslav

last: Tomas

last: Makovicky

first: Maria

last: Urbanova

first: Bozena

last: Smolkova

first: Eythimios

last: Koniaris

first: Ioanna

last: Aggelioudaki

first: Agap

last: i Kataki

first: Vita

last: Rovite


title: Functions of Mfn1 and H3.3 in early mouse embryos by RNA-seq

first: Li-quan

last: Zhou

summary: In this study, we knocked down Mfn1/H3.3 in mouse early embryos and examined their impact on transcriptome in mouse 8-cell embryos.

overall_design: Generally, siRNA against Mfn1/H3.3 was injected into mouse zygotes, and cultured to 8-cell stage for transcriptome analysis.

first: Yin

last: Ying

first: Zhou

last: Liquan


title: Age-Related  Transcriptomic Profiling of Human Granulosa Cells Reveals mRNA-microRNA Regulatory Network Associated with Key Ovulation Dynamics [RNA-Seq]

first: Ye

last: Yuan

first: Heather

last: Rogers

first: Ahmed

last: Gad

first: Gentry

last: Cork

first: Nico

last: Menjivar

first: Dawit

last: Tesfaye


title: A feedback amplifier circuit with Notch and E2A orchestrates T-cell fate and suppresses the innate lymphoid cell lineages during thymic ontogeny [Single-cell RNA + ATAC-Seq]

city: Chiba

first: Kenta

last: Horie

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: IAAR

institute: Chiba university

summary: We performed 10x single cell multiome analysis (ATAC-seq + RNA-seq) on fetal wild-type and E47-/- N1End/d thymic cells to decipher the dynamics of chromatin structure and gene expression during thymic ontogeny.

overall_design: Live thymic cells were isolated from the fetal thymi of wild-type and E47-/- N1End/d mice at 15 days post coitum. These cells were then used to isolate nuclei and construct libraries for scRNA-seq and scATAC-seq from an identical nucleus, according to the manufacturer's protocol for Chromium Next GEM Single Cell Multiome ATAC + Gene Expression.

first: Kazuko

last: Miyazaki

first: Taishin

last: Akiyama

first: Masaki


title: Functions of Mfn1 and H3.3 in early mouse embryos by ChIP-seq

summary: In this study, we knocked down Mfn1/H3.3 in mouse early embryos and examined their impact on epigenome in mouse 8-cell embryos.

overall_design: Generally, siRNA against Mfn1/H3.3 was injected into mouse zygotes, and cultured to 8-cell stage for epigenome analysis by ChIP-seq.


title: Inhibition of acid or neutral sphingomyelinases differentially impacts RNA and protein cargo sorting to extracellular vesicles

city: Montreal

first: Eric

last: Lecuyer

state: Quebec

address: 110 Pine Ave W

country: Canada

institute: Montreal Clinical Research Institute

summary: Extracellular vesicles (EVs) form through regulated biogenesis processes involving sphingomyelinases (SMases), enzymes that metabolize sphingomyelin to produce ceramide-a lipid influencing membrane rigidity and essential for EV generation. This study explores the impact of inhibiting neutral SMase (NSM) and acid SMase (ASM) on the sorting of EV protein and RNA cargoes in human MCF7 cells. Our results revealed that NSM inhibition reduces EV nanoparticles and diminishes RNA and protein cargoes, including endosomal, spliceosomal, and translation-related proteins. Conversely, ASM inhibition increased RNA-binding proteins within and enhanced the expression of ribonucleoprotein complex-associated RNA in released EVs, including several snRNAs and 7SL RNA. Intriguingly, ASM-inhibited EVs enhanced the migration and translational activity of recipient MCF10A cells. These findings suggest an important role for SMase-dependent vesiculation in governing RNA and protein trafficking to the extracellular space, unveiling potential implications for cellular communication and function.

overall_design: To explore sphingomyelinases' impact on cargo loading in extracellular vesicles, MCF7 cells were treated with sphingomyelinase inhibitors GW4869 or FTY720. Total RNA was isolated from both MCF7 cells and extracellular vesicles (EVs) under control and drug treatment conditions. After ribosomal RNA depletion, library preparation utilized the KAPA RNA HyperPrep Kit with RiboErase (HMR) from Roche. For cellular samples, 1 µg of total RNA was utilized, while EV samples under drug-induced conditions used 2-6 ng of total RNA. Libraries underwent 7 and 16 PCR cycles for amplification. Quantification using qPCR was followed by loading at equimolar concentrations for sequencing on the Novaseq platform with the Novaseq S4 kit, aiming for a coverage of 35 million paired-end reads per sample.

first: Juan-Carlos

middle: A

last: Padilla

first: Seda

last: Barutcu

first: Jonathan

last: Boulais

first: Yiran

last: Chen

first: Easin

last: Syed

first: Janaína

middle: C

last: da Silva

first: Eunjeong

last: Kwon

last: Lécuyer


title: The immune landscape of the “deregulated host response” in sepsis: newly emerging MDSCs with high expression of CD47 leads to B cell suppression via App-CD74 signaling

city: Chengdu

first: Feng

middle: Zhong

last: Xue

state: Sichuan

address: No. 2222, Frontier Medical Center, Xin Chuan Road, Zhong He Street

institute: Sichuan University

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

overall_design: Refer to individual Series


title: The immune landscape of the “deregulated host response” in sepsis: newly emerging MDSCs with high expression of CD47 leads to B cell suppression via App-CD74 signaling [scRNA-seq]

summary: Sepsis is defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. However, how this dysregulation occurs remains unclear. Herein, we used scRNA-seq to define the immune landscape of infection and found that when sepsis occurred, adaptive immunity was acutely and strongly suppressed, which manifested as a striking increase in the number of myeloid-derived suppressor cells (MDSCs), a decrease in the number of lymphocytes and drastic downregulation of the expression levels of B-cell-related genes and MHC class II molecules. Transcriptomic analysis showed that systemic immunosuppression occurred not only in the peripheral blood but also in all other immune compartments, including the spleen, lymph nodes, and bone marrow. Patients diagnosed with infection in the emergency department with extremely low expression levels of adaptive immunity-related genes had a high risk for developing sepsis. CD47 was identified as the key molecule that triggered this immunosuppression by inducing the production of amyloid-b precursor protein (App), which caused adaptive immunosuppression via B-cell suppression. Our study outlines a framework for how the dysregulated host response occurs and provides translational opportunities for sepsis immunotherapies.

overall_design: Comparative gene expression profiling analysis of single cell sequencing data for the PBMC in Sham mice, Mild infection mice and Critical infection (Sepsis) mice, 3 group in total.

last: Zhongxue


title: Single-Cell Resolution of Individual Variation in Hypothalamic Neurons Allows Targeted Manipulation Affecting Social Motivation

status: Public on Mar 11 2025

city: St. Louis

first: Joseph

last: Dougherty

state: MO

address: 4370 Duncan Ave

department: Genetics

institute: Washington University in St. Louis

summary: One great challenge in neuroscience is connecting molecular and cellular phenotypes to behavioral consequences. Using social motivation as a test case, we propose that individual behavioral trait variation can be leveraged to identify novel components of social reward circuits in the brain. Specifically, we hypothesized that either proportion or molecular features of distinct neuron classes in the hypothalamus can predict individual differences in social motivation. To test this, we generated high-precision single-nucleus RNA-sequencing profiles of >120,000 neurons from the hypothalamus and adjacent thalamus from 36 mice assessed for social motivation, balancing across sex and an autism-associated mutation genotype. Analysis of IEG patterns revealed that PVN Agtr1a+ neurons negatively predict social behavior. Consistent with this, FDA-approved AGTR1A antagonists increase social orienting. Next, analyzing neuronal subtype proportions as predictors of social behavior, we identified multiple neuronal populations whose relative abundance correlated with individual differences in social reward-seeking, particularly the Nxph4+ neurons of the posterior and lateral hypothalamus. Subsequent chemogenetic inhibition of these suppressed multiple aspects of social motivation. This work establishes a proof-of-principle for a new approach using single-cellsingle cell genomics to identify neural substrates for behavior and identifies cellular determinants of social motivation, which suggest therapeutic avenues for disorders with social deficits.

overall_design: Following a social operant conditioning paradigm, tuberal hypothalamus and neighboring thalamus were harvested from Myt1l mice (n=36, split by sex and genotype) 30 minutes after task completeion. Nuclei were isolated and barcoded libraries prepared using ScaleBio snRNAseq.

first: Simona

last: Sarafinovska

first: Sneha

middle: M

last: Chaturvedi

first: Din

last: Selmanovic

first: Jungeun

last: Ji

first: Emma

last: Jones

middle: D


title: Epidermal loss of PRMT5 leads to the emergence of an atypical basal keratinocyte-like cell population and defective skin stratification

city: Iowa City

last: Van Otterloo

state: Iowa

address: 801 Newton Rd

institute: University of Iowa

summary: During skin development, ectoderm-derived cells undergo precisely coordinated proliferation, differentiation, and adhesion to yield stratified epidermis. Disruptions in these processes can result in congenital anomalies including ectodermal dysplasia and harlequin ichthyosis. Protein Arginine Methyl Transferase 5 (PRMT5)—an enzyme responsible for methylating arginine residues in histones and other proteins—maintains progenitor status in germ and limb bud cells. Similarly, in vitro evidence suggests that PRMT5 prevents differentiation of basal keratinocytes, leading us to hypothesize that PRMT5 preserves the stem-cell phenotype of keratinocytes in vivo. To test this possibility, we generated conditional knockout (cKO) mice lacking Prmt5 in early ectoderm (E7.5), impacting the entire epidermis. Prmt5 cKOs exhibited gross skin defects, compromised skin barrier function, and reduced postnatal viability. Histological analyses revealed significant defects in epidermal stratification, without alterations in apoptosis or proliferation. Single-cell RNA and ATAC-seq analysis identified an atypical population of basal keratinocyte-like cells in Prmt5 cKOs, that exhibited a senescence-like program, characterized by increased Cdkn1a (p21), elevated senescence-associated secretory phenotype (SASP) molecules (Igfbp2), and decreased developmental transcription factor (Trp63) expression. Our findings suggest that PRMT5 prevents basal keratinocyte senescence by repressing Cdkn1a, shedding light on the epigenetic regulation of basal keratinocyte maintenance and senescence in congenital skin disorders.

overall_design: Bulk RNAseq analysis of E15.5 control and Prmt5 cKO back skin samples (3 independent controls and 3 independent mutants)

first: Nicole

last: Recka


title: From the Gut to the Brain: Transcriptomic Insights into Neonatal Meningitis Escherichia coli Across Diverse Host Niches

city: Gainesville

first: Subhashinie

last: Kariyawasam

state: Florida

address: 1945 SW 16th Ave

department: Comparative, Diagnostic, and Population Medicine

institute: University of Florida

summary: Neonatal meningitis caused by Escherichia coli (NMEC) is a leading cause of morbidity and mortality in newborns, and its pathogenesis relies on the ability of the bacterium to adapt and survive in diverse host environments. Despite advances in neonatal care, significant gaps remain in our understanding of how NMEC reprogram their transcriptome to survive in physiologically relevant niches. This study investigated the transcriptomic profiles of  E. coli strain RS218 (O18:H7:K1) in four under host-relevant environment —colonic fluid (CF), serum (S), human brain endothelial cells (HBECs) and cerebrospinal fluid (CSF)—to mimic the infection landscape of neonatal meningitis. High-throughput RNA sequencing (RNA-seq) was performed to profile NMEC’s transcriptomic responses in each niche, and differential gene expression analyses were conducted to identify enriched pathways.

overall_design: RNAseq profiling of NMEC strain RS218 incubated in host mimic conditions such as colonic fluid (CF), serum (S), human brain endothelial cells (HBECs) and cerebrospinal fluid (CSF)

first: Lekshmi

last: Edison


title: The immune landscape of the “deregulated host response” in sepsis: newly emerging MDSCs with high expression of CD47 leads to B cell suppression via App-CD74 signaling [RNA-seq]

summary: Sepsis is defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. However, how this dysregulation occurs remains unclear. Herein, we used scRNA-seq to define the immune landscape of infection and found that when sepsis occurred, adaptive immunity was acutely and strongly suppressed, which manifested as a striking increase in the number of myeloidderived suppressor cells (MDSCs), a decrease in the number of lymphocytes and drastic downregulation of the expression levels of B-cell-related genes and MHC class II molecules. Transcriptomic analysis  showed that systemic immunosuppression occurred not only in the peripheral blood but also in all other immune compartments, including the spleen, lymph nodes, and bone marrow. Patients diagnosed with  infection in the emergency department with extremely low expression levels of adaptive immunity related genes had a high risk for developing sepsis. CD47 was identified as the key molecule that  triggered this immunosuppression by inducing the production of amyloid-b precursor protein (App),  which caused adaptive immunosuppression via B-cell suppression. Our study outlines a framework for  how the dysregulated host response occurs and provides translational opportunities for sepsis  immunotherapies

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the Lung tissue, Kidney tissue,Liver tissue in  Sham mice , Mild infection mice and critical infection (Sepsis) mice, in addition, We also conducted an Comparative gene expression profiling analysis of RNA-seq data for immune cells that from  PBMCs, the central (bone marrow) and secondary lymphoid tissues (spleen and  lymph nodes) in different infection group, 61 groups in total

first: Zhongxue

last: Feng


title: Neoadjuvant BMS-813160, nivolumab, gemcitabine and nab-paclitaxel for pancreatic cancer

first: David

last: DeNardo

address: 660 S Euclid Ave

summary: Background: Targeting tumor-associated macrophages through C-C chemokine receptor type 2 (CCRs) in pancreatic ductal adenocarcinoma (PDAC) improves the efficacy of chemotherapy and restores T cell immunity. Methods: We conducted a phase I/II single institution study (NCT03496662) combining chemotherapy gemcitabine and nab-paclitaxel (GnP), an oral CCR2/5 inhibitor BMS-813160 and nivolumab for four 28-day cycles as a neoadjuvant therapy for patients with borderline resectable (BR) or locally advanced (LA) PDAC. The recommended phase 2 dose (RP2D) of BMS-813160 was established in the standard 3+3 design. Primary end points were safety and objective response rate (ORR). Secondary end points included resection rate, progression-free survival (PFS) and overall survival (OS). Results: 8 patients were treated with GnP alone (control arm) and 31 patients (29 response evaluable) were treated at RP2D. No grade 3 or 4 toxicities attributed to nivolumab or BMS-813160 were identified. After all 4 cycles of study treatment (N=26), ORR was 35.7%, 16.7% among BR- and LA-PDAC patients, compared to 0% of control arm patients. 78.6% BR- and 16.7% of LA-PDAC patients who completed study treatment underwent surgical resection. For intent-to-treat analyses, BR-PDAC patients had a mPFS and mOS of 14.6 and 20.4 months respectively; and LA-PDAC patients had a mPFS and mOS of 14.7 and 17 months respectively. Single cell RNAseq analysis showed enhanced proliferating CD4 and CD8 T cells and gene signatures indicative of effector function. Conclusions: Neoadjuvant BMS-813160/nivolumab/GnP was well tolerated and appears to achieve higher ORR and resectability than historical data, warranting a larger randomized phase II study.

overall_design: Single-cell RNA sequencing of pancreas tissue biopsy samples before all treatment, and after one or two cycles of treatment.

first: Patrick

last: Grierson

first: Crystal

last: Wolf

first: Rama

last: Suresh

first: Andrea

last: Wang-Gillam

first: Benjamin

last: Tan

first: Lee

last: Ratner

first: Peter

last: Oppelt

first: Olivia

last: Aranha

first: Ashley

last: Frith

first: Katrina

last: Pedersen

first: John

last: Baer

first: Emily

last: Butka

first: Faiz

last: Ahmad

first: Nick

last: Boice

first: Amberly

last: Brown

first: Yifei

last: Xu

first: Jingxia

last: Liu

first: Kian-Huat

last: Lin


title: IGF2BP3 Promotes Stemness and Leukemogenesis in Acute Myeloid Leukemia

city: GuangZhou,GuangDong Province

first: Feng

last: Huang

state: China

institute: Guangzhou Laboratory

summary: N6-methyladenosine (m6A) is the most abundant internal modification in mRNA, and its modulators have been implicated in various biological processes. Here, we demonstrate that the mRNA m6A reader IGF2BP3 is highly expressed in human acute myeloid leukemia (AML), particularly in AML leukemia stem/initiating cells (LSCs/LICs). IGF2BP3 is required for the development and maintenance of AML and the self-renewal of LSCs/LICs but dispensable for normal hematopoiesis. IGF2BP3 exhibits promising anti-AML efficacy both in vitro and in vivo, providing new therapeutic strategies for targeting AML.

overall_design: To investigate the impact of IGF2BP3 on gene expression in AML cells, we establised IGF2BP3-knockdown MOLM13 cell lines by two shRNAs together with control MOLM13 cells (shNS), or IGF2BP3-degron U937 cell lines by treated with 5‘-Ph-IAA. We then performed RNA sequencing (RNA-seq) in IGF2BP3-knockdown, IGF2BP3-degron, and control  cells.

first: Hengyou

last: Weng

first: Huilin

first: Yushuai

last: Wang