title: Gene expression profiles of p16high and p16low cells in the gonadal adipose tissue of 18 month old mice [scRNA_Adipose_CD45]

status: Public on May 31 2024

city: Minato City, Tokyo

first: Teh-Wei

last: Wang

address: 4 Chome-6-1 Shirokanedai

country: Japan

institute: IMSUT

type: Expression profiling by high throughput sequencing

summary: We used scRNA-seq analysis to investigate the cell-to-cell communication in the gonadal adipose tissue of aging mice.

overall_design: We conducted the p16CreERT2-tdTomato mice of 18 month old  to study the function of cell-to-cell communication in the gonadal adipose tissue. The tdTomato-positive CD45- cells,  tdTomato-positive CD45+cells, tdTomato-negative CD45- cells and tdTomato-negative CD45+ cells were collected through FACS and processed for library preparation.

first: Xinyi

last: Zeng

first: Makoto

last: Nakanishi


title: DMF-ChIP-seq for Highly Sensitive and Integrated Epigenomic Profiling of Low-input Cells

city: Xiamen

first: Xing

last: Xu

address: 422, Siming South Road

country: China

institute: Xiamen University

summary: Mapping genome-wide DNA-protein interactions (DPIs) provides insights into the epigenetic landscape of complex biological systems and elucidates the mechanisms of epigenetic regulation in biological progress. However, current technologies in DPI profiling still suffer from high cell demands, low detection sensitivity and large reagent consumption. To address these problems, we developed DMF-ChIP-seq that builds on digital microfluidic (DMF) technology to profile genome-wide DPIs in a highly-efficient, cost-effective and user-friendly way. The entire workflow including cell pretreatment, antibody recognition, pA-Tn5 tagmentation, fragment enrichment and PCR amplification is programmatically manipulated on a single chip. Leveraging closed sub-microliter reaction volumes and a superhydrophobic interface, DMF-ChIP-seq presented higher sensitivity in peak enrichment than other current methods, with high accuracy (Pearson Correlation Coefficient (PCC) > 0.86) and high repeatability (PCC > 0.92). Furthermore, DMF-ChIP-seq was capable of processing the samples with as few as 3 cells while maintaining a high signal-to-noise ratio. By applying DMF-ChIP-seq, H3K27ac histone modification of early embryonic cells during differentiation was profiled for the investigation of epigenomic landscape dynamics. With the benefits of high efficiency and sensitivity in DPI analysis, the system provides great promise in studying epigenetic regulation during various biological processes.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: CUT&Tag epigenomic profiles of different cell lines

first: Mingyin

last: Li

first: Fanghe

last: Lin

first: Shanshan

last: Liang

first: Jia

last: Song

first: Chaoyong

last: Yang


title: Multi-Omics Analysis of Low-input cells by Omics Carrier Microparticle [transcriptome sequencing]

city: shanghai

first: Guoqiang

last: Zhou

address: Fudan University, Shanghai, 200438, China

institute: Fudan University School of Life Sciences

summary: Rare cells exert substantial impact on tissue physiology and pathology across a spectrum of biological realms. The elucidation of their physiological functions through multi-omics analysis is pivotal. Nonetheless, advancements in trace-level cell multi-omics technology are impeded by cellular loss during experimental procedures. Mitochondrial DNA (mtDNA) editing facilitates disease modeling of mitochondrial genetic disorders in cell lines and animals, with potential for future therapeutic applications. However, the absence of technology capable of simultaneously assessing the efficiency of mitochondrial gene editors and molecular phenotypes limits the development of mitochondrial gene editors and their in vivo therapeutic applications. Here, to address these challenges, we devised a novel omics carrier microparticle, abbreviated as OmicsCam for driving low-input cells multi-omics. OmicsCam consists of three key components: miniaturized open microparticles for multi-step biochemistry, an enlarged cell chamber boundary for streamline manipulation and minimize cell loss, and tunable permeability to ensure compatibility with key steps of magnetic separation in automated systems. By refining OmicsCam's manufacturing process, optimizing cell permeation conditions, and fine-tuning multi-omics library biochemistry, we demonstrated simultaneous assessment of mtDNA editing efficiency (mtDNA sequencing), post-editing cellular transcriptome, and chromatin accessibility in minute cell samples containing as few as 25,000 cells. Moreover, we can concurrently analyze off-target effects of gene editing. The OmicsCam platform offers a powerful way for microscale cell multi-omics analysis, enabling interrogation mitochondrial gene editing efficiency and molecular phenotypes in a unified framework. This offers a holistic perspective on the consequences of genetic manipulation within the mitochondrial genome, thereby advancing our understanding of mitochondrial biology and facilitating the development of precision therapeutics for mitochondrial disorders.

overall_design: We performed the transcriptome sequencing in both mitochondrial ND4 gene-edited cell lines and their corresponding wild-type counterparts.

first: Ting


title: N-acetylglucosamine (GlcNAc) sensor Ngs1 is essential for GlcNAc-involved biological control potential of fungal insecticide Beauveria bassiana

city: Fuzhou

first: Long-Bin

last: zhang

state: Fujian

address: Jianping Road

department: College of Biological Science and Engineering

institute: Fuzhou University

summary: Beauveria bassiana is a popular and eco-friendly biopesticide. Sensing N-acetylglucosamine (GlcNAc) , a building block of both insect exoskeleton and fungal cell wall, might play a vital role during B. bassiana pathogen-pest interaction. Previous studies in Candida albicans have demonstrated that a GlcNAc sensor (termed as Ngs1) was in response to GlcNAc signal sensing and transportation. Herein, we found a Ngs1 homology in B. bassiana, and reported the alteration of transcriptomic profiles between wild-type strain and Ngs1-deletion mutants grown on cuticle broth (CB) supplemented with 1% cuticle powder of Locusta migratoria exoskeleton, followed by shaking at 150 rpm for 5 days at 25 ℃.

overall_design: First, Ngs1-deletion mutants were constructed through homologous-recombination strategy; then, aliquots of 50 mL 10^6 conidia/mL cuticle broth (CB) containing 1% cuticle powder were incubated by shaking at 150 rpm for 5 days at 25 ℃. The cultures were centrifuged by 13,200×g for 1 min at 4 ℃. Hyphal cultures were collected and used for total RNA extracted; subsequently, the extracted RNA were sent to Novogene Company (Beijing, China) for RNA sequencing using Illumina Hiseq 2000.

last: Zhang

first: Wu-Wei-Jie


title: Effect of ZNF582 on gene expression in human head and neck squamous cell carcinoma

city: Beijing

first: Yaqing

last: Mao

address: No.22, Zhongguancun South Avenue

institute: Peking University School and Hospital of Stomatology

summary: Head and neck squamous cell carcinoma (HNSCC) is highly aggressive and associated with poor prognosis. The molecular mechanisms underlying HNSCC progression are important for the development of novel diagnostics and interventions. The bio-functional effects and potential mechanisms of ZNF582 are still unknown. We established HNSCC cell lines with ZNF582 overexpressed. High-throughput RNA-sequencing was performed to identify the altered signaling pathways in HNSCC with ZNF582 overexpression.

overall_design: To investigate the effect of ZNF582 on gene expression in human head and neck squamous cell carcinoma, HN6 cell line with ZNF582 overexpressed were established, and high-throughput RNA-sequencing was performed to identify the altered signaling pathways.

first: Shuo

last: Liu

first: Lingfei

last: Jia

first: Xin

last: Peng


title: Gene expession profiles of p16high and p16low adipocyte progenitor cells of gonadal adipose tissue in the cancer cachexia mouse model

first: Teh-Wei

summary: We used bulk RNA-seq analysis to investigate the gene expression patterns of p16high adipocyte progenitor cells compared with p16low adipocyte progenitor cells in the gonadal adipose tissue of tumor bearing mice.

overall_design: We examined the p16CreERT2-tdTomato mice combined with allograft model of PDAC to study the function of p16high adipocyte cells of gonadal adipose tissue in the cancer cachexia mouse model. The tdTomato-positive and negative adipocyte progenitor cells were collected through FACS and processed for library preparation.


title: Human γδ T cells in diverse tissues exhibit site-specific maturation dynamics across the lifespan

city: New York City

first: Joshua

middle: Ian

last: Gray

state: New York

address: 630 168th Street

department: CCTI

country: USA

institute: Columbia University

summary: During ontogeny, γδ T cells emerge from the thymus and directly seed peripheral tissues for in situ immunity, though their functional role in humans is largely defined from blood. Here, we analyzed the phenotype, transcriptome, function, and repertoire of human γδ T cells in blood, mucosal and lymphoid tissues from 176 donors across the lifespan, revealing distinct profiles in children compared to adults. In early life, clonally diverse Vd1 subsets predominate across blood and tissues, comprising naïve and differentiated effector and tissue repair functions, while cytolytic Vd2 subsets populate blood, spleen and lungs. Over age, both subsets exhibit clonal expansions disseminated across sites and express elevated cytolytic signatures. In adults, Vd2 cells predominate in blood, while Vd1 cells are enriched across tissues and express residency profiles. These results indicate that antigenic exposures over childhood drive the functional evolution and tissue compartmentalization of γδ T cells, leading to age-dependent roles in immunity.

overall_design:
Adult and pediatric tissues were processed to a single cell suspension as described in the methods. Gd T cells were isolated by fluorescence-activated cellular sorting (FACS). DNA was isolated from sorted cell pellets using the DNA micro kit (Qiagen) and DNA concentrations were assessed using the NanoDrop (Thermo Scientific). TCRγ and TCRα/δ chains were amplified and sequenced to the survey-level by Adaptive Biotechnologies (Seattle, WA) using the ImmunoSEQ™ assay and their preprocessing pipeline which also removes PCR and sequencing errors.

***************************************************************
Adaptive Biotechnologies does not release raw data.
***************************************************************

middle: I

first: Donna

middle: L

last: Farber


title: Mapping genome-wide binding profile of ChCUC1 by DNA Affinity Purification sequencing (DAP-seq)

city: Cologne

first: Miltos

last: Tsiantis

state: North Rhine-Westphalia

address: Carl-von-Linné-Weg, 10

department: Department of Comparative Development and Genetics

country: Germany

institute: Max Planck Institue for Plant Breeding Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The mechanism underlying CUC genes regulating leaf marginal patterning remains largely unknown. To this end, we employed DAP-seq to identify the downstream regulating genes of ChCUC1. The aim of this project is to map genome-wide CUC genes binding sites.

overall_design: A genomic DNA library is first prepared according to general library construction methods that include fragmentation of genomic DNA followed by ligation with Illumina-based sequencing adaptors. Oxford genomic DNA were used for library construction. To allow for high-throughput expression of affinity-tagged ChCUC1, ChCUC1 open reading frames (ORFs) are transferred to the Gateway-compatible pIX-HALO expression vector, which contains an N-terminal HaloTag affinity tag sequence. The pIX-HALO-CUC construct is then expressed using plant (wheat germ)-based in vitro transcription/translation coupled system. Purified proteins are then combined with the adaptor-ligated genomic DNA library and can bind to genomic DNA fragments in a sequence-specific manner. After washing away the unbound fragments, the beads are boiled to denature the protein and release the DNA into solution. This DNA is then PCR-amplified to attach multiplexing index sequences and enrich for TF-bound fragments. Samples are pooled and the resulting final library is sequenced using an Illumina sequencing platform.

first: Ziliang

last: Hu


title: Effect of ChCUC1 induction on gene expression in Cardamine hirsuta leaf development

summary: Here we investigate the function of CUC1(CUP-SHAPED COTYLEDON1) in the diversification of leaf forms between simple-leaved Arabidopsis thaliana and compound-leaved Cardamine hirsuta. CUC transcription factors are conserved regulators in leaf margin dissection and leaflet formation. ChCUC1, ChCUC2 and ChCUC3 function redundantly and are required for the leaflet formation in C. hirsuta. Recently we discovered that ChCUC1 has species species-specific expression in young leaves of C.hirsuta. Moreover, interspecies gene transfer of ChCUC1 allele into A.thaliana is sufficient to increase leaf complexity. On this basis, we hypothesize that redeployment of ChCUC1 in leaves contributes to the formation of leaflets instead of serrations. However, the mechanism underlying ChCUC1 regulating cell division, cell polarity, cytoskeleton and thus leaf marginal patterning remains elusive. To this end, we make use of chromatin immunoprecipitation sequencing(ChIP-seq), transcriptomic, comparative genetics and advanced imaging approaches to identify the downstream regulating genes of ChCUC1.

overall_design: To this end, we generated RCOp::LhG4:GR; Op::ChCUC1:Venus transgenic line in C. hirsuta. We harvested 12-days-old seedlings harboring RCOp::LhG4:GR; Op::ChCUC1:Venus, which were incubated in liquid MS medium with 10 μM Dexamethasone (induction) or 0.1% DMSO (control). Seedlings without cotyledons, roots, and mature leaves were harvested at 2, 4, 6, and 8 hours after treatment. For each replicate, twenty seedlings were collected for RNA isolation. Three independent replicates treated with Dexamethasone were used as the experimental group, and three independent replicates treated with DMSO were used as the control group.


title: High Multiplex Translocation Sequencing Reveals the Versatile Role of Condensin II in Chromosomal Translocations

city: La Jolla

first: Amir

last: Gamliel

state: CA

address: 9500 Gilman Dr.

department: Medicine

institute: University of California San Diego

summary: Chromosomal translocations play pivotal roles in various physiological and pathological processes, such as immunoglobulin production and tumor progression; however, the infrequency of chromosomal translocation events has impeded the exploration of the underlying mechanisms. To tackle this challenge, we devised a strategy to report and enrich cells with translocations in vitro, in conjunction with a novel method termed High Multiplex Translocation Sequencing (HMTS), to capture genome-wide translocations from multiple bait regions simultaneously. Analysis of HMTS data unveiled a preference for translocations to occur at Topologically Associating Domain (TAD) boundaries, and experimental disruption of the TAD boundary indeed led to a reduction in translocation frequency, exemplified by translocations involving ERG. Knockdown of Cohesin or condensin II was observed distinct roles in translocations. Cohesin deficiency promoted long-distance translocations, while condensin II deficiency promoted short distance translocation, inside TAD, and decreased intra-chromatin long-distance translocation, particularly at TAD boundaries. For inter-chromatin, although condensin II deficiency also decreased the translocation at TAD boundaries, and highly transcription regions while paradoxically slightly increased inter-chromatin translocation ratio, suggesting that condensin II physiologically mediated inter-chromatin  interaction at TAD boundary regions but simultaneously restricted interaction from other regions, such as centromere. Our new translocation sequencing method revealed the versatile role of condensin II in controlling intra-chromatin short-distance, long-distance, and inter-chromosome translocations.

overall_design: We sought to investigate whether disruption of TAD boundaries would affect the translocation frequency of genes located near TAD boundaries. To address this question, we deleted a fragment containing two CTCF-peaks near the TAD boundary of ERG gene. These two CTCF motifs are oriented in a convergent manner with neighboring CTCF motifs. We confirmed the deletion of the CTCF peak region by PCR analysis and Sanger sequencing. Subsequenty, we used in situ Hi-c to confirm whether the TAD boudnary where disrupted following the deletion of the pair of CTCF peaks.

first: Wubin

last: Ma

first: Dario

last: Meluzzi

first: Michael

middle: G

last: Rosenfeld


title: Prevention of cyclophosphamide-induced immune suppression by polysaccharides from Apocynum Venetum flowers via enhancing immunity, reducing oxidative stress and regulating gut microbial in mice

city: Kaifeng

first: zhao

last: qingchun

address: North section of Jinming Avenue, Kaifeng City, Henan Province

institute: National R&D Center for Edible Fungus Processing Technology

summary: Introduction: Emerging proof suggests that Apocynum venetum flowers polysaccharides (AVFP) has immunomodulatory effects in vitro. However, the action mechanism of AVFP is still unclear in vivo. The purpose of this study is to probe into the potential mechanism of AVFP on immunosuppressed mice through investigating organ index, cytokine levels, anti-oxidative stress capacity, transcriptomics and gut microbiota. Methods: Immunocompromised mouse model induced by cyclophosphamide (CXT) was divided into 6 groups. Enzyme-labeled method, HE, transcriptomics and high-throughput sequencing were used to detect the regulatory effects of AVFP on immunocompromised mice, as well as the function of AVFP on the concentration of short-chain fatty acids (SCFAs) by high-performance liquid chromatographic analysis (HPLC). Pearson was used to analyze the correlation between intestinal microbiota and biochemical indexes. Results: The experimental results illustrated that AVFP has protective effects against CXT-induced immunosuppression in mice via prominently increasing organ index, levels of anti-inflammatory factors in serum as well as enhancing antioxidant capacity of the liver. Meanwhile, it could also signally decrease the level of pro-inflammatory cytokines in serum, the activity of transaminase in serum and the content of free radicals in liver. Transcriptomics results discovered that AVFP could play a role in immune regulation via participating in NF-κB signaling pathway, regulating the immune-related genes Bcl3, Hp, Lbp, Cebpd, Gstp2 and Lcn2. Intestinal microbiota results illustrated that AVFP could increase abundance of beneficial bacteria, reduce abundance of harmful bacteria, while dramatically improved the content of SCFAs, modulated immune responses and improved host metabolism. Spearman analysis further assessed the correlation between gut microbiota and biochemical indicators. Conclusion: These findings demonstrated that AVFP could enhance the immune effects of the immunosuppressed mice and improve the body's ability to resist oxidative stress.

overall_design: Transcriptomic analysis was performed on 9 spleen samples from Control, Mod and AVFP-M groups. Firstly, took 60 mg of tissue and pulverized it into powder in liquid nitrogen, centrifuged after homogenizing, added 0.3 mL of isoamyl alcohol to the supernatant, and centrifuged. After that, 1 mL75% ethanol was added to wash twice, and then centrifuged. In the end, DEPC-treated water was added to dissolve RNA, followed by identification and quantification of total RNA using Nano Drop and an Agilent 2100 Bioanalyzer.

first: Qingchun

last: Zhao

first: Jinmei

last: Wang

first: Haiyang

last: Liang


title: Aged skin exacerbates experimental osteoarthritis via enhanced IL-36R signaling

city: Guangzhou

first: Dalin

last: Chen

address: 295 Changxing Road

institute: Guangdong Institute of Orthopedics

summary: To investigate  skin aging is an important driver of experimental osteoarthritis(OA) progression in mice via enhanced IL-36 receptor (IL-36R) signaling. we generated epidermis keratinocyte conditional knockout mice (IL-36Ra-cKO) with topical administration of capsid-mutant Adeno-associated virus 2 (AAV2) vector23 encoding Cre recombinase (AAV2-Cre) to IL-36Rafl/fl mice.  Subsequently, epidermal skin tissues were collected from IL-36Rafl/fl and IL-36Ra-cKO mice for RNA sequencing analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for IL-36Rafl/fl and IL-36Ra-cKO mice epidermal skin tissues

first: Chong

first: Changsheng

last: Yang

first: Liangyu

first: Panpan

first: Zilin

last: Zou

first: Honghao

last: Li

first: Yun

last: Xiao

first: Junfeng

last: Wu

first: Qinwei

last: Cheng

first: Chengliang

first: Ee

last: Ke

first: Bin

last: Huang

first: Xiaochun

last: Bai

first: Kai


title: Targeting Immunoproteasome in Macrophages Suppresses M1 Polarization and Ameliorates Experimental Emphysema via Activating NRF1 and NRF2-P62 Axis [Cut & Tag]

city: Shenzhen

first: xing

last: shi

state: Guangdong

address: Luohu

department: Department of Respiratory and Critical Care Medicine

institute: Shenzhen Institute of Respiratory Disease

summary: Chronic obstructive pulmonary disease (COPD) stands as the prevailing chronic airway ailment, characterized by chronic bronchitis and emphysema. Current medications fall short in treatment of these diseases, underscoring the urgent need for effective therapy. Prior research indicated immunoproteasome inhibition can alleviate various inflammatory diseases by modulating immune cell functions. However, its therapeutic potential in COPD remains largely unexplored. Here, we observed elevated expression of immunoproteasome subunits LMP2 and LMP7 in bronchoalveolar lavage (BAL) macrophages collected from mouse with LPS/elastase-induced emphysema and M1 polarized macrophages in vitro. Subsequently, intranasal administration of the immunoproteasome-specific inhibitor ONX-0914 significantly mitigated emphysema-associated airway inflammation and improved lung function in mice, by suppressing M1 macrophage polarization. Mechanistically, ONX-0914 activated autophagy, and endoplasmic reticulum (ER) stress was not necessary for ONX- 0914-induced M1 suppression. Intriguingly, ONX-0914 upregulated the autophagy receptor p62/SQSTM1, which proved vital for the inhibitory effect of ONX-0914 on M1 polarization. Additionally, our research identified that the nuclear factor erythroid 2-related factor-2 (NRF2), but not NRF1, was responsible for the induction of p62. Finally, silencing both NRF1 and NRF2 partially counteracted ONX-0914-mediated M1 polarization inhibition. In summary, our findings suggest that targeting the immunoproteasome in macrophages holds promise as a therapeutic strategy for emphysema.

overall_design: The CUT&Tag sequencing for NRF2 binding sites analysis in mouse bronchoalveolar lavage macrophages M1, and M1+ONX-0914.


title: Analysis of MLLT3 genomic distribution and related chromatin features in cultured cord blood hematopoietic stem-progenitor cells [ChIP-seq]

city: Los Angeles

first: Vincenzo

last: Calvanese

address: 615 Charles E Young Dr S

institute: UCLA

summary: MLLT3 binds to TSS of genes active in CB-HSPC.

overall_design: MLLT3 was immunoprecipitated from sonicated chromatin (3.5 to 5M cells per IP). DNA was amplified with Nugen Ovation V2 kit and sequenced in single end 50bp in multiplexed run on an Illumina HiSeq4000 instrument.

first: Anastasia

last: Vavilina

first: Iman

last: Fares

first: Hanna

middle: K

last: Mikkola


title: RNA sequencing analysis of the genes regulated by ZntR in Vibrio parahaemolyticus.

city: Yangzhou

first: Chengkun

last: Zheng

address: No.48 East Wenhui Road

institute: Yangzhou university

summary: The transcriptome of the wild type strain and ΔzntR of Vibrio parahaemolyticus was compared by RNA sequencing analysis. The data revealed that some genes, such as zntA, were significantly differentially expressed in the mutant.

overall_design: The transcription profiles of the ΔzntR mutant grown in Tryptic Soy Broth were compared with that of the wild type strain. Each strain contains three biological replications.

first: Mengxian

last: Wang

first: Yimeng

last: Zhai


title: IRE1α-XBP1 sustains cytokine responses of group 3 innate lymphoid cells in inflammatory bowel disease

city: St. Louis

first: Siyan

last: Cao

state: MO

address: 660 S Euclid Ave

department: Gastroenterology

institute: Washington University in St. Louis

summary:
Group 3 innate lymphoid cells (ILC3s) are key players in intestinal homeostasis. Endoplasmic reticulum (ER) stress is linked to inflammatory bowel disease (IBD). Herein, we used cell culture, novel mouse models, and human specimens to examine if ER stress in ILC3s impacts IBD pathophysiology. We show that mouse intestinal ILC3s exhibited a 24h-rhythmic expression pattern of the master ER stress response regulator, IRE1α-XBP1. Proinflammatory cytokine IL-23 selectively stimulated IRE1α-XBP1 in mouse ILC3s through mitochondrial reactive oxygen species (mtROS). IRE1α-XBP1 was activated in ILC3s of mice exposed to experimental colitis and in inflamed human IBD specimens. Mice with Ire1α deletion in ILC3s (Ire1αΔRorc) showed reduced expression of ER stress response and cytokine genes including Il22 in ILC3s and were highly vulnerable to infections and colitis. Administration of IL-22 counteracted their colitis susceptibility. In human ILC3s, IRE1 inhibitors suppressed cytokine production, which was upregulated by an IRE1 activator. Moreover, the frequencies of intestinal XBP1s+ ILC3s in Crohn’s disease patients before administration of ustekinumab, an anti-IL-12/IL-23 antibody, positively correlated with response to treatment. We demonstrate that a non-canonical mtROS-IRE1α-XBP1 pathway augments cytokine production by ILC3s and identify XBP1+ ILC3s as a potential biomarker for predicting response to anti-IL-23 therapies in IBD.
Group 3 innate lymphoid cells (ILC3s) have recently emerged as important regulators and potential drug targets for IBD. However, the response of ILC3s to environmental stimuli during intestinal inflammation remains elusive. IRE1a-XBP1 serves as the regulatory hub of the unfolded protein response (UPR) that plays a vital role in intestinal inflammation.

overall_design: ILC3s of mice with genotypes Ire1f/f and Ire1f/f,Rorc-Cre that were exposed to experimental colitis.


title: Subungual melanoma and atypical lentiginous melanocytic proliferations: New insights for the use of molecular analyses

city: nice

first: Ilaria

last: Di Mauro

address: 28 avenue de valombrose

country: France

institute: CHU de Nice

summary: In the study, researchers investigated acral melanomas, particularly subungual melanomas (SUM), which are primarily characterized by whole genome copy number variations (CNV) such as amplifications, gains, and losses. Previous research has utilized various cytogenetic or molecular analyses ranging from targeted methods focused on specific genes to comprehensive whole genome and whole transcriptome sequencing techniques. To differentiate between malignant and benign lesions, fluorescence in situ hybridization (FISH) methods have been commonly employed, utilizing probes targeting genes like CCND1, RREB1, MYB, CDKN2A, or MYC either individually or in combination.In this study a Comparative Genomic Hybridization on array (array-CGH) was performed to detect whole genome CNV. This approach aimed to improve the classification of malignant and benign lesions in a cohort consisting of 31 SUM cases and 8 subungual lentiginous melanocytic proliferations with or without atypia.

overall_design:
The study employed a Comparative Genomic Hybridization on array (array-CGH) methodology to identify whole genome copy number variations (CNV) within a cohort comprising 31 cases of subungual melanomas (SUM) and 8 cases of subungual lentiginous melanocytic proliferations, with or without atypia.
Please note that CGH/SNP-array showed CNA only in 14 samples of SUM. For the remaining cases, no quantitative abnormalities have been detected, and therefore they are not included in the records.

first: Christophe

last: Perrin

first: Bérengère

last: Dadone-Montaudié


title: RNA-seq of MLLT3-L and MLLT3-S overexpressing cultured HSPC, compared to non-overexpressing and uncultured FL-HSPC

summary: MLLT3 preserves the FL-HSPC gene expression signature in culture.

overall_design:
FL-HSPC were infected with Control or MLLT3-OE lentivirus and cultured for 4 weeks on OP9M2. Sorted HSPC were profiled before (n=3) or after (n=6) culture.

The raw data for reanalysis Samples GSM7996837-GSM7996840 are included in BioProject PRJNA437152.


title: Genomic profiles and survival prognosticators in African-American patients with acute myeloid leukemia

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: Genomic profiles and prognostic biomarkers in patients with acute myeloid leukemia (AML) from ancestry diverse populations are underexplored. We analyzed the exomes and transcriptomes of 100 Black patients with AML (Alliance) and compared somatic mutation frequencies with those of 323 White patients (BeatAML). Seventy-three percent of 162 recurrent gene mutations identified in Black patients, including a novel PHIP alteration detected in 7% of patients, were found in only ≤1 White patient. Black patients with myelodysplasia-related AML were younger than White patients suggesting intrinsic and/or extrinsic dysplasia-causing stressors. On multivariable outcome analyses of Black patients, NPM1 and NRAS mutations associated with inferior disease-free and IDH1/2 mutations with reduced overall survival. Inflammatory profiles, cell type distributions and transcriptional profiles differed between Black and White NPM1-mutated patients. Incorporation of ancestry-specific risk markers into the 2022 European LeukemiaNet genetic-risk stratification changed risk-group assignment for one-third of Black patients and improved their outcome prediction.

overall_design:
Single-cell RNA sequencing studies of Black and White NPM1-mutated patients provide first evidence of differences in cell-type distribution and differentially activated pathways for patients of different ancestry.
**** The raw sequencing data will be available in dbGAP***

first: Andrew

last: Stiff

first: Bailee

middle: N

last: Kain

first: Maarten

last: Fornerod

first: H

last: Grimes

first: Elaine

middle: R

last: Mardis

first: Ann-Kathrin

last: Eisfeld


title: Carnitine Palmitoyltransferase 1 facilitates fatty acid oxidation in a noncell autonomous manner [TKO_RNAseq]

city: Baltimore

first: Michael

middle: J.

last: Wolfgang

state: MD

address: 855 N Wolfe Street

department: Institute for Basic Biomedical Sciences

institute: The Johns Hopkins University School of Medicine

summary: Mitochondrial fatty acid oxidation is facilitated by the combined activities of Carnitine Palmitoyltransferase 1 and Carnitine Palmitoyltransferase 2 which generate and utilize acylcarnitines respectively.  We compared the response of mice with liver specific deficiencies in Cpt1a and Cpt1b, Cpt2, or the triple deletion of all three acyltransferases. We discovered that they display unique metabolic, physiological and molecular phenotypes.  The loss of Cpt1a and Cpt1b or Cpt2 resulted in particular transcriptional outputs in hepatocytes. We show that much of the transcriptional signature is suppressed when deleting both Cpt2 and Ppara, showing the contribution of Ppara. Our results utilize stringent genetic mouse models to characterize the differential phenotypes of mice lacking Cpt1a and Cpt1b or Cpt2 and also show the contribution of a major transcription factor, Ppara.

overall_design: To characterize transcriptional contribution of Cpt1 or Cpt2, littermate control mice and mice lacking Cpt1a and Cpt1b, Cpt2, all three Cpt1a Cpt1b and Cpt2, or Cpt2 and Ppara were fasted for 24 hours and livers were collected for RNA-sequencing by Novogene Corporation Inc.

first: Joseph

last: Choi

first: Danielle

last: Smith

first: Susanna

last: Scafidi

first: Ryan

last: Riddle


title: Gene expression profiles of p16high and p16low adipocyte progenitor cells in the gonadal adipose tissue of 18 month old mice [scRNA_Adipose]

city: Minato City, Tokyo

first: Teh-Wei

last: Wang

address: 4 Chome-6-1 Shirokanedai

institute: IMSUT

summary: We used scRNA-seq analysis to investigate the expression profiles of p16high adipocyte progenitor cells compared with p16low adipocyte progenitor cells in the gonadal adipose tissue of aging mice.

overall_design: We conducted the p16CreERT2-tdTomato mice of 18 month old  to study the function of p16high adipocyte progenitor cells in the gonadal adipose tissue. The tdTomato-positive CD31- CD45- cells and tdTomato-negative CD31- CD45- cells were collected through FACS and processed for library preparation.

first: Xinyi

last: Zeng

first: Makoto

last: Nakanishi


title: Targeting Immunoproteasome in Macrophages Suppresses M1 Polarization and Ameliorates Experimental Emphysema via Activating NRF1 and NRF2-P62 Axis

first: xing

last: shi

overall_design:
The RNA sequencing for mouse peritoneal macrophages M0, M0+ONX-0914, M1, M1+ONX-0914, M2, and M2+ONX-0914.

***Submitters state that raw data has been lost and thus is not provided******


title: Carnitine Palmitoyltransferase 1 facilitates fatty acid oxidation in a noncell autonomous manner [CPT1a_RNAseq]

summary: Mitochondrial fatty acid oxidation is facilitated by the combined activities of Carnitine Palmitoyltransferase 1 and Carnitine Palmitoyltransferase 2 which generate and utilize acylcarnitines respectively.  We compared the response of mice with liver specific deficiencies in the liver enriched Cpt1a or the ubiquitous Cpt2 and discovered that they display unique metabolic, physiological and molecular phenotypes.  The loss of Cpt1a or Cpt2 resulted in the induction of the muscle enriched isoenzyme, Cpt1b, in hepatocytes in a Ppara dependent manner. Primary component analysis also revealed overall differential grouping between mouse with deletions of either Cpt1a or Cpt2. Our results utilize stringent genetic mouse models to elucidate that the sequential steps to facilitate mitochondrial fatty acid oxidation may have other factors.

overall_design:
To characterize transcriptional contribution of Cpt1a or Cpt2, littermate control mice and mice lacking either Cpt1a or Cpt2 were fasted for 24 hours and livers were collected for RNA-sequencing by Novogene Corporation Inc.
Cpt2 samples were submitted to GEO previously in GSE240396.


title: Analysis of MLLT3 genomic distribution and related chromatin features in cultured cord blood hematopoietic stem-progenitor cells, and RNA-seq of MLLT3-L and MLLT3-S overexpressing cultured HSPC compared to non-overexpressing and uncultured FL-HSPC

first: Vincenzo

last: Calvanese

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

overall_design: Refer to individual Series


title: Single-Cell RNA Sequencing Investigation of the Duodenal Mucosa in Canine Chronic Inflammatory Enteropathy and Health

city: Fort Collins

first: Dylan

middle: T

last: Ammons

state: CO

address: 200 W Lake St

department: Clinical Sciences

institute: Colorado State University

summary: We used single-cell RNA sequencing to characterize the heterogeneity duodenal tissue in healthy and chronic inflammatory enteropathy (CIE) affected dogs.

overall_design: The complete dataset consists of 150bp paired end sequencing data obtained using a 10x Genomics single-cell RNA sequencing platform (Chromium Next GEM Single Cell 3ʹ Kit v3.1 protocol). The final dataset consists of data from 7 biologically distinct dogs (3 healthy and 4 diagnosed with CIE).

first: Steven

last: Dow


title: FTO alleviates psoriasis-like dermatitis through the regulation of FN1

city: Nanjing

first: Zhang

last: Min

address: Jiangwangmiao Street, Xuanwu District

institute: Hospital for Skin Diseases

summary: FTO was found to inhibit keratinocyte inflammation and proliferation in both in vitro and in vivo settings, independent of m6A demethylase function. RNA-seq was used to identify fibronectin (FN1,FN) as a potential target for FTO. FTO does not rely on demethylase activity to decrease FN1 expression. The anti-inflammatory and anti-proliferative effects of FTO on psoriasis partly depend on FN1. FTO may regulate the skipping of EDA exon in FN1.

overall_design: RNA sequencing was conducted on HaCaT cells that were either overexpressing an empty vector, wild-type FTO, or a mutant type that disrupts the demethylase activity.

first: Min

last: Zhang

first: Chao

last: Luan

first: Jiaan

first: Kun

last: Chen


title: Human regulatory memory B cells defined by expression of TIM-1 and TIGIT are dysfunctional in Multiple Sclerosis.

city: Boston

first: Shannan

last: Ho Sui

address: 401 Park Drive

institute: Harvard

summary: Regulatory B cells (Bregs) play a pivotal role in suppressing immune responses, yet there is still a lack of cell surface markers that can rigorously identify them. In mouse models for multiple sclerosis (MS), TIM-1 or TIGIT expression on B cells is required for maintaining self-tolerance and regulating autoimmunity to the central nervous system. Here we investigated the activities of human memory B cells that differentially express TIM-1 and TIGIT to determine their potential regulatory function in healthy donors and patients with relapsing-remitting (RR) MS. FACS-sorted TIM-1+/-TIGIT+/- memory B (memB) cells co-cultured with allogenic CD4+ T cells were analyzed for proliferation and induction of inflammatory markers using flow cytometry and cytokine quantification, to determine Th1/Th17 cell differentiation. Transcriptional differences were assessed by SMARTSeq2 RNA sequencing analysis.  TIM-1-TIGIT- double negative (DN) memB cells strongly induce T cell proliferation and pro-inflammatory cytokine expression. The TIM-1+ memB cells enabled low levels of CD4+ T cell activation and gave rise to T cells that co-express IL-10 with IFNg and IL-17A or FoxP3. T cells cultured with the TIM-1+TIGIT+ double positive (DP) memB cells exhibited reduced proliferation and IFNg, IL-17A, TNFa, and GM-CSF expression, and exhibited strong regulation in Breg suppression assays. The functional activity suggests the DP memB cells are a bonafide Breg population. However, MS DP memB cells were less inhibitory than HC DP memB cells. A retrospective longitudinal study of anti-CD20 treated patients found that post-treatment DP memB cell frequency and absolute number were associated with response to therapy. Transcriptomic analyses indicated that the dysfunctional MS-derived DP memB/Breg population exhibited increased expression of genes associated with T cell activation and survival (CD80, ZNF10, PIK3CA), and had distinct gene expression compared to the TIGIT+ or TIM-1+ memB cells. These findings demonstrate that TIM-1/TIGIT expressing memory B cell subsets have distinct functionalities. Co-expression of TIM-1 and TIGIT defines a regulatory memory B cell subset that is functionally impaired in MS.

overall_design: Peripheral blood was obtained from RRMS (Natalizumab treated) patients and age- and sex-matched healthy volunteers with signed informed consent as approved by the Institutional Review Board of Brigham and Women’s Hospital. Peripheral blood mononuclear cells (PBMCs) were isolated, incubated with fluorochrome-labelled monoclonal antibodies, and then sorted on FACS Aria III. 1000 cells of each TIM-1/TIGIT expressing memory B cells were sorted and collected. The plates were stored at -80 C and processed by the BROAD Institute Genomics platform for Smart-Seq2 RNA-seq. The Trombetta protocol was used sequentially to clean up the lysate, reverse transcribe the mRNA, amplify the transcriptome, PCR clean up, Nextera XT sequencing-library construction, and DNA SPRI bead cleanup. Illumina NextSeq500 was used to run 2 × 38bp paired sequencing at the BROAD Genomics platform. Sequencing reads were quality-controlled, mapped and quantified using the bcbio-nextgen bulk RNA-seq pipeline (version 1.2.8-1c563f1).


title: Targeting Immunoproteasome in Macrophages Suppresses M1 Polarization and Ameliorates Experimental Emphysema via Activating NRF1 and NRF2-P62 Axis [ATAC-Seq]

overall_design: The Assay for Transposase-Accessible Chromatin with Sequencing (ATAC-Seq) for mouse bronchoalveolar lavage macrophages M1, and M1+ONX-0914.


title: Contribution of DNA methylation profiling in the classification of TRIO::TERT sarcomas

first: Ilaria

last: Di Mauro

summary: DNA methylation profiling has emerged as a valuable tool for tumor classification, exemplified by the German Cancer Research Center's creation of online classifiers for CNS tumors and sarcomas. Identification of rare molecular events, such as TRIO::TERT fusion in undifferentiated sarcomas, through DNA methylation profiling and transcriptome analysis aims to define distinct molecular subgroups within sarcomas of uncertain diagnosis, potentially improving classification and treatment strategies.In this study, we present 8 cases of sarcomas characterized by TRIO::TERT fusion, establishing it as a distinct molecular subtype of sarcomas. This fusion represents a consistent molecular feature across all analyzed tumors, suggesting its pivotal role in sarcomatogenesis. Identifying TRIO::TERT transcript sarcoma as a new tumor type may enhance diagnostic strategies for improved patient management.

overall_design: screening of 5 cases of TRIO-TERT sarcoma by SNP array with affymetrix platform

first: Charlotte

last: Paoli

first: Philipp

last: Sievers

first: Franck

last: Tirode

first: Daniel

last: Pissaloux

first: Marie

last: Karanian

first: Isabelle

last: Monticelli

first: Martin

last: Hasselblatt

first: Julien

last: Boyer

first: Esma

last: Saada-Bouzid

first: Fanny

last: Burel-Vandenbos

first: Bérengère

last: Dadone-Montaudié


title: Mapping genome-wide binding profile of ChCUC1 by Chromatin Immunoprecipatation sequencing (ChIP-seq)

first: Miltos

last: Tsiantis

summary: The mechanism underlying CUC genes regulating leaf marginal patterning remains largely unknown. To this end, we employed MOBE-ChIP-seq to identify the downstream regulating genes of ChCUC1. The aim of this project is to map genome-wide binding sites of ChCUC1 gene .

overall_design: Low input ChIP-seq

first: Ziliang

last: Hu


title: Histone acetylation by HBO1 activates Wnt/β-catenin signaling to promote leukemogenesis in B-cell acute lymphoblastic leukemia

first: Ning

last: Chang

address: 253 Industrial Avenue

institute: Zhujiang Hospital, Southern Medical University

summary:
To investigate the underlying mechanism by which HBO1 promotes B-ALL progression, we established NALM-6 cell lines in which HBO1 has been knocked down by shRNA.
We then performed gene expression profiling analysis of NALM-6/shHBO1 cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NALM-6 cells and its KD derivatives (shHBO1).

first: Hao

last: Wang

first: Yingqi

last: Qiu

first: Honghao

last: Zhang

first: Yuhua

last: Li


title: Genome-wide analysis of the histone modification H3K9ac in Oryza sativa infested with Spodoptera frugiperda

city: 福州

first: Rong

middle: rong

last: Xue

state: 福建

address: 福建省福州市仓山区

institute: 福建农林大学

summary: The histone 3 lysine 9 acetylation (H3K9ac) is an epigenetic marker widely distributed in plant genome, which could eThe histone 3 lysine 9 acetylation (H3K9ac) is an epigenetic marker widely distributed in plant genome, which could enhance gene transcription involved in stress-responsive gene expression. The physiological and molecular mechanisms underlying plant responses to insects are being increasingly studied, while epigenetic modifications such as histone acetylation and their potential regulation at the genomic level of transcription of hidden genes in plants damaged by insects remain largely unknown. In current study, we provided the genome-wide profiles of H3K9ac in rice (Oryza sativa) infested by fall armyworm (Spodoptera frugiperda, FAW) using chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-seq). RNA-seq data revealed that 3269 and 4609 genes were up-regulated at 3 h and 12 h after infestation with FAW, respectively.  ChIP-Seq analysis revealed 1617 and 2617 genes modified by H3K9ac in rice infested with FAW at 3 h and 12 h, respectively, and H3K9ac was mainly enriched in the transcription start sites of genes.

overall_design: Examination of H3K9ac histone modifications in whole rice seedlings

first: Rongrong

first: Ruiqing

last: Guo

first: Jie


title: The miRNA stabilized into the blood through the gastrointestinal system of mice after intragastric administration of Lycium chinense Mill

first: Xiaozhu

last: Tang

address: Xianlin Road

institute: Nanjing University of Chinese University

type: Non-coding RNA profiling by high throughput sequencing

summary: Osteoporosis, the leading cause of death among older people, is characterized by low bone mineral density (BMD) and reduced bone strength. Here, we report that miR162a, a Lycium chinense Mill-encoded microRNA, directly targets bone marrow and inhibits osteoporosis. MiR162a is stable in mice’s stomach and synthetic miR162a agomir could pass through mouse Gastrointestinal tract (GI) tract and enter the sera, bone marrow and organs.

sample_organism:
Mus musculus
Lycium chinense

platform_organism:
Mus musculus
Lycium chinense

overall_design: To verify whether plant miRNA could be absorbed into blood of mice, we intragastric gavaged C57 BL/6J mice with Lycium chinense Mill at a dose of 10 mL/kg. After 14 days, the blood was drawn and subjected to Illumina deep-sequencing technology


title: Dystrophin Deficiency Derives Phenotype Switching in Vascular Smooth Muscle Cells

city: Tampa

first: Wanling

last: xuan

state: FL

address: 12901 Bruce B Down Blvd

department: DPS

institute: University of South Florida

summary: To investigate how dystrophin deficiency affects phenotype of vascular smooth muscle cells

overall_design: Comparative gene expression profiling analysis of RNA-seq data for normail iPS cells derived vascular smooth muscle cells and DMD iPS cells derived vascular smooth muscle cells

last: Xuan

first: Muhammad

last: Ashraf


title: Massively parallel saturation genome editing of an essential mitochondrial targeting sequence

city: Ann Arbor

first: Anthony

last: Antonellis

state: MI

address: 1241 Catherine St

department: Human Genetics

institute: University of Michigan


title: Massively parallel saturation genome editing of an essential mitochondrial targeting sequence (Tn5)

summary: We employed saturation genome editing (SGE) to assess the functional consequences of synonymous, missense, and nonsense variants across KARS1 exon 2. Deep DNA sequencing of fixed-amplicon PCR products targeting the endogenous KARS1 Exon 2 locus was used to determine variant frequencies as part of a larger study to identify a set of reproducible enrichment scores indicating effects of variants on KARS1 function.

overall_design: Tagmented libraries were prepared for homology-directed repair template pDNA and genomic DNA collected from HAP1 cells (4 biological replicates for two different sgRNAs) transfected with sgRNA only or sgRNA + HDR template at two passages post-puromycin selection (p1, p2) to assess overall sgRNA efficacy and HDR knock-in rates for saturation genome editing.

first: Megan

last: Forrest


title: Massively parallel saturation genome editing of an essential mitochondrial targeting sequence (TileSeq)

overall_design: Variant frequencies in homology-directed repair template libraries (2x replicates), and 4 biological replicates for two different sgRNAs were determined at the initial cell population stage (p0) and at three subsequent passages (p1, p2, p3).


title: Single-cell RNA-sequencing reveals peripheral T helper cells promoting the development of IgG4-related disease by enhancing B cell activation and differentiation

city: Shanghai

first: Zongfei

last: Ji

address: No. 180, Fenglin Road

institute: Zhongshan hospital, Fudan University

summary: We aim to investigate a comprehensive cell landscape from retroperitoneal fibrotic lesions of IgG4-RD through single-cell RNA-sequencing (scRNA-seq).

overall_design: 3 IgG4-related disease (IgG4-RD) tissues and 3 control tissues

first: Weiqi

last: Lu


title: ST105-02: Deciphering and comparison of tumor mutational burden of MBT2 and LM8 mouse cancer cell lines

city: Lyon

first: joel

last: lachuer

address: 8 avenue rockefeller

institute: university Lyon1

summary: The aim of this project is to use high-throughput transcriptomic approach to decipher the tumor mutational burden (TMB) of two cancer cell lines, MBT2 (urothelial) and LM8 (osteosarcoma), syngeneic of the C3H/HeN mouse strain, and to compare them as biomarker of immunogenicity (Rizvi NA et al. Science, 2015, Sha D et al. Cancer Discovery, 2020).

overall_design: The two cell lines MBT2 and LM8 have been grown in-vitro and harvested without any supplemental treatment for RNA extraction in duplicate.

first: Sylvain

last: Thierry

first: Mathilde

last: Boucard-Jourdin


title: DDX24 in Vascular Smooth Muscle Cells Is Essential for Vascular Development via Direct Association with FANCA mRNA

city: Zhuhai

first: Yujiao

last: Gong

address: No. 52 Mei Hua Dong Road

institute: The Fifth Affiliated Hospital of Sun Yat-sen University

summary: To investigate the role of DDX24 in vascular smooth muscle cells, RNA-seq of HASMC with DDX24 knockdown was performed.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HASMC cell and HASMC cell with DDX24 knockdown.

first: Yan

last: Liang

first: Jiaxing

last: Wei

last: Liu


title: ST105-01: UNBIASED IN-VIVO AND IN-SILICO TL-532 MECANISM OF ACTION BY RNA-SEQUENCING

summary: Tollys characterized and patented a family of TLR3 proprietary ligands, including the drug candidate TL-532 considered in this study. The aim of this project is to use unbiassed high-throughput transcriptomic approach to decipher signaling pathways linked to the mechanisms of action of the drug candidate TL-532 (including induction of programmed death, immunological activation, TH1 and BDCA3 response, cytokines and chemokines expression, angiogenesis, infiltrates, etc.), induced early (3h, 6h and 24h post-treatment), after a single locoregional treatment, at a dose known to be very effective in this model.

overall_design: Tumor mRNA profiles of Mock treated or TL-532 treated mice were recovered after 3h, 6h and 24h post treatment respectively and generated by deep sequencing, in triplicate,

last: THIERRY

last: BOUCARD-JOURDIN

first: Chloé

last: RENOUX


title: p53-R172H cooperates with Brd4 to induce Csf-1 expression and lung metastasis:  H3K27ac profile of mouse ESCC cells with Trp53R172/- or Trp53+/+

city: New York

first: Spyros

last: Karaiskos

state: NY

department: Herbert Irving Cancer Center

institute: Columbia University

summary:
TP53 mutations are frequent in esophageal squamous cell carcinoma (ESCC), and other SCCs, and are associated with a proclivity for metastasis. Here, we report that the Colony-Stimulating Factor-1 (CSF-1) expression is upregulated significantly in a p53-R175H (R172H in mice)-mediated manner in lung metastatic lesions of ESCC. The p53-R172H-dependent Csf-1 signaling through its cognate receptor Csf-1r increases tumor cell invasion and lung metastasis, which is mediated in part through the phosphorylation of Stat3 and epithelial-to-mesenchymal transition. In Trp53R172H tumor cells, p53 binds to the Csf-1 promoter and the Csf-1 locus is enriched with H3K27ac, which likely is permissive for fostering an interaction between Brd4 and p53-R172H to regulate the Csf-1 transcription. Inhibition of Brd4 not only reduces tumor invasion and lung metastasis but also reduces the Csf-1 level in circulation. Overall, our results establish that the p53-R175H-mediated Brd4-Csf-1 axis promotes ESCC lung metastasis and suggest avenues for therapeutic strategies for this difficult to treat disease.
To elucidate the mechanism for how Trp53R172H regulates Csf-1 transcription, we conducted Cleavage Under Targets and Release Using Nuclease sequencing (CUT&RUN-seq) for histone 3 lysine 27 acetylation (H3K27ac), which is an active enhancer and promoter marker [48], on Trp53R172H/- or Trp53+/+ ESCC cells. The genome-wide analysis revealed 1189 genes having enriched and 1454 genes having depleted H3K27ac in Trp53R172H/- tumor cells compared to Trp53+/+ cells (|log2fold change| > 1.5). Notably, H3K27ac peaks were enriched across Vim gene encoding the mesenchymal marker Vimentin and were reduced across Cdh1 gene encoding the epithelial marker E- Cadherin in Trp53R172H tumor cells compared to Trp53+/+ cells. Interestingly, H3K27ac peaks were enriched across Csf-1 locus including the promoter site in Trp53R172H/- ESCC cells compared to Trp53+/+ tumor cells, suggesting that the Csf-1 locus was accessible and active in the presence of p53-R172H. The epigenetic reader Brd4 binds to acetylated histone lysine residues at promoters and super-enhancers to regulate transcription initiation [29]. We therefore investigated if Brd4 was recruited to enriched H3K27ac sites in ESCC cells to upregulate Csf-1. We found that global Brd4 level in Trp53R172H/- tumor cells was ~2-fold higher than in Trp53-/- cells and ~3-fold higher than in Trp53+/+ cells suggesting gain-of-function properties of p53-R172.

overall_design: Gizem, Efe

first: Saul

last: Carcamo

first: Dan

last: Hasson

first: Anil

last: Rustgi


title: Methyl Gallate Alleviates Acute Ulcerative Colitis by Modulating Gut Microbiota and Inhibiting TLR4/NF-κB Pathway [16S]

city: Luzhou

first: Lai

last: Jia

address: Xianglin Road

institute: Southwest Medical University

summary: Ulcerative colitis (UC) is a complex immune-mediated inflammatory disease. In recent years, the incidence of UC has increased rapidly, however, its exact etiology and mechanism are still unclear. Based on the definite anti-inflammatory and antibacterial activities of Sanguisorba officinalis L., we studied its monomer methyl gallate (MG). In this study, we employed flow cytometry and detected nitric oxide production, finding MG regulated macrophage polarization and inhibited the expression of proinflammatory cytokines in vitro. MG also exhibited anti-inflammatory activity with ameliorating body weight loss, improving colon length and histological damage in dextran sulfate sodium-induced UC mice. Meanwhile, transcription sequencing and 16S rRNA sequencing analyzed the key signaling pathways and changes in the gut microbiota of MG for UC treatment, proving MG could alleviate inflammation by regulating the TLR4/NF-κB pathway in vivo and in vitro. Additionally, MG altered the diversity and composition of the gut microbiota and changed the abundance of metabolic products. In conclusion, our results are the first to demonstrate MG has obvious therapeutic effects against acute UC, which is related to macrophage polarization, improved intestinal flora dysbiosis and inhibition of TLR4/NF-κB signaling pathway activation, and may be a promising therapeutic agent for UC treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for colon tissue (normal group, model group and MG groups).

first: Ping

last: Zhou

first: Jia

last: Lai

first: Wenjun

last: Zou

first: Jianming

last: Wu


title: Long noncoding RNA GATA2AS regulates human erythroid differentiation by controlling erythroid transcription factors binding and regulatory landscape

city: Bethesda

first: Ann

last: Dean

address: 50 South Drive, Bldg 50

department: NIDDK

institute: NIH

summary: To study how GATA2AS regulates erythroid differentiation, GATA2AS ChIRP-seq, RNA-seq, LRF and KLF1 ChIP-seq, H3K27ac ChIP-seq and ATAC-seq were performed.

overall_design: GATA2AS ChIRP-seq was performed in wild type Hudep2 cells. RNA-seq were performed in KO control and GATA2AS KO Hudep2 cells on day 0/4/7/9 during differentiation and  in KD control and GATA2AS KD CD34 cells on day 6/10/14 during differentiation. LRF and KLF1 ChIP-seq were performed in KO control and GATA2AS KO Hudep2 cells to investigate how GATA2AS affects LRF and KLF1 binding. H3K27ac ChIP-seq and ATAC-seq were performed in  KO control and GATA2AS KO Hudep2 cells to study how GATA2AS affects regulatory landscape.

first: Guoyou


title: IGF2BP1 regulate proliferation of multiple myeloma with chromosome 1q gain via CDC5L in a M6A way [CLIP-seq]

first: Jiadai

last: Xu

state: Shanghai

address: Fenglin Road 180, Shanghai, China

department: Hematology

institute: Zhongshan Hospital, Fudan University

summary: Combination analysis of m6A-seq, IGF2BP1-KD RNA-seq, IGF2BP1 CLIP-seq in H929 cells

first: Liang

last: Ren

first: Yawen

last: Wang

first: Peng


title: Methyl Gallate Alleviates Acute Ulcerative Colitis by Modulating Gut Microbiota and Inhibiting TLR4/NF-κB Pathway

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

sample_organism:
Mus musculus
mouse gut metagenome

platform_organism:
Mus musculus
mouse gut metagenome

overall_design: Refer to individual Series


title: IGF2BP1 regulate proliferation of multiple myeloma with chromosome 1q gain via CDC5L in a M6A way


title: SOX9 manipulation in human melanoma cell culture [RNA-seq]

city: Saint Louis

first: Charles

last: Kaufman

address: 660 S Euclid Ave

department: Oncology

institute: Washington University in St. Louis

summary: RNA-seq profiling to compare gene expression in non-transfected A375 cells and A375 cells transfected with SOX9-HA.

overall_design: RNA-seq from 3 external replicates of non-transfected vs. 5µg SOX9-HA transfected A375 human melanoma cells, with singular replicates of other transfection conditions.

first: Eva

last: Kramer


title: Genome-wide DNA methylation analysis of high-grade serous ovarian cancer_after chemotherapy

city: Chuo-ku

first: Takahiro

last: Ebata

state: Tokyo

address: 5-1-1, Tsukiji

institute: National Cancer Center Research Institute

type: Methylation profiling by genome tiling array

summary: DNA methylation in high-grade serous ovarian cancer_after chemotherapy

overall_design: Bisulfite converted DNA from the 30 samples were hybridised to the Infinium MethylationEPIC BeadChip Kit

first: Satoshi

last: Yamashita

first: Hiroshi

last: Yoshida

first: Toshikazu

last: Ushijima


title: HIF2α-regulated genes in small intestine epithelial cells from  collagen induced arthritis model

city: Erlangen

first: Pang

last: Lyu

address: Glückstr. 6

department: Department of Internal Medicine 3

institute: University Hospital Erlangen

summary: HIF2α works as an important transcription factor to induce target genes mediating cell proliferation, meabolism and inflammation. To gain new insights into  HIF2α modulated genes, we used high-throughput sequencing to analyze potential HIF2a regulated genes in small intestine cells from collagen induced arthritis model mice.

overall_design: RNA-seq was used to define differentially expressed genes in small intestine epithelial cells from collagen induced arthritis model of intestinal specific HIF2α ko mice and littermate control mice.

first: Jinming

last: Wen

first: Aline

last: Bozec


title: SOX9 manipulation in human melanoma cell culture [CUT&RUN]

summary: CUT&RUN profiling to compare SOX9 and SOX10 binding in non-transfected A375 cells and A375 cells transfected with SOX9-HA.

overall_design: We sought to evaluate the impact of SOX9 overexpression on binding profiles in human melanoma cell culture. Using A375 or SKMel5 human melanoma cell lines, binding profiles for proteins of interest were compared between non-transfected cells and cells transfected with tagged SOX9. CUT&RUN binding profiles of up to 5 proteins-- H3K4me3, IgG, SOX9, SOX10, as well as either HA or Myc in transfected samples-- were evaluated in up to 3 (transfected)-4 (non-transfected) external replicates for A375 cells and 1 (transfected) -2 (non-transfected) external replicates for SKMel5 cells.


title: Methyl Gallate Alleviates Acute Ulcerative Colitis by Modu-lating Gut Microbiota and Inhibiting TLR4/NF-κB Pathway [RNA-seq]

first: Lai

last: Jia

first: Ping

last: Zhou

first: Jia

first: Wenjun


title: PITX2 knockout induces key findings of electrical remodeling as seen in persistent atrial fibrillation

city: Muenster

first: Amer

last: Ghalawinji

address: Domagkstrasse 3

department: Institute of Human Genetics

institute: WWU

summary: Introduction: Atrial fibrillation (AF) is the most common arrhythmia and affects around 1% of the population with increasing incidence and substantial morbidity. Functional effects of genetic variants associated with AF should help to identify targets involved in AF initiation and/or subsequent remodeling. Gene variants next to the gene of the transcription factor PITX2 (paired-like homeodomain transcription factor 2) showed the strongest association with AF. A significant number of AF patients showed reduced PITX2 levels in the left atrium. Mouse models have been used to study functional aspects of PITX2 gene deletion (“knock out”), but there are substantial differences in atrial electrophysiology between mouse and human . HiPSC-CM should be able to bridge the gap, provided the cells reproduce typical characteristics of human atrium.   Methods: PITX2 knock out samples from a control cell line of human induced pluripotent stem cells (hiPSC) were obtained. Differentiation and generation of Atrial-like engineered heart tissue (aEHT) was performed. RNA-sequencing (RNA-Seq), Quantitative Real-time PCR (RT-qPCR), Protein analysis by Western Blot, Contraction and force analysis, action potential measurements, Calcium current measurements and differential gene expression analysis were run on the samples.  Results: Effective knock out of PITX2 was confirmed by mRNA sequencing and WB. It was shown that PITX2 deficiency reduces contraction force. PITX2 deficiency induces action potential triangulation with more negative maximum diastolic potential.  Activation of muscarinic receptors shortens APD in both PITX2  knockout and controls but hyperpolarization is lost in PITX2 knock out. It was shown that Ca2+ current density is smaller in PITX2 knock out than controls. We found that more negative MDP in PITX2 knock out is not associated with higher IK1.    Conclusion: We improved atrial differentiation, coming very close to human atrial electrophysiology. We demonstrate that PITX2 deficiency induces key characteristics known from persistent AF.

overall_design: Control group (Cell line of human induced pluripotent stem cells): 3 samples; Study group (PITX2 Knockout): 3 samples

first: Carl

last: Schulz

first: Marc

middle: D

last: Lemoine

first: Giulia

last: Mearini

first: Jascha

last: Sani

first: Jussi

last: Koivumäki

first: Monika

last: Stoll

first: Paulus

last: Kirchhof

first: Arne

last: Hansen

first: Thomas

last: Eschenhagen

first: Torsten

last: Christ


title: Investigating a Novel Interaction of c-MET and BACH1 in Head and Neck Squamous Cell Carcinoma Metastasis

status: Public on May 30 2024

city: Washington

first: Kennedy

middle: Davis

last: Brock

state: DC

address: 2300 I St NW Rm 437, Ross Hall

department: Biochemistry

institute: George Washington University

summary: Metastasis is estimated to be responsible for 90% of cancer deaths, and fewer than 10% of patients with metastatic head and neck squamous cell carcinoma (HNSCC) survive beyond 5 years.  HNSCC is responsible for upwards of 270,000 global deaths annually, with up to 30% more cases projected annually by 2030.  The proto-oncogene MET encodes for the tyrosine kinase receptor c-MET, which is overexpressed in over 80% of human papilloma virus (HPV)-negative HNSCC cases and particularly enriched in metastatic lymph nodes.  c-MET is activated by its ligand, hepatocellular growth factor (HGF), and is known to promote cancer cell migration, proliferation, and metastasis through a variety of downstream effectors.  Thus far, unfortunately, inhibition of c-MET has shown low efficacy as a single-agent therapy in clinical trials, which indicates a need for further understanding of the mechanisms underlying c-MET-mediated metastasis in HNSCC.  We show here that human HNSCC cells upregulate expression of the transcription factor BACH1 through c-MET activation upon HGF treatment.  In accordance with previous reports, HGF activation increased expression of epithelial-mesenchymal transition (EMT) markers.  Similarly, BACH1 suppression reduced expression of these EMT markers.  By pharmacological inhibition of c-MET by FDA-approved capmatinib in combination with hemin treatment to reduce BACH1 expression, migration was reduced compared to either treatment alone in scratch-wound migration assays.  Collectively, these data indicate that BACH1 and c-MET are both necessary for the regulation of EMT and migration in HNSCC.  Our data suggest the potential for combination therapy targeting both c-MET and BACH1 to reduce HNSCC metastasis.

overall_design: HNSCC cell lines FaDu, Detroit562, and Cal27 were established as paired shControl and shBACH1 cells lines.  Each cell line was then cultured and treated for 0, 3, or 6 hours with HGF and RNA collected for sequencing.

first: Bok-Soon

last: Lee

first: Jiyoung


title: RNA-Sequencing of LBH transcriptomes in human breast cancer cell lines

city: Miami

first: Karoline

middle: J

last: Briegel

state: Florida

address: 1600 NW 10th Avenue

department: Surgery

institute: University of Miami Miller School of Medicine

summary:
Purpose:  Gene expression analysis of knockdown and overexpression of LBH (Limb-Bud-and-Heart) in human breast cancer cell lines using RNA-Seq
Methods: RNA was collected and analyzed from three biological replicates of each condition (LBH vs vector) for LBH overexpression (OE) in two human breast cancer cell lines (BT549, MCF7). Additionally, RNA was collected  and analyzed from three biological replicates of each condition (siLBH vs non-target/NT siRNA) for LBH knockdown (KD) in two human triple negative breast cancer cells lines (HCC1395, MDA-MB-231). High-throughput sequencing used Illumina platforms.
Results: Using an optimized data analysis workflow, we mapped about 60 million sequence reads per sample to the human genome (build hg19).
Conclusions: Our study represents the first gene profiling analysis of LBH transcriptomes in human breast cancer cell lines, with biologic replicates, generated by RNA-seq technology.

overall_design: RNA was collected and analyzed from three biological replicates of each condition (LBH vs vector control) for LBH overexpression in two human breast cancer cell lines (BT549, MCF7). Additionally, RNA was collected and analyzed from three biological replicates of each condition (siLBH vs scramble siRNA control) for LBH knockdown in two human triple negative breast cancer cells lines (HCC1395, MDA-MB-231). The resulting sequenced reads were mapped. Comparisons of transcriptomes between the different study groups allow identification of LBH regulated genes which may underly breast cancer progression.

first: Koteswararao

last: Garikapati


title: RNA sequencing to compare gene expression in control and Glut1 knockdown hepatic stellate cells

city: Austin

first: Ningling

last: Kang

state: Minnesota

address: 801 16th Ave NE

institute: The Hormel Institute

summary:
Primary human hepatic stellate cells (HSCs) isolated from healthy donors were purchased from Sciencell. HSC cells were transfected with viruses encoding control or Glut1 shRNA and stimulated with TGFbeta1 (5 ng/ml) for 24 hours.
Cells were collected for RNA isolation and RNA sequencing. The goal of this study is to identify genes transcriptionally regulated by Glut1.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HSC cells

first: Yuanguo

last: Wang


title: IL-23 stabilizes an effector Treg program in the tumor microenvironment

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: Regulatory T cells (Tregs) are crucial for the maintenance of immune tolerance and restrict immunopathology during inflammation, yet they limit efficient anti-tumor immunity in the tumor microenvironment (TME). Effector Tregs (eTregs) are thought to be the cellular subset equipped with the strongest immunosuppressive and cancer promoting properties. Here we found by in preclinical cancer models, that Treg specific deletion of IL23R reduces tumor growth. Using heterozygous conditional knock-out mice in which Il23r KO and Il23r WT Tregs coexist in the same tumor microenvironment, we found that IL-23 sensing represents a crucial signal driving the maintenance and stabilization of eTregs involving the transcription factor Foxp3.

overall_design: single cell RNA sequencing of tumor infiltrating CD4+ T cells from female heterozygous Il23r conditional KO mice (Il23rfl/fl X Foxp3-Cre(+/-)) was performed on day 13 after tumor inoculation with B16F10 tumor cells.

first: Tobias

last: Wertheimer

first: Pascale

last: Zwicky

first: Sonia

last: Tugues

first: Burkhard

last: Becher


title: Identifying CSTF2-bound RNA Sequences in HUH7 Cells using RIP-seq

city: Guangzhou

first: Qiangnu

last: Zhang

state: None Selected

address: 1017 Dongmen Bei Lu, 518020Shenzhen, China

institute: Guangzhou Medical University

summary: CSTF2, an RNA-binding protein, and its target genes in hepatocellular carcinoma remain unreported. Screening for potential CSTF2-bound RNA sequences was performed using RIP-seq technique in HUH7 cells.

overall_design: To identify RNA sequences in HUH7 cells that potentially bind to CSTF2, RIP-seq analysis can be performed.


title: SOX9 manipulation in human melanoma cell culture

first: Charles

last: Kaufman


title: Single cell RNA sequencing of peritoneal cells from macrophage-Cd36-/- and macrophage-Cd36 fl/fl mice  at the resolution phase of sterile inflammation.

city: New York City

first: Dimitris

last: Nasias

state: New York

address: 550 1st Avenue

department: Langone Medical School

institute: New York University

summary: Monocytes and macrophages as components of innate immunity are critical for both homeostasis and inflammation. The scavenger receptor CD36, highly expressed in macrophages, promotes immunological responses mediated by recognition of molecular patterns on pathogens or endogenous ligands on apoptotic cells. CD36 mediated lipid uptake also allows metabolic adaptations that influence macrophage phenotype and polarization. CD36 binds diverse lipids including fatty acids and various lipoproteins, which could exert differential effects on macrophage conversion. Previous studies reported opposite outcomes due to CD36-mediated lipid uptake; macrophages converted to either an inflammatory or an alternatively activated phenotype. To determine the role of this receptor in vivo in the presence of physiological lipid sources, we created macrophage-specific CD36 knockout mice. Using zymosan-induced peritonitis to activate immune cells, we show through single cell RNA sequencing analysis that a broad variety of resident and infiltrated immune cells are present in the peritoneum 72h after the initial stimulus. CD36 deficiency did not affect the numbers of cells during the infiltration and resolution phases, but CD36 deficiency altered the macrophage transcriptome. Pathways related to innate immunity, antigen presentation and oxidative phosphorylation were upregulated in macrophages with CD36 deficiency, whereas those related to efferocytosis, adaptive immunity and B cell activation were downregulated. Despite these gene changes, neither immunoglobulin production nor peritoneal efferocytosis was altered by macrophage CD36 deficiency, nor were there changes in the numbers of circulating white blood cells. Thus, CD36 deficiency does not reduce the inflammatory phenotype of induced peritoneal macrophages.

overall_design: We established the peritonitis model with high dosage of zymosan (1mg/ animal) in macrophage-Cd36-/- and macrophage-Cd36 fl/fl mice.  Total peritoneal cells were isolated with 1x PBS and were analyzed using sc-RNAseq.

first: Julie

last: De Bermont

first: Ni-Huiping

last: Son

first: Nada

middle: A

last: Abumrad

first: Ira

last: Goldberg


title: A Missense Variant in CASKIN1's Proline-Rich Region Segregates with Psychosis in a Three-Generation Family

city: Baltimore

first: Dimitrios

last: Avramopoulos

state: Maryland

address: 733 North Broadway

department: Genetic Medicine

institute: Johns Hopkins University

summary: The polygenic nature of schizophrenia (SCZ) implicates many variants in disease development. Rare variants of high penetrance have been shown to contribute to the disease prevalence. Whole-exome sequencing of a large three-generation family with SCZ and bipolar disorder identified a single segregating novel, rare, non-synonymous variant in the gene CASKIN1. The variant D1204N is absent from all databases, and CASKIN1 has a gnomAD missense score Z = 1.79 and pLI = 1, indicating its strong intolerance to variation. We find that introducing variants in the proline-rich region where the D1204N resides results in significant cellular changes in iPSC-derived neurons, consistent with CASKIN1’s known functions. We observe significant transcriptomic changes in 368 genes (padj < 0.05) involved in neuronal differentiation and nervous system development. We also observed nominally significant changes in the frequency of action potentials during differentiation, where the speed at which the edited and unedited cells reach the same level of activity differs. Our results suggest that CASKIN1 is an excellent gene candidate for psychosis development with high penetrance in this family.

overall_design: iPS cells from a healthy donor were edited to introduce changes in the CASKIN1 gene and 5 edited and 5 unedited clones  differentiated to excitatory neurons. RNA was extracted and subjected to RNA sequencing, after which the transcriptomes of edited and unedited cells were compared. Details in our publication HGG Adv. 2024 May 3;5(3):100303. doi: 10.1016/j.xhgg.2024.100303 PMID: 37479784

first: Marah

last: Wahbeh

first: D


title: RNA sequencing of NlCSP11-infiltrated Nicotiana benthamiana

city: Shanghai

first: Li

last: Wan

address: 300 Feng Lin Road

department: CAS Center for Excellence in Molecular Plant Sciences

institute: Chinese Academy of Sciences

summary: In order to find the differentially expressed RNAs and signaling pathways related to the dwarf phenotype induced by NlCSP11, 35S-NlCSP11,  35S-XopQ and 35S-GFP control were infiltrated into Nicotiana benthamiana. We analyzed the differentially expressed RNAs in the infiltrated leaves (NlCSP11_Z/XopQ_Z) and the upper uninfiltrated leaves (NlCSP11_U/XopQ_U) of N. benthamiana.  KEGG annotation revealed a large number of differentially expressed RNAs involved in plant-pathogen interactions, indicating that NlCSP11 resulted in a more strong systemic resistance in N. benthamiana.

overall_design: In order to find the RNAs and signaling pathways related to the dwarf phenotype induced by NlCSP11, 35S-NlCSP11, 35S-XopQ and 35S-GFP control were infiltrated into the local leaves  and the upper leaves of Nicotiana benthamiana.

first: Weiwei

last: Rao

first: Tingting

last: Ma

last: wan


title: IGF2BP1 regulate proliferation of multiple myeloma with chromosome 1q gain via CDC5L in a M6A way [RNA-seq]

first: Jiadai

last: Xu

overall_design: Combination analysis of m6A-seq, IGF2BP1-KD RNA-seq, IGF2BP1 CLIP-seq in H929 cells

first: Liang

last: Ren

first: Yawen

last: Wang

first: Peng

last: Liu


title: Mechanism of TIA1 in spinal cord injury mice

city: Wenzhou

first: Mengxian

last: Jia

state: Zhejiang

address: Nanbaixiang Street

institute: the First Affiliated Hospital of Wenzhou Medical University

summary: Conditional knockout Tia1 could induce the changes of gene expression in injury spinal cord of mice.

overall_design: The mRNA of injury spinal cord were collected from Tia1Nestin-CKO mice and Tia1f/f mice at 7 days after SCI, then compared with the each other.


title: Gene Amplification of Mediator Subunit 30 Redirects the MYC Transcriptional Program and Oncogenesis [Cut&Tag]

city: La Jolla

first: Chunyu

last: Jin

address: 9500 Gilman Dr. MC0648

institute: University of California, San Diego

summary: Understanding the molecular mechanisms underlying tumorigenesis is crucial for developing effective cancer therapies. Here, we investigate the common co-amplification of MED30 and MYC across diverse cancer types and its impact on oncogenic transcriptional programs. Transcriptional profiling of MYC and MED30 single or both overexpression/amplification revealed the over amount of MED30 lead MYC to a new transcriptional program that associate with poor prognosis. Mechanistically, MED30 overexpression/amplification recruits other Mediator components and binding of MYC to a small subset of novel genomic regulatory sites, changing the epigenetic marks and inducing the formation of new enhancers, which drive the expression of target genes crucial for cancer progression. In vivo studies in pancreatic ductal adenocarcinoma (PDAC) further validate the oncogenic potential of MED30, as its overexpression promotes tumor growth and can be attenuated by knockdown of MYC. Using another cancer type, MED30 knockdown reduces tumor growth particularly in MYC high-expressed glioblastoma (GBM) cell lines. Overall, our study elucidates the critical role of MED30 overexprssion in orchestrating oncogenic transcriptional programs and highlights its potential as a therapeutic target for MYC-amplified cancer.

overall_design: Genomic binding map of histone marks (H3K4me3, H3K27Ac, H3K27me2), MYC, MED30 and some other subunits of mediator complex were profiled by Cut&Tag experiments in Mia PaCa-2 cell line that integrated with doxycycline (Dox) inducible MED30 or MED30-3xHA (labeled MED30C3HA) expression plasmid with or without Dox treatment. Samples with Dox treatment were labeled as OE (overexpression).

first: Guofeng

last: Zhao

first: Michael

last: Rosenfeld


title: Intratumor transforming growth factor-β signaling with extracellular matrix-related gene regulation marks chemotherapy-resistant gastric cancer

city: Koto-ku

first: Ayane

last: Nakamura

department: Cancer Chemotherapy Center

institute: Japanese Foundation for Cancer Research

summary: Drug-tolerant persister (DTP) cells remain following chemotherapy and can cause cancer relapse. However, it is unclear when acquired resistance to chemotherapy emerges. Here, we compared the gene expression profiles of gastric cancer patient-derived cells (GC PDCs) and their respective xenograft tumors with different sensitivities to 5-fluorouracil (5-FU) by using immunodeficient female BALB/c-nu mice. RNA sequencing analysis of 5-FU-treated PDCs demonstrated that DNA replication/cell cycle-related genes were transiently induced in the earlier phase of DTP cell emergence, while extracellular matrix (ECM)-related genes were sustainably upregulated during long-term cell survival in 5-FU-resistant residual tumors. NicheNet analysis, which uncovers cell-cell signal interactions, indicated the transforming growth factor-β (TGF-β) pathway as the upstream regulator in response to 5-FU treatment. This induced ECM-related gene expression in the 5-FU-resistant tumor model. In the 5-FU-resistant residual tumors, there was a marked upregulation of cancer cell-derived TGF-β1 expression and increased phosphorylation of SMAD3, a downstream regulator of the TGF-β receptor. By contrast, these responses were not observed in a 5-FU-sensitive tumor model. We further found that TGF-β-related upregulation of ECM genes was preferentially observed in non-responders to chemotherapy with 5-FU and/or oxaliplatin among 22 patient-derived xenograft tumors. These observations suggest that chemotherapy-induced activation of the TGF-β1/SMAD3/ECM-related gene axis is a potential biomarker for the emergence of drug resistance in GCs.

overall_design: Examination of RNA-sequencing in (1) JSC18-1 cells were treated with or without 5-FU at IC50 values, 1 μM for 5 days, and (2) JSC15-3 and JSC18-1 cells were treated with or without 5-FU at IC50 values, 1 μM and 0.5 μM for 14 days, and (3) their xenograft tumors in BALB/c-nu mice were treated with PBS or 5-FU (100 mg/kg).

first: Tetsuo

last: Mashima

first: Hiroyuki

last: Seimiya


title: A novel CRISPR-Cas9 strategy to target DYSTROPHIN mutations downstream of exon 44 in patient-specific DMD iPSCs

city: Minneapolis

first: Neha

last: Dhoke

address: 2231 6th St SE

institute: University of Minnesota

summary: Here, we performed CRISPR-cas9 mediated genetic correction in  DMD patient derived iPSC and then differentiated them into  in vitro myotubes. Pairing bulk RNA sequencing between Wild-type (WT), DMD and the corrected counterparts we were able to differentiate the molecular changes that occurs during the absence of dystrophin.

overall_design: We performed gene expression profiling for data obtained through bulk RNA-sequencing of 15 uniques samples. Samples included WT, DMD and DMD corrected iPSC derived myotubes.

first: Rita

last: Perlingeiro


title: GLUT1 overexpression enhances CAR T cell metabolic fitness and anti-tumor efficacy

city: New York

first: Yuzhe

last: Shi

address: 1250 First Avenue

department: Immunolgy

institute: Memorial Sloan Kettering Cancer Center

summary: The tumor microenvironment presents many obstacles to effective CAR T cell therapy, including glucose competition from tumor and myeloid cells. Using mouse models of acute lymphoblastic leukemia (ALL), renal cell carcinoma (RCC), and glioblastoma (GBM), we show that enforced expression of the glucose transporter GLUT1 enhances anti-tumor efficacy and promotes favorable CAR T cell phenotypes for two clinically relevant CAR designs, 19-28z and IL13Ra2-BBz. In the NALM6 ALL model, 19-28z-GLUT1 promotes Tscm formation and prolongs survival. RNA sequencing of these CAR T cells reveals that overexpression of GLUT1, but not GLUT3, enriches for genes involved in glycolysis, mitochondrial respiration, and memory precursor phenotypes. Extending these data, 19-28z-GLUT1 CAR T cells improve tumor control and response to rechallenge in an RCC patient derived xenograft model. Furthermore, IL13Ra2-BBz CAR T cells overexpressing GLUT1 prolong survival of mice bearing orthotopic GBMs and exhibit decreased exhaustion markers. This novel engineering approach can offer a competitive advantage to CAR T cells in harsh tumor environments where glucose is limiting.

overall_design: To understand what led to the improved anti-tumor efficacy of 19-28z-GLUT1 CAR T cells, we performed SMARTer-RNA-seq on flow-sorted CAR T cells from bone marrow at 7 days after CAR T cell infusion

first: Ivan

middle: S

last: Kotchetkov


title: Histone Modification in Cerebral Arteriovenous Malformation

city: Los Angeles

first: Xiuju

last: Wu

state: CA

address: 650 Charles Young Dr East, CHS A2-237

institute: University of California, Los Angeles

summary: Cerebral arteriovenous malformations (AVMs) are the most common vascular malformations worldwide and the leading cause of hemorrhagic strokes that result in crippling neurological deficits. Here, using newly generated mouse model, we discovered that genome-wide ocuppancy of H4K8ac and H3K27me3 decreased in mouse cerebral AVMs.

overall_design: Chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) to discover histone modification of H4K8ac and H3K27me3 in mouse model of cerebral arteriovenous malformations.


title: Mapping the follicle-specific regulation of extracellular vesicle-mediated microRNA transport in the southern white rhinoceros (Ceratotherium simum simum)

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

summary: Efforts to implement effective assisted reproductive technologies (ART) to extricate the northern white rhinoceros (NWR; Ceratotherium simum cottoni) from extinction, could be unconventionally offset from studies carried out using the southern white rhinoceros (Ceratotherium simum simum) as a relative model species. The bi-directional communication and critical transport of regulatory molecules controlling follicular growth and oocyte development are in part mediated through extracellular vesicles (EVs), which encompass a highly conserved and advanced paracrine signaling mechanism important in shuttling unique cargo such as microRNAs (miRNAs). In this study, critical miRNAs for follicular development were identified, proposing novel approaches using EV-mediated miRNA to possibly improve the in vitro technologies outcome in a multitude of species.

overall_design: Two southern white rhinoceros females (n=2) were stimulated and utilized for transrectal OPU, facilitating the in vivo collections of follicular fluid aspirate from follicles of distinct size. Prior to ultrasound-guided ablation of follicles, follicles were assigned to predetermined categories based on their established diameter: growing (G; 11-17mm), dominant (D; 18-29mm), and pre-ovulatory (P; 30-34mm). Follicular fluids were used for EV isolation from which total RNA were isolated and smallRNA sequencing were performed.

first: Nico

last: Menjivar

first: Rachel

last: Felton

first: Barbara

last: Durrant

first: Dawit

last: Tesfaye

first: Elena

last: Ruggeri


title: Adipocyte-specific inactivation of NAMPT, a key NAD+ biosynthetic enzyme, causes a metabolically-unhealthy lean phenotype in female mice during aging

city: Izumo

first: Jun

last: Yoshino

state: Shimane

address: 89-1 Enya-cho

institute: Faculty of Medicine, Shimane University

summary: Nicotinamide adenine dinucleotide (NAD+) is a universal coenzyme regulating cellular energy metabolism in many cell types. Recent studies have demonstrated the close relationships between defective NAD+ metabolism and aging and age-associated metabolic diseases. The major purpose of the present study was to test the hypothesis that NAD+ biosynthesis, mediated by a rate-limiting NAD+ biosynthetic enzyme, nicotinamide phosphoribosyltransferase (NAMPT), is essential for maintaining normal adipose tissue function and whole-body metabolic health during the aging process. To this end, we provided in-depth and comprehensive metabolic assessments for female adipocyte-specific Nampt knockout (ANKO) mice during aging. We first evaluated body fat mass in young (≤ 4-month-old), middle aged (10 to 14-month-old), and old (≥ 18-month-old) mice. Intriguingly, adipocyte-specific Nampt deletion protected against age-induced obesity without changing energy balance. However, data obtained from the hyperinsulinemic euglycemic clamp procedure demonstrated that, despite the lean phenotype, old ANKO mice had severe insulin resistance in skeletal muscle, heart, and white adipose tissue (WAT). Old ANKO mice also exhibited hyperinsulinemia and hypoadiponectinemia. Mechanistically, loss of Nampt caused marked decreases in WAT gene expression of lipogenic targets of peroxisome proliferator-activated receptor gamma (PPARγ) in an age-dependent manner. In addition, administration of a PPARγ agonist rosiglitazone restored fat mass and improved metabolic abnormalities in old ANKO mice. In conclusion, these findings highlight the importance of the NAMPT-NAD+-PPARγ axis in maintaining functional integrity and quantity of adipose tissue, and whole-body metabolic function in female mice during aging.

overall_design: We determined the effects of adipocyte-specific Nampt deletion on subcutaneous white adipose tissue gene expression profiling in young and old mice by analyzing control (flox/flox) and adipocyte-specific Nampt knockout (ANKO) mice.

first: Nathan

last: Qi

middle: P

last: Franczyk

first: Yo

last: Sasaki

first: Brian

last: Finck

last: DeBosch


title: IL-10 suppresses T cell expansion while promoting tissue-resident memory cell formation during SARS-CoV-2 infection in rhesus macaques

city: Salvador

first: Eduardo

last: Fukutani

state: Bahia

address: Marginal da - Av. Luís Viana Filho, 3230 - Imbuí, Salvador - BA

country: Brazil

institute: Fundação Oswaldo Cruz

summary: SARS-CoV-2 infection leads to vastly divergent and heterogeneous clinical outcomes ranging from asymptomatic to fatal disease. Co-morbidities, sex, age, and host genetics together with vaccine status are known to affect disease severity.  However, how the inflammatory milieu of the lung at the time of SARS-CoV-2 infection impacts control of the virus remains less well understood. Here, we identify key innate immune pathways required to limit viral replication, including the pro-inflammatory cytokine TNFα. Moreover, we demonstrate here that recent immune events in the lung proximal to the time of SARS-CoV-2 exposure can drastically impact viral control.  A diverse set of pulmonary inflammatory stimuli, ranging from prior resolved respiratory infections of S. aureus or influenza, ongoing M. tuberculosis infection, or ovalbumin/alum-induced asthma to administration of defined TLR ligands and recombinant cytokines, resulted in an antiviral state that potently limited SARS-CoV-2 replication. In addition to type I interferons, the broadly inducible inflammatory cytokines TNFα and IL-1 very effectively conditioned the lung for enhanced viral control. Collectively, our work reveals that SARS-CoV-2 may benefit from an immunologically quiescent lung microenvironment and indicates that the recent and momentary pulmonary inflammatory tone during SARS-CoV-2 exposure may contribute to the population-wide variability in COVID-19 disease outcomes.

overall_design:
Cryopreserved Bronchoalveolar lavage (BAL) cells from rhesus macaques infected with SARS-CoV-2 collected at days 0, 3, 7, 14 and 28-35 (necropsy) post-infection. This data is composed of 71 samples, whose general group distribution is as follows: aIFNg (n = 22), aIL10 (n = 24) and controls (n = 24).

Cryopreserved BAL cells from pre-infection (d0) and days 3, 7, 14, and 28-35 post infection (necropsy) were thawed and homogenized using Qiagen RLT buffer Plus (Cat # 1053393) and QIAShredder Columns (Cat # 79656). RNA was isolated using the Qiagen RNeasy Mini kit (Cat # 74134) according to manufacturer’s instructions and eluted in 25uL of RNase free water. RNA was concentrated to 25-50ng/uL using Eppendorf Vacufuge plus centrifuge concentrator. RNA quality was confirmed with Agilent TapeStation. RNA was sent to the National Cancer Institute (NCI) Center for Cancer Research Genomics Core at the Frederick National Laboratory. Digital mRNA gene expression analysis was performed with the Nanostring nCounter NHP Immunology panel V2 (Cat # 115000276). Raw read counts were obtained from RCC files using the nSolver 4.0 Data Analysis software and the NS_NHP_Immunology_V2.0 rlf file references included with the nCounter NHP Immunology panel V2 kit.

first: Christine

middle: E

last: Nelson

first: Taylor

middle: W

last: Foreman

first: Keith

last: Kauffman

first: Shunsuke

last: Sakai

first: Joel

last: Fleegle

first: Felipe

last: Gomez

first: Sydnee

last: Gould

first: Cyril

last: Le Nouën

first: Xueqiao

last: Liu

first: Tracey

last: Burdette

first: Nicole

last: Garza

first: Bernard

last: Lafont

first: Kelsie

last: Brooks

first: Cecilia

last: Arlehamn

first: Daniela

last: Weiskopf

first: Alessandro

last: Sette

first: Heather

last: Hickman

first: Ursula

last: Buchholz

first: Reed

middle: F

last: Johnson

first: Jason

middle: M

last: Brenchley

first: James

last: Oberman

first: Artur

last: Queiroz

first: Bruno

middle: B

last: Andrade

first: Laura

last: Via

first: Daniel

last: Barber


title: The roles of nuclear orphan receptor NR2F6 in anti-viral innate immunity [RNA-seq]

city: Wuhan

first: Chen-Yu

last: Wang

state: Hubei

address: 299 Bayi Road, Wuchang District

institute: Wuhan University

summary: The regulation of proper gene transcription is critical for anti-viral defense. Dynamics of enhancer activity play important roles in many biological processes, and epigenomic analysis is widely used to determine the involved enhancers and transcription factors. To determine new transcription factors in anti-DNA-virus response, we perform H3K27ac ChIP-Seq analysis to profile the active enhancer pattern in HSV-1-infected THP-1 cells. We have identified three transcription factors, NR2F6, MEF2D and MAFF, and experimentally verified their roles in promoting HSV-1 replication. NR2F6 promotes HSV-1 replication and gene expression in vitro and in vivo, which is not related with the classical cGAS/STING pathway. NR2F6 binds to the promoter of MAP3K5 and activate AP-1/c-Jun pathway, which is critical for DNA virus replication. On the contrary, NR2F6 expression is transcriptionally repressed by c-Jun upon HSV-1 infection, which forms a negative feedback loop. Meanwhile, cGAS/STING innate immunity signaling represses NR2F6 through STAT3. Taken together, we have identified new transcription factors involved in the interactive network between DNA viruses and host cells, and revealed the underlying mechanisms for anti-viral research.

overall_design:
We perform RNA-Seq analysis to profile differentially expressed gene in HSV-1-infected THP-1 cells
We perform RNA-Seq analysis to profile differentially expressed gene in HSV-1-infected NR2F6 knockdown (sgNR2F6) THP-1 cells

first: Yang

last: Chen

first: Wang

last: Chenyu

first: Long

last: Qiaoyun

first: Wei

last: Minglang

first: Tang

last: Shanbo

first: Xiao

last: Qiong

first: Wu

last: Min

first: Li

last: Lianyun

first: Chen

last: Mingkai

last: Yong


title: MeRIP-seq analysis for CSTF2 knockout in HUH7 and PLC/PRF/5 cell lines

first: Qiangnu

last: Zhang

summary: CSTF2 has been shown to have a certain oncogenic effect in hepatocellular carcinoma, but its mechanism remains unclear. Previous studies have suggested that CSTF2 can shorten the 3' untranslated region (3'UTR) of target genes. Considering that the 3'UTR contains numerous m6A modification sites, we hypothesize that CSTF2 may regulate mRNA m6A modification. We performed MeRIP-seq analysis to investigate the changes in m6A modification in CSTF2 knockout HUH7 and PLC/PRF/5 cell lines.

overall_design: We employed CRISPR-Cas9 gene editing technology to knockout CSTF2 in HUH7 and PLC/PRF/5 cell lines. Parental HUH7 and PLC/PRF/5 cell lines were used as controls. MeRIP-seq was performed to analyze the changes in RNA methylation patterns


title: Persistent gene expression and DNA methylation alterations linked to carcinogenic effects of dichloroacetic acid [RRBS]

city: Research Triangle Park

first: Brian

last: Chorley

state: NC

address: US EPA, 109 TW Alexander Dr

institute: US EPA

summary: Mechanistic understanding of transient exposures that lead to adverse health outcomes will enhance our ability to recognize biological signatures of disease. Here, we measured the transcriptomic and epigenomic alterations due to exposure to the metabolic reprogramming agent, dichloroacetic acid (DCA). Previously, we showed that exposure to DCA increased liver cancer in B6C3F1 mice after continuous or early life exposures similarly over background level. Measures from these studies did not support direct cytotoxic, mitogenic, or genotoxic modes-of-action of tumorigenesis. Using archived formalin-fixed liver samples, we utilized modern methodologies to measure gene expression and DNA methylation levels to link to previously generated phenotypic measures. Gene expression was measured by targeted RNA sequencing (TempO-seq 1500+ toxicity panel: 2754 total genes) in liver samples collected from 10-, 32-, 57-, and 78-week old mice exposed to deionized water (controls), DCA continuously at 3.5g/L in drinking water (“Direct” group), or DCA at 3.5g/L for 10-, 32-, or 57-weeks followed by control water (“Stop” groups). Genome-scaled alterations in DNA methylation were measured by Reduced Representation Bisulfite Sequencing (RRBS) at 78-weeks. Transcriptomic changes were most robust with concurrent or adjacent timepoints after exposure stoppage. DNA methylation alterations followed a similar pattern, measuring 2720 and 567 differentially methylated regions (DMRs) in 78-week Direct and 10-week “Stop” DCA exposure groups, respectively. Gene pathway analysis indicated cellular effects linked to increased oxidative metabolism, a primary mechanism of action for DCA, closer to exposure windows especially early in life. Conversely, many gene signatures and pathways reversed patterns later in life and reflected more pro-tumorigenic patterns for both current and prior DCA exposures. DNA methylation patterns linked to early gene pathway perturbations, suggesting persistence in the epigenome and possible regulatory effects. In total, results suggested that liver metabolic reprogramming effects of DCA interact with normal age mechanisms to increase tumor burden with both continuous and prior DCA exposure in the B6C3F1 rodent model.

overall_design: Male B6C3F1 mice were treated with 3.5 g/L DCA in deionized water in a stop exposure study design over a period of 78 weeks. Mice were either provided only deionized water (control), continuous DCA (direct) or in a series of stop-dosage timepoints after which the mice were switched to deionized water for the duration of the experiment. The stop group treatments were as follows: 10 weeks of DCA followed by 68 weeks of water (S1), 32 weeks of DCA and 46 weeks of water (S2) and 57 weeks of DCA with 21 weeks of water (S3). The direct group were exposed to 3.5 g/L for the entirety of the 78-week study. At each timepoint (10, 32, 57 or 78 weeks), a subset of the control, direct and stop treatment block mice were humanely euthanized with CO2 following EPA approved Animal Care and Use Committee protocols.  Portions of the livers were fresh frozen at each sacrifice timepoint along with the preparation of FFPE paraffin blocks. Figure 1 outlines study collection points and treatments. FFPE-derived samples were used to measure gene expression and frozen samples were used for DNA methylation determination.

first: Gleta

last: Carswell

last: Bennett