title: Age-related changes in human skeletal muscle transcriptome and proteome are more affected by chronic inflammation and physical inactivity than primary aging

status: Public on Jan 29 2024

city: Moscow

first: Pavel

last: Makhnovsky

address: 76A Khoroshevskoye shosse

country: Russia

institute: Institute of Biomedical Problems of the Russian Academy of Sciences

summary: Evaluation of the influence of primary and secondary aging on the manifestation of molecular and cellular hallmarks of aging is a challenging and currently unresolved issue. Our study represents the first demonstration of the distinct role of primary aging and both chronic inflammation and physical inactivity – the most important drivers of secondary aging, in the regulation of transcriptomic and proteomic profiles in human skeletal muscle. To achieve this purpose, young healthy people (n=15), young (n=8) and older (n=37) patients with knee/hip osteoarthritis, a model to study the effect of long-term inactivity and chronic inflammation on the vastus lateralis muscle, were included in the study. It was revealed that widespread and substantial age-related changes in gene expression (~4,000 genes regulating mitochondrial function, proteostasis, cell membrane, secretory and immune response) were related to the long-term physical inactivity and chronic inflammation rather than primary aging. Primary aging contributed mainly to the regulation of genes (~200) encoding nuclear proteins (regulators of DNA repair, RNA processing, and transcription), mitochondrial proteins (genes encoding respiratory enzymes, mitochondrial complex assembly factors, regulators of cristae formation and mitochondrial reactive oxygen species production), as well as regulators of proteostasis. It was found that proteins associated with aging were regulated mainly at the post-transcriptional level. The set of putative primary aging genes and their potential transcriptional regulators can be used as a resource for further targeted studies investigating the role of individual genes and related transcription factors in the emergence of a senescent cell phenotype.

overall_design: The study involved 37 older patients with advanced‐stage, symptomatic knee/hip osteoarthritis (OP; median age 72 years and interquartile range [69–77] years, M:F = 5:32), 8 young patients with the same diagnosis (YP; 39 [37–42] years, M:F = 7:1), and 15 young healthy volunteers (YH; 35 [28–38] years, M:F = 13:2). Biopsies of muscle tissue from m. vastus lateralis were taken after an overnight fast, placed in the Custodiol buffer (Dr. Franz Köhler Chemie GmbH, Germany) and processed within 10–15 minutes after the biopsy. Thus, visible fragments of connective and adipose tissue were removed; a part of the tissue was fixed for histological examination, and another part was frozen in liquid nitrogen and stored at -80 °C.

first: Daniil

last: Popov

last: Makhnovskii


title: In vivo cells from liver and brain from mice treated with control and keto diet collected in different ages - 12 and 26 months

status: Public on Jan 31 2024

city: California

first: Natalia

middle: Faraj

last: Murad

state: CA

address: 500 Parnassus Ave

department: HemOnc

country: USA

institute: University of California, San Francisco

type: Expression profiling by high throughput sequencing

summary: Beta-hydroxybutyrate (BHB) is a ketone body synthesized during fasting or strenuous exercise. Our previous study demonstrated that a cyclic ketogenic diet (KD), which induces BHB levels similar to fasting every other week, reduces midlife mortality and improves memory in aging mice. First, we analyzed hepatic gene expression in an aging KD-treated mouse cohort using bulk RNA-seq. In addition to the downregulation of TOR pathway activity, cyclic KD reduces inflammatory gene expression in the liver. We examined the brain gene expression of 12-month-old male mice fed with one-week and one-year cyclic KD. While a one-week KD increases inflammatory signaling, a one-year cyclic KD reduces neuroinflammation induced by aging.

overall_design: 16 samples of liver from 26 months old mice, 8 exposed to control diet and 8 exposed to keto diet. 28 samples from mouse brain. 12 mice 12 months old - 5 control diet and 7 keto diet. 16 samples from mice 26 months old, 8 control diet e 8 treated with keto diet.


title: Mapping catalytically engaged TOP2B in neurons reveals the principles of topoisomerase action within the genome [Re-analysis_TOP2B_mm10]

city: Dallas

first: Ram

last: Madabhushi

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Topoisomerase IIb (TOP2B) is essential for neural development and function, yet its precise molecular roles remain poorly understood. Here we trapped catalytically engaged TOP2B in DNA cleavage complexes (TOP2Bccs) and mapped their positions genome-wide in cultured mouse cortical neurons. We report that chromosome compartments set the threshold of TOP2B activity within the genome, while specific nucleosome configurations stimulate TOP2B activity within strongly transcribed regions and enhancers. Highly expressed genes that are devoid of usually associated chromatin marks, such as H3K36me3, are deficient in TOP2B activity, indicating that TOP2B may be inefficient at sensing transcription-generated torsional stress directly. Active promoters and the transcription start sites (TSS) with high RNA polymerase II (RNAPII) occupancy show elevated TOP2B ChIP-seq signals but are depleted in TOP2Bccs, indicating that TOP2B is held inactive at active promoters. Surprisingly, TOP2B inhibition with etoposide increased nascent transcription at highly expressed genes and enhancers. While ETP treatment reduced nascent transcription within long genes, these effects were independent of transcript length and instead correlated with the presence of intragenic enhancers. Together these results provide insights into the epigenetic regulation of topoisomerase activity and reveal new roles for TOP2B in neuronal transcriptional regulation.

relation:
Reanalysis of: GSM1516578
SubSeries of: GSE227463

overall_design: Re-analysis of GSM1516578: TOP2B ChIP-seq in Control with mm10 alignments - Raw FASTQ sequencing reads were analyzed for quality control using FastQC, trimmed using Trimmomatic, and aligned to the mm10 reference genome (GRCm38.p6 assembly) using BWA-MEM. BAM files were marked and filtered for duplicate reads using Sambamba and Samtools, respectively.  Peaks were called using MACS2 from biological duplicates and pseudo-replicates where each ChIP sample was normalized to input DNA. MACS2-generated bedGraph files were converted to bigWig files using Kent Utils for individual replicates and pooled replicates

first: Amir

last: Segev

first: Lance

last: Heady

first: Morgan

last: Crewe


title: Mapping catalytically engaged TOP2B in neurons reveals the principles of topoisomerase action within the genome [Re-analγsis_gH2ax_mm10]

relation:
Reanalysis of: GSM1516574
Reanalysis of: GSM1516591
SubSeries of: GSE227463

overall_design: Re-analysis of GSM1516574 and GSM1516591: γH2AX ChIP-seq with mm10 alignments in Control and Etoposide treated samples - Sequencing reads were mapped to mouse genome assembly (mm10) using BWA aligner (samse option). Bedgraph trace files were generated using HOMER software and converted to bigWig using UCSC Kent tools


title: Mapping catalytically engaged TOP2B in neurons reveals the principles of topoisomerase action within the genome [TOP2Bcc-seq]

overall_design: TOP2Bcc-seq was used to map catalytically engaged TOP2B in mouse cortical neruons


title: Mapping catalytically engaged TOP2B in neurons reveals the principles of topoisomerase action within the genome [fastGRO]

overall_design: FastGRO was used to map nascent transcription in primary cortical neurons following TOP2 inhibition


title: DNA methylation analysis of radioresistant and ALDH+ Head and Neck Squamous Cell Carcinoma cells and their parental counterparts

city: Dresden

first: Claudia

last: Peitzsch

address: Fetscherstr. 105

country: Germany

institute: Center for Regenerative Therapies Dresden (CRTD)

type: Methylation profiling by genome tiling array

summary: Background: The sensitivity of head and neck squamous cell carcinoma (HNSCC) to ionizing radiation, among others, is determined by the number of cells with high clonogenic potential and stem-like features. These cellular characteristics are dynamically regulated in response to treat-ment and may lead to an enrichment of radioresistant cells with a cancer stem cell (CSC) pheno-type. Epigenetic mechanisms, particularly DNA and histone methylation, are key regulators of gene-specific transcription and cellular plasticity. Therefore, we hypothesized that specific epi-genetic targeting may prevent irradiation-induced plasticity and may sensitize HNSCC cells to radiotherapy. Methods: We compared the DNA methylome and intracellular concentrations of tricarboxylic acid cycle metabolites in radioresistant FaDu and Cal33 cell lines with their parental controls, as well as aldehyde dehydrogenase (ALDH)-positive CSCs with negative controls. Moreover, we conducted a screen of a chemical library targeting enzymes in-volved in epigenetic regulation in combination with irradiation and analyzed the clonogenic potential, sphere formation, and DNA repair capacity to identify compounds with both radiosensi-tizing and CSC-targeting potential. Results: We identified the histone demethylase inhibitor GSK-J1, which targets UTX (KDM6A) and JMJD3 (KDM6B), leading to increased H3K27 tri-methylation, heterochromatin formation, and gene silencing. The clonogenic survival assay after siRNA-mediated knock-down of both genes radiosensitized Cal33 and SAS cell lines. Moreover, high KDM6A expression in tissue sections of patients with HNSCC was associated with improved locoregional control after primary (n = 137) and post-operative (n = 187) radio/chemotherapy. Conversely, high KDM6B expression was a prognostic factor for reduced overall survival. Conclusions: Within this study, we investigated cellular and molecular mechanisms underlying irradiation-induced cellular plasticity, a key inducer of radioresistance, with a focus on epigenetic alterations. We identified UTX (KDM6A) as a putative prognostic and therapeutic target for HNSCC patients treated with radiotherapy.

overall_design: Within this study, the human head and neck squamous cell carcinoma (HNSCC) cell lines FaDu(DD) (RRID:CVCL_VP44, ATCC) and Cal33 (RRID:CVCL_1108, Deutsche Sammlung von Mikroorganismen und Zellkulturen DSMZ GmbH) were used. Radioresistant (RR) sublines were generated from indicated parental cell lines via selection with at least 15 fractions of 4 Gy and analyzed together with age-matched controls. Moreover, cancer stem cells (CSC) were isolated from FaDu and Cal33 cells by Aldefluor assay (Stem cell technologies) according to the manufacture’s recommendation. Genomic DNA was isolated from each cell population (23 samples in total) with the Qiamp DNA Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s recommendations.  Bisulphite converted DNA from the 48 samples were hybridised to the Illumina Infinium Human MethylationEPIC V1 Beadchip.

first: Iñaki

last: Schniewind

first: María

middle: J

last: Besso

first: Wahyu

middle: W

last: Hadiwikarta

first: Ina

last: Kurth


title: Mapping catalytically engaged TOP2B in neurons reveals the principles of topoisomerase action within the genome [RNA-Seq]

overall_design: RNA-seq to in mouse cortical neruons


title: Mapping catalytically engaged TOP2B in neurons reveals the principles of topoisomerase action within the genome

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

overall_design: Refer to individual Series


title: Mapping catalytically engaged TOP2B in neurons reveals the principles of topoisomerase action within the genome [CTCF ChIP-Seq]

overall_design: CTCF ChIP-seq in mouse cortical neruons


title: Differential gene expression analysis of trisomy 21 and euploid hematopoietic progenitor cells derived from human pluripotent stem cells.

city: Boston

first: Chun-Chin

last: Chen

state: MA

address: 300 Longwood Avenue

institute: BCH

summary: Children with trisomy 21 (T21) are highly predisposed to acute myeloid leukemia, which is preceded by a pre-leukemic transient abnormal myelopoiesis driven by truncating mutations in GATA1 (GATA1s). We investigated gene expression profiles in T21 and isogenic euploid hematopoietic progenitor cells (HPCs) derived from human induced pluripotent stem cells (iPSCs), in combination GATA1s and STAG2 mutations associated with T21 myeloid leukemia. We identified upregulation of interferon alpha/gamma responses and ribosome subunit pathways in gene set enrichment analysis in T21 versus euploid CD45+ hematopoietic cells, whereas pathways regulating genome integrity including mitotic spindle and G2/M checkpoint were downregulated. GATA1s in T21 cells led to downregulation of heme metabolism and apoptosis pathways as well as a further significant increase in the average expression of genes on chromosome 21. These results suggest that T21 and GATA1s mutations cooperate to disrupt normal HPC functions and cause myeloid lineage skewing.

overall_design:
We introduced mutations in exon 2 of GATA1 by CRISPR/Cas9 to generate GATA1s-mutant single clones in T21 and isogenic euploid human iPSCs (PMID: 23045682). A STAG2 mutant clones was generated in the T21-GATA1s line by disrupting exon 5 using CRISPR/Cas9. Hematopoietic differentiation was performed using STEMdiff Hematopoietic Kit (STEMCELL #05310) following manufacturer’s protocol to derive HPCs. RNA was purified using RNeasy Micro Kit (Qiagen) and submitted for bulk RNA-seq on Illumina NextSeq platform using single-end 75bp setting. Reads were mapped to hg19 genome using Rsubread (2.12.0) in R (4.2.2). Differential analyses were performed using edgeR (3.40.2).
Submitter states that missing raw data will be deposited in dbGaP

first: R. Grant

last: Rowe


title: Momordicine-I suppresses head and neck cancer growth by reprogrammimg immunosuppressive effect of the tumor-infiltrating macrophages and B lymphocytes

status: Public on Jan 24 2024

city: St. Louis

first: Michelle

last: Brennan

state: MO

address: 1100 South Grand Blvd

department: Biochemistry & Molecular Biology

institute: Saint Louis University School of Medicine

summary: Head and neck cancer (HNC) is prevalent worldwide, and treatment options are limited. Momordicine-I (M-I), a natural component from bitter melon, shows antitumor activity against these cancers, but its mechanism of action, especially in the tumor microenvironment (TME), remains unclear. In this study, we establish that M-I reduces HNC tumor growth in two different immunocompetent mouse models using MOC2 and SCC VII cells. We demonstrate that the anticancer activity results from modulating several molecules in the monocyte/macrophage clusters in CD45+ populations in MOC2 tumors by single-cell-RNA sequencing.. Tumor-associated macrophages (TAMs) often pose a barrier to antitumor effects, but following M-I treatment, we observed a significant reduction in the expression of Sfln4, a myeloid cell differentiation factor, and Cxcl3, a neutrophil chemoattractant, in the monocyte/macrophage populations. We further find that the macrophages must be in close contact with the tumor cells to inhibit Sfln4 and Cxcl3, suggesting that these TAMs are impacted by M-I treatment. Coculturing macrophages with tumor cells shows inhibition of Agr1 expression following M-I treatment, which is indicative of switching from M2 to M1 phenotype. Furthermore, the total B-cell population in M-I-treated tumors is significantly lower, while spleen cells also show similar results when cocultured with MOC2 cells. M-I treatment also inhibits PD1, PD-L1, and FoxP3 expression in tumors. Collectively, these results uncover the potential mechanism of M-I by modulating immune cells, and this new insight can help develop M-I as a promising candidate to treat head and neck cancers, either alone or as adjuvant therapy.

overall_design: Tumors (3 mice per group-pooled) were processed for single-cell isolation followed by cell sorting using FITC-conjugated CD45 antibody and propidium iodide (PI) staining. Isolated CD45+ sorted cells were analyzed for scRNAseq.

first: Ratna

middle: B

last: Ray

first: Subhayan

last: Sur


title: Barcode-free prediction of cell lineages from scRNA-seq datasets

status: Public on Jan 28 2024

city: Lausanne

first: Almut

middle: Sophia

last: Eisele

address: Station 19

country: Switzerland

institute: EPFL

summary: The integration of lineage tracing with scRNA-seq has transformed our understanding of gene expression dynamics during development, regeneration, and disease. However, lineage tracing is technically demanding and most existing scRNA-seq datasets are devoid of lineage information. By analyzing our own (mouse embryonic stem cells;mESCs) and public lineage-annotated scRNA-seq datastes, we could identify and characterize genes displaying conserved expression levels over cell divisions in multiple cell types. This resulted in the development of  Gene Expression Memory-based Lineage Inference (GEMLI), a computational pipeline allowing to predict cell lineages over several cell divisions solely from scRNA-seq datasets.

overall_design: CGR8 mESCs were barcoded using the LARRY cellular barcoding library and grown for 48h in N2B27 medium supplemented with 2i and LIF before analysis by scRNA-seq. Extraction of LARRY lineage barcodes in the scRNA-seq data allows to link single cell transcriptomes to lineage information.

middle: S

first: Marcel

last: Tarbier

first: Alexia

middle: A

last: Dormann

first: Vicente

last: Pelechano

first: David

middle: M

last: Suter


title: DLK-gated responses in motoneurons following sciatic nerve crush

status: Public on Jan 22 2024

city: Ann Arbor

first: Catherine

last: Collins

address: 1105 N University Ave

institute: University of Michigan

summary:
To profile downstream gene-expression changes regulated by DLK, we profiled motoneurons in the lumbar spinal cord using RiboTag, following sciatic nerve crush in both control and Dlk conditional knockout (Dlk ΔMN) mice.
We found that DLK regulates the expression of many secreted proteins, which have the potential to influence the behavior of other cells, including the immune system.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of mRNAs isolated from injured, uninjured, and Naïve motoneurons from Dlk ΔMN and control animals.

first: Elham

last: Asghari Adib


title: UFL1 ablation in T cells suppresses PD-1 UFMylation to enhance anti-tumor immunity

status: Public on Jan 30 2024

city: Wuhan

first: chuan

last: he

state: China

address: Fruit lake street

department: Medical Research Institute

country: China

institute: Wuhan University

summary: To better understand the impact of Ufl1 expression in T cells on regulating tumor microenvironment dynamics, we performed single-cell RNA sequencing on purified CD45+ immune cells from MC38 xenografts harvested from Ufl1 cKO or WT C57BL/6 mice.

overall_design: MC38 tumors were established by subcutaneously injecting 1×10^5 MC38 cells into 8-week-old WT and Ufl1 cKO mice, CD45+ immune cells were sorted by FACSAria III (BD) from subcutaneous MC38 tumors for scRNA-seq analysis.

first: Chuan

last: He

first: Xixin

last: Xing


title: Effects of attenuated leptin signaling pathways on cardiac function under high-altitude hypoxia

status: Public on Jan 20 2024

city: Beijing

first: Jianan

last: Wang

address: dongdan san tiao number 5

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College

summary: Background: High-altitude hypoxia significantly impacts cardiovascular function, but the effects of adipose/metabolic factors on cardiovascular regulation remain unclear. Thus, a deeper understanding of adipose/metabolic factors’ role in cardiovascular function changes is needed. Methods: We assessed lung ventilation function, cardiovascular function, electrocardiogram, plasma CK-MB, sPecam-1, and 11 plasma adipose/metabolic factors in expeditioners at Antarctic Kunlun Station (4087m). To investigate adipose/metabolic factors’ effects and mechanisms on cardiac function, we constructed a rat model exposed to simulated hypobaric hypoxia (5000 m) with the same oxygen concentration as Kunlun Station. Echocardiography, ELISA, histology, and gene and protein expression studies were employed to examine cardiac function changes, pathological alterations, and leptin’s role in cardiac pathology under acute and chronic hypoxic exposure.  Results: The Antarctic ice plateau environment significantly altered lung ventilation function, weakened cardiac pumping and contractile function, increased systematic vascular resistance (SVR), induced adaptive changes in cardiac conduction, significantly increased plasma CK-MB and Pecam-1, and significantly reduced plasma leptin, resistin, insulin, and lipocalin-2 levels. Decreased leptin was significantly correlated to cardiopulmonary function. Rats chronically exposed to simulated hypobaric hypoxia at 5000m exhibited pulmonary arterial hypertension (PAH), right ventricular hypertrophy (RVH), impaired left ventricular systolic and diastolic function, and significant deteriorated left ventricular global longitudinal strain (GLS), lateral and radial strains of the myocardium, with increased plasma CK-MB and sPecam-1 in hypoxic rats. Protein levels of leptin/ob-Rb, JAK2/STAT3, PI3K/AKT/GSK3β, and ERK/JNK were decreased in biventricular myocardial tissues of chronic hypoxia-exposed rats, accompanied by increased myocytes hypertrophy, fibrosis, lipid deposition, cell apoptosis, and mitochondrial dysfunction, and decreased metabolic gene levels. Left ventricular transcriptome analysis revealed that decreased myocardial leptin in hypoxic rats regulated cardiac pathology via down-regulated genes related to circadian rhythm, sodium/potassium ion transport, and cell skeleton. Conclusion: Our findings suggest that leptin is a crucial metabolic factor in regulating cardiac pathological changes and cardiac contractile and diastolic function under high altitudes. These regulatory pathways may involve leptin's classical signaling pathways and genes related to circadian rhythm, sodium/potassium ion transport, and cell skeleton in the heart.

overall_design: 8 week-old male SD rats exposed to high-altitude hypobaric hypoxia for 14 days with control group exposed to normoxia

first: Shiying

last: Liu


title: DNAJB1-PRKACA fusion protein-regulated LINC00473 promotes tumor growth and alters mitochondrial fitness in fibrolamellar carcinoma

status: Public on Jan 19 2024

city: Ithaca

first: Praveen

last: Sethupathy

email: as3999@cornell.edu, pr46@cornell.edu

state: NY

address: T7 006D Veterinary Research Tower, Box 17

department: Department of Biomedical Sciences

institute: Cornell University

summary: Fibrolamellar carcinoma (FLC) is a rare liver cancer that disproportionately affects adolescents and young adults. Currently, no standard of care is available and there remains a dire need for new therapeutics. Most patients harbor the fusion oncogene DNAJB1-PRKACA (DP fusion), but clinical inhibitors are not yet developed and it is critical to identify downstream mediators of FLC pathogenesis. Here, we identify long non-coding RNA LINC00473 among the most highly upregulated genes in FLC tumors and determine that it is strongly suppressed by RNAi-mediated inhibition of the DP fusion in FLC tumor epithelial cells. We show by loss- and gain-of-function studies that LINC00473 suppresses apoptosis, increases the expression of FLC marker genes, and promotes FLC growth in cell-based and in vivo models of disease. Mechanistically, LINC00473 plays an important role in promoting glycolysis and altering mitochondrial activity. Specifically, LINC00473 knockdown leads to increased spare respiratory capacity, an indicator of mitochondrial fitness. Overall, we propose that LINC00473 could be a viable target for this devastating disease.

overall_design: RNA-seq of FLC LINC00473-overexpression (LeGO-473ox) FLC monoclone cell and empty vector (LeGO-Ctl) control FLC monoclone cell samples. Additionally, RNA-seq of tumors derived from LeGO-473ox or LeGO-Ctl cells through subcutaneous implantation into mouse flanks. Also, RNA-seq of FLC patient samples for Primary & NML tumor samples.

first: Rosanna

last: Ma

first: Alexandria

last: Shumway


title: The cells of the sensory epithelium, and not the stria vascularis, are the main cochlear cells related to the genetic pathogenesis of age-related hearing loss

status: Public on Jan 18 2024

city: Tel Aviv

first: Mai

last: Eshel

address: Klatzkin 35

department: Human Molecular Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

summary: Gene expression profile at single cell level of murine p90 cochlear duct enriched for Fbxo2+ cells

overall_design: Cochlear ducts from Three-month-old (P90) heterozygous Fbxo2VHC/+ mice were pooled and processed for nuclear extraction. 3 males and 3 females were processed separately. Venus positive nuclei were sorted using an Aria II Cell Sorter (BD) to enrich for hair cell and supporting cell nuclei.

first: Beatrice

last: Milon

first: Ran

last: Elkon

first: Ronna

last: Hertzano


title: Overexpression of FOXO1 enhances CAR T cell polyfunctionality, metabolic fitness and efficacy against solid tumors [Mouse RNAseq]

city: Melbourne

first: Kevin

middle: C

last: sek

state: VIC

address: 305 Grattan Street

department: Cancer Immunology

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Investigating the effect on CAR T cell phenotype by overexpressing FOXO1

overall_design: Murine C57BL/6 splenocytes were transduced to express a human HER2 directed CAR and a constitutively active variant of Foxo1 (Foxo1-ADA) or empty vector. CAR T cells were cultured with a CAR agonistic antibody for the HER2 CAR over 72 hours, purified and analyzed with 3' RNA seq.

first: Jack

last: Chan

first: Paul

last: Beavis

last: Sek


title: Overexpression of FOXO1 enhances CAR T cell polyfunctionality, metabolic fitness and efficacy against solid tumors [Human ATACseq CD8]

overall_design: Human PBMCs were transduced to express a human Lewis-Y directed CAR and FOXO1 or mCherry. Following transduction, CD8+ CAR T cells were sorted and analyzed by ATAC-seq


title: Cigarette smoke impairs the hematopoietic supportive property of mesenchymal stem cells via the production of reactive oxygen species and NLRP3 activation

status: Public on Jan 17 2024

city: Seoul

first: Kyung-rok

last: Yu

address: 1, Gwanak-ro, Gwanak-gu, Seoul

country: South Korea

institute: Seoul National University

summary: Mesenchymal stem cells (MSCs) play important roles in tissue homeostasis by providing a supportive microenvironmental niche for the hematopoietic system. Cigarette smoking induces systemic abnormalities, including an impeded recovery process after hematopoietic stem cell transplantation. However, the role of cigarette smoking-mediated alterations in MSC niche function have not been investigated. In the present study, we asked whether exposure to cigarette smoking extract (CSE) disrupts the hematopoietic niche function of MSCs, and pathways impacted. To investigate the effects on bone marrow (BM)-derived MSCs and support of hematopoietic stem and progenitor cells (HSPCs), we examined the impact of 3R4F as a reference CSE, and HSPC-supporting function was determined. Both direct ex vivo and systemic in vivo MSC exposure to 3R4F resulted in impaired engraftment in a humanized mouse model. Furthermore, transcriptomic profile analysis showed significantly upregulated signaling pathways related to reactive oxygen species (ROS), inflammation, and aging in 3R4F-treated MSCs. 3R4F-exposed MSCs also developed impaired HSPC-supportive function, as confirmed by colony forming unit (CFU) assays and HSPC transplantation into NSG mice, and were further restored by the ROS inhibitor N-acetyl-l-cysteine (NAC). Finally, ingenuity pathway analysis revealed the activation of NLRP3 inflammasome signaling pathway in 3R4F-treated MSCs, and pretreatment with the NLRP3 inhibitor MCC950 rescued the HSPC-supporting ability of 3R4F-treated MSCs. In conclusion, these findings indicate that exposure to CSE reduces the HSPC-supportive function of MSCs by inducing robust ROS production and subsequent NLRP3 activation.

overall_design: RNA sequencing (RNA-seq) was performed by Theragen Bio (Seongnam, South Korea) using Illumina technology as previously described, with modifications (22). Total RNA was extracted and purified from hMSCs incubated with or without 5% 3R4F using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). Libraries were generated using the Illumina TruSeq strand mRNA sample preparation kit (Illumina, San Diego, CA, USA) and sequenced on a NovaSeq 6000 (2 x 150 paired end sequencing, Illumina) according to the manufacturer's protocol.

first: Hyun Sung

last: Park

first: Byung-Chul

last: Lee

first: Kyung-Rok


title: Overexpression of FOXO1 enhances CAR T cell polyfunctionality, metabolic fitness and efficacy against solid tumors

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: A novel regulator of the PI3K/AKT pathway encoded by circ-PDE5A inhibits esophageal squamous carcinoma progression by promoting USP14-mediated deubiquitination of PIK3IP1

status: Public on Jan 15 2024

city: Guangzhou

first: kai

last: lei

address: 107 Yan Jiang West Road

department: Department of Thoracic Surgery

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

summary:
Objective: Esophageal squamous carcinoma (ESCC) is one of the most common gastrointestinal tumors, and the PI3K/AKT signaling pathway plays a key role in the development of ESCC. circRNAs have been reported to be involved in the regulation of PI3K/AKT signaling, but the underlying mechanisms are unclear. This study aimed to identify protein-coding circRNAs and investigate their function in ESCC.
Design: Differential expression of circRNAs between ESCC tissues and adjacent normal tissues was identified using circRNA microarray analysis. A novel protein encoded by circ-PDE5A was identified by LC-MS/MS. Molecular biological methods were used to explore the biological functions and regulatory mechanisms of circ-PDE5A and its encoded PDE5A-500aa novel protein in ESCC. Construction of a nanoplatform for the coupling of circRNAs to investigate the therapeutic translation value of circ-PDE5A.
Results: We found that circ-PDE5A expression was downregulated in ESCC cells and tissues, and its low expression was associated with later clinicopathological staging and poorer prognosis. Functionally, circ-PDE5A inhibited ESCC proliferation and metastasis in vitro and in vivo by encoding the novel PDE5A-500aa protein, which was identified as a key player in regulating PI3K/AKT signaling activation in ESCC. Mechanistically, the novel PDE5A-500aa protein binds directly to PIK3IP1 and promotes USP14-mediated deubiquitination of the k48-linked polyubiquitin chain at residue K198 of PIK3IP1, thereby attenuating PI3K/AKT pathway in ESCC. In addition, the circ-PDE5A plasmid-coupled reduction-responsive nanoplatform successfully inhibited ESCC growth and metastasis.
Conclusions: circ-PDE5A represents an epigenetic mechanism regulating PI3K/ATK signaling and serves as a novel and promising therapeutic target and prognostic marker for ESCC.

overall_design: To explore the specific mechanism by which circ-PDE5A affects the biological function of ESCC, we constructed KYSE30 cells with stable overexpression of circ-PDE5A and performed RNA-sequencing analysis.

first: Kai

last: Lei

first: Ruihao

last: Liang

first: Jialu

first: Minghui


title: Study on the mechanism of circ-PDE5A inhibiting the progression of esophageal squamous cell carcinoma

summary: Objective: Esophageal squamous carcinoma (ESCC) is one of the most common gastrointestinal tumors, and the PI3K/AKT signaling pathway plays a key role in the development of ESCC. circRNAs have been reported to be involved in the regulation of PI3K/AKT signaling, but the underlying mechanisms are unclear. This study aimed to identify protein-coding circRNAs and investigate their function in ESCC.  Design: Differential expression of circRNAs between ESCC tissues and adjacent normal tissues was identified using circRNA microarray analysis. A novel protein encoded by circ-PDE5A was identified by LC-MS/MS. Molecular biological methods were used to explore the biological functions and regulatory mechanisms of circ-PDE5A and its encoded PDE5A-500aa novel protein in ESCC. Construction of a nanoplatform for the coupling of circRNAs to investigate the therapeutic translation value of circ-PDE5A.  Results: We found that circ-PDE5A expression was downregulated in ESCC cells and tissues, and its low expression was associated with later clinicopathological staging and poorer prognosis. Functionally, circ-PDE5A inhibited ESCC proliferation and metastasis in vitro and in vivo by encoding the novel PDE5A-500aa protein, which was identified as a key player in regulating PI3K/AKT signaling activation in ESCC. Mechanistically, the novel PDE5A-500aa protein binds directly to PIK3IP1 and promotes USP14-mediated deubiquitination of the k48-linked polyubiquitin chain at residue K198 of PIK3IP1, thereby attenuating PI3K/AKT pathway in ESCC. In addition, the circ-PDE5A plasmid-coupled reduction-responsive nanoplatform successfully inhibited ESCC growth and metastasis.  Conclusions: circ-PDE5A represents an epigenetic mechanism regulating PI3K/ATK signaling and serves as a novel and promising therapeutic target and prognostic marker for ESCC.

overall_design: Three pairs of ESCC tissues and adjacent normal tissues were analyzed for differentially expressed circRNA using the Arraystar Human circRNA Array analysis.

last: Wang


title: Dysregulated Immune and Metabolic Pathways were associated with Poor Survival in Adult Acute Myeloid Leukemia with CEBPA bZIP in-frame Mutations

status: Public on Jan 16 2024

city: Taipei

first: Fengming

last: Tien

state: Taiwan

address: No.7, Chungshan south road

country: Taiwan

institute: National Taiwan University Hospital

summary: Acute myeloid leukemia (AML) with CEBPA bZIP in-frame mutations (CEBPAbZIP-inf) is classified within the favorable risk group by the 2022 European LeukemiaNet (ELN-2022). However, heterogeneous clinical outcomes are still observed in these patients. In this study, we aimed to investigate the mutation profiles and transcriptomic pattern associated with poor outcomes in patients with CEBPAbZIP-inf. One hundred and thirteen CEBPAbZIP-inf patients were identified in a cohort of 887 AML patients homogeneously treated with intensive chemotherapy. RNA-sequencing analysis revealed an enrichment of interferon (IFN) signaling and metabolic pathways in those with a shorter event-free survival (EFS). CEBPAbZIP-inf patients with a shorter EFS had higher expression of IFN-stimulated genes (IRF2, IRF5, OAS2, and IFI35). Genes in mitochondrial complexes I (NDUFA12 and NDUFB6) and V (ATP5PB and ATP5IF1) were overexpressed and were associated with poorer survival, and the results were independently validated in the TARGET AML cohort. In conclusion, a dysregulated immune and metabolic state were correlated with poor survival in patients with CEBPAbZIP-inf.

overall_design: Comparitive gene expression profiling of RNA-seq data for AML patients with CEBPAbZIP-inf and CEBPA wild-type

first: Hsin-An

last: Hou

first: Feng-Ming


title: Gene expression and locomotor recovery in adult rats with spinal cord injury and plasma-synthesized polypyrrole/iodine application combined with a mixed rehabilitation scheme

status: Public on Jan 26 2024

city: Mexico city

first: Angelica

last: Coyoy-Salgado

address: Av. Cuauhtémoc 330, Mexico City, Mexico

country: Mexico

institute: CONACyT-Instituto Mexicano del Seguro Social

summary:
Cell genesis and synaptic plasticity in the adult brain and spinal cord can be influenced by stress, and enriched environment and physical exercise, which promotes the re-expression in adults of a series of intrinsic and extrinsic factors that may be important to stimulte a cell to re-enter growth mode and thus promote regeneration of the damaged system.
We used microarray to identify genes that could explain some possible mechanisms involved in motor function recovery and detail the global programme of gene expression undelying plasticity and regeneration process after a spinal cord injury and identified distict classes of up-regulated and down-regulated genes during this process

overall_design: A spinal cord injury was performed in Rattus Norvergicus to RNA extraction and hybridatization on Affymetrix microarrays. We sought to obtatin spinal cord tissue after a month of produce an injury and administrated treatments.

first: Carlos

last: Orozco-Barrios


title: Nanostring analysis of neonatal brains following bacterial infection

city: ROCHESTER

first: Kathryn

last: Knoop

state: MN

address: 2511 Boulder Ridge Dr NW

department: Internal Medicine, Gastroenterology Division

institute: Mayo Clinic

summary:
Neonatal meningitis and neurocomplications are often a complication of neonatal bacterial bloodstream infections. As distinct bacterial organisms may cause different disease outcomes, we assessed two separate bacterial infections: E. coli and S. agalactiae (GBS). In this study we assessed differences in immune response within the brain tissue of neonates and the effect of gamma delta T cells to the brain during bacterial infection.
As gamma delta T cells are resident to tissues, and can contribute to bacterial infections, we compared wild-type and TCRdKO mice, which lack gamma delta T cells, in two infections models: E. coli and GBS.

overall_design:
We profiled RNA from homogenized brain from either control mice or TCRd knockout mice following acute infection with either E. coli or GBS using the NanoString Sprint Platform using Mouse Immunology panel.
We performed mRNA profiling for 547 target genes, and 14 internal reference controls.

first: Lila

last: Witt


title: Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation [ChIP-seq]

status: Public on Jan 11 2024

city: Brookline

first: Ramesh

last: Shivdasani

state: Massachusetts

address: SM1052, Smith10, 450 Brookline Ave

department: Medical Oncology

institute: DFCI

summary:
To investigate the regulation of human enteroendocrine cell differentiation, we established Neurog3ER inducible cell lines.
We then analysed active histone marks using data obtained from H3K27ac ChIP-seq at various  time points.

first: Pratik

middle: N

last: Singh


title: Single-cell characterization of human conjunctiva tissue, organoids and air-liquid interface cultures (10X)

city: Utrecht

first: Marie

last: Bannier-Hélaouët

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: We mapped the cell types present in human conjunctiva tissue, organoids and air-liquid interface cultures exposed or not to IL4/13.

overall_design: The following samples were subjected to single-cell mRNA sequencing: (1) human conjunctival organoids cultured in expansion medium for 5 days (donor 16 – palpebral – passage 5), (2) human conjunctival organoids cultured in expansion medium for 10 days and in differentiation medium for 7 days (donor 16 – palpebral – passage 4), (3) human conjunctival ALI when cells had just reached confluence (i.e. 3 days after seeding, named ALI day 0, from donor 16 – palpebral – passage 6), (4) human conjunctival ALI 3 days after shifting to air-liquid interface (donor 16 – palpebral – passage 5), (5) human conjunctival ALI 17 days after shifting to air-liquid interface (donor 16 – palpebral – passage 3, donor 4 – bulbar – passage 10), (6) human conjunctival ALI 15 days after shifting to air-liquid interface exposed to IL4/13 (donor 4 – bulbar – passage 4), and (7) human tissue from 4 pooled donors (all bulbar conjunctiva).

first: Mart

last: Lamers

first: Harry

last: Begthel

first: Ziliang

last: Ma

first: Jeroen

last: Korving

first: Amir

last: Giladi

first: Willine

last: van de Wetering

first: Carmen

last: Lopez-Iglesias

first: Nobuyo

last: Yawata

first: Mor

last: Dickman

first: Vanessa

last: LaPointe

first: Rachel

last: Kalmann

first: Saskia

last: Imhoff

first: Peter

last: Peters

first: Wei

last: Wu

first: Bart

last: Haagman

first: Hans

last: Clevers


title: RNA-sequencing of liver tissue from wild type and Gramd1c knockout mice fed with high and low cholesterol diet

city: Cleveland

first: Mark

last: Brown

state: OH

department: Cancer Bio

institute: Cleveland Clinic

summary: The Aster-C protein (encoded by the Gramd1c gene) is an endoplasmic reticulum (ER) resident protein that has been reported to transport cholesterol from the plasma membrane to the ER . Although there is a clear role for the closely-related Aster-B protein in cholesterol transport and downstream esterification in the adrenal gland, the specific role for Aster-C in tissue cholesterol homeostasis is not well understood. Here, we have examined whole body cholesterol balance in mice globally lacking Aster-C under low or high dietary cholesterol conditions.transport and metabolism under divergent dietary cholesterol conditions. These results strongly suggest that Aster-C alone is not sufficient to control whole body cholesterol balance, but can modestly impact circulating cortisol and bile acid levels when dietary cholesterol is limited.

overall_design: Liver tissue mRNA profiles of GRAMD1C wild type and knockout mice fed with high and low cholesterol diet for 4 weeks

first: Banerjee

last: Rakhee

first: J

first: Jung

last: Bryan


title: Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation [bulk ATAC-seq]

first: Ramesh

last: Shivdasani

summary:
To investigate the regulation of human enteroendocrine cell differentiation, we established Neurog3ER inducible cell lines.
We then performed chromatin analysis using data obtained from ATAC-seq of 2 independent human lines at various  time points.

first: Pratik

last: Singh


title: Oxygen enhances antiviral innate immunity through maintenance of EGLN1-catalysed proline hydroxylation of IRF3

city: 武汉

first: zixuan

last: wang

state: 湖北省

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

summary: Oxygen is essential for aerobic organisms, but little is known about its role in antiviral immunity. Here, we report that during responses to viral infection, the hypoxic conditions repress antiviral-responsive genes independently of HIF signalling. EGLN1 was identified as a key mediator of the enhancement exerted by the oxygen on antiviral innate immune responses. Under sufficient oxygen conditions, EGLN1 maintains its prolyl hydroxylase activity to catalyse hydroxylation of IRF3 at proline 10. This modification enhances IRF3 phosphorylation, dimerisation, and nuclear translocation, leading to subsequent IRF3 activation. Furthermore, mice and zebrafish with Egln1 deletion, treatment with the EGLN inhibitor, FG4592, or mice carrying an Irf3 P10A mutation are more susceptible to viral infections. These findings not only reveal a direct link between oxygen and antiviral responses, but also provide insights into the mechanisms by which oxygen regulates innate immunity

overall_design:
To investigate the function of the oxygen sensor EGLN1 in innate immune signaling pathways, we constructed wild-type MEF and EGLN1 knockdown MEF cell lines
We then performed gene expression analysis in two different cell lines with or without VSV infection by using the data provided by RNA-seq
Fastp (version 0.19.7) was used to perform basic statistics on the quality of the raw reads
The clean reads were then mapped to the mouse genome using HISAT.
Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses for the DEGs were performed using Cluster Profiler version 3.8

first: Xing

last: Liu

first: Jinghua

last: Tang

first: Zixuan

last: Wang

first: Wuhan

last: Xiao


title: Effect of Pax6 KO in mouse conjunctival organoids

first: Marie

last: Bannier-Hélaouët

summary: We sought the differences between WT and Pax6-KO mouse conjunctiva organoids.

overall_design: To determine the effect of Pax6-KO, we established 2 WT and 3 Pax6-KO clonal lines, that were each cultured for 7 days before being subjected to bulk RNA sequencing.

first: Mart

last: Lamers

first: Jeroen

last: Korving

first: Amir

last: Giladi

first: Harry

last: Begthel

first: Willine

last: van de Wetering

first: Carmen

last: Lopez-Iglesias

first: Nobuyo

last: Yawata

first: Mor

last: Dickman

first: Rachel


title: Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation [bulk RNA-seq]

first: Ramesh

summary:
To investigate the regulation of human enteroendocrine cell differentiation, we established Neurog3ER inducible cell lines.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 independent human lines at various  time points.


title: Gsα regulates macrophage foam cell formation during atherosclerosis

status: Public on Jan 06 2024

city: Jinan

first: Chang

last: Ma

state: Shandong

address: Wenhuaxi Road107#

institute: Shandong University

summary: To investigate in vivo transcriptome profiles of macrophages from CTR and Mac-GsαKO mice , we isolated and cultured peritoneal macrophages. Our data indicates that macrophages from CTR and Mac-GsαKO mice show different mRNA expressions. Compared with macrophages from CTR mice, macrophages from Mac-GsαKO mice expressed more genes related to lipid metabolism.

overall_design: Samples from macrophages isolated and cultured from CTR and Mac-GsαKO mice (aged 6-8 weeks).

first: Xiaoteng

last: Qin

first: Yihui

last: Li

first: Wencheng

last: Zhang


title: Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation [Cut&Run]

last: Shivdasani

summary:
To investigate the regulation of human enteroendocrine cell differentiation, we established Neurog3ER inducible cell lines.
We then analyzed ASCL1 and NEUROD1 binding using data obtained from CUT&RUN of at 96h.

overall_design: CUT&RUN of at 96h.

first: Pratik

last: Singh


title: Overexpression of FOXO1 enhances CAR T cell polyfunctionality, metabolic fitness and efficacy against solid tumors [Human RNAseq CD8]

first: Kevin

last: sek

overall_design: Human PBMCs were transduced to express a human Lewis-Y directed CAR and FOXO1 or mCherry. Following transduction, CAR T cells were sorted on CD8+ CAR T cells and analyzed by 3' RNA-seq

first: Jack

last: Chan

first: Paul

last: Beavis

last: Sek


title: Effect of HSV1 and hAdV8 infection in human conjunctiva air-liquid interface cultures

first: Marie

last: Bannier-Hélaouët

summary: We sought to identify the effect of HSV1 or hAdV8 infection in human conjunctival epithelium.

overall_design: We performed bulk RNA sequencing on air-liquid interface cultures infected with HSV1 for 72 hours (and the uninfected control; 2 controls and 2 infected) and with hAdV8 for 96 hours (and the uninfected control; 3 controls and 3 infected).

first: Mart

last: Lamers

first: Jeroen

last: Korving

last: Kalmann

first: Saskia

last: Imhoff

first: Peter

last: Peters

first: Bart

last: Haagman

first: Hans

last: Clevers


title: Overexpression of FOXO1 enhances CAR T cell polyfunctionality, metabolic fitness and efficacy against solid tumors [Human RNAseq CD4]

summary: Investigating the effect on CAR T cell phenotype by overexpressing FOXO1

overall_design: Human PBMCs were transduced to express a human Lewis-Y directed CAR and FOXO1 or mCherry. Following transduction, CAR T cells were sorted on CD4+ CAR T cells and analyzed by 3' RNA-seq


title: Single-Cell Analysis of Transcriptome and TCR Sequencing Reveals Immune Cell Atlas and Functional Heterogeneity of T Cell Repertoire in Murine Heart Transplantation

first: Jie

last: Wu

state: Hubei

address: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road 1277

department: Department of Cardiovascular Surgery

summary: To illustrate the  immune cell atlas and functional heterogeneity of T cell repertoire in murine heart transplantation，we established the murine heterotopic heart transplantation model and isolated CD45 positive cells from cardiac grafts and spleens for single cell transcriptome and TCR sequencing.

overall_design: 8-10 weeks male C57BL/6 (H-2b) and BALB/c(H-2d) were purchased from Charles River (Beijing, China). All mice experiments were performed in a specific pathogen-free facility according to the guidelines of the animal care and use committee of Huazhong University of Science and Technology. We established the murine heterotopic heart transplantation model as previously described. Allograft group: BALB/c (H2d) hearts were transplanted into fully MHC-mismatched C57BL/6 (H2b) recipients. Isograft group: C57BL/6 (H2b) hearts were transplanted into MHC-matched C57BL/6 (H2b) recipients. CD45+ cells were sorted from recipients’ heart grafts and spleens on Day 6 after transplantation. Each group (allograft, allo-spleen, and iso-spleen) was pooled from three mice. In brief, cardiac grafts were cut into pieces and digested with 1 mg/mL of collagenase B (Roche 11088815001) in HEPES buffer for 45 min at 37°C. After digestion, cell suspensions were collected and filtered with 70-μm cell strainers (BIOFIL), Percoll (Beijing Solarbio Science & Technology Co., Ltd.) was used to purify mononuclear cells through density centrifugation with 600g 25min RT not-brake. Splenocytes were prepared through grinding, erythrocyte lysis, washing and centrifugation (600g, 3min). CD45+ live cells were then sorted by FACSAria flow cytometer after Cardiac graft infiltrating cells and splenocytes stained with CD45-APC (Biolegend 103112) and Zombie GreenTM Fixable Viability Kit (Biolegend 423112).

first: Jikai

last: Cui

first: Heng

last: Xu


title: circZDHHC11 knockdown in ST486 cells

status: Public on Jan 04 2024

city: Groningen

first: Joost

last: Kluiver

address: Hanzeplein 1

institute: UMCG

summary: To determine the effect of circZDHHC11 knockdown on gene expression in burkitt lymphoma cell line ST486

overall_design: ST486 cells were infected with shRNAs (sh1 and sh2) against circZDHHC11 or control shRNA (NT1). Two independent experiments were performed using GFP+ sorted cells  (>98% purity) on day 5 (exp 1) or day 6 (exp 2) post-infection.

first: Yichen

last: Liu

first: Xing

last: Zhao

first: Annika

last: Seitz

first: Annie

last: Hooijsma

first: Reyhaneh

last: Ravanbakhsh

first: Sofia

last: Sheveleva

first: Debora

last: de Jong

first: Jasper

last: Koerts

first: Agnieszka

last: Dzikiewicz-Krawczyk

first: Anke

last: van den Berg

first: Lotteke

last: Ziel-Swier


title: T cell receptor repertoire profiling of murine skin transplantation in context of PD-1+ cells Ablation therapy

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: The purpose of this study was to evaluate the influence of ablating PD-1+ cells on alloreactive T cell repertoires. We established the murine skin transplantation model and obtained the draining lymph nodes (dLNs) T cells from recipients for TCR repertoires sequencing.

overall_design: PD-1DTR mice were generated via knocking IRES-DTR-P2A-EGFP-P2A-firefly Luciferase into 3’ UTR of the Pdcd1 locus with EGE (CRISPR/Cas9) system from Biocytogen (Beijing, China). 4 to 6-week-old male mice were performed with thymectomy and recovered for one month before transplantation. The murine skin transplantation model was established as previously described. In the ISO group, the dorsal sides of C57BL/6 (B6; H-2b) ears were transplanted onto the dorsum of PD-1DTR recipients. While in the PBS group and DT group, BALB/c (H-2d) ears were transplanted onto the dorsum of PD-1DTR recipients, with PBS or DT (10μg/kg) treatment. At day 9 post transplantation, dLNs of recipients were obtained with Pan T Cell Isolation Kit for TCR repertoires sequencing. Each group has 3 replicates. Each replicate was generated from isolated T cells pooled from 3 mice.

first: Jizhang

last: Yu


title: Monocytes in Type 1 diabetes families exhibit high cytolytic activity and subset abundances that correlate with clinical progression

status: Public on Jan 01 2024

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary: Monocytes are immune regulators implicated in the pathogenesis of Type 1 diabetes (T1D), an autoimmune disease that targets the insulin-producing pancreatic β-cell.  We determined that monocytes of recent onset (RO) T1D patients and their healthy siblings express proinflammatory/cytolytic transcriptomes and hyper-secrete cytokines in response to lipopolysaccharide exposure compared to unrelated healthy controls (uHC).  Flow cytometry measured elevated circulating abundances of intermediate monocytes and >2-fold more CD14+CD16+HLADR+KLRD1+PRF1+ NK-like monocytes among ROT1D patients compared to uHC.  The intermediate to nonclassical monocyte ratio among ROT1D patients correlated with the decline in functional β-cell mass during the first 24 months post-onset.  Among sibling non-progressors, flow cytometry measured temporal decreases in the intermediate to nonclassical monocyte ratio and NK-like monocyte abundances; these changes coincided with increases in peripheral activated regulatory T-cells.  In contrast, these monocyte populations exhibited stability among T1D progressors.  This study associates heightened monocyte proinflammatory/cytolytic activity with T1D susceptibility and progression and offers insight to the age-dependent decline in T1D susceptibility.

overall_design: Cryopreserved PBMC samples of 8 age-matched subjects (2 well-controlled ROT1D patients, 2 HRS, 2 LRS, 2 uHC) were thawed and incubated with the fixable Live/Dead Violet dye (Life Technologies, Grand Island, NY, USA),  generate a monocyte-enriched, single cell, PBMC population and analyzed by scRNA-seq.

first: Tarun

last: Pant

first: Chien-Wei

last: Lin

first: Shuang

last: Jia

first: Mark

middle: F

last: Roethle

first: Nathan

last: Truchan

first: Amina

last: Bedrat

first: Ashley

middle: E

last: Ciecko

first: Jeffrey

last: Woodliff

first: Yi-Guang

last: Chen


title: Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications

city: Canberra

first: AKANKSHA

last: SRIVASTAVA

state: Australian Capital Territory

address: 131 Garran Rd

department: The Shine-Dalgarno Centre for RNA Innovation

institute: Australian National University

summary: The expanding field of epitranscriptomics might rival the epigenome in the diversity of biological processes impacted. However, the identification of multiple modification types in individual RNA molecules remains challenging. We present CHEUI, a new method that detects N6-methyladenosine (m6A) and 5-methylcytidine (m5C) in individual transcript molecules in a single condition as well as differential methylation between two conditions, using nanopore signals. CHEUI processes observed and expected signals with convolutional neural networks to achieve high single-molecule accuracy and outperform other methods in detecting m6A and m5C sites and quantifying their stoichiometry. Moreover, CHEUI’s unique capability to identify different modifications in the same signal data reveals a non-random co-occurrence of m6A and m5C in transcripts in human cell lines and during mouse embryonic brain development. CHEUI unlocks the capability of studying links between multiple RNA modifications and phenotypes, enabling the discovery of new epitranscriptome functions. Furthermore, CHEUI's training and testing protocols are adaptable to other modifications, making it a versatile RNA technology.

overall_design: We performed RNA bisulfite treatment (bsRNA-seq) following the protocol from Johnson et al. (Johnson, Z., Xu, X., Pacholec, C. & Xie, H. Systematic evaluation of parameters in RNA bisulfite sequencing data generation and analysis. NAR genomics Bioinforma. 4, lqac045 (2022). There were no deviations done for the protocol except the fact that a GE50 spin column was used for the removal of the excess of bisulfite reagent (sodium bisulfide and hydroquinone) instead of a GE25. This protocol was applied to RNA fully modified with m5C or non-modified obtained from in-vitro transcripts (IVTs) m1, m2, m3, m4 built from four non-overlapping fragments from the mouse canonical pre-rRNA (~13kb long). Sequencing of the bisulfite-treated samples was performed with Illumina.


title: SRSF1 is involved in alternative mRNA splicing in granulosa cell survival

city: Beijing

first: xiaohong

last: Yao

address: No. 2 Yuanmingyuan West Road, Haidian District, Beijing

institute: China Agricultural University

summary: Granulosa cells abnormalities are one of the characteristics of premature ovarian insufficiency (POI). Abnormal expression of serine/arginine-rich splicing factor 1 (SRSF1) can causes a variety of diseases, but the role of SRSF1 in mouse granulosa cells has been poorly reported. In this study, we found that SRSF1 was expressed in the nuclei of both mouse oocytes and granulosa cells. Specific knockout of SRSF1 in granulosa cells was performed using Foxl2-creERT2 mice, and morphological staining showed that follicular development was blocked. In addition, granulosa cell proliferation decreased and cell apoptosis increased. The differential gene Gene Ontology (GO) analysis of RNA-Seq results showed abnormal expression of DNA repair, cell killing and other signaling pathways. Alternative splicing (AS) analysis showed that SRSF1 affected DNA damage in granulosa cells by regulating genes related to DNA repair. In conclusion, SRSF1 in granulosa cells affects female reproduction by controlling the development of follicles through regulating granulosa cell DNA repair related genes.

overall_design: SRSF1 was knocked out in ovarian granulosa cells, and 9dpp ovaries were taken to analyze and compare the gene expression profiles of RNA-Seq data between WT and knockout groups.

first: Xiaohong

first: Jiali

last: Liu


title: Glioblastoma vessel co-option occurs as a resistance mechanism to chemoradiation via induction of a persister cell state

city: Orsay

first: Giorgio

last: Seano

address: Bâtiment 110, Rue Henri Becquerel

department: INSERM U1021 - CNRS UMR3347

country: France

institute: Institut Curie

summary: Glioblastoma (GB) is one of the deadliest types of human cancer. Recurrence after chemoradiation is mostly caused by regrowth of highly invasive and resistant cells. There is an urgent need to better understand the underlying GB mechanisms of chemoradiation resistance and tumor spreading. Using a combination of transcriptomic analysis, longitudinal imaging, organotypic cultures, functional assays, animal studies and clinical data analyses, we demonstrated that chemoradiation and brain vasculature induce a transition to an invasive functional cell state that we named VC-Resist. Better cell survival, G2M-arrest, senescence/stemness pathways’ induction and YAP activation make this GB cell state more resistant to therapy. Notably, these persister GB cells are highly vessel co-opting, allowing homing to the perivascular niche, which in turn increases their transition to this cell state. These findings demonstrate how vessel co-option, the perivascular niche, and GB cell plasticity jointly drive resistance during GB recurrence.

overall_design: Gene expression profiling analysis of RNA-seq data for MGG4, MGG18, GL261 GBM cells based on a cells state reporter expression (Nestin reporter, high or low expression of the reporter). Profiling of MGG4 after therapies in vitro and in-vivo (TMZ-temozolomide or IR-irradiation). Profiling of MGG4 after culture with brain blood vessels (BV) and corresponding controls without blood vessels  (BV-CTL).

first: Cathy

last: Pichol-Thievend

first: Oceane

last: Anezo

first: Aafrin

last: Pettiwala

first: Guillaume

last: Bourmeau


title: Mitf is a Schwann Cell Sensor of Axonal Integrity that Drives Nerve Repair

city: La Jolla

first: Samuel

middle: L

last: Pfaff

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary:
Here we identify Mitf as a transcriptional sensor of axon damage under the control of Nrg-ErbB-PI3K-PI5K-mTorc2 signaling. Mitf regulates a core transcriptional program for generating functional repair Schwann cells following injury and during peripheral neuropathies caused by CMT4J and CMT4D. In the absence of Mitf, core genes for epithelial-to-mesenchymal transition, metabolism and dedifferentiation are misexpressed and nerve repair is disrupted. Taken together, our findings demonstrate that Schwann cells monitor axonal health using a phosphoinositide signaling system that controls Mitf, which is critical for activating cellular plasticity and counteracting neural disease.
We performed gene expression profiling analysis using data obtained from RNA-seq of sciatic nerves from Mitf mutant mice in both control and injury experiments as well as in Ndrg1 and Egr2Cre models mutants.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of sciatic nerves.

first: Lydia

last: Daboussi

first: Shawn

last: Driscoll


title: Transcriptomic Analysis Reveals that Atf3/c-Jun/Lgals3 axis is associated with Central Diabetes Insipidus after Hypothalamic Injury

first: Mingfeng

last: Zhou

state: Guangdong Province

address: No.1838 Guangzhou Avenue North

department: Department of Neurosurgery

institute: Nanfang Hospital, Southern Medical University

summary:
Purpose: To investigate the underlying regulatory mechanism of neurodegeneration induced by hypothalamic injury from basic gene expression profile, we extracted RNA from hypothalamic supraoptic nucleus (SON) and paraventricular nucleus (PVN) RNA sequencing (RNA-seq), at day 1 and day 7 after PEL surgery.
Results: We identified 1711 differentially expressed genes (DEGs, defined as adjust p value < 0.05) between PEL_1d (day 1 after PEL) and control group, 185 DEGs between PEL_7d (day 7 after PEL) and control group, respectively.
Conclusions: We revealed that RNA-seq based transcriptome characterization would expedite genetic network analyses of hypothalamic SON, PVN and permit the dissection of complex biologic functions during the process of central diabetes insipidus after PEL surgery.

overall_design: Hypothalamic SON and PVN mRNA profiles of control, PEL_1d and PEL_7d rat.

first: Songtao

last: Qi


title: YAP Drives Assembly of a Spatially Colocalized Cellular Triad Required for Heart Renewal

city: Houston

first: Jong

middle: H

last: Kim

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: After myocardial infarction (MI), the heart fails to renew, and the cardiac microenvironment is irreversibly disrupted. Inactivation of the Hippo signaling pathway can rebuild the post ischemic microenvironment and improve cardiac function. We investigated spatially resolved cellular relationships of neonatal and adult renewal-competent hearts to gain insight into inefficient mammalian heart renewal. Spatial transcriptomics (ST) and single-cell sequencing of adult control hearts and hearts expressing YAP5SA, an active version of the Hippo signaling pathway effector YAP, which models heart renewal, revealed a conserved, renewal-competent cardiomyocyte (CM) population in control hearts and amplified in YAP5SA hearts. This CM population was also found in the wildtype, renewal competent neonatal heart after myocardial infarction, as well as the adult human heart. Cardiac fibroblasts (CFs), expressing complement C3, colocalized with these CMs. In YAP5SA hearts and neonatal hearts post-MI, macrophages (MPs) expressing complement receptor C3ar1 also colocalized, creating a pro-renewal niche composed of the CM, CF and MP triad. Both C3 and C3ar1 loss-of-function in YAP5SA hearts similarly suppressed heart renewal, indicating that C3-expressing CFs, C3ar1-expressing MPs, and complement system signaling play a direct role in heart renewal

overall_design:
Single cell RNA sequencing and spatial transcriptomics were performed to examine MCM control versus MCM YAP5SA adult murine hearts

Single nucleus RNA sequencing were performed to examine wild type control and C3-/- p2 neonatal murine hearts 3 days after sham or MI surgeries.

first: Rich

middle: G

last: Li

first: Xiao

first: James

last: Martin


title: Adult Neurogenesis of the Median Eminence Contributes to Structural Reconstruction and Recovery of Body Fluid Metabolism in Hypothalamic Self-Repair

summary:
Purpose: To investigate the underlying regulatory mechanism of neurobiology induced by hypothalamic injury from basic gene expression profile, we extracted RNA from hypothalamic median eminence (ME) RNA sequencing (RNA-seq), at day 1  after control and PEL surgery.
Results: We identified 811 differentially expressed genes (DEGs, defined as adjust p value < 0.05) between PEL_1d (day 1 after PEL) and control group.
Conclusions:We revealed that RNA-seq based transcriptome characterization would expedite genetic network analyses of hypothalamic ME and permit the dissection of complex biologic functions during the process of central diabetes insipidus after PEL surgery.

overall_design: Hypothalamic ME mRNA profiles of Control and PEL_1d rats.

first: Yichao

last: Ou


title: Tumor type and cell type-specific gene expression alterations in diverse pediatric central nervous system tumors identified using single nuclei RNA-seq

status: Public on Dec 31 2023

city: Lebanon

first: Min Kyung

last: Lee

state: NH

address: 1 Medical Center Dr

institute: Dartmouth College

summary: Central nervous system (CNS) tumors are the leading cause of pediatric cancer death, and these patients have an increased risk for developing secondary neoplasms. Due to the low prevalence of pediatric CNS tumors, major advances in targeted therapies have been lagging compared to other adult tumors. We collected single nuclei RNA-seq data from 35 pediatric CNS tumors and three non-tumoral pediatric brain tissues (84,700 nuclei) and characterized tumor heterogeneity and transcriptomic alterations. We distinguished cell subpopulations associated with specific tumor types including radial glial cells in ependymomas and oligodendrocyte precursor cells in astrocytomas. In tumors, we observed pathways important in neural stem cell-like populations, a cell type previously associated with therapy resistance. Lastly, we identified transcriptomic alterations among pediatric CNS tumor types compared to non-tumor tissues, while accounting for cell type effects on gene expression. Our results suggest potential tumor type and cell type-specific targets for pediatric CNS tumor treatment.

overall_design: Nuclei were isolated from pediatric central nervous system tumors and non-tumor pediatric brain tissue and RNA was isolated following the Qiagen RNeasy Plus kit. Libraries for bulk RNA-seq were prepared following the Takara Pico v3 low-input protocol.

first: Min

middle: K

first: Brock

last: Christensen


title: Comprehesive DNA methylation profiling reveals novel biomarkers and potential pathways in epithelial ovarian cancer.

city: Teliyarganj, Prayagraj

first: Priyanka

last: Gautam

state: Uttar Pradesh

address: Department of Biotechnology, MNNIT Allahabad

department: Biotechnology

country: India

institute: Motilal Nehru National Institute of Technology

type: Methylation profiling by high throughput sequencing

summary: This study showed that MeDIP-seq could be used for methylation profiling in an efficient manner and identified a number of potential hub genes and pathways important in the ovarian cancer carcinogenesis that may deepen our understanding of the molecular mechanisms involved inthe development of ovarian cancer.

overall_design: DNA methylation profiling of 3 normal, 1 benign and 4 ovarian cancer samples.

first: Sameer

last: Gupta

first: Manisha

last: Sachan


title: The plasma miRnome and venous thromboembolism in high-grade glioma: miRNA sequencing of a nested case-control cohort

city: Wien

first: Andreas

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

type: Non-coding RNA profiling by high throughput sequencing

summary: Background: Patients with high-grade gliomas are at high risk of venous thromboembolism  (VTE). MicroRNAs (miRNAs) are small non-coding RNAs with multiple roles in tumor biology,  hemostasis and platelet function. We aimed to explore the association between plasma  miRNAs and risk of VTE in high-grade glioma.  Results: We conducted a nested-case control study within 152 patients with WHO grade IV  glioma that had been included in the Vienna Cancer and Thrombosis Study (CATS), a  prospective cohort study focused on risk factors for VTE in newly diagnosed or recurrent  cancer. At study inclusion a single blood draw was taken, and patients were thereafter  followed for a maximum of two years. During that time, 24 patients (16%) developed VTE. Of  the other 128 patients, we randomly selected 24 age- and sex-matched controls. After  sample quality control, the final group size was 21 VTE-patients and 23 without VTE. Small  RNA next-generation sequencing of plasma was performed. We observed that hsa-miR-451a  was globally the most abundant miRNA. Notably, 51% of all miRNAs showed a correlation  with platelet count. The analysis of miRNAs differentially regulated in VTE patients – with and  without platelet adjustment – identified potential VTE biomarker candidates such as has-miR-  221-3p.  Conclusion: We here provide one of the largest and deepest peripheral blood miRNA  datasets of high-grade glioma patients so far. Further, we confirm previous observations of a  considerable impact of platelet count on the blood miRNome. And, finally, we present first  VTE biomarker candidates that can serve as the starting point for future confirmatory  research.

first: Friedrich

last: Erhart

first: Georg

last: Widhalm

first: Barbara

last: Kiesel

first: Matthias

last: Hackl

last: Preusser

first: Karl

last: Rössler

first: Johannes

last: Thaler

first: Ingrid

last: Pabinger

first: Cihan

last: Ay

first: Julia

last: Riedl


title: Gene expression profile at single cell level from untreated and Enterococcus faecalis-infected skin wounds

city: Singapore

first: Guillaume

last: Thibault

address: 60 Nanyang Dr

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary: Enterococcus faecalis (E. faecalis) is a Gram-(+) opportunistic pathogen associated with predominantly nosocomial wound infections. E. faecalis has been shown to suppress or evade immune-mediated clearance by the immune system and promote persistent infection. Here, we sought to interrogate whether E. faecalis infection induces transcriptomic changes in the host at the single-cell resolution using a mouse excisional wound model. Keratinocyte, fibroblast, endothelial and immune cell populations reveal unique clusters in the infected wounds. Cell communication analysis discovered strong ligand-receptor interactions between macrophages and endothelial cells in the infected niche, whilst fibroblast and keratinocytes instruct healing cellular interactions in untreated skin wounds. We also identified differential terminal lineage driving genes, following RNA velocity in each condition. Together, results suggest that E. faecalis infection alters the skin transcriptome, which may help promote the chronicity of bacteria-infected wounds.

overall_design: A single, 6-mm full-thickness wound was created on the shaven dorsal skin of C57BL/6J mice. The wounds were inoculated with Enterococcus faecalis and all wounds were covered with Tegaderm. Tissues were harvested at day 4 with a 6-mm biopys punch with minimal adjacent healthy tissue.

first: Celik

last: Cenk

first: Thibault

last: Guillaume


title: Transcriptomic analysis of the bone reveals the mechanism of Desertliving Cistanche herb in ovariectomized rats of postmenopausal osteoporosis

city: zheng zhou

first: shuo

last: tian

address: Jinshui East Road

institute: Henan University of Chinese Medicine

summary: To investigate the function of Desertliving Cistanche herb in the postmenopausal osteoporosis, we established ovariectomized rats in which both ovaried were removed.We performed gene expression profiling alalysisi using date obtained from RNA-seq of ovariectomized rats of postmenopausal osteoporosis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the normal rats, ovariectomized rats and Desertliving Cistanche herb treatment.

first: Shuo

last: Tian

first: Dandan

last: Chen


title: Transcriptome Sequencing Reveals Molecular Signatures of Antigen-encountering T cells in Adoptive transfer Murine Heart Transplantation Model

city: Wuhan

first: Jie

last: Wu

summary: The purpose of this study was to identify the molecular signatures of antigen-encountering T cells, we established the adoptive transfer murine heterotopic heart transplantation model and isolated TEa cells from spleens for RNA sequencing.

overall_design: B6.Cg-Tg(Tcra,Tcrb)3Ayr/J(TEa TCR transgenic mice) and B6.SJL-Ptprca Pepcb/BoyJ (B6 CD45.1) mice were purchased from Jackson Laboratories (Bar Harbor, ME). TEa cells were isolated from spleen of TEa mice via CD4+ T Cell Isolation Kit (70901-100; BEAVER). And the purity was checked with FCM (>90%). The B6 CD45.1+ recipients were intravenously transferred with 5 million CD45.2+ TEa cells one day before heart transplantation. The murine heterotopic heart transplantation model was established as previously described. In Allograft group, BALB/c (H-2d) hearts were transplanted into CD45.1+ recipients. While in Isograft group, C57BL/6 (B6; H-2b) hearts were used as the grafts. On day 6, the TEa cells were sorted from the recipients’ spleens, and differentially expressed genes between the allograft and isograft groups were determined by RNA-seq. Each group has 3 replicates. Each replicate was generated from sorted TEa cells pooled from 3 mice.

first: Jikai

last: Cui

first: Heng

last: Xu

first: Jizhang

last: Yu


title: Ketogenic diet and BHB rescue the fall of long-term potentiation in an Alzheimer's mouse model and stimulates synaptic plasticity pathway enzymes

city: PADOVA

first: GIUSEPPE

last: PERSICO

state: PD

address: VIA UGO BASSI 58/B

country: Italy

institute: UNIVERSITA' DI PADOVA

summary: The Ketogenic Diet (KD) improves memory and longevity in aged C57BL/6 mice. We tested 7 months KD vs. control diet (CD) in the mouse Alzheimer's Disease (AD) model APP/PS1. KD significantly rescued Long-Term-Potentiation (LTP) to wild-type levels, not by changing Amyloid-β (Aβ) levels. KD's 'main actor' is thought to be Beta-Hydroxy-butyrate (BHB) whose levels rose significantly in KD vs. CD mice, and BHB itself significantly rescued LTP in APP/PS1 hippocampi. KD's 6 most significant pathways induced in brains by RNAseq all related to Synaptic Plasticity. KD induced significant increases in synaptic plasticity enzymes p-ERK and p-CREB in both sexes, and of brain-derived neurotrophic factor (BDNF) in APP/PS1 females. We suggest KD rescues LTP through BHB's enhancement of synaptic plasticity. LTP falls in Mild-Cognitive Impairment (MCI) of human AD. KD and BHB, because they are an approved diet and supplement respectively, may be most therapeutically and translationally relevant to the MCI phase of Alzheimer's Disease.

overall_design:
Brain Cortex of PS1/APP mice kept in standard diet (SD) or ketogenic diet (KD)
contributor: Alexey

first: Jacopo

last: Di Lucente

first: Giuseppe

last: Persico

first: Zeyu

last: Zhou

first: Lee-Way

last: Jin

first: Jon

last: Ramsey

first: Jennifer

middle: R

last: Rutkowsky

first: Claire

last: Montgomery

first: Kyoungmi

last: Kim

first: Marco

last: Giorgi

first: Izumi

last: Maezawa

first: Gino

last: Cortopassi

first: Alexey

last: Tomilov


title: HA-1-targeted T cell receptor (TCR) T cell therapy for recurrent leukemia after hematopoietic stem cell transplantation: results from a phase I clinical trial.

city: Seattle

first: Scott

last: Furlan

address: 1100 Fairview Ave N

institute: CRD

summary: Tumors escape antigen-directed immunotherapies through a variety of mechanisms. We used single-cell RNA sequencing (scRNA-seq) to examine potential mechanisms of immune escape in patients with disease relapse or progression after T cell receptor T cell (TCR-T) immunotherapy directed against the minor histocompatibility antigen HA-1.

overall_design: Mononuclear cells (MC) from bone marrow (BMMC) or peripheral blood (PBMC) were isolated from samples collected post- (all patients) +/- pre- (Pts 4, 6, 9) infusion of HA-1 TCR-T cells in patients with acute myeloid leukemia or myelodysplastic syndromes and captured for 5' single cell gene expression analysis. Two patient 5 samples were subjected to CD3 selection and CD3+ and CD3- fractions captured separately along with whole (unselected) cells; all other samples were unselected.

first: Michelle

last: Brault

first: Melinda

last: Biernacki

first: Marie

last: Bleakley


title: Integrated single-cell RNA sequencing and spatial transcriptomics analysis reveals the tumor microenvironment in patients with endometrial cancer responding to anti-PD-1 treatment

status: Public on Dec 27 2023

city: shanghai

first: Junfeng

last: Chen

address: Gaoke Xi Road 2699

institute: Tongji university

summary: The heterogeneity and complex of immune cell components have a crucial effect on endometrial cancer progression and response to treatment. However, deciphering the neoplastic subtypes and their spatial arrangement remains a formidable challenge. Here, we combine single-cell RNA sequencing (scRNA-seq) with spatial transcriptomics (ST) to identify special immune cell populations that might be involved in the important contribution to the anti-PD-1 sensitiveness of EC. Each cell is organized into discrete subpopulations, characterized by a range of distinct features, origins, and functions. These cell clusters are not only distinguished by their diversity but also arise from interplay among various subtypes. Cell number and function of CD8 cytotoxic cells and Treg cells were abnormal in anti-PD-1 patients with non-responsiveness, and we also identified several ligand-receptor associated with T cell dysfunction. Additionally, we have observed that these subclusters are distinctly localized within various tissue regions, exhibiting variations in the enrichment of immune cell types. Our findings offer valuable biological insights into emerging therapeutic targets and potential biomarkers for enhancing anti-PD-1 therapy.

overall_design: Case A : responders to anti-PD-1 therapy ; Case B：nonresponders  to anti-PD-1 therapy

first: Yunfeng

last: Song

first: Jian

last: Huang

first: Xiaoping

last: Wan

first: Yiran

last: Li


title: Comprehensive Assessment of Isoform Detection Methods for Third-Generation Sequencing Data

status: Public on Dec 25 2023

city: Haining

first: Yaqi

last: Su

state: Zhejiang

address: ZJU-UoE Institute,718 East Haizhou Rd.

institute: Zhejiang University-University of Edinburgh Institute, Zhejiang University

summary: The advancement of Third-Generation Sequencing (TGS) techniques managed to increase the sequencing length to several kilobases, which leads to a bright future for completely reserving alternative splicing (AS) events and isoform expressions. In recent years, many computational methods for isoform detection from long-read sequencing data have been developed and published. However, there is no prior comparative study that systemically evaluates the performance of the software implemented with different algorithms. Here we benchmarked nine methods implemented in seven computational tools that can identify isoform structures from TGS RNA sequencing data and analyzed their performances from various aspects using both simulated datasets produced by an in-house simulator and previously published experimental data. Our results comprehensively demonstrate the relative effectiveness of the approaches and provide guidance as well as recommendations for future research on AS analysis and further improvement of the tools for isoform detection using TGS data.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for naïve and primed H1 cells.

first: Zhejian

last: Yu

first: Ziwei

last: Xue

first: Yixin

last: Guo

first: Wanlu

last: Liu


title: Single-cell transcriptomic profiling of the neonatal oviduct and uterus reveals new insights into upper Müllerian duct regionalization

status: Public on Dec 21 2023

city: Madison

first: Fei

last: Zhao

address: 2015 Linden Drive, Room 4206/4210

department: CBS

institute: School of Veterinary Medicine, University of Wisconsin Madison

summary: The upper Müllerian duct (MD) is patterned and specified into two morphologically and functionally distinct organs, the oviduct and uterus. It is known that this regionalization process is instructed by inductive signals from the adjacent mesenchyme. However, the interaction landscape between epithelium and mesenchyme during upper MD development remains largely unknown. Here, we performed single-cell transcriptomic profiling of mouse neonatal oviducts and uteri at the initiation of MD epithelial differentiation (postnatal day 3). We identified major cell types including epithelium, mesenchyme, pericytes, mesothelium, endothelium, and immune cells in both organs with established markers. Moreover, we uncovered region-specific epithelial and mesenchymal subpopulations and then deduced region-specific ligand-receptor pairs mediating mesenchymal-epithelial interactions along the craniocaudal axis. Unexpectedly, we discovered a mesenchymal subpopulation marked by neurofilaments with specific localizations at the mesometrial pole of both the neonatal oviduct and uterus. Lastly, we analyzed and revealed organ-specific signature genes of pericytes and mesothelial cells. Taken together, our study enriches our knowledge of upper Müllerian duct development, and provides a manageable list of potential genes, pathways, and region-specific cell subtypes for future functional studies.

overall_design: Oviducts and uteri were collected from CD1 neonates at PND3 and dissociated to achieve single cell suspension. Two replicates for each organ were pooled from the same 3 and 4 neonates

first: Shuai

last: Jia


title: Monocytes in Type 1 diabetes families exhibit high cytolytic activity and subset abundances that correlate with clinical progression

city: Milwaukee

first: Martin

last: Hessner

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary: Monocytes are immune regulators implicated in the pathogenesis of Type 1 diabetes (T1D), an autoimmune disease that targets the insulin-producing pancreatic β-cell.  We determined that monocytes of recent onset (RO) T1D patients and their healthy siblings express proinflammatory/cytolytic transcriptomes and hyper-secrete cytokines in response to lipopolysaccharide exposure compared to unrelated healthy controls (uHC).  Flow cytometry measured elevated circulating abundances of intermediate monocytes and >2-fold more CD14+CD16+HLADR+KLRD1+PRF1+ NK-like monocytes among ROT1D patients compared to uHC.  The intermediate to nonclassical monocyte ratio among ROT1D patients correlated with the decline in functional β-cell mass during the first 24 months post-onset.  Among sibling non-progressors, flow cytometry measured temporal decreases in the intermediate to nonclassical monocyte ratio and NK-like monocyte abundances; these changes coincided with increases in peripheral activated regulatory T-cells.  In contrast, these monocyte populations exhibited stability among T1D progressors.  This study associates heightened monocyte proinflammatory/cytolytic activity with T1D susceptibility and progression and offers insight to the age-dependent decline in T1D susceptibility.

overall_design: RNA was extracted from monocytes negatively selected from PBMC of 4 groups. 14 ROT1D samples were collected from subjects collected 2–7 months after diagnosis from subjects with histories of good glycemic control and possessed ≥1 autoantibody.  Healthy control subjects were free of known infection at sample collection and belonged to one of the following 3 groups: 1) 15 HRSs - autoantibody-negative siblings of probands with high-risk (DR3 and/or DR4) HLA genotypes (HRS); 2) 19 LRSs - autoantibody-negative siblings of probands with lower risk (non-DR3/DR4) HLA genotypes (LRS); and 3) 14 uHCs - possessing no family history of T1D (uHC).

first: Tarun

last: Pant

first: Chien-Wei

last: Lin

first: Shuang

first: Mark

last: Roethle

first: Nathan

last: Truchan

first: Amina

last: Bedrat

first: Ashley

last: Ciecko

first: Jeffrey

last: Woodliff

first: Yi-Guang


title: Transcriptional effects of Deoxynivalenol in primary monocyte-derived cells

status: Public on Dec 18 2023

city: Magdeburg

first: Constanze

last: Nossol

address: Leipziger Str. 44

department: Medical Faculty

institute: Otto-von-Guericke University

summary: in vitro microarray study of transcriptional changes of primary monocyte-derived cells

overall_design:
three samples per experimental group were used for expression profiling
ANOVA

first: Klaus

last: Wimmers

first: Michael

last: Oster


title: mRNA and lncRNA expression profiling analysis in A549 cells treated with DMSO,  RSL3 alone, or co-treated with Fer-1

city: Beijing

first: Fumin

last: Tai

state: Beijing

address: 27 Taiping Road

institute: Beijing Institute of Radiation Medicine

summary: Ferroptosis is a new type of programmed cell death induced by iron-dependent lipid peroxidation that has been linked to several malignancies, including non-small cell lung cancer (NSCLC). Finding ferroptosis-associated genes is extremely helpful for guiding and improving ferroptosis-based anti-tumor therapy. To explore ferroptosis-associated genes, we treated A549 cells with DMSO, RSL3 alone, or co-treated with Fer-1 for 24h. Lung cancer-associated transcript 1 (LUCAT1) was identified as a novel ferroptosis suppressor via RNA-seq analysis.

overall_design: To investigate the mRNAs and lncRNAs associated with ferroptosis, we treated A549 cells with DMSO,  RSL3 (2μM) alone, or co-treated with Fer-1 (5μM) for 24h. We then performed gene expression profiling analysis using data from RNA-seq.

first: Hanjiang

last: Fu

first: Xiaofei

last: Zheng


title: Blockade of histamine receptor H1 augments immune checkpoint therapy by enhancing MHC-I expression in pancreatic cancer cells

status: Public on Dec 26 2023

city: Fukuoka

first: Zhong

last: pingshan

address: 3-1-1, Maidashi, Higashi-ku

department: Department of Surgery and Oncology

country: Japan

institute: Kyushu University

summary: Although immune checkpoint blockade (ICB) therapy has proven to be extremely effective in managing certain cancers, its efficacy in pancreatic ductal adenocarcinoma (PDAC) remains limited. Previous studies have indicated that histamine and histamine receptor H1 (HRH1) can suppress immunity by affecting immune cells. This study uncovered an unexplored role of HRH1 intrinsic to tumor cells in PDAC. When HRH1 specific to tumor cells was inhibited in PDAC mouse models, there was a noticeable increase in MHC-I expression in these cells via the activation of cholesterol biosynthesis signaling. This augmented the infiltration and efficacy of cytotoxic CD8+ T cells, synergizing anticancer immunity and mitigating resistance to ICB treatment. Our results highlight that HRH1 plays an immunosuppressive role in cancer cells. Consequently, HRH1 intervention may be a promising method to amplify the responsiveness of PDAC to immunotherapy.

overall_design: Human cell lines (MIA PaCa-2 and KP-2) were treated with Az or H2O.

first: PingShan

last: Zhong

first: Kohei

last: Nakata


title: Genetic interaction screen for FXN in K562 cells, to identify genes that are synthetic sick/buffering in the absence of robust Fe-S cluster synthesis

city: Rehovot

first: Tslil

last: Ast

address: 234 Herzl St.

institute: The Weizmann Institute of Science

summary: Friedreich’s ataxia (FA) is the most common monogenic mitochondrial disease. FA is caused by a depletion of the mitochondrial protein frataxin (FXN), an iron-sulfur (Fe-S) cluster biogenesis factor. To better understand the cellular consequences of FA, we performed genetic interaction mapping in control or FXN edited cells. This screen identified impaired mitochondrial translation downstream of FXN loss, and specifically highlighted the methyltransferase-like protein METTL17 as a candidate effector.

overall_design:
To investigate the genetic interactions of FXN, K562 cells were infected with pRDA_186 lentiviral vectors, which express sgRNA against a control locus or FXN, blasticidin resistance from the PGK promoter, and a 2A site-expressing EGFP. Cells were sorted for low GFP expression and expanded.
For the screen, the all-in-one Brunello barcoded library was utilized. This library contains 77,441 sgRNA; an average of 4 guides per gene and 1000 non–targeting control guides. Infections were performed in distinct duplicate at a predetermined MOI of ~0.5 in 12-well plates with 5µg/mL polybrene supplementation. Cells were infected for 2h under centrifugation at 1000 x g, incubated for 22h under standard culturing conditions and pooled 24 h post-centrifugation. Infections were performed with 6.5x107 cells per replicate, in order to achieve a representation of at least 300 cells per sgRNA following puromycin selection. 48 hours after infection, cells were selected with puromycin for 2 days to remove uninfected cells. Cells were passaged in fresh media every 2–3 days. Cells were harvested 11 days after initiation of treatment.

first: Vamsi

last: Mootha


title: The effects of glycemic index on prostate cancer progression in a xenograft mouse model

city: Los Angeles

first: Gloria Cecilia

last: Galvan

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

summary: Previously, we found low-carbohydrate diets slowed prostate cancer (PC) growth and increased survival vs. a Western diet in mice, by inhibiting the insulin/IGF-1 axis. Thus, we tested whether modifying carbohydrate quality to lower glycemic index (GI) without changing quantity results in similar benefits as with reduced quantity. Male SCID mice injected with LAPC-4 cells were single-housed and randomized when their tumors reached 200mm3 on average to a LoGI (48% carbohydrate kcal, from Hylon-VII) or HiGI Western diet (48% carbohydrate kcal, from sucrose). Body weight and tumor volume were measured weekly. Body composition was assessed 35 days after randomization. Blood glucose and serum insulin, IGF-1 and IGFBP3 were measured at study end when tumor volumes reached 800mm3. We analyzed gene expression of mice tumors by RNA-sequencing and human tumors using the Prostate Cancer Transcriptome Atlas. There were no significant differences in tumor volume (P>0.05), tumor proliferation (P=0.29), and overall survival (P=0.15) between groups. At 35 days after randomization, the LoGI group had 30% lower body fat (P=0.007) despite similar body weight (P=0.58). At sacrifice, LoGI mice had smaller livers (P<0.001) and lower glucose (P=0.15), insulin (P=0.11), IGF-1 (P=0.07) and IGF-1:IGFBP3 ratio (P=0.05), and higher IGFBP3 (P=0.09) vs. HiGI, although none of these metabolic differences reached statistical significance. We observed differential gene expression and pathway enrichment in mice tumors by diet. The most upregulated and downregulated gene in the LoGI group showed expression patterns more closely resembling expression in human benign prostate tissue vs. PC. In this single mouse xenograft model, consuming a low GI diet did not delay PC growth or survival vs. a high GI diet despite suggestions of decreased activation of the insulin/IGF-1 pathway. These data suggest that improving carbohydrate quality alone while consuming a high carbohydrate diet may not effectively slow PC growth.

overall_design: We investigated the effect of carbohydrate quality on prostate cancer growth and survival in a xenograft model comparing high vs. low glycemic index Western diets. Tumors from a subset of mice (n=3/group) were used for gene expression analysis by RNA-sequencing.


title: Gene expression profiles associated with myxoid liposarcoma scaffold culture compared to monolayer growth and effect of fusion oncogene FUS-DDIT3

city: Göteborg

first: Emma

last: Jonasson

address: Medicinaregatan 1F, floor 5

department: Sahlgrenska Center for Cancer Research

country: Sweden

institute: University of Gothenburg

summary: Myxoid liposarcoma (MLS) is the second most common type of liposarcoma and is characterized by the fusion oncogene FUS‐DDIT3 or the less common EWSR1‐DDIT3. FUS-DDIT3 is causative in tumor development, but the molecular function of FUS-DDIT3 remains largely unknown. In addition, the tumor microenvironment is important in MLS development. However, due to a lack of relevant experimental model systems, it has been challenging to examine the microenvironmental impact in MLS development. Therefore, we have developed an in vivo-like experimental model system utilizing cell-free scaffolds derived from myxoid liposarcoma patient-derived xenograft tumors that can be repopulated with tumor cells. To study the effect of FUS-DDIT3 expression in combination with the MLS microenvironment, we analyzed MLS cell lines as well as fibrosarcoma cells with and without ectopic FUS-DDIT3 expression cultured in scaffolds using cells cultured in monolayers as reference. We identified several gene networks and processes that are uniquely associated with FUS-DDIT3 expression as well as microenvironment. The use of in vivo-like experimental systems opens new possibilities to understand tumor development and develop treatments.

overall_design: Five cell lines were cultured in scaffolds and monolayer (2D) in 3-5 replicates and analyzed using RNA sequencing: Two MLS cell lines, 1765-92 and 2645-94, as well as HT1080 fibrosarcoma cells with and without fusion oncogene FUS-DDIT3 including native HT1080 cells, HT1080 cells expressing EGFP and HT1080 cells expressing FUS-DDIT3-EGFP.

first: Parmida

last: Ranji

first: Lisa

last: Andersson

first: Stefan

last: Filges

first: Manuel

last: Luna Santamaría

first: Soheila

last: Dolatabadi

first: Pierre

last: Åman

first: Anders

last: Ståhlberg


title: Human gene regulatory evolution is driven by divergence in cis and trans

status: Public on Dec 22 2023

city: Nashville

first: Tyler

last: Hansen

state: TN

address: 2215 Garland Ave

department: Biochemistry

country: USA

institute: Vanderbilt University

summary: Gene regulation can evolve either by cis-acting local changes to regulatory element DNA sequences or by global changes to the trans-acting regulatory environment; however, the modes favored during recent human evolution are unknown. To date, studies investigating gene regulatory divergence between closely-related species have produced limited estimates on the relative contributions of cis and trans effects on DNA regulatory element activities at a global-scale. By leveraging a comparative ATAC-STARR-seq framework, we identified 10,779 regulatory regions with divergent activity in cis and 10,608 regulatory regions with divergent activity in trans between human and rhesus macaque lymphoblastoid cell lines (LCLs). This revealed substantially more trans effects than predicted and indicates trans-regulatory mechanisms play a larger role in human evolution than previously expected. We also discover that most species-specific regulatory elements (67%) diverge in both cis and trans, suggesting these two mechanisms jointly drive divergent regulatory activity in a single sequence.

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: Comparative ATAC-STARR-seq and RNA-seq of human (GM12878) and macaque (LCL8664) lymphoblastoid cell lines

first: Sarah

last: Fong

first: John

last: Capra

first: Emily

last: Hodges


title: Alteration of DNMT1/DNMT3A by eribulin elicits global DNA methylation changes with potential therapeutic implications for triple-negative breast cancer

city: Lebanon

first: Min Kyung

last: Lee

address: 1 Medical Center Dr

institute: Dartmouth College

summary: Triple-negative breast cancer (TNBC) is an aggressive disease subtype with limited treatment options. Eribulin is a chemotherapeutic approved for the treatment of advanced breast cancer that has been shown to elicit epigenetic changes. We investigated the effect of eribulin treatment on genome-scale DNA methylation patterns in TNBC cells. Following repeated treatment, The results showed that eribulin-induced changes in DNA methylation patterns evident in persister cells. Eribulin also affected the binding of transcription factors to genomic ZEB1 binding sites and regulated several cellular pathways, including ERBB and VEGF signaling and cell adhesion. Eribulin also altered the expression of epigenetic modifiers including DNMT1, TET1, and DNMT3A/B in persister cells. Data from primary human TNBC tumors supported these findings: DNMT1 and DNMT3A levels were altered by eribulin treatment in human primary TNBC tumors. Our results suggest that eribulin modulates DNA methylation patterns in TNBC cells by altering the expression of epigenetic modifiers. These findings have clinical implications for using eribulin as a therapeutic agent.

overall_design: Bisulfite converted DNA from the untreated, eribulin and paclitaxel treated MDA-MB-231 cell lines were hybridised to the Illumina Infinium Human MethylationEPIC Beadchip.

first: Meisam

last: Bagheri

first: Min