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Liu L, Hao S, Gou S, Tang X, Zhang Y, Cai D, Xiao M, Zhang X, Zhang D, Shen J, Li Y, Chen Y, Zhao Y, Deng S, Wu X, Li M, Zhang Z, Xiao Z, Du F. Potential applications of dual haptoglobin expression in the reclassification and treatment of hepatocellular carcinoma. Transl Res 2024; 272:19-40. [PMID: 38815898 DOI: 10.1016/j.trsl.2024.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/07/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024]
Abstract
HCC is a malignancy characterized by high incidence and mortality rates. Traditional classifications of HCC primarily rely on tumor morphology, phenotype, and multicellular molecular levels, which may not accurately capture the cellular heterogeneity within the tumor. This study integrates scRNA-seq and bulk RNA-seq to spotlight HP as a critical gene within a subgroup of HCC malignant cells. HP is highly expressed in HCC malignant cells and lowly expressed in T cells. Within malignant cells, elevated HP expression interacts with C3, promoting Th1-type responses via the C3/C3AR1 axis. In T cells, down-regulating HP expression favors the expression of Th1 cell-associated marker genes, potentially enhancing Th1-type responses. Consequently, we developed a "HP-promoted Th1 response reclassification" gene set, correlating higher activity scores with improved survival rates in HCC patients. Additionally, four predictive models for neoadjuvant treatment based on HP and C3 expression were established: 1) Low HP and C3 expression with high Th2 cell infiltration; 2) High HP and low C3 expression with high Th2 cell infiltration; 3) High HP and C3 expression with high Th1 cell infiltration; 4) Low HP and high C3 expression with high Th1 cell infiltration. In conclusion, the HP gene selected from the HCC malignant cell subgroup (Malignant_Sub 6) might serve as a potential ally against the tumor by promoting Th1-type immune responses. The establishment of the "HP-promoted Th1 response reclassification" gene set offers predictive insights for HCC patient survival prognosis and neoadjuvant treatment efficacy, providing directions for clinical treatments.
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Affiliation(s)
- Lin Liu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Siyu Hao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Shuang Gou
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Xiaolong Tang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Yao Zhang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Dan Cai
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Mintao Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Xinyi Zhang
- Department of Anaesthesia and Intensive Care, Faculty of Medicine, The Chinese University of Hong Kong, China
| | - Duoli Zhang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Yan Li
- Public Center of Experimental Technology, Southwest Medical University, Sichuan Luzhou 646000, China
| | - Yu Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Shuai Deng
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Zhuo Zhang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China
| | - Fukuan Du
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan Luzhou 646000, China; Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Sichuan Luzhou, 646000, China; South Sichuan Institute of Translational Medicine, Sichuan Luzhou 646000, China.
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Xia MZ, Yan HC. Epithelial cell-related prognostic risk model in breast cancer based on single-cell and bulk RNA sequencing. Heliyon 2024; 10:e37048. [PMID: 39286180 PMCID: PMC11402982 DOI: 10.1016/j.heliyon.2024.e37048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 08/26/2024] [Accepted: 08/27/2024] [Indexed: 09/19/2024] Open
Abstract
Objective This study aims to construct an epithelial cell-related prognostic risk model for breast cancer (BRCA) and explore its significance. Methods GSE42568, GSE10780, GSE245601, and TCGA-BRCA datasets were sourced from public databases. Epithelial cell-related differentially expressed genes were identified using single-cell data analysis. Venn diagrams determined the intersecting genes between epithelial cell-related and BRCA-related genes. Batch Kaplan-Meier (K-M) survival analysis identified core intersecting genes for BRCA overall survival. Consensus clustering, enrichment, LASSO, and COX regression analyses were performed on the core intersecting genes, and then a prognostic risk model was constructed. The diagnostic and prognostic effectiveness of the risk model was subsequently evaluated and immune infiltration analysis was conducted. Finally, qRT-PCR was used to verify the expression of genes in the risk model. Results There were 374 intersecting genes between epithelial cell-related and BRCA-related genes, among which 51 core intersecting genes were associated with BRCA prognosis. Consensus clustering categorized TCGA-BRCA into C1 and C2, with shared regulation of the estrogen signaling pathway. Three genes (DIRC3, SLC6A2, TUBA3D) were independent predictors of BRCA prognosis, forming the basis for a risk model. Except for exhibiting satisfactory diagnostic efficacy, the risk score elevation correlated with poor prognosis, elevated matrix, immune, and ESTIMATE scores, and negative correlation with microsatellite instability. The in vitro results confirmed the differential expression levels of DIRC3, SLC6A2, and TUBA3D. Conclusion The prognostic risk model associated with epithelial cells demonstrates effective diagnostic performance in BRCA, serving as an independent prognostic factor for BRCA patients. Additionally, it exhibits a correlation with immune scores.
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Affiliation(s)
- Man-Zhi Xia
- General Surgery, Shaoxing Maternity and Child Health Care Hospital, Shaoxing, 312000, Zhejiang, China
| | - Hai-Chao Yan
- Department of Thyroid Surgery, The Second Affiliated Hospital of Zhejiang University College of Medicine, Hangzhou, 310009, Zhejiang, China
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3
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Xiang L, Rao J, Yuan J, Xie T, Yan H. Single-Cell RNA-Sequencing: Opening New Horizons for Breast Cancer Research. Int J Mol Sci 2024; 25:9482. [PMID: 39273429 PMCID: PMC11395021 DOI: 10.3390/ijms25179482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 08/25/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024] Open
Abstract
Breast cancer is the most prevalent malignant tumor among women with high heterogeneity. Traditional techniques frequently struggle to comprehensively capture the intricacy and variety of cellular states and interactions within breast cancer. As global precision medicine rapidly advances, single-cell RNA sequencing (scRNA-seq) has become a highly effective technique, revolutionizing breast cancer research by offering unprecedented insights into the cellular heterogeneity and complexity of breast cancer. This cutting-edge technology facilitates the analysis of gene expression profiles at the single-cell level, uncovering diverse cell types and states within the tumor microenvironment. By dissecting the cellular composition and transcriptional signatures of breast cancer cells, scRNA-seq provides new perspectives for understanding the mechanisms behind tumor therapy, drug resistance and metastasis in breast cancer. In this review, we summarized the working principle and workflow of scRNA-seq and emphasized the major applications and discoveries of scRNA-seq in breast cancer research, highlighting its impact on our comprehension of breast cancer biology and its potential for guiding personalized treatment strategies.
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Affiliation(s)
- Lingyan Xiang
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Jie Rao
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Jingping Yuan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Ting Xie
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Honglin Yan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan 430060, China
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Wang J, Alhaskawi A, Dong Y, Tian T, Abdalbary SA, Lu H. Advances in spatial multi-omics in tumors. TUMORI JOURNAL 2024:3008916241271458. [PMID: 39185632 DOI: 10.1177/03008916241271458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Single-cell techniques have convincingly demonstrated that tumor tissue usually contains multiple genetically defined cell subclones with different gene mutation sets as well as various transcriptional profiles, but the spatial heterogeneity of the microenvironment and the macrobiological characteristics of the tumor ecosystem have not been described. For the past few years, spatial multi-omics technologies have revealed the cellular interactions, microenvironment, and even systemic tumor-host interactions in the tumor ecosystem at the spatial level, which can not only improve classical therapies such as surgery, radiotherapy, and chemotherapy but also promote the development of emerging targeted therapies in immunotherapy. Here, we review some emerging spatial omics techniques in cancer research and therapeutic applications and propose prospects for their future development.
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Affiliation(s)
- Junyan Wang
- The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Ahmad Alhaskawi
- Department of Orthopedics, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Yanzhao Dong
- Department of Orthopedics, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Tu Tian
- Department of Plastic Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Sahar Ahmed Abdalbary
- Department of Orthopedics, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
- Department of Orthopedic Physical Therapy, Faculty of Physical Therapy, Nahda University in Beni Suef, Beni Suef, Egypt
| | - Hui Lu
- The First Affiliated Hospital, Zhejiang University, Hangzhou, China
- Department of Orthopedics, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
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5
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Fathima AJ, Fasla MMN. A comprehensive review on heart disease prognostication using different artificial intelligence algorithms. Comput Methods Biomech Biomed Engin 2024; 27:1357-1374. [PMID: 38424704 DOI: 10.1080/10255842.2024.2319706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/06/2024] [Accepted: 02/12/2024] [Indexed: 03/02/2024]
Abstract
Prediction of heart diseases on time is significant in order to preserve life. Many conventional methods have taken efforts on earlier prediction but faced with challenges of higher prediction cost, extended time for computation and complexities with larger volume of data which reduced prediction accuracy. In order to overcome such pitfalls, AI (Artificial Intelligence) technology has been evolved in diagnosing heart diseases through deployment of several ML (Machine Learning) and DL (Deep Learning) algorithms. It improves detection by influencing with its capacity of learning from the massive data containing age, obesity, hypertension and other risk factors of patients and extract it accordingly to differentiate on the circumstances. Moreover, storage of larger data with AI greatly assists in analysing the occurrence of the disease from past historical data. Hence, this paper intends to provide a review on different AI based algorithms used in the heart disease prognostication and delivers its benefits through researching on various existing works. It performs comparative analysis and critical assessment as encompassing accuracies and maximum utilization of algorithms focussed by traditional studies in this area. The major findings of the paper emphasized on the evolution and continuous explorations of AI techniques for heart disease prediction and the future researchers aims in determining the dimensions that have attained high and low prediction accuracies on which appropriate research works can be performed. Finally, future research is included to offer new stimulus for further investigation of AI in cardiac disease diagnosis.
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Affiliation(s)
- A Jainul Fathima
- Assistant Professor, IT Francis Xavier Engineering College, Tirunelveli - 627003, India
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Gondal MN, Shah SUR, Chinnaiyan AM, Cieslik M. A systematic overview of single-cell transcriptomics databases, their use cases, and limitations. FRONTIERS IN BIOINFORMATICS 2024; 4:1417428. [PMID: 39040140 PMCID: PMC11260681 DOI: 10.3389/fbinf.2024.1417428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 06/11/2024] [Indexed: 07/24/2024] Open
Abstract
Rapid advancements in high-throughput single-cell RNA-seq (scRNA-seq) technologies and experimental protocols have led to the generation of vast amounts of transcriptomic data that populates several online databases and repositories. Here, we systematically examined large-scale scRNA-seq databases, categorizing them based on their scope and purpose such as general, tissue-specific databases, disease-specific databases, cancer-focused databases, and cell type-focused databases. Next, we discuss the technical and methodological challenges associated with curating large-scale scRNA-seq databases, along with current computational solutions. We argue that understanding scRNA-seq databases, including their limitations and assumptions, is crucial for effectively utilizing this data to make robust discoveries and identify novel biological insights. Such platforms can help bridge the gap between computational and wet lab scientists through user-friendly web-based interfaces needed for democratizing access to single-cell data. These platforms would facilitate interdisciplinary research, enabling researchers from various disciplines to collaborate effectively. This review underscores the importance of leveraging computational approaches to unravel the complexities of single-cell data and offers a promising direction for future research in the field.
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Affiliation(s)
- Mahnoor N. Gondal
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Saad Ur Rehman Shah
- Gies College of Business, University of Illinois Business College, Champaign, MI, United States
| | - Arul M. Chinnaiyan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, United States
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
- Department of Urology, University of Michigan, Ann Arbor, MI, United States
- Howard Hughes Medical Institute, Ann Arbor, MI, United States
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, United States
| | - Marcin Cieslik
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, United States
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, United States
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7
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Yu Y, Hou W, Liu Y, Wang H, Dong L, Mai Y, Chen Q, Li Z, Sun S, Yang J, Cao Z, Zhang P, Zi Y, Liu R, Gao J, Zhang N, Li J, Ren L, Jiang H, Shang J, Zhu S, Wang X, Qing T, Bao D, Li B, Li B, Suo C, Pi Y, Wang X, Dai F, Scherer A, Mattila P, Han J, Zhang L, Jiang H, Thierry-Mieg D, Thierry-Mieg J, Xiao W, Hong H, Tong W, Wang J, Li J, Fang X, Jin L, Xu J, Qian F, Zhang R, Shi L, Zheng Y. Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling. Nat Biotechnol 2024; 42:1118-1132. [PMID: 37679545 PMCID: PMC11251996 DOI: 10.1038/s41587-023-01867-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 06/15/2023] [Indexed: 09/09/2023]
Abstract
Certified RNA reference materials are indispensable for assessing the reliability of RNA sequencing to detect intrinsically small biological differences in clinical settings, such as molecular subtyping of diseases. As part of the Quartet Project for quality control and data integration of multi-omics profiling, we established four RNA reference materials derived from immortalized B-lymphoblastoid cell lines from four members of a monozygotic twin family. Additionally, we constructed ratio-based transcriptome-wide reference datasets between two samples, providing cross-platform and cross-laboratory 'ground truth'. Investigation of the intrinsically subtle biological differences among the Quartet samples enables sensitive assessment of cross-batch integration of transcriptomic measurements at the ratio level. The Quartet RNA reference materials, combined with the ratio-based reference datasets, can serve as unique resources for assessing and improving the quality of transcriptomic data in clinical and biological settings.
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Affiliation(s)
- Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Wanwan Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yaqing Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Haiyan Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | | | - Yuanbang Mai
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qingwang Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Zhihui Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Shanyue Sun
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jingcheng Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
- Greater Bay Area Institute of Precision Medicine, Guangzhou, China
| | - Zehui Cao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Peipei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yi Zi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ruimei Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jian Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Naixin Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jingjing Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
- Nextomics Biosciences Institute, Wuhan, China
| | - Luyao Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - He Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jun Shang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Sibo Zhu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Xiaolin Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Tao Qing
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ding Bao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Bingying Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Bin Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Chen Suo
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yan Pi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Xia Wang
- National Institute of Metrology, Beijing, China
| | | | - Andreas Scherer
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- EATRIS ERIC-European Infrastructure for Translational Medicine, Amsterdam, The Netherlands
| | - Pirkko Mattila
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- EATRIS ERIC-European Infrastructure for Translational Medicine, Amsterdam, The Netherlands
| | | | - Lijun Zhang
- Nanjing Vazyme Biotech Co. Ltd., Nanjing, China
| | | | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Wenming Xiao
- Office of Oncologic Diseases, Office of New Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Jing Wang
- National Institute of Metrology, Beijing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China
- National Center of Gerontology, Beijing, China
| | - Xiang Fang
- National Institute of Metrology, Beijing, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA.
| | - Feng Qian
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China.
- National Center of Gerontology, Beijing, China.
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
- International Human Phenome Institutes, Shanghai, China.
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
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8
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Hasanaj E, Mathur S, Bar-Joseph Z. Integrating patients in time series clinical transcriptomics data. Bioinformatics 2024; 40:i151-i159. [PMID: 38940139 PMCID: PMC11256926 DOI: 10.1093/bioinformatics/btae241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024] Open
Abstract
MOTIVATION Analysis of time series transcriptomics data from clinical trials is challenging. Such studies usually profile very few time points from several individuals with varying response patterns and dynamics. Current methods for these datasets are mainly based on linear, global orderings using visit times which do not account for the varying response rates and subgroups within a patient cohort. RESULTS We developed a new method that utilizes multi-commodity flow algorithms for trajectory inference in large scale clinical studies. Recovered trajectories satisfy individual-based timing restrictions while integrating data from multiple patients. Testing the method on multiple drug datasets demonstrated an improved performance compared to prior approaches suggested for this task, while identifying novel disease subtypes that correspond to heterogeneous patient response patterns. AVAILABILITY AND IMPLEMENTATION The source code and instructions to download the data have been deposited on GitHub at https://github.com/euxhenh/Truffle.
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Affiliation(s)
- Euxhen Hasanaj
- Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA 15213, United States
| | - Sachin Mathur
- R&D Data and Computational Sciences, Sanofi, Cambridge, MA 02141, United States
| | - Ziv Bar-Joseph
- Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA 15213, United States
- R&D Data and Computational Sciences, Sanofi, Cambridge, MA 02141, United States
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, United States
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9
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Summers BS, Thomas Broome S, Pang TWR, Mundell HD, Koh Belic N, Tom NC, Ng ML, Yap M, Sen MK, Sedaghat S, Weible MW, Castorina A, Lim CK, Lovelace MD, Brew BJ. A Review of the Evidence for Tryptophan and the Kynurenine Pathway as a Regulator of Stem Cell Niches in Health and Disease. Int J Tryptophan Res 2024; 17:11786469241248287. [PMID: 38757094 PMCID: PMC11097742 DOI: 10.1177/11786469241248287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 04/03/2024] [Indexed: 05/18/2024] Open
Abstract
Stem cells are ubiquitously found in various tissues and organs in the body, and underpin the body's ability to repair itself following injury or disease initiation, though repair can sometimes be compromised. Understanding how stem cells are produced, and functional signaling systems between different niches is critical to understanding the potential use of stem cells in regenerative medicine. In this context, this review considers kynurenine pathway (KP) metabolism in multipotent adult progenitor cells, embryonic, haematopoietic, neural, cancer, cardiac and induced pluripotent stem cells, endothelial progenitor cells, and mesenchymal stromal cells. The KP is the major enzymatic pathway for sequentially catabolising the essential amino acid tryptophan (TRP), resulting in key metabolites including kynurenine, kynurenic acid, and quinolinic acid (QUIN). QUIN metabolism transitions into the adjoining de novo pathway for nicotinamide adenine dinucleotide (NAD) production, a critical cofactor in many fundamental cellular biochemical pathways. How stem cells uptake and utilise TRP varies between different species and stem cell types, because of their expression of transporters and responses to inflammatory cytokines. Several KP metabolites are physiologically active, with either beneficial or detrimental outcomes, and evidence of this is presented relating to several stem cell types, which is important as they may exert a significant impact on surrounding differentiated cells, particularly if they metabolise or secrete metabolites differently. Interferon-gamma (IFN-γ) in mesenchymal stromal cells, for instance, highly upregulates rate-limiting enzyme indoleamine-2,3-dioxygenase (IDO-1), initiating TRP depletion and production of metabolites including kynurenine/kynurenic acid, known agonists of the Aryl hydrocarbon receptor (AhR) transcription factor. AhR transcriptionally regulates an immunosuppressive phenotype, making them attractive for regenerative therapy. We also draw attention to important gaps in knowledge for future studies, which will underpin future application for stem cell-based cellular therapies or optimising drugs which can modulate the KP in innate stem cell populations, for disease treatment.
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Affiliation(s)
- Benjamin Sebastian Summers
- Applied Neurosciences Program, Peter Duncan Neurosciences Research Unit, St. Vincent’s Centre for Applied Medical Research, Sydney, NSW, Australia
- Faculty of Medicine and Health, School of Clinical Medicine, UNSW Sydney, NSW, Australia
| | - Sarah Thomas Broome
- Faculty of Science, Laboratory of Cellular and Molecular Neuroscience, School of Life Sciences, University of Technology Sydney, NSW, Australia
| | | | - Hamish D Mundell
- Faculty of Medicine and Health, New South Wales Brain Tissue Resource Centre, School of Medical Sciences, Charles Perkins Centre, University of Sydney, NSW, Australia
| | - Naomi Koh Belic
- School of Life Sciences, University of Technology, Sydney, NSW, Australia
| | - Nicole C Tom
- Formerly of the Department of Physiology, University of Sydney, NSW, Australia
| | - Mei Li Ng
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Maylin Yap
- Formerly of the Atherothrombosis and Vascular Biology Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Monokesh K Sen
- Applied Neurosciences Program, Peter Duncan Neurosciences Research Unit, St. Vincent’s Centre for Applied Medical Research, Sydney, NSW, Australia
- School of Medicine, Western Sydney University, NSW, Australia
- Faculty of Medicine and Health, School of Medical Sciences, Charles Perkins Centre, The University of Sydney, NSW, Australia
| | - Sara Sedaghat
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Michael W Weible
- School of Environment and Science, Griffith University, Brisbane, QLD, Australia
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD, Australia
| | - Alessandro Castorina
- Faculty of Science, Laboratory of Cellular and Molecular Neuroscience, School of Life Sciences, University of Technology Sydney, NSW, Australia
| | - Chai K Lim
- Faculty of Medicine, Macquarie University, Sydney, NSW, Australia
| | - Michael D Lovelace
- Applied Neurosciences Program, Peter Duncan Neurosciences Research Unit, St. Vincent’s Centre for Applied Medical Research, Sydney, NSW, Australia
- Faculty of Medicine and Health, School of Clinical Medicine, UNSW Sydney, NSW, Australia
| | - Bruce J Brew
- Applied Neurosciences Program, Peter Duncan Neurosciences Research Unit, St. Vincent’s Centre for Applied Medical Research, Sydney, NSW, Australia
- Faculty of Medicine and Health, School of Clinical Medicine, UNSW Sydney, NSW, Australia
- Departments of Neurology and Immunology, St. Vincent’s Hospital, Sydney, NSW, Australia
- University of Notre Dame, Darlinghurst, Sydney, NSW, Australia
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10
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Gondal MN, Shah SUR, Chinnaiyan AM, Cieslik M. A Systematic Overview of Single-Cell Transcriptomics Databases, their Use cases, and Limitations. ARXIV 2024:arXiv:2404.10545v1. [PMID: 38699169 PMCID: PMC11065044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Rapid advancements in high-throughput single-cell RNA-seq (scRNA-seq) technologies and experimental protocols have led to the generation of vast amounts of genomic data that populates several online databases and repositories. Here, we systematically examined large-scale scRNA-seq databases, categorizing them based on their scope and purpose such as general, tissue-specific databases, disease-specific databases, cancer-focused databases, and cell type-focused databases. Next, we discuss the technical and methodological challenges associated with curating large-scale scRNA-seq databases, along with current computational solutions. We argue that understanding scRNA-seq databases, including their limitations and assumptions, is crucial for effectively utilizing this data to make robust discoveries and identify novel biological insights. Furthermore, we propose that bridging the gap between computational and wet lab scientists through user-friendly web-based platforms is needed for democratizing access to single-cell data. These platforms would facilitate interdisciplinary research, enabling researchers from various disciplines to collaborate effectively. This review underscores the importance of leveraging computational approaches to unravel the complexities of single-cell data and offers a promising direction for future research in the field.
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Affiliation(s)
- Mahnoor N. Gondal
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI USA
| | - Saad Ur Rehman Shah
- Gies College of Business, University of Illinois Business College, Champaign, IL USA
| | - Arul M. Chinnaiyan
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI USA
- Department of Pathology, University of Michigan, Ann Arbor, MI USA
- Department of Urology, University of Michigan, Ann Arbor, MI USA
- Howard Hughes Medical Institute, Ann Arbor, MI USA
- University of Michigan Rogel Cancer Center, Ann Arbor, MI USA
| | - Marcin Cieslik
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI USA
- Department of Pathology, University of Michigan, Ann Arbor, MI USA
- University of Michigan Rogel Cancer Center, Ann Arbor, MI USA
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11
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Yan H, Ju X, Huang A, Yuan J. Advancements in technology for characterizing the tumor immune microenvironment. Int J Biol Sci 2024; 20:2151-2167. [PMID: 38617534 PMCID: PMC11008272 DOI: 10.7150/ijbs.92525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/12/2024] [Indexed: 04/16/2024] Open
Abstract
Immunotherapy plays a key role in cancer treatment, however, responses are limited to a small number of patients. The biological basis for the success of immunotherapy is the complex interaction between tumor cells and tumor immune microenvironment (TIME). Historically, research on tumor immune constitution was limited to the analysis of one or two markers, more novel technologies are needed to interpret the complex interactions between tumor cells and TIME. In recent years, major advances have already been made in depicting TIME at a considerably elevated degree of throughput, dimensionality and resolution, allowing dozens of markers to be labeled simultaneously, and analyzing the heterogeneity of tumour-immune infiltrates in detail at the single cell level, depicting the spatial landscape of the entire microenvironment, as well as applying artificial intelligence (AI) to interpret a large amount of complex data from TIME. In this review, we summarized emerging technologies that have made contributions to the field of TIME, and provided prospects for future research.
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Affiliation(s)
- Honglin Yan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | | | | | - Jingping Yuan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
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12
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Ahluwalia P, Ballur K, Leeman T, Vashisht A, Singh H, Omar N, Mondal AK, Vaibhav K, Baban B, Kolhe R. Incorporating Novel Technologies in Precision Oncology for Colorectal Cancer: Advancing Personalized Medicine. Cancers (Basel) 2024; 16:480. [PMID: 38339232 PMCID: PMC10854941 DOI: 10.3390/cancers16030480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/10/2024] [Accepted: 01/13/2024] [Indexed: 02/12/2024] Open
Abstract
Colorectal cancer (CRC) is one of the most heterogeneous and deadly diseases, with a global incidence of 1.5 million cases per year. Genomics has revolutionized the clinical management of CRC by enabling comprehensive molecular profiling of cancer. However, a deeper understanding of the molecular factors is needed to identify new prognostic and predictive markers that can assist in designing more effective therapeutic regimens for the improved management of CRC. Recent breakthroughs in single-cell analysis have identified new cell subtypes that play a critical role in tumor progression and could serve as potential therapeutic targets. Spatial analysis of the transcriptome and proteome holds the key to unlocking pathogenic cellular interactions, while liquid biopsy profiling of molecular variables from serum holds great potential for monitoring therapy resistance. Furthermore, gene expression signatures from various pathways have emerged as promising prognostic indicators in colorectal cancer and have the potential to enhance the development of equitable medicine. The advancement of these technologies for identifying new markers, particularly in the domain of predictive and personalized medicine, has the potential to improve the management of patients with CRC. Further investigations utilizing similar methods could uncover molecular subtypes specific to emerging therapies, potentially strengthening the development of personalized medicine for CRC patients.
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Affiliation(s)
- Pankaj Ahluwalia
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Kalyani Ballur
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Tiffanie Leeman
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Ashutosh Vashisht
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Harmanpreet Singh
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Nivin Omar
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Ashis K. Mondal
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Kumar Vaibhav
- Department of Neurosurgery, Augusta University, Augusta, GA 30912, USA;
| | - Babak Baban
- Departments of Neurology and Surgery, Augusta University, Augusta, GA 30912, USA;
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
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13
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Shaban N, Kamashev D, Emelianova A, Buzdin A. Targeted Inhibitors of EGFR: Structure, Biology, Biomarkers, and Clinical Applications. Cells 2023; 13:47. [PMID: 38201251 PMCID: PMC10778338 DOI: 10.3390/cells13010047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Members of the EGFR family of tyrosine kinase receptors are major regulators of cellular proliferation, differentiation, and survival. In humans, abnormal activation of EGFR is associated with the development and progression of many cancer types, which makes it an attractive target for molecular-guided therapy. Two classes of EGFR-targeted cancer therapeutics include monoclonal antibodies (mAbs), which bind to the extracellular domain of EGFR, and tyrosine kinase inhibitors (TKIs), which mostly target the intracellular part of EGFR and inhibit its activity in molecular signaling. While EGFR-specific mAbs and three generations of TKIs have demonstrated clinical efficacy in various settings, molecular evolution of tumors leads to apparent and sometimes inevitable resistance to current therapeutics, which highlights the need for deeper research in this field. Here, we tried to provide a comprehensive and systematic overview of the rationale, molecular mechanisms, and clinical significance of the current EGFR-targeting drugs, highlighting potential candidate molecules in development. We summarized the underlying mechanisms of resistance and available personalized predictive approaches that may lead to improved efficacy of EGFR-targeted therapies. We also discuss recent developments and the use of specific therapeutic strategies, such as multi-targeting agents and combination therapies, for overcoming cancer resistance to EGFR-specific drugs.
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Affiliation(s)
- Nina Shaban
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia; (D.K.); (A.B.)
- Laboratory for Translational Genomic Bioinformatics, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Dmitri Kamashev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia; (D.K.); (A.B.)
- Laboratory for Translational Genomic Bioinformatics, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Institute of Personalized Oncology, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Aleksandra Emelianova
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow 119991, Russia;
| | - Anton Buzdin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia; (D.K.); (A.B.)
- Laboratory for Translational Genomic Bioinformatics, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Institute of Personalized Oncology, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), 1200 Brussels, Belgium
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14
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Shen K, Ke S, Chen B, Gao W. Integrated analysis of single-cell and bulk RNA-sequencing reveals the poor prognostic value of ABCA1 in gastric adenocarcinoma. Discov Oncol 2023; 14:189. [PMID: 37874419 PMCID: PMC10597929 DOI: 10.1007/s12672-023-00807-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 10/17/2023] [Indexed: 10/25/2023] Open
Abstract
PURPOSE ATP-binding cassette A1 (ABCA1) is a potential prognostic marker for various tumor types. However, the biological effects and prognostic value of ABCA1 in gastric adenocarcinoma (GAC) remain unknown. METHODS GAC-associated single-cell RNA and bulk RNA-sequencing (bulk-seq) data were obtained from the Gene Expression Omnibus and The Cancer Genome Atlas databases, respectively. The differential expression of ABCA1 between GAC and normal gastric tissues was analyzed based on the bulk-seq data. Additionally, the relationship between ABCA1 expression and various clinicopathological features was explored. Furthermore, Kaplan-Meier survival and Cox regression analyses were performed to establish the prognostic value of ABCA1. The relationships between ABCA1 expression and anti-tumor drug sensitivity and immune checkpoints were also explored. Finally, the biological functions of ABCA1 were evaluated at the single-cell level, and in vitro studies were performed to assess the effects of ABCA1 on GAC cell proliferation and invasion. RESULTS ABCA1 expression is significantly elevated in GAC samples compared with that in normal gastric tissues. Clinical features and survival analysis revealed that high ABCA1 expression is associated with poor clinical phenotypes and prognosis, whereas Cox analysis identified ABCA1 as an independent risk factor for patients with GAC. Furthermore, high ABCA1 expression suppresses sensitivity to various chemotherapeutic drugs, including cisplatin and mitomycin, while upregulating immune checkpoints. ABCA1-overexpressing macrophages are associated with adverse clinical phenotypes in GAC and express unique ligand-receptor pairs that drive GAC progression. In vitro, ABCA1-knockdown GAC cells exhibit significantly inhibited proliferative and invasive properties. CONCLUSION High ABCA1 expression promotes an adverse immune microenvironment and low survival rates in patients with GAC. Furthermore, ABCA1 and ABCA1-producing macrophages may serve as novel molecular targets in GAC treatment.
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Affiliation(s)
- Kaiyu Shen
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Shuaiyi Ke
- Department of Internal Medicine, Affiliated Xianju's Hospital, XianJu People's Hospital, Zhejiang Southeast Campus of Zhejiang Provincial People's Hospital, Hangzhou Medical College, XianJu, 317399, China
| | - Binyu Chen
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Wencang Gao
- Department of Oncology, the Second Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, 310005, China.
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15
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Yaghoubi Naei V, Bordhan P, Mirakhorli F, Khorrami M, Shrestha J, Nazari H, Kulasinghe A, Ebrahimi Warkiani M. Advances in novel strategies for isolation, characterization, and analysis of CTCs and ctDNA. Ther Adv Med Oncol 2023; 15:17588359231192401. [PMID: 37692363 PMCID: PMC10486235 DOI: 10.1177/17588359231192401] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 07/19/2023] [Indexed: 09/12/2023] Open
Abstract
Over the past decade, the detection and analysis of liquid biopsy biomarkers such as circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) have advanced significantly. They have received recognition for their clinical usefulness in detecting cancer at an early stage, monitoring disease, and evaluating treatment response. The emergence of liquid biopsy has been a helpful development, as it offers a minimally invasive, rapid, real-time monitoring, and possible alternative to traditional tissue biopsies. In resource-limited settings, the ideal platform for liquid biopsy should not only extract more CTCs or ctDNA from a minimal sample volume but also accurately represent the molecular heterogeneity of the patient's disease. This review covers novel strategies and advancements in CTC and ctDNA-based liquid biopsy platforms, including microfluidic applications and comprehensive analysis of molecular complexity. We discuss these systems' operational principles and performance efficiencies, as well as future opportunities and challenges for their implementation in clinical settings. In addition, we emphasize the importance of integrated platforms that incorporate machine learning and artificial intelligence in accurate liquid biopsy detection systems, which can greatly improve cancer management and enable precision diagnostics.
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Affiliation(s)
- Vahid Yaghoubi Naei
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
- Faculty of Medicine, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Pritam Bordhan
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
- Faculty of Science, Institute for Biomedical Materials & Devices, University of Technology Sydney, Australia
| | - Fatemeh Mirakhorli
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Motahare Khorrami
- Immunology Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jesus Shrestha
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Hojjatollah Nazari
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Arutha Kulasinghe
- Faculty of Medicine, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, 1, Broadway, Ultimo New South Wales 2007, Australia
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16
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Lin J, Feng D, Liu J, Yang Y, Wei X, Lin W, Lin Q. Construction of stemness gene score by bulk and single-cell transcriptome to characterize the prognosis of breast cancer. Aging (Albany NY) 2023; 15:8185-8203. [PMID: 37602872 PMCID: PMC10496995 DOI: 10.18632/aging.204963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023]
Abstract
Breast cancer (BC) is a heterogeneous disease characterized by significant differences in prognosis and therapy response. Numerous prognostic tools have been developed for breast cancer. Usually these tools are based on bulk RNA-sequencing (RNA-Seq) and ignore tumor heterogeneity. Consequently, the goal of this study was to construct a single-cell level tool for predicting the prognosis of BC patients. In this study, we constructed a stemness-risk gene score (SGS) model based on single-sample gene set enrichment analysis (ssGSEA). Patients were divided into two groups based on the median SGS. Patients with a high SGS scores had a significantly worse prognosis than those with a low SGS, and these groups exhibited differences in several tumor characteristics, such as immune infiltration, gene mutations, and copy number variants. Our results indicate that the SGS is a reliable tool for predicting prognosis and response to immunotherapy in BC patients.
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Affiliation(s)
- Jun Lin
- Department of Anesthesiology, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Department of Anesthesiology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
- Anesthesiology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Deyi Feng
- Xiamen University, Xiamen 361100, China
| | - Jie Liu
- Department of Endoscopy, Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, China
| | - Ye Yang
- The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Xujin Wei
- The Graduate School of Fujian Medical University, Fuzhou 350001, China
| | - Wenqian Lin
- Department of Anesthesiology, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Department of Anesthesiology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
- Anesthesiology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Qun Lin
- Department of Anesthesiology, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Department of Anesthesiology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
- Anesthesiology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
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17
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Sorokin M, Buzdin AA, Guryanova A, Efimov V, Suntsova MV, Zolotovskaia MA, Koroleva EV, Sekacheva MI, Tkachev VS, Garazha A, Kremenchutckaya K, Drobyshev A, Seryakov A, Gudkov A, Alekseenko IV, Rakitina O, Kostina MB, Vladimirova U, Moisseev A, Bulgin D, Radomskaya E, Shestakov V, Baklaushev VP, Prassolov V, Shegay PV, Li X, Poddubskaya EV, Gaifullin N. Large-scale assessment of pros and cons of autopsy-derived or tumor-matched tissues as the norms for gene expression analysis in cancers. Comput Struct Biotechnol J 2023; 21:3964-3986. [PMID: 37635765 PMCID: PMC10448432 DOI: 10.1016/j.csbj.2023.07.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 07/17/2023] [Accepted: 07/30/2023] [Indexed: 08/29/2023] Open
Abstract
Normal tissues are essential for studying disease-specific differential gene expression. However, healthy human controls are typically available only in postmortal/autopsy settings. In cancer research, fragments of pathologically normal tissue adjacent to tumor site are frequently used as the controls. However, it is largely underexplored how cancers can systematically influence gene expression of the neighboring tissues. Here we performed a comprehensive pan-cancer comparison of molecular profiles of solid tumor-adjacent and autopsy-derived "healthy" normal tissues. We found a number of systemic molecular differences related to activation of the immune cells, intracellular transport and autophagy, cellular respiration, telomerase activation, p38 signaling, cytoskeleton remodeling, and reorganization of the extracellular matrix. The tumor-adjacent tissues were deficient in apoptotic signaling and negative regulation of cell growth including G2/M cell cycle transition checkpoint. We also detected an extensive rearrangement of the chemical perception network. Molecular targets of 32 and 37 cancer drugs were over- or underexpressed, respectively, in the tumor-adjacent norms. These processes may be driven by molecular events that are correlated between the paired cancer and adjacent normal tissues, that mostly relate to inflammation and regulation of intracellular molecular pathways such as the p38, MAPK, Notch, and IGF1 signaling. However, using a model of macaque postmortal tissues we showed that for the 30 min - 24-hour time frame at 4ºC, an RNA degradation pattern in lung biosamples resulted in an artifact "differential" expression profile for 1140 genes, although no differences could be detected in liver. Thus, such concerns should be addressed in practice.
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Affiliation(s)
- Maksim Sorokin
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
- Omicsway Corp., Walnut, CA 91789, USA
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Anton A. Buzdin
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- World-Class Research Center "Digital biodesign and personalized healthcare", Sechenov First Moscow State Medical University, Moscow, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), Brussels, Belgium
| | - Anastasia Guryanova
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
| | - Victor Efimov
- World-Class Research Center "Digital biodesign and personalized healthcare", Sechenov First Moscow State Medical University, Moscow, Russia
| | - Maria V. Suntsova
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Marianna A. Zolotovskaia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
- Omicsway Corp., Walnut, CA 91789, USA
| | - Elena V. Koroleva
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
| | - Marina I. Sekacheva
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Victor S. Tkachev
- Omicsway Corp., Walnut, CA 91789, USA
- Oncobox Ltd., Moscow 121205, Russia
| | - Andrew Garazha
- Omicsway Corp., Walnut, CA 91789, USA
- Oncobox Ltd., Moscow 121205, Russia
| | | | - Aleksey Drobyshev
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | | | - Alexander Gudkov
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Irina V. Alekseenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", 2, Kurchatov Square, Moscow 123182, Russian
- FSBI "National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I. Kulakov" Ministry of Healthcare of the Russian Federation, Moscow 117198, Russia
| | - Olga Rakitina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Maria B. Kostina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Uliana Vladimirova
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
- Oncobox Ltd., Moscow 121205, Russia
| | - Aleksey Moisseev
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Dmitry Bulgin
- Research Institute of Medical Primatology, 177 Mira str., Veseloye, Sochi 354376, Russia
| | - Elena Radomskaya
- Research Institute of Medical Primatology, 177 Mira str., Veseloye, Sochi 354376, Russia
| | - Viktor Shestakov
- Research Institute of Medical Primatology, 177 Mira str., Veseloye, Sochi 354376, Russia
| | | | - Vladimir Prassolov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova str., Moscow 119991, Russia
| | - Petr V. Shegay
- National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, 249036 Obninsk, Russia
| | - Xinmin Li
- UCLA Technology Center for Genomics & Bioinformatics, Department of Pathology & Laboratory Medicine, 650 Charles E Young Dr., Los Angeles, CA 90095, USA
| | | | - Nurshat Gaifullin
- Department of Physiology and General Pathology, Faculty of Medicine, Lomonosov Moscow State University, Moscow 119991, Russia
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18
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Revkov E, Kulshrestha T, Sung KWK, Skanderup AJ. PUREE: accurate pan-cancer tumor purity estimation from gene expression data. Commun Biol 2023; 6:394. [PMID: 37041233 PMCID: PMC10090153 DOI: 10.1038/s42003-023-04764-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 03/27/2023] [Indexed: 04/13/2023] Open
Abstract
Tumors are complex masses composed of malignant and non-malignant cells. Variation in tumor purity (proportion of cancer cells in a sample) can both confound integrative analysis and enable studies of tumor heterogeneity. Here we developed PUREE, which uses a weakly supervised learning approach to infer tumor purity from a tumor gene expression profile. PUREE was trained on gene expression data and genomic consensus purity estimates from 7864 solid tumor samples. PUREE predicted purity with high accuracy across distinct solid tumor types and generalized to tumor samples from unseen tumor types and cohorts. Gene features of PUREE were further validated using single-cell RNA-seq data from distinct tumor types. In a comprehensive benchmark, PUREE outperformed existing transcriptome-based purity estimation approaches. Overall, PUREE is a highly accurate and versatile method for estimating tumor purity and interrogating tumor heterogeneity from bulk tumor gene expression data, which can complement genomics-based approaches or be used in settings where genomic data is unavailable.
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Affiliation(s)
- Egor Revkov
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore
- School of Computing, National University of Singapore, Computing 1, 13 Computing Drive, Singapore, 117417, Republic of Singapore
| | - Tanmay Kulshrestha
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore
| | - Ken Wing-Kin Sung
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore
- School of Computing, National University of Singapore, Computing 1, 13 Computing Drive, Singapore, 117417, Republic of Singapore
| | - Anders Jacobsen Skanderup
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
- School of Computing, National University of Singapore, Computing 1, 13 Computing Drive, Singapore, 117417, Republic of Singapore.
- National Cancer Centre Singapore, Division of Medical Oncology, 30 Hospital Boulevard, Singapore, 168583, Republic of Singapore.
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19
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Gong Y, Bao L, Xu T, Yi X, Chen J, Wang S, Pan Z, Huang P, Ge M. The tumor ecosystem in head and neck squamous cell carcinoma and advances in ecotherapy. Mol Cancer 2023; 22:68. [PMID: 37024932 PMCID: PMC10077663 DOI: 10.1186/s12943-023-01769-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 03/27/2023] [Indexed: 04/08/2023] Open
Abstract
The development of head and neck squamous cell carcinoma (HNSCC) is a multi-step process, and its survival depends on a complex tumor ecosystem, which not only promotes tumor growth but also helps to protect tumor cells from immune surveillance. With the advances of existing technologies and emerging models for ecosystem research, the evidence for cell-cell interplay is increasing. Herein, we discuss the recent advances in understanding the interaction between tumor cells, the major components of the HNSCC tumor ecosystem, and summarize the mechanisms of how biological and abiotic factors affect the tumor ecosystem. In addition, we review the emerging ecological treatment strategy for HNSCC based on existing studies.
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Affiliation(s)
- Yingying Gong
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Lisha Bao
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Tong Xu
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Xiaofen Yi
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Jinming Chen
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Shanshan Wang
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Zongfu Pan
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China.
- Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Zhejiang Provincial People's Hospital, Hangzhou, China.
- Clinical Research Center for Cancer of Zhejiang Province, Hangzhou, People's Republic of China.
| | - Ping Huang
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China.
- Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Zhejiang Provincial People's Hospital, Hangzhou, China.
- Clinical Research Center for Cancer of Zhejiang Province, Hangzhou, People's Republic of China.
| | - Minghua Ge
- Otolaryngology & Head and Neck Center, Cancer Center, Department of Head and Neck Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China.
- Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Zhejiang Provincial People's Hospital, Hangzhou, China.
- Clinical Research Center for Cancer of Zhejiang Province, Hangzhou, People's Republic of China.
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20
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Zheng Y, Yang X. Spatial RNA sequencing methods show high resolution of single cell in cancer metastasis and the formation of tumor microenvironment. Biosci Rep 2023; 43:BSR20221680. [PMID: 36459212 PMCID: PMC9950536 DOI: 10.1042/bsr20221680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/03/2022] Open
Abstract
Cancer metastasis often leads to death and therapeutic resistance. This process involves the participation of a variety of cell components, especially cellular and intercellular communications in the tumor microenvironment (TME). Using genetic sequencing technology to comprehensively characterize the tumor and TME is therefore key to understanding metastasis and therapeutic resistance. The use of spatial transcriptome sequencing enables the localization of gene expressions and cell activities in tissue sections. By examining the localization change as well as gene expression of these cells, it is possible to characterize the progress of tumor metastasis and TME formation. With improvements of this technology, spatial transcriptome sequencing technology has been extended from local regions to whole tissues, and from single sequencing technology to multimodal analysis combined with a variety of datasets. This has enabled the detection of every single cell in tissue slides, with high resolution, to provide more accurate predictive information for tumor treatments. In this review, we summarize the results of recent studies dealing with new multimodal methods and spatial transcriptome sequencing methods in tumors to illustrate recent developments in the imaging resolution of micro-tissues.
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Affiliation(s)
- Yue Zheng
- Department of Biochemistry and Molecular Biology, Basic Medical College, Shanxi Medical University, No. 56, Xinjiang South Road, Yingze street, Yingze District, Taiyuan City, Shanxi Province 030000, China
| | - Xiaofeng Yang
- Department of Urology, First Hospital of Shanxi Medical University, No. 85, Jiefang South Road, Yingze street, Yingze District, Taiyuan City, Shanxi Province 030000, China
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21
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Alharbi F, Vakanski A. Machine Learning Methods for Cancer Classification Using Gene Expression Data: A Review. Bioengineering (Basel) 2023; 10:bioengineering10020173. [PMID: 36829667 PMCID: PMC9952758 DOI: 10.3390/bioengineering10020173] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Cancer is a term that denotes a group of diseases caused by the abnormal growth of cells that can spread in different parts of the body. According to the World Health Organization (WHO), cancer is the second major cause of death after cardiovascular diseases. Gene expression can play a fundamental role in the early detection of cancer, as it is indicative of the biochemical processes in tissue and cells, as well as the genetic characteristics of an organism. Deoxyribonucleic acid (DNA) microarrays and ribonucleic acid (RNA)-sequencing methods for gene expression data allow quantifying the expression levels of genes and produce valuable data for computational analysis. This study reviews recent progress in gene expression analysis for cancer classification using machine learning methods. Both conventional and deep learning-based approaches are reviewed, with an emphasis on the application of deep learning models due to their comparative advantages for identifying gene patterns that are distinctive for various types of cancers. Relevant works that employ the most commonly used deep neural network architectures are covered, including multi-layer perceptrons, as well as convolutional, recurrent, graph, and transformer networks. This survey also presents an overview of the data collection methods for gene expression analysis and lists important datasets that are commonly used for supervised machine learning for this task. Furthermore, we review pertinent techniques for feature engineering and data preprocessing that are typically used to handle the high dimensionality of gene expression data, caused by a large number of genes present in data samples. The paper concludes with a discussion of future research directions for machine learning-based gene expression analysis for cancer classification.
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22
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Zhou JG, Liang R, Wang HT, Jin SH, Hu W, Frey B, Fietkau R, Hecht M, Ma H, Gaipl US. Identification and characterization of circular RNAs as novel putative biomarkers to predict anti-PD-1 monotherapy response in metastatic melanoma patients - Knowledge from two independent international studies. Neoplasia 2023; 37:100877. [PMID: 36696838 PMCID: PMC9879779 DOI: 10.1016/j.neo.2023.100877] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/29/2022] [Accepted: 01/16/2023] [Indexed: 01/25/2023]
Abstract
Melanoma is the most aggressive skin malignancy with high morbidity. Anti-programmed cell death protein 1 (PD-1) monotherapy has been applied in metastatic melanoma. However, still most of the patients do not respond to anti-PD-1 and the availability of the present approved biomarkers therefore is limited. Here we combined the transcriptomic and clinical data of 163 advanced melanoma patients receiving anti-PD-1 from NIH Melanoma Genome Sequencing Project (phs000452, 122 patients) as the training and internal validation cohort, and Melanoma Institute Australia cohort (PRJEB23709, 41 patients) as the external validation cohort, respectively. Circular RNAs (circRNAs) are an evolutionarily conserved novel class of noncoding endogenous RNAs (ncRNAs) found in the eukaryotic transcriptome and were used based on RNAseq data for our analyses. 74,243 circular RNAs (circRNAs) were identified with NCLscan and CIRCexplorer2. Thereof, 70 circRNAs significantly associated with progression-free survival and overall survival. Further, a prognostic circRNAs signature consisting of HSA_CIRCpedia_1497, HSA_CIRCpedia_12559, HSA_CIRCpedia_43640, HSA_CIRCpedia_43070, and HSA_CIRCpedia_21660 could be determined with LASSO regression. This signature was a prognostic factor of overall survival and progression-free survival among the analyzed advanced melanoma patients. The concordance indexes (C-index of OStraining: 0.61, C-index of PFStraining: 0.68) also confirmed its credibility and accuracy. First enrichment analysis indicated that immune response and pathways related to tumor immune microenvironment were enriched. In conclusion, we succeeded to construct and validate novel prognostic circRNAs signature for advanced melanoma patients treated with anti-PD-1 immunotherapy.
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Affiliation(s)
- Jian-Guo Zhou
- Department of Oncology, The second affiliated Hospital of Zunyi Medical University, Zunyi, China,Translational Radiobiology, Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany,Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany,Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Rui Liang
- Biomedical Engineering College of Bioengineering, Chongqing University, Chongqing, China
| | - Hai-Tao Wang
- Thoracic Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Su-Han Jin
- Department of Orthodontic, School of Stomatology, Zunyi Medical University, Zunyi, China
| | - Wei Hu
- Department of Oncology, The second affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Benjamin Frey
- Translational Radiobiology, Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany,Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany,Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Rainer Fietkau
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany,Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Markus Hecht
- Department of Radiotherapy and Radiation Oncology, Saarland University Medical Center, Homburg, Germany
| | - Hu Ma
- Department of Oncology, The second affiliated Hospital of Zunyi Medical University, Zunyi, China.
| | - Udo S. Gaipl
- Translational Radiobiology, Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany,Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany,Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany,Corresponding author at: Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsstraße 27, 91054 Erlangen, Germany.
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23
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The Sesquiterpene Lactone-Rich Fraction of Inula helenium L. Enhances the Antitumor Effect of Anti-PD-1 Antibody in Colorectal Cancer: Integrative Phytochemical, Transcriptomic, and Experimental Analyses. Cancers (Basel) 2023; 15:cancers15030653. [PMID: 36765611 PMCID: PMC9913754 DOI: 10.3390/cancers15030653] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023] Open
Abstract
Treatment strategies combining immune checkpoint inhibitors with sesquiterpene lactones have attracted much attention as a promising approach for cancer treatment. We systemically analyzed gene expression profiles of cells in response to two major sesquiterpene lactones, alantolactone and isoalantolactone, and determined whether the sesquiterpene lactone-rich fraction of Inula helenium L. (SFIH) enhances the antitumor effect of anti-PD-1 antibody in MC38 colorectal cancer-bearing mice. Gene expression and pathway analysis using RNA sequencing data were used to identify the SFIH-driven combined activity with anti-PD-1 antibody. The results showed that SFIH significantly enhanced the antitumor effect of anti-PD-1 antibody by reducing tumor growth and increasing the survival time of mice. Specifically, SFIH exhibited antitumor activity when combined with anti-PD-1 antibody, and the effects were further enhanced compared with monotherapy. An analysis of immune cells indicated that combination treatment with SFIH and anti-PD-1 antibody significantly increased the proportion of CD8+ T cells. Moreover, combination treatment enhanced antitumor immunity by decreasing the population of myeloid-derived suppressor cells and increasing the number of M1-like macrophages. Pathway enrichment analysis revealed that combination therapy activated immune-related pathways to a greater extent than monotherapy. In conclusion, our integrative analysis demonstrates that SFIH enhances the response of murine tumors to anti-PD-1 antibody. These findings provide insight into developing integrative therapeutics and molecular data for the use of natural products as an adjunct treatment for colorectal cancer.
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24
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Peixoto C, Lopes MB, Martins M, Casimiro S, Sobral D, Grosso AR, Abreu C, Macedo D, Costa AL, Pais H, Alvim C, Mansinho A, Filipe P, Costa PMD, Fernandes A, Borralho P, Ferreira C, Malaquias J, Quintela A, Kaplan S, Golkaram M, Salmans M, Khan N, Vijayaraghavan R, Zhang S, Pawlowski T, Godsey J, So A, Liu L, Costa L, Vinga S. Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization. BMC Bioinformatics 2023; 24:17. [PMID: 36647008 PMCID: PMC9841719 DOI: 10.1186/s12859-022-05104-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 12/07/2022] [Indexed: 01/18/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer and the second most deathly worldwide. It is a very heterogeneous disease that can develop via distinct pathways where metastasis is the primary cause of death. Therefore, it is crucial to understand the molecular mechanisms underlying metastasis. RNA-sequencing is an essential tool used for studying the transcriptional landscape. However, the high-dimensionality of gene expression data makes selecting novel metastatic biomarkers problematic. To distinguish early-stage CRC patients at risk of developing metastasis from those that are not, three types of binary classification approaches were used: (1) classification methods (decision trees, linear and radial kernel support vector machines, logistic regression, and random forest) using differentially expressed genes (DEGs) as input features; (2) regularized logistic regression based on the Elastic Net penalty and the proposed iTwiner-a network-based regularizer accounting for gene correlation information; and (3) classification methods based on the genes pre-selected using regularized logistic regression. Classifiers using the DEGs as features showed similar results, with random forest showing the highest accuracy. Using regularized logistic regression on the full dataset yielded no improvement in the methods' accuracy. Further classification using the pre-selected genes found by different penalty factors, instead of the DEGs, significantly improved the accuracy of the binary classifiers. Moreover, the use of network-based correlation information (iTwiner) for gene selection produced the best classification results and the identification of more stable and robust gene sets. Some are known to be tumor suppressor genes (OPCML-IT2), to be related to resistance to cancer therapies (RAC1P3), or to be involved in several cancer processes such as genome stability (XRCC6P2), tumor growth and metastasis (MIR602) and regulation of gene transcription (NME2P2). We show that the classification of CRC patients based on pre-selected features by regularized logistic regression is a valuable alternative to using DEGs, significantly increasing the models' predictive performance. Moreover, the use of correlation-based penalization for biomarker selection stands as a promising strategy for predicting patients' groups based on RNA-seq data.
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Affiliation(s)
- Carolina Peixoto
- grid.9983.b0000 0001 2181 4263INESC-ID, Instituto Superior Técnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029 Lisbon, Portugal
| | - Marta B. Lopes
- NOVA Laboratory for Computer Science and Informatics (NOVA LINCS), NOVA School of Science and Technology, 2829-516 Caparica, Portugal ,Center for Mathematics and Applications (NOVA MATH), NOVA School of Science and Technology (FCT NOVA), 2829-516 Caparica, Portugal
| | - Marta Martins
- grid.9983.b0000 0001 2181 4263Instituto de Medicina Molecular - João Lobo Antunes, Faculdade de Medicina de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisbon, Portugal
| | - Sandra Casimiro
- grid.9983.b0000 0001 2181 4263Instituto de Medicina Molecular - João Lobo Antunes, Faculdade de Medicina de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisbon, Portugal
| | - Daniel Sobral
- grid.10772.330000000121511713Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal ,grid.10772.330000000121511713UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Ana Rita Grosso
- grid.10772.330000000121511713Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal ,grid.10772.330000000121511713UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Catarina Abreu
- grid.418341.b0000 0004 0474 1607Oncology Division, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Lisbon, Portugal
| | - Daniela Macedo
- grid.418341.b0000 0004 0474 1607Oncology Division, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Lisbon, Portugal
| | - Ana Lúcia Costa
- grid.418341.b0000 0004 0474 1607Oncology Division, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Lisbon, Portugal
| | - Helena Pais
- grid.418341.b0000 0004 0474 1607Oncology Division, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Lisbon, Portugal
| | - Cecília Alvim
- grid.418341.b0000 0004 0474 1607Oncology Division, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Lisbon, Portugal
| | - André Mansinho
- grid.9983.b0000 0001 2181 4263Instituto de Medicina Molecular - João Lobo Antunes, Faculdade de Medicina de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisbon, Portugal ,grid.418341.b0000 0004 0474 1607Oncology Division, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Lisbon, Portugal
| | - Pedro Filipe
- grid.418341.b0000 0004 0474 1607Oncology Division, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Lisbon, Portugal
| | - Pedro Marques da Costa
- grid.418341.b0000 0004 0474 1607Oncology Division, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Lisbon, Portugal
| | - Afonso Fernandes
- grid.9983.b0000 0001 2181 4263Instituto de Medicina Molecular - João Lobo Antunes, Faculdade de Medicina de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisbon, Portugal
| | - Paula Borralho
- grid.9983.b0000 0001 2181 4263Instituto de Medicina Molecular - João Lobo Antunes, Faculdade de Medicina de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisbon, Portugal
| | - Cristina Ferreira
- grid.418341.b0000 0004 0474 1607Oncology Division, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Lisbon, Portugal
| | - João Malaquias
- grid.418341.b0000 0004 0474 1607Oncology Division, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Lisbon, Portugal
| | - António Quintela
- grid.418341.b0000 0004 0474 1607Oncology Division, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Lisbon, Portugal
| | - Shannon Kaplan
- grid.185669.50000 0004 0507 3954Illumina Inc., 5200 Illumina Way, San Diego, CA 92122 USA
| | - Mahdi Golkaram
- grid.185669.50000 0004 0507 3954Illumina Inc., 5200 Illumina Way, San Diego, CA 92122 USA
| | - Michael Salmans
- grid.185669.50000 0004 0507 3954Illumina Inc., 5200 Illumina Way, San Diego, CA 92122 USA
| | - Nafeesa Khan
- grid.185669.50000 0004 0507 3954Illumina Inc., 5200 Illumina Way, San Diego, CA 92122 USA
| | - Raakhee Vijayaraghavan
- grid.185669.50000 0004 0507 3954Illumina Inc., 5200 Illumina Way, San Diego, CA 92122 USA
| | - Shile Zhang
- grid.185669.50000 0004 0507 3954Illumina Inc., 5200 Illumina Way, San Diego, CA 92122 USA
| | - Traci Pawlowski
- grid.185669.50000 0004 0507 3954Illumina Inc., 5200 Illumina Way, San Diego, CA 92122 USA
| | - Jim Godsey
- grid.185669.50000 0004 0507 3954Illumina Inc., 5200 Illumina Way, San Diego, CA 92122 USA
| | - Alex So
- grid.185669.50000 0004 0507 3954Illumina Inc., 5200 Illumina Way, San Diego, CA 92122 USA
| | - Li Liu
- grid.185669.50000 0004 0507 3954Illumina Inc., 5200 Illumina Way, San Diego, CA 92122 USA
| | - Luís Costa
- grid.9983.b0000 0001 2181 4263Instituto de Medicina Molecular - João Lobo Antunes, Faculdade de Medicina de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisbon, Portugal ,grid.418341.b0000 0004 0474 1607Oncology Division, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Lisbon, Portugal
| | - Susana Vinga
- grid.9983.b0000 0001 2181 4263INESC-ID, Instituto Superior Técnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029 Lisbon, Portugal ,grid.9983.b0000 0001 2181 4263IDMEC, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
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25
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Miller AR, Wijeratne S, McGrath SD, Schieffer KM, Miller KE, Lee K, Mathew M, LaHaye S, Fitch JR, Kelly BJ, White P, Mardis ER, Wilson RK, Cottrell CE, Magrini V. Pacific Biosciences Fusion and Long Isoform Pipeline for Cancer Transcriptome-Based Resolution of Isoform Complexity. J Mol Diagn 2022; 24:1292-1306. [PMID: 36191838 DOI: 10.1016/j.jmoldx.2022.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 08/05/2022] [Accepted: 09/13/2022] [Indexed: 01/13/2023] Open
Abstract
Genomic profiling using short-read sequencing has utility in detecting disease-associated variation in both DNA and RNA. However, given the frequent occurrence of structural variation in cancer, molecular profiling using long-read sequencing improves the resolution of such events. For example, the Pacific Biosciences long-read RNA-sequencing (Iso-Seq) transcriptome protocol provides full-length isoform characterization, discernment of allelic phasing, and isoform discovery, and identifies expressed fusion partners. The Pacific Biosciences Fusion and Long Isoform Pipeline (PB_FLIP) incorporates a suite of RNA-sequencing software analysis tools and scripts to identify expressed fusion partners and isoforms. In addition, sequencing of a commercial reference (Spike-In RNA Variants) with known isoform complexity was performed and demonstrated high recall of the Iso-Seq and PB_FLIP workflow to benchmark our protocol and analysis performance. This study describes the utility of Iso-Seq and PB_FLIP analysis in improving deconvolution of complex structural variants and isoform detection within an institutional pediatric and adolescent/young adult translational cancer research cohort. The exemplar case studies demonstrate that Iso-Seq and PB_FLIP discover novel expressed fusion partners, resolve complex intragenic alterations, and discriminate between allele-specific expression profiles.
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Affiliation(s)
- Anthony R Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Saranga Wijeratne
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Sean D McGrath
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Kathleen M Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Katherine E Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Kristy Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio
| | - Mariam Mathew
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio
| | - Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - James R Fitch
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Benjamin J Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio; Department of Neurosurgery, The Ohio State University College of Medicine, Columbus, Ohio
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio.
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio
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Costa VG, Costa SM, Saramago M, Cunha MV, Arraiano CM, Viegas SC, Matos RG. Developing New Tools to Fight Human Pathogens: A Journey through the Advances in RNA Technologies. Microorganisms 2022; 10:2303. [PMID: 36422373 PMCID: PMC9697208 DOI: 10.3390/microorganisms10112303] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 09/18/2024] Open
Abstract
A long scientific journey has led to prominent technological advances in the RNA field, and several new types of molecules have been discovered, from non-coding RNAs (ncRNAs) to riboswitches, small interfering RNAs (siRNAs) and CRISPR systems. Such findings, together with the recognition of the advantages of RNA in terms of its functional performance, have attracted the attention of synthetic biologists to create potent RNA-based tools for biotechnological and medical applications. In this review, we have gathered the knowledge on the connection between RNA metabolism and pathogenesis in Gram-positive and Gram-negative bacteria. We further discuss how RNA techniques have contributed to the building of this knowledge and the development of new tools in synthetic biology for the diagnosis and treatment of diseases caused by pathogenic microorganisms. Infectious diseases are still a world-leading cause of death and morbidity, and RNA-based therapeutics have arisen as an alternative way to achieve success. There are still obstacles to overcome in its application, but much progress has been made in a fast and effective manner, paving the way for the solid establishment of RNA-based therapies in the future.
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Affiliation(s)
| | | | | | | | | | - Sandra C. Viegas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal; (V.G.C.); (S.M.C.); (M.S.); (M.V.C.); (C.M.A.)
| | - Rute G. Matos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal; (V.G.C.); (S.M.C.); (M.S.); (M.V.C.); (C.M.A.)
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Postel MD, Culver JO, Ricker C, Craig DW. Transcriptome analysis provides critical answers to the "variants of uncertain significance" conundrum. Hum Mutat 2022; 43:1590-1608. [PMID: 35510381 PMCID: PMC9560997 DOI: 10.1002/humu.24394] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/16/2022] [Accepted: 04/26/2022] [Indexed: 12/30/2022]
Abstract
While whole-genome and exome sequencing have transformed our collective understanding of genetics' role in disease pathogenesis, there are certain conditions and populations for whom DNA-level data fails to identify the underlying genetic etiology. Specifically, patients of non-White race and non-European ancestry are disproportionately affected by "variants of unknown/uncertain significance" (VUS), limiting the scope of precision medicine for minority patients and perpetuating health disparities. VUS often include deep intronic and splicing variants which are difficult to interpret from DNA data alone. RNA analysis can illuminate the consequences of VUS, thereby allowing for their reclassification as pathogenic versus benign. Here we review the critical role transcriptome analysis plays in clarifying VUS in both neoplastic and non-neoplastic diseases.
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Affiliation(s)
- Mackenzie D. Postel
- Department of Translational GenomicsUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Julie O. Culver
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Charité Ricker
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - David W. Craig
- Department of Translational GenomicsUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
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Huang R, Wang X, Yin X, Zhou Y, Sun J, Yin Z, Zhu Z. Combining bulk RNA-sequencing and single-cell RNA-sequencing data to reveal the immune microenvironment and metabolic pattern of osteosarcoma. Front Genet 2022; 13:976990. [PMID: 36338972 PMCID: PMC9626532 DOI: 10.3389/fgene.2022.976990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/15/2022] [Indexed: 11/20/2022] Open
Abstract
Background: Osteosarcoma (OS) is a kind of solid tumor with high heterogeneity at tumor microenvironment (TME), genome and transcriptome level. In view of the regulatory effect of metabolism on TME, this study was based on four metabolic models to explore the intertumoral heterogeneity of OS at the RNA sequencing (RNA-seq) level and the intratumoral heterogeneity of OS at the bulk RNA-seq and single cell RNA-seq (scRNA-seq) level. Methods: The GSVA package was used for single-sample gene set enrichment analysis (ssGSEA) analysis to obtain a glycolysis, pentose phosphate pathway (PPP), fatty acid oxidation (FAO) and glutaminolysis gene sets score. ConsensusClusterPlus was employed to cluster OS samples downloaded from the Target database. The scRNA-seq and bulk RNA-seq data of immune cells from GSE162454 dataset were analyzed to identify the subsets and types of immune cells in OS. Malignant cells and non-malignant cells were distinguished by large-scale chromosomal copy number variation. The correlations of metabolic molecular subtypes and immune cell types with four metabolic patterns, hypoxia and angiogenesis were determined by Pearson correlation analysis. Results: Two metabolism-related molecular subtypes of OS, cluster 1 and cluster 2, were identified. Cluster 2 was associated with poor prognosis of OS, active glycolysis, FAO, glutaminolysis, and bad TME. The identified 28608 immune cells were divided into 15 separate clusters covering 6 types of immune cells. The enrichment scores of 5 kinds of immune cells in cluster-1 and cluster-2 were significantly different. And five kinds of immune cells were significantly correlated with four metabolic modes, hypoxia and angiogenesis. Of the 28,608 immune cells, 7617 were malignant cells. The four metabolic patterns of malignant cells were significantly positively correlated with hypoxia and negatively correlated with angiogenesis. Conclusion: We used RNA-seq to reveal two molecular subtypes of OS with prognosis, metabolic pattern and TME, and determined the composition and metabolic heterogeneity of immune cells in OS tumor by bulk RNA-seq and single-cell RNA-seq.
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Affiliation(s)
- Ruichao Huang
- Department of Orthopedics, Zhengzhou Central Hospital affiliated to Zhengzhou University, Zhengzhou, China
| | - Xiaohu Wang
- Department of Orthopedics, Zhengzhou Central Hospital affiliated to Zhengzhou University, Zhengzhou, China
| | - Xiangyun Yin
- Department of Orthopedics, Zhengzhou Central Hospital affiliated to Zhengzhou University, Zhengzhou, China
- Advanced Medical Research Center of Zhengzhou University, Zhengzhou Central Hospital affiliated to Zhengzhou University, Zhengzhou, China
| | - Yaqi Zhou
- Department of Orthopedics, Zhengzhou Central Hospital affiliated to Zhengzhou University, Zhengzhou, China
| | - Jiansheng Sun
- Department of Orthopedics, Zhengzhou Central Hospital affiliated to Zhengzhou University, Zhengzhou, China
| | - Zhongxiu Yin
- Nanchang University Queen Mary School, Nanchang, China
| | - Zhi Zhu
- Department of Orthopedics, Zhengzhou Central Hospital affiliated to Zhengzhou University, Zhengzhou, China
- *Correspondence: Zhi Zhu,
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Chen Y, Zheng A, Zhang Y, Xiao M, Zhao Y, Wu X, Li M, Du F, Chen Y, Chen M, Li W, Li X, Sun Y, Gu L, Xiao Z, Shen J. Dysregulation of B7 family and its association with tumor microenvironment in uveal melanoma. Front Immunol 2022; 13:1026076. [PMID: 36311731 PMCID: PMC9615147 DOI: 10.3389/fimmu.2022.1026076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/20/2022] [Indexed: 11/25/2022] Open
Abstract
Background Uveal melanoma (UVM) is the most common primary intraocular malignancy in adults with a poor prognosis. B7 family is an important modulator of the immune response. However, its dysregulation and underlying molecular mechanism in UVM still remains unclear. Methods Data were derived from TCGA and GEO databases. The prognosis was analyzed by Kaplan-Meier curve. The ESTIMATE algorithm, CIBERSORT algorithm, and TIMER database were used to demonstrate the correlation between B7 family and tumor immune microenvironment in UVM. Single-cell RNA sequencing was used to detect the expression levels of the B7 family in different cell types of UVM. UVM was classified into different types by consistent clustering. Enrichment analysis revealed downstream signaling pathways of the B7 family. The interaction between different cell types was visualized by cell chat. Results The expression level of B7 family in UVM was significantly dysregulated and negatively correlated with methylation level. The expression of B7 family was associated with prognosis and immune infiltration, and B7 family plays an important role in the tumor microenvironment (TME). B7 family members were highly expressed in monocytes/macrophages of UVM compared with other cell types. Immune response and visual perception were the main functions affected by B7 family. The result of cell chat showed that the interaction between photoreceptor cells and immune-related cells was mainly generated by HLA-C-CD8A. CABP4, KCNJ10 and RORB had the strongest correlation with HLA-C-CD8A, and their high expression was significantly correlated with poor prognosis. CABP4 and RORB were specifically expressed in photoreceptor cells. Conclusions Dysregulation of the B7 family in UVM is associated with poor prognosis and affects the tumor immune microenvironment. CABP4 and RORB can serve as potential therapeutic targets for UVM, which can be regulated by the B7 family to affect the visual perception and immune response function of the eye, thus influencing the prognosis of UVM.
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Affiliation(s)
- Yao Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- Pidu District People’s Hospital, Chengdu, Sichuan, China
| | - Anfu Zheng
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Yao Zhang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Mintao Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Fukuan Du
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Yu Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Meijuan Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Wanping Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Xiaobing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Yuhong Sun
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Li Gu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Zhangang Xiao
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- *Correspondence: Jing Shen, ; Zhangang Xiao,
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
- *Correspondence: Jing Shen, ; Zhangang Xiao,
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Xu J, Qin S, Yi Y, Gao H, Liu X, Ma F, Guan M. Delving into the Heterogeneity of Different Breast Cancer Subtypes and the Prognostic Models Utilizing scRNA-Seq and Bulk RNA-Seq. Int J Mol Sci 2022; 23:ijms23179936. [PMID: 36077333 PMCID: PMC9456551 DOI: 10.3390/ijms23179936] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Breast cancer (BC) is the most common malignancy in women with high heterogeneity. The heterogeneity of cancer cells from different BC subtypes has not been thoroughly characterized and there is still no valid biomarker for predicting the prognosis of BC patients in clinical practice. Methods: Cancer cells were identified by calculating single cell copy number variation using the inferCNV algorithm. SCENIC was utilized to infer gene regulatory networks. CellPhoneDB software was used to analyze the intercellular communications in different cell types. Survival analysis, univariate Cox, least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox analysis were used to construct subtype specific prognostic models. Results: Triple-negative breast cancer (TNBC) has a higher proportion of cancer cells than subtypes of HER2+ BC and luminal BC, and the specifically upregulated genes of the TNBC subtype are associated with antioxidant and chemical stress resistance. Key transcription factors (TFs) of tumor cells for three subtypes varied, and most of the TF-target genes are specifically upregulated in corresponding BC subtypes. The intercellular communications mediated by different receptor–ligand pairs lead to an inflammatory response with different degrees in the three BC subtypes. We establish a prognostic model containing 10 genes (risk genes: ATP6AP1, RNF139, BASP1, ESR1 and TSKU; protective genes: RPL31, PAK1, STARD10, TFPI2 and SIAH2) for luminal BC, seven genes (risk genes: ACTR6 and C2orf76; protective genes: DIO2, DCXR, NDUFA8, SULT1A2 and AQP3) for HER2+ BC, and seven genes (risk genes: HPGD, CDC42 and PGK1; protective genes: SMYD3, LMO4, FABP7 and PRKRA) for TNBC. Three prognostic models can distinguish high-risk patients from low-risk patients and accurately predict patient prognosis. Conclusions: Comparative analysis of the three BC subtypes based on cancer cell heterogeneity in this study will be of great clinical significance for the diagnosis, prognosis and targeted therapy for BC patients.
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Duan W, Zhang B, Li X, Chen W, Jia S, Xin Z, Jian Q, Jian F, Chou D, Chen Z. Single-cell transcriptome profiling reveals intra-tumoral heterogeneity in human chordomas. Cancer Immunol Immunother 2022; 71:2185-2195. [DOI: 10.1007/s00262-022-03152-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
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Xiao K, Li S, Ding J, Wang Z, Wang D, Cao X, Zhang Y, Dong Z. Expression and clinical value of circRNAs in serum extracellular vesicles for gastric cancer. Front Oncol 2022; 12:962831. [PMID: 36059681 PMCID: PMC9428625 DOI: 10.3389/fonc.2022.962831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/28/2022] [Indexed: 12/24/2022] Open
Abstract
Objective At present, there are still no effective diagnosis methods for gastric cancer (GC). Increasing evidences indicate that Extracellular Vesicle circular RNAs (EV circRNAs) play a crucial role in several diseases. However, their correlations with GC are not clarified. This study aims to investigate the expression profile of serum EV circRNAs in GC and evaluate its potential clinical value. Methods High-throughput RNA sequencing (RNA-seq) was used to assess circRNA expression profiles between 4 patients with GC and 4 healthy controls. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were employed to determine the biological functions of differentially expressed (DE) circRNAs. A circRNA-miRNA-mRNA network was constructed using bioinformatics tools. Reverse transcription-quantitative polymerase chain reaction (RT-q)PCR was used to validate the dysregulated circRNAs. Receiver operating characteristic (ROC) curves were used to evaluate the diagnostic value of circRNAs for GC. Results A total of 4692 circRNAs were detected in the serum EVs of healthy controls and patients with GC, most of which were novel (98%) and intergenic (52%). 7 circRNAs were upregulated and 4 circRNAs were downregulated (|log2Fold Change| > 2, P < 0.05). GO and KEGG pathway enrichment analyses revealed that DE circRNAs were primarily involved in glutathione metabolism, protein folding, and drug metabolism-cytochrome P450. Of these, 3 circRNAs (Chr10q11, Chr1p11, and Chr7q11) were identified to be significantly overexpressed in patients with GC compared with healthy controls using RT-qPCR. The combination of 3 EV circRNAs and carcinoembryonic antigen (CEA) produced an area under the curve (AUC) of 0.866 (95%CI: 0.803-0.915) with a sensitivity and specificity of 80.4% and 81.8%, respectively. Additionally, the expression levels of 3 EV circRNAs were significantly correlated with tumor size, lymph node metastasis, and TNM stage. The circRNA-miRNA-mRNA network showed that the 3 identified circRNAs were predicted to interact with 13 miRNAs and 91 mRNAs. Conclusion Our results illustrate that the panel of EV circRNAs in serum are aberrantly expressed and may act as the suitable biomarkers for gastric cancer.
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Affiliation(s)
- Ke Xiao
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Shirong Li
- Department of Laboratory Medicine, Weifang People’s Hospital, Weifang, China
| | - Juan Ding
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Zhen Wang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Ding Wang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Xiangting Cao
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Yi Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
- *Correspondence: Zhaogang Dong, ; Yi Zhang,
| | - Zhaogang Dong
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
- *Correspondence: Zhaogang Dong, ; Yi Zhang,
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Gindin T, Hsiao SJ. Analytical Principles of Cancer Next Generation Sequencing. Clin Lab Med 2022; 42:395-408. [DOI: 10.1016/j.cll.2022.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Liu L, Liu Z, Gao J, Liu X, Weng S, Guo C, Hu B, Wang Z, Zhang J, Shi J, Guo W, Zhang S. CD8+ T cell trajectory subtypes decode tumor heterogeneity and provide treatment recommendations for hepatocellular carcinoma. Front Immunol 2022; 13:964190. [PMID: 35967384 PMCID: PMC9363578 DOI: 10.3389/fimmu.2022.964190] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction Mounting evidence has revealed that the interactions and dynamic alterations among immune cells are critical in shaping the tumor microenvironment and ultimately map onto heterogeneous clinical outcomes. Currently, the underlying clinical significance of immune cell evolutions remains largely unexplored in hepatocellular carcinoma (HCC). Methods A total of 3,817 immune cells and 1,750 HCC patients of 15 independent public datasets were retrieved. The Seurat and Monocle algorithms were used to depict T cell evolution, and nonnegative matrix factorization (NMF) was further applied to identify the molecular classification. Subsequently, the prognosis, biological characteristics, genomic variations, and immune landscape among distinct clusters were decoded. The clinical efficacy of multiple treatment approaches was further investigated. Results According to trajectory gene expression, three heterogeneous clusters with different clinical outcomes were identified. C2, with a more advanced pathological stage, presented the most dismal prognosis relative to C1 and C3. Eight independent external cohorts validated the robustness and reproducibility of the three clusters. Further explorations elucidated C1 to be characterized as lipid metabolic HCC, and C2 was referred to as cell-proliferative HCC, whereas C3 was defined as immune inflammatory HCC. Moreover, C2 also displayed the most conspicuous genomic instability, and C3 was deemed as “immune-hot”, having abundant immune cells and an elevated expression of immune checkpoints. The assessments of therapeutic intervention suggested that patients in C1 were suitable for transcatheter arterial chemoembolization treatment, and patients in C2 were sensitive to tyrosine kinase inhibitors, while patients in C3 were more responsive to immunotherapy. We also identified numerous underlying therapeutic agents, which might be conducive to clinical transformation in the future. Conclusions Our study developed three clusters with distinct characteristics based on immune cell evolutions. For specifically stratified patients, we proposed individualized treatment strategies to improve the clinical outcomes and facilitate the clinical management.
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Affiliation(s)
- Long Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Research Centre for Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering and Research Center for Diagnosis and Treatment of Hepatobiliary and Pancreatic Surgical Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jie Gao
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Research Centre for Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering and Research Center for Diagnosis and Treatment of Hepatobiliary and Pancreatic Surgical Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xudong Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Research Centre for Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering and Research Center for Diagnosis and Treatment of Hepatobiliary and Pancreatic Surgical Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chunguang Guo
- Department of Endovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bowen Hu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Research Centre for Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering and Research Center for Diagnosis and Treatment of Hepatobiliary and Pancreatic Surgical Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhihui Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Research Centre for Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering and Research Center for Diagnosis and Treatment of Hepatobiliary and Pancreatic Surgical Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jiakai Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Research Centre for Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering and Research Center for Diagnosis and Treatment of Hepatobiliary and Pancreatic Surgical Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jihua Shi
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Research Centre for Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering and Research Center for Diagnosis and Treatment of Hepatobiliary and Pancreatic Surgical Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Research Centre for Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering and Research Center for Diagnosis and Treatment of Hepatobiliary and Pancreatic Surgical Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Research Centre for Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Engineering and Research Center for Diagnosis and Treatment of Hepatobiliary and Pancreatic Surgical Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Shuijun Zhang,
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Garg T, Weiss CR, Sheth RA. Techniques for Profiling the Cellular Immune Response and Their Implications for Interventional Oncology. Cancers (Basel) 2022; 14:3628. [PMID: 35892890 PMCID: PMC9332307 DOI: 10.3390/cancers14153628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 12/07/2022] Open
Abstract
In recent years there has been increased interest in using the immune contexture of the primary tumors to predict the patient's prognosis. The tumor microenvironment of patients with cancers consists of different types of lymphocytes, tumor-infiltrating leukocytes, dendritic cells, and others. Different technologies can be used for the evaluation of the tumor microenvironment, all of which require a tissue or cell sample. Image-guided tissue sampling is a cornerstone in the diagnosis, stratification, and longitudinal evaluation of therapeutic efficacy for cancer patients receiving immunotherapies. Therefore, interventional radiologists (IRs) play an essential role in the evaluation of patients treated with systemically administered immunotherapies. This review provides a detailed description of different technologies used for immune assessment and analysis of the data collected from the use of these technologies. The detailed approach provided herein is intended to provide the reader with the knowledge necessary to not only interpret studies containing such data but also design and apply these tools for clinical practice and future research studies.
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Affiliation(s)
- Tushar Garg
- Division of Vascular and Interventional Radiology, Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (T.G.); (C.R.W.)
| | - Clifford R. Weiss
- Division of Vascular and Interventional Radiology, Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (T.G.); (C.R.W.)
| | - Rahul A. Sheth
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Sinjab A, Rahal Z, Kadara H. Cell-by-Cell: Unlocking Lung Cancer Pathogenesis. Cancers (Basel) 2022; 14:3424. [PMID: 35884485 PMCID: PMC9320562 DOI: 10.3390/cancers14143424] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/08/2022] [Accepted: 07/12/2022] [Indexed: 01/09/2023] Open
Abstract
For lung cancers, cellular trajectories and fates are strongly pruned by cell intrinsic and extrinsic factors. Over the past couple of decades, the combination of comprehensive molecular and genomic approaches, as well as the use of relevant pre-clinical models, enhanced micro-dissection techniques, profiling of rare preneoplastic lesions and surrounding tissues, as well as multi-region tumor sequencing, have all provided in-depth insights into the early biology and evolution of lung cancers. The advent of single-cell sequencing technologies has revolutionized our ability to interrogate these same models, tissues, and cohorts at an unprecedented resolution. Single-cell tracking of lung cancer pathogenesis is now transforming our understanding of the roles and consequences of epithelial-microenvironmental cues and crosstalk during disease evolution. By focusing on non-small lung cancers, specifically lung adenocarcinoma subtype, this review aims to summarize our knowledge base of tumor cells-of-origin and tumor-immune dynamics that have been primarily fueled by single-cell analysis of lung adenocarcinoma specimens at various stages of disease pathogenesis and of relevant animal models. The review will provide an overview of how recent reports are rewriting the mechanistic details of lineage plasticity and intra-tumor heterogeneity at a magnified scale thanks to single-cell studies of early- to late-stage lung adenocarcinomas. Future advances in single-cell technologies, coupled with analysis of minute amounts of rare clinical tissues and novel animal models, are anticipated to help transform our understanding of how diverse micro-events elicit macro-scale consequences, and thus to significantly advance how basic genomic and molecular knowledge of lung cancer evolution can be translated into successful targets for early detection and prevention of this lethal disease.
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Affiliation(s)
- Ansam Sinjab
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Z.R.); (H.K.)
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Long Q, Yuan Y, Li M. RNA-SSNV: A Reliable Somatic Single Nucleotide Variant Identification Framework for Bulk RNA-Seq Data. Front Genet 2022; 13:865313. [PMID: 35846154 PMCID: PMC9279659 DOI: 10.3389/fgene.2022.865313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
The usage of expressed somatic mutations may have a unique advantage in identifying active cancer driver mutations. However, accurately calling mutations from RNA-seq data is difficult due to confounding factors such as RNA-editing, reverse transcription, and gap alignment. In the present study, we proposed a framework (named RNA-SSNV, https://github.com/pmglab/RNA-SSNV) to call somatic single nucleotide variants (SSNV) from tumor bulk RNA-seq data. Based on a comprehensive multi-filtering strategy and a machine-learning classification model trained with comprehensively curated features, RNA-SSNV achieved the best precision–recall rate (0.880–0.884) in a testing dataset and robustly retained 0.94 AUC for the precision–recall curve in three validation adult-based TCGA (The Cancer Genome Atlas) datasets. We further showed that the somatic mutations called by RNA-SSNV tended to have a higher functional impact and therapeutic power in known driver genes. Furthermore, VAF (variant allele fraction) analysis revealed that subclonal harboring expressed mutations had evolutional selection advantage and RNA had higher detection power to rescue DNA-omitted mutations. In sum, RNA-SSNV will be a useful approach to accurately call expressed somatic mutations for a more insightful analysis of cancer drive genes and carcinogenic mechanisms.
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Affiliation(s)
- Qihan Long
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Precision Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Disease Genome Research, Sun Yat-Sen University, Guangzhou, China
| | - Yangyang Yuan
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Precision Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Disease Genome Research, Sun Yat-Sen University, Guangzhou, China
| | - Miaoxin Li
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Precision Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Disease Genome Research, Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Key Laboratory of Tropical Disease Control (SYSU), Ministry of Education, Guangzhou, China
- *Correspondence: Miaoxin Li,
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Pan Y, Cao W, Mu Y, Zhu Q. Microfluidics Facilitates the Development of Single-Cell RNA Sequencing. BIOSENSORS 2022; 12:bios12070450. [PMID: 35884253 PMCID: PMC9312765 DOI: 10.3390/bios12070450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 12/12/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) technology provides a powerful tool for understanding complex biosystems at the single-cell and single-molecule level. The past decade has been a golden period for the development of single-cell sequencing, with scRNA-seq undergoing a tremendous leap in sensitivity and throughput. The application of droplet- and microwell-based microfluidics in scRNA-seq has contributed greatly to improving sequencing throughput. This review introduces the history of development and important technical factors of scRNA-seq. We mainly focus on the role of microfluidics in facilitating the development of scRNA-seq technology. To end, we discuss the future directions for scRNA-seq.
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Affiliation(s)
- Yating Pan
- Research Center for Analytical Instrumentation, State Key Laboratory of Industrial Control Technology, College of Control Science and Engineering, Zhejiang University, Hangzhou 310027, China; (Y.P.); (W.C.)
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wenjian Cao
- Research Center for Analytical Instrumentation, State Key Laboratory of Industrial Control Technology, College of Control Science and Engineering, Zhejiang University, Hangzhou 310027, China; (Y.P.); (W.C.)
| | - Ying Mu
- Research Center for Analytical Instrumentation, State Key Laboratory of Industrial Control Technology, College of Control Science and Engineering, Zhejiang University, Hangzhou 310027, China; (Y.P.); (W.C.)
- Correspondence: (Y.M.); (Q.Z.); Tel.: +86-88208383 (Y.M.); +86-88208383 (Q.Z.)
| | - Qiangyuan Zhu
- Research Center for Analytical Instrumentation, State Key Laboratory of Industrial Control Technology, College of Control Science and Engineering, Zhejiang University, Hangzhou 310027, China; (Y.P.); (W.C.)
- Huzhou Institute of Zhejiang University, Huzhou 313002, China
- Correspondence: (Y.M.); (Q.Z.); Tel.: +86-88208383 (Y.M.); +86-88208383 (Q.Z.)
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Chen X, Li M, Tang Y, Liang Q, Hua C, He H, Song Y, Cheng H. Gene Expression Profile Analysis of Human Epidermal Keratinocytes Expressing Human Papillomavirus Type 8 E7. Pathol Oncol Res 2022; 28:1610176. [PMID: 35665406 PMCID: PMC9156622 DOI: 10.3389/pore.2022.1610176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/21/2022] [Indexed: 11/13/2022]
Abstract
Background: Human papillomavirus type 8 (HPV8) has been implicated in the progress of non-melanoma skin cancers and their precursor lesions. The HPV8 E7 oncoprotein plays a key role in the tumorigenesis of HPV-associated cutaneous tumors. However, the exact role of HPV8 E7 in human epidermal carcinogenesis has not been fully elucidated. Methods: To investigate the potential carcinogenic effects of HPV8 E7 on epithelial cells, we used RNA-sequencing technology to analyze the gene expression profile of HPV8 E7-overexpressed normal human epidermal keratinocytes (NHEKs). Results: RNA-sequencing revealed 831 differentially expressed genes (DEGs) between HPV8 E7-expressing NHEKs and control cells, among which, 631 genes were significantly upregulated, and 200 were downregulated. Gene ontology annotation enrichment analysis showed that HPV8 E7 mainly affected the expression of genes associated with protein heterodimerization activity, DNA binding, nucleosomes, and nucleosome assembly. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that overexpression of HPV8 E7 affected the expression of gene clusters associated with viral carcinogenesis and transcriptional misregulation in cancer and necroptosis signaling pathways that reportedly play crucial roles in HPV infection promotion and cancer progression. We also found the DEGs, such as HKDC1 and TNFAIP3, were associated with epigenetic modifications, immune regulation, and metabolic pathways. Conclusion: Our results demonstrate that the pro-carcinogenic effect of HPV8 expression in epithelial cells may be attributed to the regulatory effect of oncogene E7 on gene expression associated with epigenetic modifications and immune and metabolic status-associated gene expression. Although our data are based on an in vitro experiment, it provides the theoretical evidence that the development of squamous cell carcinoma can be caused by HPV.
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Affiliation(s)
- Xianzhen Chen
- Department of Dermatology and Venereology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou, China
| | - Ma Li
- Department of Dermatology and Venereology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou, China
| | - Yi Tang
- Department of Dermatology and Venereology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou, China.,Department of Dermatology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Qichang Liang
- Department of Dermatology and Venereology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou, China
| | - Chunting Hua
- Department of Dermatology and Venereology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou, China
| | - Huiqin He
- Department of Gastroenterology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou, China
| | - Yinjing Song
- Department of Dermatology and Venereology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou, China
| | - Hao Cheng
- Department of Dermatology and Venereology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou, China
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FFPE-Based NGS Approaches into Clinical Practice: The Limits of Glory from a Pathologist Viewpoint. J Pers Med 2022; 12:jpm12050750. [PMID: 35629172 PMCID: PMC9146170 DOI: 10.3390/jpm12050750] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 01/02/2023] Open
Abstract
The introduction of next-generation sequencing (NGS) in the molecular diagnostic armamentarium is deeply changing pathology practice and laboratory frameworks. NGS allows for the comprehensive molecular characterization of neoplasms, in order to provide the best treatment to oncologic patients. On the other hand, NGS raises technical issues and poses several challenges in terms of education, infrastructures and costs. The aim of this review is to give an overview of the main NGS sequencing platforms that can be used in current molecular diagnostics and gain insights into the clinical applications of NGS in precision oncology. Hence, we also focus on the preanalytical, analytical and interpretative issues raised by the incorporation of NGS in routine pathology diagnostics.
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Dlamini Z, Skepu A, Kim N, Mkhabele M, Khanyile R, Molefi T, Mbatha S, Setlai B, Mulaudzi T, Mabongo M, Bida M, Kgoebane-Maseko M, Mathabe K, Lockhat Z, Kgokolo M, Chauke-Malinga N, Ramagaga S, Hull R. AI and precision oncology in clinical cancer genomics: From prevention to targeted cancer therapies-an outcomes based patient care. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100965] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Zhang L, Chen D, Song D, Liu X, Zhang Y, Xu X, Wang X. Clinical and translational values of spatial transcriptomics. Signal Transduct Target Ther 2022; 7:111. [PMID: 35365599 PMCID: PMC8972902 DOI: 10.1038/s41392-022-00960-w] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/04/2022] [Accepted: 03/09/2022] [Indexed: 02/06/2023] Open
Abstract
The combination of spatial transcriptomics (ST) and single cell RNA sequencing (scRNA-seq) acts as a pivotal component to bridge the pathological phenomes of human tissues with molecular alterations, defining in situ intercellular molecular communications and knowledge on spatiotemporal molecular medicine. The present article overviews the development of ST and aims to evaluate clinical and translational values for understanding molecular pathogenesis and uncovering disease-specific biomarkers. We compare the advantages and disadvantages of sequencing- and imaging-based technologies and highlight opportunities and challenges of ST. We also describe the bioinformatics tools necessary on dissecting spatial patterns of gene expression and cellular interactions and the potential applications of ST in human diseases for clinical practice as one of important issues in clinical and translational medicine, including neurology, embryo development, oncology, and inflammation. Thus, clear clinical objectives, designs, optimizations of sampling procedure and protocol, repeatability of ST, as well as simplifications of analysis and interpretation are the key to translate ST from bench to clinic.
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Affiliation(s)
- Linlin Zhang
- Zhongshan Hospital, Department of Pulmonary and Critical Care Medicine, Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Shanghai, 200000, China
| | - Dongsheng Chen
- Suzhou Institute of Systems Medicine, Suzhou, 215123, Jiangsu, China
| | - Dongli Song
- Zhongshan Hospital, Department of Pulmonary and Critical Care Medicine, Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Shanghai, 200000, China
| | - Xiaoxia Liu
- Zhongshan Hospital, Department of Pulmonary and Critical Care Medicine, Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Shanghai, 200000, China
| | - Yanan Zhang
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Tsinghua University, Shenzhen, 518055, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Xiangdong Wang
- Zhongshan Hospital, Department of Pulmonary and Critical Care Medicine, Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Shanghai, 200000, China.
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Ahmed R, Zaman T, Chowdhury F, Mraiche F, Tariq M, Ahmad IS, Hasan A. Single-Cell RNA Sequencing with Spatial Transcriptomics of Cancer Tissues. Int J Mol Sci 2022; 23:3042. [PMID: 35328458 PMCID: PMC8955933 DOI: 10.3390/ijms23063042] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/02/2022] [Accepted: 03/07/2022] [Indexed: 01/27/2023] Open
Abstract
Single-cell RNA sequencing (RNA-seq) techniques can perform analysis of transcriptome at the single-cell level and possess an unprecedented potential for exploring signatures involved in tumor development and progression. These techniques can perform sequence analysis of transcripts with a better resolution that could increase understanding of the cellular diversity found in the tumor microenvironment and how the cells interact with each other in complex heterogeneous cancerous tissues. Identifying the changes occurring in the genome and transcriptome in the spatial context is considered to increase knowledge of molecular factors fueling cancers. It may help develop better monitoring strategies and innovative approaches for cancer treatment. Recently, there has been a growing trend in the integration of RNA-seq techniques with contemporary omics technologies to study the tumor microenvironment. There has been a realization that this area of research has a huge scope of application in translational research. This review article presents an overview of various types of single-cell RNA-seq techniques used currently for analysis of cancer tissues, their pros and cons in bulk profiling of transcriptome, and recent advances in the techniques in exploring heterogeneity of various types of cancer tissues. Furthermore, we have highlighted the integration of single-cell RNA-seq techniques with other omics technologies for analysis of transcriptome in their spatial context, which is considered to revolutionize the understanding of tumor microenvironment.
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Affiliation(s)
- Rashid Ahmed
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar
- Biomedical Research Centre, Qatar University, Doha 2713, Qatar
- Department of Biotechnology, Faculty of Natural and Applied Sciences, Mirpur University of Science and Technology, Mirpur 10250 AJK, Pakistan;
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA;
| | - Tariq Zaman
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA;
| | - Farhan Chowdhury
- Department of Mechanical Engineering and Energy Processes, Southern Illinois University Carbondale, Carbondale, IL 62901, USA;
| | - Fatima Mraiche
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha 2713, Qatar;
| | - Muhammad Tariq
- Department of Biotechnology, Faculty of Natural and Applied Sciences, Mirpur University of Science and Technology, Mirpur 10250 AJK, Pakistan;
| | - Irfan S. Ahmad
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA;
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
| | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar
- Biomedical Research Centre, Qatar University, Doha 2713, Qatar
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Identifying Potential New Gene Expression-Based Biomarkers in the Peripheral Blood Mononuclear Cells of Hepatitis B-Related Hepatocellular Carcinoma. Can J Gastroenterol Hepatol 2022; 2022:9541600. [PMID: 35265561 PMCID: PMC8901362 DOI: 10.1155/2022/9541600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/13/2021] [Accepted: 01/22/2022] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE The analysis of the gene expression of peripheral blood mononuclear cells (PBMCs) is important to clarify the pathogenesis of hepatocellular carcinoma (HCC) and the detection of suitable biomarkers. The purpose of this investigation was to use RNA-sequencing to screen the appropriate differentially expressed genes (DEGs) in the PBMCs for the HCC. METHODS The comprehensive transcriptome of extracted RNA of PBMC (n = 20) from patients with chronic hepatitis B (CHB), liver cirrhosis, and early stage of HCC (5 samples per group) was carried out using RNA-sequencing. All raw RNA-sequencing data analyses were performed using conventional RNA-sequencing analysis tools. Next, gene ontology (GO) analyses were carried out to elucidate the biological processes of DEGs. Finally, relative transcript abundance of selected DEGs was verified using qRT-PCR on additional validation groups. RESULTS Specifically, 13, 1262, and 1450 DEGs were identified for CHB, liver cirrhosis, and HCC, when compared with the healthy controls. GO enrichment analysis indicated that HCC is closely related to the immune response. Seven DEGs (TYMP, TYROBP, CD14, TGFBI, LILRA2, GNLY, and GZMB) were common to HCC, cirrhosis, and CHB when compared to healthy controls. The data revealed that the expressions of these 7 DEGs were consistent with those from the RNA-sequencing results. Also, the expressions of 7 representative genes that had higher sensitivity were obtained by receiver operating characteristic analysis, which indicated their important diagnostic accuracy for HBV-HCC. CONCLUSION This study provides us with new horizons into the biological process and potential prospective clinical diagnosis and prognosis of HCC in the near future.
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Zhang J, Song C, Tian Y, Yang X. Single-Cell RNA Sequencing in Lung Cancer: Revealing Phenotype Shaping of Stromal Cells in the Microenvironment. Front Immunol 2022; 12:802080. [PMID: 35126365 PMCID: PMC8807562 DOI: 10.3389/fimmu.2021.802080] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022] Open
Abstract
The lung tumor microenvironment, which is composed of heterogeneous cell populations, plays an important role in the progression of lung cancer and is closely related to therapeutic efficacy. Increasing evidence has shown that stromal components play a key role in regulating tumor invasion, metastasis and drug resistance. Therefore, a better understanding of stromal components in the tumor microenvironment is helpful for the diagnosis and treatment of lung cancer. Rapid advances in technology have brought our understanding of disease into the genetic era, and single-cell RNA sequencing has enabled us to describe gene expression profiles with unprecedented resolution, enabling quantitative analysis of gene expression at the single-cell level to reveal the correlations among heterogeneity, signaling pathways, drug resistance and microenvironment molding in lung cancer, which is important for the treatment of this disease. In this paper, several common single-cell RNA sequencing methods and their advantages and disadvantages are briefly introduced to provide a reference for selection of suitable methods. Furthermore, we review the latest progress of single-cell RNA sequencing in the study of stromal cells in the lung tumor microenvironment.
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Barrón-Gallardo CA, Garcia-Chagollán M, Morán-Mendoza AJ, Delgadillo-Cristerna R, Martínez-Silva MG, Aguilar-Lemarroy A, Jave-Suárez LF. Transcriptomic Analysis of Breast Cancer Patients Sensitive and Resistant to Chemotherapy: Looking for Overall Survival and Drug Resistance Biomarkers. Technol Cancer Res Treat 2022; 21:15330338211068965. [PMID: 34981997 PMCID: PMC8733364 DOI: 10.1177/15330338211068965] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Worldwide breast cancer ranks first in mortality and incidence rates in women over 20 years old. Rather than one disease, breast cancer is a heterogeneous group of diseases that express distinct molecular profiles. Neoadjuvant chemotherapy is an important therapeutic strategy for breast cancer patients independently of their molecular subtype, with the drawback of resistance development. In addition, chemotherapy has adverse effects that combined with resistance could contribute to lower overall survival. Although great efforts have been made to find diagnostic and prognostic biomarkers for breast cancer and for response to targeted and immune therapy for this pathology, little has been explored regarding biomarkers of response to anthracyclines and taxanes based neoadjuvant chemotherapy. This work aimed to evaluate the molecular profile of patients who received neoadjuvant chemotherapy to identify differentially expressed genes (DEGs) that could be used as biomarkers of chemotherapy response and overall survival. Breast cancer patients who were candidates for neoadjuvant chemotherapy were enrolled in this study. After treatment and according to their pathological response, they were assigned as sensitive or resistant. To evaluate DEGs, Gene Ontology, Kyoto Encyclopedia Gene and Genome (KEGG), and protein–protein interactions, RNA-seq information from all patients was obtained by next-generation sequencing. A total of 1985 DEGs were found, and KEGG analysis indicated a great number of DEGs in metabolic pathways, pathways in cancer, cytokine–cytokine receptor interactions, and neuroactive ligand-receptor interactions. A selection of 73 DEGs was used further for an analysis of overall survival using the METABRIC study and the ductal carcinoma dataset of The Cancer Genome Atlas (TCGA) database. Nine DEGs correlated with overall survival, of which the subexpression of C1QTNF3, CTF1, OLFML3, PLA2R1, PODN, KRT15, HLA-A, and the overexpression of TUBB and TCP1 were found in resistant patients and related to patients with lower overall survival.
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Affiliation(s)
- Carlos A Barrón-Gallardo
- Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Mariel Garcia-Chagollán
- Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | | | | | | | | | - Luis F Jave-Suárez
- 37767Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
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Qi CL, Huang ML, Zou Y, Yang R, Jiang Y, Sheng JF, Kong YG, Tao ZZ, Feng HY, Hua QQ, Bu LH, Chen SM. The IRF2/CENP-N/AKT signaling axis promotes proliferation, cell cycling and apoptosis resistance in nasopharyngeal carcinoma cells by increasing aerobic glycolysis. J Exp Clin Cancer Res 2021; 40:390. [PMID: 34893086 PMCID: PMC8662847 DOI: 10.1186/s13046-021-02191-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 11/21/2021] [Indexed: 12/15/2022] Open
Abstract
Background Centromere protein N (CENP-N) has been reported to be highly expressed in malignancies, but its role and mechanism in nasopharyngeal carcinoma (NPC) are unknown. Methods Abnormal CENP-N expression from NPC microarrays of GEO database was analyzed. CENP-N expression level was confirmed in NPC tissues and cell lines. Stable CENP-N knockdown and overexpression NPC cell lines were established, and transcriptome sequencing after CENP-N knockdown was performed. In vitro and in vivo experiments were performed to test the impact of CENP-N knockdown in NPC cells. ChIP and dual luciferase reporter assays were used to verify the combination of IRF2 and CENP-N. Western blot analysis, cellular immunofluorescence, immunoprecipitation and GST pulldown assays were used to verify the combination of CENP-N and AKT. Results CENP-N was confirmed to be aberrantly highly expressed in NPC tissues and cell lines and to be associated with high 18F-FDG uptake in cancer nests and poor patient prognosis. Transcriptome sequencing after CENP-N knockdown revealed that genes with altered expression were enriched in pathways related to glucose metabolism, cell cycle regulation. CENP-N knockdown inhibited glucose metabolism, cell proliferation, cell cycling and promoted apoptosis. IRF2 is a transcription factor for CENP-N and directly promotes CENP-N expression in NPC cells. CENP-N affects the glucose metabolism, proliferation, cell cycling and apoptosis of NPC cells in vitro and in vivo through the AKT pathway. CENP-N formed a complex with AKT in NPC cells. Both an AKT inhibitor (MK-2206) and a LDHA inhibitor (GSK2837808A) blocked the effect of CENP-N overexpression on NPC cells by promoting aerobic glycolysis, proliferation, cell cycling and apoptosis resistance. Conclusions The IRF2/CENP-N/AKT axis promotes malignant biological behaviors in NPC cells by increasing aerobic glycolysis, and the IRF2/CENP-N/AKT signaling axis is expected to be a new target for NPC therapy. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-02191-3.
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Affiliation(s)
- Cheng-Lin Qi
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, 238 Jie-Fang Road, Wuhan, Hubei, 430060, P.R. China
| | - Mao-Ling Huang
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, 238 Jie-Fang Road, Wuhan, Hubei, 430060, P.R. China
| | - You Zou
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, 238 Jie-Fang Road, Wuhan, Hubei, 430060, P.R. China
| | - Rui Yang
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, 238 Jie-Fang Road, Wuhan, Hubei, 430060, P.R. China
| | - Yang Jiang
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, 238 Jie-Fang Road, Wuhan, Hubei, 430060, P.R. China
| | - Jian-Fei Sheng
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, 238 Jie-Fang Road, Wuhan, Hubei, 430060, P.R. China
| | - Yong-Gang Kong
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, 238 Jie-Fang Road, Wuhan, Hubei, 430060, P.R. China
| | - Ze-Zhang Tao
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, 238 Jie-Fang Road, Wuhan, Hubei, 430060, P.R. China.,Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, 238 Jie-Fang Road, Wuhan, Hubei, 430060, P.R. China
| | - Hong-Yan Feng
- PET-CT/MRI Center, Molecular Imaging Center, Renmin Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Qing-Quan Hua
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, 238 Jie-Fang Road, Wuhan, Hubei, 430060, P.R. China.,Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, 238 Jie-Fang Road, Wuhan, Hubei, 430060, P.R. China
| | - Li-Hong Bu
- PET-CT/MRI Center, Molecular Imaging Center, Renmin Hospital of Wuhan University, Wuhan, People's Republic of China.
| | - Shi-Ming Chen
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, 238 Jie-Fang Road, Wuhan, Hubei, 430060, P.R. China. .,Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, 238 Jie-Fang Road, Wuhan, Hubei, 430060, P.R. China.
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Ahmed R, Augustine R, Valera E, Ganguli A, Mesaeli N, Ahmad IS, Bashir R, Hasan A. Spatial mapping of cancer tissues by OMICS technologies. Biochim Biophys Acta Rev Cancer 2021; 1877:188663. [PMID: 34861353 DOI: 10.1016/j.bbcan.2021.188663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 11/15/2021] [Accepted: 11/26/2021] [Indexed: 12/14/2022]
Abstract
Spatial mapping of heterogeneity in gene expression in cancer tissues can improve our understanding of cancers and help in the rapid detection of cancers with high accuracy and reliability. Significant advancements have been made in recent years in OMICS technologies, which possess the strong potential to be applied in the spatial mapping of biopsy tissue samples and their molecular profiling to a single-cell level. The clinical application of OMICS technologies in spatial profiling of cancer tissues is also advancing. The current review presents recent advancements and prospects of applying OMICS technologies to the spatial mapping of various analytes in cancer tissues. We benchmark the current state of the art in the field to advance existing OMICS technologies for high throughput spatial profiling. The factors taken into consideration include spatial resolution, types of biomolecules, number of different biomolecules that can be detected from the same assay, labeled versus label-free approaches, and approximate time required for each assay. Further advancements are still needed for the widespread application of OMICs technologies in performing fast and high throughput spatial mapping of cancer tissues as well as their effective use in research and clinical applications.
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Affiliation(s)
- Rashid Ahmed
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar; Biomedical Research Center (BRC), Qatar University, Doha 2713, Qatar; Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana Champaign, IL, USA
| | - Robin Augustine
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar; Biomedical Research Center (BRC), Qatar University, Doha 2713, Qatar
| | - Enrique Valera
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana Champaign, IL, USA; Department of Bioengineering, University of Illinois at Urbana Champaign, IL, USA
| | - Anurup Ganguli
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana Champaign, IL, USA; Department of Bioengineering, University of Illinois at Urbana Champaign, IL, USA
| | - Nasrin Mesaeli
- Department of Biochemistry, Weill Cornell Medicine in Qatar, Qatar Foundation, Doha, Qatar
| | - Irfan S Ahmad
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana Champaign, IL, USA
| | - Rashid Bashir
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana Champaign, IL, USA; Department of Bioengineering, University of Illinois at Urbana Champaign, IL, USA; Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
| | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar; Biomedical Research Center (BRC), Qatar University, Doha 2713, Qatar.
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Helmy M, Agrawal R, Ali J, Soudy M, Bui TT, Selvarajoo K. GeneCloudOmics: A Data Analytic Cloud Platform for High-Throughput Gene Expression Analysis. FRONTIERS IN BIOINFORMATICS 2021; 1:693836. [PMID: 36303746 PMCID: PMC9581002 DOI: 10.3389/fbinf.2021.693836] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 10/14/2021] [Indexed: 11/18/2022] Open
Abstract
Gene expression profiling techniques, such as DNA microarray and RNA-Sequencing, have provided significant impact on our understanding of biological systems. They contribute to almost all aspects of biomedical research, including studying developmental biology, host-parasite relationships, disease progression and drug effects. However, the high-throughput data generations present challenges for many wet experimentalists to analyze and take full advantage of such rich and complex data. Here we present GeneCloudOmics, an easy-to-use web server for high-throughput gene expression analysis that extends the functionality of our previous ABioTrans with several new tools, including protein datasets analysis, and a web interface. GeneCloudOmics allows both microarray and RNA-Seq data analysis with a comprehensive range of data analytics tools in one package that no other current standalone software or web-based tool can do. In total, GeneCloudOmics provides the user access to 23 different data analytical and bioinformatics tasks including reads normalization, scatter plots, linear/non-linear correlations, PCA, clustering (hierarchical, k-means, t-SNE, SOM), differential expression analyses, pathway enrichments, evolutionary analyses, pathological analyses, and protein-protein interaction (PPI) identifications. Furthermore, GeneCloudOmics allows the direct import of gene expression data from the NCBI Gene Expression Omnibus database. The user can perform all tasks rapidly through an intuitive graphical user interface that overcomes the hassle of coding, installing tools/packages/libraries and dealing with operating systems compatibility and version issues, complications that make data analysis tasks challenging for biologists. Thus, GeneCloudOmics is a one-stop open-source tool for gene expression data analysis and visualization. It is freely available at http://combio-sifbi.org/GeneCloudOmics.
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Affiliation(s)
- Mohamed Helmy
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Computer Science, Lakehead University, Thunder Bay, ON, Canada
| | - Rahul Agrawal
- Department of Geology and Geophysics, Indian Institute of Technology (IIT) Kharagpur, Kharagpur, India
| | - Javed Ali
- Department of Geology and Geophysics, Indian Institute of Technology (IIT) Kharagpur, Kharagpur, India
| | - Mohamed Soudy
- Proteomics and Metabolomics Unit, Children Cancer Hospital (CCHE-57357), Cairo, Egypt
| | - Thuy Tien Bui
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Kumar Selvarajoo
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore (NUS), Singapore, Singapore
- *Correspondence: Kumar Selvarajoo,
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Wang H, Yu S, Cai Q, Ma D, Yang L, Zhao J, Jiang L, Zhang X, Yu Z. The Prognostic Model Based on Tumor Cell Evolution Trajectory Reveals a Different Risk Group of Hepatocellular Carcinoma. Front Cell Dev Biol 2021; 9:737723. [PMID: 34660596 PMCID: PMC8511531 DOI: 10.3389/fcell.2021.737723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/30/2021] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related death worldwide, and heterogeneity of HCC is the major barrier in improving patient outcome. To stratify HCC patients with different degrees of malignancy and provide precise treatment strategies, we reconstructed the tumor evolution trajectory with the help of scRNA-seq data and established a 30-gene prognostic model to identify the malignant state in HCC. Patients were divided into high-risk and low-risk groups. C-index and receiver operating characteristic (ROC) curve confirmed the excellent predictive value of this model. Downstream analysis revealed the underlying molecular and functional characteristics of this model, including significantly higher genomic instability and stronger proliferation/progression potential in the high-risk group. In summary, we established a novel prognostic model to overcome the barriers caused by HCC heterogeneity and provide the possibility of better clinical management for HCC patients to improve their survival outcomes.
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Affiliation(s)
- Haoren Wang
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Yunnan University, Kunming, China
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shizhe Yu
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Yunnan University, Kunming, China
- Department of Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qiang Cai
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Yunnan University, Kunming, China
| | - Duo Ma
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Yunnan University, Kunming, China
| | - Lingpeng Yang
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Yunnan University, Kunming, China
| | - Jian Zhao
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Yunnan University, Kunming, China
| | - Long Jiang
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Yunnan University, Kunming, China
| | - Xinyi Zhang
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Yunnan University, Kunming, China
| | - Zhiyong Yu
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Yunnan University, Kunming, China
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