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Chu Y, Zhang S, Wan W, Yang J, Zhang Y, Nie C, Xing W, Tong S, Liu J, Tian G, Wang B, Ji L. Pathological image profiling identifies onco-microbial, tumor immune microenvironment, and prognostic subtypes of colorectal cancer. APMIS 2024; 132:416-429. [PMID: 38403979 DOI: 10.1111/apm.13387] [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: 09/20/2023] [Accepted: 02/02/2024] [Indexed: 02/27/2024]
Abstract
Histology slide, tissue microbes, and the host gene expression can be independent prognostic factors of colorectal cancer (CRC), but the underlying associations and biological significance of these multimodal omics remain unknown. Here, we comprehensively profiled the matched pathological images, intratumoral microbes, and host gene expression characteristics in 527 patients with CRC. By clustering these patients based on histology slide features, we classified the patients into two histology slide subtypes (HSS). Onco-microbial community and tumor immune microenvironment (TIME) were also significantly different between the two subtypes (HSS1 and HSS2) of patients. Furthermore, variation in intratumoral microbes-host interaction was associated with the prognostic heterogeneity between HSS1 and HSS2. This study proposes a new CRC classification based on pathological image features and elucidates the process by which tumor microbes-host interactions are reflected in pathological images through the TIME.
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Affiliation(s)
- Yuwen Chu
- School of Electrical & Information Engineering, Anhui University of Technology, Anhui, China
- Geneis Beijing Co., Ltd., Beijing, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Shuo Zhang
- School of management, Harbin Institute of Technology, Harbin, China
| | - Wei Wan
- Department of Colorectal and Anal Surgery, Yidu Central Hospital of Weifang, Shandong, China
| | - Jialiang Yang
- Geneis Beijing Co., Ltd., Beijing, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Yumeng Zhang
- Geneis Beijing Co., Ltd., Beijing, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
- School of Mathematics and Statistics, Hainan Normal University, Haikou, China
| | - Chuanqi Nie
- School of Electrical & Information Engineering, Anhui University of Technology, Anhui, China
- Geneis Beijing Co., Ltd., Beijing, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Weipeng Xing
- School of Electrical & Information Engineering, Anhui University of Technology, Anhui, China
- Geneis Beijing Co., Ltd., Beijing, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Shanhe Tong
- School of Electrical & Information Engineering, Anhui University of Technology, Anhui, China
- Geneis Beijing Co., Ltd., Beijing, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Jinyang Liu
- Geneis Beijing Co., Ltd., Beijing, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Geng Tian
- Geneis Beijing Co., Ltd., Beijing, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Bing Wang
- School of Electrical & Information Engineering, Anhui University of Technology, Anhui, China
| | - Lei Ji
- Geneis Beijing Co., Ltd., Beijing, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
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Norris AC, Mansueto AJ, Jimenez M, Yazlovitskaya EM, Jain BK, Graham TR. Flipping the script: Advances in understanding how and why P4-ATPases flip lipid across membranes. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119700. [PMID: 38382846 DOI: 10.1016/j.bbamcr.2024.119700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 11/15/2023] [Accepted: 02/16/2024] [Indexed: 02/23/2024]
Abstract
Type IV P-type ATPases (P4-ATPases) are a family of transmembrane enzymes that translocate lipid substrates from the outer to the inner leaflet of biological membranes and thus create an asymmetrical distribution of lipids within membranes. On the cellular level, this asymmetry is essential for maintaining the integrity and functionality of biological membranes, creating platforms for signaling events and facilitating vesicular trafficking. On the organismal level, this asymmetry has been shown to be important in maintaining blood homeostasis, liver metabolism, neural development, and the immune response. Indeed, dysregulation of P4-ATPases has been linked to several diseases; including anemia, cholestasis, neurological disease, and several cancers. This review will discuss the evolutionary transition of P4-ATPases from cation pumps to lipid flippases, the new lipid substrates that have been discovered, the significant advances that have been achieved in recent years regarding the structural mechanisms underlying the recognition and flipping of specific lipids across biological membranes, and the consequences of P4-ATPase dysfunction on cellular and physiological functions. Additionally, we emphasize the requirement for additional research to comprehensively understand the involvement of flippases in cellular physiology and disease and to explore their potential as targets for therapeutics in treating a variety of illnesses. The discussion in this review will primarily focus on the budding yeast, C. elegans, and mammalian P4-ATPases.
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Affiliation(s)
- Adriana C Norris
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | | | - Mariana Jimenez
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | | | - Bhawik K Jain
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Todd R Graham
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
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Yazlovitskaya EM, Graham TR. Type IV P-Type ATPases: Recent Updates in Cancer Development, Progression, and Treatment. Cancers (Basel) 2023; 15:4327. [PMID: 37686603 PMCID: PMC10486736 DOI: 10.3390/cancers15174327] [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: 07/11/2023] [Revised: 08/15/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Adaptations of cancer cells for survival are remarkable. One of the most significant properties of cancer cells to prevent the immune system response and resist chemotherapy is the altered lipid metabolism and resulting irregular cell membrane composition. The phospholipid distribution in the plasma membrane of normal animal cells is distinctly asymmetric. Lipid flippases are a family of enzymes regulating membrane asymmetry, and the main class of flippases are type IV P-type ATPases (P4-ATPases). Alteration in the function of flippases results in changes to membrane organization. For some lipids, such as phosphatidylserine, the changes are so drastic that they are considered cancer biomarkers. This review will analyze and discuss recent publications highlighting the role that P4-ATPases play in the development and progression of various cancer types, as well as prospects of targeting P4-ATPases for anti-cancer treatment.
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Affiliation(s)
| | - Todd R. Graham
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
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Chen LC, Huang SP, Shih CT, Li CY, Chen YT, Huang CY, Yu CC, Lin VC, Lee CH, Geng JH, Bao BY. ATP8B1: A prognostic prostate cancer biomarker identified via genetic analysis. Prostate 2023; 83:602-611. [PMID: 36794287 DOI: 10.1002/pros.24495] [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: 09/06/2022] [Revised: 01/10/2023] [Accepted: 01/23/2023] [Indexed: 02/17/2023]
Abstract
BACKGROUND Controlling the asymmetric distribution of phospholipids across biological membranes plays a pivotal role in the life cycle of cells; one of the most important contributors that maintain this lipid asymmetry are phospholipid-transporting adenosine triphosphatases (ATPases). Although sufficient information regarding their association with cancer exists, there is limited evidence linking the genetic variants of phospholipid-transporting ATPase family genes to prostate cancer in humans. METHODS In this study, we investigated the association of 222 haplotype-tagging single-nucleotide polymorphisms (SNPs) in eight phospholipid-transporting ATPase genes with cancer-specific survival (CSS) and overall survival (OS) of 630 patients treated with androgen-deprivation therapy (ADT) for prostate cancer. RESULTS After multivariate Cox regression analysis and multiple testing correction, we found that ATP8B1 rs7239484 was remarkably associated with CSS and OS after ADT. A pooled analysis of multiple independent gene-expression datasets demonstrated that ATP8B1 was under-expressed in tumor tissues and that a higher ATP8B1 expression was associated with a better patient prognosis. Moreover, we established highly invasive sublines using two human prostate cancer cell lines to mimic cancer progression traits in vitro. The expression of ATP8B1 was consistently downregulated in both highly invasive sublines. CONCLUSION Our study indicates that rs7239484 is a prognostic factor for patients treated with ADT and that ATP8B1 can potentially attenuate prostate cancer progression.
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Affiliation(s)
- Lih-Chyang Chen
- Department of Medicine, Mackay Medical College, New Taipei City, Taiwan
| | - Shu-Pin Huang
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Ph.D. Program in Environmental and Occupational Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Chieh-Tien Shih
- Department of Medicine, Mackay Medical College, New Taipei City, Taiwan
| | - Chia-Yang Li
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Yei-Tsung Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chao-Yuan Huang
- Department of Urology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chia-Cheng Yu
- Division of Urology, Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
- Department of Urology, School of Medicine, National Yang-Ming University, Taipei, Taiwan
- Department of Pharmacy, Tajen University, Pingtung, Taiwan
| | - Victor C Lin
- Department of Urology, E-Da Hospital, Kaohsiung, Taiwan
- School of Medicine for International Students, I-Shou University, Kaohsiung, Taiwan
| | - Cheng-Hsueh Lee
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Jiun-Hung Geng
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Urology, Kaohsiung Municipal Hsiao-Kang Hospital, Kaohsiung, Taiwan
| | - Bo-Ying Bao
- Department of Pharmacy, China Medical University, Taichung, Taiwan
- Sex Hormone Research Center, China Medical University Hospital, Taichung, Taiwan
- Department of Nursing, Asia University, Taichung, Taiwan
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