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van den Driest L, Kelly P, Marshall A, Johnson CH, Lasky-Su J, Lannigan A, Rattray Z, Rattray NJ. A gap analysis of UK biobank publications reveals SNPs associated with intrinsic subtypes of breast cancer. Comput Struct Biotechnol J 2024; 23:2200-2210. [PMID: 38817965 PMCID: PMC11137368 DOI: 10.1016/j.csbj.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 06/01/2024] Open
Abstract
Breast cancer is a multifaceted disease and a leading cause of cancer morbidity and mortality in females across the globe. In 2020 alone, 2.3 million women were diagnosed and 685,000 died of breast cancer worldwide. With the number of diagnoses projected to increase to 3 million per year by 2040 it is essential that new methods of detection and disease stratification are sought to decrease this global cancer burden. Although significant improvements have been made in breast cancer diagnosis and treatment, the prognosis of breast cancer remains poor in some patient groups (i.e. triple negative breast cancer), necessitating research into better patient stratification, diagnosis and drug discovery. The UK Biobank, a comprehensive biomedical and epidemiological database with a wide variety of multiomics data (genomics, proteomics, metabolomics) offers huge potential to uncover groundbreaking discoveries in breast cancer research leading to improved patient stratification. Combining genomic, proteomic, and metabolic profiles of breast cancer in combination with histological classification, can aid treatment decisions through accurate diagnosis and prognosis prediction of tumor behaviour. Here, we systematically reviewed PubMed publications reporting the analysis of UK Biobank data in breast cancer research. Our analysis of UK Biobank studies in the past five years identified 125 publications, of which 76 focussed on genomic data analysis. Interestingly, only two studies reported the analysis of metabolomics and proteomics data, with none performing multiomics analysis of breast cancer. A meta-analysis of the 76 publications identified 2870 genetic variants associated with breast cancer across 445 genes. Subtype analysis revealed differential genetic alteration in 13 of the 445 genes and the identification of 59 well-established breast cancer genes. in differential pathways. Pathway interaction analyses illuminated their involvement in general cancer biomolecular pathways (e.g. DNA damage repair, Gene expression). While our meta-analysis only measured genetic differences in breast cancer due to current usage of UK Biobank data, minimal multi-omics analyses have been performed and the potential for harnessing multi-omics strategies within the UK Biobank cohort holds promise for unravelling the biological signatures of distinct breast cancer subtypes further in the future.
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Affiliation(s)
- Lisa van den Driest
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Patricia Kelly
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Alan Marshall
- School of Social and Political Science, University of Edinburgh, Chrystal Macmillan Building, George Square, Edinburgh EH8 9LD, UK
| | - Caroline H. Johnson
- Yale School of Public Health, Yale University, 60 College Street, New Haven, CT 06510, USA
| | - Jessica Lasky-Su
- Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Ave, Boston, MA 02115, USA
| | - Alison Lannigan
- NHS Lanarkshire, Lanarkshire, Scotland, UK
- Wishaw General Hospital, NHS Lanarkshire, 50 Netherton St, Wishaw ML2 0DP, UK
| | - Zahra Rattray
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
- NHS Lanarkshire, Lanarkshire, Scotland, UK
| | - Nicholas J.W. Rattray
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
- NHS Lanarkshire, Lanarkshire, Scotland, UK
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2
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Ma W, Tang W, Kwok JS, Tong AH, Lo CW, Chu AT, Chung BH. A review on trends in development and translation of omics signatures in cancer. Comput Struct Biotechnol J 2024; 23:954-971. [PMID: 38385061 PMCID: PMC10879706 DOI: 10.1016/j.csbj.2024.01.024] [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: 10/27/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
The field of cancer genomics and transcriptomics has evolved from targeted profiling to swift sequencing of individual tumor genome and transcriptome. The steady growth in genome, epigenome, and transcriptome datasets on a genome-wide scale has significantly increased our capability in capturing signatures that represent both the intrinsic and extrinsic biological features of tumors. These biological differences can help in precise molecular subtyping of cancer, predicting tumor progression, metastatic potential, and resistance to therapeutic agents. In this review, we summarized the current development of genomic, methylomic, transcriptomic, proteomic and metabolic signatures in the field of cancer research and highlighted their potentials in clinical applications to improve diagnosis, prognosis, and treatment decision in cancer patients.
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Affiliation(s)
- Wei Ma
- Hong Kong Genome Institute, Hong Kong, China
| | - Wenshu Tang
- Hong Kong Genome Institute, Hong Kong, China
| | | | | | | | | | - Brian H.Y. Chung
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hong Kong Genome Project
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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3
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Yang Y, Hao X, Zhang J, Gao T, Huo M, Liu W, Hu T, Ma T, Yuan B, Zhang M, Teng X, Yu H, Huang W, Wang Y. The E3 ligase TRIM22 functions as a tumor suppressor in breast cancer by targeting CCS for proteasomal degradation to inhibit STAT3 signaling. Cancer Lett 2024; 600:217157. [PMID: 39127340 DOI: 10.1016/j.canlet.2024.217157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 07/02/2024] [Accepted: 08/03/2024] [Indexed: 08/12/2024]
Abstract
Deregulation of E3 ubiquitin ligases drives the proliferation and metastasis of various cancers; however, the underlying mechanisms remain unknown. This study aimed to investigate the role of tripartite motif-containing 22 (TRIM22), a poorly investigated E3 ubiquitin ligase in the TRIM family, as a tumor suppressor in breast cancer. High expression of TRIM22 in breast cancer correlated with better prognosis. Functional experiments demonstrated that TRIM22 significantly inhibited the proliferation and invasion of breast cancer cells. Label-free proteomics and biochemical analyses revealed that the copper chaperone for superoxide dismutase (CCS), an oncoprotein that is upregulated in breast cancer and promotes the growth and invasion of breast cancer cells, was a target of TRIM22 for degradation via K27-linked ubiquitination. Notably, the ability of the coiled-coil domain-defective mutants of TRIM22 to induce CCS ubiquitination and degradation diminished, with lysine 76 of the CCS serving as the ubiquitination site. Moreover, the TRIM22-mediated inhibition of the proliferation and invasion of breast cancer cells was restored by ectopic CCS expression. RNA-sequencing experiments using Gene Set Enrichment Analysis demonstrated that TRIM22 is involved in the JAK-STAT signaling pathway. TRIM22 overexpression also improved reactive oxygen species levels in breast cancer cells and inhibited STAT3 phosphorylation, which was restored via CCS overexpression or N-acetyl-l-cysteine treatment. Chromatin immunoprecipitation-quantitative polymerase chain reaction results showed that TRIM22 overexpression decreased the enrichment of phosphorylated STAT3 in FN1, VIM and JARID2 promoters. Clinically, low TRIM22 expression correlated with high CCS expression and decreased survival rates in patients with breast cancer. Moreover, TRIM22 upregulation was associated with a better prognosis in patients with breast cancer who received classical therapy. TRIM22 expression was downregulated in many cancer types, including colon, kidney, lung, and prostate cancers. To the best of our knowledge, the E3 ubiquitin ligase TRIM22 was first reported as a tumor suppressor that inhibits the proliferation and invasion of breast cancer cells through CCS ubiquitination and degradation. TRIM22 is a potential prognostic biomarker in patients with breast cancer.
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Affiliation(s)
- Yunkai Yang
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xinhui Hao
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China; Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Jingyao Zhang
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Tianyang Gao
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Miaomiao Huo
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Wei Liu
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Ting Hu
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Tianyu Ma
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Baowen Yuan
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Min Zhang
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xu Teng
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Hefen Yu
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Wei Huang
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Yan Wang
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China; Institute of Cancer Research, Henan Academy of Innovations in Medical Sciences, Zhengzhou, Henan Province, 450000, China; Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China; Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China.
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4
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Song H, Tang X, Liu M, Wang G, Yuan Y, Pang R, Wang C, Zhou J, Yang Y, Zhang M, Jin Y, Jiang K, Wang S, Yin Y. Multi-omic analysis identifies metabolic biomarkers for the early detection of breast cancer and therapeutic response prediction. iScience 2024; 27:110682. [PMID: 39252976 PMCID: PMC11381768 DOI: 10.1016/j.isci.2024.110682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/06/2024] [Accepted: 08/02/2024] [Indexed: 09/11/2024] Open
Abstract
Reliable blood-based tests for identifying early-stage breast cancer remain elusive. Employing single-cell transcriptomic sequencing analysis, we illustrate a close correlation between nucleotide metabolism in the breast cancer and activation of regulatory T cells (Tregs) in the tumor microenvironment, which shows distinctions between subtypes of patients with triple-negative breast cancer (TNBC) and non-TNBC, and is likely to impact cancer prognosis through the A2AR-Treg pathway. Combining machine learning with absolute quantitative metabolomics, we have established an effective approach to the early detection of breast cancer, utilizing a four-metabolite panel including inosine and uridine. This metabolomics study, involving 1111 participants, demonstrates high accuracy across the training, test, and independent validation cohorts. Inosine and uridine prove predictive of the response to neoadjuvant chemotherapy (NAC) in patients with TNBC. This study deepens our understanding of nucleotide metabolism in breast cancer development and introduces a promising non-invasive method for early breast cancer detection and predicting NAC response in patients with TNBC.
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Affiliation(s)
- Huajie Song
- Department of Pathology, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xiaowei Tang
- Department of Pathology, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Miao Liu
- Breast Center, Peking University People's Hospital, Beijing 100044, China
| | - Guangxi Wang
- Department of Pathology, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yuyao Yuan
- Department of Pathology, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ruifang Pang
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen 518036, P.R. China
| | - Chenyi Wang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing 100044, China
| | - Juntuo Zhou
- Department of Pathology, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yang Yang
- Breast Center, Peking University People's Hospital, Beijing 100044, China
| | - Mengmeng Zhang
- Breast Center, Peking University People's Hospital, Beijing 100044, China
| | - Yan Jin
- Department of Pathology, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Kewei Jiang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing 100044, China
| | - Shu Wang
- Breast Center, Peking University People's Hospital, Beijing 100044, China
| | - Yuxin Yin
- Department of Pathology, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, China
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen 518036, P.R. China
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5
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Tarantino P, Hortobagyi G, Tolaney SM, Mittendorf EA. Heterogeneity of Residual Disease After Neoadjuvant Systemic Therapy in Breast Cancer: A Review. JAMA Oncol 2024:2823546. [PMID: 39264638 DOI: 10.1001/jamaoncol.2024.3679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Importance Over the past 2 decades, systemic therapy for early-stage breast cancer has gradually moved from the adjuvant to the neoadjuvant setting. Administration of systemic therapy before surgery leads to potential improvements in surgical outcomes and allows for the assessment of the pathologic response to treatment. For patients with residual disease (RD), 3 adjuvant strategies have been shown to improve outcomes: (1) adjuvant trastuzumab emtansine for ERBB2-positive disease, (2) adjuvant capecitabine for triple-negative disease, and (3) adjuvant olaparib for patients with germline BRCA variants. Furthermore, studies are testing novel drugs in the postneoadjuvant setting. Given the potential to tailor adjuvant therapy based on the response to preoperative systemic therapy, recognizing the complexities of response to neoadjuvant therapy and moving beyond the binary paradigm of RD vs experiencing a pathologic complete response is becoming increasingly necessary. Observations Novel antibody-drug conjugates, anti-ERBB2 tyrosine kinase inhibitors, and immune checkpoint inhibitors are being evaluated as additional rescue options in phase 3 trials for patients with RD after neoadjuvant treatment. Concomitantly, the prognostic role of RD has been refined by the introduction of the residual cancer burden. In addition, the genomic landscape of RD has been found to be associated with long-term prognosis, as has the immune background of the disease evaluated via the presence of tumor-infiltrating lymphocytes. Lastly, the dynamics of circulating tumor DNA may allow for further improvement in prognostication by understanding which patients harbor detectable minimal RD. Conclusions and Relevance Escalating adjuvant treatment has led to meaningful survival improvements among patients with breast cancer and RD after neoadjuvant therapy. Uncovering the anatomic and biological intricacies of RD will allow for increased precision in postneoadjuvant treatments, moving beyond the binary paradigm of RD vs pathologic complete response, toward more tailored rescue strategies in the adjuvant setting.
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Affiliation(s)
- Paolo Tarantino
- Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Gabriel Hortobagyi
- Department of Breast Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Sara M Tolaney
- Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Elizabeth A Mittendorf
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
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6
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Fan X, Chen L, Chen M, Zhang N, Chang H, He M, Shen Z, Zhang L, Ding H, Xie Y, Huang Y, Ke W, Xiao M, Zang X, Xu H, Fang W, Li S, Cao C, Xu Y, Shan S, Wu W, Chen C, Xue X, Wang L. Pan-omics-based characterization and prediction of highly multidrug-adapted strains from an outbreak fungal species complex. Innovation (N Y) 2024; 5:100681. [PMID: 39228856 PMCID: PMC11369464 DOI: 10.1016/j.xinn.2024.100681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 07/28/2024] [Indexed: 09/05/2024] Open
Abstract
Strains from the Cryptococcus gattii species complex (CGSC) have caused the Pacific Northwest cryptococcosis outbreak, the largest cluster of life-threatening fungal infections in otherwise healthy human hosts known to date. In this study, we utilized a pan-phenome-based method to assess the fitness outcomes of CGSC strains under 31 stress conditions, providing a comprehensive overview of 2,821 phenotype-strain associations within this pathogenic clade. Phenotypic clustering analysis revealed a strong correlation between distinct types of stress phenotypes in a subset of CGSC strains, suggesting that shared determinants coordinate their adaptations to various stresses. Notably, a specific group of strains, including the outbreak isolates, exhibited a remarkable ability to adapt to all three of the most commonly used antifungal drugs for treating cryptococcosis (amphotericin B, 5-fluorocytosine, and fluconazole). By integrating pan-genomic and pan-transcriptomic analyses, we identified previously unrecognized genes that play crucial roles in conferring multidrug resistance in an outbreak strain with high multidrug adaptation. From these genes, we identified biomarkers that enable the accurate prediction of highly multidrug-adapted CGSC strains, achieving maximum accuracy and area under the curve (AUC) of 0.79 and 0.86, respectively, using machine learning algorithms. Overall, we developed a pan-omic approach to identify cryptococcal multidrug resistance determinants and predict highly multidrug-adapted CGSC strains that may pose significant clinical concern.
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Affiliation(s)
- Xin Fan
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
- Beijing Research Center for Respiratory Infectious Diseases, Beijing 100020, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Chen
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Changzheng Hospital, Shanghai 200003, China
| | - Na Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Chang
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Mingjie He
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhenghao Shen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lanyue Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Ding
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuyan Xie
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yemei Huang
- Department of Respiratory and Critical Care, Emergency and Critical Care Medical Center, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Weixin Ke
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Meng Xiao
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Xuelei Zang
- Department of Respiratory and Critical Care, Emergency and Critical Care Medical Center, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Heping Xu
- Department of Clinical Laboratory, First Affiliated Hospital of Xiamen University, Xiamen 361003, China
| | - Wenxia Fang
- Institute of Biological Science and Technology, Guangxi Academy of Sciences, Nanning 530007, China
| | - Shaojie Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cunwei Cao
- Department of Dermatology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
- Guangxi Key Laboratory of Mycosis Prevention and Treatment, Nanning 530021, China
| | - Yingchun Xu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Shiguang Shan
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Wenjuan Wu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Changbin Chen
- The Unit of Pathogenic Fungal Infection & Host Immunity, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
- Nanjing Advanced Academy of Life and Health, Nanjing 211135, China
| | - Xinying Xue
- Department of Respiratory and Critical Care, Emergency and Critical Care Medical Center, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
- Department of Respiratory and Critical Care, Shandong Second Medical University, Weifang 261035, China
| | - Linqi Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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7
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Sun Z, Liu H, Zhao Q, Li JH, Peng SF, Zhang Z, Yang JH, Fu Y. Immune-related cell death index and its application for hepatocellular carcinoma. NPJ Precis Oncol 2024; 8:194. [PMID: 39245753 PMCID: PMC11381516 DOI: 10.1038/s41698-024-00693-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 08/28/2024] [Indexed: 09/10/2024] Open
Abstract
Regulated cell death (RCD) plays a crucial role in the immune microenvironment, development, and progression of hepatocellular carcinoma (HCC). However, reliable immune-related cell death signatures have not been explored. In this study, we collected 12 RCD modes (e.g., apoptosis, ferroptosis, and cuproptosis), including 1078 regulators, to identify immune-related cell death genes based on HCC immune subgroups. Using a developed competitive machine learning framework, nine genes were screened to construct the immune-related cell death index (IRCDI), which is available for online application. Multi-omics data, along with clinical features, were analyzed to explore the HCC malignant heterogeneity. To validate the efficacy of this model, more than 18 independent cohorts, including survival and diverse treatment cohorts and datasets, were utilized. These findings were further validated using in-house samples and molecular biological experiments. Overall, the IRCDI may have a wide application in individual therapeutic decision-making and improving outcomes for HCC patients.
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Affiliation(s)
- Zhao Sun
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Hao Liu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Qian Zhao
- Clinical Systems Biology Key Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jie-Han Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - San-Fei Peng
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zhen Zhang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jing-Hua Yang
- Clinical Systems Biology Key Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| | - Yang Fu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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8
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You C, Su GH, Zhang X, Xiao Y, Zheng RC, Sun SY, Zhou JY, Lin LY, Wang ZZ, Wang H, Chen Y, Peng WJ, Jiang YZ, Shao ZM, Gu YJ. Multicenter radio-multiomic analysis for predicting breast cancer outcome and unravelling imaging-biological connection. NPJ Precis Oncol 2024; 8:193. [PMID: 39244594 PMCID: PMC11380684 DOI: 10.1038/s41698-024-00666-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 07/24/2024] [Indexed: 09/09/2024] Open
Abstract
Radiomics offers a noninvasive avenue for predicting clinicopathological factors. However, thorough investigations into a robust breast cancer outcome-predicting model and its biological significance remain limited. This study develops a robust radiomic model for prognosis prediction, and further excavates its biological foundation and transferring prediction performance. We retrospectively collected preoperative dynamic contrast-enhanced MRI data from three distinct breast cancer patient cohorts. In FUSCC cohort (n = 466), Lasso was used to select features correlated with patient prognosis and multivariate Cox regression was utilized to integrate these features and build the radiomic risk model, while multiomic analysis was conducted to investigate the model's biological implications. DUKE cohort (n = 619) and I-SPY1 cohort (n = 128) were used to test the performance of the radiomic signature in outcome prediction. A thirteen-feature radiomic signature was identified in the FUSCC cohort training set and validated in the FUSCC cohort testing set, DUKE cohort and I-SPY1 cohort for predicting relapse-free survival (RFS) and overall survival (OS) (RFS: p = 0.013, p = 0.024 and p = 0.035; OS: p = 0.036, p = 0.005 and p = 0.027 in the three cohorts). Multiomic analysis uncovered metabolic dysregulation underlying the radiomic signature (ATP metabolic process: NES = 1.84, p-adjust = 0.02; cholesterol biosynthesis: NES = 1.79, p-adjust = 0.01). Regarding the therapeutic implications, the radiomic signature exhibited value when combining clinical factors for predicting the pathological complete response to neoadjuvant chemotherapy (DUKE cohort, AUC = 0.72; I-SPY1 cohort, AUC = 0.73). In conclusion, our study identified a breast cancer outcome-predicting radiomic signature in a multicenter radio-multiomic study, along with its correlations with multiomic features in prognostic risk assessment, laying the groundwork for future prospective clinical trials in personalized risk stratification and precision therapy.
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Affiliation(s)
- Chao You
- Department of Radiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Guan-Hua Su
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xu Zhang
- Department of Radiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi Xiao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ren-Cheng Zheng
- Institute of Science and Technology for Brain-inspired Intelligence, Fudan University, Shanghai, China
| | - Shi-Yun Sun
- Department of Radiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jia-Yin Zhou
- Department of Radiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lu-Yi Lin
- Department of Radiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ze-Zhou Wang
- Department of Cancer Prevention, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - He Wang
- Institute of Science and Technology for Brain-inspired Intelligence, Fudan University, Shanghai, China
| | - Yan Chen
- School of Medicine, University of Nottingham, Nottingham, UK
| | - Wei-Jun Peng
- Department of Radiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi-Zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Ya-Jia Gu
- Department of Radiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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9
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Barozzi I, Slaven N, Canale E, Lopes R, Amorim Monteiro Barbosa I, Bleu M, Ivanoiu D, Pacini C, Mensa' E, Chambers A, Bravaccini S, Ravaioli S, Győrffy B, Dieci MV, Pruneri G, Galli GG, Magnani L. A Functional Survey of the Regulatory Landscape of Estrogen Receptor-Positive Breast Cancer Evolution. Cancer Discov 2024; 14:1612-1630. [PMID: 38753319 PMCID: PMC11372371 DOI: 10.1158/2159-8290.cd-23-1157] [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] [Received: 10/04/2023] [Revised: 03/12/2024] [Accepted: 05/14/2024] [Indexed: 09/05/2024]
Abstract
Only a handful of somatic alterations have been linked to endocrine therapy resistance in hormone-dependent breast cancer, potentially explaining ∼40% of relapses. If other mechanisms underlie the evolution of hormone-dependent breast cancer under adjuvant therapy is currently unknown. In this work, we employ functional genomics to dissect the contribution of cis-regulatory elements (CRE) to cancer evolution by focusing on 12 megabases of noncoding DNA, including clonal enhancers, gene promoters, and boundaries of topologically associating domains. Parallel epigenetic perturbation (CRISPRi) in vitro reveals context-dependent roles for many of these CREs, with a specific impact on dormancy entrance and endocrine therapy resistance. Profiling of CRE somatic alterations in a unique, longitudinal cohort of patients treated with endocrine therapies identifies a limited set of noncoding changes potentially involved in therapy resistance. Overall, our data uncover how endocrine therapies trigger the emergence of transient features which could ultimately be exploited to hinder the adaptive process. Significance: This study shows that cells adapting to endocrine therapies undergo changes in the usage or regulatory regions. Dormant cells are less vulnerable to regulatory perturbation but gain transient dependencies which can be exploited to decrease the formation of dormant persisters.
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Affiliation(s)
- Iros Barozzi
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Neil Slaven
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Eleonora Canale
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Rui Lopes
- Disease area Oncology, Novartis Biomedical Research, Basel, Switzerland
| | | | - Melusine Bleu
- Disease area Oncology, Novartis Biomedical Research, Basel, Switzerland
| | - Diana Ivanoiu
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Claudia Pacini
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Emanuela Mensa'
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Alfie Chambers
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Sara Bravaccini
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
- Faculty of Medicine and Surgery, "Kore" University of Enna, Enna, Italy
| | - Sara Ravaioli
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
- Department of Biophysics, Medical School, University of Pecs, Pecs, Hungary
- Cancer Biomarker Research Group, Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Budapest, Hungary
| | - Maria Vittoria Dieci
- Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Giancarlo Pruneri
- Department of Diagnostic Innovation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | | | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer, Research, London, United Kingdom
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10
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Liu J, Bao C, Zhang J, Han Z, Fang H, Lu H. Artificial intelligence with mass spectrometry-based multimodal molecular profiling methods for advancing therapeutic discovery of infectious diseases. Pharmacol Ther 2024; 263:108712. [PMID: 39241918 DOI: 10.1016/j.pharmthera.2024.108712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/22/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
Infectious diseases, driven by a diverse array of pathogens, can swiftly undermine public health systems. Accurate diagnosis and treatment of infectious diseases-centered around the identification of biomarkers and the elucidation of disease mechanisms-are in dire need of more versatile and practical analytical approaches. Mass spectrometry (MS)-based molecular profiling methods can deliver a wealth of information on a range of functional molecules, including nucleic acids, proteins, and metabolites. While MS-driven omics analyses can yield vast datasets, the sheer complexity and multi-dimensionality of MS data can significantly hinder the identification and characterization of functional molecules within specific biological processes and events. Artificial intelligence (AI) emerges as a potent complementary tool that can substantially enhance the processing and interpretation of MS data. AI applications in this context lead to the reduction of spurious signals, the improvement of precision, the creation of standardized analytical frameworks, and the increase of data integration efficiency. This critical review emphasizes the pivotal roles of MS based omics strategies in the discovery of biomarkers and the clarification of infectious diseases. Additionally, the review underscores the transformative ability of AI techniques to enhance the utility of MS-based molecular profiling in the field of infectious diseases by refining the quality and practicality of data produced from omics analyses. In conclusion, we advocate for a forward-looking strategy that integrates AI with MS-based molecular profiling. This integration aims to transform the analytical landscape and the performance of biological molecule characterization, potentially down to the single-cell level. Such advancements are anticipated to propel the development of AI-driven predictive models, thus improving the monitoring of diagnostics and therapeutic discovery for the ongoing challenge related to infectious diseases.
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Affiliation(s)
- Jingjing Liu
- School of Chinese Medicine, Hong Kong Traditional Chinese Medicine Phenome Research Center, State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Chaohui Bao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jiaxin Zhang
- School of Chinese Medicine, Hong Kong Traditional Chinese Medicine Phenome Research Center, State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Zeguang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Haitao Lu
- School of Chinese Medicine, Hong Kong Traditional Chinese Medicine Phenome Research Center, State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China; Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
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11
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Glass M, Ji Z, Davis R, Pavlisko EN, DiBernardo L, Carney J, Fishbein G, Luthringer D, Miller D, Mitchell R, Larsen B, Butt Y, Bois M, Maleszewski J, Halushka M, Seidman M, Lin CY, Buja M, Stone J, Dov D, Carin L, Glass C. A machine learning algorithm improves the diagnostic accuracy of the histologic component of antibody mediated rejection (AMR-H) in cardiac transplant endomyocardial biopsies. Cardiovasc Pathol 2024; 72:107646. [PMID: 38677634 DOI: 10.1016/j.carpath.2024.107646] [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: 04/03/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Pathologic antibody mediated rejection (pAMR) remains a major driver of graft failure in cardiac transplant patients. The endomyocardial biopsy remains the primary diagnostic tool but presents with challenges, particularly in distinguishing the histologic component (pAMR-H) defined by 1) intravascular macrophage accumulation in capillaries and 2) activated endothelial cells that expand the cytoplasm to narrow or occlude the vascular lumen. Frequently, pAMR-H is difficult to distinguish from acute cellular rejection (ACR) and healing injury. With the advent of digital slide scanning and advances in machine deep learning, artificial intelligence technology is widely under investigation in the areas of oncologic pathology, but in its infancy in transplant pathology. For the first time, we determined if a machine learning algorithm could distinguish pAMR-H from normal myocardium, healing injury and ACR. MATERIALS AND METHODS A total of 4,212 annotations (1,053 regions of normal, 1,053 pAMR-H, 1,053 healing injury and 1,053 ACR) were completed from 300 hematoxylin and eosin slides scanned using a Leica Aperio GT450 digital whole slide scanner at 40X magnification. All regions of pAMR-H were annotated from patients confirmed with a previous diagnosis of pAMR2 (>50% positive C4d immunofluorescence and/or >10% CD68 positive intravascular macrophages). Annotations were imported into a Python 3.7 development environment using the OpenSlide™ package and a convolutional neural network approach utilizing transfer learning was performed. RESULTS The machine learning algorithm showed 98% overall validation accuracy and pAMR-H was correctly distinguished from specific categories with the following accuracies: normal myocardium (99.2%), healing injury (99.5%) and ACR (99.5%). CONCLUSION Our novel deep learning algorithm can reach acceptable, and possibly surpass, performance of current diagnostic standards of identifying pAMR-H. Such a tool may serve as an adjunct diagnostic aid for improving the pathologist's accuracy and reproducibility, especially in difficult cases with high inter-observer variability. This is one of the first studies that provides evidence that an artificial intelligence machine learning algorithm can be trained and validated to diagnose pAMR-H in cardiac transplant patients. Ongoing studies include multi-institutional verification testing to ensure generalizability.
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Affiliation(s)
- Matthew Glass
- Duke Division of Artificial Intelligence and Computational Pathology, Duke University Medical Center, Durham NC, USA; Department of Anesthesiology, Duke University Medical Center, Durham NC, USA
| | - Zhicheng Ji
- Department of Biostatistics and Bioinformatics, Duke School of Medicine, Durham NC, USA
| | - Richard Davis
- Department of Pathology, Duke University Medical Center, Durham NC, USA
| | - Elizabeth N Pavlisko
- Duke Division of Artificial Intelligence and Computational Pathology, Duke University Medical Center, Durham NC, USA; Department of Pathology, Duke University Medical Center, Durham NC, USA
| | - Louis DiBernardo
- Department of Pathology, Duke University Medical Center, Durham NC, USA
| | - John Carney
- Department of Pathology, Duke University Medical Center, Durham NC, USA
| | - Gregory Fishbein
- Department of Pathology, University of California at Los Angeles, Los Angeles CA, USA
| | - Daniel Luthringer
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles CA, USA
| | - Dylan Miller
- Department of Pathology, Intermountain Healthcare, Salt Lake City UT, USA
| | - Richard Mitchell
- Department of Pathology, Brigham and Women's Hospital, Boston MA, USA
| | - Brandon Larsen
- Department of Pathology and Laboratory Medicine, Mayo Clinic, Phoenix AZ, USA
| | - Yasmeen Butt
- Department of Pathology and Laboratory Medicine, Mayo Clinic, Phoenix AZ, USA
| | - Melanie Bois
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester MN, USA
| | - Joseph Maleszewski
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester MN, USA
| | - Marc Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore MD, USA
| | - Michael Seidman
- Department of Pathology, University Health Network, Toronto ON, CA
| | - Chieh-Yu Lin
- Department of Pathology and Immunology, Washington University, St. Louis MO, USA
| | - Maximilian Buja
- Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center at Houston, Houston TX, USA
| | - James Stone
- Department of Pathology, Massachusetts General Hospital, Boston MA, USA
| | - David Dov
- Duke Division of Artificial Intelligence and Computational Pathology, Duke University Medical Center, Durham NC, USA; Pratt School of Engineering, Department of Electrical and Computer Engineering, Duke University, Durham NC, USA
| | - Lawrence Carin
- Duke Division of Artificial Intelligence and Computational Pathology, Duke University Medical Center, Durham NC, USA; Pratt School of Engineering, Department of Electrical and Computer Engineering, Duke University, Durham NC, USA
| | - Carolyn Glass
- Duke Division of Artificial Intelligence and Computational Pathology, Duke University Medical Center, Durham NC, USA; Department of Pathology, Duke University Medical Center, Durham NC, USA.
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12
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Ahmad F, Muhmood T. Clinical translation of nanomedicine with integrated digital medicine and machine learning interventions. Colloids Surf B Biointerfaces 2024; 241:114041. [PMID: 38897022 DOI: 10.1016/j.colsurfb.2024.114041] [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: 02/01/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/21/2024]
Abstract
Nanomaterials based therapeutics transform the ways of disease prevention, diagnosis and treatment with increasing sophistications in nanotechnology at a breakneck pace, but very few could reach to the clinic due to inconsistencies in preclinical studies followed by regulatory hinderances. To tackle this, integrating the nanomedicine discovery with digital medicine provide technologies as tools of specific biological activity measurement. Hence, overcome the redundancies in nanomedicine discovery by the on-site data acquisition and analytics through integrating intelligent sensors and artificial intelligence (AI) or machine learning (ML). Integrated AI/ML wearable sensors directly gather clinically relevant biochemical information from the subject's body and process data for physicians to make right clinical decision(s) in a time and cost-effective way. This review summarizes insights and recommend the infusion of actionable big data computation enabled sensors in burgeoning field of nanomedicine at academia, research institutes, and pharmaceutical industries, with a potential of clinical translation. Furthermore, many blind spots are present in modern clinically relevant computation, one of which could prevent ML-guided low-cost new nanomedicine development from being successfully translated into the clinic was also discussed.
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Affiliation(s)
- Farooq Ahmad
- State Key Laboratory of Chemistry and Utilization of Carbon Based Energy Resources, College of Chemistry, Xinjiang University, Urumqi 830017, China.
| | - Tahir Muhmood
- International Iberian Nanotechnology Laboratory (INL), Avenida Mestre José Veiga, Braga 4715-330, Portugal.
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13
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Chen C, Chen X, Hu Y, Pan B, Huang Q, Dong Q, Xue X, Shen X, Chen X. Utilizing machine learning to integrate single-cell and bulk RNA sequencing data for constructing and validating a novel cell adhesion molecules related prognostic model in gastric cancer. Comput Biol Med 2024; 180:108998. [PMID: 39137671 DOI: 10.1016/j.compbiomed.2024.108998] [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: 11/07/2023] [Revised: 05/01/2024] [Accepted: 08/02/2024] [Indexed: 08/15/2024]
Abstract
BACKGROUND Cell adhesion molecules (CAMs) play a vital role in cell-cell interactions, immune response modulation, and tumor cell migration. However, the unique role of CAMs in gastric cancer (GC) remains largely unexplored. METHODS This study characterized the genetic alterations and mRNA expression of CAMs. The role of CD34, a representative molecule, was validated in 375 GC tissues. The activity of the CAM pathway was further tested using single-cell and bulk characterization. Next, data from 839 patients with GC from three cohorts was analyzed using univariate Cox and random survival forest methods to develop and validate a CAM-related prognostic model. RESULTS Most CAM-related genes exhibited multi-omics alterations and were associated with clinical outcomes. There was a strong correlation between increased CD34 expression and advanced clinical staging (P = 0.026), extensive vascular infiltration (P = 0.003), and unfavorable prognosis (Log-rank P = 0.022). CD34 expression was also found to be associated with postoperative chemotherapy and tumor immunotherapy response. Furthermore, the CAM pathway was significantly activated and mediated poor prognosis. Additionally, eight prognostic signature genes (PSGs) were identified in the training cohort. There was a substantial upregulation of the expression of immune checkpoints and a pronounced infiltration of immune cells in GC tissues with high PSG score, which is consistent with the prediction of increased sensitivity to immunotherapy. Moreover, 9 compounds from the CTRPv2 database and 13 from the Profiling Relative Inhibition Simultaneously in Mixture (PRISM) database were identified as potential therapeutic drugs for patients with GC with high PSG score. CONCLUSION Thorough understanding of CAM pathways regulation and the innovative PSG score model hold significant implications for medical diagnosis, potentially enhancing personalized treatment strategies and improving patient outcomes in GC management.
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Affiliation(s)
- Chenbin Chen
- Department of General Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China; Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China; Department of General Surgery, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Xietao Chen
- Department of General Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China; Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yuanbo Hu
- Department of General Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China; Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China; Department of General Surgery, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Bujian Pan
- Department of General Surgery, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Qunjia Huang
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China; Department of Pathology, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Qiantong Dong
- Department of General Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Xiangyang Xue
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China; Department of General Surgery, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
| | - Xian Shen
- Department of General Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China; Department of General Surgery, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
| | - Xiaodong Chen
- Department of General Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
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14
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Liu Y, Wang R, Zhang C, Huang L, Chen J, Zeng Y, Chen H, Wang G, Qian K, Huang P. Automated Diagnosis and Phenotyping of Tuberculosis Using Serum Metabolic Fingerprints. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2406233. [PMID: 39159075 DOI: 10.1002/advs.202406233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/23/2024] [Indexed: 08/21/2024]
Abstract
Tuberculosis (TB) stands as the second most fatal infectious disease after COVID-19, the effective treatment of which depends on accurate diagnosis and phenotyping. Metabolomics provides valuable insights into the identification of differential metabolites for disease diagnosis and phenotyping. However, TB diagnosis and phenotyping remain great challenges due to the lack of a satisfactory metabolic approach. Here, a metabolomics-based diagnostic method for rapid TB detection is reported. Serum metabolic fingerprints are examined via an automated nanoparticle-enhanced laser desorption/ionization mass spectrometry platform outstanding by its rapid detection speed (measured in seconds), minimal sample consumption (in nanoliters), and cost-effectiveness (approximately $3). A panel of 14 m z-1 features is identified as biomarkers for TB diagnosis and a panel of 4 m z-1 features for TB phenotyping. Based on the acquired biomarkers, TB metabolic models are constructed through advanced machine learning algorithms. The robust metabolic model yields a 97.8% (95% confidence interval (CI), 0.964-0.986) area under the curve (AUC) in TB diagnosis and an 85.7% (95% CI, 0.806-0.891) AUC in phenotyping. In this study, serum metabolic biomarker panels are revealed and develop an accurate metabolic tool with desirable diagnostic performance for TB diagnosis and phenotyping, which may expedite the effective implementation of the end-TB strategy.
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Affiliation(s)
- Yajing Liu
- Department of Ultrasound in Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, P. R. China
| | - Ruimin Wang
- State Key Laboratory for Oncogenes and Related Genes School of Biomedical Engineering Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Chao Zhang
- Department of Ultrasound in Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, P. R. China
| | - Lin Huang
- State Key Laboratory for Oncogenes and Related Genes School of Biomedical Engineering Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Jifan Chen
- Department of Ultrasound in Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, P. R. China
| | - Yiqing Zeng
- Department of Ultrasound in Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, P. R. China
| | - Hongjian Chen
- Post-Doctoral Research Center, Zhejiang SUKEAN Pharmaceutical Co., Ltd, Hangzhou, 311225, P. R. China
| | - Guowei Wang
- Department of Ultrasound in Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, P. R. China
| | - Kun Qian
- State Key Laboratory for Oncogenes and Related Genes School of Biomedical Engineering Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Pintong Huang
- Department of Ultrasound in Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, P. R. China
- Research Center for Life Science and Human Health, Binjiang Institute of Zhejiang University, Hangzhou, 310053, P. R. China
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15
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de Gonzalo-Calvo D, Karaduzovic-Hadziabdic K, Dalgaard LT, Dieterich C, Perez-Pons M, Hatzigeorgiou A, Devaux Y, Kararigas G. Machine learning for catalysing the integration of noncoding RNA in research and clinical practice. EBioMedicine 2024; 106:105247. [PMID: 39029428 PMCID: PMC11314885 DOI: 10.1016/j.ebiom.2024.105247] [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: 03/08/2024] [Revised: 06/17/2024] [Accepted: 07/02/2024] [Indexed: 07/21/2024] Open
Abstract
The human transcriptome predominantly consists of noncoding RNAs (ncRNAs), transcripts that do not encode proteins. The noncoding transcriptome governs a multitude of pathophysiological processes, offering a rich source of next-generation biomarkers. Toward achieving a holistic view of disease, the integration of these transcripts with clinical records and additional data from omic technologies ("multiomic" strategies) has motivated the adoption of artificial intelligence (AI) approaches. Given their intricate biological complexity, machine learning (ML) techniques are becoming a key component of ncRNA-based research. This article presents an overview of the potential and challenges associated with employing AI/ML-driven approaches to identify clinically relevant ncRNA biomarkers and to decipher ncRNA-associated pathogenetic mechanisms. Methodological and conceptual constraints are discussed, along with an exploration of ethical considerations inherent to AI applications for healthcare and research. The ultimate goal is to provide a comprehensive examination of the multifaceted landscape of this innovative field and its clinical implications.
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Affiliation(s)
- David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.
| | | | | | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology and Department of Internal Medicine III, University Hospital Heidelberg, Germany; German Center for Cardiovascular Research (DZHK) - Partner Site Heidelberg/Mannheim, Germany
| | - Manel Perez-Pons
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Artemis Hatzigeorgiou
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece; Hellenic Pasteur Institute, Athens, Greece
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Georgios Kararigas
- Department of Physiology, Faculty of Medicine, University of Iceland, Reykjavik, Iceland.
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16
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Shahrouzi P, Forouz F, Mathelier A, Kristensen VN, Duijf PHG. Copy number alterations: a catastrophic orchestration of the breast cancer genome. Trends Mol Med 2024; 30:750-764. [PMID: 38772764 DOI: 10.1016/j.molmed.2024.04.017] [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: 02/26/2024] [Revised: 04/12/2024] [Accepted: 04/26/2024] [Indexed: 05/23/2024]
Abstract
Breast cancer (BCa) is a prevalent malignancy that predominantly affects women around the world. Somatic copy number alterations (CNAs) are tumor-specific amplifications or deletions of DNA segments that often drive BCa development and therapy resistance. Hence, the complex patterns of CNAs complement BCa classification systems. In addition, understanding the precise contributions of CNAs is essential for tailoring personalized treatment approaches. This review highlights how tumor evolution drives the acquisition of CNAs, which in turn shape the genomic landscapes of BCas. It also discusses advanced methodologies for identifying recurrent CNAs, studying CNAs in BCa and their clinical impact.
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Affiliation(s)
- Parastoo Shahrouzi
- Department of Medical Genetics, Institute of Basic Medical Science, Faculty of Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway.
| | - Farzaneh Forouz
- School of Pharmacy, University of Queensland, Woolloongabba, Brisbane, Australia
| | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway; Center for Bioinformatics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway; Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Vessela N Kristensen
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway; Division of Medicine, Department of Clinical Molecular Biology and Laboratory Science (EpiGen), Akershus University Hospital, Lørenskog, Norway; Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Pascal H G Duijf
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway; Centre for Cancer Biology, UniSA Clinical and Health Sciences, University of South Australia and SA Pathology, Adelaide, Australia.
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17
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Dupont V, Xhaard C, Behm-Ansmant I, Bresso E, Thuillier Q, Branlant C, Lopez-Sublet M, Deleuze JF, Zannad F, Girerd N, Rossignol P. Multiomic profiling of new-onset kidney function decline: insights from the STANISLAS study cohort with a 20-year follow-up. Clin Kidney J 2024; 17:sfae224. [PMID: 39135941 PMCID: PMC11317839 DOI: 10.1093/ckj/sfae224] [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: 04/11/2024] [Indexed: 08/15/2024] Open
Abstract
Background Identifying the biomarkers associated with new-onset glomerular filtration rate (GFR) decrease in an initially healthy population could offer a better understanding of kidney function decline and help improving patient management. Methods Here we described the proteomic and transcriptomic footprints associated with new-onset kidney function decline in an initially healthy and well-characterized population with a 20-year follow-up. This study was based on 1087 individuals from the familial longitudinal Suivi Temporaire Annuel Non-Invasif de la Santé des Lorrains Assurés Sociaux (STANISLAS) cohort who attended both visit 1 (from 1993 to 1995) and visit 4 (from 2011 to 2016). New-onset kidney function decline was approached both in quantitative (GFR slope for each individual) and qualitative (defined as a decrease in GFR of >15 ml/min/1.7 m2) ways. We analysed associations of 445 proteins measured both at visit 1 and visit 4 using Olink Proseek® panels and 119 765 genes expressions measured at visit 4 with GFR decline. Associations were assessed using multivariable models. The Bonferroni correction was applied. Results We found several proteins (including PLC, placental growth factor (PGF), members of the tumour necrosis factor receptor superfamily), genes (including CCL18, SESN3), and a newly discovered miRNA-mRNA pair (MIR1205-DNAJC6) to be independently associated with new-onset kidney function decline. Complex network analysis highlighted both extracellular matrix and cardiovascular remodelling (since visit 1) as well as inflammation (at visit 4) as key features of early GFR decrease. Conclusions These findings lay the foundation to further assess whether the proteins and genes herein identified may represent potential biomarkers or therapeutic targets to prevent renal function impairment.
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Affiliation(s)
- Vincent Dupont
- Department of Nephrology, University hospital of Reims, Reims, France
- FCRIN INI-CRCT (Cardiovascular and Renal Clinical Trialists)
- CNRS UMR 7369, Université de Reims Champagne-Ardenne, Reims, France
| | - Constance Xhaard
- FCRIN INI-CRCT (Cardiovascular and Renal Clinical Trialists)
- Université de Lorraine, Centre d'Investigations Cliniques- Plurithématique 14-33, Inserm U1116, CHRU Nancy, France
| | | | - Emmanuel Bresso
- FCRIN INI-CRCT (Cardiovascular and Renal Clinical Trialists)
- Université de Lorraine, Centre d'Investigations Cliniques- Plurithématique 14-33, Inserm U1116, CHRU Nancy, France
| | | | | | - Marilucy Lopez-Sublet
- FCRIN INI-CRCT (Cardiovascular and Renal Clinical Trialists)
- AP-HP, Hopital Avicenne, Centre d'Excellence Europeen en Hypertension Arterielle, Service de Medecine Interne, INSERM UMR 942 MASCOT, Paris 13-Universite Paris Nord, Bobigny, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Faiez Zannad
- FCRIN INI-CRCT (Cardiovascular and Renal Clinical Trialists)
- Université de Lorraine, Centre d'Investigations Cliniques- Plurithématique 14-33, Inserm U1116, CHRU Nancy, France
| | - Nicolas Girerd
- FCRIN INI-CRCT (Cardiovascular and Renal Clinical Trialists)
- Université de Lorraine, Centre d'Investigations Cliniques- Plurithématique 14-33, Inserm U1116, CHRU Nancy, France
| | - Patrick Rossignol
- FCRIN INI-CRCT (Cardiovascular and Renal Clinical Trialists)
- Medicine and Nephrology-dialysis departments, Princess Grace Hospital, and Monaco Private Hemodialysis Centre, Monaco, Monaco
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18
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Zhou J, Bai Y, Zhang Y, Wang Z, Sun S, Lin L, Gu Y, You C. A preoperative radiogenomic model based on quantitative heterogeneity for predicting outcomes in triple-negative breast cancer patients who underwent neoadjuvant chemotherapy. Cancer Imaging 2024; 24:98. [PMID: 39080809 PMCID: PMC11289960 DOI: 10.1186/s40644-024-00746-z] [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: 01/11/2024] [Accepted: 07/24/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is highly heterogeneous, resulting in different responses to neoadjuvant chemotherapy (NAC) and prognoses among patients. This study sought to characterize the heterogeneity of TNBC on MRI and develop a radiogenomic model for predicting both pathological complete response (pCR) and prognosis. MATERIALS AND METHODS In this retrospective study, TNBC patients who underwent neoadjuvant chemotherapy at Fudan University Shanghai Cancer Center were enrolled as the radiomic development cohort (n = 315); among these patients, those whose genetic data were available were enrolled as the radiogenomic development cohort (n = 98). The study population of the two cohorts was randomly divided into a training set and a validation set at a ratio of 7:3. The external validation cohort (n = 77) included patients from the DUKE and I-SPY 1 databases. Spatial heterogeneity was characterized using features from the intratumoral subregions and peritumoral region. Hemodynamic heterogeneity was characterized by kinetic features from the tumor body. Three radiomics models were developed by logistic regression after selecting features. Model 1 included subregional and peritumoral features, Model 2 included kinetic features, and Model 3 integrated the features of Model 1 and Model 2. Two fusion models were developed by further integrating pathological and genomic features (PRM: pathology-radiomics model; GPRM: genomics-pathology-radiomics model). Model performance was assessed with the AUC and decision curve analysis. Prognostic implications were assessed with Kaplan‒Meier curves and multivariate Cox regression. RESULTS Among the radiomic models, the multiregional model representing multiscale heterogeneity (Model 3) exhibited better pCR prediction, with AUCs of 0.87, 0.79, and 0.78 in the training, internal validation, and external validation sets, respectively. The GPRM showed the best performance for predicting pCR in the training (AUC = 0.97, P = 0.015) and validation sets (AUC = 0.93, P = 0.019). Model 3, PRM and GPRM could stratify patients by disease-free survival, and a predicted nonpCR was associated with poor prognosis (P = 0.034, 0.001 and 0.019, respectively). CONCLUSION Multiscale heterogeneity characterized by DCE-MRI could effectively predict the pCR and prognosis of TNBC patients. The radiogenomic model could serve as a valuable biomarker to improve the prediction performance.
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Affiliation(s)
- Jiayin Zhou
- Department of Radiology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yansong Bai
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200000, China
| | - Ying Zhang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Zezhou Wang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Department of Cancer Prevention, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Shanghai Municipal Hospital Oncological Specialist Alliance, Shanghai, 200000, China
| | - Shiyun Sun
- Department of Radiology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Luyi Lin
- Department of Radiology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yajia Gu
- Department of Radiology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Chao You
- Department of Radiology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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Paverd H, Zormpas-Petridis K, Clayton H, Burge S, Crispin-Ortuzar M. Radiology and multi-scale data integration for precision oncology. NPJ Precis Oncol 2024; 8:158. [PMID: 39060351 PMCID: PMC11282284 DOI: 10.1038/s41698-024-00656-0] [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: 01/19/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
In this Perspective paper we explore the potential of integrating radiological imaging with other data types, a critical yet underdeveloped area in comparison to the fusion of other multi-omic data. Radiological images provide a comprehensive, three-dimensional view of cancer, capturing features that would be missed by biopsies or other data modalities. This paper explores the complexities and challenges of incorporating medical imaging into data integration models, in the context of precision oncology. We present the different categories of imaging-omics integration and discuss recent progress, highlighting the opportunities that arise from bringing together spatial data on different scales.
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Affiliation(s)
- Hania Paverd
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
| | | | - Hannah Clayton
- Department of Oncology, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
| | - Sarah Burge
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
| | - Mireia Crispin-Ortuzar
- Department of Oncology, University of Cambridge, Cambridge, UK.
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK.
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20
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Enoma D. Genomics in Clinical trials for Breast Cancer. Brief Funct Genomics 2024; 23:325-334. [PMID: 38146120 DOI: 10.1093/bfgp/elad054] [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: 08/30/2023] [Revised: 11/29/2023] [Accepted: 12/01/2023] [Indexed: 12/27/2023] Open
Abstract
Breast cancer (B.C.) still has increasing incidences and mortality rates globally. It is known that B.C. and other cancers have a very high rate of genetic heterogeneity and genomic mutations. Traditional oncology approaches have not been able to provide a lasting solution. Targeted therapeutics have been instrumental in handling the complexity and resistance associated with B.C. However, the progress of genomic technology has transformed our understanding of the genetic landscape of breast cancer, opening new avenues for improved anti-cancer therapeutics. Genomics is critical in developing tailored therapeutics and identifying patients most benefit from these treatments. The next generation of breast cancer clinical trials has incorporated next-generation sequencing technologies into the process, and we have seen benefits. These innovations have led to the approval of better-targeted therapies for patients with breast cancer. Genomics has a role to play in clinical trials, including genomic tests that have been approved, patient selection and prediction of therapeutic response. Multiple clinical trials in breast cancer have been done and are still ongoing, which have applied genomics technology. Precision medicine can be achieved in breast cancer therapy with increased efforts and advanced genomic studies in this domain. Genomics studies assist with patient outcomes improvement and oncology advancement by providing a deeper understanding of the biology behind breast cancer. This article will examine the present state of genomics in breast cancer clinical trials.
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Affiliation(s)
- David Enoma
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 2500 University Dr NW, Calgary, Alberta, T2N 1N4, Canada
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21
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Pan JW, Tan ZC, Ng PS, Zabidi MMA, Nur Fatin P, Teo JY, Hasan SN, Islam T, Teoh LY, Jamaris S, See MH, Yip CH, Rajadurai P, Looi LM, Taib NAM, Rueda OM, Caldas C, Chin SF, Lim J, Teo SH. Gene expression signature for predicting homologous recombination deficiency in triple-negative breast cancer. NPJ Breast Cancer 2024; 10:60. [PMID: 39030225 PMCID: PMC11271517 DOI: 10.1038/s41523-024-00671-1] [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: 08/16/2023] [Accepted: 07/10/2024] [Indexed: 07/21/2024] Open
Abstract
Triple-negative breast cancers (TNBCs) are a subset of breast cancers that have remained difficult to treat. A proportion of TNBCs arising in non-carriers of BRCA pathogenic variants have genomic features that are similar to BRCA carriers and may also benefit from PARP inhibitor treatment. Using genomic data from 129 TNBC samples from the Malaysian Breast Cancer (MyBrCa) cohort, we developed a gene expression-based machine learning classifier for homologous recombination deficiency (HRD) in TNBCs. The classifier identified samples with HRD mutational signature at an AUROC of 0.93 in MyBrCa validation datasets and 0.84 in TCGA TNBCs. Additionally, the classifier strongly segregated HRD-associated genomic features in TNBCs from TCGA, METABRIC, and ICGC. Thus, our gene expression classifier may identify triple-negative breast cancer patients with homologous recombination deficiency, suggesting an alternative method to identify individuals who may benefit from treatment with PARP inhibitors or platinum chemotherapy.
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Affiliation(s)
- Jia-Wern Pan
- Cancer Research Malaysia, Subang Jaya, Malaysia.
| | | | - Pei-Sze Ng
- Cancer Research Malaysia, Subang Jaya, Malaysia
| | | | | | | | | | - Tania Islam
- Department of Surgery, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Li-Ying Teoh
- Department of Surgery, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Suniza Jamaris
- Department of Surgery, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Mee-Hoong See
- Department of Surgery, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | | | - Pathmanathan Rajadurai
- Subang Jaya Medical Centre, Subang Jaya, Malaysia
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya, Malaysia
| | - Lai-Meng Looi
- Department of Pathology, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Nur Aishah Mohd Taib
- Department of Surgery, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Oscar M Rueda
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Carlos Caldas
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Robinson Way, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Suet-Feung Chin
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Joanna Lim
- Cancer Research Malaysia, Subang Jaya, Malaysia
| | - Soo-Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Malaysia
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
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22
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Sohrabei S, Moghaddasi H, Hosseini A, Ehsanzadeh SJ. Investigating the effects of artificial intelligence on the personalization of breast cancer management: a systematic study. BMC Cancer 2024; 24:852. [PMID: 39026174 PMCID: PMC11256548 DOI: 10.1186/s12885-024-12575-1] [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: 10/26/2023] [Accepted: 06/27/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND Providing appropriate specialized treatment to the right patient at the right time is considered necessary in cancer management. Targeted therapy tailored to the genetic changes of each breast cancer patient is a desirable feature of precision oncology, which can not only reduce disease progression but also potentially increase patient survival. The use of artificial intelligence alongside precision oncology can help physicians by identifying and selecting more effective treatment factors for patients. METHOD A systematic review was conducted using the PubMed, Embase, Scopus, and Web of Science databases in September 2023. We performed the search strategy with keywords, namely: Breast Cancer, Artificial intelligence, and precision Oncology along with their synonyms in the article titles. Descriptive, qualitative, review, and non-English studies were excluded. The quality assessment of the articles and evaluation of bias were determined based on the SJR journal and JBI indices, as well as the PRISMA2020 guideline. RESULTS Forty-six studies were selected that focused on personalized breast cancer management using artificial intelligence models. Seventeen studies using various deep learning methods achieved a satisfactory outcome in predicting treatment response and prognosis, contributing to personalized breast cancer management. Two studies utilizing neural networks and clustering provided acceptable indicators for predicting patient survival and categorizing breast tumors. One study employed transfer learning to predict treatment response. Twenty-six studies utilizing machine-learning methods demonstrated that these techniques can improve breast cancer classification, screening, diagnosis, and prognosis. The most frequent modeling techniques used were NB, SVM, RF, XGBoost, and Reinforcement Learning. The average area under the curve (AUC) for the models was 0.91. Moreover, the average values for accuracy, sensitivity, specificity, and precision were reported to be in the range of 90-96% for the models. CONCLUSION Artificial intelligence has proven to be effective in assisting physicians and researchers in managing breast cancer treatment by uncovering hidden patterns in complex omics and genetic data. Intelligent processing of omics data through protein and gene pattern classification and the utilization of deep neural patterns has the potential to significantly transform the field of complex disease management.
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Affiliation(s)
- Solmaz Sohrabei
- Department of Health Information Technology and Management, Medical Informatics, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Moghaddasi
- Department of Health Information Technology and Management, Medical Informatics, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Azamossadat Hosseini
- Department of Health Information Technology and Management, Health Information Management, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Seyed Jafar Ehsanzadeh
- Department of English Language, School of Health Management and Information Sciences, Iran University of Medical Sciences, Tehran, Iran
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23
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Chen L, Zhang W, Shi H, Zhu Y, Chen H, Wu Z, Zhong M, Shi X, Li Q, Wang T. Metabolism score and machine learning models for the prediction of esophageal squamous cell carcinoma progression. Cancer Sci 2024. [PMID: 38992901 DOI: 10.1111/cas.16279] [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: 03/28/2024] [Revised: 06/19/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024] Open
Abstract
The incomplete prediction of prognosis in esophageal squamous cell carcinoma (ESCC) patients is attributed to various therapeutic interventions and complex prognostic factors. Consequently, there is a pressing demand for enhanced predictive biomarkers that can facilitate clinical management and treatment decisions. This study recruited 491 ESCC patients who underwent surgical treatment at Huashan Hospital, Fudan University. We incorporated 14 blood metabolic indicators and identified independent prognostic indicators for overall survival through univariate and multivariate analyses. Subsequently, a metabolism score formula was established based on the biochemical markers. We constructed a nomogram and machine learning models utilizing the metabolism score and clinically significant prognostic features, followed by an evaluation of their predictive accuracy and performance. We identified alkaline phosphatase, free fatty acids, homocysteine, lactate dehydrogenase, and triglycerides as independent prognostic indicators for ESCC. Subsequently, based on these five indicators, we established a metabolism score that serves as an independent prognostic factor in ESCC patients. By utilizing this metabolism score in conjunction with clinical features, a nomogram can precisely predict the prognosis of ESCC patients, achieving an area under the curve (AUC) of 0.89. The random forest (RF) model showed superior predictive ability (AUC = 0.90, accuracy = 86%, Matthews correlation coefficient = 0.55). Finally, we used an RF model with optimal performance to establish an online predictive tool. The metabolism score developed in this study serves as an independent prognostic indicator for ESCC patients.
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Affiliation(s)
- Lu Chen
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - WenXin Zhang
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Huanying Shi
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Yongjun Zhu
- Department of Cardiovascular Thoracic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Haifei Chen
- Department of Pharmacy, Baoshan Campus of Huashan Hospital, Fudan University, Shanghai, China
| | - Zimei Wu
- Department of Pharmacy, Baoshan Campus of Huashan Hospital, Fudan University, Shanghai, China
| | - Mingkang Zhong
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaojin Shi
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Qunyi Li
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Tianxiao Wang
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
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24
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Cao L, Zhu G, Wang X, Kuang Z, Song X, Ma X, Zhu X, Gao R, Li J. Yiqi Wenyang Jiedu prescription for preventing and treating postoperative recurrence and metastasis of gastric cancer: a randomized controlled trial protocol. Front Oncol 2024; 14:1326970. [PMID: 39035732 PMCID: PMC11257841 DOI: 10.3389/fonc.2024.1326970] [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: 10/24/2023] [Accepted: 06/17/2024] [Indexed: 07/23/2024] Open
Abstract
Introduction Postoperative recurrence and metastasis of gastric cancer (GC) are primary factors that contribute to poor prognosis. GC recurs at a rate of approximately 70%-80% within 2 years after local treatment and approximately 90% within 5 years. "Yang-deficient toxic node" is the core pathogenesis of GC recurrence and metastasis. The Yiqi Wenyang Jiedu prescription (YWJP), a form of complementary and alternative medicine in China, is an empirical remedy to prevent postoperative recurrence and metastasis of GC. Taking the main therapeutic principles of "nourishing Qi and warming Yang, strengthening Zhengqi, and detoxifying" can aid in preventing the recurrence and metastasis of GC in patients during the watchful waiting period after surgery and adjuvant chemotherapy. This approach aims to enhance the quality of life of patients. However, high-quality evidence to support this hypothesis is lacking. This study will aim to investigate the efficacy and safety of YWJP to prevent and treat postoperative metastasis and GC recurrence. Methods The study will be a multicenter, randomized, double-blind, placebo-parallel-controlled clinical trial. A total of 212 patients who completed adjuvant chemotherapy within 8 months of radical gastrectomy will be enrolled. Patients in the intervention group will receive the YWJP, whereas those in the control group will receive a placebo. The main outcome was the disease-free survival (DFS) rate 2 years after surgery. The secondary outcomes included DFS time, overall survival, annual cumulative recurrence and rate of metastasis after 1-3 years, cumulative annual survival after 1-3 years, fat distribution-related indicators, tumor markers, peripheral blood inflammatory indicators, prognostic nutritional index, symptoms and quality of life evaluation, medication compliance, and adverse reaction rate. Discussion There is a lack of effective therapy after the completion of adjuvant therapy during the postoperative period of watchful waiting. This study will be the first randomized clinical trial to evaluate whether complementary and alternative medical interventions can effectively prevent recurrence and metastasis during the watchful waiting period after GC surgery and to provide evidence for surveillance treatment management after GC surgery. Clinical trial registration ClinicalTrials.gov, identifier NCT05229809.
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Affiliation(s)
- Luchang Cao
- Department of Oncology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Guanghui Zhu
- Department of Oncology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
| | - Xinmiao Wang
- Department of Oncology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ziyu Kuang
- Department of Oncology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaotong Song
- Department of Oncology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xinyi Ma
- Department of Oncology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaoyu Zhu
- Department of Oncology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ruike Gao
- Department of Oncology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jie Li
- Department of Oncology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
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25
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van der Voort A, van der Hoogt KJJ, Wessels R, Schipper RJ, Wesseling J, Sonke GS, Mann RM. Diffusion-weighted imaging in addition to contrast-enhanced MRI in identifying complete response in HER2-positive breast cancer. Eur Radiol 2024:10.1007/s00330-024-10857-7. [PMID: 38967659 DOI: 10.1007/s00330-024-10857-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 04/15/2024] [Accepted: 04/26/2024] [Indexed: 07/06/2024]
Abstract
OBJECTIVES The aim of this study is to investigate the added value of diffusion-weighted imaging (DWI) to dynamic-contrast enhanced (DCE)-MRI to identify a pathological complete response (pCR) in patients with HER2-positive breast cancer and radiological complete response (rCR). MATERIALS AND METHODS This is a single-center observational study of 102 patients with stage I-III HER2-positive breast cancer and real-world documented rCR on DCE-MRI. Patients were treated between 2015 and 2019. Both 1.5 T/3.0 T single-shot diffusion-weighted echo-planar sequence were used. Post neoadjuvant systemic treatment (NST) diffusion-weighted images were reviewed by two readers for visual evaluation and ADCmean. Discordant cases were resolved in a consensus meeting. pCR of the breast (ypT0/is) was used to calculate the negative predictive value (NPV). Breast pCR-percentages were tested with Fisher's exact test. ADCmean and ∆ADCmean(%) for patients with and without pCR were compared using a Mann-Whitney U-test. RESULTS The NPV for DWI added to DCE is 86% compared to 87% for DCE alone in hormone receptor (HR)-/HER2-positive and 67% compared to 64% in HR-positive/HER2-positive breast cancer. Twenty-seven of 39 non-rCR DWI cases were false positives. In HR-positive/HER2-positive breast cancer the NPV for DCE MRI differs between MRI field strength (1.5 T: 50% vs. 3 T: 81% [p = 0.02]). ADCmean at baseline, post-NST, and ∆ADCmean were similar between patients with and without pCR. CONCLUSION DWI has no clinically relevant effect on the NPV of DCE alone to identify a pCR in early HER2-positive breast cancer. The added value of DWI in HR-positive/HER2-positive breast cancer should be further investigated taken MRI field strength into account. CLINICAL RELEVANCE STATEMENT The residual signal on DWI after neoadjuvant systemic therapy in cases with early HER2-positive breast cancer and no residual pathologic enhancement on DCE-MRI breast should not (yet) be considered in assessing a complete radiologic response. KEY POINTS Radiologic complete response is associated with a pathologic complete response (pCR) in HER2+ breast cancer but further improvement is warranted. No relevant increase in negative predictive value was observed when DWI was added to DCE. Residual signal on DW-images without pathologic enhancement on DCE-MRI, does not indicate a lower chance of pCR.
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Affiliation(s)
- Anna van der Voort
- Department of Medical Oncology, the Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Kay J J van der Hoogt
- Department of Radiology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
- GROW School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Ronni Wessels
- Department of Radiology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Robert-Jan Schipper
- Department of Radiology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Surgery, Catharina Hospital, Eindhoven, The Netherlands
| | - Jelle Wesseling
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gabe S Sonke
- Department of Medical Oncology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
- University of Amsterdam, Amsterdam, The Netherlands
| | - Ritse M Mann
- Department of Radiology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
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26
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Hoang DT, Dinstag G, Shulman ED, Hermida LC, Ben-Zvi DS, Elis E, Caley K, Sammut SJ, Sinha S, Sinha N, Dampier CH, Stossel C, Patil T, Rajan A, Lassoued W, Strauss J, Bailey S, Allen C, Redman J, Beker T, Jiang P, Golan T, Wilkinson S, Sowalsky AG, Pine SR, Caldas C, Gulley JL, Aldape K, Aharonov R, Stone EA, Ruppin E. A deep-learning framework to predict cancer treatment response from histopathology images through imputed transcriptomics. NATURE CANCER 2024:10.1038/s43018-024-00793-2. [PMID: 38961276 DOI: 10.1038/s43018-024-00793-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 06/06/2024] [Indexed: 07/05/2024]
Abstract
Advances in artificial intelligence have paved the way for leveraging hematoxylin and eosin-stained tumor slides for precision oncology. We present ENLIGHT-DeepPT, an indirect two-step approach consisting of (1) DeepPT, a deep-learning framework that predicts genome-wide tumor mRNA expression from slides, and (2) ENLIGHT, which predicts response to targeted and immune therapies from the inferred expression values. We show that DeepPT successfully predicts transcriptomics in all 16 The Cancer Genome Atlas cohorts tested and generalizes well to two independent datasets. ENLIGHT-DeepPT successfully predicts true responders in five independent patient cohorts involving four different treatments spanning six cancer types, with an overall odds ratio of 2.28 and a 39.5% increased response rate among predicted responders versus the baseline rate. Notably, its prediction accuracy, obtained without any training on the treatment data, is comparable to that achieved by directly predicting the response from the images, which requires specific training on the treatment evaluation cohorts.
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Affiliation(s)
- Danh-Tai Hoang
- Biological Data Science Institute, College of Science, Australian National University, Canberra, Australian Capital Territory, Australia.
| | | | - Eldad D Shulman
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Leandro C Hermida
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | - Katherine Caley
- Biological Data Science Institute, College of Science, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Stephen-John Sammut
- Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, UK
- The Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - Sanju Sinha
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Neelam Sinha
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Christopher H Dampier
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Chani Stossel
- Oncology Institute, Sheba Medical Center at Tel-Hashomer, Tel Aviv University, Tel Aviv, Israel
| | - Tejas Patil
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Arun Rajan
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Wiem Lassoued
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Julius Strauss
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Shania Bailey
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Clint Allen
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Jason Redman
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Peng Jiang
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Talia Golan
- Oncology Institute, Sheba Medical Center at Tel-Hashomer, Tel Aviv University, Tel Aviv, Israel
| | - Scott Wilkinson
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Adam G Sowalsky
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Sharon R Pine
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Carlos Caldas
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - James L Gulley
- Genitourinary Malignancy Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Eric A Stone
- Biological Data Science Institute, College of Science, Australian National University, Canberra, Australian Capital Territory, Australia.
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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27
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Fu C, Ji W, Cui Q, Chen A, Weng H, Lu N, Yang W. GSDME-mediated pyroptosis promotes anti-tumor immunity of neoadjuvant chemotherapy in breast cancer. Cancer Immunol Immunother 2024; 73:177. [PMID: 38954046 PMCID: PMC11219631 DOI: 10.1007/s00262-024-03752-z] [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: 02/23/2024] [Accepted: 06/02/2024] [Indexed: 07/04/2024]
Abstract
Paclitaxel and anthracycline-based chemotherapy is one of the standard treatment options for breast cancer. However, only about 6-30% of breast cancer patients achieved a pathological complete response (pCR), and the mechanism responsible for the difference is still unclear. In this study, random forest algorithm was used to screen feature genes, and artificial neural network (ANN) algorithm was used to construct an ANN model for predicting the efficacy of neoadjuvant chemotherapy for breast cancer. Furthermore, digital pathology, cytology, and molecular biology experiments were used to verify the relationship between the efficacy of neoadjuvant chemotherapy and immune ecology. It was found that paclitaxel and doxorubicin, an anthracycline, could induce typical pyroptosis and bubbling in breast cancer cells, accompanied by gasdermin E (GSDME) cleavage. Paclitaxel with LDH release and Annexin V/PI doubule positive cell populations, and accompanied by the increased release of damage-associated molecular patterns, HMGB1 and ATP. Cell coculture experiments also demonstrated enhanced phagocytosis of macrophages and increased the levels of IFN-γ and IL-2 secretion after paclitaxel treatment. Mechanistically, GSDME may mediate paclitaxel and doxorubicin-induced pyroptosis in breast cancer cells through the caspase-9/caspase-3 pathway, activate anti-tumor immunity, and promote the efficacy of paclitaxel and anthracycline-based neoadjuvant chemotherapy. This study has practical guiding significance for the precision treatment of breast cancer, and can also provide ideas for understanding molecular mechanisms related to the chemotherapy sensitivity.
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Affiliation(s)
- Changfang Fu
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
- Anhui Provincial Key Laboratory of Precision Pharmaceutical Preparations and Clinical Pharmacy, Hefei, 230001, Anhui, China
| | - Wenbo Ji
- Clinical Pharmacy Department, Anhui Provincial Children's Hospital, Hefei, 230000, Anhui, China
| | - Qianwen Cui
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
| | - Anling Chen
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
| | - Haiyan Weng
- Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Nannan Lu
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China.
| | - Wulin Yang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China.
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, China.
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28
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Huang H, Chen G, Zhang Z, Wu G, Zhang Z, Yu A, Wang J, Quan C, Li Y, Zhou M. Deciphering the role of cuproptosis-related lncRNAs in shaping the lung cancer immune microenvironment: A comprehensive prognostic model. J Cell Mol Med 2024; 28:e18519. [PMID: 38973477 PMCID: PMC11228428 DOI: 10.1111/jcmm.18519] [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: 12/19/2023] [Revised: 05/21/2024] [Accepted: 06/19/2024] [Indexed: 07/09/2024] Open
Abstract
Cuproptosis plays an important role in cancer, but its role in lung cancer remains unknown. Transcriptional profiles, clinical details and mutation data were acquired from the Cancer Genome Atlas database through a variety of methods. The analysis of this publicly available data was comprehensively performed using R software along with its relevant packages, ensuring a thorough examination of the information. In this study, we conducted a detailed analysis of cuproptosis-related genes and lncRNA co-expression, identifying 129 relevant lncRNAs and establishing a prognostic model with four key lncRNAs (LINC00996, RPARP-AS1, SND1-IT1, TMPO-AS1). Utilizing data from TCGA and GEO databases, the model effectively categorized patients into high- and low-risk groups, showing significant survival differences. Correlation analysis highlighted specific relationships between individual lncRNAs and cuproptosis genes. Our survival analysis indicated a higher survival rate in the low-risk group across various cohorts. Additionally, the model's predictive accuracy was confirmed through independent prognostic analysis and ROC curve evaluations. Functional enrichment analysis revealed distinct biological pathways and immune functions between risk groups. Tumour mutation load analysis differentiated high- and low-risk groups by their mutation profiles. Drug sensitivity analysis and immune infiltration studies using the CIBERSORT algorithm further elucidated the potential treatment responses in different risk groups. This comprehensive evaluation underscores the significance of lncRNAs in cuproptosis and their potential as biomarkers for lung cancer prognosis and immune microenvironment.
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Affiliation(s)
- Hai Huang
- Tuberculosis ward No.2, Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Wuhan, Hubei, China
| | - Guoxi Chen
- Tuberculosis ward No.2, Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Wuhan, Hubei, China
| | - Zongqi Zhang
- Tuberculosis ward No.2, Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Wuhan, Hubei, China
| | - Gang Wu
- Department of Tuberculosis control, Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Affiliated to Jianghan University, Wuhan, Hubei, China
| | - Zhengbin Zhang
- Department of Tuberculosis control, Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Affiliated to Jianghan University, Wuhan, Hubei, China
| | - Aiping Yu
- Infectious disease prevention and control department, Dongxihu Centers for Disease Prevention and Control, Wuhan, Hubei, China
| | - Jianjie Wang
- Department of Tuberculosis control, Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Affiliated to Jianghan University, Wuhan, Hubei, China
| | - Chao Quan
- Department of Tuberculosis control, Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Affiliated to Jianghan University, Wuhan, Hubei, China
| | - Yuehua Li
- Department of Tuberculosis control, Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Affiliated to Jianghan University, Wuhan, Hubei, China
| | - Meilan Zhou
- Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Affiliated to Jianghan University, Wuhan, Hubei, China
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29
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Shao J, Ma J, Yu Y, Zhang S, Wang W, Li W, Wang C. A multimodal integration pipeline for accurate diagnosis, pathogen identification, and prognosis prediction of pulmonary infections. Innovation (N Y) 2024; 5:100648. [PMID: 39021525 PMCID: PMC11253137 DOI: 10.1016/j.xinn.2024.100648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 05/19/2024] [Indexed: 07/20/2024] Open
Abstract
Pulmonary infections pose formidable challenges in clinical settings with high mortality rates across all age groups worldwide. Accurate diagnosis and early intervention are crucial to improve patient outcomes. Artificial intelligence (AI) has the capability to mine imaging features specific to different pathogens and fuse multimodal features to reach a synergistic diagnosis, enabling more precise investigation and individualized clinical management. In this study, we successfully developed a multimodal integration (MMI) pipeline to differentiate among bacterial, fungal, and viral pneumonia and pulmonary tuberculosis based on a real-world dataset of 24,107 patients. The area under the curve (AUC) of the MMI system comprising clinical text and computed tomography (CT) image scans yielded 0.910 (95% confidence interval [CI]: 0.904-0.916) and 0.887 (95% CI: 0.867-0.909) in the internal and external testing datasets respectively, which were comparable to those of experienced physicians. Furthermore, the MMI system was utilized to rapidly differentiate between viral subtypes with a mean AUC of 0.822 (95% CI: 0.805-0.837) and bacterial subtypes with a mean AUC of 0.803 (95% CI: 0.775-0.830). Here, the MMI system harbors the potential to guide tailored medication recommendations, thus mitigating the risk of antibiotic misuse. Additionally, the integration of multimodal factors in the AI-driven system also provided an evident advantage in predicting risks of developing critical illness, contributing to more informed clinical decision-making. To revolutionize medical care, embracing multimodal AI tools in pulmonary infections will pave the way to further facilitate early intervention and precise management in the foreseeable future.
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Affiliation(s)
- Jun Shao
- Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, West China School of Medicine, Sichuan University, Chengdu 610041, China
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610213, China
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu 610213, China
| | - Jiechao Ma
- AI Lab, Deepwise Healthcare, Beijing 100080, China
| | - Yizhou Yu
- Department of Computer Science, The University of Hong Kong, Hong Kong SAR, China
| | - Shu Zhang
- AI Lab, Deepwise Healthcare, Beijing 100080, China
| | - Wenyang Wang
- Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, West China School of Medicine, Sichuan University, Chengdu 610041, China
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610213, China
| | - Weimin Li
- Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, West China School of Medicine, Sichuan University, Chengdu 610041, China
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610213, China
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu 610213, China
| | - Chengdi Wang
- Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, West China School of Medicine, Sichuan University, Chengdu 610041, China
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610213, China
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu 610213, China
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30
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Zhang X, Chen R, Huo Z, Li W, Jiang M, Su G, Liu Y, Cai Y, Huang W, Xiong Y, Wang S. Blood-based molecular and cellular biomarkers of early response to neoadjuvant PD-1 blockade in patients with non-small cell lung cancer. Cancer Cell Int 2024; 24:225. [PMID: 38951894 PMCID: PMC11218110 DOI: 10.1186/s12935-024-03412-3] [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: 02/23/2024] [Accepted: 06/22/2024] [Indexed: 07/03/2024] Open
Abstract
BACKGROUND Despite the improved survival observed in PD-1/PD-L1 blockade therapy, a substantial proportion of cancer patients, including those with non-small cell lung cancer (NSCLC), still lack a response. METHODS Transcriptomic profiling was conducted on a discovery cohort comprising 100 whole blood samples, as collected multiple times from 48 healthy controls (including 43 published data) and 31 NSCLC patients that under treatment with a combination of anti-PD-1 Tislelizumab and chemotherapy. Differentially expressed genes (DEGs), simulated immune cell subsets, and germline DNA mutational markers were identified from patients achieved a pathological complete response during the early treatment cycles. The predictive values of mutational markers were further validated in an independent immunotherapy cohort of 1661 subjects, and then confirmed in genetically matched lung cancer cell lines by a co-culturing model. RESULTS The gene expression of hundreds of DEGs (FDR p < 0.05, fold change < -2 or > 2) distinguished responders from healthy controls, indicating the potential to stratify patients utilizing early on-treatment features from blood. PD-1-mediated cell abundance changes in memory CD4 + and regulatory T cell subset were more significant or exclusively observed in responders. A panel of top-ranked genetic alterations showed significant associations with improved survival (p < 0.05) and heightened responsiveness to anti-PD-1 treatment in patient cohort and co-cultured cell lines. CONCLUSION This study discovered and validated peripheral blood-based biomarkers with evident predictive efficacy for early therapy response and patient stratification before treatment for neoadjuvant PD-1 blockade in NSCLC patients.
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Affiliation(s)
- Xi Zhang
- School of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China.
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, 710069, Shaanxi, Xi'an, China.
| | - Rui Chen
- School of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Zirong Huo
- School of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Wenqing Li
- School of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Mengju Jiang
- School of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Guodong Su
- School of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Yuru Liu
- School of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Yu Cai
- School of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Wuhao Huang
- Department of Lung Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, Tianjin, 300060, China
| | - Yuyan Xiong
- School of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, 710069, Shaanxi, Xi'an, China
| | - Shengguang Wang
- Department of Lung Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, Tianjin, 300060, China.
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31
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Lee S, Sun M, Hu Y, Wang Y, Islam MN, Goerlitz D, Lucas PC, Lee AV, Swain SM, Tang G, Wang XS. iGenSig-Rx: an integral genomic signature based white-box tool for modeling cancer therapeutic responses using multi-omics data. BMC Bioinformatics 2024; 25:220. [PMID: 38898383 PMCID: PMC11186173 DOI: 10.1186/s12859-024-05835-1] [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: 05/14/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024] Open
Abstract
Multi-omics sequencing is poised to revolutionize clinical care in the coming decade. However, there is a lack of effective and interpretable genome-wide modeling methods for the rational selection of patients for personalized interventions. To address this, we present iGenSig-Rx, an integral genomic signature-based approach, as a transparent tool for modeling therapeutic response using clinical trial datasets. This method adeptly addresses challenges related to cross-dataset modeling by capitalizing on high-dimensional redundant genomic features, analogous to reinforcing building pillars with redundant steel rods. Moreover, it integrates adaptive penalization of feature redundancy on a per-sample basis to prevent score flattening and mitigate overfitting. We then developed a purpose-built R package to implement this method for modeling clinical trial datasets. When applied to genomic datasets for HER2 targeted therapies, iGenSig-Rx model demonstrates consistent and reliable predictive power across four independent clinical trials. More importantly, the iGenSig-Rx model offers the level of transparency much needed for clinical application, allowing for clear explanations as to how the predictions are produced, how the features contribute to the prediction, and what are the key underlying pathways. We anticipate that iGenSig-Rx, as an interpretable class of multi-omics modeling methods, will find broad applications in big-data based precision oncology. The R package is available: https://github.com/wangxlab/iGenSig-Rx .
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Affiliation(s)
- Sanghoon Lee
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15206, USA
| | - Min Sun
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Yiheng Hu
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Yue Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Md N Islam
- Genomics and Epigenomics Shared Resource (GESR), Georgetown University Medical Center, Washington, DC, 20057, USA
| | - David Goerlitz
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, 20057, USA
| | - Peter C Lucas
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- National Surgical Adjuvant Breast and Bowel Project (NSABP), Pittsburgh, PA, 15213, USA
| | - Adrian V Lee
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Sandra M Swain
- National Surgical Adjuvant Breast and Bowel Project (NSABP), Pittsburgh, PA, 15213, USA
| | - Gong Tang
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- National Surgical Adjuvant Breast and Bowel Project (NSABP), Pittsburgh, PA, 15213, USA
| | - Xiao-Song Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA.
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA.
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15206, USA.
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32
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Cai R, Chen Q, Zhao D, Wang Y, Zhou L, Zhang K, Shan J, Li Z, Chen Y, Zhang H, Feng G, Zhu X, Deng R, Tang J. A High Immune-Related Index with the Suppression of cGAS-STING Pathway is a Key Determinant to Herceptin Resistance in HER2+ Breast Cancer. Int J Biol Sci 2024; 20:3497-3514. [PMID: 38993569 PMCID: PMC11234227 DOI: 10.7150/ijbs.94868] [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: 01/30/2024] [Accepted: 06/10/2024] [Indexed: 07/13/2024] Open
Abstract
Resistance to HER2-targeted therapy is the major cause of treatment failure in patients with HER2+ breast cancer (BC). Given the key role of immune microenvironment in tumor development, there is a lack of an ideal prognostic model that fully accounts for immune infiltration. In this study, WGCNA analysis was performed to discover the relationship between immune-related signaling and prognosis of HER2+ BC. After Herceptin-resistant BC cell lines established, transcriptional profiles of resistant cell line and RNA-sequencing data from GSE76360 cohort were analyzed for candidate genes. 85 samples of HER2+ BC from TCGA database were analyzed by the Cox regression, XGBoost and Lasso algorithm to generalize a credible immune-related prognostic index (IRPI). Correlations between the IRPI signature and tumor microenvironment were further analyzed by multiple algorithms, including single-cell RNA sequencing data analysis. Patients with high IRPI had suppressive tumor immune microenvironment and worse prognosis. The suppression of type I interferon signaling indicated by the IRPI in Herceptin-resistant HER2+ BC was validated. And we elucidated that the suppression of cGAS-STING pathway is the key determinant underlying immune escape in Herceptin-resistant BC with high IRPI. A combination of STING agonist and DS-8201 could serve as a new strategy for Herceptin-resistant HER2+ BC.
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Affiliation(s)
- Ruizhao Cai
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qingshan Chen
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dechang Zhao
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yan Wang
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ling Zhou
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Kaiming Zhang
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jialu Shan
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhiling Li
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yuhong Chen
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Hailiang Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Gongkan Feng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiaofeng Zhu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Rong Deng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jun Tang
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
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Liu Y, Huang J, Chen JC, Chen W, Pan Y, Qiu J. Predicting treatment response in multicenter non-small cell lung cancer patients based on federated learning. BMC Cancer 2024; 24:688. [PMID: 38840081 PMCID: PMC11155008 DOI: 10.1186/s12885-024-12456-7] [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: 04/24/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Multicenter non-small cell lung cancer (NSCLC) patient data is information-rich. However, its direct integration becomes exceptionally challenging due to constraints involving different healthcare organizations and regulations. Traditional centralized machine learning methods require centralizing these sensitive medical data for training, posing risks of patient privacy leakage and data security issues. In this context, federated learning (FL) has attracted much attention as a distributed machine learning framework. It effectively addresses this contradiction by preserving data locally, conducting local model training, and aggregating model parameters. This approach enables the utilization of multicenter data with maximum benefit while ensuring privacy safeguards. Based on pre-radiotherapy planning target volume images of NSCLC patients, a multicenter treatment response prediction model is designed by FL for predicting the probability of remission of NSCLC patients. This approach ensures medical data privacy, high prediction accuracy and computing efficiency, offering valuable insights for clinical decision-making. METHODS We retrospectively collected CT images from 245 NSCLC patients undergoing chemotherapy and radiotherapy (CRT) in four Chinese hospitals. In a simulation environment, we compared the performance of the centralized deep learning (DL) model with that of the FL model using data from two sites. Additionally, due to the unavailability of data from one hospital, we established a real-world FL model using data from three sites. Assessments were conducted using measures such as accuracy, receiver operating characteristic curve, and confusion matrices. RESULTS The model's prediction performance obtained using FL methods outperforms that of traditional centralized learning methods. In the comparative experiment, the DL model achieves an AUC of 0.718/0.695, while the FL model demonstrates an AUC of 0.725/0.689, with real-world FL model achieving an AUC of 0.698/0.672. CONCLUSIONS We demonstrate that the performance of a FL predictive model, developed by combining convolutional neural networks (CNNs) with data from multiple medical centers, is comparable to that of a traditional DL model obtained through centralized training. It can efficiently predict CRT treatment response in NSCLC patients while preserving privacy.
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Affiliation(s)
- Yuan Liu
- School of Radiology, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Jinzao Huang
- Department of Radiology, Cathay General Hospital, Taipei, China
- Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming Chiao- Tung University, Taipei, China
| | - Jyh-Cheng Chen
- Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming Chiao- Tung University, Taipei, China
- Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung, China
| | - Wei Chen
- School of Radiology, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Yuteng Pan
- School of Radiology, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Jianfeng Qiu
- School of Radiology, Second Affiliated Hospital of Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China.
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Wang N, Dong G, Qiao R, Yin X, Lin S. Bringing Artificial Intelligence (AI) into Environmental Toxicology Studies: A Perspective of AI-Enabled Zebrafish High-Throughput Screening. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:9487-9499. [PMID: 38691763 DOI: 10.1021/acs.est.4c00480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
The booming development of artificial intelligence (AI) has brought excitement to many research fields that could benefit from its big data analysis capability for causative relationship establishment and knowledge generation. In toxicology studies using zebrafish, the microscopic images and videos that illustrate the developmental stages, phenotypic morphologies, and animal behaviors possess great potential to facilitate rapid hazard assessment and dissection of the toxicity mechanism of environmental pollutants. However, the traditional manual observation approach is both labor-intensive and time-consuming. In this Perspective, we aim to summarize the current AI-enabled image and video analysis tools to realize the full potential of AI. For image analysis, AI-based tools allow fast and objective determination of morphological features and extraction of quantitative information from images of various sorts. The advantages of providing accurate and reproducible results while avoiding human intervention play a critical role in speeding up the screening process. For video analysis, AI-based tools enable the tracking of dynamic changes in both microscopic cellular events and macroscopic animal behaviors. The subtle changes revealed by video analysis could serve as sensitive indicators of adverse outcomes. With AI-based toxicity analysis in its infancy, exciting developments and applications are expected to appear in the years to come.
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Affiliation(s)
- Nan Wang
- College of Environmental Science and Engineering, Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, Tongji University, Shanghai 200092, People's Republic of China
- Key Laboratory of Yangtze River Water Environment, Ministry of Education; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, People's Republic of China
| | - Gongqing Dong
- College of Environmental Science and Engineering, Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, Tongji University, Shanghai 200092, People's Republic of China
- Key Laboratory of Yangtze River Water Environment, Ministry of Education; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, People's Republic of China
| | - Ruxia Qiao
- College of Environmental Science and Engineering, Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, Tongji University, Shanghai 200092, People's Republic of China
- Key Laboratory of Yangtze River Water Environment, Ministry of Education; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, People's Republic of China
| | - Xiang Yin
- College of Environmental Science and Engineering, Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, Tongji University, Shanghai 200092, People's Republic of China
- Key Laboratory of Yangtze River Water Environment, Ministry of Education; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, People's Republic of China
| | - Sijie Lin
- College of Environmental Science and Engineering, Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, Tongji University, Shanghai 200092, People's Republic of China
- Key Laboratory of Yangtze River Water Environment, Ministry of Education; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, People's Republic of China
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Xiao T, Kong S, Zhang Z, Hua D, Liu F. A review of big data technology and its application in cancer care. Comput Biol Med 2024; 176:108577. [PMID: 38739981 DOI: 10.1016/j.compbiomed.2024.108577] [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: 11/19/2023] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 05/16/2024]
Abstract
The development of modern medical devices and information technology has led to a rapid growth in the amount of data available for health protection information, with the concept of medical big data emerging globally, along with significant advances in cancer care relying on data-driven approaches. However, outstanding issues such as fragmented data governance, low-quality data specification, and data lock-in still make sharing challenging. Big data technology provides solutions for managing massive heterogeneous data while combining artificial intelligence (AI) techniques such as machine learning (ML) and deep learning (DL) to better mine the intrinsic connections between data. This paper surveys and organizes recent articles on big data technology and its applications in cancer, dividing them into three different types to outline their primary content and summarize their critical role in assisting cancer care. It then examines the latest research directions in big data technology in cancer and evaluates the current state of development of each type of application. Finally, current challenges and opportunities are discussed, and recommendations are made for the further integration of big data technology into the medical industry in the future.
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Affiliation(s)
- Tianyun Xiao
- Hebei Key Laboratory of Data Science and Application, North China University of Science and Technology, Tangshan, Hebei, 063210, China; The Key Laboratory of Engineering Computing in Tangshan City, North China University of Science and Technology, Tangshan, Hebei, 063210, China; College of Science, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Shanshan Kong
- College of Science, North China University of Science and Technology, Tangshan, Hebei, 063210, China.
| | - Zichen Zhang
- Hebei Key Laboratory of Data Science and Application, North China University of Science and Technology, Tangshan, Hebei, 063210, China; The Key Laboratory of Engineering Computing in Tangshan City, North China University of Science and Technology, Tangshan, Hebei, 063210, China; College of Science, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Dianbo Hua
- Beijing Sitairui Cancer Data Analysis Joint Laboratory, Beijing, 101149, China
| | - Fengchun Liu
- Hebei Key Laboratory of Data Science and Application, North China University of Science and Technology, Tangshan, Hebei, 063210, China; The Key Laboratory of Engineering Computing in Tangshan City, North China University of Science and Technology, Tangshan, Hebei, 063210, China; College of Science, North China University of Science and Technology, Tangshan, Hebei, 063210, China; Hebei Engineering Research Center for the Intelligentization of Iron Ore Optimization and Ironmaking Raw Materials Preparation Processes, North China University of Science and Technology, Tangshan, Hebei, China; Tangshan Intelligent Industry and Image Processing Technology Innovation Center, North China University of Science and Technology, Tangshan, Hebei, China
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Schlam I, Corti C, Sammons S, Mittendorf EA, Tolaney SM. Checkpoint inhibition for early-stage hormone receptor-positive breast cancer. Expert Opin Biol Ther 2024; 24:511-520. [PMID: 38913933 DOI: 10.1080/14712598.2024.2370395] [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: 04/03/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024]
Abstract
INTRODUCTION Most patients with breast cancer have early-stage hormone receptor (HR)-positive, human epidermal growth factor receptor-2 (HER2)-negative disease. Even though the prognosis for most of these patients is good, there is a need to identify patients at risk for poor outcomes and to develop strategies to mitigate this risk. AREAS COVERED The addition of immunotherapy to standard neoadjuvant chemotherapy represents a promising option for select patients with HR-positive early breast cancer. Three randomized clinical trials have shown favorable results to date. In this review, we discuss the findings of I-SPY2, CheckMate 7FL (NCT04109066), and KEYNOTE-756 (NCT03725059). EXPERT OPINION Despite the promising results of these trials, there are unanswered questions that need to be considered before incorporating neo/adjuvant immunotherapy in the treatment paradigm of early-stage HR-positive breast cancer. One example of an unanswered question is patient selection. Because the regimens used in these protocols are associated with long-term toxicities, identifying the patients who are more likely to derive a benefit from these agents, such as through the use of biomarkers, is critical. A second example is the optimal integration of adjuvant therapies that improve invasive disease-free survival, such as abemaciclib and ribociclib, which are not safely administered concurrently with immunotherapy.
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Affiliation(s)
- Ilana Schlam
- Department of Hematology and Oncology, Tufts Medical Center, Boston, MA, USA
- School of Medicine, Tufts University, Boston, MA, USA
| | - Chiara Corti
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology (DIPO), University of Milan, Milan, Italy
| | - Sarah Sammons
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Elizabeth A Mittendorf
- Breast Oncology Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Sara M Tolaney
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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Wang Z, Lin R, Li Y, Zeng J, Chen Y, Ouyang W, Li H, Jia X, Lai Z, Yu Y, Yao H, Su W. Deep learning-based multi-modal data integration enhancing breast cancer disease-free survival prediction. PRECISION CLINICAL MEDICINE 2024; 7:pbae012. [PMID: 38912415 PMCID: PMC11190375 DOI: 10.1093/pcmedi/pbae012] [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: 02/21/2024] [Revised: 05/19/2024] [Accepted: 05/22/2024] [Indexed: 06/25/2024] Open
Abstract
Background The prognosis of breast cancer is often unfavorable, emphasizing the need for early metastasis risk detection and accurate treatment predictions. This study aimed to develop a novel multi-modal deep learning model using preoperative data to predict disease-free survival (DFS). Methods We retrospectively collected pathology imaging, molecular and clinical data from The Cancer Genome Atlas and one independent institution in China. We developed a novel Deep Learning Clinical Medicine Based Pathological Gene Multi-modal (DeepClinMed-PGM) model for DFS prediction, integrating clinicopathological data with molecular insights. The patients included the training cohort (n = 741), internal validation cohort (n = 184), and external testing cohort (n = 95). Result Integrating multi-modal data into the DeepClinMed-PGM model significantly improved area under the receiver operating characteristic curve (AUC) values. In the training cohort, AUC values for 1-, 3-, and 5-year DFS predictions increased to 0.979, 0.957, and 0.871, while in the external testing cohort, the values reached 0.851, 0.878, and 0.938 for 1-, 2-, and 3-year DFS predictions, respectively. The DeepClinMed-PGM's robust discriminative capabilities were consistently evident across various cohorts, including the training cohort [hazard ratio (HR) 0.027, 95% confidence interval (CI) 0.0016-0.046, P < 0.0001], the internal validation cohort (HR 0.117, 95% CI 0.041-0.334, P < 0.0001), and the external cohort (HR 0.061, 95% CI 0.017-0.218, P < 0.0001). Additionally, the DeepClinMed-PGM model demonstrated C-index values of 0.925, 0.823, and 0.864 within the three cohorts, respectively. Conclusion This study introduces an approach to breast cancer prognosis, integrating imaging and molecular and clinical data for enhanced predictive accuracy, offering promise for personalized treatment strategies.
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Affiliation(s)
- Zehua Wang
- Guangdong Key Laboratory of Cross-Application of Data Science and Technology, Beijing Normal University-Hong Kong Baptist University United International College, Zhuhai 519087, China
| | - Ruichong Lin
- Faculty of Innovation Engineering, Macau University of Science and Technology, Taipa, Macao 999078, China
- Department of Computer and Information Engineering, Guangzhou Huali College, Guangzhou 511325, China
| | - Yanchun Li
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Jin Zeng
- Guangzhou National Laboratory, Guangzhou 510005, China
| | - Yongjian Chen
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm 17177, Sweden
| | - Wenhao Ouyang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Centre, Phase I Clinical Trial Centre, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Han Li
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
| | - Xueyan Jia
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macao 999078, China
| | - Zijia Lai
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Centre, Phase I Clinical Trial Centre, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Yunfang Yu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Centre, Phase I Clinical Trial Centre, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macao 999078, China
| | - Herui Yao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Centre, Phase I Clinical Trial Centre, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Weifeng Su
- Guangdong Key Laboratory of Cross-Application of Data Science and Technology, Beijing Normal University-Hong Kong Baptist University United International College, Zhuhai 519087, China
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Zheng R, Su R, Fan Y, Xing F, Huang K, Yan F, Chen H, Liu B, Fang L, Du Y, Zhou F, Wang D, Feng S. Machine Learning-Based Integrated Multiomics Characterization of Colorectal Cancer Reveals Distinctive Metabolic Signatures. Anal Chem 2024; 96:8772-8781. [PMID: 38743842 DOI: 10.1021/acs.analchem.4c01171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The metabolic signature identification of colorectal cancer is critical for its early diagnosis and therapeutic approaches that will significantly block cancer progression and improve patient survival. Here, we combined an untargeted metabolic analysis strategy based on internal extractive electrospray ionization mass spectrometry and the machine learning approach to analyze metabolites in 173 pairs of cancer samples and matched normal tissue samples to build robust metabolic signature models for diagnostic purposes. Screening and independent validation of metabolic signatures from colorectal cancers via machine learning methods (Logistic Regression_L1 for feature selection and eXtreme Gradient Boosting for classification) was performed to generate a panel of seven signatures with good diagnostic performance (the accuracy of 87.74%, sensitivity of 85.82%, and specificity of 89.66%). Moreover, seven signatures were evaluated according to their ability to distinguish between cancer and normal tissues, with the metabolic molecule PC (30:0) showing good diagnostic performance. In addition, genes associated with PC (30:0) were identified by multiomics analysis (combining metabolic data with transcriptomic data analysis) and our results showed that PC (30:0) could promote the proliferation of colorectal cancer cell SW480, revealing the correlation between genetic changes and metabolic dysregulation in cancer. Overall, our results reveal potential determinants affecting metabolite dysregulation, paving the way for a mechanistic understanding of altered tissue metabolites in colorectal cancer and design interventions for manipulating the levels of circulating metabolites.
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Affiliation(s)
- Ran Zheng
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130021, China
| | - Rui Su
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130021, China
| | - Yusi Fan
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Software, Jilin University, Changchun 130021, China
| | - Fan Xing
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130021, China
| | - Keke Huang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130021, China
| | - Fei Yan
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130021, China
| | - Huanwen Chen
- School of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang 330004, China
| | - Botong Liu
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130021, China
| | - Laiping Fang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130021, China
| | - Yechao Du
- Department of General Surgery Center, First Hospital of Jilin University, 1 Xinmin Street Changchun, Jilin 130012, China
| | - Fengfeng Zhou
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Software, Jilin University, Changchun 130021, China
| | - Daguang Wang
- Department of Gastric Colorectal and Anal Surgery, First Hospital of Jilin University, 1 Xinmin Street Changchun, Jilin 130012, China
| | - Shouhua Feng
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130021, China
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Ivanova M, Pescia C, Trapani D, Venetis K, Frascarelli C, Mane E, Cursano G, Sajjadi E, Scatena C, Cerbelli B, d’Amati G, Porta FM, Guerini-Rocco E, Criscitiello C, Curigliano G, Fusco N. Early Breast Cancer Risk Assessment: Integrating Histopathology with Artificial Intelligence. Cancers (Basel) 2024; 16:1981. [PMID: 38893102 PMCID: PMC11171409 DOI: 10.3390/cancers16111981] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/13/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
Effective risk assessment in early breast cancer is essential for informed clinical decision-making, yet consensus on defining risk categories remains challenging. This paper explores evolving approaches in risk stratification, encompassing histopathological, immunohistochemical, and molecular biomarkers alongside cutting-edge artificial intelligence (AI) techniques. Leveraging machine learning, deep learning, and convolutional neural networks, AI is reshaping predictive algorithms for recurrence risk, thereby revolutionizing diagnostic accuracy and treatment planning. Beyond detection, AI applications extend to histological subtyping, grading, lymph node assessment, and molecular feature identification, fostering personalized therapy decisions. With rising cancer rates, it is crucial to implement AI to accelerate breakthroughs in clinical practice, benefiting both patients and healthcare providers. However, it is important to recognize that while AI offers powerful automation and analysis tools, it lacks the nuanced understanding, clinical context, and ethical considerations inherent to human pathologists in patient care. Hence, the successful integration of AI into clinical practice demands collaborative efforts between medical experts and computational pathologists to optimize patient outcomes.
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Affiliation(s)
- Mariia Ivanova
- Division of Pathology, European Institute of Oncology IRCCS, 20141 Milan, Italy; (M.I.); (C.P.); (K.V.); (C.F.); (E.M.); (G.C.); (E.S.); (F.M.P.); (E.G.-R.)
| | - Carlo Pescia
- Division of Pathology, European Institute of Oncology IRCCS, 20141 Milan, Italy; (M.I.); (C.P.); (K.V.); (C.F.); (E.M.); (G.C.); (E.S.); (F.M.P.); (E.G.-R.)
| | - Dario Trapani
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology IRCCS, 20141 Milan, Italy; (D.T.); (C.C.); (G.C.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Konstantinos Venetis
- Division of Pathology, European Institute of Oncology IRCCS, 20141 Milan, Italy; (M.I.); (C.P.); (K.V.); (C.F.); (E.M.); (G.C.); (E.S.); (F.M.P.); (E.G.-R.)
| | - Chiara Frascarelli
- Division of Pathology, European Institute of Oncology IRCCS, 20141 Milan, Italy; (M.I.); (C.P.); (K.V.); (C.F.); (E.M.); (G.C.); (E.S.); (F.M.P.); (E.G.-R.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Eltjona Mane
- Division of Pathology, European Institute of Oncology IRCCS, 20141 Milan, Italy; (M.I.); (C.P.); (K.V.); (C.F.); (E.M.); (G.C.); (E.S.); (F.M.P.); (E.G.-R.)
| | - Giulia Cursano
- Division of Pathology, European Institute of Oncology IRCCS, 20141 Milan, Italy; (M.I.); (C.P.); (K.V.); (C.F.); (E.M.); (G.C.); (E.S.); (F.M.P.); (E.G.-R.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Elham Sajjadi
- Division of Pathology, European Institute of Oncology IRCCS, 20141 Milan, Italy; (M.I.); (C.P.); (K.V.); (C.F.); (E.M.); (G.C.); (E.S.); (F.M.P.); (E.G.-R.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Cristian Scatena
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy;
| | - Bruna Cerbelli
- Department of Medical-Surgical Sciences and Biotechnologies, Sapienza University of Rome, 00185 Rome, Italy;
| | - Giulia d’Amati
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome, 00185 Rome, Italy;
| | - Francesca Maria Porta
- Division of Pathology, European Institute of Oncology IRCCS, 20141 Milan, Italy; (M.I.); (C.P.); (K.V.); (C.F.); (E.M.); (G.C.); (E.S.); (F.M.P.); (E.G.-R.)
| | - Elena Guerini-Rocco
- Division of Pathology, European Institute of Oncology IRCCS, 20141 Milan, Italy; (M.I.); (C.P.); (K.V.); (C.F.); (E.M.); (G.C.); (E.S.); (F.M.P.); (E.G.-R.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Carmen Criscitiello
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology IRCCS, 20141 Milan, Italy; (D.T.); (C.C.); (G.C.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Giuseppe Curigliano
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology IRCCS, 20141 Milan, Italy; (D.T.); (C.C.); (G.C.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Nicola Fusco
- Division of Pathology, European Institute of Oncology IRCCS, 20141 Milan, Italy; (M.I.); (C.P.); (K.V.); (C.F.); (E.M.); (G.C.); (E.S.); (F.M.P.); (E.G.-R.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
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40
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Rashid MM, Selvarajoo K. Advancing drug-response prediction using multi-modal and -omics machine learning integration (MOMLIN): a case study on breast cancer clinical data. Brief Bioinform 2024; 25:bbae300. [PMID: 38904542 PMCID: PMC11190965 DOI: 10.1093/bib/bbae300] [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: 03/25/2024] [Revised: 05/30/2024] [Accepted: 06/11/2024] [Indexed: 06/22/2024] Open
Abstract
The inherent heterogeneity of cancer contributes to highly variable responses to any anticancer treatments. This underscores the need to first identify precise biomarkers through complex multi-omics datasets that are now available. Although much research has focused on this aspect, identifying biomarkers associated with distinct drug responders still remains a major challenge. Here, we develop MOMLIN, a multi-modal and -omics machine learning integration framework, to enhance drug-response prediction. MOMLIN jointly utilizes sparse correlation algorithms and class-specific feature selection algorithms, which identifies multi-modal and -omics-associated interpretable components. MOMLIN was applied to 147 patients' breast cancer datasets (clinical, mutation, gene expression, tumor microenvironment cells and molecular pathways) to analyze drug-response class predictions for non-responders and variable responders. Notably, MOMLIN achieves an average AUC of 0.989, which is at least 10% greater when compared with current state-of-the-art (data integration analysis for biomarker discovery using latent components, multi-omics factor analysis, sparse canonical correlation analysis). Moreover, MOMLIN not only detects known individual biomarkers such as genes at mutation/expression level, most importantly, it correlates multi-modal and -omics network biomarkers for each response class. For example, an interaction between ER-negative-HMCN1-COL5A1 mutations-FBXO2-CSF3R expression-CD8 emerge as a multimodal biomarker for responders, potentially affecting antimicrobial peptides and FLT3 signaling pathways. In contrast, for resistance cases, a distinct combination of lymph node-TP53 mutation-PON3-ENSG00000261116 lncRNA expression-HLA-E-T-cell exclusions emerged as multimodal biomarkers, possibly impacting neurotransmitter release cycle pathway. MOMLIN, therefore, is expected advance precision medicine, such as to detect context-specific multi-omics network biomarkers and better predict drug-response classifications.
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Affiliation(s)
- Md Mamunur Rashid
- Biomolecular Sequence to Function Division, BII, (ASTAR), Singapore 138671, Republic of Singapore
| | - Kumar Selvarajoo
- Biomolecular Sequence to Function Division, BII, (ASTAR), Singapore 138671, Republic of Singapore
- Synthetic Biology Translational Research Program, Yong Loo Lin School of Medicine, NUS, Singapore 117456, Republic of Singapore
- School of Biological Sciences, Nanyang Technological University (NTU), Singapore 639798, Republic of Singapore
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Devaux Y, Zhang L, Lumley AI, Karaduzovic-Hadziabdic K, Mooser V, Rousseau S, Shoaib M, Satagopam V, Adilovic M, Srivastava PK, Emanueli C, Martelli F, Greco S, Badimon L, Padro T, Lustrek M, Scholz M, Rosolowski M, Jordan M, Brandenburger T, Benczik B, Agg B, Ferdinandy P, Vehreschild JJ, Lorenz-Depiereux B, Dörr M, Witzke O, Sanchez G, Kul S, Baker AH, Fagherazzi G, Ollert M, Wereski R, Mills NL, Firat H. Development of a long noncoding RNA-based machine learning model to predict COVID-19 in-hospital mortality. Nat Commun 2024; 15:4259. [PMID: 38769334 PMCID: PMC11106268 DOI: 10.1038/s41467-024-47557-1] [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: 12/11/2023] [Accepted: 04/03/2024] [Indexed: 05/22/2024] Open
Abstract
Tools for predicting COVID-19 outcomes enable personalized healthcare, potentially easing the disease burden. This collaborative study by 15 institutions across Europe aimed to develop a machine learning model for predicting the risk of in-hospital mortality post-SARS-CoV-2 infection. Blood samples and clinical data from 1286 COVID-19 patients collected from 2020 to 2023 across four cohorts in Europe and Canada were analyzed, with 2906 long non-coding RNAs profiled using targeted sequencing. From a discovery cohort combining three European cohorts and 804 patients, age and the long non-coding RNA LEF1-AS1 were identified as predictive features, yielding an AUC of 0.83 (95% CI 0.82-0.84) and a balanced accuracy of 0.78 (95% CI 0.77-0.79) with a feedforward neural network classifier. Validation in an independent Canadian cohort of 482 patients showed consistent performance. Cox regression analysis indicated that higher levels of LEF1-AS1 correlated with reduced mortality risk (age-adjusted hazard ratio 0.54, 95% CI 0.40-0.74). Quantitative PCR validated LEF1-AS1's adaptability to be measured in hospital settings. Here, we demonstrate a promising predictive model for enhancing COVID-19 patient management.
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Affiliation(s)
- Yvan Devaux
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg.
| | - Lu Zhang
- Bioinformatics Platform, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Andrew I Lumley
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg
| | | | - Vincent Mooser
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Simon Rousseau
- The Meakins-Christie Laboratories at the Research Institute of the McGill University Heath Centre Research Institute, & Department of Medicine, Faculty of Medicine, McGill University, Montréal, QC, Canada
| | - Muhammad Shoaib
- Luxembourg Center for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg
| | - Venkata Satagopam
- Luxembourg Center for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg
| | - Muhamed Adilovic
- Faculty of Engineering and Natural Sciences, International University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | | | - Costanza Emanueli
- National Heart and Lung Institute, Imperial College London, London, England, UK
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Milan, Italy
| | - Simona Greco
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Milan, Italy
| | - Lina Badimon
- Cardiovascular Program-ICCC, Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU); CIBERCV, Autonomous University of Barcelona, Barcelona, Spain
| | - Teresa Padro
- Cardiovascular Program-ICCC, Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU); CIBERCV, Autonomous University of Barcelona, Barcelona, Spain
| | - Mitja Lustrek
- Department of Intelligent Systems, Jozef Stefan Institute, Ljubljana, Slovenia
| | - Markus Scholz
- Group Genetical Statistics and Biomathematical Modelling, Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Maciej Rosolowski
- Group Genetical Statistics and Biomathematical Modelling, Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Marko Jordan
- Department of Intelligent Systems, Jozef Stefan Institute, Ljubljana, Slovenia
| | | | - Bettina Benczik
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary; Pharmahungary Group, Szeged, Hungary
| | - Bence Agg
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary; Pharmahungary Group, Szeged, Hungary
| | - Peter Ferdinandy
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary; Pharmahungary Group, Szeged, Hungary
| | - Jörg Janne Vehreschild
- Medical Department 2 (Hematology/Oncology and Infectious Diseases), Center for Internal Medicine, Goethe University Frankfurt, University Hospital, Frankfurt, Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Cologne, Germany
- German Centre for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | | | - Marcus Dörr
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany; German Centre of Cardiovascular Research (DZHK), Greifswald, Germany
| | - Oliver Witzke
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | | | | | - Andy H Baker
- Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, Scotland
- CARIM Institute and Department of Pathology, University of Maastricht, Maastricht, The Netherlands
| | - Guy Fagherazzi
- Deep Digital Phenotyping Research Unit, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Markus Ollert
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-Sur-Alzette, Luxembourg
- Department of Dermatology and Allergy Center, Odense Research Center for Anaphylaxis (ORCA), University of Southern Denmark, Odense, Denmark
| | - Ryan Wereski
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
| | - Nicholas L Mills
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
- Usher Institute, University of Edinburgh, Edinburgh, UK
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Blise KE, Sivagnanam S, Betts CB, Betre K, Kirchberger N, Tate BJ, Furth EE, Dias Costa A, Nowak JA, Wolpin BM, Vonderheide RH, Goecks J, Coussens LM, Byrne KT. Machine Learning Links T-cell Function and Spatial Localization to Neoadjuvant Immunotherapy and Clinical Outcome in Pancreatic Cancer. Cancer Immunol Res 2024; 12:544-558. [PMID: 38381401 PMCID: PMC11065586 DOI: 10.1158/2326-6066.cir-23-0873] [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: 10/24/2023] [Revised: 01/12/2024] [Accepted: 02/19/2024] [Indexed: 02/22/2024]
Abstract
Tumor molecular data sets are becoming increasingly complex, making it nearly impossible for humans alone to effectively analyze them. Here, we demonstrate the power of using machine learning (ML) to analyze a single-cell, spatial, and highly multiplexed proteomic data set from human pancreatic cancer and reveal underlying biological mechanisms that may contribute to clinical outcomes. We designed a multiplex immunohistochemistry antibody panel to compare T-cell functionality and spatial localization in resected tumors from treatment-naïve patients with localized pancreatic ductal adenocarcinoma (PDAC) with resected tumors from a second cohort of patients treated with neoadjuvant agonistic CD40 (anti-CD40) monoclonal antibody therapy. In total, nearly 2.5 million cells from 306 tissue regions collected from 29 patients across both cohorts were assayed, and over 1,000 tumor microenvironment (TME) features were quantified. We then trained ML models to accurately predict anti-CD40 treatment status and disease-free survival (DFS) following anti-CD40 therapy based on TME features. Through downstream interpretation of the ML models' predictions, we found anti-CD40 therapy reduced canonical aspects of T-cell exhaustion within the TME, as compared with treatment-naïve TMEs. Using automated clustering approaches, we found improved DFS following anti-CD40 therapy correlated with an increased presence of CD44+CD4+ Th1 cells located specifically within cellular neighborhoods characterized by increased T-cell proliferation, antigen experience, and cytotoxicity in immune aggregates. Overall, our results demonstrate the utility of ML in molecular cancer immunology applications, highlight the impact of anti-CD40 therapy on T cells within the TME, and identify potential candidate biomarkers of DFS for anti-CD40-treated patients with PDAC.
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Affiliation(s)
- Katie E. Blise
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR USA
- The Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
| | - Shamilene Sivagnanam
- The Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR USA
| | - Courtney B. Betts
- The Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR USA
- Current affiliation: Akoya Biosciences, 100 Campus Drive, 6 Floor, Marlborough, MA USA
| | - Konjit Betre
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR USA
| | - Nell Kirchberger
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR USA
| | - Benjamin J. Tate
- The Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
- Immune Monitoring and Cancer Omics Services, Oregon Health & Science University, Portland, OR USA
| | - Emma E. Furth
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Andressa Dias Costa
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA USA
| | - Jonathan A. Nowak
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA USA
| | - Brian M. Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA USA
| | - Robert H. Vonderheide
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Jeremy Goecks
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR USA
- The Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
- Current affiliation: Department of Machine Learning, H. Lee Moffitt Cancer Center, Tampa, FL USA
- Current affiliation: Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL USA
| | - Lisa M. Coussens
- The Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR USA
| | - Katelyn T. Byrne
- The Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR USA
- Lead contact: Katelyn T. Byrne, Department of Cell, Developmental and Cancer Biology, RLSB 6N032 Mail Code CL6C, 2730 S. Moody Ave, Portland, OR 97201
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Chen HY, Pan Y, Chen JY, Chen J, Liu LL, Yang YB, Li K, Ma Q, Shi L, Yu RS, Shao GL. Machine Learning Methods Based on CT Features Differentiate G1/G2 From G3 Pancreatic Neuroendocrine Tumors. Acad Radiol 2024; 31:1898-1905. [PMID: 38052672 DOI: 10.1016/j.acra.2023.10.040] [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: 08/05/2023] [Revised: 10/16/2023] [Accepted: 10/23/2023] [Indexed: 12/07/2023]
Abstract
RATIONALE AND OBJECTIVES To identify CT features for distinguishing grade 1 (G1)/grade 2 (G2) from grade 3 (G3) pancreatic neuroendocrine tumors (PNETs) using different machine learning (ML) methods. MATERIALS AND METHODS A total of 147 patients with 155 lesions confirmed by pathology were retrospectively included. Clinical-demographic and radiological CT features was collected. The entire cohort was separated into training and validation groups at a 7:3 ratio. Least absolute shrinkage and selection operator (LASSO) algorithm and principal component analysis (PCA) were used to select features. Three ML methods, namely logistic regression (LR), support vector machine (SVM), and K-nearest neighbor (KNN) were used to build a differential model. Receiver operating characteristic (ROC) curves and precision-recall curves for each ML method were generated. The area under the curve (AUC), accuracy rate, sensitivity, and specificity were calculated. RESULTS G3 PNETs were more likely to present with invasive behaviors and lower enhancement than G1/G2 PNETs. The LR classifier yielded the highest AUC of 0.964 (95% confidence interval [CI]: 0.930, 0.972), with 95.4% accuracy rate, 95.7% sensitivity, and 92.9% specificity, followed by SVM (AUC: 0.957) and KNN (AUC: 0.893) in the training group. In the validation group, the SVM classier reached the highest AUC of 0.952 (95% CI: 0.860, 0.981), with 91.5% accuracy rate, 97.3% sensitivity, and 70% specificity, followed by LR (AUC: 0.949) and KNN (AUC: 0.923). CONCLUSIONS The LR and SVM classifiers had the best performance in the training group and validation group, respectively. ML method could be helpful in differentiating between G1/G2 and G3 PNETs.
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Affiliation(s)
- Hai-Yan Chen
- Department of Radiology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China (H.-Y.C., J.-Y.C., L.-L.L., Y.-B.Y., K.L., Q.M., L.S.)
| | - Yao Pan
- Department of Radiology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang, China (Y.P., R.-S.Y.)
| | - Jie-Yu Chen
- Department of Radiology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China (H.-Y.C., J.-Y.C., L.-L.L., Y.-B.Y., K.L., Q.M., L.S.)
| | - Jia Chen
- Research Center for Healthcare Data Science, Zhejiang Lab, Hangzhou 311121, Zhejiang Province, China (J.C.)
| | - Lu-Lu Liu
- Department of Radiology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China (H.-Y.C., J.-Y.C., L.-L.L., Y.-B.Y., K.L., Q.M., L.S.)
| | - Yong-Bo Yang
- Department of Radiology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China (H.-Y.C., J.-Y.C., L.-L.L., Y.-B.Y., K.L., Q.M., L.S.)
| | - Kai Li
- Department of Radiology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China (H.-Y.C., J.-Y.C., L.-L.L., Y.-B.Y., K.L., Q.M., L.S.)
| | - Qian Ma
- Department of Radiology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China (H.-Y.C., J.-Y.C., L.-L.L., Y.-B.Y., K.L., Q.M., L.S.)
| | - Lei Shi
- Department of Radiology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China (H.-Y.C., J.-Y.C., L.-L.L., Y.-B.Y., K.L., Q.M., L.S.)
| | - Ri-Sheng Yu
- Department of Radiology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang, China (Y.P., R.-S.Y.)
| | - Guo-Liang Shao
- Department of Interventional Radiology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang Province, China (G.-L.S.); Clinical Research Center of Hepatobiliary and pancreatic diseases of Zhejiang Province, Hangzhou 310006, Zhejiang Province, China (G.-L.S.).
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Sammut SJ, Galson JD, Minter R, Sun B, Chin SF, De Mattos-Arruda L, Finch DK, Schätzle S, Dias J, Rueda OM, Seoane J, Osbourn J, Caldas C, Bashford-Rogers RJM. Predictability of B cell clonal persistence and immunosurveillance in breast cancer. Nat Immunol 2024; 25:916-924. [PMID: 38698238 PMCID: PMC11065701 DOI: 10.1038/s41590-024-01821-0] [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: 02/20/2024] [Accepted: 03/15/2024] [Indexed: 05/05/2024]
Abstract
B cells and T cells are important components of the adaptive immune system and mediate anticancer immunity. The T cell landscape in cancer is well characterized, but the contribution of B cells to anticancer immunosurveillance is less well explored. Here we show an integrative analysis of the B cell and T cell receptor repertoire from individuals with metastatic breast cancer and individuals with early breast cancer during neoadjuvant therapy. Using immune receptor, RNA and whole-exome sequencing, we show that both B cell and T cell responses seem to coevolve with the metastatic cancer genomes and mirror tumor mutational and neoantigen architecture. B cell clones associated with metastatic immunosurveillance and temporal persistence were more expanded and distinct from site-specific clones. B cell clonal immunosurveillance and temporal persistence are predictable from the clonal structure, with higher-centrality B cell antigen receptors more likely to be detected across multiple metastases or across time. This predictability was generalizable across other immune-mediated disorders. This work lays a foundation for prioritizing antibody sequences for therapeutic targeting in cancer.
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MESH Headings
- Humans
- Female
- Breast Neoplasms/immunology
- B-Lymphocytes/immunology
- Immunologic Surveillance
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, B-Cell/metabolism
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/immunology
- T-Lymphocytes/immunology
- Monitoring, Immunologic
- Exome Sequencing
- Antigens, Neoplasm/immunology
- Neoplasm Metastasis
- Clone Cells
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Affiliation(s)
- Stephen-John Sammut
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
- The Royal Marsden Hospital NHS Foundation Trust, London, UK.
| | | | | | - Bo Sun
- Wellcome Centre for Human Genetics, Oxford, UK
- Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, UK
| | - Suet-Feung Chin
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Leticia De Mattos-Arruda
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | | | | | | | - Oscar M Rueda
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Joan Seoane
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Institució Catalana de Recerca i Estudis Avançats (ICREA), Universitat Autònoma de Barcelona (UAB), CIBERONC, Barcelona, Spain
| | | | - Carlos Caldas
- School of Clinical Medicine, University of Cambridge, Cambridge, UK.
| | - Rachael J M Bashford-Rogers
- Wellcome Centre for Human Genetics, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
- Oxford Cancer Centre, Oxford, UK.
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45
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Eisenstein M. AI assistance for planning cancer treatment. Nature 2024; 629:S14-S16. [PMID: 38811703 DOI: 10.1038/d41586-024-01431-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
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46
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Rosano D, Sofyali E, Dhiman H, Ghirardi C, Ivanoiu D, Heide T, Vingiani A, Bertolotti A, Pruneri G, Canale E, Dewhurst HF, Saha D, Slaven N, Barozzi I, Li T, Zemlyanskiy G, Phillips H, James C, Győrffy B, Lynn C, Cresswell GD, Rehman F, Noberini R, Bonaldi T, Sottoriva A, Magnani L. Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells. Cancer Discov 2024; 14:866-889. [PMID: 38527495 PMCID: PMC11061610 DOI: 10.1158/2159-8290.cd-23-1161] [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] [Received: 10/05/2023] [Revised: 01/10/2024] [Accepted: 02/20/2024] [Indexed: 03/27/2024]
Abstract
Patients with estrogen receptor-positive breast cancer receive adjuvant endocrine therapies (ET) that delay relapse by targeting clinically undetectable micrometastatic deposits. Yet, up to 50% of patients relapse even decades after surgery through unknown mechanisms likely involving dormancy. To investigate genetic and transcriptional changes underlying tumor awakening, we analyzed late relapse patients and longitudinally profiled a rare cohort treated with long-term neoadjuvant ETs until progression. Next, we developed an in vitro evolutionary study to record the adaptive strategies of individual lineages in unperturbed parallel experiments. Our data demonstrate that ETs induce nongenetic cell state transitions into dormancy in a stochastic subset of cells via epigenetic reprogramming. Single lineages with divergent phenotypes awaken unpredictably in the absence of recurrent genetic alterations. Targeting the dormant epigenome shows promising activity against adapting cancer cells. Overall, this study uncovers the contribution of epigenetic adaptation to the evolution of resistance to ETs. SIGNIFICANCE This study advances the understanding of therapy-induced dormancy with potential clinical implications for breast cancer. Estrogen receptor-positive breast cancer cells adapt to endocrine treatment by entering a dormant state characterized by strong heterochromatinization with no recurrent genetic changes. Targeting the epigenetic rewiring impairs the adaptation of cancer cells to ETs. See related commentary by Llinas-Bertran et al., p. 704. This article is featured in Selected Articles from This Issue, p. 695.
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Affiliation(s)
- Dalia Rosano
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Center, The Institute of Cancer Research, London, United Kingdom
| | - Emre Sofyali
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Heena Dhiman
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Center, The Institute of Cancer Research, London, United Kingdom
| | - Chiara Ghirardi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Diana Ivanoiu
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Timon Heide
- Human Technopole, Milan, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | | | | | - Giancarlo Pruneri
- Istituto Nazionale Tumori, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milano, Milano, Italy
| | - Eleonora Canale
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Hannah F. Dewhurst
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Debjani Saha
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Neil Slaven
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Centre for Cancer Research, Medical University of Vienna, Austria
| | - Tong Li
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Grigory Zemlyanskiy
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Henry Phillips
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Chela James
- Human Technopole, Milan, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
- RCNS Cancer Biomarker Research Group, Budapest, Hungary
- Department of Biophysics, Medical School, University of Pecs, Pecs, Hungary
| | - Claire Lynn
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - George D. Cresswell
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - Farah Rehman
- Charing Cross Hospital, Imperial College NHS Trust, London, United Kingdom
| | - Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milano, Milano, Italy
| | - Andrea Sottoriva
- Human Technopole, Milan, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Center, The Institute of Cancer Research, London, United Kingdom
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47
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Su MC, Lee AM, Zhang W, Maeser D, Gruener RF, Deng Y, Huang RS. Computational Modeling to Identify Drugs Targeting Metastatic Castration-Resistant Prostate Cancer Characterized by Heightened Glycolysis. Pharmaceuticals (Basel) 2024; 17:569. [PMID: 38794139 PMCID: PMC11124089 DOI: 10.3390/ph17050569] [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: 03/29/2024] [Revised: 04/22/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
Metastatic castration-resistant prostate cancer (mCRPC) remains a deadly disease due to a lack of efficacious treatments. The reprogramming of cancer metabolism toward elevated glycolysis is a hallmark of mCRPC. Our goal is to identify therapeutics specifically associated with high glycolysis. Here, we established a computational framework to identify new pharmacological agents for mCRPC with heightened glycolysis activity under a tumor microenvironment, followed by in vitro validation. First, using our established computational tool, OncoPredict, we imputed the likelihood of drug responses to approximately 1900 agents in each mCRPC tumor from two large clinical patient cohorts. We selected drugs with predicted sensitivity highly correlated with glycolysis scores. In total, 77 drugs predicted to be more sensitive in high glycolysis mCRPC tumors were identified. These drugs represent diverse mechanisms of action. Three of the candidates, ivermectin, CNF2024, and P276-00, were selected for subsequent vitro validation based on the highest measured drug responses associated with glycolysis/OXPHOS in pan-cancer cell lines. By decreasing the input glucose level in culture media to mimic the mCRPC tumor microenvironments, we induced a high-glycolysis condition in PC3 cells and validated the projected higher sensitivity of all three drugs under this condition (p < 0.0001 for all drugs). For biomarker discovery, ivermectin and P276-00 were predicted to be more sensitive to mCRPC tumors with low androgen receptor activities and high glycolysis activities (AR(low)Gly(high)). In addition, we integrated a protein-protein interaction network and topological methods to identify biomarkers for these drug candidates. EEF1B2 and CCNA2 were identified as key biomarkers for ivermectin and CNF2024, respectively, through multiple independent biomarker nomination pipelines. In conclusion, this study offers new efficacious therapeutics beyond traditional androgen-deprivation therapies by precisely targeting mCRPC with high glycolysis.
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Affiliation(s)
- Mei-Chi Su
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA; (M.-C.S.); (A.M.L.); (R.F.G.)
| | - Adam M. Lee
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA; (M.-C.S.); (A.M.L.); (R.F.G.)
| | - Weijie Zhang
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455, USA; (W.Z.); (D.M.)
| | - Danielle Maeser
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455, USA; (W.Z.); (D.M.)
| | - Robert F. Gruener
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA; (M.-C.S.); (A.M.L.); (R.F.G.)
| | - Yibin Deng
- Department of Urology, Masonic Cancer Center, University of Minnesota Medical School, Minneapolis, MN 55455, USA;
| | - R. Stephanie Huang
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA; (M.-C.S.); (A.M.L.); (R.F.G.)
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455, USA; (W.Z.); (D.M.)
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48
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Yoneyama M, Zormpas-Petridis K, Robinson R, Sobhani F, Provenzano E, Steel H, Lightowlers S, Towns C, Castillo SP, Anbalagan S, Lund T, Wennerberg E, Melcher A, Coles CE, Roxanis I, Yuan Y, Somaiah N. Longitudinal Assessment of Tumor-Infiltrating Lymphocytes in Primary Breast Cancer Following Neoadjuvant Radiation Therapy. Int J Radiat Oncol Biol Phys 2024:S0360-3016(24)00566-2. [PMID: 38677525 DOI: 10.1016/j.ijrobp.2024.04.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 04/16/2024] [Accepted: 04/21/2024] [Indexed: 04/29/2024]
Abstract
PURPOSE Tumor-infiltrating lymphocytes (TILs) have prognostic significance in several cancers, including breast cancer. Despite interest in combining radiation therapy with immunotherapy, little is known about the effect of radiation therapy itself on the tumor-immune microenvironment, including TILs. Here, we interrogated longitudinal dynamics of TILs and systemic lymphocytes in patient samples taken before, during, and after neoadjuvant radiation therapy (NART) from PRADA and Neo-RT breast clinical trials. METHODS AND MATERIALS We manually scored stromal TILs (sTILs) from longitudinal tumor samples using standardized guidelines as well as deep learning-based scores at cell-level (cTIL) and cell- and tissue-level combination analyses (SuperTIL). In parallel, we interrogated absolute lymphocyte counts from routine blood tests at corresponding time points during treatment. Exploratory analyses studied the relationship between TILs and pathologic complete response (pCR) and long-term outcomes. RESULTS Patients receiving NART experienced a significant and uniform decrease in sTILs that did not recover at the time of surgery (P < .0001). This lymphodepletive effect was also mirrored in peripheral blood. Our SuperTIL deep learning score showed good concordance with manual sTILs and importantly performed comparably to manual scores in predicting pCR from diagnostic biopsies. The analysis suggested an association between baseline sTILs and pCR, as well as sTILs at surgery and relapse, in patients receiving NART. CONCLUSIONS This study provides novel insights into TIL dynamics in the context of NART in breast cancer and demonstrates the potential for artificial intelligence to assist routine pathology. We have identified trends that warrant further interrogation and have a bearing on future radioimmunotherapy trials.
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Affiliation(s)
- Miki Yoneyama
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, United Kingdom
| | - Konstantinos Zormpas-Petridis
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, United Kingdom; Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Ruth Robinson
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, United Kingdom; The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Faranak Sobhani
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Elena Provenzano
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Harriet Steel
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, United Kingdom
| | - Sara Lightowlers
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom; Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Catherine Towns
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Simon P Castillo
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Selvakumar Anbalagan
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, United Kingdom
| | - Tom Lund
- Integrated Pathology Unit, The Institute of Cancer Research and The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Erik Wennerberg
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, United Kingdom
| | - Alan Melcher
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, United Kingdom
| | - Charlotte E Coles
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom; Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Ioannis Roxanis
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Yinyin Yuan
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom.
| | - Navita Somaiah
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, United Kingdom; The Royal Marsden NHS Foundation Trust, London, United Kingdom.
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49
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Tang M, Jiang S, Huang X, Ji C, Gu Y, Qi Y, Xiang Y, Yao E, Zhang N, Berman E, Yu D, Qu Y, Liu L, Berry D, Yao Y. Integration of 3D bioprinting and multi-algorithm machine learning identified glioma susceptibilities and microenvironment characteristics. Cell Discov 2024; 10:39. [PMID: 38594259 PMCID: PMC11003988 DOI: 10.1038/s41421-024-00650-7] [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: 06/27/2023] [Accepted: 01/18/2024] [Indexed: 04/11/2024] Open
Abstract
Glioma, with its heterogeneous microenvironments and genetic subtypes, presents substantial challenges for treatment prediction and development. We integrated 3D bioprinting and multi-algorithm machine learning as a novel approach to enhance the assessment and understanding of glioma treatment responses and microenvironment characteristics. The bioprinted patient-derived glioma tissues successfully recapitulated molecular properties and drug responses of native tumors. We then developed GlioML, a machine learning workflow incorporating nine distinct algorithms and a weighted ensemble model that generated robust gene expression-based predictors, each reflecting the diverse action mechanisms of various compounds and drugs. The ensemble model superseded the performance of all individual algorithms across diverse in vitro systems, including sphere cultures, complex 3D bioprinted multicellular models, and 3D patient-derived tissues. By integrating bioprinting, the evaluative scope of the treatment expanded to T cell-related therapy and anti-angiogenesis targeted therapy. We identified promising compounds and drugs for glioma treatment and revealed distinct immunosuppressive or angiogenic myeloid-infiltrated tumor microenvironments. These insights pave the way for enhanced therapeutic development for glioma and potentially for other cancers, highlighting the broad application potential of this integrative and translational approach.
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Affiliation(s)
- Min Tang
- Shanghai University of Traditional Chinese Medicine, Shanghai, China.
- Department of NanoEngineering, University of California San Diego, La Jolla, CA, USA.
| | - Shan Jiang
- Department of Statistics, University of California Davis, Davis, CA, USA
| | - Xiaoming Huang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- National Center for Neurological Disorders, Shanghai, China
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai, China
- Immunology Laboratory, Neurosurgical Institute of Fudan University, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China
| | - Chunxia Ji
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- National Center for Neurological Disorders, Shanghai, China
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai, China
- Immunology Laboratory, Neurosurgical Institute of Fudan University, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China
| | - Yexin Gu
- Cyberiad Biotechnology Ltd., Shanghai, China
| | - Ying Qi
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- National Center for Neurological Disorders, Shanghai, China
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai, China
- Immunology Laboratory, Neurosurgical Institute of Fudan University, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China
| | - Yi Xiang
- Department of NanoEngineering, University of California San Diego, La Jolla, CA, USA
| | - Emmie Yao
- Department of NanoEngineering, University of California San Diego, La Jolla, CA, USA
| | - Nancy Zhang
- Department of Human Biology, University of California San Diego, La Jolla, CA, USA
| | - Emma Berman
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Di Yu
- Department of Human Biology, University of California San Diego, La Jolla, CA, USA
| | - Yunjia Qu
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Longwei Liu
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - David Berry
- Department of NanoEngineering, University of California San Diego, La Jolla, CA, USA
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, USA
| | - Yu Yao
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
- National Center for Neurological Disorders, Shanghai, China.
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai, China.
- Immunology Laboratory, Neurosurgical Institute of Fudan University, Shanghai, China.
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China.
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50
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Zhang W, Mou M, Hu W, Lu M, Zhang H, Zhang H, Luo Y, Xu H, Tao L, Dai H, Gao J, Zhu F. MOINER: A Novel Multiomics Early Integration Framework for Biomedical Classification and Biomarker Discovery. J Chem Inf Model 2024; 64:2720-2732. [PMID: 38373720 DOI: 10.1021/acs.jcim.4c00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
In the context of precision medicine, multiomics data integration provides a comprehensive understanding of underlying biological processes and is critical for disease diagnosis and biomarker discovery. One commonly used integration method is early integration through concatenation of multiple dimensionally reduced omics matrices due to its simplicity and ease of implementation. However, this approach is seriously limited by information loss and lack of latent feature interaction. Herein, a novel multiomics early integration framework (MOINER) based on information enhancement and image representation learning is thus presented to address the challenges. MOINER employs the self-attention mechanism to capture the intrinsic correlations of omics-features, which make it significantly outperform the existing state-of-the-art methods for multiomics data integration. Moreover, visualizing the attention embedding and identifying potential biomarkers offer interpretable insights into the prediction results. All source codes and model for MOINER are freely available https://github.com/idrblab/MOINER.
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Affiliation(s)
- Wei Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Wei Hu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Mingkun Lu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Hanyu Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Hongning Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Hongquan Xu
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Lin Tao
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Haibin Dai
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jianqing Gao
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
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