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Song P, Tian Y, Chen S, Zhang S, Li X, You Z, Fu J, Xu W, Li Z, Luan J, Zhao Q, Wang C, Pang F. A novel method for simultaneous detection of hematological tumors and infectious pathogens by metagenomic next generation sequencing of plasma. Clin Chim Acta 2024; 557:117874. [PMID: 38484907 DOI: 10.1016/j.cca.2024.117874] [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: 11/24/2023] [Revised: 02/23/2024] [Accepted: 03/11/2024] [Indexed: 03/21/2024]
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) is valuable for pathogen identification; however, distinguishing between infectious diseases and conditions with potentially similar clinical manifestations, including malignant tumors, is challenging. Therefore, we developed a method for simultaneous detection of infectious pathogens and cancer in blood samples. METHODS Plasma samples (n = 244) were collected from 150 and 94 patients with infections and hematological malignancies, respectively, and analyzed by mNGS for pathogen detection, alongside human tumor chromosomal copy number variation (CNV) analysis (≥5Mbp or 10Mbp CNV region). Further, an evaluation set, comprising 87 plasma samples, was analyzed by mNGS and human CNV analysis, to validate the feasibility of the method. RESULTS Among 94 patients with hematological malignancy, sensitivity values of CNV detection for tumor diagnosis were 69.15 % and 32.98 % for CNV region 5Mbp and 10Mbp, respectively, with corresponding specificities of 92.62 % and 100 % in the infection group. Area under the ROC curve (AUC) values for 5Mbp and 10Mbp region were 0.825 and 0.665, respectively, which was a significant difference of 0.160 (95 % CI: 0.110-0.210; p < 0.001), highlighting the superiority of 5Mbp output region data. Six patients with high-risk CNV results were identified in the validation study: three with history of tumor treatment, two eventually newly-diagnosed with hematological malignancies, and one with indeterminate final diagnosis. CONCLUSIONS Concurrent CNV analysis alongside mNGS for infection diagnosis is promising for detecting malignant tumors. We recommend adopting a CNV region of 10Mbp over 5Mbp for our model, because of the lower false-positive rate (FPR).
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Affiliation(s)
- Pingping Song
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China
| | - Yaxian Tian
- Department of Central Laboratory, Liaocheng People's Hospital, Liaocheng, China
| | - Shuai Chen
- Department of Clinical Laboratory, Liaocheng Third People's Hospital, Liaocheng, China
| | - Sheng Zhang
- Department of Pathology, Liaocheng Third People's Hospital, Liaocheng, China
| | - Xuan Li
- The Key Laboratory of Molecular Pharmacology, Liaocheng People's Hospital, Liaocheng, China
| | - Zhiqing You
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China
| | - Juanjuan Fu
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China
| | - Wenbin Xu
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China
| | - Zhen Li
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China
| | - Jing Luan
- Department of Hematology, Liaocheng People's Hospital, Liaocheng, China
| | - Qigang Zhao
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China
| | - Chengtan Wang
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China.
| | - Feng Pang
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China.
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Sánchez S, Juárez U, Domínguez J, Molina B, Barrientos R, Martínez-Hernández A, Carnevale A, Grether-González P, Mayen DG, Villarroel C, Lieberman E, Yokoyama E, Del Castillo V, Torres L, Frias S. Frequent copy number variants in a cohort of Mexican-Mestizo individuals. Mol Cytogenet 2023; 16:2. [PMID: 36631885 PMCID: PMC9835318 DOI: 10.1186/s13039-022-00631-z] [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: 11/01/2022] [Accepted: 12/13/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The human genome presents variation at distinct levels, copy number variants (CNVs) are DNA segments of variable lengths that range from several base pairs to megabases and are present at a variable number of copies in human genomes. Common CNVs have no apparent influence on the phenotype; however, some rare CNVs have been associated with phenotypic traits, depending on their size and gene content. CNVs are detected by microarrays of different densities and are generally visualized, and their frequencies analysed using the HapMap as default reference population. Nevertheless, this default reference is inadequate when the samples analysed are from people from Mexico, since population with a Hispanic genetic background are minimally represented. In this work, we describe the variation in the frequencies of four common CNVs in Mexican-Mestizo individuals. RESULTS In a cohort of 147 unrelated Mexican-Mestizo individuals, we found that the common CNVs 2p11.2 (99.6%), 8p11.22 (54.5%), 14q32.33 (100%), and 15q11.2 (71.1%) appeared with unexpectedly high frequencies when contrasted with the HapMap reference (ChAS). Yet, while when comparing to an ethnically related reference population, these differences were significantly reduced or even disappeared. CONCLUSION The findings in this work contribute to (1) a better description of the CNVs characteristics of the Mexican Mestizo population and enhance the knowledge of genome variation in different ethnic groups. (2) emphasize the importance of contrasting CNVs identified in studied individuals against a reference group that-as best as possible-share the same ethnicity while keeping this relevant information in mind when conducting CNV studies at the population or clinical level.
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Affiliation(s)
- Silvia Sánchez
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México ,grid.9486.30000 0001 2159 0001Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ulises Juárez
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México
| | - Julieta Domínguez
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México
| | - Bertha Molina
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México
| | - Rehotbevely Barrientos
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México
| | - Angélica Martínez-Hernández
- grid.452651.10000 0004 0627 7633Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica, Ciudad de Mexico, México
| | - Alessandra Carnevale
- grid.452651.10000 0004 0627 7633Laboratorio de Enfermedades Mendelianas, Instituto Nacional de Medicina Genómica, Ciudad de Mexico, México
| | - Patricia Grether-González
- grid.419218.70000 0004 1773 5302Departamento de Genética y Genómica Humana, Instituto Nacional de Perinatología, Ciudad de Mexico, México ,grid.413678.fPresent Address: Centro Médico ABC, Campus Santa Fe, Ciudad de Mexico, México
| | - Dora Gilda Mayen
- Unidad de Genética Aplicada. Hospital Ángeles Lomas, Huixquilucan, Edo. de México México
| | - Camilo Villarroel
- grid.419216.90000 0004 1773 4473Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - Esther Lieberman
- grid.419216.90000 0004 1773 4473Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - Emiy Yokoyama
- grid.419216.90000 0004 1773 4473Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - Victoria Del Castillo
- grid.419216.90000 0004 1773 4473Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - Leda Torres
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México
| | - Sara Frias
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México ,grid.9486.30000 0001 2159 0001Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
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Zhou Z, Wu J, Ma W, Dong F, Wang J. Pan-Cancer analyses of Necroptosis-Related genes as a potential target to predict immunotherapeutic outcome. J Cell Mol Med 2022; 27:204-221. [PMID: 36583248 PMCID: PMC9843528 DOI: 10.1111/jcmm.17634] [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: 09/14/2022] [Revised: 11/14/2022] [Accepted: 11/22/2022] [Indexed: 12/31/2022] Open
Abstract
Necroptosis is a unique programmed death mechanism of necrotic cells. However, its role and specific mechanism in cancer remain unclear, and a systematic pan-cancer analysis of necroptosis is yet to be conducted. Thus, we performed a specific pan-cancer analysis using The Cancer Genome Atlas and Genotype-Tissue Expression databases to analyse necroptosis expression in terms of cancer prognosis, DNA methylation status, tumour mutative burden, microsatellite instability, immune cell infiltration in different types of cancer and molecular mechanisms. For the first time, we explored the correlation between necroptosis and immunotherapy prognosis. Thus, our study provides a relatively comprehensive understanding of the carcinogenicity of necroptosis in different types of cancer. It is suggested that necroptosis can be used to evaluate the sensitivity of different patients to immunotherapy and may become a potential target for tumour immunotherapy.
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Affiliation(s)
- Zheng Zhou
- Bengbu Medical College Graduate SchoolBengbuChina,Department of Head and Neck Surgery, Centre of Otolaryngology‐Head and Neck Surgery, Zhejiang Provincial People's HospitalPeople's Hospital of Hangzhou Medical CollegeHangzhouChina
| | - Jiajun Wu
- Bengbu Medical College Graduate SchoolBengbuChina,Department of Head and Neck Surgery, Centre of Otolaryngology‐Head and Neck Surgery, Zhejiang Provincial People's HospitalPeople's Hospital of Hangzhou Medical CollegeHangzhouChina
| | - Wenli Ma
- Bengbu Medical College Graduate SchoolBengbuChina,Department of Head and Neck Surgery, Centre of Otolaryngology‐Head and Neck Surgery, Zhejiang Provincial People's HospitalPeople's Hospital of Hangzhou Medical CollegeHangzhouChina
| | - Feilin Dong
- Zhejiang Provincial Key Laboratory of Diagnosis and Treatment of Endocrine Gland DiseasesHangzhouChina
| | - Jiafeng Wang
- Department of Head and Neck Surgery, Centre of Otolaryngology‐Head and Neck Surgery, Zhejiang Provincial People's HospitalPeople's Hospital of Hangzhou Medical CollegeHangzhouChina,Zhejiang Provincial Key Laboratory of Diagnosis and Treatment of Endocrine Gland DiseasesHangzhouChina
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Zhou X, Sun Q, Xu C, Zhou Z, Chen X, Zhu X, Huang Z, Wang W, Shi Y. A systematic pan-cancer analysis of PXDN as a potential target for clinical diagnosis and treatment. Front Oncol 2022; 12:952849. [PMID: 35982948 PMCID: PMC9380648 DOI: 10.3389/fonc.2022.952849] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/01/2022] [Indexed: 11/22/2022] Open
Abstract
Peroxidasin (PXDN), also known as vascular peroxidase-1, is a newly discovered heme-containing peroxidase; it is involved in the formation of extracellular mesenchyme, and it catalyzes various substrate oxidation reactions in humans. However, the role and specific mechanism of PXDN in tumor are unclear, and no systematic pan-cancer studies on PXDN have been reported to date. This study employed data from multiple databases, including The Cancer Genome Atlas and The Genotype-Tissue Expression, to conduct a specific pan-cancer analysis of the effects of PXDN expression on cancer prognosis. Further, we evaluated the association of PXDN expression with DNA methylation status, tumor mutation burden, and microsatellite instability. Additionally, for the first time, the relationship of PXDN with the tumor microenvironment and infiltration of fibroblasts and different immune cells within different tumors was explored, and the possible molecular mechanism of the effect was also discussed. Our results provide a comprehensive understanding of the carcinogenicity of PXDN in different tumors and suggest that PXDN may be a potential target for tumor immunotherapy, providing a new candidate that could improve cancer clinical diagnosis and treatment.
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Affiliation(s)
- Xiaohu Zhou
- Department of Hepatobiliary and Pancreatic Surgery, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiang Sun
- Department of Hepatobiliary and Pancreatic Surgery, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chang Xu
- Department of Hepatobiliary and Pancreatic Surgery, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zheng Zhou
- Department of Head and Neck Surgery, Centre of Otolaryngology-Head and Neck Surgery, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, Hangzhou, China
| | - Xiaoquan Chen
- Department of pediatric, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiuping Zhu
- Department of Pharmacy, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhaoshuai Huang
- Department of Hepatobiliary and Pancreatic Surgery, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Weilin Wang
- Department of Hepatobiliary and Pancreatic Surgery, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Weilin Wang, ; Yanjun Shi,
| | - Yanjun Shi
- Department of Hepatobiliary and Pancreatic Surgery, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Weilin Wang, ; Yanjun Shi,
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