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Tsang HF, Cheung YS, Yu CSA, Chan CSS, Wong CBT, Yim KYA, Pei X, Wong SCC. Menstrual Blood as a Diagnostic Specimen for Human Papillomavirus Genotyping and Genital Tract Infection Using Next-Generation Sequencing as a Novel Diagnostic Tool. Diagnostics (Basel) 2024; 14:686. [PMID: 38611599 PMCID: PMC11012019 DOI: 10.3390/diagnostics14070686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/04/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Menstrual blood (MB) is a convenient specimen type that can be self-collected easily and non-invasively by women. This study assessed the potential application of MB as a diagnostic specimen to detect genital tract infections (GTIs) and human papillomavirus (HPV) infections in women. METHOD Genomic DNA was extracted from MB samples. Pacific Bioscience (Pacbio) 16S ribosomal DNA (rDNA) high-fidelity (HiFi) long-read sequencing and HPV PCR were performed. RESULTS MB samples were collected from women with a pathological diagnosis of CIN1, CIN2, CIN3 or HPV infection. The sensitivity and positive predictive value (PPV) of high-risk HPV detection using MB were found to be 66.7%. A shift in vaginal flora and a significant depletion in Lactobacillus spp. in the vaginal microbiota communities were observed in the MB samples using 16S rDNA sequencing. CONCLUSIONS In this study, we demonstrated that MB is a proper diagnostic specimen of consideration for non-invasive detection of HPV DNA and genotyping using PCR and the diagnosis of GTIs using metagenomic next-generation sequencing (mNGS). MB testing is suitable for all women who menstruate and this study has opened up the possibility of the use of MB as a diagnostic specimen to maintain women's health.
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Affiliation(s)
- Hin-Fung Tsang
- Department of Clinical Laboratory and Pathology, Hong Kong Adventist Hospital, Hong Kong SAR, China
| | - Yui-Shing Cheung
- Department of Obstetrics and Gynaecology, Queen Elizabeth Hospital, Hong Kong SAR, China; (Y.-S.C.); (C.-S.S.C.)
| | - Chi-Shing Allen Yu
- Codex Genetics Limited, Hong Kong SAR, China; (C.-S.A.Y.); (C.-B.T.W.); (K.-Y.A.Y.)
| | - Chung-Sum Sammy Chan
- Department of Obstetrics and Gynaecology, Queen Elizabeth Hospital, Hong Kong SAR, China; (Y.-S.C.); (C.-S.S.C.)
| | - Chi-Bun Thomas Wong
- Codex Genetics Limited, Hong Kong SAR, China; (C.-S.A.Y.); (C.-B.T.W.); (K.-Y.A.Y.)
| | - Kay-Yuen Aldrin Yim
- Codex Genetics Limited, Hong Kong SAR, China; (C.-S.A.Y.); (C.-B.T.W.); (K.-Y.A.Y.)
| | - Xiaomeng Pei
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China;
| | - Sze-Chuen Cesar Wong
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China;
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Xue VW, Ng SSM, Tsang HF, Wong HT, Leung WW, Wong YN, Wong YKE, Yu ACS, Yim AKY, Cho WCS, Tai WCS, Wong SCC. The non-invasive diagnosis of colorectal cancer via a SOX9-based gene panel. Clin Exp Med 2023; 23:2421-2432. [PMID: 36637582 DOI: 10.1007/s10238-022-00970-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 12/01/2022] [Indexed: 01/14/2023]
Abstract
Colorectal cancer (CRC) threatens human health seriously. Early diagnosis of CRC is critical to improving patient survival. Meanwhile, non-invasive detection through tumor-circulating markers can be an important auxiliary diagnosis. In this study, we performed targeted RNA sequencing in paired tumor and adjacent normal fresh frozen tissues from 68 patients, and we also measured circulating mRNA levels in 4 time-point plasma samples collected before and after operation or chemotherapy. Our results showed that SOX9 (6.73-fold with adjusted p value < 1 × 10-45), MYC (20.59-fold with adjusted p value < 1 × 10-57), and MMP7 (131.94-fold with adjusted p value < 1 × 10-78) highly expressed in tumor compared with adjacent normal tissues. Besides, the circulating mRNA of SOX9 (41.14-fold with adjusted p value < 1 × 10-13) in CRC was significantly higher than in the normal control as well. Moreover, a SOX9-based 9-gene panel (SOX9, GSK3A, FZD4, LEF1, DVL1, FZD7, NFATC1, KRT19, and RUVBL1) showed the non-invasive diagnostic value of CRC (AUC: 0.863 (0.766-0.960), TPR: 0.92, TNR: 0.87). In summary, SOX9 expression consistently increases in tumor and plasma samples from CRC patients, which indicates the important role of SOX9 in CRC progression and its potential in non-invasive diagnosis of CRC.
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Affiliation(s)
- Vivian Weiwen Xue
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Department of Pharmacology, Shenzhen University Health Science Center, Shenzhen, China
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Simon Siu Man Ng
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Kowloon, Hong Kong Special Administrative Region, China
| | - Hin Fung Tsang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Heong Ting Wong
- Department of Pathology, Kiang Wu Hospital, Santo António, Macau Special Administrative Region, China
| | - Wing Wa Leung
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Kowloon, Hong Kong Special Administrative Region, China
| | - Yee Ni Wong
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Kowloon, Hong Kong Special Administrative Region, China
| | - Yin Kwan Evelyn Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Allen Chi Shing Yu
- Codex Genetics Limited, Kowloon, Hong Kong Special Administrative Region, China
| | - Aldrin Kay Yuen Yim
- Codex Genetics Limited, Kowloon, Hong Kong Special Administrative Region, China
| | - William Chi Shing Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong Special Administrative Region, China
| | - William Chi Shing Tai
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Sze Chuen Cesar Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China.
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Tsang HF, Yu ACS, Yim AKY, Jin N, Wu YO, Cheng HYL, Cheung WL, Leung WMS, Lam KW, Hung TN, Chan L, Chiou J, Pei XM, Lee OYA, Cho WCS, Wong SCC. The clinical characteristics of pediatric patients infected by SARS-CoV-2 Omicron variant and whole viral genome sequencing analysis. PLoS One 2023; 18:e0282389. [PMID: 36897843 PMCID: PMC10004545 DOI: 10.1371/journal.pone.0282389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 02/13/2023] [Indexed: 03/11/2023] Open
Abstract
Pediatric population was generally less affected clinically by SARS-CoV-2 infection. Few pediatric cases of COVID-19 have been reported compared to those reported in infected adults. However, a rapid increase in the hospitalization rate of SARS-CoV-2 infected pediatric patients was observed during Omicron variant dominated COVID-19 outbreak. In this study, we analyzed the B.1.1.529 (Omicron) genome sequences collected from pediatric patients by whole viral genome amplicon sequencing using Illumina next generation sequencing platform, followed by phylogenetic analysis. The demographic, epidemiologic and clinical data of these pediatric patients are also reported in this study. Fever, cough, running nose, sore throat and vomiting were the more commonly reported symptoms in children infected by Omicron variant. A novel frameshift mutation was found in the ORF1b region (NSP12) of the genome of Omicron variant. Seven mutations were identified in the target regions of the WHO listed SARS-CoV-2 primers and probes. On protein level, eighty-three amino acid substitutions and fifteen amino acid deletions were identified. Our results indicate that asymptomatic infection and transmission among children infected by Omicron subvariants BA.2.2 and BA.2.10.1 are not common. Omicron may have different pathogenesis in pediatric population.
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Affiliation(s)
- Hin Fung Tsang
- Department of Clinical Laboratory and Pathology, Hong Kong Adventist Hospital, Hong Kong, China
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China
- * E-mail: (HFT); (SCCW)
| | | | | | - Nana Jin
- Codex Genetics Limited, Hong Kong, China
| | - Yu On Wu
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Hennie Yuk Lin Cheng
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - WL Cheung
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Wai Ming Stanley Leung
- Department of Clinical Laboratory and Pathology, Hong Kong Adventist Hospital, Hong Kong, China
| | - Ka Wai Lam
- Department of Clinical Laboratory and Pathology, Hong Kong Adventist Hospital, Hong Kong, China
| | - Tin Nok Hung
- Department of Clinical Laboratory and Pathology, Hong Kong Adventist Hospital, Hong Kong, China
| | - Loiston Chan
- Department of Clinical Laboratory and Pathology, Hong Kong Adventist Hospital, Hong Kong, China
| | - Jiachi Chiou
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Xiao Meng Pei
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China
| | - On Ying Angela Lee
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China
| | | | - Sze Chuen Cesar Wong
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
- * E-mail: (HFT); (SCCW)
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