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Corver WE, Ter Haar NT. High-Resolution Multiparameter DNA Flow Cytometry for Accurate Ploidy Assessment and the Detection and Sorting of Tumor and Stromal Subpopulations from Paraffin-Embedded Tissues. Curr Protoc 2023; 3:e825. [PMID: 37428889 DOI: 10.1002/cpz1.825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
This article contains detailed protocols for the simultaneous flow cytometric identification of tumor cells and stromal cells and measurement of DNA content of formalin-fixed, paraffin-embedded (FFPE) tissues. The vimentin-positive stromal cell fraction can be used as an internal reference for accurate DNA content assessments of FFPE carcinoma tissues. This allows clear detection of keratin-positive tumor cells with a DNA index lower than 1.0 (near-haploidy) and of keratin-positive tumor cells with a DNA index close to 1.0 in overall DNA aneuploid samples, thus improving DNA ploidy assessment in FFPE carcinomas. Furthermore, the protocol is useful for studying molecular genetic alterations and intratumor heterogeneity in archival FFPE samples. Keratin-positive tumor cell fractions can be sorted for further molecular genetic analysis, while DNA from the sorted vimentin-positive stromal cells can serve as a reference when normal tissue of the patient is not available. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Multiparameter DNA content analysis of FFPE carcinomas Alternate Protocol 1: Immunocytochemistry for keratin and vimentin, and DNA labeling for blue and red excitation Alternate Protocol 2: Immunocytochemistry for keratin and vimentin, and DNA labeling for blue excitation Support Protocol: Sorting cell population from FFPE carcinomas.
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Huang J, Qian Z, Gong Y, Wang Y, Guan Y, Han Y, Yi X, Huang W, Ji L, Xu J, Su M, Yuan Q, Cui S, Zhang J, Bao C, Liu W, Chen X, Zhang M, Gao X, Wu R, Zhang Y, Xu H, Zhu S, Zhu H, Yang L, Xu X, Zhou P, Liang Z. Comprehensive genomic variation profiling of cervical intraepithelial neoplasia and cervical cancer identifies potential targets for cervical cancer early warning. J Med Genet 2018; 56:186-194. [PMID: 30567904 PMCID: PMC6581088 DOI: 10.1136/jmedgenet-2018-105745] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/13/2018] [Accepted: 11/16/2018] [Indexed: 12/31/2022]
Abstract
Background To better understand the pathogenesis of cervical cancer (CC), we systematically analysed the genomic variation and human papillomavirus (HPV) integration profiles of cervical intraepithelial neoplasia (CIN) and CC. Methods We performed whole-genome sequencing or whole-exome sequencing of 102 tumour-normal pairs and human papillomavirus probe capture sequencing of 45 CCs, 44 CIN samples and 25 normal cervical samples, and constructed strict integrated workflow of genomic analysis. Results Mutational analysis identified eight significantly mutated genes in CC including four genes (FAT1, MLL3, MLL2 and FADD), which have not previously been reported in CC. Targetable alterations were identified in 55.9% of patients. In addition, HPV integration breakpoints occurred in 97.8% of the CC samples, 70.5% of the CIN samples and 42.8% of the normal cervical samples with HPV infection. Integrations of high-risk HPV strains in CCs, including HPV16, 18, 33 and 58, also occurred in the CIN samples. Moreover, gene mutations were detected in 52% of the CIN specimens, and 54.8% of these mutations occurred in genes that also mutated in CCs. Conclusion Our results lay the foundation for a deep understanding of the molecular mechanisms and finding new diagnostic and therapeutic targets of CC.
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Affiliation(s)
- Jian Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome at Shanghai, Shanghai, China
| | - Zhaoyang Qian
- Binhai Genomics Institute, BGI-Tianjin, Tianjin, China
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | | | - Yanzhou Wang
- Department of Obstetrics and Gynecology, Southwestern Hospital, Third Military Medical University, Chongqing, China
| | | | - Yingxin Han
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Yi
- Geneplus-Beijing, Beijing, China
| | - Wanqiu Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Liyan Ji
- Geneplus-Beijing, Beijing, China
| | - Jiajia Xu
- Binhai Genomics Institute, BGI-Tianjin, Tianjin, China
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Mengyuan Su
- Binhai Genomics Institute, BGI-Tianjin, Tianjin, China
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Qing Yuan
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shujian Cui
- Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome at Shanghai, Shanghai, China
| | - Jinling Zhang
- Shenzhen People’s Hospital, Second Clinical Medical College of Jinan University, Shenzhen, China
| | - Chaohui Bao
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Weilong Liu
- Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People’s Hospital, Guangdong Medical University, Shenzhen, Guangdong, China
| | - Xi Chen
- Binhai Genomics Institute, BGI-Tianjin, Tianjin, China
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Ming Zhang
- Binhai Genomics Institute, BGI-Tianjin, Tianjin, China
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Xiaohuan Gao
- Binhai Genomics Institute, BGI-Tianjin, Tianjin, China
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Renhua Wu
- Binhai Genomics Institute, BGI-Tianjin, Tianjin, China
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Yinxin Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Huicheng Xu
- Department of Obstetrics and Gynecology, Southwestern Hospital, Third Military Medical University, Chongqing, China
| | - Shida Zhu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Hongmei Zhu
- Binhai Genomics Institute, BGI-Tianjin, Tianjin, China
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | | | - Xun Xu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Pingyu Zhou
- STD Institute, Shanghai Skin Disease Hospital, Tong Ji University, Shanghai, China
| | - Zhiqing Liang
- Department of Obstetrics and Gynecology, Southwestern Hospital, Third Military Medical University, Chongqing, China
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Ren T, Suo J, Liu S, Wang S, Shu S, Xiang Y, Lang JH. Using low-coverage whole genome sequencing technique to analyze the chromosomal copy number alterations in the exfoliative cells of cervical cancer. J Gynecol Oncol 2018; 29:e78. [PMID: 30022638 PMCID: PMC6078888 DOI: 10.3802/jgo.2018.29.e78] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/19/2018] [Accepted: 06/11/2018] [Indexed: 01/28/2023] Open
Abstract
Objectives We analyzed the chromosomal-arm-level copy number alterations (CNAs) in the cervical exfoliative cell and tissue samples by using the low-coverage whole genomic sequencing technique. Methods In this study, we retrospectively collected 55 archived exfoliated cervical cell suspension samples and the corresponding formalin-fixed and paraffin-embedded tissue section samples including 27 invasive cervical cancer and 28 control cases. We also collected 19 samples of the cervical exfoliative cells randomly from women to verify the new algorithm model. We analyzed the CNAs in cervical exfoliated cell and tissue samples by using the low-coverage next generation of sequencing. Results In the model-building study, multiple chromosomal-arm-level CNAs were detected in both cervical exfoliated cell and tissue samples of all cervical cancer cases. By analyzing the consistency of CNAs between exfoliated cells and cervical tissue samples, as well as the heterogeneity in individual patient, we also established a C-score algorithm model according to the chromosomal-arm-level changes of 1q, 2q, 3p, 7q. The C-score model was then validated by the pathological diagnosis of all 74 exfoliated cell samples (including 55 cases in model-building group and 19 cases in verification group). In our result, a cutoff value of C-score >6 showed 100% sensitivity and 100% specificity in the diagnosis of cervical cancer. Conclusion In this study, we found that CNAs of cervical exfoliated cell samples could robustly distinguish invasive cervical cancer from cancer-free tissues. And we have also developed a C-score algorithm model to process the sequencing data in a more standardized and automated way.
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Affiliation(s)
- Tong Ren
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Jing Suo
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Shikai Liu
- Department of Obstetrics and Gynecology, Cangzhou Central Hospital, Cangzhou, China
| | - Shu Wang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
| | - Shan Shu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yang Xiang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Jing He Lang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
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Migdalska-Sęk M, Karowicz-Bilińska A, Pastuszak-Lewandoska D, Czarnecka KH, Nawrot E, Domańska-Senderowska D, Kiszałkiewicz J, Brzeziańska-Lasota E. Assessment of the frequency of genetic alterations (LOH/MSI) in patients with intraepithelial cervical lesions with HPV infection: a pilot study. Med Oncol 2016; 33:51. [PMID: 27090798 DOI: 10.1007/s12032-016-0763-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 04/06/2016] [Indexed: 12/13/2022]
Abstract
In the present study, we analyzed (1) the type of HPV infection and (2) the frequency of loss of heterozygosity and microsatellite imbalance (LOH/MSI) in normal cytology and cervical intraepithelial neoplasia (CIN1-3). The cytological material included: low-grade squamous intraepithelial lesions (CIN1, n = 11), high-grade lesions (CIN2 and CIN3, n = 13), and cytologically normal cells from non-neoplastic cervical samples (n = 8). HPV genotyping was done using RealLine HPV 16/18 kit. We used 20 microsatellite markers from: 1p31.2, 3p14.3, 3p21.3, 3p22.2, 3p24.2, 3p25.3, 7q32.2, 9p21.3, 11p15.5, 12q23.2, and 16q22.1. LOH/MSI was correlated with clinicopathological parameters. The presence of HPV DNA was revealed in 78.13 % samples, including normal cytology. LOH/MSI was the most frequent for: 3p25.3 (39 %), 3p22.2 (20.83 %), 3p24.2 (20 %), and 3p14.3 (16.67 %). It was demonstrated that D3S1234 (FHIT; 3p14.3), D3S1611 (MLH1; 3p22.2), D3S1583 (RARB; 3p24.2), D3S1317 and D3S3611 (VHL; 3p25.3) could differentiate patients with CIN2/CIN3 versus CIN1, showing significantly higher frequency in CIN2/CIN3. LOH/MSI frequency for other than 3p markers was lower, 10-22.2 %. The simultaneous occurrence of LOH/MSI for several markers (OFAL) was higher in CIN2/CIN3. Significant differences in OFAL were found between samples with versus without HPV infection. In HPV-positive patients, significant differences in OFAL were found between normal cytology, CIN1 and CIN2/CIN3. HPV infection influences the increase in LOH/MSI frequency, especially in tumor suppressor gene loci. Several studied microsatellite markers seem to be useful for CIN grading. Hopefully, the obtained results, if confirmed on larger patient cohort, would allow creating a panel of markers supporting clinical diagnosis in patients with HPV infection.
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Affiliation(s)
- Monika Migdalska-Sęk
- Department of Molecular Bases of Medicine, 1st Chair of Internal Diseases, Medical University of Lodz, Pomorska St. No. 251, 92-213, Lodz, Poland.
| | - Agata Karowicz-Bilińska
- Department of Pregnancy Pathology, 1st Chair of Gynecology and Obstetrics, Medical University of Lodz, Wileńska 37, 94-029, Lodz, Poland
| | - Dorota Pastuszak-Lewandoska
- Department of Molecular Bases of Medicine, 1st Chair of Internal Diseases, Medical University of Lodz, Pomorska St. No. 251, 92-213, Lodz, Poland
| | - Karolina H Czarnecka
- Department of Molecular Bases of Medicine, 1st Chair of Internal Diseases, Medical University of Lodz, Pomorska St. No. 251, 92-213, Lodz, Poland
| | - Ewa Nawrot
- Department of Molecular Bases of Medicine, 1st Chair of Internal Diseases, Medical University of Lodz, Pomorska St. No. 251, 92-213, Lodz, Poland
| | - Daria Domańska-Senderowska
- Department of Molecular Bases of Medicine, 1st Chair of Internal Diseases, Medical University of Lodz, Pomorska St. No. 251, 92-213, Lodz, Poland
| | - Justyna Kiszałkiewicz
- Department of Molecular Bases of Medicine, 1st Chair of Internal Diseases, Medical University of Lodz, Pomorska St. No. 251, 92-213, Lodz, Poland
| | - Ewa Brzeziańska-Lasota
- Department of Molecular Bases of Medicine, 1st Chair of Internal Diseases, Medical University of Lodz, Pomorska St. No. 251, 92-213, Lodz, Poland
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The microRNA-218~Survivin axis regulates migration, invasion, and lymph node metastasis in cervical cancer. Oncotarget 2015; 6:1090-100. [PMID: 25473903 PMCID: PMC4359219 DOI: 10.18632/oncotarget.2836] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/24/2014] [Indexed: 11/26/2022] Open
Abstract
Cervical cancer is the third most common cancer in women worldwide. In the present study, global microRNA profiling for 79 cervical cancer patient samples led to the identification of miR-218 down-regulation in cervical cancer tissues compared to normal cervical tissues. Lower miR-218 expression was associated significantly with worse overall survival (OS), disease-free survival (DFS), and pelvic/aortic lymph node recurrence. In vitro, miR-218 over-expression decreased clonogenicity, migration, and invasion. Survivin (BIRC5) was subsequently identified as an important cervical cancer target of miR-218 using in silico prediction, mRNA profiling, and quantitative real-time PCR (qRT-PCR). Concordant with miR-218 over-expression, survivin knockdown by siRNA decreased clonogenicity, migration, and invasion. YM155, a small molecule survivin inhibitor, significantly suppressed tumor growth and lymph node metastasis in vivo. Our findings demonstrate that the miR-218~survivin axis inhibits cervical cancer progression by regulating clonogenicity, migration, and invasion, and suggest that the inhibition of survivin could be a potential therapeutic strategy to improve outcome in this disease.
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Houldsworth J. FHACT: the FISH-based HPV-associated cancer test that detects nonrandom gain at four genomic loci as biomarkers of disease progression. Expert Rev Mol Diagn 2014; 14:921-34. [DOI: 10.1586/14737159.2014.965685] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Kuglik P, Smetana J, Vallova V, Moukova L, Kasikova K, Cvanova M, Brozova L. Genome-wide screening of DNA copy number alterations in cervical carcinoma patients with CGH+SNP microarrays and HPV-FISH. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2014; 7:5071-5082. [PMID: 25197380 PMCID: PMC4152070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 06/24/2014] [Indexed: 06/03/2023]
Abstract
Alterations in the genome that lead to changes in DNA sequence copy number are characteristic features of solid tumors. We used CGH+SNP microarray and HPV-FISH techniques for detailed screening of copy number alterations (CNAs) in a cohort of 26 patients with cervical carcinoma (CC). This approach identified CNAs in 96.2% (25/26) of tumors. Array-CGH discovered CNAs in 73.1% (19/26) of samples, HPV-FISH experiments revealed CNAs in additional 23.1% (6/26) of samples. Common gains of genetic sequences were observed in 3q (50.0%), 1q (42.4%), 19q (23.1%), while losses were frequently found in 11q (30.8%), 4q (23.1%) and 13q (19.2%). Chromosomal regions involved in loss of heterozygosity were observed in 15.4% of samples in 8q21, 11q23, 14q21 and 18q12.2. Incidence of gain 3q was associated with HPV 16 and HPV 18 positive samples and simultaneous presence of gain 1q (P = 0.033). We did not found a correlation between incidence of CNAs identified by array-CGH and HPV strain infection and incidence of lymph node metastases. Subsequently, HPV-FISH was used for validation of array-CGH results in 23 patients for incidence of hTERC (3q26) and MYC (8q24) amplification. Using HPV-FISH, we found chromosomal lesions of hTERC in 87.0% and MYC in 65.2% of specimens. Our findings confirmed the important role of HPV infection and specific genomic alterations in the development of invasive cervical cancer. This study also indicates that CGH+SNP microarrays allow detecting genome-wide CNAs and copy-neutral loss of heterozygosity more precisely, however, it may be less sensitive than FISH in samples with low level clonal CNAs.
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Affiliation(s)
- Petr Kuglik
- Laboratory of Molecular Cytogenetics, Institute of Experimental Biology, Faculty of Science, Masaryk UniversityBrno, Czech Republic
- Department of Medical Genetics, University HospitalBrno, Czech Republic
| | - Jan Smetana
- Laboratory of Molecular Cytogenetics, Institute of Experimental Biology, Faculty of Science, Masaryk UniversityBrno, Czech Republic
- Department of Medical Genetics, University HospitalBrno, Czech Republic
| | - Vladimira Vallova
- Laboratory of Molecular Cytogenetics, Institute of Experimental Biology, Faculty of Science, Masaryk UniversityBrno, Czech Republic
- Department of Medical Genetics, University HospitalBrno, Czech Republic
| | - Lucie Moukova
- Department of Gynecological Oncology, Masaryk Memorial Cancer InstituteBrno, Czech Republic
| | - Katerina Kasikova
- Laboratory of Molecular Cytogenetics, Institute of Experimental Biology, Faculty of Science, Masaryk UniversityBrno, Czech Republic
- Department of Medical Genetics, University HospitalBrno, Czech Republic
| | - Michaela Cvanova
- Institute of Biostatistics and Analyses, Faculty of Medicine and Faculty of Science, Masaryk UniversityBrno, Czech Republic
| | - Lucie Brozova
- Institute of Biostatistics and Analyses, Faculty of Medicine and Faculty of Science, Masaryk UniversityBrno, Czech Republic
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