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Bronk JK, Kapadia C, Wu X, Chapman BV, Wang R, Karpinets TV, Song X, Futreal AM, Zhang J, Klopp AH, Colbert LE. Feasibility of a novel non-invasive swab technique for serial whole-exome sequencing of cervical tumors during chemoradiation therapy. PLoS One 2022; 17:e0274457. [PMID: 36201462 PMCID: PMC9536567 DOI: 10.1371/journal.pone.0274457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/29/2022] [Indexed: 11/06/2022] Open
Abstract
Background Clinically relevant genetic predictors of radiation response for cervical cancer are understudied due to the morbidity of repeat invasive biopsies required to obtain genetic material. Thus, we aimed to demonstrate the feasibility of a novel noninvasive cervical swab technique to (1) collect tumor DNA with adequate throughput to (2) perform whole-exome sequencing (WES) at serial time points over the course of chemoradiation therapy (CRT). Methods Cervical cancer tumor samples from patients undergoing chemoradiation were collected at baseline, at week 1, week 3, and at the completion of CRT (week 5) using a noninvasive swab-based biopsy technique. Swab samples were analyzed with whole-exome sequencing (WES) with mutation calling using a custom pipeline optimized for shallow whole-exome sequencing with low tumor purity (TP). Tumor mutation changes over the course of treatment were profiled. Results 216 samples were collected and successfully sequenced for 70 patients (94% of total number of tumor samples collected). A total of 33 patients had a complete set of samples at all four time points. The mean mapping rate was 98% for all samples, and the mean target coverage was 180. Estimated TP was greater than 5% for all samples. Overall mutation frequency decreased during CRT but mapping rate and mean target coverage remained at >98% and >180 reads at week 5. Conclusion This study demonstrates the feasibility and application of a noninvasive swab-based technique for WES analysis which may be applied to investigate dynamic tumor mutational changes during treatment to identify novel genes which confer radiation resistance.
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Affiliation(s)
- Julianna K. Bronk
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Chiraag Kapadia
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiaogang Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Bhavana V. Chapman
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Rui Wang
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Tatiana V. Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Andrew M. Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Ann H. Klopp
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail: (LEC); (AHK)
| | - Lauren E. Colbert
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail: (LEC); (AHK)
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Qin J, Zhu Y, Ding Y, Niu T, Zhang Y, Wu H, Zhu L, Yuan B, Qiao Y, Lu J, Liu K, Dong Z, Jin G, Chen X, Zhao J. DNA polymerase β deficiency promotes the occurrence of esophageal precancerous lesions in mice. Neoplasia 2021; 23:663-675. [PMID: 34144266 PMCID: PMC8217306 DOI: 10.1016/j.neo.2021.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/10/2021] [Accepted: 05/03/2021] [Indexed: 01/12/2023] Open
Abstract
Esophageal mucosa undergoes mild, moderate, severe dysplasia, and other precancerous lesions and eventually develops into carcinoma in situ, and understanding the developmental progress of esophageal precancerous lesions is beneficial to prevent them from developing into cancer. DNA polymerase β (Polβ), a crucial enzyme of the base excision repair system, plays an important role in repairing damaged DNA and maintaining genomic stability. Abnormal expression or deletion mutation of Polβ is related to the occurrence of esophageal cancer, but the role of Polβ deficiency in the esophageal precancerous lesions is still unclear. Here, esophageal mucosa Polβ-knockout mice were used to explore the relationship of Polβ deficiency with esophageal precancerous lesions. First, we found the degree and number of esophageal precancerous lesions in Polβ-KO mice were more serious than those in Polβ-Loxp mice after N-nitrosomethylbenzylamine (NMBA) treatment. Whole exome sequencing revealed that deletion of Polβ increased the frequency of gene mutations. Gene expression prolife analysis showed that the expression of proteins correlated to cell proliferation and the cell cycle was elevated in Polβ-KO mice. We also found that deletion of Polβ promoted the proliferation and clone formation as well as accelerated cell cycle progression of human immortalized esophageal epithelial cell line SHEE treated with NMBA. Our findings indicate that Polβ knockout promotes the occurrence of esophageal precancerous lesions.
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Affiliation(s)
- Jiace Qin
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China; Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou, China
| | - Yanyan Zhu
- Department of Dermatology, The Second Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Yongwei Ding
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China; Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou, China
| | - Tingting Niu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China; Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou, China
| | - Yangyang Zhang
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China; Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou, China
| | - Huiting Wu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China; Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou, China
| | - Lili Zhu
- Department of Pathology, the First Affiliated Hospital and School of Medicine, Zhejiang University, Hangzhou, China
| | - Baoyin Yuan
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China; Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou, China
| | - Yan Qiao
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China; Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou, China
| | - Jing Lu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China; Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou, China
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China; Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou, China; The China-US (Henan) Hormel Cancer Institute, Zhengzhou, China
| | - Ziming Dong
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China; Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou, China
| | - Ge Jin
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China.
| | - Xinhuan Chen
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China; Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou, China.
| | - Jimin Zhao
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China; Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou, China; State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, China.
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Southern A, El-Bahrawy M. Advances in understanding the molecular pathology of gynecological malignancies: the role and potential of RNA sequencing. Int J Gynecol Cancer 2021; 31:1159-1164. [PMID: 34016704 DOI: 10.1136/ijgc-2021-002509] [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: 02/08/2021] [Revised: 05/04/2021] [Accepted: 05/07/2021] [Indexed: 11/03/2022] Open
Abstract
For many years technological limitations restricted the progress of identifying the underlying genetic causes of gynecologicalcancers. However, during the past decade, high-throughput next-generation sequencing technologies have revolutionized cancer research. RNA sequencing has arisen as a very useful technique in expanding our understanding of genome changes in cancer. Cancer is characterized by the accumulation of genetic alterations affecting genes, including substitutions, insertions, deletions, translocations, gene fusions, and alternative splicing. If these aberrant genes become transcribed, aberrations can be detected by RNA sequencing, which will also provide information on the transcript abundance revealing the expression levels of the aberrant genes. RNA sequencing is considered the technique of choice when studying gene expression and identifying new RNA species. This is due to the quantitative and qualitative improvement that it has brought to transcriptome analysis, offering a resolution that allows research into different layers of transcriptome complexity. It has also been successful in identifying biomarkers, fusion genes, tumor suppressors, and uncovering new targets responsible for drug resistance in gynecological cancers. To illustrate that we here review the role of RNA sequencing in studies that enhanced our understanding of the molecular pathology of gynecological cancers.
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Affiliation(s)
- Alba Southern
- Surgery and Cancer, Imperial College London, London, UK
| | - Mona El-Bahrawy
- Metabolism, Digestion and Reproduction, Imperial College London, London, UK .,Pathology, Alexandria University Faculty of Medicine, Alexandria, Egypt
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A novel function of IMPA2, plays a tumor-promoting role in cervical cancer. Cell Death Dis 2020; 11:371. [PMID: 32409648 PMCID: PMC7224180 DOI: 10.1038/s41419-020-2507-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/10/2020] [Accepted: 04/14/2020] [Indexed: 12/19/2022]
Abstract
Discovery of genes and molecular mechanism involved in cervical cancer development would promote the prevention and treatment. By comparing gene expression profiles of cervical carcinoma in situ (CCIS) and adjacent normal tissues, we identified a potential cancer-promoting gene, IMPA2. This study aimed to elucidate the role of IMPA2 and underlying molecular mechanisms in cervical cancer progression. To do this expression of IMPA2 was compared between human cervical cancer and corresponding adjacent normal cervical tissues firstly. CCK-8 assay, clone formation assay, wound healing assay, transwell assay, and tumor formation in nude mice were performed to demonstrate the effect of IMPA2 in cervical cancer proliferation and metastasis. Further proteomic profiling and western blotting explored the molecular pathway involved in the IMPA2-regulating process. The results showed that IMPA2 gene expression was upregulated in cervical cancer. Consistently, silencing of IMPA2 suppressed tumor formation in BALB/c nude mice. Short hairpin RNA (shRNA)-mediated IMPA2 silencing significantly inhibited proliferation and colony-forming abilities of cervical cancer cells, while IMPA2 overexpression had little impact. Also, IMPA2 silencing suppressed cellular migration, but overexpression promoted migration. Proteomics analysis revealed the involvement of mitogen-activated protein kinase (MAPK) pathway in tumor-promoting action of IMPA2. Significantly, the inhibition of IMPA2 activated ERK phosphorylation, and its inhibitory effects can be restored by using selective ERK inhibitor, FR180204. In conclusion, IMPA2 acts as an oncogene in the proliferation and migration of cervical cancer. IMPA2 downregulated ERK phosphorylation to promote cervical cancer. These findings identify a new mechanism underlying cervical cancer and suggest a regulating effect of IMPA2 in MAPK signaling pathway.
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RNA-based high-risk HPV genotyping and identification of high-risk HPV transcriptional activity in cervical tissues. Mod Pathol 2020; 33:748-757. [PMID: 31537894 DOI: 10.1038/s41379-019-0369-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 08/30/2019] [Accepted: 09/02/2019] [Indexed: 01/09/2023]
Abstract
Nearly all cervical cancers are initiated by a persistent infection with one of the high-risk human papillomaviruses (high-risk HPV). High-risk HPV DNA testing is highly sensitive but cannot distinguish between active, productive infections and dormant infections or merely deposited virus. A solution for this shortcoming may be the detection of transcriptional activity of viral oncogenes instead of mere presence of high-risk HPVs. In this study, fresh-frozen cervical tissues (n = 22) were subjected to high-risk HPV DNA detection using the line probe assay and to targeted RNA next-generation sequencing using single-molecule molecular inversion probes. Targeted RNA sequencing was applied for (1) RNA-based genotyping of high-risk HPV, giving information on specific HPV-subtype (2) discrimination of E2, E6, and E7 transcripts and (3) discovery of possible non-HPV cancer biomarkers. Data were analyzed using computational biology. Targeted RNA sequencing enabled reliable genotyping of high-risk HPV subtypes and allowed quantitative detection of E2, E6, and E7 viral gene expression, thereby discriminating cervical lesions from normal cervical tissues. Moreover, targeted RNA sequencing identified possible cervical cancer biomarkers other than high-risk HPV. Interestingly, targeted RNA sequencing also provided high-quality transcription profiles from cervical scrape samples, even after 1 week of dry storage or storage in Preservcyt fixative. This proof of concept study shows that targeted RNA sequencing can be used for high-risk HPV genotyping and simultaneous detection of high-risk HPV gene activity. Future studies are warranted to investigate the potential of targeted RNA sequencing for risk assessment for the development of cervical lesions, based on molecular analysis of cervical scrapes.
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