Integrated multi-omic analysis of low-grade ovarian serous carcinoma collected from short and long-term survivors
Abstract Background Low-grade serous ovarian cancer (LGSOC) is a rare disease that occurs more frequently in younger women than those with high-grade disease. The current treatment is suboptimal and a better understanding of the molecular pathogenesis of this disease is required. In this study, we c...
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BMC
2022-12-01
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| Series: | Journal of Translational Medicine |
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| Online Access: | https://doi.org/10.1186/s12967-022-03820-x |
| _version_ | 1811198400078544896 |
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| author | Kwong-Kwok Wong Nicholas W. Bateman Chun Wai Ng Yvonne T. M. Tsang Charlotte S. Sun Joseph Celestino Tri V. Nguyen Anais Malpica R. Tyler Hillman Jianhua Zhang P. Andrew Futreal Christine Rojas Kelly A. Conrads Brian L. Hood Clifton L. Dalgard Matthew D. Wilkerson Neil T. Phippen Thomas P. Conrads George L. Maxwell Anil K. Sood David M. Gershenson |
| author_facet | Kwong-Kwok Wong Nicholas W. Bateman Chun Wai Ng Yvonne T. M. Tsang Charlotte S. Sun Joseph Celestino Tri V. Nguyen Anais Malpica R. Tyler Hillman Jianhua Zhang P. Andrew Futreal Christine Rojas Kelly A. Conrads Brian L. Hood Clifton L. Dalgard Matthew D. Wilkerson Neil T. Phippen Thomas P. Conrads George L. Maxwell Anil K. Sood David M. Gershenson |
| author_sort | Kwong-Kwok Wong |
| collection | DOAJ |
| description | Abstract Background Low-grade serous ovarian cancer (LGSOC) is a rare disease that occurs more frequently in younger women than those with high-grade disease. The current treatment is suboptimal and a better understanding of the molecular pathogenesis of this disease is required. In this study, we compared the proteogenomic analyses of LGSOCs from short- and long-term survivors (defined as < 40 and > 60 months, respectively). Our goal was to identify novel mutations, proteins, and mRNA transcripts that are dysregulated in LGSOC, particularly in short-term survivors. Methods Initially, targeted sequencing of 409 cancer-related genes was performed on 22 LGSOC and 6 serous borderline ovarian tumor samples. Subsequently, whole-genome sequencing analysis was performed on 14 LGSOC samples (7 long-term survivors and 7 short-term survivors) with matched normal tissue samples. RNA sequencing (RNA-seq), quantitative proteomics, and phosphoproteomic analyses were also performed. Results We identified single-nucleotide variants (SNVs) (range: 5688–14,833 per sample), insertion and deletion variants (indels) (range: 880–1065), and regions with copy number variants (CNVs) (range: 62–335) among the 14 LGSOC samples. Among all SNVs and indels, 2637 mutation sites were found in the exonic regions. The allele frequencies of the detected variants were low (median12%). The identified recurrent nonsynonymous missense mutations included KRAS, NRAS, EIF1AX, UBR5, and DNM3 mutations. Mutations in DNM3 and UBR5 have not previously been reported in LGSOC. For the two samples, somatic DNM3 nonsynonymous missense mutations in the exonic region were validated using Sanger sequencing. The third sample contained two missense mutations in the intronic region of DNM3, leading to a frameshift mutation detected in RNA transcripts in the RNA-seq data. Among the 14 LGSOC samples, 7754 proteins and 9733 phosphosites were detected by global proteomic analysis. Some of these proteins and signaling pathways, such as BST1, TBXAS1, MPEG1, HBA1, and phosphorylated ASAP1, are potential therapeutic targets. Conclusions This is the first study to use whole-genome sequencing to detect somatic mutations in LGSOCs with matched normal tissues. We detected and validated novel mutations in DNM3, which were present in 3 of the 14 samples analyzed. Additionally, we identified novel indels, regions with CNVs, dysregulated mRNA, dysregulated proteins, and phosphosites that are more prevalent in short-term survivors. This integrated proteogenomic analysis can guide research into the pathogenesis and treatment of LGSOC. |
| first_indexed | 2024-04-12T01:30:35Z |
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| institution | Directory Open Access Journal |
| issn | 1479-5876 |
| language | English |
| last_indexed | 2024-04-12T01:30:35Z |
| publishDate | 2022-12-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Translational Medicine |
| spelling | doaj.art-3d3ade2fb20a4c199fb227538f7a10f62022-12-22T03:53:31ZengBMCJournal of Translational Medicine1479-58762022-12-0120111510.1186/s12967-022-03820-xIntegrated multi-omic analysis of low-grade ovarian serous carcinoma collected from short and long-term survivorsKwong-Kwok Wong0Nicholas W. Bateman1Chun Wai Ng2Yvonne T. M. Tsang3Charlotte S. Sun4Joseph Celestino5Tri V. Nguyen6Anais Malpica7R. Tyler Hillman8Jianhua Zhang9P. Andrew Futreal10Christine Rojas11Kelly A. Conrads12Brian L. Hood13Clifton L. Dalgard14Matthew D. Wilkerson15Neil T. Phippen16Thomas P. Conrads17George L. Maxwell18Anil K. Sood19David M. Gershenson20Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer CenterGynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical CenterDepartment of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer CenterDepartment of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer CenterDepartment of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer CenterDepartment of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer CenterDepartment of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer CenterDepartment of Pathology, The University of Texas MD Anderson Cancer CenterDepartment of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer CenterGenomic Medicine, The University of Texas MD Anderson Cancer CenterGenomic Medicine, The University of Texas MD Anderson Cancer CenterGynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical CenterGynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical CenterGynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical CenterDepartment of Anatomy, Physiology and Genetics and Center for Military Precision Health, Uniformed Services University of the Health SciencesDepartment of Anatomy, Physiology and Genetics and Center for Military Precision Health, Uniformed Services University of the Health SciencesGynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical CenterWomen’s Health Integrated Research Center at Inova Health System, Women’s Service LineWomen’s Health Integrated Research Center at Inova Health System, Women’s Service LineDepartment of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer CenterDepartment of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer CenterAbstract Background Low-grade serous ovarian cancer (LGSOC) is a rare disease that occurs more frequently in younger women than those with high-grade disease. The current treatment is suboptimal and a better understanding of the molecular pathogenesis of this disease is required. In this study, we compared the proteogenomic analyses of LGSOCs from short- and long-term survivors (defined as < 40 and > 60 months, respectively). Our goal was to identify novel mutations, proteins, and mRNA transcripts that are dysregulated in LGSOC, particularly in short-term survivors. Methods Initially, targeted sequencing of 409 cancer-related genes was performed on 22 LGSOC and 6 serous borderline ovarian tumor samples. Subsequently, whole-genome sequencing analysis was performed on 14 LGSOC samples (7 long-term survivors and 7 short-term survivors) with matched normal tissue samples. RNA sequencing (RNA-seq), quantitative proteomics, and phosphoproteomic analyses were also performed. Results We identified single-nucleotide variants (SNVs) (range: 5688–14,833 per sample), insertion and deletion variants (indels) (range: 880–1065), and regions with copy number variants (CNVs) (range: 62–335) among the 14 LGSOC samples. Among all SNVs and indels, 2637 mutation sites were found in the exonic regions. The allele frequencies of the detected variants were low (median12%). The identified recurrent nonsynonymous missense mutations included KRAS, NRAS, EIF1AX, UBR5, and DNM3 mutations. Mutations in DNM3 and UBR5 have not previously been reported in LGSOC. For the two samples, somatic DNM3 nonsynonymous missense mutations in the exonic region were validated using Sanger sequencing. The third sample contained two missense mutations in the intronic region of DNM3, leading to a frameshift mutation detected in RNA transcripts in the RNA-seq data. Among the 14 LGSOC samples, 7754 proteins and 9733 phosphosites were detected by global proteomic analysis. Some of these proteins and signaling pathways, such as BST1, TBXAS1, MPEG1, HBA1, and phosphorylated ASAP1, are potential therapeutic targets. Conclusions This is the first study to use whole-genome sequencing to detect somatic mutations in LGSOCs with matched normal tissues. We detected and validated novel mutations in DNM3, which were present in 3 of the 14 samples analyzed. Additionally, we identified novel indels, regions with CNVs, dysregulated mRNA, dysregulated proteins, and phosphosites that are more prevalent in short-term survivors. This integrated proteogenomic analysis can guide research into the pathogenesis and treatment of LGSOC.https://doi.org/10.1186/s12967-022-03820-xLow-grade serous ovarian cancerWhole-genome sequencingGlobal proteomicsGlobal phosphoproteomicsRNAseq |
| spellingShingle | Kwong-Kwok Wong Nicholas W. Bateman Chun Wai Ng Yvonne T. M. Tsang Charlotte S. Sun Joseph Celestino Tri V. Nguyen Anais Malpica R. Tyler Hillman Jianhua Zhang P. Andrew Futreal Christine Rojas Kelly A. Conrads Brian L. Hood Clifton L. Dalgard Matthew D. Wilkerson Neil T. Phippen Thomas P. Conrads George L. Maxwell Anil K. Sood David M. Gershenson Integrated multi-omic analysis of low-grade ovarian serous carcinoma collected from short and long-term survivors Journal of Translational Medicine Low-grade serous ovarian cancer Whole-genome sequencing Global proteomics Global phosphoproteomics RNAseq |
| title | Integrated multi-omic analysis of low-grade ovarian serous carcinoma collected from short and long-term survivors |
| title_full | Integrated multi-omic analysis of low-grade ovarian serous carcinoma collected from short and long-term survivors |
| title_fullStr | Integrated multi-omic analysis of low-grade ovarian serous carcinoma collected from short and long-term survivors |
| title_full_unstemmed | Integrated multi-omic analysis of low-grade ovarian serous carcinoma collected from short and long-term survivors |
| title_short | Integrated multi-omic analysis of low-grade ovarian serous carcinoma collected from short and long-term survivors |
| title_sort | integrated multi omic analysis of low grade ovarian serous carcinoma collected from short and long term survivors |
| topic | Low-grade serous ovarian cancer Whole-genome sequencing Global proteomics Global phosphoproteomics RNAseq |
| url | https://doi.org/10.1186/s12967-022-03820-x |
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