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Nesic K, Hurley RM, McGehee C, Kondrashova O, Harrell MI, Zapparoli GV, Musafer A, Wong ME, Weroha J, Hou X, Li H, Negron V, Peterson K, Schneider P, Swisher EM, Southey M, Dobrovic A, Wakefield M, Kaufmann SH, Scott CL. Abstract IA02: DNA repair gene promoter methylation patterns adapt and influence PARP inhibitor response. Clin Cancer Res 2020. [DOI: 10.1158/1557-3265.ovca19-ia02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
PARP inhibitor (PARPi) resistance in high-grade serous ovarian carcinoma (HGSOC) can be acquired as a result of restored homologous recombination (HR) due to secondary or reversion mutations in HR genes, such as BRCA1, BRCA2, and RAD51C, or due to loss of BRCA1 promoter methylation (meBRCA1). We have demonstrated that homozygous meBRCA1 can be lost or reverted to heterozygous methylation following treatment with platinum-based chemotherapy, resulting in HR-competent PARPi-resistant tumors. RAD51C promoter methylation (meRAD51C) is detected in approximately 2% of HGSOC cases and, as with meBRCA1, is associated with gene silencing and HR deficiency. We are exploring PARPi response in meRAD51C preclinical models to determine clinical relevance. Two patient-derived xenograft (PDX) models of HGSOC with RAD51C gene silencing caused by meRAD51C have distinct meRAD51C profiles (measured by methylation-specific high-resolution melt analysis and targeted bisulfite next-generation sequencing), and different responses to PARPi treatment pressure. PDX PH039 loses methylation and regains RAD51C expression after only 2 cycles of PARPi retreatment (niraparib), resulting in PARPi-refractory tumors by cycle 3-4. Illumina EPIC methylation array analysis of PH039 revealed increasing global methylation losses following each round of PARPi treatment. Lack of meRAD51C stability and rapid development of PARPi resistance in PH039 may be due to the high degree of meRAD51C heterogeneity within the tumor favoring selection of pre-existing HR-competent clones under PARPi pressure. In contrast, PDX 183 has a relatively homogeneous and stable meRAD51C profile. We have multiple examples of using unique PDX models to demonstrate various important features of PARPi resistance, including loss of promoter methylation for BRCA1 vs. RAD51C. Thus, meRAD51C confers response to PARPi in HGSOC, but PARPi treatment pressure can cause loss of methylation and drug resistance in some tumors. The contrasting PARPi responses of these PDX provide a platform for the study of meRAD51C stability in vivo and may present therapeutic opportunities to improve meRAD51C durability and PARPi responses in patients.
Citation Format: Kasenija Nesic, Rachel M Hurley, Cordelia McGehee, Olga Kondrashova, Maria I. Harrell, Giada V. Zapparoli, Ashan Musafer, Ming E. Wong, John Weroha, Xiaonan Hou, Hu Li, Vivian Negron, Kevin Peterson, Paula Schneider, Elizabeth M. Swisher, Melissa Southey, Alexander Dobrovic, Matthew Wakefield, Scott H. Kaufmann, Clare L. Scott. DNA repair gene promoter methylation patterns adapt and influence PARP inhibitor response [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr IA02.
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Affiliation(s)
- Kasenija Nesic
- *Authors contributed equally to this work
- 1Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,
| | - Rachel M Hurley
- *Authors contributed equally to this work
- 2Mayo Clinic, Rochester, MN,
| | - Cordelia McGehee
- *Authors contributed equally to this work
- 2Mayo Clinic, Rochester, MN,
| | - Olga Kondrashova
- 1Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,
| | | | - Giada V. Zapparoli
- 4Olivia Newton John Cancer Research Institute, Heidelberg, VIC, Australia,
| | - Ashan Musafer
- 4Olivia Newton John Cancer Research Institute, Heidelberg, VIC, Australia,
| | | | | | | | - Hu Li
- 2Mayo Clinic, Rochester, MN,
| | | | | | | | | | | | - Alexander Dobrovic
- 4Olivia Newton John Cancer Research Institute, Heidelberg, VIC, Australia,
| | - Matthew Wakefield
- *Authors contributed equally to this work
- 1Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,
| | - Scott H. Kaufmann
- *Authors contributed equally to this work
- 2Mayo Clinic, Rochester, MN,
| | - Clare L. Scott
- *Authors contributed equally to this work
- 1Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,
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Kondrashova O, Topp M, Nesic K, Lieschke E, Ho GY, Harrell MI, Zapparoli GV, Hadley A, Holian R, Boehm E, Heong V, Sanij E, Pearson RB, Krais JJ, Johnson N, McNally O, Ananda S, Alsop K, Hutt KJ, Kaufmann SH, Lin KK, Harding TC, Traficante N, deFazio A, McNeish IA, Bowtell DD, Swisher EM, Dobrovic A, Wakefield MJ, Scott CL. Methylation of all BRCA1 copies predicts response to the PARP inhibitor rucaparib in ovarian carcinoma. Nat Commun 2018; 9:3970. [PMID: 30266954 PMCID: PMC6162272 DOI: 10.1038/s41467-018-05564-z] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 06/25/2018] [Indexed: 01/17/2023] Open
Abstract
Accurately identifying patients with high-grade serous ovarian carcinoma (HGSOC) who respond to poly(ADP-ribose) polymerase inhibitor (PARPi) therapy is of great clinical importance. Here we show that quantitative BRCA1 methylation analysis provides new insight into PARPi response in preclinical models and ovarian cancer patients. The response of 12 HGSOC patient-derived xenografts (PDX) to the PARPi rucaparib was assessed, with variable dose-dependent responses observed in chemo-naive BRCA1/2-mutated PDX, and no responses in PDX lacking DNA repair pathway defects. Among BRCA1-methylated PDX, silencing of all BRCA1 copies predicts rucaparib response, whilst heterozygous methylation is associated with resistance. Analysis of 21 BRCA1-methylated platinum-sensitive recurrent HGSOC (ARIEL2 Part 1 trial) confirmed that homozygous or hemizygous BRCA1 methylation predicts rucaparib clinical response, and that methylation loss can occur after exposure to chemotherapy. Accordingly, quantitative BRCA1 methylation analysis in a pre-treatment biopsy could allow identification of patients most likely to benefit, and facilitate tailoring of PARPi therapy.
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Affiliation(s)
- Olga Kondrashova
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Monique Topp
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medicine and Health Sciences, Monash University, Clayton, VIC, 3168, Australia
| | - Ksenija Nesic
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Elizabeth Lieschke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Gwo-Yaw Ho
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
- Research Division, Peter MacCallum Cancer Centre, Grattan Street, Parkville, VIC, 3010, Australia
| | - Maria I Harrell
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, 98195, USA
| | - Giada V Zapparoli
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Alison Hadley
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Robert Holian
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- School of Medicine, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Emma Boehm
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- School of Medicine, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Valerie Heong
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
| | - Elaine Sanij
- Research Division, Peter MacCallum Cancer Centre, Grattan Street, Parkville, VIC, 3010, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Richard B Pearson
- Research Division, Peter MacCallum Cancer Centre, Grattan Street, Parkville, VIC, 3010, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3168, Australia
| | - John J Krais
- Fox Chase Cancer Centre, Philadelphia, PA, 19111, USA
| | - Neil Johnson
- Fox Chase Cancer Centre, Philadelphia, PA, 19111, USA
| | - Orla McNally
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
| | | | - Kathryn Alsop
- Research Division, Peter MacCallum Cancer Centre, Grattan Street, Parkville, VIC, 3010, Australia
| | - Karla J Hutt
- Department of Medicine and Health Sciences, Monash University, Clayton, VIC, 3168, Australia
| | - Scott H Kaufmann
- Departments of Oncology and Molecular Pharmacology, Mayo Clinic, Rochester, MN, 55905, USA
| | | | | | - Nadia Traficante
- Research Division, Peter MacCallum Cancer Centre, Grattan Street, Parkville, VIC, 3010, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Anna deFazio
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney Medical School, The University of Sydney and Department of Gynaecological Oncology, Westmead Hospital, Sydney, NSW, 2145, Australia
| | - Iain A McNeish
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Kensington, London, SW7 2AZ, United Kingdom
| | - David D Bowtell
- Research Division, Peter MacCallum Cancer Centre, Grattan Street, Parkville, VIC, 3010, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Elizabeth M Swisher
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, 98195, USA
| | - Alexander Dobrovic
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, VIC, 3086, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Matthew J Wakefield
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Melbourne Bioinformatics, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Clare L Scott
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.
- Department of Medicine and Health Sciences, Monash University, Clayton, VIC, 3168, Australia.
- Research Division, Peter MacCallum Cancer Centre, Grattan Street, Parkville, VIC, 3010, Australia.
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Hurley RM, Nesic K, McGehee C, Kondrashova O, Harrell MI, Schneider PA, Hou X, Correia C, Flatten KS, Zapparoli GV, Dobrovic A, Lin KK, Harding TC, Hendrickson AEW, Swisher EM, Wakefield M, Weroha SJ, Scott CL, Kaufmann SH. Abstract 5885: Loss of RAD51C promoter hypermethylation confers PARP inhibitor resistance. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-5885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Acquired PARP inhibitor (PARPi) resistance in high-grade serous ovarian cancer (HGSOC) as a result of restored homologous recombination has been observed following secondary mutations that restore full-length protein in BRCA1, BRCA2, RAD51C, and RAD51D. Additionally, loss of BRCA1 methylation has also been shown to confer resistance. However, little is known about the role of RAD51C methylation in acquired PARPi resistance. In ARIEL2 Part 1, a phase 2 study of the PARPi rucaparib in ovarian carcinoma, four (2%) tumors demonstrated RAD51C methylation. The present study utilizes HGSOC patient derived xenografts (PDXs) and recurrent samples from ARIEL2 to assess the role of RAD51C methylation in the development of PARPi resistance.
Methods: To drive PARPi resistance, PDX039, an extremely PARPi-sensitive model lacking demonstrable mutations in DNA repair genes, was treated cyclically with niraparib (100 mg/kg) for 21 days, after which the tumor was allowed to regrow and re-established in new mice for the next treatment round. To evaluate the frequency of methylation change, RAD51C methylation was analyzed in 12 rucaparib-treated mice (300 or 450 mg/kg) harboring PDX183, a PARPi-sensitive model without mutations in DNA repair genes. Global changes in gene expression following development of PARPi resistance were assessed by RNA sequencing. RAD51C promoter methylation was evaluated by bisulfite sequencing. Subsequent functional analysis included qRT-PCR, IHC, and western blot. DNA damage response pathways are being evaluated by immunofluorescence ex vivo following niraparib, rucaparib, or IR.
Results: PDX039 grew through PARPi treatment by the third and fourth cycle of therapy. RAD51C was the only DNA repair gene to show significant change in RNAseq analysis (log2 fold-change=8.43; p=2e-192), corresponding with a loss of RAD51C methylation. Moreover, after just one round of PARPi treatment, RAD51C methylation was lost in 1 of 12 PARPi-treated PDX183 xenografts. RAD51C methylation loss ultimately resulted in restoration of expression, for which functional analysis is ongoing. Analysis of patient samples is currently underway.
Conclusions: In HGSOC PDX models, RAD51C methylation affords PARPi sensitivity in the absence of DNA repair gene mutations. Treatment pressure with PARPi can reverse RAD51C methylation and restore RAD51C expression. Isolated changes in methylation of the RAD51C locus are sufficient to restore HR and convey PARPi resistance.
Citation Format: Rachel M. Hurley, Ksenija Nesic, Cordelia McGehee, Olga Kondrashova, Maria I. Harrell, Paula A. Schneider, Xiaonan Hou, Cristina Correia, Karen S. Flatten, Giada V. Zapparoli, Alexander Dobrovic, Kevin K. Lin, Thomas C. Harding, Andrea E. Wahner Hendrickson, Elizabeth M. Swisher, Matthew Wakefield, S. John Weroha, Clare L. Scott, Scott H. Kaufmann. Loss of RAD51C promoter hypermethylation confers PARP inhibitor resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5885.
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Affiliation(s)
| | - Ksenija Nesic
- 2The Walter and Eliza Hall Institute, Melbourne, Australia
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Clare L. Scott
- 2The Walter and Eliza Hall Institute, Melbourne, Australia
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Garsed DW, Alsop K, Fereday S, Emmanuel C, Kennedy CJ, Etemadmoghadam D, Gao B, Gebski V, Garès V, Christie EL, Wouters MC, Milne K, George J, Patch AM, Li J, Arnau GM, Semple T, Gadipally SR, Chiew YE, Hendley J, Mikeska T, Zapparoli GV, Amarasinghe K, Grimmond SM, Pearson JV, Waddell N, Hung J, Stewart CJ, Sharma R, Allan PE, Rambau PF, McNally O, Mileshkin L, Hamilton A, Ananda S, Grossi M, Cohen PA, Leung YC, Rome RM, Beale P, Blomfield P, Friedlander M, Brand A, Dobrovic A, Köbel M, Harnett P, Nelson BH, Bowtell DDL, deFazio A. Homologous Recombination DNA Repair Pathway Disruption and Retinoblastoma Protein Loss Are Associated with Exceptional Survival in High-Grade Serous Ovarian Cancer. Clin Cancer Res 2017; 24:569-580. [DOI: 10.1158/1078-0432.ccr-17-1621] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/07/2017] [Accepted: 10/11/2017] [Indexed: 11/16/2022]
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Busuttil RA, Zapparoli GV, Haupt S, Fennell C, Wong SQ, Pang JMB, Takeno EA, Mitchell C, Di Costanzo N, Fox S, Haupt Y, Dobrovic A, Boussioutas A. Role of p53 in the progression of gastric cancer. Oncotarget 2015; 5:12016-26. [PMID: 25427447 PMCID: PMC4322971 DOI: 10.18632/oncotarget.2434] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 09/02/2014] [Indexed: 12/20/2022] Open
Abstract
Intestinal metaplasia (IM) is a premalignant lesion associated with gastric cancer (GC) but is poorly described in terms of molecular changes. Here, we explored the role of TP53, a commonly mutated gene in GC, to determine if p53 protein expression and/or the presence of somatic mutations in TP53 can be used as a predictive marker for patients at risk of progressing to GC from IM. Immunohistochemistry and high resolution melting were used to determine p53 protein expression and TP53 mutation status respectively in normal gastric mucosa, IM without concurrent GC (IM-GC), IM with concurrent GC (IM+GC) and GC. This comparative study revealed an incremental increase in p53 expression levels with progression of disease from normal mucosa, via an IM intermediate to GC. TP53 mutations however, were not detected in IM but occurred frequently in GC. Further, we identified increased protein expression of Mdm2/x, both powerful regulators of p53, in 100% of the IM+GC cohort with these samples also exhibiting high levels of wild-type p53 protein. Our data suggests that TP53 mutations occur late in gastric carcinogenesis contributing to the final transition to cancer. We also demonstrated involvement of Mdmx in GC.
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Affiliation(s)
- Rita A Busuttil
- Cancer Genetics and Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia. Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia. Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
| | - Giada V Zapparoli
- Molecular Pathology Research and Development Laboratory, Department of Pathology Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia. Translational Genomics and Epigenomics Laboratory, Ludwig Institute for Cancer Research, Olivia Newton-John Cancer and Wellness Centre, Heidelberg, VIC, Australia
| | - Sue Haupt
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia. Molecular Pathology Research and Development Laboratory, Department of Pathology Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia. Tumour Suppression Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Christina Fennell
- Cancer Genetics and Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Stephen Q Wong
- Molecular Pathology Research and Development Laboratory, Department of Pathology Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Jia-Min B Pang
- Molecular Pathology Research and Development Laboratory, Department of Pathology Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia. Department of Pathology, University of Melbourne, Parkville, VIC, Australia
| | - Elena A Takeno
- Molecular Pathology Research and Development Laboratory, Department of Pathology Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Catherine Mitchell
- Molecular Pathology Research and Development Laboratory, Department of Pathology Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Natasha Di Costanzo
- Cancer Genetics and Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Stephen Fox
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia. Molecular Pathology Research and Development Laboratory, Department of Pathology Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia. Department of Pathology, University of Melbourne, Parkville, VIC, Australia
| | - Ygal Haupt
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia. Translational Genomics and Epigenomics Laboratory, Ludwig Institute for Cancer Research, Olivia Newton-John Cancer and Wellness Centre, Heidelberg, VIC, Australia. Tumour Suppression Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia. Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Alexander Dobrovic
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia. Molecular Pathology Research and Development Laboratory, Department of Pathology Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia. Translational Genomics and Epigenomics Laboratory, Ludwig Institute for Cancer Research, Olivia Newton-John Cancer and Wellness Centre, Heidelberg, VIC, Australia. Department of Pathology, University of Melbourne, Parkville, VIC, Australia
| | - Alex Boussioutas
- Cancer Genetics and Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia. Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia. Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia. Department of Gastroenterology, Royal Melbourne Hospital, Parkville, VIC, Australia
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Zapparoli GV, Jorissen RN, Hewitt CA, McBean M, Westerman DA, Dobrovic A. Quantitative threefold allele-specific PCR (QuanTAS-PCR) for highly sensitive JAK2 V617F mutant allele detection. BMC Cancer 2013; 13:206. [PMID: 23617802 PMCID: PMC3658971 DOI: 10.1186/1471-2407-13-206] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 03/26/2013] [Indexed: 02/03/2023] Open
Abstract
Background The JAK2 V617F mutation is the most frequent somatic change in myeloproliferative neoplasms, making it an important tumour-specific marker for diagnostic purposes and for the detection of minimal residual disease. Sensitive quantitative assays are required for both applications, particularly for the monitoring of minimal residual disease, which requires not only high sensitivity but also very high specificity. Methods We developed a highly sensitive probe-free quantitative mutant-allele detection method, Quantitative Threefold Allele-Specific PCR (QuanTAS-PCR), that is performed in a closed-tube system, thus eliminating the manipulation of PCR products. QuantTAS-PCR uses a threefold approach to ensure allele-specific amplification of the mutant sequence: (i) a mutant allele-specific primer, (ii) a 3′dideoxy blocker to suppress false-positive amplification from the wild-type template and (iii) a PCR specificity enhancer, also to suppress false-positive amplification from the wild-type template. Mutant alleles were quantified relative to exon 9 of JAK2. Results We showed that the addition of the 3′dideoxy blocker suppressed but did not eliminate false-positive amplification from the wild-type template. However, the addition of the PCR specificity enhancer near eliminated false-positive amplification from the wild-type allele. Further discrimination between true and false positives was enabled by using the quantification cycle (Cq) value of a single mutant template as a cut-off point, thus enabling robust distinction between true and false positives. As 10,000 JAK2 templates were used per replicate, the assay had a sensitivity of 1/10-4 per replicate. Greater sensitivity could be reached by increasing the number of replicates analysed. Variation in replicates when low mutant-allele templates were present necessitated the use of a statistics-based approach to estimate the load of mutant JAK2 copies. QuanTAS-PCR showed comparable quantitative results when validated against a commercial assay. Conclusions QuanTAS-PCR is a simple, cost-efficient, closed-tube method for JAK2 V617F mutation quantification that can detect very low levels of the mutant allele, thus enabling analysis of minimal residual disease. The approach can be extended to the detection of other recurrent single nucleotide somatic changes in cancer.
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Affiliation(s)
- Giada V Zapparoli
- Department of Pathology, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, Victoria 3002, Australia
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