1
|
Parkman GL, Turapov T, Kircher DA, Burnett WJ, Stehn CM, O’Toole K, Culver KM, Chadwick AT, Elmer RC, Flaherty R, Stanley KA, Foth M, Lum DH, Judson-Torres RL, Friend JE, VanBrocklin MW, McMahon M, Holmen SL. Genetic Silencing of AKT Induces Melanoma Cell Death via mTOR Suppression. Mol Cancer Ther 2024; 23:301-315. [PMID: 37931033 PMCID: PMC10932877 DOI: 10.1158/1535-7163.mct-23-0474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/08/2023] [Accepted: 10/30/2023] [Indexed: 11/08/2023]
Abstract
Aberrant activation of the PI3K-AKT pathway is common in many cancers, including melanoma, and AKT1, 2 and 3 (AKT1-3) are bona fide oncoprotein kinases with well-validated downstream effectors. However, efforts to pharmacologically inhibit AKT have proven to be largely ineffective. In this study, we observed paradoxical effects following either pharmacologic or genetic inhibition of AKT1-3 in melanoma cells. Although pharmacological inhibition was without effect, genetic silencing of all three AKT paralogs significantly induced melanoma cell death through effects on mTOR. This phenotype was rescued by exogenous AKT1 expression in a kinase-dependent manner. Pharmacological inhibition of PI3K and mTOR with a novel dual inhibitor effectively suppressed melanoma cell proliferation in vitro and inhibited tumor growth in vivo. Furthermore, this single-agent-targeted therapy was well-tolerated in vivo and was effective against MAPK inhibitor-resistant patient-derived melanoma xenografts. These results suggest that inhibition of PI3K and mTOR with this novel dual inhibitor may represent a promising therapeutic strategy in this disease in both the first-line and MAPK inhibitor-resistant setting.
Collapse
Affiliation(s)
- Gennie L. Parkman
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
- Department of Oncological Sciences, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
| | - Tursun Turapov
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
| | - David A. Kircher
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
- Department of Oncological Sciences, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
| | - William J. Burnett
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
| | - Christopher M. Stehn
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
| | - Kayla O’Toole
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
- Department of Oncological Sciences, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
| | - Katie M. Culver
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
| | - Ashley T. Chadwick
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
| | - Riley C. Elmer
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
| | - Ryan Flaherty
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
| | - Karly A. Stanley
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
| | - Mona Foth
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
| | - David H. Lum
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
| | - Robert L. Judson-Torres
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
- Department of Oncological Sciences, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
- Department of Dermatology, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
| | | | - Matthew W. VanBrocklin
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
- Department of Oncological Sciences, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
- Department of Surgery, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
| | - Martin McMahon
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
- Department of Oncological Sciences, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
- Department of Dermatology, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
| | - Sheri L. Holmen
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
- Department of Oncological Sciences, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
- Department of Surgery, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
| |
Collapse
|
2
|
Actionable Mutation Profile of Sun-Protected Melanomas in South America. Am J Dermatopathol 2022; 44:741-747. [PMID: 35503891 DOI: 10.1097/dad.0000000000002213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
ABSTRACT Melanomas that arise in sun-protected sites, including acral and oral mucosal melanomas, are likely under the control of unique, specific mechanisms that lead to mutagenesis through various pathways. In this study, we examined somatic mutations in tumors by targeted sequencing using a custom Ion Ampliseq Panel, comprising hotspots of 14 genes that are frequently mutated in solid tumors. Tumor DNA was extracted from 9 formalin fixation, paraffin-embedded sun-protected melanomas (4 primary oral mucosal melanomas and 5 acral lentiginous melanomas), and we identified mutations in the NRAS, PIK3CA, EGFR, HRAS, ERBB2, and ROS1 genes. This study reveals new actionable mutations that are potential targets in the treatment of photo-protected melanomas. Additional studies on more of these melanoma subtypes could confirm our findings and identify new mutations.
Collapse
|
3
|
Parkman GL, Foth M, Kircher DA, Holmen SL, McMahon M. The role of PI3'-lipid signalling in melanoma initiation, progression and maintenance. Exp Dermatol 2022; 31:43-56. [PMID: 34717019 PMCID: PMC8724390 DOI: 10.1111/exd.14489] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 09/11/2021] [Accepted: 10/19/2021] [Indexed: 01/03/2023]
Abstract
Phosphatidylinositol-3'-kinases (PI3Ks) are a family of lipid kinases that phosphorylate the 3' hydroxyl (OH) of the inositol ring of phosphatidylinositides (PI). Through their downstream effectors, PI3K generated lipids (PI3K-lipids hereafter) such as PI(3,4,5)P3 and PI(3,4)P2 regulate myriad biochemical and biological processes in both normal and cancer cells including responses to growth hormones and cytokines; the cell division cycle; cell death; cellular growth; angiogenesis; membrane dynamics; and autophagy and many aspects of cellular metabolism. Engagement of receptor tyrosine kinase by their cognate ligands leads to activation of members of the Class I family of PI3'-kinases (PI3Kα, β, δ & γ) leading to accumulation of PI3K-lipids. Importantly, PI3K-lipid accumulation is antagonized by the hydrolytic action of a number of PI3K-lipid phosphatases, most notably the melanoma suppressor PTEN (lipid phosphatase and tensin homologue). Downstream of PI3K-lipid production, the protein kinases AKT1-3 are believed to be key effectors of PI3'-kinase signalling in cells. Indeed, in preclinical models, activation of the PI3K→AKT signalling axis cooperates with alterations such as expression of the BRAFV600E oncoprotein kinase to promote melanoma progression and metastasis. In this review, we describe the different classes of PI3K-lipid effectors, and how they may promote melanomagenesis, influence the tumour microenvironment, melanoma maintenance and progression to metastatic disease. We also provide an update on both FDA-approved or experimental inhibitors of the PI3K→AKT pathway that are currently being evaluated for the treatment of melanoma either in preclinical models or in clinical trials.
Collapse
Affiliation(s)
- Gennie L. Parkman
- Department of Oncological Sciences, University of Utah Health Sciences Center, Salt Lake City, Utah, USA
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Mona Foth
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - David A. Kircher
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Sheri L. Holmen
- Department of Oncological Sciences, University of Utah Health Sciences Center, Salt Lake City, Utah, USA
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah, USA
- Department of Surgery, University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Martin McMahon
- Department of Oncological Sciences, University of Utah Health Sciences Center, Salt Lake City, Utah, USA
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah, USA
- Department of Dermatology, University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| |
Collapse
|
4
|
Resistance to Molecularly Targeted Therapies in Melanoma. Cancers (Basel) 2021; 13:cancers13051115. [PMID: 33807778 PMCID: PMC7961479 DOI: 10.3390/cancers13051115] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 12/12/2022] Open
Abstract
Malignant melanoma is the most aggressive type of skin cancer with invasive growth patterns. In 2021, 106,110 patients are projected to be diagnosed with melanoma, out of which 7180 are expected to die. Traditional methods like surgery, radiation therapy, and chemotherapy are not effective in the treatment of metastatic and advanced melanoma. Recent approaches to treat melanoma have focused on biomarkers that play significant roles in cell growth, proliferation, migration, and survival. Several FDA-approved molecular targeted therapies such as tyrosine kinase inhibitors (TKIs) have been developed against genetic biomarkers whose overexpression is implicated in tumorigenesis. The use of targeted therapies as an alternative or supplement to immunotherapy has revolutionized the management of metastatic melanoma. Although this treatment strategy is more efficacious and less toxic in comparison to traditional therapies, targeted therapies are less effective after prolonged treatment due to acquired resistance caused by mutations and activation of alternative mechanisms in melanoma tumors. Recent studies focus on understanding the mechanisms of acquired resistance to these current therapies. Further research is needed for the development of better approaches to improve prognosis in melanoma patients. In this article, various melanoma biomarkers including BRAF, MEK, RAS, c-KIT, VEGFR, c-MET and PI3K are described, and their potential mechanisms for drug resistance are discussed.
Collapse
|
5
|
Louveau B, Jouenne F, Têtu P, Sadoux A, Gruber A, Lopes E, Delyon J, Serror K, Marco O, Da Meda L, Ndiaye A, Lermine A, Dumaz N, Battistella M, Baroudjian B, Lebbe C, Mourah S. A Melanoma-Tailored Next-Generation Sequencing Panel Coupled with a Comprehensive Analysis to Improve Routine Melanoma Genotyping. Target Oncol 2020; 15:759-771. [PMID: 33151472 DOI: 10.1007/s11523-020-00764-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Tumor molecular deciphering is crucial in clinical management. Pan-cancer next-generation sequencing panels have moved towards exhaustive molecular characterization. However, because of treatment resistance and the growing emergence of pharmacological targets, tumor-specific customized panels are needed to guide therapeutic strategies. OBJECTIVE The objective of this study was to present such a customized next-generation sequencing panel in melanoma. METHODS Melanoma patients with somatic molecular profiling performed as part of routine care were included. High-throughput sequencing was performed with a melanoma tailored next-generation sequencing panel of 64 genes involved in molecular classification, prognosis, theranostic, and therapeutic resistance. Single nucleotide variants and copy number variations were screened, and a comprehensive molecular analysis identified clinically relevant alterations. RESULTS Four hundred and twenty-one melanoma cases were analyzed (before any treatment initiation for 94.8% of patients). After bioinformatic prioritization, we uncovered 561 single nucleotide variants, 164 copy number variations, and four splice-site mutations. At least one alteration was detected in 368 (87.4%) lesions, with BRAF, NRAS, CDKN2A, CCND1, and MET as the most frequently altered genes. Among patients with BRAFV600 mutated melanoma, 44.5% (77 of 173) harbored at least one concurrent alteration driving potential resistance to mitogen-activated protein kinase inhibitors. In patients with RAS hotspot mutated lesions and in patients with neither BRAFV600 nor RAS hotspot mutations, alterations constituting potential pharmacological targets were found in 56.9% (66 of 116) and 47.7% (63 of 132) of cases, respectively. CONCLUSIONS Our tailored next-generation sequencing assay coupled with a comprehensive analysis may improve therapeutic management in a significant number of patients with melanoma. Updating such a panel and implementing multi-omic approaches will further enhance patients' clinical management.
Collapse
Affiliation(s)
- Baptiste Louveau
- Department of Pharmacology and Solid Tumor Genomics, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 1 Avenue Claude Vellefaux, 75475, Paris Cedex 10, France.,Université de Paris, Paris, France.,INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology and Immunotherapy (HIPI), Paris, France
| | - Fanélie Jouenne
- Department of Pharmacology and Solid Tumor Genomics, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 1 Avenue Claude Vellefaux, 75475, Paris Cedex 10, France.,Université de Paris, Paris, France.,INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology and Immunotherapy (HIPI), Paris, France
| | - Pauline Têtu
- Department of Dermatology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Aurélie Sadoux
- Department of Pharmacology and Solid Tumor Genomics, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 1 Avenue Claude Vellefaux, 75475, Paris Cedex 10, France
| | - Aurélia Gruber
- Department of Pharmacology and Solid Tumor Genomics, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 1 Avenue Claude Vellefaux, 75475, Paris Cedex 10, France
| | - Eddie Lopes
- Department of Pharmacology and Solid Tumor Genomics, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 1 Avenue Claude Vellefaux, 75475, Paris Cedex 10, France
| | - Julie Delyon
- Université de Paris, Paris, France.,INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology and Immunotherapy (HIPI), Paris, France.,Department of Dermatology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Kevin Serror
- Department of Plastic, Reconstructive and Esthetic Surgery, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Oren Marco
- Department of Plastic, Reconstructive and Esthetic Surgery, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Laetitia Da Meda
- Department of Dermatology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Aminata Ndiaye
- MOABI-APHP Bioinformatics Platform-WIND-DSI, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Alban Lermine
- MOABI-APHP Bioinformatics Platform-WIND-DSI, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Nicolas Dumaz
- INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology and Immunotherapy (HIPI), Paris, France
| | - Maxime Battistella
- Université de Paris, Paris, France.,INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology and Immunotherapy (HIPI), Paris, France.,Department of Pathology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Barouyr Baroudjian
- Department of Dermatology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Céleste Lebbe
- Université de Paris, Paris, France.,INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology and Immunotherapy (HIPI), Paris, France.,Department of Dermatology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Samia Mourah
- Department of Pharmacology and Solid Tumor Genomics, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 1 Avenue Claude Vellefaux, 75475, Paris Cedex 10, France. .,Université de Paris, Paris, France. .,INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology and Immunotherapy (HIPI), Paris, France.
| |
Collapse
|
6
|
Fattore L, Campani V, Ruggiero CF, Salvati V, Liguoro D, Scotti L, Botti G, Ascierto PA, Mancini R, De Rosa G, Ciliberto G. In Vitro Biophysical and Biological Characterization of Lipid Nanoparticles Co-Encapsulating Oncosuppressors miR-199b-5p and miR-204-5p as Potentiators of Target Therapy in Metastatic Melanoma. Int J Mol Sci 2020; 21:E1930. [PMID: 32178301 PMCID: PMC7139872 DOI: 10.3390/ijms21061930] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/06/2020] [Accepted: 03/10/2020] [Indexed: 02/06/2023] Open
Abstract
Uncontrolled MAPK signaling is the main oncogenic driver in metastatic melanomas bearing mutations in BRAF kinase. These tumors are currently treated with the combination of BRAF/MEK inhibitors (MAPKi), but this therapy is plagued by drug resistance. In this context we recently discovered that several microRNAs are involved in the development of drug resistance. In particular miR-204-5p and miR-199b-5p were found to function as antagonists of resistance because their enforced overexpression is able to inhibit melanoma cell growth in vitro either alone or in combination with MAPKi. However, the use of miRNAs in therapy is hampered by their rapid degradation in serum and biological fluids, as well as by the poor intracellular uptake. Here, we developed lipid nanoparticles (LNPs) encapsulating miR-204-5p, miR-199b-5p individually or in combination. We obtained LNPs with mean diameters < 200 nm and high miRNA encapsulation efficiency. These formulations were tested in vitro on several melanoma cell lines sensitive to MAPKi or rendered drug resistant. Our results show that LNPs encapsulating combinations of the two oncosuppressor miRNAs are highly efficient in impairing melanoma cell proliferation and viability, affect key signaling pathways involved in melanoma cell survival, and potentiate the efficacy of drugs inhibiting BRAF and MEK. These results warrant further assessment of the anti-tumor efficacy of oncosuppressor miRNAs encapsulating LNPs in in vivo tumor models.
Collapse
Affiliation(s)
- Luigi Fattore
- Istituto Nazionale Tumori IRCCS, "Fondazione G. Pascale", 80131 Naples, Italy; (L.F.); (G.B.); (P.A.A.)
| | - Virginia Campani
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy; (V.C.); (L.S.); (G.D.R.)
| | - Ciro Francesco Ruggiero
- IRCCS, Istituto Nazionale Tumori “Regina Elena”, Via Elio Chianesi 53, 00144 Rome, Italy; (C.F.R.); (V.S.)
| | - Valentina Salvati
- IRCCS, Istituto Nazionale Tumori “Regina Elena”, Via Elio Chianesi 53, 00144 Rome, Italy; (C.F.R.); (V.S.)
| | - Domenico Liguoro
- Department of Molecular and Clinical Medicine, University of Roma “Sapienza”, 00185 Rome, Italy; (D.L.); (R.M.)
| | - Lorena Scotti
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy; (V.C.); (L.S.); (G.D.R.)
| | - Gerardo Botti
- Istituto Nazionale Tumori IRCCS, "Fondazione G. Pascale", 80131 Naples, Italy; (L.F.); (G.B.); (P.A.A.)
| | - Paolo Antonio Ascierto
- Istituto Nazionale Tumori IRCCS, "Fondazione G. Pascale", 80131 Naples, Italy; (L.F.); (G.B.); (P.A.A.)
| | - Rita Mancini
- Department of Molecular and Clinical Medicine, University of Roma “Sapienza”, 00185 Rome, Italy; (D.L.); (R.M.)
| | - Giuseppe De Rosa
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy; (V.C.); (L.S.); (G.D.R.)
| | - Gennaro Ciliberto
- IRCCS, Istituto Nazionale Tumori “Regina Elena”, Via Elio Chianesi 53, 00144 Rome, Italy; (C.F.R.); (V.S.)
| |
Collapse
|
7
|
Romano G, Chen PL, Song P, McQuade JL, Liang RJ, Liu M, Roh W, Duose DY, Carapeto FCL, Li J, Teh JLF, Aplin AE, Chen M, Zhang J, Lazar AJ, Davies MA, Futreal PA, Amaria RN, Zhang DY, Wargo JA, Kwong LN. A Preexisting Rare PIK3CAE545K Subpopulation Confers Clinical Resistance to MEK plus CDK4/6 Inhibition in NRAS Melanoma and Is Dependent on S6K1 Signaling. Cancer Discov 2018; 8:556-567. [PMID: 29496665 PMCID: PMC5932238 DOI: 10.1158/2159-8290.cd-17-0745] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 01/22/2018] [Accepted: 02/23/2018] [Indexed: 12/14/2022]
Abstract
Combined MEK and CDK4/6 inhibition (MEKi + CDK4i) has shown promising clinical outcomes in patients with NRAS-mutant melanoma. Here, we interrogated longitudinal biopsies from a patient who initially responded to MEKi + CDK4i therapy but subsequently developed resistance. Whole-exome sequencing and functional validation identified an acquired PIK3CAE545K mutation as conferring drug resistance. We demonstrate that PIK3CAE545K preexisted in a rare subpopulation that was missed by both clinical and research testing, but was revealed upon multiregion sampling due to PIK3CAE545K being nonuniformly distributed. This resistant population rapidly expanded after the initiation of MEKi + CDK4i therapy and persisted in all successive samples even after immune checkpoint therapy and distant metastasis. Functional studies identified activated S6K1 as both a key marker and specific therapeutic vulnerability downstream of PIK3CAE545K-induced resistance. These results demonstrate that difficult-to-detect preexisting resistance mutations may exist more often than previously appreciated and also posit S6K1 as a common downstream therapeutic nexus for the MAPK, CDK4/6, and PI3K pathways.Significance: We report the first characterization of clinical acquired resistance to MEKi + CDK4i, identifying a rare preexisting PIK3CAE545K subpopulation that expands upon therapy and exhibits drug resistance. We suggest that single-region pretreatment biopsy is insufficient to detect rare, spatially segregated drug-resistant subclones. Inhibition of S6K1 is able to resensitize PIK3CAE545K-expressing NRAS-mutant melanoma cells to MEKi + CDK4i. Cancer Discov; 8(5); 556-67. ©2018 AACR.See related commentary by Sullivan, p. 532See related article by Teh et al., p. 568This article is highlighted in the In This Issue feature, p. 517.
Collapse
Affiliation(s)
- Gabriele Romano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Pei-Ling Chen
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ping Song
- Department of Bioengineering, Rice University, Houston, Texas
| | - Jennifer L McQuade
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Roger J Liang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mingguang Liu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Whijae Roh
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dzifa Y Duose
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Fernando C L Carapeto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jun Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jessica L F Teh
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Andrew E Aplin
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
- Department of Cutaneous Biology and Dermatology, Thomas Jefferson University, Philadelphia, Pennsylvania
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Merry Chen
- Department of Neurooncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexander J Lazar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael A Davies
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rodabe N Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David Y Zhang
- Department of Bioengineering, Rice University, Houston, Texas
| | - Jennifer A Wargo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Neurooncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lawrence N Kwong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| |
Collapse
|
8
|
Hernandez B, Adissu HA, Wei BR, Michael HT, Merlino G, Simpson RM. Naturally Occurring Canine Melanoma as a Predictive Comparative Oncology Model for Human Mucosal and Other Triple Wild-Type Melanomas. Int J Mol Sci 2018; 19:E394. [PMID: 29385676 PMCID: PMC5855616 DOI: 10.3390/ijms19020394] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 01/19/2018] [Accepted: 01/22/2018] [Indexed: 02/07/2023] Open
Abstract
Melanoma remains mostly an untreatable fatal disease despite advances in decoding cancer genomics and developing new therapeutic modalities. Progress in patient care would benefit from additional predictive models germane for human disease mechanisms, tumor heterogeneity, and therapeutic responses. Toward this aim, this review documents comparative aspects of human and naturally occurring canine melanomas. Clinical presentation, pathology, therapies, and genetic alterations are highlighted in the context of current basic and translational research in comparative oncology. Somewhat distinct from sun exposure-related human cutaneous melanomas, there is growing evidence that a variety of gene copy number alterations and protein structure/function mutations play roles in canine melanomas, in circumstances more analogous to human mucosal melanomas and to some extent other melanomas with murine sarcoma viral oncogene homolog B (BRAF), Neuroblastoma RAS Viral (V-Ras) Oncogene Homolog (NRAS), and neurofibromin 1 tumor suppressor NF1 triple wild-type genotype. Gaps in canine genome annotation, as well as an insufficient number and depth of sequences covered, remain considerable barriers to progress and should be collectively addressed. Preclinical approaches can be designed to include canine clinical trials addressing immune modulation as well as combined-targeted inhibition of Rat Sarcoma Superfamily/Mitogen-activated protein kinase (RAS/MAPK) and/or Phosphatidylinositol-3-Kinase/Protein Kinase B/Mammalian target of rapamycin (PI3K/AKT/mTOR) signal transduction, pathways frequently activated in both human and canine melanomas. Future investment should be aimed towards improving understanding of canine melanoma as a predictive preclinical surrogate for human melanoma and for mutually benefiting these uniquely co-dependent species.
Collapse
Affiliation(s)
- Belen Hernandez
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
- Medical Research Scholars Program, Office of Clinical Research Training and Medical Education, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Hibret A Adissu
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
| | - Bih-Rong Wei
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
- Leidos Biomedical Research, Inc., Frederick, MD 21704, USA.
| | - Helen T Michael
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
- NIH Comparative Biomedical Scientist Training Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
| | - Glenn Merlino
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
| | - R Mark Simpson
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
| |
Collapse
|
9
|
The next generation of metastatic melanoma: uncovering the genetic variants for anti-BRAF therapy response. Oncotarget 2018; 7:25135-49. [PMID: 26863566 PMCID: PMC5041894 DOI: 10.18632/oncotarget.7175] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/24/2016] [Indexed: 12/12/2022] Open
Abstract
Metastatic melanoma (MM) is a highly aggressive cancer with a median overall survival of 6-9 months, notwithstanding the numerous efforts in development of new therapeutic approaches. To this aim we tested the clinical applicability of the Ion Torrent Personal Genome Machine to simultaneously screen MM patients in order to individuate new or already known SNPs and mutations able to predict the duration of response to BRAF inhibitors. An Ampliseq Custom Panel, including 11 crucial full length genes involved in melanoma carcinogenesis and therapy response pathways, was created and used to analyze 25 MM patients. We reported BRAFV600 and NRASQ61 mutations in 68% and 24% of samples, respectively. Moreover, we more frequently identified the following alterations related to BRAF status: PIK3CAI391M (44%) and KITD737N (36%) mutations, CTLA4T17A (52%), MC1RV60L (32%) and MITFS473A (60%) polymorphisms. Considering the progression free survival (PFS), statistical analyses showed that BRAFV600 patients without any of these more frequent alterations had a higher median PFS. Protein structure changes seem to be due to these variants by in silico analysis. In conclusion, a Next-Generation Sequencing approach with custom panel may provide new information to evaluate tumor-specific therapeutic susceptibility and individual prognosis to improve the care of MM patients.
Collapse
|
10
|
Testa U, Castelli G, Pelosi E. Melanoma: Genetic Abnormalities, Tumor Progression, Clonal Evolution and Tumor Initiating Cells. Med Sci (Basel) 2017; 5:E28. [PMID: 29156643 PMCID: PMC5753657 DOI: 10.3390/medsci5040028] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 10/31/2017] [Accepted: 11/08/2017] [Indexed: 12/11/2022] Open
Abstract
Melanoma is an aggressive neoplasia issued from the malignant transformation of melanocytes, the pigment-generating cells of the skin. It is responsible for about 75% of deaths due to skin cancers. Melanoma is a phenotypically and molecularly heterogeneous disease: cutaneous, uveal, acral, and mucosal melanomas have different clinical courses, are associated with different mutational profiles, and possess distinct risk factors. The discovery of the molecular abnormalities underlying melanomas has led to the promising improvement of therapy, and further progress is expected in the near future. The study of melanoma precursor lesions has led to the suggestion that the pathway of tumor evolution implies the progression from benign naevi, to dysplastic naevi, to melanoma in situ and then to invasive and metastatic melanoma. The gene alterations characterizing melanomas tend to accumulate in these precursor lesions in a sequential order. Studies carried out in recent years have, in part, elucidated the great tumorigenic potential of melanoma tumor cells. These findings have led to speculation that the cancer stem cell model cannot be applied to melanoma because, in this malignancy, tumor cells possess an intrinsic plasticity, conferring the capacity to initiate and maintain the neoplastic process to phenotypically different tumor cells.
Collapse
Affiliation(s)
- Ugo Testa
- Department of Oncology, Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Germana Castelli
- Department of Oncology, Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Elvira Pelosi
- Department of Oncology, Istituto Superiore di Sanità, 00161 Rome, Italy.
| |
Collapse
|
11
|
Morgese F, Soldato D, Pagliaretta S, Giampieri R, Brancorsini D, Torniai M, Rinaldi S, Savini A, Onofri A, Scarpelli M, Berardi R. Impact of phosphoinositide-3-kinase and vitamin D3 nuclear receptor single-nucleotide polymorphisms on the outcome of malignant melanoma patients. Oncotarget 2017; 8:75914-75923. [PMID: 29100280 PMCID: PMC5652674 DOI: 10.18632/oncotarget.18304] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 04/27/2017] [Indexed: 12/31/2022] Open
Abstract
Background Several studies associating single nucleotide polymorphisms (SNPs) frequencies with tumors outcome have been conducted, nevertheless malignant melanoma literature data are inconclusive. Therefore we evaluate the impact of different genotypes for phosphoinositide-3-kinase (PI3K) and vitamin D3 nuclear receptor (VDR) SNPs on melanoma patients’ outcome. Materials and methods Genomic DNA of 88 patients was extracted from blood and tumor samples. SNPs were determined by PCR using TaqMan assays. We selected polymorphisms of the regulatory and catalytic subunit of PI3K (PIK3R1 and PIK3CA genes, respectively), analyzing rs2699887C>T of PIK3CA and rs3730089G>A of PIK3R1 SNPs. Furthermore we considered the following VDR SNPs: rs2228570A>G (Fok1), rs731236A>G (Taq1) and rs1544410C>T (Bsm1). Progression free survival (PFS) and overall survival (OS) were estimated with the Kaplan-Meier method and with Mantel-Haenszel log-rank test. Results The statistical analysis for Fok1 of VDR showed a significant difference in PFS after the first line therapy (median PFS= 21.2 months in the homozygous recessive genotype group vs. 3.3 months of homozygous dominant and heterozygous ones, p= 0.03). In particular, in homozygous recessive patients for Fok1 SNPs of VDR a high rate of histological regression and BRAF (B- Rapidly Accelerated Fibrosarcoma gene) mutation were observed. Furthermore, more efficacy of BRAF +/- MEK (MAPK-ERK-Kinase) inhibitors therapies in homozygous recessive patients vs. homozygous dominant and heterozygous ones was shown. Conclusions Our study showed a significant correlation between homozygous recessive genotype of Fok1 SNPs of VDR gene and an increased PFS in patients who underwent a first line therapy with BRAF inhibitors.
Collapse
Affiliation(s)
- Francesca Morgese
- Clinica Oncologica, Università Politecnica delle Marche, Azienda Ospedaliero-Universitaria Ospedali Riuniti "Umberto I°-G.M. Lancisi-G. Salesi", Ancona, Italy
| | - Davide Soldato
- Clinica Oncologica, Università Politecnica delle Marche, Azienda Ospedaliero-Universitaria Ospedali Riuniti "Umberto I°-G.M. Lancisi-G. Salesi", Ancona, Italy
| | - Silvia Pagliaretta
- Clinica Oncologica, Università Politecnica delle Marche, Azienda Ospedaliero-Universitaria Ospedali Riuniti "Umberto I°-G.M. Lancisi-G. Salesi", Ancona, Italy
| | - Riccardo Giampieri
- Clinica Oncologica, Università Politecnica delle Marche, Azienda Ospedaliero-Universitaria Ospedali Riuniti "Umberto I°-G.M. Lancisi-G. Salesi", Ancona, Italy
| | - Donatella Brancorsini
- Section of Pathological Anatomy and Histopathology, Deparment of Neuroscience, Università Politecnica delle Marche, Azienda Ospedaliero-Universitaria Ospedali Riuniti "Umberto I°-G.M. Lancisi-G. Salesi", Ancona, Italy
| | - Mariangela Torniai
- Clinica Oncologica, Università Politecnica delle Marche, Azienda Ospedaliero-Universitaria Ospedali Riuniti "Umberto I°-G.M. Lancisi-G. Salesi", Ancona, Italy
| | - Silvia Rinaldi
- Clinica Oncologica, Università Politecnica delle Marche, Azienda Ospedaliero-Universitaria Ospedali Riuniti "Umberto I°-G.M. Lancisi-G. Salesi", Ancona, Italy
| | - Agnese Savini
- Clinica Oncologica, Università Politecnica delle Marche, Azienda Ospedaliero-Universitaria Ospedali Riuniti "Umberto I°-G.M. Lancisi-G. Salesi", Ancona, Italy
| | - Azzurra Onofri
- Clinica Oncologica, Università Politecnica delle Marche, Azienda Ospedaliero-Universitaria Ospedali Riuniti "Umberto I°-G.M. Lancisi-G. Salesi", Ancona, Italy
| | - Marina Scarpelli
- Section of Pathological Anatomy and Histopathology, Deparment of Neuroscience, Università Politecnica delle Marche, Azienda Ospedaliero-Universitaria Ospedali Riuniti "Umberto I°-G.M. Lancisi-G. Salesi", Ancona, Italy
| | - Rossana Berardi
- Clinica Oncologica, Università Politecnica delle Marche, Azienda Ospedaliero-Universitaria Ospedali Riuniti "Umberto I°-G.M. Lancisi-G. Salesi", Ancona, Italy
| |
Collapse
|
12
|
Hambright HG, Ghosh R. Autophagy: In the cROSshairs of cancer. Biochem Pharmacol 2016; 126:13-22. [PMID: 27789215 DOI: 10.1016/j.bcp.2016.10.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 10/21/2016] [Indexed: 12/18/2022]
Abstract
Two prominent features of tumors that contribute to oncogenic survival signaling are redox disruption, or oxidative stress phenotype, and high autophagy signaling, making both phenomena ideal therapeutic targets. However, the relationship between redox disruption and autophagy signaling is not well characterized and the clinical impact of reactive oxygen species (ROS)-generating chemotherapeutics on autophagy merits immediate attention as autophagy largely contributes to chemotherapeutic resistance. In this commentary we focus on melanoma, using it as an example to provide clarity to current literature regarding the roles of autophagy and redox signaling which can be applicable to initiation and maintenance of most tumor types. Further, we address the crosstalk between ROS and autophagy signaling during pharmacological intervention and cell fate decisions. We attempt to elucidate the role of autophagy in regulating cell fate following treatment with ROS-generating agents in preclinical and clinical settings and discuss the emerging role of autophagy in cell fate decisions and as a cell death mechanism. We also address technical aspects of redox and autophagy evaluation in experimental design and data interpretation. Lastly, we present a provocative view of the clinical relevance, emerging challenges in dual targeting of redox and autophagy pathways for therapy, and the future directions to be addressed in order to advance both basic and translational aspects of this field.
Collapse
Affiliation(s)
- Heather Graham Hambright
- Department of Urology, University of Texas Health Science Center at San Antonio, South Texas Research Facility Campus, 8403 Floyd Curl Drive, San Antonio, TX 78229, USA; Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, South Texas Research Facility Campus, 8403 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Rita Ghosh
- Department of Urology, University of Texas Health Science Center at San Antonio, South Texas Research Facility Campus, 8403 Floyd Curl Drive, San Antonio, TX 78229, USA; Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, South Texas Research Facility Campus, 8403 Floyd Curl Drive, San Antonio, TX 78229, USA; Department of Pharmacology, University of Texas Health Science Center at San Antonio, South Texas Research Facility Campus, 8403 Floyd Curl Drive, San Antonio, TX 78229, USA; Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, South Texas Research Facility Campus, 8403 Floyd Curl Drive, San Antonio, TX 78229, USA.
| |
Collapse
|
13
|
Kircher DA, Silvis MR, Cho JH, Holmen SL. Melanoma Brain Metastasis: Mechanisms, Models, and Medicine. Int J Mol Sci 2016; 17:E1468. [PMID: 27598148 PMCID: PMC5037746 DOI: 10.3390/ijms17091468] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 08/02/2016] [Accepted: 08/26/2016] [Indexed: 12/15/2022] Open
Abstract
The development of brain metastases in patients with advanced stage melanoma is common, but the molecular mechanisms responsible for their development are poorly understood. Melanoma brain metastases cause significant morbidity and mortality and confer a poor prognosis; traditional therapies including whole brain radiation, stereotactic radiotherapy, or chemotherapy yield only modest increases in overall survival (OS) for these patients. While recently approved therapies have significantly improved OS in melanoma patients, only a small number of studies have investigated their efficacy in patients with brain metastases. Preliminary data suggest that some responses have been observed in intracranial lesions, which has sparked new clinical trials designed to evaluate the efficacy in melanoma patients with brain metastases. Simultaneously, recent advances in our understanding of the mechanisms of melanoma cell dissemination to the brain have revealed novel and potentially therapeutic targets. In this review, we provide an overview of newly discovered mechanisms of melanoma spread to the brain, discuss preclinical models that are being used to further our understanding of this deadly disease and provide an update of the current clinical trials for melanoma patients with brain metastases.
Collapse
Affiliation(s)
- David A Kircher
- Department of Oncological Sciences, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA.
| | - Mark R Silvis
- Department of Surgery, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA.
| | - Joseph H Cho
- Department of Oncological Sciences, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA.
| | - Sheri L Holmen
- Department of Oncological Sciences, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA.
- Department of Surgery, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA.
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA.
| |
Collapse
|
14
|
Pfarr N, Penzel R, Klauschen F, Heim D, Brandt R, Kazdal D, Jesinghaus M, Herpel E, Schirmacher P, Warth A, Weichert W, Endris V, Stenzinger A. Copy number changes of clinically actionable genes in melanoma, non-small cell lung cancer and colorectal cancer-A survey across 822 routine diagnostic cases. Genes Chromosomes Cancer 2016; 55:821-33. [PMID: 27218826 DOI: 10.1002/gcc.22378] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/19/2016] [Accepted: 05/19/2016] [Indexed: 12/29/2022] Open
Abstract
Targeted deep massive parallel sequencing has been implemented in routine molecular diagnostics for high-throughput genetic profiling of formalin-fixed paraffin-embedded (FFPE) cancer samples. This approach is widely used to interrogate simple somatic mutations but experience with the analysis of copy number variations (CNV) is limited. Here, we retrospectively analyzed CNV in 822 cancer cases (135 melanoma, 468 non-small cell lung cancers (NSCLC), 219 colorectal cancers (CRC)). We observed a decreasing frequency of CNV in clinically actionable genes from melanoma to NSCLC to CRC. The overall cohort displayed 168 (20%) amplifications in 17 druggable targets. The majority of BRAF mutant melanomas (54%) showed co-occurring CNV in other genes, mainly affecting CDKN2A. Subsets showed clustered deletions in ABL1, NOTCH1, RET or STK11, GNA11, and JAK3. Most NRAS mutant melanomas (49%) harbored CNVs in other genes with CDKN2A and FGFR3 being most frequently affected. Five BRAF/NRASwt tumors had co-amplifications of KDR, KIT, PDGFRA and another six mutated KIT. Among all NSCLC, we identified 14 EGFRamp (with ten EGFRmut) and eight KRASamp (with seven KRASmut). KRASmut tumors displayed frequent amplifications of MYC (n = 10) and MDM2 (n = 5). Fifteen KRAS/EGFR/BRAFwt tumors had MET mutations/amplifications. In CRC, amplified IGF2 was most prevalent (n = 13) followed by MYC (n = 9). Two cases showed amplified KRAS wildtype alleles. Two of the KRASmut cases harbored amplifications of NRAS and three KRASwt cases amplification of EGFR. In conclusion, we demonstrate that our approach i) facilitates detection of CNV, ii) enables detection of known CNV patterns, and iii) uncovers new CNV of clinically actionable genes in FFPE tissue samples across cancers. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Nicole Pfarr
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Institute of Pathology, Technical University Munich (TUM), Munich, Germany
| | - Roland Penzel
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Daniel Heim
- Institute of Pathology, Charité University Hospital, Berlin, Germany
| | - Regine Brandt
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Daniel Kazdal
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Moritz Jesinghaus
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Institute of Pathology, Technical University Munich (TUM), Munich, Germany
| | - Esther Herpel
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Arne Warth
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Lung Research (DZL), Heidelberg, Germany
| | - Wilko Weichert
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Institute of Pathology, Technical University Munich (TUM), Munich, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Volker Endris
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany. .,National Center for Tumor Diseases (NCT), Heidelberg, Germany.
| |
Collapse
|