Actionable Mutations in Solid Tumors

Amy M. Sion, PharmD BCOP
Clinical Pharmacy Specialist—Genitourinary/Head and Neck/Oncology Research
Medical University of South Carolina, Hollings Cancer Center
Charleston, SC

Emma Dion
PharmD candidate (2020)
University of South Carolina College of Pharmacy
Columbia, SC

It has long been understood that cancer develops due to an accumulation of genomic mutations in healthy cells. Alterations in oncogenes and tumor suppressor proteins, like p53, lead to dysregulation of cell cycle control resulting in transformation of normal cells to a cancer phenotype. The identification of mutations that drive the onset of cancer has led not only to a better understanding of cancer physiology but also to significant advancements in the development of drugs that target specific mutations in a tumor. Precision oncology is the term used to describe personalized cancer treatment based on the genetic changes in an individual patient’s tumor. The utility of precision oncology in clinical practice has been made possible by advances in technology such as next-generation sequencing (NGS), along with intensive research efforts made possible by funding from programs like the $200 million Precision Medicine Initiative announced by President Barack Obama in 2015.¹ This article summarizes the principles of precision oncology and provides guidance to pharmacists on using genomic information in clinical practice.

Types of Mutations and Clinical Significance

It is important to understand the type and function of a mutation and its biological significance when using genomic analyses to design a patient treatment plan. Tumor cells have both inherited and somatic variants in their genome. Hereditary mutations, referred to as germline mutations, are gene changes in the germ cells (sperm or oocyte) that are passed to every cell in the offspring.² Many germline mutations in cancer are known, such as BRCA1/2, TP53, ATM, and PALB2, and they are most often associated with increased cancer susceptibility and more aggressive cancer phenotypes.³

Alternatively, somatic mutations are not present in germ cells and develop spontaneously in an individual’s DNA over time. These acquired changes in human oncogenes are known to play a role in the development of cancer. Moreover, the number of somatic mutations in the tumor can change over time, potentially leading to treatment resistance and disease progression.

Understanding common terms used to describe the clinical significance of cancer mutations is also essential. An actionable mutation is defined as a genetic aberration in a patient’s tumor that is targetable with an available anticancer treatment or is the target of novel therapeutics in development. A driver mutation is a mutation that may not be targetable with a specific treatment but is known to play a role in cancer development, resistance, or progression. Passenger mutations are nonpathogenic and are thought to have little or no biological significance to cancer biology but are linked to driver mutations on the same gene.^2-4 Thus, given the diversity of genetic aberrations in cancer, it is essential to understand the clinical relevance of each type of mutation in solid tumors.

Further, some genomic aberrations are predictive of treatment response, prognostic of outcomes, or both, depending on the tumor type. For example, mutations in the RAS genes KRAS and NRAS predict a poor response to epidermal growth factor receptor (EGFR) therapies, like cetuximab and panitumumab, in colorectal cancer. In non-small-cell lung cancer (NSCLC) tumors, the presence of a KRAS mutation predicts a poor response to EGFR tyrosine kinase inhibitors, like erlotinib. Prognostically, NSCLC tumors with mutant KRAS demonstrate poor survival compared with tumors having wild-type KRAS.⁵ To date, no therapies specifically targeting Ras proteins have been approved by the U.S. Food and Drug Administration (FDA), so the clinical significance of KRAS in solid tumors remains as a predictor of treatment responses and a prognostic marker of clinical outcomes.

The presence of a germline BRCA1/2 mutation is known to increase the risk of developing breast and ovarian cancer. More so, it is well known that breast cancer patients with BRCA1/2 mutations have an overall worse prognosis compared to patients with sporadic breast cancer, and the presence of a BRCA1 mutation is associated with triple negative breast cancer, which has a worse prognosis than hormone receptor or human epidermal growth factor receptor 2 (HER2)–positive disease.³ Likewise, the pivotal study by Antoniou and colleagues analyzed more than 8,000 cases of breast and ovarian cancer and showed that the cumulative risk of ovarian cancer development was 39% in patients with BRCA1 and 11% in patients with and BRCA2.⁶ Interestingly, the presence of BRCA1/2 mutations in ovarian cancer has been shown to prolong survival and confer sensitivity to platinum chemotherapy.⁷

Next-Generation Sequencing

The use of precision oncology to guide treatment decisions has increased because of recent advancements in NGS. NGS is a genomic profiling technology based on high-throughput DNA and RNA sequencing platforms that analyze specific gene panels for molecular changes and actionable driver mutations.⁸ NGS technology can be used to analyze DNA or RNA from tumor tissue or circulating tumor DNA (ctDNA) from the blood, also called a liquid biopsy. ctDNA is composed of small fragments of tumor DNA shed by the tumor into the blood when cells undergo apoptosis.⁹ Studies have shown that genomic changes detected using NGS from liquid biopsy have a strong correlation to NGS testing from tumor tissue. A liquid biopsy can be used in cases where tumor tissue is not available, cannot be obtained, or is of poor quality. Two FDA-approved liquid biopsy assays are available, Guardant360 and FoundationACT, which currently analyze more than 70 genes that are relevant in solid tumors.^10,11 For FDA-approved targeted therapies, companion NGS tests, both tissue- and liquid-based, are used to detect the presence of the associated mutation.

Taking Action on an Actionable Mutation

Essential questions need to be addressed when one is analyzing NGS reports to guide treatment decisions in solid tumors. Is a mutation benign or pathogenic (i.e., is it a driver mutation)? Is it prognostic of outcomes or predictive of response to certain therapies? Is the mutation a variant of known significance? Is there an approved targeted therapy?

Moreover, it is as important to identify mutations that do not convey response to targeted agents as it is to identify ones that correlate with efficacy. For example, fusions in neurotrophic-tropomyosin receptor kinase (NTRK) genes are known drivers of oncogenesis, and various solid tumors harboring

NTRK fusions have been shown to have response rates of up to 79% to NTRK inhibitors, like larotrectinib. On the other hand, point mutations in NTRK are associated with a lack of response to NTRK inhibitors. Therefore, an NTKR inhibitor should be used only in a patient with an NTRK fusion-positive tumor.¹²

For FDA-approved targeted therapies, the relevance of a specific mutation and the efficacy of the associated treatment have been validated in clinical trials. (Table 1 - see PDF) summarizes known actionable mutations and their matched anticancer therapies. Although most targeted agents are approved for a specific tumor type harboring a mutation, clinical guidelines may recommend that these agents be used off-label in a different tumor type with the same mutation. Further, when a mutation of known significance is identified but no approved therapy exists, a clinical trial should be considered.

Last, it is important to consider the appropriate time to reevaluate NGS throughout the course of treatment in patients with advanced disease. The frequency of existing somatic mutations can fluctuate with a treatment response, and new somatic mutations may develop with disease progression; therefore, NGS may be most beneficial at the time of treatment failure or progression.

Microsatellite Instability and Deficient DNA Mismatch Repair

Microsatellite instability and deficient DNA mismatch repair (dMMR) can be conceptually hard to understand. Microsatellites are known short sequences of DNA with repeated nucleotides (e.g., CTGTGTGTGTGCA) that are inherited in all cells throughout the body. When a tumor cell contains a microsatellite with a different sequence compared to the same microsatellite in a normal cell, this is called microsatellite instability, or MSI. The frequency of abnormal microsatellites in a tumor determines whether it is characterized by an MSI-Low or MSI-High phenotype.

Tumors with dMMR are not able to repair DNA damage because of germline mutations in mismatch repair genes, allowing cancer cells to proliferate with aberrant DNA. Microsatellites are susceptible to errors during DNA replication because of the repetitive nucleotides, but without a functional DNA repair system, these errors are not repaired in proliferating tumor cells. MSI status is therefore a surrogate marker for dMMR in solid tumors.¹³ MSI-H/dMMR status may be a useful biomarker for identifying a patient’s response to anti-programmed-death 1 (PD-1) and anti-programmed-death-ligand 1 (PD-L1) immunotherapies. Cancers that are considered MSI-H/dMMR harbor thousands of mutations that code for neoantigens that potentially increase the immunogenicity of the tumor and upregulate immune checkpoint blockade proteins. Hence, pembrolizumab is approved for tumors with MSI-H or dMMR regardless of the tumor’s origin.¹⁴

Likewise, in tumors with BRCA1/2 mutations, the intrinsic DNA repair processes are often dysregulated. Poly (ADP-ribose) polymerase (PARP) is an enzyme that plays a critical role in DNA repair in BRCA1/2 deficient solid tumors. Currently, four PARP inhibitors have been approved for use in ovarian and breast cancers with BRCA1/2 mutations, and recent clinical trials have demonstrated efficacy of these agents in treating prostate and pancreatic cancers with BRCA1/2 deficiency.^15,16

The Role of the Pharmacist in Precision Oncology

Because genomic-based decision making has become a routine part of oncology clinical practice, it is important for pharmacists to know where to find up-to-date information on the clinical significance and actionability of a genomic variant. OncoKB and the Catalogue of Somatic Mutations in Cancer (COSMIC) are comprehensive and curated databases that provide evidence-based information about the clinical significance of somatic mutations in cancer. (Table 2 - see PDF) provides a list of resources for interpreting genomic variants in cancer. It is recommended that each patient’s genomic report undergo a comprehensive review under the guidance of a molecular tumor board (MTB) if one exists at the institution. If an MTB does not exist, it is recommended that all NGS findings be presented at an interdisciplinary tumor board when determining the best treatment approach for the patient.¹⁷

Walko and colleagues published a report in 2016 detailing three pharmacist-led precision oncology models at different institutions.¹⁸ Their report showed the different roles an oncology pharmacist can play in the implementation of precision medicine in clinical practice, including but not limited to participation in an MTB, selection of therapy, and procurement of off-label medications. Their report also recommends the development of continuing education programs for oncology pharmacists and the incorporation of precision oncology modules into residency programs and school of pharmacy curricula. As the genomic-guided approach to cancer care expands in practice, it will be imperative that practicing pharmacists have a strong understanding of precision oncology principles and access to appropriate tools and educational resources for confident decision making.

References

1. Schaffhausen J. What precisely is precision medicine? Trends Pharmacol Sci. 2017;38:1-2.
2. U.S. National Institutes of Health. National Cancer Institute Dictionary of Cancer Terms: Germline mutation. Available at https://www.cancer.gov/publications/dictionaries/cancer-terms/def/germline-mutation, Accessed February 4, 2020.
3. Sun J, Meng H, Yao L, et al. Germline mutations in cancer susceptibility genes in a large series of unselected breast cancer patients. Clin Cancer Res. 2017;23;6113-6119.
4. Brown AL, Li M, Goncearenco A, Panchenko AR. Finding driver mutations in cancer: elucidating the role of background mutational processes. PLoS Comput Biol. 2019;15:e1006981.
5. Eberhard DA, Johnson BE, Amler LC, et al. Mutations in the epidermal growth factor receptor and in KRAS are predictive and prognostic indicators in patients with non-small-cell lung cancer treated with chemotherapy alone and in combination with erlotinib. J Clin Oncol. 2005;23:5900-5909.
6. Antoniou A, Pharoah PD, Narod S, et al. Average risks of breast and ovarian cancer associated with BRCA1 or BRCA2 mutations detected in case series unselected for family history: a combined analysis of 22 studies. Am J Hum Genet. 2003;72:1117-1130.
7. Neff RT, Senter L, Salani R. BRCA mutation in ovarian cancer: testing, implications and treatment considerations. Ther Adv Med Oncol. 2017;9:519-531.
8. Allegretti M, Fabi A, Buglioni S, et al. Tearing down the walls: FDA approves next generation sequencing (NGS) assays for actionable cancer genomic aberrations. J Exp Clin Cancer Res. 2018;37:47.
9. U.S. National Library of Medicine. What is circulating tumor DNA and how is it used to diagnose and manage cancer? Genetics Home Reference. https://ghr.nlm.nih.gov/primer/testing/circulatingtumordna. Accessed February 4, 2020.
10. NewBridge Pharmaceuticals. The Guardant 360 Assay. Available at https://www.guardant360.com. Accessed February 4, 2020.
11. Foundation Medicine. What is FoundationOne Liquid? Available at https://www.foundationmedicine.com/genomic-testing/foundation-one-liquid. Accessed February 4, 2020.
12. Okamura R, Boichard A, Kato S, et al. Analysis of NTRK alterations in pan-cancer adult and pediatric malignancies: implications for NTRK-targeted therapeutics. JCO Precis Oncol. 2018; 2018.
13. Zhao P, Li L, Jiang X, Li Q. Mismatch repair deficiency/microsatellite instability-high as a predictor for anti-PD-1/PD-L1 immunotherapy efficacy. J Hematol Oncol. 2019;12:54.
14. Marabelle A, Le DT, Ascierto PA, et al. Efficacy of pembrolizumab in patients with noncolorectal high microsatellite instability/mismatch repair-deficient cancer: results from the phase II KEYNOTE-158 Study. J Clin Oncol. 2020;38:1-10.
15. Yap TA, Plummer R, Azad NS, Helleday T. The DNA damaging revolution: PARP inhibitors and beyond. Am Soc Clin Oncol Educ Book. 2019;39:185-195.
16. Golan T, Hammel P, Reni M, et al. Maintenance olaparib for germline BRCA-mutated metastatic pancreatic cancer. N Engl J Med. 2019;381:317-327.
17. Knepper TC, Bell GC, Hicks JK, et al. Key lessons learned from Moffitt’s molecular tumor board: the Clinical Genomics Action Committee experience. Oncologist. 2017;22:144-151.
18. Walko C, Kiel PJ, Kolesar J. Precision medicine in oncology: new practice models and roles for oncology pharmacists. Am J Health Syst Pharm. 2016;73:1935-1942.
19. National Comprehensive Cancer Network. NCCN Clinical Practice Guidelines in Oncology. Bladder Cancer. Version 3.2020 (January 17, 2020). Available at https://www.nccn.org/professionals/physician_gls/pdf/bladder.pdf. Accessed February 28, 2020.
20. National Comprehensive Cancer Network. NCCN Clinical Practice Guidelines in Oncology. Breast Cancer. Version 3.2020 (March 6, 2020). Available at https://www.nccn.org/professionals/physician_gls/pdf/breast.pdf. Accessed February 12, 2020.
21. National Comprehensive Cancer Network. NCCN Clinical Practice Guidelines in Oncology. Colon Cancer. Version 2.2020 (March 3, 2020). Available at https://www.nccn.org/professionals/physician_gls/pdf/colon.pdf. Accessed March 4, 2020.
22. National Comprehensive Cancer Network. NCCN Clinical Practice Guidelines in Oncology. Cutaneous Melanoma. Version 1.2020 (December 19, 2019). Available at https://www.nccn.org/professionals/physician_gls/pdf/cutaneous_melanoma.pdf. Accessed February 4, 2020.
23. National Comprehensive Cancer Network. NCCN Clinical Practice Guidelines in Oncology. Non-Small Cell Lung Cancer. Version 3.2020 (February 11, 2020). Available at https://www.nccn.org/professionals/physician_gls/pdf/nscl.pdf. Accessed February 28, 2020.
24. National Comprehensive Cancer Network. NCCN Clinical Practice Guidelines in Oncology. Ovarian Cancer Including Fallopian Tube Cancer and Primary Peritoneal Cancer. Version 1.2020 (March 11, 2020). Available at https://www.nccn.org/professionals/physician_gls/pdf/ovarian.pdf. Accessed February 4, 2020.
25. National Comprehensive Cancer Network. NCCN Clinical Practice Guidelines in Oncology. Pancreatic Adenocarcinoma. Version 1.2020 (November 26, 2019). Available at https://www.nccn.org/professionals/physician_gls/pdf/pancreatic.pdf. Accessed February 28, 2020.
26. National Comprehensive Cancer Network. NCCN Clinical Practice Guidelines in Oncology. Prostate Cancer. Version 4.2019. Version 1.2020 (March 16, 2020). Available at https://www.nccn.org/professionals/physician_gls/pdf/prostate.pdf. Accessed March 19, 2020.
27. National Comprehensive Cancer Network. NCCN Clinical Practice Guidelines in Oncology. Soft Tissue Sarcoma. Version 6.2019 (February 10, 2020). Available at https://www.nccn.org/professionals/physician_gls/pdf/sarcoma.pdf. Accessed February 28, 2020.
28. Tsang H, Addepalli K, Davis SR. Resources for interpreting variants in precision genomic oncology applications. Front Oncol. 2017;7:214.
29. Chakravarty D, Gao J, Phillips SM, et al. OncoKB: a precision oncology knowledge base. JCO Precis Oncol. 2017; 2017. Epub May 16, 2017.