Quantifying the Benefits of Genome-Driven Oncology

<b/> The excitement surrounding genomically selected cancer therapy has led many to question whether this treatment paradigm is living up to its initial promise. The MOSCATO study suggests that a genome-driven strategy for cancer therapy improves outcomes in a significant minority of patients who undergo molecular screening. Cancer Discov; 7(6); 552-4. ©2017 AACR.See related article by Massard et al., p. 586.

HER kinase inhibition in patients with HER2- and HER3-mutant cancers

Somatic mutations of ERBB2 and ERBB3 (which encode HER2 and HER3, respectively) are found in a wide range of cancers. Preclinical modelling suggests that a subset of these mutations lead to constitutive HER2 activation, but most remain biologically uncharacterized. Here we define the biological and therapeutic importance of known oncogenic HER2 and HER3 mutations and variants of unknown biological importance by conducting a multi-histology, genomically selected, 'basket' trial using the pan-HER kinase inhibitor neratinib (SUMMIT; clinicaltrials.gov identifier NCT01953926). Efficacy in HER2-mutant cancers varied as a function of both tumour type and mutant allele to a degree not predicted by preclinical models, with the greatest activity seen in breast, cervical and biliary cancers and with tumours that contain kinase domain missense mutations. This study demonstrates how a molecularly driven clinical trial can be used to refine our biological understanding of both characterized and new genomic alterations with potential broad applicability for advancing the paradigm of genome-driven oncology.

Accelerating Discovery of Functional Mutant Alleles in Cancer

Most mutations in cancer are rare, which complicates the identification of therapeutically significant mutations and thus limits the clinical impact of genomic profiling in patients with cancer. Here, we analyzed 24,592 cancers including 10,336 prospectively sequenced patients with advanced disease to identify mutant residues arising more frequently than expected in the absence of selection. We identified 1,165 statistically significant hotspot mutations of which 80% arose in 1 in 1,000 or fewer patients. Of 55 recurrent in-frame indels, we validated that novel AKT1 duplications induced pathway hyperactivation and conferred AKT inhibitor sensitivity. Cancer genes exhibit different rates of hotspot discovery with increasing sample size, with few approaching saturation. Consequently, 26% of all hotspots in therapeutically actionable oncogenes were novel. Upon matching a subset of affected patients directly to molecularly targeted therapy, we observed radiographic and clinical responses. Population-scale mutant allele discovery illustrates how the identification of driver mutations in cancer is far from complete.Significance: Our systematic computational, experimental, and clinical analysis of hotspot mutations in approximately 25,000 human cancers demonstrates that the long right tail of biologically and therapeutically significant mutant alleles is still incompletely characterized. Sharing prospective genomic data will accelerate hotspot identification, thereby expanding the reach of precision oncology in patients with cancer. Cancer Discov; 8(2); 174-83. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 127.

Fusions in solid tumours: diagnostic strategies, targeted therapy, and acquired resistance

Structural gene rearrangements resulting in gene fusions are frequent events in solid tumours. The identification of certain activating fusions can aid in the diagnosis and effective treatment of patients with tumours harbouring these alterations. Advances in the techniques used to identify fusions have enabled physicians to detect these alterations in the clinic. Targeted therapies directed at constitutively activated oncogenic tyrosine kinases have proven remarkably effective against cancers with fusions involving ALK, ROS1, or PDGFB, and the efficacy of this approach continues to be explored in malignancies with RET, NTRK1/2/3, FGFR1/2/3, and BRAF/CRAF fusions. Nevertheless, prolonged treatment with such tyrosine-kinase inhibitors (TKIs) leads to the development of acquired resistance to therapy. This resistance can be mediated by mutations that alter drug binding, or by the activation of bypass pathways. Second-generation and third-generation TKIs have been developed to overcome resistance, and have variable levels of activity against tumours harbouring individual mutations that confer resistance to first-generation TKIs. The rational sequential administration of different inhibitors is emerging as a new treatment paradigm for patients with tumours that retain continued dependency on the downstream kinase of interest.

Basket Studies: Redefining Clinical Trials in the Era of Genome-Driven Oncology

Understanding a tumor's detailed molecular profile has become increasingly necessary to deliver the standard of care for patients with advanced cancer. Innovations in both tumor genomic sequencing technology and the development of drugs that target molecular alterations have fueled recent gains in genome-driven oncology care. "Basket studies," or histology-agnostic clinical trials in genomically selected patients, represent one important research tool to continue making progress in this field. We review key aspects of genome-driven oncology care, including the purpose and utility of basket studies, biostatistical considerations in trial design, genomic knowledgebase development, and patient matching and enrollment models, which are critical for translating our genomic knowledge into clinically meaningful outcomes.

Abstract 375: Oncologist use and perception of large panel next generation tumor sequencing

At Memorial Sloan Kettering, we have used a clinically validated custom hybridization capture-based NGS assay (MSK-IMPACT) to sequence the tumors of more than 10,000 patients. We sought to determine physician perception and use of these results, including whether they changed management and the reasoning behind this decision-making. All physicians who ordered MSK-IMPACT testing for patients where it was not considered routine were asked to complete a questionnaire quarterly (Table). Physician determination of genomic “actionability” was compared to OncoKB, a curated knowledge base of somatic variants (OncoKB.org).

Responses were received from 146 of 258 physicians emailed (57%) regarding 1932 of 9147 patients (21%). Physician respondents comprised a diversity of cancer specialties including medical oncology (67%), pediatric oncology (8%), surgery (6%), radiation oncology (5%), and neuro-oncology (5%). A total of 49 cancer types were represented. Physicians indicated that sequencing altered management in 331 (20%) of profiled patients in need of a treatment change. Among those in whom treatment was reportedly not altered, physicians indicated the presence of at least one actionable alteration in 55% (805/1474) of cases. However, only 45% of these cases harbored a genomic variant annotated as actionable by OncoKB. Among patients in whom physicians deemed the report non-actionable, 12% had OncoKB annotated actionable variants. Across the cases annotated as potentially actionable by OncoKB, physicians identified an actionable alteration in 81% of cases. At the time of data analysis, 297 (15%) patients had been enrolled in at least one clinical trial of targeted therapy at MSKCC including 224 (12%) patients on genomically-matched trials, 76% of whom participated after IMPACT profiling. As the clinical adoption of NGS panels expands, continued education of physicians as well as maintained knowledge bases for annotation will be necessary to expand the utility of this approach and the opportunity for precision medicine.

QuestionsResponses, N (%)DID alter treatment, as follows:1. Patient enrolled to a therapeutic protocol at MSKCC265 (14)2. Patient enrolled to a therapeutic protocol at another institution15 (1)3. Patient treated with off-label use of an FDA approved therapy43 (2)DID NOT alter treatment, as follows:4. Actionable mutation(s) identified, but no therapeutic protocol was available175 (9)5. Actionable mutation(s) identified, but patient declined participation in, or was ineligible for, available therapeutic protocol115 (6)6. Actionable mutation(s) identified, but patient deteriorated, progressed, or died before results could be used176 (9)7. Actionable mutation(s) identified and therapeutic study available, but patient has not recurred/progressed since MSK-IMPACT result339 (18)8. No actionable mutation identified669 (35)Other135 (7)TOTAL1932

Citation Format: Alison M. Schram, Dalicia Reales, Jesse Galle, Roy Cambria, Robert Durany, Darren Feldman, Eric Sherman, Jonathan Rosenberg, Gabriella D'Andrea, Shrujal Baxi, Yelena Janjigian, William Tap, Maura Dickler, José Baselga, Barry Taylor, Debyani Chakravarty, Jianjiong Gao, Nikolaus D. Schultz, David B. Solit, Michael F. Berger, David M. Hyman. Oncologist use and perception of large panel next generation tumor sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 375. doi:10.1158/1538-7445.AM2017-375

A Next-Generation TRK Kinase Inhibitor Overcomes Acquired Resistance to Prior TRK Kinase Inhibition in Patients with TRK Fusion-Positive Solid Tumors

Larotrectinib, a selective TRK tyrosine kinase inhibitor (TKI), has demonstrated histology-agnostic efficacy in patients with TRK fusion-positive cancers. Although responses to TRK inhibition can be dramatic and durable, duration of response may eventually be limited by acquired resistance. LOXO-195 is a selective TRK TKI designed to overcome acquired resistance mediated by recurrent kinase domain (solvent front and xDFG) mutations identified in multiple patients who have developed resistance to TRK TKIs. Activity against these acquired mutations was confirmed in enzyme and cell-based assays and in vivo tumor models. As clinical proof of concept, the first 2 patients with TRK fusion-positive cancers who developed acquired resistance mutations on larotrectinib were treated with LOXO-195 on a first-in-human basis, utilizing rapid dose titration guided by pharmacokinetic assessments. This approach led to rapid tumor responses and extended the overall duration of disease control achieved with TRK inhibition in both patients.Significance: LOXO-195 abrogated resistance in TRK fusion-positive cancers that acquired kinase domain mutations, a shared liability with all existing TRK TKIs. This establishes a role for sequential treatment by demonstrating continued TRK dependence and validates a paradigm for the accelerated development of next-generation inhibitors against validated oncogenic targets. Cancer Discov; 7(9); 963-72. ©2017 AACR.See related commentary by Parikh and Corcoran, p. 934This article is highlighted in the In This Issue feature, p. 920.

Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients

Tumor molecular profiling is a fundamental component of precision oncology, enabling the identification of genomic alterations in genes and pathways that can be targeted therapeutically. The existence of recurrent targetable alterations across distinct histologically defined tumor types, coupled with an expanding portfolio of molecularly targeted therapies, demands flexible and comprehensive approaches to profile clinically relevant genes across the full spectrum of cancers. We established a large-scale, prospective clinical sequencing initiative using a comprehensive assay, MSK-IMPACT, through which we have compiled tumor and matched normal sequence data from a unique cohort of more than 10,000 patients with advanced cancer and available pathological and clinical annotations. Using these data, we identified clinically relevant somatic mutations, novel noncoding alterations, and mutational signatures that were shared by common and rare tumor types. Patients were enrolled on genomically matched clinical trials at a rate of 11%. To enable discovery of novel biomarkers and deeper investigation into rare alterations and tumor types, all results are publicly accessible.

Genomic Characterization of Renal Medullary Carcinoma and Treatment Outcomes

BACKGROUND

Renal medullary carcinoma (RMC) is a rare and aggressive type of kidney cancer that primarily affects young adults with sickle cell trait; outcomes are poor despite treatment. Identifying molecular features of this tumor could provide biologic rationale for novel targeted therapies. The objective was to report on clinical outcomes with systemic therapy and characterize molecular features.

PATIENTS AND METHODS

This was a retrospective analysis on 36 patients given a pathologic diagnosis of RMC at one institution from 1995 to 2015. Tumors were analyzed for expression of SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily B, Member 1 (SMARCB1) through immunohistochemistry and for genomic alterations with fluorescence in situ hybridization for SMARCB1, and targeted next-generation sequencing. Time from initiation of therapy to progression of disease and overall survival were calculated using the Kaplan-Meier method.

RESULTS

The median age in the cohort was 28 (range, 12-72) years, and all patients tested had sickle cell trait. Overall survival was 5.8 months (95% confidence interval [CI], 4.1-10.9) and for 12 patients who received platinum-based therapy, median progression-free survival was 2.5 months (95% CI, 1.2-not reached). A total of 10 available tumors underwent analysis with fluorescence in situ hybridization for SMARCB1; this revealed loss of heterozygosity with concurrent translocation in 8, and biallelic loss in 2. Next-generation targeted sequencing showed no recurring mutations.

CONCLUSIONS

Outcome was generally poor in this cohort of patients with RMC. Uniform loss of SMARCB1 is a key molecular feature in this tumor and mechanism of loss appears to be mostly through translocations and deletions.

The activity, safety, and evolving role of brigatinib in patients with ALK-rearranged non-small cell lung cancers

Brigatinib (AP26113) is a dimethylphosphine oxide group-containing tyrosine kinase inhibitor (TKI) constructed around a bisanilinopyrimidine scaffold with potent activity against the anaplastic lymphoma kinase (ALK) and several other targets. Despite the activity of first- and second-generation ALK inhibitors in advanced ALK-rearranged lung cancers, the development of acquired resistance represents an ongoing challenge. Later generation ALK inhibitors such as brigatinib are important potential tools in the management of patients with acquired resistance characterized by continued dependency on ALK. Brigatinib is active in vitro against many ALK kinase domain mutations that may mediate acquired resistance to other ALK TKIs, with reported activity (IC50 <50 nM) against ALK C1156Y, I1171S/T, V1180L, L1196M, L1152R/P, E1210K, and G1269A. In patients with ALK-rearranged lung cancers who receive brigatinib after crizotinib, substantial and durable responses and intracranial disease control can be achieved based on early-phase clinical trial data. The drug is also being explored in TKI-naïve patients. From a safety perspective, early pulmonary toxicity has been observed, prompting the decision to pursue lead-in dosing for the drug. Early data point to ALK G1202R and ALK E1210K as potential mechanisms of clinical resistance to brigatinib.

Precision oncology: Charting a path forward to broader deployment of genomic profiling

In this Perspective, David Hyman and coauthors discuss clinical research on the application of genomic information in oncology.

Haemophagocytic lymphohistiocytosis in adults: a multicentre case series over 7 years

Haemophagocytic lymphohistiocytosis (HLH) is a syndrome of uncontrolled immune activation that has gained increasing attention over the past decade. Although classically known as a familial disorder of children caused by mutations that affect cytotoxic T-cell function, an acquired form of HLH in adults is now widely recognized. This is often seen in the setting of malignancy, infection or rheumatological disorders. We performed a retrospective review across 3 tertiary care centres and identified 68 adults with HLH. The average age was 53 years (range 18-77 years) and 43 were male (63%). Underlying disorders included malignancy in 33 patients (49%), infection in 22 (33%), autoimmune disease in 19 (28%) and idiopathic HLH in 15 (22%). Patients were treated with disease-specific therapy and immunomodulatory agents. After a median follow-up of 32·2 months, 46 patients had died (69%). The median overall survival was 4 months (95% CI: 0·0-10·2 months). Patients with malignancy had a worse prognosis compared to those without (median survival 2·8 months versus 10·7 months, P = 0·007). HLH is a devastating disorder with a high mortality. Further research is needed to improve treatment and outcomes.

Primary cutaneous Candida tropicalis infection in a patient with B-cell lymphoma

We report the case of a 61-year-old man with diffuse large B-cell lymphoma who presented with a tender skin lesion on the left side of the flank of 5 weeks' duration after undergoing myeloablative chemotherapy. Prior treatment with intravenous vancomycin showed minimal response. Clinical examination revealed a tender, indurated, erythematous plaque on the left side of the flank. A skin biopsy demonstrated a lymphohistiocytic and neutrophilic infiltrate with deep dermal necrosis and fungal forms in the dermis and subcutis. A tissue culture grew Candida tropicalis; however, blood cultures remained negative for yeast. A diagnosis of primary cutaneous candidiasis was made based on the lack of response to antibiotics, tissue evidence of C tropicalis, and negative blood cultures. Although rare, primary cutaneous candidiasis should be considered in immunocompromised patients presenting with cellulitis or an abscess that is unresponsive to treatment.

A germline JAK2 SNP is associated with predisposition to the development of JAK2(V617F)-positive myeloproliferative neoplasms

Polycythemia vera, essential thrombocythemia and primary myelofibrosis are myeloproliferative neoplasms (MPN) characterized by multilineage clonal hematopoiesis. Given that the identical somatic activating mutation in the JAK2 tyrosine kinase gene (JAK2(V617F)) is observed in most individuals with polycythemia vera, essential thrombocythemia and primary myelofibrosis, there likely are additional genetic events that contribute to the pathogenesis of these phenotypically distinct disorders. Moreover, family members of individuals with MPN are at higher risk for the development of MPN, consistent with the existence of MPN predisposition loci. We hypothesized that germline variation contributes to MPN predisposition and phenotypic pleiotropy. Genome-wide analysis identified an allele in the JAK2 locus (rs10974944) that predisposes to the development of JAK2(V617F)-positive MPN, as well as three previously unknown MPN modifier loci. We found that JAK2(V617F) is preferentially acquired in cis with the predisposition allele. These data suggest that germline variation is an important contributor to MPN phenotype and predisposition.