The pharmacogenomics of drug resistance to protein kinase inhibitors

Dysregulation of growth factor cell signaling is a major driver of most human cancers. This has led to development of numerous drugs targeting protein kinases, with demonstrated efficacy in the treatment of a wide spectrum of cancers. Despite their high initial response rates and survival benefits, the majority of patients eventually develop resistance to these targeted therapies. This review article discusses examples of established mechanisms of drug resistance to anticancer therapies, including drug target mutations or gene amplifications, emergence of alternate signaling pathways, and pharmacokinetic variation. This reveals a role for pharmacogenomic analysis to identify and monitor for resistance, with possible therapeutic strategies to combat chemoresistance

Exploring Clinical and Genetic Factors to Optimize the Use of Tyrosine Kinase Inhibitors in Clinical Practice

Multi-targeted tyrosine kinase inhibitors (TKIs) are widely prescribed anticancer agents that provide significant benefit in survival across a range of cancers; however, 20-30% of individuals do not respond, demonstrating intrinsic resistance. The goal of this dissertation was to identify demographic, clinical, and genetic factors predictive of inefficacy to the multi-targeted TKIs. A retrospective analysis of 108,825 cancer patients revealed a heightened incidence of a Stevens-Johnson syndrome (SJS), a life-threatening adverse event, in cancer patients and suggested that TKIs may trigger the reaction, necessitating drug discontinuation. In a retrospective study of outcomes in routine clinical practice, chart reviews of 266 patients treated with multi-targeted TKIs identified a resistance rate of 21%. Duration of TKI treatment was significantly longer in non-resistant patients; however, there were no significant differences in demographics, tumor type treated, or TKI received. Similar rates of resistance in the subgroups suggest that there may be unidentified shared markers of resistance to these agents. A methodology study to determine the utility of archived formalin-fixed paraffin-embedded (FFPE) samples for genetic analyses was conducted. FFPE tumor samples representing a range of ages, tissue sources, and diagnoses were obtained for next-generation sequencing (NGS). We found no association between age of FFPE samples and sequencing failure; however, there was an association between DNA yield and ability to generate NGS. Both failed samples were derived from bone, suggesting that bone is not an ideal source for FFPE-derived DNA. To identify genetic predictors of intrinsic resistance, cancer patients treated with multi-targeted TKIs were classified as resistant or non-resistant, and tumor FFPE samples were used to generate NGS and copy number variation (CNV). NTRK1, KDR, TGFBR2, and PTPN11 were more commonly mutated in resistant patients and CDK4, CDKN2B, and ERBB2 demonstrated differential patterns of CNVs between groups. In combined analysis using random forest and a decision tree, CNV in CDK4 and CDKN2B were the most important features, and alone could differentiate 55% of individuals as resistant or non-resistant, thus implicating the cyclin-dependent pathway as an important factor in resistance to multi-targeted TKIs. This dissertation presents foundational evidence for the personalization of multi-targeted TKI prescribing and management.Doctor of Philosoph

Clinical impact of clonal hematopoiesis in hematopoietic cell transplantation: a review, metaanalysis, and call to action

Hematopoietic cell transplantation (HCT) is the only potentially curative treatment option for many patients with hematologic malignancies. While HCT outcomes have improved drastically over the years, patients and clinicians continue to face numerous survivorship challenges, such as relapse, graft-versushost disease, and secondary malignancies. Recent literature suggests that clonal hematopoiesis (CH), the presence of a recurrent somatic mutation in hematopoietic cells, in HCT patients or donors may be associated with outcomes in autologous and allogeneic HCT. Herein, we perform a review of the literature and summarize reported associations between CH and clinical outcomes in HCT. For commonly reported outcomes, we used meta-analysis methods to provide estimates of effect sizes when combining results. A total of 32 articles with relevant and independent contributions were included, covering both autologous (n = 19) and allogeneic (n = 13) HCT. The articles report variable risk for developing outcomes according to CH characteristics, patient disease status, and method of HCT. Using meta-analysis of available results, HCT outcomes with statistically significant effects by CH status include therapy-related myeloid neoplasms (OR 3.65, 95%CI 2.18-6.10) and overall survival (HR 1.38, 95%CI 1.20-1.58) in autologous HCT and relapse (HR 0.80, 95%CI 0.68-0.94) in allogeneic HCT. However, heterogeneity, biases, and limitations in the literature provide challenges for informing the translation of CH to clinical decision-making. We conclude with a call to action and discussion of next steps to build upon the current literature and provide granularity to the true clinical impact of CH in the setting of HCT

Tumor exome sequencing and copy number alterations reveal potential predictors of intrinsic resistance to multi-targeted tyrosine kinase inhibitors

Multi-targeted tyrosine kinase inhibitors (TKIs) have broad efficacy and similar FDA-approved indications, suggesting shared molecular drug targets across cancer types. Irrespective of tumor type, 20-30% of patients treated with multi-targeted TKIs demonstrate intrinsic resistance, with progressive disease as a best response. We conducted a retrospective cohort study to identify tumor (somatic) point mutations, insertion/deletions, and copy number alterations (CNA) associated with intrinsic resistance to multi-targeted TKIs. Using a candidate gene approach (n=243), tumor next-generation sequencing and CNA data was associated with resistant and non-resistant outcomes. Resistant individuals (n=11) more commonly harbored somatic point mutations in NTRK1, KDR, TGFBR2, and PTPN11 and CNA in CDK4, CDKN2B, and ERBB2 compared to non-resistant (n=26, p<0.01). Using a random forest classification model for variable reduction and a decision tree classification model, we were able to differentiate intrinsically resistant from non-resistant patients. CNA in CDK4 and CDKN2B were the most important analytical features, implicating the cyclin D pathway as a potentially important factor in resistance to multi-targeted TKIs. Replication of these results in a larger, independent patient cohort has potential to inform personalized prescribing of these widely utilized agents

Key Lessons Learned from Moffitt's Molecular Tumor Board: The Clinical Genomics Action Committee Experience

The increasing practicality of genomic sequencing technology has led to its incorporation into routine clinical practice. Successful identification and targeting of driver genomic alterations that provide proliferative and survival advantages to tumor cells have led to approval and ongoing development of several targeted cancer therapies. Within many major cancer centers, molecular tumor boards are constituted to shepherd precision medicine into clinical practice

The Method for Assigning Priority Levels (MAPLe): A new decision-support system for allocating home care resources

<p>Abstract</p> <p>Background</p> <p>Home care plays a vital role in many health care systems, but there is evidence that appropriate targeting strategies must be used to allocate limited home care resources effectively. The aim of the present study was to develop and validate a methodology for prioritizing access to community and facility-based services for home care clients.</p> <p>Methods</p> <p>Canadian and international data based on the Resident Assessment Instrument – Home Care (RAI-HC) were analyzed to identify predictors for nursing home placement, caregiver distress and for being rated as requiring alternative placement to improve outlook.</p> <p>Results</p> <p>The Method for Assigning Priority Levels (MAPLe) algorithm was a strong predictor of all three outcomes in the derivation sample. The algorithm was validated with additional data from five other countries, three other provinces, and an Ontario sample obtained after the use of the RAI-HC was mandated.</p> <p>Conclusion</p> <p>The MAPLe algorithm provides a psychometrically sound decision-support tool that may be used to inform choices related to allocation of home care resources and prioritization of clients needing community or facility-based services.</p

Cancer therapy shapes the fitness landscape of clonal hematopoiesis.

Acquired mutations are pervasive across normal tissues. However, understanding of the processes that drive transformation of certain clones to cancer is limited. Here we study this phenomenon in the context of clonal hematopoiesis (CH) and the development of therapy-related myeloid neoplasms (tMNs). We find that mutations are selected differentially based on exposures. Mutations in ASXL1 are enriched in current or former smokers, whereas cancer therapy with radiation, platinum and topoisomerase II inhibitors preferentially selects for mutations in DNA damage response genes (TP53, PPM1D, CHEK2). Sequential sampling provides definitive evidence that DNA damage response clones outcompete other clones when exposed to certain therapies. Among cases in which CH was previously detected, the CH mutation was present at tMN diagnosis. We identify the molecular characteristics of CH that increase risk of tMN. The increasing implementation of clinical sequencing at diagnosis provides an opportunity to identify patients at risk of tMN for prevention strategies

Cancer therapy shapes the fitness landscape of clonal hematopoiesis.

Acquired mutations are pervasive across normal tissues. However, understanding of the processes that drive transformation of certain clones to cancer is limited. Here we study this phenomenon in the context of clonal hematopoiesis (CH) and the development of therapy-related myeloid neoplasms (tMNs). We find that mutations are selected differentially based on exposures. Mutations in ASXL1 are enriched in current or former smokers, whereas cancer therapy with radiation, platinum and topoisomerase II inhibitors preferentially selects for mutations in DNA damage response genes (TP53, PPM1D, CHEK2). Sequential sampling provides definitive evidence that DNA damage response clones outcompete other clones when exposed to certain therapies. Among cases in which CH was previously detected, the CH mutation was present at tMN diagnosis. We identify the molecular characteristics of CH that increase risk of tMN. The increasing implementation of clinical sequencing at diagnosis provides an opportunity to identify patients at risk of tMN for prevention strategies