Pharmacogenetics in the cancer clinic: from candidate gene studies to next-generation sequencing

A Pilot Study on the Whole Exome Sequencing of Prostate Cancer in the Indian Phenotype Reveals Distinct Polymorphisms

Prostate cancer (PCa) is the third most common cancer among men in India, and no next-generation sequencing (NGS) studies have been attempted earlier. Recent advances in NGS have heralded the discovery of biomarkers from Caucasian/European and Chinese ancestry, but not much is known about the Indian phenotype/variant of PCa. In a pilot study using the whole exome sequencing of benign/PCa patients, we identified characteristic mutations specific to the Indian sub-population. We observed a large number of mutations in DNA repair genes, viz. helicases, TP53, and BRCA besides the variants of unknown significance with a possibly damaging rare variant (rs730881069/chr19:55154172C/TR136Q) in the TNNI3 gene that has been previously reported as a semi-conservative amino acid substitution. Our pilot study attempts to bring an understanding of PCa prognosis and recurrence for the Indian phenotype.

Pharmacogenetics of treatments for pancreatic cancer

Introduction: Despite clinical efforts, pancreatic ductal adenocarcinoma (PDAC) has a dismal prognosis. The scarcity of effective therapies can be reflected by the lack of reliable biomarkers to adapt anticancer drugs prescription to tumors' and patients' features. Areas covered: Pharmacogenetics should provide the way to select patients who may benefit from a specific therapy that best matches individual and tumor genetic profile, but it has not yet led to gains in outcome. This review describes PDAC pharmacogenetics findings, critically reappraising studies on polymorphisms and -omics profiles correlated to response to gemcitabine, FOLFIRINOX, and nab-paclitaxel combinations, as well as limitations of targeted therapies. Further, we question whether personalized approaches will benefit patients to any significant degree, supporting the need of new strategies within well-designed trials and validated genomic tests for treatment decision-making. Expert opinion: A major challenge in PDAC is the identification of subgroups of patients who will benefit from treatments. Minimally-invasive tests to analyze biomarkers of drug sensitivity/toxicity should be developed alongside anticancer treatments. However, progress might fall below expectations because of tumor heterogeneity and clonal evolution. Whole-genome sequencing and liquid biopsies, as well as prospective validation in selected cohorts, should overcome the limitations of traditional pharmacogenetic approaches.

Genomic analysis in the clinic: benefits and challenges for health care professionals and patients in Brazil

Despite significant advances in the diagnosis and treatment of genetic diseases in the last two decades, there is still a significant proportion where a causative mutation cannot be identified and a definitive genetic diagnosis remains elusive. New genome-wide or high-throughput multiple gene tests have brought new hope to the field, since they can offer fast, cost-effective and comprehensive analysis of genetic variation. This is particularly interesting in disorders with high genetic heterogeneity. There are, however, limitations and concerns regarding the implementation of genomic analysis in everyday clinical practice, including some particular to emerging and developing economies, as Brazil. They include the limited number of actionable genetic variants known to date, difficulties in determining the clinical validity and utility of novel variants, growth of direct-to-consumer genetic testing using a genomic approach and lack of proper training of health care professionals to adequately request, interpret and use genetic information. Despite all these concerns and limitations, the availability of genomic tests has grown at an extremely rapid pace and commercially available services include initiatives in almost all areas of clinical genetics, including newborn and carrier screening. We discuss the benefits and limitations of genomic testing, as well as the ethical implications and the challenges for genetic education and enough available and qualified health care professionals, to ensure the adequate process of informed consent, meaningful interpretation and use of genomic data and definition of a clear regulatory framework in the particular context of Brazil.

Germ line polymorphisms as predictive markers for pre-surgical radiochemotherapy in locally advanced rectal cancer: a 5-year literature update and critical review

PURPOSE

Locally advanced rectal cancer is currently treated with pre-surgical radiotherapy and chemotherapy. Approximately one-half of patients obtain a relevant shrinkage/disappearance of tumour, with major clinical advantages. The remaining patients, in contrast, show no benefit and possibly need alternative treatment. To provide the best therapeutic option for each individual patient, predictive markers have been widely researched. This review was undertaken to evaluate recent progress made in this field.

METHODS

A systematic literature search was performed using PubMed and Scopus database, focused on germ line gene polymorphisms as biomarkers and response and toxicity as outcomes. Because an exhaustive previous review was available describing findings up to 2008, we restricted our analysis to the last 5 years.

RESULTS

Ten original research articles were found, reporting promising results for some candidate genes in drug metabolism (TYMS, MTHFR), DNA repair (XRCC1, OGG1, CCND1) and inflammation (SOD2, TGFB1)/immunity (IL13) pathways, but with no firm conclusion. All the studies had small sample size and were defined as exploratory. This review highlights pivotal molecular, clinical, genetic and statistical issues in the investigation of genetic polymorphisms as outcome predictors for rectal cancer and offers suggestions for future development.

CONCLUSIONS

What emerges is a clear need for new proposals, especially in view of the increasing evidence for tumour-host and gene-gene interactions during anticancer treatment, together with stronger adherence to proper methodological requirements.

Genetic markers for toxicity of adjuvant oxaliplatin and fluoropyrimidines in the phase III TOSCA trial in high-risk colon cancer patients

We investigated 17 polymorphisms in 11 genes (TS, MTHFR, ERCC1, XRCC1, XRCC3, XPD, GSTT1, GSTP1, GSTM1, ABCC1, ABCC2) for their association with the toxicity of fluoropyrimidines and oxaliplatin in colorectal cancer patients enrolled in a prospective randomized trial of adjuvant chemotherapy. The TOSCA Italian adjuvant trial was conducted in high-risk stage II–III colorectal cancer patients treated with 6 or 3 months of either FOLFOX-4 or XELOX adjuvant chemotherapy. In the concomitant ancillary pharmacogenetic study, the primary endpoint was the association of polymorphisms with grade 3–4 CTCAE toxicity events (grade 2–4 for neurotoxicity). In 517 analyzed patients, grade ≥ 3 neutropenia and grade ≥ 2 neurotoxicity events occurred in 150 (29%) and in 132 patients (24.8%), respectively. Diarrhea grade ≥ 3 events occurred in 34 (6.5%) patients. None of the studied polymorphisms showed clinically relevant association with toxicity. Hopefully, genome-wide association studies will identify new and more promising genetic variants to be tested in future studies.

A snapshot of challenges and solutions in cancer drug development and therapy

Cancer chemotherapy has transitioned from the use of cytotoxic drugs to the era of agents with an apparent selectivity for a cancer-specific target. The past decade has provided evidence that therapy with such agents can be curative in subsets of patients. It is anticipated that incorporation of pharmacological principles for novel therapeutics will result in further refinement of outcome measures as well as the discovery of new treatment modalities for multiple malignant diseases.