Prediction of cancer driver mutations in protein kinases as potential targets

A historical overview of protein kinases and their. These 158 drivers were confined to 66 of the 210 cancer samples. This is manifest by altered expression andor activity of cell cycle related. Mechanisms of receptor tyrosine kinase activation in cancer. Protein kinase c pkc is a family of phospholipiddependent serinethreonine kinases, which can be further classified into three pkc isozymes subfamilies. Significantly, protein kinases are the second most targeted group of drug targets, after the gproteincoupled receptors. Prediction and prioritization of rare oncogenic mutations in the. Protein kinases can modify the function of a protein in almost every conceivable way. Table s12 displayed the support validation evidences for kinases in published paper and the immunohistochemistry results of kinases in 11 stomach cancer tissues from human protein atlas. Targeting protein kinases for cancer therapy david j.

Thus, recent structural studies have not only facilitated our understanding of the functional consequences of specific cancer driver mutations in protein kinases, but have also exposed synergies between largescale resequencing studies of kinase coding regions in tumors and targeted, diseaseoriented crystallography that could lead to a. Proliferation is an important part of cancer development and progression. Protein kinase pk domain mutations were the most common followed by small gtpbinding. Frontiers integration of random forest classifiers and. Kinases play a key role in cancer biology, and serve as potential clinically useful targets for designing cancer therapies. Resequencing studies of protein kinase coding regions have emphasized the importance of sequence and structure determinants of cancer causing kinase mutations in understanding of the mutationdependent activation process. Nek10 may also be subject of direct mutations in cancer.

Introduction egfr is a member of the erbb family of. Mar 15, 2008 prediction of cancer driver mutations in protein kinases. Hence, the protein kinases have been widely considered to represent an important class of candidates as drug targets for cancer therapy. Prediction of cancer driver mutations in protein kinases article pdf available in cancer research 686. We have developed a computational method, called cancer specific highthroughput annotation of somatic mutations chasm, to identify and prioritize those missense mutations most likely to generate functional changes. Point mutations of protein kinases and individualised cancer therapy. In the present study, we aimed to investigate the correlation of twelve targeted protein kinases with cca recurrence. Prediction of cancer driver mutations in protein kinases. It analyzes genomic, transcriptomic and proteomic data sets and provides information on deregulated drug targets, enriched biological pathways and deregulated subnetworks, as well as mutations and their potential effects on putative drug targets and genes of interest. To discover potential candidate targets, the center applies computational methods to rnaseq data from the cancer genome atlas and the. Oct 31, 2011 early studies in lower eukaryotes have defined a role for the members of the nima related kinase nek family of protein kinases in cell cycle control. Sequence and structure signatures of cancer mutation. Cancer driver mutations in protein kinase genes request pdf.

Structurefunctional prediction and analysis of cancer mutation. A central goal of cancer research involves the discovery and. Significantly, protein kinases are the second most targeted group of drug targets, after the gproteincoupled. Protein kinases are the most common protein domains implicated in cancer, where somatically acquired mutations are known to be functionally linked to a variety of cancers. The presence of oncogenic driver mutations leads to a phenomenon called oncogene addiction wherein tumor cells tend to be dependent on the specific mutant. Since kinases are prominent therapeutic targets for intervention within the cancer cell, studying the impact that genomic alterations within. Activating genomic alterations of protein and lipid kinases. Protein kinases as drug targets in cancer bentham science. Our predictions determine the potential of a gene to play a role as a cancer driver in particular tumor types, and is.

Table 1 lists these four molecular targets with their respective detection methods and inhibitors. By carefully inspecting predictions of machine learning models in the context of dynamic and energetic signatures of mutational sites for oncogenic protein kinases, this study offered instructive strategy for simulationbased postprocessing of machine learning predictions and detailed functional specification of cancer driver mutations. Schork nj 2008 prediction of cancer driver mutations in protein kinases. Cancer driver mutations in protein kinase genes sciencedirect. As a result, protein kinases are important therapeutic targets for combating. At the highest level mokca provides the full list of 518 human protein kinases listed alphabetically by gene name to facilitate browsing, with each entry labelled with the number of mutations found, the cancer driver selection pressure and rank, and an iconic representation of the tumour types in which mutations in that protein kinase have. Integrated computational approaches to driver prediction. Distribution of the cancer driver log candl mutations across protein domains. Protein kinase signaling networks in cancer sciencedirect. Deep phospho and phosphotyrosine proteomics identified.

Cancer associated mutations are preferentially distributed in protein kinase functional sites article in proteins structure function and bioinformatics 774. Perturbation of these signaling networks by mutations or abnormal protein expression underlies the cause of many diseases including cancer. Glioblastoma is the most common malignant brain tumor and has a poor prognosis. Apr 10, 2020 the potential for targeting kinases in the treatment of cancer was the theme of the keystone symposium protein kinases and cancer. Prediction and prioritization of rare oncogenic mutations in. Concomitant driver mutations in advanced egfrmutated non. The distribution of domains for mutations that are listed in candl, as defined by interpro database, are shown. A large number of somatic mutations accumulate during the process of tumorigenesis. Pdf somatic mutations in protein kinases pks are frequent driver events in many human tumors.

Statistical analysis of pathogenicity of somatic mutations in cancer. Mutated kinases as targets for cancer drugs sciencedirect. Co mutations in other cancer driver genes oncogenes or tumor. Complete with fullcolor presentations, targeting protein kinases for cancer therapy defines the structural features of protein kinases and examines their cellular functions. Comprehensive characterization of cancer driver genes and. Nrg1 emerges as a potentially actionable target in lung.

Cancerspecific highthroughput annotation of somatic. Many of these kinases are associated with human cancer initiation and progression. The recently available pan cancer dataset of 3,185 tumor genomes and 12 cancer types from the cancer genome atlas tcga comprises the largest collection of somatic cancer mutations. Sequence and structure signatures of cancer mutation hotspots in. In many cancers, protein kinases are deregulated, and therefore, are the most often used therapeutic targets in the treatment of cancer. Cancer driver log candl the journal of molecular diagnostics.

Mokca databasemutations of kinases in cancer nucleic. Pdf structurefunctional prediction and analysis of. Structurefunctional prediction and analysis of cancer. Mutational profiling of kinases in glioblastoma bmc cancer. The recent development of smallmolecule kinase inhibitors for the treatment of diverse types of cancer has proven successful in clinical therapy. While the frequent recurrence of some driver mutations in human cancers helps. At the root of the socalled precision medicine or precision oncology, which is our focus here. Point mutations of protein kinases and individualised. Sequence and structure signatures of cancer mutation hotspots in protein kinases. Oct 07, 2019 present study provided pathway crosstalk and protein interaction network for understanding potential tumorigenesis genes underlying hcc. Prediction of cancer driver mutations in protein kinases cancer. Protein stability differences calculated between the wildtype and mutants for predicted cancer driver mutations in the erbb kinases using foldx approach.

These driver mutations can shed light on the understanding of cancer initiation and progression and can also provide potential opportunities for targeted treatments. Phosphoproteomics enables molecular subtyping and nomination. The growing body of genetic, molecular and functional information about protein kinases genes, combined with their prominent role as therapeutic targets for cancer intervention have. Rapidly improving technologies for sequencing the human genome and the commercial availability of genetic tests for signs of predisposition to disease are just two indicators that an age of personalized medicine is rapidly approaching. Differentiating driver mutations that are functionally relevant from passenger mutations is a major challenge in cancer genomics. Targeted sequencing studies of many different cancers have shown that the. Jan 01, 2009 protein kinases are a superfamily involved in many crucial cellular processes, including signal transmission and regulation of cell cycle. We analyzed the distribution of pathogenic somatic point mutations drivers in the protein kinase.

Although protein kinases are key players in cancer development and progression, accurate predictions of drivers in other protein families, such as transcription factors or phosphatases, will also be useful in determining a more holistic picture of tumorigenesis and cancer treatment. Transcriptionassociated cyclindependent kinases as. Structural and biochemical characterization of protein kinases that confer oncogene addiction and harbor a large number of diseaseassociated mutations, including ret and met kinases, have provided insights into molecular mechanisms associated with the protein kinase activation in human cancer. Oncogenic driver mutations in lung cancer springerlink.

A subset of these mutations contribute to tumor progression known as driver mutations whereas the majority of these mutations are effectively neutral known as passenger mutations. These driver mutations seem to be involved heavily in nucleotide binding, possibly driven by resistance to inhibitors mimicking atp, and regulatory functions, especially movements from the inactive to active conformation. Cancer is a genetic disease that develops through a series of somatic mutations, a subset of which drive cancer progression. Identifying driver mutations in sequenced cancer genomes. Erbb2 protein expression summary the human protein atlas. These cancer mutation hotspots occur in functionally important protein kinase segments figure 7, containing an abundance of predicted cancer driver mutations.

Identifying hepatocellular carcinoma driver genes by. Researchers develop new method for spotting critical cancer drivers. Namely, whole genome sequencing of 210 primary tumors and immortalized human cancer cell lines uncovered more than a somatic mutations within the coding sequences of the 518 predicted human protein kinases 82, 83. Mutated cancer genes mutational cancer driver genes cosmic somatic mutations in cancer genes cosmic amplifications cosmic somatic mutations cosmic other mutations cosmic missense mutations disease related genes fda approved drug targets biotech drugs small molecule drugs mapped to nextprot nextprot evidence at protein level protein evidence. Protein kinases are the most common protein domains implicated in. The probability distribution of the gbm chasm scores should then be similar to the chasm score distribution of a mixture of known driver and synthetic passenger mutations 21. Members of the protein kinase family are amongst the most commonly mutated genes in human cancer, and both mutated and activated protein kinases have proved to be tractable targets for the development of new anticancer therapies 5. Ultimately, the determination that a mutation is functional requires experimental validation, using in vitro or in vivo models to demonstrate that a mutation leads to at least one of the characteristics of the cancer phenotype, such as dna repair deficiency. Recent exon resequencing studies of gene families involved in cellular signaling pathways, such as tyrosine kinases, tyrosine phosphatases, and phosphatidylinositol 3kinases have identified many potential tumorigenic driver mutations 4555. Cancerassociated mutations are preferentially distributed. Protein kinases are a superfamily involved in many crucial cellular processes, including signal transmission and regulation of cell cycle.

Recent rnai screens and cancer genomic sequencing studies have revealed that many more kinases than anticipated contribute to tumorigenesis and are potential targets for inhibitor drug development intervention. However, a major hurdle to achieve the maximum potential of targeted. The 14 driver genes identified from this study are of great translational value in hcc diagnosis and treatment, as well as in clinical study on the pathogenesis of hcc. Pdf prediction of cancer driver mutations in protein kinases. Abnormality in cellular phosphorylation is closely related to oncogenesis. Protein phosphorylation can increase or decrease enzyme activity and it can alter other biological activities such as transcription and translation. Following the sequencing of a cancer genome, the next step is to identify driver mutations that are responsible for the cancer phenotype. Targets for t cell based immunotherapy must be on the cell surface, either as a peptide that is presented by major histocompatibility complex mhc class i protein complexes or as a cell surface protein variant.

According to these authors the cell cycle kinases are pks that, by cooperating with other protein families, allow systematic and coordinated cell cycle progression. According to a proposed mechanism, structural effect of kinase mutations with a high oncogenic potential. The mutational landscape of phosphorylation signaling in. Research paper concomitant driver mutations in advanced. Prediction and prioritization of rare oncogenic mutations. For example, algorithms such as active driver focus on phosphorylation and kinase domain site. Cancer driver annotation predicts missense driver mutations in cancers based on a set of 96 structural, evolutionary, and gene features using functional prediction algorithms, such as sift sorting intolerant from tolerant and chasm cancer specific highthroughput annotation of somatic mutations. Protein kinases that are mutated in cancer represent attractive targets, as they may result in cellular dependency on the mutant kinase or its associated pathway for survival, a condition known as oncogene addiction. Segments involved directly in catalytic functions, such as the ploop, catalytic loop, and activation loop tend to be populated by cancer causing mutations. In this article, structural modeling, molecular dynamics, and free energy simulations of a. Most co mutations did not impact the response to firstline erlotinibtreatment, but may represent potential additional therapeutic targets.

However, an identification of predictive factor on opisthorchis viverrini ovassociated cca recurrence is not well elucidated. Thus, while protein kinases have a clear role in tumorigenesis, commonly mutated protein kinases in cancer appear to be the exception to the rule. The list of highconfidence protein kinase cancer drivers includes kinases with wellestablished roles in cancer development, such as various receptor tyrosine kinases, as. We focus on the differential effects of activating point mutations that increase protein kinase activity and kinaseinactivating mutations that decrease activity. Point mutations of protein kinases and individualised cancer. Expansion of the nek family throughout evolution has been accompanied by their broader involvement in checkpoint regulation and cilia biology. Resequencing studies of protein kinase coding regions have emphasized the importance of sequence and structure determinants of cancer causing kinase mutations in understanding of the mutation dependent activation process. While recurrent mutations in a gene provides supporting evidence of driver status, novel computational methods and model systems are greatly improving our ability to identify genes important in carcinogenesis. Combining kinase biology with chemistry and pharmacology applications, this book enlists emerging data to drive the discovery of new cancer fighting drugs. Protein kinases genes, tumorigenesis, and cancer treatment. Our study is a comprehensive assessment of the performance of different algorithms in predicting cancer driver mutations and provides deep insights into the best practice of computationally prioritizing cancer mutation candidates for endusers and for the future development of new algorithms. Drugtarget interaction prediction methods oup academic. One parameter for distinguishing driver and passenger mutations is. Thus, kinase inhibitors, especially tyrosine kinase inhibitors tkis, have been developed as anti cancer drugs.

Computational modeling of structurally conserved cancer. Somatic mutations in the genes encoding rtks typically cluster in evolutionally conserved residues, such as the dfg motif in the kinase activation loop and around the. Author summary selective inhibition of specific panels of multiple protein targets provides an unprecedented potential for improving therapeutic efficacy of anticancer agents. Nek family of kinases in cell cycle, checkpoint control and. Since kinases are prominent therapeutic targets for intervention within the cancer cell, studying the. Alterations of the nrg1 gene that are present at low rates in certain solid tumors have emerged as potentially actionable oncogenic drivers, with targeted therapies making their way to early clinical studies and into some basket trials. We have developed a computational method, called cancer specific highthroughput annotation of somatic mutations chasm, to identify and prioritize those missense mutations most likely to generate. Protein stability changes induced by cancer driver mutations in the inactive and active states of egfr kinase a, erbb2 kinase b, erbb3 kinase c, and erbb4 kinase d. The description of 518 protein kinases constituting the kinome enabled systematic mutation analysis of kinases in colon cancer 2, 6, and other types of cancer, including glioblastoma 5, 21. Significance of oncogenic driver mutations in lung cancer severity and therapy. Nek family of kinases in cell cycle, checkpoint control. Although cancer genome sequencing studies are beginning to reveal the mutational patterns of genes in various cancers, identifying the small subset of causative mutations from the large subset of noncausative mutations, which accumulate as a consequence of. Structurefunctional prediction and analysis of cancer mutation effects in protein kinases article pdf available in computational and mathematical methods in medicine 2014. We also present a systematic computational analysis that combines sequence and structurebased prediction models to characterize the effect of cancer mutations in protein kinases.

Cancer progresses by accumulation of mutations in a subset of genes that confer growth advantage. Mokca databasemutations of kinases in cancer nucleic acids. A historical overview of protein kinases and their targeted. The 518 protein kinase genes encoded in the human genome. Mutant kinases and other critically altered proteins in cancer cells may thus prove to be good drug targets.

Akt1 protein expression summary the human protein atlas. Transcriptionassociated cyclindependent kinases as targets and biomarkers for cancer therapy. Predicting breast cancer driver gene is a cumbersome task, as it. Cancer driver predictions were performed by using the svm approach as described in our earlier work 70, 71. Among the 16 kinases we identified, 10 kinases have been validated as potential targets in different cancers. Cancers arise due to the accumulation of mutations in critical target genes that confer a. Comprehensive assessment of computational algorithms in. T1 point mutations of protein kinases and individualised cancer therapy. The y axis denotes break represents the percentage of genes. Characterization of potential driver mutations involved in human.

As a consequence of this role, kinases have been reported to be associated with many types of cancer and are considered as potential therapeutic targets. The ability to differentiate between drivers and passengers will be critical to the success of upcoming largescale cancer dna resequencing projects. Combing the cancer genome for novel kinase drivers and. Prediction and prioritization of rare oncogenic mutations in the cancer kinome using novel features and multiple classifiers. Identification of the key roles of protein kinases in signaling pathways leading to development of cancer has caused pharmacological interest to concentrate extensively on targeted therapies as a more specific and effective way for blockade of cancer progression. A activating point mutations in genes coding for kinases lead to the expression of a constitutively activated kinase. Such mutations either lead to an amino acid substitution in the catalytic site, rendering it active.

We assumed that the gbm mutations are a mixture of drivers and passengers and wanted to estimate the proportion of drivers in the mixture. Cancer recurrence is one of the most concerning clinical problems of cholangiocarcinoma cca patients after treatment. Thus, while protein kinases have a clear role in tumorigenesis, commonly mutated protein kinases in cancer. Moreover, mutations of nek family members have been identified as drivers behind the development of. Although the predicted cancer driver mutations did fall at the. Our predictions determine the potential of a gene to play a role as a cancer driver in particular tumor types, and is independent of specific. We examined nucleic acid variations in the human kinome and several. Hunting for cancer mutations through genomic sequence comparisons. While protein kinases have a prominent role in tumorigenesis, commonly mutated protein kinases in cancer appeared to be the exception to the rule and most of kinase driver mutations are expected to be distributed across many protein kinase genes 27. Overall, our analyses indicate that our method is capable of accurately determining driver mutations in protein kinases.

Sequence and structure signatures of cancer mutation hotspots. The higher the oncogenic potential of the cancer drive, the larger the ball denoting structural position of the respective mutation. Frontiers integration of random forest classifiers and deep. Largescale sequencing of cancer genomes has uncovered thousands of dna alterations, but the functional relevance of the majority of these mutations to tumorigenesis is unknown. Akt1 is one of 3 closely related serinethreonine protein kinases akt1, akt2 and akt3 called the akt kinase, and which regulate many processes including metabolism, proliferation, cell survival, growth and angiogenesis ref, ref, ref, ref. We introduce a computational systems pharmacology strategy, which uses the concept of target inhibition networks to predict effective multitarget combinations for treating specific cancer types. Pkc isozymes are known to be involved in cell proliferation, survival, invasion, migration, apoptosis, angiogenesis, and drug resistance. A recently published book, targeting protein kinases for cancer therapy, provides a solution. Early on, therapies were disease andor protein targeted, such as. Review protein kinases, their function and implication in.