Genetic Alterations In Cancer Research Articles

Molecular biology techniques for loss of heterozygosity detection: the glioma example

In recent years, many oncology institutions have implemented the use of molecular approaches to assess and manage cancer patients. One commonly observed type of genetic alteration in cancer is the loss of heterozygosity (LOH). In the clinical setting, this molecular genetic marker is an important tool for disease prognosis, diagnosis and treatment. For example, the loss of 1p/19q is a classical molecular marker for oligodendroglioma assessment. In addition, this marker is associated with a favorable prognosis and chemosensitivity in oligodendroglial tumors. Interpretation of the clinical significance of molecular markers requires that health professionals and biomedical scientists understand the basic theoretical fundamentals of molecular diagnostic techniques. Although there are different methodologies to assess LOH, including high-performance techniques, this review aims to describe the polymerase chain reaction (PCR)-based LOH assays and fluorescence in situ hybridization (FISH), which are the molecular techniques most used for evaluation of 1p/19q status in pathology laboratories.

Inactivation of p53 in Human Keratinocytes Leads to Squamous Differentiation and Shedding via Replication Stress and Mitotic Slippage

Tumor suppressor p53 is a major cellular guardian of genome integrity, and its inactivation is the most frequent genetic alteration in cancer, rising up to 80% in squamous cell carcinoma (SCC). By adapting the small hairpin RNA (shRNA) technology, we inactivated endogenous p53 in primary epithelial cells from the epidermis of human skin. We show that either loss of endogenous p53 or overexpression of a temperature-sensitive dominant-negative conformation triggers a self-protective differentiation response, resulting in cell stratification and expulsion. These effects follow DNA damage and exit from mitosis without cell division. p53 preserves the proliferative potential of the stem cell compartment and limits the power of proto-oncogene MYC to drive cell cycle stress and differentiation. The results provide insight into the role of p53 in self-renewal homeostasis and help explain why p53 mutations do not initiate skin cancer but increase the likelihood that cancer cells will appear.

Erratum to: The RNA editing enzyme APOBEC1 induces somatic mutations and a compatible mutational signature is present in esophageal adenocarcinomas

AbstractNo abstract

FISH molecular testing in cytological preparations from solid tumors.

Many of the exciting new developments in solid tumor molecular cytogenetics impact classical and molecular pathology. Fluorescence in situ hybridization to identify specific DNA target sequences in nuclei of non-dividing cells in solid neoplasms has contributed to the integration of molecular cytogenetics into cytology in spite of the remarkable promiscuity of cancer genes. Indeed, although it is a low-throughput assay, fluorescence in situ hybridization enables the direct disclosure and localization of genetic markers in single nuclei. Gene fusions are among the most prominent genetic alterations in cancer, providing markers that may be determinant in needle biopsies that are negative or suspicious for malignancy, and may contribute to the correct classification of the tumors. In view of the expanding use of fluorescence in situ hybridization in cytology, future challenges include automated sample evaluation and the specification of common criteria for interpreting and reporting results.

The RNA editing enzyme APOBEC1 induces somatic mutations and a compatible mutational signature is present in esophageal adenocarcinomas.

BackgroundThe AID/APOBECs are deaminases that act on cytosines in a diverse set of pathways and some of them have been linked to the onset of genetic alterations in cancer. Among them, APOBEC1 is the only family member to physiologically target RNA, as the catalytic subunit in the Apolipoprotein B mRNA editing complex. APOBEC1 has been linked to cancer development in mice but its oncogenic mechanisms are not yet well understood.ResultsWe analyze whether expression of APOBEC1 induces a mutator phenotype in vertebrate cells, likely through direct targeting of genomic DNA. We show its ability to increase the inactivation of a stably inserted reporter gene in a chicken cell line that lacks any other AID/APOBEC proteins, and to increase the number of imatinib-resistant clones in a human cellular model for chronic myeloid leukemia through induction of mutations in the BCR-ABL1 fusion gene. Moreover, we find the presence of an AID/APOBEC mutational signature in esophageal adenocarcinomas, a type of tumor where APOBEC1 is expressed, that mimics the one preferred by APOBEC1 in vitro.ConclusionsOur findings suggest that the ability of APOBEC1 to trigger genetic alterations represents a major layer in its oncogenic potential. Such APOBEC1-induced mutator phenotypes could play a role in the onset of esophageal adenocarcinomas. APOBEC1 could be involved in cancer promotion at the very early stages of carcinogenesis, as it is highly expressed in Barrett's esophagus, a condition often associated with esophageal adenocarcinoma.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-014-0417-z) contains supplementary material, which is available to authorized users.

No evidence of correlation between p53 codon 72 G > C gene polymorphism and cancer risk in Indian population: a meta-analysis.

p53 is a tumor suppressor gene, which is activated in response to several forms of cellular stress and exerts multiple antiproliferative functions, making it the most frequent target for genetic alteration in cancer. Various studies have evaluated the association between p53 codon 72 G > C (rs1042522) polymorphism and risk of cancer. However, results from the published studies remained inconclusive. The aim of this study is to investigate the precise association between this variant and a risk of cancer in a large-scale meta-analysis. We searched the PubMed (MEDLINE) and Google Scholar web databases for studies regarding the association of p53 codon 72 G > C polymorphism and risk of cancer in the Indian population. Pooled odds ratio (OR) with 95 % confidence interval (CI) were calculated by using random effect model to assess the association. Twenty studies with 3,258 cancer cases and 4,260 healthy controls were included. Overall, no significant association was detected for C allele carrier (C vs. G: OR = 1.135, 95 % CI = 0.930 to 1.386, p = 0.211) and homozygous (CC vs. GG: OR = 1.200, 95 % CI = 0.810 to 1.779, p = 0.364), heterozygous (CG vs. GG: OR = 1.204, 95 % CI = 0.921 to 1.575, p = 0.175), dominant (CC + CG vs. GG: OR = 1.231, 95 % CI = 0.932 to 1.625, p = 0.144), and recessive (CC vs. GG + GC: OR = 1.078, 95 % CI = 0.792 to 1.468, p = 0.632) genetic models, respectively. No significant publication bias was observed by using Begg's funnel plot and Egger's test. Present meta-analysis indicated that the p53 codon 72 G > C polymorphism was not associated with cancer risk. This suggests that this polymorphism may not be an independent risk factor for cancer in the Indian population.

Vemurafenib and panitumumab combination tailored therapy in BRAF-mutated metastatic colorectal cancer

As the knowledge on cancer genetic alterations progresses, it fosters the need for more personalized therapeutic intervention in modern cancer management. Recently, mutations in KRAS, BRAF, and PIK3CA genes have emerged as important mechanisms of resistance to EGFR-targeted therapy in metastatic colorectal cancer (mCRC). Here we report the first case of a mCRC patient whose disease had progressed on standard lines of treatment and for which we devised a personalized therapeutic approach consisting of vemurafenib (ZelborafTM) and panitumumab (VectibixTM), based on the following molecular profile: BRAFV600E-mutant, amplified EGFR (double positive) and WT KRAS, WT PIK3CA, not-amplified HER2 (triple negative). This new combination therapy was well tolerated and resulted in a strong control of the disease. In particular, the vemurafenib-panitumumab combination appears to limit the typical toxicity of single agents, since no cutaneous toxic effects typically associated with vemurafenib were observed. Here we report the first clinical evidence that the combination of an anti-EGFR (panitumumab) and an inhibitor of BRAFV600E (vemurafenib) is well tolerated and results in a strong disease control in an extensively pretreated mCRC patient.

The Structural Basis of PI3K Cancer Mutations: From Mechanism to Therapy

While genetic alteration in the p85α-p110α (PI3K) complex represents one of the most frequent driver mutations in cancer, the wild-type complex is also required for driving cancer progression through mutations in related pathways. Understanding the mechanistic basis of the function of the phosphoinositide 3-kinase (PI3K) is essential for designing optimal therapeutic targeting strategies. Recent structural data of the p85α/p110α complex unraveled key insights into the molecular mechanisms of the activation of the complex and provided plausible explanations for the well-established biochemical data on p85/p110 dimer regulation. A wealth of biochemical and biologic information supported by recent genetic findings provides a strong basis for additional p110-independent function of p85α in the regulation of cell survival. In this article, we review the structural, biochemical, and biologic mechanisms through which p85α regulates the cancer cell life cycle with an emphasis on the recently discovered genetic alterations in cancer. As cancer progression is dependent on multiple biologic processes, targeting key drivers such as the PI3K may be required for efficacious therapy of heterogeneous tumors typically present in patients with late-stage disease.

IndividualizedPath: identifying genetic alterations contributing to the dysfunctional pathways in glioblastoma individuals.

Due to the extensive complexity and high genetic heterogeneity of genetic alterations in cancer, comprehensively depicting the molecular mechanisms of cancer remains difficult. Characterizing personalized pathogenesis in cancer individuals can help to reveal new details of the complex mechanisms. In this study, we proposed an integrative method called IndividualizedPath to identify genetic alterations and their downstream risk pathways from the perspective of individuals through combining the DNA copy number, gene expression data and topological structures of biological pathways. By applying the method to TCGA glioblastoma multiforme (GBM) samples, we identified 394 gene-pathway pairs in 252 GBM individuals. We found that genes with copy number alterations showed high heterogeneity across GBM individuals, whereas they affected relatively consistent biological pathways. A global landscape of gene-pathway pairs showed that EGFR linked with multiple cancer-related biological pathways confers the highest risk of GBM. GBM individuals with MET-pathway pairs showed significantly shorter survival times than those with only MET amplification. Importantly, we found that the same risk pathways were affected by different genes in distinct groups of GBM individuals with a significant pattern of mutual exclusivity. Similarly, GBM subtype analysis revealed some subtype-specific gene-pathway pairs. In addition, we found that some rare copy number alterations had a large effect on contribution to numerous cancer-related pathways. In summary, our method offers the possibility to identify personalized cancer mechanisms, which can be applied to other types of cancer through the web server (http://bioinfo.hrbmu.edu.cn/IndividualizedPath/).

The RNA editing enzyme APOBEC1 induces somatic mutations and a compatible mutational signature is present in esophageal adenocarcinomas

The AID/APOBECs are deaminases that act on cytosines in a diverse set of pathways and some of them have been linked to the onset of genetic alterations in cancer. Among them, APOBEC1 is the only family member to physiologically target RNA, as the catalytic subunit in the Apolipoprotein B mRNA editing complex. APOBEC1 has been linked to cancer development in mice but its oncogenic mechanisms are not yet well understood. We analyze whether expression of APOBEC1 induces a mutator phenotype in vertebrate cells, likely through direct targeting of genomic DNA. We show its ability to increase the inactivation of a stably inserted reporter gene in a chicken cell line that lacks any other AID/APOBEC proteins, and to increase the number of imatinib-resistant clones in a human cellular model for chronic myeloid leukemia through induction of mutations in the BCR-ABL1 fusion gene. Moreover, we find the presence of an AID/APOBEC mutational signature in esophageal adenocarcinomas, a type of tumor where APOBEC1 is expressed, that mimics the one preferred by APOBEC1 in vitro. Our findings suggest that the ability of APOBEC1 to trigger genetic alterations represents a major layer in its oncogenic potential. Such APOBEC1-induced mutator phenotypes could play a role in the onset of esophageal adenocarcinomas. APOBEC1 could be involved in cancer promotion at the very early stages of carcinogenesis, as it is highly expressed in Barrett's esophagus, a condition often associated with esophageal adenocarcinoma.

Gene amplification: mechanisms and involvement in cancer.

Gene amplification was recognized as a physiological process during the development of Drosophila melanogaster. Intriguingly, mammalian cells use this mechanism to overexpress particular genes for survival under stress, such as during exposure to cytotoxic drugs. One well-known example is the amplification of the dihydrofolate reductase gene observed in methotrexate-resistant cells. Four models have been proposed for the generation of amplifications: extrareplication and recombination, the breakage-fusion-bridge cycle, double rolling-circle replication, and replication fork stalling and template switching. Gene amplification is a typical genetic alteration in cancer, and historically many oncogenes have been identified in the amplified regions. In this regard, novel cancer-associated genes may remain to be identified in the amplified regions. Recent comprehensive approaches have further revealed that co-amplified genes also contribute to tumorigenesis in concert with known oncogenes in the same amplicons. Considering that cancer develops through the alteration of multiple genes, gene amplification is an effective acceleration machinery to promote tumorigenesis. Identification of cancer-associated genes could provide novel and effective therapeutic targets.

The TRAIL of oncogenes to apoptosis

Despite the significant advances in clinical research, surgical resection, radiotherapy and chemotherapy are still used as the primary method for cancer treatment. As compared to conventional therapies that often induce systemic toxicity and eventually contribute to tumor resistance, the TNF-related apoptosis-inducing ligand (TRAIL) is a promising anticancer agent that selectively triggers apoptosis in various cancer cells by interacting with its proapoptotic receptors DR4 and KILLER/DR5, while sparing the normal surrounding tissue. The intensive studies of TRAIL signaling pathways over the past decade have provided clues for understanding the molecular mechanisms of TRAIL-induced apoptosis in carcinogenesis and identified an array of therapeutic responses elicited by TRAIL and its receptor agonists. Analysis of its activity at the molecular level has shown that TRAIL improves survival either as monotherapies or combinatorial therapies with other mediators of apoptosis or anticancer chemotherapy. Combinatorial treatments amplify the activities of anticancer agents and widen the therapeutic window by overcoming tumor resistance to apoptosis and driving cancer cells to self-destruction. Although TRAIL sensitivity varies widely depending on the cell type, nontransformed cells are largely resistant to death mediated by TRAIL Death Receptors (DRs). Genetic alterations in cancer can contribute in tumor progression and often play an important role in evasion of apoptosis by tumor cells. Remarkably, RAS, MYC and HER2 oncogenes have been shown to sensitise tumor cells to TRAIL induced cell death. Here, we summarise the cross-talk of oncogenic and apoptotic pathways and how they can be exploited toward efficient combinatorial therapeutic protocols.

Targeted Sequencing of Cancer-Related Genes in Colorectal Cancer Using Next-Generation Sequencing

Recent advance in sequencing technology has enabled comprehensive profiling of genetic alterations in cancer. We have established a targeted sequencing platform using next-generation sequencing (NGS) technology for clinical use, which can provide mutation and copy number variation data. NGS was performed with paired-end library enriched with exons of 183 cancer-related genes. Normal and tumor tissue pairs of 60 colorectal adenocarcinomas were used to test feasibility. Somatic mutation and copy number alteration were analyzed. A total of 526 somatic non-synonymous sequence variations were found in 113 genes. Among these, 278 single nucleotide variations were 232 different somatic point mutations. 216 SNV were 79 known single nucleotide polymorphisms in the dbSNP. 32 indels were 28 different indel mutations. Median number of mutated gene per tumor was 4 (range 0–23). Copy number gain (>X2 fold) was found in 65 genes in 40 patients, whereas copy number loss (<X0.5 fold) was found in 103 genes in 39 patients. The most frequently altered genes (mutation and/or copy number alteration) were APC in 35 patients (58%), TP53 in 34 (57%), and KRAS in 24 (40%). Altered gene list revealed ErbB signaling pathway as the most commonly involved pathway (25 patients, 42%). Targeted sequencing platform using NGS technology is feasible for clinical use and provides comprehensive genetic alteration data.

Existing and Emerging Technologies for Tumor Genomic Profiling

Ongoing global genome characterization efforts are revolutionizing our knowledge of cancer genomics and tumor biology. In parallel, information gleaned from these studies on driver cancer gene alterations--mutations, copy number alterations, translocations, and/or chromosomal rearrangements--an be leveraged, in principle, to develop a cohesive framework for individualized cancer treatment. These possibilities have been enabled, to a large degree, by revolutionary advances in genomic technologies that facilitate systematic profiling for hallmark cancer genetic alterations at increasingly fine resolutions. Ongoing innovations in existing genomics technologies, as well as the many emerging technologies, will likely continue to advance translational cancer genomics and precision cancer medicine.

Using Cytogenetic Rearrangements for Cancer Prognosis and Treatment (Pharmacogenetics)

Chromosomal rearrangements including translocations, deletions, inversions, and insertions are common genetic alterations in cancer. Over 1,000 recurrent chromosome rearrangements have been reported so far in different human tumors ( http://cgap.nci.nih.gov/Chromosomes/Mitelman ). Most of these chromosome rearrangements are associated with specific tumor types and bear distinctive diagnostic and prognostic significance. Molecular characterization of these rearrangements has revealed numerous cancer genes, including novel fusion genes, and their normal and aberrant interactions involved in tumorigenesis, and has identified myriad therapeutic targets. With the help of advanced high-throughput technologies, many cryptic chromosome rearrangements undetectable by conventional cytogenetics have recently been discovered and delineated. The understanding of the mechanisms responsible for the formation of recurrent chromosome rearrangements and their biological functions has led to novel treatment regimens that target tumor cells specifically, with minimal impact to normal cells. Here, we review common recurrent chromosome rearrangements in both hematopoietic malignancies and solid tumors, and their clinical significance, with a focus on acquired fusion genes and their therapeutic implications (i.e., pharmacogenetics).

Genomic characterization of meningiomas.

2020 Background: Understanding the genetic alterations in cancer has lead to groundbreaking discoveries in targeted therapies. Meningiomas are among the most common primary brain tumors, with approximately 18,000 new cases diagnosed annually. Though certain genes have been associated with the development of meningiomas, most notably the tumor suppressor gene neurofibromatosis 2 (NF2), the genetic changes that drive meningiomas remain poorly understood. Our objective was to comprehensively characterize the somatic genetic alterations of meningiomas to gain insight into the molecular pathways that drive this disease. Methods: Fresh frozen specimens and paired blood were collected from 16 consented patients. DNA was extracted from regions of high tumor purity determined by evaluation of H&amp;E slides. Whole-genome sequencing from 10 tumor-normal pairs and whole-exome sequencing from 6 tumor-normal pairs was carried out. We performed an unbiased screen for point mutations, insertions-deletions, rearrangements and copy-number changes across the exomes and genomes. Recurrent (potential driver) events were then analyzed with additional algorithms for statistical significance. Results: Alterations in the NF2 gene were present in 9 of 16 patients. Multiple novel rearrangements and recurrent non-NF2 mutations were also identified in the cohort. Massive genomic rearrangement termed chromothripsis was observed in chromosome 1 in one sample, which has never previously been described in meningiomas, and represents a potentially new mechanism of malignant transformation in this tumor type. Conclusions: While NF2 mutations appear to drive a majority of these tumors, our analysis has uncovered additional potential driver genes in meningiomas, particularly in those tumors negative for NF2 alterations. To our knowledge, this is the first study to comprehensively characterize the totality of somatic genetic alterations in meningiomas, and brings us closer to the development of new therapeutic targets for this disease.

Abstract 4027: Regulation of p16INK4A and TGF-beta by DNA hydroxymethylation in glioblastoma multiforme

Abstract Glioblastoma multiforme (GBM) is the most prevalent form of primary brain cancer in adults. Cancer stem cells (CSCs) are thought to drive the growth and metastasis of tumors, and are readily isolated from GBM patient tumors. These GBM CSCs are maintained under serum-free conditions in neurosphere media, and form tumors upon orthotopic injection in mice. However, when grown in the presence of serum, GBM CSCs undergo morphological changes, have reduced proliferation, exhibit loss of stem cell markers, and have reduced tumorigenicity following orthotopic implantation into the brains of immune compromised mice. Upon return to serum-free neurosphere media, these GBM CSCs revert to neurospheres. We set out to define the transcriptional incongruities between these culture condition-dependent states, and the underlying epigenetic changes which regulate these differences in gene expression. Although genetic alterations in cancer are irreversible, epigenetic changes are inherently reversible, and we hypothesize that the plasticity between culture condition-dependent states is mediated by epigenetic regulation of genes relevant to the ability of these cells to form tumors. Recently, a novel epigenetic mark, 5-hydroxymethylcytosine (5hmC), has been shown to be enriched at regulatory elements within polycomb target genes in embryonic stem cells, and is frequently found at genes that are involved in the maintenance of stem cells. We found that 5hmC levels of several polycomb target genes, including p16INK4A and several components of the TGF-beta pathway involved in epithelial to mesenchymal transition (EMT), are altered in neurospheres compared to CSCs cultured in serum. Loss of p16INK4A expression has recently been associated with increased CSC abundance in breast cancer, and our results suggest that a similar trend exists in GBM. Furthermore, our results suggest that 5hmC is involved in the regulation of polycomb target genes in CSCs, including p16INK4A and components of the TGF-beta pathway. These findings implicate 5hmC in the maintenance of CSCs and regulation of EMT. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4027. doi:1538-7445.AM2012-4027

Radiation/Paclitaxel Treatment of p53-Abnormal Non-Small Cell Lung Cancer Xenograft Tumor and Associated Mechanism

Mutations in key tumor suppressor genes such as tumor protein 53 (TP53) and phosphatase and tensin homolog deleted on chromosome ten (PTEN) are the main genetic alterations in cancers. TP53 mutations have been found in most patients with non-small cell lung cancer (NSCLC), whereas PTEN mutations are rarely found in lung cancer, though most NSCLCs lack PTEN protein synthesis. However, the signaling involved in radio- and chemotherapy of NSCLC with wild-type PTEN and nonfunctional p53 is not clearly understood. In this study, we established a xenograft tumor model with H358 NSCLC cells expressing wild-type PTEN, but nonfunctional p53. Protein expression and phosphorylation of PTEN and its downstream signal molecules in NSCLC tissues were detected by Western blot. We demonstrated that radiation and paclitaxel alone inhibited tumor growth, but a combined therapy of radiation and paclitaxel was more effective in inhibiting NSCLC tumor growth. Interestingly, both radiation and paclitaxel significantly increased PTEN protein expression and phosphorylation. Further identification of the affected PTEN downstream molecules showed that Akt phosphorylation at Ser(473) and Thr(308) residues was significantly decreased, whereas Bax and cleaved caspase-3 levels were significantly increased in tumor tissues treated with both radiation and paclitaxel. The combined treatment was more effective than either treatment alone in regulating the studied molecules. We also found that paclitaxel, but not radiation, inhibited phosphoinositide 3-kinase (PI3K) activity. Our study suggested that a PTEN-PI3K-Akt-Bax signaling cascade is involved in the therapeutic effect of combined radiation/paclitaxel treatment in NSCLC without p53 expression. Our study also suggested that PTEN is an ideal target in tumors with wild-type PTEN and a lack of functional p53.

Gene alterations in the PI3K/PTEN/AKT pathway as a mechanism of drug-resistance (Review)

The most common therapeutic approach for many cancers is chemotherapy. However, many patients relapse after treatment due to the development of chemoresistance. Recently, targeted therapies represent novel approaches to destroy cancer cells. The PI3K/PTEN/AKT pathway is a key signaling pathway involved in the regulation of cell growth. Dysregulated signaling of this pathway may be associated with activating mutations of PI3K-related genes. Analyses of these mutations reveal that they increase the PI3K signal, stimulate downstream Akt signaling, promote growth factor-independent growth and increase cell invasion and metastasis. In this review, we summarize the PI3K/PTEN/AKT pathway genetic alterations in cancer and their potential clinical applications.

Structural and Functional Impact of Cancer-Related Missense Somatic Mutations

A number of large-scale cancer somatic genome sequencing projects are now identifying genetic alterations in cancers. Evaluation of the effects of these mutations is essential for understanding their contribution to tumorigenesis. We have used SNPs3D, a software suite originally developed for analyzing nonsynonymous germ-line variants, to identify single-base mutations with a high impact on protein structure and function. Two machine learning methods are used: one identifying mutations that destabilize protein three-dimensional structure and the other utilizing sequence conservation and detecting all types of effects on in vivo protein function. Incorporation of detailed structure information into the analysis allows detailed interpretation of the functional effects of mutations in specific cases. Data from a set of breast and colorectal tumors were analyzed. In known cancer genes, mutations approaching 100% of mutations are found to impact protein function, supporting the view that these methods are appropriate for identifying driver mutations. Overall, 50–60% of all somatic missense mutations are predicted to have a high impact on structural stability or to more generally affect the function of the corresponding proteins. This value is similar to the fraction of all possible missense mutations that have a high impact and is much higher than the corresponding one for human population single-nucleotide polymorphisms, at about 30%. The majority of mutations in tumor suppressors destabilize protein structure, while mutations in oncogenes operate in more varied ways, including destabilization of less active conformational states. The set of high-impact mutations encompasses the possible drivers.